@article {pmid40935925,
year = {2025},
author = {Zhou, Y and Wang, H and Sun, J and Wicaksono, WA and Liu, C and He, Y and Qin, Y and Berg, G and Li, L and Lin, H and Chai, Y and Bai, Y and Ma, Z and Cernava, T and Chen, Y},
title = {Phenazines contribute to microbiome dynamics by targeting topoisomerase IV.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40935925},
issn = {2058-5276},
support = {LZ23C140004//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; U21A20219//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Phenazines are highly prevalent, natural bioactive substances secreted by microbes. However, their mode of action and potential involvement in shaping microbiomes remain elusive. Here we performed a comprehensive analysis of over 1.35 million bacterial genomes to identify phenazine-producing bacteria distributed across 193 species in 34 families. Analysis of rhizosphere microbiome and public rhizosphere metagenomic datasets revealed that phenazines could shape the microbial community by inhibiting Gram-positive bacteria, which was verified by pairwise interaction assays using Phenazine-1-carboxamide (PCN)-producing Pseudomonas chlororaphis. PCN induced DNA damage in Bacillus subtilis, a model Gram-positive target, where it directly bound to the bacterial topoisomerase IV, inhibiting its decatenation activity and leading to cell death. A two-species consortium of phenazine-producing Pseudomonas and resistant B. subtilis exhibited superior synergistic activity in preventing Fusarium crown rot in wheat plants. This work advances our understanding of a prevalent microbial interaction and its potential for biocontrol.},
}

@article {pmid40935888,
year = {2025},
author = {Otani, K and Nakatsu, G and Fujimoto, K and Miyaoka, D and Sato, N and Nadatani, Y and Nishida, Y and Maruyama, H and Ominami, M and Fukunaga, S and Hosomi, S and Tanaka, F and Imoto, S and Uematsu, S and Watanabe, T and Fujiwara, Y},
title = {Development of gastric mucosa-associated microbiota in autoimmune gastritis with neuroendocrine tumors.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {40935888},
issn = {1435-5922},
support = {JP22K08040//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: Autoimmune gastritis (AIG) is a chronic atrophic gastritis that affects the gastric corpus, leading to achlorhydria, hypergastrinemia, and a precursor of neuroendocrine tumors (NETs). This study aimed to elucidate the underlying mechanisms of gastric NET formation in AIG by analyzing gastric mucosa-associated microbiota and host tissue-derived metabolite profiles.

METHODS: A total of 19 patients diagnosed with AIG and 12 controls uninfected with Helicobacter pylori underwent gastric mucosal biopsies for microbiome analysis using next-generation sequencing with primers targeting the V3-V4 region of the 16S rRNA gene, and metabolome analysis using capillary electrophoresis time-of-flight mass spectrometry.

RESULTS: Microbiome analysis revealed significantly reduced α-diversity indices in patients with AIG when compared with the control group. β-Diversity analysis showed distinct microbial compositions among the control, NET-negative, and NET-positive groups. The NET-positive group exhibited a significantly higher abundance of Proteobacteria and Fusobacteriota, particularly Haemophilus parainfluenzae, Fusobacterium periodonticum, and Fusobacterium nucleatum, whereas Firmicutes, including Streptococcus salivarius and Veillonella atypica, were significantly decreased compared with the NET-negative group. Metabolome analysis revealed a shift away from glycolysis and tricarboxylic acid cycle activity toward alternative metabolic pathways in patients with AIG. Integrated analysis of gastric microbiota signatures (GMS) and tissue metabotypes demonstrated significant associations among GMS, tissue metabotypes, and NET diagnosis.

CONCLUSIONS: These findings highlight marked shifts in gastric mucosa-associated microbiota profiles in patients with AIG who developed gastric NETs. Tissue-specific metabolic alterations may precede mucosal dysbiosis in patients with AIG and promote the development of a microenvironment implicated in NET formation.},
}

@article {pmid40935766,
year = {2025},
author = {Medina Evora, G and Brauer, M and Letellier, E},
title = {Host and microbiome lipid metabolism in colorectal cancer development and therapy.},
journal = {Trends in cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.trecan.2025.08.005},
pmid = {40935766},
issn = {2405-8025},
abstract = {Colorectal cancer (CRC) remains one of the most prevalent cancers, with treatment largely dependent on surgery and chemotherapy, underscoring the need for novel or adjunct therapies. Cancer cells reprogram their lipid metabolism to support proliferation, invasiveness, and chemoresistance, making it a promising therapeutic target. Although several inhibitors of lipogenesis, lipases, lipid uptake, and lipid storage are under investigation in CRC, none have yet shown sufficient efficacy. Importantly, the tumor microenvironment (TME) and the microbiome influence CRC lipid metabolism by supplying compensatory lipids and engaging in crosstalk that affects the efficacy of lipid-targeting therapies. This review describes the role of lipids in CRC and explores how the TME and the gut/tumor microbiome may contribute to current challenges in the development of effective lipid-targeting therapies.},
}

@article {pmid40935747,
year = {2025},
author = {Strobel, KM and Perez, KM and Benjamin, H and Hoban, R},
title = {Human milk as therapy: neurodevelopment and neonatal brain injury.},
journal = {Seminars in perinatology},
volume = {},
number = {},
pages = {152140},
doi = {10.1016/j.semperi.2025.152140},
pmid = {40935747},
issn = {1558-075X},
abstract = {Human milk (HM) is the gold standard for infant feeding due to its associations with significant reductions in short and long-term serious morbidities. It is also associated with improved brain growth and development and neurodevelopmental outcomes, particularly in the preterm population. The myriad of bioactives found in HM, such as growth factors, stem cells, human milk oligosaccharides, and the human milk microbiome, presumably play a large role in these outcomes. Given the significant improvements in infant outcomes, components of HM are now being studied as targeted neurological therapy for brain injury. This narrative review will summarize the unique components of HM that are thought to be responsible for brain health and how they may affect brain structure and development in the term and preterm neonate. Neurodevelopmental improvements seen with HM feeding will also be reviewed. Finally, pre-clinical and clinical studies utilizing whole HM or HM components to treat brain injury will be summarized so that providers can better share the science of this remarkable biologic with multi-disciplinary teams and families.},
}

@article {pmid40935212,
year = {2025},
author = {Wang, Z and Zhu, Y and Wang, G and Sun, M and Yao, W and Ba, Q},
title = {Eucommia alleviates high fat diet-induced MASLD via the F. prausnitzii/butyrate/GPR43/GLP-1 signaling.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {120587},
doi = {10.1016/j.jep.2025.120587},
pmid = {40935212},
issn = {1872-7573},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) has become the most prevalent chronic liver disorder worldwide, and remains without truly effective therapies. Eucommia ulmoides Oliver (Eucommia), a traditional Chinese medicinal herb, is widely known for its hepatoprotective actions, but its therapeutic potential in MASLD and underlying mechanisms remain largely unexplored.

AIM OF THE STUDY: In vitro and in vivo studies, the protective effect of Eucommia bark extract (EBE) on MASLD was elucidated, and investigate its hepatoprotective mechanism.

MATERIALS AND METHODS: A high-fat diet (HFD)-induced MASLD mouse model was used to evaluate the therapeutic efficacy of EBE. Mice were orally administered EBE throughout HFD feeding, and metabolic parameters, liver histology, and key signaling pathways were systematically assessed. To investigate the underlying mechanisms, gut microbiota composition was analyzed by 16S rRNA sequencing, and fecal microbiota transplantation from EBE-treated donors was performed to determine the microbiota-mediated effects.

RESULTS: EBE dramatically attenuated HFD-induced weight gain, oxidative stress, inflammation, lipid accumulation, and fibrosis in MASLD mice. Mechanistically, EBE raised circulating glucagon-like peptide-1 (GLP-1) levels, enhanced adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) phosphorylation downstream of GLP-1 receptor (GLP-1R), thereby suppressing lipogenesis and promoting lipophagy. Although EBE did not directly trigger GLP-1 release in STC-1 cells, microbiome profiling revealed a selective bloom of Faecalibacterium prausnitzii (F. prausnitzii) - a major butyric acid producer-leading to elevated colonic butyric acid. Butyrate activated G protein-coupled receptor 43 (GPR43) on enteroendocrine cells to drive GLP-1 synthesis, a response abolished by GPR43 knockdown. Crucially, fecal microbiota transplantation from EBE-treated donors recapitulated these metabolic improvements in recipient mice.

CONCLUSION: EBE ameliorates MASLD by reshaping the gut microbiota to enrich F. prausnitzii-derived butyrate, which in turn stimulates endogenous GLP-1 secretion and activates the hepatic GLP-1R/AMPK axis to preserves lipid metabolism disorders.},
}

@article {pmid40935093,
year = {2025},
author = {Marangi, M and Palladino, G and Valzano, F and Scicchitano, D and Turroni, S and Rampelli, S and Candela, M and Arena, F},
title = {Genetic characterization of enteric protozoan microorganisms in newly arrived migrants in Italy and correlation with the gut microbiome layout.},
journal = {Travel medicine and infectious disease},
volume = {},
number = {},
pages = {102901},
doi = {10.1016/j.tmaid.2025.102901},
pmid = {40935093},
issn = {1873-0442},
abstract = {The prevalence of the enteric protozoan microorganisms, its genetic characterization as well as its associated gut microbiome has been molecularly and 16S metagenomic characterized in a cohort of newly arrived migrants in Italy from African countries over the period 2022-2024. Out of 199 individuals, 92 (46.2 %) were found to be carrier of protozoan microorganisms with a higher prevalence of Blastocystis sp. (15.5 %), followed by Giardia duodenalis (12.6 %), Dientamoeba fragilis (7.5 %), Cryptosporidium parvum (6.5 %), and Entamoeba histolytica (4 %). Subtypes ST1, ST2 and ST3 were genetically characterized for Blastocystis sp., assemblages A and B for G. duodenalis, subtypes families IIa and IIc for C. parvum and genotype 1 for D. fragilis. High prevalence of Butyrivibrio, Lachnospiraceae UGC 10 and Paraprevotella, were identified in the protozoan non-carrier individual group. This work shed lights on the circulation of enteric protozoan microorganisms in apparently healthy migrants from African countries and the potential relationship with the host-microbiome composition. Moreover, these results give an overview of the importance of microbiological surveys among migrants and asylum seekers arriving to hosting countries in order to evaluate the reliable risk of several microorganisms introduction though migration. Ultimately, further investigation of interplays between the intestinal microbiota and protozoan microorganisms will provide new approaches in the diagnosis and treatment of intestinal infections.},
}

@article {pmid40934984,
year = {2025},
author = {Yan, W and Zhu, A and Zhong, B and Chen, Q},
title = {Indole modulates lipoteichoic acid-induced inflammatory response in duck intestinal epithelial cells.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108030},
doi = {10.1016/j.micpath.2025.108030},
pmid = {40934984},
issn = {1096-1208},
abstract = {The microbial metabolite indole not only affects gut microbiome function but also regulates intestinal homeostasis and the immune response. Indole is primarily located in the intestinal tract; however, its effects on duck intestinal epithelial cells (IECs) under lipoteichoic acid (LTA) stimulation remain unknown. In this study, primary duck IECs were isolated, and their identity was verified using immunofluorescence staining and specific gene expression profiling. The proliferative activity of IECs was detected using the CCK-8 method. The viability of IECs under varying LTA concentrations was detected using the MTT assay. The mRNA levels of TNF-α and IL-1β under varying LTA concentrations and of TNF-α, IL-6, TGF-β1, claudin-1, and ZO-1 under varying indole concentrations were detected using quantitative real-time polymerase chain reaction (qRT-PCR). The expression levels of NF-κB-Rel and NF-κB-p65 in IECs subjected to a combination of LTA (40 μg/mL, 24 h) and indole (50 mg/L, 24 h) were detected using qRT-PCR and western blotting, respectively. We observed a reduction in IEC viability with increasing LTA concentrations. In vitro, LTA (40 μg/mL, 24 h) treatment significantly induced the mRNA expression of TNF-α and IL-1β in IECs (p < 0.001). However, indole (50 mg/L, 24 h) treatment significantly reduced their expression (p < 0.01), whereas it significantly increased mRNA levels of TGF-β1, claudin-1, and ZO-1 (p < 0.01) under LTA (40 μg/mL, 24 h) treatment. The mRNA expression of NF-κB-Rel significantly decreased in the LTA + indole group (p < 0.001) compared to that in the LTA group. Grayscale value analyses revealed that the LTA + indole group had lower phosphorylated-NF-κB-p65/NF-κB-p65 ratios for the total and cytoplasmic protein fractions of IECs than those of the LTA group (p < 0.001). In conclusion, indole reduces the inflammatory response in LTA-treated duck IECs by regulating the NF-κB signaling pathway, which may also maintain the function of the intestinal epithelial barrier by enhancing the mRNA expression of genes encoding tight junction proteins (claudin-1 and ZO-1) in ducks.},
}

@article {pmid40934939,
year = {2025},
author = {Ramasamy, B and Sharma, DK and Callary, SA and Ramadass, B and Solomon, LB and Atkins, GJ},
title = {Role of gut microbiota disruption in prosthetic joint infection: a scoping review.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101193},
doi = {10.1016/j.lanmic.2025.101193},
pmid = {40934939},
issn = {2666-5247},
abstract = {Prosthetic joint infection (PJI) is a serious complication of joint replacement surgery. Emerging evidence suggests that gut dysbiosis (characterised by reduced microbial diversity, altered immune responses, and increased intestinal permeability) could facilitate bacterial translocation from the gut to prosthetic joints and contribute to the development of PJI. In this scoping review, we analysed eight studies (three preclinical and five clinical) that investigated the potential link between gut microbiota alteration (dysbiosis) and PJIs. Preclinical models indicated that animals experiencing gut dysbiosis had higher rates of PJI, with a study testing the Trojan horse hypothesis showing that neutrophils carrying viable meticillin-resistant Staphylococcus aureus from the gut seeded the prosthetic joints without detectable bloodstream infection. Clinical research identified higher levels of zonulin (a marker of intestinal barrier integrity) and inflammatory markers, decreased gut microbial diversity, and presence of gut commensals within the joint tissues of patients with PJI. However, few studies used stool sequencing or adhered to microbiome research guidelines, thereby restricting conclusions. This Review highlights the need for future research that includes gut microbiota profiling, tight junction biomarker characterisation, and intervention trials (eg, testing the effect of probiotic use) to elucidate the role of gut dysbiosis in PJI. Investigating the gut microbiota before arthroplasty and incorporating suitable control groups could help to identify any causative relationships. The findings of this Review suggest that gut dysbiosis could be a modifiable risk factor for PJI, warranting the exploration of osteomicrobiology and gut-joint axis mechanisms in arthroplasty outcomes.},
}

@article {pmid40934913,
year = {2025},
author = {Martinez-Martinez, D and Peres, TV and Gehling, K and Quintaneiro, L and Cabrera, C and Cherevatenko, M and Cutty, SJ and Best, L and Marinos, G and Zimmerman, J and Safoor, A and Chrysostomou, D and Mokochinski, JB and Montoya, A and Brodesser, S and Zatorska, M and Scott, T and Andrew, I and Kramer, H and Begum, M and Zhang, B and Golding, BT and Marchesi, JR and Hirabayashi, S and Kaleta, C and Barr, AR and Frezza, C and Cochemé, HM and Cabreiro, F},
title = {Chemotherapy modulation by a cancer-associated microbiota metabolite.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101397},
doi = {10.1016/j.cels.2025.101397},
pmid = {40934913},
issn = {2405-4720},
abstract = {Understanding how the microbiota produces regulatory metabolites is of significance for cancer and cancer therapy. Using a host-microbe-drug-nutrient 4-way screening approach, we evaluated the role of nutrition at the molecular level in the context of 5-fluorouracil toxicity. Notably, our screens identified the metabolite 2-methylisocitrate, which was found to be produced and enriched in human tumor-associated microbiota. 2-methylisocitrate exhibits anti-proliferative properties across genetically and tissue-diverse cancer cell lines, three-dimensional (3D) spheroids, and an in vivo Drosophila gut tumor model, where it reduced tumor dissemination and increased survival. Chemical landscape interaction screens identified drug-metabolite signatures and highlighted the synergy between 5-fluorouracil and 2-methylisocitrate. Multi-omic analyses revealed that 2-methylisocitrate acts via multiple cellular pathways linking metabolism and DNA damage to regulate chemotherapy. Finally, we converted 2-methylisocitrate into its trimethyl ester, thereby enhancing its potency. This work highlights the great impact of microbiome-derived metabolites on tumor proliferation and their potential as promising co-adjuvants for cancer treatment.},
}

@article {pmid40934886,
year = {2025},
author = {Miao, Z and Hu, S and Wu, P and Lai, Y and Chen, LT and Huang, M and Zhang, K and He, H and Xu, F and Li, F and Yuan, J and Hu, Y and Liu, G and Huang, K and Shuai, M and Ye, M and Liang, X and Xiao, C and Gou, W and Shi, R and Wang, X and Jiang, Z and Shi, MQ and Wu, YY and Wang, XH and Lu, S and Fu, Y and Hu, W and Qiu, X and Pan, A and Pan, XF and Zheng, JS},
title = {Maternal gut microbiome during early pregnancy predicts preterm birth.},
journal = {Cell host & microbe},
volume = {33},
number = {9},
pages = {1623-1639.e8},
doi = {10.1016/j.chom.2025.08.004},
pmid = {40934886},
issn = {1934-6069},
abstract = {Preterm birth, the leading cause of infant mortality and morbidity, lacks robust biomarkers for early risk prediction. Here, we characterized the maternal gut microbiome in 5,313 Chinese pregnant women from two independent cohorts and identified eleven genera and one species associated with preterm birth during early pregnancy. We demonstrated that microbial risk scores (MRSs), generated from selected microbial genera or species, could effectively segregate pregnant women with shorter gestational duration and at higher preterm birth risk. The MRS showed interaction with host polygenic susceptibility to amplify preterm birth risk. Among bacteria comprising the MRS, Clostridium innocuum exhibited the most promising replicable microbial feature for preterm birth. The C. innocuum exhibited 17β-estradiol-degrading activity, and the estradiol-degrading gene k141_29441_57, validated through functional prediction and heterologous expression in E. coli, was enriched in women with preterm birth. These findings open new avenues for microbiome-targeted predictive and therapeutic strategies to mitigate adverse pregnancy outcomes.},
}

@article {pmid40934885,
year = {2025},
author = {Kujawska, M and Seki, D and Chalklen, L and Malsom, J and Kiu, R and Goatcher, S and Christoforou, I and Mitra, S and Crouch, L and Hall, LJ},
title = {Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts.},
journal = {Cell host & microbe},
volume = {33},
number = {9},
pages = {1502-1517.e13},
doi = {10.1016/j.chom.2025.08.008},
pmid = {40934885},
issn = {1934-6069},
abstract = {Animals harbor divergent microbiota, including various Bifidobacterium species, yet their evolutionary relationships and functional adaptations remain understudied. Using samples from insects, reptiles, birds, and mammals, we integrated taxonomic, genomic, and predicted functional annotations to uncover how Bifidobacterium adapts to host-specific environments. Host phylogeny is a major determinant of gut microbial composition. Distinct microbiota in mammalian and avian hosts reflect evolutionary adaptations to dietary niches, such as carnivory, and ecological pressures. At a strain-resolved level, Bifidobacterium and their hosts exhibit strong co-phylogenetic associations, driven by vertical transmission and dietary selection. Functional analyses highlight striking host-specific adaptations in Bifidobacterium, particularly in carbohydrate metabolism and oxidative stress responses. In mammals, Bifidobacterium strains are enriched in glycoside hydrolases tailored to complex carbohydrate-rich diets, including multi-domain GH13_28 α-amylases associated with degradation of resistant starch. Together, these findings deepen our understanding of host-microbe co-evolution and the critical role of microbiota in shaping animal health and adaptation.},
}

@article {pmid40934881,
year = {2025},
author = {Wang, S},
title = {Run to boost your gut microbiome that can help fight cancer.},
journal = {Cell host & microbe},
volume = {33},
number = {9},
pages = {1464-1465},
doi = {10.1016/j.chom.2025.07.022},
pmid = {40934881},
issn = {1934-6069},
abstract = {Exercise is beneficial to physical health, and it also helps to promote efficacy following immunotherapy. In a recent paper published in Cell, Phelps et al. identified that the gut microbiota plays a critical role in how exercise improves checkpoint inhibitor efficacy in melanoma.},
}

@article {pmid40934669,
year = {2025},
author = {Osti, JF and Pereira Leal, RM and de Souza, AJ and Paulon Rezende, LG and Viana, DG and Andreote, FD and Mendonça, RS and Jakelaitis, A and Regitano, JB},
title = {Complex interplay between composted manure application, metal contamination, and antibiotic resistance genes profile under tropical field conditions.},
journal = {Environment international},
volume = {203},
number = {},
pages = {109783},
doi = {10.1016/j.envint.2025.109783},
pmid = {40934669},
issn = {1873-6750},
abstract = {Manure applications in agricultural soils are a major driver of antibiotic resistance gene (ARG) dissemination, yet long-term effects of composted manure applications under tropical real field conditions remain unclear. This study assessed how successive composted manure applications influence soil physicochemical attributes, bacteriome and resistome profiles in the Brazilian Cerrado, including one site with naturally high heavy metal content. Across all sites, multidrug resistance genes were most abundant, followed by macrolide-lincosamide-streptogramin (MLS), tetracycline, β-lactam and glycopeptides resistance, aligning with predominance of Actinomycetota and Pseudomonadota as key ARG hosts. Manure increased soil pH and available phosphorus (P), with pH significantly shaping bacterial communities and pH and P the resistome in uncontaminated sites (2 and 3). However, in the metal-rich site (1), Cu was the dominant driver. Manure increased ARG richness and changed resistome structure but did not affect clinically relevant genes or resistome diversity. Metal resistance genes (MRGs), particularly for Cu and Zn, strongly influenced resistome dynamics, highlighting co-selection. Integrons integrase genes (intl) abundance increased in metal-depleted but not in metal-rich soils. While composting appears to mitigate ARG spread, particularly for clinically relevant genes, the high antibiotic use in livestock, large manure volumes, and potential for ARG persistence in tropical soils highlight the need for further research on manure treatment strategies and ARG fate in these environments. Environmental Implication. Our study highlights the environmental risks of antibiotic resistance gene (ARG) dissemination in tropical agricultural soils, emphasizing the role of manure application and heavy metal contamination in shaping soil resistome. While composted manure increased bacterial diversity and ARG richness, it did not significantly impact clinically relevant genes and resistome diversity, suggesting that composting may help mitigate ARG spread but does not eliminate it. Metals were the dominant drivers of ARG selection in the contaminated site, underscoring the role of co-selection mechanisms in maintaining resistance. However, manure applications increased integrons abundance, raising concerns about horizontal gene transfer and potential ARG proliferation into pathogens. These findings stress the urgent need for improved manure management policies in Brazil, where high antibiotic use in livestock and large manure volumes pose significant environmental and public health risks. Developing sustainable manure treatment strategies and monitoring ARG persistence are essential to limit antibiotic resistance proliferation in tropical agricultural ecosystems.},
}

@article {pmid40934553,
year = {2025},
author = {Zonneveld, KL and Bustos-Diaz, ED and Francisco, BG and Angelica, CJ},
title = {The cycad coralloid root: is there evidence for plant-microbe coevolution?.},
journal = {Current opinion in microbiology},
volume = {88},
number = {},
pages = {102660},
doi = {10.1016/j.mib.2025.102660},
pmid = {40934553},
issn = {1879-0364},
abstract = {Cycads are survivors, ancient plants originating in the Carboniferous. We hypothesize that cycad resilience and recent diversification could be partially explained by their specialized coral-like (coralloid) roots and their microbiome and that these symbiotic partners are co-evolving. The coralloid root is unique in gymnosperms and rare in vascular plants. Coralloid roots and their associated microbes have been studied since the late 19th century, but a deeper understanding of their taxonomy and function has taken place only recently. And yet, we are at the 'tip of the root' as there are many open questions regarding this specialized organ and its evolutionary history. This review provides an overview of cycad coralloid roots and their microbiome, the technical limitations of their study to date, and the exciting questions that remain to be answered.},
}

@article {pmid40934079,
year = {2025},
author = {Khan, MW and Cruz de Jesus, V and Mittermuller, BA and Schroth, RJ and Hu, P and Chelikani, P},
title = {Integrative analysis of taste genetics and the dental plaque microbiome in early childhood caries.},
journal = {Cell reports},
volume = {44},
number = {9},
pages = {116245},
doi = {10.1016/j.celrep.2025.116245},
pmid = {40934079},
issn = {2211-1247},
abstract = {Early childhood caries (ECC) is a multifactorial disease mainly caused by the oral microbiome; however, it is also influenced by host genetics and environmental factors. This study investigates the interplay between genetic variants in taste-related genes and the microbiome in ECC. Using a case-control design involving 538 children, we obtained dental plaque microbiome profiles and genetic variants across 55 candidate genes. Including the socioeconomic factor index (SEFI) as one of the confounders, we find a significant association of three taste-gene variants with ECC and microbial diversity. However, there are no specific associations between the variants and cariogenic species. Furthermore, our analysis indicates that Streptococcus mutans is a partial mediator between these genetic variants and ECC outcomes. A combined machine learning model identifies Streptococcus mutans, rural-urban status, a bitter taste receptor variant, Candida dubliniensis, and SEFI as the top ECC-associated factors. Our findings underscore the need for multiomics approaches in ECC risk assessment.},
}

@article {pmid40933888,
year = {2025},
author = {Liu, Y and He, J and Lyu, D and Yang, X and Zhang, H and Tu, S and Yao, Y and Wei, M and Li, Y and Zhao, Z and Huang, R and Lu, B and Xu, X and Pan, X},
title = {Uncovering the research evolution and hotspots of metabolism in renal cell carcinoma over the last decade.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1537805},
doi = {10.3389/fonc.2025.1537805},
pmid = {40933888},
issn = {2234-943X},
abstract = {BACKGROUND: The vital role metabolism plays in RCC, a global disease with huge disease burden, has been widely acknowledged. However, bibliometric analysis remains underexplored in the context of metabolism in RCC.

METHODS: The Web of Science database was adopted to obtain relevant publications for further bibliometric analysis of countries, institutions, authors, journals, publications, references and keywords. Literature reading and keyword co-occurrence analysis were employed to figure out major points and hotspots in this field. The analysis was conducted by biblioshiny based on Bibliometrix package in R version 4.3.2.

RESULTS: From 15 May 2015 to 15 May 2025, 3010 relevant publications were retrieved. China was the most productive country and USA was the country with the highest total citations. The most productive institution was "Harvard University". WANG Y published 46 publications with an H-index of 16. Core journals were identified with Bradford's law. Additionally, three major points and hotspots were identified and discussed through bibliometric analysis and targeted literature reading.

CONCLUSION: Our research provided a reference for future basic and clinical research through summarizing past research findings, analyzing current research hotspots, and prospecting the future development of research. "Metabolic alterations in RCC", "Metabolic syndrome and RCC", "Microbiome and RCC" were major points and hot spots in this field. In the future, a broader metabolic map could be made and more researches concerning metabolism during RCC treatment and drug resistance might bring more clinical significance.},
}

@article {pmid40933872,
year = {2025},
author = {Yáñez Ramil, U and Jezierska, S and Krupa, M and Bogado Pascottini, O},
title = {Fundamentals of microbiome-based therapies for reproductive tract inflammatory diseases in domestic animals.},
journal = {Animal reproduction},
volume = {22},
number = {3},
pages = {e20250030},
doi = {10.1590/1984-3143-AR2025-0030},
pmid = {40933872},
issn = {1984-3143},
abstract = {Reproductive tract inflammatory diseases (RTID) present significant health challenges in domestic animals, impacting welfare, fertility, and productivity. Traditionally, antibiotics have been the primary treatment for these conditions, however, the rise of antimicrobial resistance calls for alternative approaches. The microbiome of the female reproductive tract plays a vital role in maintaining reproductive health, and emerging evidence suggests that microbiome-based therapies, such as 'natural' or 'synthetic' microbiome transplantation, may offer sustainable solutions for RTID management. This review explores the composition and dynamics of the reproductive microbiome in both healthy and diseased states in cows, mares, sows, dogs, and cats. It also examines current treatments and the potential for microbiome-based interventions to replace or complement antibiotic therapies. Although research on microbiome-based therapies for preventing or treating RTID in domestic animals is virtually non-existent, vaginal and uterine microbiomes transplantation in mice and women show promise but require further investigation to evaluate their efficacy and safety across species with varying reproductive physiologies. Additionally, synthetic microbiome therapies present a controlled and reproducible alternative, though they face challenges in design, engraftment, and regulatory approval. The transition from antibiotic dependence to microbiome-based solutions marks a paradigm shift in veterinary medicine, but successful implementation demands a deeper understanding of host-microbiome interactions, rigorous safety protocols, and species-specific research.},
}

@article {pmid40933845,
year = {2025},
author = {Fitri, DK and Tuygunov, N and Wan Harun, WHA and Purwasena, IA and Cahyanto, A and Zakaria, MN},
title = {Key virulence genes associated with Streptococcus mutans biofilm formation: a systematic review.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1654428},
doi = {10.3389/froh.2025.1654428},
pmid = {40933845},
issn = {2673-4842},
abstract = {INTRODUCTION: Streptococcus mutans is central to plaque-induced oral diseases due to its robust biofilm-forming ability. Understanding the genetic and regulatory basis of this process is critical for developing targeted anti-virulence strategies that preserve the balance of the oral microbiome. This systematic review aims to gather and evaluate existing evidence on the virulence genes associated with Streptococcus mutans biofilm formation.

METHODS: A comprehensive search of PubMed, Scopus, and Web of Science was conducted in accordance with PRISMA guidelines. Studies investigating the genetic and regulatory mechanisms of biofilm formation, as well as the effects of experimental treatments, were included, and the risk of bias was assessed using the QUIN tool.

RESULTS: Key virulence genes were identified, including glucosyltransferases (gtfB, gtfC, gtfD), glucan-binding proteins (gbpB, gbpC), and two-component systems (vicRK, liaSR). These genes contribute to adhesion, extracellular polysaccharide synthesis, and environmental adaptation, processes critical for biofilm development. Various anti-virulence strategies, such as quorum sensing inhibitors and gene-targeted compounds, show promise in controlling biofilm formation without compromising bacterial viability, thereby preserving the homeostasis of the normal oral flora, which is essential for maintaining overall oral health.

CONCLUSION: While key virulence genes have been well characterized, further research is needed to clarify how their regulation is influenced by environmental conditions. Insights from this review may support the development of novel therapeutic approaches that reduce Streptococcus mutans pathogenicity while maintaining oral microbial balance.

https://www.crd.york.ac.uk/PROSPERO/view/CRD42024577977, PROSPERO CRD42024577977.},
}

@article {pmid40933614,
year = {2025},
author = {Chen, L and Li, W and Mo, D and Meng, X and Yao, L and Zhang, X and Liu, H},
title = {Comprehensive Analysis of the Microbiome and Metabolome: Unveiling Interactions Between Intestinal Flora and Metabolites in Schizophrenia.},
journal = {Neuropsychiatric disease and treatment},
volume = {21},
number = {},
pages = {1955-1971},
doi = {10.2147/NDT.S523570},
pmid = {40933614},
issn = {1176-6328},
abstract = {BACKGROUND: Schizophrenia (SZ) is a complex, multifactorial neurodevelopmental disorder characterized as a severe mental illness. Despite extensive research, its etiology and pathogenesis remain largely elusive. Recent studies suggest that the intestinal microbiota and its metabolites may play critical roles in the onset and regulation of SZ. This study aims to examine the characteristics of the intestinal microbiota and metabolomics in patients with SZ and to explore their correlation with clinical symptoms.

METHODS: This study involved thirty-five patients diagnosed with schizophrenia (SZ group) and thirty healthy control participants (HC group). Fecal samples were collected and analyzed using microbiome (16S rRNA gene sequencing) and metabolome (UPLC-MS) techniques. Bioinformatics and statistical analyses were conducted to interpret the data.

RESULTS: Age, sex, and BMI were comparable between the SZ and HC groups. Microbial diversity sequencing identified 837 operational taxonomic units (OTUs) across both groups. Although alpha diversity metrics showed no significant difference, beta diversity metrics revealed notable disparities. At the genus level, differences were observed in nine bacterial groups: Turicibacter, Toprococcus, Campylobacter, Eubacterium, Blautia, Sarcina, Catenibacterium, Lactobacillus, and Porphyromonas. At the family level, Erysipelotrichaceae, Turicibacteraceae, Campylobacteraceae, Desulfovibrionaceae, Lactobacillaceae, and Lachnospiraceae showed significant variations. Metabolomics analysis identified 946 metabolites, with 54 showing significant differences, primarily in caffeine metabolism and cysteine and methionine metabolism. Notably, correlations were found between differential gut microbes and metabolites, and between these metabolites and psychiatric clinical symptoms.

CONCLUSION: The study reveals significant abnormalities in the intestinal flora and metabolites of SZ patients, correlating with clinical severity. These findings offer new insights into the interactions between the gut microbiome and metabolites, potentially contributing to the understanding of the pathophysiology of schizophrenia.},
}

@article {pmid40933561,
year = {2025},
author = {Mascia, L and D'Albo, R and Cavalli, I and Giaccari, L and Della Giovampaola, M and Donati, B},
title = {Organ crosstalk: brain-lung interaction.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1655813},
doi = {10.3389/fmed.2025.1655813},
pmid = {40933561},
issn = {2296-858X},
abstract = {The interaction between the brain and the lungs is bidirectional: ICU patients with acute brain injury develop pulmonary complications, while ARDS patients frequently manifest neurological sequelae. Research is indeed focusing on both aspects of this cross-talk. On one side, ARDS survivors experience poor neurological outcomes both in the short and long term, with high incidence of delirium and post- discharge neurocognitive impairment. The underlying mechanisms have been investigated either in the pre-clinical and in the clinical field. Ventilator associated brain injury is the new recent term used to indicate the brain damage consequent to mechanical ventilation and leading to neuroinflammation and increased brain cells apoptosis. Moreover, prolonged hypoxia, deep sedation, loss of cerebral autoregulation and complications from vv-ECMO during ARDS are potentially sources of brain damage. On the other side, pulmonary complications in patients with acute brain injury follow a double-hit model, recently implemented in a triple-hit hypothesis. According to this theory, the primary brain injury leads to sympathetic hyperactivity, with inflammation and oxidative stress. Thus, the lungs become more vulnerable to develop complications such as neurogenic pulmonary edema and pneumonia. Finally, immune dysregulation and microbiome alterations due to brain-lung cross-talk lead to the worsening of lung injury. In this context, mechanical ventilation strategies aiming to guarantee adequate gas exchange and brain oxygen delivery are essential to prevent this phenomenon cascade. This review purpose is to examine the mechanisms behind brain-lung cross talk, starting from pathophysiological mechanisms, in order to suggest potential new research and therapeutic approaches.},
}

@article {pmid40933132,
year = {2025},
author = {Li, X and Lu, H},
title = {Enhanced metagenomic strategies for elucidating the complexities of gut microbiota: a review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626002},
doi = {10.3389/fmicb.2025.1626002},
pmid = {40933132},
issn = {1664-302X},
abstract = {The human gastrointestinal tract (GIT) is inhabited by a heterogeneous and dynamic microbial community that influences host health at multiple levels both metabolically, immunologically and via neurological pathways. Though the gut microbiota-overwhelmingly Bacteroidetes and Firmicutes-has essential functions in nutrient metabolism, immune regulation, and resistance to pathogens, its dysbiosis is likewise associated with pathologies, such as inflammatory bowel disease (IBD), obesity, type 2 diabetes (T2D), and neurodegenerative diseases. While conventional metagenomic techniques laid the groundwork for understanding microbial composition, next-generation enhanced metagenomic techniques permit an unprecedented resolution in exploring the functional and spatial complexity of gut communities. Advanced frameworks such as high-throughput sequencing, bioinformatic and multi-omics technologies are expanding the understanding of microbial gene regulation, metagenomic pathways, and host-microbe communication. Beyond taxonomic profiling, they map niche-specific activities of gut microbiota along a dichotomy of facultative mutualism, evidenced by relations of beneficial symbionts, represented here by Enterobacteriaceae. In this review, we critically consider the latest approaches (e.g., long-read sequencing, single-cell metagenomics and AI-guided annotation) that mitigate biases stemming from DNA extraction, sequencing depth and functional inference.},
}

@article {pmid40933130,
year = {2025},
author = {He, J and Gao, LY and Luo, YP and Chai, M and Wang, HF and Yang, LH and Zhao, K and Maimaiti, Y and Nie, YJ and Chen, W},
title = {Aspergillus Niger 129B promotes plant growth by inducing the interaction between SAUR32 and PP2C72.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1637235},
doi = {10.3389/fmicb.2025.1637235},
pmid = {40933130},
issn = {1664-302X},
abstract = {INTRODUCTION: Plant growth-promoting fungi (PGPF) play a fundamental role in plant development, such as nutrient acquisition and root growth. However, the growth promotion mechanisms regulated by Aspergillus niger are poorly characterized.

METHODS: We examined the growth-promoting effects of Aspergillus niger 129B on tomato plant root, stem, and leaf development through a combination of phenotype analyses and plant biomass measurement. Subsequently, molecular and genetic experiments were conducted to reveal the mechanism promoting root, stem, and leaf development.

RESULTS: It demonstrated that 129B significantly promoted the growth of tomato plants. Plant transcriptome and metabolome analysis revealed that this effect was associated with the plant hormone signaling pathway, particularly the expression of SAUR32 and PP2C72 genes. In addition, 129B could promote the development of root, stem, and leaf tissues by downregulating the expression of SAUR32 and PP2C72 genes. Importantly, we found that the promotion of tissue development may be attributed to the interaction between SAUR32 and PP2C72; the expression of SAUR32 proteins, which act as inhibitors of PP2C72 phosphatases, triggered root H[+] efflux.

DISCUSSION: Our findings concluded that 129B-induced plant promotion is dependent on the interaction between SAUR32 and PP2C72, providing novel insights into beneficial plant-microbiome interactions.},
}

@article {pmid40933056,
year = {2025},
author = {Shoshin, DE and Sizova, EA and Yausheva, EV and Ryazantseva, KV and Nechitajlo, KS and Kamirova, AM},
title = {Ultrafine Metallic Particles as Inducers of Digestive Processes in Rumen: Dry Matter Digestibility of Feed and Enzymatic Activity.},
journal = {Scientifica},
volume = {2025},
number = {},
pages = {9556646},
doi = {10.1155/sci5/9556646},
pmid = {40933056},
issn = {2090-908X},
abstract = {The ban on the use of antibiotics in animal husbandry encourages an active search for highly effective alternatives with additional properties, one of which is ultrafine particles (UFP) of metallic nature. The objective of the presented work was to conduct a comprehensive analysis of newly synthesized UFP Co3O4 and Mn2O3, including determination of their biological activity on the model of luminescent bacterial strain and potentiating effect on rumen digestion in ruminants using an in situ method. In parallel, the activity of proteinase, lipase, amylase, and cellulase, as well as nitrogen forms, microbial biomass, and the number of protozoa in 1 mL of rumen fluid, were determined. The minimum inhibitory concentrations for Mn2O3 and Co3O4 UFP were 3.9 × 10[-2] and 1.2 × 10[-3] mg/mL, respectively. The digestibility coefficient with the introduction of Mn2O3 UFP (39.0 mg/kg dry matter of feed) increased relative to the control by 6.6% (p = 0.012); Co3O4 UFP (0.6 mg/kg) by 12.7% (p = 0.012). Cellulolytic, amylolytic, and lipolytic activities in the group with Mn2O3 UFP increased by 18.2%, 515.5%, and 122.6% times compared to control, respectively. Proteinase activity decreased by 7.7% compared to control. Similar indicators in the group with Co3O4 UFP were +35.1%, +210.3%, +74.2, and +8.8%. Other indicators changed accordingly. Thus, UFP Mn2O3 and Co3O4 demonstrated significant potential as effectors of digestive processes in the rumen, stimulating the reproduction of protozoa and the enzymatic activity of the microbiome, which in combination ensured an increase in the digestibility of dry matter of feed. In other words, they can be used in the future as feed additives for ruminants. However, to fully understand the mechanisms of their action, it is also necessary to analyze the microbiome and metabolic pathways in the rumen.},
}

@article {pmid40933007,
year = {2025},
author = {Le, J and Hakimjavadi, H and Parsana, R and Chamala, S and Michail, S},
title = {Fecal Microbiota Transplantation Induces Sustained Gut Microbiome Changes in Pediatric Ulcerative Colitis: A Combined Randomized and Open-Label Study.},
journal = {Gastro hep advances},
volume = {4},
number = {10},
pages = {100741},
doi = {10.1016/j.gastha.2025.100741},
pmid = {40933007},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation (FMT) is a promising tool to modulate the gut microbiome in pediatric ulcerative colitis (UC). We investigated the long-term impact of FMT on the gut microbiome and identified microbial signatures associated with disease severity and clinical outcomes.

METHODS: This study combined a randomized, double-blind trial comparing FMT to autologous placebo with an open-label extension to assess FMT's effects on the gut microbiome in pediatric UC patients over 48 weeks. Stool samples were collected at baseline and postintervention, and clinical response was evaluated using the Pediatric Ulcerative Colitis Activity Index. Shotgun metagenomic sequencing characterized the fecal microbiome's composition and functional potential. Taxon set enrichment analysis identified microbial taxon sets associated with UC and FMT.

RESULTS: FMT induced significant, sustained increases in gut microbial diversity over 48 weeks. Key changes included decreases in Klebsiella oxytoca and increases in Coprobacter fastidiosus post-FMT. Microbial signatures were associated with disease severity, including increased indole producers and decreased mucin degraders in mild UC compared to remission. Patients with clinical improvement post-FMT showed decreased Fusobacterium nucleatum and Veillonella parvula. Klebsiella pneumoniae and Klebsiella variicola decreased after open-label FMT.

CONCLUSION: FMT induces sustained changes in the pediatric UC gut microbiome, with distinct microbial signatures associated with disease severity and clinical outcomes. However, the high autologous placebo response rate underscores the need for further research to elucidate the mechanisms underlying FMT and placebo responses. Our study provides insights into the gut microbiome's role in pediatric UC, laying the foundation for developing personalized microbiome-targeted therapies. ClinicalTrials.gov number, NCT02291523.},
}

@article {pmid40932704,
year = {2025},
author = {Rühle, A and Krausz, M and Monroy Ordonez, EB and Heyer, J and Thomsen, AR and Schäfer, H and Kafkaletos, A and Bronsert, P and Kesselring, R and Al-Ahmad, A and Schlueter, N and Wüster, J and Knopf, A and Grosu, AL and Proietti, M and Henke, M and Berlin, C and Nicolay, NH},
title = {Oral Lachnoanaerobaculum Levels and Survival in Patients With Head and Neck Cancer.},
journal = {JAMA otolaryngology-- head & neck surgery},
volume = {},
number = {},
pages = {},
doi = {10.1001/jamaoto.2025.2816},
pmid = {40932704},
issn = {2168-619X},
abstract = {IMPORTANCE: The oral microbiome plays a critical role in cancer treatment responses, yet its influence on outcomes in patients with head and neck squamous cell carcinoma (HNSCC) undergoing (chemo)radiotherapy remains poorly understood. Identifying specific microbiome signatures associated with treatment effectiveness could provide novel prognostic biomarkers and therapeutic targets.

OBJECTIVE: To investigate the association between salivary Lachnoanaerobaculum spp abundance and treatment outcomes in patients with HNSCC undergoing (chemo)radiotherapy and to explore potential mechanisms.

This prognostic study analyzed saliva samples from patients with HNSCC who were enrolled in 2 independent prospective biomarker studies (SALIVA and ZissTrans) and underwent definitive (chemo)radiotherapy. Oral microbiome composition was assessed using 16S rRNA gene sequencing. Tumor-infiltrating lymphocytes (TILs) were evaluated via immunohistochemistry in patients with available data. Findings were further assessed using data from The Cancer Microbiome Atlas and The Cancer Genome Atlas. Sample collection occurred from 2008 to 2011 (SALIVA) and from 2017 to 2022 (ZissTrans), and the data for this study were analyzed from July to December 2024.

EXPOSURE: Definitive (chemo)radiotherapy.

MAIN OUTCOMES AND MEASURES: The primary outcome was locoregional recurrence-free survival (LRFS) and a secondary outcome was overall survival (OS). Additional secondary analyses evaluated the association between Lachnoanaerobaculum spp levels and TIL levels, and the incidence of severe radiation-induced oral mucositis.

RESULTS: The analysis included 92 patients with HNSCC (mean [SD] age, 61.1 [7.9] years; 15 female [16.3%] 77 male [83.7%] individuals) and found that higher Lachnoanaerobaculum spp abundance was associated with substantially improved LRFS (median, 69 vs 11 months; hazard ratio [HR], 0.50; 95% CI, 0.29-0.86) and OS (median, 75 vs 27 months; HR, 0.54; 95% CI, 0.30-0.98). This finding was confirmed by multivariable Cox regression (LRFS: HR, 0.50; 95% CI, 0.25-1.00; OS: HR, 0.37; 95% CI, 0.16-0.85). TILs were evaluated in 76 patients (82.2%) and showed that increased Lachnoanaerobaculum spp levels were associated with higher CD4-positive and CD8-positive TIL counts. Lachnoanaerobaculum spp abundance showed no meaningful association with severe radiation-induced oral mucositis. Data from The Cancer Microbiome Atlas (n = 157) indicated that higher intratumoral Lachnoanaerobaculum spp levels were associated with improved OS (HR, 0.62; 95% CI, 0.39-0.98). Transcriptomic analyses in The Cancer Genome Atlas cohort further supported an immune-stimulated tumor microenvironment in Lachnoanaerobaculum-high tumors.

CONCLUSIONS AND RELEVANCE: This prognostic study found that higher salivary Lachnoanaerobaculum spp abundance was associated with improved tumor control and survival in patients with HNSCC undergoing (chemo)radiotherapy. These findings support further investigation into microbiome-targeted interventions to improve HNSCC treatment effectiveness.},
}

@article {pmid40932624,
year = {2025},
author = {Zhu, W and Xu, X and Nagarajan, V and Guo, J and Gupta, A and Peng, Z and Zhang, A and Liu, J and Mattapallil, MJ and Jittayasothorn, Y and Horai, R and Belkaid, Y and Constantinides, MG and St Leger, AJ and Caspi, RR},
title = {TLR2 supports γδ T cell IL-17A response to ocular surface commensals by metabolic reprogramming.},
journal = {The Journal of experimental medicine},
volume = {222},
number = {11},
pages = {},
doi = {10.1084/jem.20251046},
pmid = {40932624},
issn = {1540-9538},
support = {R00EY025761/NH/NIH HHS/United States ; R01EY032482/NH/NIH HHS/United States ; EY000184/EY/NEI NIH HHS/United States ; },
mesh = {*Toll-Like Receptor 2/metabolism/immunology ; *Interleukin-17/metabolism/immunology/genetics ; Animals ; *Receptors, Antigen, T-Cell, gamma-delta/metabolism/immunology ; Mice ; *Conjunctiva/immunology/microbiology ; Mice, Inbred C57BL ; *Corynebacterium/immunology ; Signal Transduction ; Mice, Knockout ; Metabolic Reprogramming ; },
abstract = {The ocular surface is a mucosal barrier tissue colonized by commensal microbes, which tune local immunity by eliciting IL-17 from conjunctival γδ T cells to prevent pathogenic infection. The commensal Corynebacterium mastitidis (C. mast) elicits protective IL-17 responses from conjunctival Vγ4 T cells through a combination of γδ TCR ligation and IL-1 signaling. Here, we identify Vγ6 T cells as a major C. mast-responsive subset in the conjunctiva and uncover its unique activation requirements. We demonstrate that Vγ6 cells require both extrinsic (via dendritic cells) and intrinsic TLR2 stimulation for optimal IL-17A response. Mechanistically, intrinsic TLR2 signaling was associated with epigenetic changes and enhanced expression of genes involved in fatty acid oxidation to support Il17a transcription. We identify a key transcription factor, IκBζ, which is upregulated by TLR2 stimulation and is essential for this program. Our study highlights the importance of intrinsic TLR2 signaling in driving metabolic reprogramming and production of IL-17A in microbiome-specific mucosal γδ T cells.},
}

*Toll-Like Receptor 2/metabolism/immunology
*Interleukin-17/metabolism/immunology/genetics
Animals
*Receptors, Antigen, T-Cell, gamma-delta/metabolism/immunology
Mice
*Conjunctiva/immunology/microbiology
Mice, Inbred C57BL
*Corynebacterium/immunology
Signal Transduction
Mice, Knockout
Metabolic Reprogramming

@article {pmid40932530,
year = {2025},
author = {Liu, B and Liu, Y and Xu, S and Wu, Q and Wu, D and Zhan, L and Liao, Y and Mai, Y and Zheng, M and Wang, S and Chen, Y and Huang, Z and Luo, X and Xie, Z and Pan, X and Yu, G and Xie, L},
title = {EasyMultiProfiler: an efficient multi-omics data integration and analysis workflow for microbiome research.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40932530},
issn = {1869-1889},
abstract = {Host-microbiome interactions are crucial for physiological homeostasis and disease progression. While traditional microbiome research provided foundational insights, multi-omics approaches enable a more comprehensive and systems-level understanding. However, integrating multi-omics data presents significant methodological challenges, including inconsistent sample coverage, heterogeneous data formats, and complex analytical workflows, which collectively impair reproducibility and reliability. To address these critical challenges, we developed the EasyMultiProfiler (EMP), a streamlined and efficient analytical workflow. EMP utilizes SummarizedExperiment and MultiAssayExperiment classes to establish a unified multi-omics data storage and analysis framework. Its architecture comprises five interconnected functional modules: data extraction, preparation, support, analysis, and visualization, integrated into a user-friendly and natural language-style workflow. This design offers an efficient and standardized solution, directly resolving data integration issues, workflow standardization, and result reproducibility. EMP provides researchers and clinicians with a robust and flexible platform to systematically extract biologically relevant insights from complex multi-omics datasets, overcoming key barriers in contemporary microbiome research.},
}

@article {pmid40932394,
year = {2025},
author = {Yang, H and Xie, D and Wei, P and Ge, J and Li, Y},
title = {A case study of ChatGPT-assisted building of a microbiome-based machine learning model for biologists.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0008225},
doi = {10.1128/jmbe.00082-25},
pmid = {40932394},
issn = {1935-7877},
abstract = {Machine learning is a widespread technology that is shaping how biologists interact with data. However, there are many practical challenges in teaching machine learning to biology students, who often do not have a strong programming background. To address these challenges, we present an educational study utilizing publicly available salivary microbiome data sets to develop a machine learning model using Python. With the assistance of ChatGPT, most students successfully built a simple random forest model. Evaluation metrics, such as accuracy and area under the curve, indicated that the overall performance of the model was favorable and accurately predicted oral malodor diseases. This work establishes a pedagogical framework for integrating machine learning into biology curricula, bridging the gap between data science and life science education.},
}

@article {pmid40932298,
year = {2025},
author = {Flammer, ER and Christopher, MW and Powers, ER and Broncucia, H and Steck, AK and Gitelman, SE and Garrett, TJ and Ismail, HM},
title = {Serum Metabolomics Reveals Potential Differences in Gut Microbiota-Associated Metabolites in Twins Discordant for Type 1 Diabetes.},
journal = {Diabetes},
volume = {},
number = {},
pages = {},
doi = {10.2337/db25-0156},
pmid = {40932298},
issn = {1939-327X},
support = {DK-129799//National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health/ ; },
abstract = {We believed this cohort of twins discordant for type 1 diabetes (T1D) would allow for control over genetic variability to examine environmental factors. We aimed to identify differences in microbial and microbiota-associated metabolites in twins discordant for T1D to examine the effect of the gut microbiome on T1D. Thirteen metabolites were identified as significantly different. Our results show dysregulation of several microbial metabolites in twin pairs, suggesting the role of the gut microbiome in T1D pathogenesis.},
}

@article {pmid40932281,
year = {2025},
author = {Tang, X and Chen, T and Zhai, X and Huang, J and Sun, Y and Yang, Y and Zhao, Z and Pan, Y and Huang, Y and Li, X and Fan, G},
title = {Phytoplasma-induced alterations in endophytic bacterial communities in Paulownia: implications for witches' broom.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0148925},
doi = {10.1128/spectrum.01489-25},
pmid = {40932281},
issn = {2165-0497},
abstract = {UNLABELLED: Paulownia witches' broom (PaWB), caused by phytoplasma, threatens global Paulownia cultivation. Although phytoplasma is known to manipulate host physiology, their influence on the plant-associated microbiome, particularly at the tissue-specific level, remains unclear. Here, we integrated scanning electron microscopy, nested PCR, and 16S rRNA sequencing to investigate the morphological characteristics, phytoplasma infection, and bacterial communities across four compartments (leaves, branches, roots, and rhizosphere) in healthy, symptomatic, and asymptomatic P. fortunei trees. We found that PaWB induces pronounced external morphological abnormalities without significantly altering internal tissue structures. Notably, phytoplasma was detected not only in symptomatic tissues but also at low abundance in asymptomatic compartments, indicating a latent infection state. Phytoplasma proliferation in symptomatic leaves and branches was accompanied by a dramatic loss of bacterial diversity and a collapse in microbial interaction network complexity, while the root and rhizosphere microbiota remained comparatively stable. Random forest modeling identified Candidatus phytoplasma and ten other bacterial genera as key predictors of PaWB status. Microbial function predictions further revealed that disrupted carbohydrate degradation and tryptophan metabolism in diseased tissues may promote the expansion of opportunistic microbes, potentially exacerbating PaWB symptom development. Our study provides the first compelling evidence that phytoplasma infection drives tissue-specific microbiome collapse in Paulownia, disrupting microbial networks and reprogramming functional pathways well before visible symptoms emerge. These previously unrecognized microbial and metabolic signatures represent robust early-warning biomarkers and offer strategic targets for precision diagnostics and disease intervention, marking a significant advance in our understanding and management of PaWB.

IMPORTANCE: Paulownia witches' broom (PaWB) disease poses a severe threat to global Paulownia cultivation, yet its microbiome-related mechanisms remain poorly understood. Here, we show that phytoplasma infection alters the external P. fortunei morphology and disrupts the composition, structure, and function of endophytic bacterial communities in aerial tissues. These microbial shifts are closely linked to symptom development, with latent infections also detected in asymptomatic tissues. Eleven microbial markers, including Candidatus Phytoplasma, enable accurate disease prediction. Predictions of functional shifts in carbohydrate and tryptophan metabolism further implicate microbiome alterations in symptom development. Our study contributes to a deeper understanding of the complex interaction mechanism among Paulownia, microorganisms and phytoplasma during the occurrence of PaWB and offer a theoretical foundation for sustainable management of PaWB.},
}

@article {pmid40931708,
year = {2025},
author = {Soghli, N and Khormali, A and Mahboubi, D and Peng, A and Miguez, PA},
title = {Recent advancements in artificial intelligence-powered cancer prediction from oral microbiome.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.70000},
pmid = {40931708},
issn = {1600-0757},
support = {CA233037/NH/NIH HHS/United States ; DE030427/NH/NIH HHS/United States ; },
abstract = {Oral cancer is a major global health burden, ranking sixth in prevalence, with oral squamous cell carcinoma (OSCC) being the most common type. Importantly, OSCC is often diagnosed at late stages, underscoring the need for innovative methods for early detection. The oral microbiome, an active microbial community within the oral cavity, holds promise as a biomarker for the prediction and progression of cancer. Emerging computational techniques in the artificial intelligence (AI) field have enabled the analysis of complex microbiome data sets to unravel the association between oral microbiome composition and oral cancer. This review provides a comprehensive overview of learning-based algorithms applied to oral microbiome data for cancer prediction. In particular, this work discusses how typical machine learning (ML) algorithms, such as logistic regression, random forests, and artificial neural networks, identify the unique microbial patterns associated with oral cancer and other malignancies. A search was conducted in Pubmed covering a 10-year period. The goal was to identify previous studies focused on the role of the oral microbiome in oral cancer prediction using AI-powered tools. The search strategy identified 3382 records in total, of which 44 studies met the inclusion criteria. While AI has shown a transformative power in understanding and revealing the oral microbiome's role in cancer studies, its application in clinical settings requires further efforts on standardization of protocols, curation of diverse cohorts, and validation through large-scale multi-centric and longitudinal studies. The integration of AI with oral microbiome analysis holds significant promise for improving early detection, risk stratification, and personalized treatment strategies for OSCC. By identifying unique microbial patterns associated with cancer, AI-driven models offer a noninvasive, cost-effective tool to predict disease progression and guide clinical decision-making. However, translating these advancements into routine clinical practice requires standardized protocols, diverse patient cohorts, and validation through large-scale, longitudinal studies. Once implemented, this approach could transform oral cancer management, enabling timely interventions and improving patient outcomes.},
}

@article {pmid40931615,
year = {2025},
author = {Bergmann, KC and Zuberbier, T},
title = {Diversity and Dosage Determine the Efficacy of the Probiotic SYN-53 in Allergic Rhinoconjunctivitis: A Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70045},
pmid = {40931615},
issn = {1398-9995},
support = {//Synformulas/ ; },
abstract = {SYN-53, a multi-strain probiotic food supplement, was recently shown to significantly alleviate allergic rhinoconjunctivitis (ARC) and its symptoms. The diversity and dosage of bacterial strains administered via SYN-53 have been proposed as key drivers of its efficacy. The aim of this study was to assess the role of bacterial diversity and dosage by comparing SYN-53 to a low dose variant (SYN-53-LD), a low diversity variant (SYN-4), and a placebo in the management of ARC. This double-blind, parallel-group, placebo-controlled clinical trial included subjects with moderate-to-severe grass pollen allergy. Following baseline exposure in an allergen exposure chamber (AEC), 166 subjects were randomized to undergo three weekly 3-day intake cycles of SYN-53, SYN-53-LD, SYN-4, or placebo, followed by a final allergen exposure. During AEC exposure, symptoms were continuously measured via assessment of the Total Symptom Score (TSS). SYN-53 was significantly superior in reducing TSSMAX compared with its low dose variant SYN-53-LD (∆TSSMAX [Mean ± SE]: -5.19 ± 0.80 vs. -2.27 ± 0.65; p = 0.0372), its low diversity variant SYN-4 (-3.41 ± 0.52; p = 0.0482), and placebo (-2.82 ± 0.78; p = 0.0329). No significant differences to placebo were seen for either SYN-53-LD (p = 0.7377) or SYN-4 (p = 0.5152). SYN-53 and its variants were well tolerated, and adverse events were not different from placebo. Our findings reaffirm the efficacy of SYN-53 in the management of ARC and demonstrate that the effectiveness of this multi-strain probiotic is intricately linked to the diversity of bacterial strains and dosage administered.},
}

@article {pmid40931587,
year = {2025},
author = {Gunasekera, L and Ray, JC and Butzkueven, H and O'Brien, TJ and Hutton, E and Kaul, N},
title = {The Hypometabolic State of the Migraine Brain: Is a Ketogenic Diet the Answer?.},
journal = {Brain and behavior},
volume = {15},
number = {9},
pages = {e70860},
doi = {10.1002/brb3.70860},
pmid = {40931587},
issn = {2162-3279},
mesh = {Humans ; *Diet, Ketogenic/methods ; *Migraine Disorders/metabolism/diet therapy/physiopathology ; *Brain/metabolism ; },
abstract = {BACKGROUND: Migraine pathophysiology involves a constellation of metabolic abnormalities. These interlinked contributory factors include mitochondrial dysfunction, an altered gut microbiome, neuroinflammation, oxidative stress, weight imbalance, and altered glucose metabolism. The ketogenic diet is an emerging therapy which may restore hypometabolism seen in chronic migraine. We describe contributions of metabolic dysfunction to chronic migraine pathophysiology and discuss the role of ketogenic diet therapy to improve cerebral metabolism.

METHODS: A literature search of articles from OVID Medline, Embase, and Cochrane Library were reviewed until May 6, 2024. A total of 50 articles were included comprising case reports, case series, observational clinical trials, and narrative review articles.

RESULTS: Migraine pathophysiology involves significant hypometabolism, seen on functional imaging studies, so therapeutics which target these underlying deficiencies may ameliorate chronic migraine symptoms. The ketogenic diet reduces migraine days, pain intensity, and acute analgesic use. Current studies are limited by small sample sizes, inconsistent methodology precluding direct comparison between studies or pooling of results, and limited longitudinal follow-up.

CONCLUSION: While there is biological plausibility to reason that a ketogenic diet could correct metabolic mismatch in people with migraine, further randomized clinical trials with larger sample sizes are required to confirm the positive results of preliminary, uncontrolled studies.},
}

Humans
*Diet, Ketogenic/methods
*Migraine Disorders/metabolism/diet therapy/physiopathology
*Brain/metabolism

@article {pmid40931350,
year = {2025},
author = {Ye, G and Hong, H and Li, T and Li, J and Wu, JQ and Jiang, S and Meng, ZT and Yuan, HT and Xue, W and Li, AL and Zhou, T and Li, TT and Li, T},
title = {MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {276},
pmid = {40931350},
issn = {1474-760X},
support = {No. 32100421//China National Natural Science Foundation/ ; No. 82341098//China National Natural Science Foundation/ ; No. 82130052//China National Natural Science Foundation/ ; No. NSS2021CI05002//Nanhu Laboratory/ ; No. 2024ZYYDSA400333//The Central Government Guides Local Science and Technology Development Fund Projects/ ; },
abstract = {Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information. It represents a valuable resource for researchers in discovering potential novel microbial lineages and understanding their ecological roles. MAGdb is publicly available at https://magdb.nanhulab.ac.cn/ .},
}

@article {pmid40931263,
year = {2025},
author = {Xiang, K and Huang, L and Liu, J and Chen, W},
title = {Segmental analysis of esophageal and gastric fundus microbiome diversity in reflux esophagitis.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {40931263},
issn = {1874-9356},
abstract = {Microbiome dysbiosis in reflux esophagitis has been extensively studied. However, limited research has examined microbiota across different segments of the upper gastrointestinal tract in reflux esophagitis. In this study, we investigated microbial alterations in three esophageal segments (upper, middle, and lower) and the gastric fundus of reflux esophagitis patients and healthy controls. In healthy individuals, the gastric fundus harbored a microbiota composition distinct from that of all esophageal segments. In reflux esophagitis patients, the regional distinction was absent, with similar microbial profiles across the esophagus and gastric fundus. At the genus level, notable compositional shifts were observed between the healthy and reflux esophagitis groups. In controls, the microbiota was dominated by Streptococcus (24.45%), Achromobacter (14.14%), and Prevotella (6.58%). In reflux esophagitis patients, Streptococcus (20.03%) remained the dominant genus, followed by an increased abundance of Prevotella (9.38%). Multilevel LEfSe analysis identified Prevotella as a potential microbial marker of reflux esophagitis. These findings indicate that reflux esophagitis is associated with widespread microbiota alterations extending throughout the esophageal tract and the gastric fundus.},
}

@article {pmid40930684,
year = {2025},
author = {Cappas, VM and Roy, R and Davenport, ER and Sykes, DG},
title = {The microbiome and volatile organic compounds reflecting the state of decomposition in an indoor environment.},
journal = {Science & justice : journal of the Forensic Science Society},
volume = {65},
number = {5},
pages = {101302},
doi = {10.1016/j.scijus.2025.101302},
pmid = {40930684},
issn = {1876-4452},
mesh = {*Volatile Organic Compounds/analysis ; *Microbiota ; Humans ; *Postmortem Changes ; },
abstract = {Given that a variety of factors can affect the decomposition process, it can be difficult to determine the post-mortem interval (PMI). The process is highly dependent on microbial activity, and volatile organic compounds (VOCs) are a by-product of this activity. Given both have been proposed to assist in PMI determination, a deeper understanding of this relationship is needed. The current study investigates the temporal evolution of the microbiome and VOC profile of a decomposing human analog (swine) in a controlled, indoor environment. Microbial communities were sampled at six-time points up to the active decay phase (72 swabs in total). VOC headspace samples were collected every six hours with six sampling times in common with the swab times. Sampling locations included the abdominal area, anus, right ear canal, and right nostril. Bacterial communities were found to significantly change during decomposition (p < 0.001), and communities shifted differently based on sample location. The families Moraxellaceae, Planococcaceae, Lactobacillaceae, and Staphylococcaceae drove these community shifts. From random forest analysis, the nostril sampling location was determined to be the best location to predict stage of decomposition. Individual VOCs exhibited large temporal shifts through decomposition stage in contrast to smaller shifts when evaluated based on functional groups. Finally, pairwise linear regression models between abdominal area bacteria and selected VOCs were assessed; Planococcaceae and Tissierellaceae were significantly correlated to indole. Overall, this study provides an exploratory analysis to support the connection between the microbiome, VOCs, and their relationship throughout decomposition.},
}

*Volatile Organic Compounds/analysis
*Microbiota
Humans
*Postmortem Changes

@article {pmid40930564,
year = {2025},
author = {Rauber, C and Roberti, MP and Vehreschild, MJ and Tsakmaklis, A and Springfeld, C and Teufel, A and Ettrich, T and Jochheim, L and Kandulski, A and Missios, P and Mohr, R and Reichart, A and Waldschmidt, DT and Sauer, LD and Sander, A and Schirmacher, P and Jäger, D and Michl, P and Dill, MT},
title = {Protocol: Faecal microbiota transfer in liver cancer to overcome resistance to atezolizumab/bevacizumab - a multicentre, randomised, placebo-controlled, double-blind phase II trial (the FLORA trial).},
journal = {BMJ open},
volume = {15},
number = {9},
pages = {e097802},
doi = {10.1136/bmjopen-2024-097802},
pmid = {40930564},
issn = {2044-6055},
mesh = {Humans ; *Liver Neoplasms/therapy/drug therapy ; *Bevacizumab/therapeutic use ; Double-Blind Method ; *Fecal Microbiota Transplantation/methods ; *Antibodies, Monoclonal, Humanized/therapeutic use ; *Carcinoma, Hepatocellular/therapy/drug therapy ; Drug Resistance, Neoplasm ; Clinical Trials, Phase II as Topic ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; Immune Checkpoint Inhibitors/therapeutic use ; Gastrointestinal Microbiome ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; },
abstract = {INTRODUCTION: Combined vascular endothelial growth factor/programmed death-ligand 1 blockade through atezolizumab/bevacizumab (A/B) is the current standard of care in advanced hepatocellular carcinoma (HCC). A/B substantially improved objective response rates compared with tyrosine kinase inhibitor sorafenib; however, a majority of patients will still not respond to A/B. Strong scientific rationale and emerging clinical data suggest that faecal microbiota transfer (FMT) may improve antitumour immune response on PD-(L)1 blockade. Early trials in melanoma with FMT and reinduction of immune checkpoint blockade (ICI) therapy in patients with anti-PD-1-refractory metastatic melanoma were reported in 2021 and demonstrated reinstatement of response to ICI therapy in many patients. Due to anatomical vicinity and the physiological relevance of the gut-liver axis, we hypothesise HCC to be a particularly attractive cancer entity to further assess a potential benefit of FMT in combination with ICI towards increased antitumour immunity. Additionally, HCC often occurs in patients with liver cirrhosis, where liver function is prognostically relevant. There is evidence that FMT may increase hepatic function and therefore could positively affect outcome in this patient population.

METHODS AND ANALYSIS: This prospective, multicentre, randomised, placebo-controlled, double-blind phase II clinical trial has been designed to assess immunogenicity and safety of FMT via INTESTIFIX 001 combined with A/B in advanced HCC in comparison to A/B with placebo. Primary endpoints are measured as tumour CD8+ T cell infiltration after 2 cycles of treatment with vancomycin, A/B+INTESTIFIX 001 in comparison to vancomycin-placebo, A/B+INTESTIFIX 001-placebo and safety of the therapeutic combination in advanced HCC. INTESTIFIX 001 is an encapsulated FMT preparation by healthy donors with a high alpha-diversity in their gut microbiome for oral administration, manufactured by the Cologne Microbiota Bank (CMB). Sample size was calculated to achieve a specific expected accuracy for the primary immunological endpoint. 48 subjects will be randomised to reach a goal of 42 usable measurements in the modified intention-to-treat set. Subjects will be randomised in a 2:1 ratio to A/B or placebo (28 A/B, 14 placebo).

ETHICS AND DISSEMINATION: The study was approved by ethics committee review and the German Federal Ministry of Drugs and Medical Devices. The trial is registered under EU CT no. 2023-506887-15-00. The outcome of the study will be disseminated via peer-reviewed publications and at international conferences.

TRIAL REGISTRATION NUMBER: NCT05690048.},
}

Humans
*Liver Neoplasms/therapy/drug therapy
*Bevacizumab/therapeutic use
Double-Blind Method
*Fecal Microbiota Transplantation/methods
*Antibodies, Monoclonal, Humanized/therapeutic use
*Carcinoma, Hepatocellular/therapy/drug therapy
Drug Resistance, Neoplasm
Clinical Trials, Phase II as Topic
Randomized Controlled Trials as Topic
Multicenter Studies as Topic
Immune Checkpoint Inhibitors/therapeutic use
Gastrointestinal Microbiome
Antineoplastic Combined Chemotherapy Protocols/therapeutic use

@article {pmid40930373,
year = {2025},
author = {Korobkova, L and Thornton, ME and Collin, MA and Morin, EL and Aoued, H and Sannigrahi, S and Bhinderwala, N and Garza, KM and Siebert, ER and Walum, H and Cabeen, RP and Grubbs, BH and Sanchez, MM and Dias, BG},
title = {RNA in plasma extracellular vesicles of adolescent rhesus macaques reveal immune, bioenergetic and microbial imprints of early life adversity - an exploratory analysis.},
journal = {Biological psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biopsych.2025.08.020},
pmid = {40930373},
issn = {1873-2402},
abstract = {BACKGROUND: Exposure to early life adversity (ELA), including childhood maltreatment, is one of the most significant risk factors for the emergence of psychosomatic disorders in adolescence and adulthood. Most investigations into biological processes that have been perturbed by ELA have profiled DNA methylation in whole blood and coalesced around perturbations of immunobiology being centrally insulted by ELA.

METHODS: To identify novel molecular signatures that are enduringly perturbed by childhood maltreatment, we isolated circulating extracellular vesicles (EVs) from plasma collected from adolescent rhesus macaques that had either experienced nurturing maternal care (CONT, n = 7, 4M 3F) or maltreatment in infancy (MALT, n = 6, 3M 3F). Next, we profiled the RNA found in these EVs.

RESULTS: RNA associated with genes related to translation, ATP synthesis, mitochondrial function and immune response were downregulated in circulating EVs collected from adolescent macaques that had experienced maltreatment during infancy, while those involved in ion transport, metabolism and cell differentiation were upregulated in these EVs. Additionally, a significant proportion of EV RNA aligned to the microbiome and maltreatment during infancy altered the diversity of microbiome-associated RNA signatures found in EVs.

CONCLUSIONS: Our findings provide evidence that alterations in RNA associated with immune function, cellular energetics and the microbiome in circulating EVs may serve as enduring biomarkers of prior exposure to ELA. As a corollary, perturbations of these RNA profiles may offer novel molecular insight into how biology can remain altered long after the shadow of ELA has passed.},
}

@article {pmid40930337,
year = {2025},
author = {Mohammed, V and Muthuramamoorthy, M and Arasu, MV and Arockiaraj, J},
title = {Gut microbiome and mitochondrial crosstalk in Schizophrenia, a mental disability: Emerging mechanisms and therapeutic targets.},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {106371},
doi = {10.1016/j.neubiorev.2025.106371},
pmid = {40930337},
issn = {1873-7528},
abstract = {Gut-mitochondria is an emerging paradigm in understanding the pathophysiology of complex neuropsychiatric disorders such as Schizophrenia (SCZ). This bidirectional communication network connects the gastrointestinal microbiota with mitochondrial function and brain health, offering novel insights into disease onset and progression. SCZ, characterized by hallucinations, delusions, cognitive impairments, and social withdrawal, has traditionally been attributed to genetic and neurochemical imbalances. However, growing evidence highlights the role of systemic factors specifically, gut microbiome dysbiosis and mitochondrial dysfunction as key contributors to its etiology. Gut dysbiosis in SCZ involves a decrease in health-promoting microbiota such as Faecalibacterium and Roseburia, as well as an increase in pro-inflammatory taxa such as Proteobacteria. The dysbiosis leads to elevated levels of microbial metabolites like lipopolysaccharide (LPS) and trimethylamine-N-oxide (TMAO), which can overcome the intestinal barrier, induce systemic inflammation, and activate toll-like receptors and microglia which drive neuroinflammatory cascades. Simultaneously, mitochondrial dysfunction marked by impaired oxidative phosphorylation, ATP depletion, reactive oxygen species (ROS) accumulation, and mtDNA mutations exacerbates synaptic deficits and neurotransmitter dysregulation, particularly in dopaminergic, glutamatergic, and GABAergic systems. In this review we summarize what we currently know about the gut-mitochondria axis as being core to SCZ pathogenesis via molecular biology, neuroimmunology, and the microbiome. We also identify potential diagnostic biomarkers and therapeutic options that could include the use of probiotics, prebiotics, mitochondrial-targeted antioxidants, and dietary modifications in restoring gut and mitochondrial homeostasis. If the gut-mitochondria axis is linked, such programs may provide improved personalization, efficacy, and mechanistic precision, for future treatments of SCZ.},
}

@article {pmid40930256,
year = {2025},
author = {Kong, E and Cucco, A and Custovic, A and Fontanella, S},
title = {Machine learning in allergy research: A bibliometric review.},
journal = {Immunology letters},
volume = {},
number = {},
pages = {107088},
doi = {10.1016/j.imlet.2025.107088},
pmid = {40930256},
issn = {1879-0542},
abstract = {The emergence of big data and analytic approaches initiated research efforts to characterise different subtypes of allergic diseases, including tracking disease progression and identifying patterns that may offer insight into their development and progression. Triangulation from different data sources and study types may help to elucidate the directionality of relationships between variables at a very individual level by modelling the complex interdependencies between multiple dimensions (e.g., genome, transcriptome, epigenome, microbiome, and metabolome), thereby moving away from associative to a more causal analysis. To ascertain the role of machine learning in allergy research, we conducted a comprehensive systematic review of the current literature. the findings highlight and underscore the potential of using AI/ML approaches in advancing our understanding of allergic diseases, which ultimately enhances patient care through improved prevention, diagnosis, and management strategies. It is important to emphasise that there is no single 'best' analytical method, highlighting the importance of cross-disciplinary collaborations. A team science approach is crucial for ensuring the application of appropriate methodologies tailored to the research question at hand and that context-specific interpretations are being made, supported by critical appraisal from both the front- (e.g., clinicians) and back-end (e.g., analysts) of research processes.},
}

@article {pmid40930091,
year = {2025},
author = {Minich, JJ and Allsing, N and Din, MO and Tisza, MJ and Maleta, K and McDonald, D and Hartwick, N and Mamerto, A and Brennan, C and Hansen, L and Shaffer, J and Murray, ER and Duong, T and Knight, R and Stephenson, K and Manary, MJ and Michael, TP},
title = {Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.08.020},
pmid = {40930091},
issn = {1097-4172},
abstract = {The human gut microbiome is linked to child malnutrition, yet traditional microbiome approaches lack resolution. We hypothesized that complete metagenome-assembled genomes (cMAGs), recovered through long-read (LR) DNA sequencing, would enable pangenome and microbial genome-wide association study (GWAS) analyses to identify microbial genetic associations with child linear growth. LR methods produced 44-64× more cMAGs per gigabase pair (Gbp) than short-read methods, with PacBio (PB) yielding the most accurate and cost-effective assemblies. In a Malawian longitudinal pediatric cohort, we generated 986 cMAGs (839 circular) from 47 samples and applied this database to an expanded set of 210 samples. Machine learning identified species predictive of linear growth. Pangenome analyses revealed microbial genetic associations with linear growth, while genome instability correlated with declining length-for-age Z score (LAZ). This resource demonstrates the power of comparing cMAGs with health trajectories and establishes a new standard for microbiome association studies.},
}

@article {pmid40930012,
year = {2025},
author = {Wei, X and Zhao, X},
title = {Blood meal modulates midgut bacterial community structure and metabolic function in Aedes albopictus.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {56},
number = {},
pages = {101628},
doi = {10.1016/j.cbd.2025.101628},
pmid = {40930012},
issn = {1878-0407},
abstract = {The transmission of mosquito-borne diseases is intrinsically linked to mosquito blood-feeding behavior, yet the metabolic adaptations of the midgut microbiota in response to blood meals remain poorly understood. This study aimed to characterize the structural and functional changes in the midgut microbiota of Aedes albopictus following blood feeding and to elucidate their potential physiological implications. In this study, we employed 16S rRNA gene amplification coupled with PacBio Sequel II sequencing to characterize shifts in the midgut microbiota of Aedes albopictus before and after blood feeding on mice. Following blood feeding, we observed a significant restructuring of the microbial composition. This shift was characterized by a marked enrichment of Acinetobacter and Wolbachia, with Wolbachia displacing Flavisolibacter as the dominant taxon. Functionally, blood feeding promoted the upregulation of pathways related to mobile genetic elements and stress tolerance, largely driven by Lactobacillaceae. Furthermore, we presented the first comprehensive analysis of blood meal-induced metabolic network remodeling in the mosquito midgut microbiota. Post-prandial microbiota exhibited enhanced metabolic capacity for pyruvate and glycine catabolism. These findings reveal that blood meals induce rapid microbial metabolic adaptation aimed at nutrient utilization and oxidative management. This study provides insight into how microbiota dynamics support mosquito host adaptation under nutritional stress and offers potential targets for microbiome-based strategies to interfere with vector competence.},
}

@article {pmid40929977,
year = {2025},
author = {Han, F and Guo, Y and Zhao, C and Zhang, W and Zhang, M and Zhou, W},
title = {Halophilic heterotrophic ammonia assimilation biosystem shows stronger resilience and decreased ARGs abundance under sulfamethoxazole gradient stress compared with halophilic nitrification biosystem.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139749},
doi = {10.1016/j.jhazmat.2025.139749},
pmid = {40929977},
issn = {1873-3336},
abstract = {Differences of niche and nitrogen metabolism between halophilic nitrification (AN) and heterotrophic ammonia assimilation (HAA) biosystems determine microbiome resilience and antibiotic resistance genes (ARGs) transfer under antibiotic stress. However, the underlying mechanism of this difference remains unclear. This study compared the bioresponses and ARGs characteristics of the two biosystems under sulfamethoxazole (SMX) stress. Results revealed that both biosystems maintained above 90 % NH4[+] -N and 95 % SMX removal efficiencies at SMX concentrations below 1 mg/L. However, exposure to 5 mg/L SMX impaired both NH4[+]-N and SMX removal efficiencies. HAA biosystem exhibited stronger robustness and resilience than the AN biosystem under SMX stress. The microbial products synthesis, extracellular protein structure, and extracellular electron transfer in both biosystems displayed distinct responses to SMX. Metagenomic results revealed SMX shock decreased the abundance of ammonia-oxidizing bacteria and ammonia-monooxygenase gene in the AN biosystem, while the rapid turnover of heterotrophic microorganisms and the flexibility of ammonia assimilation genes maintained the HAA function in the HAA biosystem. Furthermore, SMX stress induced ARGs enrichment in the AN biosystem, whereas the abundance and diversity of ARGs in the HAA biosystem decreased under SMX stress. These findings highlighted the potential of novel HAA biosystem for antibiotics degradation and ARGs control.},
}

@article {pmid40929913,
year = {2025},
author = {Fakhruddin, KS and Kamal, I and Maglaperidze, T and Marya, A and Samaranayake, L and Porntaveetus, T},
title = {Autism and the Oral Microbiome: A Systematic Review of Host-microbial Interactions and Diversity.},
journal = {International dental journal},
volume = {75},
number = {6},
pages = {100957},
doi = {10.1016/j.identj.2025.100957},
pmid = {40929913},
issn = {1875-595X},
abstract = {BACKGROUND: Emerging evidence suggests a link between the oral microbiome and autism spectrum disorder (ASD), a neurodevelopmental condition characterised by social and behavioural impairments. The vast microbial reservoirs in the gut complement those of the oral cavity, suggesting a potential oral-gut-brain axis that may influence ASD and perhaps other neurological diseases, such as Parkinson's syndrome and Alzheimer's disease. For the first time, this systematic review synthesises the current knowledge of oral microbiome composition, diversity, and functionality in ASD and its potential diagnostic and therapeutic implications.

METHODS: A comprehensive literature search was conducted using Medline (PubMed), Embase, Scopus, and Google Scholar for peer-reviewed case-control and cross-sectional studies published between January 2000 and January 2025. Study quality was assessed using the Newcastle-Ottawa scale.

RESULTS: Nine studies (n = 8533; 2536 ASD and 5937 controls) met the inclusion criteria. The overall findings on microbial diversity were inconsistent; some studies reported alterations in ASD, while others found no significant differences. Functional profiling revealed enrichment of pathways involved in dopamine and GABA degradation, as well as disruptions in lysine metabolism, suggesting possible links to neurotransmitter imbalances in ASD. Although external factors such as selective eating, oral hygiene, and cognitive function were proposed to influence microbial profiles, statistical evidence supporting these associations was lacking. Moreover, no consistent link was found between oral microbiota features and core ASD symptoms like repetitive behaviours or communication deficits.

CONCLUSION: This review highlights subtle yet potentially significant alterations in the oral microbiome of individuals with ASD, particularly in metabolic pathways that affect neurotransmitters. While direct associations with clinical symptoms remain unsubstantiated, the findings emphasise the importance of future multi-omics and longitudinal studies to clarify the oral microbiome's role in ASD pathophysiology and to explore its potential in personalised therapeutic strategies.},
}

@article {pmid40929825,
year = {2025},
author = {Wang, Q and Yang, R and Yang, N and Wen, C},
title = {Can myostatin editing together with gut microbiota modulation produce more and tastier meat?.},
journal = {Meat science},
volume = {231},
number = {},
pages = {109950},
doi = {10.1016/j.meatsci.2025.109950},
pmid = {40929825},
issn = {1873-4138},
abstract = {The growing global population and economic development have increased the demand for meat with desired texture and flavor requirements. While intensive breeding and advancements in nutrition and management practices have driven significant improvements in meat production, sustainable solutions are still needed to further enhance both meat yield and quality. The Myostatin (MSTN) gene, which acts as an inhibitor of muscle growth and differentiation, has been extensively studied. Suppressing MSTN activity has been shown to induce muscle hyperplasia and/or hypertrophy in various animal species, resulting in increased skeletal muscle mass. However, MSTN deficiency also decreases fat mass, which can negatively impact meat flavor and quality. In addition to genetic regulation, the gut microbiome plays a crucial role in muscle development and fat accumulation. Emerging evidence suggests a complex interplay between the gut microbiota and the host, which may influence meat production and quality. Interestingly, MSTN-modified animals may exhibit altered gut microbiota, indicating the potential to manipulate gut microbiota to increase meat quality. Thus, integrating these insights is crucial to satisfy the growing consumer demand for high-quality meat while ensuring sustainable production practices. This review aims to provide a comprehensive overview of the effect of MSTN on muscle mass and fat accumulation, as well as the opportunities and challenges associated with using gene editing in farm animals to enhance meat quantity. Moreover, it emphasizes the importance of the gut microbiota in modulating muscle growth and fat deposition, highlighting the potential for gut microbiota manipulation to improve meat quality.},
}

@article {pmid40929788,
year = {2025},
author = {Rubio López, JM},
title = {[Oil and life: The impact of olive oil on human health. A review of the evidence supporting the recommendation for extra virgin olive oil consumption].},
journal = {Semergen},
volume = {51},
number = {8},
pages = {102582},
doi = {10.1016/j.semerg.2025.102582},
pmid = {40929788},
issn = {1578-8865},
abstract = {Extra virgin olive oil (EVOO) is a key functional food in the Mediterranean diet, renowned for its multiple health benefits. Rich in monounsaturated fatty acids, such as oleic acid, and bioactive compounds like polyphenols and tocopherols, EVOO helps reduce LDL cholesterol, increase HDL cholesterol, and protect against oxidative stress. Regular consumption is associated with a lower incidence of cardiovascular, metabolic, and neurodegenerative diseases. Studies such as PREDIMED and the Seven Countries Study have demonstrated its role in preventing cardiovascular events and reducing blood pressure. Additionally, EVOO contributes to cancer prevention, lowering the risk of specific types like breast and colon cancer. It also improves insulin sensitivity and intestinal microbiota health, promoting metabolic and cognitive balance. Recommended for its positive impact on health, EVOO should be a staple in a healthy daily diet, not only as a substitute for saturated fats but as an essential ingredient to enhance quality of life and prevent chronic diseases. The information search period covers the years 2000 to April 2025, in accordance with the inclusion criteria defined for the studies. These criteria prioritize relevant and up-to-date publications, while allowing exceptions for earlier works of historical significance.},
}

@article {pmid40929463,
year = {2025},
author = {Ogasawara, N},
title = {EVOLVING TRENDS AND EMERGING THEMES IN GUT MICROBIOTA RESEARCH: A COMPREHENSIVE BIBLIOMETRIC ANALYSIS (2015-2024).},
journal = {Arquivos de gastroenterologia},
volume = {62},
number = {},
pages = {e25023},
doi = {10.1590/S0004-2803.24612025-023},
pmid = {40929463},
issn = {1678-4219},
mesh = {*Bibliometrics ; *Gastrointestinal Microbiome/physiology ; Humans ; *Biomedical Research/trends ; },
abstract = {BACKGROUND: This study aims to analyze research trends and emerging insights into gut microbiota studies from 2015 to 2024 through bibliometric analysis techniques. By examining bibliographic data from the Web of Science (WoS) Core Collection, it seeks to identify key research topics, evolving themes, and significant shifts in gut microbiota research. The study employs co-occurrence analysis, principal component analysis (PCA), and burst detection analysis to uncover latent patterns and the development trajectory of this rapidly expanding field.

METHODS: This study uses a bibliometric approach to analyze 89,512 gut microbiota research articles published between 2015 and 2024 in the WoS Core Collection. Data preprocessing involved cleaning bibliographic data and identifying the 50 most frequent keywords. A co-occurrence matrix was constructed to capture keyword relationships, and a heatmap visualization illustrated these interconnections. PCA applied for dimensionality reduction, visualizing keyword distributions. Burst detection analysis using Kleinberg's algorithm identified rapidly growing research topics. Finally, the study contextualized its findings by linking results to broader research developments and discussing future research directions and potential opportunities.

RESULTS: The bibliometric analysis of gut microbiota research from 2015 to 2024 revealed significant trends and emerging themes. The total number of publications on gut microbiota increased approximately 5.82 times during this period, indicating a rapid expansion of the field. Co-occurrence analysis identified key thematic clusters, with "diet", "microbiome", and "immune function" emerging as central research topics. PCA further clarified topic relationships, revealing strong associations between gut microbiota and metabolic diseases, inflammation, and neurological disorders. Burst analysis of key terms demonstrated a shift in research focus, with increasing attention on the role of gut microbiota in precision medicine, neuroinflammation, and host-microbiome interactions. These findings provide a comprehensive overview of gut microbiota research trends, offering insights into critical developments and guiding future investigations into microbiome-based therapies and disease prevention.

CONCLUSION: This study provides a comprehensive bibliometric analysis of gut microbiota research from 2015 to 2024, highlighting key trends and emerging directions. The findings show that gut microbiota studies have expanded to include diet, health, and disease. The strong link between "diet" and "microbiota" in this study suggests dietary interventions are central to this future research. Rapidly growing keywords like "intestinal", "disease", and "mice" indicate a focus on translational and experimental research. These insights reveal the shifting landscape of gut microbiota research and emphasize the need for further exploration of diet-microbiota interactions, personalized nutrition, and clinical applications.},
}

*Bibliometrics
*Gastrointestinal Microbiome/physiology
Humans
*Biomedical Research/trends

@article {pmid40929253,
year = {2025},
author = {Golan, Y and Nyquist, SK and Liu, Z and Ennis, D and Zhao, J and Blair, E and Khan, AR and Prahl, M and Gaw, SL and Yassour, M and Engelhardt, BE and Flaherman, VJ and Ahituv, N},
title = {Genomic characterization of normal and aberrant human milk production.},
journal = {Science advances},
volume = {11},
number = {37},
pages = {eadr7174},
doi = {10.1126/sciadv.adr7174},
pmid = {40929253},
issn = {2375-2548},
mesh = {Humans ; *Milk, Human/metabolism/microbiology ; Female ; Lipid Droplets/metabolism ; Transcriptome ; *Lactation/genetics ; *Genomics/methods ; Glycoproteins/genetics/metabolism ; Gene Expression Profiling ; Breast Feeding ; Adult ; Glycolipids/genetics/metabolism ; Microbiota/genetics ; Infant ; },
abstract = {Breastfeeding is essential for reducing infant morbidity and mortality, yet exclusive breastfeeding rates remain low, often because of insufficient milk production. The molecular causes of low milk production are not well understood. Fresh milk samples from 30 lactating individuals, classified by milk production levels across postpartum stages, were analyzed using genomic and microbiome techniques. Bulk RNA sequencing of milk fat globules (MFGs), milk cells, and breast tissue revealed that MFG-derived RNA closely mirrors luminal milk cells. Transcriptomic and single-cell RNA analyses identified changes in gene expression and cellular composition, highlighting key genes (GLP1R, PLIN4, and KLF10) and cell-type differences between low and high producers. Infant microbiome diversity was influenced by feeding type but not maternal milk production. This study provides a comprehensive human milk transcriptomic catalog and highlights that MFG could serve as a useful biomarker for milk transcriptome analysis, offering insights into the genetic factors influencing milk production.},
}

Humans
*Milk, Human/metabolism/microbiology
Female
Lipid Droplets/metabolism
Transcriptome
*Lactation/genetics
*Genomics/methods
Glycoproteins/genetics/metabolism
Gene Expression Profiling
Breast Feeding
Adult
Glycolipids/genetics/metabolism
Microbiota/genetics
Infant

@article {pmid40928899,
year = {2025},
author = {Khan, ZA and Labala, RK and Ju, LS and Gravenstein, N and Setlow, B and Martynyuk, AE},
title = {The contribution of the brain-gut-microbiome axis to intergenerational abnormalities in a rat model of perioperative neurocognitive disorder.},
journal = {Anesthesiology},
volume = {},
number = {},
pages = {},
doi = {10.1097/ALN.0000000000005745},
pmid = {40928899},
issn = {1528-1175},
abstract = {BACKGROUND: The brain-gut-microbiome (BGM) axis is a communication network through which the brain and gastrointestinal microbiota interact via neural, hormonal, immune, and gene expression mechanisms. Gut microbiota dysbiosis is thought to contribute to neurocognitive disorders, including perioperative neurocognitive disorder (PND), and to various metabolic abnormalities. Recently, we reported that sevoflurane induces neurocognitive deficits in exposed rats as well as their future offspring, with male offspring being particularly affected (intergenerational PND). In this study, we examined in the same animals whether the intergenerational effects of sevoflurane involve abnormalities in the BGM axis, and whether they are mitigated by paternal pretreatment with either the Na+-K+-Cl- (NKCC1) Cl- transporter inhibitor bumetanide or the glucocorticoid receptor inhibitor RU486, as previously demonstrated for neurocognitive deficits.

METHODS: Male Sprague Dawley rats (F0 generation) were exposed to 2.1% sevoflurane for 3 hours on postnatal days 56, 58, and 60 (F0M_S group). Prior to each sevoflurane exposure, distinct experimental groups of F0 males received bumetanide (F0M_BS group) or RU486 (F0M_RS group). These males were mated on postnatal day 90 to produce offspring (F1 generation). Gut microbiota were profiled using 16S rRNA gene sequencing, and brain changes analyzed via RNA sequencing of hippocampal samples.

RESULTS: F1 male offspring of F0M_S sires exhibited heightened corticosterone responses to stress, increased inflammatory markers, altered hippocampal transcriptomes, gut microbiota dysbiosis, elevated serum low-density lipoprotein cholesterol levels, and increased body weight. The only abnormality observed in F1 females was a shift in microbial diversity. F0M_S displayed profound alterations in hippocampal transcriptome, while microbial diversity was the only parameter affected in their gut microbiota. Bumetanide or RU486 mitigated most abnormalities, except increased body weight in F1 males.

CONCLUSION: Paternal sevoflurane exposure in rats induces BGM axis abnormalities, particularly in male offspring, despite the absence of direct anesthetic exposure. Pretreatment with bumetanide or RU486 showed therapeutic efficacy.},
}

@article {pmid40928712,
year = {2025},
author = {Noble, O and Jeon, D and Lewis, M and Fan, C and Nasir, K and Abraham, BP},
title = {From Gut Inflammation to Cardiovascular Conflagration: Mapping IBD's Cardiometabolic Risks.},
journal = {Current atherosclerosis reports},
volume = {27},
number = {1},
pages = {89},
pmid = {40928712},
issn = {1534-6242},
mesh = {Humans ; *Cardiovascular Diseases/etiology/epidemiology ; *Inflammatory Bowel Diseases/complications ; *Inflammation ; Gastrointestinal Microbiome ; Dysbiosis ; Risk Factors ; Heart Disease Risk Factors ; },
abstract = {PURPOSE OF REVIEW: This review aims to characterize the known cardiovascular (CV) manifestations associated with inflammatory bowel disease (IBD) and the underlying mechanisms driving these associations.

RECENT FINDINGS: Gut dysbiosis, a hallmark of patients with IBD, can result in both local and systemic inflammation, thereby potentially increasing the risk of cardiovascular disease (CVD) in the IBD population. Micronutrient deficiencies, anemia, and sarcopenia independently increase the risk of CVD and are frequent comorbidities of patients with IBD. IBD is a chronic inflammatory condition with significant and underrecognized cardiovascular complications. Patients with IBD frequently develop coronary artery disease (CAD) in the absence of traditional risk factors such as obesity and smoking and experience an earlier onset of CVD compared to the general population. Moreover, IBD has been associated with increased risks of arrhythmia, myocarditis, pericarditis, heart failure, and venous thromboembolism. Nontraditional risk factors related to IBD, including disease activity, prolonged disease duration, and cardiovascular risks associated with certain IBD medications, significantly contribute to the increased risk of CVD. While additional prospective research is required to fully elucidate the mechanisms driving CVD in IBD patients, current evidence suggests that minimizing disease activity, optimizing nutritional status, addressing gut dysbiosis, and mitigating the traditional risk factors could significantly reduce the burden of CVD in the IBD population. As our understanding of the link between IBD and cardiovascular disease grows, healthcare providers must closely monitor cardiovascular health and risk factors in patients with IBD, particularly during flares, active disease, and hospitalizations.},
}

Humans
*Cardiovascular Diseases/etiology/epidemiology
*Inflammatory Bowel Diseases/complications
*Inflammation
Gastrointestinal Microbiome
Dysbiosis
Risk Factors
Heart Disease Risk Factors

@article {pmid40928706,
year = {2025},
author = {Zou, X and Zhou, X and Wang, C and Zheng, Y and Li, Y and Suo, H},
title = {The composition, influencing factors, and physiological functions of bifidobacteria in the infant gut: a review.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo02271a},
pmid = {40928706},
issn = {2042-650X},
abstract = {Bifidobacteria are naturally found in the human gut and quickly establish dominance shortly after birth, playing a crucial role in the development and stability of the infant gut microbiota. A growing body of research suggests that host and environmental factors shape the colonization and the relative abundance of bifidobacteria in the infant gut during early life. Understanding the factors that influence bifidobacterial colonization and maintaining normal colonization levels are keys to ensuring gut health. Bifidobacteria exhibit antibacterial, anti-inflammatory, and pathogen-resistant properties, and have the ability to maintain intestinal microbiota homeostasis. Clinically, they have been widely used to manage manifestations of various conditions, such as constipation, diarrhea, inflammatory bowel disease, and liver injury. This review focuses on the composition of bifidobacteria in the infant gut, the relevant factors influencing their colonization and abundance, and their physiological functions, to advance a deeper comprehension of the health-protective role and mechanisms of bifidobacteria within the host microbiome. This information provides an important basis for further understanding the underlying mechanisms of action, and lays the foundation for developing Bifidobacterium-based interventions to promote the healthy development of the infant gut microbiome and prevent related diseases.},
}

@article {pmid40928632,
year = {2025},
author = {Mafe, AN and Smart, OO and Edo, GI and Akpoghelie, PO and Gaaz, TS and Yousif, E and Isoje, EF and Igbuku, UA and Ismael, SA and Essaghah, AEA and Ahmed, DS and Ozsahin, DU and Umar, H},
title = {Genesis, Health Benefits, and Future Perspectives of Probiotics: Exploring Endogenous and Exogenous Classes, Innovations, and Research Gaps.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40928632},
issn = {1867-1314},
abstract = {Probiotics are live beneficial microorganisms that confer health benefits to the host when administered in adequate amounts, have gained considerable scientific and commercial interest for their ability to support gut health, strengthen immunity, and reduce disease risk. This review traces the genesis of probiotic science from its origins in traditional fermented foods to contemporary clinical applications, offering a conceptual understanding of its evolution. A clear distinction is drawn between endogenous probiotics, naturally resident in the human microbiome, and exogenous probiotics, introduced via dietary supplements and functional foods. The broad spectrum of documented health benefits is examined, encompassing digestive, immune, metabolic, neurological, and dermatological outcomes. Recent innovations are highlighted, including bioengineered probiotic strains with targeted therapeutic functions, the integration of probiotics with prebiotics as synbiotics, and advanced delivery systems such as microencapsulation and nanotechnology. Special attention is given to regulatory frameworks, with global comparisons and a focused case study on Argentina, alongside a structured roadmap for translating research into market-ready products. The review also addresses inclusivity in probiotic use, emphasizing safety considerations across diverse populations, and underscores the strain-specific nature of probiotic effects. Current challenges such as commercialization gaps, regulatory inconsistencies, and underexplored applications in non-digestive health domains are critically discussed. The conclusion calls for interdisciplinary collaboration among microbiologists, nutritionists, clinicians, and technologists to accelerate innovation, ensure equitable access, and maximize the potential of probiotics in promoting health and preventing disease.},
}

@article {pmid40928460,
year = {2025},
author = {Cole, AL and Marzahn, MR and Valdespino, EL and Patel, R and Cole, AM},
title = {Nasal microbiome inhabitants with anti-Staphylococcus aureus activity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0102425},
doi = {10.1128/spectrum.01024-25},
pmid = {40928460},
issn = {2165-0497},
abstract = {UNLABELLED: Staphylococcus aureus (SA) colonizes most mammals but also represents a danger in clinical settings because it evolves resistance against antibiotics, and SA infections represent a leading cause of death worldwide. SA nasal carriage provides the bacterial reservoir for opportunistic infection because clinical strains often match the patient's own nasally carried strain. The global SA carriage rate is typically reported as 25%-30% after sampling subjects once or twice and defining carrier status using culture-based methods. Here, we collected nasal swabs from 31 healthy subjects twice weekly for an average of 5 months and determined that 23 of 31 subjects (74.9%) presented SA colonies at least once during longitudinal sampling. We explored the nasal microbiota of individuals who rarely or never tested SA-positive and evaluated 25 nasal isolates for anti-SA properties using culture conditions modeling the nasal mucosa. We determined that members of the Gammaproteobacteria class, including Klebsiella spp., Serratia marcescens, and Enterobacter hormaechei, inhibited SA survival. Firmicutes Dolosigranulum pigrum and Streptococcus mitis/oralis also inhibited SA recovery from nasal tissues. Klebsiella spp. (aerogenes, variicola, pneumoniae) activity was contact-independent and not mediated by sequestration of iron or other vital nutrients. K. aerogenes was the most potent SA inhibitor (>99% reduction), and its action was mediated by secreted cationic peptide(s) or protein(s). Collectively, this project determined that most people may be nasally colonized with SA throughout life. It also represents an important step toward explaining why some hosts don't exhibit detectable nasal SA and highlights a potential source of naturally occurring and novel antibiotics targeting SA.

IMPORTANCE: Staphylococcus aureus (SA) is a common member of the human microbiota, colonizing people transiently throughout life, and SA nasal carriage is an important reservoir for the spread of this bacterium. The global economic toll of SA infections is enormous, and antibiotic-resistant strains continue to emerge. Therefore, new approaches to decolonize carriers of SA are urgently needed. To better understand the dynamics of nasal SA carriage versus non-carriage, we monitored subjects longitudinally and isolated and identified species that associate with SA culture-negative noses. While several members of the Gammaproteobacteria class demonstrated anti-SA activity, the nasal Klebsiella spp. potently inhibited (>99%) SA survival in a contact-independent manner. For multiple nasal isolates of K. aerogenes from our donor cohort, this inhibition was attributed to a small, cationic, proteinaceous molecule(s). The secreted products of nasal Gammaproteobacteria (e.g., Klebsiella/Serratia spp.) warrant further investigation as potential sources of new SA decolonization agents.},
}

@article {pmid40928445,
year = {2025},
author = {Gallo, RL},
title = {Drugs and Bugs in Atopic Dermatitis: Benefits to the Skin Microbiome from Targeted Immunotherapies.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.08.001},
pmid = {40928445},
issn = {1523-1747},
}

@article {pmid40928296,
year = {2025},
author = {Martinez, A and Ruth, N and Hatch, A and Chain, P and Shakya, M},
title = {Aerosol biome of a cafeteria and medical facility in Los Alamos, New Mexico, USA.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0076625},
doi = {10.1128/mra.00766-25},
pmid = {40928296},
issn = {2576-098X},
abstract = {Aerosol sampling with next-generation sequencing was used to characterize microbial communities in a cafeteria and medical facility waiting room in Los Alamos, New Mexico, USA. We detected sequences from human, bacteria, archaea, fungi, other eukaryotes, and viruses, providing insights into the diversity of the aerosol microbiome.},
}

@article {pmid40928248,
year = {2025},
author = {Hourigan, D and Field, D and Murray, E and Sugrue, I and O'Connor, PM and Hill, C and Ross, RP},
title = {Nisin-like biosynthetic gene clusters are widely distributed across microbiomes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0154525},
doi = {10.1128/mbio.01545-25},
pmid = {40928248},
issn = {2150-7511},
abstract = {Bacteriocins are antimicrobial peptides/proteins that can have narrow or broad inhibitory spectra and remarkable potency against clinically relevant pathogens. One such bacteriocin that is extensively used in the food industry and with potential for biotherapeutic application is the post-translationally modified peptide, nisin. Recent studies have shown the impact of nisin on the gastrointestinal microbiome, but relatively little is known of how abundant nisin production is in nature, the breadth of existing variants, and their antimicrobial potency. Whether or not nisin production and immunity are widespread in gut microbiomes could be a deciding factor in determining the suitability of nisin as a prospective therapeutic for human and/or animal infections. Here, we used publicly available data sets to determine the presence of widespread and diverse nisin biosynthetic gene clusters (nBGCs) across the biosphere. We show that 30% of these nBGCs are predicted to be located on mobile genetic elements, with some found in pathogenic bacteria. Furthermore, we highlight evidence of horizontal gene transfer of nBGCs between genera, including Streptococcus suis, Enterococcus hirae, and Staphylococcus aureus. In all, we describe 107 novel nisin-like peptides. Five representatives were heterologously expressed and all exhibited antimicrobial activity. We further characterized nisin VP, a novel natural nisin variant produced by Velocimicrobium porci isolated from the porcine gut. The peptide has a completely novel hinge region "AIQ" not detected in other nisin variants to date. While nisin VP could be induced by nisin A, the latter could not be induced by nisin VP.IMPORTANCEOur research reveals the heretofore underappreciated presence of diverse and widespread nisin-like biosynthetic gene clusters in microbiomes across the globe. Notably, different clusters share similar biosynthetic machinery but differ in sequence, suggesting gene transfer and adaptation. We identify >100 new nisin-like variants, including several in species not previously known to produce nisin. This emphasizes the widespread dissemination of nisin-like gene clusters and the diversity of novel core peptides with biotherapeutic potential. These findings point to a role for nisin in microbial competition in microbiomes. We heterologously expressed nine nisin variants, five of which are completely novel peptides, using the nisin A biosynthetic machinery and confirmed that all exhibited antimicrobial activity.},
}

@article {pmid40928236,
year = {2025},
author = {Liu, D and Hu, J and Zhang, D and Ren, S and Zhao, L and Gao, H and Hu, S and Xu, S and Liang, G},
title = {Use of the CHM13-T2T genome improves metagenomic analysis by minimizing host DNA contamination.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0084025},
doi = {10.1128/msystems.00840-25},
pmid = {40928236},
issn = {2379-5077},
abstract = {Human-associated metagenomic data often contain human nucleic acid information, which can affect the accuracy of microbial classification or raise ethical concerns. These reads are typically removed through alignment to the human genome using various metagenomic mapping tools or human reference genomes, followed by filtration before metagenomic analysis. In this study, we conducted a comprehensive analysis to identify the optimal combination of alignment software and human reference genomes using benchmarking data. Our findings show that the combination of bwa-mem and the telomere-to-telomere human genome (CHM13-T2T) is the most effective in removing human reads in simulated data. We also analyzed CHM13-T2T-derived sequences in RefSeq to understand how CHM13-T2T reduces false positive results. Finally, we assessed clinical samples and found that CHM13-T2T effectively reduces host-derived contamination, particularly in low microbial biomass samples. This study provides a thorough overview of the application of CHM13-T2T in metagenomic analysis and highlights its significance in improving microbial classification accuracy.IMPORTANCEHuman gene sequences account for a large proportion of metagenomic sequences. To gain accurate and precise microbiome information, effective host-derived contamination removal methods are required. Both the alignment algorithm and the reference genome could influence the effectiveness of this process. The telomere-to-telomere human genome (CHM13-T2T) is a state-of-the-art human genome with 216 Mbp of additional new sequences compared with the commonly used GRCh38.p14. Our findings show the optimal dehosting effect of CHM13-T2T combined with the bwa-mem software in metagenomic analysis. We also investigate the reasons for the superiority of CHM13-T2T. Our study provides insights into optimal strategies for host sequence removal from metagenomic data. A standard reference is proposed for future metagenomic analysis, which can improve the accuracy of microbial identification.},
}

@article {pmid40928232,
year = {2025},
author = {Allman, HM and Bernate, EP and Franck, E and Oliaro, FJ and Hartmann, EM and Crofts, TS},
title = {Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0103925},
doi = {10.1128/msystems.01039-25},
pmid = {40928232},
issn = {2379-5077},
abstract = {A significant challenge in the field of microbiology is the functional annotation of novel genes from microbiomes. The increasing pace of sequencing technology development has made solving this challenge in a high-throughput manner even more important. Functional metagenomics offers a sequence-naive and cultivation-independent solution. Unfortunately, most methods for constructing functional metagenomic libraries require large input masses of metagenomic DNA, putting many sample types out of reach. Here, we show that our functional metagenomic library preparation method, METa assembly, can be used to prepare useful libraries from much lower input DNA quantities. Standard methods of functional metagenomic library preparation generally call for 5-60 µg of input metagenomic DNA. We demonstrate that the threshold for input DNA mass can be lowered at least to 30.5 ng, a 3-log decrease from prior art. We prepared functional metagenomic libraries using between 30.5 ng and 100 ng of metagenomic DNA and found that despite their limited input mass, they were sufficient to link MFS transporters lacking substrate-specific annotations to tetracycline resistance and capture a gene encoding a novel GNAT family acetyltransferase that represents a new streptothricin acetyltransferase, satB. Our preparation of functional metagenomic libraries from aquatic samples and a human stool swab demonstrates that METa assembly can be used to prepare functional metagenomic libraries from microbiomes that were previously incompatible with this approach.IMPORTANCEBacterial genes in microbial communities, including those that give resistance to antibiotics, are often so novel that sequencing-based approaches cannot predict their functions. Functional metagenomic libraries offer a high-throughput, sequence-naive solution to this problem, but their use is often held back due to their need for large quantities of metagenomic DNA. We demonstrate that our functional metagenomic library preparation method, METa assembly, can prepare these libraries using as little as ~30 ng of DNA, approximately 1,000-fold less than other methods. We use METa assembly to prepare functional metagenomic libraries from low-biomass aquatic and fecal swab microbiomes and show that they are home to novel tetracycline efflux pumps and a new family of streptothricin resistance gene, respectively. The efficiency of the METa assembly library preparation method makes many otherwise off-limits, low-biomass microbiome samples compatible with functional metagenomics.},
}

@article {pmid40928221,
year = {2025},
author = {Arosoaie, A and Hennessy, E},
title = {Teaching critical histories of microbiology: two case studies.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0021024},
doi = {10.1128/jmbe.00210-24},
pmid = {40928221},
issn = {1935-7877},
abstract = {In recent years, microbiologists have emphasized the importance of understanding the historical relation between microbiomes and public health as a means of contributing to social equity. Consistent with critical engaged and anti-racist pedagogical practices, we developed a curricular intervention-HEALing the Sciences-that centers critical histories of science as means to educate scientists about how science has contributed to and replicated inequities in society. Here, we describe two case studies that our interdisciplinary team designed, implemented, and assessed specifically for a module on the history of microbiology. Both case studies, "Germs and Jim Crow" and "Ghosting Race," encourage participants to think critically about the field of microbiology's historical contributions to the maintenance of racial disparities in ways that remain relevant to the present. In this manuscript, we expand on the implementation and assessment of the case studies, suggesting possible modifications that would enable instructors to adopt and adapt the research design we have developed. We have taught these case studies via remote synchronous instruction to a cohort of microbiologists, including graduate students, faculty, and research staff, who provided extensive qualitative feedback through surveys that suggest both the effectiveness of the material and possible modifications for improvement. We hope these case studies will provide STEM educators in microbiology and beyond with useful pedagogical tools to advance anti-racist efforts in the academe.},
}

@article {pmid40928220,
year = {2025},
author = {Dong, L and Yang, J and Wu, H and Sun, Y and Liu, J and Yuan, H and Wang, M and Dai, Y and Teng, F and Jing, G and Yang, F},
title = {Metagenomic research on the structural difference of plaque microbiome from different caries stages and the construction of a caries diagnostic model.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0004425},
doi = {10.1128/msystems.00044-25},
pmid = {40928220},
issn = {2379-5077},
abstract = {Development of dental caries is a dynamic process; yet, there is limited knowledge on microbial differences at various stages of caries at higher resolution. To investigate the shifting microbiome profiles across different caries stages, 30 children were enrolled in this study, including 15 caries-active patients and 15 caries-free individuals. Plaque samples were collected from the buccal surface of caries-free subjects, defined as confident health (CH; n = 15). For caries-active individuals, plaque samples were collected from non-cavitated surfaces (defined as relative health [RH], n = 15), enamel caries (EC; n = 15), and dentin caries samples (DC; n = 15). All the above samples were sequenced through the 2bRAD sequencing platform to reveal the microbial community structures in each group. We identified significant differences in microbial community structures from different caries stages. First, the CH group showed the highest species richness (P < 0.05), and then followed by the RH and EC groups with lower richness, and the lowest richness was found in the DC group, yet no significant difference was found among the last three groups (P > 0.05). Second, the microbial structure exhibited the greatest difference between CH and DC groups, followed by the distance between RH/EC and DC groups, and the smallest difference was found between RH and EC groups. Third, specific species were found with a significant difference during the different caries stages. Therefore, we developed a diagnostic model using deep learning methods based on neural networks to diagnose different caries stages with an AUC of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.IMPORTANCEThe diagnosis and treatment of dental caries are crucial for human oral health. Previous studies have focused on the microbial differences between caries and healthy teeth, but there was not enough knowledge on the microbial differences at different stages of dental caries. Our findings could provide a high-resolution understanding of the microbial divergencies among different stages of dental caries and thus build microbial-based diagnostic models for differentiating dental caries status using deep learning methods with an accuracy of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.},
}

@article {pmid40928120,
year = {2025},
author = {Lauwens, K and Saghi, M and Germonpré, PJ and Zayed, N and Boon, N and Bernaerts, K and Teughels, W and Van Holm, W},
title = {Can We Combine Mouthrinses With Probiotics? An Evaluation of Their Compatibility and Combined Therapy on Oral Biofilms.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70033},
pmid = {40928120},
issn = {1600-0765},
abstract = {AIM: Multiple oral pathologies requiring antiseptic mouthrinses for prevention or treatment. However, nonselective elimination of the microbes may also harm beneficial commensal, healthy bacteria. Promicrobial strategies, such as probiotics, aim to rebalance the oral microbiome rather than eradicate it; however, we hypothesised that their incorporation might be challenged due to the microbiome's inherent resistance to outsiders. In this study, their combined effect on an in vitro oral biofilm model was assessed. Instead of comparing mouthrinses to probiotics, could they be combined to obtain the best of both worlds?

METHODS: The compatibility of two commonly used Limosilactobacillus reuteri strains with 13 commercially available mouthrinses was tested by evaluating probiotic survival in the mouthrinses and their combined effect on a multispecies in vitro biofilm model.

RESULTS: Differences in compatibility were observed. Several mouthrinses showed moderate compatibility and improved the probiotics incorporation into biofilms. One mouthrinse (O7 Active Oxygen) demonstrated the most favourable compatibility, enabling abundant probiotic incorporation and beneficial biofilm composition changes.

CONCLUSION: The combination of mouthrinses and probiotics has the potential to improve the treatment of oral pathologies and promote a healthier oral microbiome, although compatibility varies.},
}

@article {pmid40927984,
year = {2025},
author = {Dethier, L and Jespersen, JRP and Lloyd, J and Pupi, E and Li, R and Zhou, W and Liu, F and Bai, Y and Halkier, BA and Xu, D},
title = {Isolation of a Novel Plant Growth-Promoting Dyella sp. From a Danish Natural Soil.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70186},
doi = {10.1111/1758-2229.70186},
pmid = {40927984},
issn = {1758-2229},
support = {2022YFF1001800//National Science and Technology Infrastructure Program/ ; NNF20OC0060824//Novo Nordisk Fonden/ ; //Tencent Foundation (XPLORER-2023-1017)/ ; },
mesh = {*Soil Microbiology ; Plant Roots/microbiology/growth & development ; *Arabidopsis/growth & development/microbiology ; Denmark ; Seedlings/growth & development/microbiology ; Phylogeny ; Solanum lycopersicum/growth & development/microbiology ; Biomass ; RNA, Ribosomal, 16S/genetics ; Plant Development ; },
abstract = {Natural soils are reservoirs of potentially beneficial microbes that can improve plant performance. Here, we isolated 75 bacterial strains from surface-sterilised roots of Arabidopsis thaliana (Arabidopsis) grown in a natural soil derived from an alder swamp. Culture-dependent isolation of individual strains from the roots, followed by monoassociation-based screening, identified seven bacteria that promoted Arabidopsis seedling weight. Of those, we identified a new species from the Dyella genus which increased the biomass of Arabidopsis and tomato seedlings in agar, as well as the shoot biomass of Arabidopsis grown in both the alder swamp soil and potting soil. Dyella sp. A4 specifically promoted the elongation of lateral roots without affecting lateral root number and primary root elongation. The new Dyella sp. A4 expands the toolbox of biostimulants for plant growth promotion via modulating root architecture.},
}

*Soil Microbiology
Plant Roots/microbiology/growth & development
*Arabidopsis/growth & development/microbiology
Denmark
Seedlings/growth & development/microbiology
Phylogeny
Solanum lycopersicum/growth & development/microbiology
Biomass
RNA, Ribosomal, 16S/genetics
Plant Development

@article {pmid40927879,
year = {2025},
author = {Wang, X and Wang, J and Chen, J and Bezemer, TM and Song, Z and Wanek, W and Liu, G and Zhang, C},
title = {Environmental Stresses Constrain Soil Microbial Community Functions by Regulating Deterministic Assembly and Niche Width.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70096},
doi = {10.1111/mec.70096},
pmid = {40927879},
issn = {1365-294X},
support = {2023YFF1305103//National Key Research and Development Program of China/ ; 42130717//National Sciences Foundation of China/ ; 42177449//National Sciences Foundation of China/ ; 2024JC-JCQN-35//Shaanxi Provincial Science Fund for Distinguished Young Scholars/ ; },
abstract = {Increasing evidence indicates that the loss of soil microbial α-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial α-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal α- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal α-diversity declined under high environmental stress across three soil layers (0-20 cm, 20-40 cm and 40-60 cm). Metagenomic-based analyses showed that the diversity of functional genes decreased along the stress gradients. High stress enhanced the abundance of genes associated with broad functional categories (e.g., glycolysis/gluconeogenesis, TCA cycle, DNA replication/repair and cell growth/death) but reduced the abundance of genes linked to specialised functional categories (e.g., C, N, S and methane metabolism). Phylogenetic null models and niche analyses indicated that stochastic assembly processes predominated in high-diversity communities, in which bacterial and fungal taxa had a narrow ecological niche. However, in low-diversity communities, deterministic assembly processes were dominant, and taxa had wide niches, correlating with the reduction in gene abundance observed for broad and specialised functional categories. Given the essential role of the microbiome in regulating ecosystem functions, our findings suggest that low-diversity-induced deterministic community assembly processes and a wide niche under high environmental stress may regulate microbial functions. These findings emphasise the ecological mechanisms through which microbial biodiversity regulates terrestrial ecosystem functioning.},
}

@article {pmid40927726,
year = {2025},
author = {Eiman, L and Moazzam, K and Anjum, S and Kausar, H and Sharif, EAM and Ibrahim, WN},
title = {Gut dysbiosis in cancer immunotherapy: microbiota-mediated resistance and emerging treatments.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1575452},
pmid = {40927726},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/therapy ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/microbiology ; *Immunotherapy/methods ; Animals ; *Drug Resistance, Neoplasm ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Tumor Microenvironment/immunology ; },
abstract = {Cancer is a multifaceted disease driven by a complex interplay of genetic predisposition, environmental factors and lifestyle habits. With the accelerating pace of cancer research, the gut microbiome has emerged as a critical modulator of human health and immunity. Disruption in the gut microbial populations and diversity, known as dysbiosis, has been linked with the development of chronic inflammation, oncogenesis, angiogenesis and metastasis. This review discusses the microbial species associated with various types of cancer and the pathways involved in their tumorigenic effect including mechanisms like inflammatory cytokine response, immune modulation, genotoxicity and modification of the tumor microenvironment. Diagnostic tools such as metagenomics, metabolomics, and the use of dysbiosis indexes help in the detection of gut bacterial imbalances, enabling early detection of cancer and potential intervention. Gut dysbiosis diminishes the efficacy of cancer treatments including immunotherapies, and creates immunotherapy resistance by altering drug metabolism and driving immunometabolic reprogramming, allowing tumor cells to evade immune attack. Immunometabolic reprogramming through gut microbiota modulation provides a new avenue to be explored that can restore anti-tumor immunity and reverse resistance to cancer treatments. This review also highlights the use of fecal microbiota transplantation and probiotics to mitigate chances of dysbiosis-related cancer progression. Through a comprehensive assessment of the role of gut microbiota in cancer, this review underscores the need for the use of gut microbial biomarkers for cancer detection and microbiome-targeting strategies to individualize cancer treatment.},
}

Humans
*Dysbiosis/immunology/therapy
*Gastrointestinal Microbiome/immunology
*Neoplasms/therapy/immunology/microbiology
*Immunotherapy/methods
Animals
*Drug Resistance, Neoplasm
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Tumor Microenvironment/immunology

@article {pmid40927712,
year = {2025},
author = {Mattavelli, E and Agustoni, F and Tartara, A and De Simeis, F and Perrone, L and Caccialanza, R and Pedrazzoli, P and Da Prat, V},
title = {Nutritional status, immunonutrition, and gut microbiome: a coming of age for immunotherapy?.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1612567},
pmid = {40927712},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immunotherapy/methods ; *Nutritional Status ; *Neoplasms/therapy/immunology ; Body Composition ; Animals ; Immunonutrition Diet ; },
abstract = {In the last decades, immunotherapy has revolutionized cancer treatment. Despite its success, a significant number of patients fail to respond, and the underlying causes of ineffectiveness remain poorly understood. Factors such as nutritional status and body composition are emerging as key predictors of immunotherapy outcomes. In particular, poor nutritional status, sarcopenia, and low skeletal muscle mass are associated with poorer survival and immunotherapy response in several cancers. Conversely, certain parameters of body composition, such as adiposity, may have beneficial effects on immunotherapy efficacy. Nutritional status and body composition can be targeted through tailored nutritional support, making it a potential strategy to improve immunotherapy outcomes. Specific nutrients and modulation of the gut microbiota may further enhance immune functions, offering promising avenues for clinical improvement. Despite the promising potential of tailored nutritional support, clinical evidence remains limited, and further research is needed to establish optimal strategies to optimize immunotherapy response and effectiveness.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Immunotherapy/methods
*Nutritional Status
*Neoplasms/therapy/immunology
Body Composition
Animals
Immunonutrition Diet

@article {pmid40927699,
year = {2025},
author = {Wang, X and Zhao, R and Guo, J and Yang, K and Xu, B},
title = {The Role of Plasma Metabolites in Mediating the Effect of Gut Microbiota on Obstructive Sleep Apnea: A Two-Step, Two-Sample Mendelian Randomization Study.},
journal = {Nature and science of sleep},
volume = {17},
number = {},
pages = {2119-2130},
pmid = {40927699},
issn = {1179-1608},
abstract = {BACKGROUND: Recent research has increasingly underscored a significant correlation between gut microbiota and obstructive sleep apnea (OSA). Probiotics have emerged as promising adjunctive interventions for OSA. Metabolites and their related biochemical pathways have emerged as important contributors to the development of OSA. This study aimed to estimate the causal association between gut microbiota and OSA and to quantify the mediating effects of metabolites.

METHODS: We employed two-step, two-sample Mendelian randomization techniques, utilizing single nucleotide polymorphisms as genetic instruments for exposures and mediators. Summary statistics were obtained from genome-wide association studies of gut microbiota (the Dutch Microbiome Project, n=7,738), plasma metabolites (the Canadian Longitudinal Study on Aging cohort, n=8,299), and OSA (FinnGen database, n=410,385). To ensure the robustness of our findings, sensitivity analyses and heterogeneity tests were systematically conducted.

RESULTS: In the Dutch Microbiome Project, species Parabacteroides merdae, genus Faecalibacterium, species Faecalibacterium prausnitzii and species Bifidobacterium longum demonstrated a potential protective association with OSA. We included the top 10 metabolites with potential biological significance as candidate mediators. Among them, only 2-hydroxypalmitate was associated with a reduced risk of OSA. 2-hydroxypalmitate partially mediated the association between species Parabacteroides merdae and OSA, with a mediation proportion of 20.53%.

CONCLUSION: The study highlighted the protective effect of species Parabacteroides merdae against OSA. It also revealed the mediating role of 2-hydroxypalmitate in the relationship between species Parabacteroides merdae and OSA.},
}

@article {pmid40927664,
year = {2025},
author = {Lee, T and Kim, HY and Han, JH and Shin, JE and Song, NY and Chung, WY and Kang, CM},
title = {Longitudinal analysis of oral microbiome changes during the neonatal period in full-term and preterm newborns.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2555575},
pmid = {40927664},
issn = {2000-2297},
abstract = {BACKGROUND: The neonatal period is critical for oral microbiome establishment, but temporal patterns in preterm newborns remain unclear. This study examined longitudinal microbiome changes in full-term and preterm newborns and assessed perinatal and clinical influences.

METHODS: Oral swabs were collected from 98 newborns (23 full-term, 75 preterm). Samples were obtained at birth and Day 2 for full-term, and at birth, Day 7, and Day 28 for preterm newborns. 16S rRNA gene sequencing was used to analyze microbial diversity, taxonomic shifts, and virulence-related genes.

RESULTS: Preterm newborns showed persistently lower α-diversity and delayed succession compared with full-term newborns. Full-term infants transitioned rapidly from Proteobacteria-dominant to Firmicutes- and Actinobacteria-rich communities, while preterm infants maintained Proteobacteria longer. Diversity in preterm newborns was significantly affected by gestational age, birthweight, delivery mode, feeding type, and β-lactam exposure. Breastfeeding supported more stable diversity, whereas cesarean delivery and formula feeding reduced diversity. Functional profiling revealed greater abundance of virulence-associated genes in preterm newborns, suggesting differences in early host-microbe interactions. .

CONCLUSIONS: Preterm newborns exhibit delayed oral microbiome development, influenced by multiple modifiable factors. Supportive strategies, such as breastfeeding and prudent antibiotic use, may help foster microbial stability and potentially reduce infection risk in this vulnerable population.},
}

@article {pmid40927580,
year = {2025},
author = {Lee, CY and Zven, SE and Sathya, SA and Abukhalaf, D and Sahoo, S and Samal, P and Prescott, SM},
title = {Using molecular methods to diagnose, classify, and treat neonatal sepsis: a scoping review.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1625449},
pmid = {40927580},
issn = {2296-2360},
abstract = {INTRODUCTION: Neonatal sepsis is a dysregulated immune response to bloodstream infection causing serious disease and death. Our review seeks to integrate the knowledge gained from studies of multiple molecular methods- such as genomics, metabolomics, transcriptomics, and the gut microbiome- in the setting of neonatal sepsis that may improve the diagnosis, classification, and treatment of the disease. Sepsis claims over 200,000 lives annually worldwide and remains a top 10 cause of infant mortality in the US. Diagnosis and treatment of neonatal sepsis remains a challenge as its mechanisms are poorly understood.

METHODS: We conducted a scoping review of literature published between 2018 and 2024. Of 1,043 articles screened, 30 were included in the final review.

RESULTS: The gut microbiome is associated with both pathogenicity and protection in the setting of neonatal sepsis, while expression levels of immune response and regulation help classify neonatal response to septic events. Metabolomic studies reveal possible biomarkers to detect, classify, and predict neonatal sepsis morbidity and mortality, and proteomic studies confirm mechanisms predicted by the other models.

DISCUSSION: Studies using molecular methods foster greater understanding of neonatal sepsis and show promise to improve diagnosis, classification, and therapeutic intervention. Future research using multi-omic analyses may further elucidate the development and progression of inflammatory processes that occur as sepsis progresses.},
}

@article {pmid40927538,
year = {2025},
author = {Alao, JO and Lau, KEM and White, D and Lee, K and Puli'uvea, C and Bartley, J},
title = {Acoustic therapy for allergic rhinitis and chronic rhinosinusitis: modulating microbiome, immunity and well-being.},
journal = {Frontiers in allergy},
volume = {6},
number = {},
pages = {1649031},
pmid = {40927538},
issn = {2673-6101},
abstract = {Allergic rhinitis (AR) and chronic rhinosinusitis (CRS) are common respiratory conditions that significantly impact patient health and contribute to substantial healthcare burdens. While conventional treatments offer symptom relief, many patients continue to experience persistent symptoms, side effects, or resistance to standard therapies. This highlights the growing need for novel, non-invasive, and sustainable therapeutic strategies to manage chronic airway inflammation. This review examines acoustic therapy, an emerging non-pharmacological treatment that uses sound wave-induced vibrations as a potential adjunctive therapy for AR and CRS. Acoustic therapy shows potential benefits, including enhanced nitric oxide production, improved mucociliary clearance, and modulation of immune responses by activating mechanosensitive pathways and disrupting pathogenic biofilms. Preliminary clinical findings across some trials have reported improvements in peak nasal inspiratory flow ranging from approximately 17% to 31%, significant reductions in nasal congestion and symptom scores, such as Total Nasal Symptom Score, Sino-Nasal Outcome Test-22 (SNOT-22), and enhancements in sleep quality and patient-reported outcomes. Given this limited but expanding body of evidence, we integrate interdisciplinary insights from respiratory medicine, immunology, and microbiome science to provide a translational framework for future research. We highlight the need for rigorously designed clinical trials to assess acoustic therapy's therapeutic efficacy, safety, and long-term impact. As this field evolves, acoustic therapy holds significant potential to address unmet needs in chronic respiratory diseases and contributes to improved patient care.},
}

@article {pmid40927460,
year = {2025},
author = {Feng, Y and Chang, Q and Zhou, H and Zhang, W and Xie, L and Deng, X and Chen, T and Liu, W},
title = {Effects of gut microbiota on cognitive impairment in Parkinson's disease: a comprehensive Mendelian randomization and case-control study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1620449},
pmid = {40927460},
issn = {1664-302X},
abstract = {BACKGROUND: Increasing evidence suggests a potential role of the gut microbiota in Parkinson's disease (PD). However, the relationship between the gut microbiome (GM) and PD dementia (PDD) remains debated, with their causal effects and underlying mechanisms not yet fully understood.

METHODS: Utilizing data from large-scale genome-wide association studies (GWASs), this study applied bidirectional and mediating Mendelian randomization (MR) to investigate the causal relationship and underlying mechanisms between the GM and PDD. In our analysis, inverse-variance weighting (IVW) was used as the primary method. Clinical validation was performed using metagenomic sequencing and bioinformatic analysis. The relationships between the GM and PDD were visualized using receiver operating characteristic (ROC) curves, confusion matrices, and correlation analyses.

RESULTS: Our study revealed a significant causal impact of five GM genera, 10 metabolites, two metabolite ratios, and 22 immune cells on PDD. Notably, the maltose to sucrose ratio was identified as a mediator of the positive causal effect of Subdoligranulum on PDD, with a mediation value of 13.2%. The clinical samples confirmed the efficacy of Subdoligranulum sp. in distinguishing patients with PDD from normal controls (area under the curve (AUC) = 0.80, 95% CI: 0.674-0.924). In addition, correlation analysis revealed a potential negative association between Subdoligranulum abundance and the Mini-Mental State Examination (MMSE) scores (r = -0.316, p = 0.006). Finally, bioinformatic analysis suggested that Subdoligranulum may influence PDD risk through the regulation of starch and sucrose metabolism pathways.

CONCLUSION: Our study confirms the potential role of Subdoligranulum in PDD progression, potentially mediated through starch and sucrose metabolism. These findings highlight the importance of the gut-brain axis in PDD and may provide insights into targeted interventions for PDD.},
}

@article {pmid40927458,
year = {2025},
author = {Li, Y and Duan, Y and Zhang, J and Petropoulos, E and Zhao, J and Wu, F and Wang, L and Chen, Y and Wang, X},
title = {Structure and function of the topsoil microbiome in Chinese terrestrial ecosystems.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1595810},
pmid = {40927458},
issn = {1664-302X},
abstract = {While soil microorganisms underpin terrestrial ecosystem functioning, how their functional potential adapts across environmental gradients remains poorly understood, particularly for ubiquitous taxa. Employing a comprehensive metagenomic approach across China's six major terrestrial ecosystems (41 topsoil samples, 0-20 cm depth), we reveal a counterintuitive pattern: oligotrophic environments (deserts, karst) harbor microbiomes with significantly greater metabolic pathway diversity (KEGG) compared to resource-rich ecosystems. We provide a systematic catalog of key functional genes governing biogeochemical cycles in these soils, identifying: 6 core CAZyme genes essential for soil organic carbon (SOC) decomposition and biosynthesis; 62 nitrogen (N)-cycling genes (KOs) across seven critical enzymatic clusters; 15 sulfur (S)-cycling genes (KOs) within three key enzymatic clusters. These functional gene abundances exhibit distinct, geography-driven clustering patterns, strongly correlated with eight environmental drivers (latitude, NDVI, pH, EC, SOC, TN, C:N ratio, and MAP). This work provides a predictive framework and actionable genetic targets (e.g., specific CAZyme, N/S cycling genes) for potentially manipulating soil microbiomes to enhance ecosystem resilience and biogeochemical functions under stress.},
}

@article {pmid40927450,
year = {2025},
author = {Montecillo, JAV and Lee, JH and Yoo, HJ and Lee, YY and Park, CM and Cho, A and Lee, H and Kim, JM and Lee, NY and Park, SH and Park, NJ and Han, HS and Chong, GO and Seo, I},
title = {Characterization of Streptococcus mitis subsp. carlssonii isolated from human vagina: prevalence, phenotypic, and genomic insights.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1625724},
pmid = {40927450},
issn = {1664-302X},
abstract = {The genus Streptococcus is a heterogenous group of commensal and pathogenic bacteria. Members of this genus are classified into two major groups, the pyogenic group and the viridans group streptococci (VGS). VGS are frequently found as normal members of the human microbiome and are regarded as commensals. In this work, we characterized a VGS strain isolated from the vaginal swab sample of a Korean patient diagnosed with endometrial cancer. Phylogenetic, phenotypic, and genome-based analyses confirmed the classification of the strain K0074 as a member of the S. mitis complex. Based on the phylogenetic analyses, the species belonged to the recently established Streptococcus mitis subsp. carlssonii. The strain was found to be rare in the vaginal microbiome, but prevalent in the oral and nasal microbiome samples. K0074 neither triggered an inflammatory response nor caused cytolytic and cytotoxic effects on human cervical cancer cell line. Genome analysis uncovered the genetic basis of the strain's metabolism, virulence factors, and potential antimicrobial resistance phenotypes. Moreover, comparative genomics of the strain and closely related species and subspecies highlighted their striking differences in gene properties and biological functions. Overall, the new strain exhibited low virulence and pathogenic potentials and thus, is regarded as a commensal member of the human microflora. The genetic divergence of K0074 from closely related strains offers a compelling foundation for future investigations into the strain's potential functional specialization and its adaptation within the vaginal microbiome.},
}

@article {pmid40927373,
year = {2025},
author = {Lv, Y and Zhou, Y and Lu, H and Dong, H and He, Z},
title = {Determinants of piglet gut microbiome colonization: roles of genetics, nutrition, therapeutics, and the impact of enteric pathogens like PEDV.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1626239},
pmid = {40927373},
issn = {2235-2988},
mesh = {Animals ; Swine ; *Gastrointestinal Microbiome/drug effects ; *Swine Diseases/microbiology/virology/drug therapy/immunology ; *Porcine epidemic diarrhea virus/pathogenicity ; *Coronavirus Infections/veterinary/microbiology/virology/drug therapy ; Drugs, Chinese Herbal/therapeutic use/pharmacology ; Intestinal Mucosa/microbiology/immunology ; Immunity, Mucosal ; Diarrhea ; },
abstract = {The gut microbiota of piglets is crucial for intestinal health and immune function, yet highly susceptible to various factors. Multiple factors such as Genetic and Sow Factors, feeding environment, diet and pathogen combine to shape the gut microbiota of piglets. PEDV, a highly pathogenic and transmissible virus, disrupts the gut microbiota by damaging the intestinal epithelial barrier, leading to microbial imbalance, weakened gut immunity, and severe diarrhea. In this review, we systematically investigated the factors affecting microbial colonization in the gastrointestinal tract of piglets and the effects of PEDV infection on intestinal microecology, intestinal epithelial barrier and mucosal immunity. Meanwhile, the unique potential of Chinese herbal medicines compound represented by Qiwen Huangbai San in repairing the barrier, remodeling the flora and enhancing the immunity was discussed in depth. Through the above multidimensional perspectives, this review aims to provide a scientific basis and an effective preventive strategy for the construction of a comprehensive prevention and control program centered on Chinese herbs to alleviate the intestinal damage caused by PEDV in piglets.},
}

Animals
Swine
*Gastrointestinal Microbiome/drug effects
*Swine Diseases/microbiology/virology/drug therapy/immunology
*Porcine epidemic diarrhea virus/pathogenicity
*Coronavirus Infections/veterinary/microbiology/virology/drug therapy
Drugs, Chinese Herbal/therapeutic use/pharmacology
Intestinal Mucosa/microbiology/immunology
Immunity, Mucosal
Diarrhea

@article {pmid40927228,
year = {2025},
author = {Nireeksha, and Maniangat Luke, A and Kumari N, S and Hegde, MN and Hegde, NN},
title = {Metabolic interplay of SCFA's in the gut and oral microbiome: a link to health and disease.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1646382},
pmid = {40927228},
issn = {2673-4842},
abstract = {Short-chain fatty acids (SCFAs), primarily acetate (C2), propionate (C3), and butyrate (C4), are crucial microbial metabolites formed by the fermentation of dietary fibers by gut microbiota in the colon. These SCFAs, characterized by fewer than six carbon atoms, serve as an essential energy source for colonic epithelial cells and contribute approximately 10% of the body's total energy requirement. They are central to maintaining gut health through multiple mechanisms, including reinforcing intestinal barrier function, exerting anti-inflammatory effects, regulating glucose and lipid metabolism, and influencing host immune responses. Butyrate, in particular, plays a pivotal role in protecting the gut mucosa and modulating inflammatory processes. Beyond their intestinal functions, SCFAs affect systemic metabolic outcomes such as body weight regulation and appetite control by modulating the secretion of gut hormones and interacting with G-protein coupled receptors. Despite strong experimental evidence, mainly from animal models, clinical applications of SCFA modulation remain in preliminary stages, with limited translational findings in human therapeutics.In parallel, the oral microbiome also produces SCFAs, such as propionic, butyric, isobutyric, and isovaleric acids, as metabolic by-products in biofilm ecosystems like dental plaque. These acids contribute to interspecies communication, "cross-feeding" dynamics, and possibly biofilm stability or pathogenicity, especially in caries and periodontal disease. SCFAs in the oral cavity may act as signaling molecules or competitive factors, modulating microbial behavior and ecological balance within the oral niche. Collectively, these insights highlight SCFAs as integral to host-microbiota interactions, both in the gut and oral environments, with potential implications for targeted microbiome-based therapies in health and disease.},
}

@article {pmid40926848,
year = {2025},
author = {Sizova, EA and Shoshin, DE and Yausheva, EV and Ivanishcheva, AP and Nechitailo, KS and Ryazantseva, KV},
title = {Influence of lactulose as a composition of organic-mineral feed additive on broiler chicken productivity, feed digestibility, and microbiome.},
journal = {Veterinary world},
volume = {18},
number = {7},
pages = {2095-2105},
pmid = {40926848},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The global demand for efficient poultry production necessitates alternatives to antibiotic growth promoters. This study aimed to evaluate the effects of a novel four-component organic-mineral feed additive (OMFA), comprising lactulose, arginine, ultrafine silicon dioxide particles, and succinic acid, and a three-component variant (without lactulose) on growth performance, nutrient digestibility, elemental tissue composition, and the cecal microbiota of Arbor Acres broiler chickens.

MATERIALS AND METHODS: One hundred and five one-day-old broiler chicks were randomly allocated into three groups: Control, Group I (four-component OMFA), and Group II (three-component OMFA). Growth metrics were recorded weekly over a 42-day period. Nutrient digestibility was assessed through balance experiments, while elemental tissue composition was measured by inductively coupled plasma mass spectrometry. Cecal microbiota profiling was conducted using 16S ribosomal RNA gene sequencing on the MiSeq platform. Statistical analyses were performed using the Mann-Whitney U-test.

RESULTS: Group I showed an 11.2% increase in body weight gain and a 9.6% reduction in feed conversion ratio compared to controls (p = 0.074; p = 0.063). Group II demonstrated superior weight gain (17.9%) but incurred a 3.6% increase in feed costs. Digestibility of crude fat and protein improved significantly in Group II (p = 0.037). Elemental analysis indicated that lactulose supplementation enhanced the accumulation of magnesium, calcium, manganese, cobalt, zinc, and chromium in muscle tissue. Microbiota analysis revealed that Group I increased Ruminococcaceae abundance and suppressed Pseudobdellovibrionaceae, while Group II favored the proliferation of Helicobacteraceae, Rikenellaceae, and Bacteroidaceae.

CONCLUSION: Both OMFA formulations enhanced productivity and modulated gut microbiota. The four-component OMFA improved feed efficiency and mineral deposition, while the three-component version elicited greater weight gains. These findings support the incorporation of OMFA as a strategic tool in antibiotic-free poultry production. Further studies are warranted to elucidate the metabolic interactions among additive components and their long-term effects on gut health and performance.},
}

@article {pmid40926846,
year = {2025},
author = {Prihambodo, TR and Mulianda, R and Wulandari, W and Anggrahini, S and Qomariyah, N and Ella, A and Winarti, E and Yusriani, Y and Suyatno, S and Firison, J and Fitra, D and Harahap, AE and Sari, DAP and Hidayat, T and Jayanegara, A},
title = {Scopus-based bibliometric analysis of research trends in silage feed and its impact on rumen fermentation in ruminants.},
journal = {Veterinary world},
volume = {18},
number = {7},
pages = {1972-1990},
pmid = {40926846},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Silage plays a pivotal role in ruminant nutrition, significantly influencing rumen fermentation, animal productivity, and environmental sustainability. Despite extensive research on silage and fermentation, a comprehensive synthesis of global trends and collaborations in this domain has not been systematically explored. This study aimed to conduct a bibliometric analysis of global research on silage feed and its effects on rumen fermentation in ruminants. It sought to identify publication trends, leading contributors, research themes, and international collaboration networks, thereby informing future directions in ruminant nutrition research.

MATERIALS AND METHODS: A total of 1,007 documents published between 1961 and 2024 were retrieved from the Scopus database using targeted keywords. Bibliometric and network analyses were performed using VOSviewer, Bibliometrix (R package), and Microsoft Excel. Inclusion criteria were limited to peer-reviewed English-language articles focused on silage feed and rumen fermentation in ruminants. Data cleaning and preprocessing involved harmonization of author names, keywords, and institutional affiliations.

RESULTS: Publication output has increased significantly since 2010, with China, the United States, and Canada emerging as the top contributors. Major research themes include silage quality, microbial fermentation, methane mitigation, and feed efficiency. Core journals identified include Journal of Dairy Science and Journal of Animal Science. Leading institutions such as China Agricultural University and the University of Florida demonstrated high productivity and citation impact. Keyword analysis highlighted emerging trends, including microbiome, methanogenesis, and sustainability. Collaboration network analysis revealed strong regional clusters, with North America and Europe forming central hubs, while Asia and South America showed growing but less integrated networks.

CONCLUSION: Research on silage and rumen fermentation has evolved from foundational studies to interdisciplinary approaches integrating microbiology, environmental science, and precision agriculture. The field is rapidly expanding, with increasing emphasis on reducing methane emissions and enhancing livestock performance through improved silage practices. However, global collaboration remains fragmented, particularly in underrepresented regions. Future research should focus on metagenomics, smart technologies (e.g., Artificial Intelligence and Internet of Things), and policy-driven strategies to optimize feed systems and support sustainable livestock production.},
}

@article {pmid40926716,
year = {2025},
author = {Zhang, Y and Li, H and Jiang, N and Ru, Q},
title = {The Role of Traditional Chinese Medicine in the Management of Nonalcoholic Fatty Liver Disease: Targeting Gut Microbiome.},
journal = {The American journal of Chinese medicine},
volume = {},
number = {},
pages = {1-34},
doi = {10.1142/S0192415X25500788},
pmid = {40926716},
issn = {1793-6853},
abstract = {The incidence of non-alcoholic fatty liver disease (NAFLD) has increased and become a serious global public health problem in recent years. The currently generally used clinical treatments have disadvantages such as side effects, limitations, and poor patient compliance. Traditional Chinese medicine (TCM) has a pharmacological effect with multiple components, multiple targets, and multiple pathways, emphasizing a "holistic concept" and "differential diagnosis and treatment," which is compatible with the complex pathogenesis of GM and NAFLD. Previous studies have demonstrated a close relationship between the gut microbiome (GM) and the occurrence and progression of NAFLD. However, the mechanisms between GM and NAFLD are complex. This paper not only analyzes the relationship between the GM and the pathogenesis of NAFLD but also discusses in detail how various TCM active metabolites and Chinese herbal formulas could exert a therapeutic effect on NAFLD by regulating the GM and its metabolites. Furthermore, this paper innovatively explores how TCM regulates the abundance of five major bacterial phyla, and their representative genera, to improve the pathogenesis of NAFLD. In summary, this review article proposes innovative ideas and options for the prevention and treatment of NAFLD with focus on GM regulation, and provides a theoretical basis for the development of new drugs from traditional Chinese medicine.},
}

@article {pmid40926562,
year = {2025},
author = {Mendes-Frias, A and Vieira, MC and Araújo, M and Duarte-Oliveira, C and Feys, S and Micheli, C and Gaifem, J and Gonçalves, LG and Osório, NS and Longatto-Filho, A and Castro, AG and Torrado, E and Cunha, C and Carvalho, A and Duarte, IF and Silva, NA and Rodrigues, F and Silvestre, R},
title = {Branched-Chain Amino Acids Exacerbate Colitis Progression by Lowering Colonic Fumarate Levels.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf125},
pmid = {40926562},
issn = {1536-4844},
support = {//FCT/MCTES/ ; },
abstract = {BACKGROUND: Ulcerative colitis (UC) is a gastrointestinal inflammatory condition with an unclear etiology. Recent findings suggest that metabolites play a pivotal role in promoting intestinal health. We have previously observed a significant enrichment in colonic branched-chain amino acids (BCAAs) in resistant mice to colitis suggesting the potential role of these metabolites in UC development.

METHODS: C57BL6/J mice underwent a 20-day BCAA supplementation regimen, followed by induction of colitis using dextran sulfate sodium (DSS). Disease activity index (DAI), immune cell profiling, and histological and transcriptomic analysis were evaluated. 16S rRNA sequencing and metabolomic profiling of stool extracts were performed. Additionally, mice were treated with dimethyl fumarate (DMF) post-supplementation to explore therapeutic interventions.

RESULTS: BCAA supplementation exacerbated colitis severity in mice, as evidenced by worsened DAI, increased histological damage, and significant alterations in immune cell populations, including decreased type 3 innate lymphoid cells and increased Th17 and regulatory T cells. Microbiota analysis showed a shift toward a decreased abundance of Lactobacillus spp. and an increase in pathobionts. Metabolomic profiling indicated significantly reduced colonic fumarate levels and increased pro-inflammatory metabolites. DMF treatment attenuated BCAA-induced pro-inflammatory phenotype, improved disease outcomes, and modulated the immune response in a microbiome-dependent manner.

CONCLUSIONS: BCAA supplementation exacerbates DSS-induced colitis in mice. This effect is mediated by detrimental changes in gut microbiota composition and metabolome. DMF treatment shows promise to mitigate these adverse effects, suggesting potential therapeutic avenues to manage BCAA-induced colitis exacerbation and reinforcing the role of microbiome in UC. These findings underscore the caution needed with the use of BCAAs during inflammatory conditions.},
}

@article {pmid40926344,
year = {2025},
author = {Sarango Flores, S and Cordovez, V and Oyserman, BO and Arias Giraldo, LM and Stopnisek, N and Raaijmakers, JM and van 't Hof, P},
title = {Microbiome-Mediated Resistance of Wild Tomato to the Invasive Insect Prodiplosis longifila.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70190},
doi = {10.1111/1758-2229.70190},
pmid = {40926344},
issn = {1758-2229},
support = {024.004.014/NWO_/Dutch Research Council/Netherlands ; CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Research Grant/ ; },
mesh = {*Solanum lycopersicum/microbiology/parasitology/immunology ; Animals ; *Microbiota ; *Soil Microbiology ; *Diptera/physiology ; Ecuador ; Plant Roots/microbiology/parasitology ; Introduced Species ; Bacteria/classification/genetics/isolation & purification ; Plant Leaves/parasitology ; },
abstract = {Plant roots are colonised by diverse communities of microorganisms that can affect plant growth and enhance plant resistance to (a) biotic stresses. We investigated the role of the indigenous soil microbiome in the resistance of tomato to the invasive sap-sucking insect Prodiplosis longifila (Diptera: Cecidomyiidae). Native and agricultural soils were sampled from the Andes in Southern Ecuador and tested, in greenhouse bioassays, for leaf tissue damage caused by P. longifila on domesticated Solanum lycopersicum cv. Moneymaker and wild tomato S. pimpinellifolium. We observed no significant differences in insect damage between domesticated and wild tomatoes grown in live native or agricultural soils. However, when grown in sterilised native and agricultural soils, wild tomato was more severely affected by the insect than the domesticated tomato. Microbiome analyses revealed that soil sterilisation impacted overall rhizobacterial diversity and abundance in wild tomato. Particularly, Actinoplanes abundance was reduced upon sterilisation, which significantly correlated with loss of insect resistance. Metagenome analyses and genome assembly of Micromonosporaceae (Actinoplanes family) suggested a putative association between motility, chemotaxis, membrane transport, chorismate, and lanthipeptide biosynthesis and insect resistance. This indicates that wild S. pimpinellifolium, in contrast to domesticated S. lycopersicum, relies on specific members of the root-associated microbiome for P. longifila protection.},
}

*Solanum lycopersicum/microbiology/parasitology/immunology
Animals
*Microbiota
*Soil Microbiology
*Diptera/physiology
Ecuador
Plant Roots/microbiology/parasitology
Introduced Species
Bacteria/classification/genetics/isolation & purification
Plant Leaves/parasitology

@article {pmid40926280,
year = {2025},
author = {Hao, W and Luo, Q and Szabo, IM and Gasparoni, G and Tierling, S and Quan, W and Chang, HF and Wu, G and Schulze-Hentrich, J and Liu, Y},
title = {Intestinal epithelial Dicer1 regulates gut microbiome and Alzheimer's pathology in App-knock-in mice.},
journal = {Alzheimer's research & therapy},
volume = {17},
number = {1},
pages = {202},
pmid = {40926280},
issn = {1758-9193},
mesh = {Animals ; *Ribonuclease III/genetics/metabolism ; *Gastrointestinal Microbiome/physiology/genetics ; *Alzheimer Disease/pathology/metabolism/genetics ; Mice ; *DEAD-box RNA Helicases/genetics/metabolism ; *Intestinal Mucosa/metabolism ; Amyloid beta-Protein Precursor/genetics ; Brain/pathology/metabolism ; Mice, Transgenic ; Disease Models, Animal ; Male ; Gene Knock-In Techniques ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) patients and animal models exhibit an altered gut microbiome that is associated with pathological changes in the brain. Intestinal miRNA enters bacteria and regulates bacterial metabolism and proliferation. This study aimed to investigate whether the manipulation of miRNA could alter the gut microbiome and AD pathologies.

METHODS: The enzyme producing miRNA was deleted in App-knock-in mice by conditional knock-out of Dicer1 gene in intestinal epithelial cells. 16S rDNA sequencing/microbiome analysis was performed in both the gut and brain. Barrier integrity, inflammatory activation and T cell differentiation in the gut were analyzed by measuring transcripts of relevant marker genes. AD-associated pathologies in the brain, including amyloid pathology, neuroinflammation and synaptic impairment, were investigated by immunohistochemistry, ELISA, quantitative Western blot, mRNA-sequencing/transcriptomic analysis, real-time PCR and behavior tests. To investigate the mechanisms controlling Aβ level, β- and γ-secretase activities, protein levels of LRP1 and ABCB1 in isolated blood microvessels, CD68 immunofluorescence around Aβ deposits and transcription of neprilysin and IDE genes in the brain were analyzed.

RESULTS: Deletion of Dicer1 in intestinal epithelial cells of App-knock-in mice reduced the absolute number and altered the composition of bacteria in both the gut and brain, and inhibited inflammatory activation in the gut, but had no effect on the differentiation of CD4-positive T lymphocytes. It lowered Aβ load in the brain, possibly by inhibiting β-secretase activity, and increasing the expression of LRP1 and ABCB1 at the blood-brain barrier. Deletion of intestinal Dicer1 increased Il-10 transcription and decreased Ccl-2 transcription in the brain tissue. Transcriptomic analysis further showed that Dicer1 deletion reduced transcription of Ndufa2 and Ndufa5 genes. In behavior tests, deletion of intestinal Dicer1 induced anxiety symptoms without improving cognitive function in AD mice.

CONCLUSIONS: Deletion of Dicer1 in intestinal epithelial cells modulates the microbiome in both the gut and brain, and AD pathologies in the brain of App-knock-in mice. Future studies should focus on the identification of AD-specific miRNAs in the gut that can be therapeutically utilized to alter the gut microbiome and prevent AD progression.},
}

Animals
*Ribonuclease III/genetics/metabolism
*Gastrointestinal Microbiome/physiology/genetics
*Alzheimer Disease/pathology/metabolism/genetics
Mice
*DEAD-box RNA Helicases/genetics/metabolism
*Intestinal Mucosa/metabolism
Amyloid beta-Protein Precursor/genetics
Brain/pathology/metabolism
Mice, Transgenic
Disease Models, Animal
Male
Gene Knock-In Techniques

@article {pmid40926269,
year = {2025},
author = {Abdel-Rasol, MA and El-Sayed, WM},
title = {Nuclear receptors in metabolic, inflammatory, and oncologic diseases: mechanisms, therapeutic advances, and future directions.},
journal = {European journal of medical research},
volume = {30},
number = {1},
pages = {843},
pmid = {40926269},
issn = {2047-783X},
mesh = {Humans ; *Receptors, Cytoplasmic and Nuclear/metabolism/agonists/genetics ; *Neoplasms/metabolism/drug therapy/therapy ; *Inflammation/metabolism/drug therapy ; *Metabolic Diseases/metabolism/drug therapy ; Animals ; },
abstract = {Nuclear receptors (NRs) are a superfamily of ligand-activated transcription factors that regulate gene expression in response to metabolic, hormonal, and environmental signals. These receptors play a critical role in metabolic homeostasis, inflammation, immune function, and disease pathogenesis, positioning them as key therapeutic targets. This review explores the mechanistic roles of NRs such as PPARs, FXR, LXR, and thyroid hormone receptors (THRs) in regulating lipid and glucose metabolism, energy expenditure, cardiovascular health, and neurodegeneration. The therapeutic landscape for NRs has expanded with the approval of drugs like PPARγ agonists (pioglitazone, rosiglitazone) for diabetes, FXR agonists (obeticholic acid) for liver diseases, and selective TR agonists (resmetirom) for Metabolic dysfunction-Associated Steatohepatitis (MASH). However, challenges such as tissue-specific activation, drug resistance in chronic diseases, and potential carcinogenic risks continue to limit the full clinical efficacy of NR-targeted therapies. Emerging therapeutic strategies, including selective nuclear receptor modulators (SNRMs), dual and pan-NR agonists, and gene therapy approaches, aim to enhance receptor specificity while minimizing adverse effects. Furthermore, advances in artificial intelligence-driven drug discovery, CRISPR-based gene therapy, and microbiome-targeted interventions hold significant promise for refining the therapeutic efficacy and safety of NR-based treatments. A deeper understanding of NR crosstalk with metabolic, inflammatory, and oncogenic pathways will be crucial for developing next-generation therapies to overcome resistance mechanisms and improve clinical outcomes. These advancements, combined with precision medicine approaches, are poised to revolutionize NR-targeted therapies, offering more precise, effective, and safer treatments for a range of metabolic, inflammatory, and oncological diseases.},
}

Humans
*Receptors, Cytoplasmic and Nuclear/metabolism/agonists/genetics
*Neoplasms/metabolism/drug therapy/therapy
*Inflammation/metabolism/drug therapy
*Metabolic Diseases/metabolism/drug therapy
Animals

@article {pmid40926211,
year = {2025},
author = {Selten, G and de Jonge, R},
title = {Bacillus drives functional states in synthetic plant root bacterial communities.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {270},
pmid = {40926211},
issn = {1474-760X},
support = {NNF19SA0059362//Novo Nordisk Fonden/ ; },
mesh = {*Plant Roots/microbiology ; *Microbiota ; *Bacillus/physiology ; Biofilms/growth & development ; Quorum Sensing ; },
abstract = {BACKGROUND: Plant roots release root exudates to attract microbes that form root communities, which in turn promote plant health and growth. Root community assembly arises from millions of interactions between microbes and the plant, leading to robust and stable microbial networks. To manage the complexity of natural root microbiomes for research purposes, scientists have developed reductionist approaches using synthetic microbial inocula (SynComs). Recently, an increasing number of studies employed SynComs to investigate root microbiome assembly and dynamics under various conditions or with specific plant mutants. These studies have identified bacterial traits linked to root competence, but if and how these traits shape root microbiome dynamics across conditions is not well understood.

RESULTS: To explore whether bacterial trait selection follows recurrent patterns, we conducted a meta-analysis of nine SynCom studies involving plant roots. Surprisingly, we observed that root communities frequently assemble into two distinct functional states. Further analysis revealed that these states are characterized by differences in the abundance of Bacilli. We propose that these Bacilli-associated functional states are driven by microbial interactions such as quorum sensing and biofilm formation and that host activities, including root exudation and immune responses, influence these functional states.

CONCLUSIONS: Whether natural root communities also organize into distinct functional states remains unclear, but the implications could be significant. Functional diversification within root communities may influence the effectiveness of plant-beneficial bioinoculants, particularly Bacilli-based inoculants. To optimize microbiome-driven plant benefits, a deeper understanding of the mechanisms underlying functional state differentiation in root microbiomes is needed.},
}

*Plant Roots/microbiology
*Microbiota
*Bacillus/physiology
Biofilms/growth & development
Quorum Sensing

@article {pmid40926119,
year = {2025},
author = {Masson, SWC and Simpson, RC and Cutler, HB and Carlos, PW and Marian, OC and Yau, B and Potter, M and Madsen, S and Cooke, KC and Craw, NR and Fuller, OK and Harney, DJ and Larance, M and Cooney, GJ and Morahan, G and Shanahan, ER and Kebede, MA and Hodgkins, C and Payne, RJ and Stöckli, J and James, DE},
title = {Genetic variance in the murine defensin locus modulates glucose homeostasis.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {40926119},
issn = {1460-2075},
support = {FL200100096//Department of Education and Training | Australian Research Council (ARC)/ ; Y23G-MASS//Diabetes Australia/ ; },
abstract = {Insulin resistance is a heritable risk factor for many chronic diseases; however, the genetic drivers remain elusive. In seeking these, we performed genetic mapping of insulin sensitivity in 670 chow-fed Diversity Outbred in Australia (DOz) mice and identified a genome-wide significant locus (QTL) on chromosome 8 encompassing 17 defensin genes. By taking a systems genetics approach, we identified alpha-defensin 26 (Defa26) as the causal gene in this region. To validate these findings, we synthesized Defa26 and performed diet supplementation experiments in two mouse strains with distinct endogenous Defa26 expression levels. In the strain with relatively lower endogenous expression (C57BL/6J) supplementation improved insulin sensitivity and reduced gut permeability, while in the strain with higher endogenous expression (A/J) it caused hypoinsulinemia, glucose intolerance and muscle wasting. Based on gut microbiome and plasma bile acid profiling this appeared to be the result of disrupted microbial bile acid metabolism. These data illustrate the danger of single strain over-reliance and provide the first evidence of a link between host-genetics and insulin sensitivity which is mediated by the microbiome.},
}

@article {pmid40926100,
year = {2025},
author = {Gibson, TE and Kim, Y and Acharya, S and Kaplan, DE and DiBenedetto, N and Lavin, R and Berger, B and Allegretti, JR and Bry, L and Gerber, GK},
title = {Learning ecosystem-scale dynamics from microbiome data with MDSINE2.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40926100},
issn = {2058-5276},
support = {BRICS HR0011-15-C-0094//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; R01GM130777//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM149270//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM143056//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21AI154075//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM141861//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30DK056338//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; MTM2 2025512//National Science Foundation (NSF)/ ; },
abstract = {Although dynamical systems models are a powerful tool for analysing microbial ecosystems, challenges in learning these models from complex microbiome datasets and interpreting their outputs limit use. We introduce the Microbial Dynamical Systems Inference Engine 2 (MDSINE2), a Bayesian method that learns compact and interpretable ecosystems-scale dynamical systems models from microbiome timeseries data. Microbial dynamics are modelled as stochastic processes driven by interaction modules, or groups of microbes with similar interaction structure and responses to perturbations, and additionally, noise characteristics of data are modelled. Our open-source software package provides multiple tools for interpreting learned models, including phylogeny/taxonomy of modules, and stability, interaction topology and keystoneness. To benchmark MDSINE2, we generated microbiome timeseries data from two murine cohorts that received faecal transplants from human donors and were then subjected to dietary and antibiotic perturbations. MDSINE2 outperforms state-of-the-art methods and identifies interaction modules that provide insights into ecosystems-scale interactions in the gut microbiome.},
}

@article {pmid40926099,
year = {2025},
author = {Dohlman, AB and Pan, X and Zitvogel, L and Iliev, ID},
title = {The multi-kingdom cancer microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40926099},
issn = {2058-5276},
support = {R01CA286920, R01DK113136, R01DK121977, R01 AI178683 and R01AI163007//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Microbial influence on cancer development and therapeutic response is a growing area of cancer research. Although it is known that microorganisms can colonize certain tissues and contribute to tumour initiation, the use of deep sequencing technologies and computational pipelines has led to reports of multi-kingdom microbial communities in a growing list of cancer types. This has prompted discussions on the role and scope of microbial presence in cancer, while raising the possibility of microbiome-based diagnostic, prognostic and therapeutic tools. However, additional investigation and thorough validation of cancer microbiome findings are required before this translational potential can be realized. Here we provide historical context and a conceptual framework for the so-called cancer microbiome and summarize experimental studies into tumour-associated bacteria, fungi and other microorganisms. We also discuss the current evidence for microbial colonization of tumours and their varied influence on the disease, including recent debates. Finally, we consider outstanding questions and discuss our outlook for the field.},
}

@article {pmid40926031,
year = {2025},
author = {Pasricha, TS and Kulkarni, S},
title = {Dopaminergic signalling in gastrointestinal health and disease.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {40926031},
issn = {1759-5053},
abstract = {Enteric dopaminergic signalling has a critical role in gastrointestinal motility, maintaining mucosal integrity and modulating the gut microbiome. In this Review, we provide an overview of dopamine metabolism and signalling pathways in the central nervous system and periphery and their effects on gastrointestinal health and disease. We describe the physiological role of enteric dopamine, including a discussion of therapeutic opportunities and future research needs. With rising interest in the gut-first hypothesis of Parkinson disease, an area of great interest is how dopaminergic depletion in the gut could indicate future neurological dysfunction. In addition, dopamine signalling has been found to influence microbiome colonization resistance against enteric pathogens and immunoregulation. Emerging data on the effect of dopamine replacement therapy on gastrointestinal symptoms, across a range of conditions from neurodegenerative disease to inflammatory bowel disease, are also explored.},
}

@article {pmid40925937,
year = {2025},
author = {Josephs-Spaulding, J and Rettig, HC and Zimmermann, J and Chkonia, M and Mischnik, A and Franzenburg, S and Graspeuntner, S and Rupp, J and Kaleta, C},
title = {Metatranscriptomics-based metabolic modeling of patient-specific urinary microbiome during infection.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {183},
pmid = {40925937},
issn = {2055-5008},
support = {EXC2167//DFG Excellence Cluster Precision Medicine in Chronic Inflammation/ ; EXC2167//DFG Excellence Cluster Precision Medicine in Chronic Inflammation/ ; EXC2167//DFG Excellence Cluster Precision Medicine in Chronic Inflammation/ ; EXC2167//DFG Excellence Cluster Precision Medicine in Chronic Inflammation/ ; EXC2167//DFG Excellence Cluster Precision Medicine in Chronic Inflammation/ ; EXC2167//DFG Excellence Cluster Precision Medicine in Chronic Inflammation/ ; EXC2167//DFG Excellence Cluster Precision Medicine in Chronic Inflammation/ ; EXC2167//DFG Excellence Cluster Precision Medicine in Chronic Inflammation/ ; EXC2167//DFG Excellence Cluster Precision Medicine in Chronic Inflammation/ ; 407495230//DFG Research Infrastructure Next Generation Sequencing Competence Network/ ; 407495230//DFG Research Infrastructure Next Generation Sequencing Competence Network/ ; 407495230//DFG Research Infrastructure Next Generation Sequencing Competence Network/ ; 440395346//Kiel University Computing Centre/ ; 440395346//Kiel University Computing Centre/ ; },
mesh = {Humans ; *Urinary Tract Infections/microbiology/urine ; Female ; *Microbiota ; *Uropathogenic Escherichia coli/genetics/isolation & purification ; *Escherichia coli Infections/microbiology/urine ; Gene Expression Profiling ; Systems Biology ; Middle Aged ; Transcriptome ; Adult ; },
abstract = {Urinary tract infections (UTIs) are among the most common bacterial infections and are increasingly complicated by multidrug resistance (MDR). While Escherichia coli is frequently implicated, the contribution of broader microbial communities remains less understood. Here, we integrate metatranscriptomic sequencing with genome-scale metabolic modeling to characterize active metabolic functions of patient-specific urinary microbiomes during acute UTI. We analyzed urine samples from 19 female patients with confirmed uropathogenic E. coli (UPEC) infections, reconstructing personalized community models constrained by gene expression and simulated in a virtual urine environment. This systems biology approach revealed marked inter-patient variability in microbial composition, transcriptional activity, and metabolic behavior. We identified distinct virulence strategies, metabolic cross-feeding, and a modulatory role for Lactobacillus species. Comparisons between transcript-constrained and unconstrained models showed that integrating gene expression narrows flux variability and enhances biological relevance. These findings highlight the metabolic heterogeneity of UTI-associated microbiota and point to microbiome-informed diagnostic and therapeutic strategies for managing MDR infections.},
}

Humans
*Urinary Tract Infections/microbiology/urine
Female
*Microbiota
*Uropathogenic Escherichia coli/genetics/isolation & purification
*Escherichia coli Infections/microbiology/urine
Gene Expression Profiling
Systems Biology
Middle Aged
Transcriptome
Adult

@article {pmid40925904,
year = {2025},
author = {Rashwan, HH and Marzouk, NH and Youness, RA and El-Hadidi, M and Ramadan, R and Mysara, M},
title = {Unravelling novel microbial players in the breast tissue of TNBC patients: a meta-analytic perspective.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {182},
pmid = {40925904},
issn = {2055-5008},
mesh = {Humans ; *Triple Negative Breast Neoplasms/microbiology/pathology ; *Microbiota ; Female ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Breast/microbiology ; },
abstract = {Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer (BC), accounting for nearly 40% of BC-related deaths. Emerging evidence suggests that the breast tissue microbiome harbors distinct microbial communities; however, the microbiome specific to TNBC remains largely unexplored. This study presents the first comprehensive meta-analysis of the TNBC tissue microbiome, consolidating 16S rRNA amplicon sequencing data from 200 BC samples across four independent cohorts. Our analysis highlights the enrichment of Azospirillum genus as well as butyrate-producing species, namely Gemmiger formicilis and Anaerobutyricum soehngenii, potentially influencing TNBC aggressiveness and clinical outcomes. Additionally, our functional analyses reveal the involvement of the TNBC microbiome in several pathways associated with chronic inflammation, increased cellular proliferation, invasion, and metastasis. This study uncovers novel microbial players in TNBC that could explain its aggressiveness and poor prognosis, and warrants further investigation into microbiome-driven interventions.},
}

Humans
*Triple Negative Breast Neoplasms/microbiology/pathology
*Microbiota
Female
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification/metabolism
*Breast/microbiology

@article {pmid40925897,
year = {2025},
author = {Oguri, N and Kobayashi, C and Ozawa, Y and Kimura, T and Nishinarita, Y and Wada, H and Nemoto, N and Narita, M and Tanigaki, S and Hanawa, T and Miyoshi, J and Hisamatsu, T},
title = {Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8032},
pmid = {40925897},
issn = {2041-1723},
mesh = {Female ; Humans ; Pregnancy ; *Vagina/microbiology ; Infant, Newborn ; Adult ; Japan ; RNA, Ribosomal, 16S/genetics ; Longitudinal Studies ; *Pregnancy Outcome ; *Gastrointestinal Microbiome/genetics ; *Lactobacillus crispatus/genetics/isolation & purification/physiology ; Postpartum Period ; *Microbiota ; Cohort Studies ; Lactobacillus/genetics ; East Asian People ; },
abstract = {The maternal microbiome during pregnancy and the peripartum period plays a critical role in maternal health outcomes and establishing the neonatal gut microbiome, with long-term implications for offspring health. However, a healthy microbiome during these key periods has not been definitively characterized. This longitudinal study examines maternal and neonatal microbiomes using 16S rRNA amplicon sequencing in a Japanese cohort throughout pregnancy and the postpartum period. Forty-two mothers and their forty-five offspring participate in the study. The maternal vaginal microbiome remains relatively stable during pregnancy but significantly changes in the postpartum period. Among Lactobacillus species, the Lactobacillus crispatus group is predominant. A higher abundance of Lactobacillus early in pregnancy is associated with a favorable gestational period. The maternal gut microbiome is associated with the vaginal microbiome throughout pregnancy. The neonatal gut microbiome substantially changes in early life, with bacterial composition influenced by delivery mode. Over time, bacteria shared with the maternal gut microbiome become dominant in the neonatal gut. This study provides insights into microbiome dynamics in Japanese mothers and their offspring during pregnancy and the postpartum period. Identification of common patterns across diverse populations may help define keystone microbes essential for human health and inform the development of microbiome-based interventions.},
}

Female
Humans
Pregnancy
*Vagina/microbiology
Infant, Newborn
Adult
Japan
RNA, Ribosomal, 16S/genetics
Longitudinal Studies
*Pregnancy Outcome
*Gastrointestinal Microbiome/genetics
*Lactobacillus crispatus/genetics/isolation & purification/physiology
Postpartum Period
*Microbiota
Cohort Studies
Lactobacillus/genetics
East Asian People

@article {pmid40925319,
year = {2025},
author = {Kisielius, V and Barra Caracciolo, A and Mingoli, A and Parisi, E and Martinez I Quer, A and Garbini, GL and Grenni, P and Carvalho, PN},
title = {Decentralized wastewater management using treatment wetlands: Effective removal of antibiotics, resistance genes and organic micropollutants.},
journal = {The Science of the total environment},
volume = {1000},
number = {},
pages = {180406},
doi = {10.1016/j.scitotenv.2025.180406},
pmid = {40925319},
issn = {1879-1026},
abstract = {Treatment wetlands (TW) are a popular choice for decentralized wastewater treatment, with substantial documentation on their capacity to manage conventionally monitored pollutants. However, most insights into their effectiveness against emerging contaminants come from lab and mesocosm studies with a limited number of compounds, highlighting knowledge gaps in their performance at full scale. This study provides a first long-term, full-scale assessment of TW ability to remove a large number of organic micropollutants (OMPs) and manage antibiotic resistance under real-world conditions. The TW, with Phragmites australis as the plant species, operational for 10 years with a vertical flow bed followed by an aerated bed, serves a Danish village with a 100 population equivalent. We have monitored its performance over 18 consecutive months (each 3 weeks), analysing organic carbon, nitrogen and OMPs (e.g. pharmaceuticals including antibiotics). Moreover, the microbial community structure (abundance and biodiversity) and possible presence of Antibiotic resistance genes (ARGs) in wastewater and reed rhizosphere at different points of the TW were analysed in four seasonal samplings. The findings demonstrated robust nutrient and OMP removal, with slight performance reductions in winter, likely due to plant dormancy and lower temperatures. Due to the small population served by the TW, antibiotics entered the system sporadically but at peak concentrations. The sul1, sul2 genes associated with sulfonamide resistance and intI1 gene were detected in all microbiological samples. The vertical flow bed effectively reduced OMPs (including antibiotics) and ARGs thanks to the removal action of the reed-microbiome system. The TW was a biofilter for targeted emerging contaminants, limiting their transfer in the water cycle and this study uniquely demonstrates that full-scale TWs can achieve high removal efficiencies for both antibiotics and ARGs, offering new insights into their practical application and operation for decentralized wastewater management.},
}

@article {pmid40925203,
year = {2025},
author = {Kapoor, B and Gulati, M},
title = {Gut microbiome and rheumatoid arthritis: Revisiting the gut-joint axis.},
journal = {International immunopharmacology},
volume = {165},
number = {},
pages = {115503},
doi = {10.1016/j.intimp.2025.115503},
pmid = {40925203},
issn = {1878-1705},
abstract = {Over the past few decades, the scientific perspective on gut microbiota has undergone a profound transformation, particularly with the emergence and advancement of microbiome research. Next-generation sequencing technologies have emerged as a foundational tool in microbiome research, facilitating comprehensive characterization of microbial communities across diverse sample types and ecological niches. Significant alterations in gut microbiota composition have been observed in disease states compared to healthy individuals, suggesting a direct association between gut dysbiosis and host health status. Initially, alterations in gut microbiota were primarily thought to be associated with gastrointestinal disorders. With advancing research, however, it has become evident that gut dysbiosis is also implicated in a broad spectrum of extra-intestinal conditions, including neurological, dermatological, metabolic, and musculoskeletal diseases. The present review provides a comprehensive analysis of preclinical and clinical studies elucidating the role of gut dysbiosis in the pathogenesis and progression of rheumatoid arthritis. Advancements in the understanding of the gut-joint axis have facilitated the development of novel therapeutic modalities, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, that have been comprehensively discussed in present review.},
}

@article {pmid40925184,
year = {2025},
author = {Lin, Z and Qiao, Y and Ge, J and Lu, L and Xie, R and Tian, S},
title = {Novel plant growth-promoting endophytic bacteria, Stenotrophomonas maltophilia SaRB5, facilitate phytoremediation by plant growth and cadmium absorption in Salix suchowensis.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118967},
doi = {10.1016/j.ecoenv.2025.118967},
pmid = {40925184},
issn = {1090-2414},
abstract = {Seven plant growth-promoting bacteria (PGPB) were isolated from extracts of surface-sterilized Sedum alfredii Hance. Among the seven isolates, the strain SaRB5 identified as Stenotrophomonas maltophilia through 16S rDNA sequence analysis, exhibited highest levels of heavy metal resistance and plant growth-promoting traits. SaRB5 tolerated high concentrations of cadmium (Cd) (1.5 mg·kg[-1]) and demonstrated production of indole-3-acetic acid and siderophores when grown with or without Cd. Whole genome sequence alignment and comparative genomic analysis revealed thirty genes associated with plant growth and Cd tolerance metabolism in strain SaRB5, including trpA, trpB, czcB, and others. Pot experiments indicated that SaRB5-treated willow biomass increased by 71.7 % and extracted 129.2 % more Cd. Meanwhile,the inoculation of SaRB5 enhanced the release of organic acids, amino acids, and salicylic acid from plants into the soil, consequently facilitating the recruitment of specific beneficial microbiota at the rhizoplane (including Bradyrhizobium, Mesorhizobium, Romboutsia, and Turicibacter). The recruitment of Bradyrhizobium and Mesorhizobium and the strong upregulation of the nifH gene suggest that SaRB5 inoculation favored efficient nitrogen-fixing microbes at the rhizoplane. Romboutsia and Turicibacter had an impact on the mobilization of iron-manganese oxide-bound Cd and its uptake. This study suggests that SaRB5 enhances phytoremediation not only through the direct effects of the inoculum itself but also by impacting the indigenous rhizoplane bacterial community.},
}

@article {pmid40925130,
year = {2025},
author = {Sahu, KK and Yadav, K and Pradhan, M and Sharma, M and Dubey, A and Sucheta, and Kirubakaran, JJ},
title = {Pharmacological insights into gut microbiota modulation in systemic lupus erythematosus: Mechanisms, treatment strategies, and clinical implications.},
journal = {The Journal of pharmacology and experimental therapeutics},
volume = {392},
number = {9},
pages = {103659},
doi = {10.1016/j.jpet.2025.103659},
pmid = {40925130},
issn = {1521-0103},
abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by widespread inflammation and immune system dysregulation. Recent research suggests that the gut microbiota may play a role in the development of SLE by modulating immune system responses, affecting cytokine production, and altering the activity of T and B cells lymphocytes. As a result, there is a growing interest in microbiota-targeted therapies, including probiotics, dietary changes, and fecal microbiota transplantation. These methods may help restore the balance of microbes and reduce disease activity, but there are still a number of problems to solve. For example, microbiota composition varies greatly from person to person, and it is not clear how dysbiosis causes disease onset. There are also safety concerns about fecal microbiota transplantation. Experimental and clinical studies have started to shed light on the complicated ways in which microbial communities and immune function affect each other in SLE. These studies provide useful information, but their results are often inconsistent. As research continues, integrative methods like metagenomics and metabolomics may help find microbial signatures linked to disease, helping create more accurate and personalized treatments. The gut microbiome is a promising yet still developing area of research that could help us learn more about autoimmune diseases and their treatment, such as SLE. SIGNIFICANCE STATEMENT: Grasping the complex interplay between gut microbiota and systemic lupus erythematosus (SLE) has provided an avenue for therapeutic intervention. This study emphasizes the importance of gut dysbiosis in immune dysregulation, with connections between microbial translocation, molecular mimicry, and inflammatory pathways as contributing factors to the progression of SLE. This work sets the stage for novel and targeted approaches to treating SLE and improving patient outcomes by investigating microbiota-centric treatment options, such as probiotics, dietary interventions, and fecal microbiota transplantation.},
}

@article {pmid40924818,
year = {2025},
author = {Mabry, SJ and Cao, X and Zhu, Y and Rowe, C and Patel, S and González-Arancibia, C and Romanazzi, T and Saleeby, DP and Elam, A and Lee, HT and Turkmen, S and Lauzon, SN and Hernandez, CE and Sun, H and Wu, H and Carter, AM and Galli, A},
title = {Fusobacterium nucleatum enhances amphetamine-induced behavioral responses through a butyrate-driven epigenetic mechanism.},
journal = {Science signaling},
volume = {18},
number = {903},
pages = {eadx7729},
doi = {10.1126/scisignal.adx7729},
pmid = {40924818},
issn = {1937-9145},
mesh = {Animals ; *Fusobacterium nucleatum/metabolism/physiology ; *Butyrates/pharmacology/metabolism ; *Amphetamine/pharmacology ; *Epigenesis, Genetic/drug effects ; Drosophila melanogaster/microbiology/genetics ; *Behavior, Animal/drug effects ; Dopamine Plasma Membrane Transport Proteins/metabolism/genetics ; Dopamine/metabolism ; Gastrointestinal Microbiome/drug effects ; Male ; *Amphetamine-Related Disorders/microbiology/metabolism/genetics ; },
abstract = {Amphetamines are psychostimulants that are commonly used to treat neuropsychiatric disorders and are prone to misuse. The pathogenesis of amphetamine use disorder (AUD) is associated with dysbiosis (an imbalance in the body's microbiome) and bacterially produced short-chain fatty acids (SCFAs), which are implicated in the gut-brain axis. Amphetamine exposure in both rats and humans increases the amount of intestinal Fusobacterium nucleatum, which releases SFCAs. Here, we found that colonization of gnotobiotic Drosophila melanogaster with F. nucleatum or supplementing the flies' diet with the SCFA butyrate enhanced the psychomotor and reward properties of amphetamine. Butyrate inhibits histone deacetylases (HDACs), and knockdown of HDAC1 recapitulated the effects induced by F. nucleatum or butyrate. The enhancement in amphetamine-induced behaviors was mediated by an increase in the amount of released dopamine that resulted from amphetamine-induced reversal of dopamine transporter (DAT) function, termed nonvesicular dopamine release (NVDR). The magnitude of amphetamine-induced NVDR was partially mediated by an increase in DAT abundance stimulated at a transcriptional level, and the administration of F. nucleatum or butyrate enhanced NVDR by increasing DAT expression. The findings indicate that F. nucleatum supports AUD through epigenetic regulation of dopamine signaling and identify potential targets for AUD treatment.},
}

Animals
*Fusobacterium nucleatum/metabolism/physiology
*Butyrates/pharmacology/metabolism
*Amphetamine/pharmacology
*Epigenesis, Genetic/drug effects
Drosophila melanogaster/microbiology/genetics
*Behavior, Animal/drug effects
Dopamine Plasma Membrane Transport Proteins/metabolism/genetics
Dopamine/metabolism
Gastrointestinal Microbiome/drug effects
Male
*Amphetamine-Related Disorders/microbiology/metabolism/genetics

@article {pmid40924218,
year = {2025},
author = {Samonty, I and Hasan, MZ and Hossain, MR and Mahamud, AGMSU},
title = {The PGPB paradox: A critical review of field performance and practical constraints in agriculture.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {9},
pages = {321},
pmid = {40924218},
issn = {1573-0972},
mesh = {*Agriculture/methods ; *Soil Microbiology ; Crops, Agricultural/microbiology/growth & development ; Rhizosphere ; *Bacteria/metabolism ; Biological Control Agents ; Fertilizers ; },
abstract = {While PGPB have historically been applied in agriculture, their formal recognition in the last century has driven intensive research into their role as sustainable tools for improving crop yield and stress tolerance. As they are primarily sourced from wild or native environments, the widespread enthusiasm has led to heightened expectations surrounding their potential, often based on the assumption that biological solutions are inherently safer and more effective than synthetic inputs. However, despite their popularity, increasing reports of inconsistent or limited performance under real-world, field conditions have raised critical questions about their credibility as biofertilizers and biocontrol agents. This commentary critically evaluates the reasons behind the limited success of PGPB in field settings, based on the latest scientific evidence. Particular focus is placed on the microbial conflict in the rhizosphere, the inability of PGPB inoculants to adapt in complex environmental conditions, limitations in modern agricultural practices, formulation challenges, and regulatory gaps. The paper recommends the need for a paradigm shift in PGPB research and deployment strategies to better align laboratory successes with the challenges and outcomes seen in actual field conditions. Such an approach is vital for reducing over-reliance on underperforming technologies and promoting more resilient, context-specific solutions for sustainable agriculture, especially in under-resourced regions.},
}

*Agriculture/methods
*Soil Microbiology
Crops, Agricultural/microbiology/growth & development
Rhizosphere
*Bacteria/metabolism
Biological Control Agents
Fertilizers

@article {pmid40924210,
year = {2025},
author = {Arad, N and Spraker, J and Garcia, K and Pauli, D and Arnold, AE},
title = {Biosynthetic potential of the culturable foliar fungi associated with field-grown lettuce.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {197},
pmid = {40924210},
issn = {1432-0614},
support = {DGE-2022055//National Science Foundation/ ; ARZT-1361340-H25-242//National Institute of Food and Agriculture/ ; },
mesh = {*Lactuca/microbiology ; *Plant Leaves/microbiology ; Multigene Family ; *Biosynthetic Pathways/genetics ; Alternaria/genetics/isolation & purification/metabolism ; Arizona ; Genome, Fungal ; Endophytes/genetics/isolation & purification/metabolism ; Phylogeny ; *Fungi/genetics/isolation & purification/metabolism/classification ; Fusarium/genetics/isolation & purification/metabolism ; },
abstract = {Fungal endophytes and epiphytes associated with plant leaves can play important ecological roles through the production of specialized metabolites encoded by biosynthetic gene clusters (BGCs). However, their functional capacity, especially in crops like lettuce (Lactuca sativa L.), remains poorly understood. We sequenced the genomes of nine fungal isolates, representing Fusarium sp., Fulvia sp., Alternaria alternata, and Alternaria postmessia, from leaves of lettuce grown under field conditions in Arizona, USA. We used antibiotics and secondary metabolite analysis shell (antiSMASH) and the database for automated carbohydrate-active enzyme annotation (dbCAN3), to predict BGCs and carbohydrate-active enzymes (CAZymes) for each strain, and then compared them to conspecific strains from other environments and substrates. Foliar lettuce-associated fungi featured 39-95 BGCs per genome, with substantial overlap between isolates occurring in association with lettuce leaves vs. from other substrates. Species identity was a significant determinant of BGC count, while host type, isolation source, and lifestyle were not. Several BGCs, including those for alternariol and 1,3,6,8-Tetrahydroxynaphthalene (T4HN), showed 100% similarity to characterized minimum information about a biosynthetic gene cluster (MIBiG) clusters based on antiSMASH predictions. Although analysis by biosynthetic gene similarity clustering and prospecting engine (BiG-SCAPE) identified gene cluster families (GCFs) across the dataset, these reference-matching clusters were not always grouped, reflecting methodological differences in how the tools assess similarity. Comparative CAZyme analysis in a focal species (Fulvia sp.) revealed higher gene counts in a foliar lettuce-derived isolate than in tomato (Solanum lycopersicum)-associated strains, challenging assumptions about host chemical complexity. These results highlight the importance of phylogenetic context in shaping fungal functional potential and suggest that selection on microbial traits in edible leafy crops may be more subtle and species-specific than previously assumed. KEY POINTS: • Lettuce-associated fungi feature diverse biosynthetic potential • Phylogeny predicts fungal BGC content more strongly than ecological lifestyle • Findings support genome-informed microbiome strategies for leafy crops.},
}

*Lactuca/microbiology
*Plant Leaves/microbiology
Multigene Family
*Biosynthetic Pathways/genetics
Alternaria/genetics/isolation & purification/metabolism
Arizona
Genome, Fungal
Endophytes/genetics/isolation & purification/metabolism
Phylogeny
*Fungi/genetics/isolation & purification/metabolism/classification
Fusarium/genetics/isolation & purification/metabolism

@article {pmid40923525,
year = {2025},
author = {Prasad, R and Angelova, A and Subramanian, P and Namasivayam, S and Chen, Q and Banks, K and Levy, S and Maxwell, GL and Hourigan, SK},
title = {Parity influences on the infant gut microbiome development: a longitudinal cohort study.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2557980},
doi = {10.1080/19490976.2025.2557980},
pmid = {40923525},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Female ; Infant ; *Parity ; RNA, Ribosomal, 16S/genetics ; Pregnancy ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Adult ; Delivery, Obstetric ; Infant, Newborn ; Cohort Studies ; Cesarean Section ; },
abstract = {Parity, the number of pregnancies carried beyond 20 weeks, influences the maternal gut microbiome. However, whether parity modulates the infant microbiome longitudinally remains underexplored. To address this, 746 infants in a longitudinal cohort study were assessed. Serial infant stool samples collected at 2, 6, 12, and 24 months underwent 16S ribosomal RNA gene sequencing. Mothers were stratified by parity: 1 = 32.6%, 2 = 42.0%, 3 = 18.6%, 4, 5, 6 or 7 = 6.8%. Although no differences in alpha diversity were found with parity, significant differences were found in microbiome composition (beta diversity, Bray-Curtis) by parity at each time point through the first year of life (p < 0.001). Delivery mode (vaginal delivery (VD) = 60.5%, Cesarean section (CS) = 39.5%) was a significant contributor to infant microbiome composition at 2 months (p = 0.002). In VD infants, parity-related differences in microbiota composition were evident up to 6 months (p ≤ 0.002), however in CS delivered infants, early life parity-related differences were absent. In conclusion, our brief report showed a significant effect of parity on early infant gut microbiome composition. However, the effect of parity diminished with CS delivery, which we hypothesize is due to decreased mother-to-infant microbiome transfer with CS. These results demonstrate the necessity of including parity in longitudinal infant microbiome analyses.},
}

Humans
*Gastrointestinal Microbiome
Longitudinal Studies
Female
Infant
*Parity
RNA, Ribosomal, 16S/genetics
Pregnancy
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Male
Adult
Delivery, Obstetric
Infant, Newborn
Cohort Studies
Cesarean Section

@article {pmid40923499,
year = {2025},
author = {Van Hecke, T and Jakobsen, LMA and Tian, X and Van Pee, J and Elias Masiques, N and Vermeersch, AS and Deforce, D and Van Nieuwerburgh, F and Van Royen, G and De Vrieze, J and Bertram, HC and De Smet, S},
title = {Metabolic consequences and gut microbiome alterations in rats consuming pork or a plant-based meat analogue.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo02197a},
pmid = {40923499},
issn = {2042-650X},
abstract = {It is unknown how human health is affected by the current increased consumption of ultra-processed plant-based meat analogues (PBMA). In the present study, rats were fed an experimental diet based on pork or a commercial PBMA, matched for protein, fat, and carbohydrate content for three weeks. Rats on the PBMA diet exhibited metabolic changes indicative of lower protein digestibility and/or dietary amino acid imbalance, alongside increased mesenteric (+38%) and retroperitoneal (+20%) fat depositions despite lower food and energy intake. In contrast, rats on the pork diet demonstrated signs of a disturbed gut-liver axis with increased liver weight (+15%) and blood low-density lipoprotein (+86%), which may have been facilitated by gut microbial changes. The colon of rats on the PBMA diet was characterized by an outgrowth of bacterial groups including Muribaculaceae, Roseburia and various Eubacterium spp. known to improve cholesterol metabolism, whereas a remarkable outgrowth of Akkermansia, Oscillospiraceae and Desulfovibrionaceae in rats on the pork diet may be conducive to colon mucin degradation. Effects on oxidative stress parameters were equivocal, with increased lipid oxidation (+27%) in the colon mucosa of PBMA-fed rats, whereas lower blood levels of the endogenous antioxidant glutathione (-30%) were found in pork-fed. Overall, the present rat study reveals major differences in the physiological and microbiota-related responses to diets containing either conventional pork or PBMA, which could have implications for human health.},
}

@article {pmid40923448,
year = {2025},
author = {He, MC and Ferrini, A and Parvizi, J},
title = {Periprosthetic joint infection: Time to think outside the box.},
journal = {Knee surgery, sports traumatology, arthroscopy : official journal of the ESSKA},
volume = {},
number = {},
pages = {},
doi = {10.1002/ksa.70056},
pmid = {40923448},
issn = {1433-7347},
abstract = {Despite undisputed success of orthopaedic procedures, surgical site infections (SSI) such as periprosthetic joint infection (PJI) continues to compromise the outcome and result in major clinical and economic burden. The overall rate of infection is expected to rise in the future resulting in significant associated mortality and morbidity. Traditional concepts have largely attributed the source of PJI to exogenous pathogens. However, recent studies indicate that pathogens from the patient's own microbiome, colonizing the skin, nasal passages, gut microbiota, and even the surgical site play a major role in causing SSIs. Immune cell-mediated 'Trojan Horse' pathways have been posited as the mechanism of how bacteria reach and persist at the surgical site. In light of these developing insights, novel therapeutic strategies are under investigation. Some exciting developments include the use of membrane-permeable antibiotics, bacteriophage therapy targeting intracellular pathogens as well as probiotics, prebiotics, or faecal microbiota transplantation. Overall, targeting the endogenous microbiome represents a promising frontier for improving the prevention and management of PJI in the era of rapidly increasing total joint arthroplasty procedures.},
}

@article {pmid40923363,
year = {2025},
author = {Huang, F and Sun, K and Diao, L and Lu, K and Fan, Y and Xie, G},
title = {Glycyrrhizin alleviates renal damage in MRL/lpr mice by modulating gut microbiota dysbiosis and regulating the RTK-PKCα axis: insights from reverse network pharmacology.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01743b},
pmid = {40923363},
issn = {2042-650X},
abstract = {The present investigation elucidates the therapeutic potential of glycyrrhizin, the predominant triterpene saponin isolated from Glycyrrhiza glabra (licorice), in the management of systemic lupus erythematosus (SLE), an autoimmune disorder characterized by multisystemic involvement and therapeutic recalcitrance. Comprehensive interrogation of multiple disease-specific databases facilitated the identification of crucial SLE-associated molecular targets and hub genes, with MAPK1, MAPK3, TP53, JUN, and JAK2 demonstrating the highest degree of network centrality. Subsequent molecular docking simulations and binding affinity assessments revealed compounds with exceptional complementarity to these pivotal molecular targets, establishing Glycyrrhiza glabra as a pharmacologically promising botanical source and glycyrrhizin as its principal bioactive constituent meriting comprehensive mechanistic investigation. Experimental validation employing the MRL/lpr murine lupus model demonstrated that glycyrrhizin treatment significantly diminished circulating autoantibody titers and markedly ameliorated the characteristic glomerulonephritis and tubular interstitial damage associated with lupus nephritis. Concomitant 16S rDNA gene sequencing-based microbiome profiling revealed that glycyrrhizin administration induced substantial modulation of the intestinal microbial ecosystem, specifically attenuating the abundance of Ruminococcus genus, a bacterial taxon previously implicated in the pathogenesis and exacerbation of lupus nephritis. Transcriptomic analysis utilizing Gene Expression Omnibus (GEO) repository datasets confirmed glycyrrhizin's profound regulatory effects on calcium signaling pathways. Mechanistically, glycyrrhizin suppresses renal receptor tyrosine kinase (RTK)-protein kinase C alpha (PKCα) axis activation, thereby interrupting key inflammatory and fibrotic signaling cascades. Collectively, these findings provide compelling evidence that glycyrrhizin confers nephroprotective effects in lupus nephritis through orchestrated dual mechanisms: (1) restoration of gut microbiota homeostasis, and (2) suppression of the renal RTK-PKCα signaling axis, thereby attenuating inflammatory cascades and preserving renal architectural integrity. These mechanistic insights advance our understanding of glycyrrhizin's therapeutic potential and establish a robust scientific foundation for its clinical translation in SLE management strategies.},
}