@article {pmid40221592,
year = {2025},
author = {Butler, MI and Kittel-Schneider, S and Wagner-Skacel, J and Mörkl, S and Clarke, G},
title = {The Gut Microbiome in Anxiety Disorders.},
journal = {Current psychiatry reports},
volume = {},
number = {},
pages = {},
pmid = {40221592},
issn = {1535-1645},
abstract = {PURPOSE OF REVIEW: We aim to update readers on the latest evidence regarding the role of the gut microbiome in generalized anxiety disorder (GAD), panic disorder (PD), agoraphobia, and social anxiety disorder (SAD). This review summarises the literature on microbiome composition and function in these conditions, provides insights about causality and mechanisms and evaluates current evidence for microbiome-based interventions in anxiety disorders.

RECENT FINDINGS: Most studies exploring the microbiome in anxiety disorders are small, cross-sectional studies. Nevertheless, some consistent findings emerge. Bacterial taxa such as Eubacterium, Coprococcus and Faecalibacterium may be depleted in GAD. Studies in PD and SAD are scarce and, to our knowledge, there have been no studies conducted in agoraphobia. Probiotics may help reduce anxiety symptoms, although the majority of studies have been in non-clinical cohorts. Large, prospective studies are required to further elucidate the role of the microbiome-gut-brain axis in anxiety disorders. Microbiome-based interventions hold promise, but randomised controlled trials in clinical populations with relevant diagnoses are now warranted and urgently required.},
}

@article {pmid40221450,
year = {2025},
author = {Kim, KS and Noh, J and Kim, BS and Koh, H and Lee, DW},
title = {Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {57},
pmid = {40221450},
issn = {2055-5008},
support = {RS-2021-NR056579//National Research Foundation of Korea (NRF)/ ; RS-2023-KH141436//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; 200118770//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; Colitis, Ulcerative/microbiology ; DNA, Bacterial/genetics ; Republic of Korea ; Phylogeny ; Feces/microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {Understanding the role of human gut microbiota in health and disease requires insights into its taxonomic composition and functional capabilities. This study evaluates whether concatenating paired-end reads enhances data output for gut microbiome analysis compared to the merging approach across various regions of the 16S rRNA gene. We assessed this approach in both mock communities and Korean cohorts with or without ulcerative colitis. Our results indicate that using the direct joining method for the V1-V3 or V6-V8 regions improves taxonomic resolution compared to merging paired-end reads (ME) in post-sequencing data. While predicting microbial function based on 16S rRNA sequencing has inherent limitations, integrating sequencing reads from both the V1-V3 and V6-V8 regions enhanced functional predictions. This was confirmed by whole metagenome sequencing (WMS) of Korean cohorts, where our approach improved taxa detection that was lost using the ME method. Thus, we propose that the integrated dual 16S rRNA sequencing technique serves as a valuable tool for microbiome research by bridging the gap between amplicon sequencing and WMS.},
}

*RNA, Ribosomal, 16S/genetics
Humans
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/genetics/isolation & purification
*Metagenomics/methods
Sequence Analysis, DNA/methods
Metagenome
Colitis, Ulcerative/microbiology
DNA, Bacterial/genetics
Republic of Korea
Phylogeny
Feces/microbiology
Biodiversity
High-Throughput Nucleotide Sequencing

@article {pmid40221415,
year = {2025},
author = {Xu, C and Sun, P and Jiang, Q and Meng, Y and Dong, L and Wang, X and Hu, X and Li, C and Li, G and Zheng, R and You, X and Yang, X},
title = {Tissue-resident Klebsiella quasipneumoniae contributes to progression of idiopathic pulmonary fibrosis by triggering macrophages mitophagy in mice.},
journal = {Cell death discovery},
volume = {11},
number = {1},
pages = {168},
pmid = {40221415},
issn = {2058-7716},
support = {81973383//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82204488//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Idiopathic pulmonary fibrosis (IPF) is a progressive and chronic interstitial lung disease with unclear underlying pathogenic mechanisms. Dysbiosis of the lung microbiota is believed to be associated with the development of fibrosis; however, the roles of the microbiome in the respiratory functions of hosts with IPF remain poorly understood. To investigate the relationship between the lung microbiome and the pathological processes of idiopathic pulmonary fibrosis under laboratory conditions, C57BL/6 J mice were exposed to bleomycin and observed at 7, 14, 21, and 28 days post-exposure. 16S rDNA analysis revealed that the lung microbial community exhibited dysbiosis in the bleomycin-induced pulmonary fibrosis model, characterized by an abnormally high proportion of Klebsiella quasipneumoniae (K. quasipneumoniae), as confirmed by RNA fluorescence in situ hybridization. Throughout the progression of experimental pulmonary fibrosis, Tax4Fun analysis indicated that the abundance of K. quasipneumoniae differed significantly between model mice and control mice, correlating with the sustained activation of reactive oxygen species (ROS) pathways. Importantly, the dysbiosis of K. quasipneumoniae may serve as a critical factor triggering increased ROS levels, accompanied by macrophage mitophagy, ultimately leading to the overexpression of TGF-β1, a key player in the pathogenesis of pulmonary fibrosis. These findings suggest that lung microbiota dysbiosis exacerbates the progression of bleomycin-induced pulmonary fibrosis related to macrophage mitophagy.},
}

@article {pmid40221043,
year = {2025},
author = {Badhan, A and Wang, Y and Terry, S and Gruninger, R and Guan, LL and McAllister, TA},
title = {Interplay of rumen microbiome and the cattle host in modulating feed efficiency and methane emissions.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-26063},
pmid = {40221043},
issn = {1525-3198},
abstract = {Given that the majority of energy and protein supplied to cattle arises as a result of ruminal fermentation, the rumen microbiome plays a key role in determining host feed efficiency and methane (CH4) emissions. Some reports suggests that a less diverse rumen microbiome is associated with improved feed efficiency, while other studies suggest that microbial diversity does not differ between low- and high-efficiency cattle of the same breed, fed identical diets. While reducing enteric CH4 emissions offers a dual benefit in terms of improved feed efficiency and a reduced environmental footprint; recent findings indicate that these outcomes are not always consistent in ruminants. The composition of the rumen microbiome is mainly determined by diet but is also influenced by host genetics and physiological parameters such as rumen volume, rate of passage and rumination. Reduced microbial diversity may impair the ability of cattle to adapt to frequent changes in diet and the environment. Hydrogen exchange and capture are the energetic foundation of the rumen microbiome, and considerable resources have been invested in developing additives that redirect hydrogen flow toward alternative sinks and away from the reduction of CO2 to CH4. These additives reduce enteric CH4 emissions by 30-80%, yet the anticipated gains in feed efficiency remain inconsistent. Strategies to improve the feed efficiency of cattle production must consider the multifaceted interactions among the host, rumen microbiome, and diet to ensure the sustainable intensification of cattle production while maintaining the social license for milk and meat production.},
}

@article {pmid40221038,
year = {2025},
author = {Flynn, A and Leech, J and McFadden, M and McAloon, C and Paul-Murphy, J and Crispie, F and Cotter, PD and McAloon, C and Kennedy, E},
title = {The effects of offering adequate-quality or high-quality colostrum on the passive immunity, health, growth and fecal microbiome development of dairy heifer calves.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-26165},
pmid = {40221038},
issn = {1525-3198},
abstract = {Colostrum quality is influenced by multiple factors, including its microbial load, which is determined by the cleanliness of collection and storage conditions. Additionally, the dam's diet and immune status play a crucial role in shaping colostrum quality by affecting immunoglobulin (IgG) concentrations. While many factors contribute to colostrum quality, this study will specifically use IgG content as the primary measure of quality. It is well established that feeding low-quality colostrum negatively affects calf health and growth, while feeding good-quality colostrum leads to better outcomes. However, it remains unclear if feeding colostrum above the recommended quality threshold offers additional benefits for calf health and growth. This study compared the effects of adequate versus high-quality colostrum on dairy heifer calf growth, health, and the development of the fecal microbiome during the first 15 weeks of life. We also measured the levels of apparent efficacy of absorption of IgG in both groups. Colostrum quality was initially determined and measured before feeding using a Brix refractometer (only feeding a minimum of 21% Brix); 93 heifer calves were assigned to treatment based on this data. Subsequently, laboratory analyses were conducted using radial immunodiffusion assays to measure the exact IgG levels in the colostrum; 72 calves were selected for continuation in the experiment based on the highest (n = 36) and lowest (n = 36) IgG levels in the colostrum. For these 72 calves, laboratory analyses were conducted using radial immunodiffusion assays to measure the exact IgG levels in the colostrum at the point of feeding and in the calf serum at 24 h post-feeding. To ensure a fair comparison, the groups were balanced for calf birthweight, breed, and dam parity. Serum IgG at 24 h, weight, and health data were analyzed in SAS using linear mixed models and logistic regression. Alpha and β diversity were analyzed using R with ANOVA, PERMANOVA, and Benjamini-Hochberg p-value adjustments. Calves fed colostrum with a high IgG content (123.0 mg/ml IgG) exhibited higher rates of passive transfer compared with those fed adequate-quality colostrum (85.2 mg/ml IgG). Both groups had passive transfer rates > 23 mg/ml IgG. Health outcomes were similar between the 2 groups, and average daily gain during the pre-weaning period was comparable, with calves gaining an average of 0.62 kg per day. Measures of α and β diversity in the fecal microbiome showed similar development in both groups. Apparent absorption efficacy was lower in calves fed high-quality colostrum (24.9%) compared with those fed adequate-quality colostrum (29.3%). The findings of this study support current recommendations for colostrum quality and suggest that calves may have a limited capacity to absorb higher concentrations of IgG. While feeding higher-quality colostrum did not lead to significant improvements in growth, health, or microbiome diversity, it demonstrated that adequate-quality colostrum can be equally effective when combined with best practice management. Further research is needed to better understand the relationships between immunoglobulin absorption efficiency, calf health, microbiome development, and growth performance.},
}

@article {pmid40220988,
year = {2025},
author = {Puel, EM and Taruhn, LF and Damé-Teixeira, N and Stefani, CM and Lataro, RM},
title = {Is there a link between the abundance of nitrate-reducing bacteria and arterial hypertension? A systematic review.},
journal = {Nitric oxide : biology and chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.niox.2025.04.001},
pmid = {40220988},
issn = {1089-8611},
abstract = {CONTEXT: Nitric oxide is a vasodilator molecule that acts on blood pressure (BP) control, and its production can occur through the reduction of nitrates by oral or intestinal nitrate-reducing bacteria. However, the relationship between nitrate-reducing bacteria and arterial hypertension (HTN) remains under debate.

OBJECTIVE: Systematically review if there is an association between the abundance of oral and intestinal nitrate-reducing bacteria and the occurrence of HTN in humans.

MEDLINE, Scopus, Cochrane Library, EMBASE, LILACS, Web of Science, Livivo, ProQuest Dissertations, and Google Scholar were searched for eligible articles until February 10th, 2024. Studies were included if they: (1) were observational studies or clinical trials; (2) included adults (≥ 18 years old) with HTN (systolic BP ≥130 mmHg and/or diastolic BP >80 mmHg and/or use of BP lowering medication); (3) compared (or not) to no-HTN adults; and (4) used next-generation sequencing microbiome analysis to identify bacterial taxa in the oral and/or gut nitrate-reducing bacteria.

RESULTS: The search identified 9365 articles, and 28 were included in the study after applying the inclusion and exclusion criteria; 23 articles assessed the gut microbiota, 4 assessed the oral microbiota, and 1 that assessed both. Depletion of nitrate-reducing bacteria was not consistently showed in the studies. The included studies reported reduction, increase, and no change in the nitrate-reducing bacteria genera or species in oral or gut microbiota.

CONCLUSION: We found no association between the abundance of oral and gut nitrate-reducing bacteria and the occurrence of HTN in humans.

REGISTRATION: PROSPERO identification number CRD42022315891.},
}

@article {pmid40220894,
year = {2025},
author = {Kinnunen, O and Kruglova, A and Jensen, MM and Kuokkanen, A and Smets, BF and Mikola, A},
title = {Shift in activated sludge microbiomes associated with nitrite accumulation and high nitrous oxide emissions.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121591},
doi = {10.1016/j.envres.2025.121591},
pmid = {40220894},
issn = {1096-0953},
abstract = {Nitrous oxide (N2O) emissions can constitute over half of the carbon footprint of a wastewater treatment plant (WWTP), and emission peaks frequently correlate with nitrite (NO2[-]) concentrations. However, connections between the microbiome and high N2O and NO2[-] levels are not well-documented. Here, we characterize the microbiomes in several parallel lines of a WWTP during massive N2O emissions (20% of influent nitrogen load) with prolonged NO2[-] accumulation in most lines, aiming to identify key differences between communities in lines with high and low NO2[-] concentrations. The abundance of nitrite-oxidizing bacteria (NOB) was extremely low in the lines with NO2[-] accumulation, which also had slightly lower abundances of ammonia-oxidizing bacteria (AOB). Some incomplete denitrifiers were more abundant in the lines with NO2[-] accumulation. Lines without NO2[-] had a higher relative abundance of filamentous bacteria and better floc formation. These findings confirmed our hypothesis that loss of NOB caused NO2[-] accumulation, inducing increased N2O emissions. AOB are suspected to be the main source of N2O during the studied period, with a likely contribution from heterotrophic denitrifiers. A few species were identified as interesting candidates for further study regarding their potential role in increased N2O emission from WWTPs. Long-term microbiome monitoring is necessary to understand the changes in the microbiome that might initiate NO2[-] accumulation and high N2O emissions.},
}

@article {pmid40220854,
year = {2025},
author = {Olah, P and Reuvers, N and Radai, Z and Varadi, A and van Lierop, A and Wachtmeister, T and Plante, S and Chaskar, P and Thomas, C and Julia, V and Alenius, H and Homey, B},
title = {Microbe-Host Interaction in Rosacea and its Modulation Through Topical Ivermectin.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.03.031},
pmid = {40220854},
issn = {1523-1747},
abstract = {Rosacea is characterized by inflammatory lesions, often accompanied by an increased density of the common skin mite Demodex folliculorum. Although rosacea shows a high prevalence and significantly affects the quality of life of patients, the underlying mechanisms, especially the role of cutaneous dysbiosis are largely unknown. Hence, we aimed to systematically characterize disease severity of rosacea patients in the context of mite density, the cutaneous microbiome and the host's transcriptome before and after 30 days of topical 1% ivermectin cream treatment. At day 30, a marked decrease in mite density was observed in 87.5% of patients. At day 0, distinct microbial community changes included the decrease in Cutibacterium acnes abundance, while Staphylococcus epidermidis colonization increased when compared to healthy volunteers. Interestingly, the insect symbiont Snodgrassella alvi was recovered from a highly Demodex-colonized patient and eradicated by day 30 of treatment. Although topical ivermectin did not affect bacterial dysbiosis, the host's transcriptome significantly normalized and an "ivermectin transcriptomic signature" was defined. Findings of the present study support that rosacea lesions are associated with dysbiosis. However, improvement of clinical signs during topical ivermectin is not associated with normalization of the bacterial microbiome, but rather a decrease of transcriptomic dysregulation and mite density.},
}

@article {pmid40220779,
year = {2025},
author = {Porcari, S and Ianiro, G and , },
title = {Microbiome testing in clinical practice - Authors' reply.},
journal = {The lancet. Gastroenterology & hepatology},
volume = {10},
number = {5},
pages = {414-415},
doi = {10.1016/S2468-1253(25)00063-9},
pmid = {40220779},
issn = {2468-1253},
}

@article {pmid40220778,
year = {2025},
author = {Singh, A and Bhardwaj, A and Midha, V and Sood, A},
title = {Microbiome testing in clinical practice.},
journal = {The lancet. Gastroenterology & hepatology},
volume = {10},
number = {5},
pages = {414},
doi = {10.1016/S2468-1253(24)00432-1},
pmid = {40220778},
issn = {2468-1253},
}

@article {pmid40220558,
year = {2025},
author = {Darriaut, R and Roose-Amsaleg, C and Vanhove, M and Monard, C},
title = {Microbiome engineering to palliate microbial dysbiosis occurring in agroecosystems.},
journal = {Microbiological research},
volume = {297},
number = {},
pages = {128178},
doi = {10.1016/j.micres.2025.128178},
pmid = {40220558},
issn = {1618-0623},
abstract = {Plant health and productivity are closely tied to the fluctuations of soil microbiomes, which regulate biogeochemical processes and plant-soil interactions. However, environmental and anthropogenic stressors, including climate change, intensive agricultural practices, and industrial activities, disrupt these microbial communities. This microbial imbalance reduces soil fertility, plant health, and biodiversity, threatening agroecosystem sustainability. This review explores the mechanisms driving microbial dysbiosis in soil and plant environments. Plants under stress release chemical signals through root exudates, dynamically recruiting beneficial microbes to counteract microbial imbalances. Moreover, this review evaluates traditional methods to alleviate these stress-induced microbial alterations, such as microbial inoculants and organic soil amendments, alongside innovative strategies like phage therapy, CRISPR, and small RNA-based technologies. Despite these advancements, the practical implementation of microbiome interventions faces significant challenges. These include regulatory hurdles, economic constraints, and the need for long-term field studies to validate efficacy and ensure environmental safety.},
}

@article {pmid40220550,
year = {2025},
author = {Silva, CJFD and Silva, CVFD and Cardoso, AM and de Oliveira Santos, E},
title = {Exploring clinical parameters and salivary microbiome profiles associated with metabolic syndrome in a population of Rio de Janeiro, Brazil.},
journal = {Archives of oral biology},
volume = {175},
number = {},
pages = {106251},
doi = {10.1016/j.archoralbio.2025.106251},
pmid = {40220550},
issn = {1879-1506},
abstract = {OBJECTIVES: This study investigates for the first time the association between metabolic syndrome and oral microbial profiles in a population-based sample from Rio de Janeiro, Brazil.

DESIGN: We assessed 66 volunteers, collecting detailed sociodemographic, anthropometric, and clinical data alongside salivary samples for metagenomic analysis.

RESULTS: Our findings reveal significant differences in anthropometric parameters, including waist circumference, glycemia, High-Density Lipoprotein (HDL), and triglycerides between the metabolic syndrome and control groups. Increased abundance of Bacteroidetes and Bacteroidia was observed in the metabolic syndrome group, suggesting a potential link between these phyla and metabolic dysregulation. While no significant differences in alpha diversity were found between the overall groups, stratification by body mass index (BMI) indicated that the normal weight subgroup without Metabolic Syndrome exhibited notable variations compared to overweight and obese individuals.

CONCLUSIONS: This study identifies specific shifts in oral microbiota composition that are associated with metabolic syndrome, highlighting their potential as microbial biomarkers for this condition. These findings suggest a link between oral dysbiosis and metabolic dysregulation, providing new insights into the pathophysiology of metabolic syndrome. Additionally, the results pave the way for the development of non-invasive diagnostics tools and targeted therapies that leverage the oral microbiome's role in systemic health.},
}

@article {pmid40220427,
year = {2025},
author = {Sun, X and Qin, B and Guo, A and Gui, J and Weng, J and Ye, J and Feng, S and Sang, M},
title = {Withaferin A maintained microbiome and metabolome features in A53T transgenic mice via multi-omics integrated analysis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {141},
number = {},
pages = {156725},
doi = {10.1016/j.phymed.2025.156725},
pmid = {40220427},
issn = {1618-095X},
abstract = {BACKGROUND: Withaferin A (WFA), a naturally occurring compound, has shown promise as a therapeutic agent for Parkinson's disease (PD), a neurodegenerative disorder associated with motor and gastrointestinal dysfunctions. However, its effects on gut microbiota metabolism remain poorly understood.

PURPOSE: This study aimed to elucidate the neuroprotective mechanisms of WFA in a PD mouse model by investigating its regulation of gut microbiota composition, metabolic pathways, and correlations with brain spatial metabolomics.

METHODS: Human SNCA-transgenic (A53T) mice were treated with WFA and evaluated using behavioral tests, immunohistochemistry, Western blot, and ELISA to assess motor/cognitive functions and PD-related pathology. Gut microbiota composition was analyzed via 16S rRNA sequencing, while untargeted fecal metabolomics and brain spatial metabolomics were employed to identify metabolic alterations.

RESULTS: WFA significantly improved motor performance, alleviated cognitive deficits, restored intestinal barrier integrity, and reduced neuroinflammation. It elevated the abundance of anti-inflammatory gut bacteria (e.g., Bifidobacterium, Dubosiella, Akkermansia) and reversed 55 fecal metabolites linked to sphingolipid metabolism, serotonergic synapses, and neuroactive ligand- receptor interactions. Spatial metabolomics revealed WFA's regulation of sphingolipid signaling pathways, including sphingosine kinase (Sphk1), ceramidase, sphingosine 1-phosphate receptor (S1PR5), and endocannabinoid receptor CB2 expression. Correlation analysis indicated a link between brain metabolite content and gut microbiota abundance.

CONCLUSION: Our findings highlight a potential mechanism of WFA that repairs neurons by modulating the sphingolipid signaling pathway within the microbiota-gut-brain axis.},
}

@article {pmid40220252,
year = {2025},
author = {Rezaei, AR and Ates, F and Sulik, A and Toczyłowski, K},
title = {'Smart', microbiome-sparing antibacterial therapy with a focus on the novel Lolamicin: an overview.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {40220252},
issn = {1439-0973},
abstract = {PURPOSE: Antibiotic resistance (AR) is an escalating worldwide health emergency, requiring inventive strategies for antibiotic treatment. This review examines the tactics used in designing smart antibiotics, with a specific emphasis on the mechanism of action of lolamicin, a newly developed microbiome-sparing antibiotic.

METHODS: We review the recent advances in smart antibiotic development, particularly those aiming to preserve the gut microbiome while effectively targeting pathogens. The study focuses on lolamicin's selective targeting mechanism, its inhibition of the LolCDE complex in Gram-negative bacteria.

RESULTS: Lolamicin works by blocking the LolCDE complex, which is crucial for transporting lipoproteins in Gramnegative bacteria. It offers a significant improvement compared to conventional antibiotics and other microbiomesparing options by safeguarding the microbiome and reducing the development of resistance. However, its limited range of effectiveness - namely against certain harmful bacteria such as Pseudomonas aeruginosa - and the possibility of bacteria becoming resistant to it, remain areas of concern.

CONCLUSION: Lolamicin presents a hopeful resolution by selectively attacking Gram-negative bacteria while leaving the beneficial gut flora unharmed. Further investigation and rigorous clinical testing are essential to fully harness its promise and confirm its long-term utility in combating antibiotic resistance.},
}

@article {pmid40220199,
year = {2025},
author = {Wasim, R and Sumaiya, and Ahmad, A and Anwar, A and Salman, A},
title = {Microbial imbalance in the gut: a new frontier in Rheumatoid arthritis research.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {40220199},
issn = {1568-5608},
abstract = {A chronic autoimmune illness that causes joint destruction and inflammation, rheumatoid arthritis (RA) often results in disability. Genetic, environmental, and immune system variables all have a role in the pathophysiology of RA. The complex community of bacteria that live in the gastrointestinal system, known as the gut microbiota, has been implicated in the onset and progression of RA in recent years, according to mounting data. An imbalance in the gut microbiota's composition, known as dysbiosis, has been noted in RA patients. This imbalance may impact inflammatory pathways and immunological responses, which in turn may contribute to the development and severity of the illness. Research has shown that some bacterial species, including Firmicutes, Bacteroidetes, and Proteobacteria, are either more abundant or less prevalent in RA patients than in healthy people. The gut-immune system axis may be modulated, immunological tolerance may be affected, and pro-inflammatory cytokine production may be enhanced by these microbial changes, all of which may lead to systemic inflammation linked to RA. Moreover, changes in intestinal permeability and a rise in microbial metabolite translocation may make autoimmune reactions worse. Probiotics, antibiotics, and dietary changes have also been investigated as possible treatment approaches to help RA patients regain the balance of their gut microbiota. Still up for debate, however, are the precise ways in which the gut microbiome affects RA. Comprehending the complex connection between gut microbiota and RA may give new perspectives on managing and preventing the condition, as well as future prospects for medicines that target the microbiome.},
}

@article {pmid40220189,
year = {2025},
author = {Knoppersen, RS and Bose, T and Coutinho, TA and Hammerbacher, A},
title = {Inside the Belly of the Beast: Exploring the Gut Bacterial Diversity of Gonipterus sp. n. 2.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {27},
pmid = {40220189},
issn = {1432-184X},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Eucalyptus/parasitology/chemistry ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Diet ; South Africa ; *Coleoptera/microbiology/physiology ; Gas Chromatography-Mass Spectrometry ; Introduced Species ; Biodiversity ; },
abstract = {The Eucalyptus snout beetle (Gonipterus sp. n. 2) is a destructive invasive pest of Eucalyptus plantations, responsible for significant defoliation and wood yield losses globally. Native to Australia, this beetle has adapted to thrive on diverse Eucalyptus hosts, overcoming their chemical defences. However, the mechanisms by which Gonipterus tolerates or utilises these plant defence metabolites remain poorly understood. In South Africa, Gonipterus sp. n. 2 poses a significant threat to Eucalyptus plantations by causing extensive defoliation and leading to substantial reductions in growth and wood production. This study investigates the relationship between diet, host Eucalyptus species, and the gut microbiome of Gonipterus sp. n. 2. Using controlled feeding experiments, beetles were reared on artificial, semi-artificial, and natural diets, as well as two Eucalyptus genotypes with distinct secondary metabolite profiles. High-throughput 16S rDNA sequencing and gas chromatography-mass spectrometry (GC-MS) revealed significant shifts in gut bacterial diversity and composition across diets. Natural diets supported the most diverse microbial communities, while artificial diets fostered a homogenised microbiome dominated by opportunistic taxa like Serratia. Host-specific effects were observed in frass microbiota, with substantial biotransformation of monoterpenes into less toxic derivatives. The results highlight the plasticity of Gonipterus gut microbiota, which enables metabolic adaptability and resilience in diverse environments. This microbial flexibility underpins the invasiveness of Gonipterus, emphasising the role of gut symbionts in overcoming host chemical defences. Understanding these interactions offers novel insights for microbiome-targeted pest management strategies, providing a sustainable approach to mitigate the impact of Gonipterus on global Eucalyptus forestry.},
}

Animals
*Gastrointestinal Microbiome
*Eucalyptus/parasitology/chemistry
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Diet
South Africa
*Coleoptera/microbiology/physiology
Gas Chromatography-Mass Spectrometry
Introduced Species
Biodiversity

@article {pmid40220054,
year = {2025},
author = {Brubaker, L and Horsley, H and Khasriya, R and Wolfe, AJ},
title = {Microbiologist in the Clinic: Antibiotic Dependent in her 30 s.},
journal = {International urogynecology journal},
volume = {},
number = {},
pages = {},
pmid = {40220054},
issn = {1433-3023},
abstract = {In this third episode of the Microbiologist in the Clinic series, clinicians and laboratory scientists share their perspectives about a 32 y/o female who has become antibiotic-dependent for her urinary symptoms. Despite escalating methods of antibiotic administration, the patient has persistent and recurrent "UTI" symptoms. Extensive testing has not provided guidance for her treating clinicians. The challenges of this clinical presentation are discussed with evidence for evaluation and treatment.},
}

@article {pmid40219702,
year = {2025},
author = {Xiao, Y and Yue, X and Zhang, X and Yang, Y and Zhang, Y and Sun, L},
title = {The role of bacteriophage in inflammatory bowel disease and its therapeutic potential.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/1040841X.2025.2492154},
pmid = {40219702},
issn = {1549-7828},
abstract = {Inflammatory bowel disease (IBD) refers to a group of chronic inflammatory disorders impacting the gastrointestinal (GI) tract. It represents a significant public health challenge due to its rising global incidence and substantial impact on patients' quality of life. Emerging research suggests a pivotal role of the human microbiome in IBD pathogenesis. Bacteriophages, integral components of the human microbiome, are indicated to influence the disease onset, progression, and therapeutic strategies. Here, we review the effect of bacteriophages on the pathogenesis of IBD and, more specifically, on the gut bacteria, the systemic immunity, and the susceptibility genes. Additionally, we explore the potential therapeutic use of the bacteriophages to modify gut microbiota and improve the health outcomes of IBD patients. This review highlights the potential of therapeutic bacteriophages in regulating gut microbiota and modulating the immune response to improve health outcomes in IBD patients. Future studies on personalized bacteriophage therapy and its integration into clinical practice could advance treatment strategies for IBD.},
}

@article {pmid40219669,
year = {2025},
author = {Murray, J and Kefayat, A and Finlayson, M and Seenan, JP and Hsu, R and Din, S},
title = {RCPE in association with the American College of Gastroenterology and the Scottish Society of Gastroenterology - Gastroenterology: A global perspective.},
journal = {The journal of the Royal College of Physicians of Edinburgh},
volume = {},
number = {},
pages = {14782715251332318},
doi = {10.1177/14782715251332318},
pmid = {40219669},
issn = {2042-8189},
abstract = {On 6 November 2024, the Royal College of Physicians of Edinburgh (RCPE) hosted its annual gastroenterology symposium, marking the first collaboration with the American College of Gastroenterology (ACG) and the Scottish Society of Gastroenterology (SSG). The event addressed key global challenges in gastroenterology, including obesity, liver disease, inflammatory bowel disease (IBD), the gut microbiome, endoscopy quality and artificial intelligence (AI) applications. Discussions emphasised the growing burden of metabolic dysfunction-associated steatotic liver disease (MASLD), with promising pharmacologic and endoscopic interventions emerging. Advances in microbiome-targeted therapies, including faecal microbiota transplantation (FMT), were explored for recurrent Clostridium difficile infection and IBD. Professor David Rubin delivered the esteemed Sir Stanley Davidson lecture, highlighting the era of disease modification in IBD, emphasising early intervention and personalised treatment strategies. The symposium also addressed the role of AI in improving endoscopic detection rates and optimising resource allocation. This international collaboration underscored the importance of a multidisciplinary approach to tackling global digestive diseases, integrating clinical innovation, policy interventions and technological advancements. The event fostered knowledge exchange among global experts, aiming to advance patient care and improve long-term outcomes in gastroenterology.},
}

@article {pmid40219624,
year = {2025},
author = {Kanbay, M and Ozbek, L and Guldan, M and Abdel-Rahman, SM and Sisman, U and Mallamaci, F and Zoccali, C},
title = {Nutrition, cognition and chronic kidney disease: A comprehensive review of interactions and interventions.},
journal = {European journal of clinical investigation},
volume = {},
number = {},
pages = {e70045},
doi = {10.1111/eci.70045},
pmid = {40219624},
issn = {1365-2362},
abstract = {BACKGROUND: Cognitive impairment is a prevalent complication in chronic kidney disease (CKD), ranging from mild deficits in early stages to more severe conditions, such as mild cognitive impairment and dementia in advanced stages. CKD patients exhibit reduced performance in memory, attention, language, visuospatial abilities and executive functions.

RESULTS AND DISCUSSION: Contributing factors include uraemic toxins, structural brain changes, blood-brain barrier dysfunction, anaemia and comorbidities like diabetes mellitus. Malnutrition, affecting nearly half of CKD patients, exacerbates cognitive decline through inflammation, oxidative stress and protein-energy wasting. Nutritional deficiencies, particularly in protein, vitamin D, B vitamins, omega-3 fatty acids and antioxidants, are linked to impaired cognition. Emerging evidence highlights the role of the gut-brain axis, with gut-derived uraemic toxins and microbiome alterations contributing to cognitive dysfunction. Processed foods and microplastics further compound risks by promoting inflammation and neurotoxicity. Dialysis and kidney transplantation offer opportunities for cognitive recovery, though challenges remain, particularly in haemodialysis patients. Nutritional interventions, including tailored protein intake, micronutrient supplementation and dietary counselling, are critical for mitigating cognitive decline. Addressing CKD comorbidities, such as anaemia and diabetes through targeted nutritional and pharmacological strategies, improves outcomes. Integrating psychological and social support enhances quality of life, given the high prevalence of anxiety and depression in CKD patients.

CONCLUSIONS: Future research should focus on personalized nutrition, gut microbiota modulation and routine cognitive assessments to optimise care. A holistic approach combining medical, nutritional and psychosocial strategies is essential for improving cognitive and overall health in CKD patients.},
}

@article {pmid40219203,
year = {2025},
author = {Aizaz, M and Lubna, and Hashmi, SS and Khan, MA and Jan, R and Bilal, S and Kim, KM and Al-Harrasi, A and Asaf, S},
title = {Unraveling the Complexities of Flowering in Ornamental Plants: The Interplay of Genetics, Hormonal Networks, and Microbiome.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/plants14071131},
pmid = {40219203},
issn = {2223-7747},
abstract = {In ornamental plants, one of the most complex life processes, i.e., flowering, is regulated by interaction between the microbiota, hormones, and genes. Flowering plays an integral role in overall development and is quintessential for reproduction. Considering its importance, this review explores the complex mechanisms that determine the induction of flowering, highlighting the relationship between hormonal and genetic networks as well as the growing significance of the microbiome. Important genes involved in genetic control include FT, SOC1, and LFY. These genes react to environmental stimuli like photoperiod and vernalization. Auxins, cytokinin, and gibberellins are only a few hormone pathways important for floral growth and timing. The importance of plant-microbe interactions has been emphasized by current research, which shows that the microbiome affects flowering through processes like hormone production and availability of food. A comprehensive understanding of flowering induction is possible by integrating results from microbiota, hormones, and genetics studies, which may improve the breeding and culture of ornamental plants. For researchers to understand the complexity of flowering in ornamental plants and develop unique breeding strategies and improved floral qualities, it is critical to use interdisciplinary approaches, as this comprehensive investigation demonstrates.},
}

@article {pmid40219101,
year = {2025},
author = {Fouad, N and El-Zayat, EM and Amr, D and El-Khishin, DA and Abd-Elhalim, HM and Hafez, A and Radwan, KH and Hamwieh, A and Tadesse, W},
title = {Characterizing Wheat Rhizosphere Bacterial Microbiome Dynamics Under Salinity Stress: Insights from 16S rRNA Metagenomics for Enhancing Stress Tolerance.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/plants14071033},
pmid = {40219101},
issn = {2223-7747},
abstract = {Salinity is one of the most important abiotic stress factors affecting wheat production. Salt in the soil is a major environmental stressor that can affect the bacterial community in the rhizosphere of wheat. The bacteria in the plant's rhizosphere promote growth and stress tolerance, which vary by variety and location. Nevertheless, the soil harbors some of the most diverse microbial communities, while the rhizosphere selectively recruits according to the needs of plants in a complex harmonic regulation. The microbial composition and diversity under normal and saline conditions were assessed by comparing the rhizosphere of wheat with soil using 16S rRNA gene amplicon sequencing, highlighting the number of operational taxonomic units (OTUs). Taxonomic analyzes showed that the bacterial community was predominantly and characteristically composed of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Fibrobacteres, representing the usual microbial profile for the rhizosphere of wheat. Idiomarinaceae, Rheinheimera, Halomonas, and Pseudomonas (a strain of Proteobacteria), together with Gracilibacillus (a strain of Firmicutes Bacilli), were recognized as microbial signatures for the rhizosphere microbiome under saline conditions. This was observed even with unchanged soil type and genotype. These patterns occurred despite the same soil type and genotype, with salinity being the only variable. The collective action of these bacterial phyla in the rhizosphere not only improves nutrient availability but also induces systemic resistance in the plants. This synergistic effect improves plant resistance to salt stress and supports the development of salt-tolerant wheat varieties. These microbial signatures could improve our understanding of plant-microbe interactions and support the development of microbiome-based solutions for salt stress.},
}

@article {pmid40219037,
year = {2025},
author = {Theodoridis, X and Papaemmanouil, A and Papageorgiou, N and Savopoulos, C and Chourdakis, M and Triantafyllou, A},
title = {The Association Between Lifestyle Interventions and Trimethylamine N-Oxide: A Systematic-Narrative Hybrid Literature Review.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071280},
pmid = {40219037},
issn = {2072-6643},
mesh = {Humans ; *Methylamines/blood ; *Exercise/physiology ; *Life Style ; Cardiovascular Diseases/prevention & control ; *Diet, Healthy ; Dietary Supplements ; Biomarkers/blood ; Diet ; Diet, Mediterranean ; },
abstract = {BACKGROUND: Trimethylamine N-oxide (TMAO) is a gut- and food-derived molecule. Elevated TMAO concentrations have been associated with an increased risk of cardiovascular disease (CVD) and all-cause mortality, highlighting its significance as a potential biomarker for adverse health outcomes. Given these associations, it is hypothesized that lifestyle interventions, such as healthy dietary patterns and exercise, could reduce TMAO concentrations. The aim of this systematic-narrative hybrid literature review was to evaluate the relationship between various lifestyle interventions and TMAO.

METHODS: MEDLINE (via PubMed[®]), Scopus[®], and grey literature were searched until July 2024 for eligible clinical trials. Case reports, case series, case studies and observational studies were excluded, as well as studies that investigated food products, nutraceuticals, dietary supplements or have been conducted in the pediatric population.

RESULTS: In total, 27 studies were included in this review. While some dietary interventions, such as plant-based, high-dairy, very low-calorie ketogenic diet or the Mediterranean diet, were associated with lower TMAO concentrations, others-including high-protein and high-fat diets-were linked to an increase in TMAO concentrations. Studies that incorporated a combination of nutrition and exercise-based intervention presented neutral results.

CONCLUSIONS: The relationship between dietary interventions and TMAO concentration remains controversial. While certain interventions show promise in reducing TMAO levels, others yield mixed or contradictory outcomes. Further research, including well-structured RCTs, is needed to investigate the aforementioned associations.},
}

Humans
*Methylamines/blood
*Exercise/physiology
*Life Style
Cardiovascular Diseases/prevention & control
*Diet, Healthy
Dietary Supplements
Biomarkers/blood
Diet
Diet, Mediterranean

@article {pmid40219016,
year = {2025},
author = {Rouskas, K and Guela, M and Pantoura, M and Pagkalos, I and Hassapidou, M and Lalama, E and Pfeiffer, AFH and Decorte, E and Cornelissen, V and Wilson-Barnes, S and Hart, K and Mantovani, E and Dias, SB and Hadjileontiadis, L and Gymnopoulos, LP and Dimitropoulos, K and Argiriou, A},
title = {The Influence of an AI-Driven Personalized Nutrition Program on the Human Gut Microbiome and Its Health Implications.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071260},
pmid = {40219016},
issn = {2072-6643},
support = {817732//European Union/ ; 2024NA119000001//Sus.Agri.Food National program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Adult ; Female ; Male ; Feces/microbiology ; *Artificial Intelligence ; *Precision Medicine/methods ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics ; Diet ; },
abstract = {Background/Objectives: Personalized nutrition programs enhanced with artificial intelligence (AI)-based tools hold promising potential for the development of healthy and sustainable diets and for disease prevention. This study aimed to explore the impact of an AI-based personalized nutrition program on the gut microbiome of healthy individuals. Methods: An intervention using an AI-based mobile application for personalized nutrition was applied for six weeks. Fecal and blood samples from 29 healthy participants (females 52%, mean age 35 years) were collected at baseline and at six weeks. Gut microbiome through 16s ribosomal RNA (rRNA) amplicon sequencing, anthropometric and biochemical data were analyzed at both timepoints. Dietary assessment was performed using food frequency questionnaires. Results: A significant increase in richness (Chao1, 220.4 ± 58.5 vs. 241.5 ± 60.2, p = 0.024) and diversity (Faith's phylogenetic diversity, 15.5 ± 3.3 vs. 17.3 ± 2.8, p = 0.0001) was found from pre- to post-intervention. Following the intervention, the relative abundance of genera associated with the reduction in cholesterol and heart disease risk (e.g., Eubacterium coprostanoligenes group and Oscillobacter) was significantly increased, while the abundance of inflammation-associated genera (e.g., Eubacterium ruminantium group and Gastranaerophilales) was decreased. Alterations in the abundance of several butyrate-producing genera were also found (e.g., increase in Faecalibacterium, decrease in Bifidobacterium). Further, a decrease in carbohydrate (272.2 ± 97.7 vs. 222.9 ± 80.5, p = 0.003) and protein (113.6 ± 38.8 vs. 98.6 ± 32.4, p = 0.011) intake, as well as a reduction in waist circumference (78.4 ± 12.1 vs. 77.2 ± 11.2, p = 0.023), was also seen. Changes in the abundance of Oscillospiraceae_UCG_002 and Lachnospiraceae_UCG_004 were positively associated with changes in olive oil intake (Rho = 0.57, p = 0.001) and levels of triglycerides (Rho = 0.56, p = 0.001). Conclusions: This study highlights the potential for an AI-based personalized nutrition program to influence the gut microbiome. More research is now needed to establish the use of gut microbiome-informed strategies for personalized nutrition.},
}

Humans
*Gastrointestinal Microbiome/physiology
Adult
Female
Male
Feces/microbiology
*Artificial Intelligence
*Precision Medicine/methods
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics
Diet

@article {pmid40219015,
year = {2025},
author = {Lee, NK and Lee, Y and Shin, DS and Choi, YM and Lee, J and Park, E and Paik, HD},
title = {Effect of Lactiplantibacillus plantarum DSW3805 Isolated from Kimchi for Gut Health Attenuating Colonic Inflammation in a Dextran Sulfate Sodium-Induced Mouse Model.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071259},
pmid = {40219015},
issn = {2072-6643},
mesh = {Animals ; Dextran Sulfate ; *Probiotics/pharmacology ; *Colitis/chemically induced/microbiology/therapy ; Mice ; Disease Models, Animal ; Gastrointestinal Microbiome ; *Fermented Foods/microbiology ; Colon/pathology/microbiology/metabolism ; *Lactobacillus plantarum/isolation & purification ; Male ; Fatty Acids, Volatile/metabolism ; Cytokines/metabolism ; Inflammation ; Lactobacillaceae ; Mice, Inbred C57BL ; },
abstract = {Background/Objectives:Lactiplantibacillus plantarum DSW3805 was isolated from Korean kimchi samples to examine its effect in a dextran sulfate sodium (DSS)-induced mouse model. Methods: To induce colitis, mice were treated with DSS for one week before sacrifice (n = 8 per group, total n = 40). Lacticaseibacillus rhamnosus GG (10[9] CFU/day) or probiotics (L. plantarum DSW3805; 10[8] or 10[9] CFU/day) were administered for two weeks. To assess colitis damage, we evaluated the disease activity index, colon tissue, inflammatory factors, the microbiome, short-chain fatty acids, and intestine-related factors. Results: DSS induced colonic tissue damage (colon length, mucus thickness, and colonic crypts), and L. plantarum DSW3805 alleviated the tissue damage. Induced inflammation was reduced by inhibiting TNF-α, IFN-γ, IL-1β, IL-6, IgA, IgG, LTB4, PGE2, and NF-κB protein expression. The ratio of Firmicutes to Bacteroidetes in the PC group (DSS-treated control) was lower than that in the NC (DSS-nontreated control); L. plantarum DSW3805 increased the ratio. Higher concentrations of acetic, propionic, and butyric acids were detected in probiotic groups. In addition, harmful factors, such as calprotectin and β-glucuronidase, were reduced in the probiotic groups. Conclusions:L. plantarum DSW3805 alleviates gut damage by colitis; therefore, it can be used as a functional food to improve gut health.},
}

Animals
Dextran Sulfate
*Probiotics/pharmacology
*Colitis/chemically induced/microbiology/therapy
Mice
Disease Models, Animal
Gastrointestinal Microbiome
*Fermented Foods/microbiology
Colon/pathology/microbiology/metabolism
*Lactobacillus plantarum/isolation & purification
Male
Fatty Acids, Volatile/metabolism
Cytokines/metabolism
Inflammation
Lactobacillaceae
Mice, Inbred C57BL

@article {pmid40219004,
year = {2025},
author = {Cedillo-Flores, R and Cuevas-Budhart, MA and Cavero-Redondo, I and Kappes, M and Ávila-Díaz, M and Paniagua, R},
title = {Impact of Gut Microbiome Modulation on Uremic Toxin Reduction in Chronic Kidney Disease: A Systematic Review and Network Meta-Analysis.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071247},
pmid = {40219004},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Renal Insufficiency, Chronic/microbiology/therapy ; *Uremic Toxins/metabolism/blood ; Synbiotics/administration & dosage ; Prebiotics/administration & dosage ; Probiotics/administration & dosage ; Network Meta-Analysis as Topic ; Dysbiosis ; Randomized Controlled Trials as Topic ; Male ; Female ; Cresols/blood ; },
abstract = {Background/Objectives: Chronic kidney disease is associated with increased intestinal barrier permeability, leading to heightened inflammation and oxidative stress. These changes contribute to complications such as cardiovascular disease, anemia, altered mineral metabolism, and CKD progression. Interventions using prebiotics, probiotics, and synbiotics may mitigate dysbiosis and improve intestinal barrier function, Under this premise, the objective of this network meta-analysis was to evaluate the effect of probiotics, prebiotics, and synbiotics in reducing uremic toxins produced by the gut microbiota in CKD patients. Methods: A systematic review and network meta-analysis of randomized clinical trials (RCTs) was performed in the following databases: Web of Science, Scopus, the Cochrane Register of Controlled Trials, and PubMed published between 2019 and 2023. The analysis focused on the use of prebiotics, probiotics, and synbiotics in CKD patients at stages 3 to 5, as per KDIGO guidelines, and their association with reductions in uremic toxins such as Indoxyl Sulfate, p-Cresyl Sulfate, urea, and creatinine. The risk of bias was assessed using the Cochrane risk of bias tool (RoB 2), with evaluations conducted independently by two reviewers, and a third consulted for disagreements. The study follows the PRISMA statement. Results: The studies included 331 patients, primarily male, across CKD stages 3a to 5. The interventions positively impacted the gut microbiota composition, leading to reductions in free and total p-Cresyl Sulfate (SUCRA: 72.6% and 66.2, respectively) and indoxyl sulfate (SUCRA: 88.5% and 83.1%). Conclusions: The findings suggest that modulating the gut microbiota through these interventions can effectively reduce specific uremic toxins. However, further trials are necessary to better understand microbiota modulation and its impact on intestinal bacterial composition (PROSPERO number: CRD42023438901).},
}

Humans
*Gastrointestinal Microbiome/physiology
*Renal Insufficiency, Chronic/microbiology/therapy
*Uremic Toxins/metabolism/blood
Synbiotics/administration & dosage
Prebiotics/administration & dosage
Probiotics/administration & dosage
Network Meta-Analysis as Topic
Dysbiosis
Randomized Controlled Trials as Topic
Male
Female
Cresols/blood

@article {pmid40218992,
year = {2025},
author = {Vanderpeet, CL and Dorey, ES and Neal, ES and Mullins, T and McIntyre, DH and Callaway, LK and Barrett, HL and Dekker Nitert, M and Cuffe, JSM},
title = {Dietary Fibre Modulates Gut Microbiota in Late Pregnancy Without Altering SCFA Levels, and Propionate Treatement Has No Effect on Placental Explant Function.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071234},
pmid = {40218992},
issn = {2072-6643},
support = {APP1028575//National Health and Medical Research Council/ ; },
mesh = {Humans ; Female ; *Dietary Fiber/administration & dosage/pharmacology ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; *Propionates/pharmacology ; *Fatty Acids, Volatile/blood/metabolism ; *Placenta/drug effects/physiology/metabolism ; Adult ; Feces/microbiology ; Butyrates/blood ; Bacteria ; },
abstract = {Background/Objectives: Dietary fibre promotes health, partly by mediating gut microbiota and short-chain fatty acid (SCFA) production. Pregnancy alters the relationship between dietary composition and the gut microbiota, and it is unclear if fibre intake during late pregnancy alters the abundance of SCFA bacteria and circulating SFCA concentrations. The aim of this study was to determine the impact of dietary fibre on faecal microbiome composition and circulating concentrations of SCFA acetate, butyrate, and propionate in late pregnancy. We also aimed to assess the impact of propionate treatment on placental function using cultured placental explants. Methods: 16S rRNA gene amplicon sequencing was performed on faecal DNA collected at 28 weeks of gestation from participants enrolled in the SPRING cohort study consuming a low or adequate fibre diet. Circualting SCFA were assessed. Placental explants were treated with sodium propionate. Results: Fibre intake did not impact microbial diversity or richness but did impact the abundance of specific bacterial genera. Pregnant participants with low-fibre diets had a greater abundance of Bacteroides and Sutterella, and dietary fibre intake (mg/day) negatively correlated with genera, including Sutterella, Bilophila, and Bacteroides. SCFA concentrations did not differ between groups but circulating concentrations of acetate, propionate, and butyrate did correlate with the abundance of key bacterial genera. Propionate treatment of placental explants did not alter mRNA expression of fatty acid receptors, antioxidants, or markers of apoptosis, nor did it impact pAMPK levels. Conclusions: This study demonstrates that the impact of dietary fibre on SCFA concentrations in pregnant women is modest, although this relationship may be difficult to discern given that other dietary factors differed between groups. Furthermore, this study demonstrates that propionate does not impact key pathways in placental tissue, suggesting that previous associations between this SCFA and placental dysfunction may be due to other maternal factors.},
}

Humans
Female
*Dietary Fiber/administration & dosage/pharmacology
Pregnancy
*Gastrointestinal Microbiome/drug effects
*Propionates/pharmacology
*Fatty Acids, Volatile/blood/metabolism
*Placenta/drug effects/physiology/metabolism
Adult
Feces/microbiology
Butyrates/blood
Bacteria

@article {pmid40218980,
year = {2025},
author = {Slöcker-Barrio, M and López-Herce Cid, J and Solana-García, MJ},
title = {The Interplay Between Nutrition and Microbiota and the Role of Probiotics and Symbiotics in Pediatric Infectious Diseases.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071222},
pmid = {40218980},
issn = {2072-6643},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; Child ; *Communicable Diseases/microbiology/therapy/immunology ; Prebiotics/administration & dosage ; *Gastrointestinal Microbiome ; Dietary Supplements ; *Nutritional Status ; *Child Nutritional Physiological Phenomena ; Immunocompromised Host ; },
abstract = {The interplay between nutrition and infectious diseases has been a central theme in health sciences for the last decades due to its great impact on the pediatric population, especially in immunocompromised patients and critically ill children. As conventional treatment and the development of antimicrobials for most infections standard treatment is either limited or not possible, alternative treatment options should be explored. Recent research shows that early enteral nutrition and nutritional supplements (such as probiotics and symbiotics) could have a pivotal role in promoting a healthy microbiome and subsequently preventing and improving outcomes for certain pediatric infectious diseases. However, understanding the specific mechanism of action and tailoring nutritional interventions remains a significant challenge. The optimal dose range for different probiotic strains and prebiotics and the most effective combination for each treatment indication needs further investigation and is yet to be defined. Additionally, in the era of personalized medicine, goal- and patient-directed treatment are key to optimizing and improving outcomes and minimizing potential complications and side effects, especially in complex and immunocompromised patients. The main objectives of this narrative review are 1. to explore the relationship and the complex interactions between microbiota and the human immune system; 2. to describe the influence of nutrition on infectious diseases; 3. to evaluate the impact of supplementation with probiotics and symbiotics in the prevention and treatment of the most relevant infections in children; and 4. to identify knowledge gaps and potential research priorities regarding the use of these supplements in pediatric patients.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
Child
*Communicable Diseases/microbiology/therapy/immunology
Prebiotics/administration & dosage
*Gastrointestinal Microbiome
Dietary Supplements
*Nutritional Status
*Child Nutritional Physiological Phenomena
Immunocompromised Host

@article {pmid40218978,
year = {2025},
author = {Zwierz, M and Suprunowicz, M and Mrozek, K and Pietruszkiewicz, J and Oracz, AJ and Konarzewska, B and Waszkiewicz, N},
title = {Vitamin B12 and Autism Spectrum Disorder: A Review of Current Evidence.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071220},
pmid = {40218978},
issn = {2072-6643},
support = {B.SUB.25.437//Medical University of Białystok/ ; },
mesh = {Humans ; *Vitamin B 12/blood/administration & dosage ; *Autism Spectrum Disorder/etiology/blood ; Pregnancy ; Female ; *Vitamin B 12 Deficiency/complications/blood ; Gastrointestinal Microbiome ; Maternal Nutritional Physiological Phenomena ; Dysbiosis ; Brain ; Infant ; },
abstract = {Vitamin B12 (cobalamin) plays a crucial role in neurodevelopment, particularly during pregnancy and early childhood. It is essential for DNA synthesis, red blood cell formation, and nervous system function. Maternal B12 levels are particularly important, as they influence fetal brain development. Inadequate maternal intake during pregnancy may lead to altered neurodevelopmental trajectories and increase the risk of ASD. Postnatally, insufficient dietary cobalamin in infants and young children could further contribute to cognitive and behavioral impairments. One potential mechanism linking low B12 levels to ASD involves its role in the gut microbiota balance. Dysbiosis, commonly observed in individuals with ASD, is associated with increased gut permeability, low-grade inflammation, and disruptions in the gut-brain axis, all of which may contribute to ASD symptoms. Additionally, B12 is essential for neurotransmitter metabolism, particularly in the synthesis of serotonin and dopamine, which regulate mood, cognition, and behavior. Cobalamin also plays a key role in neuronal myelination, which ensures efficient signal transmission in the nervous system. Disruptions in these processes could underlie some of the cognitive and behavioral features associated with ASD. Despite growing evidence, the link between B12 and ASD remains inconclusive due to inconsistent findings across studies. Research suggests that B12 levels may serve as a potential biomarker for disease progression and treatment response. However, many studies rely on single-time-point measurements, failing to account for individual variability, genetic predispositions, dietary intake, and environmental factors, all of which can influence B12 levels and ASD risk. Further longitudinal studies are needed to clarify this relationship.},
}

Humans
*Vitamin B 12/blood/administration & dosage
*Autism Spectrum Disorder/etiology/blood
Pregnancy
Female
*Vitamin B 12 Deficiency/complications/blood
Gastrointestinal Microbiome
Maternal Nutritional Physiological Phenomena
Dysbiosis
Brain
Infant

@article {pmid40218973,
year = {2025},
author = {Lutz, M and Arancibia, M and Moran-Kneer, J and Manterola, M},
title = {Ultraprocessed Foods and Neuropsychiatric Outcomes: Putative Mechanisms.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071215},
pmid = {40218973},
issn = {2072-6643},
support = {CIDI 003/2025//C-ESTRES (Center for Translational Studies in Stress and Mental Health), Universidad de Valpa-raíso, Chile/ ; },
mesh = {Humans ; Gastrointestinal Microbiome ; *Food Handling ; *Mental Disorders/etiology ; *Fast Foods/adverse effects ; Oxidative Stress ; *Diet/adverse effects ; },
abstract = {A body of evidence indicates an association between ultraprocessed foods (UPFs) and health outcomes. Most of it has been obtained through preclinical studies, although a number of observational studies substantiate how a high intake of these products increases the risk of neuropsychiatric disorders, and an increasing amount of dietary intervention studies confirm these findings. The aim of this narrative review is to describe some of the putative mechanisms involved in the deleterious effects of a high intake of UPFs on neuropsychiatric outcomes. A myriad of unhealthy actions may be associated with the consumption of UPFs, and some mechanisms are being discussed. They include UPFs' high caloric density; their high sugar, sodium, and additives content and low amounts of fiber; and a high palatability that induces overconsumption, acting as obesogens. Moreover, thermal treatment of these foods generates oxidative products such as glycotoxins, lipotoxins, and acrolein, all of which affect the brain. The chemical products act, directly or indirectly, on the gut microbiome and affect the gut-brain axis, causing neuroinflammation, oxidative stress, and neurodegeneration. UPFs also exert various epigenetic effects that affect mental health and might explain the intergenerational inheritance of neuropsychiatric disorders. A diet containing a high proportion of these foods has a low nutritional density, including bioactive protective agents such as antioxidant and anti-inflammatory compounds that promote eubiosis. The evidence shows that UPFs intake affects neuropsychiatric outcomes such as neurodegeneration, cognitive decline, dementia, and mood disorders and reinforces the need to promote a healthy dietary pattern throughout all life stages, thus interfering with the current commercial determinants of health.},
}

Humans
Gastrointestinal Microbiome
*Food Handling
*Mental Disorders/etiology
*Fast Foods/adverse effects
Oxidative Stress
*Diet/adverse effects

@article {pmid40218958,
year = {2025},
author = {Porter Starr, KN and Connelly, MA and Wallis, J and North, R and Zhang, Q and Song, K and González-Delgado, JM and Brochu, HN and Icenhour, CR and Iyer, LK and Miller, MG and Huffman, KM and Kraus, WE and Bales, CW},
title = {Effects of Blueberry Consumption on Fecal Microbiome Composition and Circulating Metabolites, Lipids, and Lipoproteins in a Randomized Controlled Trial of Older Adults with Overweight or Obesity: The BEACTIVE Trial.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071200},
pmid = {40218958},
issn = {2072-6643},
support = {N/A//U.S. Highbush Blueberry Council grant/ ; },
mesh = {Humans ; *Blueberry Plants ; *Feces/microbiology ; Male ; Female ; Aged ; *Obesity/microbiology/blood/diet therapy ; Middle Aged ; *Overweight/microbiology/blood/diet therapy ; *Gastrointestinal Microbiome ; *Lipids/blood ; *Lipoproteins/blood ; Biomarkers/blood ; Diet ; },
abstract = {Background/Objectives: Generous consumption of phytonutrient-rich foods, including blueberries, provides benefits to multiple physiologic and metabolic systems. This study explored the potential that regular, generous blueberry intake could favorably modulate fecal microbiome composition in sedentary older (>60 years) men and women with overweight or obesity (BMI ≥ 25 to 32 kg/m[2]). Methods: Participants (n = 55) were randomized to daily consumption of either lyophilized blueberry powder (equivalent to 1.5 cups of blueberries) or an indistinguishable placebo powder; both groups participated in weekly supervised exercise classes. Fecal samples were collected at 0 and 12 weeks and frozen. Following this, 16S rRNA gene sequencing was used to profile each participant's fecal microbiome. Blood biomarkers of cardiometabolic health were measured via nuclear magnetic resonance spectroscopy (NMR) pre- and post-treatment. Results: Comparing the baseline and endpoint results for the blueberry (n = 15) and placebo (n = 19) groups, there were no significant overall compositional differences or differences in the level of diversity in the fecal microbiome. However, in subjects whose diet included blueberry powder, there was a significant enrichment (p = 0.049) in the relative abundance of Coriobacteriales incertae sedis, a taxonomic group of bacteria that facilitates the metabolism of dietary polyphenols. The placebo group exhibited significant reductions in total cholesterol, LDL-C, non-HDL-C, total LDL-P, large LDL-P, and ApoB, while the blueberry group exhibited significant reductions in total HDL-P and ApoA-I after 12 weeks compared to baseline. Conclusions: Generous blueberry consumption may upregulate the ability of the older human gut to utilize dietary polyphenols by altering the fecal microbiome. Longer, larger-scale studies with blueberries or blueberry powder are needed to observe improvements in cardiometabolic risk factors in older adults with overweight or obesity.},
}

Humans
*Blueberry Plants
*Feces/microbiology
Male
Female
Aged
*Obesity/microbiology/blood/diet therapy
Middle Aged
*Overweight/microbiology/blood/diet therapy
*Gastrointestinal Microbiome
*Lipids/blood
*Lipoproteins/blood
Biomarkers/blood
Diet

@article {pmid40218949,
year = {2025},
author = {Lee, SB and Yoo, B and Baeg, C and Yun, J and Ryu, DW and Kim, G and Kim, S and Shin, H and Lee, JH},
title = {A 12-Week, Randomized, Double-Blind, Placebo-Controlled Study to Evaluate the Efficacy and Safety of Lactobacillus plantarum LMT1-48 on Body Fat Loss.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071191},
pmid = {40218949},
issn = {2072-6643},
mesh = {Humans ; *Lactobacillus plantarum ; *Probiotics/administration & dosage/adverse effects/therapeutic use ; Double-Blind Method ; Male ; Female ; *Obesity/therapy/microbiology ; Middle Aged ; Adult ; Gastrointestinal Microbiome ; *Adipose Tissue ; Feces/microbiology ; Body Mass Index ; Treatment Outcome ; Body Composition ; Absorptiometry, Photon ; },
abstract = {OBJECTIVES: This study aims to evaluate the efficacy and safety of probiotics for body fat reduction in obese individuals.

METHODS: A total of 106 participants with a body mass index between 25 and 30 kg/m[2] were randomly assigned to either the experimental group treating with Lactobacillus plantarum LMT1-48 or the placebo group in the placebo-controlled clinical trial. Body composition was assessed by dual-energy X-ray absorptiometry and computed tomography. Fecal samples between the groups were contrasted via DNA sequencing for evaluation of the microbiota and its diversity.

RESULTS: After 12 weeks of follow-up period, the body fat mass decreased significantly, from 30.0 ± 4.4 to 28.3 ± 4.1 kg in the experimental group (p = 0.009). The percentage of body fat in the two groups showed a similar trend (p = 0.004).

CONCLUSIONS: LMT1-48 also positively influenced the microbial taxa linked to obesity analyzed by gut microbiome sequencing. LMT1-48 is a safe and collaborative agent to reduce obesity.},
}

Humans
*Lactobacillus plantarum
*Probiotics/administration & dosage/adverse effects/therapeutic use
Double-Blind Method
Male
Female
*Obesity/therapy/microbiology
Middle Aged
Adult
Gastrointestinal Microbiome
*Adipose Tissue
Feces/microbiology
Body Mass Index
Treatment Outcome
Body Composition
Absorptiometry, Photon

@article {pmid40218922,
year = {2025},
author = {Chatsirisakul, O and Leenabanchong, N and Siripaopradit, Y and Chang, CW and Buhngamongkol, P and Pongpirul, K},
title = {Strain-Specific Therapeutic Potential of Lactiplantibacillus plantarum: A Systematic Scoping Review.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071165},
pmid = {40218922},
issn = {2072-6643},
support = {FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; N/A//Second Century Fund (C2F)/ ; },
mesh = {Humans ; *Probiotics/therapeutic use ; *Lactobacillus plantarum/classification/physiology ; Female ; Oral Health ; Dermatitis, Atopic/therapy ; Dental Caries/therapy ; Species Specificity ; },
abstract = {Objectives: This systematically scoping review aims to evaluate the therapeutic potential and clinical benefits of specific Lactiplantibacillus plantarum (L. plantarum) strains in human health, identifying their strain-specific effects across various medical conditions. Methods: Following the PRISMA for Scoping Reviews (PRISMA-ScR) guidelines and employing the PICO framework, a comprehensive literature search was conducted in the PubMed and Embase databases to identify relevant studies published up to December 2023. Inclusion criteria were rigorously applied to ensure the selection of high-quality studies focusing on the clinical application of distinct L. plantarum stains. Results: This review analyzed several unique strains of L. plantarum across 69 studies, identifying several therapeutic benefits. L. plantarum 299v effectively improved gastrointestinal symptoms, enhanced oral health, and reduced systemic inflammation. L. plantarum IS-10506 exhibited notable immunomodulatory effects, especially in managing atopic dermatitis. L. plantarum LB931 showed promise in decreasing pathogenic colonization, supporting women's vaginal health. Additionally, L. plantarum CCFM8724 demonstrated potential in reducing early childhood caries, highlighting its promise in pediatric oral care. Conclusions: The therapeutic potential of L. plantarum is extensive, with certain strains exhibiting promising clinical benefits for specific health concerns. The findings of this review advocate for the integration of L. plantarum strains into clinical practice, emphasizing the need for further research to elucidate their mechanisms of action, optimal dosages, and long-term safety profiles.},
}

Humans
*Probiotics/therapeutic use
*Lactobacillus plantarum/classification/physiology
Female
Oral Health
Dermatitis, Atopic/therapy
Dental Caries/therapy
Species Specificity

@article {pmid40218905,
year = {2025},
author = {Minaya, DM and Hoss, A and Bhagat, A and Guo, TL and Czaja, K},
title = {Sex-Specific Effect of a High-Energy Diet on Body Composition, Gut Microbiota, and Inflammatory Markers in Rats.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071147},
pmid = {40218905},
issn = {2072-6643},
support = {1R01DC013904/GF/NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Rats, Sprague-Dawley ; *Body Composition ; Rats ; *Obesity/etiology/microbiology ; Feces/chemistry/microbiology ; Biomarkers/blood ; *Inflammation ; Sex Factors ; Weight Gain ; Cytokines/blood ; *Energy Intake ; *Diet ; },
abstract = {Background/Objectives: A high-energy-density (HED) diet promotes body weight gain, fat accumulation, and gut dysbiosis, contributing to obesity. The aim of this study was to characterize the initial response to HED diet consumption, as well as identify any sex differences in body composition, systemic inflammation, gut microbiome, and fecal fat excretion in rats. Methods: Male and female Sprague-Dawley rats were fed a low-energy-density (LED) diet for 10 days and were then switched to an HED diet for four weeks. Food intake, body weight, and body composition were measured routinely. Serum samples were collected to measure inflammatory cytokines/chemokines. Fecal samples were collected for microbiome analysis and lipid content. Results: After the HED diet, all rats gained body weight and fat mass, with males exhibiting increased susceptibility to weight gain. Males displayed either a diet-induced obesity phenotype (DIO-P) or a diet-resistant (DR) phenotype, as characterized by their differential body weight gain. Males showed elevated TGF-β levels, while females exhibited increases in Interferon gamma-inducible protein 10 (IP-10), regulated on activation, normal T cell expressed and secreted (RANTES) protein, and basic fibroblast growth factor (FGFb). Changes in gut microbiota composition revealed a reduction in beneficial species, like Bacteroides uniformis and Parabacteroides distasonis, and an increase in species such as Akkermansia muciniphila. Sex differences in fat metabolism were shown in the greater fecal fat excretion observed in males. Conclusions: Our study demonstrates that short-term consumption of a high-energy diet elicits notable sex-specific differences in body weight, body composition, inflammatory markers, gut microbiota, and fat excretion in Sprague-Dawley rats. While we recognize that this study has a small sample size and a short-term intervention, our findings highlight the critical role of sex as a biological variable in diet-induced obesity research.},
}

Animals
*Gastrointestinal Microbiome/physiology
Male
Female
Rats, Sprague-Dawley
*Body Composition
Rats
*Obesity/etiology/microbiology
Feces/chemistry/microbiology
Biomarkers/blood
*Inflammation
Sex Factors
Weight Gain
Cytokines/blood
*Energy Intake
*Diet

@article {pmid40218904,
year = {2025},
author = {Jayasinghe, T and Jenkins, J and Medara, N and Choowong, P and Dharmarathne, G and Kong, F and Cho, H and Kim, SH and Zhang, Y and Franco-Duarte, R and Eberhard, J and Spahr, A},
title = {Dietary Fibre Modulates Body Composition, Blood Glucose, Inflammation, Microbiome, and Metabolome in a Murine Model of Periodontitis.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071146},
pmid = {40218904},
issn = {2072-6643},
support = {Philanthropic funding received for the Chair of Oral Lifespan, School of Dentistry, The University of Sydney.//Philanthropic funding received for the Chair of Oral Lifespan, School of Dentistry, The University of Sydney./ ; },
mesh = {Animals ; *Dietary Fiber/administration & dosage/pharmacology ; Male ; *Periodontitis/microbiology/metabolism/diet therapy/blood ; *Metabolome/drug effects ; Mice, Inbred C57BL ; *Blood Glucose/metabolism ; Mice ; *Body Composition/drug effects ; Disease Models, Animal ; *Inflammation ; *Microbiota ; Gastrointestinal Microbiome ; Feces/microbiology ; },
abstract = {Background: Dietary fibre plays a crucial role in metabolic regulation, inflammation, and microbiome composition. However, its impact on systemic and oral health, particularly in periodontitis, remains unclear. This study investigated the effects of high- and low-fibre diets on body composition, glycaemic control, inflammation, microbiome, and metabolome in a murine model of experimental periodontitis. Methods: Thirty-six male C57BL/6 mice were randomised to a high-fibre (40% fibre) or low-fibre (5% fibre) diet for eight weeks. Body weight, fat mass, lean mass, fasting blood glucose, serum inflammatory markers, alveolar bone loss, and root length were assessed. Oral and faecal microbiome composition was analysed using 16S rRNA sequencing. Metabolomic and short-chain fatty acid (SCFA) profiling was conducted using liquid chromatography-mass spectrometry (LC-MS). Results: Mice on the high-fibre diet exhibited significantly lower body weight (p < 0.0001), fat mass (p = 0.0007), and lean mass (p < 0.0001) compared to the low-fibre group. Fasting blood glucose levels were significantly lower in the high-fibre group (p = 0.0013). TNF-α and IFN-γ levels were significantly elevated in the low-fibre group (p < 0.0001), suggesting a heightened pro-inflammatory state. While alveolar bone loss and root length did not differ significantly, microbiome analysis revealed distinct bacterial compositions (PERMANOVA, p < 0.05), with fibre-fermenting taxa enriched in high-fibre-fed mice. Metabolomic analysis identified 19 significantly altered metabolites, indicating dietary adaptations. Conclusions: A high-fibre diet improves glycaemic control, reduces systemic inflammation, and alters microbial and metabolic profiles in experimental periodontitis. These findings highlight dietary fibre's role in modulating metabolic and inflammatory pathways relevant to periodontal and systemic diseases.},
}

Animals
*Dietary Fiber/administration & dosage/pharmacology
Male
*Periodontitis/microbiology/metabolism/diet therapy/blood
*Metabolome/drug effects
Mice, Inbred C57BL
*Blood Glucose/metabolism
Mice
*Body Composition/drug effects
Disease Models, Animal
*Inflammation
*Microbiota
Gastrointestinal Microbiome
Feces/microbiology

@article {pmid40218900,
year = {2025},
author = {Al-Refai, W and Keenan, S and Camera, DM and Cooke, MB},
title = {The Influence of Vegan, Vegetarian, and Omnivorous Diets on Protein Metabolism: A Role for the Gut-Muscle Axis?.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071142},
pmid = {40218900},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Muscle, Skeletal/metabolism ; *Diet, Vegan ; *Diet, Vegetarian ; *Diet ; *Dietary Proteins/metabolism ; Vegans ; },
abstract = {There has been a growing interest globally in vegan and vegetarian diets over the last decade for a combination of health, ethical, environmental, spiritual, and social reasons. In line with this popularity, research examining the role of plant-based food sources, including vegan and vegetarian diets, in supporting skeletal muscle remodeling and anabolism in humans has also received considerable attention. The emergence of the microbiota-gut-muscle axis, a bidirectional pathway where the gut microbiota impacts skeletal muscle and vice versa, has been suggested as a potential mediator of food and nutrition's influence on the mechanistic processes that regulate muscle mass and function. Considering inherent nutritional differences between vegan, vegetarian, and omnivorous diets related to the fiber and macronutrient content, presence of anti-nutritional factors, and diverse food and supplemental sources for obtaining protein, it stands to reason that the regulation of the microbiota-gut-muscle axis via diet-induced changes in gut microbiota composition and function may be dissimilar. However, whether this translates into differential effects on the skeletal muscle is unclear. This review article aims to provide a contemporary perspective for how variations in gut microbiota linked to vegan, vegetarian, and omnivorous diets may be a potential mechanism for influencing protein metabolism in skeletal muscle mass via a purported microbiota-gut-muscle axis.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Muscle, Skeletal/metabolism
*Diet, Vegan
*Diet, Vegetarian
*Diet
*Dietary Proteins/metabolism
Vegans

@article {pmid40218866,
year = {2025},
author = {Altendorfer, B and Benedetti, A and Mrowetz, H and Bernegger, S and Bretl, A and Preishuber-Pflügl, J and Bessa de Sousa, DM and Ladek, AM and Koller, A and Le Faouder, P and Bertrand-Michel, J and Trost, A and Aigner, L},
title = {Omega-3 EPA Supplementation Shapes the Gut Microbiota Composition and Reduces Major Histocompatibility Complex Class II in Aged Wild-Type and APP/PS1 Alzheimer's Mice: A Pilot Experimental Study.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071108},
pmid = {40218866},
issn = {2072-6643},
support = {2023-PRE-008-Altendorfer//PMU-Research and Innovation Fund/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Alzheimer Disease/microbiology ; *Eicosapentaenoic Acid/pharmacology/administration & dosage ; Pilot Projects ; Mice ; Mice, Transgenic ; *Dietary Supplements ; Female ; Hippocampus/metabolism ; Amyloid beta-Protein Precursor/genetics ; Disease Models, Animal ; *Histocompatibility Antigens Class II/metabolism ; *Genes, MHC Class II/drug effects ; Fatty Acids, Omega-3 ; },
abstract = {Background/Objectives: Neuroinflammation, a hallmark of Alzheimer's disease (AD), is characterized by elevated levels of inflammatory signaling molecules, including cytokines and eicosanoids, as well as increased microglial reactivity, and is augmented by gut microbiota dysbiosis via the gut-brain axis. We conducted a pilot experiment to elucidate the anti-inflammatory effects of dietary omega-3 polyunsaturated fatty acid (ω-3 PUFA) eicosapentaenoic acid (EPA) on the gut microbiota and neuroinflammation. Methods: Female APP/PS1 mice (TG) and non-transgenic littermates (WT), 13-14 months old, were fed a diet supplemented with 0.3% EPA or control chow for 3 weeks. The gut microbiota composition, hippocampal and plasma eicosanoids levels, platelet activation, and microglial phagocytosis, as well as the brain and retinal genes and protein expression, were analyzed. Results: EPA supplementation decreased the percentage of Bacteroidetes and increased bacteria of the phylum Firmicutes in APP/PS1 and WT mice. Inflammatory lipid mediators were elevated in the hippocampus of the TG mice, accompanied by a reduction in the endocannabinoid docosahexaenoyl ethanolamide (DHEA). Dietary EPA did not affect hippocampal lipid mediators, but reduced the levels of arachidonic-derived 5-HETE and N-arachidonoylethanolamine (AEA) in WT plasma. Moreover, EPA supplementation decreased major histocompatibility complex class II (MHCII) gene expression in the retina in both genotypes, and MHCII+ cells in the hippocampus of TG mice. Conclusions: This pilot study showed that short-term EPA supplementation shaped the gut microbiota by increasing butyrate-producing bacteria of the Firmicutes phylum and decreasing Gram-negative LPS-producing bacteria of the Bacteroidetes phylum, and downregulated the inflammatory microglial marker MHCII in two distinct regions of the central nervous system (CNS). Further investigation is needed to determine whether EPA-mediated effects on the microbiome and microglial MHCII have beneficial long-term effects on AD pathology and cognition.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Alzheimer Disease/microbiology
*Eicosapentaenoic Acid/pharmacology/administration & dosage
Pilot Projects
Mice
Mice, Transgenic
*Dietary Supplements
Female
Hippocampus/metabolism
Amyloid beta-Protein Precursor/genetics
Disease Models, Animal
*Histocompatibility Antigens Class II/metabolism
*Genes, MHC Class II/drug effects
Fatty Acids, Omega-3

@article {pmid40218348,
year = {2025},
author = {Du, H and Li, K and Guo, W and Na, M and Zhang, J and Zhang, J and Na, R},
title = {Physiological and Microbial Community Dynamics in Does During Mid-Gestation to Lactation and Their Impact on the Growth, Immune Function, and Microbiome Transmission of Offspring Kids.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/ani15070954},
pmid = {40218348},
issn = {2076-2615},
support = {BR22-13-02//Basic scientific research business fee project for universities directly under the Inner Mongolia Autonomous Region/ ; NMGIRT2322//Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; },
abstract = {This study investigated changes in physiological processes and rumen microbial communities in does from mid-gestation to lactation and identified potential associations between these physiological changes and the rumen microbiome. Additionally, we studied the transmission mechanisms of microorganisms between the dam and offspring. Our study demonstrates significant changes in maternal physiological metabolism, immune status, and rumen microbiota from mid-pregnancy through lactation. We identified potential associations between these physiological changes and the rumen microbiome. Moreover, the findings highlight that alterations in maternal physiological metabolism and immune status significantly influence the growth and immune development of offspring kids. Additionally, we observed that the maternal microbiota serves as a key source of gastrointestinal microbial communities in young animals, with early colonization of maternally derived microbes in the offspring's gastrointestinal tract playing a role in shaping their immune system development. The results for primary outcomes are as follows: The serum levels of estrogen and progesterone in pregnant does were greater than those observed during lactation, while the concentration of growth hormone, triiodothyronine, and glucose exhibited an upward trend during lactation. During late gestation, the serum IL-10 concentration in does decreased, while the TNF-α concentration increased. Additionally, on day 140 of gestation, does showed a significant decrease in IgG, total protein, and globulin levels. From mid-gestation to lactation, the abundance of dominant phyla and genera, including Firmicutes, Bacteroidetes, Patescibacteria, Bacteroidales_RF16_group, Clostridia_UCG-014, RF39, and Eubacterium_ventriosum_group, in the rumen of does underwent significant changes. LEfSe analysis identified a series of marker microorganisms in the rumen of does at different physiological stages. A correlation was observed between these dominant bacteria and the serum physiological indicators of the does. Notably, rumen volatile fatty acids also exhibited a correlation with serum physiological indicators. In addition, serum physiological indicators of does were significantly correlated with the growth and immune indicators of their kids. Microbiological origin analysis revealed that the gastrointestinal microbiome of kids primarily originated from the rumen, birth canal, and milk of does. Further analysis identified a correlation between the kids' serum immunometric indicators and certain gastrointestinal microorganisms. In particular, the jejunum microbiota of 28-day-old lactating kids, including Alysiella, Neisseria, and Muribaculaceae, showed a significant positive correlation with serum IL-6 and IL-10 levels. Meanwhile, these genera were dominant in the saliva and milk of does, suggesting a direct microbial transfer from dam to offspring. These microbial communities may play a significant role in modulating the metabolism and immune responses of the offspring, thereby influencing their immune system development.},
}

@article {pmid40218330,
year = {2025},
author = {Li, W and Zeng, X and Wang, L and Yin, L and Wang, Q and Yang, H},
title = {Comparative Analysis of Gut Microbiota Diversity Across Different Digestive Tract Sites in Ningxiang Pigs.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/ani15070936},
pmid = {40218330},
issn = {2076-2615},
support = {2025JJ50141//The Natural Science Foundation Project of Hunan Province/ ; 2022RC3060//Science and Technology Innovation Program of Hunan Province/ ; 24A0044//Hunan Provincial Department of Education key project/ ; },
abstract = {BACKGROUND: Microbial communities in the gastrointestinal tract play a critical role in nutrient absorption, metabolism, and overall health of animals. Understanding the structure and function of tissue-specific microbial communities in Ningxiang pigs is essential for optimizing their growth, development, and nutritional efficiency. However, the diversity and functional roles of microbiota in different nutrient absorption tissues remain underexplored.

METHODS: We collected samples from four key nutrient absorption tissues (NFC: Cecal Content, NFI: Ileal Content, NFL: Colonic Content, NFG: Gastric Content, N = 6) of Ningxiang pigs and performed 16S rRNA gene sequencing to analyze microbial community composition. Bioinformatics analyses included alpha and beta diversity assessments, linear discriminant analysis effect size (LEfSe) for biomarker identification, and PICRUSt2-based functional prediction. Comparative metabolic abundance analysis was conducted to explore functional differences among tissues.

RESULTS: Alpha diversity indices (ACE, Chao1, Simpson, and Shannon) revealed significant differences in microbial richness and evenness among the four tissues. At the phylum level, Firmicutes dominated the microbiota, while Bacteroidota was prominent in NFC and NFL. LEfSe analysis identified tissue-specific dominant microbial groups, such as f_Prevotellaceae in NFC, o_Lactobacillales in NFG, f_Clostridiaceae in NFI, and f_Muribaculaceae in NFL. Functional profiling using PICRUSt2 showed that the microbiota was primarily involved in organismal systems (e.g., aging, digestion), cellular processes (e.g., cell growth, transport), environmental information processing (e.g., signaling), genetic information processing (e.g., transcription, translation), and metabolic regulation (e.g., amino acid and carbohydrate metabolism). Comparative metabolic abundance analysis highlighted distinct functional profiles across tissues, with significant differences observed in pathways related to the immune system, energy metabolism, lipid metabolism, transcriptional and translational regulation, and aging.

CONCLUSIONS: Our findings demonstrate that tissue-specific microbial communities in Ningxiang pigs exhibit distinct structural and functional characteristics, which are closely associated with nutrient absorption and metabolic regulation. These results provide valuable insights into the roles of microbiota in the growth and health of Ningxiang pigs and pave the way for future studies on microbe-mediated nutritional interventions.},
}

@article {pmid40218302,
year = {2025},
author = {Gao, Z and Tian, J and Zhang, Q and Sun, H and Jiang, Q and Zhang, T},
title = {Effects of Dietary Protein and Fat Levels on Growth Performance, Nutrient Digestibility, Serum Indexes, and Rectal Fecal Microbiota of Sika Deer (Cervus nippon) Fawns in Early Wintering Period.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/ani15070908},
pmid = {40218302},
issn = {2076-2615},
support = {CAASASTIP-2021-ISAPS//Agricultural Science and Technology Innovation Program of China/ ; },
abstract = {This study examined the effects of dietary crude protein (CP: 18%, 15%) and crude fat (EE: 8%, 4%) levels, and their interactions, on growth performance, nutrient digestibility, serum indices, and rectal fecal microbiota in sika deer fawns during early wintering. A two-month 2 × 2 factorial experiment was conducted using 32 healthy five-month-old male fawns randomly assigned to four groups: P18E8 (18% CP, 8% EE), P18E4 (18% CP, 4% EE), P15E8 (15% CP, 8% EE), and P15E4 (15% CP, 4% EE). The P18E4 group showed the highest total weight gain and average daily gain (p < 0.05), along with greater apparent digestibility of dry matter, crude protein, calcium, and fiber fractions (p < 0.05). Serum urea content was significantly lower in this group, indicating improved nitrogen utilization (p < 0.05). Dominant fecal microbiota at the phylum level across all groups included Firmicutes_A and Bacteroidota, with the P18E4 group showing a unique genus composition within Bacteroidota, known for enhancing fiber digestion. In summary, a diet with 18% CP and 4% EE optimized growth performance, nutrient digestibility, and gut microbiota composition, providing a strategy for improving the health and productivity of sika deer fawns during overwintering.},
}

@article {pmid40217936,
year = {2025},
author = {Boscia, G and Spataro, F and Desantis, V and Solimando, AG and Vacca, A and Ria, R and Savastano, A},
title = {Ocular Side Effects of Dupilumab: A Comprehensive Overview of the Literature.},
journal = {Journal of clinical medicine},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/jcm14072487},
pmid = {40217936},
issn = {2077-0383},
abstract = {Dupilumab, a monoclonal antibody targeting the interleukin (IL)-4 receptor alpha subunit and IL-13, has markedly advanced the treatment of atopic conditions such as dermatitis, asthma, and chronic rhinosinusitis. However, its expanding use has brought increased attention to a range of ocular adverse events-conjunctivitis, blepharitis, keratitis, corneal ulcers, and cicatricial conjunctivitis-that remain underrecognized and frequently underestimated in clinical practice. These manifestations often emerge in patients with atopic dermatitis and display varying severity, posing diagnostic and therapeutic challenges. Rather than isolated phenomena, these effects appear to stem from a complex interplay of goblet cell depletion, mucin deficiency, immune dysregulation, and microbiome alterations, including Demodex proliferation. Current management strategies remain largely empirical, lacking standardized protocols, and are often guided by anecdotal evidence. In this review, we critically appraise the existing literature, synthesize emerging pathogenic hypotheses, and highlight the unmet clinical need for evidence-based treatment algorithms. We advocate for a multidisciplinary approach and future research aimed at elucidating mechanisms, refining risk stratification, and minimizing ocular toxicity without compromising the therapeutic benefits of dupilumab. Furthermore, we intend to provide a more practical and straightforward resource for the reader based on the current literature on approaching the topic.},
}

@article {pmid40217873,
year = {2025},
author = {Cucu, CI and Giurcăneanu, C and Mihai, MM and Andronic, T and Ancuta, I and Popa, MI and Macovei, IS and Popa, LG},
title = {Unraveling the Skin Microbiome in Hidradenitis Suppurativa: Implications for Treatment and Disease Progression.},
journal = {Journal of clinical medicine},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/jcm14072424},
pmid = {40217873},
issn = {2077-0383},
support = {Publish, not Perish//Carol Davila University of Medicine and Pharmacy/ ; },
abstract = {Background: Hidradenitis suppurativa (HS) is a chronic, disabling, and disfiguring inflammatory disease with a complex, incompletely elucidated pathogenesis. The role of skin dysbiosis in the development and progression of HS has not yet been clarified. Methods: We performed an observational, prospective culture-based study that included 40 HS patients and analyzed the bacterial load and diversity in HS skin lesions, their correlation with disease severity, and several host and environmental factors. Additionally, we investigated the prevalence of antibiotic resistance and determined the resistance profile of bacterial strains isolated from chronic HS lesions. Results: An impressive number and diversity of bacterial strains were isolated from both superficial and deep HS lesions. 201 aerobic and anaerobic bacterial strains were isolated, polymicrobial growth being detected in the majority of samples. The most frequently isolated bacteria were Staphylococcus epidermidis, Staphylococcus aureus, Staphylococcus lugdunensis, Peptoniphilus spp., and Enterococcus faecalis in superficial lesions and Staphylococcus epidermidis, Staphylococcus aureus, and Corynebacterium tuberculostearicum in deep lesions. A significantly higher bacterial density and diversity was found in male patients, regardless of the affected area and in patients with severe HS. The proportion of bacterial strains resistant to antibiotics was lower in our study (8.95%) compared to the previously reported data. Conclusions: Our findings indicate dysbiosis as a key player in the initiation and maintenance of the inflammatory process in HS. Further large-scale, prospective studies are required to comprehensively characterize the microbiological landscape of HS and shed light on its contribution in the pathogenesis of the disease.},
}

@article {pmid40217801,
year = {2025},
author = {Bekbossynova, M and Saliev, T and Ivanova-Razumova, T and Andossova, S and Kali, A and Myrzakhmetova, G},
title = {Beyond Cholesterol: Emerging Risk Factors in Atherosclerosis.},
journal = {Journal of clinical medicine},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/jcm14072352},
pmid = {40217801},
issn = {2077-0383},
support = {BR21881970//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Atherosclerosis remains a leading cause of cardiovascular morbidity and mortality worldwide, traditionally linked to elevated cholesterol levels, particularly low-density lipoprotein cholesterol (LDL-C). However, despite aggressive lipid-lowering strategies, residual cardiovascular risk persists, underscoring the need to explore additional contributing factors. This review examines emerging risk factors beyond cholesterol, including chronic inflammation, gut microbiota composition, oxidative stress, and environmental exposures. Inflammation plays a pivotal role in atherogenesis, with markers such as C-reactive protein (CRP), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α) serving as indicators of disease activity. The gut microbiome, particularly metabolites like trimethylamine N-oxide (TMAO), has been implicated in vascular inflammation and plaque development, while beneficial short-chain fatty acids (SCFAs) demonstrate protective effects. Oxidative stress further exacerbates endothelial dysfunction and plaque instability, driven by reactive oxygen species (ROS) and lipid peroxidation. Additionally, environmental factors, including air pollution, heavy metal exposure, endocrine disruptors, and chronic psychological stress, have emerged as significant contributors to cardiovascular disease. Understanding these novel risk factors offers a broader perspective on atherosclerosis pathogenesis and provides new avenues for targeted prevention and therapeutic interventions.},
}

@article {pmid40217595,
year = {2025},
author = {Batir-Marin, D and Ștefan, CS and Boev, M and Gurău, G and Popa, GV and Matei, MN and Ursu, M and Nechita, A and Maftei, NM},
title = {A Multidisciplinary Approach of Type 1 Diabetes: The Intersection of Technology, Immunotherapy, and Personalized Medicine.},
journal = {Journal of clinical medicine},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/jcm14072144},
pmid = {40217595},
issn = {2077-0383},
abstract = {Background: Type 1 diabetes (T1D) is a chronic autoimmune disorder characterized by the destruction of pancreatic β-cells, leading to absolute insulin deficiency. Despite advancements in insulin therapy and glucose monitoring, achieving optimal glycemic control remains a challenge. Emerging technologies and novel therapeutic strategies are transforming the landscape of T1D management, offering new opportunities for improved outcomes. Methods: This review synthesizes recent advancements in T1D treatment, focusing on innovations in continuous glucose monitoring (CGM), automated insulin delivery systems, smart insulin formulations, telemedicine, and artificial intelligence (AI). Additionally, we explore biomedical approaches such as stem cell therapy, gene editing, immunotherapy, gut microbiota modulation, nanomedicine-based interventions, and trace element-based therapies. Results: Advances in digital health, including CGM integration with hybrid closed-loop insulin pumps and AI-driven predictive analytics, have significantly improved real-time glucose management. AI and telemedicine have enhanced personalized diabetes care and patient engagement. Furthermore, regenerative medicine strategies, including β-cell replacement, CRISPR-based gene editing, and immunomodulatory therapies, hold potential for disease modification. Probiotics and microbiome-targeted therapies have demonstrated promising effects in maintaining metabolic homeostasis, while nanomedicine-based trace elements provide additional strategies to regulate insulin sensitivity and oxidative stress. Conclusions: The future of T1D management is shifting toward precision medicine and integrated technological solutions. While these advancements present promising therapeutic avenues, challenges such as long-term efficacy, safety, accessibility, and clinical validation must be addressed. A multidisciplinary approach, combining biomedical research, artificial intelligence, and nanotechnology, will be essential to translate these innovations into clinical practice, ultimately improving the quality of life for individuals with T1D.},
}

@article {pmid40217575,
year = {2025},
author = {Ochi, T and Fujiki, R and Fukuyo, M and Rahmutulla, B and Nakagawa, T and Ota, M and Ikeda, JI and Matsui, Y and Yoshino, I and Suzuki, H and Kaneda, A},
title = {Association of Intratumoral Bacterial Abundance With Lung Cancer Prognosis in Chiba University Hospital Cohort.},
journal = {Cancer science},
volume = {},
number = {},
pages = {},
doi = {10.1111/cas.70080},
pmid = {40217575},
issn = {1349-7006},
support = {22zf0127008s0301//Japan Agency for Medical Research and Development/ ; //Chiba University/ ; //Chiba Foundation for Health Promotion and Disease Prevention/ ; },
abstract = {The relationship between cancer prognosis and intratumoral microbiome has recently gained attention. Regarding lung cancer, most studies have focused on bacteria outside tumors, such as sputum or lavage fluid, with few examining intratumoral bacteria and their impact on prognosis. In this study, we extracted DNA from lung tumor samples of 507 patients undergoing surgery at Chiba University Hospital and quantified intratumoral bacterial abundance using bacteria-specific PCR primers. Bacteria were detected in 77.1% of cases, and bacterial abundance was significantly higher in lung adenocarcinoma than in squamous cell carcinoma. Patients were categorized into three groups (High, Low, and Very-Low) based on bacterial abundance, and associations with clinicopathological factors were analyzed. In lung squamous cell carcinoma, higher bacterial abundance was significantly associated with worse recurrent-free survival and overall survival and was found to be a poor prognostic factor independent of pathological tumor stage. In conclusion, intratumoral bacterial abundance was found in the majority of lung cancer tissues, with variations based on pathology. This abundance may serve as a useful marker for stratifying lung squamous cell carcinoma with distinct prognoses.},
}

@article {pmid40217292,
year = {2025},
author = {Diop, K and Mbaye, B and Nili, S and Filin, A and Benlaifaoui, M and Malo, J and Renaud, AS and Belkaid, W and Hunter, S and Messaoudene, M and Lee, KA and Elkrief, A and Routy, B},
title = {Coupling culturomics and metagenomics sequencing to characterize the gut microbiome of patients with cancer treated with immune checkpoint inhibitors.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {21},
pmid = {40217292},
issn = {1757-4749},
abstract = {BACKGROUND: The gut microbiome represents a novel biomarker for melanoma and non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICI). Gut microbiome metagenomics profiling studies of patients treated with immunotherapy identified bacteria associated with ICI efficacy, while others have been linked to resistance. However, limitations of metagenomics sequencing, such as complex bioinformatic processing requirements, necessity of a threshold for positive detection, and the inability to detect live organisms, have hindered our ability to fully characterize the gut microbiome. Therefore, combining metagenomics with high-throughput culture-based techniques (culturomics) represents an ideal strategy to fully characterize microbiome composition to more robustly position the microbiome as a biomarker of response to ICI.

METHODS: We performed culturomics using fecal samples from 22 patients from two academic centres in Canada and the United Kingdom with NSCLC and cutaneous melanoma treated with ICI (cancer group), comparing their microbiome composition to that of 7 healthy volunteers (HV), along with matching shotgun metagenomics sequencing.

RESULTS: For culturomics results, 221 distinct species were isolated. Among these 221 distinct species, 182 were identified in the cancer group and 110 in the HV group. In the HV group, the mean species richness was higher compared to the cancer group (34 vs. 18, respectively, p = 0.002). Beta diversity revealed separate clusters between groups (p = 0.004). Bifidobacterium spp. and Bacteroides spp. were enriched in HV, while cancer patients showed an overrepresentation of Enterocloster species, as well as Veillonella parvula. Next, comparing cancer patients' clinical outcomes to ICI, we observed that among the 20 most abundant bacteria present in non-responder patients, 2 belonged to the genus Enterocloster, along with an enrichment of Hungatella hathewayi and Cutibacterium acnes. In contrast, responders to ICI exhibited a predominance of Bacteroides spp. In NSCLC patients, metagenomics analysis revealed that of the 154 bacteria species isolated through culturomics, 61/154 (39%) were also identified by metagenomics sequencing. Importantly, 94 individual species were uniquely detected by culturomics.

CONCLUSION: These findings highlight that culturomics and metagenomics can serve as complementary tools to characterize the microbiome in patients with cancer. This integrated approach uncovers specific microbiome signatures that differentiate HV from cancer patients, and identifies specific species associated with therapy response and resistance.},
}

@article {pmid40217129,
year = {2025},
author = {Quinn-Bohmann, N and Carr, AV and Diener, C and Gibbons, SM},
title = {Moving from genome-scale to community-scale metabolic models for the human gut microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40217129},
issn = {2058-5276},
support = {R01DK133468//U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)/ ; },
abstract = {Metabolic models of individual microorganisms or small microbial consortia have become standard research tools in the bioengineering and systems biology fields. However, extending metabolic modelling to diverse microbial communities, such as those in the human gut, remains a practical challenge from both modelling and experimental validation perspectives. In complex communities, metabolic models accounting for community dynamics, or those that consider multiple objectives, may provide optimal predictions over simpler steady-state models, but require a much higher computational cost. Here we describe some of the strengths and limitations of microbial community-scale metabolic models and argue for a robust validation framework for developing personalized, mechanistic and accurate predictions of microbial community metabolic behaviours across environmental contexts. Ultimately, quantitatively accurate microbial community-scale metabolic models could aid in the design and testing of personalized prebiotic, probiotic and dietary interventions that optimize for translationally relevant outcomes.},
}

@article {pmid40217111,
year = {2025},
author = {Zhu, Q and Zhang, G and Cao, M and Huang, H and He, D and Zang, Z and Xing, J and Zhan, M and Pei, S and Deng, X and Li, J and Meng, G and Xu, J and Dai, D and Hu, G and Zheng, M and Liu, C and Qin, J and Xiao, Y},
title = {Microbiota-shaped neutrophil senescence regulates sexual dimorphism in bladder cancer.},
journal = {Nature immunology},
volume = {},
number = {},
pages = {},
pmid = {40217111},
issn = {1529-2916},
abstract = {Sex disparities have been epidemiologically demonstrated in non-reproductive cancers, yet how the sex-specific intrinsic microbiome orchestrates the immune system to affect these disparities is unclear. Here we identify a subpopulation of RETNLG[+]LCN2[+] senescence-like neutrophils (RLSNs) that preferentially accumulate in the male tumor microenvironment and exert a strong immunosuppressive effect to limit antitumor immunity, resulting in poor prognosis for patients with bladder cancer. This difference in enrichment of RLSNs between sexes can be attributed to intestinal bacterium Alistipes shahii, which preferentially populates in females rather than males. A. shahii-associated metabolite lurasidone directly targets iron sequestrator LCN2 in RLSNs. By freeing Fe[2+], lurasidone induces ferroptosis, thereby eliminating RLSNs and promoting antitumor immunity in females. In males lacking A. shahii and lurasidone, RLSNs have a survival advantage. Together, these findings demonstrate that a microbiota-lurasidone-LCN2 circuit regulates sexual disparity in bladder cancer and indicates the therapeutic potential of lurasidone for male cancer patients.},
}

@article {pmid40217076,
year = {2025},
author = {Gilbert, JA and Azad, MB and Bäckhed, F and Blaser, MJ and Byndloss, M and Chiu, CY and Chu, H and Dugas, LR and Elinav, E and Gibbons, SM and Gilbert, KE and Henn, MR and Ishaq, SL and Ley, RE and Lynch, SV and Segal, E and Spector, TD and Strandwitz, P and Suez, J and Tropini, C and Whiteson, K and Knight, R},
title = {Clinical translation of microbiome research.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40217076},
issn = {1546-170X},
abstract = {The landscape of clinical microbiome research has dramatically evolved over the past decade. By leveraging in vivo and in vitro experimentation, multiomic approaches and computational biology, we have uncovered mechanisms of action and microbial metrics of association and identified effective ways to modify the microbiome in many diseases and treatment modalities. This Review explores recent advances in the clinical application of microbiome research over the past 5 years, while acknowledging existing barriers and highlighting opportunities. We focus on the translation of microbiome research into clinical practice, spearheaded by Food and Drug Administration (FDA)-approved microbiome therapies for recurrent Clostridioides difficile infections and the emerging fields of microbiome-based diagnostics and therapeutics. We highlight key examples of studies demonstrating how microbiome mechanisms, metrics and modifiers can advance clinical practice. We also discuss forward-looking perspectives on key challenges and opportunities toward integrating microbiome data into routine clinical practice, precision medicine and personalized healthcare and nutrition.},
}

@article {pmid40217075,
year = {2025},
author = {Zitvogel, L and Derosa, L and Routy, B and Loibl, S and Heinzerling, L and de Vries, IJM and Engstrand, L and , and Segata, N and Kroemer, G},
title = {Impact of the ONCOBIOME network in cancer microbiome research.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40217075},
issn = {1546-170X},
abstract = {The European Union-sponsored ONCOBIOME network has spurred an international effort to identify and validate relevant gut microbiota-related biomarkers in oncology, generating a unique and publicly available microbiome resource. ONCOBIOME explores the effects of the microbiota on gut permeability and metabolism as well as on antimicrobial and antitumor immune responses. Methods for the diagnosis of gut dysbiosis have been developed based on oncomicrobiome signatures associated with the diagnosis, prognosis and treatment responses in patients with cancer. The mechanisms explaining how dysbiosis compromises natural or therapy-induced immunosurveillance have been explored. Through its integrative approach of leveraging multiple cohorts across populations, cancer types and stages, ONCOBIOME has laid the theoretical and practical foundations for the recognition of microbiota alterations as a hallmark of cancer. ONCOBIOME has launched microbiota-centered interventions and lobbies in favor of official guidelines for avoiding diet-induced or iatrogenic (for example, antibiotic- or proton pump inhibitor-induced) dysbiosis. Here, we review the key advances of the ONCOBIOME network and discuss the progress toward translating these into oncology clinical practice.},
}

@article {pmid40216855,
year = {2025},
author = {Novielli, P and Magarelli, M and Romano, D and Di Bitonto, P and Stellacci, AM and Monaco, A and Amoroso, N and Bellotti, R and Tangaro, S},
title = {Leveraging explainable AI to predict soil respiration sensitivity and its drivers for climate change mitigation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12527},
pmid = {40216855},
issn = {2045-2322},
mesh = {*Soil/chemistry ; *Soil Microbiology ; *Climate Change ; Carbon Dioxide/analysis/metabolism ; Machine Learning ; *Artificial Intelligence ; Global Warming ; Temperature ; },
abstract = {Global warming is one of the most pressing and critical problems facing the world today. It is mainly caused by the increase in greenhouse gases in the atmosphere, such as carbon dioxide (CO2). Understanding how soils respond to rising temperatures is critical for predicting carbon release and informing climate mitigation strategies. Q10, a measure of soil microbial respiration, quantifies the increase in CO2 release caused by a [Formula: see text] Celsius rise in temperature, serving as a key indicator of this sensitivity. However, predicting Q10 across diverse soil types remains a challenge, especially when considering the complex interactions between biochemical, microbiome, and environmental factors. In this study, we applied explainable artificial intelligence (XAI) to machine learning models to predict soil respiration sensitivity (Q10) and uncover the key factors driving this process. Using SHAP (SHapley Additive exPlanations) values, we identified glucose-induced soil respiration and the proportion of bacteria positively associated with Q10 as the most influential predictors. Our machine learning models achieved an accuracy of [Formula: see text], precision of [Formula: see text], an AUC-ROC of [Formula: see text], and an AUC-PRC of [Formula: see text], ensuring robust and reliable predictions. By leveraging t-SNE (t-distributed Stochastic Neighbor Embedding) and clustering techniques, we further segmented low Q10 soils into distinct subgroups, identifying soils with a higher probability of transitioning to high Q10 states. Our findings not only highlight the potential of XAI in making model predictions transparent and interpretable, but also provide actionable insights into managing soil carbon release in response to climate change. This research bridges the gap between AI-driven environmental modeling and practical applications in agriculture, offering new directions for targeted soil management and climate resilience strategies.},
}

*Soil/chemistry
*Soil Microbiology
*Climate Change
Carbon Dioxide/analysis/metabolism
Machine Learning
*Artificial Intelligence
Global Warming
Temperature

@article {pmid40216810,
year = {2025},
author = {Sarandi, E and Tsoukalas, D and Rudofsky, G and Fragoulakis, V and Liapi, C and Paramera, E and Papakonstantinou, E and Krueger Krasagakis, S and Tsatsakis, A},
title = {Identifying the metabolic profile of Hashimoto's thyroiditis from the METHAP clinical study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12410},
pmid = {40216810},
issn = {2045-2322},
mesh = {Humans ; *Hashimoto Disease/metabolism/blood/urine ; Female ; Male ; Biomarkers/blood/urine/metabolism ; Case-Control Studies ; Adult ; *Metabolome ; Middle Aged ; Metabolomics/methods ; Gas Chromatography-Mass Spectrometry ; },
abstract = {Hashimoto's thyroiditis (HT), one of the most common autoimmune diseases and the leading cause of hypothyroidism, is linked to metabolic and cellular dysfunctions that contribute to disease aetiopathogenesis. This case-control study aimed to identify potent metabolic biomarkers of HT employing machine learning techniques. 62 euthyroid patients with HT and 58 healthy individuals were included from the metabolic biomarkers in Hashimoto's thyroiditis and psoriasis (METHAP) clinical trial. Quantification of 73 metabolites was performed using gas-chromatography/mass spectrometry in plasma and urine samples of fasted participants. Changes in the tricarboxylic acid cycle, carbohydrate, neurotransmitter, microbiome and lipid metabolism were identified in the HT group. Ordinary least squares and beta regression modeling associated the presence of HT with methylmalonic acid, 4-hydroxyphenylpyruvic acid, palmitic acid, palmitoleic acid, myristoleic acid and total saturated fatty acids, adjusting for confounders. Artificial neural network analysis had good predictive accuracy with an AUC of 0.8, while debiased sparse partial correlation network analysis identified metabolite-metabolite interactions distinct for HT. These findings provide insights into novel biomarkers associated with HT, and we discuss their biological relevance and clinical significance. Hashimoto's thyroiditis is associated with mitochondrial dysfunction, micronutrient decreased bioavailability, microbiome imbalances, and carbohydrate and fatty acids dysfunctional metabolism.},
}

Humans
*Hashimoto Disease/metabolism/blood/urine
Female
Male
Biomarkers/blood/urine/metabolism
Case-Control Studies
Adult
*Metabolome
Middle Aged
Metabolomics/methods
Gas Chromatography-Mass Spectrometry

@article {pmid40216789,
year = {2025},
author = {Shekarriz, S and Szamosi, JC and Whelan, FJ and Lau, JT and Libertucci, J and Rossi, L and Fontes, ME and Wolfe, M and Lee, CH and Moayyedi, P and Surette, MG},
title = {Detecting microbial engraftment after FMT using placebo sequencing and culture enriched metagenomics to sort signals from noise.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3469},
pmid = {40216789},
issn = {2041-1723},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Metagenomics/methods ; *Colitis, Ulcerative/therapy/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Placebos ; Adult ; Middle Aged ; },
abstract = {Fecal microbiota transplantation (FMT) has shown efficacy for the treatment of ulcerative colitis but with variable response between patients and trials. The mechanisms underlying FMT's therapeutic effects remains poorly understood but is generally assumed to involve engraftment of donor microbiota into the recipient's microbiome. Reports of microbial engraftment following FMT have been inconsistent between studies. Here, we investigate microbial engraftment in a previous randomized controlled trial (NCT01545908), in which FMT was sourced from a single donor, using amplicon-based profiling, shotgun metagenomics, and culture-enriched metagenomics. Placebo samples were included to estimate engraftment noise, and a significant level of false-positive engraftment was observed which confounds the prediction of true engraftment. We show that analyzing engraftment across multiple patients from a single donor enhances the accuracy of detection. We identified a unique set of genes engrafted in responders to FMT which supports strain displacement as the primary mechanism of engraftment in our cohort.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Metagenomics/methods
*Colitis, Ulcerative/therapy/microbiology
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Male
Female
Placebos
Adult
Middle Aged

@article {pmid40216734,
year = {2025},
author = {Vallazhath, A and Thimmappa, PY and Joshi, HB and Hebbar, KR and Nayak, A and Umakanth, S and Saoji, AA and Manjunath, NK and Hadapad, BS and Joshi, MB},
title = {A comprehensive review on the implications of Yogic/Sattvic diet in reducing inflammation in type 2 diabetes.},
journal = {Nutrition & diabetes},
volume = {15},
number = {1},
pages = {14},
pmid = {40216734},
issn = {2044-4052},
support = {DST/SATYAM/2020/247 (G)//Department of Science and Technology, Ministry of Science and Technology (DST)/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/diet therapy/complications ; *Inflammation/diet therapy/prevention & control ; Insulin Resistance ; *Yoga ; Gastrointestinal Microbiome ; },
abstract = {Chronic inflammation in type 2 diabetes (T2D), characterized by constitutively activated immune cells and elevated pro-inflammatory mediators along with hyperglycaemia and increased free fatty acids and branched chain amino acid levels, significantly alters the immuno-metabolic axis. Over the years, dietary intervention has been explored as an effective strategy for managing T2D. Evidence from experimental and clinical studies indicates that various diets, including Mediterranean, Nordic, Palaeolithic and ketogenic diets, increase insulin sensitivity, decrease gluconeogenesis, and adiposity, and exert anti-inflammatory effects, thus preserving immuno-metabolic homeostasis in individuals with T2D. Indian dietary sources are categorized as Sattvic, Rajasic, and Tamasic, depending on their impact on health and behaviour. The Yogic diet, commonly recommended during yoga practice, is predominantly Sattvic, emphasizing plant-based whole foods while limiting processed and high-glycaemic-index items. Yogic diet is also recommended for Mitahara, emphasizing mindful eating, which is attributed to calorie restriction. Adopting a Yogic diet, featuring low-fat vegetarian principles, strongly reduces inflammatory mediator levels. This diet not only ameliorates insulin resistance and maintains a healthy body weight but also regulates immunomodulation, enhances gut microbiome diversity and provides essential phytonutrients, collectively preventing inflammation. Although, preliminary studies show aforementioned beneficial role of Yogic diet in improving diabetes associated metabolic and inflammatory changes, precise cellular and molecular mechanisms are not yet understood. Hence, further studies are warranted to decipher the mechanisms. This review summarizes the multiple roles of Yogic diet and related dietary components in mitigating inflammation and enhancing glycaemic control in T2D.},
}

Humans
*Diabetes Mellitus, Type 2/diet therapy/complications
*Inflammation/diet therapy/prevention & control
Insulin Resistance
*Yoga
Gastrointestinal Microbiome

@article {pmid40216167,
year = {2025},
author = {Sangfuang, N and Xie, Y and McCoubrey, LE and Taub, M and Favaron, A and Mai, Y and Gaisford, S and Basit, AW},
title = {Investigating the bidirectional interactions between senotherepeutic agents and human gut microbiota.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {},
number = {},
pages = {107098},
doi = {10.1016/j.ejps.2025.107098},
pmid = {40216167},
issn = {1879-0720},
abstract = {Biological ageing is a time-dependent process that has implications for health and disease. Cellular senescence is a key driver in ageing and age-related diseases. Senotherapeutic agents have been shown to slow biological ageing by eliminating senescent mammalian cells. Given the increasing awareness of the gut microbiome in regulating human health, this study aimed to investigate the effects of senotherapeutic agents as pharmacological interventions on the human gut microbiota. In this study, the bidirectional effects of four senotherapeutic agents, quercetin, fisetin, dasatinib, and sirolimus, with the gut microbiota sourced from healthy human donors were investigated. The results revealed that quercetin was completely biotransformed by the gut microbiota within six hours, while dasatinib was the most stable of the four compounds. Additionally, metagenomic analysis confirmed that all four compounds increased the abundance of bacterial species associated with healthy ageing (e.g., Bacteroides fragilis, Bifidobacterium longum, and Veillonella parvula), and decreased the abundance of pathogenic bacteria primarily associated with age-related diseases (e.g., Enterococcus faecalis and Streptococcus spp.). The findings from this study provide a comprehensive understanding of the pharmacobiomics of senotherapeutic interventions, highlighting the potential of microbiome-targeted senolytics in promoting healthy ageing.},
}

@article {pmid40216091,
year = {2025},
author = {Kyriazopoulou, E and Stylianakis, E and Damoraki, G and Koufargyris, P and Kollias, I and Katrini, K and Drakou, E and Marousis, K and Spyrou, A and Symbardi, S and Alexiou, N and Alexiou, Z and Lada, M and Poulakou, G and Chrysos, G and Adamis, G and Giamarellos-Bourboulis, EJ},
title = {Procalcitonin-Guided Early Stop of Antibiotics Prevents Gut Inflammation and Preserves Gut Microbiome: Data from the PROGRESS Controlled Trial.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107507},
doi = {10.1016/j.ijantimicag.2025.107507},
pmid = {40216091},
issn = {1872-7913},
abstract = {The PROGRESS randomized trial (ClinicalTrials.gov NCT03333304) showed that early stop of antibiotics guided by procalcitonin (PCT) decreased the incidence of infections by multidrug resistant organisms and/or Clostridioides difficile and was associated with survival benefit. We investigated if benefit is associated with microbiome dysbiosis. Patients with sepsis due to lung infection, acute pyelonephritis or primary bacteremia were randomized to standard-of-care (SoC) duration of antibiotics or early stop using PCT. Faecal samples were collected before, 7 and 28 days after randomization and analyzed by 16S rRNA Nanopore sequencing. Calprotectin was measured by an enzyme immunoassay. Median (Q1-Q3) antimicrobial duration was 5 days in PCT (5-7.5) and 11 days (8-15) in SoC arm, respectively (p < 0.001). Faecal calprotectin did not differ at baseline. By day 7, it was significantly increased in SoC (p=0.002) but it was unchanged in the PCT arm. Microbiome alpha- and beta-diversity were similar at baseline in PCT (n=81) and SoC (n=76) treated patients. Shannon's index was significantly decreased in SoC by day 7 from baseline (median [Q1-Q3], 2.88 [2.37-3.39] at day 1 vs 2.24 [1.52-3.08] at day 7; pt-test=0.0013); this was not the case for the PCT arm (median [Q1-Q3], 2.73 [2.26-3.4] at day 1 vs 2.43 [1.81-3.21] at day 7; pt-test=0.037, Bonferroni corrected alpha = 0.0125). Relative abundances of Actinomycetota and Pseudomonadota were decreased in PCT arm by day 7 and relative abundance of Bacillota was increased. Early PCT-guided stop of antibiotics contributes to decreased microbiome dysbiosis by day 7.},
}

@article {pmid40216077,
year = {2025},
author = {Armengaud, J and Cardon, T and Cristobal, S and Matallana-Surget, S and Bertile, F},
title = {Novel model organisms and proteomics for a better biological understanding.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105441},
doi = {10.1016/j.jprot.2025.105441},
pmid = {40216077},
issn = {1876-7737},
abstract = {The concept of « model organisms » is being revisited in the light of the latest advances in multi-omics technologies that can now capture the full range of molecular events that occur over time, regardless of the organism studied. Classic, well-studied models, such as Escherichia coli, Saccharomyces cerevisiae, to name a few, have long been valuable for hypothesis testing, reproducibility, and sharing common platforms among researchers. However, they are not suitable for all types of research. The complexity of unanswered questions in biology demands more elaborated systems, particularly to study plant and animal biodiversity, microbial ecosystems and their interactions with their hosts if any. More integrated systems, known as « holobionts », are emerging to describe and unify host organisms and associated microorganisms, providing an overview of all their possible interactions and trajectories. Comparative evolutionary proteomics offers interesting prospects for extrapolating knowledge from a few selected model organisms to others. This approach enables a deeper characterization of the diversity of proteins and proteoforms across the three branches of the tree of life, i.e. Bacteria, Archaea, and Eukarya. It also provides a powerful means to address remaining biological questions, such as identifying the key molecular players in organisms when they are confronted to environmental challenges, like anthropogenic toxicants, pathogens, dietary shifts or climate stressors, and proposing long-term sustainable solutions. SIGNIFICANCE: In this commentary, we reevaluated the concept of "model organisms" in light of advancements in multi-omics technologies. Traditional models have proven invaluable for hypothesis testing, reproducibility, and fostering shared research frameworks. However, we discussed that they are not universally applicable. To address complexities such as biodiversity and understand microbial ecosystems and their host interactions, integrated systems like "holobionts," which encompass host organisms and their associated microbes, are gaining prominence. Comparative evolutionary proteomics further enhances our understanding by enabling detailed exploration of protein diversity across organisms. This approach also facilitates the identification of critical molecular players in organisms facing environmental challenges, such as pollutants, pathogens, dietary changes, or climate stress, and contributes to developing sustainable long-term solutions.},
}

@article {pmid40216042,
year = {2025},
author = {Ma, H and Qiao, Q and Yu, Z and Wang, W and Li, Z and Xie, Z and Su, Y and Zhang, X and Sun, Y and Wang, P and Zhang, Z},
title = {Integrated multi-omics analysis and experimental validation reveals the mechanism of tenuifoliside A activity in Alzheimer's disease.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {119797},
doi = {10.1016/j.jep.2025.119797},
pmid = {40216042},
issn = {1872-7573},
abstract = {Alzheimer's disease (AD) is characterized by progressive cognitive dysfunction and memory loss. Tenuifoliside A (TFSA) is a constituent of RADIX POLYGALAE, a medicinal herb traditionally used in the clinical treatment of AD in China. However, the therapeutic mechanism of this compound is unknown.

AIM OF THE STUDY: To investigate the effects and pharmacological mechanisms of TFSA in ameliorating AD symptoms in APP/PS1 mice.

MATERIALS AND METHODS: The neuroprotective effects of TFSA were assessed using behavioral tests, transmission electron microscopy, and immunofluorescence staining. The differential metabolites in the feces of model mice were obtained from non-targeted metabolomics analysis. Differential abundances of microbiota in the gut were investigated by 16S rRNA sequencing, and correlations among differential metabolites and microbiota were investigated using an integrated approach.

RESULTS: Cognitive impairment and Aβ burden were mitigated in APP/PS1 mice treated with TFSA. TFSA intervention led to an increase in the diversity of gut microbiota and a reduction in the relative abundance of Firmicutes, Bacteroidetes, and Proteobacteria. There were 71 differential metabolites in mice given high dose of TFSA. In comparison to the AD group, the mice treated with TFSA exhibited a notable enrichment in various pathways including glucose and lipid metabolism, tryptophan metabolism. Based on integrated metabolomics and 16S rRNA sequencing, 23 metabolite-microbiota pairs were different between the TFSA and AD groups, and there was an especially strong correlation between Alistipes and 2,3-dinor-8-epi-prostaglandin F2α. Validation experiment demonstrated TFSA ameliorates AD by regulating metabolism pathways and inhibiting neuroinflammation.

CONCLUSIONS: This study offers a theoretical basis for elucidating the molecular mechanism of TFSA's amelioration of AD. Although the potential pharmacological mechanisms of TFSA are still unknown, we have demonstrated that TFSA inhibits neuroinflammation and improves AD symptoms in APP/PS1 mice by remodeling the microbiota and its metabolites.},
}

@article {pmid40215444,
year = {2025},
author = {Kerwin, AH and Ohdera, A and Bier, J and Goodman, D and Mammone, M and Sharp, V and Echeandía, A and Medina, M},
title = {Cassiopea xamachana microbiome across anatomy, development, and geography.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0319944},
doi = {10.1371/journal.pone.0319944},
pmid = {40215444},
issn = {1932-6203},
mesh = {Animals ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Larva/microbiology ; *Hydrozoa/microbiology/growth & development/anatomy & histology ; Female ; Phylogeny ; Symbiosis ; Male ; Geography ; },
abstract = {The upside-down jellyfish holobiont, Cassiopea xamachana, is a useful model system for tri-partite interactions between the cnidarian host, the photosymbiont, and the bacterial microbiome. While the interaction between the host and photosymbiont has been well studied, less is understood of the associated bacterial community. To date, the bacterial microbiome of wild C. xamachana has remained largely uncharacterized. Thus, wild medusae (n=6) and larvae (n=3) were collected from two sites in the Florida Keys. Bacterial community composition was characterized via amplicon sequencing of the 16S rRNA gene V4 region. The medusa bacterial community was dominated by members of the Alphaproteobacteria and Gammaproteobacteria, while Planctomycetota, Actinomycetota, Bacteroidota, and Bacillota were also present, among others. Community composition was consistent between locations and across medusa structures (oral arm, bell, and gonad). The larval bacterial community clustered apart from the medusa community in beta diversity analysis and was characterized by the presence of several Pseudomonadota taxa that were not present in the medusa, including the Alteromonas, Pseudoalteromonas, and Thalassobius genera. A bacterial isolate library encompassing much of the amplicon sequencing diversity was also developed and tested via metabolic assays in a separate culture-dependent analysis of isolates from medusa bells, oral arms, and laplets. Most characteristics were not correlated with host sex or medusa structure, but gelatinase production was more common in laplet isolates, while lactose fermentation was more common in female oral arm isolates. The Endozoicomonas genus was dominant in both amplicon sequencing and in our isolate library, and was equally prevalent across all medusa structures and in both sexes. Understanding the bacterial component of the C. xamachana holobiont will allow us to further develop this important model cnidarian holobiont.},
}

Animals
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Larva/microbiology
*Hydrozoa/microbiology/growth & development/anatomy & histology
Female
Phylogeny
Symbiosis
Male
Geography

@article {pmid40214948,
year = {2025},
author = {Côco, LZ and de Souza Belisário, E and Vasquez, EC and Pereira, TMC and Aires, R and Campagnaro, BP},
title = {Probiotics: a promising future in the treatment of ulcerative colitis?.},
journal = {Pharmacological reports : PR},
volume = {},
number = {},
pages = {},
pmid = {40214948},
issn = {2299-5684},
support = {305740/2019-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 309431/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 308220/2021-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Edital 15/2022 - PROFIX: 708/2022//Fundação de Amparo à Pesquisa e Inovação do Espírito Santo/ ; Edital 15/2022 - PROFIX: 630/2022//Fundação de Amparo à Pesquisa e Inovação do Espírito Santo/ ; },
abstract = {Ulcerative colitis is an idiopathic and chronic inflammatory bowel disease, characterized by inflammation of the mucosa of the colon and rectum. Clinical manifestations commonly include abdominal pain, diarrhea (with or without hematochezia), and weight loss. The pathogenesis of ulcerative colitis is multifactorial, involving a combination of genetic predispositions and lifestyle factors. High consumption of processed food, sedentary habits, alcohol intake, and stress are among the lifestyle factors implicated in disease onset and progression. Current treatment strategies focus on managing symptoms and inducing remission, however, the chronic nature of the disease, along with the adverse effects of conventional therapies, often compromises patient's quality of life. Therefore, exploring alternative therapies that can prolong remission and reduce symptom burden is important. Experimental evidence suggests that probiotics may extend remission duration in ulcerative colitis. Moreover, probiotics exhibit efficacy in amelioration clinical symptoms by reducing inflammation markers, preserving, and restoring intestinal epithelial. This review explores the advantages of the administration of probiotics in the treatment of ulcerative colitis, elucidating their mechanism of action.},
}

@article {pmid40214782,
year = {2025},
author = {Koponen, K and McDonald, D and Jousilahti, P and Meric, G and Inouye, M and Lahti, L and Niiranen, T and Männistö, S and Havulinna, A and Knight, R and Salomaa, V},
title = {Associations of alcohol with the human gut microbiome and prospective health outcomes in the FINRISK 2002 cohort.},
journal = {European journal of nutrition},
volume = {64},
number = {4},
pages = {153},
pmid = {40214782},
issn = {1436-6215},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; Male ; Middle Aged ; Adult ; Prospective Studies ; *Alcohol Drinking/adverse effects ; Aged ; Feces/microbiology ; Finland/epidemiology ; Cohort Studies ; *Ethanol ; Bacteria/classification ; },
abstract = {BACKGROUND AND AIMS: Alcohol remains a global risk factor for non-communicable diseases with the gut microbiome emerging as a novel elucidator. We investigated how gut microbiome associates with alcohol on population level, if there is mediation reflected in health outcomes, and how functional potential is related.

METHODS: Our sample consisted of 4575 shallow-shotgun sequenced fecal samples from the FINRISK 2002 cohort (25-74yrs., 52.5% women). Alcohol (g 100% alcohol/week) use was self-reported. Diversity and differential species abundances were analyzed using multiple linear regression. Compositional differences were analyzed using PERMANOVA, and prospective associations with Cox-regression. Connections between alcohol, microbiome, inflammatory markers, and outcomes were assessed using serial mediation. Functional associations were assessed using KEGG-orthologies and multiple linear regression.

RESULTS: High-risk alcohol consumers had significantly lower bacterial diversity when compared to low-risk consumers (mean±SD:4.04±0.41 vs. 4.11±0.43, p = 9.56 × 10[- 4]). Alcohol also associated with significant shifts in overall composition (PERMANOVA; p ≤ 1.00 × 10[- 4]) and differential abundances of 344 species (ANCOM-BC2; q ≤ 0.05). These shifts were characterized by an increase in relative abundances of Gram-negative bacteria, the top genera of which were Bacteroides and Prevotella, and a decrease in putatively beneficial species in genera such as Lactobacillus, Bifidobacterium, and Akkermansia. Prospective associations with all-cause mortality (HR:1.12 [1.02-1.23]), and liver disease (HR:1.53 [1.22-1.92]) were observed. The association between alcohol and liver disease had a mediating link via a proinflammatory beta-diversity principal coordinate (OR:1.04 [1.001-1.10]). Functional associations were observed with 1643 KO-groups (q < 0.05, npositive=431, nnegative=1212). Antioxidative and gut integrity maintaining functions were diminished and lipopolysaccharide synthesis enriched.

CONCLUSIONS: Alcohol use is associated with community-level shifts in composition towards enriched Gram-negative bacteria, and diminished levels of putatively beneficial bacteria. Alcohol use associates with a proinflammatory gut microbiome profile that mediates alcohol's effect on incident liver disease risk, possibly via increased proliferation of endotoxins through the gut epithelial lining.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Female
Male
Middle Aged
Adult
Prospective Studies
*Alcohol Drinking/adverse effects
Aged
Feces/microbiology
Finland/epidemiology
Cohort Studies
*Ethanol
Bacteria/classification

@article {pmid40214675,
year = {2025},
author = {Liu, S and Liu, J and Mei, Y and Zhang, W},
title = {Gut microbiota affects PD-L1 therapy and its mechanism in melanoma.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {5},
pages = {169},
pmid = {40214675},
issn = {1432-0851},
support = {BLSA [2024] No. 2, 2024300CC0020//The grants of Science and Technology Projects of Beijing Life Science Academy/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Melanoma/immunology/drug therapy/microbiology/pathology/metabolism ; *B7-H1 Antigen/antagonists & inhibitors/metabolism/immunology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Tumor Microenvironment/immunology ; Animals ; Immunotherapy/methods ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism ; },
abstract = {Immune checkpoint inhibitors (ICIs), particularly PD-1/PD-L1 blockade, have shown great success in treating melanoma. PD-L1 (B7-H1, CD274), a ligand of PD-1, binds to PD-1 on T cells, inhibiting their activation and proliferation through multiple pathways, thus dampening tumor-reactive T cell activity. Studies have linked PD-L1 expression in melanoma with tumor growth, invasion, and metastasis, making the PD-1/PD-L1 pathway a critical target in melanoma therapy. However, immune-related adverse events are common, reducing the effectiveness of anti-PD-L1 treatments. Recent evidence suggests that the gut microbiome significantly influences anti-tumor immunity, with the microbiome potentially reprogramming the tumor microenvironment and overcoming resistance to anti-PD-1 therapies in melanoma patients. This review explores the mechanisms of PD-1/PD-L1 in melanoma and examines how gut microbiota and its metabolites may help address resistance to anti-PD-1 therapy, offering new insights for improving melanoma treatment strategies.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Melanoma/immunology/drug therapy/microbiology/pathology/metabolism
*B7-H1 Antigen/antagonists & inhibitors/metabolism/immunology
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Tumor Microenvironment/immunology
Animals
Immunotherapy/methods
Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism

@article {pmid40214509,
year = {2025},
author = {Khazaei, M and Parsasefat, M and Bahar, A and Tahmasebi, H and Oksenych, V},
title = {Behavioral Cooperation or Conflict of Human Intestinal Roundworms and Microbiomes: A Bio-Activity Perspective.},
journal = {Cells},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/cells14070556},
pmid = {40214509},
issn = {2073-4409},
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome ; *Nematoda/physiology ; *Intestines/parasitology/microbiology ; },
abstract = {Human infections are greatly impacted by intestinal nematodes. These nematodes, which encompass the large roundworms, have a direct impact on human health and well-being due to their close cohabitation with the host's microorganisms. When nematodes infect a host, the microbiome composition changes, and this can impact the host's ability to control the parasites. We aimed to find out if the small intestinal roundworms produce substances that have antimicrobial properties and respond to their microbial environment, and if the immune and regulatory reactions to nematodes are altered in humans lacking gut microbes. There is no doubt that different nematodes living in the intestines can alter the balance of intestinal bacteria. Nonetheless, our knowledge about the parasite's influence on the gut microbiome remains restricted. The last two decades of study have revealed that the type of iron utilized can influence the activation of unique virulence factors. However, some roundworm proteins like P43, which makes up a large portion of the worm's excretory-secretory product, have an unknown role. This review explores how the bacterial iron regulatory network contributes to the adaptability of this opportunistic pathogen, allowing it to successfully infect nematodes in different host environments.},
}

Humans
Animals
*Gastrointestinal Microbiome
*Nematoda/physiology
*Intestines/parasitology/microbiology

@article {pmid40214493,
year = {2025},
author = {Rahim, MA and Seo, H and Barman, I and Hossain, MS and Shuvo, MSH and Song, HY},
title = {Insights into Autophagy in Microbiome Therapeutic Approaches for Drug-Resistant Tuberculosis.},
journal = {Cells},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/cells14070540},
pmid = {40214493},
issn = {2073-4409},
support = {RS-2023-00219563//National Research Foundation of Korea/ ; P248400003//Korea Institute for Advancement of Technology (KIAT)/ ; Soonchunhyang University Research Fund//Soonchunhyang University/ ; },
mesh = {Humans ; *Autophagy ; *Tuberculosis, Multidrug-Resistant/therapy/microbiology ; *Microbiota ; Mycobacterium tuberculosis/drug effects ; Animals ; Antitubercular Agents/therapeutic use/pharmacology ; },
abstract = {Tuberculosis, primarily caused by Mycobacterium tuberculosis, is an airborne lung disease and continues to pose a significant global health threat, resulting in millions of deaths annually. The current treatment for tuberculosis involves a prolonged regimen of antibiotics, which leads to complications such as recurrence, drug resistance, reinfection, and a range of side effects. This scenario underscores the urgent need for novel therapeutic strategies to combat this lethal pathogen. Over the last two decades, microbiome therapeutics have emerged as promising next-generation drug candidates, offering advantages over traditional medications. In 2022, the Food and Drug Administration approved the first microbiome therapeutic for recurrent Clostridium infections, and extensive research is underway on microbiome treatments for various challenging diseases, including metabolic disorders and cancer. Research on microbiomes concerning tuberculosis commenced roughly a decade ago, and the scope of this research has broadened considerably over the last five years, with microbiome therapeutics now viewed as viable options for managing drug-resistant tuberculosis. Nevertheless, the understanding of their mechanisms is still in its infancy. Although autophagy has been extensively studied in other diseases, research into its role in tuberculosis is just beginning, with preliminary developments in progress. Against this backdrop, this comprehensive review begins by succinctly outlining tuberculosis' characteristics and assessing existing treatments' strengths and weaknesses, followed by a detailed examination of microbiome-based therapeutic approaches for drug-resistant tuberculosis. Additionally, this review focuses on establishing a basic understanding of microbiome treatments for tuberculosis, mainly through the lens of autophagy as a mechanism of action. Ultimately, this review aims to contribute to the foundational comprehension of microbiome-based therapies for tuberculosis, thereby setting the stage for the further advancement of microbiome therapeutics for drug-resistant tuberculosis.},
}

Humans
*Autophagy
*Tuberculosis, Multidrug-Resistant/therapy/microbiology
*Microbiota
Mycobacterium tuberculosis/drug effects
Animals
Antitubercular Agents/therapeutic use/pharmacology

@article {pmid40214226,
year = {2025},
author = {Costello, MK and McClure, JC and Brown, JA and Amorín de Hegedüs, R and Mantovani, HC and Ricke, SC},
title = {The gastrointestinal tract microbiome of Holstein × Angus cross cattle is negatively impacted by the pre-harvest process.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0259924},
doi = {10.1128/aem.02599-24},
pmid = {40214226},
issn = {1098-5336},
abstract = {Stress during the beef pre-harvest period can induce an inflammatory response and acidotic conditions in the gastrointestinal tract (GIT), which affects the gastrointestinal tract microbiome. The objective of this study was to characterize the status of the GIT microbiome at harvest in beef cattle entering a small USDA processing facility. Nine beef cattle were shipped from a producer in Columbia County, WI, to the USDA processing facility at the University of Wisconsin-Madison and were harvested across four dates. Digesta samples were collected from eight GIT locations: rumen solids, rumen liquids, abomasum, duodenum, jejunum, ileum, cecum, and large intestines. After DNA extraction, the V4 region of the 16S rRNA gene was amplified and sequenced on the Illumina MiSeq platform. Sequences were analyzed for alpha and beta diversity metrics, core microbiome, differential abundance, and co-occurrence network analyses. Harvest date, finishing weight, and GIT location had a significant impact on microbial diversity and community composition (P < 0.05), and there was an interaction between GIT location and harvest date (P < 0.05). Taxonomic composition shifted throughout the GIT, though Prevotella and Treponema were core members in several different GIT locations. The co-occurrence analysis revealed microorganisms potentially associated with clinical infections, with Moryella in the rumen and Acinetobacter in the hindgut emerging as the highest scoring hubs. These results suggest that the pre-harvest period may negatively impact the beef cattle GIT microbiome. Modulating the GIT microbiome during the pre-harvest period may offer an opportunity to improve food safety.IMPORTANCEWith the global rise in antimicrobial resistance and the threat of foodborne illness, determining intervention strategies prior to harvest is a promising solution. The period between transportation from the feedlot to harvest may increase the risk of foodborne illness. During this period, cattle are withheld feed to reduce gastrointestinal tract (GIT) contents during carcass dressing. Feed withdrawal has many unintended consequences, such as acidosis and an increase in GIT pathogenic bacteria, that may result in foodborne pathogens on the final product. These consequences have yet to be thoroughly investigated in dairy-beef cross cattle, which have been rising in prominence in the United States. The GIT microbiome of dairy-beef cross cattle has been scarcely characterized despite its influence on preventing the proliferation of common pathogens in the GIT. Therefore, it is necessary to determine the impacts of feed withdrawal on the GIT microbiome and its relation to foodborne illness.},
}

@article {pmid40214217,
year = {2025},
author = {Geniselli da Silva, V and Mullaney, JA and Roy, NC and Smith, NW and Wall, C and Tatton, CJ and McNabb, WC},
title = {Complementary foods in infants: an in vitro study of the faecal microbial composition and organic acid production.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo00414d},
pmid = {40214217},
issn = {2042-650X},
abstract = {The transition from breastmilk to complementary foods is critical for maturing the colonic microbiota of infants. Dietary choices at weaning can lead to long-lasting microbial changes, potentially influencing health later in life. However, the weaning phase remains underexplored in colonic microbiome research, and the current understanding of how complementary foods impact the infant's colonic microbiota is limited. To address this knowledge gap, this study assessed the influence of 13 food ingredients on the in vitro microbial composition and production of organic acids by the faecal microbiota in New Zealand infants aged 5 to 11 months. To better represent real feeding practices, ingredients were combined with infant formula, other complementary foods, or both infant formula and other foods. Among the individual food ingredients, fermentation with peeled kūmara (sweet potato) increased the production of lactate and the relative abundance of the genus Enterococcus. Fermentation with blackcurrants, strawberries, or raspberries enhanced acetate and propionate production. Additionally, fermentation with blackcurrants increased the relative abundance of the genus Parabacteroides, while raspberry fermentation increased the relative abundance of the genera Parabacteroides and Eubacterium. When combined with infant formula or with blackcurrants, fermenting black beans increased butyrate production and stimulated the relative abundance of Clostridium sensu stricto 1. These foods are promising candidates for future clinical trials.},
}

@article {pmid40214103,
year = {2025},
author = {Hoedt, EC and Carroll, G and Stephensen, B and Morrison, M and Vishnoi, V and Cuskelly, A and Draganic, B and McManus, B and Clarke, L and Shah, K and Smith, SR and Talley, NJ and Keely, S and Pockney, P},
title = {Preoperative Antibiotics and Mechanical Bowel Preparation Impact the Colonic Mucosa Associated Microbiota But Not Anastomotic Leak Rate After Colorectal Resection.},
journal = {Diseases of the colon and rectum},
volume = {},
number = {},
pages = {},
doi = {10.1097/DCR.0000000000003775},
pmid = {40214103},
issn = {1530-0358},
abstract = {BACKGROUND: Alterations in the gastrointestinal microbiome have been associated with increased anastomotic leak risk. Oral antibiotics and bowel preparations may both reduce anastomotic leaks rates.

OBJECTIVE: Within patients undergoing colorectal surgery, we aimed to examine the impact of oral antibiotic use, bowel preparation and other perioperative factors on the mucosa associated microbiota and investigated association with anastomotic leak rates.

DESIGN: We opportunistically sampled Australian patients undergoing colorectal resection for any indication with anastomosis, mucosal swabs were taken from the proximal and distal extent of the resected specimen immediately after extraction.

SETTINGS: A single site, public tertiary referral hospital of 694 beds with an accredited specialist colorectal unit in Newcastle, Australia.

PATIENTS: Of 192 patients; 31 patients were identified as receiving oral antibiotics pre-surgery. Thirty-one patients received mechanical preparation and 58 received enema pre-surgery.

MAIN OUTCOME MEASURES: The influence of patient factors on mucosa-associated microbiota composition and associations to rate of anastomotic leaks.

RESULTS: The leak rate was 15% (N = 28/192). Preoperative oral antibiotic manipulation and bowel preparation minimally affected the mucosa-associated microbiota, but neither were associated with anastomotic leaks. Erythromycin (N = 14/192) had the greatest impact on the mucosa-associated microbiota. Of the different bowel preparation regimes, excluding patients given antibiotics, only fleet enemas (N = 58/161) had a significant impact on the mucosa-associated microbiota. Bowel preparation was not associated with occurrence of anastomotic leaks. There were only subtle differences observed in the mucosa-associated microbiota between anastomotic leaks and non-anastomotic leaks patients.

LIMITATIONS: Antibiotic recipient numbers included were modest.

CONCLUSIONS: This is the largest series of routine colorectal anastomoses for which the mucosa-associated microbiota adjacent the anastomoses was examined. We show that antibiotics and bowel preparation in the preoperative period exert only limited effects on the mucosa-associated microbiota and conclude that there are no obvious mucosa-associated microbiota characteristics that are predictive for an anastomotic leak.},
}

@article {pmid40213471,
year = {2025},
author = {Kurz, C and Arbeeva, L and Azcarate-Peril, MA and Stewart, DA and Lascelles, BDX and Loeser, RF and Nelson, AE},
title = {Exploring associations among pro-inflammatory cytokines, osteoarthritis, and gut microbiome composition in individuals with obesity using machine learning.},
journal = {Osteoarthritis and cartilage open},
volume = {7},
number = {2},
pages = {100603},
pmid = {40213471},
issn = {2665-9131},
abstract = {OBJECTIVE: To investigate potentially novel and modifiable mechanisms of the effects of gut microbiome composition on obesity-related osteoarthritis (OA), focusing on cross-sectional relationships between microbiota, cytokines, and lipopolysaccharide (LPS).

DESIGN: Johnston County OA Project participants (n ​= ​64) with (cases) and without (controls) OA in hands and knees, with age ≥55 years and obesity (BMI ≥30 ​kg/m[2]), provided samples for multiplex cytokine, LPS, and fecal microbiota analysis. Latent Dirichlet Allocation (LDA), a machine learning method to detect latent groups within data, was used to identify microbial enterotypes. LDA regression models were used to evaluate associations of enterotypes with demographics, cytokines associated with OA, and LPS.

RESULTS: We identified 5 enterotypes. Enterotypes 3, 4 (most prevalent in our sample), and 5, dominated respectively by genera Akkermansia, Bacteroides, Ruminococcus/Phascolarctobacterium, were positively associated with control status, and inversely associated with levels of at least two cytokines associated with OA in our sample. We observed no associations of enterotypes with LPS levels. Enterotype 3 was inversely associated with thrombopoietin and IL-4 levels (b [95 ​% CIs] -0.19 [-0.43, 0.05] and -0.17 [-0.42, 0.08]), enterotype 5 with osteopontin and thrombopoietin (-0.23 [-0.49, 0.03] and -0.24 [-0.51, 0.04]), and enterotype 4 was inversely associated with all 3 of these cytokines (b -0.20 to -0.35).

CONCLUSION: Three of five identified enterotypes were inversely associated with OA status and levels of OA associated cytokines. These exploratory analyses revealed associations between the gut microbiome, cytokines, and OA outcomes, suggesting potentially cytokine-mediated mechanisms of the effects of gut composition on OA in obese individuals, and providing a basis for further investigation of the underlying causal mechanisms.},
}

@article {pmid40213273,
year = {2025},
author = {Subedi, S and Dang, UJ},
title = {Multivariate Poisson lognormal distribution for modeling counts from modern biological data: An overview.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {1255-1264},
pmid = {40213273},
issn = {2001-0370},
abstract = {Modern biological data are often multivariate discrete counts, and there has been a dearth of statistical distributions to directly model such counts in an efficient manner. While mixed Poisson distributions, e.g., negative binomial distribution, are often the distribution of choice for univariate data, multivariate statistical distributions and their algorithmic implementations tend to have different drawbacks, e.g., non-tractable distributions, non-closed form solutions for parameter estimates, constrained correlation structures, and slow convergence during iterative parameter estimation. Herein, we provide an overview of the Poisson lognormal and multivariate Poisson lognormal distributions. These distributions can be written in an hierarchical fashion. An efficient variational approximation-based parameter estimation strategy as well as a hybrid approach for full Bayesian posterior estimation is available for such models, allowing for scaling up and modeling high-dimensional data. We provide comparisons of the univariate Poisson, the negative binomial, and the Poisson lognormal distributions in terms of the estimated mean-variance relationships using simulations and example real datasets. We also discuss the properties of the multivariate Poisson lognormal distribution, and ability to directly model count data including zero counts, over-dispersion, both positive and negative covariance elements, and the mapping from correlations in the latent space vs. the observed space. Finally, we illustrate their use through two model-based clustering examples using a mixtures of distributions approach in RNA-seq and microbiome data.},
}

@article {pmid40213158,
year = {2025},
author = {Wang, Y and Cheng, N and Zhang, Q and Chang, F and Wang, T and Kan, M and Han, Y and Zhai, B and Huang, K and He, X},
title = {Longitudinal multi-omics analysis of the gut-liver axis: Unraveling the molecular mechanisms of metabolic homeostasis regulation by Pd@Pt nanozymes.},
journal = {Materials today. Bio},
volume = {32},
number = {},
pages = {101685},
pmid = {40213158},
issn = {2590-0064},
abstract = {Recently, the nanozyme Pd@Pt has garnered attention due to its notable specific surface area and superior enzyme-like catalytic activity, leading to extensive examination and application in previous studies. However, the comprehensive impact of Pd@Pt nanozyme on treating metabolic disorders, such as diabetes and its associated conditions, remains largely unexplored. This research aimed to clarify how Pd@Pt influences metabolic balance at both the transcriptome and microbiome levels and to explore the interactions between microbiota and genes. We conducted an examination of mice subjected to a high-fat diet (HFD) following treatment with Pd@Pt. Transcriptome analysis was performed to identify differentially expressed genes (DEGs), and microbiome analysis was conducted to identify significant bacterial correlations associated with Pd@Pt exposure. The results indicated enhancements in glucose metabolism dysfunctions in the treated mice. Transcriptome analysis revealed that DEGs after Pd@Pt administration were enriched in the PI3K-Akt, NF-κB, and MAPK signaling pathways in the liver. Microbiome analysis identified four significant bacteria that exhibited a strong negative correlation with Pd@Pt exposure, while ten bacteria showed a positive correlation. Furthermore, a correlation network established among the gut microbiota, metabolites, and DEGs demonstrated a robust association. This research enhances our understanding of the mechanisms by which Pd@Pt affects the regulation of metabolic diseases in HFD-exposed environments and proposes a novel strategy for utilizing nanozymes in human health management.},
}

@article {pmid40212922,
year = {2025},
author = {Wang, C and Li, C and You, F and Zhou, Y and Tu, G and Liu, R and Yi, P and Wu, X and Nie, H},
title = {Multi-Omics Analysis of Gut Microbiome and Host Metabolism in Different Populations of Chinese Alligators (alligator sinensis) During Various Reintroduction Phases.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71221},
pmid = {40212922},
issn = {2045-7758},
abstract = {Reintroduction plays a significant role in the self-maintenance and reconstruction of wild animal populations, serving as a communication bridge between captive and wild animals. The Chinese alligator (Alligator sinensis) is a distinct and endangered reptile species found in China. The mechanisms by which artificially bred Chinese alligators adapt following their release into the wild remain poorly understood. This study aims to elucidate the alterations in gut microbiomes and metabolic phenotypes of Chinese alligators during their reintroduction. During the Chinese alligator's reintroduction, Fusobacterium and Cetobacterium became more abundant, while typical pathogens declined significantly. The gut type of the Chinese alligator changed from Acinetobacter to Cetobacterium. The construction of the gut microbial community was dominated by neutral (random) processes and shifted towards deterministic processes with the progression of reintroduction. In terms of species function, reintroduction significantly upregulated the expression of host immune-related genes and significantly decreased the expression of gut bacterial pathogenic genes and antibiotic resistance genes. Metagenomic and metabolomic KEGG enrichment analyses indicate that glucoside hydrolase families 13 and 23-alongside glycolysis and gluconeogenesis pathways-may play pivotal roles in energy metabolism, host-pathogen interactions, and homeostasis maintenance for Chinese alligators. Differential metabolite analysis identified significant upregulation of metabolites related to neuroendocrine immune modulation and significant down-regulation of anti-inflammatory metabolites during Chinese alligator reintroduction. Association analysis showed that there were significant co-metabolic effects between microorganisms and metabolites, which coordinated host adaptive interaction. This study provides insights into the synergistic mechanisms of host adaptation and wild environment adaptation for Chinese alligators.},
}

@article {pmid40212761,
year = {2024},
author = {Moysidou, CM and van Niekerk, DC and Stoeger, V and Pitsalidis, C and Draper, LA and Withers, AM and Hughes, K and McCoy, R and Acharya, R and Hill, C and Owens, RM},
title = {Modelling Human Gut-Microbiome Interactions in a 3D Bioelectronic Platform.},
journal = {Small science},
volume = {4},
number = {6},
pages = {2300349},
pmid = {40212761},
issn = {2688-4046},
abstract = {The role of the gut microbiome in various aspects of health and disease is now a well-established concept in modern biomedicine. Numerous studies have revealed links between host health and microbial activity, spanning from digestion and metabolism to autoimmune disorders, stress and neuroinflammation. However, the exact mechanisms underlying this complex cross-talk still remain a mystery. Conventionally, studies examining host-microbiome interactions rely on animal models, but translation of such findings into human systems is challenging. Bioengineered models represent a highly promisingapproach for tackling such challenges. Here, a bioelectronic platform, the e-transmembrane, is used to establish a 3D model of human intestine, to study the effects of microbiota on gut barrier integrity. More specifically, how postbiotics and live bacteria impact the morphology and function of the intestinal barrier is evaluated. e-Transmembrane devices provide a means for in-line and label-free continuous monitoring of host-microbe cross-talk using electrochemical impedance spectroscopy, revealing distinct patterns that emerge over 24 hours. Microscopy and quantification of molecular biomarkers further validate the differential effects of each bacterial intervention on the host tissue. In addition, a framework to better study and screen drug candidates and potential therapeutic/dietary interventions, such as postbiotics and probiotics, in more physiologically relevant human models is provided.},
}

@article {pmid40212655,
year = {2025},
author = {Iriarte-Mesa, C and Bergen, J and Danielyan, K and Crudo, F and Marko, D and Kählig, H and Del Favero, G and Kleitz, F},
title = {Functionalization of Silica Nanoparticles for Tailored Interactions with Intestinal Cells and Chemical Modulation of Paracellular Permeability.},
journal = {Small science},
volume = {5},
number = {1},
pages = {2400112},
pmid = {40212655},
issn = {2688-4046},
abstract = {The intestinal compartment confines the gut microbiome while enabling food passage and absorption of active molecules. For the rational design of oral formulations aiming to overcome physiological barriers of the gut, it is crucial to understand how cells respond to the presence of nanoparticulate materials. Taking advantage of the versatility and biocompatibility of dendritic mesoporous silica nanoparticles (DMSNs), several post-grafting strategies are developed to diversify the surface properties of spherical DMSNs and then probe interactions with the intestinal coculture cell model Caco-2/HT29-MTX-E12. Herein, the functionalization of DMSNs with polyethylene glycol, phosphonate, methyl, and farnesol moieties enables the investigation of both particle penetration through the mucus layer and pathways relevant to intracellular uptake. Contributions of surface chemistry, charge, and colloidal stability are correlated with the modulation of particle movement through the mucus and the organization of cell-cell junctions. Hydrophilic and negative functionalities favor particle distribution toward the intestinal monolayer. Instead, hydrophobic DMSNs are hindered by the mucus, possibly limiting cell contact. Hybrid surfaces, combining phosphonate and long carbon chain functions, support diffusion through the mucus and foster the paracellular permeability as well as the transient barrier relapse, as indicated by increased cell-cell distances and reorganization of tight junctions.},
}

@article {pmid40212495,
year = {2025},
author = {Mouselimis, D and Özcan, F and Wiech, T and Lüring, C},
title = {A Revision of an Infected Total Hip Arthroplasty leading to Oxalate Nephropathy: A Case Report.},
journal = {Journal of orthopaedic case reports},
volume = {15},
number = {4},
pages = {90-94},
pmid = {40212495},
issn = {2250-0685},
abstract = {INTRODUCTION: Although one of the most successful orthopedic procedures, total hip arthroplasty (THA) conveys a not negligible risk for complications.

CASE REPORT: A 72-year-old patient after a THA received an operative revision 2 times due to persistent hematoma and early periprothetic infection. Post-operative renal failure requiring hemodialysis has been caused by a histologically confirmed oxalate nephropathy (ON). Post-operative antibiotic treatment altering the gut microbiome has been assumed as the most likely cause of ON. It is the first presented case of ON as a post-operative complication after a hip arthroplasty revising operation.

CONCLUSION: Acute post-operative renal injury conveys significant danger for the patients. An interdisciplinary approach is needed as many cases require complex diagnostic and therapeutical procedures offered by experts on the field.},
}

@article {pmid40212383,
year = {2025},
author = {Yu, Y and Geng, S and Bu, C and Cao, G and Han, Y and Xie, D and Hong, Y},
title = {Dry ginger and Schisandra chinensis modulate intestinal flora and bile acid metabolism to treatment asthma.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1541335},
pmid = {40212383},
issn = {1664-302X},
abstract = {BACKGROUND AND AIMS: Zingiber officinale Rosc (Dry ginger) and Schisandra chinensis (Turcz.) Baill (Schisandra chinensis) drug pairs (DSP) are often used as drug pairs for the treatment of asthma, and these two traditional Chinese medicines (TCM) are also the core components of multiple TCM. However, its specific pharmacological mechanism needs further research. The aim of this study is to investigate the effects of DSP on intestinal flora and bile acid metabolism in rats with asthma caused by cold, and to provide experimental evidence for its clinical application.

MATERIALS AND METHODS: Sixty male rats are divided into five groups, 12 rats per group. Except for control groups, other groups of rats use the method of "abdominal injection of "OVA + ice water swimming" to establish cold cough rats models. After the administration cycle is over, an optical microscope count method is used to detect eosinophils (EOS) and neutrophils (Neu) in bronchoalveolar lavage fluid (BALF); Enzyme-Linked Immunosorbent Assay (ELISA) method detects Immunoglobulin E (IgE), Interleukin-13 (IL-13), Interleukin-4 (IL-4), Tumor Necrosis Factor-α (TNF-α), Interferon-γ (INF-γ); Western Blot (WB) and Reverse Transcription-Polymerase Chain Reaction (RT-PCR) analysis was used to detect Forkhead box protein P3 (Foxp3) and Transforming Growth Factor-beta 1 (TGF-β1) proteins expression. In addition, Using 16S rDNA sequencing reveal the role of intestinal flora in asthma and the effect on the gut microbiome after DSP treatment. We also examined Farnesoid X Receptor (FXR) proteins expression, and finally used ultra performance UPLC-MS/MS to analyze bile acids (BAs) contentin in rats.

RESULTS: DSP inhibits asthma inflammation. It alleviates inflammatory factors, suppresses the inflammatory response in asthmatic rats by regulating FOXP3 and TGF-β1 in Treg cells, and reduces tissue damage. After DSP treatment, intestinal flora changed: harmful bacteria like Streptococcus decreased, while beneficial bacteria such as Candidatus - Arthromitus and Ligilactobacillus increased. These changes can be potential markers for DSP-intervened asthma. Also, DSP increased FXR protein expression and changed the bile acid spectrum: Deoxycholic acid (DCA) increased, allocholic acid (ACA), glycolithocholic acid (GLCA), glycochenodeoxycholic acid (GCDCA) andglycoursodeoxycholic acid (GUDCA) decreased.

CONCLUSION: This study has preliminarily revealed that DSP has the effect of alleviating inflammation levels, also regulate the expression of FOXP3 and TGF-β1 proteins, and has an impact on the gut microbiota and bile acid metabolism, thereby exerting an improving effect on asthma and providing a reference for the clinical application of traditional Chinese medicine in the treatment of asthma.},
}

@article {pmid40212372,
year = {2025},
author = {Kang, Y and Sun, Y and Cui, J and Song, Y and Sun, Z and Li, H and Niu, R and Qiao, H},
title = {Combined microbiome and metabolomics analysis of yupingfeng san fermented by Bacillus coagulans: insights into probiotic and herbal interactions.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19206},
pmid = {40212372},
issn = {2167-8359},
mesh = {*Fermentation ; *Probiotics/metabolism ; *Metabolomics ; *Drugs, Chinese Herbal/metabolism ; *Bacillus coagulans/metabolism ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Yupingfeng san is a traditional Chinese medicine formula composed of siler, atractylodes, and astragalus. The herbal medicine fermentation process relies on the role of probiotics. Bacillus coagulans is a probiotic commonly used to ferment food and drugs. It produces a variety of beneficial metabolites during fermentation. However, the study on the interaction between B. coagulans and yupingfeng san is still blank.

METHODS: During solid-state fermentation of yupingfeng san, we used metabolomics technology and 16S rDNA sequencing to analyze the differential metabolites and microbial flora of B. coagulans at 0, 3, 7, 11, and 15 d, which corresponded to groups A0, B3, B7, B11, and B15, respectively. This research explored the correlation between microorganisms and metabolites in fermented compound Chinese medicine.

RESULTS: The results revealed a significant difference in species β diversity between group A0 and the B groups (P < 0.01). At the phylum level, in fermentation groups B3, B7, B11, and B15, the Cyanobacteria relative abundance decreased by 6.69%, 9.09%, 5.74%, and 2.24%, respectively (P < 0.05). The Firmicutes relative abundance increased by 39.73%, 35.65%, 49.09%, and 68.66% (P < 0.05), respectively. The Proteobacteria relative abundance decreased by 39.86% and 26.70%, respectively, in groups B11 and B15 (P < 0.05). The relative abundance of Actinobacteria increased initially with extended fermentation time, and then gradually decreased after reaching its peak in group B7. At the genus level, compared with group A0, the relative abundance of Actinobacteria increased to its highest level of 21.12% in fermentation group B3 and decreased to 9.51% after a fermentation time of 15 d. The abundance of Leuconostoc in fermentation groups B3, B7, and B11 was significantly higher than in group A0 (20.93%, 20.73%, and 21.00%, respectively, P < 0.05). Pediococcus in fermentation groups B3, B7, B11, and B15 was also significantly higher than in group A0 (4.20%, 2.35%, 18.84%, and 52.01%, P < 0.05). Both Pediococcus and Leuconostoc, which belong to lactic acid bacteria, increased fivefold, accounting for a total abundance of 62%. After yupingfeng san fermentation, using nontargeted metabolomics, we identified 315 differential metabolites. This results showed a decrease in the content of alkene and an increase in the contents of acids, lipids, ketones, and amino acids. In addition, in group B3, the contents of quercetin, paeoniflorin-3-O-glucoside, netin, iristin, anthocyanin, caffeic acid, rosmarinic acid, liquiritin, and isoliquiritin were significantly upregulated.

CONCLUSION: In this study, the composition and metabolic profile of yupingfeng san after the fermentation of B. coagulans were studied, and it was found that the fermentation group showed rich species diversity, in which the abundance of Leuconostoc and Weisseria increased significantly, while the opportunistic pathogens such as Pseudomonas aeruginosa and Enterobacter decreased significantly. The analysis of metabolic products showed that the contents of acids, lipids and ketones were significantly increased, rich in a variety of beneficial microorganisms and small molecular compounds with antibacterial effects, and these changes worked together to inhibit the growth of pathogens and maintain intestinal health. The study not only helps to elucidate the assembly mechanism and functional expression of microorganisms after Chinese traditional medicine fermentation, but also provides a solid scientific basis for the development of efficient and safe micro-ecological feed additives.},
}

*Fermentation
*Probiotics/metabolism
*Metabolomics
*Drugs, Chinese Herbal/metabolism
*Bacillus coagulans/metabolism
*Microbiota
RNA, Ribosomal, 16S/genetics

@article {pmid40212280,
year = {2025},
author = {Agranyoni, O and Rowley, T and Johnson, SB and Volk, H and Schleif, W and Hernandez, RG and Klein, LM and Yolken, RH and Sabunciyan, S},
title = {Oral microbiome composition is associated with depressive symptoms during pregnancy.},
journal = {Brain, behavior, & immunity - health},
volume = {45},
number = {},
pages = {100978},
pmid = {40212280},
issn = {2666-3546},
abstract = {BACKGROUND: Oral microbiome dysbiosis has been linked to systemic disease with an underlying inflammatory etiology. However, the possible association of the oral microbiome in antenatal depression has received little attention.

METHODS: Participants were pregnant women in the PREDICT prenatal cohort study (n = 400) who provided saliva during pregnancy. Using 16S rRNA sequencing, we determined the association between composition of the salivary microbiome and a continuous measure of depressive symptoms (Center for Epidemiological Studies-Depression Scale (CES-D): 0-60) as well as clinically significant depressive symptoms during pregnancy (CES-D score> 16, n = 46) compared with women without clinically significant symptoms (n = 327).

RESULTS: CES-D scores were associated with differences in bacterial levels in the salivary microbiome. Women with clinically significant depressive symptoms (CES-D≥16) had significantly lower abundance in nine bacterial taxa, including the Neisseria genus, which has previously been positively associated with oral health and negatively correlated with pro-inflammatory cytokines, mental health, and infant birth weight. Findings were not explained by body mass index, smoking, antibiotic administration, oral health problems, or gestational week. Prediction tools based on 16S sequences indicated that significantly lower levels of several pathways related to the biosynthesis of Menaquinol, Ectoine biosynthesis, and D-glucarate degradation, were associated with women with depressive symptoms.

CONCLUSIONS: Our findings underscore the potential relationship between the oral microbiome and antenatal depression, highlighting microbiome measures as a promising source of biomarkers for maternal mental health. This study suggests previously unexplored aspects for understanding the microbiome's composition in women with mental health problems, emphasizing the need for further longitudinal investigations to elucidate the temporal dynamics of the oral microbiome in pregnancy.},
}

@article {pmid40212162,
year = {2025},
author = {Aleali, MS and Mahapatro, A and Maddineni, G and Paladiya, R and Jeanty, H and Mohanty, E and Mirchandani, M and Jahanshahi, A and Devulapally, P and Alizadehasl, A and Tariq, MD and Hosseini Jebelli, SF and Aliabadi, AY and Hashemi, SM and Amini-Salehi, E},
title = {The impact of gut microbiome modulation on anthropometric indices in metabolic syndrome: an umbrella review.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {4},
pages = {2263-2277},
pmid = {40212162},
issn = {2049-0801},
abstract = {BACKGROUND: Metabolic syndrome (MetS) is a complex disorder characterized by a cluster of metabolic risk factors. Recent research highlights the gut microbiome's role in metabolic regulation, suggesting that modulation through probiotics, prebiotics, and synbiotics may provide a novel approach to managing MetS. This umbrella review aims to integrate insights from existing meta-analyses to explore how changes in gut microbiota influence key body measurement indicators in individuals with MetS.

METHODS: A systematic search of PubMed, Scopus, and Web of Science databases identified meta-analyses that assessed the impact of probiotics, prebiotics, or synbiotics on anthropometric indices in MetS patients.

RESULTS: The results indicated that microbial therapy leads to a significant reduction in body mass index (BMI) (SMD: -0.22; 95% CI: -0.35 to -0.09; P < 0.01) and waist circumference (WC) (SMD: -0.47; 95% CI: -0.80 to -0.15; P < 0.01). However, microbial therapy did not significantly affect body fat mass (SMD: -0.30; 95% CI: -0.64 to 0.02; P = 0.06), body fat percentage (SMD: -0.29; 95% CI: -0.62 to 0.03; P = 0.07), waist-to-hip ratio (SMD: -0.09; 95% CI: -0.46 to 0.28; P = 0.63), and weight (SMD: -0.06; 95% CI: -0.21 to 0.08; P = 0.37).

CONCLUSIONS: Gut microbial modulation, mainly through probiotics and synbiotics, shows promise in reducing BMI and WC in MetS patients. However, its effects on other anthropometric indices remain uncertain, warranting further high-quality research to fully understand microbial interventions' therapeutic potential.},
}

@article {pmid40212158,
year = {2025},
author = {Abbas, AH and Haji, MR and Shimal, AA and Kurmasha, YH and Al-Janabi, AAH and Azeez, ZT and Al-Ali, ARS and Al-Najati, HMH and Al-Waeli, ARA and Abdulhadi, NASA and Al-Tuaama, AZH and Al-Ashtary, MM and Hussin, OA},
title = {A multidisciplinary review of long COVID to address the challenges in diagnosis and updated management guidelines.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {4},
pages = {2105-2117},
pmid = {40212158},
issn = {2049-0801},
abstract = {Long COVID has emerged as a significant challenge since the COVID-19 pandemic, which was declared as an outbreak in March 2020, marked by diverse symptoms and prolonged duration of disease. Defined by the WHO as symptoms persisting or emerging for at least two months post-SARS-CoV-2 infection without an alternative cause, its prevalence varies globally, with estimates of 10-20% in Europe, 7.3% in the USA, and 3.0% in the UK. The condition's etiology remains unclear, involving factors, such as renin-angiotensin system overactivation, persistent viral reservoirs, immune dysregulation, and autoantibodies. Reactivated viruses, like EBV and HSV-6, alongside epigenetic alterations, exacerbate mitochondrial dysfunction and energy imbalance. Emerging evidence links SARS-CoV-2 to chromatin and gut microbiome changes, further influencing long-term health impacts. Diagnosis of long COVID requires detailed systemic evaluation through medical history and physical examination. Management is highly individualized, focusing mainly on the patient's symptoms and affected systems. A multidisciplinary approach is essential, integrating diverse perspectives to address systemic manifestations, underlying mechanisms, and therapeutic strategies. Enhanced understanding of long COVID's pathophysiology and clinical features is critical to improving patient outcomes and quality of life. With a growing number of cases expected globally, advancing research and disseminating knowledge on long COVID remain vital for developing effective diagnostic and management frameworks, ultimately supporting better care for affected individuals.},
}

@article {pmid40212131,
year = {2025},
author = {Mubeen, M and Shazad, A and Aziz, M and Poudel, S},
title = {Role of gut microbiota and trimethylamine N-oxide in preeclampsia: pathophysiological insights and therapeutic opportunities.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {4},
pages = {1790-1793},
pmid = {40212131},
issn = {2049-0801},
abstract = {Preeclampsia (PE) is a condition where a sudden rise in blood pressure (>140/90 mmHg) after the 20th week of gestation poses a significant threat to maternal as well as fetal health. PE causes maternal organ damage and several fetal abnormalities which may prove fatal, leading to a high mortality rate. Several studies have been conducted on the role of the gut microbiome, linking its connection to the development of various diseases including PE. One such derivative of gut microbiota is trimethylamine N-oxide (TMAO), a metabolite shown to be involved in the progression of PE by disrupting the normal microbiome, promoting inflammation and oxidative stress. The objective of this editorial is to provide a general overview of PE, assess the negative effect of TMAO leading to diseases such as PE, and provide an outline for its potential exploitation as a treatment strategy. Although the current findings offer important insights into the mechanisms related to TMAO, further trials can confirm its clinical relevance and investigate its potential as a diagnostic biomarker and a therapeutic target.},
}

@article {pmid40212081,
year = {2024},
author = {Tuerhongjiang, G and Guo, M and Qiao, X and Liu, J and Xi, W and Wei, Y and Liu, P and Lou, B and Wang, C and Sun, L and Yuan, X and Liu, H and Xiong, Y and Ma, Y and Li, H and Zhou, B and Li, L and Yuan, Z and Wu, Y and She, J},
title = {Gut Microbiota Regulate Saturated Free Fatty Acid Metabolism in Heart Failure.},
journal = {Small science},
volume = {4},
number = {9},
pages = {2300337},
pmid = {40212081},
issn = {2688-4046},
abstract = {AIMS: Heart failure (HF) is associated with profound changes in cardiac metabolism. At present, there is still a lack of relevant research to explore the key microbiome and their metabolites affecting the progression of HF. Herein, the interaction of gut microbiota and circulating free fatty acid (FFA) in HF patients and mice is investigated.

METHODS AND RESULTS: In HF patients, by applying metagenomics analysis and targeted FFA metabolomics, enriched abundance of Clostridium sporogenes (C.sp) in early and late stage of HF patients, which negatively correlated to saturated free fatty acid (SFA) levels, is identified. KEGG analysis further indicates microbiota gene enrichment in FFA degradation in early HF, and decreased gene expression in FFA synthesis in late HF. In HF mice (C57BL/6J) induced by isoproterenol (ISO), impaired intestinal permeability is observed, and decreased fecal C.sp and increased SFA are further validated. At last, by supplementing C.sp to ISO-induced HF mice, the cardiac function, fibrosis, and myocardial size are partially rescued, together with decreased circulating SFA levels.

CONCLUSIONS: Clostridium abundance is increased in HF, compensating cardiac function deterioration via downregulation of circulating SFA levels. The results demonstrate that the gut microbiota-SFA axis plays an important role in HF protection, which may provide a strategic advantage for the probiotic therapy development in HF.},
}

@article {pmid40211980,
year = {2025},
author = {Elena Schmitz, J and Rahmann, S},
title = {A comprehensive review and evaluation of species richness estimation.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf158},
pmid = {40211980},
issn = {1477-4054},
mesh = {*Biodiversity ; Computer Simulation ; Animals ; Computational Biology/methods ; Algorithms ; },
abstract = {MOTIVATION: The statistical problem of estimating the total number of distinct species in a population (or distinct elements in a multiset), given only a small sample, occurs in various areas, ranging from the unseen species problem in ecology to estimating the diversity of immune repertoires. Accurately estimating the true richness from very small samples is challenging, in particular for highly diverse populations with many rare species. Depending on the application, different estimation strategies have been proposed that incorporate explicit or implicit assumptions about either the species distribution or about the sampling process. These methods are scattered across the literature, and an extensive overview of their assumptions, methodology, and performance is currently lacking.

RESULTS: We comprehensively review and evaluate a variety of existing methods on real and simulated data with different compositions of rare and abundant species. Our evaluation shows that, depending on species composition, different methods provide the most accurate richness estimates. Simple methods based on the observed number of singletons yield accurate asymptotic lower bounds for several of the tested simulated species compositions, but tend to underestimate the true richness for heterogeneous populations and small samples containing 1% to 5% of the population. When the population size is known, upsampling (extrapolating) estimators such as PreSeq and RichnEst yield accurate estimates of the total species richness in a sample that is up to 10 times larger than the observed sample.

AVAILABILITY: Source code for data simulation and richness estimation is available at https://gitlab.com/rahmannlab/speciesrichness.},
}

*Biodiversity
Computer Simulation
Animals
Computational Biology/methods
Algorithms

@article {pmid40211775,
year = {2025},
author = {Kumar, N and Das, A and Kumari, N and Jain, U and Singh, G and Pandey, DP and Bodakhe, SH},
title = {"Preventive Role of Intermittent Fasting and Vitamin E in Mitigating Propylthiouracil-Induced Hypothyroidism Progression in Rat Model".},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-25},
doi = {10.1017/S0007114525000832},
pmid = {40211775},
issn = {1475-2662},
abstract = {Thyroid disorders are increasingly prevalent globally and are considered metabolic-lifestyle diseases. While medications can manage thyroid dysfunction, they are usually lifelong, costly, and not always practical. Intermittent fasting (IF), a highly adaptable dietary regimen, has been shown to influence lifestyle, gut microbiome, and circadian rhythms. Our study hypothesized that IF, combined with vitamin supplementation, could reduce the risk of thyroid disorders due to their antioxidant effects. In this study, experimental animals were divided into five groups: Euthyroid, hypothyroidism control, IF + vitamin E, vitamin E, and IF. Hypothyroidism was induced using propylthiouracil (PTU) over 24 days, and IF and vitamin E (66 mg/ml) were administered based on the experimental group. The hypothyroid animals exhibited increased anxiety, weight gain, lipid peroxidation, and a significant reduction in thyroid hormone levels, locomotor activity, and antioxidant levels-clear signs of thyroid dysfunction's impact on metabolism and overall health. Our proposed therapies IF and vitamin E effectively mitigated thyroid damage. Drawing inspiration from ancient Ayurveda and modern healthcare strategies, these cost-effective and practical regimens offer a promising solution to managing thyroid disorders globally.},
}

@article {pmid40211688,
year = {2025},
author = {Ge, SX and Niu, YM and Ren, LL and Zong, SX},
title = {Inheritance or Recruitment? The Assembly Mechanisms and Functional Dynamics of Microbial Communities in the Life Cycle of a Wood-Feeding Beetle.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17751},
doi = {10.1111/mec.17751},
pmid = {40211688},
issn = {1365-294X},
support = {2021YFD1400900//National Key R&D Program of China/ ; },
abstract = {Microbial partners enhance the metabolic capabilities of insects, enabling their adaptation to diverse ecological niches. Xylophagous insects have larvae that can digest lignocellulose and cope with plant secondary metabolites (PSMs). However, there is little information in terms of microbiome sources, dynamics and species contributions. This limits our understanding of the interaction between xylophagous insects and the microbiome. Monochamus saltuarius (Cerambycidae) is a significant borer of conifers. We used combined qPCR, host genomic and microbiome metagenomic datasets, as well as in vitro validation experiments to study the dynamics of the associated microbiome and its interactions with M. saltuarius. We evaluated microbial metabolic/biosynthetic contributions and validated their related functions. Our findings revealed that insect growth and development altered the quantity and community composition of associated bacteria and fungi. The egg microbiome was particularly susceptible to alteration due to oviposition pits. Bacterial transmission largely persisted between developmental stages, while fungal re-acquisition primarily originated from the external environment. By reconstructing community pathway maps, we identified the cooperative interactions between the insect and its gut microbiome. As larvae transitioned from phloem to xylem feeding, the functional role of the gut microbiome in various pathways was weakened. Remarkably, high-contribution bacterial species largely overlapped across different functional roles, and these species also showed considerable overlap between phloem and xylem feeding periods. Overall, our study highlights the unique interaction between xylophagous insects and their microbiome, which enhances their ability in lignocellulose digestion, PSMs degradation and the acquisition of essential amino acids, as well as vitamins.},
}

@article {pmid40211685,
year = {2025},
author = {Kim, JW and Choi, EC and Lee, KJ},
title = {Standardizing the approach to clinical-based human microbiome research: from clinical information collection to microbiome profiling and human resource utilization.},
journal = {Osong public health and research perspectives},
volume = {},
number = {},
pages = {},
doi = {10.24171/j.phrp.2024.0319},
pmid = {40211685},
issn = {2210-9099},
abstract = {OBJECTIVES: This study presents the standardized protocols developed by the Clinical-Based Human Microbiome Research and Development Project (cHMP) in the Republic of Korea.

METHODS: It addresses clinical metadata collection, specimen handling, DNA extraction, sequencing methods, and quality control measures for microbiome research.

RESULTS: The cHMP involves collecting samples from healthy individuals and patients across various body sites, including the gastrointestinal tract, oral cavity, respiratory system, urogenital tract, and skin. These standardized procedures ensure consistent data quality through controlled specimen collection, storage, transportation, DNA extraction, and sequencing. Sequencing encompasses both amplicon and whole metagenome methods, followed by stringent quality checks. The protocols conform to international guidelines, ensuring that the data generated are both reliable and comparable across microbiome studies.

CONCLUSION: The cHMP underscores the importance of methodological standardization in enhancing data integrity, reproducibility, and advancing microbiome-based research with potential applications for improving human health outcomes.},
}

@article {pmid40211627,
year = {2025},
author = {Yakubu, I and Yeon, E and Kong, HG},
title = {Microbial Community Responses to Alternate Wetting and Drying in the System of Rice Intensification.},
journal = {The plant pathology journal},
volume = {41},
number = {2},
pages = {231-239},
doi = {10.5423/PPJ.NT.01.2025.0001},
pmid = {40211627},
issn = {1598-2254},
support = {//Chungbuk National University/ ; },
abstract = {Continuous flooding in rice production presents significant challenges, such as increased labor intensity and soil degradation. However, when properly implemented, alternate wetting and drying can mitigate these issues. Despite its potential advantages, the effects of different water management practices on the soil microbiome are not well understood. This study explored how intermittent flooding and drying influence the soil microbiome by analyzing microbial communities under varying moisture conditions using Illumina sequencing. The results showed notable shifts in the abundance of Bacillota and Actinomycetota in response to fluctuations in water levels, although the overall microbial abundance returned to its original state under stable moisture conditions. In contrast, the abundance of Chloroflexota, which increased during waterlogging, remained elevated even under dry conditions. Additionally, microbial interactions were more pronounced during waterlogging compared to both moist and dry conditions. Overall, this research underscores the significant role of water management in shaping soil bacterial communities.},
}

@article {pmid40211625,
year = {2025},
author = {Lee, SM and Tae, HS and Kong, HG and Lee, B and Chang, YK and Ryu, CM},
title = {Foliar Application of Chlorella Supernatant Protects Turfgrass against Clarireedia jacksonii by Eliciting Induced Resistance and Modulating the Rhizosphere Microbiota.},
journal = {The plant pathology journal},
volume = {41},
number = {2},
pages = {210-224},
doi = {10.5423/PPJ.FT.01.2025.0009},
pmid = {40211625},
issn = {1598-2254},
support = {ABC-2010-0029728//Ministry of Science, ICT and Future Planning/ ; 918017-4//Ministry of Agriculture, Food and Rural Affairs/ ; RS-2023-00249410//National Research Foundation of Korea/ ; //Korea Reseach Institute of Bioscience & BioTechnology/ ; },
abstract = {Large-scale culture of the microalga Chlorella produces valuable products. Cultivation also generates tons of supernatant waste that require detoxification and disposal. Recent research has focused on recycling waste supernatant as a plant protectant and biofertilizer, although, to date, most studies have considered its use as a biological control of pathogens infecting dicot plants. By contrast, the current study evaluated whether Chlorella supernatant could protect turfgrass (Agrostis stolonifera), a monocot plant widely used as a turfgrass, against dollar spot disease caused by the fungal pathogen Clarireedia jacksonii (formerly Sclerotinia homoeocarpa) under greenhouse and field conditions. Foliar application of supernatants from Chlorella sp. ABC001 and HS2 cultures reduced the incidence of dollar spot disease in turfgrass under both greenhouse and field conditions without directly inhibiting growth. The effects of supernatant application on the rhizosphere microbiome were investigated using 16S rRNA amplicon sequencing. Application of ABC001 and HS2 supernatants modulated the structure of the rhizosphere microbiome and enriched specific microbial taxa that improved turfgrass health in the presence of C. jacksonii. The application of waste Chlorella supernatant therefore offers an alternative method for protecting monocot plants against fungal pathogens, while also enhancing the composition of soil microbes in the rhizosphere.},
}

@article {pmid40211604,
year = {2025},
author = {Rajczewski, AT and Blakeley-Ruiz, JA and Meyer, A and Vintila, S and McIlvin, MR and Van Den Bossche, T and Searle, BC and Griffin, TJ and Saito, MA and Kleiner, M and Jagtap, PD},
title = {Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e202400187},
doi = {10.1002/pmic.202400187},
pmid = {40211604},
issn = {1615-9861},
support = {R35GM138362/NH/NIH HHS/United States ; R01GM135709/GM/NIGMS NIH HHS/United States ; OCE-2123055//National Science Foundation/ ; 2021-67013-34537//U.S. Department of Agriculture National Institute of Food and Agriculture/ ; [1286824N]//Research Foundation Flanders/ ; T32DK007737//National Institute of Diabetes and Digestive and Kidney Diseases:/ ; },
abstract = {Mass spectrometry (MS)-based metaproteomics is used to identify and quantify proteins in microbiome samples, with the frequently used methodology being data-dependent acquisition mass spectrometry (DDA-MS). However, DDA-MS is limited in its ability to reproducibly identify and quantify lower abundant peptides and proteins. To address DDA-MS deficiencies, proteomics researchers have started using Data-independent acquisition mass spectrometry (DIA-MS) for reproducible detection and quantification of peptides and proteins. We sought to evaluate the reproducibility and accuracy of DIA-MS metaproteomic measurements relative to DDA-MS using a mock community of known taxonomic composition. Artificial microbial communities of known composition were analyzed independently in three laboratories using DDA- and DIA-MS acquisition methods. In this study, DIA-MS yielded more protein and peptide identifications than DDA-MS in each laboratory for the particular instruments and software parameters chosen. In addition, the protein and peptide identifications were more reproducible in all laboratories and provided an accurate quantification of proteins and taxonomic groups in the samples. We also identified some limitations of current DIA tools when applied to metaproteomic data, highlighting specific needs to improve DIA tools enabling analysis of metaproteomic datasets from complex microbiomes. Ultimately, DIA-MS represents a promising strategy for MS-based metaproteomics due to its large number of detected proteins and peptides, reproducibility, deep sequencing capabilities, and accurate quantitation.},
}

@article {pmid40211528,
year = {2025},
author = {Liu, Y and Feng, D and Zhang, H and Wang, L},
title = {Dissecting Causal Relationships Between Gut Microbiota, 1400 Blood Metabolites, and Intervertebral Disc Degeneration.},
journal = {Neurospine},
volume = {22},
number = {1},
pages = {211-221},
doi = {10.14245/ns.2449172.586},
pmid = {40211528},
issn = {2586-6583},
abstract = {OBJECTIVE: The precise mechanisms driving intervertebral disc degeneration (IVDD) development remain unclear, but evidence suggests a significant involvement of gut microbiota (GM) and blood metabolites. We aimed to investigate the causal relationships between GM, IVDD, and blood metabolites using Mendelian randomization (MR) analysis.

METHODS: We utilized the summary statistics of GM from the MiBioGen consortium, 1400 blood metabolites from the genome-wide association studies (GWAS) Catalog, and IVDD data from the FinnGen repository, which are sourced from the largest GWAS conducted to date. Employing bidirectional MR analyses, we investigated the causal relationships between GM and IVDD. Additionally, we conducted 2 mediation analyses, 2-step MR and multivariable MR (MVMR), to identify potential mediating metabolites.

RESULTS: Five bacterial genera were causally associated with IVDD, while IVDD did not show a significant causal effect on GM. In the 2-step MR analysis, Eubacteriumfissicatenagroup, RuminococcaceaeUCG003, Lachnoclostridium, and Marvinbryantia genera, along with metabolites X-24949, Pimeloylcarnitine/3-methyladipoylcarnitine (C7-DC), X-24456, histidine, 2-methylserine, Phosphocholine, and N-delta-acetylornithine, were all significantly associated with IVDD (all p < 0.05). MVMR analysis revealed that the associations between Eubacteriumfissicatenagroup genus and IVDD were mediated by X-24949 (8.1%, p = 0.024); Lachnoclostridium genus and IVDD were mediated by histidine (18.1%, p = 0.013); and RuminococcaceaeUCG003 genus and IVDD were mediated by C7-DC (-7.5%, p = 0.041).

CONCLUSION: The present MR study offers evidence supporting the causal relationships between several specific GM taxa and IVDD, as well as identifying potential mediating metabolites.},
}

@article {pmid40211458,
year = {2025},
author = {Akagawa, S and Tsuji, S and Nakai, Y and Urakami, C and Yamagishi, M and Akagawa, Y and Kaneko, K},
title = {Faecalibacterium in the Gut Microbiota Predicts Tolerance Acquisition in Pediatric Hen's Egg Allergy.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16556},
pmid = {40211458},
issn = {1398-9995},
support = {//Nipponham Foundation for the Future of Food/ ; //Kansai Medical University/ ; },
}

@article {pmid40211390,
year = {2025},
author = {Wang, Z and Gao, X and Ji, H and Shao, M and Ni, B and Fei, S and Sun, L and Chen, H and Tan, R and Du, M and Gu, M},
title = {Characterization of gut microbiota and metabolites in renal transplant recipients during COVID-19 and prediction of one-year allograft function.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {420},
pmid = {40211390},
issn = {1479-5876},
support = {82170769//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Kidney Transplantation ; *COVID-19/metabolism/microbiology/complications ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; Adult ; *Metabolome ; SARS-CoV-2 ; Allografts ; Transplant Recipients ; Feces/microbiology ; Aged ; },
abstract = {BACKGROUND: The gut-lung-kidney axis is pivotal in immune-related kidney diseases, with gut dysbiosis potentially exacerbating the severity of Coronavirus disease 2019 (COVID-19) in recipients of kidney transplant. This study aimed to characterize the gut microbiome and metabolome in renal transplant recipients with COVID-19 pneumonia over a one-year follow-up period.

METHODS: A total of 30 renal transplant recipients were enrolled, comprising 17 with COVID-19 pneumonia, six with mild COVID-19, and seven without COVID-19. Fecal samples were collected at the onset of infection for gut microbiome and metabolome analysis. Generalized Estimating Equations (GEE) model and Latent Class Growth Mixed Model (LCGMM) were employed to dissect the relationships among clinical characteristics, laboratory tests, and gut microbiota and metabolites.

RESULTS: Four microbial phyla (Deferribacteres, TM7, Fusobacteria, and Gemmatimonadetes) and 13 genera were significantly enriched across three recipients groups, correlating with baseline inflammatory response and allograft function. Additionally, 52 differentially expressed metabolites were identified, with seven significantly correlating with eight altered microbiota genera. LCGMM revealed two distinct classes of recipients, with those suffering from COVID-19 pneumonia exhibiting significantly elevated serum creatinine (Scr) trajectories over the one-year period. GEE further identified 12 genera and 181 metabolites closely associated with these trajectories; a multivariable model incorporating gut metabolites of 1-Caffeoylquinic Acid and PMK was found to effectively predict one-year allograft function.

CONCLUSIONS: Our study indicates a possible interaction between the composition of the gut microbiota and metabolites community and COVID-19 in renal transplant recipients, particularly in relation to disease severity and the prediction of one-year allograft function.},
}

Humans
*Kidney Transplantation
*COVID-19/metabolism/microbiology/complications
*Gastrointestinal Microbiome/physiology
Female
Male
Middle Aged
Adult
*Metabolome
SARS-CoV-2
Allografts
Transplant Recipients
Feces/microbiology
Aged

@article {pmid40211330,
year = {2025},
author = {Zhang, Z and Jiang, C and Xing, YQ and Yang, T and Zou, L and Jia, Z and Zhao, L and Han, X and Qu, X and Zhang, Z and Zong, J and Wang, S},
title = {Unveiling the interplay among skin microbiota, cytokines, and T2DM: an insightful Mendelian randomization study.},
journal = {Nutrition & metabolism},
volume = {22},
number = {1},
pages = {29},
pmid = {40211330},
issn = {1743-7075},
support = {82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 82074426, 82104864, 82204822//National Natural Science Foundation of China/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2023JH2/101300096//Applied Basic Research Project of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; 2021-BS-215, 2022-MS-25, 2023-MS-13//Natural Science Foundation of Liaoning Province/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; XLYC1802014//Liaoning Revitalization Talents Program/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; 2017226015//Liaoning Key Research and Development Planning Project/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; LJKMZ20221286//Basic Research Projects of Liaoning Provincial Department of Education/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; XZ202301ZR0030G, XZ2023ZR-ZY82(Z)//Natural Science Foundation of Tibet Autonomous Region/ ; },
abstract = {BACKGROUND: Previous observational studies have indicated a correlation between the skin microbiome and Type 2 diabetes (T2DM). It is hypothesized that this causal relationship may be influenced by inflammatory responses. However, these factors as determinants of T2DM remain largely unexplored.

METHOD: This study incorporated data from the GWAS database on the skin microbiome, 91 types of inflammatory cytokines, and T2DM. We employed two-sample MR and multivariable MR methods to assess the correlation between the skin microbiome and T2DM, and to investigate whether this correlation is affected by inflammatory cytokines.

RESULTS: The results of the two-sample MR analysis indicate that within the skin microbiome, genetically predicted genus: Acinetobacter, class: Alphaproteobacteria, genus: Bacteroides, ASV005[Propionibacterium granulosum], and ASV072[Rothia mucilaginosa] are associated with an increased risk of T2DM, while phylum: Proteobacteria, genus: Enhydrobacter, family: Clostridiales, ASV006[Staphylococcus hominis] serve as protective factors against T2DM. Among the inflammatory cytokines, levels of Macrophage colony-stimulating factor 1, Tumor necrosis factor receptor superfamily member 9, Urokinase-type plasminogen activator, and C-C motif chemokine 28 are associated with an increased risk of T2DM. Multivariable MR analysis further revealed that Macrophage colony-stimulating factor 1 levels act as a mediating factor between ASV072[Rothia mucilaginosa] and T2DM.

CONCLUSION: In this study, we found a connection between the skin microbiome and T2DM, with inflammatory cytokines playing a key role in this relationship. This research helps us better understand this complex link and shows that addressing inflammation is important for preventing and treating diabetes. This could greatly benefit public health by reducing the impact of diabetes and its complications. Our results suggest that future studies should explore the specific biological interactions between the skin microbiome and diabetes to develop more effective risk management and treatment strategies from a microbial perspective.},
}

@article {pmid40211272,
year = {2025},
author = {Li, N and Wang, Y and Zhang, H and Ma, L and Huang, X and Qiao, Y and Li, H and Zhao, H and Li, P},
title = {Urobiome of patients with diabetic kidney disease in different stages is revealed by 2bRAD-M.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {414},
pmid = {40211272},
issn = {1479-5876},
support = {82104601//The National Natural Science Foundation of China/ ; 82174144//National Natural Science Foundation of China/ ; U23A20504//National Natural Science Foundation of China/ ; 82174296//National Natural Science Foundation of China/ ; 2023-NHLHCRFDJMS-05//National High Level Hospital Clinical Research Funding/ ; ZRJY2024-GG11//Elite Medical Professionals project of China-Japan Friendship Hospital/ ; },
mesh = {Humans ; *Diabetic Nephropathies/microbiology/urine ; *Microbiota/genetics ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Diabetes Mellitus, Type 2/microbiology ; Bacteria/genetics ; Case-Control Studies ; Aged ; },
abstract = {BACKGROUND: Knowledge of the urinary microbiome (urobiome) in diabetic kidney disease (DKD) remains limited. The most commonly used 16S rRNA sequencing technique can only provide bacterial identification at the genus level. As a novel technique, 2bRAD sequencing for microbiome (2bRAD-M) can be used to identify the low-biomass microbiome at the species level. In this study, we used 2bRAD-M to compare the urobiome composition of patients with DKD at different stages with healthy individuals and those with type 2 diabetes mellitus (T2DM), with the expectation that we would find discriminative species correlated with DKD.

METHOD: Healthy controls, patients with DKD with microalbuminuria (DKD1 group) or macroalbuminuria (DKD2 group), and patients with T2DM were recruited (n = 20 for each group). The first-morning urine was collected for 2bRAD-M testing. The albumin-to-creatinine ratio (ACR) was also measured with urine samples. Serum samples were collected for detecting clinical indicators. The microbial diversity and composition based on abundance were calculated. Differential bacteria for different groups were identified. Besides, the correlation between discriminative bacteria and clinical indices was also analyzed.

RESULTS: Urobiome diversity was significantly reduced in the DKD groups. In the DKD1 group, was the dominant genus, followed by Pseudomonas_E, whereas in the DKD2 group, Pseudomonas_E became the dominant genus and Escherichia was notably reduced. Both Bifidobacterium and Streptococcus, which were the top genera in the control group, were substantially decreased in the DKD groups. The discriminative species for DKD1 included Escherichia coli and Acinetobacter johnsonii, while for DKD2, Pseudomonas_E oleovorans, Enterococcus faecalis, and Morganella morganii were identified. Pseudomonas_E, Enterococcus and Morganella showed a strong correlation with renal function indicators and urinary protein levels.

CONCLUSION: The urobiome diversity and composition in patients with DKD were markedly different from those in healthy individuals and T2DM patients. These findings provide valuable insights into the onset and progression of DKD, driven by changes in the urinary bacterial community structure.},
}

Humans
*Diabetic Nephropathies/microbiology/urine
*Microbiota/genetics
Male
Female
Middle Aged
RNA, Ribosomal, 16S/genetics
Diabetes Mellitus, Type 2/microbiology
Bacteria/genetics
Case-Control Studies
Aged

@article {pmid40211121,
year = {2025},
author = {Polizel, GHG and Diniz, WJS and Cesar, ASM and Ramírez-Zamudio, GD and Cánovas, A and Dias, EFF and Fernandes, AC and Prati, BCT and Furlan, É and Pombo, GDV and Santana, MHA},
title = {Impacts of prenatal nutrition on metabolic pathways in beef cattle: an integrative approach using metabolomics and metagenomics.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {359},
pmid = {40211121},
issn = {1471-2164},
support = {2021/03265-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/12105-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {Animals ; Cattle ; Female ; *Metabolomics/methods ; Pregnancy ; *Metabolic Networks and Pathways ; *Metagenomics/methods ; Male ; Metabolome ; Rumen/microbiology ; Microbiota ; *Prenatal Nutritional Physiological Phenomena ; *Animal Nutritional Physiological Phenomena ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: This study assessed the long-term metabolic effects of prenatal nutrition in Nelore bulls through an integrated analysis of metabolome and microbiome data to elucidate the interconnected host-microbe metabolic pathways. To this end, a total of 126 cows were assigned to three supplementation strategies during pregnancy: NP (control)- only mineral supplementation; PP- protein-energy supplementation during the last trimester; and FP- protein-energy supplementation throughout pregnancy. At the end of the finishing phase, blood, fecal, and ruminal fluid samples were collected from 63 male offspring. The plasma underwent targeted metabolomics analysis, and fecal and ruminal fluid samples were used to perform 16 S rRNA gene sequencing. Metabolite and ASV (amplicon sequence variant) co-abundance networks were constructed for each treatment using the weighted gene correlation network analysis (WGCNA) framework. Significant modules (p ≤ 0.1) were selected for over-representation analyses to assess the metabolic pathways underlying the metabolome (MetaboAnalyst 6.0) and the microbiome (MicrobiomeProfiler). To explore the metabolome-metagenome interplay, correlation analyses between host metabolome and microbiome were performed. Additionally, a holistic integration of metabolic pathways was performed (MicrobiomeAnalyst 2.0).

RESULTS: A total of one and two metabolite modules associated with the NP and FP were identified, respectively. Regarding fecal microbiome, three, one, and two modules for the NP, PP, and FP were identified, respectively. The rumen microbiome demonstrated two modules correlated with each of the groups under study. Metabolite and microbiome enrichment analyses revealed the main metabolic pathways associated with lipid and protein metabolism, and regulatory mechanisms. The correlation analyses performed between the host metabolome and fecal ASVs revealed 13 and 12 significant correlations for NP and FP, respectively. Regarding the rumen, 16 and 17 significant correlations were found for NP and FP, respectively. The NP holistic analysis was mainly associated with amino acid and methane metabolism. Glycerophospholipid and polyunsaturated fatty acid metabolism were over-represented in the FP group.

CONCLUSIONS: Prenatal nutrition significantly affected the plasma metabolome, fecal microbiome, and ruminal fluid microbiome of Nelore bulls, providing insights into key pathways in protein, lipid, and methane metabolism. These findings offer novel discoveries about the molecular mechanisms underlying the effects of prenatal nutrition.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Animals
Cattle
Female
*Metabolomics/methods
Pregnancy
*Metabolic Networks and Pathways
*Metagenomics/methods
Male
Metabolome
Rumen/microbiology
Microbiota
*Prenatal Nutritional Physiological Phenomena
*Animal Nutritional Physiological Phenomena
Gastrointestinal Microbiome

@article {pmid40211032,
year = {2025},
author = {Hindson, J},
title = {Diet-driven microbiome restoration associated with cardiometabolic benefits.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {40211032},
issn = {1759-5053},
}

@article {pmid40210899,
year = {2025},
author = {Ni Lochlainn, M and Bowyer, RCE and Moll, JM and García, MP and Wadge, S and Baleanu, AF and Nessa, A and Sheedy, A and Akdag, G and Hart, D and Raffaele, G and Seed, PT and Murphy, C and Harridge, SDR and Welch, AA and Greig, C and Whelan, K and Steves, CJ},
title = {Author Correction: Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3393},
doi = {10.1038/s41467-025-58771-w},
pmid = {40210899},
issn = {2041-1723},
}

@article {pmid40210877,
year = {2025},
author = {Wagner, J and Handley, A and Donato, CM and Lyons, EA and Pavlic, D and Ong, DS and Bonnici, R and Bogdanovic-Sakran, N and Parker, EPK and Bronowski, C and Thobari, JA and Satria, CD and Nirwati, H and Witte, D and Jere, KC and Mpakiza, A and Watts, E and Turner, A and Boniface, K and Mandolo, J and Justice, F and Bar-Zeev, N and Iturriza-Gomara, M and Buttery, JP and Cunliffe, NA and Soenarto, Y and Bines, JE},
title = {Early-life gut microbiome associates with positive vaccine take and shedding in neonatal schedule of the human neonatal rotavirus vaccine RV3-BB.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3432},
pmid = {40210877},
issn = {2041-1723},
support = {1164384//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1058454//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1164384//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1111055//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1058454//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1164384//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1111055//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1058454//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1164384//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1111055//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1054584//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1164384//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1111055//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1058454//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 1111055//Bill and Melinda Gates Institute for Population and Reproductive Health (Gates Institute)/ ; 1012425//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 1012425//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 1012425//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 1012425//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 1012425//Department of Health | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Rotavirus Vaccines/immunology/administration & dosage ; *Rotavirus Infections/prevention & control/immunology/virology ; Infant ; Infant, Newborn ; Rotavirus/immunology ; Female ; Immunoglobulin A/immunology ; Feces/virology/microbiology ; Virus Shedding/immunology ; Male ; Vaccines, Attenuated/immunology/administration & dosage ; Antibodies, Viral/immunology/blood ; Immunization Schedule ; Malawi ; Indonesia ; Seroconversion ; Vaccination ; },
abstract = {Rotavirus vaccines are less effective in high mortality regions. A rotavirus vaccine administered at birth may overcome challenges to vaccine uptake posed by a complex gut microbiome. We investigated the association between the microbiome and vaccine responses following RV3-BB vaccine (G3P[6]) administered in a neonatal schedule (dose 1: 0-5 days), or infant schedule (dose 1: 6-8 weeks) in Indonesia (Phase 2b efficacy study) (n = 478 samples/193 infants) (ACTRN12612001282875) and in Malawi (Immunigenicity study) (n = 355 samples/186 infants) (NCT03483116). Vaccine responses assessed using anti-rotavirus IgA seroconversion (IgA), stool shedding of vaccine virus and vaccine take (IgA seroconversion and/or shedding). Here we report, high alpha diversity, beta diversity differences and high abundance of Bacteroides is associated with positive vaccine take and shedding following RV3-BB administered in the neonatal schedule, but not with IgA seroconversion, or in the infant schedule. Higher alpha diversity was associated with shedding after three doses of RV3-BB in the neonatal schedule compared to non-shedders, or the placebo group. High abundance of Streptococcus and Staphylococcus is associated with no shedding in the neonatal schedule group. RV3-BB vaccine administered in a neonatal schedule modulates the early microbiome environment and presents a window of opportunity to optimise protection from rotavirus disease.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Rotavirus Vaccines/immunology/administration & dosage
*Rotavirus Infections/prevention & control/immunology/virology
Infant
Infant, Newborn
Rotavirus/immunology
Female
Immunoglobulin A/immunology
Feces/virology/microbiology
Virus Shedding/immunology
Male
Vaccines, Attenuated/immunology/administration & dosage
Antibodies, Viral/immunology/blood
Immunization Schedule
Malawi
Indonesia
Seroconversion
Vaccination

@article {pmid40210868,
year = {2025},
author = {Fu, Y and Guzior, DV and Okros, M and Bridges, C and Rosset, SL and González, CT and Martin, C and Karunarathne, H and Watson, VE and Quinn, RA},
title = {Balance between bile acid conjugation and hydrolysis activity can alter outcomes of gut inflammation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3434},
pmid = {40210868},
issn = {2041-1723},
support = {1R01DK140854//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
mesh = {Animals ; *Bile Acids and Salts/metabolism ; Humans ; Gastrointestinal Microbiome/genetics ; Mice, Knockout ; Mice ; Amidohydrolases/metabolism/genetics ; Hydrolysis ; Acyltransferases/genetics/metabolism ; Taurocholic Acid/pharmacology/metabolism ; Disease Models, Animal ; *Colitis/metabolism/pathology/microbiology ; Male ; Inflammatory Bowel Diseases/metabolism/microbiology ; Female ; Mice, Inbred C57BL ; Clostridiales/metabolism/genetics ; Crohn Disease/metabolism/microbiology/genetics ; },
abstract = {Conjugated bile acids (BAs) are multi-functional detergents in the gastrointestinal (GI) tract produced by the liver enzyme bile acid-CoA:amino acid N-acyltransferase (BAAT) and by the microbiome from the acyltransferase activity of bile salt hydrolase (BSH). Humans with inflammatory bowel disease (IBD) have an enrichment in both host and microbially conjugated BAs (MCBAs), but their impacts on GI inflammation are not well understood. We investigated the role of host-conjugated BAs in a mouse model of colitis using a BAAT knockout background. Baat[-/-] KO mice have severe phenotypes in the colitis model that were rescued by supplementation with taurocholate (TCA). Gene expression and histology showed that this rescue was due to an improved epithelial barrier integrity and goblet cell function. However, metabolomics also showed that TCA supplementation resulted in extensive metabolism to secondary BAs. We therefore investigated the BSH activity of diverse gut bacteria on a panel of conjugated BAs and found broad hydrolytic capacity depending on the bacterium and the amino acid conjugate. The complexity of this microbial BA hydrolysis led to the exploration of bsh genes in metagenomic data from human IBD patients. Certain bsh sequences were enriched in people with Crohn's disease particularly that from Ruminococcus gnavus. This study shows that both host and microbially conjugated BAs may provide benefits to those with IBD, but this is dictated by a delicate balance between BA conjugation/deconjugation based on the bsh genes present.},
}

Animals
*Bile Acids and Salts/metabolism
Humans
Gastrointestinal Microbiome/genetics
Mice, Knockout
Mice
Amidohydrolases/metabolism/genetics
Hydrolysis
Acyltransferases/genetics/metabolism
Taurocholic Acid/pharmacology/metabolism
Disease Models, Animal
*Colitis/metabolism/pathology/microbiology
Male
Inflammatory Bowel Diseases/metabolism/microbiology
Female
Mice, Inbred C57BL
Clostridiales/metabolism/genetics
Crohn Disease/metabolism/microbiology/genetics

@article {pmid40210576,
year = {2025},
author = {Park, DE and Aziz, M and Salazar, JE and Pham, T and Nelson, SG and Villani, J and Weber, NO and Price, LB and Hungate, BA and Liu, CM},
title = {The nasal microbiome modulates risk for SARS-CoV-2 infection.},
journal = {EBioMedicine},
volume = {},
number = {},
pages = {105660},
doi = {10.1016/j.ebiom.2025.105660},
pmid = {40210576},
issn = {2352-3964},
abstract = {BACKGROUND: The nasal microbiome may influence host risk for COVID-19 by modulating the expression of key proteins that facilitate SARS-CoV-2 entry, including angiotensin-converting enzyme 2 (ACE2), which binds the virus, and transmembrane serine protease 2 (TMPRSS2), which activates viral entry into nasal epithelial cells. This study examined whether the expression levels of ACE2 and TMPRSS2 in the nasal cavity predict the risk of SARS-CoV-2 infection and whether the host nasal microbiome modulates their expression.

METHODS: Using 1548 self-collected nasal swabs from a population-based surveillance testing of community-dwelling adults in Washington D.C., we conducted two retrospective case-control studies (cross-sectional: n = 111 cases and 343 controls; longitudinal: n = 97 cases, 286 controls) and a nasal microbiome study (n = 428). Cases, defined as individuals with a positive SARS-CoV-2 test, were matched with controls based on age and test date. Pre-infection samples were analysed. We measured nasal ACE2/TMPRSS2 expression using RT-qPCR and characterized the nasal microbiome using 16S rRNA gene-based qPCR and sequencing. We used machine learning and regression analysis to determine if nasal ACE2/TMPRSS2 expression predicts SARS-CoV-2 infection and whether the nasal microbiome influences their expression.

FINDINGS: Elevated nasal ACE2/TMPRSS2 expression was associated with 3.6-fold increased risk of contracting COVID-19 (95% CI = 1.71-7.47) compared to those with no detectable levels of ACE2 or TMPRSS2. Before testing positive for SARS-CoV-2, cases also had significantly higher and more unstable ACE2/TMPRSS2 expression in their nasal cavity than controls. Having high densities of Staphylococcus aureus, Haemophilus influenzae, or Moraxella catarrhalis/nonliquefaciens was linked to increased nasal ACE2/TMPRSS2 expression. In contrast, having high densities of Dolosigranulum pigrum was associated with decreased nasal ACE2/TMPRSS2 expression.

INTERPRETATION: These results suggest that natural variation in the nasal microbiome significantly impacts ACE2/TMPRSS2 expression in the nasal cavity and the near-term risk of SARS-CoV-2 infection in adults. Modifying the nasal microbiome could potentially reduce COVID-19 risk.

FUNDING: Research reported in this article was supported by the Milken Institute School of Public Health, the George Washington University and the National Institute of Allergy and Infectious Diseases, National Institutes of Health under award number R01AI168182. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.},
}

@article {pmid40210439,
year = {2025},
author = {Smith, BJ and Zhao, C and Dubinkina, V and Jin, X and Zahavi, L and Shoer, S and Moltzau-Anderson, J and Segal, E and Pollard, KS},
title = {Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279543.124},
pmid = {40210439},
issn = {1549-5469},
abstract = {Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for understanding the causes and consequences of this intraspecific diversity. The enormous size of pangenome references, strain mixing within samples, and inconsistent sequencing depth present challenges for existing tools that analyze samples one at a time. To address this gap, we updated the MIDAS pangenome profiler, now released as version 3, and developed StrainPGC, an approach to strain-specific gene content estimation that combines strain tracking and correlations across multiple samples. We validate our integrated analysis using a complex synthetic community of strains from the human gut and find that StrainPGC outperforms existing approaches. Analyzing a large, publicly available metagenome collection from inflammatory bowel disease patients and healthy controls, we catalog the functional repertoires of thousands of strains across hundreds of species, capturing extensive diversity missing from reference databases. Finally, we apply StrainPGC to metagenomes from a clinical trial of fecal microbiota transplantation for the treatment of ulcerative colitis. We identify two Escherichia coli strains, from two different donors, that are both frequently transmitted to patients but have notable differences in functional potential. StrainPGC and MIDAS v3 together enable precise, intraspecific pangenomic investigations using large collections of metagenomic data without microbial isolation or de novo assembly.},
}