@article {pmid39854381,
year = {2025},
author = {Holley, L and Creasey, HN and Bedenice, D and Reed, S and Romualdo da Silva, DR and Trautwein, V and Mazan, M and Widmer, G},
title = {Nebulization of 2% lidocaine has no detectable impact on the healthy equine respiratory microbiota.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0316079},
doi = {10.1371/journal.pone.0316079},
pmid = {39854381},
issn = {1932-6203},
mesh = {Animals ; Horses/microbiology ; *Microbiota/drug effects ; *Lidocaine/administration & dosage/pharmacology ; *Bronchoalveolar Lavage Fluid/microbiology ; *Nebulizers and Vaporizers/microbiology ; Male ; Female ; Trachea/microbiology ; Cross-Over Studies ; Bacteria/genetics/classification/drug effects/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Respiratory System/microbiology ; },
abstract = {Glucocorticosteroids remain the most common pharmaceutical approach for the treatment of equine asthma but can be associated with significant side effects, including respiratory microbiome alterations. The goal of the study was to assess the impact of 2% lidocaine nebulization, a projected alternative treatment of equine asthma, on the healthy equine respiratory microbiota. A prospective, randomized, controlled, blinded, 2-way crossover study was performed, to assess the effect of 1 mg/kg 2% lidocaine (7 treatments over 4 days) on the equine respiratory microbiota compared to control horses (saline and no treatment). Clinical assessments and respiratory samples, including nasal wash, endoscopic tracheal aspirate and bronchoalveolar lavage fluid, were obtained at each sample collection timepoint. The profile of the respiratory bacterial microbiota was evaluated using 16S amplicon sequencing, and clinical data compared using related samples analyses, based on data normality. The treatment did not affect the clinical data or alter the tracheal and nasal microbiota in healthy horses. However, time explained 12.6% of microbiota variation among samples. A significant difference in bacterial composition was observed between nasal and tracheal samples, showing the greatest relative abundance of Actinobacteria and Firmicutes, respectively. Bacterial DNA from bronchoalveolar lavage fluid did not amplify with generic primers targeting the V4 variable region of the prokaryotic small subunit ribosomal RNA gene, despite attempting multiple DNA extraction methods and PCR protocols, and after excluding PCR inhibition. This observation indicates that bronchoalveolar lavage fluid of healthy horses has a low bacterial load.},
}

Animals
Horses/microbiology
*Microbiota/drug effects
*Lidocaine/administration & dosage/pharmacology
*Bronchoalveolar Lavage Fluid/microbiology
*Nebulizers and Vaporizers/microbiology
Male
Female
Trachea/microbiology
Cross-Over Studies
Bacteria/genetics/classification/drug effects/isolation & purification
RNA, Ribosomal, 16S/genetics
Prospective Studies
Respiratory System/microbiology

@article {pmid39854335,
year = {2025},
author = {Hendrycks, W and Mullens, N and Bakengesa, J and Kabota, S and Tairo, J and Backeljau, T and Majubwa, R and Mwatawala, M and De Meyer, M and Virgilio, M},
title = {Deterministic and stochastic effects drive the gut microbial diversity in cucurbit-feeding fruit flies (Diptera, Tephritidae).},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0313447},
doi = {10.1371/journal.pone.0313447},
pmid = {39854335},
issn = {1932-6203},
mesh = {Animals ; *Tephritidae/microbiology/physiology ; *Gastrointestinal Microbiome ; *Larva/microbiology ; Stochastic Processes ; Bacteria/classification/genetics ; Biodiversity ; },
abstract = {Insect diversity is closely linked to the evolution of phytophagy, with most phytophagous insects showing a strong degree of specialisation for specific host plants. Recent studies suggest that the insect gut microbiome might be crucial in facilitating the dietary (host plant) range. This requires the formation of stable insect-microbiome associations, but it remains largely unclear which processes govern the assembly of insect microbiomes. In this study, we investigated the role of deterministic and stochastic processes in shaping the assembly of the larval microbiome of three tephritid fruit fly species (Dacus bivittatus, D. ciliatus, Zeugodacus cucurbitae). We found that deterministic and stochastic processes play a considerable role in shaping the larval gut microbiome. We also identified 65 microbial ASVs (Amplicon sequence variants) that were associated with these flies, most belonging to the families Enterobacterales, Sphingobacterales, Pseudomonadales and Betaproteobacterales, and speculate about their relationship with cucurbit specialisation. Our data suggest that the larval gut microbiome assembly fits the "microbiome on a leash" model.},
}

Animals
*Tephritidae/microbiology/physiology
*Gastrointestinal Microbiome
*Larva/microbiology
Stochastic Processes
Bacteria/classification/genetics
Biodiversity

@article {pmid39854266,
year = {2025},
author = {},
title = {Correction to: Microbiome characterization of skin biopsies in Spanish patients with hidradenitis suppurativa shows a decrease in D1 and H1 lineages of Cutibacterium acnes.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf029},
pmid = {39854266},
issn = {1365-2133},
}

@article {pmid39854190,
year = {2025},
author = {Jiang, Z and Tabuchi, C and Gayer, SG and Bapat, SP},
title = {Immune Dysregulation in Obesity.},
journal = {Annual review of pathology},
volume = {20},
number = {1},
pages = {483-509},
doi = {10.1146/annurev-pathmechdis-051222-015350},
pmid = {39854190},
issn = {1553-4014},
mesh = {Humans ; *Obesity/immunology/metabolism ; Animals ; *Adipose Tissue/immunology/metabolism ; Inflammation/immunology/metabolism ; Homeostasis/immunology ; T-Lymphocytes/immunology ; Immune System/immunology/metabolism ; },
abstract = {The immune system plays fundamental roles in maintaining physiological homeostasis. With the increasing prevalence of obesity-a state characterized by chronic inflammation and systemic dyshomeostasis-there is growing scientific and clinical interest in understanding how obesity reshapes immune function. In this review, we propose that obesity is not merely an altered metabolic state but also a fundamentally altered immunological state. We summarize key seminal and recent findings that elucidate how obesity influences immune function, spanning its classical role in microbial defense, its contribution to maladaptive inflammatory diseases such as asthma, and its impact on antitumor immunity. We also explore how obesity modulates immune function within tissue parenchyma, with a particular focus on the role of T cells in adipose tissue. Finally, we consider areas for future research, including investigation of the durable aspects of obesity on immunological function even after weight loss, such as those observed with glucagon-like peptide-1 (GLP-1) receptor agonist treatment. Altogether, this review emphasizes the critical role of systemic metabolism in shaping immune cell functions, with profound implications for tissue homeostasis across various physiological contexts.},
}

Humans
*Obesity/immunology/metabolism
Animals
*Adipose Tissue/immunology/metabolism
Inflammation/immunology/metabolism
Homeostasis/immunology
T-Lymphocytes/immunology
Immune System/immunology/metabolism

@article {pmid39854186,
year = {2025},
author = {Zhang, X and Chang, KM and Yu, J and Loomba, R},
title = {Unraveling Mechanisms of Genetic Risks in Metabolic Dysfunction-Associated Steatotic Liver Diseases: A Pathway to Precision Medicine.},
journal = {Annual review of pathology},
volume = {20},
number = {1},
pages = {375-403},
doi = {10.1146/annurev-pathmechdis-111523-023430},
pmid = {39854186},
issn = {1553-4014},
mesh = {Humans ; *Precision Medicine ; *Genetic Predisposition to Disease ; Gastrointestinal Microbiome ; Non-alcoholic Fatty Liver Disease/genetics/metabolism/therapy ; Risk Factors ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing global health problem, affecting ∼1 billion people. This condition is well established to have a heritable component with strong familial clustering. With the extraordinary breakthroughs in genetic research techniques coupled with their application to large-scale biobanks, the field of genetics in MASLD has expanded rapidly. In this review, we summarize evidence regarding genetic predisposition to MASLD drawn from family and twin studies. Significantly, we delve into detailed genetic variations associated with diverse pathogenic mechanisms driving MASLD. We highlight the interplay between these genetic variants and their connections with metabolic factors, the gut microbiome, and metabolites, which collectively influence MASLD progression. These discoveries are paving the way for precise medicine, including noninvasive diagnostics and therapies. The promising landscape of novel genetically informed drug targets such as RNA interference is explored. Many of these therapies are currently under clinical validation, raising hopes for more effective MASLD treatment.},
}

Humans
*Precision Medicine
*Genetic Predisposition to Disease
Gastrointestinal Microbiome
Non-alcoholic Fatty Liver Disease/genetics/metabolism/therapy
Risk Factors

@article {pmid39854185,
year = {2025},
author = {Guglietta, S and Li, X and Saxena, D},
title = {Role of Fungi in Tumorigenesis: Promises and Challenges.},
journal = {Annual review of pathology},
volume = {20},
number = {1},
pages = {459-482},
doi = {10.1146/annurev-pathmechdis-111523-023524},
pmid = {39854185},
issn = {1553-4014},
mesh = {Humans ; *Neoplasms/microbiology/immunology/therapy ; *Carcinogenesis/immunology ; *Fungi/pathogenicity/physiology ; Gastrointestinal Microbiome/immunology ; Animals ; Mycobiome/immunology ; Antifungal Agents/therapeutic use ; Mycoses/microbiology/immunology/therapy ; },
abstract = {The mycobiome plays a key role in the host immune responses in homeostasis and inflammation. Recent studies suggest that an imbalance in the gut's fungi contributes to chronic, noninfectious diseases such as obesity, metabolic disorders, and cancers. Pathogenic fungi can colonize specific organs, and the gut mycobiome has been linked to the development and progression of various cancers, including colorectal, breast, head and neck, and pancreatic cancers. Some fungal species can promote tumorigenesis by triggering the complement system. However, in immunocompromised patients, fungi can also inhibit this activation and establish life-threatening infections. Interestingly, the interaction of the fungi and bacteria can also induce unique host immune responses. Recent breakthroughs and advancements in high-throughput sequencing of the gut and tumor mycobiomes are highlighting novel diagnostic and therapeutic opportunities for cancer. We discuss the latest developments in the field of cancer and the mycobiome and the potential benefits and challenges of antifungal therapies.},
}

Humans
*Neoplasms/microbiology/immunology/therapy
*Carcinogenesis/immunology
*Fungi/pathogenicity/physiology
Gastrointestinal Microbiome/immunology
Animals
Mycobiome/immunology
Antifungal Agents/therapeutic use
Mycoses/microbiology/immunology/therapy

@article {pmid39854172,
year = {2025},
author = {MacCann, R and Li, J and Leon, AAG and Negi, R and Alalwan, D and Tinago, W and McGettrick, P and Cotter, AG and Landay, A and Sabin, C and O'Toole, PW and Mallon, PW and , },
title = {Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf043},
pmid = {39854172},
issn = {1537-6613},
abstract = {BACKGROUND: Inflammation and innate immune activation are associated with chronic HIV infection, despite effective treatment. Although gut microbiota alterations are linked to systemic inflammation, the relationships between the gut microbiome, inflammation and HIV remain unclear.

METHODS: The UPBEAT-CAD sub-study, examining cardiovascular disease (CVD) risk in HIV, enrolled participants matched on HIV status and traditional CVD risk factors. Subclinical CVD was assessed using coronary computed tomography angiography (CCTA). 34 biomarkers were measured using quantitative immunoassays. Microbiota composition was analysed by 16S rRNA sequencing of stool samples, with taxonomic assignment via the SPINGO pipeline. Differentially abundant species were identified by Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) and correlated to biomarkers, diet and CCTA outcomes using Spearman correlation.

RESULTS: Among 81 participants (median age 51 years, 73% male), people with HIV (n=44 , 54%) had a higher prevalence of hypercholesterolaemia (p <0.025) and statin use (p <0.001). A significant separation in gut microbiome β-diversity was observed between people with and without HIV. ANCOM-BC analysis identified 42 differentially abundant species and 10 genera in those with HIV. Enrichment of Bifidobacterium pseudocatenulatum, Megamonas hypermegale and Selenomonas ruminantium and depletion of Fusicatenenibacter correlated with lower plaque burden. Depletion of SCFA-producing Ruminococcus bromii correlated with higher plaque burden and fat intake, while depletion of Bacteroides spp and Alistepes spp correlated with elevated inflammatory biomarkers (D-dimer, CD40-ligand, CRP and IFN-γ).

CONCLUSION: Significant gut microbiota differences in people with HIV were linked to subclinical CVD, diet, and inflammation, suggesting a role for the microbiome in cardiovascular risk in HIV infection.},
}

@article {pmid39854158,
year = {2025},
author = {Lau, RI and Su, Q and Ng, SC},
title = {Long COVID and gut microbiome: insights into pathogenesis and therapeutics.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2457495},
doi = {10.1080/19490976.2025.2457495},
pmid = {39854158},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Fecal Microbiota Transplantation ; *COVID-19/therapy/microbiology ; *Probiotics/therapeutic use ; *Dysbiosis/therapy/microbiology ; *SARS-CoV-2 ; *Post-Acute COVID-19 Syndrome ; Prebiotics/administration & dosage ; },
abstract = {Post-acute coronavirus disease 2019 syndrome (PACS), following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or coronavirus disease 2019 (COVID-19), is typically characterized by long-term debilitating symptoms affecting multiple organs and systems. Unfortunately, there is currently a lack of effective treatment strategies. Altered gut microbiome has been proposed as one of the plausible mechanisms involved in the pathogenesis of PACS; extensive studies have emerged to bridge the gap between the persistent symptoms and the dysbiosis of gut microbiome. Recent clinical trials have indicated that gut microbiome modulation using probiotics, prebiotics, and fecal microbiota transplantation (FMT) led to improvements in multiple symptoms related to PACS, including fatigue, memory loss, difficulty in concentration, gastrointestinal upset, and disturbances in sleep and mood. In this review, we highlight the latest evidence on the key microbial alterations observed in PACS, as well as the use of microbiome-based therapeutics in managing PACS symptoms. These novel findings altogether shed light on the treatment of PACS and other chronic conditions.},
}

*Gastrointestinal Microbiome
Humans
*Fecal Microbiota Transplantation
*COVID-19/therapy/microbiology
*Probiotics/therapeutic use
*Dysbiosis/therapy/microbiology
*SARS-CoV-2
*Post-Acute COVID-19 Syndrome
Prebiotics/administration & dosage

@article {pmid39854015,
year = {2025},
author = {Loo, QY and Chuah, KH and Hian, WX and Khoo, XH and Lee, YY and Mahadeva, S},
title = {Impact of Positive Glucose, Lactose, and Fructose Hydrogen Breath Tests on Symptoms and Quality of Life in Irritable Bowel Syndrome.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.16891},
pmid = {39854015},
issn = {1440-1746},
support = {PV039-2019//UMSC C.A.R.E Fund Research Grant/ ; 304/PPSP/6150155/M145//Morinaga Milk Industry Co. Ltd./ ; },
abstract = {BACKGROUND: Gas production due to fermentation from fructose malabsorption (FM) or lactose malabsorption (LM) and small intestinal bacterial overgrowth (SIBO) contribute to the development of gastrointestinal symptoms in patients with irritable bowel syndrome (IBS). However, the impact of the carbohydrate malabsorption, unlike SIBO, is relatively unknown.

METHODOLOGY: A multicenter, prospective study of consecutive adults with IBS who underwent a hydrogen breath test (HBT) (glucose, 75 g; lactose, 25 g; or fructose, 25 g) was conducted. The proportion of patients who tested positive for glucose, fructose and lactose HBT were evaluated. The symptom severity, psychology, and quality of life of subjects with SIBO were compared with those having LM and/or FM. Independent factors associated with severe IBS (IBS-symptom severity scale: IBS-SSS > 300) were explored.

RESULTS: A total of 116 subjects were included (median age 56 years, male 35.3%). Of these, 23.3% (27/116), 85.7% (24/28), and 44.4% (16/36) of them tested positive for glucose, lactose, and fructose HBT, respectively. Among those with a positive HBT (n = 65), patients with SIBO were more likely to have the diarrhea-predominant subtype of IBS (77.8% vs. 47.4%, p = 0.014). Severe IBS was associated with SIBO, compared with LM/FM (SIBO: 36.4% vs. LM: 9.1%/FM 13.3%, p = 0.016). With multivariate analysis, SIBO (OR 5.25, p = 0.028) and depression (OR 5.59, p = 0.030) were independently associated with severe IBS.

CONCLUSION: Although LM and FM commonly co-exist in IBS, their clinical relevance appears to be less significant than that of SIBO. The connection between SIBO with depression reinforces the importance of the microbiome-gut-brain axis in IBS.},
}

@article {pmid39853943,
year = {2025},
author = {Dyson, G and Barrett, M and Schlupp, L and Prinz, E and Hannebut, N and Szymczak, A and Brawner, CM and Jeffries, MA},
title = {Ketogenic Diet-Associated Worsening of Osteoarthritis Histologic Secerity, Increased Pain Sensitivity and Gut Microbiome Dysbiosis in Mice.},
journal = {ACR open rheumatology},
volume = {7},
number = {1},
pages = {e11794},
doi = {10.1002/acr2.11794},
pmid = {39853943},
issn = {2578-5745},
support = {K08AR070891/AR/NIAMS NIH HHS/United States ; R33AR078075/AR/NIAMS NIH HHS/United States ; R61AR078075/AR/NIAMS NIH HHS/United States ; PR191652//Congressionally Directed Medical Research Programs/ ; P20GM125528/GM/NIGMS NIH HHS/United States ; },
abstract = {OBJECTIVES: Dietary interventions are a potentially powerful treatment option for knee osteoarthritis (OA). The objective of this study was to evaluate a well-formulated ketogenic diet (KD) in the context of knee OA histology and pain using the destabilization of the medial meniscus (DMM) mouse model and correlate with gut microbiome and systemic cytokine levels.

METHODS: Adult male mice underwent unilateral DMM or sham surgery and were then fed eight weeks of KD or chow. At baseline and every two weeks, mechanical allodynia of the operated and contralateral knees was assessed via analgesiometry. Knee joints were collected for histology, gut microbiome analysis was performed on cecal material via 16S sequencing, and serum cytokines were analyzed via Bio-Plex assay.

RESULTS: KD mice had worse histopathologic OA after DMM (mean ± SEM Osteoarthritis Research Society International score: KD-DMM: 4.0 ± 0.5 vs chow-DMM: 2.7 ± 0.08; P = 0.02). KD mice had increased mechanical allodynia postsurgery (P = 0.005 in mixed-effects model). The gut microbiome changed substantially with KD: 59 clades were altered by KD in DMM and 39 by KD in sham (36 were shared, 25 overlapped with previous murine OA studies). Several clades were correlated on an individual-mouse level with both histology and allodynia (eg, Lactobacillus histology P = 0.004, allodynia P = 1 × 10[-4]). Serum analysis showed four cytokines increased with KD (interleukin [IL]-1β, IL-2, IL-3, and IL-13).

CONCLUSION: KD started immediately after OA induction via DMM is associated with worsened histologic outcomes. KD also worsens mechanical allodynia after either DMM or sham surgery. KD induces significant gut microbiome dysbiosis in clades previously associated with murine OA.},
}

@article {pmid39853798,
year = {2025},
author = {Lutz, KC and Neugent, ML and Bedi, T and De Nisco, NJ and Li, Q},
title = {A Generalized Bayesian Stochastic Block Model for Microbiome Community Detection.},
journal = {Statistics in medicine},
volume = {44},
number = {3-4},
pages = {e10291},
doi = {10.1002/sim.10291},
pmid = {39853798},
issn = {1097-0258},
support = {2113674//National Science Foundation/ ; 2210912//National Science Foundation/ ; AT-2030-20200401//Welch Foundation/ ; 1F32DK128975-01A1/NH/NIH HHS/United States ; 1R01DK131267-01/NH/NIH HHS/United States ; 1R01GM141519/NH/NIH HHS/United States ; },
mesh = {*Bayes Theorem ; Humans ; *Microbiota/genetics ; *Markov Chains ; Computer Simulation ; Female ; Monte Carlo Method ; Stochastic Processes ; Models, Statistical ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; },
abstract = {Advances in next-generation sequencing technology have enabled the high-throughput profiling of metagenomes and accelerated microbiome studies. Recently, there has been a rise in quantitative studies that aim to decipher the microbiome co-occurrence network and its underlying community structure based on metagenomic sequence data. Uncovering the complex microbiome community structure is essential to understanding the role of the microbiome in disease progression and susceptibility. Taxonomic abundance data generated from metagenomic sequencing technologies are high-dimensional and compositional, suffering from uneven sampling depth, over-dispersion, and zero-inflation. These characteristics often challenge the reliability of the current methods for microbiome community detection. To study the microbiome co-occurrence network and perform community detection, we propose a generalized Bayesian stochastic block model that is tailored for microbiome data analysis where the data are transformed using the recently developed modified centered-log ratio transformation. Our model also allows us to leverage taxonomic tree information using a Markov random field prior. The model parameters are jointly inferred by using Markov chain Monte Carlo sampling techniques. Our simulation study showed that the proposed approach performs better than competing methods even when taxonomic tree information is non-informative. We applied our approach to a real urinary microbiome dataset from postmenopausal women. To the best of our knowledge, this is the first time the urinary microbiome co-occurrence network structure in postmenopausal women has been studied. In summary, this statistical methodology provides a new tool for facilitating advanced microbiome studies.},
}

*Bayes Theorem
Humans
*Microbiota/genetics
*Markov Chains
Computer Simulation
Female
Monte Carlo Method
Stochastic Processes
Models, Statistical
Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
Metagenome

@article {pmid39853408,
year = {2025},
author = {Wang, X and Yi, F and Zou, C and Yan, Q and Bashir, MH and Ahmed, W and Mahmood, SU and Wu, J and Ali, S},
title = {Exposure to spaceflight enhances the virulence of Purpureocillium lilacinum against Tetranychus cinnabarinus: modulation of the host's enzyme activities and microbiome.},
journal = {Archives of microbiology},
volume = {207},
number = {2},
pages = {43},
pmid = {39853408},
issn = {1432-072X},
mesh = {Animals ; *Tetranychidae/microbiology/genetics ; Virulence ; *Hypocreales/pathogenicity/genetics/enzymology ; Microbiota/physiology ; Antioxidants/metabolism ; },
abstract = {Multiple studies have been conducted to investigate the impact of space conditions on human, plant, and microbial life. This research investigated the virulence of spaceflight mutants of the entomopathogenic fungus Purpureocillium lilacinum (HP7, HP36, HP52) and its original strain (SP535) against Tetranychus cinnabarinus as well as examination of the T. cinnabarinus immune response, including alterations in enzyme profiles and microbiome composition post fungal application. Our observations revealed contrasting, time-specific differences in pathogenicity and tissue infection between the ground-based isolate and spaceflight mutant isolates. Analysis of detoxifying and antioxidant enzymes showed a significant reduction in enzyme activities T. cinnabarinus infected with the most virulent spaceflight mutants at 36 h post-fungal infection, compared to ground-based isolates. Additionally, the microbiota was reduced due to a fungal infection, partly due to decreased antioxidant enzyme activities. Our findings indicate that changes in the microbiota of T. cinnabarinus following infection with P. lilacinum (both ground-based and spaceflight mutant isolates) resulted in variations in metabolism and genetic information-related KEGG pathways. This data can help identify potential changes in the host immune system that drive increased virulence after spaceflight mutation.},
}

Animals
*Tetranychidae/microbiology/genetics
Virulence
*Hypocreales/pathogenicity/genetics/enzymology
Microbiota/physiology
Antioxidants/metabolism

@article {pmid39853324,
year = {2025},
author = {Dasinger, JH and Abais-Battad, JM and McCrorey, MK and Van Beusecum, JP},
title = {Recent Advances on Immunity and Hypertension: The New Cells on the Kidney Block.},
journal = {American journal of physiology. Renal physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajprenal.00309.2024},
pmid = {39853324},
issn = {1522-1466},
support = {R00HL157549//HHS | National Institutes of Health (NIH)/ ; T32GM12055//HHS | National Institutes of Health (NIH)/ ; T32GM1523862//HHS | National Institutes of Health (NIH)/ ; IK2BX005605//U.S. Department of Veterans Affairs (VA)/ ; PTRF2023-10//Dialysis Clinics (DCI)/ ; MUSC COM-PPG//MUSC | College of Medicine, Medical University of South Carolina (College of Medicine)/ ; P30AR072582//HHS | National Institutes of Health (NIH)/ ; R56HL169434//HHS | National Institutes of Health (NIH)/ ; },
abstract = {Over the last 50 years, contribution of the immune system has been identified in the development of hypertension and renal injury. Both human and experimental animal models of hypertension have demonstrated that innate and adaptive immune cells, along with their cytokines and chemokines, modulate blood pressure fluctuations and end organ renal damage. Numerous cell types of the innate immune system, specifically monocytes, macrophages, and dendritic cells present antigenic peptides to T cells promoting inflammation and the elevation of blood pressure. These T cells and other adaptive immune cells, migrate to vascular and tubular cells of the kidney and promote end-organ fibrosis, damage, and ultimately hypertensive injury. Through the development of high throughput screening, novel renal and immune cell subsets have been identified as possible contributors and regulators of renal injury and hypertension. In this review, we will consider classical immunological cells and their contribution to renal inflammation, and novel cell subsets, including renal stromal cells, that could potentially shed new light on renal injury and hypertension. Lastly, we will discuss how interorgan inflammation contributes to the development of hypertension and hypertension-related multi-organ damage, and the clinical implications of the immunological components of renal injury and hypertension.},
}

@article {pmid39853270,
year = {2025},
author = {Cardones, AR and Emiola, A and Hall, R and Sung, AD and Zhang, JY and Petty, AJ and Puza, C and Bohannon, LM and Bush, AT and Lew, MV and Fleming, E and Jin, YJ and Nichols, KR and Jain, V and Gregory, SG and Sullivan, KM and Chao, NJ and Oh, J},
title = {Cutaneous dysbiosis characterizes the post-allogeneic hematopoietic stem cell transplantation period.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2021004792},
pmid = {39853270},
issn = {2473-9537},
abstract = {Gut dysbiosis is linked to mortality and the development of graft-versus-host disease (GVHD) after hematopoietic stem cell transplantation (HSCT), but the impact of cutaneous dysbiosis remains unexplored. We performed a pilot observational study and obtained retroauricular and forearm skin swabs from 12 adult patients prior to conditioning chemotherapy/radiation, and at 1-week, 1-month and 3-months after allogeneic HSCT, and performed shotgun metagenomic sequencing. The cutaneous microbiome among HSCT patients was enriched for gram-negative bacteria such as E coli and Pseudomonas, fungi, and viruses. Enrichment with bacteriophages and Polyomavirus sp, was observed among patients who died within 1-year, while we observed longitudinal stability of the cutaneous microbiome at the 3-month time point among those who survived beyond 1 year post-HSCT, although these may simply be a reflection of the overall medical status of the patients. There was no association with fungal abundance and any of the outcomes observed. The cutaneous microbiome may be a reservoir of pathobionts among allogeneic HSCT patients. Our findings suggest that cutaneous dysbiosis exists post-HSCT, but the ultimate implication of this to patient outcomes remains to be seen. Larger studies are required.},
}

@article {pmid39853059,
year = {2025},
author = {Guo, D and Liu, C and Zhu, H and Cheng, Y and Huo, X and Guo, Y and Qian, H},
title = {Food-Induced Adverse Reactions: A Review of Physiological Food Quality Control, Mucosal Defense Mechanisms, and Gastrointestinal Physiology.},
journal = {Toxics},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/toxics13010061},
pmid = {39853059},
issn = {2305-6304},
abstract = {Although food is essential for the survival of organisms, it can also trigger a variety of adverse reactions, ranging from nutrient intolerances to celiac disease and food allergies. Food not only contains essential nutrients but also includes numerous substances that may have positive or negative effects on the consuming organism. To protect against potentially harmful components, all animals have evolved defense mechanisms, which are similar to antimicrobial defenses but often come at the cost of the organism's health. When these defensive responses are exaggerated or misdirected, they can lead to adverse food reactions, where the costs outweigh the benefits. Furthermore, due to the persistent toxicity of harmful food components, the failure of defense mechanisms can also result in pathological effects triggered by food. This article review presents a food quality control framework that aims to clarify how these reactions relate to normal physiological processes. Organisms utilize several systems to coexist with symbiotic microbes, regulate them, and concurrently avoid, expel, or neutralize harmful pathogens. Similarly, food quality control systems allow organisms to absorb necessary nutrients while defending against low-quality or harmful components in food. Although many microbes are lethal in the absence of antimicrobial defenses, diseases related to microbiome dysregulation, such as inflammatory bowel disease, have significantly increased. Antitoxin defenses also come with costs and may fail due to insufficiencies, exaggerations, or misdirected actions, ultimately leading to adverse food reactions. With the changes in human diet and lifestyle, the failure of defense mechanisms has contributed to the rising incidence of food intolerances. This review explores the mechanisms of antitoxin defenses and analyzes how their failure can lead to adverse food reactions, emphasizing the importance of a comprehensive understanding of food quality control mechanisms for developing more effective treatments for food-triggered diseases.},
}

@article {pmid39853010,
year = {2024},
author = {Alexiev, A and Stretch, E and Kasschau, KD and Wilson, LB and Truong, L and Tanguay, RL and Sharpton, TJ},
title = {Clearing the Air on Pollutant Disruptions of the Gut-Brain Axis: Developmental Exposure to Benzo[a]pyrene Disturbs Zebrafish Behavior and the Gut Microbiome in Adults and Subsequent Generations.},
journal = {Toxics},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/toxics13010010},
pmid = {39853010},
issn = {2305-6304},
support = {1R01ES030226/ES/NIEHS NIH HHS/United States ; T32ES007060/ES/NIEHS NIH HHS/United States ; },
abstract = {Developmental exposure to benzo[a]pyrene (BaP), a ubiquitous environmental pollutant, has been linked to various toxic effects, including multigenerational behavioral impairment. While the specific mechanisms driving BaP neurotoxicity are not fully understood, recent work highlights two important determinants of developmental BaP neurotoxicity: (1) the aryl hydrocarbon receptor (AHR), which induces host metabolism of BaP, and (2) the gut microbiome, which may interact with BaP to affect its metabolism, or be perturbed by BaP to disrupt the gut-brain axis. We utilized the zebrafish model to explore the role of AHR, the gut microbiome, and their interaction, on BaP-induced neurotoxicity. We tested (1) how developmental BaP exposure and AHR2 perturbation in zebrafish link to adult behavior, (2) how these variables associate with the structure and function of the adult zebrafish gut metagenome, and (3) whether these associations are multigenerational. Our findings reveal a reticulated axis of association between BaP exposure, developmental AHR2 expression, the zebrafish gut metagenome, and behavior. Results indicate that AHR2 is a key modulator of how BaP elicits neurotoxicity and microbiome dysbiosis. Additionally, this axis of association manifests generationally. These findings demonstrate the importance of studying pollutant-microbiome interactions and elucidate the role of specific host genes in neurotoxicity and dysbiosis.},
}

@article {pmid39852495,
year = {2025},
author = {Gómez-Lama Cabanás, C and Mercado-Blanco, J},
title = {Groundbreaking Technologies and the Biocontrol of Fungal Vascular Plant Pathogens.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/jof11010077},
pmid = {39852495},
issn = {2309-608X},
support = {2021ICT246//Ayudas Extraordinarias a la Incorporación de Científicos Titulares OEP 2020-2021/ ; 202440E003//CSIC 'Proyecto Intramural'/ ; },
abstract = {This review delves into innovative technologies to improve the control of vascular fungal plant pathogens. It also briefly summarizes traditional biocontrol approaches to manage them, addressing their limitations and emphasizing the need to develop more sustainable and precise solutions. Powerful tools such as next-generation sequencing, meta-omics, and microbiome engineering allow for the targeted manipulation of microbial communities to enhance pathogen suppression. Microbiome-based approaches include the design of synthetic microbial consortia and the transplant of entire or customized soil/plant microbiomes, potentially offering more resilient and adaptable biocontrol strategies. Nanotechnology has also advanced significantly, providing methods for the targeted delivery of biological control agents (BCAs) or compounds derived from them through different nanoparticles (NPs), including bacteriogenic, mycogenic, phytogenic, phycogenic, and debris-derived ones acting as carriers. The use of biodegradable polymeric and non-polymeric eco-friendly NPs, which enable the controlled release of antifungal agents while minimizing environmental impact, is also explored. Furthermore, artificial intelligence and machine learning can revolutionize crop protection through early disease detection, the prediction of disease outbreaks, and precision in BCA treatments. Other technologies such as genome editing, RNA interference (RNAi), and functional peptides can enhance BCA efficacy against pathogenic fungi. Altogether, these technologies provide a comprehensive framework for sustainable and precise management of fungal vascular diseases, redefining pathogen biocontrol in modern agriculture.},
}

@article {pmid39852475,
year = {2025},
author = {Obi, LU and Roopnarain, A and Tekere, M and Zhou, J and Li, H and Wang, Y and Zhang, Y and Adeleke, RA},
title = {Dynamics and Insights into the Unique Ecological Guild of Fungi in Bacteria-Bioaugmented Anaerobic Digesters.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/jof11010056},
pmid = {39852475},
issn = {2309-608X},
support = {WRC: Grant No. K5/2543//Water Research Commission/ ; },
abstract = {Anaerobic digesters host a variety of microorganisms, and they work together to produce biogas. While bacterial and archaeal communities have been well explored using molecular techniques, fungal community structures remain relatively understudied. The present study aims to investigate the dynamics and potential ecological functions of the predominant fungi in bacteria-bioaugmented anaerobic digesters. Eight different anaerobic digesters that contained chopped water hyacinth and cow dung as feedstock at 2% total solids were respectively inoculated with eight different bacterial strains and digested anaerobically in controlled conditions. The diversity and dynamics of the fungal community of the digesters before and after digestion were monitored using high-throughput sequencing of the fungal ITS2 sub-region of the ribosomal gene. The functional potential of the fungal community was predicted using ecological guild analysis. The dominant fungal phyla were (with relative abundance ≥1%) Ascomycota and Neocallimastigomycota. Ascomycota exhibited over 90% dominance in all treatments after anaerobic digestion (AD). Aspergillus sp. was consistently dominant across treatments during AD, while prominent anaerobic fungal genera Anaeromyces, Cyllamyces, and Caeomyces decreased. Ecological guild analysis at genus level showed that the majority of the identified fungi were saprophytes, and diversity indices indicated decreased richness and diversity after AD, suggesting a negative impact of AD on fungal communities in the anaerobic digesters. The multivariate structure of the fungal communities showed clustering of treatments with similar fungal taxa. The findings from this study provide insights into the fungal ecological guild of different bacteria-bioaugmented anaerobic digesters, highlighting their potentials in bacteria-augmented systems. Identification of an anaerobic fungal group within the phylum Ascomycota, beyond the well-known fungal phylum Neocallimastigomycota, offers a new perspective in optimizing the AD processes in specialized ecosystems.},
}

@article {pmid39852437,
year = {2024},
author = {Horng, HC and Xu, JW and Kuo, YS and Chen, YS and Chiu, YH and Tsui, KH and Tung, YT},
title = {Dual Mechanisms of Action: Anti-Candida and Anti-Inflammatory Potential of Lactobacillus Fermentation Broth in Treating Vulvovaginal Candidiasis.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/jof11010018},
pmid = {39852437},
issn = {2309-608X},
abstract = {Vulvovaginal candidiasis (VVC), a condition predominantly caused by Candida albicans, affects millions of women worldwide, prompting the need for alternative treatments due to the side effects and increasing resistance associated with conventional imidazole antifungals. This study investigated VAGINNE[®], a novel fermentation broth derived from Lactobacillus species, as a potential VVC treatment. Using a BALB/c mouse model of C. albicans infection, we evaluated VAGINNE[®]'s effects on vaginal microbiome composition, inflammatory markers, and tissue integrity. Our findings revealed that VAGINNE[®] treatment enhanced the growth of beneficial Lactobacillus species while suppressing C. albicans proliferation, leading to a more balanced vaginal microbiome. Additionally, VAGINNE[®] significantly reduced pro-inflammatory cytokines (IL-17A, IL-22, IL-23) in vaginal tissues and systemic inflammatory markers (IL-6, IL-1β) in plasma. Histological analysis showed minimal fungal invasion and preserved vaginal epithelial integrity in VAGINNE[®]-treated mice compared to untreated controls. These results suggest that VAGINNE[®] could serve as an effective anti-Candida and anti-inflammatory agent for managing VVC, offering a promising alternative to traditional antifungal treatments. By promoting a healthy vaginal microbiome, reducing inflammation, and maintaining tissue health, this probiotic-based approach presents a novel strategy for addressing VVC, particularly in cases of drug resistance or adverse reactions to standard therapies. This study underscores the potential of microbiome-modulating strategies in managing vaginal infections, paving the way for more targeted and side-effect-free VVC treatments.},
}

@article {pmid39852393,
year = {2025},
author = {Ou, Z and Fu, X and Norbäck, D and Lin, R and Wen, J and Sun, Y},
title = {MiMeJF: Application of Coupled Matrix and Tensor Factorization (CMTF) for Enhanced Microbiome-Metabolome Multi-Omic Analysis.},
journal = {Metabolites},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/metabo15010051},
pmid = {39852393},
issn = {2218-1989},
support = {42377106//National Natural Science Foundation of China/ ; },
abstract = {Background/Objectives: The integration of microbiome and metabolome data could unveil profound insights into biological processes. However, widely used multi-omic data analyses often employ a stepwise mining approach, failing to harness the full potential of multi-omic datasets and leading to reduced detection accuracy. Synergistic analysis incorporating microbiome/metabolome data are essential for deeper understanding. Method: This study introduces a Coupled Matrix and Tensor Factorization (CMTF) framework for the joint analysis of microbiome and metabolome data, overcoming these limitations. Two CMTF frameworks were developed to factorize microbial taxa, functional pathways, and metabolites into latent factors, facilitating dimension reduction and biomarker identification. Validation was conducted using three diverse microbiome/metabolome datasets, including built environments and human gut samples from inflammatory bowel disease (IBD) and COVID-19 studies. Results: Our results revealed biologically meaningful biomarkers, such as Bacteroides vulgatus and acylcarnitines associated with IBD and pyroglutamic acid and p-cresol associated with COVID-19 outcomes, which provide new avenues for research. The CMTF framework consistently outperformed traditional methods in both dimension reduction and biomarker detection, offering a robust tool for uncovering biologically relevant insights. Conclusions: Despite its stringent data requirements, including the reliance on stratified microbial-based pathway abundances and taxa-level contributions, this approach provides a significant step forward in multi-omics integration and analysis, with potential applications across biomedical, environmental, and agricultural research.},
}

@article {pmid39852383,
year = {2025},
author = {Yuan, JD and Wang, LW and Fu, SY and E, RG and Ren, XQ and Sun, H and Liu, F and Wang, B and An, JH and Zhao, MR and He, JF and He, XL},
title = {Heat Tolerance Differences Between Hu Sheep and Hu Crossbred Sheep in Microbial Community Structure and Metabolism.},
journal = {Metabolites},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/metabo15010040},
pmid = {39852383},
issn = {2218-1989},
support = {2022JBGS0012//Inner Mongolia Autonomous Region Science and Technology Plan Project/ ; 2023CXYJJM03//Innovation Fund of Inner Mongolia Academy of Agricultural and Animal Husbandry Science/ ; 2023QN03019//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; ZD20232314//the Erdos Major Project of Science & Technology/ ; none//the Inner Mongolia Autonomous Region Mutton Sheep industry technology system/ ; },
abstract = {BACKGROUND: The frequent occurrence of extreme temperature events causes significant economic losses to the livestock industry. Therefore, delving into the differences in the physiological and molecular mechanisms of heat stress across different sheep breeds is crucial for developing effective management and breeding strategies.

METHODS: This study explores the differences in heat tolerance mechanisms between Hu sheep and Xinggao sheep by comparing their growth performance under normal and heat stress conditions, as well as examining the differences in physiological, biochemical, and antioxidant indicators related to heat tolerance, serum metabolomics, and gut microbiomics in a heat stress environment.

RESULTS: The results indicate that with changes in the temperature-humidity index (THI), Hu sheep exhibit superior stability in respiratory rate (RR) and rectal temperature (RT) fluctuations compared to Xinggao sheep. In terms of biochemical indicators and antioxidant capacity, the levels of creatinine (Cr) and superoxide dismutase (SOD) in Hu sheep serum are significantly higher than those in Xinggao sheep. In comparison, alkaline phosphatase (ALP) and malondialdehyde (MDA) levels are significantly lower. Metabolomic results showed that, compared to Hu sheep, Xinggao sheep exhibited higher cortisol (COR) and dopamine (DA) levels under heat stress conditions, a stronger lipid mobilization capacity, and elevated levels of tricarboxylic acid (TCA) cycle-related metabolites. Furthermore, gut microbiome analysis results indicate that Hu sheep demonstrate stronger cellulose degradation capabilities, as evidenced by significantly higher abundances of microorganisms such as Ruminococcus, Fibrobacter, and Bacteroidales_RF16_group, compared to Xinggao sheep.

CONCLUSIONS: In summary, Hu sheep exhibit stronger heat tolerance compared to Xinggao sheep. These findings provide an important theoretical basis for the breeding and selection of heat-tolerant meat sheep varieties and offer strong support for the region's livestock industry in addressing the challenges posed by global warming.},
}

@article {pmid39852369,
year = {2025},
author = {Lauwers, S and Weyns, AS and Breynaert, A and Van Rillaer, T and Van Huynegem, V and Fransen, E and Bittremieux, W and Lebeer, S and Tuenter, E and Hermans, N},
title = {Comparison of In Vitro Biotransformation of Olive Polyphenols Between Healthy Young and Elderly.},
journal = {Metabolites},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/metabo15010026},
pmid = {39852369},
issn = {2218-1989},
abstract = {BACKGROUND: Olive leaves are a rich source of polyphenols, predominantly secoiridoids, flavonoids, and simple phenols, which exhibit various biological properties. Extracts prepared from olive leaves are associated with hypoglycemic, hypotensive, diuretic, and antiseptic properties. Upon ingestion, a substantial fraction of these polyphenols reaches the colon where they undergo extensive metabolism by the gut microbiota. Host characteristics, like age, can influence the composition of the gut microbiome, potentially affecting the biotransformation of these compounds. Therefore, it can be hypothesised that differences in the gut microbiome between young and elderly individuals may impact the biotransformation rate and the type and amount of metabolites formed.

METHODS: An in vitro biotransformation model was used to mimic the conditions in the stomach, small intestine and colon of two age groups of healthy participants (20-30 years old, ≥65 years old), using oleuropein as a single compound and an olive leaf extract as test compounds. The bacterial composition and metabolite content were investigated.

RESULTS: The study revealed that, while the same metabolites were formed in both age groups, in the young age group, less metabolite formation was observed, likely due to a reduced viable cell count. Most biotransformation reactions took place within the first 24 h of colon incubation, and mainly, deglycosylation, hydrolysis, flavonoid ring cleavage, and demethylation reactions were observed. A bacterial composition analysis showed a steep drop in α-diversity after 24 h of colon incubation, likely due to favourable experimental conditions for certain bacterial species.

CONCLUSIONS: Both age groups produced the same metabolites, suggesting that the potential for polyphenols to exert their health-promoting benefits persists in healthy older individuals.},
}

@article {pmid39851614,
year = {2025},
author = {Srila, W and Sripilai, K and Binlateh, T and Thammanichanon, P and Tiskratok, W and Noisa, P and Jitprasertwong, P},
title = {Relationship Between the Salivary Microbiome and Oral Malodor Metabolites in Older Thai Individuals with Periodontitis and the Cytotoxic Effects of Malodor Compounds on Human Oral Squamous Carcinoma (HSC-4) Cells.},
journal = {Dentistry journal},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/dj13010036},
pmid = {39851614},
issn = {2304-6767},
support = {NRIIS number 4285350//National Science, Research, and Innovation Fund (NSRF)/ ; //Thailand Science Research and Innovation/ ; //Suranaree University of Technology/ ; },
abstract = {Background/Objectives: Halitosis is primarily caused by the activity of oral microorganisms. In this study, we employed metagenomic sequencing and metabolomic approaches to investigate the differences in salivary microbiota and metabolite profiles between individuals with halitosis and periodontitis and healthy controls. Additionally, we expanded the study to examine how oral malodorous compounds interact with human oral squamous carcinoma (HSC-4) cells. Methods: Saliva samples were collected and analyzed using Ultra-High Performance Liquid Chromatography-Mass Spectrometry (UHPLC-MS) to identify metabolites. We then assessed the correlations between the microbiota and metabolites. Furthermore, the impact of oral malodorous substances on HSC-4 cells was investigated by evaluating apoptosis, antioxidant activity, and inflammatory properties. Results: The microbiota and metabolite profiles showed significant differences between the halitosis with periodontitis group and the periodontally healthy group. The halitosis with periodontitis group exhibited significantly higher relative abundances of eight genera: Tannerella, Selenomonas, Bacteroides, Filifactor, Phocaeicola, Fretibacterium, Eubacterium saphenum, and Desulfobulbus. In contrast, the periodontally healthy group showed significantly higher relative abundances of Family XIII UCG-001, Haemophilus, and Streptobacillus. Two metabolites, 2,3-dihydro-1H-indole and 10,11-dihydro-12R-hydroxy-leukotriene E4, were significantly higher in individuals with halitosis and periodontitis. In the treatment of HSC-4 cells with metabolites, dimethyl sulfide (DMS) did not show significant effects while indole appeared to induce cell death in HSC-4 cells by triggering apoptotic pathways. Additionally, both indole and DMS affected the inflammatory and antioxidant properties of HSC-4 cells. Conclusions: This study provides insights into the mechanisms of halitosis by exploring the correlations between microbiota and metabolite profiles. Furthermore, oral metabolites were shown to impact the cellular response of HSC-4 cells.},
}

@article {pmid39851512,
year = {2025},
author = {Monti, E and Vianello, C and Leoni, I and Galvani, G and Lippolis, A and D'Amico, F and Roggiani, S and Stefanelli, C and Turroni, S and Fornari, F},
title = {Gut Microbiome Modulation in Hepatocellular Carcinoma: Preventive Role in NAFLD/NASH Progression and Potential Applications in Immunotherapy-Based Strategies.},
journal = {Cells},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/cells14020084},
pmid = {39851512},
issn = {2073-4409},
support = {25187//Italian Association for Cancer Research/ ; PNRR - M4C2-I1.3 Project PE_00000019 "HEAL ITALIA"//EUROPEAN UNION - NEXTGENERATIONEU/ ; },
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology/immunology/pathology/therapy ; *Carcinoma, Hepatocellular/immunology/pathology/microbiology/therapy ; *Gastrointestinal Microbiome ; *Liver Neoplasms/immunology/pathology/microbiology/therapy ; *Immunotherapy/methods ; *Disease Progression ; Animals ; },
abstract = {Hepatocellular carcinoma (HCC) is a heterogeneous tumor associated with several risk factors, with non-alcoholic fatty liver disease (NAFLD) emerging as an important cause of liver tumorigenesis. Due to the obesity epidemics, the occurrence of NAFLD has significantly increased with nearly 30% prevalence worldwide. HCC often arises in the background of chronic liver disease (CLD), such as nonalcoholic steatohepatitis (NASH) and cirrhosis. Gut microbiome (GM) alterations have been linked to NAFLD progression and HCC development, with several investigations reporting a crucial role for the gut-liver axis and microbial metabolites in promoting CLD. Moreover, the GM affects liver homeostasis, energy status, and the immune microenvironment, influencing the response to immunotherapy with interesting therapeutic implications. In this review, we summarize the main changes in the GM and derived metabolites (e.g., short-chain fatty acids and bile acids) occurring in HCC patients and influencing NAFLD progression, emphasizing their potential as early diagnostic biomarkers and prognostic tools. We discuss the weight loss effects of diet-based interventions and healthy lifestyles for the treatment of NAFLD patients, highlighting their impact on the restoration of the intestinal barrier and GM structure. We also describe encouraging preclinical findings on the modulation of GM to improve liver functions in CLD, boost the antitumor immune response (e.g., probiotic supplementations or anti-hypercholesterolemic drug treatment), and ultimately delay NAFLD progression to HCC. The development of safe and effective strategies that target the gut-liver axis holds promise for liver cancer prevention and treatment, especially if personalized options will be considered.},
}

Humans
*Non-alcoholic Fatty Liver Disease/microbiology/immunology/pathology/therapy
*Carcinoma, Hepatocellular/immunology/pathology/microbiology/therapy
*Gastrointestinal Microbiome
*Liver Neoplasms/immunology/pathology/microbiology/therapy
*Immunotherapy/methods
*Disease Progression
Animals

@article {pmid39851261,
year = {2025},
author = {Zhao, X and Qiu, Y and Liang, L and Fu, X},
title = {Interkingdom signaling between gastrointestinal hormones and the gut microbiome.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2456592},
doi = {10.1080/19490976.2025.2456592},
pmid = {39851261},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; *Dysbiosis/microbiology ; *Gastrointestinal Hormones/metabolism ; *Bacteria/metabolism/classification/genetics ; Fecal Microbiota Transplantation ; Signal Transduction ; Homeostasis ; Inflammatory Bowel Diseases/microbiology/metabolism ; Gastrointestinal Tract/microbiology/metabolism ; },
abstract = {The interplay between the gut microbiota and gastrointestinal hormones plays a pivotal role in the health of the host and the development of diseases. As a vital component of the intestinal microecosystem, the gut microbiota influences the synthesis and release of many gastrointestinal hormones through mechanisms such as modulating the intestinal environment, producing metabolites, impacting mucosal barriers, generating immune and inflammatory responses, and releasing neurotransmitters. Conversely, gastrointestinal hormones exert feedback regulation on the gut microbiota by modulating the intestinal environment, nutrient absorption and utilization, and the bacterial biological behavior and composition. The distributions of the gut microbiota and gastrointestinal hormones are anatomically intertwined, and close interactions between the gut microbiota and gastrointestinal hormones are crucial for maintaining gastrointestinal homeostasis. Interventions leveraging the interplay between the gut microbiota and gastrointestinal hormones have been employed in the clinical management of metabolic diseases and inflammatory bowel diseases, such as bariatric surgery and fecal microbiota transplantation, offering promising targets for the treatment of dysbiosis-related diseases.},
}

*Gastrointestinal Microbiome/physiology
Humans
Animals
*Dysbiosis/microbiology
*Gastrointestinal Hormones/metabolism
*Bacteria/metabolism/classification/genetics
Fecal Microbiota Transplantation
Signal Transduction
Homeostasis
Inflammatory Bowel Diseases/microbiology/metabolism
Gastrointestinal Tract/microbiology/metabolism

@article {pmid39850963,
year = {2024},
author = {Ciernikova, S and Sevcikova, A and Mego, M},
title = {Exploring the microbiome-gut-testis axis in testicular germ cell tumors.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1529871},
pmid = {39850963},
issn = {2235-2988},
mesh = {Humans ; *Testicular Neoplasms/microbiology ; Male ; *Neoplasms, Germ Cell and Embryonal/microbiology ; *Gastrointestinal Microbiome ; *Testis/microbiology ; *Dysbiosis/microbiology ; Microbiota ; Tumor Microenvironment ; },
abstract = {The microbiome-gut-testis axis has emerged as a significant area of interest in understanding testicular cancer, particularly testicular germ cell tumors (TGCTs), which represent the most common malignancy in young men. The interplay between the gut and testicular microbiomes is hypothesized to influence tumorigenesis and reproductive health, underscoring the complex role of microbial ecosystems in disease pathology. The microbiome-gut-testis axis encompasses complex interactions between the gut microbiome, systemic immune modulation, and the local microenvironment of the testis. Dysbiosis in the gut or testicular microbiomes may contribute to altered immune responses, inflammation, and hormonal imbalances, potentially playing a role in the pathogenesis of TGCTs. Concurrently, seminal microbiomes have been linked to variations in sperm quality, fertility potential, and possibly cancer susceptibility, underscoring the need for further evaluation. This review explores the emerging role of the microbiome-gut-testis axis in the context of testicular cancer, highlighting its implications for disease onset, progression, treatment efficacy, and toxicity. Identifying potential microbial biomarkers, followed by microbiota modulation to restore a balanced microbial community, might offer a novel supportive strategy for improving treatment efficacy in refractory TGCT patients while reducing chemotherapy-induced toxicity. We suggest a better understanding of the association between dysregulated microbial environments and TGCTs emphasizes potential pathways by which the gut microbiome might influence testicular cancer.},
}

Humans
*Testicular Neoplasms/microbiology
Male
*Neoplasms, Germ Cell and Embryonal/microbiology
*Gastrointestinal Microbiome
*Testis/microbiology
*Dysbiosis/microbiology
Microbiota
Tumor Microenvironment

@article {pmid39850945,
year = {2024},
author = {Valitutti, F and Mennini, M and Monacelli, G and Fagiolari, G and Piccirillo, M and Di Nardo, G and Di Cara, G},
title = {Intestinal permeability, food antigens and the microbiome: a multifaceted perspective.},
journal = {Frontiers in allergy},
volume = {5},
number = {},
pages = {1505834},
pmid = {39850945},
issn = {2673-6101},
abstract = {The gut barrier encompasses several interactive, physical, and functional components, such as the gut microbiota, the mucus layer, the epithelial layer and the gut mucosal immunity. All these contribute to homeostasis in a well-regulated manner. Nevertheless, this frail balance might be disrupted for instance by westernized dietary habits, infections, pollution or exposure to antibiotics, thus diminishing protective immunity and leading to the onset of chronic diseases. Several gaps of knowledge still exist as regards this multi-level interaction. In this review we aim to summarize current evidence linking food antigens, microbiota and gut permeability interference in diverse disease conditions such as celiac disease (CeD), non-celiac wheat sensitivity (NCWS), food allergies (FA), eosinophilic gastrointestinal disorder (EOGID) and irritable bowel syndrome (IBS). Specific food elimination diets are recommended for CeD, NCWS, FA and in some cases for EOGID. Undoubtfully, each of these conditions is very different and quite unique, albeit food antigens/compounds, intestinal permeability and specific microbiota signatures orchestrate immune response and decide clinical outcomes for all of them.},
}

@article {pmid39850896,
year = {2024},
author = {Deng, Y and Dong, ZX and Yang, GH and Krimsky, WS and Tai, YH and Peng, H and Huang, GT and Xu, JX and Sarkar, SA and Peng, J and Qian, K},
title = {Streptococcus intermedius promotes synchronous multiple primary lung cancer progression through apoptosis regulation.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1482084},
pmid = {39850896},
issn = {1664-3224},
mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; *Apoptosis ; Male ; *Disease Progression ; *Streptococcus intermedius ; Female ; Middle Aged ; Aged ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; Lung/microbiology/pathology ; },
abstract = {BACKGROUND: Dysbiosis of the lung microbiome can contribute to the initiation and progression of lung cancer. Synchronous multiple primary lung cancer (sMPLC) is an increasingly recognized subtype of lung cancer characterized by high morbidity, difficulties in early detection, poor prognosis, and substantial clinical challenges. However, the relationship between sMPLC pathogenesis and changes in the lung microbiome remains unclear.

METHODS: In this study, 16S rRNA sequencing was performed on clinical samples to analyze lung microbiome composition. Real-time quantitative PCR (qPCR) was used to quantify bacterial abundance in lung tissues. In addition, flow cytometry was conducted to evaluate cell cycle progression and apoptosis in lung tumor cells.

RESULTS: Clinical cohort studies demonstrated that sMPLC occurrence is associated with disturbances in the lung microbiome. Notably, Streptococcus intermedius was enriched in the lungs of sMPLC patients compared with non-tumor controls and accumulated preferentially in tumor tissues. S. intermedius shortened the cell cycle and inhibited apoptosis in lung cancer cells. Analyses of oral and gut microbiomes in different patient cohorts revealed a strong correlation between oral microbiome imbalances and lung microbiome composition in sMPLC patients.

CONCLUSIONS: These findings characterize the lung microbiota in sMPLC and identify S. intermedius as a potentially influential bacterial strain. This study provides significant new insights into the diagnosis and treatment of sMPLC.},
}

Humans
*Lung Neoplasms/microbiology/pathology
*Apoptosis
Male
*Disease Progression
*Streptococcus intermedius
Female
Middle Aged
Aged
Microbiota
RNA, Ribosomal, 16S/genetics
Dysbiosis/microbiology
Lung/microbiology/pathology

@article {pmid39850876,
year = {2024},
author = {Yoneda, K and Sendo, S and Okano, T and Shimizu, H and Yamada, H and Nishimura, K and Ueda, Y and Saegusa, J},
title = {Impact of dysregulated microbiota-derived C18 polyunsaturated fatty acid metabolites on arthritis severity in mice with collagen-induced arthritis.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1444892},
pmid = {39850876},
issn = {1664-3224},
mesh = {Animals ; *Arthritis, Experimental/microbiology/metabolism ; Mice ; *Gastrointestinal Microbiome ; Male ; *Fatty Acids, Unsaturated/metabolism ; Severity of Illness Index ; Linoleic Acids, Conjugated/metabolism ; Dysbiosis ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred DBA ; Disease Models, Animal ; },
abstract = {OBJECTIVE: We aimed to evaluate microbiome and microbiota-derived C18 dietary polyunsaturated fatty acids (PUFAs), such as conjugated linoleic acid (CLA), and to investigate their differences that correlate with arthritis severity in collagen-induced arthritis (CIA) mice.

METHODS: On day 84 after induction, during the chronic phase of arthritis, cecal samples were analyzed using 16S rRNA sequencing, and plasma and cecal digesta were evaluated using liquid chromatography-tandem mass spectrometry. Differences in microbial composition between 10 control (Ctrl) and 29 CIA mice or between the mild and severe subgroups based on arthritis scores were identified. The cecal metabolite profile and its correlation with the microbiome were evaluated with respect to arthritis severity.

RESULTS: The hydroxy and oxo metabolite levels were higher in CIA mice than in Ctrl mice, some of which, including 10-hydroxy-cis-6-18:1, were positively correlated with arthritis scores. The 9-trans,11-trans CLA levels in CIA mice had a negative linear correlation with arthritis scores. Microbial diversity was lower in severe CIA mice than in mild CIA or Ctrl mice. The abundance of Lactobacillus relatively increased in the severe subgroup of CIA mice compared with that in the mild subgroup and was positively correlated with arthritis severity.

CONCLUSION: Alterations in gut microbiota and microbiota-derived C18 PUFA metabolites are associated in CIA mice and correlated with arthritis scores, indicating that plasma or fecal C18 PUFA metabolites can be potential biomarkers for arthritis severity and dysbiosis.},
}

Animals
*Arthritis, Experimental/microbiology/metabolism
Mice
*Gastrointestinal Microbiome
Male
*Fatty Acids, Unsaturated/metabolism
Severity of Illness Index
Linoleic Acids, Conjugated/metabolism
Dysbiosis
RNA, Ribosomal, 16S/genetics
Mice, Inbred DBA
Disease Models, Animal

@article {pmid39850838,
year = {2025},
author = {Akter, A and Teddleton, H and Caldwell, M and Pighetti, G and Myer, PR and Henniger, MT and Schneider, L and Shepherd, E},
title = {Prevalence of nasopharyngeal bacteria during naturally occurring bovine respiratory disease in commercial stocker cattle.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18858},
pmid = {39850838},
issn = {2167-8359},
mesh = {Animals ; Cattle ; *Nasopharynx/microbiology ; Prevalence ; *Bovine Respiratory Disease Complex/microbiology/epidemiology ; Male ; RNA, Ribosomal, 16S/genetics ; Microbiota/drug effects ; Bacteria/isolation & purification/genetics/drug effects/classification ; Cattle Diseases/microbiology/epidemiology ; },
abstract = {Bovine respiratory disease (BRD) is one of the most common economic and health challenges to the beef cattle industry. Prophylactic use of antimicrobial drugs can alter the microbial communities in the respiratory tract. Considering that the bovine upper respiratory tract microbiome has been associated with generalized health, understanding the microenvironment that influences this microbiome may provide insights into the pathogenesis of BRD. This study aimed to determine temporal variation in nasopharyngeal (NP) microbiome in naturally occurring BRD in newly received stocker calves. Mixed breed steers (n = 40) were purchased from an auction market and housed in a commercial stocker farm. Clinical signs were used to identify BRD affected animals, and calves were categorized based on the number of treatments (NumTrt) received (0, 1, 2). On days 0, 7, 14, and 21, NP samples were collected, and subsequent DNA were isolated and sequenced. After sequencing, 16S rRNA V4 gene was amplified and utilized for NP bacterial determination. The difference in relative abundance based on day and NumTrt was measured using repeated measures ANOVA (PROC GLIMMIX; SAS 9.4). Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, and Verrucomicrobiota were the top phyla and Mycoplasma, Histophilus, Geobacillus, Saccharococcus, Lactobacillus, and Pasteurella were the top genera. In healthy calves, the relative abundance of Mycoplasma differed by day (P = 0.01), whereas on day 7, calves had five times greater abundance compared to day 0 (d 0: 0.06 ± 0.05; d 7: 0.30 ± 0.05). No differences were observed in the alpha diversity matrices based on day or NumTrt (P > 0.05). Results of this study suggest compositional variations in NP microbial populations occur during disease conditions.},
}

Animals
Cattle
*Nasopharynx/microbiology
Prevalence
*Bovine Respiratory Disease Complex/microbiology/epidemiology
Male
RNA, Ribosomal, 16S/genetics
Microbiota/drug effects
Bacteria/isolation & purification/genetics/drug effects/classification
Cattle Diseases/microbiology/epidemiology

@article {pmid39850835,
year = {2025},
author = {Zhang, Q and Zhen, M and Wang, X and Zhao, F and Dong, Y and Wang, X and Gao, S and Wang, J and Shi, W and Zhang, Y},
title = {Antibiotic exposure enriches streptococci carrying resistance genes in periodontitis plaque biofilms.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18835},
pmid = {39850835},
issn = {2167-8359},
mesh = {Humans ; *Biofilms/drug effects/growth & development ; *Periodontitis/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Streptococcus/drug effects/genetics ; Female ; Male ; Adult ; *Dental Plaque/microbiology ; *Amoxicillin/pharmacology/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Drug Resistance, Bacterial/genetics ; Microbiota/drug effects/genetics ; Tetracycline/pharmacology/therapeutic use ; Metronidazole/pharmacology/therapeutic use ; Clindamycin/pharmacology/therapeutic use ; },
abstract = {BACKGROUND: Periodontitis is not always satisfactorily treated with conventional scaling and root planing, and adjunctive use of antibiotics is required in clinical practice. Therefore, it is important for clinicians to understand the diversity and the antibiotic resistance of subgingival microbiota when exposed to different antibiotics.

MATERIALS AND METHODS: In this study, subgingival plaques were collected from 10 periodontitis patients and 11 periodontally healthy volunteers, and their microbiota response to selective pressure of four antibiotics (amoxicillin, metronidazole, clindamycin, and tetracycline) were evaluated through 16S rRNA gene amplicon and metagenomic sequencing analysis. Additionally, sensitive and resistant strains were isolated and cultured in vitro for resistance evaluation.

RESULTS: Cultivation of subgingival microbiota revealed the oral microbiota from periodontitis patients were more resistant to antibiotics than that of healthy. Significant differences were also observed for the microbial community between with and without antibiotics (especially amoxicillin and tetracycline) treated in periodontitis group.

CONCLUSION: Overall, after the two antibiotics (amoxicillin and tetracycline) exposed, the oral subgingival microbiota in periodontitis patients exhibited different diversity and composition. Streptococcus may account for oral biofilm-specific antibiotic resistance in periodontitis. This provides information for personalized treatment of periodontitis.},
}

Humans
*Biofilms/drug effects/growth & development
*Periodontitis/microbiology/drug therapy
*Anti-Bacterial Agents/pharmacology/therapeutic use
*Streptococcus/drug effects/genetics
Female
Male
Adult
*Dental Plaque/microbiology
*Amoxicillin/pharmacology/therapeutic use
RNA, Ribosomal, 16S/genetics
Middle Aged
Drug Resistance, Bacterial/genetics
Microbiota/drug effects/genetics
Tetracycline/pharmacology/therapeutic use
Metronidazole/pharmacology/therapeutic use
Clindamycin/pharmacology/therapeutic use

@article {pmid39850636,
year = {2024},
author = {Iannotti, FA},
title = {I. IDC Key-note Lecture: Influence of gut microbiome in Duchenne muscular dystrophy.},
journal = {Journal of stem cells & regenerative medicine},
volume = {20},
number = {2},
pages = {56-57},
pmid = {39850636},
issn = {0973-7154},
}

@article {pmid39850611,
year = {2025},
author = {Pardali, EC and Gkouvi, A and Gkouskou, KK and Manolakis, AC and Tsigalou, C and Goulis, DG and Bogdanos, DP and Grammatikopoulou, MG},
title = {Autoimmune protocol diet: A personalized elimination diet for patients with autoimmune diseases.},
journal = {Metabolism open},
volume = {25},
number = {},
pages = {100342},
pmid = {39850611},
issn = {2589-9368},
abstract = {The autoimmune protocol diet (AIP) is a personalized elimination diet that aims to determine and exclude the foods that might trigger immune responses, leading to inflammation and symptomatology associated with autoimmune diseases. Focusing on gut health and the importance of the gut microbiome in immune regulation and overall well-being, the AIP starts by eliminating foods that might create negative effects on the patients and continues by developing a personalized and tailored diet plan for them. This comprehensive approach aims to mitigate symptoms and improve quality of life of individuals with autoimmune conditions. This review presents and critically appraises current knowledge on the AIP protocol, highlight any oversights, and discuss findings from relevant clinical trials.},
}

@article {pmid39850469,
year = {2024},
author = {Leonov, G and Varaeva, Y and Livantsova, E and Vasilyev, A and Vladimirskaya, O and Korotkova, T and Nikityuk, D and Starodubova, A},
title = {Periodontal pathogens and obesity in the context of cardiovascular risks across age groups.},
journal = {Frontiers in oral health},
volume = {5},
number = {},
pages = {1488833},
pmid = {39850469},
issn = {2673-4842},
abstract = {BACKGROUND: Cardiovascular diseases (CVDs) are the leading cause of mortality and morbidity among noncommunicable diseases. Over the past decade, there has been a notable increase in the prevalence of CVDs among young individuals. Obesity, a well-known risk factor for CVDs, is also associated with various comorbidities that may contribute to cardiovascular risk. The relationship between periodontal pathogens and CVD risk factors, including obesity, smoking, lipid metabolism disorders, and inflammatory markers, remains underexplored.

METHODS: This study examined the relationship between six periodontal pathogens (Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Treponema denticola, Tannerella forsythia, Prevotella intermedia, and Fusobacterium nucleatum) and CVD risk factors among 189 subjects stratified by age and body mass index (BMI). Body composition was assessed via bioimpedance analysis, and blood samples were analyzed for lipid profiles, glucose, and proinflammatory cytokines. Oral samples were collected for polymerase chain reaction (PCR) analysis to identify periodontal pathogens. Cardiovascular and diabetes risk scores were calculated using the SCORE and FINDRISC scales.

RESULTS: The prevalence of periodontal pathogens in the population was 33.0% for P. gingivalis, 47.8% for P. intermedia, 63.4% for A. actinomycetemcomitans, 46.6% for T. forsythia, 46.6% for T. denticola, and 89.2% for F. nucleatum. Significant age- and BMI-related differences were observed in pathogen prevalence, particularly with P. gingivalis, P. intermedia, and T. denticola. Young obese individuals exhibited a higher prevalence of P. intermedia and T. forsythia. P. gingivalis was found to be associated with hypertension and dyslipidemia, while P. intermedia was linked to hypertension and obesity. T. denticola was associated with obesity, dyslipidemia and smoking, whereas T. forsythia was linked to dyslipidemia alone.

CONCLUSIONS: This study highlights the potential connection between periodontal pathogens and risk factors associated with cardiovascular disease, including smoking, elevated BMI, increased adipose tissue, hypertension, and dyslipidemia. Further research is required to determine the causal relationships between oral microbiome dysbiosis, obesity and, systemic diseases and to develop an effective strategy for preventing oral health-related CVD risk factors in young adults.},
}

@article {pmid39850273,
year = {2024},
author = {Lloren, KKS and Senevirathne, A and Lee, JH},
title = {Advancing vaccine technology through the manipulation of pathogenic and commensal bacteria.},
journal = {Materials today. Bio},
volume = {29},
number = {},
pages = {101349},
pmid = {39850273},
issn = {2590-0064},
abstract = {Advancements in vaccine technology are increasingly focused on leveraging the unique properties of both pathogenic and commensal bacteria. This revolutionary approach harnesses the diverse immune modulatory mechanisms and bacterial biology inherent in different bacterial species enhancing vaccine efficacy and safety. Pathogenic bacteria, known for their ability to induce robust immune responses, are being studied for their potential to be engineered into safe, attenuated vectors that can target specific diseases with high precision. Concurrently, commensal bacteria, which coexist harmlessly with their hosts and contribute to immune system regulation, are also being explored as novel delivery systems and in microbiome-based therapy. These bacteria can modulate immune responses, offering a promising avenue for developing effective and personalized vaccines. Integrating the distinctive characteristics of pathogenic and commensal bacteria with advanced bacterial engineering techniques paves the way for innovative vaccine and therapeutic platforms that could address a wide range of infectious diseases and potentially non-infectious conditions. This holistic approach signifies a paradigm shift in vaccine development and immunotherapy, emphasizing the intricate interplay between the bacteria and the immune systems to achieve optimal immunological outcomes.},
}

@article {pmid39850178,
year = {2024},
author = {Gandhi, DN and Pande, DN and Harikrishna, A and Advilkar, A and Basavan, I and Ansari, R},
title = {Beyond the Brain: Attention Deficit/Hyperactivity Disorder and the Gut-Brain Axis.},
journal = {Cureus},
volume = {16},
number = {12},
pages = {e76291},
pmid = {39850178},
issn = {2168-8184},
abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a complex neurodevelopmental condition, predominantly affecting children, characterized by inattention, hyperactivity, and impulsivity. A growing body of evidence has highlighted the potential influence of the gut microbiota on the onset and presentation of ADHD symptoms. The gut microbiota, a diverse microbial ecosystem residing within the gastrointestinal tract, exerts multiple effects on systemic physiology, including immune modulation, metabolic regulation, and neuronal signalling. The bidirectional gut-brain axis serves as a conduit for communication between gut microbes and the central nervous system, implicating its disruption in neurodevelopmental disorders such as ADHD. This comprehensive literature review aims to shed light on how alterations in the gut microbiota influence the development and manifestation of ADHD symptoms. Examining potential mechanisms involving gut microbial metabolites and their impact on neurotransmitter modulation, neuro-endocrine signalling and neuroinflammation, we dissect the intricate interplay shaping ADHD pathology. Insights into these complex interactions hold promise for personalized therapeutic interventions aimed at modulating the gut microbiota to ameliorate ADHD symptoms. Discussions encompass dietary interventions, faecal microbiota-targeted therapies, and emerging probiotic approaches, underscoring their potential as adjunctive or alternative strategies in managing ADHD. Further research elucidating the precise mechanisms driving these interactions may pave the way for targeted and personalized interventions for individuals grappling with ADHD.},
}

@article {pmid39850127,
year = {2024},
author = {Fakhraldeen, SA and Madhusoodhanan, R and Habibi, N and Al-Haddad, S and Alagarsamy, S and Habeebullah, SFK and Al-Zakri, WM and Thuslim, F and Fernandes, L and Al-Yamani, F and Al-Said, T},
title = {Shotgun metagenomics reveals the interplay between microbiome diversity and environmental gradients in the first marine protected area in the northern Arabian Gulf.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1479542},
pmid = {39850127},
issn = {1664-302X},
abstract = {INTRODUCTION: The northwest Arabian Gulf encounters significant anthropogenic pressures, including nutrient enrichment from coastal development and effluent discharge.

METHODS: This study presents the first shotgun metagenomics-based characterization of microbial communities in Kuwaiti waters of the northwest Arabian Gulf, focusing on Kuwait's first Marine Protected Area (MPA) in Sulaibikhat Bay, a vital nursery ground for commercially important fish.

RESULTS: Analysis revealed significantly higher microbial diversity within the MPA compared to adjacent waters, with Rhodobacteraceae (27.8%) and Flavobacteriaceae (15.3%) being dominant. Elevated inorganic phosphorus, nitrogen, and salinity were key factors driving this diversity. Multivariate analysis highlighted phosphate as a critical component affecting the MPA microbial community structure, particularly for the families Microbacteriaceae, Flavobacteriaceae, and Rhodobacteraceae.

DISCUSSION: This study underscores the ecological importance of MPAs and highlights the impact of nutrient enrichment and other environmental stressors on microbial diversity, emphasizing the need to reduce nutrient influx to mitigate eutrophication and enhance marine ecosystem resilience in stressed environments.},
}

@article {pmid39849992,
year = {2025},
author = {Tamminga, SM and Van Der Wal, MM and Saager, ES and Van Der Gang, LF and Boesjes, CM and Hendriks, A and Pannekoek, Y and De Bruin, MS and Van Wijk, F and Van Sorge, NM},
title = {Single-cell sequencing of human Langerhans cells identifies altered gene expression profiles in patients with atopic dermatitis.},
journal = {ImmunoHorizons},
volume = {9},
number = {2},
pages = {},
doi = {10.1093/immhor/vlae009},
pmid = {39849992},
issn = {2573-7732},
support = {//Infection and Immunity Boost/ ; //Dutch Health Council/ ; },
mesh = {Humans ; *Dermatitis, Atopic/immunology/microbiology/genetics ; *Langerhans Cells/immunology/metabolism ; *Staphylococcus aureus/immunology/genetics ; *Single-Cell Analysis ; Skin/microbiology/pathology/immunology ; Transcriptome ; Male ; Adult ; Female ; Chemokine CCL17/genetics/metabolism ; Th2 Cells/immunology/metabolism ; T-Lymphocytes, Regulatory/immunology/metabolism ; Sequence Analysis, RNA ; Lymphocyte Activation/immunology ; },
abstract = {Atopic dermatitis (AD) is characterized by dysregulated T cell immunity and skin microbiome dysbiosis with predominance of Staphylococcus aureus, which is associated with exacerbating AD skin inflammation. Specific glycosylation patterns of S. aureus cell wall structures amplify skin inflammation through interaction with Langerhans cells (LCs). Nevertheless, the role of LCs in AD remains poorly characterized. Here, we performed single cell RNA sequencing of primary epidermal LCs and dermal T cells, isolated from skin biopsies of AD patients and healthy control subjects, alongside specific glycoanalysis of S. aureus strains isolated from the AD lesions. Our findings revealed 4 LC subpopulations ie, 2 steady-state clusters [LC1 and LC1H] and 2 proinflammatory/matured subsets [LC2 and migratory LCs]. The latter 2 subsets were enriched in AD skin. AD LCs showed enhanced expression of C-type lectin receptors, the high-affinity IgE receptor, and activation of prostaglandin and leukotriene biosynthesis pathways, upregulated transcriptional signatures related to T cell activation pathways, and increased expression of CCL17 compared with healthy LCs. Correspondingly, T helper 2 and T regulatory cell populations were increased in AD lesions. Complementary, we performed bulk RNA sequencing of primary LCs stimulated with the S. aureus strains isolated from the AD lesions, which showed upregulation of T helper 2-related pathways. Our study provides proof-of-concept for a role of LCs in connecting the S. aureus-T cell axis in the AD inflammatory cycle.},
}

Humans
*Dermatitis, Atopic/immunology/microbiology/genetics
*Langerhans Cells/immunology/metabolism
*Staphylococcus aureus/immunology/genetics
*Single-Cell Analysis
Skin/microbiology/pathology/immunology
Transcriptome
Male
Adult
Female
Chemokine CCL17/genetics/metabolism
Th2 Cells/immunology/metabolism
T-Lymphocytes, Regulatory/immunology/metabolism
Sequence Analysis, RNA
Lymphocyte Activation/immunology

@article {pmid39849986,
year = {2025},
author = {Liu, Y and Geng, Y and Jiang, Y and Li, P and Li, YZ and Zhang, Z},
title = {Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf012},
pmid = {39849986},
issn = {1751-7370},
abstract = {One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial survival. The powerful effects of antimicrobial toxins result in simple combinations of microorganisms failing to coexist under laboratory conditions, but it is unclear whether they also have a negative impact on the biodiversity of natural communities. Here, we revealed that microbial communities worldwide universally possess functional potential for antimicrobial toxin production. Counterintuitively, the biodiversity of global microbial communities increases, rather than decreases, as the abundance of antimicrobial toxins in rare taxa rises. Rare taxa may encode more antimicrobial toxins than abundant taxa, which is associated with the maintenance of the high biodiversity of microbial communities amid complex interactions. Our findings suggest that the antagonistic interaction caused by antimicrobial toxins may play a positive role in microbial community biodiversity at the global scale.},
}

@article {pmid39849793,
year = {2025},
author = {Gul, P and Khan, J and Li, Q and Liu, K},
title = {Moringa oleifera in a modern time: A comprehensive review of its nutritional and bioactive composition as a natural solution for managing diabetes mellitus by reducing oxidative stress and inflammation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {201},
number = {},
pages = {115671},
doi = {10.1016/j.foodres.2025.115671},
pmid = {39849793},
issn = {1873-7145},
mesh = {*Moringa oleifera/chemistry ; *Oxidative Stress/drug effects ; Humans ; *Hypoglycemic Agents/pharmacology ; *Diabetes Mellitus/drug therapy ; Animals ; *Inflammation/drug therapy ; *Plant Extracts/pharmacology ; Antioxidants/pharmacology ; Anti-Inflammatory Agents/pharmacology ; Nutritive Value ; Seeds/chemistry ; },
abstract = {Globally, diabetes mellitus (DM) and its complications are considered among the most significant public health problems. According to numerous scientific studies, Plants and their bioactive compounds may reduce inflammation and oxidative stress (OS), leading to a reduction in the progression of DM. Moringa oleifera (MO), widely used in Ayurvedic and Unani medicine for centuries because of its health-promoting characteristics, particularly its ability to control DM and its related complications. MO is a multi-purpose plant that has an impressive range of nutritional components including proteins, amino acids (Essential and non-essential amino acids), carbs, fats, fiber, vitamins, and phenolic compounds. In the modern era, scientists have paid close attention to the anti-diabetic, anti-oxidative and anti-inflammatory attributes and other medicinal properties, of MO leaves and seeds. MO leaves and seeds have modulatory effects on DM that are likely influenced by multiple mechanisms. Some of these mechanisms include direct effects, but other mechanisms involve inhibition the production of inflammatory markers, modulation of the gut microbiome, reduction of OS, enhancement of glucose metabolism through hexokinase and glucose 6-phosphate dehydrogenase, improve insulin sensitivity and glucose uptake in the liver and muscles. Overall, these findings suggest that MO may play a role in lowering the risk of DM and its related outcomes. The purpose of this review is to provide a comprehensive overview of the nutritional and bioactive profiles of MO leaves and seeds, as well as to investigate their possible anti-diabetic effects by modulating oxidative stress and inflammation. Our results indicate that MO may be a beneficial natural resource for management of DM and related issues by lowering oxidative stress and inflammation. Furthermore, studies on MO has yielded promising findings in diabetic animal models, indicating antioxidant and anti-inflammatory properties. However, human trials have shown less solid results, most likely due to a lack of studies, different techniques, and dosages. More clinical research is needed to fully understand MO's anti-diabetic potential, notably in lowering oxidative stress and inflammation, both of which are critical in controlling diabetes complications.},
}

*Moringa oleifera/chemistry
*Oxidative Stress/drug effects
Humans
*Hypoglycemic Agents/pharmacology
*Diabetes Mellitus/drug therapy
Animals
*Inflammation/drug therapy
*Plant Extracts/pharmacology
Antioxidants/pharmacology
Anti-Inflammatory Agents/pharmacology
Nutritive Value
Seeds/chemistry

@article {pmid39849752,
year = {2025},
author = {Eg Gadegaard, IS and Eskildsen, MH and Østergaard, SK and Nielsen, JL and Rasmussen, JT},
title = {Xanthine oxidase-lactoperoxidase system: Dose-dependent antibacterial effects and global gene expression changes in infant oral microbiota.},
journal = {Food research international (Ottawa, Ont.)},
volume = {201},
number = {},
pages = {115596},
doi = {10.1016/j.foodres.2024.115596},
pmid = {39849752},
issn = {1873-7145},
mesh = {*Lactoperoxidase/metabolism/genetics ; *Xanthine Oxidase/metabolism/genetics ; Humans ; Infant ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; *Mouth/microbiology ; Saliva/microbiology/enzymology ; Reactive Oxygen Species/metabolism ; Bacteria/drug effects/genetics ; Gene Expression Regulation, Bacterial ; Milk/microbiology ; },
abstract = {Xanthine oxidase (XO) and lactoperoxidase (LPO) are highly abundant enzymes in milk. Their substrates, xanthine and thiocyanate, are found in elevated amounts in infant saliva, leading to a proposed interaction between milk and saliva referred to as the XO-LPO system. This system is suggested to generate reactive oxygen and nitrogen species with potential antibacterial effects. The antibacterial activity of the XO-LPO system was assessed on bacteria cultured from the oral cavities of five infants, where a reduction in bacterial growth rate was observed at 40 µg mL[-1] of each enzyme and with complete inhibition achieved at 200 µg mL[-1]. Gene expression analysis showed that XO-LPO treatment led to downregulation of several reactive oxygen species-related genes, suggesting a transient bacterial stress response. The study also observed downregulation of key glycolytic enzymes, indicating that XO-LPO treatment affects bacterial metabolism at transcriptional level, suggesting a possible mechanism of action for the XO-LPO system. Collectively, these findings offer new insights into the XO-LPO system, revealing novel aspects of the interaction between lactation and microbiome influence.},
}

*Lactoperoxidase/metabolism/genetics
*Xanthine Oxidase/metabolism/genetics
Humans
Infant
*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects
*Mouth/microbiology
Saliva/microbiology/enzymology
Reactive Oxygen Species/metabolism
Bacteria/drug effects/genetics
Gene Expression Regulation, Bacterial
Milk/microbiology

@article {pmid39849717,
year = {2025},
author = {Faubel, N and Blanco-Morales, V and Sentandreu, V and Barberá, R and Garcia-Llatas, G},
title = {Modulation of microbiota composition and markers of gut health after in vitro dynamic colonic fermentation of plant sterol-enriched wholemeal rye bread.},
journal = {Food research international (Ottawa, Ont.)},
volume = {201},
number = {},
pages = {115570},
doi = {10.1016/j.foodres.2024.115570},
pmid = {39849717},
issn = {1873-7145},
mesh = {*Bread/microbiology/analysis ; *Fermentation ; *Gastrointestinal Microbiome/physiology ; *Phytosterols/metabolism ; *Secale/chemistry ; Humans ; *Fatty Acids, Volatile/metabolism ; *Colon/microbiology/metabolism ; *Dietary Fiber/metabolism ; *Sitosterols/metabolism ; Prebiotics ; Stigmasterol/metabolism ; Bifidobacterium/metabolism ; Biomarkers ; Lactobacillus/metabolism ; Cholesterol/analogs & derivatives ; },
abstract = {A human oral phase followed by a dynamic gastrointestinal digestion and colonic fermentation (simgi®) has been applied to wholemeal rye bread (WRB) and PS-enriched WRB (PS-WRB). The aim of this study was to evaluate the impact of these solid and high-fiber food matrices on the metabolism of PS, modulation of the microbiota and production of short-chain fatty acids (SCFA) and ammonium ion after a simulated chronic intake (5 days). In both breads, campesterol, campestanol, stigmasterol, β-sitosterol, sitostanol, Δ5-avenasterol, Δ5,24-stigmastadienol, Δ7-stigmastenol, and Δ7-avenasterol were identified, of which only β-sitosterol was metabolized to sitostenone after PS-WRB treatment. The presence of fiber in both breads exerted a prebiotic effect after fermentation by the increase in Firmicutes (Lactobacillus genus, maximum abundance of 89-99 %) and Actinobacteria (Bifidobacterium genus, maximum abundance of 30-31 %), reflected in an increase of SCFA content. The reduction of proteolytic activity confirmed by the decrease in ammonium ion contents is related to a reduction in the Proteobacteria phylum. Thus, PS-WRB could be considered as a healthy staple food choice since, besides the known hypocholesterolemic effect of PS, rye bread fiber preserves the beneficial microbiota and exerts a positive impact on markers of gut health.},
}

*Bread/microbiology/analysis
*Fermentation
*Gastrointestinal Microbiome/physiology
*Phytosterols/metabolism
*Secale/chemistry
Humans
*Fatty Acids, Volatile/metabolism
*Colon/microbiology/metabolism
*Dietary Fiber/metabolism
*Sitosterols/metabolism
Prebiotics
Stigmasterol/metabolism
Bifidobacterium/metabolism
Biomarkers
Lactobacillus/metabolism
Cholesterol/analogs & derivatives

@article {pmid39849623,
year = {2025},
author = {Liu, Y and Ma, J and Li, X and Zhao, H and Ai, Q and Zhang, L and Tong, Y and Meng, L and Yang, H},
title = {No microorganism was detected in amniotic fluid of healthy pregnancies from the second trimester to the delivery.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {20},
pmid = {39849623},
issn = {2049-2618},
mesh = {Humans ; Female ; Pregnancy ; *Amniotic Fluid/microbiology ; *Pregnancy Trimester, Second ; Adult ; *Bacteria/classification/isolation & purification/genetics ; *RNA, Ribosomal, 16S/genetics ; Cesarean Section ; Chorioamnionitis/microbiology ; Microbiota ; Infant, Newborn ; Premature Birth/microbiology ; Pregnancy Outcome ; DNA, Bacterial/genetics ; Cohort Studies ; },
abstract = {BACKGROUND: The early colonization and establishment of the microbiome in newborns is a crucial step in the development of the immune system and host metabolism. However, the exact timing of initial microbial colonization remains a subject of ongoing debate. While numerous studies have attempted to determine the presence or absence of intrauterine bacteria, the majority of them have drawn conclusions based on sequencing data from maternal or infant samples taken at a single time point. In this study, we aimed to investigate the microbial population in amniotic fluid (AF) from the second trimester until the time of delivery using multiple microbiological methods.

METHODS: AF samples were collected during the second trimester (19-21 gestational weeks) and at the time of delivery. Cohort 1 included 51 women who underwent the term and elective cesarean section, with both their second trimester and delivery AF samples (n = 55, respectively) analyzed. Cohort 2 contained 22 women who experienced infection-related adverse pregnancy outcomes (including preterm birth, histological chorioamnionitis, and stillbirth), with only their second trimester AF samples (n = 24) examined. Additionally, multiple procedural negative controls and technical positive controls were applied to this study to remove potential contamination. Microbial profiles were assessed through cultivation, quantitative real-time polymerase chain reaction, 16S ribosomal RNA gene sequencing, and cytokine analysis.

RESULTS: In cohort 1, the bacterial load and community structure in the second trimester AF samples were indistinguishable from negative controls. Although marginally higher bacterial loads and different bacterial communities were observed in the delivery AF samples compared to negative controls, these bacterial DNA were not considered biologically functional due to the absence of maternal inflammatory responses. In cohort 2, the bacterial load and community structure of the second trimester AF samples differed significantly from those of negative controls, with Ureaplasma and Lactobacillus identified as the most prevalent genera against negative controls.

CONCLUSIONS: Our study demonstrates that no microorganisms were detected in the AF of healthy pregnancies from the second trimester to the delivery. The presence of Ureaplasma and Lactobacillus in the second trimester AF may be associated with infection-related adverse pregnancy outcomes. Video Abstract.},
}

Humans
Female
Pregnancy
*Amniotic Fluid/microbiology
*Pregnancy Trimester, Second
Adult
*Bacteria/classification/isolation & purification/genetics
*RNA, Ribosomal, 16S/genetics
Cesarean Section
Chorioamnionitis/microbiology
Microbiota
Infant, Newborn
Premature Birth/microbiology
Pregnancy Outcome
DNA, Bacterial/genetics
Cohort Studies

@article {pmid39849517,
year = {2025},
author = {Muhammad, A and Qian, Z and Li, Y and Lei, X and Iqbal, J and Shen, X and He, J and Zhang, N and Sun, C and Shao, Y},
title = {Enhanced bioaccumulation and toxicity of Fenpropathrin by polystyrene nano(micro)plastics in the model insect, silkworm (Bombyx mori).},
journal = {Journal of nanobiotechnology},
volume = {23},
number = {1},
pages = {38},
pmid = {39849517},
issn = {1477-3155},
support = {32250410276//National Natural Science Foundation of China/ ; LZ22C170001//Zhejiang Provincial Natural Science Foundation of China/ ; CARS-18-ZJ0302//China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; *Bombyx/metabolism ; *Polystyrenes/toxicity/chemistry ; *Bioaccumulation ; *Gastrointestinal Microbiome/drug effects ; Particle Size ; Adsorption ; Nanoparticles/toxicity/chemistry ; Pyrethrins/toxicity/metabolism ; Larva/drug effects/metabolism ; Microplastics/toxicity ; },
abstract = {BACKGROUND: Nano(micro)plastics (NMPs) and agrochemicals are ubiquitous pollutants. The small size and physicochemical properties of NMPs make them potential carriers for pollutants, affecting their bioavailability and impact on living organisms. However, little is known about their interactions in terrestrial ecosystems. This study investigates the adsorption of Fenpropathrin (FPP) onto two different sizes of polystyrene NMPs and examines their impacts on an insect model, silkworm Bombyx mori. We analyzed the systemic effects of acute exposure to NMPs and FPP, individually and combined, at organismal, tissue, cellular, and gut microbiome levels.

RESULTS: Our results showed that NMPs can adsorb FPP, with smaller particles having higher adsorption capacity, leading to size-dependent increases in the bioaccumulation and toxicity of FPP. These effects led to higher mortality, reduced body weight, delayed development, and decreased cocoon production in silkworms. Additionally, the pollutants caused physical and oxidative damage to the midgut and altered gene expression related to juvenile hormone (JH) and silk protein synthesis. The gut microbiome analysis revealed significant changes and reduced abundance of potentially beneficial bacteria. Thus, the aggravated toxicity induced by NMPs was size-dependent, with smaller particles (NPs) having a greater impact.

CONCLUSIONS: This study demonstrates the role of NMPs as carriers for contaminants, increasing their bioavailability and toxicity in terrestrial ecosystems. These findings have significant implications for ecosystem health and biodiversity.},
}

Animals
*Bombyx/metabolism
*Polystyrenes/toxicity/chemistry
*Bioaccumulation
*Gastrointestinal Microbiome/drug effects
Particle Size
Adsorption
Nanoparticles/toxicity/chemistry
Pyrethrins/toxicity/metabolism
Larva/drug effects/metabolism
Microplastics/toxicity

@article {pmid39849464,
year = {2025},
author = {Qin, L and Lv, W},
title = {Dietary content and eating behavior in ulcerative colitis: a narrative review and future perspective.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {12},
pmid = {39849464},
issn = {1475-2891},
mesh = {Humans ; *Colitis, Ulcerative/physiopathology ; *Gastrointestinal Microbiome/physiology ; *Diet/methods ; *Feeding Behavior/physiology ; Dysbiosis ; Intestinal Mucosa ; Risk Factors ; },
abstract = {Ulcerative colitis (UC) has experienced a steady increase in global incidence and prevalence recently. Current research into UC pathogenesis focuses on the complex interplay of genetic and environmental factors with the immune system and gut microbiome, leading to disruption of the intestinal barrier. Normally, the microbiome, intestinal epithelium, and immune system interact to maintain intestinal homeostasis. However, when this equilibrium is disturbed, a harmful cycle of dysbiosis, immune dysregulation, and inflammation emerges, resulting in intestinal barrier dysfunction and UC progression. Among various risk factors, diet significantly influences epithelial barrier integrity and architectural stability through both direct and indirect mechanisms, shaping the entire UC continuum from pre-clinical prevention to active phase treatment and remission maintenance. This review provides insights into the impact of dietary content and eating behaviors on UC, focusing on specific food, food groups, nutrients, and intermittent fasting, while providing a detailed explanation of why the gut microbiota may mediate the sustained effects of diet across all stages of UC. Additionally, it addresses the limitations of current studies, explores underexamined areas in UC dietary research and proposes potential directions for future research and expansion.},
}

Humans
*Colitis, Ulcerative/physiopathology
*Gastrointestinal Microbiome/physiology
*Diet/methods
*Feeding Behavior/physiology
Dysbiosis
Intestinal Mucosa
Risk Factors

@article {pmid39849445,
year = {2025},
author = {Xie, H and Chen, Z and Wu, G and Wei, P and Gong, T and Chen, S and Xu, Z},
title = {Application of metagenomic next-generation sequencing (mNGS) to describe the microbial characteristics of diabetic foot ulcers at a tertiary medical center in South China.},
journal = {BMC endocrine disorders},
volume = {25},
number = {1},
pages = {18},
pmid = {39849445},
issn = {1472-6823},
support = {[2021]76//the High-level Hospital and Clinical Specialty Discipline Construction Programme for Fujian Medical Development, China/ ; 2023J01692//Fujian Provincial Natural Science Foundation of China/ ; 2022J01243//Fujian Provincial Natural Science Foundation of China/ ; 2020Y9094//the Joint Funds for the innovation of science and Technology，Fujian province, China/ ; 2023Y9213//the Joint Funds for the innovation of science and Technology，Fujian province, China/ ; 2021Y9068//the Joint Funds for the innovation of science and Technology，Fujian province, China/ ; 82002034//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Diabetic Foot/microbiology/diagnosis ; China/epidemiology ; *High-Throughput Nucleotide Sequencing/methods ; *Tertiary Care Centers ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Aged ; Microbiota/genetics ; Adult ; },
abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) are characterized by dynamic wound microbiome, the timely and accurate identification of pathogens in the clinic is required to initiate precise and individualized treatment. Metagenomic next-generation sequencing (mNGS) has been a useful supplement to routine culture method for the etiological diagnosis of DFUs. In this study, we utilized a routine culture method and mNGS to analyze the same DFU wound samples and the results were compared.

METHODS: Forty samples from patients with DFUs at a tertiary medical center in South China were collected, the microorganisms were identified with mNGS and routine culture method simultaneously.

RESULTS: The results showed that the positive detection rate of microorganisms in DFUs with mNGS was much higher (95% vs. 60%). Thirteen strains of microorganisms were detected with routine culture method, and seventy-seven strains were detected with mNGS. Staphylococcus aureus was the most common microorganism detected with culture method, while Enterococcus faecalis was the most common microorganism detected with mNGS. The false negative rate of the culture method was 35%, that was, 14 samples with negative results with culture method were found to be positive with mNGS.

CONCLUSION: The mNGS method had a higher positive detection rate and identified a broader spectrum of microorganisms in DFUs, thus, mNGS provided a more comprehensive understanding of the microbiome of DFUs to facilitate the development of timely and optimal treatment.

TRIAL REGISTRATION: The study was conducted in accordance with the Declaration of Helsinki and approved by the Ethical Review Committee of the Fujian Medical University Union Hospital (approval number 2021KY054).},
}

Humans
*Diabetic Foot/microbiology/diagnosis
China/epidemiology
*High-Throughput Nucleotide Sequencing/methods
*Tertiary Care Centers
Male
Female
*Metagenomics/methods
Middle Aged
Aged
Microbiota/genetics
Adult

@article {pmid39849406,
year = {2025},
author = {Iqbal, NT and Khan, H and Khalid, A and Mahmood, SF and Nasir, N and Khanum, I and de Siqueira, I and Van Voorhis, W},
title = {Chronic inflammation in post-acute sequelae of COVID-19 modulates gut microbiome: a review of literature on COVID-19 sequelae and gut dysbiosis.},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {31},
number = {1},
pages = {22},
pmid = {39849406},
issn = {1528-3658},
support = {3U01AI151698//Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Humans ; *COVID-19/immunology/complications ; *Dysbiosis ; *Gastrointestinal Microbiome ; *Post-Acute COVID-19 Syndrome ; *SARS-CoV-2/physiology ; *Brain-Gut Axis ; Inflammation ; },
abstract = {BACKGROUND: Long COVID or Post-acute sequelae of COVID-19 is an emerging syndrome, recognized in COVID-19 patients who suffer from mild to severe illness and do not recover completely. Most studies define Long COVID, through symptoms like fatigue, brain fog, joint pain, and headache prevailing four or more weeks post-initial infection. Global variations in Long COVID presentation and symptoms make it challenging to standardize features of Long COVID. Long COVID appears to be accompanied by an auto-immune multi-faceted syndrome where the virus or viral antigen persistence causes continuous stimulation of the immune response, resulting in multi-organ immune dysregulation.

MAIN TEXT: This review is focused on understanding the risk factors of Long COVID with a special emphasis on the dysregulation of the gut-brain axis. Two proposed mechanisms are discussed here. The first mechanism is related to the dysfunction of angiotensin-converting enzyme 2 receptor due to Severe Acute Respiratory Syndrome Corona Virus 2 infection, leading to impaired mTOR pathway activation, reduced AMP secretion, and causing dysbiotic changes in the gut. Secondly, gut-brain axis dysregulation accompanied by decreased production of short-chain fatty acids, impaired enteroendocrine cell function, and increased leakiness of the gut, which favors translocation of pathogens or lipopolysaccharide in circulation causing the release of pro-inflammatory cytokines. The altered Hypothalamic-Pituitary-Adrenal axis is accompanied by the reduced level of neurotransmitter, and decreased stimulation of the vagus nerve, which may cause neuroinflammation and dysregulation of serum cortisol levels. The dysbiotic microbiome in Long COVID patients is characterized by a decrease in beneficial short chain fatty acid-producing bacteria (Faecalibacterium, Ruminococcus, Dorea, and Bifidobacterium) and an increase in opportunistic bacteria (Corynebacterium, Streptococcus, Enterococcus). This dysbiosis is transient and may be impacted by interventions including probiotics, and dietary supplements.

CONCLUSIONS: Further studies are required to understand the geographic variation, racial and ethnic differences in phenotypes of Long COVID, the influence of viral strains on existing and emerging phenotypes, to explore long-term effects of gut dysbiosis, and gut-brain axis dysregulation, as well as the potential role of diet and probiotics in alleviating those symptoms.},
}

Humans
*COVID-19/immunology/complications
*Dysbiosis
*Gastrointestinal Microbiome
*Post-Acute COVID-19 Syndrome
*SARS-CoV-2/physiology
*Brain-Gut Axis
Inflammation

@article {pmid39849320,
year = {2025},
author = {Taba, N and Fischer, K and Estonian Biobank Research Team, and Org, E and Aasmets, O},
title = {A novel framework for assessing causal effect of microbiome on health: long-term antibiotic usage as an instrument.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2453616},
doi = {10.1080/19490976.2025.2453616},
pmid = {39849320},
issn = {1949-0984},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Estonia ; Irritable Bowel Syndrome/microbiology/drug therapy ; Depression/microbiology ; Microbiota/drug effects ; },
abstract = {Assessing causality is undoubtedly one of the key questions in microbiome studies for the upcoming years. Since randomized trials in human subjects are often unethical or difficult to pursue, analytical methods to derive causal effects from observational data deserve attention. As simple covariate adjustment is not likely to account for all potential confounders, the idea of instrumental variable (IV) analysis is worth exploiting. Here we propose a novel framework of antibiotic instrumental variable regression (AB-IVR) for estimating the causal relationships between microbiome and various diseases. We rely on the recent studies showing that antibiotic treatment has a cumulative long-term effect on the microbiome, resulting in individuals with higher antibiotic usage to have a more perturbed microbiome. We apply the AB-IVR method on the Estonian Biobank data and show that the microbiome has a causal role in numerous diseases including migraine, depression and irritable bowel syndrome. We show with a plethora of sensitivity analyses that the identified causal effects are robust and propose ways for further methodological developments.},
}

Humans
*Anti-Bacterial Agents/pharmacology
*Gastrointestinal Microbiome/drug effects
Estonia
Irritable Bowel Syndrome/microbiology/drug therapy
Depression/microbiology
Microbiota/drug effects

@article {pmid39849235,
year = {2025},
author = {Scholz, KJ and Höhne, A and Wittmer, A and Häcker, G and Hellwig, E and Cieplik, F and Waidner, B and Al-Ahmad, A},
title = {Co-culture of Helicobacter pylori with oral microorganisms in human saliva.},
journal = {Clinical oral investigations},
volume = {29},
number = {1},
pages = {79},
pmid = {39849235},
issn = {1436-3771},
mesh = {Humans ; *Saliva/microbiology ; *Helicobacter pylori/isolation & purification ; *Coculture Techniques ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Candida/isolation & purification ; Actinomyces/isolation & purification ; Streptococcus mutans/isolation & purification ; Mouth/microbiology ; Colony Count, Microbial ; Streptococcus/isolation & purification ; },
abstract = {OBJECTIVE: Helicobacter pylori is known for colonizing the gastric mucosa and instigating severe upper gastrointestinal diseases such as gastritis, gastroduodenal ulcers, and gastric cancer. To date, there is no data available on the oral cavity as transmission site, whether H. pylori can survive in the oral cavity or in human saliva. The aim of the study was to investigate the influence of oral microorganisms and human saliva on the survival of H. pylori in human saliva.

METHODS: H. pylori strains KE, a motile derivate of type strain H. pylori 26695, and H. pylori SS1, a clinical isolate from a gastric biopsy, were grown in human pooled saliva (pooled from 4 healthy human donors, 0.22 μm filter-sterilized) or in BBF (Brucella browth formula; control) either as mono-cultures or in co-culture with Streptococcus mutans, Streptococcus oralis, Actinomyces naeslundii, Lacticaseibacillus casei and Candida dubliniensis. Bacterial survival of H. pylori and the oral microorganisms were investigated using colony forming units (CFU) assay and MALDI-TOF MS at baseline and after 24, 48 and 168 h.

RESULTS: In saliva, H. pylori KE demonstrated enhanced survival in co-culture with S. mutans, A. naeslundii, and C. dubliniensis, enduring for at least 48 h. In contrast, L. casei and S. oralis inhibited H. pylori KE in saliva. H. pylori KE could not be cultured after 168 h in saliva, neither in mono- nor co-culture. In contrast, H. pylori SS1 in saliva could be cultured after 168 h in co-culture with S. mutans and C. dubliniensis, but not in mono-culture. In BBF, H. pylori KE could be cultured after 168 h with S. mutans, L. casei and C. dubliniensis, and H. pylori SS1 with L. casei and C. dubliniensis, but not with S. mutans. Notably, the co-cultured microorganisms survived at high CFU numbers similar to those of the monocultures.

CONCLUSION: The study suggests that H. pylori can transiently survive in human saliva and even with presence of certain oral microorganisms. However, it may not be a permanent resident of the oral microbiota. The co-survival with oral microorganisms emphasizes the necessity for studying the role of the oral microbiota in the infectious and transmission cycle of H. pylori.},
}

Humans
*Saliva/microbiology
*Helicobacter pylori/isolation & purification
*Coculture Techniques
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Candida/isolation & purification
Actinomyces/isolation & purification
Streptococcus mutans/isolation & purification
Mouth/microbiology
Colony Count, Microbial
Streptococcus/isolation & purification

@article {pmid39849165,
year = {2025},
author = {Sandhu, S and Kumar, S and Singh, P and Singh, BP and Jurel, SK and Lal, N and Mohit, and Sharma, V and Rai, N and Chand, P},
title = {Metagenomic profiling of plaque microbiota in Indian subjects: identified hidden ecological tapestry.},
journal = {Current genetics},
volume = {71},
number = {1},
pages = {3},
pmid = {39849165},
issn = {1432-0983},
mesh = {Humans ; *Dental Plaque/microbiology ; *Metagenomics/methods ; Male ; *Microbiota/genetics ; Female ; India/epidemiology ; Adult ; *Metagenome ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Young Adult ; Adolescent ; Bacteria/genetics/classification/isolation & purification ; Streptococcus/genetics/isolation & purification/classification ; },
abstract = {Dental plaque biofilms are the primary etiologic factor for various chronic oral infectious diseases. In recent years, dental plaque shows enormous potential to know about an individual microbiota. Various microbiome studies of oral cavity from different geographical locations reveals abundance of microbial species. Although, the representation of Indian population in this respect is limited, which make us curious to undergo this study. This study investigates the dental plaque microbiota of North Indian individuals based on their age, gender, and dietary patterns; specifically, food preference and availability of water source using 16 S rRNA metagenomics analysis. The findings from this study revealed that Streptococcus levels are high across genders, age groups, and water source, highlighting its role as a predominant dental caries associated species like Streptococcus mutans, Streptococcus pyogenes, Streptococcus sobrinus and Streptococcus oralis in the studied population groups. Additionally, the abundance of Actinomyces is observed higher in young individuals and females whereas Fusobacterium and Leptotrichia were high in elderly individuals. Moreover, non-vegetarians have higher abundance of Streptococcus and Fusobacterium, whereas vegetarians show higher abundance of Prevotella and Leptotrichia. The study also highlights the influence of water type on bacterial composition of dental plaque in the studied population i.e., individuals consuming underground water has high abundance of Streptococcus, whereas individuals consuming RO water exhibit elevated Prevotella and Leptotrichia. Insights emerged from the analysis illuminates the complex dynamics of microbiota in dental plaque among North Indians. This study also highlight that this variation of microbiome is influenced by age, gender, and dietary habits (vegetarian or non-vegetarian lifestyle). These results will fill a significant knowledge gap regarding the Indian dental plaque microbiome but also offer a foundation to conduct metagenome studies and potential therapeutic implications for future personalized oral health interventions.},
}

Humans
*Dental Plaque/microbiology
*Metagenomics/methods
Male
*Microbiota/genetics
Female
India/epidemiology
Adult
*Metagenome
*RNA, Ribosomal, 16S/genetics
Middle Aged
Young Adult
Adolescent
Bacteria/genetics/classification/isolation & purification
Streptococcus/genetics/isolation & purification/classification

@article {pmid39848958,
year = {2025},
author = {Escobar Marcillo, DI and Privitera, GF and Rollo, F and Latini, A and Giuliani, E and Benevolo, M and Giuliani, M and Pichi, B and Pellini, R and Donà, MG},
title = {Microbiome analysis in individuals with human papillomavirus oral infection.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2953},
pmid = {39848958},
issn = {2045-2322},
mesh = {Humans ; *Microbiota ; *Papillomavirus Infections/virology/microbiology ; Female ; Male ; Adult ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; HIV Infections/microbiology/virology/complications ; Mouth/microbiology/virology ; Papillomaviridae/genetics/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; Human Papillomavirus Viruses ; },
abstract = {Microbiome gained attention as a cofactor in cancers originating from epithelial tissues. High-risk (hr)HPV infection causes oropharyngeal squamous cell carcinoma but only in a fraction of hrHPV+ individuals, suggesting that other factors play a role in cancer development. We investigated oral microbiome in cancer-free subjects harboring hrHPV oral infection (n = 33) and matched HPV- controls (n = 30). DNA purified from oral rinse-and-gargles of HIV-infected (HIV+) and HIV-uninfected (HIV-) individuals were used for 16S rRNA gene V3-V4 region amplification and sequencing. Analysis of differential microbial abundance and differential pathway abundance was performed, separately for HIV+ and HIV- individuals. Significant differences in alpha (Chao-1 and Shannon indices) and beta diversity (unweighted UniFrac distance) were observed between hrHPV+ and HPV-negative subjects, but only for the HIV- individuals. Infection by hrHPVs was associated with significant changes in the abundance of Saccharibacteria in HIV+ and Gracilibacteria in HIV- subjects. At the genus level, the greatest change in HIV+ individuals was observed for Bulleidia, which was significantly enriched in hrHPV+ subjects. In HIV- individuals, those hrHPV+ showed a significant enrichment of Parvimonas and depletion of Alloscardovia. Our data suggest a possible interplay between hrHPV infection and oral microbiome, which may vary with the HIV status.},
}

Humans
*Microbiota
*Papillomavirus Infections/virology/microbiology
Female
Male
Adult
*RNA, Ribosomal, 16S/genetics
Middle Aged
HIV Infections/microbiology/virology/complications
Mouth/microbiology/virology
Papillomaviridae/genetics/isolation & purification
Bacteria/genetics/classification/isolation & purification
Human Papillomavirus Viruses

@article {pmid39848248,
year = {2025},
author = {Abdill, RJ and Graham, SP and Rubinetti, V and Ahmadian, M and Hicks, P and Chetty, A and McDonald, D and Ferretti, P and Gibbons, E and Rossi, M and Krishnan, A and Albert, FW and Greene, CS and Davis, S and Blekhman, R},
title = {Integration of 168,000 samples reveals global patterns of the human gut microbiome.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.12.017},
pmid = {39848248},
issn = {1097-4172},
abstract = {The factors shaping human microbiome variation are a major focus of biomedical research. While other fields have used large sequencing compendia to extract insights requiring otherwise impractical sample sizes, the microbiome field has lacked a comparably sized resource for the 16S rRNA gene amplicon sequencing commonly used to quantify microbiome composition. To address this gap, we processed 168,464 publicly available human gut microbiome samples with a uniform pipeline. We use this compendium to evaluate geographic and technical effects on microbiome variation. We find that regions such as Central and Southern Asia differ significantly from the more thoroughly characterized microbiomes of Europe and Northern America and that composition alone can be used to predict a sample's region of origin. We also find strong associations between microbiome variation and technical factors such as primers and DNA extraction. We anticipate this growing work, the Human Microbiome Compendium, will enable advanced applied and methodological research.},
}

@article {pmid39847933,
year = {2025},
author = {Malla, MA and Nomalihle, M and Featherston, J and Kumar, A and Amoah, ID and Ismail, A and Bux, F and Kumari, S},
title = {Comprehensive profiling and risk assessment of antibiotic resistomes in surface water and plastisphere by integrated shotgun metagenomics.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137180},
doi = {10.1016/j.jhazmat.2025.137180},
pmid = {39847933},
issn = {1873-3336},
abstract = {The ever-increasing microplastics (MPs) and antibiotic-resistance genes (ARGs) in aquatic ecosystems has become a serious global challenging issue. However, the impact of different pollution sources on microbiome and antibiotic resistome in surface water (SW) and plastisphere (PS) remains largely elusive. Here, shotgun metagenomics was used to analyze microbiome structure and antibiotic resistome in SW and PS under the influence of different pollution sources. Pseudomonas were the most abundant genus, followed by Flavobacterium, Acinetobacter, Acidovorax, and Limnohabitans. However, their relative abundance varied significantly both across the sampling sites and habitats i.e. SW and PS (p < 0.05). Additionally, various ARGs were detected in SW and PS, with PS (372) having significantly more potential ARGs than SW (293). The results further showed significant variations in the relative abundance of potential pathogenic bacteria across the sampling sites and habitats (p < 0.05). Further moreover, significant differences were observed in antibiotic resistome risk scores, ARGs and MGEs across different habitats. Over all, this study suggests that pollution source and water quality parameters had a significant impact on microbiome composition and antibiotic resistome in SW and PS.},
}

@article {pmid39848913,
year = {2025},
author = {McLean, H and Mikaberidze, A and Deakin, G and Xu, X and Papp-Rupar, M},
title = {The interplay between scion genotype, root microbiome, and Neonectria ditissima apple canker.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf014},
pmid = {39848913},
issn = {1574-6941},
abstract = {Severity of European apple canker caused by Neonectria ditissima can vary between locations and apple genotypes. We investigated how location, cold storage/planting season, and apple scion genotype affect root-associated microbial communities. Additionally, we investigated whether differences in abundance of specific taxa could be associated with canker lesion counts. Seven scion cultivars grafted onto M9 rootstocks were inoculated with N. ditissima in the nursery and then planted in December 2018 or stored at 2 °C until planting in April 2019 at three sites in Kent, UK. We assessed canker lesions and collected root samples in June 2021. Quantitative PCR and 16S/ITS amplicon sequencing was used to analyse microbial communities. Site was the primary factor affecting microbiome size, diversity, and composition. Cold storage/planting season had small but significant effects, indicating that differences in the microbiome at planting can persist long-term. Scion genotype had a limited effect on diversity but did influence the abundance of specific root associated taxa. Bacterial α-diversity was associated with canker count in a site-dependent manner. Increased abundances of particular fungal (Rhizophagus irregularis and Epicoccum nigrum) and bacterial (Amycolatopsis and Bradyrhizobium) root associated taxa were associated with fewer cankers.},
}

@article {pmid39848566,
year = {2025},
author = {Olesen, CM and Edslev, SM and Aasbjerg, GN and Yüksel, YT and Agner, T and Kamstrup, MR},
title = {Subtype specific alterations in the skin microbiome of patients with cutaneous T-cell lymphoma.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.01.009},
pmid = {39848566},
issn = {1523-1747},
}

@article {pmid39848564,
year = {2025},
author = {Lewis, N and Villani, A and Lagopoulos, J},
title = {Gut dysbiosis as a driver of neuroinflammation in attention-deficit/hyperactivity disorder: A review of current evidence.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2025.01.031},
pmid = {39848564},
issn = {1873-7544},
abstract = {There is mounting evidence for the involvement of the immune system, neuroinflammation and disturbed gut microbiota, or dysbiosis, in attentive-deficit/hyperactivity disorder (ADHD). Gut dysbiosis is strongly implicated in many physical, autoimmune, neurological, and neuropsychiatric conditions, however knowledge of its particular pathogenic role in ADHD is sparse. As such, this narrative review examines and synthesizes the available evidence related to inflammation, dysbiosis, and neural processes in ADHD. Minimal differences in microbiota diversity measures between cases and controls were found, however many relative abundance differences were observed at all classification levels (phylum to strain). Compositional differences of taxa important to key gut-brain axis pathways, in particular Bacteroides species and Faecalibacterium, may contribute to inflammation, brain functioning differences, and symptoms, in ADHD. We have identified one possible model of ADHD etiopathogenesis involving systemic inflammation, an impaired blood-brain barrier, and neural disturbances as downstream consequences of gut dysbiosis. Nevertheless, studies conducted to date have varied degrees of methodological rigour and involve diverse participant characteristics and analytical techniques, highlighting a need for additional research.},
}

@article {pmid39848413,
year = {2025},
author = {Koszła, O and Kukula-Koch, W and Jóźwiak, K and Jastrząb, R and Marć, MA and Mytych, J and Tabęcka-Łonczyńska, A and Skóra, B and Szychowski, KA and Sołek, P},
title = {Biotransformation of Ganoderma lucidum and Hericium erinaceus for ex vivo gut-brain axis modulation and mood-related outcomes in humans: CREB/BDNF signaling and microbiota-driven synergies.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {119393},
doi = {10.1016/j.jep.2025.119393},
pmid = {39848413},
issn = {1872-7573},
abstract = {BACKGROUND: The human gut microbiota plays a crucial role in various aspects of health, extending beyond digestion and nutrient absorption. Ganoderma lucidum (Reishi) and Hericium erinaceus (Lion's Mane), traditional medicinal mushrooms, have garnered interest due to their potential to exert positive health effects. The aim of our study was to investigate the molecular impact of Reishi and Lion's Mane on mood regulation through the gut-brain axis.

METHODS: We utilized a dynamic simulator of the human intestinal microbial ecosystem (SHIME), followed by HPLC-ESI-QTOF-MS/MS and a series of biochemical and molecular assays, including MTT for cell viability, fluorogenic probes for redox balance (ROS and GSH), and Western blot for protein analysis.

RESULTS: Chromatographic analysis confirmed the presence of bioactive compounds in both mushrooms, including triterpenoids (ganoderic acids) and polysaccharides in G. lucidum, as well as hericenones and erinacines in H. erinaceus. We observed concentration-dependent changes in metabolic activity and redox balance due to microbiome cell-free supernatant treatment (M-CFSs). M-CFSs also influenced the Nrf2 pathway and activated heat shock proteins, which may confer neuroprotective effects. Notably, M-CFSs upregulated neurotrophic factors such as BDNF, CDNF, and MANF, crucial for neuronal function. Our study revealed alterations in intracellular signaling cascades, most notably the CREB/BDNF pathway. Moreover, the Akt/mTOR and ERK1/2 showed no significant changes, while Akt/GSK3α/β displayed only partial modifications. The overlapping effects of synaptic activity and activation of the gut-brain axis appear to contribute to mood enhancement.

CONCLUSIONS: These pilot findings suggest a potential role for G. lucidum and H. erinaceus in mood disorder regulation through multifaceted mechanisms involving the gut microbiota. The study underscores the importance of understanding the synergistic interactions between medicinal fungi, gut microbiota, and neural processes to develop novel or preventive strategies for mental health disorders.},
}

@article {pmid39848238,
year = {2025},
author = {Szajewska, H},
title = {An Overview of Early-Life Gut Microbiota Modulation Strategies.},
journal = {Annals of nutrition & metabolism},
volume = {},
number = {},
pages = {1-6},
doi = {10.1159/000541492},
pmid = {39848238},
issn = {1421-9697},
abstract = {BACKGROUND: The gut microbiota, or microbiome, is essential for human health. Early-life factors such as delivery mode, diet, and antibiotic use shape its composition, impacting both short- and long-term health outcomes. Dysbiosis, or alterations in the gut microbiota, is linked to conditions such as allergies, asthma, obesity, diabetes, inflammatory bowel disease, and necrotizing enterocolitis in preterm infants.

SUMMARY: This article reviews current strategies to influence the early-life gut microbiome and their potential health impacts. It also briefly summarizes guidelines on using biotics for gastrointestinal and allergic diseases in children. Key strategies include vaginal or fecal microbiota transplantation for cesarean-born infants, breastfeeding, and biotic-supplemented formulas. While vaginal microbial transfer and maternal fecal microbiota transplantation show short-term benefits, further research is needed to determine long-term safety and efficacy. Breast milk, rich in human milk oligosaccharides, promotes a healthy microbiota and offers protection against infections. Biotic-supplemented formulas can improve the gut microbiota in formula-fed infants and show clinical effects, though each biotic must be evaluated separately. Probiotics given as dietary supplements outside of infant formulas show promise for treating gastrointestinal disorders but require further investigation.},
}

@article {pmid39848217,
year = {2025},
author = {Arya, S and George, AB and O'Dwyer, J},
title = {The architecture of theory and data in microbiome design: towards an S-matrix for microbiomes.},
journal = {Current opinion in microbiology},
volume = {83},
number = {},
pages = {102580},
doi = {10.1016/j.mib.2025.102580},
pmid = {39848217},
issn = {1879-0364},
abstract = {Designing microbiomes for applications in health, bioengineering, and sustainability is intrinsically linked to a fundamental theoretical understanding of the rules governing microbial community assembly. Microbial ecologists have used a range of mathematical models to understand, predict, and control microbiomes, ranging from mechanistic models, putting microbial populations and their interactions as the focus, to purely statistical approaches, searching for patterns in empirical and experimental data. We review the success and limitations of these modeling approaches when designing novel microbiomes, especially when guided by (inevitably) incomplete experimental data. Although successful at predicting generic patterns of community assembly, mechanistic and phenomenological models tend to fall short of the precision needed to design and implement specific functionality in a microbiome. We argue that to effectively design microbiomes with optimal functions in diverse environments, ecologists should combine data-driven techniques with mechanistic models - a middle, third way for using theory to inform design.},
}

@article {pmid39847963,
year = {2025},
author = {Wang, S and Wang, Z and Wang, N and Wang, S and Zeng, S and Xu, Z and Liu, D and Zhao, X and Liu, F and Xu, J and Cai, Y and Ying, H},
title = {Efficient conversion of corn straw to feed protein through solid-state fermentation using a thermophilic microbial consortium.},
journal = {Waste management (New York, N.Y.)},
volume = {194},
number = {},
pages = {298-308},
doi = {10.1016/j.wasman.2025.01.023},
pmid = {39847963},
issn = {1879-2456},
abstract = {Solid-state fermentation of lignocellulosic waste to produce feed protein is a means of realising solid waste. However, low efficiency and susceptibility to microbial contamination remain significant challenges in feed protein production through room-temperature solid-state fermentation. In this study, thermophilic microbiomes were enriched. After adaptive and nitrogen acclimation, microbiomes with the combined functions of 'thermophilic-rapid decomposition-nitrogen conversion' were obtained and used for feed protein production. High-throughput sequencing and Kyoto Encyclopedia of Genes and Genomes metabolic pathway prediction techniques were used to assess the mechanisms underlying microbial involvement in substance conversion. The results showed that the microbiomes decomposed 78.21 %-81.73 % of straw within 7 days. After nitrogen acclimation, the nitrogen utilisation rate and the true protein content of the microbiomes improved by 19.22 %-26.96 % and 56.14 %-71.99 %, respectively. Fed-batch enzymatic saccharification and fermentation reduced the fermentation time by 28.5 %. Domesticated microbiomes increased the abundance of bacteria and fungi in the fermentation system, enhancing carbon metabolism and the urea cycle. This study presents a novel approach for the high-value utilisation of lignocellulose waste.},
}

@article {pmid39847486,
year = {2025},
author = {Xu, H and Jia, Z and Liu, J and Liu, R and Wei, W and Li, X},
title = {Protocol for correlating the gut microbiome and metabolomics in patients with intracranial aneurysms.},
journal = {STAR protocols},
volume = {6},
number = {1},
pages = {103582},
doi = {10.1016/j.xpro.2024.103582},
pmid = {39847486},
issn = {2666-1667},
abstract = {Gut-microbiome-combined metabolomics studies in cerebrovascular disease highlight the microbiota-gut-brain axis in neurological disorders. Here, we present a protocol for correlating the gut microbiome and metabolomics in patients with intracranial aneurysms. We describe steps for sample collection, fecal genomic DNA extraction, rRNA PCR amplification, sequencing library construction, and rRNA sequencing. We then detail procedures for metabolite extraction, liquid chromatography-tandem mass spectrometry (LC-MS/MS) non-targeted metabolomics sequencing, and ELISA for cerebrospinal fluid and plasma samples. Finally, we perform combined multi-omics analysis. For complete details on the use and execution of this protocol, please refer to Xu et al.[1].},
}

@article {pmid39846984,
year = {2025},
author = {Chung, V and Alistar, A and Becerra, C and Kasi, A and Borazanci, E and Jameson, GS and Roe, DJ and Wertheim, BC and Cridebring, D and Truitt, M and Downes, M and Barrett, MT and Korn, R and Lee, K and Han, H and Evans, R and Von Hoff, DD},
title = {Pembrolizumab ± paricalcitol in metastatic pancreatic cancer postmaximal cytoreduction.},
journal = {The oncologist},
volume = {30},
number = {1},
pages = {},
doi = {10.1093/oncolo/oyae323},
pmid = {39846984},
issn = {1549-490X},
support = {SU2C-AACR-CT03-16//AACR/ ; //Merck Sharp & Dohme LLC/ ; //Merck & Co., Inc/ ; },
mesh = {Humans ; *Ergocalciferols/pharmacology/therapeutic use/administration & dosage ; *Pancreatic Neoplasms/drug therapy/pathology ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; Male ; Female ; Middle Aged ; Aged ; Double-Blind Method ; Cytoreduction Surgical Procedures/methods ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; Neoplasm Metastasis ; Adult ; },
abstract = {LESSONS LEARNED: Intravenous paricalcitol did not improve the efficacy of pembrolizumab, likely related to the short half-life.

BACKGROUND: Immunotherapy has limited benefit in the treatment of advanced pancreatic cancer with the tumor microenvironment playing a key role in immune resistance. In preclinical studies, vitamin D receptor (VDR) agonists have been shown to sensitize pancreatic tumors to PD-1 blockade.

METHODS: This was a randomized, double-blinded, placebo-controlled, phase II trial to evaluate pembrolizumab with or without paricalcitol as maintenance therapy for patients with metastatic pancreatic ductal adenocarcinoma (PDAC). Participants were ≥18 years; histologically or cytologically confirmed metastatic PDAC showing no disease progression after frontline systemic therapy, and achieving maximal cytoreduction (eg, with no further antitumor effect), Eastern Cooperative Oncology Group (ECOG) status of 0 or 1; adequate organ function. Study treatment included: pembrolizumab 200 mg IV every 3 weeks and either paricalcitol 25 mcg IV 3 times per week or placebo. The primary objective was to evaluate 6-month progression free survival (PFS). Secondary objectives include evaluating the toxicity of the combination and overall survival (OS).

RESULTS: There was no significant difference in 6-month PFS, median PFS, median OS, nor treatment-related AEs between the 2 arms.

CONCLUSIONS AND RELEVANCE: Paricalcitol did not improve the efficacy of pembrolizumab likely related to its short half-life of only 5-7 hours. Microbiome analysis revealed significant difference between long-term (>12 weeks) and short-term (<12 weeks) survival groups across treatment arms. Modulation of the tumor microenvironment will likely require more sustained VDR activity.

TRIAL REGISTRATION: Clinicaltrials.gov, ID: NCT03331562.},
}

Humans
*Ergocalciferols/pharmacology/therapeutic use/administration & dosage
*Pancreatic Neoplasms/drug therapy/pathology
*Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology
Male
Female
Middle Aged
Aged
Double-Blind Method
Cytoreduction Surgical Procedures/methods
Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology
Neoplasm Metastasis
Adult

@article {pmid39846747,
year = {2025},
author = {Godsil, M and Ritz, NL and Venkatesh, S and Meeske, AJ},
title = {Gut phages and their interactions with bacterial and mammalian hosts.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0042824},
doi = {10.1128/jb.00428-24},
pmid = {39846747},
issn = {1098-5530},
abstract = {The mammalian gut microbiome is a dense and diverse community of microorganisms that reside in the distal gastrointestinal tract. In recent decades, the bacterial members of the gut microbiome have been the subject of intense research. Less well studied is the large community of bacteriophages that reside in the gut, which number in the billions of viral particles per gram of feces, and consist of considerable unknown viral "dark matter." This community of gut-residing bacteriophages, called the gut "phageome," plays a central role in the gut microbiome through predation and transformation of native gut bacteria, and through interactions with their mammalian hosts. In this review, we will summarize what is known about the composition and origins of the gut phageome, as well as its role in microbiome homeostasis and host health. Furthermore, we will outline the interactions of gut phages with their bacterial and mammalian hosts, and plot a course for the mechanistic study of these systems.},
}

@article {pmid39846536,
year = {2024},
author = {Hao, N and Zhang, H and Jia, H and Zhao, Y and Li, J and Feng, X and Tang, B and Zhao, B and Liu, Y},
title = {Residual Dynamics of Chlorantraniliprole and Fludioxonil in Soil and Their Effects on the Microbiome.},
journal = {Journal of xenobiotics},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/jox15010004},
pmid = {39846536},
issn = {2039-4713},
support = {2023YFD1400104//National Key Research and Development Program of China/ ; },
abstract = {The increased use of chlorantraniliprole and fludioxonil has sparked concerns about their residues and impact on the soil microbiome, highlighting an urgent issue requiring attention. This study investigates the residue dynamics of corn after chlorantraniliprole and fludioxonil treatments, as well as their effects on soil enzyme activity and microbial community structure. High-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis showed a significant decrease in chlorantraniliprole and fludioxonil residues in the soil after combined application, especially with chlorantraniliprole. This application caused a temporary reduction in urease and sucrase activities. Furthermore, high-throughput sequencing of the soil microbiome revealed a decrease in the relative abundance of Talaromyces during fludioxonil application, while Mortierela and Gibberella increased. Additionally, Vicianmibacteraceae and Vicianminbactererales saw significant increases after chlorantraniliprole application. The combined application of chlorantraniliprole and fludioxonil not only decreased the population of harmful microorganisms but also lowered residue levels in the soil when compared to individual applications. This ultimately enhanced the efficacy of control measures and promoted environmental compatibility.},
}

@article {pmid39846512,
year = {2025},
author = {Wang, S and Wang, X and Liu, Y and Yao, Q},
title = {Single and Synergistic Effects of Microplastics and Difenoconazole on Oxidative Stress, Transcriptome, and Microbiome Traits in Honey Bees.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c09141},
pmid = {39846512},
issn = {1520-5118},
abstract = {Microplastics (MPs) and pesticides are identified as two environmental pollutants. In the present study, we showed evidence of toxic effects on honey bees from chronic oral exposure to food containing difenoconazole alone (Dif) and in a binary mixture with polystyrene (PS)-MPs (Dif + PS). We observed a disrupted gut microbial community structure in bees after difenoconazole exposure, and the gut microbiota structure richness increased at the phylum and genus levels in Dif + PS group. Transcriptomic analysis revealed that difenoconazole exposure caused 98 differentially expressed genes (DEGs), while 41 DEGs were identified in Dif + PS group. PS-MPs seemed to mitigate oxidative damage and changes in the transcriptome profile in honey bees caused by difenoconazole to some extent. However, coexposure increased the disordered microbial community composition. Our study highlights the importance of investigating possible additive and synergic activities between stressors to comprehensively understand the effects of pollutants on pollinating insects.},
}

@article {pmid39846370,
year = {2025},
author = {Chen, X and Guo, X},
title = {Microbiome analysis reveals the potential mechanism of herbal sitz bath complementary therapy in accelerating postoperative recovery from perianal abscesses.},
journal = {IET systems biology},
volume = {19},
number = {1},
pages = {e12114},
doi = {10.1049/syb2.12114},
pmid = {39846370},
issn = {1751-8857},
support = {2018-2020:TCM Advantage Disease Cultivation and Co//Shanghai Three-Year Action Plan for Further Accelerating the Development of Traditional Chinese Medicine/ ; JSKJ-KTZY-2021-04//Shanghai Jinshan District health special project support/ ; },
mesh = {Humans ; *Abscess/microbiology/drug therapy/therapy ; Male ; *Microbiota/drug effects ; Female ; Middle Aged ; Adult ; Wound Healing/drug effects ; Complementary Therapies/methods ; Anus Diseases/microbiology/drug therapy/surgery ; RNA, Ribosomal, 16S/genetics ; Baths ; },
abstract = {The herbal sitz bath formula, as a complementary therapy, effectively alleviates postoperative wound pain and accelerates healing time in patients with perianal abscesses. To investigate its mechanism of action, this study conducted 16S rRNA gene sequencing and bioinformatics analysis on wound exudate samples from patients after perianal abscess surgery. Patients were randomly divided into two groups: one receiving the herbal sitz bath as an adjunctive therapy and the other without this adjunctive therapy. Samples were collected on the first and eighth days after surgery to compare the differences in microbial community composition between the two groups on the eighth day and between the first and eighth days within each group. The study revealed that the herbal sitz bath significantly altered the structure of the microbial community, increasing its diversity and abundance. By reducing Enterococcus and increasing Bifidobacterium, Faecalibacterium, and Ruminococcus, the therapy enhanced the wound's anti-infective capacity and accelerated healing. This study explored the potential mechanism of the herbal sitz bath formula as an adjunctive therapy in promoting postoperative recovery from perianal abscesses, providing valuable data for further research on the role of microorganisms in wound care. These findings contribute to optimising postoperative treatment regimens and facilitating patient recovery.},
}

Humans
*Abscess/microbiology/drug therapy/therapy
Male
*Microbiota/drug effects
Female
Middle Aged
Adult
Wound Healing/drug effects
Complementary Therapies/methods
Anus Diseases/microbiology/drug therapy/surgery
RNA, Ribosomal, 16S/genetics
Baths

@article {pmid39846192,
year = {2025},
author = {Yu, W and Yang, J and Teng, LW and Zhao, XL and Zhu, ZY and Cui, S and Du, WG and Liu, ZS and Zeng, ZG},
title = {Reciprocal translocation experiments reveal gut microbiome plasticity and host specificity in a Qinghai-Xizang Plateau lizard.},
journal = {Zoological research},
volume = {46},
number = {1},
pages = {139-151},
doi = {10.24272/j.issn.2095-8137.2024.284},
pmid = {39846192},
issn = {2095-8137},
mesh = {Animals ; *Lizards/microbiology/physiology ; *Gastrointestinal Microbiome/physiology ; *Altitude ; Female ; China ; Host Specificity ; },
abstract = {Animal adaptation to environmental challenges is a complex process involving intricate interactions between the host genotype and gut microbiome composition. The gut microbiome, highly responsive to external environmental factors, plays a crucial role in host adaptability and may facilitate local adaptation within species. Concurrently, the genetic background of host populations influences gut microbiome composition, highlighting the bidirectional relationship between host and microbiome. Despite this, our understanding of gut microbiome plasticity and its role in host adaptability remains limited, particularly in reptiles. To clarify this issue, we conducted a reciprocal translocation experiment with gravid females of the Qinghai toad-headed lizards (Phrynocephalus vlangalii) between high-altitude (2 600 m a.s.l.) and superhigh-altitude (3 600 m a.s.l.) environments on Dangjin Mountain of the Qinghai-Xizang Plateau, China. One year later, we assessed the phenotypes and gut microbiomes of their offspring. Results revealed significant plasticity in gut microbiome diversity and structure in response to contrasting elevations. High-altitude conditions increased diversity, and maternal effects appeared to enable high-altitude lizards to maintain elevated diversity when exposed to superhigh-altitude environments. Additionally, superhigh-altitude lizards displayed distinct gut microbiome structures with notable host specificity, potentially linked to their lower growth rates. Overall, these findings underscore the importance of the gut microbiome in facilitating reptilian adaptation to rapid environmental changes across altitudinal gradients. Furthermore, this study provides critical insights into microbial mechanisms underpinning local adaptation and adaptative plasticity, offering a foundation for future research on host-microbiome interactions in evolutionary and ecological contexts.},
}

Animals
*Lizards/microbiology/physiology
*Gastrointestinal Microbiome/physiology
*Altitude
Female
China
Host Specificity

@article {pmid39846059,
year = {2025},
author = {Cyphert, EL and Clare, S and Dash, A and Nixon, JC and Raphael, J and Harrison, J and Heilbronner, A and Kim, HJ and Cunningham, M and Lebl, D and Schwab, F and Hernandez, CJ and Stein, EM},
title = {A Pilot Study of the Gut Microbiota in Spine Fusion Surgery Patients.},
journal = {HSS journal : the musculoskeletal journal of Hospital for Special Surgery},
volume = {21},
number = {1},
pages = {65-72},
pmid = {39846059},
issn = {1556-3316},
abstract = {BACKGROUND: The microbiome has been identified as a contributor to bone quality. As skeletal health is critical to success of orthopedic surgery, the gut microbiome may be a modifiable factor associated with postoperative outcomes. For spine fusion surgery in particular, de novo bone formation and sufficient bone mineral density are essential for successful outcomes. Given the prevalence and complexity of these procedures, the identification of novel factors that may be related to operative success is important.

QUESTIONS/PURPOSES: We sought to investigate how the composition of the microbiota related to bone health in a focused spinal fusion surgery cohort.

METHODS: We investigated the composition of the microbiome in a cohort of 31 patients prior to spinal fusion surgery, as well as changes in the microbiome over 6 weeks postoperatively. Preoperative areal bone mineral density (BMD) was measured by dual-energy X-ray absorptiometry.

RESULTS: Composition of gut microbiota differed among spinal fusion patients with low bone mass (T-score ≤ -1.0) and those with normal BMD (P = .03). There was no significant change in composition of the gut microbiota between preoperative evaluation and 6 weeks postoperatively.

CONCLUSIONS: Our findings in this small sample suggest there may be a relationship between BMD and composition of the gut microbiome in patients who undergo spinal fusion surgery. Further work is needed to investigate these relationships as well as potential interventions to foster a favorable microbial composition in spinal fusion surgery patients.},
}

@article {pmid39846052,
year = {2025},
author = {Kortright-Maldonado, K and Reyes-Torres, BE and Cabrera-Lopez, LS and Rodríguez-Henríquez, P and Tenorio-Aguirre, EK and Martínez-Sánchez, FD},
title = {Navigating antiphospholipid syndrome: from personalized therapies to cutting-edge research.},
journal = {Rheumatology advances in practice},
volume = {9},
number = {1},
pages = {rkaf005},
pmid = {39846052},
issn = {2514-1775},
abstract = {APS is an autoimmune disorder characterized by thrombosis and pregnancy complications, primarily driven by aPLs such as LA, aCL and anti-β2 glycoprotein I (a-β2GPI). Despite advances in anticoagulation therapies, managing refractory APS cases remains challenging. Emerging therapies, including rituximab, eculizumab and HCQ, show potential in addressing the underlying mechanisms of APS. Additionally, research into genetic and environmental factors, particularly the gut microbiome's role through molecular mimicry, suggests new therapeutic pathways. Diagnostic advancements, such as the adjusted Global Antiphospholipid Syndrome Score (aGAPSS), metabolomic profiling and MRI, have improved risk stratification and early detection. Non-traditional biomarkers like anti-phosphatidylserine/prothrombin (aPS/PT) and anti-Domain I antibodies further enhance risk assessment. Future research should aim to validate these approaches, optimizing patient outcomes and minimizing long-term APS complications.},
}

@article {pmid39845884,
year = {2024},
author = {Song, S and Ning, L and Yu, J},
title = {Elucidating the causal relationship between gut microbiota, metabolites, and diabetic nephropathy in European patients: Revelations from genome-wide bidirectional mendelian randomization analysis.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1391891},
pmid = {39845884},
issn = {1664-2392},
mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome ; *Diabetic Nephropathies/genetics/microbiology/metabolism ; *Genome-Wide Association Study ; Europe/epidemiology ; },
abstract = {OBJECTIVE: Previous observational studies suggest a potential link between gut microbiota, metabolites, and diabetic nephropathy. However, the exact causal relationship among these factors remains unclear.

METHOD: We conducted a two-sample bidirectional Mendelian randomization study using summary statistics from the IEU OpenGWAS Project database to investigate gut microbiota, metabolites, and diabetic nephropathy. A range of methods, including inverse variance weighting, MR-Egger, weighted median, and simple median, were applied to examine causal associations. Sensitivity analyses were performed to assess the robustness of the results. Additionally, reverse Mendelian randomization analysis was conducted, treating significant gut microbiota as the outcome, to evaluate effects and perform sensitivity testing. This comprehensive approach provided an in-depth assessment of the interactions among gut microbiota, metabolites, and diabetic nephropathy.

RESULT: The Inverse Variance Weighted estimates revealed that the abundance of Lachnospiraceae, Parasutterella, and Eubacterium exhibited negative causal effects on diabetic nephropathy, while Coprococcus, Sutterella, Faecalibacterium prausnitzii, and Bacteroides vulgatus showed protective causal effects against the condition. However, reverse Mendelian randomization analysis did not identify any significant associations between diabetic nephropathy and the identified gut microbiota. Furthermore, the estimates indicated that Cholesterol, Pyridoxate, Hexanoylcarnitine, X-12007, Octanoylcarnitine, 10-nonadecenoate (19:1n9), X-12734, and the average number of double bonds in a fatty acid chain had negative causal effects on diabetic nephropathy. In contrast, Methionine, Glycodeoxycholate, X-06351, 1-stearoylglycerol (1-monostearin), 5-dodecenoate (12:1n7), X-13859, 2-hydroxyglutarate, Glycoproteins, Phospholipids in IDL, and the concentration of small HDL particles demonstrated protective causal effects. Notably, sensitivity analyses did not detect any heterogeneity or horizontal pleiotropy, ensuring the robustness of the findings.

CONCLUSION: Modulating gut microbiota diversity and composition offers a promising strategy for improving the incidence and prognosis of diabetic nephropathy. This highlights the need for future clinical trials focusing on microbiome-based interventions, potentially utilizing microbiome-dependent metabolites. Such approaches could transform the treatment and management of diabetic nephropathy and its associated risk factors, paving the way for more effective therapeutic strategies to combat this debilitating condition.},
}

Humans
*Mendelian Randomization Analysis
*Gastrointestinal Microbiome
*Diabetic Nephropathies/genetics/microbiology/metabolism
*Genome-Wide Association Study
Europe/epidemiology

@article {pmid39845840,
year = {2024},
author = {Chu, C and Behera, TR and Huang, Y and Qiu, W and Chen, J and Shen, Q},
title = {Corrigendum: Research progress of gut microbiome and diabetic nephropathy.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1549438},
doi = {10.3389/fmed.2024.1549438},
pmid = {39845840},
issn = {2296-858X},
abstract = {[This corrects the article DOI: 10.3389/fmed.2024.1490314.].},
}

@article {pmid39845646,
year = {2024},
author = {Hadrich, I and Turki, M and Chaari, I and Abdelmoula, B and Gargouri, R and Khemakhem, N and Elatoui, D and Abid, F and Kammoun, S and Rekik, M and Aloulou, S and Sehli, M and Mrad, AB and Neji, S and Feiguin, FM and Aloulou, J and Abdelmoula, NB and Sellami, H},
title = {Gut mycobiome and neuropsychiatric disorders: insights and therapeutic potential.},
journal = {Frontiers in cellular neuroscience},
volume = {18},
number = {},
pages = {1495224},
pmid = {39845646},
issn = {1662-5102},
abstract = {BACKGROUND: The human gut mycobiome, a minor but integral component of the gut microbiome, has emerged as a significant player in host homeostasis and disease development. While bacteria have traditionally been the focus of gut microbiome studies, recent evidence suggests that fungal communities (mycobiota) may also play a crucial role in modulating health, particularly in neuropsychiatric disorders.

OBJECTIVE: This review aims to provide a comprehensive overview of current knowledge on the relationship between the gut mycobiome and neuropsychiatric disorders, exploring the potential of targeting fungal communities as a novel therapeutic strategy.

METHODS: We summarized recent findings from metagenomic analyses that characterize the diversity and composition of gut mycobiota and discuss how these communities interact with the host and other microorganisms via the gut-brain axis. Key methodologies for studying mycobiota, such as high-throughout sequencing and bioinformatics approaches, were also reviewed to highlight advances in the field.

RESULTS: Emerging research links gut mycobiota dysbiosis to conditions such as schizophrenia, Alzheimer's disease, autism spectrum disorders, bipolar disorder, and depression. Studies indicate that specific fungal populations, such as Candida and Saccharomyces, may influence neuroinflammation, gut permeability and immune responses, thereby affecting mental health outcomes.

CONCLUSION: Understanding the gut mycobiome's role in neuropsychiatric disorders opens new avenues for therapeutic interventions, including antifungal treatments, probiotics, and dietary modifications. Future research should integrate multi-omics approaches to unravel the complex interkingdom interactions within the gut ecosystem, paving the way for personalized medicine in mental health care.},
}

@article {pmid39845431,
year = {2025},
author = {Wang, W and Xian, M and Chen, R and Li, J and Wu, L},
title = {Gradient disparities in allergy and the gut microbiome among rural, migrant, and urban populations across China.},
journal = {The World Allergy Organization journal},
volume = {18},
number = {1},
pages = {101018},
pmid = {39845431},
issn = {1939-4551},
abstract = {BACKGROUND: While much of the evidence linking the rapid urbanization and the increasing prevalence of allergen sensitization, but little is known regarding rural-to-urban migrants. The aim of this study was to identify the disparities in allergy, the gut microbiome and factors among native urban, migrating, and native rural Chinese.

METHODS: We redesigned the dataset of the China Alliance of Research on Respiratory Allergic Disease secondary survey, and after stratified sampling, a subsample of 2422 subjects were enrolled for the analysis of a questionnaire, skin prick tests (SPT), and specific immunoglobulin E (sIgE) titer measurements against 8 common allergens. Fecal microbiotal composition was also sequenced by 16S rRNA and regression-based analyses with covariate adjustment applied.

RESULTS: From urban to migrant and rural populations, IgE sensitization was predominantly directed against Dermatophagoides pteronyssinus (Der p). The titers of Der p-sIgE decreased sequentially across the 3 respective populations and co-sensitization to other allergens also showed a sequential decrease. Rural-to-urban migrants showed a low prevalence of Der p-SPT and Der p-sIgE initially, but developed substantial IgE titers and their gut microbiotal diversity, as well as species richness, appeared to change along with residential time spent in the urban area. High-fat diet, using a mattress, an SPT wheal size from Der p ≥ 6 mm, and duration of immigration >5 years were significantly associated with sIgE positivity in the migrants.

CONCLUSION: The Der p-sIgE responses and the composition of gut microbiota differs synchronously with extended living time in an urban area. Studies in immigrants provide a unique opportunities to evaluate the effects of environmental factors in the pathogenesis of allergic disorders.},
}

@article {pmid39845316,
year = {2024},
author = {Yang, HS and Zhang, J and Feng, HX and Qi, F and Kong, FJ and Zhu, WJ and Liang, CY and Zhang, ZR},
title = {Characterizing microbial communities and their correlation with genetic mutations in early-stage lung adenocarcinoma: implications for disease progression and therapeutic targets.},
journal = {Frontiers in oncology},
volume = {14},
number = {},
pages = {1498524},
pmid = {39845316},
issn = {2234-943X},
abstract = {BACKGROUND: Lung adenocarcinoma (LUAD), the most prevalent form of lung cancer. The transition from adenocarcinoma in situ (AIS), and minimally invasive adenocarcinoma (MIA) to invasive adenocarcinoma (IAC) is not fully understood. Intratumoral microbiota may play a role in LUAD progression, but comprehensive stage-wise analysis is lacking.

METHODS: Tumor and bronchoalveolar lavage fluid (BALF) samples from patients with AIS/MIA or IAC were collected for next-generation sequencing to characterize microbial diversity and composition. DNA extraction involved lysing samples with nuclease and protease, followed by homogenization and elution. Sequencing libraries were prepared and sequenced on the Illumina platform. Whole exome sequencing was performed to identify somatic mutations and genetic variants. Bioinformatics analysis, including taxonomic annotation with Kraken2 and de novo assembly with MEGAHIT, was conducted to process metagenomic data. Correlation analysis was performed to link microbial species with mutated genes using custom R scripts.

RESULTS: Metagenomic analysis revealed a distinct microbial profile in IAC compared to AIS/MIA, with increased abundance of Bacteroidetes and Firmicutes in the IAC group. Bosea sp. and Microbacterium paludicola, were less abundant in IAC, suggesting a potential protective role in early-stage disease. Conversely, Mycolicibacterium species were more prevalent in IAC, indicating a possible contribution to disease progression. Genetic sequencing identified PTPRZ1 strongly correlating with microbial composition, suggesting a mechanistic link between microbiota and genetic alterations in LUAD.

CONCLUSION: This study characterizes microbial communities in various stages of LUAD, revealing links between microbiota and genetic mutations. The unique microbiota suggests its role in LUAD progression and as a therapeutic target.},
}

@article {pmid39845057,
year = {2024},
author = {Tan, JW and Eicher, SD and Kritchevsky, JE and Bryan, KA and Dickey, A and Chitko-McKown, CG and McDaneld, TG},
title = {Insights into microbial compositions of the respiratory tract of neonatal dairy calves in a longitudinal probiotic trial through 16S rRNA sequencing.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1499531},
pmid = {39845057},
issn = {1664-302X},
abstract = {INTRODUCTION: Probiotics are a promising intervention for modulating the microbiome and the immune system, promoting health benefits in cattle. While studies have characterized the calf lung bacterial profile with and without oral probiotics, simultaneous probiotic effects on the bacterial populations of multiple sites along the respiratory tract have not been characterized.

METHODS: This study utilized the same pre-weaning diary calf group from our previous studies to characterize the bacterial populations present in the nostril and tonsil across control and treatment groups and nine sampling time points. DNA was exacted from the nostril and tonsil swabs and lung lavage fluids, and 16S ribosomal RNA gene hypervariable regions 1-3 were subsequently sequenced.

RESULTS: Temporal variation in alpha bacterial diversity within the nostril, tonsil, and lung samples was observed, indicating distinct bacterial compositions among sampling time points. Oral probiotic treatment did not change alpha diversity in any respiratory tissue, however, spatial variability in bacterial taxa composition was observed among the three respiratory tract regions. While the majority of differentially abundant taxa in probiotic treated calves were unique to their anatomical location, a few were common to two anatomical locations and one Finegoldia amplicon sequence variant was differentially abundant in all three anatomical locations.

DISCUSSION: In conclusion, these findings contribute to the understanding of the dynamic nature of bacterial diversity and the potential effects of probiotics within the bovine respiratory tract and provides insight for future studies of probiotics on animal health, disease prevention, and management.},
}

@article {pmid39845049,
year = {2024},
author = {Wu, R and Mai, Z and Song, X and Zhao, W},
title = {Hotspots and research trends of gut microbiome in polycystic ovary syndrome: a bibliometric analysis (2012-2023).},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1524521},
pmid = {39845049},
issn = {1664-302X},
abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is a common gynecological condition affecting individuals of reproductive age and is linked to the gut microbiome. This study aimed to identify the hotspots and research trends within the domain of the gut microbiome in PCOS through bibliometric analysis.

METHODS: Utilizing bibliometric techniques, we examined the literature on the gut microbiome in PCOS from the Web of Science Core Collection spanning the period from 2012 to 2023. Analytical tools such as CiteSpace, VOSviewer, and Bibliometric R packages were employed to evaluate various metrics, including countries/regions, institutions, authors, co-cited authors, authors' H-index, journals, co-references, and keywords.

RESULTS: A total of 191 publications were identified in the field of gut microbiome in PCOS, with an increase in annual publications from 2018 to 2023. People's Republic of China was the most productive country, followed by the United States of America (USA), India. Shanghai Jiao Tong University, Fudan University, and Beijing University of Chinese Medicine were the top three most publications institutions. Thackray VG was identified as the most prolific author, holding the highest H-index, while Liu R received the highest total number of citations. The journal "Frontiers in Endocrinology" published the most articles in this domain. The most frequently co-cited reference was authored by Qi XY. The analysis of keyword burst detection identified "bile acids" (2021-2023) as the leading frontier keyword. Additionally, "gut dysbiosis," "phenotypes," "adolescents," "metabolomics," "metabolites," "fecal microbiota transplantation," and "IL-22" have emerged as the primary keywords reflecting recent research trends.

CONCLUSION: This bibliometric analysis explores how the gut microbiome influences endocrine and metabolic disorders related to PCOS, emphasizing its role in the development of PCOS and treatments targeting the gut microbiome. The findings serve as a valuable resource for researchers, enabling them to identify critical hotspots and emerging areas of investigation in this field.},
}

@article {pmid39845046,
year = {2024},
author = {Almuhaideb, E and Hasan, NA and Grim, C and Rashed, SM and Parveen, S},
title = {Comparative evaluation of specimen type and processing conditions for studying oyster microbiomes.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1504487},
pmid = {39845046},
issn = {1664-302X},
abstract = {Metagenomic sequencing is increasingly being employed to understand the assemblage and dynamics of the oyster microbiome. Specimen collection and processing steps can impact the resultant microbiome composition and introduce bias. To investigate this systematically, a total of 54 farmed oysters were collected from Chesapeake Bay between May and September 2019. Six different specimen types and processing methods were evaluated for microbial community composition using shotgun metagenomics, namely fresh oyster homogenate (FOH), oyster homogenate after simulated temperature abuse (AOH), Luria broth-enriched oyster homogenate (EOH), dissected stomach homogenate (DSH), hemolymph (HLM), and stomach-gut content (SGC). In general, DSH, EOH, and FOH yielded the highest DNA concentration, while EOH had the highest microbial reads, followed by DSH, HLM, and FOH. HLM produced the highest bacterial species alpha diversity, followed by AOH, EOH, and SGC. Although alpha diversities did not differ significantly, beta-diversity measurements showed significant dissimilarity among methods (p < 0.05) indicating that the specimen types and processing steps do play an important role in representing the composition of the bacterial community. Bacterial species that had the highest log mean abundance included Cyanobium sp. PCC 7001 in FOH, Vibrio vulnificus in AOH, EOH, and DSH, and lastly Synechococcus sp. CB0205 in the DSH, HML, and SGC samples. EOH displayed higher bacterial hits, distinct microbial composition, and higher values of bacterial, phages, and antimicrobial resistance gene reads. Therefore, if studying the overall oyster microbial community, prioritizing optimum specimen collection and processing methods that align with the overall goal of the study is recommended.},
}

@article {pmid39845039,
year = {2024},
author = {Du, J and Zheng, P and Gao, W and Liang, Q and Leng, L and Shi, L},
title = {All roads lead to Rome: the plasticity of gut microbiome drives the extensive adaptation of the Yarkand toad-headed agama (Phrynocephalus axillaris) to different altitudes.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1501684},
pmid = {39845039},
issn = {1664-302X},
abstract = {The gut microbiome was involved in a variety of physiological processes and played a key role in host environmental adaptation. However, the mechanisms of their response to altitudinal environmental changes remain unclear. In this study, we used 16S rRNA sequencing and LC-MS metabolomics to investigate the changes in the gut microbiome and metabolism of the Yarkand toad-headed agama (Phrynocephalus axillaris) at different altitudes (-80 m to 2000 m). The results demonstrated that Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phylum, Lachnospiraceae and Oscillospiraceae were the most abundant family, and the low-altitude populations had higher richness than high-altitude populations; Akkermansiaceae appeared to be enriched in high-altitude populations and the relative abundance tended to increase with altitude. The gut microbiome of three populations of P. axillaris at different altitudes was clustered into two different enterotypes, low-altitude populations and high-altitude populations shared an enterotype dominated by Akkermansia, Kineothrix, Phocaeicola; intermediate-altitude populations had an enterotype dominated by Mesorhizobium, Bradyrhizobium. Metabolites involved in amino acid and lipid metabolism differed significantly at different altitudes. The above results suggest that gut microbiome plasticity drives the extensive adaptation of P. axillaris to multi-stress caused by different altitudes. With global warming, recognizing the adaptive capacity of wide-ranging species to altitude can help plan future conservation strategies.},
}

@article {pmid39845038,
year = {2024},
author = {Peters, B and Leonhardt, SD and Schloter, M and Keller, A},
title = {Direct and indirect effects of land use on microbiomes of trap-nesting solitary bee larvae and nests.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1513096},
pmid = {39845038},
issn = {1664-302X},
abstract = {INTRODUCTION: The global decline in biodiversity and insect populations highlights the urgent need to conserve ecosystem functions, such as plant pollination by solitary bees. Human activities, particularly agricultural intensification, pose significant threats to these essential services. Changes in land use alter resource and nest site availability, pesticide exposure and other factors impacting the richness, diversity, and health of solitary bee species. In this study, we investigated yet another facet currently less well investigated in such context: Microbial communities associated with wild bees play crucial roles in larval development, metabolism, immunity and overall bee health. However, the drivers and dynamics of healthy microbiome in solitary bees are still poorly understood, especially regarding the direct and indirect effects of land use on the diversity and composition of these microbial communities.

METHODS: We examined bacterial communities in the offspring and nest materials of the Megachilid trap-nesting solitary bee, Osmia bicornis, along a gradient of land use intensification by 16S rRNA gene metabarcoding. Given that landscape composition, climatic conditions, and food resources are known to influence microbial compositions in solitary bee species, we hypothesized that land use changes would alter resources available for food and nest material collection and thereby affecting the microbiomes in offspring and their nest environments. We anticipated reduced microbial diversity and altered composition with increased land use intensification, which is known to decrease the number and diversity of resources, including the pool of floral and soil bacteria in the surrounding environment.

RESULTS: As expected, we observed significant shifts in the bacterial composition and diversity of bees and their nests across varying degrees of land use intensity, differing in management types and the availability of flowers. The Shannon diversity of bacteria in nest materials (larval pollen provision, soil nest enclosure) and larval guts decreased with increasing land use intensity. However, the pupae microbiome remained unaffected, indicating a reorganization of the microbiome during metamorphosis, which is not significantly influenced by land use and available resources.

DISCUSSION: Our findings provide new insights into the factors shaping environmental transmission and changes in solitary bee microbiomes. This understanding is crucial for comprehending the impacts of intensive land use on wild bee health and developing strategies to mitigate these effects.},
}

@article {pmid39845034,
year = {2024},
author = {Meng, WJ and Wen, ZL and Kasanen, R and Sun, H and Asiegbu, FO},
title = {Microbial communities in the phyllosphere and endosphere of Norway spruce under attack by Heterobasidion.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1489900},
pmid = {39845034},
issn = {1664-302X},
abstract = {Heterobasidion annosum species complex has been regarded as the most destructive disease agent of conifer trees in boreal forests. Tree microbiome can regulate the plant-pathogen interactions by influencing both host resistance and pathogen virulence. Such information would help to improve the future health of forests and explore strategies to enhance ecosystem stability. In this study, using next-generation sequencing technology, we investigated the microbial community in different tree regions (needles, upper stem, and lower stem) of Norway spruce with and without wood decay symptoms. The primary purpose was to uncover signature characteristic microbiome harbored by asymptomatic trees compared to diseased trees. Additionally, the study was to explore the inter-kingdom and intra-kingdom interactions in microbiome (bacteria and fungi) of symptomatic versus asymptomatic trees. The results showed that in upper stem, species richness (Chao1) of fungi and bacteria were both higher in asymptomatic trees than symptomatic trees (P < 0.05). Compared to symptomatic trees, asymptomatic trees harbored a higher abundance of Actinobacteriota, bacterial genera of Methylocella, Conexibacter, Jatrophihabitans, and fungal genera of Mollisia. Fungal communities from the same anatomic region differed between the symptomatic and asymptomatic trees. Bacterial communities from the two stem regions were also distinct between the symptomatic and asymptomatic trees. The symptomatic trees possessed a less stable microbial network with more positive correlations compared to the asymptomatic trees. In the lower stem, at intra-kingdom level, the distribution of correlation numbers was more even in the bacterial network compared to the fungal network. In conclusion, the Heterobasidion attack decreased the microbial community species richness and shifted the community structure and functional structure to varying degrees. The microbial network was enlarged and became more unstable at both inter-kingdom and intra-kingdom level due to the Heterobasidion infection.},
}

@article {pmid39845032,
year = {2024},
author = {Cai, Y and Tang, H and Xiang, G and Yi, H and Zhong, J and Xie, Z and Hu, Q and El Bouhi, R and Zhou, P and Zhang, Y and Yan, H},
title = {Deciphering of differences in gut microbiota and plasma metabolites profile between non-obese and obese Golden Retrievers dogs.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1514633},
pmid = {39845032},
issn = {1664-302X},
abstract = {INTRODUCTION: Golden Retrievers have a high risk of obesity, which is prevalent in dogs and is associated with inflammation and cancer, impairing the health and life expectancy of companion animals. Microbial and metabolite biomarkers have been proposed for identifying the presence of obesity in humans and rodents. However, the effects of obesity on the microbiome and metabolome of Golden Retrievers remains unknown. Therefore, this study was designed to evaluate the signatures of serum biochemistry indexes, gut microbiota and plasma metabolites in non-obese and obese Golden Retrievers, aiming to recognize potential biomarkers of canine obesity.

METHODS: A total of 8 non-obese (Ctrl group) and 8 obese (Obe group) Golden Retrievers were included in the present study to collect blood and feces samples for measurements. The fecal microbiome and plasma metabolome were determined using 16S rRNA amplicon sequencing and liquid chromatography-mass spectrometry, respectively.

RESULTS: Results showed that the alanine aminotransferase activity and total bilirubin concentration, which have been measured using serum biochemistry analysis, were higher in the Obe group than in the Ctrl group (p < 0.05). Moreover, there was a significant difference in gut microbiota composition between the two groups (p < 0.05). The phyla Proteobacteria, Fusobacteriota, and Bacteroidota as well as genera Fusobacterium, Prevotella, Faecalibacterium, Escherichia-Shigell, and Alloprevotella were more abundant, while phylum Firmicutes and genera Peptoclostridium, Blautia, Turicibacter, Allobaculum, and Erysipelatoclostridium were less abundant in the Obe group compared to the Ctrl group (p < 0.05). Plasma concentrations of citrulline and 11-dehydrocorticosterone were significantly higher in the Obe group than those in the Ctrl group (p < 0.05). Close correlations between serum biochemistry parameters, gut microbiome, and plasma metabolites were observed in the current study.

CONCLUSION: The obesity-induced shifts in serum biochemistry indexes, gut microbiota, and plasma metabolites profiles suggest that obese Golden Retrievers exhibit a different microbiome and metabolome than non-obese ones, and the certain metabolites like citrulline and 11-dehydrocorticosterone could be considered as potential biomarkers to recognize obese Golden Retrievers.},
}

@article {pmid39845029,
year = {2024},
author = {Bouchez, T and Liu, B and Garza, DR},
title = {Healthy gut microbiomes are host-controllable microbiomes.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1497083},
pmid = {39845029},
issn = {1664-302X},
}

@article {pmid39844957,
year = {2025},
author = {Martins, V and Abdallah, C and Teixeira, A and Moreira, C and Nóbrega, M and Lanoue, A and Gerós, H},
title = {Subregional pedoclimatic conditions with contrasted UV-radiation shape host-microbiome and metabolome phenotypes in the grape berry.},
journal = {Food chemistry: X},
volume = {25},
number = {},
pages = {102139},
pmid = {39844957},
issn = {2590-1575},
abstract = {This study used integrative omics to address the response of key elements of the grapevine holobiont to contrasted pedoclimatic conditions found in distinct subregions of Douro Valley (Portugal). A metabolic OPLS-DA model predicted with 100 % accuracy the geographic origin of berries; higher UV radiation, higher temperature and lower precipitation stimulated the accumulation of phenolic acids, flavonols and malvidin conjugates, in detriment of amino acids, organic acids, flavan-3-ols, proanthocyanidins and non-malvidin anthocyanins. Metabarcoding showed a trade-off between bacteria and fungal diversity among subregions, with Pseudomonas, Lactobacillus, Aspergillus and Penicillium acting as intraregional microbial markers. The high phenotypic plasticity of berries and the role of microbes in this process are relevant upon current projections for increased UV radiation and temperature in Southern European viticulture, in a climate change scenario, with predicted impacts on regional wine quality and on the development of adaptation strategies for resilient viticulture.},
}

@article {pmid39844919,
year = {2025},
author = {Naim, W and Manetsberger, J and Lavilla Lerma, L and Benomar, N and Caballero Gómez, N and Cuesta-Bertomeu, IS and Gata Díaz, JÁ and Abriouel, H},
title = {Impact of disinfection methods used in the slaughterhouse environment on microbiome diversity throughout the meat production chain.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100336},
pmid = {39844919},
issn = {2666-5174},
abstract = {Slaughterhouse environments are prone to microbial contamination, influenced by factors like set-up, size and area as well as disinfection practices. Thus, effective control measures are crucial to prevent the spread of pathogens and their contaminant genes (antimicrobial resistance genes and virulence factors) throughout the food chain. In the present study, we assessed the microbial contamination in environmental surfaces of three slaughterhouses located in the Jaén province (Spain). We also evaluated the impact of different disinfection strategies on microbial loads and diversity by means of culture dependent and independent methods. The results revealed a statistically significant inter- and intra-specific differences in microbial loads including the most important pathogens such as pseudomonads, staphylococci, Escherichia coli, Salmonella sp. and Campylobacter jejuni. Disinfection strategies using routine disinfectant (used by the slaughterhouse), HLE disinfectant, UV, or combinations thereof showed varying effectiveness. The newly developed sustainable HLE disinfectant was most effective, while UV had the lowest disinfection strength, and routine disinfectants failed to eradicate all pathogens. Metagenomic analysis identified Pseudomonadota as the dominant phylum, followed by Actinomycetota and Bacteroidota. Results furthermore indicated shifts from sacrifice to cold rooms, with an increase in Gammaproteobacteria, particularly Moraxellaceae (represented by Psychrobacter cryohalolentis) over Acinetobacter sp. In conclusion, this study highlights the potential of HLE disinfectant (alone or in combination with the routine disinfectant) as a more effective disinfection measure on environmental surfaces, particularly for combating multi-drug resistant pathogens compared to other disinfection methods currently used.},
}

@article {pmid39844346,
year = {2025},
author = {Melville, DW and Meyer, M and Kümmerle, C and Alvarado-Barrantes, KA and Wilhelm, K and Sommer, S and Tschapka, M and Risely, A},
title = {Delayed feeding disrupts diurnal oscillations in the gut microbiome of a neotropical bat in captivity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf012},
pmid = {39844346},
issn = {1574-6941},
abstract = {Diurnal rhythms of the gut microbiota are emerging as an important yet often overlooked facet of microbial ecology. Feeding is thought to stimulate gut microbial rhythmicity, but this has not been explicitly tested. Moreover, the role of the gut environment is entirely unexplored, with rhythmic changes to gut pH rather than feeding per se possibly affecting gut microbial fluctuations. In this study, we experimentally manipulated the feeding schedule of captive lesser long-nosed bats, Leptonycteris yerbabuenae, to dissociate photic and feeding cues, and measured the fecal microbiota and gut pH every two hours. We detected strong diurnal rhythms in both microbial alpha- and beta diversity as well as in pH within the control group. However, a delay in feeding disrupted oscillations of gut microbial diversity and composition, but did not affect rhythms in gut pH. The oscillations of some genera, such as Streptococcus, which aid in metabolizing nutrients, shifted in accordance with the delayed feeding cue and were correlated with pH. For other bacterial genera, oscillations were disturbed and no connection to pH was found. Our findings suggest that the rhythmic proliferation of bacteria matches peak feeding times, providing evidence that diurnal rhythms of the gut microbiota likely evolved to optimize their metabolic support to the host's circadian phenotype.},
}

@article {pmid39844274,
year = {2025},
author = {Camper, BT and Kanes, AS and Laughlin, ZT and Manuel, RT and Bewick, SA},
title = {Transgressive hybrids as hopeful holobionts.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {19},
pmid = {39844274},
issn = {2049-2618},
mesh = {*Hybridization, Genetic ; *Symbiosis ; *Microbiota ; Animals ; Biological Evolution ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: Hybridization between evolutionary lineages has profound impacts on the fitness and ecology of hybrid progeny. In extreme cases, the effects of hybridization can transcend ecological timescales by introducing trait novelty upon which evolution can act. Indeed, hybridization can even have macroevolutionary consequences, for example, as a driver of adaptive radiations and evolutionary innovations. Accordingly, hybridization is now recognized as a motor for macrobial evolution. By contrast, there has been substantially less progress made towards understanding the positive eco-evolutionary consequences of hybridization on holobionts. Rather, the emerging paradigm in holobiont literature is that hybridization disrupts symbiosis between a host lineage and its microbiome, leaving hybrids at a fitness deficit. These conclusions, however, have been drawn based on results from predominantly low-fitness hybrid organisms. Studying "dead-end" hybrids all but guarantees finding that hybridization is detrimental. This is the pitfall that Dobzhansky fell into over 80 years ago when he used hybrid sterility and inviability to conclude that hybridization hinders evolution. Goldschmidt, however, argued that rare saltational successes-so-called hopeful monsters-disproportionately drive positive evolutionary outcomes. Goldschmidt's view is now becoming a widely accepted explanation for the prevalence of historical hybridization in extant macrobial lineages. Aligning holobiont research with this broader evolutionary perspective requires recognizing the importance of similar patterns in host-microbiome systems. That is, rare and successful "hopeful holobionts" (i.e., hopeful monsters at the holobiont scale) might be disproportionately responsible for holobiont evolution. If true, then it is these successful systems that we should be studying to assess impacts of hybridization on the macroevolutionary trajectories of host-microbiome symbioses.

RESULTS: In this paper, we explore the effects of hybridization on the gut (cloacal) and skin microbiota in an ecologically successful hybrid lizard, Aspidoscelis neomexicanus. Specifically, we test the hypothesis that hybrid lizards have host-associated (HA) microbiota traits strongly differentiated from their progenitor species. Across numerous hybrid microbiota phenotypes, we find widespread evidence of transgressive segregation. Further, microbiota restructuring broadly correlates with niche restructuring during hybridization. This suggests a relationship between HA microbiota traits and ecological success.

CONCLUSION: Transgressive segregation of HA microbiota traits is not only limited to hybrids at a fitness deficit but also occurs in ecologically successful hybrids. This suggests that hybridization may be a mechanism for generating novel and potentially beneficial holobiont phenotypes. Supporting such a conclusion, the correlations that we find between hybrid microbiota and the hybrid niche indicate that hybridization might change host microbiota in ways that promote a shift or an expansion in host niche space. If true, hybrid microbiota restructuring may underly ecological release from progenitors. This, in turn, could drive evolutionary diversification. Using our system as an example, we elaborate on the evolutionary implications of host hybridization within the context of holobiont theory and then outline the next steps for understanding the role of hybridization in holobiont research. Video Abstract.},
}

*Hybridization, Genetic
*Symbiosis
*Microbiota
Animals
Biological Evolution
Bacteria/genetics/classification

@article {pmid39844033,
year = {2025},
author = {Wang, Y and Cui, P and Cao, M and Ai, L and Zeng, L and Li, X and Chen, D and Gong, F and Fang, L and Zhou, C},
title = {Chronic restraint stress affects the diurnal rhythms of gut microbial composition and metabolism in a mouse model of depression.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {38},
pmid = {39844033},
issn = {1471-2180},
support = {YJSCX202306//Postgraduate Innovation Fund of Yongchuan Hospital Affiliated to Chongqing Medical University/ ; 82200829//National Natural Science Foundation of China/ ; 81701361//National Natural Science Foundation of China/ ; CSTB2022NSCQ-MSX0998//Natural Science Foundation of Chongqing/ ; CSTB2022NSCQ-MSX0250//Natural Science Foundation of Chongqing/ ; CSTB2022NSCQ-MSX0329//Natural Science Foundation of Chongqing/ ; KJQN202200467//Chongqing Education Commission of China/ ; KJQN202200460//Chongqing Education Commission of China/ ; YJRC202102//Science Foundation funded project of Yongchuan Hospital of Chongqing Medical University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Depression/microbiology/metabolism/physiopathology ; *Circadian Rhythm/physiology ; Mice ; *Disease Models, Animal ; *Mice, Inbred C57BL ; *Feces/microbiology ; Male ; *Stress, Psychological/microbiology/physiopathology ; Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Restraint, Physical ; Dysbiosis/microbiology ; Behavior, Animal ; },
abstract = {BACKGROUND: Depression is a common mental disorder accompanied by gut microbiota dysbiosis, which disturbs the metabolism of the host. While diurnal oscillation of the intestinal microbiota is involved in regulating host metabolism, the characteristics of the intestinal microbial circadian rhythm in depression remain unknown. Our aim was to investigate the microbial circadian oscillation signature and related metabolic pathways in a mouse model with depression-like behaviours.

METHODS: Chronic restraint stress (CRS) was used to induce depressive-like behaviours in C57BL/6J mice. The open field test (OFT) and forced swimming test (FST) were used to evaluate anxiety- and depressive-like behaviours in the control and CRS groups. Afterwards, faecal samples from the two groups were collected every four hours from ZT2 (9:00 am) to ZT22 (5:00 am). Faecal 16 S rRNA gene sequencing and metabolomics analysis were performed, and the microbial circadian rhythm was analysed via the MetaCycle package in R/RStudio.

RESULTS: CRS mice exhibited depressive-like behaviours after 4 weeks of restriction. Alpha- and beta-diversity analyses revealed that the microbial composition in control and CRS mice oscillated throughout the day. The circadian rhythm analyses revealed that at the phylum level, Bacteroidota, Firmicutes, Cyanobacteria and Patescibacteria showed circadian rhythmicity in the CRS group. At the genus level, Dubosiella and Romboutsia showed circadian rhythmicity in the control group, and Dubosiella abundance was correlated with tryptophan and galactose metabolism. In the CRS group, Bacteroides, Parabacteroides, and Rikenellaceae_RC9_gut_group showed circadian rhythmicity; among these genera, Parabacteroides was related to tryptophan metabolism, axon regeneration, phenylalanine metabolism and tyrosine metabolism.

CONCLUSION: Our data highlight the importance of observing the diurnal oscillation of the microbiome in host with depressive-like states. Rhythmicity in the microbiome may affect the host by regulating distinct metabolic pathways during the light and dark phases. A better combination of microbiota composition and oscillation would help to offer novel insight into key genera and their potential effects on depression.},
}

Animals
*Gastrointestinal Microbiome
*Depression/microbiology/metabolism/physiopathology
*Circadian Rhythm/physiology
Mice
*Disease Models, Animal
*Mice, Inbred C57BL
*Feces/microbiology
Male
*Stress, Psychological/microbiology/physiopathology
Bacteria/classification/genetics/isolation & purification/metabolism
RNA, Ribosomal, 16S/genetics
Restraint, Physical
Dysbiosis/microbiology
Behavior, Animal

@article {pmid39843765,
year = {2025},
author = {Zhong, L and Li, T and Zhang, X and Li, H},
title = {Clioquinol 3% Cream Improves Clinical Symptoms and Restores the Skin Microbiome in Interdigital Tinea Pedis.},
journal = {Mycopathologia},
volume = {190},
number = {1},
pages = {18},
pmid = {39843765},
issn = {1573-0832},
support = {YWJKJJHKYJJ-TY2010//Beijing Medical and Health Foundation/ ; },
mesh = {Humans ; *Microbiota/drug effects ; Male ; Female ; *Tinea Pedis/drug therapy/microbiology ; Middle Aged ; Adult ; *Clioquinol/administration & dosage ; Prospective Studies ; *Skin/microbiology ; Longitudinal Studies ; Treatment Outcome ; Aged ; Fungi/drug effects/classification/isolation & purification ; Young Adult ; Antifungal Agents/administration & dosage/therapeutic use/pharmacology ; Administration, Topical ; Skin Cream/administration & dosage ; Severity of Illness Index ; Bacteria/classification/isolation & purification/drug effects/genetics ; },
abstract = {BACKGROUND: Interdigital tinea pedis is a common type of tinea pedis that occurs between toes and is easy to recur. Recently, the skin microbiome analysis of interdigital tinea pedis showed changes in bacterial microbiome in addition to fungal infection.

OBJECTIVES: To investigate the efficacy and safety of clioquinol 3% cream in treating interdigital tinea pedis as well as characterize changes in the skin microbiome during treatment.

METHODS: The clinical characteristics and skin microbiome of patients with interdigital tinea pedis were investigated in a longitudinal prospective study. In total 28 participants were rcruited to use the clioquinol 3% cream topically to the target skin lesions twice a day for 1 week. Disease severity evaluation, fungal microscopic examination, and sample collection for skin microbiome analysis were performed at baseline, after treatment, and 1 week post-treatment.

RESULTS: Compared with baseline, the disease severity, lesion score, pruritus score, and malodor score of the patients significantly decreased after treatment and at 1 week post-treatment (P < 0.05). The fungal profiles after treatment and 1 week post-treatment revealed significantly decreased abundance of Trichophyton and significantly increased abundances of Cladosporium, Alternaria, and Aspergillus, which led to higher fungal diversity than pretreatment samples. The bacterial profiles after treatment and 1 week post-treatment revealed significantly decreased abundances of Brevibacterium, Finegoldia, and Facklamia. The abundance of Streptococcus and bacterial diversity were also significantly decreased at 1 week post-treatment. The disease severity was positively associated with the abundance of Trichophyton, Arthroderma, Finegoldia, Facklamia, Brevibacterium, Corynebacterium, and Porphyromonas.

CONCLUSIONS: The clioquinol 3% cream was efficient on treating interdigital tinea pedis by decreasing the abundance of pathogenic fungus, recovering the normal balance of the fungal and bacterial communities, and restore species diversity.},
}

Humans
*Microbiota/drug effects
Male
Female
*Tinea Pedis/drug therapy/microbiology
Middle Aged
Adult
*Clioquinol/administration & dosage
Prospective Studies
*Skin/microbiology
Longitudinal Studies
Treatment Outcome
Aged
Fungi/drug effects/classification/isolation & purification
Young Adult
Antifungal Agents/administration & dosage/therapeutic use/pharmacology
Administration, Topical
Skin Cream/administration & dosage
Severity of Illness Index
Bacteria/classification/isolation & purification/drug effects/genetics

@article {pmid39843757,
year = {2025},
author = {Pitashny, M and Kesten, I and Shlon, D and Hur, DB and Bar-Yoseph, H},
title = {The Future of Microbiome Therapeutics.},
journal = {Drugs},
volume = {},
number = {},
pages = {},
pmid = {39843757},
issn = {1179-1950},
abstract = {The human microbiome exerts profound influence over various biological processes within the body. Unlike many host determinants, it represents a readily accessible target for manipulation to promote health benefits. However, existing commercial microbiome-directed products often exhibit low efficacy. Advancements in technology are paving the way for the development of novel microbiome therapeutics, across a wide range of indications. In this narrative review, we provide an overview of state-of-the-art technologies in late-stage development, examining their advantages and limitations. By covering a spectrum, from fecal-derived products to live biotherapeutics, phage therapy, and synthetic biology, we illuminate the path toward the future of microbiome therapeutics.},
}

@article {pmid39843735,
year = {2025},
author = {Stephen-Victor, E and Kuziel, GA and Martinez-Blanco, M and Jugder, BE and Benamar, M and Wang, Z and Chen, Q and Lozano, GL and Abdel-Gadir, A and Cui, Y and Fong, J and Saint-Denis, E and Chang, I and Nadeau, KC and Phipatanakul, W and Zhang, A and Farraj, FA and Holder-Niles, F and Zeve, D and Breault, DT and Schmitz-Abe, K and Rachid, R and Crestani, E and Rakoff-Nahoum, S and Chatila, TA},
title = {RELMβ sets the threshold for microbiome-dependent oral tolerance.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39843735},
issn = {1476-4687},
abstract = {Tolerance to dietary antigens is critical for avoiding deleterious type 2 immune responses resulting in food allergy (FA) and anaphylaxis[1,2]. However, the mechanisms resulting in both the maintenance and failure of tolerance to food antigens are poorly understood. Here we demonstrate that the goblet-cell-derived resistin-like molecule β (RELMβ)[3,4] is a critical regulator of oral tolerance. RELMβ is abundant in the sera of both patients with FA and mouse models of FA. Deletion of RELMβ protects mice from FA and the development of food-antigen-specific IgE and anaphylaxis. RELMβ disrupts food tolerance through the modulation of the gut microbiome and depletion of indole-metabolite-producing Lactobacilli and Alistipes. Tolerance is maintained by the local production of indole derivatives driving FA protective RORγt[+] regulatory T (Treg) cells[5] through activation of the aryl hydrocarbon receptor. RELMβ antagonism in the peri-weaning period restores oral tolerance and protects genetically prone offspring from developing FA later in life. Together, we show that RELMβ mediates a gut immune-epithelial circuit regulating tolerance to food antigens-a novel mode of innate control of adaptive immunity through microbiome editing-and identify targetable candidates in this circuit for prevention and treatment of FA.},
}

@article {pmid39843625,
year = {2025},
author = {Jarquín-Díaz, VH and Dayaram, A and Soilemetzidou, ES and Desvars-Larrive, A and Bohner, J and Buuveibaatar, B and Kaczensky, P and Walzer, C and Greenwood, AD and Löber, U},
title = {Unraveling the distinctive gut microbiome of khulans (Equus hemionus hemionus) in comparison to their drinking water and closely related equids.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2767},
pmid = {39843625},
issn = {2045-2322},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Equidae/microbiology ; *RNA, Ribosomal, 16S/genetics ; Horses/microbiology ; *Drinking Water/microbiology ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Phylogeny ; },
abstract = {The microbial composition of host-associated microbiomes is influenced by co-evolutionary interactions, host genetics, domestication, and the environment. This study investigates the contribution of environmental microbiota from freshwater bodies to the gastrointestinal microbiomes of wild khulans (Equus hemionus hemionus, n = 21) and compares them with those of captive khulans (n = 12) and other equids-Przewalski's horse (n = 82) and domestic horse (n = 26). Using PacBio technology and the LotuS pipeline for 16S rRNA gene sequencing, we analyze microbial diversity and conduct differential abundance, alpha, and beta diversity analyses. Results indicate limited microbial sharing between wild khulans and their waterhole environments, suggesting minimal environmental influence on their gut microbiomes and low levels of water contamination by khulans. Wild khulans exhibit greater microbial diversity and richness compared to captive ones, likely due to adaptations to the harsh nutritional conditions of the Gobi desert. Conversely, captive khulans show reduced microbial diversity, potentially affected by dietary changes during captivity. These findings highlight the significant impact of environment and lifestyle on the gut microbiomes of equids.},
}

Animals
*Gastrointestinal Microbiome
*Equidae/microbiology
*RNA, Ribosomal, 16S/genetics
Horses/microbiology
*Drinking Water/microbiology
Bacteria/classification/genetics/isolation & purification
Biodiversity
Phylogeny

@article {pmid39843550,
year = {2025},
author = {Radlinski, LC and Bäumler, AJ},
title = {Microbiome science needs more microbiologists.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39843550},
issn = {2058-5276},
}

@article {pmid39843522,
year = {2025},
author = {Bray, AS and Broberg, CA and Hudson, AW and Wu, W and Nagpal, RK and Islam, M and Valencia-Bacca, JD and Shahid, F and Hernandez, GE and Nutter, NA and Walker, KA and Bennett, EF and Young, TM and Barnes, AJ and Ornelles, DA and Miller, VL and Zafar, MA},
title = {Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {940},
pmid = {39843522},
issn = {2041-1723},
support = {AI178595//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI166642//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI173244//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Klebsiella pneumoniae/genetics/metabolism ; *Type VI Secretion Systems/genetics/metabolism ; Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Klebsiella Infections/microbiology ; Gene Expression Regulation, Bacterial ; Gastrointestinal Tract/microbiology ; Bacterial Proteins/metabolism/genetics ; DNA Transposable Elements/genetics ; Female ; Mice, Inbred C57BL ; },
abstract = {Microbial species must compete for space and nutrients to persist in the gastrointestinal (GI) tract, and our understanding of the complex pathobiont-microbiota interactions is far from complete. Klebsiella pneumoniae, a problematic, often drug-resistant nosocomial pathogen, can colonize the GI tract asymptomatically, serving as an infection reservoir. To provide insight on how K. pneumoniae interacts with the resident gut microbiome, we conduct a transposon mutagenesis screen using a murine model of GI colonization with an intact microbiota. Among the genes identified were those encoding a type VI secretion system (T6SS), which mediates contact-dependent killing of gram-negative bacteria. From several approaches, we demonstrate that the T6SS is critical for K. pneumoniae gut colonization. Metagenomics and in vitro killing assays reveal that K. pneumoniae reduces Betaproteobacteria species in a T6SS-dependent manner, thus identifying specific species targeted by K. pneumoniae. We further show that T6SS gene expression is controlled by several transcriptional regulators and that expression only occurs in vitro under conditions that mimic the gut environment. By enabling K. pneumoniae to thrive in the gut, the T6SS indirectly contributes to the pathogenic potential of this organism. These observations advance our molecular understanding of how K. pneumoniae successfully colonizes the GI tract.},
}

*Klebsiella pneumoniae/genetics/metabolism
*Type VI Secretion Systems/genetics/metabolism
Animals
*Gastrointestinal Microbiome/genetics
Mice
*Klebsiella Infections/microbiology
Gene Expression Regulation, Bacterial
Gastrointestinal Tract/microbiology
Bacterial Proteins/metabolism/genetics
DNA Transposable Elements/genetics
Female
Mice, Inbred C57BL

@article {pmid39843462,
year = {2025},
author = {Wolf, S and Jayawickrama, C and Carlson, CA and Deutsch, C and Davis, EW and Daniels, BN and Chan, F and Giovannoni, SJ},
title = {Microbial carbon oxidation in seawater below the hypoxic threshold.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2838},
pmid = {39843462},
issn = {2045-2322},
mesh = {*Seawater/microbiology ; *Oxidation-Reduction ; *Carbon/metabolism ; *Oxygen/metabolism ; Microbiota ; Phytoplankton/metabolism ; Ecosystem ; Bacteria/metabolism/genetics ; },
abstract = {Global oxygen minimum zones (OMZs) often reach hypoxia but seldom reach anoxia. Recently it was reported that Michaelis Menten constants (Km) of oxidative enzymes are orders of magnitude higher than respiratory Km values, and in the Hypoxic Barrier Hypothesis it was proposed that, in ecosystems experiencing falling oxygen, oxygenase enzyme activities become oxygen-limited long before respiration. We conducted a mesocosm experiment with a phytoplankton bloom as an organic carbon source and controlled dissolved oxygen (DO) concentrations in the dark to determine whether hypoxia slows carbon oxidation and oxygen decline. Total oxygen utilization (TOU) in hypoxic treatment (ca. 7.1 µM O2) was 21.7% lower than the oxic treatment (ca. 245.1 µM O2) over the first 43 days of the experiment. In addition, following the restoration of fully oxic conditions to the hypoxic treatment, TOU accelerated, demonstrating that oxidative processes are sensitive to DO concentrations found in large volumes of the ocean. Microbial amplicon-based community composition diverged between oxic treatments, indicating a specialized microbiome that included Thioglobaceae (SUP05 Gammaproteobacteria), OM190 (Planctomycetota), ABY1 (Patescibacteria), and SAR86 subclade D2472, thrived in the hypoxic treatment, while the genus Candidatus Actinomarina and SAR11 alphaproteobacteria were sharply inhibited. Our findings support the hypothesis that oxygenase kinetics might slow the progression of ocean deoxygenation in oxygen-poor regions and be a factor in the evolution of microbial taxa adapted to hypoxic environments.},
}

*Seawater/microbiology
*Oxidation-Reduction
*Carbon/metabolism
*Oxygen/metabolism
Microbiota
Phytoplankton/metabolism
Ecosystem
Bacteria/metabolism/genetics

@article {pmid39843444,
year = {2025},
author = {Bechtold, EK and Ellenbogen, JB and Villa, JA and de Melo Ferreira, DK and Oliverio, AM and Kostka, JE and Rich, VI and Varner, RK and Bansal, S and Ward, EJ and Bohrer, G and Borton, MA and Wrighton, KC and Wilkins, MJ},
title = {Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {944},
pmid = {39843444},
issn = {2041-1723},
support = {EAR-2029686//National Science Foundation (NSF)/ ; PRFB-2109592//National Science Foundation (NSF)/ ; DEB-1754756//National Science Foundation (NSF)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0007144//U.S. Department of Energy (DOE)/ ; DE-SC0012088//U.S. Department of Energy (DOE)/ ; DESC0023297//U.S. Department of Energy (DOE)/ ; DE-SC0023456//U.S. Department of Energy (DOE)/ ; DE-SC0023456//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC0022191//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021350//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021350//U.S. Department of Energy (DOE)/ ; DESC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; },
mesh = {*Methane/metabolism ; *Wetlands ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Fresh Water/microbiology ; Metagenome ; Bacteria/metabolism/genetics/classification ; Climate Change ; },
abstract = {Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from high methane-emitting wetlands. Microorganisms drive methane cycling, but little is known about their conservation across wetlands. To address this, we integrate 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual methane flux data across 9 wetlands, creating the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This resource is used to link microbiome composition to function and methane emissions, focusing on methane-cycling microbes and the networks driving carbon decomposition. We identify eight methane-cycling genera shared across wetlands and show wetland-specific metabolic interactions in marshes, revealing low connections between methanogens and methanotrophs in high-emitting wetlands. Methanoregula emerged as a hub methanogen across networks and is a strong predictor of methane flux. In these wetlands it also displays the functional potential for methylotrophic methanogenesis, highlighting the importance of this pathway in these ecosystems. Collectively, our findings illuminate trends between microbial decomposition networks and methane flux while providing an extensive publicly available database to advance future wetland research.},
}

*Methane/metabolism
*Wetlands
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Fresh Water/microbiology
Metagenome
Bacteria/metabolism/genetics/classification
Climate Change

@article {pmid39843443,
year = {2025},
author = {Wu, X and Tjahyo, AS and Volchanskaya, VSB and Wong, LH and Lai, X and Yong, YN and Osman, F and Tay, SL and Govindharajulu, P and Ponnalagu, S and Tso, R and Teo, HS and Khoo, K and Fan, H and Goh, CC and Yap, CPL and Leow, MK and Henry, CJ and Haldar, S and Lim, KJ},
title = {A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {942},
pmid = {39843443},
issn = {2041-1723},
mesh = {Humans ; *Prediabetic State/diet therapy/metabolism/therapy/blood/microbiology ; Middle Aged ; *Gastrointestinal Microbiome ; Male ; Female ; *Fabaceae ; Aged ; *Caloric Restriction/methods ; Single-Blind Method ; Singapore ; Blood Glucose/metabolism ; Glycated Hemoglobin/metabolism ; Body Mass Index ; Cholesterol, LDL/blood/metabolism ; },
abstract = {Healthy dietary patterns rich in legumes can improve metabolic health, although their additional benefits in conjunction with calorie restriction have not been well-established. We investigated effects of a calorie-restricted, legume-enriched, multicomponent intervention diet compared with a calorie-restricted control diet in 127 Chinese prediabetes participants, living in Singapore. The study was a 16-week, single-blind, parallel-design, randomized controlled trial (n = 63 intervention group (IG), n = 64 control group (CG); mean ± SD age 62.2 ± 6.3 years, BMI 23.8 ± 2.6 kg/m[2]). Primary outcomes were markers of glycemia and all measurements were taken at 2 or 4-weekly intervals. At the end of 16 weeks, both groups had significantly lower BMI (q(Time) = 1.92 ×10[-42], β = -0.02) compared with baseline, with minimal difference between groups. The IG had significantly greater reductions in LDL cholesterol (q(Treatment×Time) = 0.01, β = -0.16), total cholesterol (q(Treatment×Time) = 0.02, β = -0.3) and HbA1c (q(Treatment×Time) = 0.04, β = -0.004) compared with CG, alongside increases in fiber degrading species in IG, mediated through metabolites such as bile acids and amino acids. A legume-enriched, multicomponent intervention diet can improve metabolic health in a prediabetes population, in addition to benefits obtained from calorie restriction alone, partially mediated through changes in gut microbial composition and function. Trial registration: Clinical Trials NCT04745702.},
}

Humans
*Prediabetic State/diet therapy/metabolism/therapy/blood/microbiology
Middle Aged
*Gastrointestinal Microbiome
Male
Female
*Fabaceae
Aged
*Caloric Restriction/methods
Single-Blind Method
Singapore
Blood Glucose/metabolism
Glycated Hemoglobin/metabolism
Body Mass Index
Cholesterol, LDL/blood/metabolism

@article {pmid39843249,
year = {2025},
author = {Aqeel, A and Kay, MC and Zeng, J and Petrone, BL and Yang, C and Truong, T and Brown, CB and Jiang, S and Carrion, VM and Bryant, S and Kirtley, MC and Neshteruk, CD and Armstrong, SC and David, LA},
title = {Grocery intervention and DNA-based assessment to improve diet quality in pediatric obesity: a pilot randomized controlled study.},
journal = {Obesity (Silver Spring, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/oby.24205},
pmid = {39843249},
issn = {1930-739X},
support = {//Chan Zuckerberg Initiative/ ; //Burroughs Wellcome Fund Pathogenesis of Infectious Disease Award/ ; //Duke Microbiome Center/ ; 1KL2TR002554/TR/NCATS NIH HHS/United States ; UL1TR002553/TR/NCATS NIH HHS/United States ; //Duke Clinical and Translational Science Award/ ; R01-DK116187-06A1/DK/NIDDK NIH HHS/United States ; R01-DK128611-01A1/DK/NIDDK NIH HHS/United States ; },
abstract = {OBJECTIVE: We assessed the impact of a food-provisioning intervention on diet quality in children with obesity.

METHODS: Participants (n = 33, aged 6-11 years) were randomly assigned to either usual care (intensive health behavior and lifestyle treatment) or intervention (usual care + food provisioning; high-fiber, low-dairy diet) for 4 weeks. The primary outcome was a change in child diet quality at Week 4. Secondary outcomes were changes in weight, food insecurity, gut microbiome composition (16S ribosomal RNA), and dietary intake, measured via an objective DNA-based biomarker (i.e., FoodSeq). Genomic dietary data were analyzed against a larger pediatric adolescent obesity cohort (n = 195, aged 10-18 years) from similar households.

RESULTS: Intervention demonstrated changes across all assessed diet components and was more effective than usual care in increasing whole grain (β = 0.20, 95% CI: 0.05 to 0.34; p = 0.013) and fiber (β = 2.52, 95% CI: 1.28 to 3.76; p < 0.001) and decreasing dairy (β = -1.31, 95% CI: -2.02 to -0.60; p = 0.001). FoodSeq results, highly concordant with grocery orders (adjusted R[2] = 0.65; p < 0.001), indicated a dietary shift toward low-energy-density plant taxa in the intervention relative to a prior survey of diet in a related cohort (β = 8.64, 95% CI: 5.18 to 12.14; p < 0.001). No significant changes were observed in microbiome, weight, or food insecurity.

CONCLUSIONS: Our study supports the potential of dietitian-guided food provisioning for improving diet quality in children with obesity and demonstrates an objective genomic approach for evaluating dietary shifts.},
}

@article {pmid39843118,
year = {2025},
author = {Liu, Y and Liu, Q and Ma, M and Zhang, J and Liu, M and Mosenthin, R and Zhao, L and Huang, S and Ma, Q},
title = {Dietary arabinogalactan modulates immunity and improves gut barrier in broilers via regulating metabolome and gut microbiome.},
journal = {Carbohydrate polymers},
volume = {352},
number = {},
pages = {123223},
doi = {10.1016/j.carbpol.2025.123223},
pmid = {39843118},
issn = {1879-1344},
mesh = {Animals ; *Galactans/chemistry/pharmacology ; *Chickens/immunology ; *Gastrointestinal Microbiome/drug effects ; *Metabolome/drug effects ; Dietary Supplements ; Animal Feed ; Larix/chemistry ; },
abstract = {The extraction of polysaccharides from wood by-products is recognized as a green re-utilization approach to shape a recycling-oriented society. In this research, we identified the structural properties of arabinogalactan (AG) extracted from Larix sibirica Ledeb wood chips and verified its efficacy as an additive in broiler framing. Results showed that the molecular weight of AG is 19.805 KDa. Methylation analysis and NMR spectra indicate that AG has a 1,6-linked Galp backbone, side residues mainly branched at C-1,3,6 on β-D-Galp. The Ara residues were substituted at C-3 of 1,6-linked Galp consisting of α-L-Araf-(1→3)-α-L-Araf-(1 → 3)-α-L-Araf (1→ and α-L-Araf-(1 → 4) β-D-Galp-(1 → 3)-β-D-Galp-(1→. As a dietary supplement in broiler model, AG treatment improved the body weight of broilers especially breast and leg muscle weight. Furthermore, AG could regulate host immune response, gut microbiota composition, and metabolic activity, especially promoting lipid metabolism. By means of serum non-targeted metabolomics analysis, enrichment of pantothenate and CoA biosynthesis and beta-alanine metabolism pathways could be determined. AG treatment led to a rise in bacteria that produce SCFAs, with elevated concentrations of acetic and butyric acids. In conclusion, AG can be considered as a potential dietary supplement to beneficially affect host's health status.},
}

Animals
*Galactans/chemistry/pharmacology
*Chickens/immunology
*Gastrointestinal Microbiome/drug effects
*Metabolome/drug effects
Dietary Supplements
Animal Feed
Larix/chemistry

@article {pmid39842720,
year = {2025},
author = {Mahdavi, S and Anthony, NM and Sikaneta, T and Tam, PY},
title = {Perspective: Multi-omics and Artificial Intelligence for Personalized Nutritional Management of Diabetes in Patients Undergoing Peritoneal Dialysis.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100378},
doi = {10.1016/j.advnut.2025.100378},
pmid = {39842720},
issn = {2156-5376},
abstract = {Managing diabetes in patients on peritoneal dialysis (PD) is challenging due to the combined effects of dietary glucose, glucose from dialysate, and other medical complications. Advances in technology that enable continuous biological data collection are transforming traditional management approaches. This review explores how multi-omics technologies and artificial intelligence (AI) are enhancing glucose management in this patient population. Continuous glucose monitoring (CGM) offers significant advantages over traditional markers like hemoglobin A1c (HbA1c). Unlike HbA1c, which reflects an average glucose level, CGM provides real-time, dynamic glucose data that allow clinicians to make timely adjustments, leading to better glycemic control and outcomes. Multi-omics approaches are valuable for understanding genetic factors that influence susceptibility to diabetic complications, particularly those related to advanced glycation end-products (AGEs). Identifying genetic polymorphisms that modify a patient's response to AGEs allows for personalized treatments, potentially reducing the severity of diabetes-related pathologies. Metabolomic analyses of peritoneal dialysis effluent are also promising, as they help identify early biomarkers of metabolic dysregulation. Early detection can lead to timely interventions and more tailored treatment strategies, improving long-term patient care. AI integration is revolutionizing diabetes management for PD patients by processing vast datasets from CGM, genetic, metabolic and microbiome profiles. AI can identify patterns and predict outcomes that may be difficult for humans to detect, enabling highly personalized recommendations for diet, medication, and dialysis management. Furthermore, AI can assist clinicians by automating data interpretation, improving treatment plans and enhancing patient education. Despite the promise of these technologies, there are limitations. CGM, multi-omics and AI require significant investment in infrastructure, training and validation studies. Additionally, integrating these approaches into clinical practice presents logistical and financial challenges. Nevertheless, personalized, data-driven strategies offer great potential for improving outcomes in diabetes management for PD patients.},
}

@article {pmid39842611,
year = {2025},
author = {Erkert, L and Ruder, B and Kabisch, M and Gamez Belmonte, R and Patankar, JV and Gonzalez Acera, M and Schödel, L and Chiriac, MT and Cineus, R and Gnafakis, S and Leupold, T and Thoma, OM and Stolzer, I and Taut, A and Thonn, V and Zundler, S and Günther, C and Diefenbach, A and Kühl, AA and Hegazy, AN and Waldner, M and Basic, M and Bleich, A and , },
title = {TIFA renders intestinal epithelial cells responsive to microbial ADP-heptose and drives colonic inflammation in mice.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mucimm.2025.01.003},
pmid = {39842611},
issn = {1935-3456},
abstract = {Intestinal immune homeostasis relies on intestinal epithelial cells (IECs), which provide an efficient barrier, and warrant a state of tolerance between the microbiome and the mucosal immune system. Thus, proper epithelial microbial sensing and handling of microbes is key to preventing excessive immunity, such as seen in patients with inflammatory bowel disease (IBD). To date, the molecular underpinnings of these processes remain incompletely understood. This study identifies TIFA as a driver of intestinal inflammation and an epithelial signaling hub between the microbiome and mucosal immune cells. TIFA was constitutively expressed in crypt epithelial cells and was highly induced in the intestine of mice and IBD patients with intestinal inflammation. We further identified IL-22 signaling via STAT3 as key mechanism driving TIFA expression in IECs. At the molecular level, we demonstrate that TIFA expression is essential for IEC responsiveness to the bacterial metabolite ADP-heptose. Most importantly, ADP-heptose-induced TIFA signaling orchestrates an inflammatory cellular response in the epithelium, with NF-κB and inflammasome activation, and high levels of chemokine production. Finally, mice lacking TIFA were protected from intestinal inflammation when subjected to a model of experimental colitis. In conclusion, our study implicates that targeting TIFA may be a strategy for future IBD therapy.},
}