@article {pmid40052570,
year = {2025},
author = {Shen, M and Gao, S and Zhu, R and Wang, W and Gao, W and Tao, L and Chen, W and Zhu, X and Yang, Y and Xu, T and Zhao, T and Jiao, N and Zhi, M and Zhu, L},
title = {Multimodal Metagenomic Analysis Reveals Microbial InDels as Superior Biomarkers for Pediatric Crohn's Disease.},
journal = {Journal of Crohn's & colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjaf039},
pmid = {40052570},
issn = {1876-4479},
abstract = {BACKGROUND AND AIMS: The gut microbiome is closely associated with pediatric Crohn's disease (CD), while the multidimensional microbial signature and their capabilities for distinguishing pediatric CD are underexplored. This study aims to characterize the microbial alterations in pediatric CD and develop a robust classification model.

METHODS: A total of 1,175 fecal metagenomic sequencing samples, predominantly from three cohorts of pediatric CD patients, were re-analyzed from raw sequencing data using uniform process pipelines to obtain multidimensional microbial alterations in pediatric CD, including taxonomic profiles, functional profiles, and multi-type genetic variants. Random forest algorithms were used to construct classification models after comparing multiple machine learning algorithms.

RESULTS: We found pediatric CD samples exhibited reduced microbial diversity and unique microbial characteristics. Pronounced abundance differences in 45 species and 1,357 KO genes. Particularly, Enterocloster bolteae emerged as a pivotal pediatric CD-associated species. Additionally, we identified a vast amount of microbial genetic variants linked to pediatric CD, including 192 structural variants, 1,256 insertions/deletions (InDels), and 3,567 single nucleotide variants, with a considerable portion of these variants occurred in non-genic regions. The InDel-based model outperformed other predictive models against multidimensional microbial signatures, achieving an AUC of 0.982. The robustness and disease specificity were further confirmed in an independent CD cohort (AUC=0.996) and five other microbiome-associated pediatric cohorts.

CONCLUSIONS: Our study provided a comprehensive landscape of microbial alterations in pediatric CD and introduced a highly effective diagnostic model rooted in microbial InDels, which contributes to the development of the non-invasive diagnostic tools and targeted therapies.},
}

@article {pmid40052450,
year = {2025},
author = {Qian, Z and Chen, S and Liao, X and Xie, J and Xu, Y and Zhong, H and Ou, L and Zuo, X and Xu, X and Peng, J and Wu, J and Cai, S},
title = {Decreased intestinal abundance of Akkermansia muciniphila is associated with metabolic disorders among people living with HIV.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2474730},
doi = {10.1080/07853890.2025.2474730},
pmid = {40052450},
issn = {1365-2060},
mesh = {Humans ; Male ; *HIV Infections/complications/microbiology ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; *Akkermansia ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; Prospective Studies ; Feces/microbiology ; Metagenomics/methods ; Hyperlipidemias/microbiology ; Metabolic Diseases/microbiology/epidemiology ; Verrucomicrobia/isolation & purification ; Overweight/microbiology/complications ; },
abstract = {BACKGROUND: Previous studies have shown changes in gut microbiota after human immunodeficiency virus (HIV) infection, but there is limited research linking the gut microbiota of people living with HIV (PLWHIV) to metabolic diseases.

METHODS: A total of 103 PLWHIV were followed for 48 weeks of anti-retroviral therapy (ART), with demographic and clinical data collected. Gut microbiome analysis was conducted using metagenomic sequencing of fecal samples from 12 individuals. Nonalcoholic fatty liver disease (NAFLD) was diagnosed based on controlled attenuation parameter (CAP) values of 238 dB/m from liver fibro-scans. Participants were divided based on the presence of metabolic disorders, including NAFLD, overweight, and hyperlipidemia. Akkermansia abundance in stool samples was measured using RT-qPCR, and Pearson correlation and logistic regression were applied for analysis.

RESULTS: Metagenomic sequencing revealed a significant decline in gut Akkermansia abundance in PLWHIV with NAFLD. STAMP analysis of public datasets confirmed this decline after HIV infection, while KEGG pathway analysis identified enrichment of metabolism-related genes. A prospective cohort study with 103 PLWHIV followed for 48 weeks validated these findings. Akkermansia abundance was significantly lower in participants with NAFLD, overweight, and hyperlipidemia at baseline, and it emerged as an independent predictor of NAFLD and overweight. Negative correlations were observed between Akkermansia abundance and both CAP values and body mass index (BMI) at baseline and at week 48. At the 48-week follow-up, Akkermansia remained a predictive marker for NAFLD.

CONCLUSIONS: Akkermansia abundance was reduced in PLWHIV with metabolic disorders and served as a predictive biomarker for NAFLD progression over 48 weeks of ART.},
}

Humans
Male
*HIV Infections/complications/microbiology
Female
*Gastrointestinal Microbiome
Middle Aged
Adult
*Akkermansia
*Non-alcoholic Fatty Liver Disease/microbiology/metabolism
Prospective Studies
Feces/microbiology
Metagenomics/methods
Hyperlipidemias/microbiology
Metabolic Diseases/microbiology/epidemiology
Verrucomicrobia/isolation & purification
Overweight/microbiology/complications

@article {pmid40051875,
year = {2025},
author = {De Troyer, L and Audenaert, K and Ommeslag, S and Debode, J and De Gelder, L and De Zutter, N},
title = {The biocontrol agent Streptomyces rimosus subsp. rimosus tempers shifts in the wheat spicosphere microbiome induced by Fusarium Head Blight.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1540242},
pmid = {40051875},
issn = {1664-462X},
abstract = {INTRODUCTION: Fusarium Head Blight (FHB) is a major fungal disease in wheat caused by Fusarium graminearum, inducing severe yield losses. Biological control agents (BCAs) can be an effective and sustainable approach to mitigate this phytopathogen. In this study, Streptomyces rimosus subsp. rimosus LMG19352 was used as a BCA to mitigate F. graminearum on wheat ears. Moreover, we aimed to assess the impact of BCA inoculation on non-target microorganisms present on the wheat spikes. Therefore, we evaluated shifts in the fungal and bacterial spicosphere microbiome (i) over time from flowering to mid-grain filling stage and (ii) across inoculations with F. graminearum and/or S. rimosus subsp. rimosus LMG19352.

METHODS: FHB symptoms were determined by multispectral imaging, and Illumina MiSeq was used to amplify 16S V3-V4 rDNA for bacteria and ITS2 for fungi, whereafter a correlation network analysis was performed.

RESULTS: The biocontrol potential of S. rimosus subsp. rimosus LMG19352 against F. graminearum was confirmed, as FHB symptoms were significantly reduced. Based on the microbial abundances, S. rimosus subsp. rimosus LMG19352 compensated for shifts in the spicosphere microbiome community induced by FHB. These results were supported by a network analysis, revealing a more complex and stable microbiome in the presence of the BCA compared to the infected control.

DISCUSSION: To our knowledge, this study is the first to reveal the potential of a bacterial BCA to temper shifts in the wheat microbiome caused by a phytopathogen, and thereby acting as a promising BCA.},
}

@article {pmid40051835,
year = {2025},
author = {Zhou, J and Sun, Z and Wang, X and Wang, S and Jiang, W and Tang, D and Xia, T and Xiao, F},
title = {Low-temperature cold plasma promotes wound healing by inhibiting skin inflammation and improving skin microbiome.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1511259},
pmid = {40051835},
issn = {2296-4185},
abstract = {Wound healing includes four consecutive and overlapping stages of hemostasis, inflammation, proliferation, and remodeling. Factors such as aging, infection, and chronic diseases can lead to chronic wounds and delayed healing. Low-temperature cold plasma (LTCP) is an emerging physical therapy for wound healing, characterized by its safety, environmental friendliness, and ease of operation. This study utilized a self-developed LTCP device to investigate its biological effects and mechanisms on wound healing in adult and elderly mice. Histopathological studies found that LTCP significantly accelerated the healing rate of skin wounds in mice, with particularly pronounced effects in elderly mice. LTCP can markedly inhibit the expression of pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) and senescence-associated secretory phenotype factors (MMP-3, MMP-9), while significantly increasing the expression of tissue repair-related factors, such as VEGF, bFGF, TGF-β, COL-I, and α-SMA. It also regulated the expression of genes related to cell proliferation and migration (Aqp5, Spint1), inflammation response (Nlrp3, Icam1), and angiogenesis (Ptx3, Thbs1), promoting cell proliferation and inhibit apoptosis. Furthermore, LTCP treatment reduced the relative abundance of harmful bacteria such as Delftia, Stenotrophomonas, Enterococcus, and Enterobacter in skin wounds, while increasing the relative abundance of beneficial bacteria such as Muribaculaceae, Acinetobacter, Lachnospiraceae NK4A136_group, and un_f__Lachnospiraceae, thereby improving the microbial community structure of skin wounds. These research findings are of significant implications for understanding the mechanism of skin wound healing, as well as for the treatment and clinical applications of skin wounds, especially aging skin.},
}

@article {pmid40051690,
year = {2025},
author = {Waller, ME and Gutierrez, A and Ticer, TD and Glover, JS and Baatz, JE and Wagner, CL and Engevik, MA and Chetta, KE},
title = {Profiling the response of individual gut microbes to free fatty acids (FFAs) found in human milk.},
journal = {Journal of functional foods},
volume = {125},
number = {},
pages = {},
pmid = {40051690},
issn = {1756-4646},
abstract = {Preterm infants have an immature intestinal environment featuring microbial dysbiosis. Human milk can improve the composition of the neonatal gut microbiome by supporting commensal species. Milk free fatty acids (FFAs) provide nutritional energy, participate in endogenous signaling, and exert antimicrobial effects. This study examined the growth of individual commensal and pathobiont microbes in response to unesterified unsaturated FFAs found in milk: oleic, linoleic, arachidonic, and docosahexaenoic acid. Select species of commensal and pathobiont genera (Bifidobacterium, Lactobacillus, Streptococcus, Staphylococcus, Enterococcus, Acinetobacter, Pseudomonas, Escherichia, and Klebsiella) were cultured with FFAs. The growth of all commensals, except for L. johnsonii, was significantly inhibited by the highest concentration (1 %) of all FFAs. L. johnsonii was only inhibited by arachidonic acid. In contrast, suppression of pathobionts in response to FFAs was less pronounced. Higher concentrations (0.1 %, 1 %) of docosahexaenoic acid significantly inhibited the growth of five of eight pathobionts. Meanwhile, for oleic, linoleic, and arachidonic acid, only two of eight pathobionts were significantly affected. Intriguingly, the effects for these FFAs were highly complex. For example, S. agalactiae growth was enhanced with 1 % oleic acid but suppressed at 0.01 %; however, the effects were directionally opposite for linoleic acid, i.e., suppressed at 1 % but enhanced at 0.01 %. Our genome analyses suggest that pathobiont survival may be related to the number of gene copies for fatty acid transporters. Overall, the effect of FFAs was dose-dependent and species-specific, where commensal growth was broadly inhibited while pathobionts were either unaffected or exhibited complex, bi-directional responses.},
}

@article {pmid40051624,
year = {2025},
author = {De Martinis, ECP and Alves, VF and Pereira, MG and Andrade, LN and Abichabki, N and Abramova, A and Dannborg, M and Bengtsson-Palme, J},
title = {Applying 3D cultures and high-throughput technologies to study host-pathogen interactions.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1488699},
pmid = {40051624},
issn = {1664-3224},
mesh = {Humans ; *Host-Pathogen Interactions ; *Cell Culture Techniques, Three Dimensional/methods ; Animals ; High-Throughput Screening Assays/methods ; Microbiota ; High-Throughput Nucleotide Sequencing ; },
abstract = {Recent advances in cell culturing and DNA sequencing have dramatically altered the field of human microbiome research. Three-dimensional (3D) cell culture is an important tool in cell biology, in cancer research, and for studying host-microbe interactions, as it mimics the in vivo characteristics of the host environment in an in vitro system, providing reliable and reproducible models. This work provides an overview of the main 3D culture techniques applied to study interactions between host cells and pathogenic microorganisms, how these systems can be integrated with high-throughput molecular methods, and how multi-species model systems may pave the way forward to pinpoint interactions among host, beneficial microbes and pathogens.},
}

Humans
*Host-Pathogen Interactions
*Cell Culture Techniques, Three Dimensional/methods
Animals
High-Throughput Screening Assays/methods
Microbiota
High-Throughput Nucleotide Sequencing

@article {pmid40051478,
year = {2025},
author = {Park, H and Yeo, S and Lee, T and Han, Y and Ryu, CB and Huh, CS},
title = {Culture-based characterization of gut microbiota in inflammatory bowel disease.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1538620},
pmid = {40051478},
issn = {1664-302X},
abstract = {Inflammatory bowel disease (IBD) is characterized by disruptions in the gut microbiome. While most studies on gut dysbiosis in IBD rely on sequencing-based methods, we employed a streamlined culturomics approach to obtain a more comprehensive understanding of gut microbiota imbalance in patients with IBD that may not be captured by sequencing alone. A total of 367 bacteria were identified at the species level, including 211 species from ulcerative colitis patients, 164 species from Crohn's disease (CD) patients, and 263 species from healthy individuals. Consistent with our 16S rRNA gene amplicon sequencing results, a significant decrease in microbial diversity and a severe imbalance, especially in CD patients, were also observed in the culture-based analysis. Our culturomics approach provided additional insights, highlighting dysbiosis in unique anaerobic and Gram-negative species in CD patients. Moreover, species-level findings for Bifidobacterium and Enterobacterales emphasized specific species expansions in IBD patients. Notably, Mediterraneibacter gnavus, Thomasclavelia ramosa, Parabacteroides merdae, and Collinsella aerofaciens are of particular clinical interest due to their correlation with inflammatory biomarkers. This comprehensive analysis underscores the value of integrating a culture-based approach with a genome-based approach to provide complementary insights and therapeutic targets in IBD.},
}

@article {pmid40051134,
year = {2025},
author = {Bi, O and Caballero-Lima, D and Sikkink, S and Westgate, G and Kauser, S and Elies, J and Thornton, MJ},
title = {Do Melanocytes Have a Role in Controlling Epidermal Bacterial Colonisation and the Skin Microbiome?.},
journal = {Experimental dermatology},
volume = {34},
number = {3},
pages = {e70071},
doi = {10.1111/exd.70071},
pmid = {40051134},
issn = {1600-0625},
support = {//Innovate UK/ ; },
mesh = {Humans ; *Melanocytes ; *Microbiota ; *Staphylococcus epidermidis ; *Keratinocytes/microbiology/immunology ; Corynebacterium ; Epidermis/microbiology/immunology ; Fibroblasts/microbiology ; Melanins/metabolism ; Propionibacteriaceae ; Skin/microbiology/immunology ; alpha-MSH/metabolism ; Cells, Cultured ; Immunity, Innate ; },
abstract = {In addition to producing melanin to protect epidermal keratinocytes against DNA damage, melanocytes may have important roles in strengthening innate immunity against pathogens. We have developed a functional, pigmented, human full-thickness 3D skin equivalent to determine whether the presence of melanocytes impacts epidermal bacterial growth and regulates the expression of genes involved in the immune response. We introduced primary epidermal melanocytes to construct a 3-cell full-thickness skin equivalent with primary dermal fibroblasts and epidermal keratinocytes. Immunohistochemistry verified the appropriate ratio and spatial organisation of melanocytes. Alpha-MSH induced melanogenesis, confirming an appropriate physiological response. We compared this 3-cell skin equivalent with the 2-cell version without melanocytes in response to inoculation with 3 species of bacteria: Staphylococcus epidermidis, Corynebacterium striatum, and Cutibacterium acnes. There was a significant decrease in the colonisation of bacteria in the skin equivalents containing functional melanocytes. There was increased expression of immune-response genes (S100A9, DEFB4A, IL-4R) following microorganism exposure; however, there were marked differences between the unpigmented and pigmented skin equivalents. This physiologically relevant human 3D-skin equivalent opens up new avenues for studying complex skin pigmentation disorders, melanoma, and UV damage, as well as the rapidly evolving field of the skin microbiome and the balance between commensal and pathogenic species.},
}

Humans
*Melanocytes
*Microbiota
*Staphylococcus epidermidis
*Keratinocytes/microbiology/immunology
Corynebacterium
Epidermis/microbiology/immunology
Fibroblasts/microbiology
Melanins/metabolism
Propionibacteriaceae
Skin/microbiology/immunology
alpha-MSH/metabolism
Cells, Cultured
Immunity, Innate

@article {pmid40051043,
year = {2025},
author = {Cresci, GAM},
title = {Understanding how foods and enteral feedings influence the gut microbiome.},
journal = {Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/ncp.11285},
pmid = {40051043},
issn = {1941-2452},
support = {//This study funding was provided by a research grant from Nestlé Health Science./ ; },
abstract = {The gut microbiome supports both gut and overall health. Diet is known to be one of the driving factors that influences the gut microbiome. The foods we eat, the dietary and nondietary components they contain, various food consumption patterns, and the ratio of nutrients consumed have been shown to impact gut microbiome composition and function. Studies indicate that many acute and chronic diseases are associated with alterations to the gut microbiome. There are many patients who rely on enteral tube feeding for their nutrition support. More recently, enteral tube feeding formulations of "real food" have become commercially available. However, little is known about how enteral tube feeding impacts the gut microbiome in patients requiring this specialized form of nutrition therapy. This review summarizes the existing evidence regarding the food sources of commonly consumed macronutrients and their impact on the gut microbiome. Also presented is what is known regarding "standard" and real food enteral formulations on the gut microbiome. Existing evidence is suggestive that real food enteral formulations positively impact the gut microbiome. Still, more research is needed on ready-to-feed formulations, particularly in patients with various clinical conditions, and how gut microbiome modulation impacts clinical outcomes.},
}

@article {pmid40050995,
year = {2025},
author = {Garrigues, Q and Apper, E and Mercier, F and Rodiles, A and Rovere, N and Chastant, S and Mila, H},
title = {Composition of the fecal, vaginal and colostrum microbiotas of dams at parturition and their relationship with neonatal outcomes in dogs.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {23},
pmid = {40050995},
issn = {2524-4671},
abstract = {BACKGROUND: Microbial seeding in early life is critical for the host's short- and long-term health, and the mother is the first source of bacteria for the newborn. The objective of this study was to characterize the maternal fecal, vaginal, and colostral microbiotas in the canine species one day after parturition and to evaluate the relationship between the microbial profiles of 36 dams and the neonatal outcomes of 284 newborns.

RESULTS: The first part of the study revealed the presence of 2 fecal, 3 vaginal, and 2 colostral microbial clusters on the basis of the core microbiota of the dams. Among these three maternal microbiotas, only the vaginal microbiome was found to be associated with neonatal outcomes. Compared with those in the other clusters, females in Cluster 1, with the lowest stillbirth and neonatal mortality ratios, presented a greater abundance of Moraxellaceae in their vaginal microbiota; Cluster 2, with a greater abundance of Pasteurellaceae, mostly from the Haemophilus genus; and Cluster 3 (with the highest stillbirth and neonatal mortality ratios), a greater abundance of Enterobacteriaceae, mostly E. coli. Moreover, Cluster 3 dams presented significantly lower species richness according to the Shannon index than did dams from the other clusters.

CONCLUSIONS: This study underscores the strong association between maternal microbiota, particularly the vaginal microbiota, and newborn health. The results of this study call for further research to gain a deeper understanding of the optimal vaginal microbiota composition in canine species and the ways to modulate it to improve neonatal outcomes.},
}

@article {pmid40050994,
year = {2025},
author = {Talat, A and Bashir, Y and Khalil, N and Brown, CL and Gupta, D and Khan, AU},
title = {Antimicrobial resistance transmission in the environmental settings through traditional and UV-enabled advanced wastewater treatment plants: a metagenomic insight.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {27},
pmid = {40050994},
issn = {2524-6372},
support = {BT/PR40148/BTIS/137/20/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {BACKGROUND: Municipal wastewater treatment plants (WWTPs) are pivotal reservoirs for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). Selective pressures from antibiotic residues, co-selection by heavy metals, and conducive environments sustain ARGs, fostering the emergence of ARB. While advancements in WWTP technology have enhanced the removal of inorganic and organic pollutants, assessing ARG and ARB content in treated water remains a gap. This metagenomic study meticulously examines the filtration efficiency of two distinct WWTPs-conventional (WWTPC) and advanced (WWTPA), operating on the same influent characteristics and located at Aligarh, India.

RESULTS: The dominance of Proteobacteria or Pseudomonadota, characterized the samples from both WWTPs and carried most ARGs. Acinetobacter johnsonii, a prevailing species, exhibited a diminishing trend with wastewater treatment, yet its persistence and association with antibiotic resistance underscore its adaptive resilience. The total ARG count was reduced in effluents, from 58 ARGs, representing 14 distinct classes of antibiotics in the influent to 46 and 21 in the effluents of WWTPC and WWTPA respectively. However, an overall surge in abundance, particularly influenced by genes such as qacL, blaOXA-900, and rsmA was observed. Numerous clinically significant ARGs, including those against aminoglycosides (AAC(6')-Ib9, APH(3'')-Ib, APH(6)-Id), macrolides (EreD, mphE, mphF, mphG, mphN, msrE), lincosamide (lnuG), sulfonamides (sul1, sul2), and beta-lactamases (blaNDM-1), persisted across both conventional and advanced treatment processes. The prevalence of mobile genetic elements and virulence factors in the effluents possess a high risk for ARG dissemination.

CONCLUSIONS: Advanced technologies are essential for effective ARG and ARB removal. A multidisciplinary approach focused on investigating the intricate association between ARGs, microbiome dynamics, MGEs, and VFs is required to identify robust indicators for filtration efficacy, contributing to optimized WWTP operations and combating ARG proliferation across sectors.},
}

@article {pmid40050988,
year = {2025},
author = {Fujita, H and Yoshida, S and Suzuki, K and Toju, H},
title = {Alternative stable states of microbiome structure and soil ecosystem functions.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {28},
pmid = {40050988},
issn = {2524-6372},
support = {Fellowship//Japan Society for the Promotion of Science/ ; 20K06820//Japan Society for the Promotion of Science/ ; 20K20586//Japan Society for the Promotion of Science/ ; JPMJPR16Q6//Japan Science and Technology Agency/ ; RGP0029/2019//Human Frontier Science Program/ ; JPNP18016//New Energy and Industrial Technology Development Organization/ ; },
abstract = {BACKGROUND: Theory predicts that biological communities can have multiple stable states in terms of their species/taxonomic compositions. The presence of such alternative stable states has been examined in classic ecological studies on the communities of macro-organisms (e.g., distinction between forest and savanna vegetation types). Nonetheless, it remains an essential challenge to extend the target of the discussion on multistability from macro-organismal systems to highly species-rich microbial systems. Identifying alternative stable states of taxonomically diverse microbial communities is a crucial step for predicting and controlling microbiome processes in light of classic ecological studies on community stability.

RESULTS: By targeting soil microbiomes, we inferred the stability landscapes of community structure based on a mathematical framework of statistical physics. We compiled a dataset involving 11 archaeal, 332 bacterial, and 240 fungal families detected from > 1,500 agroecosystem soil samples and applied the energy landscape analysis to estimate the stability/instability of observed taxonomic compositions. The statistical analysis suggested that both prokaryotic and fungal community structure could be classified into several stable states. We also found that the inferred alternative stable states differed greatly in their associations with crop disease prevalence in agroecosystems. We further inferred "tipping points", through which transitions between alternative stable states could occur.

CONCLUSION: Our results suggest that the structure of complex soil microbiomes can be categorized into alternative stable states, which potentially differ in ecosystem-level functioning. Such insights into the relationship between structure, stability, and functions of ecological communities will provide a basis for ecosystem restoration and the sustainable management of agroecosystems.},
}

@article {pmid40050917,
year = {2025},
author = {Zou, B and Liu, S and Dong, C and Shen, H and Lv, Y and He, J and Li, X and Ruan, M and Huang, Z and Shu, S},
title = {Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {288},
pmid = {40050917},
issn = {1479-5876},
mesh = {Humans ; *Crohn Disease/therapy/microbiology ; Child ; Female ; Male ; Prospective Studies ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Adolescent ; Biodiversity ; Feces/microbiology ; Biomarkers/metabolism ; Treatment Outcome ; },
abstract = {BACKGROUND: Clinical data on oral fecal microbiota transplantation (FMT), a promising therapy for Crohn's disease (CD), are limited. Herein, we determined the short-term safety and feasibility of FMT for pediatric patients with active CD.

METHODS: In this open-label, parallel-group, single-center prospective trial, patients with active CD were treated with oral FMT capsules combined with partial enteral nutrition (PEN) (80%). The control group comprised pediatric patients with active CD treated with PEN (80%) and immunosuppressants. Thirty-three patients (11.6 ± 1.82 years)-17 in the capsule and 16 in the control groups-were analyzed. Data regarding the adverse events, clinical reactions, intestinal microbiome composition, and biomarker parameters were collected and compared post-treatment.

RESULTS: At week 10, the clinical and endoscopic remission rates did not differ between the two groups. By week 10, the mean fecal calprotectin level, C-reactive protein level, erythrocyte sedimentation rate, simple endoscopic score for CD, and pediatric CD activity index decreased significantly in the capsule group (all P < 0.05). The main adverse event was mild-to-moderate constipation. Core functional genera, Agathobacter, Akkermansia, Roseburia, Blautia, Subdoligranulum, and Faecalibacterium, were lacking pre-treatment. Post-treatment, the implantation rates of these core functional genera increased significantly, which positively correlated with the anti-inflammatory factor, interleukin (IL)-10, and negatively correlated with the pro-inflammatory factor, IL-6. The combination of these six functional genera distinguished healthy children from those with CD (area under the curve = 0.96).

CONCLUSIONS: Oral FMT capsules combined with PEN (80%) could be an effective therapy for children with active CD. The six core functional genera identified here may be candidate biomarkers for identifying children with CD.

TRIAL REGISTRATION: ClinicalTrials.gov, retrospectively registered, ID# NCT05321758, NCT05321745, date of registration: 2022-04-04.},
}

Humans
*Crohn Disease/therapy/microbiology
Child
Female
Male
Prospective Studies
*Gastrointestinal Microbiome
*Fecal Microbiota Transplantation
Adolescent
Biodiversity
Feces/microbiology
Biomarkers/metabolism
Treatment Outcome

@article {pmid40050732,
year = {2025},
author = {Kim, K and Won, S},
title = {Robust phylogenetic tree-based microbiome association test using repeatedly measured data for composition bias.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {75},
pmid = {40050732},
issn = {1471-2105},
support = {NRF-2021R1A5A1033157//National Research Foundation/ ; NRF-2023M3E5D3009803//National Research Foundation of Korea/ ; 2024ER210800//Korea National Institute of Health/ ; },
mesh = {*Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Humans ; },
abstract = {BACKGROUND: The effects of microbiota on the host phenotypes can differ substantially depending on their age. Longitudinally measured microbiome data allow for the detection of the age modification effect and are useful for the detection of microorganisms related to the progression of disease whose identification change over time. Moreover, longitudinal analysis facilitates the estimation of the within-subject covariate effect, is robust to the between-subject confounders, and provides better evidence for the causal relationship than cross-sectional studies. However, this method of analysis is limited by compositional bias, and few statistical methods can estimate the effect of microbiota on host diseases with repeatedly measured 16S rRNA gene data. Herein, we propose mTMAT, which is applicable to longitudinal microbiome data and is robust to compositional bias.

RESULTS: mTMAT normalized the microbial abundance and utilized the ratio of the pooled abundance for association analysis. mTMAT is based on generalized estimating equations with a robust variance estimator and can be applied to repeatedly measured microbiome data. The robustness of mTMAT against compositional bias is underscored by its utilization of abundance ratios.

CONCLUSIONS: With extensive simulation studies, we showed that mTMAT is statistically relatively powerful and is robust to compositional bias. mTMAT enables detection of microbial taxa associated with host diseases using repeatedly measured 16S rRNA gene data and can provide deeper insights into bacterial pathology.},
}

*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
*Phylogeny
Humans

@article {pmid40050684,
year = {2025},
author = {Badar, A and Aqueel, R and Nawaz, A and Ijaz, UZ and Malik, KA},
title = {Microbiota transplantation for cotton leaf curl disease suppression-core microbiome and transcriptome dynamics.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {380},
pmid = {40050684},
issn = {2399-3642},
support = {BB/T010649/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {*Gossypium/microbiology/genetics ; *Plant Diseases/microbiology/prevention & control ; *Microbiota ; *Transcriptome ; Disease Resistance/genetics ; Rhizosphere ; Gene Expression Regulation, Plant ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; },
abstract = {Microbiota transplantation is a strong tool for managing plant disease. This study investigates the effects of microbiota transplantation on Cotton Leaf Curl Disease (CLCuD) resistance in Gossypium hirsutum, a species with good fiber length but high susceptibility to biotic stresses. Using metabarcoding for V3-V4 16S rRNA gene amplicon, microbial fractions from both rhizosphere and phyllosphere of CLCuD-resistant species Gossypium arboreum, and susceptible cotton varieties are analyzed. Unique bacterial taxa have been identified associated with disease resistance. Interspecies and intraspecies microbiota transplantation is conducted, followed by CLCuD incidence assays. It is seen that rhizospheric microbiota transplantation from G. arboreum FDH228 significantly suppresses CLCuD in G. hirsutum varieties, outperforming exogenous salicylic acid application. While phyllospheric transplants also reduce disease incidence, they are less effective than rhizospheric transplants. Differential expression analysis DESeq2 is utilized to identify key bacterial genera correlated with CLCuD suppression, including Pseudoxanthomonas and Stenotrophomonas in the rhizosphere of G. arboreum FDH228. Functional pathway analysis reveals upregulation of stress response and metabolism in tolerant species. Transcriptomics reveals upregulation of genes involved in protein phosphorylation and stress response in interspecies rhizospheric microbiota transplants. This study highlights microbiota transplantation as a sustainable method for controlling CLCuD along with specific microbial and genetic mechanisms contributing to CLCuD resistance.},
}

*Gossypium/microbiology/genetics
*Plant Diseases/microbiology/prevention & control
*Microbiota
*Transcriptome
Disease Resistance/genetics
Rhizosphere
Gene Expression Regulation, Plant
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification

@article {pmid40050613,
year = {2025},
author = {Jimenez-Sanchez, M and Celiberto, LS and Yang, H and Sham, HP and Vallance, BA},
title = {The gut-skin axis: a bi-directional, microbiota-driven relationship with therapeutic potential.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2473524},
doi = {10.1080/19490976.2025.2473524},
pmid = {40050613},
issn = {1949-0984},
mesh = {Humans ; *Skin/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; *Dysbiosis/microbiology ; Gastrointestinal Tract/microbiology ; Homeostasis ; Skin Diseases/microbiology/therapy ; },
abstract = {This review explores the emerging term "gut-skin axis" (GSA), describing the bidirectional signaling that occurs between the skin and the gastrointestinal tract under both homeostatic and disease conditions. Central to GSA communication are the gut and skin microbiota, the microbial communities that colonize these barrier surfaces. By influencing diverse host pathways, including innate immune, vitamin D receptor, and Aryl hydrocarbon receptor signaling, a balanced microbiota contributes to both tissue homeostasis and host defense. In contrast, microbiota imbalance, or dysbiosis at one site, can lead to local barrier dysfunction, resulting in the activation of signaling pathways that can disrupt tissue homeostasis at the other site, potentially leading to inflammatory skin conditions such as atopic dermatitis and psoriasis, or gut diseases like Inflammatory Bowel Disease. To date, most research on the GSA has examined the impact of the gut microbiota and diet on skin health, but recent studies show that exposing the skin to ultraviolet B-light can beneficially modulate both the gut microbiome and intestinal health. Thus, despite the traditional focus of clinicians and researchers on these organ systems as distinct, the GSA offers new opportunities to better understand the pathogenesis of cutaneous and gastrointestinal diseases and promote health at both sites.},
}

Humans
*Skin/microbiology
*Gastrointestinal Microbiome/physiology
Animals
*Dysbiosis/microbiology
Gastrointestinal Tract/microbiology
Homeostasis
Skin Diseases/microbiology/therapy

@article {pmid40050500,
year = {2025},
author = {Dave, M and Tattar, R},
title = {Antimicrobial resistance genes in the oral microbiome.},
journal = {Evidence-based dentistry},
volume = {},
number = {},
pages = {},
pmid = {40050500},
issn = {1476-5446},
abstract = {A COMMENTARY ON: Sukumar S, Rahmanyar Z, El Jurf H Q et al. Mapping the oral resistome: a systematic review. J Med Microbiol 2024; https://doi.org/10.1099/jmm.0.001866 .

DESIGN: This systematic review, without meta-analysis, aimed to map the oral resistome by analysing clinical studies that detected bacterial antimicrobial resistance genes (ARGs) in the oral cavity using molecular techniques.

DATA SOURCES: The researchers used Medline, Embase, Web of Science, CINAHL and Scopus databases from January 2015 to August 2023.

STUDY SELECTION: This systematic review included cross-sectional or longitudinal clinical studies that detected ARGs using molecular techniques; specifically polymerase chain reaction (PCR) or next-generation sequencing (NGS) metagenomics for samples from the oral cavity (saliva, gingival biofilm, pulp, or oral mucosa). Studies were excluded if they were in vitro or animal studies, literature reviews and not focused on ARG detection.

DATA EXTRACTION AND SYNTHESIS: Five reviewers independently screened titles and abstracts based on inclusion criteria. Full-text reports were then independently assessed for eligibility by three reviewers. Extracted data encompassed publication details, sample size, country, molecular methods used, number of ARGs detected, participants' health status, antibiotic exposure, and sample location within the oral cavity.

RESULTS: Out of 580 initially identified studies, 15 met the inclusion criteria. These studies, published between 2015 and 2023 from 12 different countries, employed either PCR (n = 10) or NGS metagenomics (n = 5) to detect ARGs from a pool of 1486 participants (1 study did not report on the number of participants). PCR-based studies identified an average of 7 ARGs (range 1-20), while NGS studies identified an average of 34 ARGs (range 7-70). In total, 159 unique ARGs conferring resistance to 22 antibiotic classes were identified across six regions of the oral cavity. The supragingival biofilm and saliva exhibited the highest richness of ARGs, defined by the number of unique ARGs detected. Genes conferring resistance to 19 antibiotic classes were present in the supragingival biofilm. Notably, 49 ARGs, including tetracycline and macrolide resistance genes, were found across all sampled locations, indicating a widespread distribution within the oral cavity. Thirteen studies reported on bacterial species associated with ARGs. NGS studies identified a mean of 65 ARG-carrying bacterial species, compared to a mean of 4 species in PCR studies. Specifically, 25 ARG-carrying species were identified in PCR studies, while NGS studies identified 177 species. Four studies reported ARGs associated with streptococcal species implicated in distant-site infections such as infective endocarditis. ESKAPE pathogens (group of highly virulent multidrug-resistant bacteria) were detected with ARGs in various oral sites using both PCR and NGS methods. Comparisons between healthy and diseased states revealed that a healthy oral microbiome harbours a more diverse resistome at the antibiotic class level. The supragingival resistome demonstrated the richest composition in both health and disease, with tetracycline ARGs predominating in the supragingival and saliva resistomes in cases of dental caries.

CONCLUSIONS: The analysis of the oral resistome from these 15 studies identified three ARGs present in all sites of the oral cavity, suggesting the presence of a core resistome. NGS studies provided greater insights compared to PCR studies; however, the overall research base is limited. Further comprehensive studies are necessary to fully map the oral resistome.},
}

@article {pmid40050445,
year = {2025},
author = {Akhi, R and Lavrinienko, A and Hakula, M and Tjäderhane, L and Hindström, R and Nissinen, A and Wang, C and Auvinen, J and Kullaa, AM and Ylöstalo, P and Salo, T and Kaikkonen, K and Koskimäki, JJ and Hörkkö, S},
title = {Oral microbiome diversity associates with carotid intima media thickness in middle-aged male subjects.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {66},
pmid = {40050445},
issn = {2730-664X},
abstract = {BACKGROUND: Although there have been significant advancements in reducing the burden of cardiovascular disease (CVD) by modifying traditional CVD risk factors, substantial risks persist, particularly among male subjects who exhibit heightened susceptibility to atherosclerosis. In this context, we aim to study the link between oral microbiome and carotid intima media thickness (cIMT).

METHODS: The Northern Finland Birth Cohort of 1966 (mean age 46 years, n = 869) underwent an extensive health examination, including the measurement of cIMT. The oral microbiome was also investigated using high-throughput 16S rRNA gene sequencing.

RESULTS: Here we show that oral microbiome diversity links with atherosclerosis risk factors, namely smoking, glycemic balance, low-grade inflammation, and periodontitis. After excluding CVD-influencing factors (n = 339), oral microbiome genera (p = 0.030), Shannon index (p = 0.001), β-diversity Bray-Curtis (p < 0.001), and Jaccard (p < 0.001) are associated with cIMT in males, but not in the female sub-cohort. Furthermore, in the male sub-cohort (n = 131), the genera Prevotella, Megasphaera, and Veillonella associate positively with cIMT, while Absconditabacteria, Capnocytophaga, Gemella, Fusobacterium, Neisseria, Aggregatibacter, Tannerella, Treponema, Cardiobacterium, and Bacteroidales associate inversely with cIMT. We examine the involvement of serum total immunoglobulins and antibodies to phosphorylcholine (PCho) and malondialdehyde-acetaldehyde LDL (MAA-LDL) with cIMT. Subjects with high cIMT have lower levels of serum total IgA (p = 0.009), IgA to PCho (p = 0.017), and IgG to PCho (p = 0.008). The relative abundance of cIMT-associated genera correlates with serum IgA antibodies.

CONCLUSIONS: This middle-aged birth cohort study shows that male oral microbiome diversity links to cIMT, suggesting a potential sex-specific interaction between the oral microbiome and atherosclerosis.},
}

@article {pmid40050220,
year = {2025},
author = {Huang, X and Zhao, W and Feng, R and Zhou, Y and Wang, J and Xiao, J and Li, L and Shan, X and Feng, Y and Ming, Y and Cao, J and Kang, X and Wu, L and Chen, H and Duan, X},
title = {Linking gut microbiome profiles and white matter integrity to social behavior in young autistic children: from the perspective of individual variation.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2025.02.031},
pmid = {40050220},
issn = {2095-9281},
}

@article {pmid40049993,
year = {2025},
author = {Sargison, ND and Chaudhry, U and Costa-Junior, L and Kutcher, JR and Li, K and Sargison, FA and Zahid, O},
title = {The diagnosis and vector potential of Ornithonyssus bacoti tropical rat mites in northern Europe.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {58},
number = {},
pages = {101204},
doi = {10.1016/j.vprsr.2025.101204},
pmid = {40049993},
issn = {2405-9390},
mesh = {Animals ; *Mites/microbiology/physiology ; *Mite Infestations/veterinary/parasitology/diagnosis ; RNA, Ribosomal, 16S/genetics/analysis ; Europe ; Rodent Diseases/parasitology/diagnosis/microbiology/epidemiology ; Rats ; Male ; Female ; Microbiota ; },
abstract = {The mesostigmatid tropical rat mite, Ornithonyssus bacoti, is an important cause of disease in small rodents, and of gamasoidosis in humans when they come into contact with infestations. Most reports of O. bacoti infestations are from warmer parts of the Americas, southern Europe and Asia; and infection has only rarely been recorded in northern Europe. In 2021 and 2024, two separate cases of gamasoidosis were identified in student flats in the city of Edinburgh, UK. Further investigation highlighted the value of combining conventional morphological and 16S ribosomal DNA sequencing methods in establishing the species identity of the mites; hence confirming the diagnosis of gamasoidosis. The bacterial microbiome associated with the mites was explored by conventional culture and metabarcoding microbiome sequencing of the ribosomal16S v3-v4 hypervariable region. The results highlight the utility of the mixed approach; and show the presence of potentially pathogenic bacteria and recognised causes of opportunistic nosocomial infections, along with known mite gut and intracellular symbionts. The results indicate the potential for O. bacoti mites as vectors of bacterial infections. The clinical presentation of gamasoidosis is indistinguishable from non-specific arthropod-bite reactions; and the cause is seldom confirmed because the temporarily parasitic mites spend most of their time in the environment. The two confirmed index cases may, therefore, represent a more widespread emerging problem; putatively associated with an increase in urban rodent populations.},
}

Animals
*Mites/microbiology/physiology
*Mite Infestations/veterinary/parasitology/diagnosis
RNA, Ribosomal, 16S/genetics/analysis
Europe
Rodent Diseases/parasitology/diagnosis/microbiology/epidemiology
Rats
Male
Female
Microbiota

@article {pmid40049951,
year = {2025},
author = {Zhao, Y and Wang, P and Wang, D and Zhao, W and Wang, J and Ge, Z and Liu, Y and Zhao, X},
title = {Gut microbiota and metabolic profile affected by pectic domains during in vitro rat fecal fermentation: A comparative study between different glycans rich in pectic monosaccharides.},
journal = {Carbohydrate polymers},
volume = {356},
number = {},
pages = {123365},
doi = {10.1016/j.carbpol.2025.123365},
pmid = {40049951},
issn = {1879-1344},
mesh = {Animals ; *Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; *Pectins/metabolism ; *Fermentation ; Rats ; Male ; Galactans/metabolism/chemistry ; Monosaccharides/metabolism ; Xylans/metabolism ; Glucans/metabolism ; Polysaccharides/metabolism/chemistry ; Metabolome ; Rats, Sprague-Dawley ; Hexuronic Acids ; },
abstract = {This study aimed to investigate in vitro rat fecal fermentation behavior of pectic polymers and glycans that constitute typical pectic fragments, i.e. homogalacturonan (HG), arabinan (AB), arabinogalactan (AG), rhamnogalacturonan (RG), and xyloglucan (XG). Results showed that galacturonic acid proportion of HG (73.85 mol%) was the highest, followed by pectin (67.99 mol%), whereas arabinose (70.23 mol%) and galactose (86.22 mol%) enriched in AB and AG, respectively. Absolute quantitative microbiome revealed that Bacteroides showed dramatic growth in RG and AG; higher absolute abundances of Bifidobacterium (5.06E+09 and 3.36E+09 copies/g feces, respectively) were found in AB and XG; Escherichia Shigella, Enterococcus, and Klebsiella were inhibited after fermentation with pectin and HG by >95 %. Untargeted metabolomics indicated that the differential metabolite in AG and RG were 7-ketodeoxycholic acid and 9,10-epoxyoctadecanoic acid, respectively, both of which were positively related to arabinose and galactose (p < 0.001). Besides, another characteristic monosaccharide, rhamnose was positively correlated with succinic acid (p < 0.05), and Parvibacter (p < 0.001). Overall, this work help to understand the interactions among pectin structure, gut microbiota and metabolites, thereby guiding the targeted design of the nutrient-directed pectins in future personalized diets.},
}

Animals
*Feces/microbiology
*Gastrointestinal Microbiome/physiology
*Pectins/metabolism
*Fermentation
Rats
Male
Galactans/metabolism/chemistry
Monosaccharides/metabolism
Xylans/metabolism
Glucans/metabolism
Polysaccharides/metabolism/chemistry
Metabolome
Rats, Sprague-Dawley
Hexuronic Acids

@article {pmid40049897,
year = {2025},
author = {Jiang, Y and Luo, J and Guo, X and Qiao, Y and Li, Y and Zhang, Y and Zhou, R and Vaculík, M and Li, T},
title = {Phyllosphere microbiome assists the hyperaccumulating plant in resisting heavy metal stress.},
journal = {Journal of environmental sciences (China)},
volume = {154},
number = {},
pages = {563-574},
doi = {10.1016/j.jes.2024.05.032},
pmid = {40049897},
issn = {1001-0742},
mesh = {*Metals, Heavy/metabolism/toxicity ; *Microbiota/drug effects ; *Soil Pollutants/metabolism/toxicity ; Sedum/metabolism/microbiology/drug effects ; Soil Microbiology ; Biodegradation, Environmental ; },
abstract = {Phyllosphere microbiome plays an irreplaceable role in maintaining plant health under stress, but its structure and functions in heavy metal-hyperaccumulating plants remain elusive. Here, the phyllosphere microbiome, inhabiting hyperaccumulating (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii grown in soils with varying heavy metal concentration, was characterized. Compared with NHE, the microbial community α-diversity was greater in HE. Core phyllosphere taxa with high relative abundance (>10 %), including Streptomyces and Nocardia (bacteria), Cladosporium and Acremonium (fungi), were significantly related to cadmium (Cd) and zinc (Zn) concentration and biomass of host plants. Moreover, microbial co-occurrence networks in HE exhibited greater complexity than those in NHE. Additionally, proportions of positive associations in HE bacterial networks increased with the rising heavy metal concentration, indicating a higher resistance of HE phyllosphere microbiome to heavy metal stress. Furthermore, in contrast to NHE, microbial community functions, primarily involved in heavy metal stress resistance, were more abundant in HE, in which microbiome assisted hosts to resist heavy metal stress better. Collectively, this study indicated that phyllosphere microbiome of the hyperaccumulator played an indispensable role in assisting hosts to resist heavy metal stress, and provided new insights into phyllosphere microbial application potential in phytoremediation.},
}

*Metals, Heavy/metabolism/toxicity
*Microbiota/drug effects
*Soil Pollutants/metabolism/toxicity
Sedum/metabolism/microbiology/drug effects
Soil Microbiology
Biodegradation, Environmental

@article {pmid40049661,
year = {2025},
author = {Yang, YP and Xu, LB and Lu, Y and Wang, J and Nie, YH and Sun, Q},
title = {Dynamic alterations in bacterial and fungal microbiome and inflammatory cytokines following SRV-8 infection in cynomolgus monkeys.},
journal = {Zoological research},
volume = {46},
number = {2},
pages = {325-338},
doi = {10.24272/j.issn.2095-8137.2024.278},
pmid = {40049661},
issn = {2095-8137},
mesh = {Animals ; *Cytokines/genetics/metabolism ; *Macaca fascicularis ; *Bacteria/classification/isolation & purification/genetics ; Gastrointestinal Microbiome ; Monkey Diseases/microbiology/immunology ; Mycobiome/genetics ; Fungi/physiology ; },
abstract = {While viral infections can disturb the host gut microbiome, the dynamic alterations in microbial composition following infection remain poorly characterized. This study identified SRV-8-infected monkeys and classified them into five groups based on infection progression. 16S rRNA amplicon sequencing revealed significant alterations in the relative and inferred absolute abundance of bacterial genera UCG-002, Agathobacter, Coprococcus, and Holdemanella during the early stage of SRV-8 infection, coinciding with provirus formation. These microbial shifts were accompanied by functional modifications in bacterial communities at the same stage. In contrast, ITS amplicon sequencing indicated no significant differences in fungal composition between healthy wild-type and SRV-8-infected monkeys. Spearman correlation analyses demonstrated close interactions between intestinal bacteria and fungi following SRV-8 infection. Additionally, SRV-8 seropositive groups exhibited significantly elevated mRNA expression levels of pro-inflammatory (TNF-α, IFN-γ, IL-1β, and IL-6) and anti-inflammatory (IL-10) cytokine genes, highlighting close associations between inflammatory cytokines and immune responses. Overall, these findings provide a comprehensive characterization of bacterial and fungal microbiota dynamics and inflammatory cytokine responses associated with SRV-8 infection, clarifying the pathobiological mechanisms underlying SRV-8 infection from the perspective of the gut microbiome.},
}

Animals
*Cytokines/genetics/metabolism
*Macaca fascicularis
*Bacteria/classification/isolation & purification/genetics
Gastrointestinal Microbiome
Monkey Diseases/microbiology/immunology
Mycobiome/genetics
Fungi/physiology

@article {pmid40049555,
year = {2025},
author = {Song, W and Huang, L},
title = {Targeting Tumor-Associated Microbiome: A New Aspect of Modulating Tumor Microenvironment for Cancer Therapy.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115554},
doi = {10.1016/j.addr.2025.115554},
pmid = {40049555},
issn = {1872-8294},
}

@article {pmid40049533,
year = {2025},
author = {Zheng, Z and Xu, M and Xiao, K and Yu, K},
title = {Association between oral microbiome and depression: A population-based study.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jad.2025.03.018},
pmid = {40049533},
issn = {1573-2517},
abstract = {OBJECTIVE: Depression is a global mental health issue, particularly affecting adolescents and young adults. While the role of gut microbiota in depression has been extensively studied, the influence of the oral microbiome remains underexplored. Recent studies suggest that the oral microbiome may affect systemic and brain health through the oral-brain axis. This study aimed to investigate the relationship between oral microbiota diversity and depression using data from 6212 participants in the National Health and Nutrition Examination Survey (NHANES) 2009-2012.

METHODS: Oral microbiota diversity was assessed through oral rinse samples using 16S rRNA sequencing, focusing on α-diversity metrics (observed ASVs and Faith's phylogenetic diversity) and β-diversity measures. Depressive symptoms were evaluated with the Patient Health Questionnaire (PHQ-9) questionnaire. Weighted regression models were employed to assess associations between α-diversity and depression, while linear regression was used to examine the relationship between α-diversity and PHQ-9 scores. β-diversity differences were analyzed via permutational analysis of variance (PERMANOVA).

RESULTS: 10.04 % of the participants were diagnosed with depression. Higher α-diversity in the oral microbiome was negatively correlated with depression: observed ASVs (OR: 0.713 [CI: 0.508-0.999], P = 0.050) and Faith's phylogenetic diversity (OR: 0.584 [CI: 0.367-0.931], P = 0.025). Linear regression indicated that greater α-diversity was associated with lower PHQ-9 scores, reflecting fewer depressive symptoms. Furthermore, β-diversity analysis revealed significant differences in the microbiome composition between depressed and non-depressed individuals.

CONCLUSION: Reduced oral microbiome diversity is associated with an increased risk and severity of depression. The study underscores the importance of exploring the oral-brain axis and highlights the need for further research into the mechanisms and therapeutic strategies targeting this relationship.},
}

@article {pmid40049396,
year = {2025},
author = {Yoshimura, Y and Wakabayashi, H and Nagano, F and Matsumoto, A and Shimazu, S and Shiraishi, A and Kido, Y and Bise, T and Hamada, T and Yoneda, K and Maeda, K},
title = {Gut Microbiome Diversity is Associated with Muscle Mass, Strength and Quality in Post-Stroke Patients.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.02.027},
pmid = {40049396},
issn = {2405-4577},
abstract = {BACKGROUND: The gut microbiome has emerged as a potential influencer of muscle health; however, its role in hospitalized patients remains unclear. This study aimed to investigate the association between gut microbiome diversity and skeletal muscle mass, strength, and quality in hospitalized post-stroke patients.

METHODS: We conducted a cross-sectional study of post-stroke patients admitted to a rehabilitation facility. Gut microbiome diversity was assessed using 16S ribosomal ribonucleic acid (rRNA) gene sequencing, calculating Operational Taxonomic Unit (OTU) Richness, Faith's Phylogenetic Diversity (PD), and Shannon index. Muscle health was evaluated using skeletal muscle index (SMI) for muscle mass, handgrip strength (HGS) for muscle strength, and bioimpedance analysis-derived phase angle (PhA) for muscle quality. Multiple linear regression analyses were performed, adjusting for potential confounders.

RESULTS: A total of 156 patients (mean age 78.4 years; 55.7% male) were analyzed. OTU Richness showed significant positive associations with SMI (β = 0.197, p = 0.025), HGS (β = 0.180, p = 0.005), and PhA (β = 0.178, p = 0.022). The Shannon index was also positively associated with SMI (β = 0.120, p = 0.041), HGS (β = 0.140, p = 0.028), and PhA (β = 0.164, p = 0.032). Faith's PD did not demonstrate significant associations with muscle health parameters.

CONCLUSIONS: Higher gut microbiome diversity, assessed by OTU Richness and Shannon index, is associated with better muscle mass, strength, and quality in post-stroke patients. These findings suggest a potential role for gut microbiota in muscle health during stroke rehabilitation.},
}

@article {pmid40049183,
year = {2025},
author = {Yu, K and Tenaglia, V and Chua, EG and Haines, R and Bahal, G and Nicol, MP and Bahal, RK},
title = {Interactions between bacteria in the human nasopharynx: a scoping review.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101062},
doi = {10.1016/j.lanmic.2024.101062},
pmid = {40049183},
issn = {2666-5247},
abstract = {Emerging evidence indicates that interactions between bacteria shape the nasopharyngeal microbiome and influence respiratory health. This Review uses the systematic scoping methodology to summarise 88 studies including observational and experimental studies, identifying key interactions between bacteria that colonise the human nasopharynx. A range of bacterial interactions were reported in the observational studies, including a variable association between Streptococcus pneumoniae and Haemophilus influenzae, a consistent positive association between S pneumoniae and Moraxella catarrhalis, and a consistent negative association between S pneumoniae and Staphylococcus aureus. Experimental studies largely validated the associations reported in the observational studies and provided insights into the mechanism and direction of interactions. In the context of respiratory health, non-pneumococcal alpha-haemolytic streptococci and the Gram-positive commensals Dolosigranulum and Corynebacterium inhibited respiratory pathogens such as H influenzae, S pneumoniae, M catarrhalis, and S aureus. These findings underscore how bacterial competition and coexistence shape the microbiome composition in this niche. This study has relevance for respiratory health and can be helpful for informing the design of potential microbiota-targeted therapies.},
}

@article {pmid40049043,
year = {2025},
author = {Huang, JN and Gao, CC and Ren, HY and Wen, B and Wang, ZN and Gao, JZ and Chen, ZZ},
title = {Multi-omics association pattern between gut microbiota and host metabolism of a filter-feeding fish in situ exposed to microplastics.},
journal = {Environment international},
volume = {197},
number = {},
pages = {109360},
doi = {10.1016/j.envint.2025.109360},
pmid = {40049043},
issn = {1873-6750},
abstract = {Microplastics (MPs) are widespread in water environments and can affect gut microbiota and host metabolism of fish, but whether changes in host metabolism under MPs are mediated by gut microbiota remains unclear. Here, silver carp, a filter-feeding fish with important ecological functions, was in-situ exposure to environmentally relevant MPs. Multi-omics analysis and fecal microbiota transplantation were used to reveal the metabolic responses of carp along gut-liver-muscle axis. After three months of in situ exposure to MPs, community structure of gut microbiota of carp was reshaped, and five dominate phyla were significantly changed, including increased Cyanobacteria, Chloroflexi and Planctomycetota but decreased Firmicutes and Fusobacteriota. Weighted gene co-expression network analysis was further performed between these phyla and liver transcription spectrum, showing that the hub gene module contained up-regulated hppD, maiA and plg and activated ubiquinone and other terpenoid-quinone biosynthesis and phenylalanine metabolism. By fecal microbiota transplantation, the key gene module associated with core microbiota phyla of carp was verified in germ-free zebrafish. Interestingly, up-regulated hppD, maiA and plg and enriched phenylalanine metabolism were also observed in this module. Subsequently, metabolome performed in carp liver also shared activated phenylalanine metabolism, including increased trans-cinnamic acid and L-tyrosine. Furthermore, high-associated mapping showed that the differentially expressed metabolites (gamma-aminobutyric acid, ornithine and L-serine) related to amino acid metabolism in carp muscle were significantly accompanied with increased L-tyrosine in its liver. Overall, MPs exposure could change gut microbiome of silver carp and alter host metabolism especially amino acid metabolism along the gut-liver-muscle axis.},
}

@article {pmid40049002,
year = {2025},
author = {Ching, XL and Samsol, S and Rusli, MU and Aqmal-Naser, M and Bidai, JA and Sonne, C and Wu, X and Ma, NL},
title = {Blood and cloacal microbiome profile of captive green turtles (Chelonia mydas) and hawksbill turtles (Eretmochelys imbricata): Water quality and conservation implications.},
journal = {Chemosphere},
volume = {375},
number = {},
pages = {144223},
doi = {10.1016/j.chemosphere.2025.144223},
pmid = {40049002},
issn = {1879-1298},
abstract = {In this study, we studied the environment factors such as plastics and heavy metals affecting the blood and cloacal microbiome of green (Chelonia mydas) and hawksbill (Eretmochelys imbricata) in captivity. By non-metric multidimensional scaling analysis, data has shown that the environment factors (p = 0.02), rather than species differences (p = 0.06), significantly influenced the composition of the cloacal microbiota of green and hawksbill turtles. The cloacal microbiota of both captive green and hawksbill turtles was dominated by several similar dominant phyla at differential abundance. Green turtles' cloacal microbiome was made up of 46% of Proteobacteria, 31% of Bacteroidota, 11% of Campylobacterota and 4% of Firmicutes, while the hawksbill turtles' cloacal microbiome was made up of 33% of Bacteroidota, 18% of Firmicutes, 17% of Proteobacteria, and 2% of Campylobacterota. Water conductivity, salinity, microplastic polymers (polycarbonate, polyethylene terephthalate, polystyrene), and copper are positively associated (p < 0.05) with blood urea nitrogen. Hematocrit and hemoglobin were found also negatively correlated (p < 0.05) with water pH, polyethylene terephthalate, iron, lead and zinc. The correlations established in this study shed light on the intricate interplay between water quality and the physiological responses of sea turtles. Recognizing these relationships is pivotal for monitoring and preserving the well-being of sea turtles in their natural habitats.},
}

@article {pmid40048957,
year = {2025},
author = {Wu, H and Liu, J and Zhang, XH and Jin, S and Li, P and Liu, H and Zhao, L and Wang, J and Zhao, S and Tian, HD and Lai, JR and Hao, Y and Liu, GR and Hou, K and Yan, M and Liu, SL and Pang, D},
title = {The combination of flaxseed lignans and PD-1/ PD-L1 inhibitor inhibits breast cancer growth via modulating gut microbiome and host immunity.},
journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy},
volume = {80},
number = {},
pages = {101222},
doi = {10.1016/j.drup.2025.101222},
pmid = {40048957},
issn = {1532-2084},
abstract = {BACKGROUND: Patients with breast cancer (BC) who benefit from the PD-1/PD-L1 inhibitor (PDi) is limited, necessitating novel strategies to improve immunotherapy efficacy of BC. Here we aimed to investigate the inhibitory effects of flaxseed lignans (FL) on the biological behaviors of BC and evaluate the roles of FL in enhancing the anticancer effects of PDi.

METHODS: HPLC was used to detect the content of enterolactone (ENL), the bacterial transformation product of FL. Transcript sequencing was performed and identified CD38 as a downstream target gene of ENL. CD38-overexpressing cells were constructed and cell proliferation, colony formation, wound healing and transwell assays were used to assess the function of ENL/CD38 axis on BC cells in vitro. Multiplexed immunohistochemistry (mIHC) and CyTOF were used to detect the changes of the tumor immune microenvironment (TIM). 16S rDNA sequencing was used to explore the changes of gut microbiota in mice. A series of in vivo experiments were conducted to investigate the anticancer effects and mechanisms of FL and PDi.

RESULTS: FL was converted to ENL by gut microbiota and FL administration inhibited the progression of BC. ENL inhibited the malignant behaviors of BC by downregulating CD38, a key gene associated with immunosuppression and PD-1/PD-L1 blockade resistance. The mIHC assay revealed that FL administration enhanced CD3[+], CD4[+] and CD8[+] cells and reduced F4/80[+] cells in TIM. CyTOF confirmed the regulatory effects of FL and FL in combination with PDi (FLcPDi) on TIM. In addition, 16S rDNA analysis demonstrated that FLcPDi treatment significantly elevated the abundance of Akkermansia and, importantly, Akkermansia administration enhanced the response to PDi in mice treated with antibiotics.

CONCLUSIONS: The FL/ENL/CD38 axis inhibited BC progression. FL enhanced the anticancer effects of PDi by modulating gut microbiota and host immunity.},
}

@article {pmid40048944,
year = {2025},
author = {Zhu, N and Cui, X and Leng, F and Lv, X and Wang, X and Guo, X and Luo, W and Wang, Y},
title = {Volatile organic compounds from medicinal plant Codonopsis radix: Unraveling rhizoplane microbiome interactions for accumulation of active components.},
journal = {Plant physiology and biochemistry : PPB},
volume = {222},
number = {},
pages = {109688},
doi = {10.1016/j.plaphy.2025.109688},
pmid = {40048944},
issn = {1873-2690},
abstract = {Plant roots emit a diverse array of volatile organic compounds (VOCs) to attract specific soil microorganisms, thereby promoting their growth and development. However, the mechanisms by which medicinal plants interact with surrounding microorganisms through VOCs to enhance their quality remain poorly understood. This study integrated microbiome, transcriptome, and metabolome analyses to investigate the VOCs that mediate interactions between rhizoplane microorganisms and Codonopsis radix plants. The research identified a total of 36 common VOCs in the roots of Codonopsis radix, with 2, 3, 5-trimethylpyrazine being the primary VOC responsible for the root's nutty flavor. Chemoheterotrophic microorganisms, including both saprophytes and arbuscular mycorrhizae, were found to be the dominant types in the rhizoplane. The rhizoplane microorganism Rugamonas was significantly positively correlated with naringin and 2-ethyl-3-methylpyrazine. Furthermore, VOCs were found to influence the accumulation of phenylpropane differential metabolites and the expression of genes involved in phenylpropane synthesis and metabolite accumulation by modulating the structure and diversity of rhizoplane microbial communities. Overall, this study provides valuable insights into the complex interactions between medicinal plants and microorganisms, as well as potential strategies for enhancing the quality of medicinal plants.},
}

@article {pmid40048904,
year = {2025},
author = {Chen, L and Zhao, B and Zhang, M and Yan, Y and Nie, C and Yu, K and Tu, Z and Xia, Y},
title = {Micron-scale heterogeneity reduction leads to increased interspecies competition in thermophilic digestion microbiome.},
journal = {Water research},
volume = {279},
number = {},
pages = {123419},
doi = {10.1016/j.watres.2025.123419},
pmid = {40048904},
issn = {1879-2448},
abstract = {Microbial spatial heterogeneity is an important determinant of larger-scale community properties, whereas most studies neglect it and therefore only provide average information, potentially obscuring the signal of microbial interactions. Our study takes a step toward addressing this problem by characterizing the spatial heterogeneity of a microbiome with micron-scale resolution. Micron-scale single clusters (40-70 μm) were randomly collected from lab-scale anaerobic digestion (AD) biosystems, and a comparative analysis was performed to evaluate differences between mesophilic and thermophilic systems. Here we reveal a cascading effect from high-temperature selection to global microbial interactions. We observed that thermophilic communities exhibited less spatial heterogeneity than mesophilic communities, which we attribute to the considerable extinction of low-abundant species by high-temperature selection. Then, the low spatial heterogeneity and the high-temperature selection acting in conjunction resulted in a high proportion of competitive interactions in thermophilic communities. Unexpectedly, however, the thermophilic AD, characterized by lower micron-scale spatial heterogeneity, showed more efficient synergistic and syntrophic cooperations involving around Clostridiales, which significantly enhanced hydrolysis performance under thermophilic conditions. In addition, the fact that high temperatures favor slower growers, along with functional redundancy-related competitive advantage, led to the selection of more proficient methanogens in more competitive environments, which are also potentially associated with enhanced methanogenic performance. In summary, our findings underscore the significance of micron-scale resolution for revealing the microbial ecology in spatially structured environments.},
}

@article {pmid40048710,
year = {2025},
author = {Zhou, Y and Hubscher, CH},
title = {Biomarker expression level changes within rectal gut-associated lymphoid tissues in spinal cord-injured rats.},
journal = {ImmunoHorizons},
volume = {9},
number = {4},
pages = {},
pmid = {40048710},
issn = {2573-7732},
support = {W81XWH-18-1-0675//Department of Defense Spinal Cord Injury Research Program/ ; 17-5//Kentucky Spinal Cord Head Injury Research Trust/ ; R01DK133195/NH/NIH HHS/United States ; },
mesh = {Animals ; Rats ; *Spinal Cord Injuries/metabolism/immunology ; *Biomarkers/metabolism ; *Lymphoid Tissue/immunology/metabolism ; *Rectum/microbiology/pathology/metabolism ; Female ; Rats, Sprague-Dawley ; Neurogenic Bowel/genetics/metabolism ; Gastrointestinal Microbiome/immunology ; Disease Models, Animal ; Intestinal Mucosa/metabolism/microbiology/immunology/pathology ; },
abstract = {Neurogenic bowel dysfunction (NBD) is common after spinal cord injury (SCI). Gut-associated lymphoid tissue (GALT), an organized structure within the mucosal immune system, is important for the maintenance of gut homeostasis and body health and serves as the first line barrier/defense against diet antigens, commensal microbiota, pathogens, and toxins in mucosal areas. The current study examined gene expression levels along six segments of anorectal tissue using real-time polymerase chain reaction (RT-PCR) in uninjured rats (28-day sham surgical controls) and at both 28- and 42-days post-T9 contusion injury. Consistent with our previous report of functional regional differences in the ano-rectum, we demonstrate the existence of GALTs located primarily within the segment at 3-4.5 cm from the rectal dentate line (termed rectal GALTs-rGALTs) in shams with upregulated gene expression levels of multiple biomarkers, including B cell and T cell-related genes, major histocompatibility complex (MHC) class II molecules, and germinal center (GC)-related genes, which was further confirmed by histologic examination. In the same rectal tissue segment following T9 SCI, inflammation-related genes were upregulated at 28 days post-injury (DPI) indicating that microbial infection and inflammation of rGALTs modified structure and function of rGALTs, while at 42 DPI rGALTs exhibited resolution of inflammation and impaired structure/function for extrafollicular B cell responses. Taken together, our data suggest that rGALTs exists in rat rectum for homeostasis of gut microbiota/barrier. SCI induces microbial infection and inflammation in rectal tissues containing rGALTs, which could contribute to development of SCI-related gut microbiome dysbiosis, NBD, and systemic diseases.},
}

Animals
Rats
*Spinal Cord Injuries/metabolism/immunology
*Biomarkers/metabolism
*Lymphoid Tissue/immunology/metabolism
*Rectum/microbiology/pathology/metabolism
Female
Rats, Sprague-Dawley
Neurogenic Bowel/genetics/metabolism
Gastrointestinal Microbiome/immunology
Disease Models, Animal
Intestinal Mucosa/metabolism/microbiology/immunology/pathology

@article {pmid40048707,
year = {2025},
author = {Hernández-Verdin, I and Kirasic, E and Mokhtari, K and Barillot, N and Rincón de la Rosa, L and Sourdeau, E and Abada, Y and Le Tarff-Tavernier, M and Nichelli, L and Rozenblum, L and Kas, A and Mathon, B and Choquet, S and Houillier, C and Hoang-Xuan, K and Alentorn, A},
title = {Gut microbiome modulates the outcome in primary central nervous system lymphoma patients undergoing chemotherapy: an ancillary study from the BLOCAGE trial.},
journal = {Neuro-oncology},
volume = {},
number = {},
pages = {},
doi = {10.1093/neuonc/noaf059},
pmid = {40048707},
issn = {1523-5866},
abstract = {BACKGROUND: Primary central nervous system lymphoma (PCNSL) treatment relies on a high-dose methotrexate based chemotherapy (HD-MTX-based CT) regimen; however, whether there is a specific microbiota composition association with treatment response and clinical outcomes remains incompletely understood.

METHODS: We conducted a prospective study of PCNSL patients, included in the clinical trial NCT02313389 and the ancillary study NCT04253496 from 2020 to 2023, where patients were treated with first line HD-MTX-based polychemotherapy without a consolidation treatment. Stool (n=52), cerebrospinal fluid (CSF, n=52), and plasma samples (n=35) were collected before and/or after therapy initiation to perform metagenomic, flow cytometry, and metabolomic analyses. Plasma metabolomic data of 90 patients also included in the BLOCAGE clinical trial was subsequently used as a validation cohort.

RESULTS: Unsupervised clustering of microbial data identified two distinct gut microbial communities, differing in Parabacteroides distasonis abundance, which correlated with progression-free survival and overall survival in both uni- and multivariate analyses. Higher P. distasonis levels were linked to increased plasma betaine/valine metabolites and enhanced CD8 T cell infiltration in the CSF, suggesting a connection between gut microbiota and immune regulation. Stratifying the validation cohort by betaine/valine content confirmed these clinical associations.

CONCLUSIONS: Our findings suggest that gut microbiome communities modulate clinical outcomes in PCNSL patients undergoing standard treatment. Moreover, after future validation in external cohorts, the quantification of Parabacteroides distasonis could potentially provide a basis for patient stratification and guide personalized therapeutic strategies in the near future.},
}

@article {pmid40048584,
year = {2025},
author = {Loublier, C and Costa, M and Taminiau, B and Lecoq, L and Daube, G and Amory, H and Cesarini, C},
title = {Longitudinal Changes in Fecal Microbiota During Hospitalization in Horses With Different Types of Colic.},
journal = {Journal of veterinary internal medicine},
volume = {39},
number = {2},
pages = {e70039},
pmid = {40048584},
issn = {1939-1676},
support = {//Fonds Spéciaux de Recherche (DYSBIOHORSIRS)/ ; //Fonds De La Recherche Scientifique - FNRS (Veterinary MD. Ph.D. VETE-CCD)/ ; },
mesh = {Animals ; Horses ; *Colic/veterinary/microbiology ; *Horse Diseases/microbiology ; *Feces/microbiology ; Male ; Female ; Prospective Studies ; Hospitalization ; Gastrointestinal Microbiome ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: Research on fecal microbiota changes during hospitalization of horses with colic is emerging.

OBJECTIVES: Describe changes of the fecal microbiota during hospitalization of horses with colic caused by inflammatory (INFL), simple (SIMPLE), and strangulated (STR) obstructions, and investigate associations with survival.

ANIMALS: Twenty-three horses with colic: 9 in INFL, 5 in STR, and 9 in SIMPLE groups. Seventeen horses survived, and 6 were euthanized.

METHODS: Prospective observational study. Fecal samples were collected on admission (D1), on days 3 (D3) and 5 (D5). Bacterial taxonomy profiling was obtained by V1V3 16S amplicon sequencing. Data were compared using a 2-way permutational analysis of variance (PERMANOVA). Linear discriminant analysis Effect Size (LEfSE) analysis identified significant bacterial population differences, with significance set at p < 0.05 and a linear discriminant analysis (LDA) cut-off > 3.0.

RESULTS: Alpha diversity indices remained stable during hospitalization within each colic group. However, at D5, the INFL group had significantly higher richness (p < 0.01) and diversity (Shannon, p < 0.001 and Simpson, p < 0.05) than other colic types. Beta diversity (Jaccard membership and Bray-Curtis indices) was significantly different in the INFL compared to SIMPLE and STR groups (both p < 0.001) but not between SIMPLE and STR. Beta diversity membership analysis by analysis of molecular variance (AMOVA) indicated a significant difference between survivors and non-survivors within the INFL group (p < 0.01). Increased relative abundances of Bacilliculturomica and Saccharofermentans were associated with survival.

CONCLUSIONS: Microbiota showed no significant variation over 5 days of hospitalization. Colic type influenced fecal microbiota more than hospitalization duration. Specific bacterial populations may differ between survival and non-survival groups.},
}

Animals
Horses
*Colic/veterinary/microbiology
*Horse Diseases/microbiology
*Feces/microbiology
Male
Female
Prospective Studies
Hospitalization
Gastrointestinal Microbiome
Bacteria/classification/genetics/isolation & purification

@article {pmid40048569,
year = {2025},
author = {Loy, M and Mahadevan, R and Mascarenhas, M and Walsh, L},
title = {Culinary Medicine.},
journal = {Pediatric annals},
volume = {54},
number = {3},
pages = {e83-e87},
doi = {10.3928/19382359-20250108-02},
pmid = {40048569},
issn = {1938-2359},
mesh = {Humans ; *Cooking ; Child ; },
abstract = {The use of food as medicine to treat illness and maintain health has ancient roots across various cultures. Despite significant scientific progress during the past 2 centuries linking diet, the microbiome, and overall health, modern challenges persist due to sociocultural factors, aggressive food marketing, and insufficient nutritional education. However, there is increasing support from health systems, insurers, nonprofits, philanthropic organizations, and government bodies to develop health policies that promote access to high-quality meals for disease prevention and management. Culinary medicine is now incorporated into undergraduate and postgraduate medical education through electives, certifications in culinary and lifestyle medicine, and continuing medical education conferences. There is substantial potential for culinary medicine to enhance patient care across diverse populations and settings, including individual consultations, group visits, schools, farms, and community gardens. Collaborative efforts among stakeholders can advance practical solutions to translate scientific knowledge into effective policy and practice. [Pediatr Ann. 2025;54(3):e83-e87.].},
}

Humans
*Cooking
Child

@article {pmid40048434,
year = {2025},
author = {Meka, AF and Bekele, GK and Abas, MK and Gemeda, MT},
title = {Exploring bioactive compound origins: Profiling gene cluster signatures related to biosynthesis in microbiomes of Sof Umer Cave, Ethiopia.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0315536},
pmid = {40048434},
issn = {1932-6203},
mesh = {*Multigene Family ; *Microbiota/genetics ; *Caves/microbiology ; Ethiopia ; Bacteria/genetics/metabolism/classification ; Soil Microbiology ; Secondary Metabolism/genetics ; },
abstract = {Sof Umer Cave is an unexplored extreme environment that hosts novel microbes and potential genetic resources. Microbiomes from caves have been genetically adapted to produce various bioactive metabolites, allowing them to survive and tolerate harsh conditions. However, the biosynthesis-related gene cluster signatures in the microbiomes of Sof Umer Cave have not been explored. Therefore, high-throughput shotgun sequencing was used to explore biosynthesis-related gene clusters (BGCs) in the microbiomes of Sof Umer Cave. The GeneAll DNA Soil Mini Kit was used to extract high-molecular-weight DNA from homogenized samples, and the purified DNA was sequenced using a NovaSeq PE150. According to the Micro-RN database, the most common microbial genera in Sof Umer Cave are Protobacteria, Actinobacteria, Verrucomicrobiota, and Cyanobacteria. The biosynthesis-related gene clusters were annotated and classified, and the BGCs were predicted using antiSMASH and NAPDOS1. A total of 460 putative regions of BGCs encoding a wide range of secondary metabolites were identified, including RiPP (47.82%), terpene (19.57%), NRPS (13.04%), hybrid (2.18%), and other newly annotated (10.87%) compounds. Additionally, the NAPDOS pipeline identified a calcium-dependent antibiotic gene cluster from Streptomyces coelicolor, an actinomycin gene cluster from Streptomyces chrysomallus, and a bleomycin gene cluster from Streptomyces verticillus. These findings highlight the untapped biosynthetic potential of the Sof Umer Cave microbiome, as well as its potential for the discovery of natural products.},
}

*Multigene Family
*Microbiota/genetics
*Caves/microbiology
Ethiopia
Bacteria/genetics/metabolism/classification
Soil Microbiology
Secondary Metabolism/genetics

@article {pmid40047941,
year = {2025},
author = {Koshy, NG and Rajan, SA and Anith, KN and Chitra, N and Soumya, VI and Scaria, TM and Beena, R},
title = {Beyond the pink: uncovering the secrets of pink pigmented facultative methylotrophs.},
journal = {Archives of microbiology},
volume = {207},
number = {4},
pages = {80},
pmid = {40047941},
issn = {1432-072X},
mesh = {*Methylobacterium/metabolism ; Plants/microbiology ; Microbiota/physiology ; Pigmentation ; Plant Development ; Agriculture/methods ; Ecosystem ; },
abstract = {Pink Pigmented Facultative Methylotrophs (PPFMs) belong to a diverse group of methylotrophic bacteria predominantly in the genus Methylobacterium, and are known for their beneficial interactions with plants. They can use single-carbon compounds, such as methanol, formate, formaldehyde and methyl amines as well as various multi-carbon substrates as sources of carbon and energy. PPFMs are characterized by their distinctive pink pigmentation and are commonly found in the phyllosphere, where they play a major role in promoting plant growth through various mechanisms; These mechanisms include the production of phytohormones, enhancing nutrient acquisition, mitigating abiotic stresses and providing biocontrol of phytopathogens. Due to their eco-friendly nature PPFMs are viewed as promising alternatives to synthetic fertilizers and pesticides in green agriculture. Furthermore, the ecological significance of PPFMs extends beyond their direct interactions with host plants. They also contribute to the resilience of ecosystems by participating in the cycling of nutrients in the environment. As the importance of the plant microbiome in agriculture becomes more recognized, the potential of PPFMs to support sustainable farming practices and contribute to environmental health is increasingly evident. This underscores their relevance in addressing global agricultural challenges.},
}

*Methylobacterium/metabolism
Plants/microbiology
Microbiota/physiology
Pigmentation
Plant Development
Agriculture/methods
Ecosystem

@article {pmid40047940,
year = {2025},
author = {Chen, P and Liu, Q and Shi, H and Liu, Z and Yang, X},
title = {Choline metabolism disorder induced by Prevotella is a risk factor for endometrial cancer in women with polycystic ovary syndrome.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {285},
pmid = {40047940},
issn = {1573-4978},
support = {2023A1515110325//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A1515012940//Guangdong Natural Science Foundation/ ; 23ptpy106//the Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; },
mesh = {Humans ; Female ; *Polycystic Ovary Syndrome/microbiology/complications/metabolism ; *Endometrial Neoplasms/microbiology ; *Prevotella ; *Choline/metabolism ; Adult ; Risk Factors ; Microbiota ; Vagina/microbiology ; Dysbiosis/complications ; RNA, Ribosomal, 16S/genetics ; Lipid Metabolism ; Transcriptome/genetics ; },
abstract = {BACKGROUND: Polycystic ovary syndrome (PCOS) is an endocrine disorder associated with an increased risk of endometrial cancer, potentially mediated by vaginal microbiota dysbiosis and hormonal disturbances. This study investigates how hormonal imbalances in PCOS patients affect the vaginal microbiome and choline metabolism, thereby influencing endometrial cancer risk.

METHODS: In this observational study, 70 women were enrolled, including 36 with PCOS and 34 controls. We analyzed their vaginal microbiota, lipid metabolism, and endometrial transcriptome using 16S rRNA sequencing, untargeted lipidomics, and transcriptomic sequencing.

RESULTS: The PCOS group showed significant differences in vaginal microbiota composition, notably an increase in LPS-producing Prevotella spp. Functional analyses indicated activation of LPS biosynthesis and inflammatory signaling pathways. Lipidomics revealed disrupted choline metabolism, with alterations in phosphocholine and total choline levels. Transcriptomic data highlighted the up-regulation of inflammatory and metabolic dysregulation pathways.

CONCLUSIONS: Hormonal imbalances in PCOS contribute to significant changes in the vaginal microbiome and metabolic pathways, increasing the risk of endometrial cancer. These findings suggest potential therapeutic targets for reducing cancer risk in this population.},
}

Humans
Female
*Polycystic Ovary Syndrome/microbiology/complications/metabolism
*Endometrial Neoplasms/microbiology
*Prevotella
*Choline/metabolism
Adult
Risk Factors
Microbiota
Vagina/microbiology
Dysbiosis/complications
RNA, Ribosomal, 16S/genetics
Lipid Metabolism
Transcriptome/genetics

@article {pmid40047510,
year = {2025},
author = {Shuman, JHB and Lin, AS and Westland, MD and Bryant, KN and Fortier, GE and Piazuelo, MB and Reyzer, ML and Judd, AM and Tsui, T and McDonald, WH and McClain, MS and Schey, KL and Algood, HM and Cover, TL},
title = {Helicobacter pylori CagA and Cag type IV secretion system activity have key roles in triggering gastric transcriptional and proteomic alterations.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0059524},
doi = {10.1128/iai.00595-24},
pmid = {40047510},
issn = {1098-5522},
abstract = {Colonization of the human stomach with cag pathogenicity island (PAI)-positive Helicobacter pylori strains is associated with increased gastric cancer risk compared to colonization with cag PAI-negative strains. To evaluate the contributions of the Cag type IV secretion system (T4SS) and CagA (a secreted bacterial oncoprotein) to gastric molecular alterations relevant for carcinogenesis, we infected Mongolian gerbils with a Cag T4SS-positive wild-type (WT) H. pylori strain, one of two Cag T4SS mutant strains (∆cagT or ∆cagY), or a ∆cagA mutant for 12 weeks. Histologic staining revealed a biphasic distribution of gastric inflammation severity in WT-infected animals and minimal inflammation in animals infected with mutant strains. Atrophic gastritis (a premalignant condition), dysplasia, and gastric adenocarcinoma were only detected in WT-infected animals with high inflammation scores. Transcriptional profiling, liquid chromatography-tandem mass spectrometry analysis of micro-extracted tryptic peptides, and imaging mass spectrometry revealed more than a thousand molecular alterations in gastric tissues from WT-infected animals with high inflammation scores compared to uninfected tissues and few alterations in tissues from other groups of infected animals. Proteins with altered abundance in animals with severe Cag T4SS-induced inflammation mapped to multiple pathways, including the complement/coagulation cascade and proteasome pathway. Proteins exhibiting markedly increased abundance in tissues from H. pylori-infected animals with severe inflammation included calprotectin components, proteins involved in proteasome activation, polymeric immunoglobulin receptor (PIGR), interferon-inducible guanylate-binding protein (GBP2), lactoferrin, lysozyme, superoxide dismutase, and eosinophil peroxidase. These results demonstrate key roles for CagA and Cag T4SS activity in promoting gastric mucosal inflammation, transcriptional alterations, and proteomic alterations relevant to gastric carcinogenesis.IMPORTANCEHelicobacter pylori colonizes the stomachs of about half of humans worldwide, and its presence is the primary risk factor for the development of stomach cancer. H. pylori strains isolated from humans can be broadly classified into two groups based on whether they contain a chromosomal cag pathogenicity island, which encodes a secreted effector protein (CagA) and components of a type IV secretion system (T4SS). In experiments using a Mongolian gerbil model, we found that severe gastric inflammation and gastric transcriptional and proteomic alterations related to gastric cancer development were detected only in animals infected with a wild-type H. pylori strain containing CagA and an intact Cag T4SS. Mutant strains lacking CagA or Cag T4SS activity successfully colonized the stomach without inducing detectable pathologic host responses. These findings illustrate two different patterns of H. pylori-host interaction.},
}

@article {pmid40047509,
year = {2025},
author = {London, LY and Lim, CH and Modliszewski, JL and Siddiqui, NY and Sysoeva, TA},
title = {Draft genomes of Klebsiella pneumoniae and Streptococcus anginosus strains found in the urine of the same female patient.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0131124},
doi = {10.1128/mra.01311-24},
pmid = {40047509},
issn = {2576-098X},
abstract = {Here, we report the draft genomes of Klebsiella pneumoniae 5008-1 and Streptococcus anginosus 5008-2 strains isolated from a catheterized urine sample obtained from an asymptomatic postmenopausal woman diagnosed with recurrent urinary tract infection and receiving vaginal estrogen cream.},
}

@article {pmid40047508,
year = {2025},
author = {Mori, A and Kudoh, M and Kuboniwa, M and Rückert-Reed, C and Busche, T and Eisenhut, M and Fukusaki, E and Bräutigam, A and Laker, B},
title = {Closed genome sequence of Fretibacterium fastidiosum, a potential contributor to periodontal disease.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0000425},
doi = {10.1128/mra.00004-25},
pmid = {40047508},
issn = {2576-098X},
abstract = {Human oral microbiome consists of diverse bacteria. Not all oral bacteria are well characterized due to challenges in cultivation in vitro. In this study, we report the closed genome sequence of one of the recently identified oral bacteria, Fretibacterium fastidiosum.},
}

@article {pmid40047452,
year = {2025},
author = {Hou, Z and Wang, M and Xu, H and Wang, M and Hannula, SE},
title = {Differential effects of pine wilt disease on root endosphere, rhizosphere, and soil microbiome of Korean white pine.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0232624},
doi = {10.1128/spectrum.02326-24},
pmid = {40047452},
issn = {2165-0497},
abstract = {Pine wilt disease (PWD), caused by pinewood nematodes, is highly destructive to pine forests in Asia and Europe, including Korean white pine (Pinus koraiensis). The microbiome in the needles and trunk of Pinus spp. are recognized to play key roles in resistance against PWD. However, the role of root and soil microbiomes in the resistance remains unclear. This study compares bacterial and fungal communities in the root endosphere, rhizosphere soil, and bulk soil of diseased versus healthy P. koraiensis. Results showed that PWD increased the α-diversity of fungi in rhizosphere soil but did not affect the microbial diversity in the root endosphere or bulk soil. The composition of bacterial and fungal communities in rhizosphere and bulk soils was significantly altered by PWD. Specifically, the relative abundance of Planctomycetes decreased, and the relative abundance of Tremellomycetes increased, while Agaricomycetes decreased in both rhizosphere and bulk soils after infestation with PWD, respectively. Relative abundances of Chloroflexi and Verrucomicrobia increased, while Proteobacteria decreased in bulk soil following PWD. Relative abundances of Leotiomycetes and Eurotiomycetes increased in the rhizosphere soil and bulk soil following PWD, respectively. Furthermore, with the host plant infestation by PWD, the relative abundance of ectomycorrhizal fungi decreases, while that of saprotrophic fungi increases in both rhizosphere and bulk soils. Our results revealed that PWD significantly affects the soil microbiomes of P. koraiensis, with varying impacts across different plant-soil compartments. This study provides insights into how root and soil microbiomes respond to PWD, enhancing our understanding of the disease's ecological consequences.IMPORTANCEThe belowground microbiome is often sensitive to infection of forest diseases and is also recognized as a potential reservoir for selection of microbial agents against PWD. Our study demonstrates that the dynamics of belowground microbiome following natural infection of PWD are compartment and taxa specific, with varying degrees of responses in both diversity and composition of bacterial or fungal communities across the root endosphere, rhizosphere soil, and bulk soil. The results highlight the importance of utilizing appropriate plant-soil compartments and microbial taxa to understand the ecological consequences of the destructive PWD.},
}

@article {pmid40047321,
year = {2025},
author = {Liang, Z and Liang, Z and Hu, HW and Howell, K and Fang, Z and Zhang, P},
title = {Food substances alter gut resistome: Mechanisms, health impacts, and food components.},
journal = {Comprehensive reviews in food science and food safety},
volume = {24},
number = {2},
pages = {e70143},
pmid = {40047321},
issn = {1541-4337},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; Phytochemicals/pharmacology ; Probiotics/pharmacology ; Animals ; Drug Resistance, Bacterial ; Functional Food ; Drug Resistance, Microbial ; Diet ; },
abstract = {Antibiotics are effective in treating bacterial infections, but their widespread use has spurred antibiotic resistance, which is linked closely with human disease. While dietary components are known to influence the gut microbiome, specific effects on the gut resistome-the collection of antibiotic-resistant genes in the gut-remain underexplored. This review outlines the mechanisms of antibiotic action and the development of resistance, emphasizing the connection between the gut resistome and human diseases such as metabolic disorders, cardiovascular disease, liver disease, and nervous system disorders. It also discusses the effects of diet habits and dietary components, including bioactive macronutrients, phytochemicals, and probiotics, on the composition of the gut resistome by enhancing antibiotic efficacy and potentially reducing resistance. This review highlights the emerging trend of increasing interest in functional foods aimed at targeting the gut resistome and a growing focus on bioactive plant compounds with the potential to modulate antibiotic resistance.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/pharmacology
Phytochemicals/pharmacology
Probiotics/pharmacology
Animals
Drug Resistance, Bacterial
Functional Food
Drug Resistance, Microbial
Diet

@article {pmid40047190,
year = {2025},
author = {Ríos-Osorio, N and Ladino, LG and Guerrero-Torres, M},
title = {Structure, biology, and function of peri-implant soft tissues in health and disease: a comprehensive review of the literature.},
journal = {Journal of periodontal & implant science},
volume = {},
number = {},
pages = {},
doi = {10.5051/jpis.2402080104},
pmid = {40047190},
issn = {2093-2278},
abstract = {The morphogenesis of peri-implant soft tissues following surgical trauma, along with the nature, topography, and design of implant-prosthetic material surfaces, leads to peri-implant tissues that exhibit unique histological and morphological characteristics. It has been shown that mucosal phenotypes with a mucosal thickness of at least 2 mm and a keratinised mucosa width of at least 2 mm promote proper integration and a biological seal at the mucosa-implant interface. This seal prevents pathogen penetration, protects the underlying peri-implant bone, and reduces susceptibility to inflammatory peri-implant diseases (IPDs). Furthermore, even under ideal conditions, peri-implant soft tissues demonstrate less mechanical resistance, stability, and hermeticity compared to periodontal tissues. These deficiencies are directly associated with both the onset and progression of IPDs such as peri-implant mucositis (PM) and peri-implantitis (PI). Over recent decades, the prevalence of PM and PI has risen, making them the primary causes of implant failure. Given that the characteristics of peri-implant mucosa are closely linked to the progression of these diseases, a deep understanding of the biology of peri-implant soft tissues is crucial for developing strategies to either avoid or minimise the impact of IPDs on implant therapy outcomes. This comprehensive review of the literature aims to provide a precise and detailed description of the structure, biology, and function of peri-implant soft tissues, starting from their formation process and linking their morphogenic characteristics to the establishment and evolution of IPDs. Additionally, the composition of the microbiome and the most relevant anti/pro-inflammatory mediators involved in the development of IPDs are summarised.},
}

@article {pmid40047100,
year = {2025},
author = {Nicol, MR and Olsem, CM},
title = {Hormones, microbes, and PrEP drugs in the female genital tract.},
journal = {Expert opinion on drug metabolism & toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17425255.2025.2476792},
pmid = {40047100},
issn = {1744-7607},
abstract = {INTRODUCTION: For HIV medications intended for HIV prevention, it is critical to achieve exposures in that will provide reliable protection to the FGT. The female genital tract (FGT) is a complex and heterogenous environment.

AREAS COVERED: We reviewed what is known about drug transport and metabolism specific to female genital tissues. We performed a literature search using key words in PubMed and Google Scholar on articles published inclusive of August 2024. We then discuss the impact of sex steroid hormones and vaginal microbiome on the genital tract pharmacology of drugs used for PrEP.

EXPERT OPINION: Better characterization of FGT pharmacology can improve PrEP options for women. Better models that can fully capture the complexities of the FGT to evaluate pharmacokinetic-pharmacodynamic relationships in the context of the complex microenvironment of the FGT will need to be developed and validated to move the field forward.},
}

@article {pmid40047092,
year = {2025},
author = {Husain, N and Kumar, A and Anbazhagan, AN and Gill, RK and Dudeja, PK},
title = {Intestinal Luminal Anion Transporters and their Interplay with Gut Microbiome and Inflammation.},
journal = {American journal of physiology. Cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpcell.00026.2025},
pmid = {40047092},
issn = {1522-1563},
support = {BX002011//U.S. Department of Veterans Affairs (VA)/ ; BX005862//U.S. Department of Veterans Affairs (VA)/ ; BX006626//U.S. Department of Veterans Affairs (VA)/ ; I01BX006177//U.S. Department of Veterans Affairs (VA)/ ; 1IK6BX005242//U.S. Department of Veterans Affairs (VA)/ ; R01DK54016//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; R56DK92441//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
abstract = {The intestine, as a critical interface between the external environment and the internal body, plays a central role in nutrient absorption, immune regulation, and maintaining homeostasis. The intestinal epithelium, composed of specialized epithelial cells, hosts apical anion transporters that primarily mediate the transport of chloride and bicarbonate ions, essential for maintaining electrolyte balance, pH homeostasis, and fluid absorption/secretion. Additionally, the intestine hosts a diverse population of gut microbiota that plays a pivotal role in various physiological processes including nutrient metabolism, immune regulation and maintenance of intestinal barrier integrity, all of which are critical for host gut homeostasis and health. The anion transporters and gut microbiome are intricately interconnected, where alterations in one can trigger changes in the other leading to compromised barrier integrity and increasing susceptibility to pathophysiological states including gut inflammation. This review focuses on the interplay of key apical anion transporters including Down Regulated in Adenoma (DRA, SLC26A3), Putative Anion Transporter-1 (PAT1, SLC26A6) and Cystic Fibrosis Transmembrane Conductance Regulator (CFTR, ABCC7) with the gut microbiome, barrier integrity and their relationship to gut inflammation.},
}

@article {pmid40047013,
year = {2025},
author = {Alverdy, J},
title = {Unpacking the sepsis controversy.},
journal = {Trauma surgery & acute care open},
volume = {10},
number = {1},
pages = {e001733},
pmid = {40047013},
issn = {2397-5776},
abstract = {Despite its many definitions and revisions, consensus statements and clinical guidelines, the term 'sepsis' continues to be referred to as a discrete clinical entity that is often claimed to be a direct cause of mortality. The assertion that sepsis can be defined as a 'life-threatening organ dysfunction caused by a dysregulated host response to infection,' has led to a field dominated by failed clinical trials informed by host-centered, pathogen-agnostic, animal experiments in which animal models do not recapitulate the clinical condition. The observations from the National Health Service from England that claim that 77.5% of sepsis deaths occur in those aged 75 years or older and those from the USA indicating that most patients dying of sepsis have also been diagnosed with 'hospice qualifying conditions,' seem to refute the assertion that sepsis is caused by, rather than associated with, a 'dysregulated host response.' This piece challenges the current conceptual framework that forms the basis of the sepsis definition. Here we posit that as a result of both its definition and the use of inappropriate animal models, ineffective clinical treatments continue to be pursued in this field.},
}

@article {pmid40046939,
year = {2025},
author = {Prokopov, AY and Gazitaeva, ZI and Sidorina, AN and Peno-Mazzarino, L and Radionov, N and Drobintseva, AO and Kvetnoy, IM},
title = {Influence of Injectable Hyaluronic Gel System on Skin Microbiota, Skin Defense Mechanisms and Integrity (Ex vivo Study).},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {18},
number = {},
pages = {459-473},
pmid = {40046939},
issn = {1178-7015},
abstract = {OBJECTIVE: The influence of injectable hyaluronic gels on skin's microbiota is unclear. As well, skin microbiota is a key factor modulating final effect of injectable gels. The ex-vivo study was aimed at alterations following hyaluronic acid injection into the dermis in non-sterile skin surface conditions.

METHODS: Ex vivo human skin explants in the presence or absence of either S. epidermidis or S. aureus, were treated with either control excipient (0.9% sodium chloride) or test product (Hyaluronic acid injectable S, HA-S). Bacterial analysis was performed, as well as skin structural integrity. Histological imaging and immunostaining analysis in the presence of skin markers: epidermal (CD1a, Toll-like receptor 2 (TLR2), Beta-defensin-3 (BD3), CCN1) and dermal (DC-SIGN, Decorin) were then performed.

RESULTS: The injection of control excipient E and test product P, both associated with bacterial deposits, induced similar noticeable increase of S. epidermidis growth over 4 days, but no noticeable effect on growth of S. aureus. The injection of control excipient, associated with bacterial deposits, showed epidermal and dermal alterations increased with time. It was observed significant increase of epidermal CD1a, TLR2, CCN1 and dermal DC-SIGN, Decorin on Day 2. The injection of test product, associated with bacterial deposits, in contrast to injection of control excipient, associated with bacterial deposits, induced very slight but significant improvement of epidermal viability as well as significant decrease of epidermal TLR2, BD3, CCN1 and dermal DC-SIGN on Day 2.

CONCLUSION: Our investigation showed that both intradermal injections, HA-based solution or control excipient, trigger short-term skin microbiota growth. We indicate strong influence of non-sterile skin surface conditions on human skin explant viability when skin barrier damaged by injection puncture and highlights differences of epidermal/dermal response depended on injected composition.},
}

@article {pmid40046910,
year = {2024},
author = {Eslami, M and Naderian, R and Ahmadpour, A and Shushtari, A and Maleki, S and Mohammadian, P and Amiri, A and Janbazi, M and Memarian, M and Yousefi, B},
title = {Microbiome structure in healthy and pregnant women and importance of vaginal dysbiosis in spontaneous abortion.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1401610},
pmid = {40046910},
issn = {2235-2988},
mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; *Dysbiosis/microbiology ; *Microbiota ; *Abortion, Spontaneous/microbiology ; Lactobacillus ; Pregnant People ; },
abstract = {The vaginal microbiome of healthy women is dominated by Lactobacillus spp. A variety of illnesses, such as vaginosis, sexually transmitted infections (STIs), failed implantation, premature birth (PTB), and preterm pre-labor membrane rupture, are brought on by an unbalanced microbiota. Pregnancy is associated with a decrease in the metabolic capacity of the vaginal resident microbiome, which is consistent with a change to a less complex Lactobacillus-dominated microbiome. Age, race, sexual intercourse, smoking, IUD, contraception, lifestyle, and diet all affect the makeup of the vaginal microbiome. Moreover, physiological events including menarche, the menstrual cycle, pregnancy, menopause, and other hormonal changes have an impact on the vaginal microbiome. The vaginal microbiome is significantly disrupted by the menstrual cycle, with significant changes toward a more varied microbiota occurring around menstruation. Several major factors maintain or disrupt the vaginal microbiome including ethnic group, menstruation cycle, and pregnancy which are discussed in this section. In the index pregnancy, the vaginal microbiota of women who had already given birth, or had just experienced an induced or spontaneous abortion, was qualitatively and quantitatively different from that of women who were having their first child. Early pregnancy vaginal microbiome depletion is a risk factor for early pregnancy miscarriage. Although, early pregnancy miscarriage is not always caused by a high bacterial diversity and quantity of lactobacilli. Lactobacillus protects against pathogens through the production of antibacterial compounds such as lactic acid and bacteriocins.},
}

Humans
Female
*Vagina/microbiology
Pregnancy
*Dysbiosis/microbiology
*Microbiota
*Abortion, Spontaneous/microbiology
Lactobacillus
Pregnant People

@article {pmid40046742,
year = {2025},
author = {Jiang, T and Du, P and Liu, D and Chen, H and Ma, Y and Hu, B and Li, J and Jiang, H and Li, X},
title = {Exploring the glucose-lowering and anti-inflammatory immune mechanism of artemether by AMPK/mTOR pathway and microbiome based on multi-omics.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1520439},
pmid = {40046742},
issn = {1663-9812},
abstract = {BACKGROUND: Diabetes mellitus (DM) is a metabolic disease with high morbidity, which significantly affects human life and health expenditures. Previous studies have demonstrated that artemether (ATM) has anti-diabetes and anti-inflammation activities, but its mechanism has not been fully elucidated. This research aimed to elucidate the impact of ATM on glucolipid metabolism in a type 2 diabetes mellitus (T2DM) model db/db mice and what kind of role the gut microbiota played, and explored the underlying mechanisms involved.

METHODS: C57BL/KsJ-db/db mice were treated with 80 and 160 mg/kg of ATM for 8 weeks, with metformin as a positive control.

RESULTS: ATM treatment (160 mg/kg) observably ameliorated insulin resistance (IR), hyperglycemia, hyperlipemia and pathological injury in the liver and pancreas. In addition, ATM significantly decreased the expression of TNF-α, IL-1β, IL-6, NF-κB and IL-17A, and significantly increased the level of IL-10 in diabetic mice. 16S rRNA sequencing and targeted GC-MS metabolomics result indicated that ATM restored gut microbiota dysbiosis based on increasing beneficial bacteria Lactobacillus and reducing pathogenic bacteria Helicobacter and Prevotella leading to the accumulation of propionic and valeric acids and the reduction of lipopolysaccharides (LPS) release, intestinal inflammation and intestinal barrier damage. Network pharmacology and metabolomics identified the AMPK/mTOR pathway as the main signaling involved in ATM improves glucolipid metabolism and inflammation in T2DM. Western blotting results revealed that ATM suppressed the phosphorylation of mTOR, P38, P65, IKBα and IRS1 whlie increased the levels of p-AMPK, TLR4, and occludin in mice liver and colon.

CONCLUSION: Taken together, ATM may modulate the composition of gut microbiota, increasing the abundance of Lactobacillus, which in turn elevates the levels of SCFAs. The elevation of SCFAs, especially propionic acid, may activate the AMPK/mTOR pathway, leading to a decrease in the levels of TNF-α, IL-1β, IL-6, NF-κB, and IL-17A, while increasing the levels of IL-10, thereby alleviating the inflammatory state and improving glucolipid metabolic disorder in T2DM. These findings laid a theoretical foundation for the clinical application of ATM in T2DM.},
}

@article {pmid40046303,
year = {2025},
author = {Ma, X and Zeng, X and Huang, Z and Li, G and Liu, R and Luo, R and Li, X and Ling, S and Wang, C and Gu, Y},
title = {Analysis of fungal microbiota diversity and potential pathogenic fungi in oral secretions and gut feces of captive giant pandas.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1522289},
pmid = {40046303},
issn = {1664-302X},
abstract = {BACKGROUND: Maintaining good oral and gut health is essential for the wellbeing of animals, and fungi are key components of the oral and gut microbiota. This study aims to explore the diversity and seasonal dynamics of oral and gut fungal communities in captive giant pandas, with a focus on their potential functional roles in health and digestion.

METHODS: In the study, we collected saliva and fecal samples from 60 captive giant pandas were collected in different seasons, oral and gut fungi were analyzed using internal transcribed spacer (ITS) amplicon sequencing. We used α and β diversity analyses to examine the differences in species diversity and composition among the different seasons. Furthermore, we validated the ITS amplicon sequencing results through fungal isolation and identification.

RESULTS: Analyses of α and β diversity revealed both the differences and similarities between the fungal communities in the oral and gut microbiomes of giant pandas. Ascomycota and Basidiomycota were predominant in both oral and gut groups, while the dominant genera in the four seasons were Cutaneotrichosporon, and unidentified_Chaetothyriales_sp. Additionally, Cladosporium and Candida were predominant in the oral and gut fungus, respectively, across all four seasons. Notably, fungal abundance and diversity in the oral microbiome were significantly higher than in the gut microbiome, a pattern observed throughout most seasons. Several potentially pathogenic fungi, such as Fusarium, Candida and Aspergillus, were detected in healthy giant pandas, with most showing increased abundance during winter. It is worth mentioning that we found a distinct bias in the functional communities of oral and gut fungi. The abundance of saprophytic fungi in the gut is relatively high, which may be related to their role in cellulose digestion.

CONCLUSION: The abundance and diversity of fungal communities in the oral cavity and gut of giant pandas exhibit significant seasonal variations. While the oral cavity hosts a higher abundance and diversity of fungi, the species composition of fungal community composition is similar to that of the intestines. The majority of gut fungi are likely derived from the oral cavity or diet, the significant seasonal variation in gut fungal community structure further suggests that long-term resident fungi may not be present in the gut.},
}

@article {pmid40046294,
year = {2025},
author = {Han, H and Xiong, H and Liu, Z and Liu, X and Wang, H and Kou, J and Yi, D and Shi, Y and Wu, H and Qiao, J},
title = {Pasteurized Akkermansia muciniphila Timepie001 ameliorates DSS-induced ulcerative colitis in mice by alleviating intestinal injury and modulating gut microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1542522},
pmid = {40046294},
issn = {1664-302X},
abstract = {INTRODUCTION: Akkermansia muciniphila (A. muciniphila), known as a next-generation probiotic, has been widely recognized for its beneficial effects in various metabolic diseases. While there is not much research whether live or pasteurized A. muciniphila has different effects on intestinal health.

METHODS: In the present study, a strain of A. muciniphila was isolated from healthy individuals, with the live and pasteurized A. muciniphila named Timepie001 and Timepie001+, respectively. They were administered to dextran sulfate sodium-induced ulcerative colitis mice to investigate their influences on the host intestinal health.

RESULTS AND CONCLUSION: The results showed that prophylactic supplementation with live and pasteurized A. muciniphila alleviates ulcerative colitis symptoms by retarding weight loss, preserving intestinal tissue structure, modulating inflammatory cytokines (TNF-α, IL-1β), and enhance the colonic mucosal barrier by upregulating the expression of tight junction protein Claudin-1. Interestingly, pasteurized A. muciniphila has a better effect compared with live A. muciniphila. Moreover, pasteurized A. muciniphila can regulates the gut microbiome to maintain intestinal homeostasis. This provides theoretical support for the widespread application of postbiotics in the food industry.},
}

@article {pmid40046174,
year = {2025},
author = {Kim, YJ and Ihrie, VM and Shi, P and Ihrie, MD and Womble, JT and Meares, AH and Granek, JA and Gunsch, CK and Ingram, JL},
title = {Glucagon-Like Peptide 1 Receptor (Glp1r) Deficiency Does Not Appreciably Alter Airway Inflammation or Gut-Lung Microbiome Axis in a Mouse Model of Obese Allergic Airways Disease and Bariatric Surgery.},
journal = {Journal of asthma and allergy},
volume = {18},
number = {},
pages = {285-305},
pmid = {40046174},
issn = {1178-6965},
abstract = {PURPOSE: High body mass index (≥30 kg/m[2]) is associated with asthma severity, and nearly 40% of asthma patients exhibit obesity. Furthermore, over 40% of patients with obesity and asthma that receive bariatric surgery no longer require asthma medication. Increased levels of glucagon-like peptide 1 (GLP-1) occur after bariatric surgery, and recent studies suggest that GLP-1 receptor (GLP-1R) signaling may regulate the gut microbiome and have anti-inflammatory properties in the lung. Thus, we hypothesized that increased GLP-1R signaling following metabolic surgery in obese and allergen-challenged mice leads to gut/lung microbiome alterations, which together contribute to improved features of allergic airways disease.

METHODS: Male and female Glp1r-deficient (Glp1r[-/-]) and replete (Glp1r[+/+]) mice were administered high fat diet (HFD) to induce obesity with simultaneous intranasal challenge with house dust mite (HDM) allergen to model allergic airway disease with appropriate controls. Mice on HFD received either no surgery, sham surgery, or vertical sleeve gastrectomy (VSG) on week 10 and were sacrificed on week 13. Data were collected with regard to fecal and lung tissue microbiome, lung histology, metabolic markers, and respiratory inflammation.

RESULTS: HFD led to metabolic imbalance characterized by lower GLP-1 and higher leptin levels, increased glucose intolerance, and alterations in gut microbiome composition. Prevalence of bacteria associated with short chain fatty acid (SCFA) production, namely Bifidobacterium, Lachnospiraceae UCG-001, and Parasutterella, was reduced in mice fed HFD and positively associated with serum GLP-1 levels. Intranasal HDM exposure induced airway inflammation. While Glp1r[-/-] genotype affected fecal microbiome beta diversity metrics, its effect was limited.

CONCLUSION: Herein, GLP-1R deficiency had surprisingly little effect on host gut and lung microbiomes and health, despite recent studies suggesting that GLP-1 receptor agonists are protective against lung inflammation.},
}

@article {pmid40045625,
year = {2025},
author = {Fan, F and Chen, L and Sun, H and Liu, JJ and Yang, K and Gu, F},
title = {Longitudinal dynamics of plasma bile acids and its associations with physiological parameters and fecal microbiome during the transition period in dairy cows.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.24.0628},
pmid = {40045625},
issn = {2765-0189},
abstract = {OBJECTIVE: The aim of this study is to investigate the dynamic changes of plasma bile acids (BA) and their associations with physiological metabolisms and fecal microbiome in transitional dairy cows.

METHODS: Twenty multiparous dairy cows were selected, the blood and fecal samples were collected at d -21, -7, +7, and +21 relative to calving. The targeted metabolome and 16s rDNA gene sequencing were applied to detect BA profiles and fecal microbial composition, respectively.

RESULTS: Totally, 32 BA species including 9 primary BAs (PBA) and 23 secondary BAs (SBA) were identified. Most of the PBAs (7 out to 9) and SBAs (15 out to 23) exhibited significant increases postpartum compared to prepartum. Notably, ursodeoxycholic acid, taurocholic acid and 7-ketodeoxycholic acid showed higher importance. Correlation analysis showed the BAs concentrations positively correlated with the concentrations of aspartate aminotransferase, total antioxidant capacity, and glutathione peroxidase, but negatively correlated with the concentrations of triglyceride significantly. A decline in bacterial alpha diversity in postpartum and significantly different β-diversity were observed. Additionally, 30 significant different genera were identified over the transition period. Among these, six and eleven biomarkers such as Alistipes and Ruminococcaceae_UCG_014 were identified at +7d and +21d, respectively. Furthermore, the abundances of choloylglycine hydrolase and 7-alpha-hydroxysteroid dehydrogenase involved in SBA biosynthesis were significantly higher postpartum as determined by PICRUSt2 analysis over the transition period.

CONCLUSION: These findings underscore a significant surge in the demand for BAs for postpartum dairy cows and highlight the potential impact of BAs on bovine health. By shedding light on these metabolic dynamics, our study offers valuable insights into strategies for optimizing the nutrition and well-being of perinatal dairy cows.},
}

@article {pmid40045464,
year = {2025},
author = {Schlicht, K and Pape, L and Rohmann, N and Knappe, C and Epe, J and Geisler, C and Pohlschneider, D and Brodesser, S and Kruse, L and Rohlfing, ME and Hartmann, K and Türk, K and Marquardt, J and Beckmann, J and von Schönfels, W and Beckmann, A and Wietzke-Braun, P and Schulte, DM and Hollstein, T and Demetrowitsch, T and Jensen-Kroll, J and Brix, F and Schreiber, S and Franke, A and Schwarz, K and Waschina, S and Laudes, M},
title = {Prediabetes and type 2 diabetes but not obesity are associated with alterations in bile acid related gut microbe-microbe and gut microbe-host community metabolism.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2474143},
doi = {10.1080/19490976.2025.2474143},
pmid = {40045464},
issn = {1949-0984},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; *Bile Acids and Salts/metabolism ; *Obesity/microbiology/metabolism ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; *Prediabetic State/microbiology/metabolism ; Female ; Bacteria/metabolism/classification/genetics/isolation & purification ; Adult ; Aged ; Taurine/metabolism ; },
abstract = {The interplay between bile acids (BAs) and metabolic diseases has gained importance in recent years, with a variety of studies investigating their relationship with diverging results. Therefore, in the present study we performed a detailed analysis of BA metabolism in 492 subjects with different metabolic phenotypes. Besides microbiomics and metabolomics this investigation included in silico analysis of community metabolism to examine metabolic interchange between different microbes as well as microbes and the human host. Our findings revealed distinct changes in the BA profiles of patients with diabetes and prediabetes, whereas obesity alone had no influence on circulating BAs. Impaired glycemic control led to increased circulating BAs, a shift toward more secondary BAs, and an increase in the ratio of glycine to taurine-conjugated BAs. Additional analyses revealed that the ratio of glycine to taurine conjugation demonstrated variations between the single BAs, cholic acid (CA), chenodeoxycholic acid (CDCA) and deoxycholic acid (DCA), regardless of the metabolic status, with CA having a higher fraction of taurine conjugation. Furthermore, we found that microbiome alterations are associated with BAs, independent of diabetes or obesity. Analysis of microbial community metabolism revealed differential relative pathway abundance in relation to diabetes, particularly those related to membrane and polyamine synthesis. Increased bacterial cross-feeding of polyamines, galactose, and D-arabinose also coincided with an increase in BA. Notably, our serum metabolome analysis mirrored several of the previously in silico predicted exchanged metabolites, especially amino acid metabolism. Therefore, targeting BA metabolism may be a future approach for the treatment of metabolic diseases, especially prediabetes and type 2 diabetes.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/metabolism
*Bile Acids and Salts/metabolism
*Obesity/microbiology/metabolism
*Gastrointestinal Microbiome
Male
Middle Aged
*Prediabetic State/microbiology/metabolism
Female
Bacteria/metabolism/classification/genetics/isolation & purification
Adult
Aged
Taurine/metabolism

@article {pmid40045434,
year = {2025},
author = {Tan, Y and Matsuzaki, J and Saito, Y and Suzuki, H},
title = {Environmental factors in gastric carcinogenesis and preventive intervention strategies.},
journal = {Genes and environment : the official journal of the Japanese Environmental Mutagen Society},
volume = {47},
number = {1},
pages = {5},
pmid = {40045434},
issn = {1880-7046},
support = {23K24188//Grant-in-Aid for Scientific Research B/ ; 24K22342//Grant-in-Aid for Challenging Research (Exploratory)/ ; },
abstract = {Gastric cancer, a significant global health concern, arises from a complex interplay of genetic and environmental factors. Helicobacter pylori (H. pylori) infection is a major risk factor that can be mitigated through eradication strategies. Epstein-Barr virus (EBV) infection causes a distinct subtype of gastric cancer called EBV-associated gastric cancer. The gastric microbiome, a dynamic ecosystem, is also involved in carcinogenesis, particularly dysbiosis and specific bacterial species such as Streptococcus anginosus. Long-term use of proton pump inhibitors and potassium-competitive acid blockers also increases the risk of gastric cancer, whereas non-steroidal anti-inflammatory drugs including aspirin may have a protective effect. Smoking significantly increases the risk, and cessation can reduce it. Dietary factors such as high intake of salt, processed meats, and red meat may increase the risk, whereas a diet rich in fruits and vegetables may be protective. Extracellular vesicles, which are small membrane-bound structures released by cells, modulate the tumor microenvironment and may serve as biomarkers for risk stratification and as therapeutic targets in gastric cancer. This review highlights the multifaceted etiology of gastric cancer and its risk factors and emphasizes the importance of a multi-pronged approach to prevention including H. pylori eradication and modification of lifestyle factors, as well as the potential of microbiome-based and EV-based interventions. Further research is needed to refine risk stratification and to develop personalized prevention strategies.},
}

@article {pmid40045431,
year = {2025},
author = {Morni, MA and William-Dee, J and Jinggong, ER and Al-Shuhada Sabaruddin, N and Azhar, NAA and Iman, MA and Larsen, PA and Seelan, JSS and Bilung, LM and Khan, FAA},
title = {Gut microbiome community profiling of Bornean bats with different feeding guilds.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {21},
pmid = {40045431},
issn = {2524-4671},
abstract = {Bats are extraordinary mammals. They have evolved to consume various dietary sources, such as insects, fruits, nectar, blood, and meat. This diversity has generated considerable interest in the scientific community, resulting in efforts to leverage bats as model organisms to study the correlation between diet and gut microbiome community. Although such studies now commonly use Next Generation Sequencing (NGS), similar studies are early in their development in Southeast Asia, especially in Malaysia, which harbours an incredibly diverse bat fauna. This study provides pioneering NGS metabarcoding information on Bornean bats. By using a high-throughput Nanopore-based 16S rRNA gene sequencing method, Bacillota, Pseudomonadota, and Campylobacterota were found in insectivorous bats and phytophagous bats. Both insectivorous and phytophagous groups harboured no dominant taxon (D = 0.076; D = 0.085). A comparative analysis of gut bacteria functional groups identified eight major groups in both phytophagous and insectivorous bats, with fermentation being the predominant group. The correlation network analysis revealed a negative correlation between the 'good bacteria' Lactobacillus and various pathogenic bacteria genera, such as Salmonella (-0.4124) and Yersinia (-0.4654), demonstrating its prebiotic characteristics. This study broadens our understanding of the bat gut microbiome from various diets, with emphasis on new data from Borneo.},
}

@article {pmid40045231,
year = {2025},
author = {Agyapong, D and Propster, JR and Marks, J and Hocking, TD},
title = {Cross-validation for training and testing co-occurrence network inference algorithms.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {74},
pmid = {40045231},
issn = {1471-2105},
support = {2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; },
mesh = {*Algorithms ; *Microbiota ; Computational Biology/methods ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.

RESULTS: Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.

CONCLUSIONS: Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.},
}

*Algorithms
*Microbiota
Computational Biology/methods
Bacteria/genetics/classification

@article {pmid40045185,
year = {2025},
author = {Freund, L and Hung, C and Topacio, TM and Diamond, C and Fresquez, A and Lyons, TW and Aronson, EL},
title = {Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {120},
pmid = {40045185},
issn = {1471-2180},
support = {NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; },
mesh = {California ; *Sulfur/metabolism ; *Microbiota ; *Lakes/microbiology ; *Seawater/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Seasons ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Biodiversity ; },
abstract = {BACKGROUND: Microorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California's largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.

RESULTS: We observed that the water column microbiome significantly varied by season (R[2] = 0.59, P = 0.003). Temperature (R[2] = 0.27, P = 0.004), dissolved organic matter (R[2] = 0.13, P = 0.004), and dissolved oxygen (R[2] = 0.089, P = 0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons.

CONCLUSIONS: Our work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea's sulfur cycle, dust proliferation, and respiratory distress experienced by the local population.},
}

California
*Sulfur/metabolism
*Microbiota
*Lakes/microbiology
*Seawater/microbiology/chemistry
*Bacteria/classification/genetics/metabolism/isolation & purification
*Seasons
Phylogeny
RNA, Ribosomal, 16S/genetics
Ecosystem
Biodiversity

@article {pmid40045177,
year = {2025},
author = {Torshizi Esfahani, A and Zafarjafarzadeh, N and Vakili, F and Bizhanpour, A and Mashaollahi, A and Karimi Kordestani, B and Baratinamin, M and Mohammadpour, S},
title = {Gut Microbiome in Colorectal Cancer: Metagenomics from Bench to Bedside.},
journal = {JNCI cancer spectrum},
volume = {},
number = {},
pages = {},
doi = {10.1093/jncics/pkaf026},
pmid = {40045177},
issn = {2515-5091},
abstract = {Colorectal cancer (CRC) is a major global health challenge. Emerging research highlights the pivotal role of the gut microbiota in influencing CRC risk, progression, and treatment response. Metagenomic approaches, especially high-throughput shotgun sequencing, have provided unprecedented insights into the intricate connections between the gut microbiome and CRC. By enabling comprehensive taxonomic and functional profiling, metagenomics has revealed microbial signatures, activities, and biomarkers associated with colorectal tumorigenesis. Furthermore, metagenomics has shown a potential to guide patient stratification, predict treatment outcomes, and inform microbiome-targeted interventions. Despite remaining challenges in multi-omics data integration, taxonomic gaps, and validation across diverse cohorts, metagenomics has propelled our comprehension of the intricate gut microbiome-CRC interplay. This review underscores the clinical relevance of microbial signatures as potential diagnostic and prognostic tools in CRC. Furthermore, it discusses personalized treatment strategies guided by this omics' approaches.},
}

@article {pmid40044961,
year = {2025},
author = {El-Baz, AM and El-Mahmoudy, AA and Saber, S and ElRakaiby, MT},
title = {The coadministration of Lactobacillus probiotic augments the antitumor effect of telmisartan in rats.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {38},
pmid = {40044961},
issn = {2191-0855},
abstract = {Colorectal cancer (CRC) is a prevalent disease with a high mortality rate and is significantly affected by microbial dysbiosis. Recent research suggests that modulation of the gut microbiome can have therapeutic benefits and that Angiotensin-II Type 1 Receptor (AT1R) can stimulate cell growth, angiogenesis, and resistance to apoptosis in various cancers. In this study, the adjunctive administration of Lactobacillus spp. and telmisartan, an AT1R blocker, was explored in the treatment of CRC. The effect of telmisartan and a mixture of probiotic species, Lactobacillus delbrueckii and Lactobacillus fermentum, was assessed on key biomarkers and selected gut microbiota taxa in 1,2-dimethylhydrazine-induced CRC in rats. Angiogenesis, inflammation, and apoptosis were assessed by measuring vascular endothelial growth factor (VEGF), carcinoembryonic antigen (CEA), Interleukin 6 (IL-6), and Annexin V levels, respectively. The relative abundance of selected gut microbial taxa, including Bacteroides spp., Clostridium spp., Clostridium coccoides, Ruminococcus spp., and Lactobacillus spp. was analyzed to determine the change in the microbial composition in the different experimental groups of the animal model. This study demonstrated that the unique combination therapy using a Lactobacillus mixture and telmisartan effectively reduced VEGF and IL-6 levels, indicating decreased angiogenesis and inflammation. Lactobacillus spp. co-administration with telmisartan boosted programmed cell death, reversed dysbiosis, improved histopathological outcomes, and reduced CEA levels. These findings offer a new perspective on the role of Lactobacillus spp. and telmisartan in CRC treatment. Further research on their adjunctive use and therapeutic potential are needed to enhance clinical efficacy.},
}

@article {pmid40044917,
year = {2025},
author = {Štůsková, K and Vavřiník, A and Hakalová, E and Čechová, J and Gramaje, D and Eichmeier, A},
title = {Arbuscular mycorrhizal fungi strongly influence the endorhizosphere of grapevine rootstock with soil type as a key factor.},
journal = {Mycorrhiza},
volume = {35},
number = {2},
pages = {17},
pmid = {40044917},
issn = {1432-1890},
support = {CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; },
mesh = {*Mycorrhizae/physiology ; *Vitis/microbiology ; *Soil Microbiology ; *Soil/chemistry ; Czech Republic ; Plant Roots/microbiology ; Mycobiome ; Basidiomycota/genetics/physiology ; Rhizosphere ; Phosphorus/metabolism/analysis ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) play a crucial role in enhancing the health and productivity of host plants, including grapevine. By forming symbiotic relationships with plant roots, AMF significantly improve water uptake and nutrient absorption, particularly phosphorus (P) and nitrogen (N). This study evaluated the microbiome composition and AMF colonization in the grapevine endorhizosphere across five wine-growing sub-regions in the Czech Republic. In all five sub-regions, in terms of composition of the fungal microbiome, the phyla Ascomycetes and Basidiomycetes were most numerous. Additionally, the study confirmed that LSU primers are more sensitive than ITS primers for AMF sequencing. While the representation of the phylum Glomeromycetes ranged from 0.07% to 5.65% in the ITS library, it was significantly higher, ranging from 83.74% to 98.71%, in the LSU library. The most significant difference compared to other sub-regions was observed in the Slovácko sub-region, where the soil had a low pH, a different texture (sandy loam), reduced micronutrient concentration, and low organic matter. The application of chemical plant protection products to grapevines also could have played a significant role, with 49 applications recorded in the Slovácko sub-region during the three years preceding sample collection. In other sub-regions, chemical treatments were conducted only 19-26 times. These factors resulted in only trace amounts of AMF being detected in Slovácko. Furthermore, it was demonstrated that AMF positively influenced the phosphorus concentration in the soil and reduced the presence of certain fungal pathogens.},
}

*Mycorrhizae/physiology
*Vitis/microbiology
*Soil Microbiology
*Soil/chemistry
Czech Republic
Plant Roots/microbiology
Mycobiome
Basidiomycota/genetics/physiology
Rhizosphere
Phosphorus/metabolism/analysis

@article {pmid40044209,
year = {2025},
author = {Wang, X and Zhang, P and Lu, H and Luo, D and Yang, D and Li, K and Qiu, S and Zeng, H and Zeng, X},
title = {Risk prediction models for dental caries in children and adolescents: a systematic review and meta-analysis.},
journal = {BMJ open},
volume = {15},
number = {3},
pages = {e088253},
pmid = {40044209},
issn = {2044-6055},
mesh = {Humans ; *Dental Caries/epidemiology ; Child ; Adolescent ; Risk Assessment/methods ; },
abstract = {OBJECTIVE: This study aimed to systematically evaluate published predictive models for dental caries in children and adolescents.

DESIGN: A systematic review and meta-analysis of observational studies.

DATA SOURCES: Comprehensive searches were conducted in PubMed, Web of Science, Cochrane Library, Cumulative Index to Nursing and Allied Health Literature, Embase, China National Knowledge Infrastructure, Wanfang Database, China Science and Technology Journal Database (VIP) and SinoMed for relevant studies published up to 18 January 2024. The search focused on caries prediction models in children and adolescents.

ELIGIBILITY CRITERIA: Eligible studies included observational research (cohort, case-control and cross-sectional designs) that developed risk prediction models for dental caries in children and adolescents aged ≤18 years. Each model was required to include a minimum of two predictors. Studies were excluded if they were not available in English or Chinese, primarily focused on oral microbiome modelling, or lacked essential details regarding study design, model construction or statistical analyses.

RESULTS: A total of 11 studies were included in the review. All models demonstrated a high risk of bias, primarily due to inappropriate statistical methods and unclear applicability resulting from insufficiently detailed presentations of the models. Logistic regression, random forests and support vector machines were the most commonly employed methods. Frequently used predictors included fluoride toothpaste use and brushing frequency. Reported area under the curve (AUC) values ranged from 0.57 to 0.91. A combined predictive model incorporating six caries predictors achieved an AUC of 0.79 (95% CI: 0.73 to 0.84).

CONCLUSIONS: Simplified predictive models for childhood caries showed moderate discriminatory performance but exhibited a high risk of bias, as assessed using the Prediction Model Risk of Bias Assessment Tool (PROBAST). Future research should adhere to PROBAST guidelines to minimise bias risk, focus on enhancing model quality, employ rigorous study designs and prioritise external validation to ensure reliable and generalisable clinical predictions.

PROSPERO REGISTRATION NUMBER: CRD42024523284.},
}

Humans
*Dental Caries/epidemiology
Child
Adolescent
Risk Assessment/methods

@article {pmid40044134,
year = {2025},
author = {Lee, SY and Lee, SB and Kwon, GH and Song, SH and Park, JH and Kim, MJ and Eom, JA and Lee, KJ and Yoon, SJ and Park, H and Won, SM and Jeong, JJ and Oh, KK and Ham, YL and Baik, GH and Kim, DJ and Sharma, SP and Suk, KT},
title = {Synbiotic combination of fructooligosaccharides and probiotics ameliorates the metabolic dysfunction-associated steatotic liver disease.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {2},
pages = {e2411002},
doi = {10.71150/jm.2411002},
pmid = {40044134},
issn = {1976-3794},
support = {//Hallym University Research Fund/ ; 2020R1I1A3073530//National Research Foundation of Korea/ ; 2020R1A6A1A03043026//National Research Foundation of Korea/ ; //Ministry of Education, Science and Technology/ ; P0020622//Korea Institute for Advancement of Technology/ ; },
mesh = {*Synbiotics/administration & dosage ; *Oligosaccharides/pharmacology ; *Probiotics/administration & dosage/pharmacology/therapeutic use ; Animals ; *Liver/metabolism/drug effects/pathology ; Male ; Mice ; Prebiotics/administration & dosage ; Mice, Inbred C57BL ; Disease Models, Animal ; Fatty Liver/metabolism ; Lipid Metabolism/drug effects ; },
abstract = {Synbiotics have become a new-age treatment tool for limiting the progression of metabolic dysfunction-associated steatotic liver disease; however, inclusive comparisons of various synbiotic treatments are still lacking. Here, we have explored and evaluated multiple synbiotic combinations incorporating three distinctive prebiotics, lactitol, lactulose and fructooligosaccharides. Of the synbiotic treatments evaluated, a combination of fructooligosaccharides and probiotics (FOS+Pro) exhibited superior protection against western diet-induced liver degeneration. This synbiotic (FOS+Pro) combination resulted in the lowest body weight gains, liver weights and liver/body weight ratios. The FOS+Pro synbiotic combination substantially alleviated liver histopathological markers and reduced serum AST and cholesterol levels. FOS+Pro ameliorated hepatic inflammation by lowering expression of proinflammatory markers including TNF-α, IL-1β, IL-6, and CCL2. FOS+Pro significantly improved steatosis by restricting the expression of lipid metabolic regulators (ACC1, FAS) and lipid transporters (CD36) in the liver. These findings are critical in suggesting that synbiotic treatments are capable of restraining western diet-induced metabolic dysfunction in the liver. Additionally, this study demonstrated that adding probiotic strains amplified the effectiveness of fructooligosaccharides but not all prebiotics.},
}

*Synbiotics/administration & dosage
*Oligosaccharides/pharmacology
*Probiotics/administration & dosage/pharmacology/therapeutic use
Animals
*Liver/metabolism/drug effects/pathology
Male
Mice
Prebiotics/administration & dosage
Mice, Inbred C57BL
Disease Models, Animal
Fatty Liver/metabolism
Lipid Metabolism/drug effects

@article {pmid40044111,
year = {2025},
author = {Pratikna, AM and Rivai, MI and Suswita, R and Putra, AE and Rachman, IA and Suchitra, A},
title = {The effect of tumor resection on intestinal microbiota dysbiosis in patients with right-sided colon cancer.},
journal = {Annals of coloproctology},
volume = {41},
number = {1},
pages = {47-56},
doi = {10.3393/ac.2024.00346.0049},
pmid = {40044111},
issn = {2287-9714},
abstract = {PURPOSE: This study aimed to determine the effect of tumor resection on dysbiosis of the intestinal microbiota in patients with right-sided colon cancer.

METHODS: This study utilized a longitudinal design to explore the outcomes of patients diagnosed with right-sided colon cancer who underwent surgical resection at Dr. M. Djamil General Hospital from July to December 2023. We excluded patients with a documented history of comorbidities, specifically those affecting the digestive system. To compare the microbiota (genus and phylum) between patients with right-sided colon cancer and the control group, we conducted bivariate analyses using the independent t-test or Mann-Whitney test. Furthermore, we employed the dependent t-test or Wilcoxon test to assess changes in the dysbiosis of the microbiota (genus and phylum) before and after resection. A P-value of <0.05 was considered statistically significant.

RESULTS: This study included a total of 21 patients diagnosed with right-sided colon cancer. In the control group, Bacteroidetes constituted the highest proportion of intestinal microbiota, accounting for 56.34%. Prior to tumor resection, the intestinal microbiota of patients exhibited Proteobacteria as the predominant phylum, representing 52.97%. Following tumor resection, Bacteroidetes remained the most prevalent, comprising 50.9% of the intestinal microbiota. Significant variations in the levels of Proteobacteria, Verrucomicrobia, and Cyanobacteria/Chloroplast were observed in the intestinal microbiota of patients with right-sided colorectal cancer before and after tumor excision (all P=0.001).

CONCLUSIONS: The microbiome of patients with right-sided colorectal cancer differed significantly from that of the control group. However, following tumor resection, the microbiome composition of these patients became more similar to that observed in the control group.},
}

@article {pmid40043878,
year = {2025},
author = {Ma, Q and Zhou, Y and Parales, RE and Jiao, S and Ruan, Z and Li, L},
title = {Effects of herbicide mixtures on the diversity and composition of microbial community and nitrogen cycling function on agricultural soil: a field experiment in Northeast China.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125965},
doi = {10.1016/j.envpol.2025.125965},
pmid = {40043878},
issn = {1873-6424},
abstract = {Herbicide mixtures application is a widespread and effective practice in modern agriculture; however, a knowledge gap exists regarding the potential ecotoxicological effects of herbicide mixtures in agricultural systems. Here, the effects of various doses of herbicide mixtures (atrazine, nicosulfuron, and mesotrione) under different varieties of maize cultivation on the structure and function of microbial communities and soil chemical parameters were clarified through field experiments. The results showed that the application of herbicide mixtures increased the bacterial and fungal community alpha diversity at jointing and maturity, indicating a prolonged effect of the herbicide mixtures. Moreover, herbicide mixtures alter the composition of bacterial and fungal communities, with sensitive taxa suppressed and herbicide-tolerant taxa enriched. The herbicide mixtures significantly reduced the abundances of Bacillus even at lower doses, but Penicillum was enriched. FAPROTAX analysis and quantitative PCR (qPCR) results showed that herbicide mixtures inhibited the soil nitrogen-cycle process and related genes AOA-amoA, AOB-amoA, and nifH at maize seedling stage. Moreover, network analysis showed that low concentrations of the herbicide mixtures increased bacterial interactions while high concentrations inhibited them, which indicated that the network complexity may be herbicide concentration dependent. A synthetic community (SynCom) consisting of six bacterial strains was established for the biodegradation of the herbicide mixtures based on the analysis of the bacterial network, which resulted in an increase in the degradation efficiency of nicosulfuron by 15.90%. Moreover, potted maize experiment showed that the addition of the SynCom alleviated the toxic effects of herbicide mixtures on the plants. In summary, this study provides a comprehensive perspective for assessing the ecological risk at taxonomic and functional levels and the biodegradation approach of herbicide mixtures residue on agricultural soils in Northeastern China.},
}

@article {pmid40043874,
year = {2025},
author = {Gan, H and Jiang, Y and Wu, L and Zhu, B and Ji, D and Liu, J and Ding, Z and Ye, X},
title = {Long-term and low-dose exposure to triclosan induces POI phenotype in female offspring mice.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125966},
doi = {10.1016/j.envpol.2025.125966},
pmid = {40043874},
issn = {1873-6424},
abstract = {Triclosan (TCS), a typical endocrine disruptor, is widely used as an antibacterial agent in consumer goods. However, there are few studies on the effects of long-term low-dose TCS exposure on ovarian function in F1 female mice. In this paper, F1 female mice were exposed to TCS (0-3000 μg/kg/day) from intrauterine to postnatal day (PND) 91 to investigate its effects on the ovary. The results revealed that the number of total follicles was decreased, while atretic follicles was increased after TCS exposure. At the hormonal level, the secretion of estradiol was reduced, while follicle-stimulating hormone and luteinizing hormone were increased after TCS exposure. Observation of vaginal smear showed that TCS disrupted the estrous cycle of F1 female mice, especially at the dose of 3000 μg/kg/day. Moreover, TCS promoted cell apoptosis by activating the p38-MAPK signaling pathway and oxidative stress in vitro. In addition, analysis of the fecal microbiome and serum metabolomics revealed that exposure to TCS may cause gut microbiota disruption and metabolic abnormalities in F1 female mice. In conclusion, long-term low-dose TCS exposure may induce primary ovarian insufficiency phenotype in F1 female mice via inducing cell apoptosis and disrupting gut microbiota and metabolism.},
}

@article {pmid40043859,
year = {2025},
author = {Lu, F and Wei, J and Guan, D and Peng, Y and Song, J and Qian, F},
title = {16S rDNA sequencing reveal synergistic effects of silkworm feces and earthworms on nutrient-poor soil microbial community structure and function in Guangxi.},
journal = {Genomics},
volume = {},
number = {},
pages = {111025},
doi = {10.1016/j.ygeno.2025.111025},
pmid = {40043859},
issn = {1089-8646},
abstract = {This study evaluates the synergistic effects of silkworm feces and earthworms on nutrient-poor acidic red soils in Guangxi, China. Using 16S rDNA amplicon sequencing, soil samples from untreated fields, silkworm feces, earthworm gut contents, and soils treated with silkworm feces combined with three earthworm densities (50, 80, and 110 worms/kg) were compared. The earthworm gut microbiome increased in diversity in a density-dependent manner, while treated soils displayed enhanced microbial richness-with the 80 worms/kg treatment showing the highest diversity (605 genera). Random Forest analysis identified key bacterial genera, and co-occurrence networks pinpointed potential keystone taxa. PICRUSt2 predicted enrichment of pathways for xenobiotic biodegradation, carbohydrate metabolism, and secondary metabolite biosynthesis. These findings demonstrate that integrating silkworm feces with an optimal earthworm density improves soil microbial diversity and function, offering insights for sustainable organic waste management and soil health.},
}

@article {pmid40043768,
year = {2025},
author = {Fernando, SC and Adams, S and Lakamp, A and Spangler, ML},
title = {Stochastic and deterministic factors that shape the rumen microbiome.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25797},
pmid = {40043768},
issn = {1525-3198},
abstract = {At the heart of degradation of complex organic matter within the rumen are its microbes. These microbes can convert unusable organic matter into useable protein and energy sources and therefore can directly influence the animal's health, performance and utilization of feed. As such, understanding stochastic and deterministic factors that contribute toward rumen microbial assembly and persistence can provide valuable information into developing methods to improve animal health, performance, and nutrient utilization through microbiome modulation. In this review, we describe how ecological concepts such as colonization history, priority effects and historical contingency may influence rumen microbial community assembly and in turn impact community composition and function. Additionally, we discuss how such ecological concepts can be used to develop novel microbial community assembly strategies to develop rumen microbiomes with long-term benefits to the host ruminant. Finally, we discuss current knowledge gaps in rumen microbiome research associated with host-microbe interactions and microbial assembly and propose potential opportunities for future microbiome studies to improve the understanding of the rumen microbiome to improve animal health and productivity.},
}

@article {pmid40043758,
year = {2025},
author = {Ghaffari, MH and Sauerwein, H and Sadri, H and Schuchardt, S and Martín-Tereso, J and Doelman, JH and Daniel, JB},
title = {Longitudinal characterization of the metabolome of dairy cows transitioning from one lactation to the next: Investigations in fecal samples.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26273},
pmid = {40043758},
issn = {1525-3198},
abstract = {The fecal metabolome comprises metabolites that are excreted or not absorbed by the animal. This study examined the changes in the fecal metabolome of dairy cows from the end of one lactation period, through the dry period, and into the subsequent lactation. Twelve Holstein cows (BW = 745 ± 71 kg, BCS = 3.43 ± 0.66) were housed in a tie-stall barn from 7 wk before to 15 wk after parturition, with dry-off occurring approximately 6 wk before the expected calving date (mean dry-off time = 42 d). Fecal samples were taken at wk -7, -5, -1, +1, +5, +10, +15 relative to calving. Targeted metabolomics identified a total of 93 metabolites, including AA, biogenic amines, bile acids (BA), and acylcarnitines (AcylCN) and some phospholipids. Principal component analysis (PCA) revealed clear metabolic shifts that showed a clear separation between the samples from the dry period and the samples from the end, early and middle of lactation, indicating significant changes in the metabolic profiles in the feces. The transition from the dry period (wk -5, -1 relative to calving) to lactation (wk +1, +5, +10, +15, -7 relative to calving) is characterized by an increase in fecal AA and metabolites, such as Glu, Met, β-alanine, and methionine sulfoxide, reflecting a shift in nitrogen metabolism to support increased protein metabolism for milk production. Higher concentrations of polyamines, such as spermidine and putrescine, were observed postpartum, indicating increased cell growth and improved tissue regeneration. Elevated gamma-aminobutyric acid (GABA) levels during lactation indicate increased microbial activity driven by a nutrient-rich diet. Results showed significant adjustments in bile acid profiles as cows transitioned into lactation. Deoxycholic acid (DCA) remained the predominant BA in feces, reflecting ongoing microbial transformation, while glycine- and taurine-conjugated BA increased postpartum, suggesting improved enterohepatic circulation and lipid absorption. Fecal acylcarnitines showed dynamic shifts with elevated levels during late gestation, a decrease in the dry period, and an increase postpartum, indicating increased fatty acid oxidation to meet energy demands. Results showed that phosphatidylcholines decreased prepartum but increased after calving. This indicates shifts in lipid metabolism reflecting energy requirements in lactation and suggests that fecal lipid composition is an indicator of metabolic adaptations in dairy cows. In particular, PCA revealed cosiderable overlap in the fecal metabolite profiles of multiparous and primiparous cows, indicating similar metabolic profiles. This was also confirmed by volcano plots, which showed no significant differences in fecal metabolism between the 2 groups across different weeks relative to calving (wk -7, -5, -1, +1, +5, +10, +15). Overall, these results emphasize the complex interactions between dietary factors, liver and gastrointestinal function, and the gut microbiome in shaping the fecal metabolite profile of dairy cows. These results underscore the value of this data set in advancing the application of fecal metabolome profiling to investigate metabolic changes during critical transitions in the lactation cycle of dairy cows.},
}

@article {pmid40043731,
year = {2025},
author = {Wang, M and Liu, YB and Tong, WM and Leung, WK and He, LL and Xu, X and Xu, D and Zhou, Q},
title = {Periodontitis History Shapes the Early Peri-Implant Microbiome Formation: A Metagenomic Analysis.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.14147},
pmid = {40043731},
issn = {1600-051X},
support = {32270188//National Natural Science Foundation of China/ ; 32070134//National Natural Science Foundation of China/ ; 2023-YBSF-162//Key Research and Development Program of Shaanxi Province, China/ ; //National Training Program of Innovation and Entrepreneurship for Undergraduates/ ; },
abstract = {AIM: This study aims to investigate the early alterations in microbiome construction and succession around dental implants in both periodontally healthy individuals and patients with a history of periodontitis during the first month after implant-crown placement.

MATERIALS AND METHODS: Ninety-five subgingival plaque samples were collected from 10 periodontally compromised patients (PCP) and nine periodontally healthy patients (PHP) at four time points with a 1-week interval and analysed using dynamic metagenomic analysis. The study compared the formation and temporal change in the peri-implant microbiome in the PCP and PHP groups during the first month after the implant crown placement. A two-year follow-up examination was conducted to assess the clinical outcomes of early peri-implant dysbiosis.

RESULTS: The results showed that PCP groups exhibited distinctively dysbiotic features in their peri-implant microbiome upon initial establishment, with an earlier and elevated emergence of periodontopathogens. This dysbiosis in the PCP group was associated with significantly higher modified sulcus bleeding index (mBI) scores compared with the PHP group. Neisseria was identified as a key driver of early peri-implant dysbiosis in patients with a periodontitis history.

CONCLUSIONS: This study established the first microbial link between periodontitis history and early peri-implant dysbiosis, highlighting the importance of early prevention strategies against peri-implant diseases in patients with a periodontitis history.},
}

@article {pmid40043672,
year = {2025},
author = {Kiššová, Z and Mátis, G and Mackei, M and Tráj, P and Márton, RA and Horváth, DG and Tóthová, C and Mudroňová, D and Karaffová, V},
title = {Research note: utilizing a novel chicken ileal explant model to assess the efficacy of probiotic Limosilactobacillus reuteri CCM 9425 against Salmonella Enteritidis infection.},
journal = {Poultry science},
volume = {104},
number = {4},
pages = {104909},
doi = {10.1016/j.psj.2025.104909},
pmid = {40043672},
issn = {1525-3171},
abstract = {The establishment of a consistent ex vivo model of poultry gut tissue for the study of intestine-microbiome interactions remains still a significant challenge. In this study a pro-inflammatory response of chicken ileal explant cultures was observed after Salmonella enterica serotype Enteritidis infection reflected by up-regulation of IL-18, TNF-α, IL-1β mRNA expression and the levelof serum amyloid A (SAA) protein. In contrast, pre-treatment of ileal explants with probiotic strain Limosilactobacillus reuteri CCM 9425 was able to suppress the infection-induced up-regulation of IL-1β, IL-18 cytokines and the SAA protein. Moreover, the applied probiotics elevated the RNA level of the gene encoding the anti-inflammatory cytokine IL-10 in the probiotic group and the pre-treatment group. Using ileal explant cultures isolated from chicken offers a reliable model of the gut, for studiing the effects of microorganisms at the level of histological tissue structure, gene expression of selected markers and protein production. In summary, regarding our results the miniature chicken ileal explants exhibited appropriate innate immune responses following exposure to bacterial infection with Salmonella Enteritidis and Limosilactobacillus reuteri, furthermore, represents a suitable model for the study of host-pathogen interactions under ex vivo conditions.},
}

@article {pmid40043655,
year = {2025},
author = {Cheng, X and Yan, Z and Li, Q and Schmitz, L and Yan, J and Ge, Y and Lan, Y and Zhao, Y and Wang, Y and Li, G and Liu, Y and Schneijderberg, M and Yang, L and Bian, H and van Dijk, ADJ and Qin, L and Cao, Q and Bisseling, T},
title = {Chinese chestnut did not induce negative plant soil feedback during centuries of growth.},
journal = {The Science of the total environment},
volume = {970},
number = {},
pages = {178883},
doi = {10.1016/j.scitotenv.2025.178883},
pmid = {40043655},
issn = {1879-1026},
abstract = {Certain tree species can reach ages of centuries, whereas lifespan of species like apple are markedly shorter. The latter is caused by negative plant-soil feedback that results in microbiome changes. We hypothesized that tree species with a long lifespan will be able to avoid such negative feedback and their root-associated microbiomes will be similar in trees of different ages. To test this, we used Chinese chestnut (Castanea mollissima) trees, ranging from 8 to 830 years old from a Ming orchard at the Great Wall. Their root-associated microbiomes were analysed by using meta-amplicon sequencing analysis. Their root-associated bacterial microbiomes were rather similar although based on linear regression models we cannot exclude that age has a weak correlation with microbiome compositions. When chestnut seedlings were grown for 3 months in soil associated with young or old trees, the plants were healthy and their growth was similar. This strongly supported that negative feedback had not occurred. Pseudomonas OTU1, a member of the core microbiome and representing >50 % of the rhizosphere community, strongly inhibited growth of chestnut pathogens and stimulated plant growth. Such properties of the microbiome, in combination with a high number of resistance genes can contribute to longevity of chestnut.},
}

@article {pmid40043583,
year = {2025},
author = {Horill, S and Zhou, XK and Jin, W},
title = {Probiotics as a possible novel therapeutic option to mitigate perioperative neurocognitive disorders: A review exploring the latest research findings.},
journal = {Journal of clinical anesthesia},
volume = {103},
number = {},
pages = {111801},
doi = {10.1016/j.jclinane.2025.111801},
pmid = {40043583},
issn = {1873-4529},
abstract = {Perioperative neurocognitive disorders (PND) refer to a constellation of symptoms that primarily affect the elderly and typically manifest as common complications after exposure to surgery and anesthesia. PND is associated with high morbidity, mortality, and progression to neurodegenerative diseases, thus exerting significant financial strains on families as well as the healthcare system. Given that an ageing global population is an inevitable trend and, with the latest advances in the healthcare system, an ever-growing number of elderly people present for surgery and anesthesia, PND is of prominent concern. The two-way communication between the intestinal flora and the brain, also known as the microbiota-gut-brain axis, plays an important role in central nervous system development, and multiple studies have highlighted the influence exerted by gut microbiome in both health and disease. Pertinent studies have corroborated the fact that anesthesia and surgery disrupt the harmony of the gut ecology, which sets off a cascade of events that initiate neuroinflammation, eventually leading to PND. Probiotics, which are live microorganisms that promote the host's health, have been shown as a viable option to restore or minimise the disruption of gut flora. Evidence exists that probiotics exhibit immunomodulatory and anti-inflammatory benefits. Given the effectiveness of probiotics in reducing neuroinflammation, research has also focused on their impact on the development of PND. This review aims to compile the data from relevant clinical trials focusing on the influence of probiotics on PND to determine whether the derived findings might be applied for the prevention and treatment of PND.},
}

@article {pmid40043555,
year = {2025},
author = {Darvishi, S and Donnachie, E and Uibel, PA and Flaskamp, M and Gasperi, C and Hapfelmeier, A and Hemmer, B},
title = {Antibiotic drug use in the five years preceding the diagnosis of multiple sclerosis.},
journal = {Multiple sclerosis and related disorders},
volume = {96},
number = {},
pages = {106366},
doi = {10.1016/j.msard.2025.106366},
pmid = {40043555},
issn = {2211-0356},
abstract = {BACKGROUND: Microbiota may play a role in autoimmune disease pathogenesis, including multiple sclerosis (MS). Antibiotic use disrupts the microbiome and may increase the risk of autoimmune diseases. We evaluated the relationship between MS diagnosis and antibiotic, antimycotic and antiviral drug use in the 5 years preceding diagnosis.

METHOD: Our population-based case-control study used German ambulatory claims data from 2012 to 2022. We defined cohorts of 13,053 MS patients, 22,898 Crohn's disease patients, and 15,037 matched controls without autoimmune diseases, aged 21-70. Logistic and Poisson regression models explored the relationship between MS diagnosis and antimicrobial usage. Two sub-analyses were performed: a separate analysis of patients with clinically isolated syndrome (CIS) and a sensitivity analysis of newly diagnosed MS patients without preceding neurological symptoms.

RESULTS: Patients with MS had higher exposure to antibiotic (Odd Ratio (OR) = 1.27, 95 % CI 1.21-1.33), antimycotic (OR = 1.27, 95 % CI 1.12-1.45), and antiviral drugs (OR = 1.28, 95 % CI 1.15-1.43) in the five years before diagnosis compared to patients with no autoimmune diseases. Similar findings were obtained for the CIS cohort and in the sensitivity analysis. Antibiotic use peaked 5 years before MS diagnosis, declining closer to diagnosis, while antiviral and antimycotic drug use showed the opposite. This effect was not observed in the sensitivity analysis and CIS cohorts. Antibiotic use was higher in Crohn's disease than in MS (OR = 0.86, 95 % CI 0.82-0.90), with no consistent differences in antimycotic and antiviral use.

CONCLUSIONS: The association and kinetic of antibiotic use before MS and CIS diagnosis supports the role of microbiota in MS pathogenesis and suggests antibiotic use to be related to the development of autoimmune diseases, including MS. Additional studies are warranted to clarify whether increased antibiotic use is part of the MS prodrome or a true risk factor for MS.},
}

@article {pmid40043439,
year = {2025},
author = {Afsari, Y and Atabi, F and Aghelan, Z and Khazaie, H and Vakili, Z and Abtahi, SH and Rezaie Pouya, M},
title = {Serum levels of 1,3-β-D-glucan is correlated with NLRP3 inflammasome activation and insomnia severity in people with chronic insomnia disorder.},
journal = {Sleep medicine},
volume = {129},
number = {},
pages = {187-191},
doi = {10.1016/j.sleep.2025.02.046},
pmid = {40043439},
issn = {1878-5506},
abstract = {This study aimed to explore the correlation between serum levels 1,3-β-D-glucan as a biomarker for gut microbiome imbalance and NLRP3 inflammasome/IL-1β axis activation and insomnia severity in humans with chronic insomnia disorder (CID). Blood samples were collected from 20 people diagnosed with CID based on the Pittsburgh Sleep Quality Index (PSQI) and video-polysomnography and 20 healthy individuals based on PSQI. 1,3-β-D-glucan, IL-1β, and NLRP3 protein serum levels were assayed using enzyme-linked immunosorbent assay (ELISA). 1,3-β-D-glucan, IL-1β, and NLRP3 protein serum concentrations in the CID group were significantly higher than in the control group. Also, we observed a significant positive correlation between the serum levels of these three factors in the CID group and a significant positive correlation between 1,3-β-D-glucan and insomnia severity index. Our findings suggest that 1,3-β-D-glucan may indicate gut microbiome imbalance in people with CID and may play an important role in the pathogenesis of chronic insomnia by activating the NLRP3/IL-1β inflammasome pathway. These results highlight the potential for dual therapeutic strategies targeting gut microbiota modulation and NLRP3 inflammasome inhibition to disrupt the neuroinflammatory cascade driving chronic insomnia.},
}

@article {pmid40043274,
year = {2025},
author = {Al, ET},
title = {FULL SUPPLEMENT: Exploring The Scalp Barrier and Microbiome In Diverse Dandruff Patients.},
journal = {Journal of drugs in dermatology : JDD},
volume = {24},
number = {3},
pages = {32730s1-32730s16},
doi = {10.36849/JDD.32730},
pmid = {40043274},
issn = {1545-9616},
mesh = {Humans ; *Dandruff/microbiology/drug therapy ; *Microbiota/drug effects ; *Scalp/microbiology ; Malassezia/isolation & purification/drug effects ; Dysbiosis/microbiology ; Antifungal Agents/administration & dosage/pharmacology ; },
abstract = {Although the exact pathophysiology of dandruff is still not completely decoded, current theories highlight the role of the microbiome on the skin surface in the patho-genesis. Several scalp microbiome studies from different populations have revealed the association of dandruff with bacterial and fungal dysbiosis. Another study comparing the major bacterial-fungal populations colonizing dandruff scalps in China and France suggests that targeting one par-ticular Malassezia species by antifungals instead of using broad-spectrum antifungals and rebalancing the dandruff scalp microbiota could be a common approach to improve dandruff condition.},
}

Humans
*Dandruff/microbiology/drug therapy
*Microbiota/drug effects
*Scalp/microbiology
Malassezia/isolation & purification/drug effects
Dysbiosis/microbiology
Antifungal Agents/administration & dosage/pharmacology

@article {pmid40043273,
year = {2025},
author = {Bitton, A and Idkowiak-Baldys, J and Bouslimani, A and Chun Wang, EH and Paturi, J and Chen, Y and Clavaud, C and Baalbaki, N},
title = {INDIVIDUAL ARTICLE: A Clinical Evaluation of Scalp Barrier Function, Ceramide Levels, and Microbiome in Diverse Dandruff Patients.},
journal = {Journal of drugs in dermatology : JDD},
volume = {24},
number = {3},
pages = {32731s3-32731s14},
doi = {10.36849/JDD.32731},
pmid = {40043273},
issn = {1545-9616},
mesh = {Humans ; *Ceramides/metabolism/analysis ; *Dandruff/microbiology ; *Microbiota/physiology ; Male ; Female ; Adult ; Middle Aged ; *Scalp/microbiology ; Malassezia/isolation & purification ; Young Adult ; Aged ; Water Loss, Insensible ; Epidermis/microbiology/metabolism ; },
abstract = {Dandruff is a common chronic scalp condition that affects approximately half the population irrespective of their origin. Dandruff scalps are characterized by flaking skin, pruritus, and minimal visible scalp inflammation. At the biological level, dandruff scalp presents a disruption of the barrier function supported by lower levels of ceramides in the stratum corneum and typically accompanied by altered microbiome diversity, including a higher abundance of Malassezia yeasts and exacerbated sebum peroxidation. This study evaluated the relationship between skin barrier integrity in association with epidermal ceramide profile, microbiome imbalance, and inflammatory markers in pathophysiology of dandruff in an ethnically diverse panel. Our results confirm a significant increase in TEWL and decrease in hydration along with an increase in erythema, dryness, flakiness, and itchiness in patients with dandruff vs normal scalps; and an elevation of IL1RA:IL1α ratio dependent on the severity of the dandruff, supporting the inflammatory association with dandruff. For the first time, a study shows that dandruff scalps have a significantly higher amount of short-chain ceramides and a significantly lower proportion of long-chain ceramides consistent with lower conformational ordering and, thus explaining a higher permeability of the skin contributing to barrier dysfunction. In addition, reduced phytosphingosine and dihydrosphingosine based ceramides (NP, AP, NDS) were also observed, supporting a weakened scalp barrier. In addition to an expected increase in Malassezia, especially Malassezia restricta, in dandruff scalp, an increase in Staphylococcus aureus and decrease in Malassezia globosa was also observed as compared to healthy scalp in the population analyzed. J Drugs Dermatol. 2025;24:3(Suppl 1):s3-14.},
}

Humans
*Ceramides/metabolism/analysis
*Dandruff/microbiology
*Microbiota/physiology
Male
Female
Adult
Middle Aged
*Scalp/microbiology
Malassezia/isolation & purification
Young Adult
Aged
Water Loss, Insensible
Epidermis/microbiology/metabolism

@article {pmid40043268,
year = {2025},
author = {A Okoye, G and Bui, H and Zadu, A and A Myles, I and S Byrd, A},
title = {The Multifaceted Effects of Berberine: Potential Uses in Dermatology.},
journal = {Journal of drugs in dermatology : JDD},
volume = {24},
number = {3},
pages = {298-301},
doi = {10.36849/JDD.8899},
pmid = {40043268},
issn = {1545-9616},
mesh = {Humans ; *Berberine/pharmacology/therapeutic use/administration & dosage ; *Skin Diseases/drug therapy ; Antioxidants/pharmacology/administration & dosage/therapeutic use ; Dermatologic Agents/therapeutic use/pharmacology/administration & dosage ; Dermatology/methods/trends ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Berberine is a natural alkaloid found in several plant species and has been utilized in traditional medicine for its antimicrobial, anti-inflammatory, and antioxidant properties. Berberine supplements are readily available over-the-counter in the United States. It has recently gained popularity on social media and is increasingly being used as complementary and alternative medicine. Berberine possesses a broad spectrum of pharmacological properties, which may be a result of its potent antioxidant properties and its regulatory effects on the gut microbiome. Acne, atopic dermatitis, pigmentary disorders, hidradenitis suppurativa, psoriasis, and skin aging are complex disorders, often requiring multifaceted treatment strategies. Berberine's broad mechanisms of action make it a promising candidate for the management of these conditions. This review explores the mechanisms of action of berberine and its clinical relevance in the management of dermatologic diseases. J Drugs Dermatol. 2025;24(3):298-301 doi:10.36849/JDD.8899.},
}

Humans
*Berberine/pharmacology/therapeutic use/administration & dosage
*Skin Diseases/drug therapy
Antioxidants/pharmacology/administration & dosage/therapeutic use
Dermatologic Agents/therapeutic use/pharmacology/administration & dosage
Dermatology/methods/trends
Gastrointestinal Microbiome/drug effects

@article {pmid40043265,
year = {2025},
author = {Whiting, C and Abdel Azim, S and Joly-Tonetti, N and Lachmann, N and Friedman, A},
title = {Effects on the Skin Microbiome by a Moisturizer Formulated for Eczema-Prone and Sensitive Skin.},
journal = {Journal of drugs in dermatology : JDD},
volume = {24},
number = {3},
pages = {275-280},
doi = {10.36849/JDD.8707},
pmid = {40043265},
issn = {1545-9616},
mesh = {Humans ; *Filaggrin Proteins ; *Microbiota/drug effects ; Female ; Adult ; *Skin Cream/administration & dosage ; Male ; *Skin/microbiology/drug effects ; *Dermatitis, Atopic/microbiology/drug therapy ; Young Adult ; Plant Extracts/administration & dosage/pharmacology ; Middle Aged ; Eczema/microbiology/drug therapy ; Administration, Cutaneous ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Cutaneous dysbiosis contributes to the pathophysiology of atopic dermatitis and potentially that of sensitive skin; regulation of the bacterial communities through skincare products is an emerging management strategy. Previous studies have highlighted the utility of ingredients that function as prebiotics, are anti-inflammatory, and have barrier-repairing properties to help shift species richness and composition toward more eubiotic states.

METHODS: In a single-site open-label study, a moisturizer containing colloidal oatmeal, Ophiopogon japonicus root extract (AD-Resyl&reg;, SILAB, France), and a patented filaggrin protein byproduct was evaluated for its effect on the bacterial communities of eczema-prone and sensitive skin (n=12). Skin swab samples from participants' cheeks were collected before and after applying the moisturizer twice daily for 21 days. Measures of alpha diversity (richness, Shannon diversity index) and beta diversity were calculated using paired, comparative analyses of sampled bacterial loads.

RESULTS: Bacterial species richness was significantly increased in 10 participants (P<0.05) without dysbiotic shifts in overall microbial composition.

CONCLUSION: These results support the use of a moisturizer containing anti-inflammatory and skin barrier-repairing ingredients for managing atopic dermatitis and add to our knowledge of the skin microbiome in sensitive skin. J Drugs Dermatol. 2025;24(3):275-280. doi:10.36849/JDD.8707.},
}

Humans
*Filaggrin Proteins
*Microbiota/drug effects
Female
Adult
*Skin Cream/administration & dosage
Male
*Skin/microbiology/drug effects
*Dermatitis, Atopic/microbiology/drug therapy
Young Adult
Plant Extracts/administration & dosage/pharmacology
Middle Aged
Eczema/microbiology/drug therapy
Administration, Cutaneous
Dysbiosis/microbiology

@article {pmid40042645,
year = {2025},
author = {Rust, C and Asmal, L and O'Hare, M and Pretorius, E and Emsley, R and Seedat, S and Hemmings, S},
title = {Investigating the gut microbiome in schizophrenia cases versus controls: South Africa's version.},
journal = {Neurogenetics},
volume = {26},
number = {1},
pages = {34},
pmid = {40042645},
issn = {1364-6753},
support = {MRC-RFA-IFSP-01-2013/SHARED ROOTS//South African Medical Research Council/ ; MRC-RFA-IFSP-01-2013/SHARED ROOTS//South African Medical Research Council/ ; MRC-RFA-IFSP-01-2013/SHARED ROOTS//South African Medical Research Council/ ; MRC-RFA-IFSP-01-2013/SHARED ROOTS//South African Medical Research Council/ ; MRC-RFA-IFSP-01-2013/SHARED ROOTS//South African Medical Research Council/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Schizophrenia/microbiology ; South Africa/epidemiology ; Male ; Female ; Adult ; *RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Middle Aged ; Bacteria/genetics/classification ; Feces/microbiology ; },
abstract = {Schizophrenia (SCZ) is a chronic and severe mental disorder with a complex molecular aetiology. Emerging evidence indicates a potential association between the gut microbiome and the development of SCZ. Considering the under-representation of African populations in SCZ research, this study aimed to explore the association between the gut microbiome and SCZ within a South African cohort. Gut microbial DNA was obtained from 89 participants (n = 41 SCZ cases; n = 48 controls) and underwent 16S rRNA (V4) sequencing. Data preparation and taxa classification were performed with the DADA2 pipeline in R studio followed by diversity analysis using QIIME2. Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) was utilised to identify differentially abundant taxa. No statistically significant differences were observed between SCZ patients and controls in terms of alpha-diversity (Shannon q = 0.09; Simpson q = 0.174) or beta-diversity (p = 0.547). Five taxa, namely Prevotella (p = 0.037), Faecalibacterium (p = 0.032), Phascolarctobacterium (p = 0.002), Dialister (p = 0.043), and SMB53 (p = 0.012), were differentially abundant in cases compared to controls, but this observation did not survive correction for multiple testing. This exploratory study suggests a potential association between the relative abundance of Prevotella, Faecalibacterium, Phascolarctobacterium, Dialister, and SMB53 with SCZ case-control status. Given the lack of significance after correcting for multiple testing, these results should be interpreted with caution. Mechanistic studies in larger samples are warranted to confirm these findings and better understand the association between the gut microbiome and SCZ.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Schizophrenia/microbiology
South Africa/epidemiology
Male
Female
Adult
*RNA, Ribosomal, 16S/genetics
Case-Control Studies
Middle Aged
Bacteria/genetics/classification
Feces/microbiology

@article {pmid40042519,
year = {2025},
author = {Gonzalez, E and Sahar, T and Haddad, M and Toupin, S and Zioud, R and Zoabi, M and Waldman, LE and Leshinsky, ZT and Ben Sasson, M and Kumar, V and Marom, Y and Midbari, A and Brereton, NJ and Shir, Y and Minerbi, A},
title = {Altered gut microbiome composition and function in individuals with complex regional pain syndrome.},
journal = {Anesthesiology},
volume = {},
number = {},
pages = {},
doi = {10.1097/ALN.0000000000005435},
pmid = {40042519},
issn = {1528-1175},
abstract = {BACKGROUND: Complex regional pain syndrome (CRPS) is a chronic pain syndrome typically affecting a limb. It is characterized by severe spontaneous and evoked pain, along with vasomotor, autonomic, and motor signs and symptoms. Although dysregulation in several physiologic systems has been suggested in CRPS, including aberrant inflammatory and immune responses, vasomotor dysfunction, and nervous system changes, the pathophysiologic mechanisms underlying the syndrome remain elusive. Effective treatment options are also limited. Previous research has highlighted the role of the gut microbiome in chronic pain, prompting us to investigate the composition and function of the gut microbiome in CRPS.

METHODS: The gut microbiomes of individuals with CRPS to age-, gender- and ethnicity-matched pain-free control participants were compared using 16S rRNA gene amplification. To minimize environmental confounders, participants were recruited from two geographically independent regions. To explore potential changes in gut-bacteria-derived metabolites targeted metabolomic analysis of feces and plasma was performed. Finally, machine learning algorithms were trained to identify the gut microbiome composition specific to CRPS patients and were tested on a validation cohort.

RESULTS: In this study, differential abundance analysis revealed significant differences in several bacterial taxa when comparing 53 CRPS patients to 52 unrelated controls, including alterations in short-chain fatty acid (SCFA) metabolizing species. Targeted stool and plasma metabolite analysis confirmed differences in fecal and plasma SCFA levels between CRPS patients and controls. Notably, the microbiome composition alone allowed accurate classification of patients and controls in a geographically independent test cohort.

CONCLUSIONS: These findings highlight unique compositional and functional changes in the gut microbiome of individuals with CRPS, thus contributing to the growing body of evidence supporting the role of the gut microbiome in chronic pain syndromes. Furthermore, they pave the way for further studies elucidating the pathophysiology of CRPS and exploring new diagnostic aids and treatment modalities.},
}

@article {pmid40042420,
year = {2025},
author = {Roseboom, TJ},
title = {[A child s first 1,000 days: its relevance to the oral care practice].},
journal = {Nederlands tijdschrift voor tandheelkunde},
volume = {132},
number = {3},
pages = {118-123},
doi = {10.5177/ntvt.2025.03.24122},
pmid = {40042420},
issn = {0028-2200},
mesh = {Humans ; Infant ; Child, Preschool ; *Oral Health ; Dental Caries/prevention & control ; Infant, Newborn ; Oral Hygiene ; Feeding Behavior ; },
abstract = {Every human life begins as a single, fertilized egg-cell. During the first 1,000 days of life, this cell develops into a 2-year-old toddler. More milestones are reached in this period of life than in any other. All organs are formed, the metabolism is set up, the microbiome is formed, the child learns to eat and drink, develops eating habits, food preferences, and learns to walk and talk. The environment in which these developments take place is crucial to health in later life. The established structures and systems will last for life and will thus have a life-long influence on the individual s general health. Due to the regular check-ups they carry out and their expertise in the field of preventive medicine, oral care providers can make an important contribution during this unique window of opportunity. This article summarizes why the first 1,000 days are important, and describes how oral care providers can contribute. Together with parents (to be) and children, they can build healthy habits, help prevent caries, obesity, diabetes, cardiovascular disease and other chronic disorders, and be part of building the health of present and future generations.},
}

Humans
Infant
Child, Preschool
*Oral Health
Dental Caries/prevention & control
Infant, Newborn
Oral Hygiene
Feeding Behavior

@article {pmid40042419,
year = {2025},
author = {Zaura, E},
title = {[The microbiome and the first 1,000 days of life].},
journal = {Nederlands tijdschrift voor tandheelkunde},
volume = {132},
number = {3},
pages = {112-117},
doi = {10.5177/ntvt.2025.03.24064},
pmid = {40042419},
issn = {0028-2200},
mesh = {Humans ; Infant, Newborn ; Infant ; *Microbiota/physiology ; Female ; Pregnancy ; },
abstract = {A healthy human being lives in symbiosis with his microbes or microbiome. The first 1,000 days of life are crucial for developing a healthy and diverse microbiome. The development of a healthy microbiome begins as early as in the womb, where the training of the fetal immune cells begins. Next, the child s microbiome is influenced by the method of delivery during the birthing process. The largest and most important phase is the postnatal period. In this last phase, the child s environment, the behaviour and lifestyle of its caregivers, and the child itself are the main determinants of developing and maintaining a healthy microbiome.},
}

Humans
Infant, Newborn
Infant
*Microbiota/physiology
Female
Pregnancy

@article {pmid40042364,
year = {2025},
author = {Wang, C and Yang, Y and Wang, N and Luan, A and Wang, H and Hu, C},
title = {Design and application of antimicrobial nanomaterials in the treatment of periodontitis.},
journal = {Nanomedicine (London, England)},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/17435889.2025.2469492},
pmid = {40042364},
issn = {1748-6963},
abstract = {Periodontitis is a chronic inflammatory disease induced by the microbiome, leading to the destruction of periodontal structures and potentially resulting in tooth loss. Using local drug delivery systems as an adjunctive therapy to scaling and root planning in periodontitis is a promising strategy. However, this administration method's effectiveness is constrained by the complexity of the periodontal environment. Nanomaterials have demonstrated significant potential in the antibacterial treatment of periodontitis, attributed to their controllable size, shape, and surface charge, high design flexibility, high reactivity, and high specific surface area. In this review, we summarize the complex periodontal microenvironment and the difficulties of local drug delivery in periodontitis, explicitly reviewing the application and design strategies of nanomaterials with unique properties in the distinct microenvironment of periodontitis. Furthermore, the review discusses the limitations of current research, proposes feasible solutions, and explores prospects for using nanomaterials in this context.},
}

@article {pmid40042343,
year = {2025},
author = {Rodenes-Gavidia, A and Illescas, V and Martínez-Blanch, J and Chenoll, E and Moreno-Muñoz, JA and Jiménez López, J and Lamelas, A},
title = {Genome sequence of Lacticaseibacillus paracasei ORD 0998 (CECT 30660), a probiotic bacterium for women's health.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0084924},
doi = {10.1128/mra.00849-24},
pmid = {40042343},
issn = {2576-098X},
abstract = {Lacticaseibacillus paracasei is commonly isolated from dairy products and the microbiome of the human reproductive and gastrointestinal tract. We report the genome assembly of Lacticaseibacillus paracasei ORD 0998 (CECT 30660) with two contigs, having a size of 3,150,431 bp and a GC content of 46.33%.},
}

@article {pmid40042318,
year = {2025},
author = {Sun, D and Liu, Y and Zhou, S and Meegaskumbura, M},
title = {Microbiome and climate: skin microbial diversity and community functions of Polypedates megacephalus (Anura: Rhacophoridae) associated with bioclimate.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0235824},
doi = {10.1128/spectrum.02358-24},
pmid = {40042318},
issn = {2165-0497},
abstract = {The microbiome inhabiting animal skin plays a crucial role in host fitness by influencing both the composition and function of microbial communities. Environmental factors, including climate, significantly impact microbial diversity and the functional attributes of these communities. However, it remains unclear how specific climatic factors affect amphibian skin microbial composition, community function, and the relationship between these two aspects. Understanding these effects is particularly important because amphibians are poikilotherms and, thus, more susceptible to temperature fluctuations. Here, we investigated the skin microbiome of the rhacophorid tree frog Polypedates megacephalus across different climatic regimes using 16S rRNA gene sequencing. Skin swab samples were collected from nine populations of P. megacephalus adults in the Guangxi region, China. The majority of the core microbiota were found to belong to the genus Pseudomonas. Our findings indicate that microbial community diversity, composition, and function are associated with changes in climatic conditions. Specifically, the taxonomic and functional diversity of the skin microbiome increased in response to higher climate variability, particularly in temperature fluctuations. Additionally, the functional traits of microbial communities changed in parallel with shifts in community diversity and composition. The significant correlations of the functional redundancy index with climatic factors suggest that environmental filtering driven by climate change impacts microbial community functional stability. These results highlight the critical influence of climatic factors on amphibian skin microbiomes and offer new insights into how microbial composition and function contribute to host adaptation in varying environmental conditions.IMPORTANCEThis study is important in understanding the association between climate variability, microbial diversity, and host adaptation in amphibians, which are particularly vulnerable to environmental changes due to their poikilothermic nature. Amphibians rely on their skin microbiome for key functions like disease resistance, yet little is known about how climate fluctuations impact these microbial communities. By analyzing the microbiome of Polypedates megacephalus across different climatic regimes, our analysis reveals that warmer climates could reduce the microbial diversity and community functional redundancy, indicating the functional stability of skin microbiome could be susceptible to climate variability, particularly in hosts adapted to relatively cooler conditions. These findings highlight the potential ecological consequences of climate change and emphasize the need to integrate microbiome health into amphibian conservation strategies.},
}

@article {pmid40042298,
year = {2025},
author = {Kensiski, A and Gavzy, SJ and Wu, L and Mas, V and Ma, B and Bromberg, JS},
title = {Immunosuppressant imprecision: multidirectional effects on metabolism and microbiome.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0017824},
doi = {10.1128/cmr.00178-24},
pmid = {40042298},
issn = {1098-6618},
abstract = {SUMMARYTransplant recipients require lifelong, multimodal immunosuppression to prevent rejection by dampening alloreactive immunity. These treatments have long been known to lack antigen specificity. Despite empirically selected long-term immunosuppression regimens, most allografts succumb to alloimmune responses that result in chronic inflammation and scarring. Additionally, immunosuppressive medications themselves contribute to unintended intestinal dysbiosis and metabolic disorders. This review focuses on the effect of immunosuppressant treatments on alloimmunity, gut microbiome, and metabolism, with a particular emphasis on the effects on metabolic disorders. We also outline the shared and unique microbial and metabolic signatures produced by each immunosuppressant class, underlining their distinct impacts on immunity and metabolic homeostasis. These observations underscore the need for a holistic understanding of these drugs' on- and off-target effects to refine therapeutic strategies, enhance immunosuppression efficacy, and ultimately enhance graft and patient survival. By characterizing these complex interactions, strategies informed by the gut microbiome and host metabolism may offer a promising adjunctive approach to optimizing immunosuppressive regimens and promoting sustained graft acceptance.},
}

@article {pmid40042272,
year = {2025},
author = {Murphree-Terry, M and Keith, JD and Oden, AM and Birket, SE},
title = {Spontaneous lung colonization in the cystic fibrosis rat model is linked to gastrointestinal obstruction.},
journal = {mBio},
volume = {},
number = {},
pages = {e0388324},
doi = {10.1128/mbio.03883-24},
pmid = {40042272},
issn = {2150-7511},
abstract = {Cystic fibrosis (CF) is a genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, resulting in CFTR protein dysfunction. CFTR dysfunction has multi-organ consequences, leading to dehydrated mucus that is adherent to epithelia. In the lungs, this leads to recalcitrant infections with bacteria such as Pseudomonas aeruginosa. In the gut, mucus-laden feces can adhere to the intestines, resulting in distal intestinal obstruction syndrome (DIOS). There is limited information on how lung colonization and DIOS are correlated in people with CF (pwCF). In this novel work, we describe the development of spontaneous lung colonization of CF pathogens in young (<3 months old) CF rats, preceding the development of DIOS. Once DIOS is established, the lung microbiome becomes predominated by taxa also observed in the feces. Induced infection with P. aeruginosa in the CF rats reflects data found in pwCF, as once CF rats are infected, they retain a higher relative abundance of P. aeruginosa than their healthy agemates. Finally, we found that ivacaftor treatment favors a healthier gut microbiome in CF rats, decreasing the relative abundance of Escherichia coli. These results indicate that the CF rat model is recapitulative of human CF disease with the spontaneous lung colonization of traditional CF pathogens and maintenance of P. aeruginosa after induced infection. Furthermore, these results indicate a possible role for the gut-lung axis in lung colonization and DIOS in CF.IMPORTANCEThese data describe for the first time the development of spontaneous lung colonization in the cystic fibrosis (CF) rat model, a hallmark aspect of human CF disease. We also find that CF rats infected with Pseudomonas aeruginosa maintain higher relative abundance following chronic infection as compared to healthy rats, similar to those is seen in people with CF. Additionally, we describe the possible contribution of the gut-lung axis linking lung health with distal intestinal obstruction syndrome, a relationship largely unexplored in the context of CF.},
}

@article {pmid40042226,
year = {2025},
author = {Ko, B and Son, J and In Won, J and Kang, BM and Choi, CW and Kim, R and Sung, JH},
title = {Gut microbe-skin axis on a chip for reproducing the inflammatory crosstalk.},
journal = {Lab on a chip},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4lc01010h},
pmid = {40042226},
issn = {1473-0189},
abstract = {The gut-skin axis has emerged as a crucial mediator of skin diseases, with mounting evidence highlighting the influence of gut microbiota on skin health. However, investigating these mechanisms has been hindered by the lack of experimental systems that enable direct study of gut microbiota-skin interactions. Here, we present the gut microbe-skin chip (GMS chip), a novel microfluidic platform designed to model microbiome-gut-skin axis interactions. The GMS chip allows the coculture of intestinal epithelial cells (Caco-2), human epidermal keratinocytes (HEKa), and gut microbes with fluidic connection mimicking the blood flow. We validated that the gut compartment, with a self-sustaining oxygen gradient, enabled coculturing gut bacteria such as Escherichia coli (E. coli) and Lactobacillus rhamnosus GG (LGG), and the skin cells properly differentiated in the chip in the presence of fluid flow. Disruption of intestinal epithelial integrity by dextran sodium sulfate (DSS) combined with lipopolysaccharides (LPS) selectively decreased skin cell viability while sparing gut cells. Notably, pretreatment with LGG showed a protective effect against the skin cell damage by enhancing the intestinal barrier function. The GMS chip effectively recapitulates the influence of gut microbiota on skin health, representing a pivotal step forward in studying gut-skin axis mechanisms and the role of the gut microbiome in skin diseases.},
}

@article {pmid40042189,
year = {2025},
author = {Shao, X and Mi, X and Kuai, X and Zhou, D and Tai, Q and Lu, Y and Zhou, C and He, S},
title = {Microbial Butyrate Modified by Melatonin Alleviates Colon Inflammation by Inhibiting GPR109A/Caspase-1-Dependent Macrophage M1 Polarization.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.4c00915},
pmid = {40042189},
issn = {1535-3907},
abstract = {Recurrent ulcerative colitis (UC) seriously affects the quality of life of patients. Melatonin affects the alteration of the gut microbiota and can effectively relieve inflammation-associated diseases. In the present study, we determined that melatonin effectively alleviated intestinal inflammation and delayed weight loss in mice. Analysis of ileocecal contents in mice via 16S-rRNA and GC-MS revealed that melatonin could elevate the diversity of the gut microbiota and the abundance of short-chain fatty acids producing bacteria and promote the secretion of butyrate. Subsequently, butyrate negatively regulates the NLRP3-mediated inflammatory signaling pathway to inhibit the secretion of proinflammatory mediators such as caspase-1 and IL-1β to restrict the further development of intestinal inflammation. The NLRP3 expression increased, and the GPR109A expression was reduced significantly in the intestinal tissues of active UC patients, which was also closely related to clinical indicators CRP and ESR closely. However, disrupting the gut microbiota with broad-spectrum antibiotics (ABX) blocks melatonin's role in reducing intestinal inflammation. Collectively, we indicate that melatonin arrests UC in mice by modulating the microbiome and the NLRP3/caspase-1 inflammatory signaling pathways to skew macrophage polarization, which may have potential implications in the development of new approaches to treat acute UC.},
}

@article {pmid40042044,
year = {2025},
author = {Shen, Y and Choi, E and Kleinberg, S},
title = {Predicting Postprandial Glycemic Responses With Limited Data in Type 1 and Type 2 Diabetes.},
journal = {Journal of diabetes science and technology},
volume = {},
number = {},
pages = {19322968251321508},
doi = {10.1177/19322968251321508},
pmid = {40042044},
issn = {1932-2968},
abstract = {BACKGROUND: A core challenge in managing diabetes is predicting glycemic responses to meals. Prior work identified significant interindividual variation in responses and developed personalized forecasts. However, intraindividual variation is still not well understood, and the most accurate approaches require invasive microbiome data. We aimed to investigate (1) whether postprandial glycemic responses (PPGRs) can be predicted with limited data and (2) sources of intraindividual variation.

METHODS: We used data collected from 397 people with Type 1 Diabetes (T1DEXI) and 100 people with Type 2 Diabetes (ShanghaiT2DM) who wore continuous glucose monitors (CGMs) and logged meals. Using dietary, demographic, and temporal features, we predicted 2 hours PPGR, and peak 2 hours postprandial glucose rise (Glumax). We evaluated the contribution of food features (eg, macronutrients, food category) and use of personal training data and investigated intraindividual variability in responses.

RESULTS: We achieved comparable accuracy to prior work for PPGR (T1DEXI R = 0.61, ShanghaiT2DM R = 0.72) and Glumax (T1DEXI R = 0.64, ShanghaiT2DM R = 0.73), without using invasive data like microbiome. Including food category features led to higher accuracy than macronutrients alone. Analysis of glycemic responses to duplicate meals identified time of day (PPGR: T1DEXI P < .05 for lunch, ShanghaiT2DM P < .001 for lunch and dinner) and menstrual cycle (Glumax: P < .05 for perimenstrual) as sources of variability.

CONCLUSIONS: We demonstrate that in individuals with T1D and T2D, glycemic responses to meals can be predicted without personalized training data or invasive physiological data.},
}

@article {pmid40041888,
year = {2025},
author = {Xu, Z and Zhang, L and Tang, Q and Yang, C and Ding, X and Wang, Z and Huang, R and Jiang, R and Maitz, J and Shi, H and Yan, X and Dong, M and Chen, J and Wang, Y},
title = {Unlocking the role of wound microbiome in diabetic, burn, and germ-free wound repair treated by natural and synthetic scaffolds.},
journal = {Acta pharmaceutica Sinica. B},
volume = {15},
number = {1},
pages = {611-626},
pmid = {40041888},
issn = {2211-3835},
abstract = {In current clinical practice, various dermal templates and skin substitutes are used to enhance wound healing. However, the role of wound commensal microbiome in regulating scaffold performance and the healing process remains unclear. In this study, we investigated the influence of both natural and synthetic scaffolds on the wound commensal microbiome and wound repair in three distinct models including diabetic wounds, burn injuries, and germ-free (GF) wounds. Remarkably, synthetic electrospun polycaprolactone (PCL) scaffolds were observed to positively promote microbiome diversity, leading to enhanced diabetic wound healing compared to the natural scaffolds Integra® (INT) and MatriDerm® (MAD). In contrast, both natural and synthetic scaffolds exhibited comparable effects on the diversity of the microbiome and the healing of burn injuries. In GF wounds with no detectable microorganisms, a reversed healing rate was noted showing natural scaffold (MAD) accelerated wound repair compared to the open or the synthetic scaffold (PCL) treatment. Furthermore, the response of the wound commensal microbiome to PCL scaffolds appears pivotal in promoting anti-inflammatory factors during diabetic wound healing. Our results emphasize that the wound commensal microbiome, mediated by different scaffolds plays an important role in the wound healing process.},
}

@article {pmid40041871,
year = {2025},
author = {Dias, NW},
title = {Editorial: Understanding the female reproductive microbiome in livestock.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1570990},
doi = {10.3389/fmicb.2025.1570990},
pmid = {40041871},
issn = {1664-302X},
}

@article {pmid40041870,
year = {2025},
author = {Kumar, S and Mukherjee, R and Gaur, P and Leal, É and Lyu, X and Ahmad, S and Puri, P and Chang, CM and Raj, VS and Pandey, RP},
title = {Unveiling roles of beneficial gut bacteria and optimal diets for health.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1527755},
pmid = {40041870},
issn = {1664-302X},
abstract = {The gut microbiome plays a pivotal role in human health, influencing digestion, immunity, and disease prevention. Beneficial gut bacteria such as Akkermansia muciniphila, Adlercreutzia equolifaciens, and Christensenella minuta contribute to metabolic regulation and immune support through bioactive metabolites like short-chain fatty acids (SCFAs). Dietary patterns rich in prebiotics, fermented foods, and plant-based bioactive compounds, including polyphenols and flavonoids, promote microbiome diversity and stability. However, challenges such as individual variability, bioavailability, dietary adherence, and the dynamic nature of the gut microbiota remain significant. This review synthesizes current insights into gut bacteria's role in health, emphasizing the mechanisms by which dietary interventions modulate microbiota. Additionally, it highlights advancements in microbiome-targeted therapies and the transformative potential of personalized nutrition, leveraging microbiota profiling and artificial intelligence (AI) to develop tailored dietary strategies for optimizing gut health and mitigating chronic inflammatory disorders. Addressing these challenges requires a multidisciplinary approach that integrates scientific innovation, ethical frameworks, and practical implementation strategies.},
}

@article {pmid40041796,
year = {2025},
author = {Bai, Y and Tang, Z and Peng, X and Huang, J and Sun, M and Liu, J and Peng, F},
title = {A new psychrophilic yeast of Kriegeriaceae (Kriegeriales) isolated from lichen in the Arctic, with the description of Licheniasvalbardensis gen. et sp. nov.},
journal = {MycoKeys},
volume = {114},
number = {},
pages = {95-113},
pmid = {40041796},
issn = {1314-4049},
abstract = {Yeasts are an important component of the microbiome in circumpolar regions that are characterized by unique environmental conditions. However, the taxonomy of yeasts remains largely unknown in high- and low-latitude regions. Curing a field survey of yeasts in the Svalbard Archipelago, Norway, a new yeast genus in Kriegeriales was isolated from dendritic lichens. Based on the phylogeny of multiple loci (ITS, LSU, SSU, rpb1, rpb2, tef1-α, and cytb), morphology, and physiological characteristics, the new genus Lichenia is proposed with the type species Licheniasvalbardensis. Additionally, 10 °C and 15 °C are the fastest growth temperatures of L.svalbardensis. It has low or no growth at temperatures above 20 °C, and there appears to be a morphogenetic transition from yeast to pseudohyphae or hyphae above 10 °C.},
}

@article {pmid40041703,
year = {2025},
author = {Sato, Y},
title = {Rumen DNA virome in beef cattle reveals an unexplored diverse community with potential links to carcass traits.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf021},
pmid = {40041703},
issn = {2730-6151},
abstract = {Rumen deoxyribonucleic acid viruses that infect and replicate within bacteria and archaea are key modulators of the prokaryotic community. These viruses influence prokaryotic community abundance, composition, and function impacting host productivity and methane production. In this study, viral genomes were assembled from the rumen of 37 Japanese Black cattle using virus-like particle metagenome sequencing, providing insights into viral diversity, functional potential, and virus-host interactions. The relationship between the rumen deoxyribonucleic acid virome and carcass traits, particularly carcass weight and marbling, was also investigated. A total of 22 942 viral operational taxonomic units of medium-quality or higher (≥5 kb length and ≥ 50% completeness), referred to as Japanese Black Rumen Viral genomes, were reconstructed. Among these, 5973 putative novel genera were identified, significantly expanding the catalog of rumen viral genomes. Hosts were predicted for 2364 viral operational taxonomic units, including carbohydrate-degrading bacteria and methanogens. Additionally, 27 auxiliary metabolic genes were categorized as glycosyl hydrolases which are responsible for the degradation of cellulose, hemicellulose, and oligosaccharides, suggesting that rumen viruses may enhance the breakdown of complex carbohydrates during infection. Furthermore, the rumen virome differed considerably between high vs low carcass weight cattle and high vs low marbling cattle. Viruses associated with Methanobrevibacter were linked to higher carcass weight. This database and the insights from this study provide primary information for the development and improvement of beef production.},
}

@article {pmid40041522,
year = {2025},
author = {Aryati, Y and Farastuti, E and Sholichah, L and Koesharyani, I and Gardenia, L and Septiningsih, E and Yamin, M and Oryzanti, P and Puspaningsih, D and Sugiani, D},
title = {Effects of honey saccharide supplementation on growth performance, amylase enzyme activity, gut microvilli, and microbiome in Cyprinus carpio.},
journal = {Veterinary world},
volume = {18},
number = {1},
pages = {228-237},
pmid = {40041522},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Prebiotics, such as saccharides in honey, play a crucial role in improving gut microbiota, digestion, and immune function. This study evaluates the effects of Kapok flower honey saccharides on growth performance, digestive enzyme activity, intestinal morphology, and gut microbiota in common carp (Cyprinus carpio).

MATERIALS AND METHODS: A completely randomized design was implemented with four honey supplementation levels (0% control, 0.5%, 0.75%, and 1%) applied to juvenile C. carpio diets over 30 days. Growth performance, feed utilization, intestinal microvilli structure, gut microbiota, and amylase activity were analyzed using advanced techniques, including high performance liquid chromatography, scanning electron microscopy, and biochemical assays.

RESULTS: Kapok flower honey contains fructooligosaccharides (FOS, 14.76%) and inulin (6.6%). Supplementation at 1% significantly improved weight gain, feed conversion ratio, and specific growth rate. Amylase activity increased with honey supplementation, peaking at 24.13 ± 3.11 U g[-1] protein for the 1% group. Gut morphology analysis revealed longer, denser intestinal microvilli and higher perimeter ratios in honey-treated groups than controls. Microbiota analysis showed increased beneficial Bacillus spp. exclusively in the honey-supplemented groups.

CONCLUSION: Honey saccharides, particularly FOS and inulin, significantly enhance the growth performance, digestive enzyme activity, and gut health of common carp. Supplementation with 1% honey is optimal, improving feed efficiency and fostering beneficial gut microbiota. These findings highlight honey as a cost-effective, natural prebiotic for aquaculture.},
}

@article {pmid40041456,
year = {2025},
author = {Farah, A and Paul, P and Khan, AS and Sarkar, A and Laws, S and Chaari, A},
title = {Targeting gut microbiota dysbiosis in inflammatory bowel disease: a systematic review of current evidence.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1435030},
pmid = {40041456},
issn = {2296-858X},
abstract = {INTRODUCTION: The dysbiosis of the gut microbiota has been identified as a central factor in the pathogenesis of inflammatory bowel disease (IBD), a chronic condition characterized by frequent recurrence and various adverse effects of traditional therapies. While treatments targeting the gut microbiota show promise, their efficacy in IBD management still requires extensive evaluation. Our systematic review analyzes recent studies to elucidate the advancements and challenges in treating IBD using microbial-based therapies.

METHODS: Through a comprehensive systematic review spanning key scientific databases-PubMed, Embase, Cochrane, Web of Science, Scopus, and Google Scholar-we scrutinized the impact of probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) on individuals with IBD. Our detailed analysis covered study and participant demographics, along with seven key outcome measures: disease activity index, inflammatory markers, serum cytokines, microbiome composition, adverse effects, and the rates of remission and relapse.

RESULTS: From 6,080 initial search hits, we included 71 studies that assessed various interventions compared to placebo or standard medical therapy. Although there was notable variation in clinical results while assessing different outcomes, overall, probiotics, prebiotics, and synbiotics enhanced the success rates in inducing remission among IBD patients. Furthermore, we noted significant reductions in levels of pro-inflammatory markers and cytokines. Additionally, the requirement for steroids, hospitalization, and poor outcomes in endoscopic and histological scores were significantly reduced in individuals undergoing FMT.

CONCLUSION: Our investigation highlights the potential of targeting gut microbiota dysbiosis with microbial-based therapies in patients with IBD. We recommend conducting larger, placebo-controlled randomized trials with extended follow-up periods to thoroughly assess these treatments' clinical efficacy and safety before widespread recommendations for clinical application.},
}