@article {pmid40505618,
year = {2025},
author = {Sanders, ME and Hill, C},
title = {The microbiome: An actor or stage for the beneficial action of probiotics, prebiotics, synbiotics, and postbiotics?.},
journal = {Cell host & microbe},
volume = {33},
number = {6},
pages = {777-789},
doi = {10.1016/j.chom.2025.04.017},
pmid = {40505618},
issn = {1934-6069},
mesh = {*Probiotics/administration & dosage ; *Prebiotics/administration & dosage ; *Synbiotics/administration & dosage ; Humans ; *Microbiota/physiology ; *Gastrointestinal Microbiome ; Animals ; },
abstract = {Probiotics, prebiotics, synbiotics, and postbiotics are required, by definition, to confer a health benefit on the host. It is often presumed the host microbiome plays a central role in the mechanism of action of these substances, collectively referred to here as "biotics." However, the definitions of both probiotics and postbiotics do not include an associated mechanism nor the involvement of the microbiome. The definitions of prebiotics and synbiotics require evidence of selective utilization by the host microbiome, but do not state that confirmatory evidence must be provided that this utilization causes the associated health benefit. In this perspective, we discuss evidence supporting a role for the microbiome in delivering these health benefits and whether or not measuring microbiome alterations can serve as important readouts of efficacy. We also discuss the possibility of expanding the biotics family with substances such as bacteriophage, fermented foods, and live dietary microbes.},
}

*Probiotics/administration & dosage
*Prebiotics/administration & dosage
*Synbiotics/administration & dosage
Humans
*Microbiota/physiology
*Gastrointestinal Microbiome
Animals

@article {pmid40505617,
year = {2025},
author = {Greathouse, KL and Choudhury, A},
title = {Precision nutrition and the gut microbiome: Harnessing AI to revolutionize cancer prevention and therapy.},
journal = {Cell host & microbe},
volume = {33},
number = {6},
pages = {766-776},
doi = {10.1016/j.chom.2025.05.011},
pmid = {40505617},
issn = {1934-6069},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Neoplasms/prevention & control/therapy/microbiology/diet therapy ; *Precision Medicine/methods ; *Artificial Intelligence ; Diet ; },
abstract = {The gut microbiome plays a pivotal role in human health, particularly in cancer prevention and treatment. Diet can significantly influence microbiome composition, but individual variability complicates intervention outcomes. We review the microbiome's influence on cancer development and therapy outcomes and evaluate dietary strategies that modulate microbial composition and metabolites. To address these complexities, we propose the digital gut twin: an artificial intelligence (AI)-driven, dynamically updated simulation that integrates nutrient databases, multi-omic microbiome profiles, host genomics, and clinical data to predict personalized responses to dietary interventions. While significant data and regulatory challenges exist that currently limit clinical implementation, emerging solutions-including pre-trained microbiome models, mechanistic simulators, automated knowledge graphs, and privacy-preserving training-provide a promising pathway toward establishing personalized diet-microbiome modulation as a core component of precision oncology.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Neoplasms/prevention & control/therapy/microbiology/diet therapy
*Precision Medicine/methods
*Artificial Intelligence
Diet

@article {pmid40505616,
year = {2025},
author = {Shenhav, L and Azad, MB and Silverman, MA},
title = {Human milk as a microbial pacemaker.},
journal = {Cell host & microbe},
volume = {33},
number = {6},
pages = {762-765},
doi = {10.1016/j.chom.2025.05.018},
pmid = {40505616},
issn = {1934-6069},
mesh = {Humans ; *Milk, Human/microbiology ; *Gastrointestinal Microbiome/physiology ; Infant ; Weaning ; Child ; Female ; },
abstract = {A Nature Medicine paper by Sawhney et al.[1] presents a strain-resolved analysis of the gut microbiome from infancy through eight years of age, identifying weaning as an evolutionary trigger for microbial adaptation. Their findings refine the timeline of microbiome development and highlight human milk as a pacemaker of microbial succession.},
}

Humans
*Milk, Human/microbiology
*Gastrointestinal Microbiome/physiology
Infant
Weaning
Child
Female

@article {pmid40505513,
year = {2025},
author = {Subramanian, M and Thaiss, CA},
title = {Microbial regulation of interoception.},
journal = {Current opinion in neurobiology},
volume = {93},
number = {},
pages = {103064},
doi = {10.1016/j.conb.2025.103064},
pmid = {40505513},
issn = {1873-6882},
abstract = {Interoceptive pathways communicate between the body and the brain to coordinate behavioral responses to changes in the internal milieu. An important contributor to the internal milieu of the body is the gastrointestinal microbiome. Here, we conceptualize the role of the microbiome and microbiome-derived metabolites in interoceptive processes that enable homeostasis maintenance. We highlight four key features that make the microbiome a valuable sensory source for interoceptive processes: its capacity to engage canonical sensory pathways, dynamic responsiveness to environmental perturbations, diurnal oscillations aligned with host circadian rhythms, and the selective gating of sensory information through the intestinal barrier. We further explore how microbiome-derived sensory information contributes to homeostasis, imparts valence to events and cues, and serves as a substrate for memory. Collectively, we present a framework for understanding interoceptive dysfunction through the lens of microbiome-host interactions.},
}

@article {pmid40504882,
year = {2025},
author = {Combrink, L and Spaan, JM and Perret, A and Maehara, T and Hyun, B and Parker, D and Johns, JL and Blouin, MS and Magnusson, K and Steinauer, ML},
title = {Does schistosome infection affect behavior through the gut-brain axis?.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {6},
pages = {e0013088},
doi = {10.1371/journal.pntd.0013088},
pmid = {40504882},
issn = {1935-2735},
abstract = {Parasitic helminths infect over 2 billion people, primarily those living in poverty. Helminth infections typically establish in early childhood and persist through critical periods of growth and development, leading to cognitive deficits and/or behavioral changes. These deficits could result from the helminths themselves or due to dysbiosis of the gut microbiota and its influence on the gut-brain axis. Using two cohorts of 3-week-old female mice, we measured levels of anxiety, fear, compulsion, spatial learning, and spatial memory, between schistosome-infected and sham-exposed mice. Additionally, we compared their fecal microbiomes using 16S rRNA gene sequencing at two time points during the chronic stage of infection. Schistosome-infected mice showed higher levels of anxiety in the open field test, reduced spatial learning in the Morris water maze task, and enhanced memory retention in the novel object task. All mice performed equally on the marble bury task. Each cohort started with unique microbiota which showed marked changes in the beta diversity of their microbiota after exposure. In both cohorts, at 7- weeks post exposure, infected mice had more Alistipes sp. and Bacteroides thetaiotaomicron and less Turicibacter sp. and Ligilactobacillus sp. than uninfected mice. At 10 weeks, infected mice had more Alistipes sp. and fewer Muribaculaceae sp. Interestingly, taxon shifts in infected mice were those typically associated with protective effects on liver disease and IL-10 gut conditions, suggesting a possible protective role of the shifted microbiome. Our analyses did not indicate associations between behavioral measures and microbiome composition; however, this could be due to the strong impact of infection on the microbiome composition. Findings here uncover behavioral and cognitive impacts of schistosome infection and shed light on the complex interplay between schistosome infection, behavioral changes, and host microbiome composition, which could ultimately support future global health efforts.},
}

@article {pmid40504797,
year = {2025},
author = {Perraud, Q and Sperandio, V},
title = {Enterohemorrhagic E. coli (EHEC) and the microbiome.},
journal = {PLoS pathogens},
volume = {21},
number = {6},
pages = {e1013224},
doi = {10.1371/journal.ppat.1013224},
pmid = {40504797},
issn = {1553-7374},
}

@article {pmid40504562,
year = {2025},
author = {Soleimani, RA and Milani, PG and Khani, N and Homayouni-Rad, A},
title = {The Overlooked Hazard: Clostridioides difficile in Preterm Infants and Immature Immune Systems-Harnessing Postbiotics for Safer Therapeutic Strategies.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf083},
pmid = {40504562},
issn = {1472-765X},
abstract = {Clostridioides difficile is a potentially harmful bacterium that can affect preterm infants more seriously than full-term infants, largely due to their immature immune systems and underdeveloped gut microbiota. Although colonization with C. difficile is often harmless in healthy babies, preterm infants are more likely to develop infections, which can lead to serious health problems. This review looks at how an immature immune system and an imbalanced gut microbiome increase the risk of C. difficile infection (CDI) in early life. To reduce this risk, researchers are exploring postbiotics-non-living bacterial products or byproducts-as a safer alternative to traditional treatments like antibiotics. Postbiotics can help by strengthening the gut barrier, reducing inflammation, and supporting the growth of beneficial bacteria. They are also considered safe for use in vulnerable populations, including infants. This review discusses the types of postbiotics, their functions, and how they may help prevent or manage CDI. It also highlights their potential for use in infant formula as a preventative strategy. Overall, postbiotics may offer a promising new way to protect preterm infants from C. difficile and support healthier immune and gut development.},
}

@article {pmid40504523,
year = {2025},
author = {Stinson, LF and Geddes, DT},
title = {Typical skin and oral bacterial species present in human milk are not the result of contamination during the sampling process.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf084},
pmid = {40504523},
issn = {1472-765X},
abstract = {Human milk has a low microbial biomass with a microbiome dominated by typical skin and oral taxa, raising concerns about contamination during sample collection. However, to date, no study has directly compared samples collected with and without aseptic technique, leaving questions related to potential contamination within the field. To address this, we compared the microbiota of hand-expressed milk samples collected from 23 mothers before and after cleansing of the hands and breast. Metataxonomic analysis showed that taxonomic profiles were largely unaffected by cleansing, with only Rothia mucilaginosa significantly more abundant in non-aseptically collected samples (P = 0.007). Although aseptically and non-aseptically collected samples were taxonomically similar, there was a higher level of bacterial richness (P = 0.003) and evenness (Shannon diversity, P = 0.0002) in non-aseptically collected samples, suggesting that multiple low-abundance taxa are introduced via skin contamination. These findings support the use of aseptic collection methods to minimise external contamination and accurately assess milk microbial diversity. Importantly, they also suggest that common skin and oral taxa detected in human milk are likely true members of the mammary microbiome.},
}

@article {pmid40504492,
year = {2025},
author = {Rosamond, KM and Esser, HJ and Assink, RB and Jaramillo-Ortiz, L and Rowe, M and Kirke, EC and Matson, KD},
title = {Host-microbiome interactions as moderators of host quality and biodiversity-disease relationships.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf091},
pmid = {40504492},
issn = {1557-7023},
abstract = {Biodiversity-disease studies typically focus on how changes in community composition (e.g., species richness, abundance, and functional or phylogenetic metrics of biodiversity) affect disease risk. In doing so, these studies tend to overlook intraspecific variation in the organisms comprising the community. Yet, intraspecific variation, which occurs to varying degrees both within and between communities, could also modulate biodiversity-disease relationships. One important driver of intraspecific variation is the microbiome. By directly and indirectly influencing health and susceptibility to infection and disease, microbiomes are integral to organismal functioning. Thus, the microbiome plays a crucial role in host quality. We define host quality as an integration of host traits related to parasite exposure, establishment, growth, and infectivity, which ultimately shape parasite fitness. The microbiome can impact host quality via a variety of mechanisms including host size and developmental stage, immune function, reproduction, nutrient acquisition, and behavior. However, the potential for such microbiome-driven changes in host quality to trigger cascading effects on community-level processes, specifically by altering parasite transmission dynamics and community competence, has not been well explored. Here, we examine and illustrate a pathway by which the microbiome may influence variation in organismal biology (i.e., host quality) of hosts in communities. Furthermore, we consider how major anthropogenic drivers of microbiome shifts, such as climate change, pollution, land use change, and domestication, might influence this pathway and thereby alter outcomes. Future studies bridging microbiome and disease ecology research will provide opportunities to unify these concepts across scales and between the plant and animal domains. To date, most microbiome research has focused on humans, crops, and laboratory animals. However, to better understand the potential for knock-on ecological effects of microbiomes, more attention must be paid to the microbiomes of wild plants and animals. Ultimately, more experimental and theoretical data are needed to clarify how the microbiome impacts host quality and disease dynamics, as well as how anthropogenic factors continuously reshape these relationships.},
}

@article {pmid40504464,
year = {2025},
author = {Chen, YR and Chen, LD and Zheng, LJ},
title = {Exploring the trimethylamine-degrading genes in the human gut microbiome.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {91},
pmid = {40504464},
issn = {2191-0855},
support = {32100082//National Natural Science Foundation of China/ ; 2023A03J0696//Science and Technology Program of Guangzhou/ ; },
abstract = {Trimethylamine (TMA), produced by gut microbes, is a precursor to a risk factor for cardiovascular diseases. Currently, TMA-degrading bacteria in the human gut have rarely been studied. This study combined TMA-enriched cultures (from 104 young male stool samples) with metagenomic profiling to identify key microbial players of TMA degradation. The results showed that the contribution of Enterococcus to methane metabolism was significantly higher in TMA-enriched culture samples. The 68.58% up-regulation of dmd-tmd (dimethylamine/trimethylamine dehydrogenase) in the TMA-enriched group indicated that the anaerobic dehydrogenase pathway participated in TMA metabolism. Notably, we first identified that taxa containing dmd-tmd belonged to Christensenella timonensis. The up-regulation of genes involved in methanogenesis (M00563) as well as the significant enrichment of M00563 (Reporter Score = 2.223) indicated that the methanogenesis pathway may play a role. We constructed gene databases for genes involved in the anaerobic dehydrogenase pathway (1526 sequences for dmd-tmd, 1319 sequences for mauA, and 326 sequences for mauB, respectively) and the aerobic oxidation pathway (2146 sequences for tmm, 1445 sequences for tdm, and 1519 sequences for dmm, respectively) based on genomes from the Integrated Microbial Genome (IMG) database, most of which belong to Pseudomonadota. Screening gut metagenomes with these databases revealed low sequence identity (< 70%), possibly because of the underrepresentation of gut-specific genomes from IMG. This study links Christensenella timonensis to TMA degradation, providing potential targets for microbiota modulation and a gene-centric framework to advance the characterization of gut microbial TMA metabolism.},
}

@article {pmid40504322,
year = {2025},
author = {Pachauri, A and Sharma, S},
title = {Unravelling the gut-skin axis: the role of gut microbiota in pathogenesis and management of psoriasis.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {40504322},
issn = {1568-5608},
abstract = {Psoriasis is a chronic, multifactorial, inflammatory skin disease, increasingly recognized as a systemic disorder influenced by the gut-skin axis, which is a dynamic bidirectional communication between intestinal microbiome and cutaneous immune response. This narrative review explores the understanding of the gut-skin axis with the latest evidence on how gut dysbiosis occurs in psoriasis, characterized by reduced microbial diversity and its shifts, and how it contributes to pathogenesis and exacerbation of psoriasis. Notably, recent scientific literature evidence suggests that the alteration of gut microbiome in psoriasis includes a decreased level of beneficial species like Faecalibacterium prausnitzii and a rise in the level of proinflammatory bacterial species like Prevotella copri. Mechanistic insights reveal that gut-derived metabolites, impaired barrier functions, and immune signaling, particularly involving IL-23 and Th17 cells, play a pivotal role in this axis, linking intestinal health to cutaneous manifestations. Both animal and human trials underscore the therapeutic potential of interventions targeting the gut microbiota, including prebiotics, probiotics, dietary modifications, and FMT, demonstrating some promising but variable effects on disease severity and systemic inflammation. Despite these advances, translating the gut-skin axis into clinical practice presents a notable challenge due to limited scientific evidence, a lack of standardised microbiome profiling, and the absence of universally accepted biomarkers to monitor and stratify therapeutic outcomes. These limitations hinder the development of personalised care approaches and the integration of the gut-skin axis as a promising frontier in many autoimmune diseases, where the gut-skin axis and the intestinal microbiome play a crucial role.},
}

@article {pmid40504059,
year = {2025},
author = {Daana, S and Rokach, Y and Abedat, S and Nachman, D and Mohsen, H and Karram, S and Zandberg, Y and Tzach-Nachman, R and Cohen, J and Amir, O and Houri-Haddad, Y and Rabea Asleh, },
title = {Periodontitis Accelerates Progression of Heart Failure With Preserved Ejection Fraction in Mice.},
journal = {JACC. Basic to translational science},
volume = {},
number = {},
pages = {101270},
doi = {10.1016/j.jacbts.2025.03.002},
pmid = {40504059},
issn = {2452-302X},
abstract = {Chronic low-grade inflammation and nitric oxide (NO) depletion are important contributors to heart failure with preserved ejection fraction (HFpEF) pathophysiology. Periodontitis (PD) is a common inflammatory disease implicated in dysregulation of NO hemostasis. Epidemiological studies have shown an association between PD and increased risk of cardiovascular disease, including heart failure. However, a causative relationship between the 2 diseases has not yet been proven. In this study, we sought to investigate the direct effect of PD induction on HFpEF progression in a mouse model. Induction of PD in HFpEF mice resulted in significant oral microbial dysbiosis, accelerated progression of diastolic dysfunction by echocardiography, and increased myocardial inflammation and fibrosis. These deleterious effects seen with PD were shown to be mediated by increased systemic blood pressure, increased systemic inflammation, and NO depletion. Our study provides evidence of potential mechanistic links between PD and HFpEF progression and suggests PD as a new therapeutic target for HFpEF.},
}

@article {pmid40503970,
year = {2025},
author = {Erkert, L and Kabisch, M and Gamez-Belmonte, R and Gonzalez-Acera, M and Patankar, JV and Schödel, L and Hofmann, K and Wagner, Y and Plattner, C and Spath, EM and Distler, U and Tenzer, S and , and Neufert, C and Neurath, MF and Becker, C},
title = {Pharmacological inhibitors of the gamma-secretase enzyme complex disrupt epithelial cell function triggering colitis in mice.},
journal = {Journal of Crohn's & colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjaf096},
pmid = {40503970},
issn = {1876-4479},
abstract = {BACKGROUND AND AIMS: Inhibiting γ-secretase mediated Notch signaling has been explored as a potential treatment for Alzheimer's disease and cancer. However, clinical trials have revealed that this approach can lead to side effects, such as gut inflammation. Notch signaling has been shown to be a key mediator of intestinal epithelial homeostasis. We aimed to investigate the molecular mechanisms of γ-secretase inhibition-associated colitis.

METHODS: Mice and small intestinal organoids were treated with γ-secretase inhibitors and analyzed for IEC differentiation and inflammation-associated markers using different molecular and histological approaches, along with transcriptomic and proteomic analyses. To evaluate the role of the microbiome in colitis development, mice undergoing pharmacological γ-secretase inhibition were treated with antibiotics. Additionally, inflammatory bowel disease (IBD) patient samples and control samples were analyzed to assess the expression of Notch signaling pathway components in IECs.

RESULTS: This study shows that pharmacological γ-secretase inhibition induces inflammation in both the small and large intestine of mice, a phenotype that could be rescued upon microbiota depletion. Inhibiting the γ-secretase induced structural disruption of the epithelium and inflammatory cytokine release. On a molecular level, epithelial organoids exhibited disrupted IEC differentiation and impaired proliferation, associated with defective Notch signaling. Finally, analysis of IBD patients revealed deregulation of Notch pathway components within IECs.

CONCLUSIONS: In conclusion, systemic use of γ-secretase inhibitors disrupts epithelial cell function by impairing IEC differentiation and triggering gut inflammation in mice. These findings should be considered when designing future therapeutic interventions involving γ-secretase inhibitors.},
}

@article {pmid40503883,
year = {2025},
author = {Pearson-Lund, AS and Williams, SD and Eaton, KR and Clark, AS and Holloway, NH and Ewen, KA and Muller, EM},
title = {Evaluating the effect of amoxicillin treatment on the microbiome of Orbicella faveolata with Caribbean yellow band disease.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0240724},
doi = {10.1128/aem.02407-24},
pmid = {40503883},
issn = {1098-5336},
abstract = {Host microbiomes play a key role in coral disease dynamics; thus, it is essential to characterize microbial communities of diseased tissues and identify how they are altered by potential treatments, especially as coral reef populations continue to decline globally. The abundance of Orbicella faveolata, a major reef-building Caribbean coral species, has significantly declined due to several stressors, including infectious disease. Caribbean yellow band disease (CYBD) often results in complete colony mortality. We applied an amoxicillin-laced Base2B ointment to CYBD lesion areas on O. faveolata within Buck Island Reef National Monument, St. Croix, USVI, trying to halt disease progression. Another CYBD lesion area on the same colony served as a paired untreated control. Microbiomes of the apparently healthy tissue adjacent to the treatment were characterized pretreatment and 2 days post-treatment, along with the paired untreated CYBD controls and nearby healthy colonies. Both microbiomes of untreated CYBD lesions and apparently healthy tissue on CYBD colonies had a significantly higher alpha diversity and significantly differed from those of nearby healthy colonies, suggesting potential systemic effects of CYBD. Amoxicillin treatment significantly changed the microbial community composition of tissues adjacent to the treatment site. The relative abundance of the bacterial family Vibrionaceae, a putative pathogen for CYBD and often associated with other coral diseases, was enriched post-treatment. However, the lesion progression rates of treated and untreated lesion areas were similar. Our results suggest that amoxicillin may disrupt the microbiome of adjacent tissue on O. faveolata, allowing for opportunistic Vibrio sp. bacteria to colonize, and may not be an effective treatment for CYBD.IMPORTANCEOrbicella faveolata, a primary reef-building coral species in the Caribbean, has been severely impacted by Caribbean yellow band disease. This disease causes tissue loss, which often culminates in the complete loss of the colony since recovery is rarely observed. The present study is significant because the development of an effective long-term treatment for Caribbean yellow band disease and understanding how the microbial partners contribute to pathogenesis are essential for conserving Caribbean coral reefs. While treatment with amoxicillin was not effective, our study uncovered valuable insights into the microbial composition of Caribbean yellow band disease in O. faveolata. In addition, this study highlights the possible unintended negative effects of treatment with amoxicillin and casts doubt on Vibrionaceae as the culprit of this disease.},
}

@article {pmid40503824,
year = {2025},
author = {Snelling, TJ and Condren, M and Huntington, JA and Warren, HE and Taylor-Pickard, J and Sinclair, LA},
title = {The rumen microbiota and metabolism of dairy cows are affected by the dietary rate of inclusion of Yucca schidigera extract.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0064125},
doi = {10.1128/spectrum.00641-25},
pmid = {40503824},
issn = {2165-0497},
abstract = {Natural plant compounds can be used to supplement livestock diets, improving feed efficiency, production, and health, while also reducing environmental impact. In the present study, a Yucca schidigera (Mohave Yucca) extract was added at four rates of inclusion (ROI) of 0, 5, 15, or 30 g/day to a ryegrass and maize silage-based diet and fed to dairy cows in a 4 × 4 Latin square experimental design. Each period was 28 days in duration, with sampling undertaken during the final week of each period. Solid phase digesta (SPD) and liquid phase digesta (LPD) samples were collected via a rumen cannula and analyzed for volatile fatty acids (VFAs), ammonia N, and microbiome using 16S rRNA gene sequencing. Total fecal and urine collection was undertaken over a 3-day period. Rumen microbial diversity was not affected by ROI (LPD: P = 0.180; SPD: P = 0.059). However, discriminant analysis found a decrease in Methanobrevibacter millerae (linear discriminant analysis, LDA = 2.15) and an increase in an unclassified species of Proteobacteria (LDA = 2.10) associated with ROI. Univariate analysis also revealed differential abundance of operational taxonomic units classified as Prevotellaceae and Fibrobacteraceae by ROI (P < 0.05). Maximum rumen ammonia N concentration decreased linearly from 228 to 109 mg/L with ROI (P = 0.044). Rumen VFA concentration was unaffected with the exception of propionate, which showed a linear increase with ROI (P = 0.010). The diurnal rumen pH range (maximum-minimum) also decreased with ROI (P = 0.004). Dry matter intake and milk yield were not affected (P > 0.05) by ROI; however, there was a linear increase in milk fat content from 38.9 to 42.0 g/kg with ROI (P < 0.05).IMPORTANCEDomestic livestock such as dairy cows are inefficient utilizers of dietary nitrogen. This increases feed costs and reduces animal production efficiency. Excreted nitrogenous compounds are also an environmental hazard, such as when they enter water courses as nitrate or are lost to the atmosphere as ammonia or nitrous oxide. Dietary protein is degraded in the rumen via the activity of the microbial population, mainly into ammonia, which may then be utilized by the microbial population to synthesize microbial protein or absorbed into the blood and potentially excreted. Manipulation of the diet or altering the microbial population may increase the utilization of dietary protein, increasing animal performance, decreasing feed costs, and reducing the environmental impact of milk production. This study examines the effect of Yucca schidigera extract on the rumen microbiome and nitrogen utilization in dairy cows.},
}

@article {pmid40503236,
year = {2025},
author = {Bartosik, T and Pjevac, P and Séneca, J and Morgenstern, C and Arnoldner, T and Gangl, K and Sinz, C and Campion, NJ and Tu, A and Stanek, V and Bangert, C and Schneider, S and Eckl-Dorna, J},
title = {Dupilumab treatment has no effect on the nasal microbiome in patients with NSAID-exacerbated respiratory disease: a longitudinal pilot study.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1508500},
pmid = {40503236},
issn = {1664-3224},
mesh = {Humans ; *Antibodies, Monoclonal, Humanized/therapeutic use ; Male ; Middle Aged ; *Microbiota/drug effects ; Pilot Projects ; Female ; Longitudinal Studies ; Aged ; Adult ; *Anti-Inflammatory Agents, Non-Steroidal/adverse effects ; Quality of Life ; RNA, Ribosomal, 16S/genetics ; Nasal Polyps/drug therapy/microbiology ; Treatment Outcome ; },
abstract = {BACKGROUND: Non-steroidal anti-inflammatory drugs-exacerbated respiratory disease (N-ERD) affects up to 10% of patients suffering from nasal polyps and has a severe impact on quality of life. Dupilumab, a monoclonal antibody targeting the IL-4 receptor α chain, leads to symptom relief and reduction in nasal type 2 mediator levels. Here, we investigated the impact of dupilumab treatment on the composition and diversity of the nasal microbiome.

METHODOLOGY: Nasal microbiome was analyzed by 16s rRNA gene amplicon sequencing in 28 patients before, 4, 12, and 24 weeks after dupilumab therapy.

RESULTS: After stringent decontamination and removal of patients whose samples contained less than 500 reads at ≥ one of the four visits, full datasets from 8 out of 28 patients remained for downstream analysis of microbiome data. All 8 patients showed significant reduction in TPS (total polyp score; p=0.0078) and an improvement in SNOT-22 (Sino-nasal outcome test-22, a quality of life questionnaire; p=0.0781) after dupilumab therapy. During 24 weeks of dupilumab therapy, there were no major changes in microbiome diversity or composition observed (Shannon index: V1-V4:p-adj=0.25, Chao 1 Index V1-V4:p-adj=0.31), and only 2 out of 8 patients showed a decrease in staphylococci abundance.

CONCLUSIONS: More than 70% of the samples did not pass quality control, this warrants further refinement of nasal microbiome sampling techniques and mandatory guidelines on stringent quality control for analysis of this low biomass data in future. Furthermore, dupilumab did not have an impact on microbiome diversity or composition.},
}

Humans
*Antibodies, Monoclonal, Humanized/therapeutic use
Male
Middle Aged
*Microbiota/drug effects
Pilot Projects
Female
Longitudinal Studies
Aged
Adult
*Anti-Inflammatory Agents, Non-Steroidal/adverse effects
Quality of Life
RNA, Ribosomal, 16S/genetics
Nasal Polyps/drug therapy/microbiology
Treatment Outcome

@article {pmid40502641,
year = {2025},
author = {Lu, L and Li, Y and Su, H and Ren, S and Liu, Y and Shao, G and Liu, W and Ji, G and Xu, H},
title = {Huangqin decoction inhibits colorectal inflammatory cancer transformation by improving gut microbiome-mediated metabolic dysfunction.},
journal = {Journal of pharmaceutical analysis},
volume = {15},
number = {5},
pages = {101138},
pmid = {40502641},
issn = {2214-0883},
abstract = {Colorectal inflammatory cancer transformation poses a major risk to patients with colitis. Patients with chronic intestinal inflammation have an approximately 2-3 folds increased risk of developing colorectal cancer (CRC). Unfortunately, there is currently no effective intervention available. Huangqin decoction (HQD), a well-known traditional Chinese medicine (TCM) formula, is frequently clinically prescribed for treating patients with colitis, and its active ingredients have effective antitumour efficacy. Nonetheless, the mechanism of HQD-mediated prevention of colorectal inflammatory cancer transformation remains unclear. A strategy integrating metagenomic, lipidomic, and messenger RNA (mRNA) sequencing analysis was used to investigate the regulatory effects of HQD on the gut microbiome, metabolism and potential mechanisms involved in colorectal inflammatory cancer transformation. Our study revealed that HQD suppressed colorectal inflammatory cancer transformation, which was associated with enhanced intestinal barrier function, decreased the inflammatory response, and regulation of the gut microbiome. Notably, cohousing experiments revealed that the transfer of the gut microbiome from HQD-treated mice largely inhibited the pathological transformation of colitis. Moreover, gut microbiome transfer from HQD-treated mice primarily resulted in the altered regulation of fatty acid metabolism, especially the remodeling of arachidonic acid metabolism, which was associated with the amelioration of pathological transformation. Arachidonic acid metabolism and the key metabolic enzyme arachidonic acid 12-lipoxygenase (ALOX12) were affected by HQD treatment, and no obvious protective effect of HQD was observed in Alox 12 [-/-] mice, which revealed that ALOX12 was a critical mediator of HQD protection against colorectal inflammatory cancer transformation. In summary, multiple omics analyses were applied to produce valuable data and theoretical support for the application of HQD as a promising intervention for the transformation of inflammatory CRC.},
}

@article {pmid40502530,
year = {2025},
author = {Smith, KB and Murack, M and Butcher, J and Hinterberger, A and Stintzi, A and Liang, J and Tata, DA and Ismail, N},
title = {Modulating effects of environmental enrichment on stress-induced changes in the gut microbiome.},
journal = {Brain, behavior, & immunity - health},
volume = {46},
number = {},
pages = {101023},
pmid = {40502530},
issn = {2666-3546},
abstract = {Environmental enrichment (EE) involves adding non-standard stimuli, such as running wheels, mazes, and cage mates, to standard animal living conditions to facilitate physical activity, cognitive stimulation, and socialization. Interestingly, exposure to EE can modulate stress and immune responses. However, it is unclear whether housing environments can modulate the effects of stress on the gut microbiome. This study aimed to explore the effects of three different housing conditions-deprived (DH), social (SH), and enriched (EE)-on the central and peripheral immune responses, the HPA axis, and the gut microbiome in 180 male and female mice. Mice were housed in either the DH, SH, or EE condition for 3 weeks starting from post-natal day 21. At 6 weeks of age, during the pubertal stress-sensitive period, mice were treated with either saline or lipopolysaccharide (LPS), a bacterial endotoxin. Eight hours post-treatment, mice were euthanized, and brain, fecal samples, and trunk blood were collected to examine peripheral and central cytokine levels, glucocorticoid receptor (GR) and mineralocorticoid receptor (MR) expressions, along with diversity in the gut microbiome. Contrary to expectations, EE and SH mice showed higher plasma concentrations of TNFα, IL6, and IL12 cytokines than DH mice following LPS treatment, with male mice exhibiting significantly higher levels of these cytokines than their female counterparts. Moreover, EE mice exhibited significantly greater hypothalamic and hippocampal expressions of GR and MR compared to DH mice. The gut microbiome analysis revealed sex-specific beta diversity patterns post-LPS treatment, with male EE and SH mice displaying a more diverse microbiome compared to female counterparts. These findings enhance our understanding of how housing conditions influence the acute immune and stress responses and modulate their effects on the gut microbiome during puberty.},
}

@article {pmid40502457,
year = {2025},
author = {Otsuka, T and Ishizaki, Y and Yoshimoto, J and Takamori, K and Watanabe, S},
title = {Searching for bacteria within acute cholecystitis using next-generation sequencers.},
journal = {Surgery open science},
volume = {26},
number = {},
pages = {113-118},
pmid = {40502457},
issn = {2589-8450},
abstract = {INTRODUCTION: A biliary microbiome comprising flora within normal gallbladders was recently uncovered through analyses targeting the bacterial 16S ribosomal RNA (16S rRNA) gene, despite the gallbladder previously being regarded as a sterile environment. In the present study, we subjected bile samples from patients with acute cholecystitis to gene analysis targeting bacterial flora.

METHODS: We targeted patients diagnosed as having Grade I or Grade II acute cholecystitis (in accordance with the Tokyo Guidelines 2018 established by the Japanese Society of Hepato-Biliary-Pancreatic Surgery) who underwent laparoscopic cholecystectomy within 24 h of diagnosis at Juntendo University Urayasu Hospital between July 2021 and January 2024 for evaluation. We drew bile sample from the gallbladder of each patient to confirm the presence of biliary bacterial flora, using both standard bacteriology (culture test) and 16S rRNA gene sequence.

RESULTS: Of the 29 samples, 15 yielded cultures positive for bacterial flora, and gene analysis revealed the presence of bacterial biliary flora in all 14 samples that had tested negative in standard bacteriology. Considering the bacterial flora of a normal gallbladder without lesions as "normal flora," bacteria other than normal flora-Propionibacterium spp., Coprococcus spp., Prevotella spp., Sediminibacterium spp., and Collinesella spp.-were detected in 25 of the 29 cases (86 %).

CONCLUSIONS: Bacteria not detected in non-inflammatory gallbladders such as Propiobacterium spp., Coprococcus spp., Prevotella spp., Sediminibacterium spp., and Collinesella spp. may play a role in the mechanism underlying development of acute cholecystitis.},
}

@article {pmid40502320,
year = {2024},
author = {Kim, N},
title = {[The Relationship of Dysbiosis of Duodenal Microbiome and Functional Dyspepsia].},
journal = {The Korean journal of helicobacter and upper gastrointestinal research},
volume = {24},
number = {4},
pages = {327-338},
pmid = {40502320},
issn = {2671-826X},
abstract = {Functional dyspepsia (FD) is a common gastrointestinal disorder characterized by chronic or recurrent epigastric pain or discomfort and postprandial fullness, without a definite organic cause. Despite the importance of FD in terms of decreased quality of life and recurrence, treatment modalities have been unsatisfactory, mainly because of their complex and heterogeneous nature. A link between microbiome dysbiosis and low-grade inflammation, along with mucosal barrier disruption of the duodenal mucosa, has been suggested and may be a potential target for FD treatment. This link supports the gut-brain (overactive visceral signaling and pain modulation) and the brain-gut (abnormal central processing) axes in FD. A definite increase in Streptococcus and a reduced abundance of Prevotella, Veillonella, and Actinomyces have also been observed. In addition, bacterial overgrowth is frequently observed in the small intestine, and rifaximin treatment improves the symptoms of FD, especially in women. This evidence highlights the importance of bacterial ecology in the development of FD symptoms. However, further research is necessary to prove the causal relationship between duodenal mucosal microbiota dysbiosis and FD.},
}

@article {pmid40502184,
year = {2025},
author = {Verna, G and De Santis, S and Islam, B and Sommella, EM and Licastro, D and Zhang, L and De Almeida Celio, F and Merciai, F and Caponigro, V and Campiglia, P and Pizarro, TT and Chieppa, M and Cominelli, F},
title = {A missense mutation in Muc2 promotes gut microbiome- and metabolome-dependent colitis-associated tumorigenesis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.31.657160},
pmid = {40502184},
issn = {2692-8205},
abstract = {UNLABELLED: Colitis-associated cancer (CAC) arises from a complex interplay between host and environmental factors, including the gut microbiome. Since ulcerative colitis (UC), a significant risk factor for CAC, is rising in prevalence worldwide, an integrative approach is essential to identify potential triggers linking inflammation to cancer. In the present study, we investigated the role of the gut microbiome using Winnie mice, a UC-like model with a relevant missense mutation in the Muc2 gene. Upon transfer from a conventional (CONV) to a specific-pathogen-free (SPF) facility, Winnie mice exhibited a more severe colitis phenotype, and notably, spontaneous CAC as early as four weeks of age, which progressively worsened over time. In contrast, CONV Winnie developed only mild colitis but with no overt signs of tumorigenesis. Notably, when rederived into germ-free (GF) conditions, SPF Winnie mice were protected from colitis or colon tumor development, indicating an essential role for the gut microbiome in the initiation and progression of CAC in these mice. Using shotgun metagenomics, metabolomics, and lipidomics, we identified a distinct pro-inflammatory microbial and metabolic signature that potentially drives the transition from colitis to CAC. Fecal microbiota transplantation (FMT), using either SPF Winnie or WT (Bl/6) donors into GF Winnie recipients, demonstrated that while colitis developed regardless of donor, only FMT from SPF Winnie donors resulted in CAC, revealing a microbiota-driven, host-specific susceptibility to tumorigenesis in Winnie mice. Our studies present a novel and relevant model of CAC, providing further evidence that the microbiome plays a key role in the pathogenesis of CAC, thereby challenging the concept of colon cancer as a strictly non-transmissible disease.

LAY SUMMARY: This study reveals a distinct metagenomic, metabolomic, and lipidomic profile associated with tumorigenesis in a murine model of ulcerative colitis, highlighting the risks of specific intestinal dysbiosis in genetically predisposed subjects.

WHAT YOU NEED TO KNOW: Background and context: Colitis-associated colorectal cancer arises from complex host-environment interactions, including gut microbiome influences, driving chronic inflammation, with the intestinal lumen environment remaining a largely unexplored potential risk factor in cancer development.New findings: Winnie mice in specific pathogen-free conditions developed severe colitis, and a novel juvenile colon dysplasia and cancer, with gut microbiome changes driving colitis-associated cancer initiation and progression.Limitations: We identified a pro-inflammatory microbial/metabolic signature promoting colitis-to-CAC transition in Winnie mice, with FMT confirming microbiota-driven tumor susceptibility. However, further research is needed to pinpoint the key bacteria-metabolite-lipid combination driving CAC.Clinical research relevance: This newly characterized microbiota-metabolome-based model of CAC, challenges the dogma of cancer as a non-transmittable disease, providing a foundation for developing microbiota-based strategies for CAC prevention and treatment.Basic research relevance: Unlike genetic or chemically induced models, the Winnie mouse model uniquely serves as a dual model for spontaneous colitis and juvenile CAC, offering a fast, 100% penetrant phenotype that enhances reliability, accelerates research, and provides valuable insights into IBD and CAC.},
}

@article {pmid40502178,
year = {2025},
author = {Tristao Santini, A and Cerqueira, AES and Moran, NA and Resende, HC and Santana, WC and de Paula, SO and da Silva, CC},
title = {Gut microbiota of Brazilian Melipona stingless bees: dominant members and their localization in different gut regions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.03.657762},
pmid = {40502178},
issn = {2692-8205},
abstract = {The gut microbiome of eusocial corbiculate bees, which include honeybees, bumblebees, and stingless bees, consists of anciently associated, host-specific bacteria that are vital for bee health. Two symbionts, Snodgrassella and Gilliamella , are ubiquitous in honeybees and bumblebees. However, their presence varies in the stingless bee clade (Meliponini), a group with pantropical distribution. They are absent or rare in the diverse genus Melipona , indicating a shift in microbiota composition in this lineage. To identify the main members of the Melipona microbiota, we combined newly collected and published data from field-collected individuals of several species. Additionally, we identified the localization of the dominant microbiota members within the gut regions of Melipona quadrifasciata anthidioides . The dominant microbiota of Melipona species includes members of the genera Bifidobacterium, Lactobacillus, Apilactobacillus, Floricoccus , and Bombella . Among these, Apilactobacillus and Bombella dominate in the crop, whereas Apilactobacillus and other members of the Lactobacillaceae dominate the ventriculus. The ileum lacks Snodgrassella or Gilliamella but contains a putative new symbiont close to Floricoccus , as well as strains of Bifidobacterium , Lactobacillaceae (including Apilactobacillus), and Bombella . The rectum is dominated by Bifidobacterium and Lactobacillus . In summary, the Melipona microbiota is compositionally distinct but shows spatial organization paralleling that of other eusocial corbiculate bees.},
}

@article {pmid40502161,
year = {2025},
author = {Tao, J and Antoine, D and Jalodia, R and Valdes, E and Boyles, SM and Hulme, W and Roy, S},
title = {Single-cell transcriptomics reveals probiotic reversal of neonatal morphine-induced gene disruptions underlying adolescent pain hypersensitivity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.30.657034},
pmid = {40502161},
issn = {2692-8205},
abstract = {Neonatal morphine is commonly administered in the Neonatal Intensive Care Unit (NICU) to manage pain. However, its long-term effects on neurodevelopment of pain pathways, remain a significant concern. The midbrain is a core region that plays a central role in pain processing and opioid-mediated analgesia. Here, we performed single-cell RNA sequencing to study gene expression in 107,427 midbrain single cells from adolescent mice neonatally exposed to either saline, morphine, or morphine with the probiotic Bifidobacterium infantis (B. infantis). We found broad alterations in transcriptomics within neurons, astrocytes, oligodendrocytes, and microglial cells. Analysis of differentially regulated genes revealed down regulation of HOX genes and upregulation of pathways related to neurotransmitter signaling and pain in adolescence that were neonatally treated with morphine. Interestingly, neonatal probiotic supplementation mitigated these morphine-induced alterations on the transcriptome. This study presents the first single-cell RNA sequencing dataset of the adolescent midbrain following neonatal morphine exposure and probiotic intervention. These findings offer new insights into the neurodevelopmental impact of early opioid exposure and highlight the therapeutic potential of microbiome-targeted interventions.},
}

@article {pmid40502158,
year = {2025},
author = {Millington, JW and Lopez, JA and Sajjadian, AM and Scheffler, RJ and DeFelice, BC and Ludington, WB and Good, BH and O'Brien, LE and Huang, KC},
title = {Gut microbe-derived lactic acid optimizes host energy metabolism during starvation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.27.656452},
pmid = {40502158},
issn = {2692-8205},
abstract = {Gut microbes convert dietary compounds into an array of metabolites that can directly provide energy to their host and indirectly impact host metabolism as systemic endocrine signals. Here, we show that gut microbe-derived metabolites can extend Drosophila melanogaster survival during starvation, despite minimal alteration of dietary energy intake. Combining survival assays with mathematical modeling and untargeted metabolomics, we identify a single, dominant mediator of starvation resilience: lactic acid produced by the commensal bacterium Lactiplantibacillus plantarum . We discover that the basis of starvation resilience is not catabolism of lactic acid using lactate dehydrogenase, but rather increased dietary energy yield through lactic acid-driven promotion of oxidative phosphorylation. Our findings emphasize the role of the microbiome as a source of endocrine cues coordinating host metabolism and underscore the potential of microbiome-derived metabolites as therapeutic molecules for manipulating metabolic health and preventing disease.},
}

@article {pmid40502111,
year = {2025},
author = {Villarreal, ES and Marinho, Y and Loya, O and Aboagye, SY and Williams, DL and Sun, J and Erzurum, S and de Jesus Perez, V and Oliveira, SD},
title = {Endothelial c-IAP2 Loss Amplifies P2X7 Receptor-Driven Inflammation and Worsens Infection-Associated Pulmonary Hypertension.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.22.655387},
pmid = {40502111},
issn = {2692-8205},
abstract = {Schistosomiasis-associated Pulmonary Hypertension (Sch-PH) is the most common form of group I PH worldwide. Recently, data revealed that the preclinical animal model of Sch-PH exhibited gut and lung microbiome dysbiosis linked to significant endothelial dysfunction and microvascular apoptosis, but the role of pro/anti-apoptosis sensors, such as the inhibitor of apoptosis protein 2 (c-IAP2) and purinergic receptor P2X7 (P2X7R), remained unclear. Using a novel Cdh5cre-ER [T2] ;cIAP1 [-/-] ;cIAP2 [fl/fl] animal model, this study investigated the contribution of endothelial c-IAP2 in this process, revealing P2X7R overexpression as a putative target in the onset of Sch-PH. Pharmacologically, inhibition of P2X7R function confirmed its role in promoting lung endothelial death and disease progression. Moreover, data suggest that microbiome-associated metabolic alterations in Sch-PH seem linked to microvascular endothelial apoptosis driven by ATP/P2X7R overactivation and suppressed c-IAP2 expression. Indeed, genetic ablation of endothelial c-IAP2 expression was sufficient to induce PH-like features in mice, with echocardiography indicating a higher pulmonary acceleration time (PAT), PAT/pulmonary ejection time (PET), and right ventricular free wall thickness after IP/IV-Egg challenge compared to controls. These findings suggest a significant contribution of lung endothelial P2X7R activation and c-IAP2 suppression to Sch-PH pathology, highlighting them as promising novel therapeutic targets for this life-threatening illness.},
}

@article {pmid40502000,
year = {2025},
author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG},
title = {The Spinal Cord-Gut Axis Regulates Gut Microbial Homeostasis: Insights from a New Murine Metagenomic Catalog.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.27.656368},
pmid = {40502000},
issn = {2692-8205},
abstract = {The spinal cord, a nexus for brain-body crosstalk, controls gut physiology and microbial homeostasis. Here, >6,500 microbial metagenome-assembled genomes were recovered de novo , from male and female C57BL/6 mice gut metagenomes before and up to 6 months after disrupting the "spinal cord-gut axis". This "Mouse B6 Gut Catalog" improved or doubled species- and strain-level representation in other published catalogs. Analyses showed that breaking the spinal cord-gut axis caused persistent microbial changes that varied by sex, spinal lesion level, and time. A key bacterium, Lactobacillus johnsonii , was consistently reduced, and feeding this to mice with a clinically relevant spinal cord injury improved host health. Genome-resolved, community-contextualized metabolic profiling showed that spinal-dependent effects on microbe-encoded carbohydrate metabolism explain the reduction of L. johnsonii . These data improve murine microbiome catalogs and emphasize that mammalian health and gut ecosystem function depend on a functional spinal cord-gut axis.},
}

@article {pmid40501963,
year = {2025},
author = {Chouhan, D and Grossman, AS and Kerns, KA and Stocke, KS and Kim, M and Dong, PT and Kumar, A and Lei, L and Lamont, RJ and McLean, JS and He, X and Bor, B},
title = {Episymbiotic Saccharibacteria suppresses epithelial immunoactivation through Type IV pili and TLR2 dependent endocytosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.30.656655},
pmid = {40501963},
issn = {2692-8205},
abstract = {Saccharibacteria are episymbionts that require host-bacteria to grow. They are positively associated with inflammatory diseases within the human microbiome, yet their mechanisms for interacting with the human host and contributing to diseases remain unknown. This study investigated interactions between a Saccharibacterium (Nanosynbacter lyticus), its host-bacteria (Schaalia odontolytica), and oral epithelial cells. The host-bacteria induced proinflammatory cytokines in epithelial cells, while Saccharibacteria were immune silent. Remarkably, Saccharibacteria dampened cytokine responses to host-bacteria during coinfection. This effect was driven by Saccharibacteria-induced clustering of TLR2 receptors, a process likely facilitated by type IV, ultimately leading to reduced TLR2-mediated cytokine signalling. High resolution imaging showed that Saccharibacteria were endocytosed by oral epithelial cells, and colocalized with endosome markers, eventually trafficking to lysosomes. Moreover, a subset of the Saccharibacteria survive endocytosis long-term, and retains their capability to reinfect host-bacteria, highlighting a mechanism for persistence in the oral microbiome and a vital role in mammalian immune system modulation.},
}

@article {pmid40501924,
year = {2025},
author = {Huang, K and Zhang, S and Wang, H and Qu, Y and Lu, Y and Roohani, Y and Li, R and Qiu, L and Li, G and Zhang, J and Yin, D and Marwaha, S and Carter, JN and Zhou, X and Wheeler, M and Bernstein, JA and Wang, M and He, P and Zhou, J and Snyder, M and Cong, L and Regev, A and Leskovec, J},
title = {Biomni: A General-Purpose Biomedical AI Agent.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.30.656746},
pmid = {40501924},
issn = {2692-8205},
abstract = {Biomedical research underpins progress in our understanding of human health and disease, drug discovery, and clinical care. However, with the growth of complex lab experiments, large datasets, many analytical tools, and expansive literature, biomedical research is increasingly constrained by repetitive and fragmented workflows that slow discovery and limit innovation, underscoring the need for a fundamentally new way to scale scientific expertise. Here, we introduce Biomni, a general-purpose biomedical AI agent designed to autonomously execute a wide spectrum of research tasks across diverse biomedical subfields. To systematically map the biomedical action space, Biomni first employs an action discovery agent to create the first unified agentic environment - mining essential tools, databases, and protocols from tens of thousands of publications across 25 biomedical domains. Built on this foundation, Biomni features a generalist agentic architecture that integrates large language model (LLM) reasoning with retrieval-augmented planning and code-based execution, enabling it to dynamically compose and carry out complex biomedical workflows - entirely without relying on predefined templates or rigid task flows. Systematic benchmarking demonstrates that Biomni achieves strong generalization across heterogeneous biomedical tasks - including causal gene prioritization, drug repurposing, rare disease diagnosis, micro-biome analysis, and molecular cloning - without any task-specific prompt tuning. Real-world case studies further showcase Biomni's ability to interpret complex, multi-modal biomedical datasets and autonomously generate experimentally testable protocols. Biomni envisions a future where virtual AI biologists operate alongside and augment human scientists to dramatically enhance research productivity, clinical insight, and healthcare. Biomni is ready to use at https://biomni.stanford.edu , and we invite scientists to explore its capabilities, stress-test its limits, and co-create the next era of biomedical discoveries.},
}

@article {pmid40501842,
year = {2025},
author = {Shamorkina, TM and Pañeda, LP and Kadavá, T and Schulte, D and Pribil, P and Heidelberger, S and Narlock-Brand, AM and Yannone, SM and Snijder, J and Heck, AJR},
title = {Deep Coverage and Extended Sequence Reads Obtained with a Single Archaeal Protease Expedite de novo Protein Sequencing by Mass Spectrometry.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.26.656138},
pmid = {40501842},
issn = {2692-8205},
abstract = {The ability to sequence proteins without reliance on a genomic template defines a critical frontier in modern proteomics. This approach, known as de novo protein sequencing, is essential for applications such as antibody sequencing, microbiome proteomics, and antigen discovery, which require accurate reconstruction of peptide and protein sequences. While trypsin remains the gold-standard protease in proteomics, its restricted cleavage specificity limits peptide diversity. This constraint is especially problematic in antibody sequencing, where the functionally critical regions often lack canonical tryptic sites. As a result, exclusively trypsin-based approaches yield sparse reads, leading to sequence gaps. Multi-protease and hybrid-fragmentation strategies can improve the sequence coverage, but they add complexity, compromise scalability and reproducibility. Here, we explore two HyperThermoacidic Archaeal (HTA)-proteases as single-enzyme solutions for de novo antibody sequencing. Each HTA-protease generated about five times more unique peptide reads than trypsin or chymotrypsin, providing high redundancy across all CDRs. Combined with EAciD fragmentation on a ZenoTOF 7600 system, this approach enabled complete, unambiguous antibody sequencing. De novo analysis using PEAKS/DeepNovo and Stitch showed up to fourfold higher alignment scores and reduced the sequence errors within the HTA-generated data. Additionally, the HTA-EAciD approach offers short digestion times, eliminates extensive cleanup, and enables analysis in a single LC-MS/MS run. This streamlined, single-protease approach delivers therefore performance comparable to multi-enzyme workflows, offering a scalable and efficient strategy for de novo protein sequencing across diverse applications.},
}

@article {pmid40501780,
year = {2025},
author = {Dubinkina, V and Smith, B and Zhao, C and Pino, C and Pollard, KS},
title = {Linkage of nucleotide and functional diversity varies across gut bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.06.658399},
pmid = {40501780},
issn = {2692-8205},
abstract = {Understanding the forces shaping genomic diversity within bacterial species is essential for interpreting microbiome evolution, ecology, and host associations. Here, we analyze over one hundred prevalent gut bacterial species using the Unified Human Gut Genome (UHGG) collection to characterize patterns of intra-specific genomic variability. Gene content divergence scales predictably with divergence in core genome single nucleotide polymorphisms (SNPs), though there is substantial variability in evolutionary dynamics across species. Overall, accessory genes exhibit consistently faster linkage decay compared to core SNPs, highlighting the fluidity of functional repertoires within species boundaries. This signal is strongest for mobile genetic elements, which show minimal linkage to core genome SNPs. Together, our findings reveal species-specific recombination regimes in the gut microbiome, underscoring the importance of accounting for horizontal gene transfer and genome plasticity in microbiome-wide association studies and evolutionary models.},
}

@article {pmid40501688,
year = {2025},
author = {Zhao, Y and Lee, TF and Zhou, B and Wang, C and Schmidt, AM and Liu, M and Li, H and Hu, J},
title = {Joint Modeling of Longitudinal Biomarker and Survival Outcomes with the Presence of Competing Risk in Nested Case-Control Studies with Application to the TEDDY Microbiome Dataset.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.23.655653},
pmid = {40501688},
issn = {2692-8205},
abstract = {MOTIVATION: Large-scale prospective cohort studies collect longitudinal biospecimens alongside time-to-event outcomes to investigate biomarker dynamics in relation to disease risk. The nested case-control (NCC) design provides a cost-effective alternative to full cohort biomarker studies while preserving statistical efficiency. Despite advances in joint modeling for longitudinal and time-to-event outcomes, few approaches address the unique challenges posed by NCC sampling, non-normally distributed biomarkers, and competing survival outcomes.

RESULTS: Motivated by the TEDDY study, we propose "JM-NCC", a joint modeling framework designed for NCC studies with competing events. It integrates a generalized linear mixed-effects model for potentially non-normally distributed biomarkers with a cause-specific hazard model for competing risks. Two estimation methods are developed. fJM-NCC leverages NCC sub-cohort longitudinal biomarker data and full cohort survival and clinical metadata, while wJM-NCC uses only NCC sub-cohort data. Both simulation studies and an application to TEDDY microbiome dataset demonstrate the robustness and efficiency of the proposed methods.},
}

@article {pmid40501659,
year = {2025},
author = {Vemuganti, V and Kang, JW and Zhang, Q and Aquino-Martinez, R and Harding, S and Harpt, JL and Deming, Y and Johnson, S and Asthana, S and Zetterberg, H and Blennow, K and Engelman, CD and Ulland, TK and Bäckhed, F and Bendlin, BB and Rey, FE},
title = {Gut bacterial metabolite imidazole propionate potentiates Alzheimer's disease pathology.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.08.657719},
pmid = {40501659},
issn = {2692-8205},
abstract = {UNLABELLED: The gut microbiome modulates metabolic, immune, and neurological functions and has been implicated in Alzheimer's disease (AD), though the specific mechanisms remain poorly defined. The bacterial metabolite imidazole propionate (ImP) has been previously associated with several AD comorbidities, such as type 2 diabetes and cardiovascular disease. Here, we show that elevated plasma ImP levels are associated with lower cognitive scores and AD biomarkers in a cohort of >1,100 cognitively unimpaired individuals. Metagenomic profiling identified gut bacteria encoding putative orthologs of the ImP-synthesizing enzyme, urocanate reductase (UrdA), whose abundance correlated with both cognitive measures and multiple AD biomarkers. Chronic ImP administration to mice activated neurodegenerative pathways, worsened AD-like neuropathology, and increased blood-brain barrier (BBB) permeability. Complementary in vitro studies showed that ImP compromised the integrity of human brain endothelial cells. Collectively, these findings implicate ImP in AD progression via both neurodegenerative and cerebrovascular mechanisms, identifying it as a potential target for early intervention.

ONE SENTENCE SUMMARY: Gut bacterial metabolite increases dementia risk.},
}

@article {pmid40501599,
year = {2025},
author = {Price, DK and West, K and Cevallos-Zea, M and Cahan, SH and Nunez, JCB and Longman, EK and Yew, JY and Mederios, MJ},
title = {Microbiome composition shapes temperature tolerance in a Hawaiian picture-winged Drosophila.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.03.657679},
pmid = {40501599},
issn = {2692-8205},
abstract = {UNLABELLED: Hawaiian picture-winged Drosophila are undergoing rapid biodiversity loss, with twelve species listed as endangered and others in decline. Gut microbiota are increasingly recognized as contributors to host adaptation that are capable of influencing stress tolerance, reproduction, and other fitness-related traits. We investigated the role of microbial communities in local adaptation using two populations of Drosophila basisetae from Hawaiian rainforests at 900 m and 1200 m elevation. Microbiome profiling of wild flies by high throughput amplicon sequencing revealed distinct bacterial and fungal communities between sites. Whole-genome resequencing of the two Drosophila populations identified weak but significant population genetic structure, with evidence of admixture and gene flow. Despite this connectivity, 16 outlier SNPs across 18 genes showed patterns consistent with divergent selection, suggesting localized adaptation. To test microbiome effects on host physiology experimentally, we conducted a fully factorial research design with microbiome inoculations in laboratory-reared flies acclimated to 18 °C (control) or 24 °C (stressful). Flies treated with low-elevation microbiota had higher survival across temperatures, whereas those treated with high-elevation microbiota produced more eggs, indicating microbiome-mediated differences in reproductive investment. Activity levels at 18 °C were higher when flies received microbiota from their native population. Measures of critical thermal maximum (CTmax) and male accessory gland size showed complex interactions among microbiome source, temperature, and fly population. These results indicate that microbes may modulate host thermal tolerance and reproduction in environmentally-dependent and population-specific ways. Our findings suggest that microbiome-host-environment interactions may contribute to both phenotypic plasticity and evolutionary adaptation to enhance resilience to environmental stress, with important implications for conservation in rapidly changing Hawaiian ecosystems.

SUMMARY STATEMENT: This study demonstrates that microbiome composition influences thermal tolerance through alterations in survival and reproduction in the Hawaiian picture wing, Drosophila basisetae , potentially contributing to adaptive phenotypic changes between populations.},
}

@article {pmid40501527,
year = {2025},
author = {Roberson, JL and Pettke, EN},
title = {Dietary Risk Factors: Fiber and Beyond.},
journal = {Clinics in colon and rectal surgery},
volume = {38},
number = {4},
pages = {253-256},
pmid = {40501527},
issn = {1531-0043},
abstract = {The incidence of diverticulosis continues to rise throughout western nations with collateral increases in the frequency of diverticulitis. However, the mechanism behind the transition from asymptomatic diverticulosis to complicated diverticulitis is incompletely understood. Dietary intake has long been investigated as one of, if not the main, links in the continuum of disease. As the world's diet continues to evolve with increasingly prevalent processed and high-fat food, longitudinal studies have emerged with a goal of finally explaining how diet influences the development of diverticulitis. While low-fiber, high-fat diets are believed to play a role in the development of an index episode of diverticulitis, the role in recurrent disease remains uncertain. More recent avenues of interest include the role of the microbiome, probiotics, and adjunct treatments such as 5-ASA and rifaximin. While robust longitudinal studies have identified an association between low-fiber, high-fat diets and the development of index diverticulitis, the impact of dietary composition and modification on disease recurrence remains unclear and fails to meet the threshold for societal recommendations.},
}

@article {pmid40501526,
year = {2025},
author = {Troester, A and Weaver, L and Jahansouz, C},
title = {The Emerging Role of the Microbiota and Antibiotics in Diverticulitis Treatment.},
journal = {Clinics in colon and rectal surgery},
volume = {38},
number = {4},
pages = {269-276},
pmid = {40501526},
issn = {1531-0043},
abstract = {Diverticular disease is the leading cause of elective colon surgery. With a rising incidence in younger populations, it continues to pose a significant burden on the health care system. Traditional etiopathogenesis implicated an infectious mechanism, while recent challenges to this theory have demonstrated the microbiome playing a significant role, along with genetic predispositions and associations with obesity and diet. Therefore, the role of antibiotics in uncomplicated disease merits reconsideration. In this review, we aim to outline the current knowledge regarding antibiotics for diverticulitis treatment, broadly define the microbiome components, functions, and modifiability, and discuss newly proposed pathogenetic mechanisms for diverticular disease that incorporate information regarding the microbiome. Analytic techniques for microbiota characterization and function continue to advance at a rapid pace. As emerging technology advances, we will continue to elucidate the role of the microbiome in diverticular disease development.},
}

@article {pmid40501476,
year = {2025},
author = {Ma, C and Yang, J and Fu, XN and Luo, JY and Liu, P and Zeng, XL and Li, XY and Zhang, SL and Zheng, S},
title = {Microbial characteristics of gut microbiome dysbiosis in patients with chronic liver disease.},
journal = {World journal of hepatology},
volume = {17},
number = {5},
pages = {106124},
pmid = {40501476},
issn = {1948-5182},
abstract = {BACKGROUND: In this study, we are committed to exploring the characteristics of the gut microbiome in three different stages of chronic liver disease (CLD): Chronic hepatitis B, liver cirrhosis, and hepatocellular carcinoma (HCC).

AIM: To delineate the gut microbiota traits in individuals with chronic liver ailments (chronic hepatitis B, cirrhosis, HCC), scrutinizes microbiome alterations during the progression of these diseases, and assesses microbiome disparities among various Child-Pugh categories in cirrhosis sufferers.

METHODS: A cohort of 60 CLD patients from the Third People's Hospital of Yunnan Province were recruited from February to August 2023, together with 37 healthy counterparts. Employing 16SrDNA high-throughput sequencing, we evaluated the diversity and composition of the gut microbiota.

RESULTS: Compared to healthy subjects, patients exhibited a reduced presence of Firmicutes and a corresponding decline in butyrate-producing genera. In contrast, an upsurge in Proteobacteria was observed in the diseased cohorts, particularly an increase in Enterobacteriaceae that intensified with the disease's progression. At the genus level, the occurrence of Escherichia_Shigella, Parabacteroides, Streptococcus, Klebsiella, and Enterococcus was higher, with Escherichia_Shigella numbers augmenting as the disease advanced. Furthermore, in cirrhosis patients, an increase in Proteobacteria was noted as liver reserve diminished, alongside a decrease in Ruminococcaceae and Bacteroidaceae.

CONCLUSION: The reduced abundance of short-chain fatty acid-producing bacteria in the intestine, alongside the increased abundance of gram-negative bacteria such as Escherichia_Shigella and Parabacteroides, may promote the progression of CLD.},
}

@article {pmid40501467,
year = {2025},
author = {Goyal, MK and Goyal, P and Goyal, O and Sood, A},
title = {Gut feeling gone wrong: Tangled relationship between disorders of gut-brain interaction and liver disease.},
journal = {World journal of hepatology},
volume = {17},
number = {5},
pages = {105582},
pmid = {40501467},
issn = {1948-5182},
abstract = {Functional gastrointestinal disorders, now termed "disorders of gut-brain interaction" (DGBI), are characterized by a spectrum of chronic gastrointestinal symptoms driven by dysregulated gut-brain interaction. DGBIs frequently coexist with liver diseases, including cirrhosis, thereby exacerbating clinical manifestations and complicating management; this overlap is underpinned by shared mechanisms, including gut dysbiosis, increased intestinal permeability, systemic inflammation, and altered neuroimmune signaling. Portal hypertension in cirrhosis promotes small intestinal bacterial overgrowth and microbial translocation, thereby triggering inflammatory pathways that worsen gut and liver function. This minireview explores the gut-liver axis as a central mediator in the interplay between DGBIs and liver disease/cirrhosis. Clinically, these interactions manifest as refractory gastrointestinal symptoms, nutritional deficiencies, and impaired quality of life. Emerging research emphasizes the need for integrative diagnostic approaches, such as combining advanced imaging, microbiome analysis, and biomarker profiling, to unravel the complex interplay between DGBIs and liver disease/cirrhosis. Therapeutic interventions targeting the gut microbiome, neuroimmune pathways, and lifestyle modification can mitigate disease burden. This review underscores the importance of a multidisciplinary framework for enhancing patient outcomes and guiding future research in this intersectional field.},
}

@article {pmid40501442,
year = {2025},
author = {Maor, M and Levy Barazany, H and Kolodkin-Gal, I},
title = {The ladder of regulatory stringency and balance: an application to the US FDA's regulation of bacterial live therapeutics.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2517377},
doi = {10.1080/19490976.2025.2517377},
pmid = {40501442},
issn = {1949-0984},
mesh = {Humans ; United States ; United States Food and Drug Administration/legislation & jurisprudence ; *Probiotics/therapeutic use ; *Fecal Microbiota Transplantation ; Bacteria/genetics ; Gastrointestinal Microbiome ; },
abstract = {The three main types of live bacterial therapies - probiotics, fecal/microbiome transplants, and engineered bacterial therapies - hold immense potential to revolutionize medicine. While offering targeted and personalized treatments for various diseases, these therapies also carry risks such as adverse immune reactions, antibiotic resistance, and the potential for unintended consequences. Therefore, developing and deploying these therapies necessitates a robust regulatory framework to protect public health while fostering innovation. In this paper, we propose a novel conceptual tool - the Ladder of Regulatory Stringency and Balance-which can assist in the design of robust regulatory regimes which encompass medicine practices based not only on definitive Randomized Controlled Trials (RCTs), but also on meta-analyses, observational studies, and clinicians experience. Regulatory stringency refers to the strictness of regulations, while regulatory balance concerns the degree of alignment between the regulatory framework governing a technology and the actual risks posed by specific products within that technology. Focusing on the US regulatory environment, we subsequently position the three types of live bacterial therapies on the Ladder. The insight gained from this exercise demonstrates that probiotics are generally positioned at the bottom of the Ladder, corresponding to low-stringency regulation, with a proportionate regulatory balance. However, probiotics intended for high-risk populations are currently subject to low-stringency regulations, resulting in under-regulation. Our analysis also supports the conclusion that fecal microbiota transplants (FMT) for recurrent Clostridium difficile infection should be positioned close to but below the threshold for under regulation by the U.S. Food and Drug Administration (FDA), and we recommend improved donor screening procedures, preservation and processing, storage, and distribution. Our framework can serve as a scale to assess regulatory gaps for live bacterial therapies and to identify potential solutions where such gaps exist.},
}

Humans
United States
United States Food and Drug Administration/legislation & jurisprudence
*Probiotics/therapeutic use
*Fecal Microbiota Transplantation
Bacteria/genetics
Gastrointestinal Microbiome

@article {pmid40501301,
year = {2025},
author = {Du, Y and Li, B and Yang, J and Zhang, Y and Qi, F and Meng, H},
title = {Analysis of Skin Microbiome in Facial and Back Acne Patients Based on High-Throughput Sequencing.},
journal = {Journal of cosmetic dermatology},
volume = {24},
number = {6},
pages = {e70259},
doi = {10.1111/jocd.70259},
pmid = {40501301},
issn = {1473-2165},
mesh = {Humans ; *Acne Vulgaris/microbiology ; *Microbiota/genetics ; *Skin/microbiology ; High-Throughput Nucleotide Sequencing ; Female ; Male ; Adult ; Young Adult ; Back ; Case-Control Studies ; Face/microbiology ; Adolescent ; Glucose/metabolism ; Sebum/metabolism ; Bacteria/isolation & purification/genetics ; Skin Microbiome ; },
abstract = {OBJECTIVE: To study the composition and diversity of microorganisms in skin lesions of patients with facial acne and back acne, analyze the relationship between microorganisms and different parts of acne.

METHODS: A total of 30 facial acne patients, 30 back acne patients, and 30 healthy controls were included. Comprehensive data on demographics, skin conditions, and state of life were collected. Skin microbiota samples were obtained using standardized protocols, through high-throughput microbial sequencing and bioinformatics analysis, to assess microbiota diversity, composition, and function, as well as their correlations with skin characteristics.

RESULTS: The diversity of skin microbiota of back acne patients decreased significantly, and the abundance of p_actinomycetes and o_propionate bacteria increased significantly. They are closely related to glucose metabolism, which may lead to increased trans epidermal water loss, decreased skin moisture content, and increased skin oil content.

CONCLUSION: The skin microbiota diversity of patients with back acne is low, and high-abundance bacteria are closely related to glucose metabolism, which may lead to the breakdown of the skin barrier and increased sebum secretion.},
}

Humans
*Acne Vulgaris/microbiology
*Microbiota/genetics
*Skin/microbiology
High-Throughput Nucleotide Sequencing
Female
Male
Adult
Young Adult
Back
Case-Control Studies
Face/microbiology
Adolescent
Glucose/metabolism
Sebum/metabolism
Bacteria/isolation & purification/genetics
Skin Microbiome

@article {pmid40500804,
year = {2025},
author = {Rocha, FI and Rodriguez-Ramos, JC and Fernando, M and Hale, L},
title = {Interrow cover crops in a semi-arid vineyard increase plant beneficial functional potential of the soil microbiome, both in vine rows and interrows, a benefit that increases with cover crop duration.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {66},
pmid = {40500804},
issn = {2524-6372},
support = {19-0689-000-SO//California Department of Food and Agriculture Healthy Soils Program/ ; 19-0689-000-SO//California Department of Food and Agriculture Healthy Soils Program/ ; 19-0689-000-SO//California Department of Food and Agriculture Healthy Soils Program/ ; 2034-13000-013//USDA ARS CRIS/ ; 2034-13000-013//USDA ARS CRIS/ ; },
abstract = {BACKGROUND: Cover crops are recognized for enhancing soil health and providing agroecosystem services, but are not widely adopted, particularly in water-limited regions. In Mediterranean vineyards, where water scarcity and soil degradation challenge productivity, interrow, cool-season cover cropping offers a promising strategy to improve microbial-mediated soil functions. However, the temporal and spatial effects of cover crops on vineyard soil microbiomes and soil health metrics remain poorly understood. This study evaluated the impacts of a California native (phacelia, Phacelia tanacetifolia) and introduced (rye, Secale cereale L.) plant species as interrow cover crops on soil properties in interrow and vine row soils across three years.

RESULTS: The study revealed distinct temporal and spatial dynamics in soil microbiomes elicited by the cover crop treatments. By the third year, phacelia exhibited the highest microbial biomass, fungal-to-bacterial ratios, and microbial network complexity. Interrow soils showed stronger responses to cover cropping, including enhanced microbial biomass and differentiation between treatments, while vine row soils demonstrated subtler but significant shifts in microbial metrics. Functional predictions indicated that cover crops reduced fungal pathogen prevalence and supported nutrient cycling processes. Deterministic processes driven by environmental selection became dominant under both treatments, promoting microbial resilience. Random Forest analysis identified NO3[-] as a key driver of microbial differentiation, with phacelia fostering communities reliant on labile organic inputs.

CONCLUSIONS: This study highlights a crucial benefit of interrow cover crops in improving soil health and enhancing microbial-mediated ecosystem functions in adjacent vine row soils, even after cover crop termination. Long-term application of cover crops offers a sustainable approach to building resilient agroecosystems in water-scarce environments, with implications for sustainable viticulture practices.},
}

@article {pmid40500778,
year = {2025},
author = {Lobato, C and Abdelfattah, A and Berg, G and Cernava, T},
title = {Defining the cultured and uncultured bacterial fractions in Cannabis seeds.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {68},
pmid = {40500778},
issn = {2524-6372},
abstract = {BACKGROUND: Seeds provide a unique environment shaped by co-evolutionary processes, hosting diverse microbial communities. While microbiome studies have uncovered an extensive diversity of microorganisms, culture-based approaches remain crucial for understanding microbial potential and functional interactions. However, the factors influencing microbial culturability within seeds are not well understood.

RESULTS: In this study, we investigated the culturing patterns of bacteria inside Cannabis seeds, assessing their phylogenetic diversity, abundance, and putative interactions. Bacteria were cultured from 54 different Cannabis accessions using germinated seeds and a range of nutrient media including those supplemented with Cannabis extracts. The cultured fraction consisted of taxa from five prominent classes-Gammaproteobacteria, Bacilli, Actinobacteria, Alphaproteobacteria, and Bacteroidia-encompassing 36 genera. Despite representing only 6.3% of the total microbiota, these cultured bacteria accounted for 89.2% of the microbial population. Almost 60% of the amplicon sequence variants (ASVs) were phylogenetically distant from cultured taxa. Rare bacterial groups such as Acidobacteriae and Verrucomicrobiae, known for their plant growth-promoting traits, were exclusively found in the uncultured fraction. Network analyses revealed that uncultured taxa are centralized and more connected to hubs, suggesting that interspecies interactions strongly influence culturability.

CONCLUSION: Our findings highlight the limitations of culture-based methods in capturing the full microbial diversity of Cannabis seeds and emphasize the importance of microbial interactions in determining culturability. The strong network connectivity of uncultured taxa suggests that interdependencies and competition within the seed microbiome may hinder the isolation of key bacterial groups. These insights provide a framework for refining cultivation strategies to recover ecologically significant microbes with potential agricultural applications.},
}

@article {pmid40500757,
year = {2025},
author = {Sussfeld, D and Lannes, R and Corel, E and Bernard, G and Martin, P and Bapteste, E and Pelletier, E and Lopez, P},
title = {New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {65},
pmid = {40500757},
issn = {2524-6372},
support = {615274/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; },
abstract = {BACKGROUND: Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN and Asgard archaea, and novel viruses. Such findings profoundly reshaped the structure of the known Tree of Life and emphasised the central role of investigating uncultured organisms. However, despite significant progresses, a large portion of proteins predicted from metagenomes remain today unannotated, both taxonomically and functionally, across many biomes and in particular in oceanic waters.

RESULTS: Here, we used an iterative, network-based approach for remote homology detection, to probe a dataset of 40 million ORFs predicted in marine environments. We assessed the environmental diversity of 53 core gene families broadly distributed across the Tree of Life, with essential functions including translational, replication and trafficking processes. For nearly half of them, we identified clusters of remote environmental homologues that showed divergence from the known genetic diversity comparable to the divergence between Archaea and Bacteria, with representatives distributed across all the oceans. In particular, we report the detection of environmental clades with new structural variants of essential SMC (Structural Maintenance of Chromosomes) genes, divergent polymerase subunits forming deep-branching clades in the polymerase tree, and variant DNA recombinases in Bacteria as well as viruses.

CONCLUSIONS: These results indicate that significant environmental diversity may yet be unravelled even in strongly conserved gene families. Protein sequence similarity network approaches, in particular, appear well-suited to highlight potential sources of biological novelty and make better sense of microbial dark matter across taxonomical scales.},
}

@article {pmid40500750,
year = {2025},
author = {Yang, B and Li, X and Wang, J and Xu, Y and Wang, L and Wu, Z and Zhao, D and Huang, L and Li, N and Chen, Q and Liu, Z},
title = {The efficacy and safety of fecal microbiota transplantation in the treatment of sarcopenia: a retrospective study.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {645},
pmid = {40500750},
issn = {1479-5876},
support = {2022YFA1304100//National Key R&D Program of China/ ; 2022YFC2010101//National Key R&D Program of China/ ; 82470701//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Sarcopenia/therapy/physiopathology/microbiology ; *Fecal Microbiota Transplantation/adverse effects ; Male ; Female ; Aged ; Retrospective Studies ; Treatment Outcome ; Middle Aged ; Resistance Training ; Inflammation ; },
abstract = {BACKGROUND: Sarcopenia, a prevalent geriatric syndrome, is influenced by factors such as inflammation, immune deficiency, and oxidative stress. In elderly individuals, alterations in the microbiome, including reduced biodiversity and functional changes, significantly contribute to the progression of the disease. Targeting the gut-muscle axis has emerged as a promising therapeutic strategy to mitigate age-related muscle atrophy and dysfunction.

METHODS: This study employed fecal microbiota transplantation (FMT) to restore intestinal homeostasis in patients with sarcopenia. Muscle mass was measured using bioelectrical impedance analysis, while muscle function was assessed through grip strength and the five-time sit-to-stand test. Inflammatory markers, including tumor necrosis factor-α (TNF-α) and C-reactive protein (CRP), were also analyzed. Eighty-seven patients received resistance training (RT) treatment, while eighty-five patients received FMT combined with RT treatment, with a follow-up period of 24 weeks.

RESULTS: After 24 weeks, the resistance training (RT) group showed a partial remission (PR) rate of 54.7% and a complete remission (CR) rate of 32.4%. The FMT plus RT group demonstrated a PR rate of 66.5% and a CR rate of 46.7%. Significant improvements induced by FMT treatment were observed in clinical markers of muscle mass, function, and inflammation.

CONCLUSIONS: These results underscore the promise of microbial-based therapies, including fecal microbiota transplantation (FMT), as groundbreaking strategies for addressing sarcopenia. The research indicates that integrating FMT with resistance training could improve muscle mass and function while alleviating inflammation in sarcopenia patients, presenting a hopeful avenue for effective management of the condition.},
}

Humans
*Sarcopenia/therapy/physiopathology/microbiology
*Fecal Microbiota Transplantation/adverse effects
Male
Female
Aged
Retrospective Studies
Treatment Outcome
Middle Aged
Resistance Training
Inflammation

@article {pmid40500582,
year = {2025},
author = {Lin, YS and Chen, JH and Zhuang, WH and Huang, JN and Chen, YH and Zhang, J and Li, J and Huang, M and Hou, JL and Qian, SJ and Chen, ZB and Zhang, YL and Xu, RT},
title = {Gut Microbiota Improve the Prediction of Stroke-Associated Pneumonia Risk and Outcomes in Acute Ischemic Stroke.},
journal = {Translational stroke research},
volume = {},
number = {},
pages = {},
pmid = {40500582},
issn = {1868-601X},
support = {2025KY1002//the Medical and Health Science and Technology Project of Zhejiang Province/ ; Y20220817//Wenzhou Municipal Science and Technology Bureau/ ; Y20210170//Wenzhou Municipal Science and Technology Bureau/ ; LQ23H090005//the Projects of Natural Science Foundation of Zhejiang Province/ ; },
abstract = {Stroke-associated pneumonia (SAP) is the most significant acute ischemic stroke (AIS) comorbidity. This investigation aimed to explore the relationship between gut microbiome composition and SAP risk in patients with moderate-to-severe AIS and to develop a robust and accessible SAP risk-prediction model for this population. This prospective study included AIS patients with an NIHSS score ≥ 9 within 48 h of onset who were admitted to the First Affiliated Hospital of Wenzhou Medical University. Rectal swabs and sputum samples were collected for 16S rRNA gene sequencing and analyzed via QIIME to evaluate microbial composition. Blood samples were subjected to untargeted metabolomics analysis via liquid chromatography‒mass spectrometry (LC‒MS). Logistic and Cox regression analyses were conducted (α = 0.05). Fifty of 104 AIS patients (48.1%) developed SAP. Microbiota abundances significantly differed between groups. Logistic regression analysis revealed that Finegoldia protected against SAP (OR 0.710, 95% CI: 0.533 - 0.946, p = 0.019), whereas Lactobacillus (OR 1.347, 95% CI: 1.015 - 1.789, p = 0.039) increased SAP risk. An improved SAP prediction model combining the A[2]DS[2] score with seven taxa yielded an AUC of 0.746 (95% CI: 0.650 - 0.841, p < 0.001). Cox regression analysis revealed that genus Clostridium (HR 1.618, 95% CI: 1.241 - 2.110, p < 0.001) was an independent risk factor for mortality, whereas genus Streptococcus (HR 0.751, 95% CI: 0.589 - 0.958, p = 0.021) was a protective factor. Our findings suggest that combining clinical indicators, gut microbiota, and blood metabolites enhances SAP prediction. Furthermore, microorganisms can potentially serve as prognostic markers and therapeutic targets for SAP in the future.},
}

@article {pmid40500467,
year = {2025},
author = {Hindson, J},
title = {Post-antibiotics microbiome restoration driven by diet.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {40500467},
issn = {1759-5053},
}

@article {pmid40500278,
year = {2025},
author = {Rodríguez Mazariegos, JR and Nam, NN and Bo, T and Wang, D and Hsu, JW and Chen, YC},
title = {Precocious puberty and gut microbiome: a systematic review and meta-analysis.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {40500278},
issn = {1530-0447},
abstract = {Central precocious puberty (CPP) is a condition that affects prepubertal children, particularly girls. Recent evidence suggests an association between the gut microbiome (GM) and CPP. This study aims to explore this association. We analyzed data from studies investigating the association between GM and CPP. Various databases were searched for relevant articles published from database inception to December 31, 2023. Standardized mean difference values were calculated and depicted in forest plots. Furthermore, subgroup analyses by type of study subject (animals vs. humans) were performed. The final analysis included 9 studies. Five were human studies, whereas the remaining four were animal (rats or mice) studies. In the precocious puberty group, the abundances (at the genus level) of Holdemania, Roseburia, Alistipes, Dialister, Enterococcus, Ruminococcus, Bilophila, and Lachnoclostridium increased significantly, whereas those of Bacteroides, Anaerostipes, Megamonas, and Gemella decreased significantly. Furthermore, for this group, the Shannon index for alpha diversity was increased in human studies and decreased in animal studies compared to the control group. Notably, the levels of major short-chain fatty acids, butyric and propionic acids, were significantly reduced in the precocious puberty group. There was an association between CPP and GM. Both subgroups revealed that microbiome profiles vary across individuals with precocious puberty. IMPACT: To our knowledge, this is the first systematic review and meta-analysis to explore the association between the gut microbiome and precocious puberty in both human and animal models. Our findings reveal distinct microbial patterns in individuals with CPP, including consistent alterations in 12 bacterial genera and significant changes in short-chain fatty acid levels. By identifying reproducible microbial signatures and metabolites associated with CPP, this study lays the groundwork for microbiome-targeted interventions alongside traditional hormonal therapies. The study addresses key methodological inconsistencies in existing literature, highlighting the need for standardized protocols in future research on the gut-puberty axis.},
}

@article {pmid40500261,
year = {2025},
author = {Dong, P and Yang, M and Hu, J and Cen, L and Zhou, P and Xu, D and Xiong, P and Li, J and He, X},
title = {Identification of a Fusobacterial RNA-binding protein involved in host small RNA-mediated growth inhibition.},
journal = {International journal of oral science},
volume = {17},
number = {1},
pages = {48},
pmid = {40500261},
issn = {2049-3169},
support = {DE030943//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; DE023810//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; DE029479//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; DE033794//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; DE031329//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
mesh = {*Fusobacterium nucleatum/genetics/metabolism/growth & development ; *RNA-Binding Proteins/metabolism/genetics ; *Bacterial Proteins/metabolism/genetics ; RNA, Bacterial/metabolism ; Humans ; RNA, Transfer/metabolism ; },
abstract = {Host-derived small RNAs are emerging as critical regulators in the dynamic interactions between host tissues and the microbiome, with implications for microbial pathogenesis and host defense. Among these, transfer RNA-derived small RNAs (tsRNAs) have garnered attention for their roles in modulating microbial behavior. However, the bacterial factors mediating tsRNA interaction and functionality remain poorly understood. In this study, using RNA affinity pull-down assay in combination with mass spectrometry, we identified a putative membrane-bound protein, annotated as P-type ATPase transporter (PtaT) in Fusobacterium nucleatum (Fn), which binds Fn-targeting tsRNAs in a sequence-specific manner. Through targeted mutagenesis and phenotypic characterization, we showed that in both the Fn type strain and a clinical tumor isolate, deletion of ptaT led to reduced tsRNA intake and enhanced resistance to tsRNA-induced growth inhibition. Global RNA sequencing and label-free Raman spectroscopy revealed the phenotypic differences between Fn wild type and PtaT-deficient mutant, highlighting the functional significance of PtaT in purine and pyrimidine metabolism. Furthermore, AlphaFold 3 prediction provides evidence supporting the specific binding between PtaT and Fn-targeting tsRNA. By uncovering the first RNA-binding protein in Fn implicated in growth modulation through interactions with host-derived small RNAs (sRNAs), our study offers new insights into sRNA-mediated host-pathogen interplay within the context of microbiome-host interactions.},
}

*Fusobacterium nucleatum/genetics/metabolism/growth & development
*RNA-Binding Proteins/metabolism/genetics
*Bacterial Proteins/metabolism/genetics
RNA, Bacterial/metabolism
Humans
RNA, Transfer/metabolism

@article {pmid40500078,
year = {2025},
author = {Liu, Z and Zhao, D and Wei, Y},
title = {Combination of L-methionine and chlorantraniliprole enhances the abundance of opportunistic pathogenic bacteria in the intestine of greater wax moth leading to increased mortality risk.},
journal = {Pesticide biochemistry and physiology},
volume = {212},
number = {},
pages = {106429},
doi = {10.1016/j.pestbp.2025.106429},
pmid = {40500078},
issn = {1095-9939},
mesh = {Animals ; *Moths/microbiology/drug effects ; *ortho-Aminobenzoates/toxicity/pharmacology ; *Insecticides/toxicity/pharmacology ; *Methionine/pharmacology/toxicity ; *Gastrointestinal Microbiome/drug effects ; Bees ; Intestines/microbiology/drug effects ; Bacteria/drug effects ; },
abstract = {Honey bees play an essential role in global crop production and agro-economic development due to their pollination properties. However, empirical evidence indicates a worldwide decline in bee colonies. The greater wax moth (GWM), a lepidopteran insect and natural enemy of honey bees, significantly contributes to this decline. Chlorantraniliprole (CH) is commonly used to control GWM in apiaries due to its efficacy and low toxicity to bees. However, long-term use of CH may lead to environmental pollution and GWM resistance. To enhance beekeeping safety and mitigate the risk of GWM resistance from prolonged CH use, we investigated the toxic effects of combining methionine (MET), which has demonstrated insecticidal activity against some lepidopteran pests, with CH on GWM. We conducted both individual and mixed exposure tests of MET and CH on GWM to finally evaluate the toxic effects of the combined treatment (MIX). The results indicated that the combination of MET and CH produced a synergistic lethal effect on GWM. Subsequent microbiome and immune-related gene expression assays, along with correlation analysis, revealed that the MIX treatment significantly reducing the abundance of Enterococcus spp., the primary genus in GWM, and induced immune stress in GWM. This phenomenon led to the proliferation of opportunistic pathogens such as Pseudomonas spp., ultimately leading to synergistic lethal effects on GWM mortality. This study provides new insights and data supporting the development of MET as a potential insecticide.},
}

Animals
*Moths/microbiology/drug effects
*ortho-Aminobenzoates/toxicity/pharmacology
*Insecticides/toxicity/pharmacology
*Methionine/pharmacology/toxicity
*Gastrointestinal Microbiome/drug effects
Bees
Intestines/microbiology/drug effects
Bacteria/drug effects

@article {pmid40499711,
year = {2025},
author = {Zhang, RR and Zhang, JS and Huang, S and Lam, WY and Chu, CH and Yu, OY},
title = {The oral microbiome of root caries: A scoping review.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {105899},
doi = {10.1016/j.jdent.2025.105899},
pmid = {40499711},
issn = {1879-176X},
abstract = {OBJECTIVE: This review characterizes shifts of the oral microbial community on carious root surfaces compared to sound root surfaces.

DATA AND SOURCES: A systematic search of English-language publications on clinical studies evaluating oral microbiomes in patients with root caries using high-throughput sequencing technologies published before April 1, 2025, was included. The search was conducted on PubMed, Cochrane Central Register of Controlled Trials, Web of Science, Embase, and Scopus. Gray literature was searched in ClinicalTrials.gov and Google Scholar.

STUDY SELECTION/RESULTS: Based on the eligibility criteria, 1,133 publications were screened, and 465 duplicates were removed. Of the remaining 16 studies assessed for full-text review, eight investigating the oral microbiome of saliva, carious roots, or dental plaque in patients with root caries were included. These studies reported the intra-community species diversity (alpha-diversity, 4/8 studies), inter-community compositional diversity (beta-diversity, 4/8 studies), dominant microbial genera/species (8/8 studies), and functional pathways (1/8 studies) of the microbial community in root caries patients. Alpha-diversity showed no significant difference between root caries and sound root surfaces in three studies, but root caries exhibited a significantly lower alpha diversity in one study. Beta-diversity differed significantly between root caries and sound root surfaces in three studies, with one study reporting no difference. The dominant microbial species in root caries varied among the included studies. However, Lactobacillus spp., Prevotella denticola, Propionibacterium acidifaciens, Streptococcus mutans, and Veillonella parvula/dispar were frequently identified in the root caries-associated microbiota. Furthermore, root caries-associated bacteria altered the predicted functional pathways, promoting organic acid production and accelerating collagen degradation.

CONCLUSION: Root caries microbiomes exhibit distinct compositional profiles, dysbiotic species predominance, and a shift in predicted functional pathways compared to healthy root surfaces.

CLINICAL SIGNIFICANCE: This review provides valuable insights into root caries' microbial landscape, potentially guiding future preventative and therapeutic strategies.},
}

@article {pmid40499683,
year = {2025},
author = {Yokomizo, S and Kaneko, N and Chen, H and Yan, L and Tsuji, S and Akagawa, S and Sameshima, J and Sueyoshi, T and Nagano, H and Miyahara, Y and Kamikaseda, Y and Kido, H and Hayashi, Y and Yamauchi, M and Kiyoshima, T and Goto, Y and Ohyama, Y and Kaneko, K and Moriyama, M and Kawano, S},
title = {Dysbiosis of the gut microbiome may contribute to the pathogenesis of oral lichen planus through Treg dysregulation.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mucimm.2025.05.009},
pmid = {40499683},
issn = {1935-3456},
abstract = {Oral lichen planus (OLP) is a chronic inflammatory disorder with autoimmune features and malignant transformation risk, lacking a definitive treatment, with CD4[+] T cells being pivotal in its pathogenesis. Dysbiosis, an imbalance in the microbiome, is linked to various autoimmune and inflammatory diseases, where CD4[+] T cells play a significant role. Given these insights, the development of OLP might be influenced by dysbiosis. This study investigates the association between dysbiosis and CD4[+] T cells in OLP. We collected stool and saliva samples from OLP patients, conducting 16S rRNA gene analysis and mass spectrometry, and assessed CD4[+] T cell characteristics in lesions through multiplex immunofluorescence and single-cell RNA sequencing. Peripheral blood samples were subjected to flow cytometry and cell culture assays. Results showed extensive gut dysbiosis in OLP patients, notably a reduction in short-chain fatty acid (SCFA)-producing bacteria essential for regulatory T cell (Treg) differentiation. While various CD4[+] T cell subsets, including Tregs, were present in tissues, these Tregs as unresponsive to specific antigens, showing reduced immunosuppressive molecule expression. The decline in SCFA-producing bacteria correlated with fewer activated Tregs in tissues and blood. These findings suggest that gut dysbiosis may contribute to OLP by impairing Treg regulation, influencing disease pathogenesis.},
}

@article {pmid40499635,
year = {2025},
author = {Wen, C and Guan, J and Uea-Anuwong, T and Shang, J and Peng, C and Tang, X and Magouras, I and Sun, Y and Li, F},
title = {Dissecting the gut microbial communities and resistomes of wild rats from different ecological areas in Hong Kong.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122108},
doi = {10.1016/j.envres.2025.122108},
pmid = {40499635},
issn = {1096-0953},
abstract = {Antimicrobial resistance (AMR) is one of the top global public health issues shared across all One Health domains. Wild rats, as one of key intersections of the animal and environmental domains, are understudied reservoirs and spreaders for AMR. Our study employed the whole-metagenome shotgun sequencing to characterize the caecal microbiome of wild rats and examine the presence of antimicrobial resistance genes (ARGs) from different ecological areas in Hong Kong. We trapped 88 live rats, belonging to the species of Rattus norvegicus (n=57), R. tanezumi (n=24), and R. andamanensis (n=7), from city regions, livestock farms, and stables of horse-riding schools (referred to as "suburbs"). We identified 9,672 ARGs belonging to 29 ARG types and 554 ARG subtypes. Among them, aminoglycosides, macrolide-lincosamide-streptogramin and chloramphenicol, known to be predominant in livestock gut resistome or manure compost were significantly more abundant in rats from livestock farms. Moreover, some ARGs with high-risk levels, including tetM, tetL, floR, mecR1 and lnuA , as well as plasmid-borne ARGs were significantly more abundant in rats from livestock farms than from city regions or suburbs. Furthermore, zoonotic antimicrobial-resistant bacteria (ARB) were detected, including but not limited to, prioritized antimicrobial-resistant Klebsiella pneumoniae, Proteus mirabilis, Escherichia coli, Enterococcus faecium, Acinetobacter baumannii, Campylobacter jejuni, and Staphylococcus aureus. Notably, resistant zoonotic bacteria of Streptococcus suis, Campylobacter coli, and Campylobacter jejuni were more abundant in wild rats from livestock farms. Our findings provides insights into the gut resistomes and zoonotic bacteria in wild rats in Hong Kong, highlighting the potential role of wild rats in the dissemination of ARGs and zoonotic pathogens, especially for those from agricultural settings.},
}

@article {pmid40499541,
year = {2025},
author = {Mannochio-Russo, H and Charron-Lamoureux, V and van Faassen, M and Lamichhane, S and Gonçalves Nunes, WD and Deleray, V and Ayala, AV and Tanaka, Y and Patan, A and Vittali, K and Rajkumar, P and El Abiead, Y and Zhao, HN and Gomes, PWP and Mohanty, I and Lee, C and Sund, A and Sharma, M and Liu, Y and Pattynama, D and Walker, GT and Norton, GJ and Khatib, L and Andalibi, MS and Wang, CX and Ellis, RJ and Moore, DJ and Iudicello, JE and Franklin, D and Letendre, S and Chin, L and Walker, C and Renwick, S and Zemlin, J and Meehan, MJ and Song, X and Kasper, D and Burcham, Z and Kim, JJ and Kadakia, S and Raffatellu, M and Bode, L and Chu, H and Zengler, K and Wang, M and Siegel, D and Knight, R and Dorrestein, PC},
title = {The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.015},
pmid = {40499541},
issn = {1097-4172},
abstract = {N-Acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of N-acyl lipids with untargeted mass spectrometry-based metabolomics, we created a reference spectral library retrieving N-acyl lipid patterns from 2,700 public datasets, identifying 851 N-acyl lipids that were detected 356,542 times. 777 are not documented in lipid structural databases, with 18% of these derived from short-chain fatty acids and found in the digestive tract and other organs. Their levels varied with diet and microbial colonization and in people living with diabetes. We used the library to link microbial N-acyl lipids, including histamine and polyamine conjugates, to HIV status and cognitive impairment. This resource will enhance the annotation of these compounds in future studies to further the understanding of their roles in health and disease and to highlight the value of large-scale untargeted metabolomics data for metabolite discovery.},
}

@article {pmid40499421,
year = {2025},
author = {Fang, Z and Hodson, ME and Hu, CJ and Li, WJ and Li, J and Monroy, AB and Tong, L and Xiao, X},
title = {Combined toxicity of polyethylene microplastics and soil salinization to earthworms is generally antagonistic or additive.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138843},
doi = {10.1016/j.jhazmat.2025.138843},
pmid = {40499421},
issn = {1873-3336},
abstract = {Microplastic (MP) accumulation and salinization frequently co-occur in terrestrial ecosystems, posing potential risks to soil health. However, their combined toxicity to soil invertebrates remains unclear. This study investigated combined effects of NaCl and polyethylene MPs (< 35, < 125, < 500 μm) on earthworms. The non-saline avoidance EC50 for < 35 μm MPs was 18 wt%, while avoidance only occurred at 50 wt% for < 125 μm MPs and not at all for < 500 μm MPs. Synergistic effects between NaCl and small MPs increased avoidance. High (10 wt%) MP concentrations by themselves did not increase earthworm mortality; mortality was lower with both MPs and 4000 mg/kg NaCl than with NaCl alone. Co-exposure to MPs and 1000 mg/kg NaCl further reduced growth rates by 16 % but increased cocoon production by 259 % compared to NaCl exposure alone. NaCl exposure induced earthworm oxidative and osmotic stress; overall stress levels were unchanged by MP co-exposure. 16S rRNA gene sequencing revealed that both NaCl and MPs significantly altered earthworm gut microbiome, suggesting potential impaired gut health. MPs more strongly impacted gut microbial community and functions when no salt was added. Overall, combined effects of NaCl and MPs on earthworms are mainly additive or antagonistic.},
}

@article {pmid38796837,
year = {2024},
author = {Tomasics, G and Schandl, L and Polyák, A and Winkler, G},
title = {[The effect of pre-, pro- and synbiotics on the carbohydrate and lipid metabolism].},
journal = {Orvosi hetilap},
volume = {165},
number = {21},
pages = {803-812},
doi = {10.1556/650.2024.33064},
pmid = {38796837},
issn = {1788-6120},
mesh = {Humans ; *Synbiotics/administration & dosage ; *Lipid Metabolism/drug effects ; *Gastrointestinal Microbiome/physiology ; *Prebiotics ; *Carbohydrate Metabolism ; *Diabetes Mellitus, Type 2/metabolism/prevention & control ; Hypoglycemic Agents/therapeutic use/pharmacology ; Diabetes Mellitus, Type 1/metabolism ; Probiotics/therapeutic use/pharmacology ; },
abstract = {The prevalence of diabetes and its precursor state – the prediabetes – is exponentially spreading worldwide. More and more data suggest the role of gut microbiome in the pathogenesis of the aforementioned conditions. It is well known that pre-, probiotics, and their combination called synbiotics may influence the composition of the gut microflora. Thus they may play a key role in the progression or retardation of the pathogenetic process of diabetes. It is also supported by more and more observations that different drugs – in particular the antidiabetic drugs − can modify the composition of the microbiome. Based on literary data, the authors review the influencing effects of pre-, pro-, and synbiotics on the carbohydrate and lipid metabolism, as well as their potential role in the pathogenesis of type 1 and type 2 diabetes, and summarize briefly the role of antidiabetic drugs on the gut microbiome composition. Orv Hetil. 2024; 165(21): 803–812.},
}

Humans
*Synbiotics/administration & dosage
*Lipid Metabolism/drug effects
*Gastrointestinal Microbiome/physiology
*Prebiotics
*Carbohydrate Metabolism
*Diabetes Mellitus, Type 2/metabolism/prevention & control
Hypoglycemic Agents/therapeutic use/pharmacology
Diabetes Mellitus, Type 1/metabolism
Probiotics/therapeutic use/pharmacology

@article {pmid38555569,
year = {2024},
author = {Rurik, I and Péter, S and Bánáti, D},
title = {[Actual challenges of nutritional science].},
journal = {Orvosi hetilap},
volume = {165},
number = {13},
pages = {483-488},
doi = {10.1556/650.2024.33013},
pmid = {38555569},
issn = {1788-6120},
mesh = {Humans ; *Nutritional Sciences ; },
abstract = {A balanced, healthy diet can ensure a longer lifespan and a better quality of life, so the huge challenge facing humanity is to provide the world’s growing population with healthy food from sustainable food systems, in sufficient quantity and quality. Malnutrition and the multiple burden of nutrition are also public health issues, as is the epidemic progression of obesity and its complications, and the increasing rates of food allergy or food intolerance to certain food substances. Our paper deals with different diets, the development of novel foods, the prospects for research on the microbiome and the nutritional aspects of healthy ageing. Sustainability and environmental aspects, animal welfare requirements, shorter food chains, reducing emissions from production and transport, controlling chemical residues of harmful substances, limiting advertising of unhealthy products, and socially responsible pricing are important. It is equally important to educate the public, develop and disseminate dietary and nutritional recommendations, develop and produce nutritious food items, and provide accurate, evidence-based consumer information. At the same time, there is a need to reduce food waste. Coordinated interventions are needed at all levels, with a strong governmental commitment. In addition to deeper study of the physiological aspects of nutrition, the main directions of research in nutrition science are the development of new technologies, new food ingredients, processing and preservation methods, and monitoring and possible optimization of the nutritional environment. Orv Hetil. 2024; 165(13): 483–488.},
}

Humans
*Nutritional Sciences

@article {pmid38142414,
year = {2023},
author = {Pállinger, É and Nagy, B and Király, A and Fülöp, V},
title = {[Immune cell functionality during pregnancy].},
journal = {Orvosi hetilap},
volume = {164},
number = {51},
pages = {2006-2015},
doi = {10.1556/650.2023.32935},
pmid = {38142414},
issn = {1788-6120},
mesh = {Pregnancy ; Female ; Humans ; *Heart Transplantation ; Trophoblasts ; },
abstract = {Immunological recognition of the fetus is the prerequisite of successful pregnancy. Decidualization enables the formation of embryo-competent tissue environment. The decidua is an independent organ performing endocrine and immunological function. On the other hand, the embryo itself is also an active participant of fertilization through the strictly regulated bidirectional communication between embryonic and maternal tissues. Immunological properties of fetomaternal interface dynamically change and pregnancy can be characterized by immunological stages. Chronology of pregnancy may be represented by the three phases “immune clock”: the implantation period is associated with the previously unimaginable inflammatory milieu, which is replaced by the anti-inflammatory environment essential to fetal growth, and followed by a second inflammatory state, which helps in labor. Adaptation to pregnancy requires great flexibility of the immune system in order to simultaneously achieve tolerance to paternal alloantigens, optimal development of the placenta and fetus, and protection against infections/xenobiotics. All this can only be achieved if a special and closely cooperating immune milieu develops at the fetal–maternal interface, where the cellular and soluble components of natural and adaptive immunity are attuned to the hormonal environment, cooperate with the microbiome and respond appropriately to the immunomodulatory effects of the trophoblasts. Characterization of the maternal immune system during pregnancy is important to understand how we can diagnose or treat immune dysregulation associated pregnancy complications, including infertility, implantation failure or pregnancy complications. Orv Hetil. 2023; 164(51): 2006–2015.},
}

Pregnancy
Female
Humans
*Heart Transplantation
Trophoblasts

@article {pmid40499249,
year = {2025},
author = {McDonagh, F and Murray, EK and Hallahan, B and Miliotis, G},
title = {Systematic examination of off-target effects of antipsychotic medications associated with microbiome disruption and heightened bacterial infection risks.},
journal = {Journal of psychiatric research},
volume = {189},
number = {},
pages = {171-183},
doi = {10.1016/j.jpsychires.2025.05.046},
pmid = {40499249},
issn = {1879-1379},
abstract = {OBJECTIVE: This systematic review aims to critically evaluate the link between antipsychotic drugs and bacterial infection risk, emphasising antimicrobial properties of antipsychotics, and microbiome changes that might heighten susceptibility to bacterial infections.

METHODS: A systematic literature search was conducted across PubMed, Scopus, and Google Scholar, up to March 2024. Peer-reviewed articles that investigated the relationship between antipsychotics, their antimicrobial effects, microbiome alterations, and bacterial infection risk were included. Data extracted included antipsychotic type, infection risks, patient demographics, and study methodologies. Risk-of-bias assessments were performed using tools such as the Newcastle-Ottawa Scale and the SYRCLE risk-of-bias tool.

RESULTS: The review analysed twenty-six studies detailing antimicrobial properties of antipsychotics, four studies on antipsychotic-induced microbiome alterations, and thirty-one studies assessing bacterial infection risk associated with antipsychotics. First-generation antipsychotics were observed to have broad antimicrobial properties, whereas second-generation antipsychotics primarily affected commensal bacteria. At least four antipsychotics were observed to disrupt the gut microbiota. A heightened risk of infection was observed among psychiatric cohorts as well as off-label antipsychotics use, with clozapine linked to a substantial increase in respiratory infection risk.

DISCUSSION: Although antipsychotics remain indispensable in psychiatric care, their association with an increased risk of bacterial infections underscores the need for judicious prescribing and vigilant monitoring. The review identifies significant knowledge gaps attributable to inconsistent research methodologies, small study cohorts, lack of controls, and focus on a limited range of antipsychotics. Further standardised research is essential to deepen our understanding of these associations and to inform improved prescribing practices and risk mitigation strategies.},
}

@article {pmid40499217,
year = {2025},
author = {Li, M and Zhang, Q and Zhao, W and Chen, J and Liu, Y and Zhou, L and Liu, Y and Wang, L and Guan, Y and He, J and Jiang, Q and Zeng, Z and Guo, X and Liu, C and Zhang, L and Zhang, Y and Luo, J and Hung, WL and He, J and Wang, R},
title = {Effects and Persistence of Bifidobacterium animalis subsp. lactis BL-99 and Fructooligosaccharides on Older Adults with Functional Constipation: A Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {The journal of nutrition, health & aging},
volume = {29},
number = {8},
pages = {100598},
doi = {10.1016/j.jnha.2025.100598},
pmid = {40499217},
issn = {1760-4788},
abstract = {Research on effects of synbiotics in older adults with functional constipation (FC) is limited. This randomized, double-blind, placebo-controlled trial evaluated a 4-week synbiotic (Bifidobacterium animalis subsp. lactis BL-99 and fructooligosaccharides [FOS]) intervention in 67 participants ≥60 years old meeting Rome IV FC criteria. Compared to placebo, the synbiotic group showed significant improvements in weekly spontaneous bowel movements (Least squares mean ± standard error: 4.94 ± 0.25 vs. 3.00 ± 0.26, P < 0.001) and whole gut transit time (37.13 ± 3.78 vs. 50.64 ± 4.22 h, P = 0.019), with benefits sustained 2 weeks post-intervention. It also reduced time per toilet attempt and alleviated rectal discomfort symptoms more effectively than placebo. Fecal microbiome analysis revealed increased abundance of beneficial Bifidobacterium species, correlating with symptom improvement (P < 0.05). These findings demonstrate that BL-99/FOS supplementation ameliorates FC symptoms in older adults, with effects sustained post-discontinuation, potentially mediated through gut microbiota modulation. Further mechanistic investigation is warranted.},
}

@article {pmid40499189,
year = {2025},
author = {Fernandes, PMB and Fernandes, AAR and Maurastoni, M and Rodrigues, SP},
title = {Lab Legends and Field Phantoms: The Tale of Virus-Resistant Plants.},
journal = {Annual review of virology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-virology-092623-101850},
pmid = {40499189},
issn = {2327-0578},
abstract = {Plant viruses present significant challenges to global agriculture, causing crop losses, threatening food security, and imposing economic burdens. Advances in biotechnology have revolutionized strategies to attack these threats, with genetically modified and genome-edited virus-resistant plants, developed using precision tools such as RNA interference and CRISPR/Cas technology, playing pivotal roles. Despite these breakthroughs, fragmented regulatory frameworks and divergent policies across regions including the European Union and the Global South hinder the global adoption of such innovations. Multifaceted approaches, including gene pyramiding, microbiome-based strategies, and pathogen-targeted defenses, show promise for enhancing plant resilience. This review explores the biological, regulatory, and ethical dimensions of deploying virus-resistant crops, emphasizing the need for harmonization of international regulation to maximize biotechnological benefits. By addressing these challenges, biotechnology can advance sustainable agriculture, secure food systems, and mitigate the effect of plant viral diseases.},
}

@article {pmid40499078,
year = {2025},
author = {Xue, K and Wang, P and Lin, Q and Xie, J and Cong, L and Yan, Z},
title = {Uncovering the Single Amino-Acid Polymorphisms of the Human Gut Ecosystem.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.5c00108},
pmid = {40499078},
issn = {1535-3907},
abstract = {Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in the gut microbial metagenome and the host genome, but they could not adequately represent the protein-level variants. Single amino-acid polymorphisms (SAP) derived from nonsynonymous SNPs can cause functional changes of proteins and are important forces of adaption. However, SAP remains quite unexplored for the human gut microbiome. Here, we present a comprehensive large-scale analysis of SAP in the gut ecosystem, introducing a rigorous computational pipeline for detecting such protein variation from 992 published human metaproteomes. We find varied yet elaborate SAP patterns, capturing both known and novel functions and adaptive strategies of gut microbes. Microbial SAP is enriched in the outermost shell, motility devices, and ribosomes. Generally, gut microbial SAP is more convergent in metabolic subpathway regions and is enriched in the initial steps of carbohydrate metabolism pathways that catalyze the formation and isomerization of phosphorylated sugars. Furthermore, microbial and host mutant peptide patterns were altered and exhibited significant correlations in both inflammatory bowel disease and type 1 diabetes. Our results highlight the functional and clinically relevant implications and potential host-microbial interactions of gut ecosystem SAP.},
}

@article {pmid40498998,
year = {2025},
author = {Marcos-Kovandzic, L and Avagliano, M and Ben Khelil, M and Srikanthan, J and Abdallah, R and Petrocelli, V and Rengassamy, J and Alfaro, A and Bied, M and Fidelle, M and Ferrere, G and Daillere, R and Arbab, A and Amine-Hneineh, R and Pages, A and Dartigues, P and Ly, P and Simon, S and Durand, S and Gottschlich, A and Ginhoux, F and Bleriot, C and Liu, P and Zhao, L and Creusot, L and Rolhion, N and Kroemer, G and Menger, L and Kobold, S and Castilla-Llorente, C and Sokol, H and Casola, S and Pasolli, E and Zitvogel, L and Bigenwald, C},
title = {Gut microbiota modulation through Akkermansia spp. supplementation increases CAR-T cell potency.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-24-1230},
pmid = {40498998},
issn = {2159-8290},
abstract = {This study investigates the clinical relevance of the gut microbiome at taxonomic and metabolic levels in anti-CD19 CAR-T cell therapy, both in patients and in a preclinical syngeneic tumor model. B cell lymphoma patients treated with CD19-CAR-T cells exhibited profound intestinal dysbiosis, exacerbated after CAR-T infusion. This dysbiosis was characterized by low bacterial richness, low sMAdCAM-1 and loss of Akkermansia species, associated with resistance to therapy. Mechanistically, oral Akkermansia massiliensis supplementation increased CAR-T cell infiltration into bone marrow, inverted the CD4/CD8 CAR-T ratio, favored Tc1 CD8+ T cell polarization and promoted release of tryptophan-derived indole metabolites, leading to better tumor control. The clinical benefit of Akkermansia spp. supplementation was abolished when CAR-T cells were genetically deficient for the indole receptor, aryl hydrocarbon receptor (Ahr). Ahr-agonistic indoles alone failed to replicate the bacterium's anticancer effects. These findings suggest Akkermansia supplementation could improve CAR-T cell potency in patients with intestinal Akkermansia deficiency.},
}

@article {pmid40498698,
year = {2025},
author = {Bußmann, A and Speckemeier, C and Ehm, A and Kollar, B and Neumann, A and Neusser, S},
title = {Approaches to predict future type 2 diabetes mellitus and chronic kidney disease: A scoping review.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0325182},
doi = {10.1371/journal.pone.0325182},
pmid = {40498698},
issn = {1932-6203},
mesh = {Humans ; *Diabetes Mellitus, Type 2/epidemiology/diagnosis ; *Renal Insufficiency, Chronic/epidemiology/diagnosis ; Risk Factors ; },
abstract = {BACKGROUND: Demographic change and changing lifestyles are leading to a steady increase in so-called population diseases such as type 2 diabetes mellitus and chronic kidney disease. Both conditions are often preceded by a latency period during which lifestyle changes and/or medications have the potential to delay or even prevent disease onset. Thus, detection of those at an increased risk of these diseases is of great importance. A scoping review was conducted to collate different prediction approaches for type 2 diabetes mellitus and chronic kidney disease.

METHODS: Literature searches were performed in PubMed, Embase, Web of Science, and Google Scholar. A stepwise approach was used, consisting of searches for systematic reviews and primary literature, and additional Google searches for novel approaches. Included was literature that (1) presented an approach for risk prediction of incident type 2 diabetes mellitus or chronic kidney disease, (2) contained information on the risk factors considered and application, (3) targeted the general population, (4) was written in English or German language, and (5) for which an abstract and full-text was available. Literature screening was carried out by two persons independently.

RESULTS: Studies extracted literature from 1940 to 2023. Prediction approaches were included from 25 literature reviews, eight primary studies and nine studies found in additional searches. Several different approaches were identified, including methods based on clinical parameters, biological parameters (blood, urine, microbiome, genetics), the combinations of those, sequential approaches, and exposure and lifestyle factors. Most of the identified approaches were risk surveys that usually ask for simple and readily available parameters. Novel approaches cover transdermal optical imaging, prediction based on facial blood flow and using deoxyribonucleic acid methylation data.

CONCLUSION: This scoping review provides an overview of different tools for the risk prediction of type 2 diabetes mellitus and chronic kidney disease. In addition to established tools, which are primarily risk surveys, innovative approaches have been developed and evaluated in recent years in which the potential of machine learning is utilized. As cardio-renal-metabolic diseases share predicting factors and given the social and economic importance of these diseases, approaches that address multiple relevant diseases such as type 2 diabetes mellitus, chronic kidney disease and cardiovascular disease can be of great interest, especially in time- and resource-constrained healthcare settings.},
}

Humans
*Diabetes Mellitus, Type 2/epidemiology/diagnosis
*Renal Insufficiency, Chronic/epidemiology/diagnosis
Risk Factors

@article {pmid40498592,
year = {2025},
author = {Wagner, AD and Ahmed, MMA and Starks, VA and Boudreau, PD},
title = {Using Repeated Lysis Steps Fractionates Between Heterotrophic and Cyanobacterial DNA Extracted from Xenic Cyanobacterial Cultures.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf135},
pmid = {40498592},
issn = {2160-1836},
abstract = {Extracting DNA from cyanobacteria can be a challenge because of their diverse morphologies, challenging cellular structure, and the heterotrophic microbiome often present within cyanobacterial cultures. As such, even with high DNA yields, the percentage of reads coming from the cyanobacterial host can be low, leading to an incomplete cyanobacterial genome assembly. In this research, we optimized a DNA isolation protocol using three iterative cell lysis steps to enrich the portion of DNA isolated coming from the cyanobacterial host rather than the heterotrophic microbiome. In order to utilize in-house nanopore sequencing, we faced a challenge using our lysis protocol: the iterative lysis approach led to more DNA shearing than is ideal for this sequencing technology. To solve this, we used two bead-based size selection steps to remove shorter molecules of DNA before nanopore sequencing. Analysis of the sequenced reads showed that, in the first lysis, the cyanobacterial sequences were only 35% of all reads. In the repeated lysis steps, however, the proportion of reads coming from the cyanobacterium increased to 75% or higher. Using our iterative lysis protocol, we were able to sequence the genomes of two fresh water cyanobacteria isolated from northern Mississippi, namely Leptolyngbya sp. BL-A-14 and Limnothrix sp. BL-A-16. The genomes of these isolates were assembled as closed chromosomes of 7.2 and 4.5 Mb for BL-A-14 and BL-A-16, respectively. As it is not always possible to prepare axenic cultures of cyanobacteria, we hope our approach will be useful for sequencing other xenic cultures of cyanobacteria.},
}

@article {pmid40498389,
year = {2025},
author = {Maître, M and Baradat, S and Froliger, M and Turlier, V and Simcic-Mori, A and Gravier, E and Géniès, C and Lauze, C and Huyghe, C and Noustens, A and Alvarez-Georges, S and Marinescu, R and Reygagne, P and Bessou-Touya, S and Mengeaud, V and Duplan, H},
title = {Scalp Microbiome Dynamics Can Contribute to the Clinical Effect of a Novel Antiseborrheic Dermatitis Shampoo Containing Patented Antifungal Actives: A Randomized Controlled Study.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {40498389},
issn = {2193-8210},
abstract = {INTRODUCTION: Scalp seborrheic dermatitis (SD) can cause physical discomfort and social embarrassment in affected individuals. Mild-to-moderate scalp SD can be managed using topical products with antifungal, antiinflammatory, and keratolytic properties.

METHODS: A two-phase, randomized, controlled study was conducted to evaluate the clinical efficacy of a newly formulated anti-SD shampoo containing two patented antifungal actives and to investigate the associated changes in the scalp microbiota. The intervention involved a 2-week intensive phase for the 42 subjects included in the study, consisting of the application of the anti-SD shampoo three times a week; a randomized [1:1], controlled, parallel-group 8-week maintenance phase consisting of the test group applying the study shampoo once a week alternately with a neutral shampoo twice a week; and the control group applying the neutral shampoo alone three times a week.

RESULTS: Following the intensive phase, the scalp condition improved substantially, as evidenced by a significant decrease in the severity of dandruff, erythema, and pruritus, associated with an improvement of SD dysbiosis. These improvements were more sustained in the test group than in the control group during the maintenance phase. The rediversification of the scalp microbiota involved a significant increase in fungal and bacterial richness along with a decrease in the level of SD-predominant Malassezia fungi and Staphylococcus bacteria and an increase in the level of low-abundant fungi genera belonging to the Ascomycota phylum.

CONCLUSIONS: The synergistic effects of antimycotic and antiinflammatory agents in the study shampoo likely contributed to rebalancing the fungal and bacterial ecosystem, thus improving scalp symptoms.

GOV IDENTIFIER: NCT06578962 (retrospectively registered on 28 August 2024).},
}

@article {pmid40498370,
year = {2025},
author = {Cullen, JT and Lawlor, PG and Cormican, P and Gardiner, GE},
title = {Investigating the impact of sanitisation of a liquid feeding system for pigs on the bacteriome and mycobiome of the liquid feeding system surfaces and liquid feed.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf143},
pmid = {40498370},
issn = {1365-2672},
abstract = {AIMS: To investigate the effect of liquid feeding system sanitisation on the bacteriome and mycobiome of feeding system surfaces and liquid feed.

METHODS AND RESULTS: High-throughput 16S and ITS2 rRNA amplicon sequencing was performed on surface swabs and feed samples collected during a previous sanitisation experiment. Results confirmed that feed pipeline surface biofilms were disrupted post-cleaning (PC). Pre-cleaning, the pipeline was dominated by Lactobacillus, Leuconostoc and Apiotrichum. Microbial diversity increased PC, with Jeotgalicoccus and Brachybacterium predominating, although Lactobacillus became predominant again between wk8-wk10 PC. Sanitisation also impacted the feed microbial profile, with decreases in Lactobacillus, Leuconostoc and Chryseobacterium in the mixing tank feed. Weissella and Kazachstania became predominant in the trough-sampled liquid feed PC. Despite sanitisation, spontaneous fermentation was still observed in the feed, evidenced by decreased abundance of spoilage-associated Pantoea and Pseudomonas between the mixing tank and troughs and a concomitant increase in Lactobacillus. Nonetheless, previously reported improvements in feed quality PC suggest the changes in the liquid feed microbiota were beneficial.

CONCLUSIONS: Intensive cleaning and subsequent daily acid-rinsing of the feeding system disrupted feed pipeline biofilms, reduced spontaneous fermentation and improved liquid feed quality. Therefore, we recommend liquid feeding system sanitisation between batches of grow-finisher pigs followed by maintenance acid-rinsing.},
}

@article {pmid40498317,
year = {2025},
author = {Viets, C and Stevens, CA},
title = {Measuring and Analyzing Bacterial Movement in Mucus.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2942},
number = {},
pages = {187-197},
pmid = {40498317},
issn = {1940-6029},
mesh = {Humans ; *Mucus/microbiology/metabolism ; Mucins/metabolism ; *Time-Lapse Imaging/methods ; *Bacteria ; Microbiota ; },
abstract = {Humans are colonized by trillions of microbes that compose the human microbiome. Much of the microbiome inhabits the mucus layers. Mucus layers, covering digestive, reproductive, ocular, and respiratory tracts, are viscous networks consisting mainly of water and mucin glycoproteins. Mucins assemble into a dense, cross-linked network that can affect bacterial swimming patterns, and studying this behavior provides valuable insights into how the body regulates interactions with both harmful and beneficial microbes. Here we present the use of time-lapse imaging to track individual bacterial cells within mucin and discuss techniques for accurately extracting cell trajectory data from these images. By integrating theoretical and experimental approaches, we also describe how to quantify bacterial movement in terms of speed, persistence, and randomness.},
}

Humans
*Mucus/microbiology/metabolism
Mucins/metabolism
*Time-Lapse Imaging/methods
*Bacteria
Microbiota

@article {pmid40498312,
year = {2025},
author = {Lisacek, F and Schnider, B and Ohayon, D and Imberty, A},
title = {Microbial Lectin-Targeting Mucus: A Glycobioinformatic Approach.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2942},
number = {},
pages = {131-143},
pmid = {40498312},
issn = {1940-6029},
mesh = {*Lectins/metabolism/chemistry ; Humans ; *Mucins/metabolism/chemistry ; *Mucus/metabolism ; Polysaccharides/metabolism/chemistry ; Protein Binding ; Microbiota ; },
abstract = {The motifs exposed on surface glycans of mucins serve as receptors to a range of proteins expressed by microorganisms. The specificity of microbial glycan-binding proteins, i.e., lectins, towards human mucin epitopes is the result of co-evolution. The binding of microbes to mucins is described in several databases hosted on the UniLectin portal. In particular, UniLectin3D provides structural details on the recognition process and LectomeXplore allows for the identification of putative lectins in the genomes of mucin-associated microbiome species. The usage of these resources is illustrated in this chapter.},
}

*Lectins/metabolism/chemistry
Humans
*Mucins/metabolism/chemistry
*Mucus/metabolism
Polysaccharides/metabolism/chemistry
Protein Binding
Microbiota

@article {pmid40498297,
year = {2025},
author = {Beraja, GE and Gruzmark, F and Pastar, I and Lev-Tov, H},
title = {What's New in Wound Healing: Treatment Advances and Microbial Insights.},
journal = {American journal of clinical dermatology},
volume = {},
number = {},
pages = {},
pmid = {40498297},
issn = {1179-1888},
abstract = {Recent advancements in wound healing are reshaping clinical practice by integrating dermatology, cutaneous microbiome research, and technology. This article discusses new diagnostic tools, such as imaging devices and microbial composition analysis, that enhance our understanding of wound environments. It highlights the importance of wound bed preparation and explores innovative treatment methods for optimal wound healing, including debridement techniques like ultrasound-assisted methods, hydrosurgery, and larval therapy. The evolution of wound management is further illustrated through the use of cellular and acellular matrix products and cellular therapies involving whole blood products. We also present the latest insights on the wound microbiome and antimicrobial treatments, including advanced dressings and antibiofilm surfactants. Finally, the potential of gene therapy for complex conditions like epidermolysis bullosa is discussed as a promising model for advancing wound healing. This review synthesizes current research to improve dermatological practices and patient outcomes in wound care.},
}

@article {pmid40498283,
year = {2025},
author = {de Miranda, NFCC and Smit, VTHBM and van der Ploeg, M and Wesseling, J and Neefjes, J},
title = {Absence of lipopolysccharide (LPS) expression in breast cancer cells.},
journal = {Cellular oncology (Dordrecht, Netherlands)},
volume = {},
number = {},
pages = {},
pmid = {40498283},
issn = {2211-3436},
support = {852832/ERC_/European Research Council/International ; },
abstract = {The relationship between bacterial activity and tumorigenesis has gained attention in recent years, complementing the well-established association between viruses and cancer. A recent study employed immunodetection of lipopolysaccharide (LPS) to demonstrate the presence of intracellular bacteria within cancer cells across various cancer types, including breast cancer. The authors proposed that these bacteria might play a role in tumor development. We sought to replicate these findings using the same experimental methods on an independent cohort of breast cancer cases. Our analysis of 129 samples revealed no evidence of LPS expression within cancer cells. Instead, LPS immunoreactivity was observed in ducts or immune cells, specifically macrophages, as expected. These discrepancies in LPS immunodetection warrant caution in interpreting the original findings, and further research is needed to clarify the potential role of intracellular bacteria in cancer development.},
}

@article {pmid40498144,
year = {2025},
author = {Frederico, G and Quirino, MW and Andretta, I and Schmitt, E and Peripolli, V and da Rosa Ulguim, R and Bianchi, I},
title = {Lactation performance and fecal microbiome of sows supplemented with antioxidant-rich polyherbal extract.},
journal = {Tropical animal health and production},
volume = {57},
number = {5},
pages = {258},
pmid = {40498144},
issn = {1573-7438},
mesh = {Animals ; Female ; *Feces/microbiology ; *Lactation/drug effects/physiology ; *Antioxidants/administration & dosage/metabolism/pharmacology ; Animal Feed/analysis ; Dietary Supplements/analysis ; *Plant Extracts/administration & dosage/pharmacology/metabolism ; Diet/veterinary ; *Sus scrofa/physiology/microbiology ; *Gastrointestinal Microbiome/drug effects ; Animal Nutritional Physiological Phenomena ; },
abstract = {This study evaluated the lactation performance and fecal microbiome of sows supplemented with an herbal extract rich in antioxidants from day 110 of gestation until weaning. Ninety-five sows (parity 1 to 8) were assigned to either the control group (n = 48; 225.3 ± 4.1 kg), fed a non-supplemented lactation diet, or the herbal group (n = 47; 224.6 ± 4.2 kg), fed the same diet supplemented with an herbal extract (Herbal C Power[®], Nuproxa, Vaud, Switzerland). Environmental conditions in the farrowing facilities were within the critical temperature and humidity range. No differences were observed in sow rectal temperature, respiratory frequency, or number of weaned piglets (P = 0.15). However, piglets from the supplemented group showed lower pre-weaning mortality (0.72% vs. 1.23%), higher weight gain (213.8 g vs. 201.1 g), and greater weaning weight (6.1 kg vs. 5.8 kg; P ≤ 0.01). Supplemented sows produced more milk (11.0 kg/day vs. 9.9 kg/day; P < 0.01), though feed and water consumption remained similar (P ≥ 0.39). Antioxidant supplementation had no significant effect on sows' body weight, backfat thickness, or weaning-to-estrus interval, but supplemented sows had lower caliper units (12.1 vs. 13.0; P = 0.03). Serum levels of AST, ALT, C-reactive protein, and TNF-α were unaffected (P ≥ 0.17). Fecal analysis revealed a higher abundance of Enterobacteriales and Enterobacteriaceae in supplemented sows (P = 0.03). Antioxidant supplementation improved litter performance, reduced piglet mortality, increased milk production, and altered sow gut microbiota; however, further studies performed under more extreme conditions are needed.},
}

Animals
Female
*Feces/microbiology
*Lactation/drug effects/physiology
*Antioxidants/administration & dosage/metabolism/pharmacology
Animal Feed/analysis
Dietary Supplements/analysis
*Plant Extracts/administration & dosage/pharmacology/metabolism
Diet/veterinary
*Sus scrofa/physiology/microbiology
*Gastrointestinal Microbiome/drug effects
Animal Nutritional Physiological Phenomena

@article {pmid40498140,
year = {2025},
author = {Meurs, J and Henderson, B and van Dun, C and Batitsta, GL and Sakkoula, E and van Diepen, JA and Gross, G and Aarts, E and Cristescu, SM},
title = {Exploring the use of exhaled breath profiling for non-invasive monitoring of cognitive functioning in children: a pilot study.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {21},
number = {4},
pages = {75},
pmid = {40498140},
issn = {1573-3890},
support = {PROJ-00405//European Regional Development Fund/ ; 818110//Horizon 2020/ ; },
mesh = {Humans ; Breath Tests/methods ; Child ; Pilot Projects ; Male ; Female ; *Cognition/physiology ; Gastrointestinal Microbiome/physiology ; Executive Function/physiology ; Exhalation ; Metabolomics/methods ; },
abstract = {INTRODUCTION: Childhood is a critical period for the development of executive functioning skills, including selective attention and inhibitory control, which are essential for cognitive development. Optimal brain development during this time requires appropriate levels of macronutrient intake. Metabolomics can offer valuable insights into which metabolites cognitive functioning and the underlying gut-brain interactions.

OBJECTIVES: This study aimed to explore to use of breathomics to investigate associations between exhaled metabolites and executive functioning in children.

METHODS: Children (8-10 years; N = 31) were recruited via flyers at schools and after-school care. The assessment of executive functioning was done using Eriksen flanker task. Breath samples were collected in Tedlar[®] bags and analyzed with proton transfer reaction-mass spectrometry (PTR-MS). On-breath peaks were selected and subjected to partial least squares (PLS) regression. Significance multivariate correlation (sMC) was used afterwards to select metabolites bearing predictive power towards executive functioning.

RESULTS: Gut microbiome-related metabolites (methane, ethanol, and butyric acid) present in exhaled breath were associated with an improved executive functioning, whereas isoprene was linked to reduced executive functioning. Additionally, increased levels of inflammatory markers, ethylene and acetaldehyde, were associated with a higher compatibility effect in error rates, suggesting diminished cognitive control. These VOCs were putatively linked with specific gut microbial taxa; for instance, reduced Bacteroidetes abundance (associated with methane production) is associated with decreased inhibitory control, while Enterobacteriaceae were linked to lipopolysaccharide-induced inflammation which is also a process that causes increased ethylene production.

CONCLUSION: This proof-of-concept study demonstrates that VOCs in exhaled breath could serve as a promising non-invasive tool for assessing gut-brain interactions related to executive functioning in children.},
}

Humans
Breath Tests/methods
Child
Pilot Projects
Male
Female
*Cognition/physiology
Gastrointestinal Microbiome/physiology
Executive Function/physiology
Exhalation
Metabolomics/methods

@article {pmid40497827,
year = {2025},
author = {Ning, W and Li, M and Jiang, L and Yang, M and Liu, M and Liu, Y},
title = {Endophytic Bacterial Community Structure and Function Response of BLB Rice Leaves After Foliar Application of Cu-Ag Nanoparticles.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/nano15110778},
pmid = {40497827},
issn = {2079-4991},
support = {RCZ202505//Xichang University Special project/ ; },
abstract = {Bacterial leaf blight (BLB) is a destructive disease caused by Xanthomonas oryzae pv. oryzae (Xoo). It has been proven that BLB adversely influences the growth and production of rice, resulting in substantial losses in yield. Nanoparticle-antimicrobial compounds possess excellent physicochemical properties, which have generated groundbreaking applications in protecting rice against BLB attacks. However, there is less research focused on the interaction between nanoparticles and the microbiome of BLB rice leaves, particularly the structure and function of endophytic bacteria, which are essential to plant health and pathogenesis. Therefore, the study explored how Cu-Ag nanoparticles influenced the endophytic bacteria's composition and functions in healthy and BLB rice leaves. The data demonstrated that the relative abundance of beneficial bacteria, Burkholderiales, Micrococcales, and Rhizobiales, increased after the introduction of Cu-Ag nanoparticles on the leaves of BLB rice. The examination of PAL activity demonstrated that nanoparticles limited the spread of Xoo in rice leaves. Furthermore, endophytic community functional prediction demonstrated that nanoparticles may regulate the physiological process associated with potential stress resistance and growth-promoting function in the endophytic communities. This investigation may enhance the understanding of interactions between nanoparticles and the composition of rice endophytic microbiome, which can contribute to the exploration and application of nanomaterials in crop pathogen management.},
}

@article {pmid40497754,
year = {2025},
author = {Cristofori, F and Castellaneta, S and Dargenio, C and Paulucci, L and La Grasta, G and Barone, M and Francavilla, R and Dargenio, VN},
title = {Unlocking the potential of the low FODMAP diet: comprehensive insights into clinical efficacy, microbiome modulation, and beyond.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2025.2519160},
pmid = {40497754},
issn = {1747-4132},
abstract = {INTRODUCTION: Functional gastrointestinal disorders (FGIDs) and inflammatory bowel diseases (IBD) present significant challenges for both pediatric and adult populations. The low FODMAP diet (LFD) has gained prominence as an evidence-based dietary intervention, offering symptom relief for abdominal pain, bloating, and altered bowel habits. However, concerns about adherence, nutritional adequacy, and long-term safety remain critical, particularly in pediatric populations.

AREAS COVERED: This narrative review examines the nature and physiological impact of FODMAPs, focusing on the practical application of the low-FODMAP diet (LFD) in adults and pediatric gastroenterology. Particular attention is given to emerging insights into its impact on gut microbiota and long-term safety.

EXPERT OPINION: While LFD effectively alleviates symptoms in FGIDs and functional symptoms in IBD, its restrictive nature demands professional supervision to mitigate nutritional risks. For pediatric patients, adherence and reintroduction protocols require optimization. Further research into personalized dietary approaches and microbiome-targeted strategies could enhance the clinical utility of the LFD, ensuring its long-term safety and efficacy for diverse patient groups.},
}

@article {pmid40497711,
year = {2025},
author = {Crosby, A and Krishnan, K and Baker, S},
title = {Andie Crosby, Calroy and Kiran Krishnan, Microbiome Labs Introducing Cartigenix HP for Pain Management.},
journal = {Alternative therapies in health and medicine},
volume = {31},
number = {4},
pages = {6-9},
pmid = {40497711},
issn = {1078-6791},
mesh = {Humans ; *Pain Management/methods ; *Microbiota ; },
abstract = {No Abstract Available.},
}

Humans
*Pain Management/methods
*Microbiota

@article {pmid40497681,
year = {2025},
author = {Fan, Y and Li, Y and Wang, L and Zhao, D and Zhou, Y and Houpt, ER and Liu, J},
title = {Fecal microbiome profiling of children with Shigella diarrhea from low- and middle-income countries.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0057325},
doi = {10.1128/spectrum.00573-25},
pmid = {40497681},
issn = {2165-0497},
abstract = {Shigella is one of the leading pathogens causing diarrhea in children globally. Stool culture remains the standard for diagnosing Shigella infections; however, quantitative PCR (qPCR) offers greater sensitivity. In this study, we evaluated the fecal microbiomes of 27 diarrheal children with and without Shigella identified by culture and quantitative PCR, respectively, aiming to characterize the fecal microbiome profiles of children with Shigella diarrhea and to explore the differences in microbiome and the mechanisms associated with the culturability of Shigella. Our results showed that Shigella qPCR positive cases were characterized by a significantly higher abundance of Shigella and other Proteobacteria, alongside a lower abundance of the probiotic genus Bifidobacterium. This profile was associated with specific virulence factors (VFGs) and antimicrobial resistance genes (ARGs), indicating a unique pathogenic module related to Shigella infection. While no significant difference in Shigella abundance was found between the Shigella culture positive and culture negative groups, genera Bifidobacterium and Ligilactobacillus were enriched in the culture positive group. Interestingly, the culture positive group also possessed a higher abundance of virulence factors associated with pathogenicity, likely resulting from the higher copy number of pINV plasmid. The fecal metagenomic analyses from diarrheal children suggested a potentially distinct intestinal microbial profile associated with Shigella infection and a possible correlation between increased pathogenicity and the Shigella culturability. These findings might contribute to a more comprehensive understanding of Shigella pathogenicity and improving diagnostic methods for Shigella.IMPORTANCEDiarrhea represents the fifth leading cause of mortality among children under the age of five, with Shigella representing the second most common pathogen responsible for diarrhea-related mortality. In the current study, we employed metagenomics to comprehensively characterize the fecal microbiome profiles of children infected with Shigella and to investigate the factors affecting Shigella culturability. We identified a distinct intestinal microbial profile associated with Shigella-infected diarrheal children, observed a correlation between increased pathogenicity and the Shigella culturability, and also proposed some potential factors that might promote the in vitro growth of Shigella strains. These findings might provide evidence for improving diagnostic methods for Shigella.},
}

@article {pmid40497338,
year = {2025},
author = {Older, EA and Mitchell, MK and Campbell, A and Lian, X and Madden, M and Wang, Y and van de Wal, LE and Zaw, T and VanderVeen, BN and Tatum, R and Murphy, EA and Chen, YH and Fan, D and Ellermann, M and Li, J},
title = {Human gut commensal Alistipes timonensis modulates the host lipidome and delivers anti-inflammatory outer membrane vesicles to suppress colitis in an Il10-deficient mouse model.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2517380},
doi = {10.1080/19490976.2025.2517380},
pmid = {40497338},
issn = {1949-0984},
mesh = {Animals ; *Interleukin-10/deficiency/genetics ; Mice ; *Gastrointestinal Microbiome ; Disease Models, Animal ; *Colitis/microbiology/immunology ; Humans ; Mice, Inbred C57BL ; Macrophages/immunology/drug effects ; *Clostridiales/physiology ; Mice, Knockout ; Lipidomics ; *Anti-Inflammatory Agents/pharmacology ; Male ; },
abstract = {Correlative studies have linked human gut microbes to specific health conditions. Alistipes is one such microbial genus negatively linked to inflammatory bowel disease (IBD). However, the protective role of Alistipes in IBD is understudied, and the underlying molecular mechanisms remain unknown. In this study, colonization of Il10-deficient mice with Alistipes timonensis DSM 27924 delays colitis development. Colonization does not significantly alter the gut microbiome composition, but instead shifts the host plasma lipidome, increasing phosphatidic acids while decreasing triglycerides. Outer membrane vesicles (OMVs) derived from Alistipes are detected in the plasma of colonized mice, carrying potentially immunomodulatory metabolites into the host circulatory system. Fractions of A. timonensis OMVs suppress LPS-induced Il6, Il1b, and Tnfa expression in vitro in murine macrophages. We detect putative bioactive lipids in the OMVs, including immunomodulatory sulfonolipids (SoLs) in the active fraction, which are also increased in the blood of colonized mice. Treating Il10-deficient mice with purified SoL B, a representative SoL, suppresses colitis development, suggesting its contribution to the anti-inflammatory phenotype observed with A. timonensis colonization. Thus, A. timonensis OMVs represent a potential mechanism for Alistipes-mediated delay of colitis in Il10-deficient mice via delivery of immunomodulatory lipids and modulation of the host plasma lipidome.},
}

Animals
*Interleukin-10/deficiency/genetics
Mice
*Gastrointestinal Microbiome
Disease Models, Animal
*Colitis/microbiology/immunology
Humans
Mice, Inbred C57BL
Macrophages/immunology/drug effects
*Clostridiales/physiology
Mice, Knockout
Lipidomics
*Anti-Inflammatory Agents/pharmacology
Male

@article {pmid40497323,
year = {2025},
author = {Hui, Y and Sandris Nielsen, D and Krych, L},
title = {De novo clustering of long-read amplicons improves phylogenetic insight into microbiome data.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2516703},
doi = {10.1080/19490976.2025.2516703},
pmid = {40497323},
issn = {1949-0984},
mesh = {*Phylogeny ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Vagina/microbiology ; Female ; Cluster Analysis ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Long-read amplicon profiling through read classification limits phylogenetic analysis of amplicons while community analysis of multicopy genes, relying on unique molecular identifier (UMI) corrections, often demands deep sequencing. To address this, we present a long amplicon consensus analysis (LACA) workflow employing multiple de novo clustering approaches based on sequence dissimilarity. LACA controls the average error rate of corrected sequences below 1% for the Oxford Nanopore Technologies (ONT) R9.4.1 and ONT R10.3 data, 0.2% for ONT R10.4.1, and 0.1% for high-accuracy ONT Duplex and Pacific Biosciences (PacBio) circular consensus sequencing (CCS) data in both simulated 16S rRNA and real 16-23S rRNA amplicon datasets. In high-accuracy PacBio CCS data, the clustering-based correction matched UMI correction, while outperforming 4× UMI correction in noisy ONT R10.3 and R9.4.1 data. Notably, LACA preserved phylogenetic fidelity in long operational taxonomic units and enhanced microbiome-wide phenotype characterization for synthetic mock communities and human vaginal samples.},
}

*Phylogeny
Humans
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Vagina/microbiology
Female
Cluster Analysis
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods

@article {pmid40497050,
year = {2025},
author = {Ma, X and Chen, Y and Li, L and Wang, T and Teng, K and Su, J and Li, L and Li, L and Li, H and Diao, W and Chen, G and Wang, J and Zhong, J},
title = {Efficient utilization of Shuanghuanglian medicine residues by microbial transformation with flavonoid glycosides-hydrolyzing strains.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1553399},
pmid = {40497050},
issn = {1664-302X},
abstract = {Shuanghuanglian, a traditional Chinese medicine, is well-known for its bioactive compounds, such as flavonoids, which offer significant health benefits. However, the production of Shuanghuanlian generates substantial pharmaceutical residues, which are often discarded as waste, posing significant environmental and economic challenges. To date, research on repurposing these medicine residues has been limited. This study utilized beneficial microbes to efficiently extract and utilize the residual bioactive compounds. Notably, a newly isolated Lactiplantibacillus plantarum strain LLB exhibited remarkable efficiency in converting flavonoid glycosides (e.g., phillyrin and luteoloside) into their corresponding aglycones. When combined synergistically with Bacillus subtilis and Saccharomyces cerevisiae, strain LLB maintained robust flavonoid glycoside conversion while enhancing lactobacilli viability in the fermented medicine residues. As a feed additive for broiler chickens, the fermented residue not only boosted antioxidant (superoxide dismutase) and anti-inflammatory (IL-10) markers, but also preserved growth performance and meat quality. Furthermore, the fermented residue modulated the gut microbiome, increasing Rikenella while reducing Elusimicrobiota and Parabacteroides abundances. Our findings demonstrate that microbial transformation of Shuanghuanglian residues offers a sustainable strategy for waste valorization and a novel feed additive for enhancing animal health.},
}

@article {pmid40497049,
year = {2025},
author = {Ren, X and Zheng, L and Huang, L and Zhao, J},
title = {The role of the gut microbiota in shaping the tumor microenvironment and immunotherapy of breast cancer.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1591745},
pmid = {40497049},
issn = {1664-302X},
abstract = {Breast cancer is the most prevalent malignancy among women worldwide and is a major contributor to cancer-related mortality. The tumor microenvironment (TME), composed of tumor cells, immune infiltrates, fibroblasts, and vascular components, is critically involved in tumor initiation, metastatic progression, and therapeutic response. In recent years, therapies targeting the TME have undergone rapid advancements, with the objective of enhancing antitumor immunity. Concurrently, mounting evidence underscores the pivotal role of the gut microbiota and its metabolites in modulating host immunity, influencing metabolic homeostasis, inflammation, and immune equilibrium. The composition and diversity of the gut microbiome influence breast cancer progression and patients' responses to immunotherapy. Therefore, modulating the gut microbiota is a promising strategy to enhance the clinical outcomes of TME-targeted immunotherapies. In this review, we discuss the influence of gut microbiota and its derived metabolites on breast cancer progression and immunotherapy prognosis and explore potential strategies to optimize immunotherapy through gut microbiota modulation.},
}

@article {pmid40496994,
year = {2025},
author = {Chen, J and Cao, J and Guo, B and Han, M and Feng, Z and Tang, J and Mo, X and Wang, J and Yang, Q and Pei, Y and Kuzyakov, Y and Ding, J and Makita, N and Yang, X and Zhang, H and Zhao, Y and Kong, D},
title = {Increased dependence on mycorrhizal fungi for nutrient acquisition under carbon limitation by tree girdling.},
journal = {Plant diversity},
volume = {47},
number = {3},
pages = {466-478},
pmid = {40496994},
issn = {2468-2659},
abstract = {Nutrient acquisition through symbiotic ectomycorrhizal fungi is carbon (C) costly but fundamental for plant growth, community, and ecosystem functioning. Here, we examined the functions of roots and mycorrhiza with respect to nutrient uptake after artificially inducing C limitation-seven months after girdling of an ectomycorrhizal tree, Pinus taeda. Root physiological activity (measured as root nitrogen content and root exudation) declined after girdling and was accompanied with 110% and 340% increases in mycorrhizal colonization and extramatrical hyphal length, respectively. Fungi colonizing roots switched to a community characterized by higher C efficiency (lower C cost) of nutrient acquisition (CENA, the amount of nutrient acquisition per unit C cost) and lower network complexity, indicating a tradeoff between CENA and stability of the fungal community. Root transcriptome analysis suggested a shift in metabolic pathways from a tricarboxylic acid cycle decomposition of carbohydrate to lipid biosynthesis to maintain closer associations with mycorrhiza for nutrient cycling after the girdling. By integrating multi-level evidence, including root transcriptome, fungal composition, and network complexity data, we demonstrate an increased dependence on mycorrhiza for nutrient acquisition under the C limitation condition, which is likely due to a shift to fungal community with higher CENA at the cost of lower stability.},
}

@article {pmid40496370,
year = {2025},
author = {Xia, Y and Liang, C and Luo, H and Zhang, Y},
title = {Therapeutic Potential of Flavonoids and Flavonoid-Rich Compounds in Irritable Bowel Syndrome.},
journal = {Drug design, development and therapy},
volume = {19},
number = {},
pages = {4895-4910},
pmid = {40496370},
issn = {1177-8881},
mesh = {*Flavonoids/pharmacology/therapeutic use/chemistry ; Humans ; *Irritable Bowel Syndrome/drug therapy/physiopathology ; Animals ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Irritable bowel syndrome (IBS) is a group of functional gastrointestinal disorders, characterized by impaired brain-gut axis (BGA) interactions, leading to symptoms such as abdominal pain, bloating, and discomfort, which significantly affect patients' quality of life. Although individuals with IBS are commonly treated with medications and lifestyle modifications, the side effects of various treatments and their inconsistent efficacy often leads to a recurrence that poses a significant burden for patients. Flavonoids, flavonoid-rich compounds extensively found in plants and known for their low toxicity, have been identified as potentially beneficial for various digestive disorders in recent years; however, clinical trials have not been widely conducted. It was suggested that flavonoids and flavonoid-rich compounds may positively influence IBS symptoms through regulation of low-grade inflammation, oxidative stress in the gut, visceral hypersensitivity (VH), intestinal motility dysfunction, dysbiosis of gut microbiome, and BGA. This article reviews the potential role of flavonoids and their compounds in the therapy of IBS, along with the associated mechanisms. Additionally, we highlight key issues that warrant further investigation and discuss the prospects and challenges of using flavonoids for managing IBS.},
}

*Flavonoids/pharmacology/therapeutic use/chemistry
Humans
*Irritable Bowel Syndrome/drug therapy/physiopathology
Animals
Gastrointestinal Microbiome/drug effects

@article {pmid40496345,
year = {2025},
author = {Seneff, S and Nigh, G and Kyriakopoulos, AM},
title = {Is Deuterium Sequestering by Reactive Carbon Atoms an Important Mechanism to Reduce Deuterium Content in Biological Water?.},
journal = {FASEB bioAdvances},
volume = {7},
number = {6},
pages = {e70019},
pmid = {40496345},
issn = {2573-9832},
abstract = {Deuterium is a natural heavy isotope of hydrogen, having a neutron as well as a proton. Deuterium disrupts ATP synthesis in mitochondria, causing increased production of reactive oxygen species and reduced synthesis of ATP. Gut microbes likely play a significant role in providing deuterium depleted short chain fatty acids (SCFAs) to human colonocytes through hydrogen gas recycling. The production of deuterium depleted (deupleted) nutrients necessarily leaves behind deuterium enriched water, unless there is a process that can sequester deuterium in small molecules that are excreted through the feces. Here, we provide evidence that a small number of classes of uniquely structured carbon-nitrogen rings and bis-allylic carbon atoms in certain biologically active small molecules may play a crucial role in sequestering deuterium for export into feces or urine. Specifically, we have identified the imidazole ring present in histidine, histamine, and microbial derivatives of histidine, the tetraterpenoid lutein, bilirubin and the derivatives urobilinogen and stercobilinogen produced by gut microbes, and the bis-allylic carbons in polyunsaturated fatty acids as likely candidates for sequestering deuterium and thereby reducing the deuterium levels in the water-based medium. Normally, carbon atoms never exchange their bound protons with deuterons from the medium, but all the above classes of molecules are important exceptions to this rule, as has been shown experimentally.},
}

@article {pmid40496249,
year = {2025},
author = {Kit, A and Conway, K and Makarowski, S and O'Regan, G and Allen, J and Shultz, SR and Bodnar, TS and Christie, BR},
title = {Can the gut-brain axis provide insight into psilocybin's therapeutic value in reducing stress?.},
journal = {Neurobiology of stress},
volume = {36},
number = {},
pages = {100732},
pmid = {40496249},
issn = {2352-2895},
abstract = {There is growing interest in exploring the therapeutic potential and mechanisms of action of psilocybin on stress-related neuropsychiatric disorders, including depression, generalized anxiety disorder (GAD), post-traumatic stress disorder (PTSD), obsessive-compulsive disorder (OCD), addiction, and disordered eating. Despite promising progressions in preclinical and clinical research, the neurobiological and physiological mechanisms underlying the therapeutic effects of psilocybin remain complex, involving multiple systems with numerous homeostatic feedback signaling pathways throughout the body. This review paper explores how psilocybin mechanistically interacts with the gut microbiota, enteric nervous system, hypothalamic-pituitary axis, and how psilocybin influences the bidirectional communication between peripheral and neuronal systems. Shifting towards a more integrated paradigm to unravel the mechanisms through which psilocybin affects the bidirectional gut-brain axis holds the promise of significantly advancing our understanding of psilocybin-based therapies from preparation of treatment, administration, to proceeding long-term integration. Such an understanding can extend beyond the treatment of psychiatric disorders, further encompassing a broader spectrum of inflammatory-related disorders.},
}

@article {pmid40496070,
year = {2025},
author = {Ali, Z and Ayub, A and Lin, Y and Anis, S and Khan, I and Younas, S and Tahir, RA and Wang, S and Li, J},
title = {Lycium b arbarum's diabetes secrets: A comprehensive review of cellular, molecular, and epigenetic targets with immune modulation and microbiome influence.},
journal = {Journal of pharmaceutical analysis},
volume = {15},
number = {5},
pages = {101130},
pmid = {40496070},
issn = {2214-0883},
abstract = {Diabetes, a metabolic disease stemming from impaired or defective insulin secretion, ranks among the most severe chronic illnesses globally. While several approved drugs exist for its treatment, they often come with multiple side effects. Therefore, there is a pressing need for safe and effective anti-diabetic medications. Traditional Chinese medicine has recognized Lycium barbarum (LB; goji berry) plant, commonly known as "wolfberry fruit" in China, for over 2,000 years. Natural compounds derived from LB show promise in reducing diabetes levels. Although research on the impact of LB on diabetes is still limited, our review aims to explore the potential of LB in reducing the risk of diabetes and examine the underlying mechanisms involved. LB can modulate diabetes through various pathways, such as inhibiting α-amylase and α-glucosidase activities, promoting β-cell proliferation, stimulating insulin secretion, inhibiting glucagon secretion, improving insulin resistance and glucose tolerance, and enhancing antioxidant and anti-inflammatory activities. Additionally, LB improves gut flora and immunomodulation, further aiding diabetes management. These findings highlight the potential clinical utility of LB in managing diabetes and its complications within the framework of evidence-based modern medicine.},
}

@article {pmid40496020,
year = {2025},
author = {Ye, HL and Meng, XQ and Li, H and Sun, X and Lin, WZ and Zhou, LJ and Zhang, J and Hou, C and Xu, S and Chen, BY and Qiu, C and Li, YL and Wang, YL and Yan, LF and Duan, SZ},
title = {Periodontitis aggravates pulmonary fibrosis by Porphyromonas gingivalis-promoted infiltration of neutrophils and Th17 cells.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1595500},
pmid = {40496020},
issn = {2235-2988},
mesh = {Animals ; *Th17 Cells/immunology ; *Porphyromonas gingivalis/immunology/pathogenicity ; *Periodontitis/complications/microbiology/immunology ; Mice ; Disease Models, Animal ; *Neutrophils/immunology ; Humans ; Mice, Inbred C57BL ; Lung/microbiology/pathology ; *Bacteroidaceae Infections/microbiology/immunology/complications ; Interleukin-17/metabolism ; RNA, Ribosomal, 16S/genetics ; Male ; *Neutrophil Infiltration ; *Pulmonary Fibrosis/microbiology/immunology/pathology ; Mouth/microbiology ; Bleomycin ; Female ; Microbiota ; },
abstract = {INTRODUCTION: Idiopathic pulmonary fibrosis (IPF) is a fatal interstitial lung disease. However, the pathogeny of IPF is poorly understood, and therapeutic options are very limited. Periodontitis (PD) is a chronic inflammatory disease that leads to dysbiosis of both the oral microbiome and host immune responses. While previous studies have suggested a PD-IPF association, insights into the mechanisms remain limited.

METHODS: The PD mouse model was established by the ligation of molars and oral inoculation of subgingival plaques from PD patients and subsequently incorporated with a bleomycin-induced pulmonary fibrosis model. The effect of PD on pulmonary fibrosis was determined. Changes of immune cells were analysed using flow cytometry. Moreover, the microbiome changes of the lungs and oral cavity were assessed by 16S rRNA gene sequencing and fluorescence in situ hybridization. Finally, the effect and mechanism of the specific PD pathogen on pulmonary fibrosis were determined.

RESULTS: PD significantly aggravated pulmonary fibrosis in mice by increasing the infiltration of neutrophils and Th17 cells. Neutrophils and Th17 cells are critical in PD-induced aggravation of pulmonary fibrosis, and Th17 cells regulate neutrophils via IL-17A. The PD pathogen Porphyromonas gingivalis (Pg) was detected enriched in both the oral cavity and lungs. Pg was further determined to exacerbate pulmonary fibrosis by increasing the expansion of neutrophils and Th17 cells in mice.

CONCLUSION: PD aggravates pulmonary fibrosis in mice, which is likely induced by Pg-promoted infiltration of neutrophils and Th17 cells. Treatment targeting PD or Pg might be a promising strategy to clinically ameliorate IPF.},
}

Animals
*Th17 Cells/immunology
*Porphyromonas gingivalis/immunology/pathogenicity
*Periodontitis/complications/microbiology/immunology
Mice
Disease Models, Animal
*Neutrophils/immunology
Humans
Mice, Inbred C57BL
Lung/microbiology/pathology
*Bacteroidaceae Infections/microbiology/immunology/complications
Interleukin-17/metabolism
RNA, Ribosomal, 16S/genetics
Male
*Neutrophil Infiltration
*Pulmonary Fibrosis/microbiology/immunology/pathology
Mouth/microbiology
Bleomycin
Female
Microbiota

@article {pmid40495681,
year = {2025},
author = {Xu, P and Uma Mageswary, M and Nisaa, AA and Balasubramaniam, SD and Samsudin, SB and Rusdi, NIBM and Jerip, ARA and Oon, CE and Bakar, MHA and Tan, JJ and Roslan, FF and Kadir, MN and Ismail, EHBE and Sany, SB and Tan, CS and Liong, MT},
title = {Impact of the Probiotic on the Modulation of Vaginal Bacterial and Fungal Microbiota in HPV-Positive Women.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70142},
doi = {10.1002/mnfr.70142},
pmid = {40495681},
issn = {1613-4133},
support = {304/PTEKIND/6501096//USM-Probionic Grant/ ; 1001/PTEKIND/8070037//USM-Industry Research Matching Grant/ ; },
abstract = {This study examined the effects of administering the probiotic Lactiplantibacillus plantarum Probio87 on the vaginal microbiota of HPV-positive women, highlighting alterations in bacterial and fungal communities and their potential influence on vaginal and overall health. In a double-blind, randomized, placebo-controlled study, participants consumed daily doses of Probio87 (1 × 10[9] CFU/sachet) or a placebo for 12 weeks. Vaginal swabs were collected, and DNA was extracted for 16S rRNA and the internal transcribed spacer (ITS) region amplification via PCR, followed by sequencing of bacterial and fungal microbiota. The probiotic group showed improved alpha and beta diversity, with an increase in beneficial Lactobacillus (p = 0.014) and Phascolarctobacterium faecium (p = 0.041), while decreasing the abundance of pathogens like Streptococcus and Candida (p = 0.011). Additionally, vaginal health questionnaires linked probiotic use to improved vaginal and mental health in HPV-positive women. L. plantarum Probio87 demonstrated clinical and psychological benefits in HPV-positive women by balancing the vaginal microbiome, reducing pathogenic species, and promoting the growth of beneficial microorganisms.},
}

@article {pmid40495582,
year = {2025},
author = {Chalmers, JC and Hernandez-Kapila, YL},
title = {The role of the oral microbiome, host response, and periodontal disease treatment in Alzheimer's disease: A primer.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12631},
pmid = {40495582},
issn = {1600-0757},
support = {//OraPharma, Bridgewater, NJ/ ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) is the leading cause of cognitive impairment and dementia in elderly patients worldwide. There is increasing evidence that periodontal disease may have an important role in the complex, multifactorial pathogenesis of AD.

AIM: This narrative review aims to (1) highlight the current understanding of the role of periodontal disease in AD, including molecular and immunological evidence, epidemiological studies, and biological mechanisms linking periodontal disease to AD; and (2) explore the potential impact of periodontal therapy as part of an individualized, multitherapeutic approach to AD.

MATERIALS AND METHODS: A literature search of the PubMed database was conducted using Boolean search strategies to identify publications related to the potential connections between periodontal disease and AD.

RESULTS: Most of the evidence for a link between periodontal disease and AD is limited to preclinical research and epidemiological investigations. A direct causal link has not yet been demonstrated in human clinical studies, but periodontal pathogenic bacteria have been detected in brain tissue and cerebrospinal fluid of patients with AD. Further, colocalization of gingipain proteases secreted by Porphyromonas gingivalis has been found in AD pathological lesions. Epidemiological studies support associations between periodontal disease and increased risk/prevalence of cognitive decline, AD, and AD mortality. Two mechanistic theories have been proposed to explain the connection between periodontitis and AD: the "microbial involvement" theory focuses on periodontal disease-associated pathogenic bacteria, whereas the "inflammatory cascade" theory focuses on proinflammatory mediators as drivers of neuroinflammation that may exacerbate pathologic lesions associated with AD. Preclinical studies of periodontal therapies targeting oral microbiota or their byproducts have investigated small-molecule gingipain inhibitors and novel therapeutics that restore oral microbial homeostasis (e.g., probiotic bacteriocin nisin). In animal models, gingipain inhibitors and nisin showed inhibitory effects on formation of pathological lesions of AD or neuroinflammation and microbiome changes, respectively; however, no impact on cognition was found with use of gingipain inhibitors in patients with mild-to-moderate AD.

CONCLUSIONS: Additional studies are needed to better understand the potential causal relationship between periodontal disease and AD, including further exploration of therapies targeting the oral-brain axis.},
}

@article {pmid40495530,
year = {2025},
author = {Rust, C and Tonge, D and van den Heuvel, LL and Asmal, L and Carr, J and Pretorius, E and Seedat, S and Hemmings, SMJ},
title = {Investigating the Blood Microbiome in Parkinson's Disease, Schizophrenia, and Posttraumatic Stress Disorder.},
journal = {Brain and behavior},
volume = {15},
number = {6},
pages = {e70629},
doi = {10.1002/brb3.70629},
pmid = {40495530},
issn = {2162-3279},
support = {//Stellenbosch University Postgraduate Scholarship Programme/ ; //South African Medical Research Council (SAMRC)/Stellenbosch University Genomics of Brain Disorders (GBD) Extramural Unit/ ; },
mesh = {Humans ; *Parkinson Disease/microbiology/blood ; *Schizophrenia/microbiology/blood ; Male ; *Stress Disorders, Post-Traumatic/microbiology/blood ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Adult ; *Microbiota/physiology/genetics ; },
abstract = {INTRODUCTION: Recent studies have challenged the idea of sterile blood, suggesting the presence of a blood microbiome. The detection of microbial nucleic acids in blood is thought to reflect the status of distant microbial niches, including the gut. However, the origins and viability of these microbes remain debated. In this study, blood microbiome signatures in Parkinson's disease (PD), schizophrenia (SCZ), and posttraumatic stress disorder (PTSD) were evaluated by extracting RNA-sequencing (RNA-seq) reads that did not map to the human genome. Furthermore, we investigated the correlation between the gut and blood microbiome in PD, SCZ, and PTSD to gain insight into possible mechanisms behind disease etiology.

METHODS: We used whole-blood samples from PD (cases: n = 14; controls: n = 19), SCZ (cases: n = 17; controls: n = 22), and PTSD (cases: n = 45; trauma-exposed [TE] controls: n = 34) cohorts. The RNA paired-end sequence reads that did not map to the human reference genome (hg38/GRCH38) were isolated using the sequence alignment/map tools (SAMtools). These unmapped reads were classified against known archaeal, bacterial, and viral microbial genomes using Kraken2 (v2.1.3; k2_standard_08gb_20240112.taz.gz database), and further taxa abundances were estimated using Bracken (v2.9). The differential abundance of blood microbial signatures between case-control groups for each cohort was assessed using DESeq2 (v1.38.3). Each cohort was analyzed separately.

RESULTS: Statistically significant differences in the abundance of Pseudomonas aeruginosa and Acinetobacter wuhouensis in PD and Salmonella enterica, Staphylococcus aureus, Pseudomonas sp. CC6-YY-74, and Shinella sumterensis in SCZ were observed compared to cohort-specific controls. We observed no statistically significant differences in microbial signatures between PTSD cases and controls.

CONCLUSION: We found blood microbial signatures associated with PD and SCZ; however, no significant blood microbial signature was observed for PTSD. These results should be interpreted with caution as biases may have been introduced due to low concentrations of microbial signatures. Further research is required to understand the biological implications of these findings, in particular, taking into account the repurposed data source, and the potential for contamination (during phlebotomy, and background contamination from DNA extraction and reagents) known to impact the analysis of low-biomass samples.},
}

Humans
*Parkinson Disease/microbiology/blood
*Schizophrenia/microbiology/blood
Male
*Stress Disorders, Post-Traumatic/microbiology/blood
Female
Middle Aged
*Gastrointestinal Microbiome
Aged
Adult
*Microbiota/physiology/genetics

@article {pmid40495477,
year = {2025},
author = {Hurst, C and Zobel, G and Young, W and Olson, T and Parkar, N and Bracegirdle, J and Hannaford, R and Anderson, RC and Dalziel, JE},
title = {Social Isolation Induces Sex-Specific Differences in Behavior and Gut Microbiota Composition in Stress-Sensitive Rats.},
journal = {Brain and behavior},
volume = {15},
number = {6},
pages = {e70621},
doi = {10.1002/brb3.70621},
pmid = {40495477},
issn = {2162-3279},
support = {//Smarter Lives: New opportunities for dairy products across the lifespan/ ; C10X1706//Ministry of Business, Innovation and Employment/ ; },
mesh = {Animals ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Rats ; *Social Isolation/psychology ; *Stress, Psychological/microbiology/physiopathology ; *Behavior, Animal/physiology ; Rats, Inbred WKY ; Anxiety ; *Sex Characteristics ; Sex Factors ; Cecum/microbiology ; },
abstract = {BACKGROUND: Social isolation (SI) is an established rat model of chronic stress. We applied this to the stress-sensitive Wistar Kyoto (WKY) strain to explore brain-to-gut interactions associated with mood. Whether SI stress-induced behavioral changes are sex-specific or if they affect the microbiome in WKY is unknown. We hypothesized individually housed (IH) animals would be more anxious than pair-housed (PH), with sex differences. Male and female rats were either IH or PH from 70 to 112 days old and behavior was assessed in modified open field (OFTmod), elevated plus maze (EPM), and novel object recognition (NOR) tests. Cecal content DNA was analyzed by shotgun metagenome sequencing.

RESULTS: IH rats, particularly females, spent more time in the center of the OFTmod where the semi-novel feed was presented compared to PH group rats. There was a tendency for greater distance traveled, or potential hyperactivity, in IH female rats. Males stayed in the EPM closed arms more than females. No treatment difference occurred for recognition memory. SI altered cecal microbiome composition in females where housing was associated with seven differentially abundant taxa and 49 differentially abundant KEGG Level 3 ortholog/gene categories. Several relationships were noted between behavioral traits and relative abundance of microbiome taxa. There was a greater shift in female microbiome composition.

CONCLUSIONS: In summary, behavioral responses to the housing treatment were minimal. IH animals, particularly females, spent more time in the center of an OFT that contained food; this may have been an indication of depression, as opposed to anxiety. Housing status had a differential impact on the microbiome for females compared to males. The associations between cecal microbiota and activity in the modified OFT suggest that dietary interventions that influence the relative abundance of Bifidobacteria, Alistipes, and Muribaculaceae should be explored.},
}

Animals
Male
Female
*Gastrointestinal Microbiome/physiology
Rats
*Social Isolation/psychology
*Stress, Psychological/microbiology/physiopathology
*Behavior, Animal/physiology
Rats, Inbred WKY
Anxiety
*Sex Characteristics
Sex Factors
Cecum/microbiology

@article {pmid40495475,
year = {2025},
author = {Wang, JY and Dunon, V and Ardevol, VN and Béguet, J and Jechalke, S and Pauwelyn, E and Lavigne, R and Smalla, K and Martin-Laurent, F and Springael, D},
title = {Dynamics of IS1071 and Its Accessory Gene Functions During Start-Up of an On-Farm Biopurification System.},
journal = {Environmental microbiology},
volume = {27},
number = {6},
pages = {e70120},
doi = {10.1111/1462-2920.70120},
pmid = {40495475},
issn = {1462-2920},
support = {222625//European Union's 7th Framework Programme (FP7) for Research and Technological Development/ ; RUN/19/001//KU Leuven/ ; C14/20/063//KU Leuven/ ; G0E8122N//the Research Foundation - Flanders (FWO) and the National Natural Science Foundation of China (NSFC)/ ; 202107650033//China Scholarship Council Fellowship/ ; },
mesh = {*DNA Transposable Elements/genetics ; *Microbiota/genetics ; *Pesticides/metabolism ; *Bacteria/genetics/metabolism/classification ; Wastewater/microbiology ; Farms ; Biodegradation, Environmental ; Betaproteobacteria/genetics/metabolism ; },
abstract = {Insertion sequences (IS) are drivers of bacterial diversification by facilitating recruitment and horizontal transfer of adaptive genes involving composite transposon structures, but their evolutionary role at the community level is rarely addressed. This study explores the dynamics of IS1071 and the cargo of IS1071-associated putative composite transposons in the establishment of a pesticide-degrading microbiome in an on-farm biopurification system (BPS)-which treats pesticide-contaminated wastewater and is considered a hotspot of microbial evolution-during the crucial start-up phase. Pesticide mineralisation assays and quantitative PCR targeting pesticide catabolic genes showed that the microbial community, upon feeding on the pesticide-contaminated wastewater, rapidly evolved into a pesticide-degrading microbiome. Concomitantly, an increase in the relative abundances of several mobile genetic elements, including IS1071, was observed, as well as a striking enrichment of xenobiotic catabolic genes in the cargo of putative IS1071-flanked composite transposons. The IS1071 cargo catabolic genes diversified over time and were mainly of Betaproteobacterial origin. Clear changes in community composition were observed both in the total bacterial community and the Betaproteobacterial community. We conclude that IS1071 supports the rapid establishment of pesticide catabolism in the BPS microbiome, highlighting the contribution of IS elements to microbial community adaptation to environmental changes.},
}

*DNA Transposable Elements/genetics
*Microbiota/genetics
*Pesticides/metabolism
*Bacteria/genetics/metabolism/classification
Wastewater/microbiology
Farms
Biodegradation, Environmental
Betaproteobacteria/genetics/metabolism

@article {pmid40495401,
year = {2025},
author = {Avendaño-Herrera, R and Tralma, L and Wicki, H and Barrios-Henríquez, F and Levipan, HA},
title = {Skin-Mucus Prokaryote Community of Atlantic Salmon (Salmo salar) in Response to Bath Challenge With Tenacibaculum dicentrarchi.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e14157},
doi = {10.1111/jfd.14157},
pmid = {40495401},
issn = {1365-2761},
support = {FONDECYT 1230068//Agencia Nacional de Investigación y Desarrollo/ ; FONDECYT Iniciación 11200708//Agencia Nacional de Investigación y Desarrollo/ ; FONDAP 1523A0007//Agencia Nacional de Investigación y Desarrollo/ ; },
abstract = {Fish skin mucus is continuously replaced by epidermal cells, making it a highly dynamic microenvironment and an effective barrier against waterborne pathogens. The objective of this study was to understand the effects of tenacibaculosis, caused by the bacterium Tenacibaculum dicentrarchi, on the skin-associated microbiome of Atlantic salmon (Salmo salar). We used a vector-free and waterborne infection model of T. dicentrarchi strain TdCh05 in Atlantic salmon smolts for 21 days. Skin swab samples were collected at 2 h and 21 days post-infection (hpi and dpi, respectively) for 16S rRNA gene amplicon sequencing using DNA or complementary DNA (cDNA) as templates. Non-metric multidimensional scaling analysis grouped the samples into distinct clusters depending on the treatment and template. Similarity-Percentage (SIMPER) analysis indicated that between ~42% and 43% of the total amplicon sequence variants (ASVs) across all samples accounted for 90% of the compositional differences among all treatments and the two templates, highlighting the contribution of Tenacibaculum ASVs. Comparisons (by SIMPER) between non-infected and TdCh05-challenged fish at 2 hpi indicated that Tenacibaculum ASVs contributed to between ~52% and 58% of the differences in compositional clustering between samples. A significant drop in skin-mucus alpha diversity in TdCh05-challenged fish was also detected, followed by alpha diversity recovery at 21 dpi. In turn, at 21 dpi, microbiome changes were related to higher interaction complexity among taxa and community instability. Furthermore, 16S cDNA-based sequencing indicated that the potential activity of the Atlantic salmon skin-associated microbiome during disease progression was primarily driven by Tenacibaculum spp. Further research is needed to elucidate the role of other potentially active components (e.g., Pseudomonadales) of the skin-associated microbiome for the onset and/or progression of tenacibaculosis.},
}

@article {pmid40495357,
year = {2025},
author = {Brunetti, K and Zhou, Z and Shuchi, S and Berry, R and White, S and Zhang, Y and Allen, MS and Yang, S and Figueroa, JD and Colon-Perez, L},
title = {Longitudinal and Concurrent Changes in Brain and Gut due to Morphine Self-Administration.},
journal = {Addiction biology},
volume = {30},
number = {6},
pages = {e70059},
doi = {10.1111/adb.70059},
pmid = {40495357},
issn = {1369-1600},
support = {28334//Brain and Behavior Research Foundation/ ; K25DA047458/NH/NIH HHS/United States ; },
mesh = {Animals ; *Morphine/administration & dosage/pharmacology ; Self Administration ; Magnetic Resonance Imaging ; Male ; *Brain/diagnostic imaging/drug effects ; Rats ; *Gastrointestinal Microbiome/drug effects ; *Analgesics, Opioid/administration & dosage/pharmacology ; Feces/microbiology ; Rats, Sprague-Dawley ; *Brain-Gut Axis/drug effects ; },
abstract = {Opioid agonists are known for their effects on the opioid and dopaminergic systems; however, new research points to complementary changes in the gut underlying maladaptive changes associated with opioid use. The gut-brain axis (GBA) is a bidirectional signaling process that permits feedback between the brain and gut and is altered in subjects with opioid use disorders, but the spatiotemporal correspondence between quantitative translational measures of gut and brain health is not clear. In this work, we determined longitudinal and concurrent changes in the brain and gut of rodents trained to self-administer morphine for 14 days. Active lever presses delivered a single infusion of morphine (0.4 mg/kg/infusion). We used MRI and 16s rDNA analysis of faecal matter to identify changes from baseline (naïve, nondrug state) to an acute phase (early in the self-administration process, after 2 days of self-administration) and a chronic phase (late in the self-administration process, after 14 days of self-administration). Animals were scanned in a 7T MRI scanner three times (baseline, acute and chronic), and before scanning, faecal matter was collected from each rat. We found early changes in gut microbiota diversity and specific abundance as early as the acute phase that persisted into the chronic phase. In MRI, we identified alterations in diffusivity indices both within subjects and between groups, showing a main effect in the striatum and thalamus. We posit that gut changes precede the effects observed in MRI, with the striatum and thalamus emerging as crucial links mediating communication between the gut and the brain.},
}

Animals
*Morphine/administration & dosage/pharmacology
Self Administration
Magnetic Resonance Imaging
Male
*Brain/diagnostic imaging/drug effects
Rats
*Gastrointestinal Microbiome/drug effects
*Analgesics, Opioid/administration & dosage/pharmacology
Feces/microbiology
Rats, Sprague-Dawley
*Brain-Gut Axis/drug effects

@article {pmid40495179,
year = {2025},
author = {Liu, W and Zhou, X and Xiao, L and Huang, X and Chang, D and Zhong, X and Zeng, M and Xian, Y and Zheng, Y and Huang, W and Huang, R and Huang, M},
title = {The gut microbiota-mediated ferroptosis pathway: a key mechanism of ginsenoside Rd against metabolism-associated fatty liver disease.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {83},
pmid = {40495179},
issn = {1749-8546},
support = {2022YFC3501200//National Key Research and Development Program of China/ ; 82274080//National Natural Science Foundation of China Projects/ ; X2024019//School Management Project of Fujian University of Traditional Chinese Medicine/ ; X2024035//School Management Project of Fujian University of Traditional Chinese Medicine/ ; 2024Y9511//Fujian Provincial Science and Technology Innovation Joint Fund Project/ ; },
abstract = {BACKGROUND: Ginsenoside Rd (G-Rd), found in Panax species, has shown therapeutic potential against metabolism-associated fatty liver disease (MAFLD), but its mechanism has not been well elucidated. This study investigated the key mechanisms of G-Rd in modulating the gut microbiome and lipid peroxidation-mediated ferroptosis pathway in MAFLD.

METHODS: A high-fat diet-induced MAFLD model was established. Ultrastructural changes in liver tissue were observed using transmission electron microscopy. Metagenomics were employed to detect alterations in gut microbiota and their metabolites. Biochemical analysis and immunohistochemistry were used to examine liver injury, blood lipids, lipid peroxidation-related indicators, and tissue iron content.

RESULTS: G-Rd significantly reduced liver injury and steatosis in MAFLD mice and downregulated the elevated relative abundance of Firmicutes and the Firmicutes/Bacteroidetes ratio. It also significantly reduced the abundances of Faecalibaculum rodentium while increasing Muribaculum intestinale, with its functional role being relevant to lipid metabolism regulation. Moreover, G-Rd ameliorated mitochondrial damage and inhibited the ferroptosis pathway in the liver, which was associated with antioxidant-related factors mediated by Nrf2 signaling. The liver protective effect of G-Rd was driven by the regulation of gut microbiota, as demonstrated by antibiotic cocktail treatment and fecal microbiota transplantation.

CONCLUSIONS: G-Rd attenuated HFD-induced MAFLD by alleviating liver oxidative stress, lipid peroxidation, and ferroptosis through modulation of the gut microbiota. The antioxidant and anti-ferroptotic actions of G-Rd, mediated via the Nrf2 pathway, were found to contribute to the amelioration of liver injury and hepatic steatosis in MAFLD.},
}

@article {pmid40495162,
year = {2025},
author = {Wei, S and Shen, R and Lu, X and Li, X and He, L and Zhang, Y and Huang, X and Shu, Z},
title = {Integrative multi-omics investigation of sleep apnea: gut microbiome metabolomics, proteomics and phenome-wide association study.},
journal = {Nutrition & metabolism},
volume = {22},
number = {1},
pages = {57},
pmid = {40495162},
issn = {1743-7075},
abstract = {BACKGROUND: Sleep apnea (SA) is linked to various diseases. This study examines the causal link between the gut microbiome and SA, exploring potential predictive factors and target proteins using a multi-omics approach with a Phenome-wide association study (PheWAS).

METHODS: Bidirectional Mendelian Randomization (MR) and Linkage Disequilibrium Score Regression (LDSC) were used to assess the genetic correlation and causal relationships between the gut microbiome and SA. Mediation analysis identified intermediate relationships involving "gut microbiome-inflammatory proteins-SA." Two-sample MR and colocalization analysis in the deCODE and UK Biobank Pharma Proteomics Project (UKB-PPP) databases identified protein quantitative trait loci (pQTL) associated with SA. Validation analysis used Fenland proteins, methylation quantitative trait loci (mQTL), and expression quantitative trait loci (eQTL). PheWAS screened 29 SA-associated SNPs and matched control SNPs (4:1 ratio) from UK Biobank data chosen through MR and LDSC analyses.

RESULTS: Inverse-variance weighted (IVW) bidirectional MR analysis did not establish a causal link between the gut microbiome and SA. C-C motif chemokine 28 showed causal relationships in both directions (forward IVW, P = 0.0336; reverse IVW, P = 0.0336). Intermediate connections were found between the Holdemanella genus and urinary plasminogen activator levels with SA. TIMP4 protein had a significant causal relationship with SA(IVW method: P > 0.05, PH4 = 96.1%; P = 7.85 × 10[-6], PH4 in deCODE = 97.4%). PRIM1 and BMP8 A were identified as potential influencers of SA through mQTL and eQTL analyses. PheWAS suggested body impedance and predicted mass as potential predictors of SA.

CONCLUSION: Bidirectional causal relationships exist between SA and inflammatory proteins, with TIMP4 identified as a pathogenic factor and potential therapeutic target. PRIM1 and BMP8 A may impact SA risk. Body impedance and predicted mass predict SA significantly.},
}

@article {pmid40494952,
year = {2025},
author = {Kerr, TD and Silver, NL and Duggal, R and Dai, J and Simmons, H and Singh, S and Shah, AA and Fredenburg, KM and Stacy, AR and McGrail, DJ},
title = {HPV status impacts oncobacteria abundance and prognostic relevance in head and neck squamous cell carcinoma.},
journal = {Oncogene},
volume = {},
number = {},
pages = {},
pmid = {40494952},
issn = {1476-5594},
support = {R00CA240689//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; K08DE029503//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
abstract = {The intratumoral microbiome is emerging as an intrinsic microenvironment feature of some cancers, most notably those along the digestive tract. Opportunistic pathogenic bacteria, such as Fusobacterium nucleatum, can enrich within certain tumors, ultimately leading to alterations in the tumor microenvironment. However, why some tumors have a higher abundance of tumor-associated bacteria, or oncobacteria, than others remains unknown. To address this question, we quantified the presence of oncobacteria in head and neck squamous cell carcinomas (HNSCCs). We found that accumulation of oncobacteria was independent of tumor stage and size, as well as patient characteristics. In contrast, we discovered that human papillomavirus (HPV)-negative tumors exhibited significantly higher accumulation of oncobacteria than HPV+ tumors. Furthermore, the abundance of oncobacteria was associated with worse overall survival in HPV+ tumors. These findings were validated in an independent cohort. Subsequent analysis of Epstein-Barr virus (EBV)+ gastric cancer suggests this phenomenon generalizes to other virally mediated cancers. Co-culture studies of HNSCC cell lines with Fusobacterium nucleatum demonstrated that HPV-negative cells have enhanced proliferation in the presence of Fusobacterium nucleatum compared to HPV+ cells, suggestive of tumor cell intrinsic determinants of oncobacteria accumulation. Together, these results illuminate tumor features that contribute to the accumulation of oncobacteria.},
}

@article {pmid40494940,
year = {2025},
author = {Yajima, S and Kobayashi, S and Hashimoto, T and Nakamura, Y and Yamashita, R and Misumi, T and Sakamoto, Y and Horasawa, S and Fujisawa, T and Imai, M and Shibuki, T and Tsukada, Y and Bando, H and Masuda, H and Yoshino, T},
title = {Physical activity and cancer biology: a narrative review of molecular mechanisms and introduction of the SCRUM-MONSTAR LIFELOG study.},
journal = {International journal of clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {40494940},
issn = {1437-7772},
support = {JP25ck0106950h0002//Japan Agency for Medical Research and Development/ ; 2024-A-05//National Cancer Center Research Development Fund/ ; },
abstract = {BACKGROUND: Physical activity (PA) has been consistently associated with improved cancer outcomes across multiple epidemiological studies. While the evidence for clinical benefits is strong, the underlying molecular mechanisms remain poorly understood. Recent technological advances now enable both continuous monitoring of PA through wearable devices and comprehensive molecular profiling through multi-omics approaches, including whole-genome sequencing (WGS)-based molecular residual disease (MRD) detection. This review examines current evidence regarding PA's effects on cancer biology and introduces the LIFELOG study, which aims to address critical knowledge gaps in this field.

METHODS: We review the current literature on PA and cancer with emphasis on molecular mechanisms, and present the design of the LIFELOG study, an ancillary study to MONSTAR-SCREEN-3. The LIFELOG study will enroll 170 post-surgical cancer patients who will wear the mSafety™ wrist device for continuous PA monitoring. We will investigate associations between PA metrics and multi-omics profiles including WGS-based MRD detection, transcriptome analyses, plasma proteomics, and gut microbiome analyses. The feasibility phase has already begun with encouraging preliminary results regarding device compliance and data quality.

DISCUSSION: Despite substantial evidence supporting PA's benefits in cancer prevention and survivorship, understanding which specific PA characteristics most effectively influence cancer outcomes remains unclear. The LIFELOG study represents the first comprehensive analysis integrating continuous PA monitoring with molecular profiling in cancer patients. By examining relationships between PA patterns and both MRD dynamics and multi-omics profiles, we aim to identify molecular mechanisms underlying exercise benefits and potentially guide development of evidence-based, precision PA interventions for cancer survivorship.

TRIAL REGISTRATION: This ancillary study (Institutional Review Board number: 2024-111, approved on November 18, 2024) is conducted under the MONSTAR-SCREEN-3 trial platform, which is registered in the UMIN Clinical Trials Registry (UMIN000053975, registered on March 27, 2024).},
}

@article {pmid40494904,
year = {2025},
author = {Mawarda, PC and van der Kaaij, R and Dini-Andreote, F and Duijker, D and Stech, M and Speksnijder, AG},
title = {Unveiling the ecological processes driving soil and lichen microbiome assembly along an urbanization gradient.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {99},
pmid = {40494904},
issn = {2055-5008},
support = {NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; PEN04908//The USDA National Institute of Food and Agriculture and Hatch Appropriations/ ; },
mesh = {*Soil Microbiology ; *Lichens/microbiology/classification ; *Microbiota ; *Urbanization ; Biodiversity ; *Bacteria/classification/genetics/isolation & purification ; Ecosystem ; Soil/chemistry ; },
abstract = {Global biodiversity loss is accelerating due to the transformation of natural landscapes into agricultural and urban areas. Yet, research on the urbanization impact on environmental and host-associated microbiomes, particularly on the ecological processes that mediate their assembly and function, remains scarce. This study investigated the effects of an urbanization gradient on the diversity and assembly processes of the soil microbiome and the microbiomes of three epiphytic lichen species (Candelaria concolor, Physcia adscendens, and Xanthoria parietina). Our findings revealed that the urbanization gradient shaped the soil microbiome, while the lichen microbiomes exhibited strong host specificity and showed no significant changes in diversity along the urbanization gradient. Heterogeneous selection and dispersal limitation primarily governed the soil community assembly and higher community turnover in medium- and highly urbanized zones compared to low-urbanized zones, indicating an increased influence of environmental pressures, altered resources, and habitat fragmentation in more urbanized areas. The lichen microbiome assembly in each species was primarily governed by undominated processes regardless of urbanization level, indicating that both selection and stochasticity contributed to, but neither dominantly influenced, their assembly. The lichen microbiomes further revealed species-specific co-occurrence networks, with microbial compositional signatures and potential functions being essential for lichen fitness and urban ecosystem health. Taken together, our study contributes to understanding how microbial communities are assembled in urban environments, bridging the gap between conceptual theories and empirical findings in the urban ecology of soil and lichen-associated microbiomes.},
}

*Soil Microbiology
*Lichens/microbiology/classification
*Microbiota
*Urbanization
Biodiversity
*Bacteria/classification/genetics/isolation & purification
Ecosystem
Soil/chemistry

@article {pmid40494898,
year = {2025},
author = {Xu, F and Guo, Y and Thomas, SC and Saxena, A and Hwang, S and Vardhan, M and Li, X},
title = {Succinate modulates oral dysbiosis and inflammation through a succinate receptor 1 dependent mechanism in aged mice.},
journal = {International journal of oral science},
volume = {17},
number = {1},
pages = {47},
pmid = {40494898},
issn = {2049-3169},
support = {DE027074//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; DE028212//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; AG055787//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; },
mesh = {Animals ; *Dysbiosis/metabolism ; Mice ; *Succinic Acid/metabolism ; Mice, Knockout ; *Receptors, G-Protein-Coupled/metabolism ; *Inflammation/metabolism ; *Aging ; Alveolar Bone Loss/metabolism ; *Mouth/microbiology ; Mice, Inbred C57BL ; Male ; Microbiota ; },
abstract = {Aging involves the accumulation of various forms of molecular and cellular damage over time. Key features of aging, such as mitochondrial dysfunction, dysbiosis, and oxidative stress, are closely linked and largely driven by inflammation. This study examines the role of succinate, a key metabolite produced and utilized by cells of both host and microbes, and its receptor, succinate receptor 1 (SUCNR1), in age-related oral dysbiosis and inflammation. We examined young and aged wild-type (WT) and SUCNR1 knockout (KO) mice for this analysis. Our findings revealed significant aging-associated alveolar bone loss and succinate elevation in aged WT mice, along with notable changes in the oral microbiome. Conversely, aged KO mice showed reduced bone loss, lower succinate levels, less inflammation, and better-maintained microbial function. These results suggest that SUCNR1 is crucial in influencing aging-related succinate elevation, oral dysbiosis, and inflammation. Analysis of gene families and pathways in the oral microbiome demonstrated distinct aging-related changes between WT and KO mice, with the functional potential being preserved in the KO-aged group. This study underscores the importance of succinate elevation and signaling through SUCNR1 in regulating inflammation, alveolar bone loss, and shifts in the oral microbiome, offering potential targets for therapeutic interventions in age-related oral health issues.},
}

Animals
*Dysbiosis/metabolism
Mice
*Succinic Acid/metabolism
Mice, Knockout
*Receptors, G-Protein-Coupled/metabolism
*Inflammation/metabolism
*Aging
Alveolar Bone Loss/metabolism
*Mouth/microbiology
Mice, Inbred C57BL
Male
Microbiota

@article {pmid40494670,
year = {2025},
author = {McDowall, LS and McDermott, K},
title = {Review: Opportunities and challenges for the pork industry from circular livestock waste management systems.},
journal = {Animal : an international journal of animal bioscience},
volume = {},
number = {},
pages = {101547},
doi = {10.1016/j.animal.2025.101547},
pmid = {40494670},
issn = {1751-732X},
abstract = {Slurry management is becoming increasingly important as countries work to decarbonise towards Net Zero goals. After feed, slurry management and application is one of the main contributors to the greenhouse gas emissions and environmental pollution associated with pork production. Whilst traditionally considered a waste product, slurry is rich in nutrients and could be harnessed to reduce environmental impacts and improve on-farm resilience. Along with reducing the environmental impacts of pork production, farmers are increasingly looking to diversify their income streams and pig slurry offers tremendous potential to achieve this. This review identifies the opportunities and challenges to the pork sector from circular, sustainable waste management systems through insect bioconversion or on-farm biogas production, with a focus on the United Kingdom. Insect bioconversion of pig slurry, through the use of Black Soldier Fly larvae, presents opportunities not only to reduce the overall volume of slurry on a farm but also to reduce heavy metal contamination, alter the microbiome and provide a myriad of additional products. These products include fertiliser in the form of insect frass, protein, oils, and chitin from the insect exoskeleton, which has applications in industries such as wastewater treatment, pharmaceuticals and healthcare. Through on-farm biogas generation, farmers, particularly those in rural areas, could reduce their reliance upon volatile energy prices and generate electricity and heat to power on-farm activities. With additional infrastructure, biogas could be upgraded to produce biofuel and CO2 could be recovered, recycled, and sold into a variety of industries. Whilst there are still a number of outstanding questions that need to be answered and challenges that need to be addressed before the wide-scale rollout of these technologies, there is huge potential to harness the power of pig slurry. When designing the farm of the future, solutions will likely need to be tailored to an individual farm due to a range of variables including the stage of production, the number of pigs, the pig diet and the availability of co-products. However, despite these potential challenges, there is still considerable opportunity for the pork sector to harness this 'waste' product to decarbonise pig production and improve farm resilience.},
}

@article {pmid40493817,
year = {2025},
author = {Poole, R and Soffa, D and Hickman, K and Ognibene, O and Stuehr, M},
title = {Reproductive microbiota in humans: characterization and role in infertility.},
journal = {Systems biology in reproductive medicine},
volume = {71},
number = {1},
pages = {229-245},
doi = {10.1080/19396368.2025.2511323},
pmid = {40493817},
issn = {1939-6376},
mesh = {Humans ; Female ; *Microbiota ; Dysbiosis/microbiology ; *Infertility/microbiology ; Male ; *Infertility, Female/microbiology ; *Reproduction ; },
abstract = {Advancements in next generation sequencing technologies, including 16S rRNA amplicon sequencing, have vastly expanded our understanding of reproductive microbiota and its role in fertility. For example, in humans, the bacterial genus of Lactobacillus is the overwhelmingly dominant commensal bacterium within reproductive tissues and fluids, such as the vagina, and is an indicator of fertility in women. Shifts away from Lactobacillus allow for opportunistic pathogenic bacteria to inhabit the reproductive tract and result in dysbiosis and infertility. The goal of this review is to explore human reproductive microbiota including bacteria that commensally inhabit reproductive tissues and fluids as well as opportunistic pathogenic bacteria that can result in dysbiosis, infertility, and disease. Continued exploration of the microbiome and its association with reproductive health will aid in the development of targeted therapeutic strategies to positively modulate bacteria and improve fertility.},
}

Humans
Female
*Microbiota
Dysbiosis/microbiology
*Infertility/microbiology
Male
*Infertility, Female/microbiology
*Reproduction