@article {pmid41731377,
year = {2026},
author = {Diouf, AM and Mbaye, AL and Deh, M and Lahlali, R and Elhoumaizi, MA and Rchiad, Z and Barakate, M},
title = {Comparative metagenomic analysis of bacterial and fungal communities associated with bayoud-resistant and susceptible date palm cultivars in the Zagora oasis-Morocco.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41731377},
issn = {1471-2180},
abstract = {BACKGROUND: Fusarium oxysporum f. sp. albedinis (Foa) is a destructive soil-borne fungal pathogen responsible for bayoud disease, which threatens date palm cultivation in North Africa. This disease has caused significant agricultural losses, particularly in Morocco, where the Zagora oasis is a key region for date palm production. Within this oasis, two cultivars—Black Bousthammi and Jihel—are mainly cultivated and exhibit complete resistance and high susceptibility to Foa, respectively. Thus, this study aimed to identify and compare the bacterial and fungal communities associated with the two cultivars and understand their assemblage regarding the disease resistance or susceptibility. Moreover, we explored the influence of each cultivar on the composition and structure of its root-associated microbiome and examined its relationship with the microbial populations present in the surrounding bulk soil, to better understand the recruitment dynamics that shape the microbiome in the roots.

RESULTS: The results revealed significant differences in microbiome composition between the bulk soil and roots of the two date palm cultivars, and between the microbiome of the resistant and susceptible cultivars as well. Moreover, we observed that date palm cultivars had a greater effect on bacterial community composition than on fungal population. Interestingly, the susceptible cultivar exhibited a higher enrichment of several beneficial genera, such as Pseudomonas, Lysinibacillus, Actinomadura, Halomonas, Kocuria, Serratia, Phyllobacterium, Bacillus, Streptomyces, and Trichoderma.

CONCLUSION: The presence of these beneficial genera, known for their antagonistic activity against phytopathogens, may reflect a recruitment pattern associated with pathogen pressure in the susceptible cultivar. This study is the first to compare the microbial communities between a bayoud-resistant and susceptible cultivar and provides insights into the potential role of the root microbiome when plants are under pathogen pressure. This reinforces the need to further elucidate the genetic and biological mechanisms that trigger microbiome assembly, which could be a key step in developing effective methods to manage the bayoud disease.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04837-8.},
}

@article {pmid41909894,
year = {2025},
author = {Hensen, T and Ahmad, S and Kastenmüller, G and Kraaij, R and Ghanbari, M and Ikram, A and Kaddurah-Daouk, R and Thiele, I},
title = {In silico metabolic modelling links microbiome-derived metabolites to risk factors of Alzheimer's disease.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2443171},
pmid = {41909894},
issn = {2993-3935},
support = {RF1 AG058942/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; },
abstract = {The gut microbiome has become increasingly recognized for its role in the pathogenesis of Alzheimer's disease (AD) and is thought to influence AD pathogenesis via metabolic crosstalk with the host. However, mechanistic pathways connecting the gut microbiome to AD pathogenesis remain unknown. To explore potential mechanistic pathways in AD pathogenesis, we created host-microbiome whole-body metabolic models personalized with 16S rRNA microbiome data and predicted emergent metabolic contributions of gut microbiomes. We analyzed 63 metabolites in blood with previously known links with AD. These in silico predictions were then associated with major risk factors for AD in a cohort of 1,065 aging non-AD individuals and subsequently used to inform targeted analyses on serum metabolomics. Our analysis identified increased host-microbial production of L-arginine in older individuals. Lower production of deoxycholate correlated with the neuroprotective APOE E2 allele and it decreased with higher global cognition. Serum metabolomics from the same individuals of cholesterol products and bile acid metabolism corroborated the modeling predictions, suggesting a potential link between the APOE genotype and cognitive health. In conclusion, this study associated metabolic gut microbiome influences on human metabolism with risk factors for AD and identified cholesterol and bile acid metabolism to potentially link with AD pathogenesis.},
}

@article {pmid41909897,
year = {2025},
author = {Gitton-Quent, O and Sola, M and Maziers, N and Hiol, A and Dechamp, N and Le Chatelier, E and Touvier, M and Galan, P and David, A and Morabito, C and Famechon, A and Quinquis, B and Mariadassou, M and Veiga, P and Dore, J and Berland, M and Deschasaux-Tanguy, M},
title = {Alterations in gut microbiota characteristics along a type 2 diabetes risk gradient linked with family history.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2527766},
pmid = {41909897},
issn = {2993-3935},
abstract = {Type 2 diabetes (T2D) is a major global health issue, with growing evidence linking it to gut microbiome changes. However, whether these alterations precede T2D onset and act as predictors, risk factors, or contributors remains unclear. This study analyzed the gut microbiota of 192 individuals from the French NutriNet-Santé cohort, divided into four groups: non-T2D adults with no (n = 47), one (n = 48), or two (n = 51) T2D-affected parents, and T2D-affected adults (n = 46). A progressive microbiota shift was observed in non-T2D groups based on parental history, converging toward the T2D profile. Changes included altered enterotype distribution, increased oral-associated species, disrupted ecological networks, and a shift in Gram-positive-to-negative ratios. Notably, Prevotella copri abundance increased, alongside bacteria potentially enhancing branched-chain amino acid (BCAA), lipopolysaccharide (LPS), and acetate production. Diet also influenced microbiota patterns, with sweet product intake, vitamin levels, and copper/zinc ratios playing roles. A gradual microbiome transition from non-diabetic to T2D participants underscores its association with family history-based risk. While these shifts may reflect or drive T2D progression, further studies are needed to confirm these findings and explore their potential for preventive strategies.},
}

@article {pmid41909899,
year = {2025},
author = {Rozenberga, M and Saksis, R and Elbere, I and Birzniece, L and Briviba, M and Konrade, I and Klovins, J},
title = {Tracking the origin of bacterial DNA in blood: Indication of localized and sporadic transfer from other body sites.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2482771},
pmid = {41909899},
issn = {2993-3935},
abstract = {Recent studies propose the existence of a blood microbiome, but its composition, origin, and dynamics remain largely unresolved. In this pilot study, we analyzed the bacterial DNA present in the blood of 10 volunteers by comparing the taxonomic profiles of 16S rRNA gene sequences from skin, vaginal, oral, and fecal samples. After applying stringent decontamination protocols, we detected bacterial DNA in all blood samples, predominantly from the Pseudomonas genus. A key finding was the identification of 32 unique Amplicon Sequence Variants (ASVs) that were identical between blood and a single body site within individual participants, with no overlap between multiple body sites or across different participants. This participant-specific overlap suggests a true biological origin of bacterial DNA in blood, likely stemming from localized bacterial migration, such as from the skin. Additionally, 27.4% of the ASVs in blood were found in other body sites, with the highest overlap observed in skin samples. Furthermore, 25.3% of blood ASVs persisted after three months, suggesting a consistent pattern in the bacterial DNA composition detected in blood over time. These findings deepen our understanding of the blood microbiome and provide a basis for future research linking blood microbiota to health and disease phenotypes.},
}

@article {pmid41909901,
year = {2025},
author = {Teo, Y and Lavrinienko, A and Albertos Torres, D and Asare, PT and Ruder, A and Dominguez-Bello, MG and Egli, A and Bokulich, NA and Vonaesch, P},
title = {Evaluating long-term stool preservation methods for maximizing the recovery of viable human fecal microbiota.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2594958},
pmid = {41909901},
issn = {2993-3935},
abstract = {UNLABELLED: The gut microbiome plays a fundamental role in human health, prompting efforts to catalog and preserve its diversity across human populations. While DNA sequencing dominates microbiome research, cultivation remains essential for mechanistic studies and therapeutic development. However, best practices for long-term stool preservation remain limited. Here, we compared the stability of eight cryopreservation treatments for maintaining viable stool microbiota over a 1-y storage period at -80 °C (freezer) or at -196 °C (liquid nitrogen) using samples from infants, children, and adults. Combining cultivation on six media with 16S rRNA sequencing, we show that ultralow-temperature cryopreservation has a minimal impact on microbiota diversity compared to fresh cultures. Standard glycerol preservation and simple snap-freezing performed comparably to more complex and costly protocols, with all cultured samples retaining donor-specific microbiota profiles after long-term cryopreservation. The lack of strong treatment-specific effects on microbiota composition suggests a shared microbial response to freeze‒thaw stress favoring taxa with broad environmental tolerance. Our findings offer practical, low-cost strategies for stool biobanking.

IMPORTANCE: The cultivation of bacterial taxa from complex communities, such as those in fecal samples, is essential for mechanistic studies and the development of microbiota-based therapeutics, including defined consortia and individual probiotic strains. Such cultivation efforts typically rely on previously stored samples; however, systematic knowledge regarding long-term preservation strategies that ensure the viability and regrowth of constituent bacterial taxa remains limited. In this study, we systematically evaluated 16 distinct cryopreservation conditions to assess their efficacy in maintaining bacterial viability. Our results show that conventional glycerol-based preservation and simple snap-freezing are comparable in performance to more elaborate and cost-intensive protocols. Moreover, we identified the duration of sample transport prior to freezing as a critical determinant of post-thaw bacterial recovery. These findings provide valuable data on the relative effectiveness of various preservation methods and support the use of low-cost, easily implementable strategies that are particularly suitable for application in resource-limited settings.},
}

@article {pmid41909902,
year = {2025},
author = {Andalib, KMS and Rodosy, FB and Habib, A},
title = {The living medicine inside us: in vitro therapeutic prospects of human gut bacteria.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2480093},
pmid = {41909902},
issn = {2993-3935},
abstract = {Gut microbial metabolism is intimately coupled to host health and disease. Recent knowledge on potential health benefits of gut microbiome lays the groundwork for development of novel therapeutic strategies. But how microbiota-derived metabolites impact on host-microbiome crosstalk remains untapped from therapeutic perspectives. In this study, six gut bacteria sourced from a fecal pool of forty healthy donors were cultured in three distinct growth media. Subsequently, the bacteria were identified through 16S rRNA gene sequencing and subjected to metabolite extraction to evaluate their anti-microbial, anti-oxidant and anti-thrombotic potential. Findings reveal strong anti-oxidant activities in the metabolic-extracts from all the isolates. Metabolites derived from Lactobacillus rhamnosus, Priestia flexa and Bacillus subtiilis inhibited the growth of clinically pathogenic strains Escherichia coli ATCC-8739, Salmonella typhi ATCC-1408 and Staphylococcus aureus ATCC-6538. Escherichia fergusonii originated metabolites demonstrated the highest efficacy in lysing blood clots compared to streptokinase. Additionally, extracts from all the isolates exhibited significant ability to delay coagulation time, competing with standard warfarin. Thus, the findings of our early-stage study provide novel insights into metabolomic functions of gut microbiota. This study underscores the significance of exploring these active metabolites for prospective therapeutic and clinical exploration at the intersection of drug discovery and live bio-therapeutics.},
}

@article {pmid41909904,
year = {2025},
author = {Ramakrishnan, M and Cross, TL and Organski, AC and Saiprasad, SM and Simpson, AMR and Tancredi, DJ and Van Haute, MJ and Christensen, CM and Lewis, ZT and Auchtung, TA and Walter, J and Hutkins, R and Savaiano, DA},
title = {Two-week supplementation of Bifidobacterium adolescentis iVS-1 reduces symptoms associated with lactose intolerance in lactose maldigesters.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2508199},
pmid = {41909904},
issn = {2993-3935},
abstract = {Probiotic supplements containing high β-galactosidase-producing bacteria may aid in the management of lactose intolerance. We previously isolated a strain of Bifidobacterium adolescentis, iVS-1, from the fecal sample of a human donor after consumption of galactooligosaccharides (GOS), a prebiotic derived from lactose. Therefore, it was hypothesized that iVS-1 might reduce symptoms associated with lactose maldigestion. Compared to other probiotic strains, iVS-1 had high β-galactosidase activity and reduced gas formation by fecal communities during in vitro fermentations of lactose or milk. A randomized placebo-controlled clinical trial was then conducted with 21 lactose maldigesters, randomized to receive either B. adolescentis iVS-1 (n = 11) or placebo (n = 10) daily for 2 weeks. Compared to the two-week run-in period, iVS-1 abundance was higher both at the end of the treatment period (p = 0.0005) and after the 2-week post-treatment period (p = 0.045). The iVS-1 group reported less overall daily symptoms during the treatment period when compared to placebo (p = 0.032) and had significant improvement for fecal urgency (p = 0.033) and diarrhea (p = 0.006). The metabolism of lactose, reduction of gas, and improvement of multiple gastrointestinal symptoms suggest that B. adolescentis iVS-1 may be an effective treatment for lactose intolerance. Trial Registration: The trial is registered at ClinicalTrials.gov (https://clinicaltrials.gov/study/NCT05668468).},
}

@article {pmid41909905,
year = {2025},
author = {Chakraborty, J and Lanchenba Singh, N and Kumar Das, B},
title = {Gut microbiome and lung cancer: mechanisms, interactions, and dietary interventions.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2501313},
pmid = {41909905},
issn = {2993-3935},
abstract = {Lung cancer continues to claim countless lives globally. Several studies have shown that the gut microbiome is vital in maintaining healthy lung function through the gut-lung axis. A comparison between the gut microflora of healthy volunteers and lung cancer patients revealed that changes in the composition of gut microflora occur in lung cancer patients. The gut microflora may contribute to lung cancer by influencing immune reactions, inflammatory pathways, bacterial metabolites modulating host metabolism, microbiome dysbiosis, genotoxicity, virulence, and bacteria-induced epigenetic alterations. Thus, it may be assumed that maintaining a healthy gut microflora could help prevent lung cancer. Nutraceuticals are specialized products designed to support health and address specific nutritional needs. They contain ingredients like vitamins, minerals, probiotics, polyphenols, and herbs to reduce the risk or impact of certain illnesses. Nutraceuticals, including probiotics and polyphenols, play a role in preventing and treating various cancers, including lung cancer, by modulating the gut microbiome. This review examines the link between the gut microbiome and lung cancer, how it contributes to cancer development, and the impact of dietary interventions - particularly probiotics, polyphenols, and dietary fibers - on lung cancer prevention and treatment.},
}

@article {pmid41909906,
year = {2025},
author = {Shibi Anilkumar, A and Thomas, SM and Veerabathiran, R},
title = {Gut microbial metabolites as a convergence point between autoimmunity and solid tumors.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2470805},
pmid = {41909906},
issn = {2993-3935},
abstract = {The human gut microbiome, a diverse community of trillions of microorganisms, is essential for controlling numerous bodily functions, such as metabolism, immune response, and epithelial barrier integrity. The gut microbiota comprises bacteria, viruses, fungi, and other microorganisms that affect human health, metabolic pathways, and immune responses. Dysbiosis, or the imbalance of gut microbial composition, has been linked to the pathogenesis of several ailments, including cardiovascular conditions, gastrointestinal conditions, allergies, obesity, autoimmune disorders, and tumors. The interaction between gut microbes and immune responses, mainly through Tregs cells and Th17 cells, underscores the microbiome's function in immune regulation. Furthermore, gut microbial metabolites act as signaling molecules and substrates for metabolic processes, impacting autoimmune disorders and cancer development. Recent research highlights the microbiome's potential role in cancer immunoediting, where gut microbial metabolites may either promote or suppress cancer progression by modulating inflammation and immunosuppression. This review delves into the critical functions of the gut microbiome, its influence on autoimmune disorders, and the emerging connection between gut microbial metabolites and cancer immunoediting, offering new insights into their impact on human health and disease.},
}

@article {pmid41909907,
year = {2025},
author = {Ishii, C and Suzuki, M and Murakami, S and Song, I and Soejima, Y and Kato, M and Fukuda, S},
title = {Ecologically robust gut environment associated with personalized metabolic responses in a Japanese cohort.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2574930},
pmid = {41909907},
issn = {2993-3935},
abstract = {The gut microbiota produces numerous metabolites that affect host physiology. However, the effects of daily diet on human fecal metabolome profiles and their robustness are not well understood, and examinations of intra-individual stability over multiple time points are limited. Here, we investigated the robustness of the human intestinal environment through fecal metabolome and microbiome profiling in response to daily dietary fluctuations. We analyzed 176 fecal samples from 25 healthy Japanese individuals subjected to three dietary regimens, including heterogeneous and homogeneous diets. Fecal metabolome and microbiome profiles were unique to each individual. Further in-depth analyses of seven of these individuals showed that these profiles were stable despite daily dietary fluctuations in six individuals. In addition, random forest classification successfully predicted each subject's identity based on their metabolome profile. The correlation analysis also revealed that the food-metabolite and food-microbiome relationships were highly personalized. The findings from this study suggest that individual diet prior to sample collection is unlikely to influence the fecal metabolome and microbiome data to an extent that is not representative of the individual's "normal" condition, which may lower barriers to future research on the gut environment and its implications for host health.},
}

@article {pmid41909910,
year = {2025},
author = {Batool, M and McMahon, S and Franklin, S and Ramont, C and Sahasrabhojane, P and Chang, CC and Hayase, T and Hayase, E and Blazier, JC and Jenq, R and Shelburne, S and Galloway-Peña, J},
title = {Gut microbiome features and resistome elements associated with colonization and infection with antibiotic-resistance threats.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2570502},
pmid = {41909910},
issn = {2993-3935},
abstract = {Infection with antimicrobial-resistant (AR) pathogens is a leading cause of morbidity and mortality among patients with hematological malignancies; however, little is known about the gut microbiome dynamics in acute myeloid leukemia patients and its impact on AR infections (ARI) and/or colonization with AR pathogens (ARC). Longitudinal stool samples collected from 154 patients undergoing induction chemotherapy were analyzed using 16S rRNA sequencing, selective and differential media culturing, MALDI-TOF, and VITEK2 to identify patients with ARC or ARI and to isolate AR infectious and colonizing bacterial strains. Shotgun metagenomic sequencing of baseline stool samples revealed taxa abundances, resistome features, and KEGG pathways associated with AR-events. Baseline observed species were lower in patients with AR-events (p = 0.01). Although several baseline taxa were more abundant in AR-event patients, they were not statistically significant when they were corrected for false discovery. Functional analysis revealed that penicillin and cephalosporin biosynthesis pathways were significantly enriched in patients with ARC. In summary, identifying the baseline microbiome, resistome, and functional pathway biomarkers may forecast an increased risk of ARI and/or ARC, thereby informing antimicrobial treatment strategies in AML patients.},
}

@article {pmid41909911,
year = {2025},
author = {Shi, J and Nguyen, SM and Yu, D and Wang, L and Liu, L and Cai, H and Wu, J and Long, J and Cai, Q and Shrubsole, MJ and Zheng, W and Shu, XO},
title = {Association of physical activity with gut microbiome among low-income black American adults in the Southern Community Cohort Study.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2589861},
pmid = {41909911},
issn = {2993-3935},
abstract = {Physical activity (PA) has been suggested to influence the gut microbiome. We evaluated this association among low-income Black American adults. This study included 489 self-identified Black American participants from the Southern Community Cohort Study. PA data, including exercise/sport- and work/home-related moderate-vigorous PA (MVPA), was collected at cohort enrollment (2002-2009). Stool samples were collected between 2018 and 2021, and microbial composition was profiled using shotgun metagenomic sequencing. General linear regression models were employed to evaluate associations between PA and gut microbial α-diversity, abundance of individual species and metabolic pathways. Among all participants, MVPA measures were not associated with Shannon α-diversity (p > 0.05) and explained approximately 0.2-0.3% variation of Bray-Curtis dissimilarity. A total of 32 bacterial species, including seven Bacteroides species, two Streptococcus species, two Prevotella species, and nine microbial metabolic pathways, including D-fucofuranose biosynthesis, xyloglucan degradation, biosynthesis of L-citrulline, L-aspartate and L-asparagine biosynthesis, and urea cycle, were significantly associated with work/home-related and/or total MVPA (all false discovery rates < 0.10). In conclusion, MVPA, particularly from work and home activities, may modulate the composition and functionality of the gut microbiome among Black American adults.},
}

@article {pmid41910033,
year = {2026},
author = {Jinato, T and Sikaroodia, M and Gilleveta, PM and Dissayabutra, T and Tangkijvanich, P and Bajaj, JS and Chuaypen, N},
title = {Gut Microbiome Signatures Differ in Cirrhosis With and Without Hepatocellular Carcinoma in a Southeast Asian Cohort.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70358},
pmid = {41910033},
issn = {1440-1746},
support = {C2F//Second Century Fund/ ; RA65/039//Ratchadapiseksompotch Fund, Faculty of Medicine Chulalongkorn University/ ; HEA_FF_68_159_3000_028//Thailand Science research and Innovation Fund Chulalongkorn University/ ; FF68//Fundamental Fund 2025/ ; B36G660004//Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; },
abstract = {BACKGROUND: Gut microbiota, microbial metabolites, and inflammatory cytokines play key roles in the pathogenesis of cirrhosis and hepatocellular carcinoma (HCC); however, data from Southeast Asia are limited. This study examined microbial composition, intestinal permeability, butyrate-related gene expression, and cytokine profiles in Thai patients with cirrhosis, with and without HCC.

METHODS: This cross-sectional study included 30 healthy controls, 33 patients with cirrhosis without HCC, and 44 patients with HCC (HCC-cirr). Fecal samples were analyzed using 16S rRNA sequencing. Microbial functional profiles were predicted using KEGG Orthology-based pathway inference. Gut permeability markers (intestinal fatty acid-binding protein [I-FABP] and lipopolysaccharide-binding protein [LBP]), butyrate-associated gene (BCoAT) expression, and cytokine profiles were assessed.

RESULTS: Alpha diversity (Chao1) was significantly lower in HCC-cirr patients than in healthy controls (p < 0.001) and patients with cirrhosis (p = 0.008). Beta diversity also differed significantly between HCC-cirr and controls (p = 0.008). Ligilactobacillus, Catenibacterium, and Alloprevotella were enriched in the cirrhosis group, whereas HCC-cirr patients showed increased Ruminococcus gnavus and reduced butyrate producers (Coprococcus, Subdoligranulum). Functional prediction suggested pathway differences between cirrhosis and HCC-cirr, including folate, sulfur, tyrosine metabolism, and steroid biosynthesis. BCoAT expression was significantly decreased in HCC (p = 0.006). Plasma LBP and I-FABP were significantly elevated in HCC-cirr (p = 0.033, p < 0.001), with I-FABP also higher than in cirrhosis (p = 0.002). Proinflammatory cytokines (GM-CSF, IL-10, IL-18, IL-1α, IL-7, IL-8, and M-CSF) were elevated in HCC-cirr.

CONCLUSIONS: Among the Thai cohort, HCC with cirrhosis was associated with distinct gut microbial changes, reduced BCoAT expression, increased gut permeability, and cytokine alterations, highlighting the contribution of gut dysbiosis and microbial by-products to liver disease progression.},
}

@article {pmid41910132,
year = {2026},
author = {Sáenz, JS and Yergaliyev, T and Rios-Galicia, B and Seifert, J and Camarinha-Silva, A},
title = {The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019126},
doi = {10.1128/msystems.00191-26},
pmid = {41910132},
issn = {2379-5077},
abstract = {UNLABELLED: Viral communities, especially phages, affect prokaryotic diversity and thus influence the host's metabolic processes. However, the makeup and role of the chicken gut virome remain poorly understood. To address this gap, we mined 1,458 chicken gut metagenomes and 56 viral-enriched samples to recover viral sequences and assemble a comprehensive collection of draft viral genomes. We identified 19,778 viral operational taxonomic units (vOTUs), of which 97% were dsDNA phages from the Caudoviricetes class, primarily targeting gut bacteria such as Lactobacillus, Limosilactobacillus, and Escherichia. Most protein-coding genes in these genomes were uncharacterized and lacked known biological functions. Additionally, the distribution of vOTUs across samples showed that the chicken virome is highly individual-specific. Yet, the viral community also exhibited strong spatial stratification along the gastrointestinal tract, with notable differences between proximal and distal regions, primarily driven by phages linked to the Lactobacillaceae family. Moreover, this study shows that the geographical region, breed, and diet drive the chicken gut viral diversity and composition. This underscores the significant novelty of the chicken gut virome and its largely unexplored functional potential, much of which would be missed if analyses were restricted to fecal samples.

IMPORTANCE: The chicken gut harbors a vast community of viruses that remain largely unexplored despite their potential to influence poultry health and productivity. By analyzing 1,514 samples from different gut regions across 15 countries, we discovered nearly 20,000 distinct viruses, most of which were previously unknown phages. The chicken virome showed strong spatial differences along the gastrointestinal tract, meaning each gut section harbors a unique viral community, underscoring that fecal samples alone miss much of the virome's diversity. We also uncovered that the geographical region, breed, and diet could drive the chicken gut viral diversity and composition. Overall, our findings greatly expand our understanding of gut virus diversity and microbiome ecology, offering a valuable foundation for developing strategies to monitor or manipulate the microbiome to improve poultry health.},
}

@article {pmid41910137,
year = {2026},
author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L},
title = {Temperature modulates gut microbiome disruption and resistome enrichment in oxytetracycline-treated channel catfish (Ictalurus punctatus).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0418725},
doi = {10.1128/spectrum.04187-25},
pmid = {41910137},
issn = {2165-0497},
abstract = {UNLABELLED: Oxytetracycline (OTC) is one of the few antibiotics approved by the U.S. Food and Drug Administration for catfish aquaculture. Unfortunately, OTC resistance has been frequently detected in production environments, with the fish gut identified as a potential hotspot for resistance selection. In aquaculture systems, water temperature is a critical factor influencing fish physiology, antibiotic pharmacokinetics, and water resistome development. However, its role in modulating OTC effects on the fish gut microbiome remains underexplored. This study examined temperature-dependent microbiome and resistome responses in channel catfish (Ictalurus punctatus) when treated with OTC at 20°C, 25°C, and 30°C. Gut contents collected at treatment completion and after withdrawal were analyzed via metagenomic sequencing. In untreated fish, temperature alone shaped microbial structure and function, with the Shannon diversity increasing with temperatures and the β-diversity differing significantly across temperature groups. After OTC exposure, microbial responses were markedly temperature dependent with few taxa affected at 20°C, whereas substantial shifts occurred at 25°C and 30°C, indicating reduced microbial resilience at higher temperatures. OTC elevated total antimicrobial resistance gene (ARG) abundance, enriching tetracycline and β-lactam resistant genes consistent with co-selection. ARG-host linkages were diffuse at 20°C but consolidated within Klebsiella, Enterococcus, Enterobacter, and Paraclostridium at 25°C and 30°C. Notably, OTC-induced dysbiosis persisted through the withdrawal period. These findings demonstrate that temperature modulates both the magnitude and persistence of OTC-driven microbiome disruption and resistome enrichment, underscoring the importance of temperature-aware antibiotic management to mitigate antimicrobial resistance risks and safeguard fish health and food safety in aquaculture.

IMPORTANCE: This study reveals that water temperature critically shapes how antibiotics affect the gut microbiome and antimicrobial resistance in channel catfish. Metagenomic sequencing results showed that oxytetracycline (OTC) treatment caused minimal disruption of the microbiome at 20°C, but induced significant community shifts and enrichment of antimicrobial resistance genes (ARGs) at 25°C and 30°C. Higher temperatures reduced microbial resilience, consolidating ARGs within key bacterial genera such as Klebsiella and Enterococcus. Importantly, OTC-induced microbiome changes and resistance persisted through the withdrawal period. These findings highlight temperature as a major driver of antibiotic impact in aquaculture, emphasizing the prudent use of antibiotics at different disease breakout temperatures.},
}

@article {pmid41910192,
year = {2026},
author = {Saqib, S and Latousakis, D and Virtanen, S and Kalliala, I and Holster, T and Juge, N and Salonen, A},
title = {Exploratory analyses of cervicovaginal mucus O-glycan composition and microbiota profiles in unexplained infertility.},
journal = {Glycobiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/glycob/cwag023},
pmid = {41910192},
issn = {1460-2423},
abstract = {In addition to the specific causes of infertility, two components of the vaginal ecosystem, the vaginal microbiota and the cervicovaginal mucus (CVM), may be associated to reduced fecundity and the success of infertility treatments. The aim of this study was to explore the composition of the CVM O-glycans and vaginal microbiota in women with unexplained infertility. We collected CVM and vaginal swab samples during medically induced ovulation from 19 women with unexplained infertility. Mucin O-glycosylation profiles were generated through Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI-ToF) mass spectrometry and taxonomic profiles of the vaginal microbiota through 16S rRNA gene amplicon sequencing. Altogether 57 O-glycan structures were identified, dominated by core 1 and 2 structures. A significant proportion, nearly 85%, of the glycans were fucosylated and five structures dominated the profiles, accounting for >50% of the glycans observed in most samples. The vaginal microbiota of the patients was dominated by Lactobacillus crispatus (79%), followed by Lactobacillus jensenii (32%) and Lactobacillus iners (21%) and Gardnerella vaginalis (5%, single sample). PERMANOVA analysis indicated significant associations between the glycan structures and dominant taxa (q = 0.0011, R2 = 0.37). This exploratory study provides initial insights into the composition and variation of CVM O-glycans in unexplained fertility and in relation to the vaginal microbiota composition, laying a groundwork for future research.},
}

@article {pmid41910204,
year = {2026},
author = {Green, L and Marchesani, A and Joyner, JL},
title = {The Atlanta Urban Watershed Harbors Antibiotic Resistant Halotolerant Bacteria.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag084},
pmid = {41910204},
issn = {1365-2672},
abstract = {AIMS: Rapid urbanization of the Chattahoochee River has decreased the water quality with higher levels of anthropogenic bacteria from nonpoint source pollution. Introduced bacteria are variable across urban watersheds but only monitored by the abundance of fecal indicator bacteria. Staphylococcus aureus is a halotolerant, opportunistic pathogen associated with aquatic pollution, but impact on the microbial ecology is not well understood in freshwater systems. Describing the halotolerant subset of the aquatic microbiome, can expand upon the health risk of bacterial pollution.

METHODS & RESULTS: Surface water samples along the Chattahoochee River were collected and halotolerant bacteria were cultured using selective agar, typical for growing Staphylococcus species. Bacteria colonies were isolated then characterized by morphology, biochemical tests, and antibiotic resistance screening. Antibiotic resistance profiles showed isolates with a high percentage of resistance to penicillin (86.2%) and novobiocin (17.2%). Biofilm formation was common with 41.4% of isolates formed moderate to strong biofilms. 16S rRNA gene sequencing identified isolates to not be Staphylococcus spp. but within two predominant groups, Bacillus spp. and Priestia spp.

CONCLUSIONS: The Priestia genus is poorly known in freshwater systems; though the combination of antibiotic resistance, biofilm formation, and spore-forming traits indicate that it has key survival characteristics. Halotolerant bacteria harbor opportunistic human pathogens and a public health risk because the bacteria have a high prevalence of antibiotic resistance and biofilm capability, which contribute to environmental persistence and reservoirs for antibiotic resistance genes. This environmental resistome is a notable and developing characteristic of the urban aquatic microbiome.},
}

@article {pmid41910238,
year = {2026},
author = {Le, NNT and Xue, S and Mu, H and Wu, J and Xi, C and Marhaba, T and Zhang, W},
title = {Soil chemistry and microbiome modulation through water irrigation containing oxygen, hydrogen, and carbon dioxide nanobubbles.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0217325},
doi = {10.1128/aem.02173-25},
pmid = {41910238},
issn = {1098-5336},
abstract = {Nanobubble technology has shown considerable promise in sustainable agriculture due to its ability to enhance seed germination, plant growth, and soil quality without leaving harmful residues. While benefits are often attributed to improved soil aeration and soil texture changes (e.g., permeability), nanobubbles may also influence soil microbiome, an essential driver of plant health and nutrient cycling. This study systematically investigated how different nanobubble types-oxygen, hydrogen, and carbon dioxide-modulate soil chemistry and microbial community structure over a 4-week period. Multivariate analyses on microbiome taxonomic composition revealed distinct microbial responses to each gas type. Oxygen and hydrogen nanobubble treatments resulted in more pronounced shifts in microbial composition and functional potential compared to carbon dioxide nanobubbles. These shifts included enrichment of bacterial taxa associated with nutrient turnover, pollutant degradation, and pathogen suppression, such as Flavobacteriaceae, Comamonadaceae, Nannocystaceae, and Blastocatellaceae. Functional predictions showed that oxygen and hydrogen nanobubbles could promote metabolic pathways related to organic compound degradation and remediation of contaminated soil. Microbial network analysis further highlighted the beneficial impacts of nanobubbles on keystone taxa, such as Flavobacteriaceae, which in turn play pivotal roles in shaping soil ecosystem functions. Together, these findings demonstrate that gas-specific nanobubble irrigation can steer soil microbiome dynamics in ways that may enhance soil fertility, resilience, and crop productivity.IMPORTANCEThis study provides new insights into how nanobubble irrigation can be used to improve soil health and agricultural sustainability. By demonstrating that oxygen and hydrogen nanobubbles selectively enrich beneficial microbial taxa linked to soil nutrient turnover, pollution degradation, and pathogen suppression, this study identifies a promising approach to enhance plant growth and soil health through new nanobubble-driven processes. The detection of keystone taxa responsive to nanobubble treatments also reveals potential microbial mechanisms underlying the interactions between nanobubbles, soil, and plant health. Together, these findings highlight nanobubble irrigation as a novel and scalable strategy for microbiome engineering that could advance sustainable crop production and environmental stewardship. Furthermore, while prior studies have primarily focused on the microbial effects of air and oxygen nanobubbles, our study systematically examined and compared the impacts of less explored nanobubble types, specifically hydrogen and carbon dioxide, demonstrating the broad versatility of nanobubbles for diverse agricultural applications.},
}

@article {pmid41910252,
year = {2026},
author = {Yang, H and Liu, W and Niu, J and Geng, B and Qiu, P and Li, H and Bao, J and Pu, X and Li, Y and Jia, X and Sun, Y and Han, Y},
title = {Integrated metagenomic-metabolomic insights into plant-microbe interactions mediated by Bacillus volatile compounds.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0252325},
doi = {10.1128/aem.02523-25},
pmid = {41910252},
issn = {1098-5336},
abstract = {Modulation of plant-microbe interactions with signaling molecules offers a promising strategy to promote plant growth and stress adaptation. However, identifying effective signaling molecules and elucidating the mechanisms for regulating the rhizosphere microbiome remain major challenges. In this study, the roles and mechanisms of Bacillus volatile compounds as potential signaling molecules in plant-microbe interactions were investigated. First, the genome and metabolism of a novel Bacillus subtilis strain capable of producing acetoin and 2,3-butanediol were studied, and the titers of the two compounds were increased to 86.76 g/L by sequential metabolic engineering. Subsequently, the effects of volatile compounds on the growth of vegetables (Brassica rapa and Solanum lycopersicum var.) were studied. Plant growth, nutrient (nitrogen, phosphorus, and potassium) utilization efficiency, and salt stress resistance were improved significantly. Compared with water as a control, significant changes in the abundance of 109 microbial genera of B. rapa's rhizosphere microbiome were identified with volatile compound application. Notably increased microbes included nitrogen-fixing, phosphate- and potassium-solubilizing, stress-resistant, plant growth-promoting, and auxin-secreting microbes. Additionally, genes involved in nitrogen, phosphorus, and potassium utilization in the rhizosphere microbiome were significantly increased, and corresponding metabolism was found. Finally, metabolomic analyses of S. lycopersicum var.'s roots and leaves revealed 67 significantly upregulated compounds with the application of volatile compounds. These compounds were primarily involved in stress resistance, oxidative stress alleviation, free radical scavenging, and auxin-related plant growth promotion. This work demonstrates that Bacillus volatile compounds regulate rhizosphere microbiome and plant-microbe interactions and enhance plant nutrient utilization efficiency, stress tolerance, and growth.IMPORTANCEPlant productivity and stress resilience are strongly influenced by interactions between plants and the rhizosphere microbiome, yet practical strategies to rationally modulate native soil microbial communities remain limited. This study demonstrates that Bacillus volatile compounds, specifically acetoin and 2,3-butanediol, function as effective signaling molecules that coordinate plant-microbe interactions in the rhizosphere. By integrating plant physiology, metagenomics, and metabolomics, we show that these volatile compounds not only enhance plant growth and nutrient use efficiency but also reprogram rhizosphere microbial communities toward functions that benefit nitrogen, phosphorus, and potassium acquisition and stress adaptation. Notably, volatile application improved plant salt tolerance, highlighting their strong ecological and physiological impact. This work provides mechanistic evidence that Bacillus-derived volatiles act as signaling molecules to activate the rhizosphere microbiome and plant metabolic responses. The findings offer a scalable and environmentally friendly strategy for improving crop performance and soil health, with broad implications for sustainable agriculture.},
}

@article {pmid41910273,
year = {2026},
author = {Tobias-Hünefeldt, SP and Woodhouse, JN and Ruscheweyh, H-J and Sunagawa, S and Russnak, V and Streit, WR and Grossart, H-P},
title = {Osmotolerance is a driver of microbial carbon processes in the Elbe estuary.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0179025},
doi = {10.1128/msystems.01790-25},
pmid = {41910273},
issn = {2379-5077},
abstract = {UNLABELLED: Estuaries are blue carbon loci, storing and exchanging carbon between aquatic, atmospheric, and terrestrial environments. Estuarine particles facilitate the transformation and transport of organic matter. The fate of particulate organic matter in estuaries is driven by structural changes in polymers that modify buoyancy, determining the proportions of sinking and suspended particles. In the open ocean and coastal ecosystems, the microbial composition and function of sinking and suspended particles differ, impacting carbon remineralization and sedimentation rates. We leverage 190 metagenomes and 73 metatranscriptomes to assess free-living, sinking, and suspended particle-associated microbial composition and function across the Elbe estuary. The salinity gradient in the Elbe estuary is the primary driver of microbiome composition and function. Transparent exopolymer particles (TEP) production was localized to freshwater, with seemingly no TEP-associated organisms detected above 20 practical salinity units (PSU). We observed differences in the function of free-living and particle-associated microbial communities, with diazotrophs enriched on particles. We observed that sinking particles may better support methanogenesis, and suspended particles showed signs of continued primary and secondary production. From this, we conclude that activities such as dredging, which resuspend sediment, will exacerbate carbon turnover and greenhouse gas emissions, and reduced dredging may lower greenhouse gas (GHG) emissions in the Elbe estuary. Many of these GHG linking processes are inhibited by salinity due to the osmosensitivity of methanogens and methanotrophs along the estuary. Changes in sea level and precipitation rates will likely directly interact with activities such as dredging, with as yet uncertain impacts on microbial carbon processing and storage.

IMPORTANCE: Estuaries, lower river areas that merge into oceans, play a large role in Earth's carbon cycle. Estuaries store carbon and manage greenhouse gases, exchanging carbon between land, water, and the air. As carbon travels down estuaries, it is processed by free-living and particle-associated microbes. We explore the relationship between environmental conditions and present and expressed genes. Based on gene profiles, methane concentrations in the water column may be related to the abundance of sinking particles, while suspended particles are linked to growth and energy acquisition. Therefore, the balance of suspended vs. sinking particles is important in highly turbid estuaries, like the Elbe estuary, where urban activities affect greenhouse gas emissions and salinity intrusions. Dredging often tips the balance toward sinking particles and therefore increased greenhouse gas emissions. Our study thereby informs future policy decisions and the impact these decisions will have on our future climate.},
}

@article {pmid41910342,
year = {2026},
author = {Dixit, K and Busi, SB and Ahmed, A and Kshirsagar, A and Jäger, C and Singh, A and Shah, V and Saroj, SD and Ahuja, V and Wilmes, P and Shouche, Y and Makharia, G and Dhotre, D},
title = {Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0085625},
doi = {10.1128/msphere.00856-25},
pmid = {41910342},
issn = {2379-5042},
abstract = {UNLABELLED: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis, and its symptoms overlap with irritable bowel syndrome (IBS). The gut microbiome is likely to play a role in the pathogenesis of NCGS. We analyzed the gut microbiome in patients with NCGS and in patients with IBS, using shotgun metagenomics and metabolomics of fecal samples. Analyses of taxonomic and functional microbial diversity revealed a higher abundance of methanogenic archaea, such as Methanobrevibacter filiformis, Methanobrevibacter boviskoreani, Methanosphaera stadtmanae, and a higher fold change in urea, uridine 5-monophosphate, and adenosine monophosphate in patients with NCGS compared to patients with IBS, who showed higher fold changes in metabolites gamma-aminobutyric acid and lactic acid. Furthermore, pangenome and metabolome analyses revealed disease-specific gene clusters, as well as genomic and metabolic features differentiating NCGS from IBS. While patients with NCGS did not show lower potential for gluten degradation, a lower synthetic potential for fructan beta-fructosidase was found in them. The present study provides an extensive analysis of taxonomic, genomic, and metabolic features that may play a role in the pathogenesis and symptom development in patients with NCGS.

IMPORTANCE: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis with symptoms that overlap with irritable bowel syndrome (IBS). Using shotgun metagenomics and metabolomics, we report deeper insights into the microbiome profile, including viral and archaeal diversity, lower fructan degradation potential, the differential abundance of metabolites, and genomic features of gut bacteria in patients with NCGS. Understanding the microbiome associated with this disorder may shed light on the possible role of the microbiome in the pathophysiology of NCGS.},
}

@article {pmid41910441,
year = {2026},
author = {Manti, M and Dimitriadis, K and Dri, E and Mavromoustakou, K and Vakka, A and Koutsopoulos, G and Tsioufis, P and Katsimichas, T and Siakavellas, S and Gazouli, M and Tsioufis, K},
title = {Transcatheter aortic valve implantation and gut microbiota: Rationale and design of the 'GUT-TAVI' cohort study.},
journal = {Science progress},
volume = {109},
number = {1},
pages = {368504261426427},
doi = {10.1177/00368504261426427},
pmid = {41910441},
issn = {2047-7163},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Transcatheter Aortic Valve Replacement/methods ; *Aortic Valve Stenosis/surgery/microbiology ; Prospective Studies ; Methylamines/blood ; Female ; Male ; Aged ; Cohort Studies ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Hemodynamics ; },
abstract = {ObjectiveAlterations in gut microbiota have been reported in patients with aortic valve stenosis (AVS), yet the impact of haemodynamic restoration following transcatheter aortic valve implantation (TAVI) on microbiota composition remains unclear. This study protocol describes a prospective cohort investigation designed to examine changes in gut microbiota and related metabolic markers after TAVI.Methods'GUT-TAVI' is a single-centre, prospective observational cohort study enrolling 40 adults with severe AVS undergoing TAVI. Stool samples will be collected at two timepoints (1 month to 1 day pre-TAVI and 3 months post-TAVI) for 16S-rRNA sequencing. Serum trimethylamine N-oxide (TMAO), standard biochemical markers, echocardiographic parameters, and dietary adherence scores will also be assessed. The primary endpoint is the change in gut microbiota composition following TAVI. Secondary analyses will examine associations between microbiota changes, haemodynamic parameters, and TMAO levels while accounting for potential confounders.ResultsAs a protocol, no results are yet available. Planned analyses include alpha- and beta-diversity comparisons, multi-variable modelling, sub-group analyses, and sensitivity analyses addressing antibiotic exposure and procedural variability.ConclusionsThis study may provide preliminary insights into how haemodynamic improvement after TAVI is associated with changes in gut microbiota and metabolic function. Findings may help inform future, larger-scale studies investigating the gut-heart axis in cardiovascular diseases.},
}

Humans
*Gastrointestinal Microbiome
*Transcatheter Aortic Valve Replacement/methods
*Aortic Valve Stenosis/surgery/microbiology
Prospective Studies
Methylamines/blood
Female
Male
Aged
Cohort Studies
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Hemodynamics

@article {pmid41910593,
year = {2026},
author = {Bartelli, TF and Baydogan, S and Sahin, I and Hoffman, KL and Petrosino, J and Blackburn, KW and Zhao, J and Wood, A and Ayvaz, T and Surathu, A and Cagigas, MN and Barcenas, EC and Mata, T and Nguyen, VK and Zulbaran-Rojas, A and Li, L and Faraoni, EY and White, JR and Ajami, N and Li, L and Yadav, D and Conwell, DL and Serrano, J and Pandol, SJ and Fogel, EL and Van Den Eden, SK and Vege, SS and Topazian, MD and Park, WG and Hart, PA and Forsmark, C and Bellin, MD and Maitra, A and Bhutani, M and Kim, M and Van Buren, G and Fisher, WE and McAllister, F and , },
title = {Whole Metagenomic Profiling Identifies a Gut Microbial Signature for Chronic Pancreatitis via Machine Learning.},
journal = {Pancreas},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPA.0000000000002618},
pmid = {41910593},
issn = {1536-4828},
abstract = {BACKGROUND: Pancreatitis significantly alters the microbial composition of the oral and intestinal compartments, causing dysbiosis that may contribute to disease mechanisms and potentially serve as a basis for diagnosis or treatment.

OBJECTIVE: To determine whether the oral or gut microbial signature can classify chronic pancreatitis (CP).

METHODS: Stool samples (n=707) were collected from participants in the Prospective Evaluation of Chronic Pancreatitis for Epidemiologic and Translational Studies (PROCEED). Samples were distributed among 200 healthy (HC), 310 CP, 49 acute pancreatitis (AP) and 148 recurrent acute pancreatitis (RAP). Additionally, saliva samples were collected for a subset of participants (n=156). Whole genome sequencing was performed to assess microbiome composition. Machine learning algorithms were utilized to identify a signature with microbial features predictive of CP.

RESULTS: Gut alpha diversity was significantly decreased in AP, RAP, and CP compared to HC, with CP exhibiting the lowest diversity. In contrast, oral microbial diversity showed no significant variation across groups. Beta diversity analysis revealed distinct gut microbiome compositions between HC and pancreatitis subtypes, with CP showing the most pronounced differences. Random forest models using gut microbial species demonstrated robust predictive performance for CP using a minimum of 10 species (Area under the curve - AUC: 0.834; accuracy: 0.774). Despite similarities in gut microbiome composition across pancreatitis subtypes, a unique gut microbial signature for CP was identified highlighting the microbiome's potential in CP diagnosis.

CONCLUSION: Our study reveals a gut microbial signature predictive of CP using machine learning models in a large US multi-institutional cohort.},
}

@article {pmid41910796,
year = {2026},
author = {Zahran, E and Elbahnaswy, S and Bruce, TJ and Hegab, YE and Palic, D},
title = {Preliminary microbiome characterization of shrimp gut and pond water in Egyptian aquaculture farms: Implications for pathogen dynamics and management practices.},
journal = {Veterinary research communications},
volume = {50},
number = {3},
pages = {},
pmid = {41910796},
issn = {1573-7446},
abstract = {UNLABELLED: Shrimp aquaculture is a rapidly expanding food sector; however, its sustainability is challenged by disease outbreaks often linked to imbalances in the microbiome. Here, we characterized the microbial communities in the intestines of shrimp and pond water from three Egyptian farms (A, B, and C) using Oxford Nanopore long-read sequencing. Descriptive comparisons of relative abundance and diversity trends revealed that pond water harbored significantly higher alpha diversity than shrimp guts. In contrast, beta diversity confirmed a strong separation between host-associated and environmental microbiomes. For the observed phyla, taxonomic profiling revealed that shrimp guts were dominated by Proteobacteria, Actinomycota, and Bacillota, whereas pond water contained additional constituents, including Cyanobacteria and Bacteroidota. Pathogen-associated genera, particularly Vibrio spp. and Pseudomonas spp., were more abundant in water samples, with farm-specific variations linked to management practices such as salinity and feed protein content. Venn analysis highlighted that pond water harbored the largest pool of unique taxa, reinforcing its role as a putative reservoir for pathogens. These findings provide the first integrative microbiome baseline for Egyptian shrimp farms, underscoring the need for microbiome-informed management to mitigate the risk of pathogens.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11259-026-11113-7.},
}

@article {pmid41910822,
year = {2026},
author = {Kumar, V and Nautiyal, CS},
title = {From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41910822},
issn = {1573-0972},
}

@article {pmid41910951,
year = {2026},
author = {Dasgupta, S},
title = {Metagenomics in Obstructive Lung Diseases: Insights into Microbial Dysbiosis, Host-Microbe Interactions, and the Gut-Lung Axis.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261419483},
doi = {10.1177/15578100261419483},
pmid = {41910951},
issn = {1557-8100},
abstract = {Obstructive lung diseases (OLDs), including asthma and chronic obstructive pulmonary disease (COPD), arise from complex interactions among microbial ecosystems, host immunity, metabolic regulation, and environmental exposures. Metagenomic approaches have substantially advanced understanding of these interactions by enabling comprehensive profiling of respiratory and gut-associated microbiomes and their functional potential. Evidence indicates that asthma is frequently associated with early-life microbial perturbations, reduced community diversity, enrichment of Streptococcus, Moraxella, and allergen-associated fungi, and gut dysbiosis that influences immune maturation and tolerance. In contrast, COPD is characterized by adult-onset dysbiosis with Proteobacteria dominance, depletion of commensal anaerobes such as Prevotella and Veillonella, and functional signatures linked to chronic inflammation, xenobiotic metabolism, and exacerbation risk. Across both diseases, alterations in gut microbial composition and metabolite profiles, including short-chain fatty acids, highlight the gut-lung axis as a key regulatory interface shaping airway immune responses. Despite these advances, critical knowledge gaps remain, including limited longitudinal data, incomplete multi-kingdom analyses, and insufficient mechanistic and translational validation of disease-associated microbiome signatures. This review integrates current metagenomic evidence to delineate disease-specific and shared microbial patterns, examines host-microbe interaction pathways within molecular and clinical contexts, and critically evaluates the implications and limitations of microbiome-based interventions. By framing microbiome research within a systems biology and public health perspective, this article underscores the importance of context-dependent interpretation and identifies priorities for future longitudinal, mechanistic, and translational studies in OLDs.},
}

@article {pmid41911313,
year = {2026},
author = {Odem, MA and Simbassa, SB and Alvarez, CF and Jeilu, O and Simar, SR and Bosserman, R and Dutta, S and Galdamez, W and Ayele, H and Hanson, BM and Proctor, DM and Krachler, AM},
title = {Shiga toxin increases intestinal transit to displace resident microbes and facilitate pathogen colonization.},
journal = {PLoS pathogens},
volume = {22},
number = {3},
pages = {e1014104},
doi = {10.1371/journal.ppat.1014104},
pmid = {41911313},
issn = {1553-7374},
abstract = {Shiga toxin (Stx)-producing Escherichia coli (STEC) is a major cause of food-borne illnesses, and disease severity correlates with the production of Shiga toxins. While clinical symptoms such as bloody diarrhea and haemolytic uremic syndrome have been attributed to Stx, its contribution to bacterial fitness is not well understood. Here, we demonstrate that Stx2 enhances STEC colonization of the zebrafish gut by facilitating the partial displacement of gut resident microbes. Infection with Stx2-producing STEC strains or direct exposure of fish to purified Stx2 induces alterations in the zebrafish microbiome structure, impacting several bacterial phyla and genera, notably Pseudomonads. We show that Stx2 is sufficient to facilitate these changes by accelerating intestinal transit, leading to increased expulsion of select gut microbes, including resident Pseudomonas species. Additionally, prokinetic drug treatment causes similar changes in gut transit and expulsion of Pseudomonas. Collectively, these findings detail a novel mode of action of Stx2 on the host, and shed light on its contribution to bacterial fitness within the host intestine.},
}

@article {pmid41911577,
year = {2026},
author = {Kaplunova, V and Alioui, H and Griguschies, T and Müller, L and Joisten-Rosenthal, V and Lautwein, T and Metzger, S and Durán, P and Loo, E},
title = {Artificial soil (ArtSoil): Recreating soil conditions in synthetic plant growth media.},
journal = {The Plant journal : for cell and molecular biology},
volume = {126},
number = {1},
pages = {e70833},
pmid = {41911577},
issn = {1365-313X},
support = {390686111//Cluster of Excellence on Plant Sciences/ ; Wolf Frommer//Alexander von Humboldt-Stiftung/ ; 391465903/GRK 2466//Deutsche Forschungsgemeinschaft/ ; 458090666//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Soil/chemistry ; *Arabidopsis/growth & development ; *Culture Media/chemistry ; Soil Microbiology ; Sucrose/metabolism ; Microbiota ; Plant Development ; },
abstract = {Controlled plant growth in laboratories can be achieved by cultivating plants under sterile or axenic conditions on predefined synthetic growth media, typically supplemented with sugar. In nature, plants do not receive exogenous sugar supplies, form symbiosis with microbes, and plant growth is influenced by soil edaphic factors. Thus, physiological and multi-omic analyses of plants grown on synthetic media will differ from those of soil-grown plants due to the influence of sucrose, and the absence of microbiota and soil edaphic factors on plant growth. The rapid advances in spatial omics call for accurate characterization of plants grown under conditions similar to soil. To address the issue, we developed Artificial Soil (ArtSoil), a growth medium containing essential nutrients for plant growth, and aqueous soil extract (ASE) to maintain soil microbiomes and edaphic factors, simultaneously eliminating the need for sugar supplementation in the medium. We compared Arabidopsis thaliana grown on conventional media and on ArtSoil under various growth conditions. We showed that complex soil microbiota in ArtSoil promote plant growth without physiological side effects induced by sucrose. We demonstrate an application for ArtSoil in single-cell transcriptomics and report microbiota-induced cell-type-specificity in immune and nitrogen signaling. We tested ArtSoil with six types of ASEs to demonstrate its potential to decouple nutrient effects from microbiota in plant growth. We conclude that ArtSoil offers a more physiologically relevant alternative to conventional media for studying plant growth within a soil-like context.},
}

*Soil/chemistry
*Arabidopsis/growth & development
*Culture Media/chemistry
Soil Microbiology
Sucrose/metabolism
Microbiota
Plant Development

@article {pmid41911622,
year = {2026},
author = {Naim, A and van Staaveren, N and Leishman, EM and Nicklas, AL and Tulpan, D and Forsythe, P and Harlander, A},
title = {Preference and behavioral responses to synbiotic supplementation via drinking water in laying hens under social stress.},
journal = {Poultry science},
volume = {105},
number = {6},
pages = {106860},
doi = {10.1016/j.psj.2026.106860},
pmid = {41911622},
issn = {1525-3171},
abstract = {Synbiotics (SYN) have the potential to enhance animal health, but their efficacy depends on both biological impact and voluntary intake, particularly under stress, when hydration and gut support are critical. This study presents the first investigation of SYN supplementation delivered exclusively through drinking water in laying hens, evaluating both preference and behavioral responses, particularly feather pecking, during a period of social stress induced by repeated mixing of unfamiliar birds. A total of 226 White Leghorn hens (37 weeks old) were housed in enriched floor pens with simultaneous access to color-coded SYN-enriched and plain water containers. Following a 2-week associative learning phase and 1-week washout, hens entered a 6-week preference testing period encompassing pre-stress, stress, and post-stress phases. Water consumption was measured at the group level, while individual jug visits were tracked using RFID technology. Feather pecking was measured (10 min/day) and feather damage assessed according to severity. Hens showed a clear preference for SYN-enriched water, consuming significantly more than plain water (p < 0.0001). While overall intake remained stable, SYN consumption fluctuated across stress phases, with the strongest preference pre-stress and a modest decline during stress. Although hens with higher rates of severe feather pecking (SFP) visited SYN-enriched water more frequently than hens with lower rates (p = 0.0288), suggesting a potential coping mechanism, overall, SFP rates remained stable across all phases. Notably, the level of SFP observed during the pre-stress phase was already sufficient to cause progressive plumage deterioration, which continued throughout the study. The proportion of birds with severe feather damage rose from 39.4% to 53.5%, while those with intact plumage dropped from 37.6% to 19.9% over time. Thus, SYN supplementation via drinking water is feasible and preferred by laying hens, even under stress. These findings highlight the potential of nutraceuticals delivered through drinking water to influence hen behavior; however, the progressive plumage deterioration despite stable SFP rates suggests that SYN supplementation alone may be insufficient, underscoring the need for integrated management strategies.},
}

@article {pmid41912274,
year = {2026},
author = {Dutton, CL and Goeckner, A and Goldwire, T and Grupstra, CGB and Houghtaling, D and Nonnamaker, LE and Subalusky, A},
title = {Bioreactors on the Move: How Animals Contribute to Microbial Community Coalescence and Shape Ecosystem Function.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70291},
doi = {10.1111/1462-2920.70291},
pmid = {41912274},
issn = {1462-2920},
support = {//Florida Atlantic University/ ; //University of Florida/ ; //United States National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Microbiota ; *Ecosystem ; *Bioreactors/microbiology ; Fishes/microbiology ; Oligochaeta/microbiology ; Bacteria/classification ; Soil Microbiology ; },
abstract = {Microbiome community coalescence-the mixing of separate microbial communities and their environments resulting in a novel community-represents an important but understudied ecological process at the animal-environment interface. Here, we propose that animals function as "mobile bioreactors" across landscapes, ingesting environmental microbes that undergo selective filtering within the animal gut that are then deposited back into the environment alongside the animal's native microbiota. This coalescence of animal and environmental microbiomes can significantly alter ecosystem processes including nutrient cycling, organic matter decomposition, and trophic interactions. We synthesize emerging evidence from terrestrial, freshwater, and marine ecosystems demonstrating how animal-facilitated microbial coalescence influences ecosystem functioning. Through case studies of hippos in African rivers, fish on coral reefs, and earthworms in soil, we illustrate how these coalescence events create novel microbial communities with distinct functional capabilities. We identify methodological approaches for investigating these phenomena and outline key knowledge gaps, particularly regarding the persistence of animal microbiota in environmental settings and their quantitative contribution to ecosystem processes. Here we highlight the importance of studying animal-environmental coalescence events with far reaching implications for our understanding of ecosystem processes, animal health, and environmental resilience.},
}

Animals
*Microbiota
*Ecosystem
*Bioreactors/microbiology
Fishes/microbiology
Oligochaeta/microbiology
Bacteria/classification
Soil Microbiology

@article {pmid41912276,
year = {2026},
author = {Luko-Sulato, K and Sulato, ET and Osman, JR and Nolasco-Jiménez, P and Morales, D and Rezende, GS and Rodrigues, CA and Maintinguer, SI and da Cunha, AF and Rosolen, V},
title = {Soil Microbiome of Tropical Seasonal and Permanent Small Wetlands.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70306},
doi = {10.1111/1758-2229.70306},
pmid = {41912276},
issn = {1758-2229},
support = {2021/06332-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2023/15396-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
mesh = {*Wetlands ; Seasons ; *Bacteria/classification/genetics/isolation & purification ; *Soil Microbiology ; *Microbiota ; *Archaea/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Tropical Climate ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; },
abstract = {Characterisation of the microbial communities of two small tropical wetlands under two distinct hydrological regimes (permanent and seasonal), across a rainy and dry season was performed by 16S rRNA amplicon sequencing. We identified 48 bacterial phyla across the two wetland types, seasons and depths and 83% of the bacterial sequences consistently corresponded to six phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Proteobacteria and Verrucomicrobia. The seasonal wetland presented a predominance of Chloroflexi, Nitrospirae, Actinobacteria and Acidobacteria, whereas the permanent wetland showed higher relative abundances of Planctomycetes, Bacteroidetes, Proteobacteria and Firmicutes. Archaeal communities also differed, with Crenarchaeota predominating in the seasonal and Euryarchaeota in the permanent wetland. Microbial communities showed pronounced compositional shifts across wetland type, season and depth, while maintaining stable alpha diversity, with depth was the dominant driver. Functional inference suggested that aerobic ammonia oxidation, nitrate reduction and sulphur compound respiration were the predominant putative metabolic pathways in the seasonal wetland and methanogenesis, fermentation, dark hydrogen oxidation, nitrogen fixation, photoautotrophy, ureolysis and hydrocarbon degradation in the permanent wetland. The permanent wetland exhibited sparse correlation with environmental drivers, consistent with long-term saturation and chronic nutrient limitation, while the seasonal wetland presented influence of pH, nutrients and SOC on microbial community structure.},
}

*Wetlands
Seasons
*Bacteria/classification/genetics/isolation & purification
*Soil Microbiology
*Microbiota
*Archaea/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Phylogeny
Tropical Climate
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA

@article {pmid41912342,
year = {2026},
author = {Engelen, MPKJ and van der Meij, BS},
title = {Targeting muscle, mitochondria, and microbiome: nutritional and exercise strategies across wasting diseases and conditions.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {29},
number = {3},
pages = {211-213},
doi = {10.1097/MCO.0000000000001220},
pmid = {41912342},
issn = {1473-6519},
}

@article {pmid41912530,
year = {2026},
author = {Jiang, J and Poulsen, CS and Boulund, U and Shah, S and Trivedi, U and Bhattacharyya, M and Neumann, AU and Dai, DLY and Petersen, C and Hoskinson, C and Moraes, TJ and Mandhane, PJ and Simons, E and Azad, MB and Subbarao, P and Bønnelykke, K and Chawes, B and Turvey, SE and Sørensen, SJ and Thorsen, J and Stokholm, J},
title = {Early life bacteria and sibling exposure associate with restoration of the infant gut microbiome after cesarean section.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71185-6},
pmid = {41912530},
issn = {2041-1723},
abstract = {Long-term gut microbiome perturbation following Cesarean section (CS) delivery has been associated with an increased risk of developing childhood asthma. Whether such CS-associated microbiome composition can be modulated by environmental exposures or ecological interactions, and thereby mitigate disease risk, is unclear. In the COPSAC2010 birth cohort (N = 700), we develop a restoration score quantifying the degree to which the 1-year gut microbiome resembled that of vaginally delivered infants. We identify predictors of this restoration score in the 1-week gut microbiome. In addition, having older siblings is linked to a higher restoration score, mediated by increased abundances of restoration-associated bacteria. The restoration score, including association with delivery mode, older siblings and later asthma as well as early bacterial drivers, is successfully replicated in the independent Canadian birth cohort, CHILD. These insights suggest that specific early-life bacteria and sibling exposure may support microbiome restoration and confer protective effects against asthma risk.},
}

@article {pmid41913243,
year = {2026},
author = {Mancin, E and Casto-Rebollo, C and Maltecca, C and Ibañez-Escriche, N and Mantovani, R and Sartori, C and Tiezzi, F},
title = {Insights into pig resilience: the Microbiome-genetic connection.},
journal = {Porcine health management},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40813-026-00506-4},
pmid = {41913243},
issn = {2055-5660},
}

@article {pmid41913289,
year = {2026},
author = {Kieri, O and Narayanan, A and Jütte, BB and Svensson, P and Aleman, S and Sönnerborg, A and Ray, S and Nowak, P},
title = {Linking gut microbiome to HIV-1 reservoir size in people living with HIV.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00828-2},
pmid = {41913289},
issn = {1757-4749},
abstract = {The gut microbiome is altered during HIV-1 infection and contributes to immune dysfunction and inflammation in people living with HIV (PLWH), these changes may persist despite effective antiretroviral therapy (ART). We explored the associations between the fecal gut microbiome and blood HIV-1 reservoir size in PLWH (n = 30) on long-term ART. The intact proviral DNA assay (IPDA) and shotgun metagenomic sequencing were performed to identify microbial species and metabolic pathways associated with the size of the HIV-1 reservoir. PLWH with a smaller intact reservoir exhibited lower evenness compared to individuals with a larger intact reservoir. We found that Phocaeicola plebeius and Lachnospira sp000437735 were significantly enriched in individuals with a smaller intact reservoir and lower intact-to-total proviral ratio, respectively. We observed a negative association between Faecalibacterium prausnitzii and a positive association of Prevotella copri, with the intact proviral reservoir size. Additionally, the metabolic pathways of glycolysis and branched-chain amino acid biosynthesis were enriched in individuals with larger reservoir. HIV reservoir size in blood is associated with gut microbiome evenness, specific metabolic pathways and microbial signatures, including Lachnospira, Prevotella, and Faecalibacterium. Our findings underscore the potential role of the gut microbiome in viral persistence, raising the possibility that modulating microbial composition could influence the HIV reservoir.},
}

@article {pmid41913604,
year = {2026},
author = {Wang, HY and Li, C and Pan, YP},
title = {[Imbalance and reconstruction of periodontal homeostasis: new perspectives on the pathogenesis, prevention and treatment of periodontitis].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {61},
number = {4},
pages = {445-451},
doi = {10.3760/cma.j.cn112144-20251209-00499},
pmid = {41913604},
issn = {1002-0098},
support = {2023YFC2506300//National Key R&D Program of China/ ; },
abstract = {Periodontal homeostasis is a dynamic equilibrium based on healthy periodontal structures, a relatively stable oral microbiome, appropriately regulated host immunity, coordinated cellular metabolism, and a functional dentition with normal occluion. This review aims to systematically elucidate the key mechanisms underlying the maintenance and disruption of periodontal homeostasis. The dysregulation of microbiota and excessive immune activation mutually reinforce each other, serving as the core driving forces for the occurrence and progression of periodontitis. On this basis, a treatment approach oriented toward "re-establishing periodontal homeostasis" is proposed. Based on microbiota remodeling and structural reconstruction, combined with host immune regulation and immunometabolic intervention, emphasizing systemic risk factor management and functional dentition reconstruction, we aim to establish a personalized, precise, and sustainable new model for periodontal prevention and treatment.},
}

@article {pmid41913620,
year = {2026},
author = {Wang, XY and Yao, YJ and Li, LL and Yan, FH},
title = {[From oral microbiome dysbiosis to renal injury: research advances in the mechanism of association between periodontitis and diabetic kidney disease].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {61},
number = {4},
pages = {582-588},
doi = {10.3760/cma.j.cn112144-20251112-00446},
pmid = {41913620},
issn = {1002-0098},
support = {82301100//National Natural Science Foundation of China/ ; BK20220198//Natural Science Foundation of Jiangsu Province/ ; 0224C001//High-Level Hospital Construction Project of Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University/ ; YKK23177//Nanjing Foundation for Development of Science and Technology/ ; },
abstract = {Periodontitis, a chronic inflammatory disease driven by dysbiosis of the oral microbiome, has increasingly been recognized for its systemic impact beyond the oral cavity. Growing evidence links periodontitis to the onset and progression of diabetic kidney disease (DKD), suggesting that disturbances of oral microbial homeostasis may influence distant organs through systemic circulation or the oral-gut-kidney axis. Such interactions can trigger systemic inflammation, immune dysregulation, oxidative stress, and metabolic disturbances, thereby accelerating renal injury. This review summarizes recent advances on the potential mechanisms linking periodontitis to DKD progression and highlights the key role of oral microbial dysbiosis and related systemic effects.},
}

@article {pmid41913730,
year = {2026},
author = {Kwoji, ID and Edwards, W and Ruffell, A and Shaw, D and Denoyelle, C and Figuiredo, A and Guadano-Procesi, I and Makkimane, J and Pantzi, K and Godfrey, A and Gentekaki, E and Stensvold, CR and Kolisko, M and Tsaousis, A},
title = {BlastoDB: first release of a community-driven multi-omics and epidemiological resource for Blastocystis biology and subtyping.},
journal = {Open research Europe},
volume = {6},
number = {},
pages = {65},
pmid = {41913730},
issn = {2732-5121},
abstract = {BlastoDB (https://www.blastodb.com/) is developed as an open-access, community-driven resource dedicated to Blastocystis, one of the most common yet understudied intestinal protists. BlastoDB will offer the scientific community up-to-date, curated information on Blastocystis by integrating epidemiological data, microbiome profiles, multi-omics datasets (genomics, transcriptomics, proteomics, and metabolomics), reference sequences for subtypes, protocols, microscopy images, and related metadata. In this initial release, we describe the data model, database architecture, curation pipelines, and web interface, which together facilitate subtype classification, comparative and integrative analyses, and cross-study synthesis of epidemiological and experimental data. We outline submission and governance workflows designed to support community contributions, training activities, and sustainable curation under the " Blastocystis under One Health" COST Action (CA21105). Finally, we highlight planned extensions, including expanded metagenomic and metatranscriptomic content, automated genome quality assessments, metagenome-assembled genomes, and geospatial and analytical dashboards. BlastoDB provides a central, FAIR-aligned hub for Blastocystis data, images, and protocols, reducing technical barriers and fostering a collaborative ecosystem for studying this globally prevalent protist.},
}

@article {pmid41913906,
year = {2026},
author = {Lu, P and Liu, M and Zhang, L and Fan, JJ and Han, G and Hou, B and Meng, Y and Wang, L and Sun, Y},
title = {Gut-Brain Axis Dysregulation in Inflammatory Bowel Disease: Implications for Coagulation Abnormalities and Extraintestinal Manifestations.},
journal = {International journal of general medicine},
volume = {19},
number = {},
pages = {590621},
pmid = {41913906},
issn = {1178-7074},
abstract = {Inflammatory bowel disease (IBD) involves chronic intestinal inflammation driven by gut-brain axis imbalance, fostering complications through an "inflammation-neuro-coagulation" triad. Current staging systems inadequately capture the dynamics of this multidimensional network. Therefore, integrated multi-omics analyses-including metagenomics, metabolomics, and single-cell transcriptomics-are essential to construct dynamic models that monitor coagulation, microbiome, and metabolism for precise assessment of disease activity and thrombotic or bleeding risks. Interventions targeting gut-brain axis nodes, such as eliminating tissue factor-positive (TF[+]) T cells or modulating vagal activity, show potential to disrupt the inflammation-coagulation cycle, although rigorous randomized trials are still needed. Artificial intelligence (AI)-assisted systems that integrate real-time biomarker monitoring with multi-omics predictions represent a novel paradigm for managing IBD-related coagulation dysfunction. Key challenges include elucidating gut-brain-liver axis regulation of coagulation and characterizing platelet functional heterogeneity. Future efforts must prioritize ethically compliant multi-omics platforms and racially stratified risk models to advance personalized coagulation management in IBD.},
}

@article {pmid41913928,
year = {2026},
author = {Mulinde, T and Sousa, LGV and Castro, J and George, SD and Muzny, CA and Cerca, N},
title = {Evidence from a broad-range PNA probe links several Prevotella species to bacterial vaginosis.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20902},
pmid = {41913928},
issn = {2167-8359},
mesh = {Female ; Humans ; *Vaginosis, Bacterial/microbiology/diagnosis ; *Prevotella/genetics/isolation & purification ; *Peptide Nucleic Acids/genetics ; Vagina/microbiology ; Sensitivity and Specificity ; Biofilms/growth & development ; Adult ; },
abstract = {BACKGROUND: Bacterial vaginosis (BV) is the most prevalent vaginal infection among reproductive-age women. It is associated with multiple adverse health outcomes in women including adverse pregnancy outcomes, an increased risk of pelvic inflammatory disease, infertility, and an increased risk of HIV and other sexually transmitted infections. BV is characterized by an imbalance in the vaginal microbiota, namely a decrease in protective Lactobacillus species and an overgrowth of facultative and strict anaerobic bacteria, leading to the development of a polymicrobial biofilm. Despite extensive research, the etiology of BV remains unclear, and its pathophysiology is not fully understood. It has been hypothesized that P. bivia, in combination with Gardnerella spp., plays an important role in the early development of the BV biofilm. We previously developed a peptide nucleic acid (PNA) probe specifically targeting P. bivia to investigate its role as a potential early colonizer. However, our recent findings have raised doubts about the specificity of this association, suggesting a broader involvement of other Prevotella species in incident BV (iBV).

METHODS: A new PNA probe targeting Prevotella spp. 23S rRNA was developed compared to the existing P. bivia-specific probe. This new probe was optimized in vitro through a variation of hybridization temperatures and times. Its performance was evaluated using a collection of 28 Prevotella strains representing 24 different species and 38 non-Prevotella spp. typically found in BV in order to assess its sensitivity and specificity. Both probes were tested on vaginal swab specimens from women with and without BV to assess the bacterial count and detection of Prevotella species.

RESULTS: In vitro validation demonstrated that the new Prevotella spp. probe achieved a specificity of 100% and sensitivity of 96%. As expected, its broader detection allowed identification of a wider range of Prevotella spp. compared to the P. bivia-specific probe, which was intentionally restricted to a single species. Application to clinical specimens revealed that the new probe identified a significantly higher count of Prevotella spp. in 6/9 (66.6%) BV-positive specimens compared to the P. bivia-specific probe. In 2/9 (22.2%) healthy control specimens, greater Prevotella spp. detection was also observed.

CONCLUSIONS: Our findings suggest that the involvement of Prevotella spp. in BV extends beyond P. bivia, implicating a wider range of species which could be present in the polymicrobial BV biofilm. The broader specificity of this new Prevotella spp. probe provides a valuable tool for future research on the vaginal microbiome and the pathogenesis of BV.},
}

Female
Humans
*Vaginosis, Bacterial/microbiology/diagnosis
*Prevotella/genetics/isolation & purification
*Peptide Nucleic Acids/genetics
Vagina/microbiology
Sensitivity and Specificity
Biofilms/growth & development
Adult

@article {pmid41914163,
year = {2026},
author = {Kozin, S and Kravtsov, A and Lyasota, O and Dorohova, A and Ivlev, V and Chikhirzhina, E and Moiseev, A and Nesterova, V and Babenkova, P and Popov, K and Fedulova, L and Dzhimak, S},
title = {Consumption of Water Similar to Martian Water in Terms of Deuterium Content by Mammals Leads to the Development of an Adaptation Syndrome and Activation of Protective Mechanisms Against Stress.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {18},
number = {1},
pages = {39086},
doi = {10.31083/FBE39086},
pmid = {41914163},
issn = {1945-0508},
support = {125011700394-5//State Task Force of the Southern Scientific Center of the Russian Academy of Sciences for 2025/ ; },
mesh = {Animals ; *Deuterium/analysis ; Rats, Wistar ; Rats ; *Adaptation, Physiological ; Male ; *Stress, Physiological ; Brain/metabolism ; *Water/chemistry ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Deuterium is unevenly distributed in natural waters, while the same applies to the content of deuterium in ice on Mars. Moreover, changes in the deuterium content of drinking water are known to affect the bodies of mammals. Thus, since plans are in place to send people to Mars in the coming years, understanding the effects of water with a Martian isotopic composition is necessary. Therefore, this study aimed to evaluate the impact of water with an increased deuterium content of 1200 ppm on the dynamics of indicators in the body of mammals.

METHODS: The study was conducted on Wistar rats. The metabolic profile of blood and the content of deuterium in it were studied in dynamics by days using nuclear magnetic resonance (NMR) spectroscopy. Additionally, the isotopic composition of brain tissue was studied in dynamics by days using isotope mass spectrometry. A further study was conducted on the functioning of the antioxidant system in blood plasma and brain tissue using PCR analysis, chemiluminescence, and biochemical analysis methods; the intestinal microbiome was also studied. The durations of the animal experiments were 31 (blood and brain study) and 38 (stress-protective activity study) days.

RESULTS: On day 23, the deuterium content in the blood plasma increased to 856 parts per million (ppm), and to 260 ppm in the brain on day 31. This increase led to an imbalance in the antioxidant/prooxidant processes. This effect was accompanied by shifts in the intensity of oxidative processes, alongside changes in enzyme activity and the expression of genes responsible for their synthesis, shifts in amino acid composition, and changes in the concentration of metabolites and microbiome molecules in the blood plasma. By the fifth and eighth days, the number of Bacteroides in the intestines had decreased by 14% and 21.8%, respectively, compared to the values measured on day zero of the experiment. Meanwhile, the population of Firmicutes-type bacteria increased by 12% and 16% on the fifth and eighth days, respectively, compared to the indicators measured on day zero of the experiment.

CONCLUSION: An increase in the concentration of deuterium in the body promotes the development of a stress reaction and the activation of compensatory mechanisms aimed at adaptation.},
}

Animals
*Deuterium/analysis
Rats, Wistar
Rats
*Adaptation, Physiological
Male
*Stress, Physiological
Brain/metabolism
*Water/chemistry
Gastrointestinal Microbiome

@article {pmid41914171,
year = {2026},
author = {Yildirim, EA and Laptev, GY and Tiurina, DG and Filippova, VA and Ilina, LA and Novikova, NI and Sokolova, KA and Ponomareva, ES and Brazhnik, EA and Zaikin, VA and Klyuchnikova, IA and Bolshakov, VN and Korochkina, EA and Vorobyov, NI and Griffin, DK and Romanov, MN},
title = {Compositional and Functional Metabolic Shifts in the Endometrial Microbiota of Cows (Bos taurus) During the Transition Period: A Metagenomic Next-Generation Sequencing Approach.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {18},
number = {1},
pages = {39439},
doi = {10.31083/FBE39439},
pmid = {41914171},
issn = {1945-0508},
support = {24-16-00131//Russian Science Foundation/ ; },
mesh = {Animals ; Female ; Cattle/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; },
abstract = {BACKGROUND: Significant alterations in feeding, housing, and physiology are observed in dairy cows during the transition period (3 weeks pre- and post-calving), in addition to changes in the composition and abundance of the endometrial microbiota. Thus, this study aimed to evaluate any changes in the composition and predicted metabolic pathways in the cow uterine microbiome during this transition period.

METHODS: Scrapings were sampled from the endometrial surface of clinically healthy cows (n = 3) in dynamics as follows: in the 10 Days period before, and on Days 3, 5, and 20 after calving. Total DNA was isolated from the samples, and the composition of the microbial community was assessed using targeted next-generation sequencing (NGS) technology. Based on the subsequent NGS data, the dynamics of the predicted metabolic pathways of the microbiota were evaluated.

RESULTS: Seven superphyla and phyla of microorganisms were found in the endometrial microbiota of cows during the transition period. Among these, the phylum Firmicutes (with a dominant class of Clostridia) and the superphylum Fusobacteriota (represented by a single class of Fusobacteriia) can be considered the dominant bacteria in the endometrium, with representation noted from 25.2 to 68.2% and from 12.3 to 51.1%, respectively. The microbiome composition underwent significant changes (p < 0.05) during the transition period. In particular, the high abundance of the Fusobacteriaceae family (up to 68.2%) in the uterus of clinically healthy cows was unexpected, given the potential association of Fusobacteriaceae with the occurrence of metritis in cows. The numbers of microorganisms in two dominant classes, Fusobacteriia and Clostridia, showed generally opposite changes in their relative abundance during the transition period. The predicted functional potential level for 32 pathways in the endometrium changed (p < 0.05) in cows during the transition period. Indeed, the activity of the predicted pathways, such as pyridoxal 5'-phosphate biosynthesis I and teichoic acid (poly-glycerol) biosynthesis, was lowered on day 3 postpartum (p < 0.05).

CONCLUSIONS: Microbiota composition and the activity of the predicted metabolic pathways in the cow endometrium underwent significant changes at different critical stages in the transition period. Moreover, even clinically healthy cows exhibited signs of dysbiotic disorders.},
}

Animals
Female
Cattle/microbiology
*Endometrium/microbiology/metabolism
*Microbiota
High-Throughput Nucleotide Sequencing
*Metagenomics

@article {pmid41914284,
year = {2026},
author = {Wang, P and Ding, L and Lang, Z and Zhang, Y and Yu, Y},
title = {Therapeutic Modulation of the Gut Microbiome in Coronary Artery Disease: Current Evidence and Future Directions.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {3},
pages = {45081},
doi = {10.31083/FBL45081},
pmid = {41914284},
issn = {2768-6698},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Coronary Artery Disease/therapy/microbiology/metabolism ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Prebiotics/administration & dosage ; Fatty Acids, Volatile/metabolism ; Bile Acids and Salts/metabolism ; Synbiotics/administration & dosage ; Methylamines/metabolism ; Diet ; },
abstract = {The gut microbiome is increasingly recognized as a modifiable contributor to coronary artery disease (CAD). This narrative review integrates mechanistic and clinical evidence regarding short-chain fatty acids (SCFAs), trimethylamine-N-oxide (TMAO), and bile acids, and appraises therapeutic modulation via diet; probiotics, prebiotics, and synbiotics; fecal microbiota transplantation (FMT); and drug-microbiome interactions. SCFAs generally confer anti-inflammatory and lipid-regulatory effects, whereas bile acid signaling exhibits context-dependent metabolic actions. Findings regarding TMAO are inconsistent; in several cohorts, associations with cardiovascular risk become null or attenuated after adjustment for renal function (estimated glomerular filtration rate [eGFR]) and dietary patterns. Most interventional studies are small, use surrogate endpoints, and vary in strains and dosing, limiting certainty. Microbiome profiles differ across geographic regions, racial and ethnic groups, and dietary patterns, underscoring the need for stratified approaches. Routine FMT in CAD remains constrained by safety, feasibility, and ethical and logistical considerations. Overall, the microbiome represents a promising yet unproven therapeutic target in CAD. Future trials should standardize interventions, rigorously control for confounders, evaluate drug-microbiome interactions, and be adequately powered to detect clinical events to enable precision medicine.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Coronary Artery Disease/therapy/microbiology/metabolism
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Prebiotics/administration & dosage
Fatty Acids, Volatile/metabolism
Bile Acids and Salts/metabolism
Synbiotics/administration & dosage
Methylamines/metabolism
Diet

@article {pmid41914628,
year = {2026},
author = {Fu, Y and Long, N and Sourn, P and Li, W and He, Z and Tan, W and Yuan, J and Chen, Y and Wu, J and Wang, S and Feng, L and Wang, Z and Ding, W},
title = {Distinct vaginal microbial signatures in pregnancies complicated by antiphospholipid syndrome: depletion of Lactobacillus johnsonii and enrichment of Bifidobacterium dentium.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0388225},
doi = {10.1128/spectrum.03882-25},
pmid = {41914628},
issn = {2165-0497},
abstract = {UNLABELLED: Antiphospholipid syndrome (APS) is a systemic autoimmune disease that contributes substantially to recurrent pregnancy loss, fetal death, intrauterine growth restriction, and preeclampsia, posing major threats to maternal and fetal health. These obstetric complications exhibit clinical similarities to those resulting from vaginal dysbiosis, yet the vaginal microbiota in APS pregnancies has not been systematically investigated. In this study, we characterized the vaginal microbiome in 33 pregnant women with APS and 90 healthy controls using 16S rRNA gene sequencing. We identified a unique microbial signature in APS pregnancies that differed from the commonly observed pattern of increased microbial diversity and Lactobacillus depletion seen in classical vaginal dysbiosis. Specifically, while overall alpha diversity and Lactobacillus dominance were preserved, we observed distinct compositional restructuring characterized by selective depletion of Lactobacillus johnsonii and marked enrichment of Bifidobacterium dentium. A logistic regression model integrating the relative abundances of these microbial biomarkers demonstrated robust diagnostic performance in differentiating pregnancies with APS from healthy pregnancies, with risk scores significantly correlating with clinical parameters and pregnancy outcomes. This study demonstrates that pregnant women with APS display a distinct vaginal microbiome pattern defined by species-specific compositional restructuring rather than global dysbiosis. These microbial alterations may contribute to APS-related pregnancy morbidity, highlighting vaginal microbial signatures as promising noninvasive biomarkers for risk stratification and potential therapeutic targets in obstetric APS management.

IMPORTANCE: Antiphospholipid syndrome (APS) is an autoimmune disease that causes recurrent miscarriage, fetal death, and pregnancy complications in women of reproductive age. While coagulation dysfunction is a known contributing factor, whether APS is accompanied by vaginal microbiota alterations and their role in adverse outcomes remains unclear. We discovered that pregnant women with antiphospholipid syndrome harbor a unique vaginal microbial community: they exhibit depletion of the protective species Lactobacillus johnsonii while showing enrichment of Bifidobacterium dentium, a bacterium typically found in the gut. Unlike typical vaginal infections that display widespread microbial dysbiosis, antiphospholipid syndrome induces only selective alterations in specific bacterial species. These microbial signatures correlated with hematological parameters and adverse pregnancy histories, including prior miscarriages. Our findings suggest that monitoring vaginal microbiota could provide a simple, noninvasive approach to identify high-risk pregnancies in women with antiphospholipid syndrome and may guide novel screening strategies for pregnancy-related disorders targeting the vaginal microbiome.},
}

@article {pmid41914631,
year = {2026},
author = {Arogundade, AA and Dumaguit, CDC and Melton, A and Buerki, S and Bittleston, LS},
title = {Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0219825},
doi = {10.1128/spectrum.02198-25},
pmid = {41914631},
issn = {2165-0497},
abstract = {Advanced sequencing technologies and improvements in bioinformatics have provided a new way to study plant-associated microbial communities, including the use of host genomic sequencing. Our study focuses on the leaf microbiome of basin big sagebrush (Artemisia tridentata subsp. tridentata), a foundational shrub of western North America. We analyzed Illumina shotgun sequences from sagebrush leaves to investigate the metagenomes of leaf-associated microbes that were sequenced alongside their plant hosts. We aimed to profile the leaf microbiome across different sample sources (magenta box, greenhouse, and field/wild), reconstruct metagenome-assembled genomes (MAGs) where possible, and investigate functional gene annotations of the resulting MAGs, specifically with regard to the potential metabolism of sagebrush chemicals. To achieve this, Illumina shotgun sequence reads (containing both host and associated microbial reads) were mapped to the reference genomes of Artemisia tridentata, Artemisia annua, and the human reference genome to remove plant host and human-associated sequences. Host-cleaned reads were then analyzed using microbial metagenomics techniques. Taxonomic profiling revealed that Phyllobacterium and Sphingomonas were the most abundant microbial genera in greenhouse-grown plants, with very little variation among the samples. Wild, field-collected samples were much more variable and were dominated by Klebsiella and Aureobasidium species. From the co-assembly of greenhouse samples, we reconstructed two high-quality MAGs (a Phyllobacterium species and a Sphingomonas species) with >98% completion and <1% contamination. Functional annotation of these MAGs uncovered genes associated with the degradation and metabolism of camphor and other essential oils such as pinene, geraniol, and limonene, which are part of sagebrush leaf chemistry.IMPORTANCEBig sagebrush (Artemisia tridentata), the foundation species of the sagebrush steppe, has broad ecological importance because its evergreen leaves offer nutrients and shade that facilitate the establishment of diverse understory plants in arid environments. Sagebrush leaves contain various secondary metabolites, including terpenoids, flavonoids, and phenolic compounds. These chemicals contribute to the plant's defense mechanisms against herbivores and pathogens. Despite this, sagebrush hosts diverse bacterial and fungal communities. We found that the microbial metagenome-assembled genomes (MAGs) we recovered contained genes that have the potential to degrade some of the chemical compounds in sagebrush leaves that could inhibit the growth of other microbes. This is the first study to mine plant genome data using host-derived sequences to generate microbial MAGs. Our results showed that MAGs can be recovered from plant host-derived sequence data, providing a new way to explore the identity and functional capabilities of difficult-to-culture microbes.},
}

@article {pmid41914733,
year = {2026},
author = {Nandi, S and Stephens, TG and Garcia, R and Sánchez-García, M and Roberson, LM and Avalos, JL and Chundawat, SPS and Bhattacharya, D},
title = {Rafts of change: microbial and functional dynamics in simulated Sargassum strandings.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0235725},
doi = {10.1128/aem.02357-25},
pmid = {41914733},
issn = {1098-5336},
abstract = {Massive influxes of pelagic Sargassum spp. across the tropical Atlantic and Caribbean regions have created urgent ecological and economic challenges that need to be addressed to stabilize local ecosystems. Use of this abundant biomass feedstock resource for biorefining and bioproducts manufacturing is a promising avenue, but this goal requires elucidating the microbial processes that regulate Sargassum degradation, which are still poorly understood. Here, we investigated the microbial degradation of the benthic Sargassum filipendula by native microbiota using multi-omics approaches. Metagenomic and meta-transcriptomic analyses identified diverse carbohydrate-active enzymes (CAZymes), including alginate lyases, fucoidanases, and cellulases, that were differentially expressed over the course of the in vitro degradation timeline. Furthermore, we identified the need for arsenic detoxification pathways in microbes utilizing Sargassum-derived substrates. We observed a suite of factors influencing microbial dynamics, including prokaryotic competition, arsenic detoxification, viruses, and substrate availability. Lineages potentially capable of degrading recalcitrant polysaccharides such as fucoidan appeared to be rapidly outcompeted by other bacteria that utilized simpler substrates like mannitol. These results highlight the metabolic potential of native marine microbial communities to degrade complex Sargassum polysaccharides and the importance of the in vitro degradation experiment time scale to capture the activities of non-dominant specialists. Our findings elucidate microbial ecosystem dynamics during Sargassum degradation and provide novel insights that can be used to advance the development of biotechnological approaches that leverage renewable Sargassum biomass as a biorefinery feedstock of the future.IMPORTANCEThis work addresses a crisis in the tropical Atlantic and Caribbean regions, the massive population growth and stranding of the floating brown seaweed Sargassum, which is wreaking havoc on ecosystems and fouling beaches vital to local tourism. One solution to this problem is to utilize the seaweed as feedstock to generate useful bioproducts. This approach requires characterizing the microbiome of Sargassum that drives its degradation in nature. To this end, we devised an in-lab degradation assay using Sargassum and identified a variety of carbohydrate-active enzymes, including alginate lyases, fucoidanases, and cellulases which break down seaweed cell wall polysaccharides. We also find that microbes compete in the closed reactors, with diversity being reduced over time. These results highlight the metabolic potential of native marine microbial communities to degrade Sargassum and elucidate microbial ecosystem dynamics during this process. These insights allow the use of renewable Sargassum as a biorefinery feedstock of the future.},
}

@article {pmid41914747,
year = {2026},
author = {Franklin, S and Sahasrabhojane, P and Hayase, T and Hayase, E and Chang, C-C and Senapati, J and Desikan, SP and Kadia, T and Lorenzi, PL and Jenq, RR and Shelburne, SA and Galloway-Peña, J},
title = {Short-chain fatty acid-producing microbes differentiate non-infectious and infectious neutropenic fever in leukemia.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0134325},
doi = {10.1128/msystems.01343-25},
pmid = {41914747},
issn = {2379-5077},
abstract = {UNLABELLED: Neutropenic fever (NF) is often the first sign of infection in patients with hematologic malignancies, but its cause is frequently unknown, leading to broad-spectrum antibiotic use without confirmed infections. Although research links gut microbiome disruptions to treatment-related infections, it typically examines NF as the outcome, leaving a gap in understanding how the microbiome and metabolic factors distinguish infectious from non-infectious cases. Stool samples from acute myeloid leukemia patients were analyzed to characterize gut microbiome composition and fecal metabolites at baseline and at fever onset. Machine learning models, network analyses, and functional profiling were used to differentiate infectious NF vs non-infectious NF at baseline and at fever onset. The baseline model (area under the receiver operating characteristic [AUROC] = 0.769) identified higher levels of Akkermansia, Enterobacter, Escherichia-Shigella, and Flavonifractor as predictors of infectious NF, while Collinsella, Lachnospiraceae, Coprococcus, and acetic acid were linked to non-infectious cases. At fever onset, Enterococcus was enriched in infectious NF, whereas Gemella, Butyrate, Lachnospiraceae, Ruminococcaceae, and Eisenbergiella abundances favored non-infectious NF outcomes (AUROC = 0.752). Network analyses also revealed greater functional diversity and microbiome-metabolome connectivity in non-infectious cases at fever onset. This study suggests that gut microbiota and metabolites may serve as biomarkers for distinguishing infectious from non-infectious neutropenic fever, warranting further validation in larger cohorts.

IMPORTANCE: Our study tackles the challenge of managing neutropenic fever (NF) in immunocompromised patients whose numbers have increased due to various immunodeficiencies and treatments that suppress immune function. Fever is often the only sign of a serious infection in these patients, yet there are neither clear patterns linking risk factors to infection nor biomarkers reliable for ruling out non-infectious causes. As a result, febrile patients are typically empirically treated for major pathogens, even in the absence of confirmed infections, which propagates antimicrobial resistance and gut dysbiosis. Our research utilizes gut microbiome and targeted metabolomic profiling from two cohorts of patients with acute myeloid leukemia undergoing chemotherapy and employs a machine learning framework to distinguish between infectious and non-infectious NFs at baseline and upon fever onset.},
}

@article {pmid41914795,
year = {2026},
author = {},
title = {Corrigenda to 'Gut microbiome and cognitive function in the Hispanic Community Health Study/Study of Latinos'.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877261432716},
doi = {10.1177/13872877261432716},
pmid = {41914795},
issn = {1875-8908},
}

@article {pmid41914849,
year = {2026},
author = {Deng, T and Wang, H and Zhang, S-F and Wu, X-Y and Yang, Z-S and Wang, D-Z and Zheng, Y},
title = {Functional determinism amid taxonomic stochasticity: insights into rules governing the assembly of algal-microbial symbioses.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0035926},
doi = {10.1128/aem.00359-26},
pmid = {41914849},
issn = {1098-5336},
abstract = {Marine algal-microbial symbioses constitute essential functional units that drive ocean biogeochemical cycles and trigger harmful algal blooms. Yet, a long-standing controversy persists regarding the mechanisms of algal-microbial symbiose assembly, specifically whether phycosphere microbiota are predominantly shaped by deterministic algal-driven selection or by stochastic environmental processes, with no definitive resolution to date. Here, we examined phycosphere communities associated with a series of Skeletonema strains, tracking their taxonomic and functional dynamics across successive growth stages. Despite pronounced taxonomic diversity, reflected in distinct community compositions, successional trajectories, and microbial networks, shotgun metagenomic analyses revealed highly conserved functional repertoires across samples, with consistently abundant core pathways, including amino acid biosynthesis, secondary metabolite and antibiotic production, and ABC transport systems. Statistical analyses further revealed a marked decoupling of taxonomy and function, with functional redundancy enabling taxonomically distinct lineages to perform equivalent metabolic roles. Based on these findings, we propose a dual assembly model in which deterministic algal host-driven selection constrains functional composition, while stochastic processes govern species-level membership. This "function-first, taxonomy-stochastic" paradigm reconciles opposing assembly theories, underscores functional resilience in the face of taxonomic turnover, and provides a conceptual foundation for the rational design of synthetic algal-microbial consortia in marine biotechnological applications.IMPORTANCEMarine algae live in close association with diverse microorganisms that influence nutrient cycling and ecosystem stability. Yet, how these algal-microbial partnerships assemble and maintain functional integrity remains unresolved. Using Skeletonema as a model, this study demonstrates that while the microbial species surrounding different algal strains vary greatly, their metabolic functions remain remarkably consistent. This finding reveals that algal hosts deterministically shape the functional needs of their microbiome, whereas the specific bacterial members fulfilling those roles are interchangeable. Such a "function-first" organization explains how algal-microbial symbioses persist despite environmental fluctuations. Understanding these assembly rules not only advances our knowledge of marine microbial ecology but also provides a conceptual foundation for engineering stable and resilient algal-microbial consortia for sustainable ocean biotechnologies.},
}

@article {pmid41914961,
year = {2026},
author = {Maigoro, AY and Lee, JH and Heo, D-R and Yun, B-R and Lee, HI and Kwon, H-W},
title = {Spatiotemporal variation in the microbiome of Aedes vexans from Korea reveals regional markers linked to environmental risk factors.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0258725},
doi = {10.1128/spectrum.02587-25},
pmid = {41914961},
issn = {2165-0497},
abstract = {Aedes vexans is a widespread mosquito species known to carry West Nile virus (WNV); however, our understanding of how its microbiome changes across different regions and seasons, particularly in temperate areas such as South Korea, remains limited. In this study, we examined the microbiome of Aedes vexans collected from 16 locations over 3 consecutive summer months. Using 16S rRNA sequencing, we found that the microbiome was largely made up of Proteobacteria, but the specific genera present, like Dickeya, Spiroplasma, and members of Enterobacterales, varied depending on the location and time of collection. Dickeya, in particular, was more common in inland areas and stayed relatively stable over time, which suggests it could serve as a useful microbial marker. We also observed a significant absence of Wolbachia, a common endosymbiont in mosquitoes, which hypothesizes potential increased risk of WNV transmission. Diversity analyses showed clear differences in microbial communities by region, and we found seasonal patterns in genera like Asaia and Pseudomonas, which were correlated to mosquito abundance and local environmental conditions. These patterns held up when we looked at co-occurrence networks between microbes. Altogether, this is the first study to track Aedes vexans microbiome across both space and time in Korea, and our findings offer new insights into mosquito ecology and the potential use of bacteria in disease control strategies.IMPORTANCEUnderstanding the dynamics of the mosquito microbiome is essential for predicting disease risk and developing targeted vector control strategies. Aedes vexans, a globally distributed species and potential vector for West Nile virus (WNV), has seen a notable population increase in South Korea, yet its microbial ecology remains poorly characterized. This study provides the first comprehensive spatiotemporal analysis of Aedes vexans microbiota across Korea, identifying key microbial taxa that vary by region and season. The absence of Wolbachia, a known antiviral symbiont, and the dominance of Dickeya, a plant-associated genus with potential ecological implications, underscore the need for microbiome-informed surveillance tools. By highlighting native microbial signatures and their environmental drivers, this work lays the groundwork for microbiota-based monitoring of vector populations and opens new avenues for symbiont-based interventions in arbovirus control.},
}

@article {pmid41915085,
year = {2026},
author = {Liang, J and Zang, S and Wang, Z and Zhang, R},
title = {Cancer and aging: complex associations and therapeutic targets.},
journal = {Molecular biomedicine},
volume = {7},
number = {1},
pages = {},
pmid = {41915085},
issn = {2662-8651},
support = {No. 202303021221201//Shanxi Provincial Basic Research Program/ ; },
mesh = {Humans ; *Aging/genetics/pathology ; *Neoplasms/therapy/pathology/genetics/metabolism/etiology ; Animals ; Cellular Senescence ; Genomic Instability ; Autophagy ; Epigenesis, Genetic ; Molecular Targeted Therapy ; },
abstract = {The incidence of cancer increases markedly with aging, and the two processes share underlying molecular mechanisms. In the context of global population aging and rising cancer incidence, nine convergent hallmark axes have been identified: genomic instability, epigenetic drift, inflammation-immunity imbalance, microbiome dysbiosis, metabolic reprogramming, telomere attrition, stem cell exhaustion, cellular senescence, and autophagy dysfunction. These hallmarks constitute an integrated regulatory network that operates synergistically, antagonistically, or through bidirectional feedback across molecular, cellular, and microenvironmental levels. Genomic instability, epigenetic remodeling, chronic inflammation, microbiome dysbiosis, and metabolic reprogramming in aging often act synergistically to promote tumorigenesis, whereas telomere attrition and stem cell exhaustion primarily exert antagonistic, tumor-suppressive effects. Cellular senescence and autophagy dysfunction display context-dependent dual roles. Importantly, this network framework has direct relevance to cancer therapeutics. Although chemotherapy, radiotherapy, and immunotherapy effectively suppress tumor progression, they frequently induce therapy-induced senescence, characterized by cell-cycle arrest and a senescence-associated secretory phenotype, thereby accelerating functional decline and increasing long-term toxicities in older patients. The proposed "synergistic-antagonistic-dual" framework linking aging and cancer not only helps explain the disproportionate cancer burden in older adults but also supports a "one drug, two targets" therapeutic paradigm. Targeting these shared pathways has delayed aging phenotypes and suppressed tumorigenesis in preclinical studies and early clinical trials, highlighting the potential of integrated interventions that concurrently address aging and cancer.},
}

Humans
*Aging/genetics/pathology
*Neoplasms/therapy/pathology/genetics/metabolism/etiology
Animals
Cellular Senescence
Genomic Instability
Autophagy
Epigenesis, Genetic
Molecular Targeted Therapy

@article {pmid41915167,
year = {2026},
author = {Venetsianou, NK and Paragkamian, S and Kalaentzis, K and Loukas, A and Damianou, C and Lagani, V and Jensen, LJ and Pafilis, E},
title = {LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02730-5},
pmid = {41915167},
issn = {1432-184X},
}

@article {pmid41915265,
year = {2026},
author = {Volk, A and Mills, M and Chae, S and Lee, J},
title = {Investigation of cyanobacteria-hosted antibiotic resistance genes in cyanoHAB-impacted drinking water sources.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41915265},
issn = {1614-7499},
abstract = {Freshwater cyanobacterial blooms (cyanoHABs) are expanding across the world, and their frequency and severity are becoming more intense due to prevalent eutrophication and a changing climate. Traditionally, the concerns about cyanoHABs have mainly focused on cyanotoxins in water. CyanoHABs are also hypothesized to play a role in the antibiotic resistome, but whether cyanobacteria host clinically relevant antibiotic resistant genes (ARGs) in the environment is largely unknown. To investigate this emerging issue, we examined whether cyanobacteria host ARGs within the broader microbiome context. We looked for the presence of cyanobacteria-hosted ARGs using shotgun metagenomic sequencing of drinking water source samples collected during the bloom season (summer and fall) from Lake Erie and Grand Lake St. Marys (GLSM). ARGs were annotated using DeepARG and Resistance Gene Identifier (RGI). Cyanobacteria were annotated to host genes conferring putative antibiotic resistance, including efflux pumps qac/EmrE, vatB, van genes, and an OXA homolog. A maximum likelihood tree with cyanobacteria and OXA reference sequences showed OXA-like homology across multiple families of cyanobacteria. Most cyanobacteria sequences clustered in a large clade with ybxI, suggesting very limited or negligible class-D beta-lactamase activity, but a small subset formed a clade with OXA-2 and OXA-46. While those hits suggest potential resistance to clinical antibiotics, overall cyanobacteria were not found to host ARGs conferring resistance to drugs of last resort in these samples. Additionally, BLAST searches of the cyanobacteria ARG contigs and coding sequences resulted in top hits for cyanobacteria, further supporting that annotated genes are likely intrinsic rather than acquired. rpoB2 and arlR ARG annotations appear to be spurious hits on housekeeping genes, which demonstrates the need to verify automated ARG annotation tool results. Selected cyanotoxins, cyanobacteria, and ARGs were also chosen for quantification. We found high levels of Microcystis in Lake Erie as well as Planktothrix and microcystin concentrations in GLSM, supporting previous trends in these water bodies. This study takes a novel approach, pairing the issues of cyanoHABs and ARGs together in two drinking water sources. In a changing climate, drinking water treatment strategies should consider the treatment and public health implications of multiple contaminants.},
}

@article {pmid41915459,
year = {2026},
author = {Gupta, RM and Ismail, HM and Siller, AF and Pesikoff, J and Devaraj, S and Balasubramanyam, A and Redondo, MJ},
title = {Impact of Body Size on Preclinical Type 1 Diabetes Development and Progression.},
journal = {Diabetes care},
volume = {},
number = {},
pages = {},
doi = {10.2337/dci25-0134},
pmid = {41915459},
issn = {1935-5548},
support = {3-SRA-2025-1738-S-B//Breakthrough Type 1 Diabetes/ ; },
abstract = {Type 1 diabetes arises from the interplay of genetic susceptibility and environmental exposures, leading to autoimmune β-cell destruction. Although disease-modifying therapies (DMTs) can delay progression to clinical (stage 3) type 1 diabetes, treatment responses remain inconsistent and transient. The marked heterogeneity of type 1 diabetes, shaped by age, sex, race/ethnicity, and genetic background, underscores the need to elucidate distinct mechanistic pathways. Among environmental contributors, obesity stands out as a compelling modifiable target. Data from The Environmental Determinants of Diabetes in the Young (TEDDY), Type 1 Diabetes TrialNet, and other longitudinal cohorts link BMI and adiposity to the onset of islet autoimmunity, progression through preclinical stages, and development of stage 3 type 1 diabetes. These associations are not uniform; heightened susceptibility to adiposity-related risk is seen among younger children, Hispanic populations, and individuals with specific HLA genotypes. Despite robust epidemiologic evidence, the biological pathways connecting elevated BMI to autoimmune β-cell destruction remain incompletely defined. Emerging data implicate a network of immunologic and metabolic disturbances, including insulin resistance, β-cell stress, chronic adipose tissue inflammation, altered adipokine signaling, and gut microbiome changes, that collectively heighten β-cell vulnerability, amplify autoreactive immune responses, and drive metabolic decompensation toward clinical disease. Elucidating these mechanisms and identifying related biomarkers are critical to advancing precision prevention. In future studies, investigators should evaluate whether modifying elevated BMI or targeting obesity-associated immunologic and metabolic pathways can alter the preclinical trajectory of type 1 diabetes. Such mechanistic understanding may help curb type 1 diabetes incidence and improve outcomes for populations most vulnerable to obesity-related risk.},
}

@article {pmid41907525,
year = {2026},
author = {González-Valdivia, C and Tong, B and Hjalmarsson, S and Guðnadóttir, U and Wagner, N and Engstrand, L and Schuppe-Koistinen, I and Fransson, E and Prast-Nielsen, S and Brusselaers, N and Hugerth, LW},
title = {The gut microbiome in early pregnancy is associated with the severity of nausea and vomiting: a nested case‒control study.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2603861},
pmid = {41907525},
issn = {2993-3935},
abstract = {Approximately 70% of all pregnancies are affected by nausea and vomiting (NVP), yet the mechanisms controlling this phenomenon are not well known. Pregnancy hormones explain a large part of this effect, mostly through human chorionic gonadotropin and fetal production of GDF15, a hormone active in the brain stem. Still, there is a wide variation in the severity of symptoms, ranging from no nausea to severe vomiting requiring hospitalization (hyperemesis gravidarum). Here, we present a nested case‒control study within the large SweMaMi cohort, wherein 337 participants with severe NVP in early pregnancy were matched 1-to-1 with moderate and mild NVP, respectively. Subjects with more severe nausea had lower richness and diversity in their fecal microbiomes. Several taxa were significantly associated with NVP score, where the most extreme are a negative correlation with Lactobacillaceae and positive correlations with Bifidobacterium dentium and Puniceicoccaceae. Finally, higher NVP score was associated with a higher abundance of bacteria encoding for the neuroactive pathways of glutamine degradation, inositol synthesis, and lactate production. In conclusion, the gut microbiota was strongly associated with NVP. Further studies with direct interventions capable of restoring the early-pregnancy gut microbiome could open up new approaches for dealing with the most common symptom of early pregnancy.},
}

@article {pmid41907632,
year = {2026},
author = {Russo, F and Tripodi, L and Caldora, F and Pandolfo, SD and Aveta, A and Nardelli, C and Imbimbo, C and Perdonà, S and Pastore, L and Castaldo, G},
title = {Identification of a weighted urinary microbial signature for bladder cancer discrimination.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1784501},
pmid = {41907632},
issn = {2234-943X},
abstract = {INTRODUCTION: Growing evidence from microbiome studies has demonstrated associations between dysbiosis and cancers, including bladder cancer (BCa). Our recent works on urobiome revealed a different microbial composition in BCa patients compared to controls. The aim of this work was to create a Weighted Composite Index (WCI) to distinguish BCa-affected patients (mBCa) from healthy controls (mHC) in a cohort of male aged over 50 years.

METHODS: Urobiome data from 51 subjects (27 mBCa and 24 mHC) were analyzed. Random Forest (RF) classifier was trained to identify genera and species which significantly contributed to discriminating between mBCa and mHC group. A weighted normalization approach was used to compute separate WCIs at genus and species levels and in-silico validation test were performed to assess the models' robustness.

RESULTS: the WCI was calculated for each patient at both genera and species levels, showing a significant difference between the two groups (p < 0.0001) in both comparisons. WCIs showed superior discriminative performances compared to any individual taxon used for the model construction. Despite the need for validation in larger independent cohorts, the in-silico validation pipeline showed a stable high sensitivity of the models.

CONCLUSIONS: Our findings identified a candidate urinary microbial signature in a biomarker discovery setting associated with bladder cancer. This hypothesis-generating approach may contribute to the identification of a non-invasive biomarker, which requires validation in larger, independent cohorts before clinical application.},
}

@article {pmid41907707,
year = {2024},
author = {Teigen, LM and Kaiser-Powers, T and Matson, M and Elkin, B and Kabage, AJ and Hamilton, M and Vaughn, BP and Sadowsky, MJ and Staley, C and Khoruts, A},
title = {Contribution of Common Sulfur-Containing Substrates to Hydrogen Sulfide Production By Human Gut Microbiota Using an In Vitro Model Standardized For Bacterial Counts.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2361246},
pmid = {41907707},
issn = {2993-3935},
abstract = {Hydrogen sulfide (H2S) produced by human gut microbiota is highly toxic and implicated in pathogenesis of gastrointestinal tract disorders. Sulfur-containing amino acid (SAA) degradation is a major contributor to its production, but SAA degradation pathways have not been extensively characterized. In vitro model systems of fecal H2S production offer a basic method to help elucidate SAA degradation pathways, but the approach is not standardized. To address this, we used fecal microbiota separated from feces and standardized for bacterial counts to measure H2S production potential in response to different substrates in healthy controls (n = 6) with repeated sampling (three samples per participant). H2S production was highest with cysteine (mean = 16.7 ppm) compared to sodium sulfate (0.7 ppm) and taurine (0.8 ppm). Sodium-sulfate-driven H2S production negatively correlated with Ruminococcus (Spearman's ρ = -0.5) and cysteine-driven H2S production negatively correlated with Firmicutes (Spearman's ρ = -0.5). These findings, using a protocol controlling for confounding variables such as bacterial counts, validate previous findings of cysteine as a primary driver of H2S production. Finally, the inclusion of samples from two patients with UC allowed for the illustration of the potential of this approach to identify functional differences in specific disease states.},
}

@article {pmid41907708,
year = {2024},
author = {Kaufman, P and O'Meara, KE and Hawrelak, J},
title = {Preventing chemotherapy-induced diarrhea and microbiota imbalances with prebiotics and probiotics in breast cancer treatment: A case report.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2379475},
pmid = {41907708},
issn = {2993-3935},
abstract = {Breast cancer (BC) is the second most common cancer in women in the United States. Of those diagnosed, 40-80% will undergo chemotherapy. Adverse effects of chemotherapy are chemotherapy-induced diarrhea (CID) and gut microbiota dysregulation. CID can lead to dehydration, metabolic acidosis, malnutrition, and gut dysbiosis. Antidiarrheal medications are the standard treatment of care; however, this has been shown to further contribute to gut dysbiosis, is not always effective in controlling diarrhea, and can lead to rebound constipation with the potential of pathogenic bacterial overgrowth. In this case report, we describe the experience of a patient-centered, personalized intervention with pre- and probiotics to preserve the microbiota and prevent CID. A 57-year-old postmenopausal female with BC undergoing adriamycin-cyclophosphamide (AC) and taxol-cyclophosphamide (TC) chemotherapies for invasive ductal carcinoma under the care of a cancer team wanted to refrain from using loperamide and instead use nutritional interventions and supplementation for preventing CID and maintaining gut health. This case report is a narrative report of the observed outcomes of one patient with BC after taking specific prebiotics and probiotics. The outcomes included the prevention of CID and other gastrointestinal adverse effects, and maintaining microbiota alpha-diversity, butyrate producing genera, and Bifidobacterium populations while inhibiting the overgrowth of Proteobacteria pathogenic bacteria.},
}

@article {pmid41907711,
year = {2024},
author = {Varshney, N and Pandey, RK and Mishra, A and Kumar, S and Jha, HC},
title = {Aurora Kinase A: Integrating Insights into Cancer, Inflammation, and Infectious Diseases.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2419069},
pmid = {41907711},
issn = {2993-3935},
abstract = {Aurora kinase A (AURKA) is crucial in regulating cell division and maintaining genomic stability, making it significant in cancer biology. This review explores AURKA's structural and functional roles, emphasizing its involvement in cell cycle progression. Beyond cancer, AURKA emerges as a multifaceted player in host cell modulation, exerting influence over inflammatory responses, cell death mechanisms, and autophagy pathways. Moreover, recent research highlights its involvement in viral and bacterial infections. Numerous viruses, for their replication and assembly, modulate host cell cycle progression. Various viruses modulated AURKA to induce viral-mediated tumor. It also emerged as a key modulator in various gut microbiome-mediated cancers. Further, it also imparts oncogenic effect by modulation in cytoplasmic and mitochondrial regions of the cell. It hampers DNA replication independent of its kinase domain. Understanding AURKA's diverse roles underscores its potential as a promising drug target, offering therapeutic avenues for various diseases. This comprehensive exploration navigates through complex landscape of AURKA biology, paving way for future investigations and therapeutic interventions.},
}

@article {pmid41907714,
year = {2024},
author = {Molinas-Vera, M and Ferreira-Sanabria, G and Peña, P and Sandoval-Espinola, WJ},
title = {The Paraguayan gut microbiome contains high abundance of the phylum Actinobacteriota and reveals the influence of health and lifestyle factors.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2332988},
pmid = {41907714},
issn = {2993-3935},
abstract = {Most gut microbiome studies are focused on populations from developed nations. However, this overlooks the role played by host genetics, lifestyle, and diet, highlighting the need to evaluate under-represented populations. Thus, we performed the first gut microbiome study from a Paraguayan cohort via 16S rRNA sequencing and PICRUSt2 analysis. We evaluated fecal samples from 60 participants from Asunción, while considering categories such as body-mass-index (BMI), sex, age, diet, lifestyle, and clinical history. Firmicutes (76.0 ± 11.6%), Actinobacteriota (10.4 ± 7.9%) and Bacteroidota (9.4 ± 11.4%) were the most abundant phyla. Similarly, the most abundant genera were Blautia (14.1 ± 7.5%), Faecalibacterium (8.07 ± 6.8%), and Bacteroides (6.7 ± 6.8%). Likewise, the most abundant microbial pathways were predicted to be involved with sugar metabolism and fermentation. Interestingly, some categories significantly impacted the gut microbiome composition and function, such as BMI (Moryella, Bifidobacterium), sex (Faecalibacterium), and others. Additionally, dysbiotic indices differed from values previously reported as homeostatic. These observations highlight the need for further studies, considering microbial species and host genetics. Thus, this work expands the knowledge of the gut microbiome from the Collective South, while contrasts found herein reinforce the need for further research with human populations traditionally understudied.},
}

@article {pmid41907715,
year = {2024},
author = {Winters, AD and Francescutti, DM and Kracht, DJ and Kuhn, DM and Angoa-Perez, M},
title = {The Effects of Ceftriaxone on Glutamate Transporter Expression and the Gut Microbiome: Implications for a Role of Antibiotic-Induced Dysbiosis in Mediating Drug Seeking and Relapse.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2393727},
pmid = {41907715},
issn = {2993-3935},
abstract = {Ceftriaxone (CTX), a beta-lactam antibiotic, is widely used in drug seeking and relapse studies due to its ability to enhance glutamate transporter (GLT-1) expression in the brain. Since increased synaptic glutamate is believed to drive drug seeking and relapse, CTX's effect on GLT-1 offers potential for treating substance abuse. However, the effect of CTX on the gut microbiome remains unexplored. Mice received CTX at 200 mg/kg per day for 4 d, and its effects on the gut microbiome were assessed. CTX led to increased striatal GLT-1 expression and induced rapid, long-lasting dysbiosis, with females showing a greater response than males. Diversity metrics were significantly altered during the acute phase of CTX treatment. Alpha diversity showed varying recovery levels depending on sex, while beta diversity indicated that CTX-treated mice remained significantly different from controls. CTX caused significant increases in Bacillota and reductions in Bacteroidota. Most taxa were rapidly reduced by CTX, but Enterococcus and Bacillales expanded significantly. Metabolomic analysis revealed significant changes in microbial pathways related to substance use disorders. These findings indicate that CTX causes immediate and persistent alterations in the gut microbiome, highlighting the importance of considering the gut microbiome as a target in substance abuse treatment.},
}

@article {pmid41907718,
year = {2024},
author = {Tannock, GW},
title = {Scoring Microbiota Function: A Proposal to Use Features of Evolutionary, Symbiotic Innovation to Recognize a "Healthy" Human Gut Microbiota.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2376543},
pmid = {41907718},
issn = {2993-3935},
abstract = {Research concerning the significance of the bacterial community of the human colon (gut microbiota or microbiome) in the etiology of diseases has depended in large part on molecular and bioinformatic tools to assemble catalogs of bacterial diversity. This article proposes that the gut microbiotas of humans are collectively a metacommunity whose functions are characteristic and consistent across all healthy humans. The pathway of evolutionary innovation in the development of the symbiosis between humans and gut microbiotas is known. Therefore, it is suggested that functional scoring of these long-lasting symbiotic innovations will reap greater benefits in delineating health or disease than can comparative taxonomic analysis. Adoption of a function-scoring approach would offer opportunities for emerging researchers, worldwide, to form multidisciplinary teams to develop essential methodologies to advance this gut microbiota research.},
}

@article {pmid41907719,
year = {2024},
author = {Dixit, K and Ahmed, A and Singh, A and Inamdar, M and Chavan, S and Bodkhe, R and Mehtab, W and Chauhan, A and Saroj, SD and Ahuja, V and Shouche, Y and Dhotre, D and Makharia, G},
title = {Site-Specific Gut Microbial Signatures in Non-Celiac Gluten Sensitivity.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2438621},
pmid = {41907719},
issn = {2993-3935},
abstract = {Gut microbiota in non-celiac gluten sensitivity (NCGS) has been poorly studied for its involvement in the disorder and site specificity. We investigated small intestinal, large intestinal and stool microbiota profiles in patients with NCGS and highly overlapping disorder irritable bowel syndrome (IBS) as well as effect of gluten-free diet (GFD) on microbiota in patients with NCGS. True NCGS patients were recruited based on serological response for anti-gliadin antibodies, 6-week gluten free diet (GFD) and symptom recurrence with gluten-rechallenge. Analyses using 16S rRNA gene amplicon and shotgun sequencing revealed community differences in core microbiome and diversity measures across sample types indicating dysbiosis mainly in mucosa-associated small intestinal microbiome of NCGS patients. Genera Elusimicrobiaum, Succinivibrio, Bacillus and Alcaligenes appeared as signatures in small intestine and stool in NCGS patients. Presence of differential taxa co-occurring at sampling sites, enabled recognition of site-specific microbial signatures. GFD led to a shift in mucosa-associated small intestinal core microbiome. Metagenome analysis revealed subtle differences in pathways for amino acid biosynthesis including L-ornithine. Mucosa-associated small intestine microbial structure was quite distinct in patients with NCGS in comparison to that with IBS.},
}

@article {pmid41907720,
year = {2024},
author = {Funahashi, K and Lee, CG and Sugitate, K and Kagata, N and Fukuda, N and Song, I and Ishii, C and Hirayama, A and Fukuda, S},
title = {Development of a Specialized Method for Simultaneous Quantification of Functional Intestinal Metabolites by GC/MS-Based Metabolomics.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2429408},
pmid = {41907720},
issn = {2993-3935},
abstract = {Intestinal metabolites produced by gut microbes play a significant role in host health. Due to their different chemical structures, they are often analyzed using multiple analyzers and methods, such as gas chromatography/mass spectrometry (GC/MS) for SCFAs and liquid chromatography/mass spectrometry (LC/MS) for bile acids (BAs), amino acids (AAs), and sugars. In this study, we aimed to develop a specialized method for the simultaneous determination of important intestinal metabolites, specifically addressing the main issue of SCFA volatilization during the dry solidification process. We discovered that these compounds can all be measured in fecal samples by GC/MS after trimethylsilyl (TMS) derivatization despite the expected volatility of SCFAs. Validating the results using SCFA standards suggested that the fecal matrix exerts a stabilizing effect. This method enabled the simultaneous quantification of 65 metabolites. For further validation in a biological context, a mouse study showed that high-MAC and high-fat diets increased SCFAs and BAs in feces, respectively, and showed a negative correlation between Alistipes and sugars, all consistent with previous studies. As a result, we successfully developed a specialized simultaneous quantification method for SCFAs, BAs, AAs, AA derivatives, and sugars in fecal samples using GC/MS-based metabolomics in conjunction with a TMS derivatization pretreatment process.},
}

@article {pmid41907847,
year = {2026},
author = {Tng, TJW and Vanan, S and Tan, EK and Zeng, L and Goh, WWB and Wong, SH and Lim, KL},
title = {Examination of shared gut microbiome signatures in aging and Parkinson's disease.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1745455},
pmid = {41907847},
issn = {1663-4365},
abstract = {Parkinson's disease (PD) is a prevalent neurodegenerative disorder that is characterized clinically by a constellation of motoric deficits including resting tremors, bradykinesia, and rigidity. In recent years, there has been increasing interest in the gut-brain axis with several studies examining the relationship between gut microbiome and PD. Although association studies have reported multidimensional microbiome changes in PD, these observed changes may be confounded by various factors, especially age. Notably, existing literature on gut microbiome tends to consider aging and PD separately. This review thus examines the gut microbiome factors associated with both aging and PD. Our comprehensive analysis of the available literature reveals significant overlaps in gut microbes that are associated with aging and PD. For example, the bacterial genera Akkermansia, and Alistipes have shown increased abundance in both conditions, while Faecalibacterium and Blautia conversely show decreased abundance. Our findings were temporally consistent with more recent studies. These shared gut microbiome signatures were identified in patients across the clinical spectrum of PD symptom severity, and may influence aging and disease pathogenesis via depletion of butyrate, a beneficial anti-inflammatory microbial metabolite, since major producers of butyrate (such as Faecalibacterium and Blautia) were constantly decreased with age (across both Asian and Western populations). Given these observations, we wish to highlight the need to consider age-related factors in understanding microbiome changes in PD; the intersection of which could reveal gut microbes and their corresponding microbial metabolites such as butyrate as potential therapeutic targets for PD.},
}

@article {pmid41907858,
year = {2026},
author = {Hashim, NT and Babiker, R and Padmanabhan, V and Islam, MS and Priya, SP and Chaitanya, NCSK and Mohammed, R and Dasnadi, SP and Ahmed, A and Gismalla, BG and Rahman, MM},
title = {Oral and cardiometabolic health through the lens of biobanks and large-scale epidemiologic research.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1774868},
pmid = {41907858},
issn = {2673-4842},
abstract = {Oral diseases and cardiometabolic disorders are among the most prevalent non-communicable conditions worldwide and share common inflammatory, metabolic, and social determinants. Over the past two decades, growing evidence has linked poor oral health-particularly periodontitis and tooth loss-to cardiometabolic outcomes such as type 2 diabetes and cardiovascular disease. However, progress in this field has long been constrained by fragmented data systems and limited availability of large-scale resources capturing both oral health exposures and cardiometabolic endpoints. Recent advances in biobank infrastructure, population-based cohorts, and electronic health record linkage have transformed this landscape, enabling robust secondary analyses at unprecedented scale. This narrative review synthesizes current evidence from major biobanks and large-scale epidemiologic datasets relevant to oral-cardiometabolic research. We describe how oral health and cardiometabolic outcomes are operationalized across data ecosystems, critically appraise the strengths and limitations of key resources, and integrate epidemiologic findings with established biological mechanisms, including chronic systemic inflammation, microbial dysbiosis, metabolic dysfunction, and vascular impairment. We further highlight the bidirectional nature of the relationship, whereby cardiometabolic disease can also exacerbate oral inflammatory conditions. Methodological challenges-such as exposure misclassification, residual confounding, and reverse causation-are discussed alongside emerging solutions, including data linkage, multi-omics integration, and advanced analytic approaches. Harnessing large-scale data sources offers a powerful opportunity to reposition oral health within cardiometabolic disease research and prevention. Strategic integration of dental and medical data has the potential to inform precision public health approaches and support more holistic models of chronic disease prevention.},
}

@article {pmid41907864,
year = {2026},
author = {Taudte, N and Liebe, L and Jänckel, N and Ramsbeck, D and Schilling, S and Potempa, J and Eick, S and Buchholz, M},
title = {Novel small molecule targeting PgQC reduces Porphyromonas gingivalis virulence.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1716188},
pmid = {41907864},
issn = {2673-4842},
abstract = {INTRODUCTION: Periodontitis, a chronic inflammatory disease affecting the periodontium, is primarily driven by dysbiosis of the oral microbiome with Porphyromonas gingivalis as a keystone pathogen. Current therapeutic approaches rely on mechanical debridement and antimicrobials, which face limitations including antibiotic resistance and microbiome disruption. Pathoblockers represent a novel therapeutic strategy that selectively targets virulence factors without bactericidal effects, potentially reducing resistance development while preserving beneficial microbiota. Here, we describe the characterization of S-0636, a novel reversible inhibitor of zinc-dependent glutaminyl cyclase (PgQC), as a compound to selectively inhibit the bacterial virulence of P. gingivalis.

METHODS: The compound's effects were assessed through enzymatic assays, bacterial growth studies, virulence factor activity measurements (gingipain activity, hemagglutination, keratinocyte invasion), selectivity testing against commensal oral bacteria, resistance development analysis over 50 passages, and cytotoxicity evaluation in human cell lines.

RESULTS: S-0636 demonstrated potent PgQC inhibition with a Ki value of 0.014 μM and has successfully reduced the intracellular PgQC activity by 50% at 8 μM and had no bactericidal effects. Treatment of P. gingivalis with S-0636 significantly decreased gingipain activity, impaired hemagglutination capacity, and reduced keratinocyte invasion by 76% at 62.5 μM. The compound showed high selectivity, with no growth inhibition of ten tested oral commensal species at concentrations up to 0.25 mM. Importantly, no resistance development was observed after 50 bacterial passages, and cytotoxicity remained minimal in human cell lines with >80% viability at 0.5 mM.

DISCUSSION: In previous studies, PgQC was suggested as an enzyme responsible for pGlu-modification and stabilization of bacterial virulence factors. The current study now validates PgQC as an attractive target for pathoblocker development, demonstrating that S-0636 effectively attenuates P. gingivalis pathogenicity through selective virulence factor inhibition while preserving bacterial viability and oral microbiome integrity. The absence of resistance development and low cytotoxicity profile support the potential clinical translation of this approach for periodontal disease management, representing a promising alternative to conventional antimicrobial therapies.},
}

@article {pmid41908157,
year = {2024},
author = {Pfavayi, LT and Sibanda, EN and Baker, S and Woolhouse, M and Mduluza, T and Mutapi, F},
title = {Diversity and composition of gut protist in young rural Zimbabwean children.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1399160},
pmid = {41908157},
issn = {2813-4338},
abstract = {BACKGROUND: The human gut microbiome harbours diverse species of archaea, bacteria, fungi, protists and viruses. To date, most gut microbiome studies have focused on bacteria, neglecting other microbial communities. Consequently, less is known about the diversity and abundance of the latter. Here, we aimed to characterise the diversity and composition of protists in the gut of preschool-aged children (PSAC) in rural Zimbabwe relative to host age, sex, and schistosome infection status.

METHODS: The gut protist of 113 PSAC (1-5 years) was examined via shotgun metagenomic sequencing and analysed for diversity. Variation in protist abundance with host and environmental factors was analysed by permutational multivariate analysis of variance (PERMANOVA). To investigate how the composition of specific taxa varies across age, sex, nutritional measures and Schistosoma hematobium infection status, analysis of the composition of microbiomes (ANCOM) was used.

RESULTS: Eighty protist genera were identified, and the most abundant genera detected was Blastocystis. The prevalence of pathogenic protists was comparatively low, with 12.4% and 3.4% of the participants' gut colonised by E. histolytica and Cryptosporidium, respectively. Of all the independent variables only S. haematobium infection showed significant relationship with the structure of the gut protist, being associated with increases in Peronospora, Pseudoperonospora, Plasmopara and Blastocystis (FDR= 0.009).

SUMMARY: This study provides data on the prevalence and diversity of the gut protists in young Zimbabwean children with an emphasis on the host factors; age, sex and schistosome infection status. Our results showed no association between the host factors investigated, including anthropometric measures adjusted for age and the intestinal protist composition and structure, but S. haematobium infection status was associated with composition of specific taxa. There is a need for more studies determining how pathogenic protist interact with non-pathogenic protist in people exhibiting clinical symptoms to inform therapy and nutraceuticals.},
}

@article {pmid41908202,
year = {2026},
author = {Awashra, A and Neiroukh, H and AbuBaha, M and Shehadeh, W and Jallad, H and Emara, A and Abu-Khazneh, O and Zahran, A and Elgendy, MS and Fkheideh, T and Sawaftah, Z and Milhem, F and Hajjeh, O and Shubietah, A},
title = {The gut-heart axis in atrial fibrillation: Pathophysiology, evidence, and therapeutic potential.},
journal = {Heart rhythm O2},
volume = {7},
number = {3},
pages = {581-597},
pmid = {41908202},
issn = {2666-5018},
abstract = {BACKGROUND: Recent advances in microbiome research highlight a bidirectional relationship between gut microbiota and atrial fibrillation (AF), the most common sustained arrhythmia worldwide. Gut dysbiosis has been implicated in systemic inflammation, metabolite imbalance, bile acid signaling, and autonomic dysfunction, whereas AF itself alters microbial homeostasis through hemodynamic and neurohormonal changes.

OBJECTIVE: This review aimed to synthesize current evidence linking gut dysbiosis to AF pathogenesis, identify mechanisms underlying this interaction, and explore the therapeutic potential of microbiota-targeted interventions.

METHODS: We conducted a narrative review of preclinical, clinical, and epidemiologic studies examining the gut-heart axis in AF. Particular emphasis was placed on microbial metabolites (eg, trimethylamine N-oxide, short-chain fatty acids, indoxyl sulfate), bile acid modulation, and inflammatory signaling. Data on interventions, including diet, probiotics, pharmacologic approaches, and fecal microbiota transplantation, were integrated to assess translational potential.

RESULTS: Evidence suggests that gut-derived signals contribute to atrial remodeling through activation of the NLRP3 inflammasome, altered calcium handling, and impaired gap junction integrity. Conversely, AF promotes dysbiosis by reducing gut perfusion, altering motility, and exposing patients to polypharmacy. Microbiota-directed strategies, particularly dietary modification and probiotics, demonstrate promise in reducing arrhythmic risk, whereas early data indicate potential biomarker roles for gut microbial signatures in AF stratification. However, causality remains uncertain, given that most studies are observational with limited sample sizes.

CONCLUSION: The gut-heart axis represents a novel paradigm in AF research. Although preliminary findings support its mechanistic and therapeutic relevance, interventional studies are needed to establish causality and guide clinical application.},
}

@article {pmid41908552,
year = {2026},
author = {Yu, N and Pang, S and Li, Y and Diao, H},
title = {Integrated microbiome-metabolome analysis reveals multiorgan toxicity of 1-nitropyrene and the limited efficacy of ferroptosis inhibitor Fer-1 in rats.},
journal = {Frontiers in toxicology},
volume = {8},
number = {},
pages = {1771766},
pmid = {41908552},
issn = {2673-3080},
abstract = {INTRODUCTION: 1-Nitropyrene (1-NP), a prevalent nitro-polycyclic aromatic hydrocarbon, is increasingly recognized as a potential metabolic disruptor, yet its systemic biological effects remain insufficiently characterized.

METHODS: This study investigated the metabolic, immunological, hepatic, and microbiome alterations induced by chronic 1-NP exposure in rats and assessed whether ferroptosis inhibition via Fer-1 could mitigate these effects.

RESULTS: Although body weight was not significantly altered overall, high-dose exposure impaired growth from week 4. Exposed groups exhibited progressively elevated fasting blood glucose and impaired glucose tolerance, indicating significant disruption of glucose homeostasis. Serum biochemistry revealed dose-dependent reductions in HDL and total cholesterol, while histopathology confirmed hepatocyte ballooning, inflammation, and steatosis consistent with NAFLD-like progression. Hematological changes, including shifts in neutrophil and lymphocyte populations, suggested chronic inflammatory activation. Untargeted metabolomics identified extensive alterations in pathways related to glycolysis, tryptophan metabolism, glycerophospholipid metabolism, and ABC transporters. Gut microbiota analysis demonstrated reduced richness and significant compositional shifts, with functional predictions linking dysbiosis to xenobiotic degradation, lipid metabolism, and phosphotransferase systems. Integrated microbiome-metabolome analysis revealed coordinated disruptions in host-microbial metabolic networks. Fer-1 intervention modified specific metabolic and microbial signatures but did not substantially alleviate major toxic outcomes.

CONCLUSION: Overall, chronic 1-NP exposure causes widespread metabolic injury driven by combined effects on host metabolism, immune regulation, hepatic function, and gut microbial ecology. These findings highlight 1-NP as a potent environmental metabolic disruptor and underscore the need for further mechanistic studies to inform mitigation strategies.},
}

@article {pmid41908560,
year = {2026},
author = {Anand, S and Shete, O and Srivastava, A and Verma, A and Goswami, S and Aggarwal, S and Luthra, K and Ghosh, TS},
title = {Urinary Microbiome Dysbiosis in Children With Congenital Uropathies at Varying Risk for Urinary Tract Infections.},
journal = {Kidney international reports},
volume = {11},
number = {4},
pages = {103799},
pmid = {41908560},
issn = {2468-0249},
abstract = {INTRODUCTION: Febrile urinary tract infections (UTIs) may occur in 30% to 50% of children with vesicoureteral reflux (VUR) or posterior urethral valves (PUVs), frequently leading to renal scarring despite chemoprophylaxis. Approximately 15% of children with uretero-pelvic junction obstruction (UPJO) may develop UTIs. However, investigations that can identify at-risk children before the first episode of UTI are lacking. In this exploratory study, we investigated the preinfection urinary microbiome in Indian children with congenital anomalies of the kidney and urinary tract (CAKUT) to determine whether microbiome alterations, metabolic potential, and antibiotic resistance profiles precede UTI.

METHODS: In this prospective cohort study with follow-up, urine samples were collected from 80 children: 36 with newly diagnosed, antibiotic-naïve CAKUT (18 UPJO, 12 VUR, 6 PUV) and 44 controls. Patients were stratified a priori into low (n = 19) and high-risk (n = 17) groups using clinically defined UTI-susceptibility criteria. V3-V4 16S ribosomal RNA sequencing was used to define urinary microbial profiles. Alpha- and beta-diversity were compared using Shannon index and permutational multivariate analysis of variance (PERMANOVA), respectively. Sliding-window and network-based analyses were used to map dysbiosis gradients. Patients were followed-up longitudinally to assess UTI incidence. Identified dysbiosis-linked microbial markers at baseline were investigated using Kaplan-Meier and Cox-proportional hazard-based analyses as predictors of UTI-risk. Metabolic functions were inferred from taxonomic data. Antibiotic resistance patterns were characterized using the Comprehensive Antibiotic Resistance Database - Resistance Gene Identifier (CARD-RGI) and the World Health Organization Access, Watch, and Reserve classification.

RESULTS: Urinary microbial alpha diversity declined significantly from controls to low-risk to high-risk groups (P = 0.002), accompanied by an increase in intragroup variability (P ≤ 0.005). PERMANOVA revealed distinct clustering by risk (R [2] = 0.11; P = 0.001). Dysbiosis scores inversely correlated with the first Kendall Principal Coordinates Analysis (PCoA) axis (ρ = -0.62; P < 0.001). With increasing risk of UTI, the commensal, control-associated genera declined along this axis while the facultative pathogens became dominant. Control-associated microbiomes favored short- and branched-chain fatty acid and spermidine production; high-risk microbiomes overproduced ammonia, putrescine, and cadaverine. Resistance to 18 of 22 routinely tested antibiotics was almost confined to the 31 risk-associated microbiomes (P = 0.001). During the median (interquartile range) follow-up of 564 (518-594) months, 14 of 36 children with CAKUT developed UTIs, and baseline depletion of health-associated microbial consortia correlated with reduced UTI-free survival. A panel of 10 species-level and 12 genus-level taxa were identified as health-associated markers negatively associated with future UTI-risk during follow-up investigation.

CONCLUSION: Children with CAKUT exhibit urinary microbiome dysbiosis before their first symptomatic UTI, characterized by loss of conserved health-associated taxa, metabolic imbalance, and broad-spectrum antibiotic resistance. These findings support the potential of microbiome-informed, noninvasive risk stratification and microbiome-tailored prophylaxis, while establishing the first Indian pediatric reference set for CAKUT-related UTI prevention.},
}

@article {pmid41908828,
year = {2026},
author = {Zhang, Z and Ku, A and Ji, R and Song, B},
title = {Multi-omics analysis reveals the mechanism of Huaganjian in alleviating cholestatic liver fibrosis.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1744312},
pmid = {41908828},
issn = {1663-9812},
abstract = {Huaganjian (HGJ) is a traditional Chinese medicinal formula with liver-protective effects. However, the pharmacological mechanisms of the effects of HGJ on cholestatic liver fibrosis (CLF) are yet to be clarified. To evaluate the effects of HGJ on CLF and elucidate the underlying mechanisms, C57BL/6J mice were fed a 0.1% 3, 5-diethoxycarbonyl-1, 4-dihydrocollidine (DDC) diet to induce CLF. The efficacy of HGJ was evaluated by measuring the biochemical indicators of liver function, fibrosis, and histology. The underlying mechanisms were investigated using an integrated multi-omics approach, including fecal 16S rRNA sequencing, serum metabolomics, and hepatic transcriptomic analysis. The findings were further validated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and Western blotting (WB). HGJ significantly alleviated liver injury, cholestasis, and fibrosis. Microbiome analysis revealed that Bifidobacterium, Turicibacter, and Clostridium_sensu_stricto_1 abundances were positively correlated with liver injury and fibrosis marker levels, and these abundances decreased following HGJ treatment. Metabolomic analysis identified 531 differential metabolites, including 299 upregulated and 232 downregulated metabolites, following HGJ intervention. Hepatic transcriptomic analysis revealed 164 differentially expressed genes, including 102 upregulated and 62 downregulated genes. Integrated multi-omics analysis revealed that HGJ alleviated CLF by modulating the glycine/serine/threonine metabolism pathway. RT-qPCR and Western blotting experiments confirmed that in this pathway, aminolevulinic acid synthase 1 levels decreased, whereas serine dehydratase and serine dehydratase-like levels increased after HGJ treatment. Overall, HGJ effectively alleviated CLF, and its mechanisms of action were closely linked to the regulation of the glycine/serine/threonine metabolism pathway.},
}

@article {pmid41908923,
year = {2025},
author = {Kurt, Ö and Scanlan, PD and Gentekaki, E and Robertson, LJ and Carmena, D and Dogruman-Al, F and Tsaousis, AD},
title = {The Blastocystis-colorectal cancer hypothesis: correlation is not causation.},
journal = {Open research Europe},
volume = {5},
number = {},
pages = {379},
pmid = {41908923},
issn = {2732-5121},
abstract = {Although superficially persuasive, claims suggesting a causal link between Blastocystis and colorectal cancer (CRC) lack robust scientific support. As Blastocystis is the most common gut protist found in human populations globally, its detection in CRC patients is unsurprising and does not imply pathogenicity. Current claims championing a causal role for Blastocystis in CRC are based on speculative correlations, a single poorly controlled animal study, and inconsistent subtype associations. We argue that linking Blastocystis to CRC is premature, misleading, and may give rise to unnecessary concern in patients that are colonised by or test positive for Blastocystis. We emphasise the need for rigorously designed investigations to establish causal roles for any microorganism in disease and the importance of conclusions being based on solid evidence, particularly in matters of public health.},
}

@article {pmid41909054,
year = {2025},
author = {Hanna, M and Huang, S and Ross, M and Reyes, A and Perera, D and Surathu, A and Cregeen, SJ and Hagan, J and Pammi, M},
title = {Microbiome Signatures and Inflammatory Biomarkers in Culture-Negative Neonatal Sepsis.},
journal = {Applied microbiology (Basel, Switzerland)},
volume = {5},
number = {3},
pages = {},
pmid = {41909054},
issn = {2673-8007},
support = {R03 HD098482/HD/NICHD NIH HHS/United States ; },
abstract = {Overuse of antibiotics is a concern in 'culture-negative sepsis' but it is unclear whether this is due to infection with viruses, fungi or other microbes that are not easily cultured, or whether it results from inflammatory processes. In a prospective study, we enrolled 50 preterm neonates with culture-positive sepsis (CP), culture-negative sepsis (CN), and asymptomatic preterm controls (CO). The microbiome of stool, skin, and blood, including bacterial, viral and fungal components and serum cytokine profiles were evaluated. The microbiome alpha or beta diversity did not differ between CN and CO groups. A MaAsLin analysis revealed increased relative abundances of specific bacterial and fungal genera in stool and skin samples in the CN group compared to CO. The virome analysis identified 24 viruses from skin samples, but they were not statistically different among the three groups. The cytokine and chemokine biomarker profiles were elevated in the CP group but were not statistically different between the CN and CO groups. Although the CN group had a longer hospital stay and higher BPD rates than the controls in unadjusted analyses, these differences were not significant after adjusting for gestational age and birth weight. The CN infants demonstrated microbial shifts without systemic immune activation or significantly worse clinical outcomes, supporting the rationale for discontinuing antibiotics in the absence of positive cultures.},
}

@article {pmid41909172,
year = {2026},
author = {Bao, Y and Xu, K and Du, Y and Feng, M and Li, L and Li, L and Yan, G and Li, X},
title = {PPARγ: a key orchestrator of epidermal barrier, immune responses, and lipid metabolism in atopic dermatitis pathogenesis and therapy.},
journal = {Frontiers in allergy},
volume = {7},
number = {},
pages = {1780908},
pmid = {41909172},
issn = {2673-6101},
abstract = {Atopic dermatitis (AD) is an immune-mediated inflammatory dermatosis characterized by epidermal barrier dysfunction, immune dysregulation, and cutaneous microbial dysbiosis. Existing therapeutic modalities for AD are limited in efficacy and durability, highlighting an unmet clinical need for novel, safe, and effective treatment strategies. Peroxisome proliferator-activated receptor gamma (PPARγ), a pivotal nuclear receptor involved in metabolic and inflammatory regulation, has emerged as a promising therapeutic target for AD. Its pleiotropic mechanisms encompass the restoration of stratum corneum integrity, modulation of aberrant immunoinflammatory signaling, normalization of cutaneous lipid metabolism, and regulation of the cutaneous microbiome and neuroimmune circuitry. This review comprehensively synthesizes the mechanistic evidence linking PPARγ to AD pathogenesis and critically appraises its potential as a novel therapeutic.},
}

@article {pmid41909251,
year = {2026},
author = {Sun, F and Yuan, M and Liao, C and Sun, Y and Yu, L and Zhuo, Y and Peng, Y and Tang, X and Zeng, Q and Song, J and Tao, X and Li, Q and Chen, M and Zhang, Y},
title = {Optimizing flue-cured tobacco planting patterns: enhanced rhizosphere nutrient availability and microbial community dynamics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1735540},
pmid = {41909251},
issn = {1664-302X},
abstract = {INTRODUCTION: Continuous monoculture of flue-cured tobacco causes soil degradation and microbial dysbiosis. While crop rotation can alleviate these obstacles, how different cropping patterns regulate soil carbon (C) and nitrogen (N) metabolic functions remains unclear.

METHODS: A four-year field experiment compared tobacco monoculture (CK), tobacco-maize rotation (TM), tobacco-rice rotation (TR), and tobacco-sweet potato intercropping (TP). Soil physicochemical properties, enzyme activities, metagenomic sequencing, and microbial network analysis were integrated.

RESULTS: TR significantly improved soil health: pH (+6.6%), organic matter (+22.1%), and urease activity (+12.5%). It enriched beneficial microbes (Pseudomonadota +16.4%, Mucoromycota +327%) and upregulated C-cycle (korA +42.3%) and N-assimilation genes (amoC +460%), while suppressing denitrification (nirK). TM increased available P/K but enriched oligotrophic taxa and reduced sucrase activity. TP triggered pathogenic fungi (Olpidium +160%), depleted beneficial microbes, and broadly suppressed C/N metabolic genes (cbbL -94.5%, nirS -21.8%).

DISCUSSION: Cropping patterns differentially reshape microbial communities and metabolic functions, determining their efficacy against continuous cropping obstacles. TR establishes efficient C/N cycling with "high assimilation, low denitrification," whereas TP induces pathogenic proliferation and metabolic suppression. This provides a functional framework for designing cropping systems to enhance soil health and tobacco productivity.},
}

@article {pmid41909261,
year = {2026},
author = {Choi, J and Shim, K and Bae, GS and Jeon, E and Hwang, EH and Kim, G and Baek, SH and Hong, JJ and Kim, DS and Kim, SH and Koo, BS},
title = {Comparative analysis of gut microbiota and host phenotypic characteristics across enterotype-like clusters in cynomolgus and rhesus macaques.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1775757},
pmid = {41909261},
issn = {1664-302X},
abstract = {Microbiome has been increasingly recognized for its close association with host physiology and diseases. Due to their close genetic relatedness to humans and standardized environmental conditions, captive macaque species serve as the most evolutionarily comparable preclinical animal models for studying human microbiome research. However, the characterization of gut microbiota and host phenotypic traits within each enterotype-like cluster of macaque species remains poorly understood. We analyzed microbiome characteristics and host metadata within enterotype-like clusters of cynomolgus and rhesus macaques housed in the same facility but with different origins of birth. At the phylum level, Bacteroidota, Firmicutes, Spirochaetota, and Proteobacteria were predominantly observed in both species. Except for Fibrobacterota at the phylum level, no significant interspecies differences were observed in bacterial composition or alpha diversity across taxonomic levels. Based on a prevalence threshold of 90%, cynomolgus macaques were found to share 12.4% of genera, while rhesus macaques shared 18.2%. Based on the relative abundance patterns of the genera Prevotella 9, Rikenellaceae RC9 gut group, and Treponema, the fecal microbiome of cynomolgus macaques was classified into three enterotype-like clusters (cluster 1, cluster 2, and cluster 3) whereas that of rhesus macaques was classified into two enterotype-like clusters. Using linear mixed-effects models, we identified species-specific associations between enterotype-like clusters and host phenotypes. In cynomolgus macaques, clustering was primarily associated with hematological and selected biochemical parameters, whereas in rhesus macaques, enterotype-like clusters were limited to body weight and hemoglobin. Despite a standardized diet and shared environments, distinct clusters and pronounced microbial individuality associated with birthplace suggest that early-life colonization is a key determinant of long-term gut microbiome structure and host phenotypes in captive primates. Also, identifying enterotype-like clusters in NHPs prior to analysis is essential for accurate and relevant human microbiome modeling, since each cluster may correspond to distinct human enterotypes and phenotypic traits.},
}

@article {pmid41909266,
year = {2026},
author = {Zhu, Z and Li, X and Cui, T and Chen, Z and Liu, Y and Chen, X and Tian, Y and Mu, Y and Wu, Y and Ji, Q and Yan, S and Cheng, Y},
title = {Temporal heterogeneity of microbial ecosystems and its formation mechanisms in Moutai-flavor Baijiu fermentation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1798174},
pmid = {41909266},
issn = {1664-302X},
abstract = {The influence of workshop age on Moutai-flavor Baijiu fermentation is recognized, but the mechanisms driving microbial community shifts remain unclear. Understanding how the physical environment selects for specific microbiota is crucial for optimizing new workshops. Through 16S/ITS sequencing of pit-entry fermented grains, Daqu, air, and cooling yards in 5-, 10-, 20-, and 30-year-old workshops, Lactobacillus emerged as a key discriminant genus, increasing from 15.02% (5-year) to 35.59% (30-year). SourceTracker analysis revealed the cooling yard as the primary microbial source, contributing 54.2% on average to fermented grains. CO2-TPD analysis showed a 3.6-fold reduction in cooling yard surface basicity (from 0.11 to 0.03 mmol·g[-1]) over 30 years, resulting in high abundances (>10%) of alkalotolerant bacteria (e.g., Alkalibacterium, Nesterenkonia) and low Lactobacillus (2.17%). Nesterenkonia was also a biomarker in 5-year fermented grains. This confirms cooling yard surface basicity drives microecological differences, revealing how long-term production practices domesticate microbial communities and providing a theoretical basis for new workshop adaptation.},
}

@article {pmid41909643,
year = {2026},
author = {Yao, Y and Hu, X and Li, R and Tan, Z and Yu, H and Lin, Z and Zhang, T and Habimana, O},
title = {Probiotic yeast engineers a protective biofilm environment to enhance bioremediation and seahorse health in aquaculture.},
journal = {Biofilm},
volume = {11},
number = {},
pages = {100357},
pmid = {41909643},
issn = {2590-2075},
abstract = {Sustainable animal farming via intensive aquaculture relies on a balanced microbial ecosystem that promotes animal well-being. This research explored the use of the probiotic yeast Saccharomyces boulardii to influence tank biofilm microbiomes for improving the health of lined seahorses, Hippocampus erectus. Following a severe mortality event at week 6 that affected both groups, the control group demonstrated partial recovery to 71.4% survival, whereas the probiotic group achieved a higher survival, with a final rate of 88.9% after a disease challenge. This recovery led to a notable reduction in enteritis occurrences with a significant increase in average body weight and a 3.9-fold increase in activity compared to control conditions. Shotgun metagenomic analysis indicated that the enhancements were significantly supported by a marked reorganization of the tank's biofilm community. Probiotic supplementation significantly reduced microbial diversity and selected for a beneficial consortium enriched in taxa with recognized roles in nutrient cycling, including Rhodobacterales (involved in sulfur cycling and pathogen antagonism) and Pirellulaceae (key in polysaccharide breakdown). This engineered biofilm has greater genetic potential for energy generation, glucose degradation, and inorganic ion transfer. Crucially, virulence factor genes and pathogen-associated sequences were substantially suppressed in probiotic-treated biofilms. Our research shows that S. boulardii acts as a crucial modulator, creating a protective biofilm that boosts bioremediation while decreasing pathogenic threats. This ecological approach to the application of probiotics (targeting the environmental rather than host-associated microbiome) may offer a sustainable means to promote health and resilience within aquaculture systems.},
}

@article {pmid41909648,
year = {2026},
author = {Kumar, V and Das, BK and Roy, S and Bhowal, P and Roy, A and Bruce, TJ and Galindo-Villegas, J},
title = {Exploring the host-pathogen interaction and genome analysis of multidrug-resistant bacterial pathogen Proteus penneri isolated from Labeo rohita.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1733414},
pmid = {41909648},
issn = {1664-3224},
mesh = {Animals ; *Fish Diseases/microbiology/immunology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Host-Pathogen Interactions/genetics ; *Cyprinidae/microbiology/immunology ; Phylogeny ; *Proteus Infections/microbiology/veterinary/immunology ; *Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Virulence ; Genomics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Multidrug-resistant (MDR) bacterial pathogens represent an escalating challenge to sustainable aquaculture, particularly in high-value freshwater species such as Labeo rohita, a cornerstone of South Asian aquaculture. This study provides the first comprehensive integration of genomic, immunological, and microbiome analyses to characterize Proteus penneri as an emerging MDR pathogen associated with severe disease manifestations in L. rohita, including exophthalmia, ulceration, and hemorrhage. Robust identification through biochemical assays, 16S rRNA sequencing, and phylogenetic analysis confirms the clinical relevance of this isolate. Functional assays demonstrated pronounced virulence, evidenced by hemolysin activity, extensive histopathological damage, and dose-dependent mortality, underscoring its pathogenic capacity in vivo. The observed resistance to multiple frontline antibiotic classes, including tetracyclines, macrolides, and carbapenems, highlights a critical therapeutic limitation in aquaculture settings. Genomic analysis further revealed a diverse repertoire of antimicrobial resistance genes, virulence determinants (notably biofilm formation and secretion systems), and mobile genetic elements, suggesting a strong potential for persistence, adaptability, and horizontal gene transfer. Infection-associated gut microbiome disruption, marked by elevated MAR indices and enrichment of virulence-associated taxa, indicates that P. penneri not only exploits host tissues but also reshapes the microbial ecosystem in ways that may exacerbate disease severity and resistance dissemination. Concurrently, heightened serum cortisol, C3, and Hsp70 levels, along with transcriptional upregulation of key immune and stress-related genes (hsp70, nod, il6, sod, c3, and myd88), reflect an intense pro-inflammatory and physiological stress response. In silico docking analyses implicating myd88-lipopolysaccharide interactions provide mechanistic insight into potential immune-modulatory strategies employed by the pathogen. Collectively, these findings delineate a multifactorial basis for P. penneri virulence and MDR, emphasizing its significance as an emerging aquaculture pathogen. Future research should prioritize functional validation of key virulence and resistance genes, longitudinal surveillance to assess transmission dynamics and AMR spread, and experimental evaluation of alternative disease mitigation strategies, including probiotics, phage therapy, and immune-modulating interventions, to reduce antibiotic reliance and enhance fish health resilience in aquaculture systems.},
}

Animals
*Fish Diseases/microbiology/immunology
*Drug Resistance, Multiple, Bacterial/genetics
*Host-Pathogen Interactions/genetics
*Cyprinidae/microbiology/immunology
Phylogeny
*Proteus Infections/microbiology/veterinary/immunology
*Genome, Bacterial
Anti-Bacterial Agents/pharmacology
Virulence
Genomics
RNA, Ribosomal, 16S/genetics

@article {pmid41909844,
year = {2026},
author = {Lin, B and Tong, S and Ba, C and Wang, X},
title = {Precision treatment of gastrointestinal tumours and liver disease interaction mechanisms based on multi-omics data and microbiome hubs.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1791531},
pmid = {41909844},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Neoplasms/therapy/microbiology ; *Gastrointestinal Microbiome ; *Liver Diseases/therapy/microbiology ; *Precision Medicine/methods ; Genomics/methods ; Proteomics/methods ; Metabolomics/methods ; Tumor Microenvironment ; Carcinogenesis ; Multiomics ; },
abstract = {The global prevalence of gastrointestinal tumours and the bottlenecks in their diagnosis and treatment are being systematically overcome by the multi-omics revolution: high-throughput technologies are driving the multidimensional integration of genomics-transcriptomics-proteomics-metabolomics to comprehensively decode the genetic architecture of tumours. Meanwhile, the gut microbiota, acting as a core regulatory hub, drives carcinogenesis through immune microenvironment remodelling and metabolic pathway hijacking, further facilitating proteome-metabolome multidimensional integration, comprehensively decoding tumour genetic architecture. The gut microbiota, acting as a core regulatory hub, drives carcinogenesis through immune microenvironment remodelling and metabolic pathway hijacking, while mediating a vicious cycle network linking liver disease and tumours via the gut-liver axis. This review examines the application of multi-omics technologies in gastrointestinal tumour research, summarises the role of gut microbiota in tumourigenesis and its interaction with liver disease, and envisions future interventions targeting the gut microbiome for early disease diagnosis and precision treatment.},
}

Humans
*Gastrointestinal Neoplasms/therapy/microbiology
*Gastrointestinal Microbiome
*Liver Diseases/therapy/microbiology
*Precision Medicine/methods
Genomics/methods
Proteomics/methods
Metabolomics/methods
Tumor Microenvironment
Carcinogenesis
Multiomics

@article {pmid41909873,
year = {2026},
author = {Yu, J and Baek, H and Jaiswal, V and Park, M and Lee, HJ},
title = {Heavy metal accumulation and fecal microbiota response in black soldier fly larvae: identification of Leminorella grimontii as a potential indicator species.},
journal = {Food science and biotechnology},
volume = {35},
number = {5},
pages = {1329-1338},
pmid = {41909873},
issn = {2092-6456},
abstract = {UNLABELLED: With growing environmental concerns about marine pollution from heavy metals, black soldier fly larvae (BSFL) are gaining attention for their potential use in sustainable waste-to-feed systems. In this study, BSFL were raised on diets containing cadmium (Cd), lead (Pb), mercury (Hg), and arsenic (As) to assess their growth, metal accumulation patterns, and changes in microbiota. While Cd mainly accumulated in the larval body, Pb, Hg, and As were primarily excreted through exuviae and feces. This pattern remained consistent even when larvae were fed naturally contaminated mackerel heads. Microbiome analysis of fecal samples showed that Leminorella grimontii had a strong positive correlation with Hg and As concentrations, suggesting its potential as a microbial indicator species for heavy metal exposure. These findings support the use of BSFL in bioconversion systems and suggest L. grimontii as a new biomarker for environmental monitoring.

GRAPHICAL ABSTRACT: Scheme 1Experimental procedure and fecal microbiome results.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-026-02114-y.},
}

@article {pmid41909880,
year = {2025},
author = {Cold, F and Heintz, JE and Ghathian, KSA and Stenbøg, PA and Hansen, LH and Carstens, AB and Petersen, AM and Halkjaer, SI and Bendtsen, F and Ytting, H},
title = {Low incidence of cytolysin-positive E. faecalis and no correlation to survival in Danish patients with alcohol-associated hepatitis: A prospective cohort study.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2549729},
pmid = {41909880},
issn = {2993-3935},
abstract = {Alcohol-associated hepatitis (AH) is a severe and life-threatening form of alcohol-associated liver disease with no approved treatments for reducing long-term mortality. Cytolysin-producing E. faecalis in the gut microbiota of AH patients has been reported as highly correlated to mortality. We investigated whether we could reproduce this correlation in a cohort of Danish patients with AH. Fecal samples from 28 hospitalized patients with AH were analyzed for cytolysin-producing E. faecalis and were followed for 1 y after hospital admission. The primary endpoint was comparison of 180-d mortality in AH patients with and without cytolysin-positive fecal samples. Three of twenty-eight (10.7%) fecal samples were identified as cytolysin-positive. There were no significant differences at baseline between cytolysin-positive and -negative patients in terms of age, Glasgow Alcoholic Hepatitis Score, Charlson Comorbidity Index or biochemical variables (INR, bilirubin, albumin). There was no difference in mortality between the groups 180 d after hospital admission; one of the three (33%) cytolysin-positive patients had died compared to 9 of the 25 (36%) cytolysin-negative (p-value for difference = 1.0). We report a low incidence of cytolysin-positive E. faecalis in hospitalized Danish AH patients and no greater risk of mortality compared to cytolysin-negative AH patients.},
}

@article {pmid41909881,
year = {2025},
author = {Liu, W and An, M and Wang, Q and Liu, Y and Shang, Y and Dong, X and Ding, H and Fu, S and Han, X and Shang, H},
title = {Gut microbiome-induced metabolites promote the role of Silybin as adjunctive drug in HIV-positive immunological nonresponders.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2569789},
pmid = {41909881},
issn = {2993-3935},
abstract = {HIV-infected immunological nonresponders (INRs) endure persistent T-cell dysfunction and chronic inflammation, facing high risk of various complications and mortality, with no effective therapies available. Silybin, the principal constituent of a plant extract, possesses anti-inflammation and immunomodulatory properties. The gut microbiome has been shown to modulate the efficacy of immune therapies and drugs. We gave 54 INRs oral silybin for three months and used multi-omics to investigate the gut-related factors influencing the efficacy of silybin. Silybin raised CD4[+] T cells counts in 52% of participants and an efficacy classification model based on baseline gut microbiome and metabolites was developed. Favorable gut bacteria produced anti-inflammatory metabolites that downregulated Ras/MAPK/PI3K-Akt signaling pathways also targeted by silybin. Our findings shed light on a novel therapeutic approach for addressing immune dysfunction in HIV-positive INRs and have important implications for personalized medical strategies in the management of HIV infection.},
}

@article {pmid41909883,
year = {2025},
author = {Abubakar, D and Abdullahi, H and Ibrahim, I},
title = {Bridging Microbiomes: Exploring Oral and Gut Microbiomes in Autoimmune Thyroid Diseases- New Insights and Therapeutic Frontiers.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2452471},
pmid = {41909883},
issn = {2993-3935},
abstract = {Autoimmune thyroid diseases (AITDs) are the most common organ-specific autoimmune disorders characterized by thyroid dysfunction and immune system deficiencies. In recent decades, the role of the microbiome in autoimmune diseases has gained increasing attention, with emerging research linking gut microbiome alterations to the development of AITDs. This review summarizes current knowledge on the relationship between AITDs and the gut microbiome. Additionally, it emphasizes the role of the oral microbiome in AITDs, an area often overlooked in autoimmune research. Beyond the microbiome, the virome and mycobiome have been recognized as critical but underexplored components of the human microbiome, potentially contributing to immune dysregulation and the pathogenesis of AITDs. The review also explores modulating the microbiome for managing AITDs, including diet adjustment, the potential use of probiotics, postbiotics, symbiotics, and even fecal microbiota transplantation (FMT) to restore a balanced microbiome that may positively influence the immune system and, by extension, the course of AITDs. This review thoroughly explores the intricate relationship between AITDs, the gut, and oral microbiomes, paving the way for precision medicine applications in AITDs. Examining microbiota-thyroid interactions highlights the potential for targeted, personalized treatments and novel therapeutic therapies, guiding future therapeutic strategies for more effective and precisely tailored AITD management approaches.},
}

@article {pmid41909884,
year = {2025},
author = {Pateriya, D and Prasoodanan P K, V and Scaria, J and Sharma, VK},
title = {Landscape of flavonoid metabolism in human gut microbiome and its association with health and disease.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2520788},
pmid = {41909884},
issn = {2993-3935},
abstract = {The positive effects of dietary flavonoids on health depend on their bioavailability in the human gut, where the flavonoid-modifying enzymes (FMEs) in gut bacteria play a crucial role in flavonoid metabolism. Thus, to comprehensively examine the role of FMEs in this process, we first constructed a database of potential FMEs containing 6,865 proteins. We identified homologs of these FMEs in gut bacterial genomes and reported species that can potentially modify flavonoids but were not previously known in this context. We examined the differential abundance of FMEs in the gut microbiomes of healthy and diseased individuals from Western and non-Western populations with distinct dietary habits. The differential enrichment of key FMEs between Western and non-Western populations and between disease and healthy samples highlights differences in gut flavonoid metabolism based on diet, population, and health status. This study reveals a comprehensive landscape of flavonoid metabolism in the human gut microbiome.},
}

@article {pmid41909885,
year = {2025},
author = {Lau, RI and Wong, MCS and Lau, LHS and Lau, AYL and Mak, IWC and Lo, OSH and Chan, NN and Dai, DLK and Hau, KC},
title = {Role of gut microbiome in pathogenesis and treatment of diseases: Multidisciplinary experts' opinion of the Asian Medical Experts Academy (AMEA).},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2558575},
pmid = {41909885},
issn = {2993-3935},
abstract = {Emerging evidence suggests the role of the gut microbiome in the health and diseases of multiple organs and systems. In the past decade, an increasing trend in the use of microbiome-based therapeutics (e.g., probiotics, prebiotics, synbiotics) has been observed in Asia and globally. However, local and global clinical guidelines on the use of microbiome-based therapeutics are limited. A multidisciplinary working group has been established to foster communication between experts from diverse medical specialties on the clinical application of microbiome-based therapeutics. Through conducting an extensive review on current evidence on the importance of the gut microbiome and the potential use of microbiome-based therapeutics in health and diseases, the experts' working group identified the unmet needs related to the use of microbiome-based therapeutics in the clinical settings in Asia and global contexts. Thirteen position statements were developed, including eight statements focusing on the role of the gut microbiome in health and disease pathogenesis, as well as six statements focusing on the potential clinical applications. A list of potential indications for microbiome-based therapeutics was also proposed based on current evidence and clinical experience. This paper is intended to serve as a reference that assists healthcare professionals in improving care for patients using microbiome-based therapeutics in Asia and globally.},
}

@article {pmid41909889,
year = {2025},
author = {Lan, Z and Chen, J and Lan, S and Li, N and Yang, B and Hou, J and Yang, X},
title = {Hydrogen-rich water attenuates radiation-induced oral mucositis in mice via antioxidant and gut microbiota-stabilizing effects: a longitudinal study.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2595392},
pmid = {41909889},
issn = {2993-3935},
abstract = {Radiation-induced oral mucositis (RIOM) frequently complicates head and neck radiotherapy, leading to severe pain, compromised nutrition, and often requiring treatment modifications. Although craniofacial-only irradiation is confined to the head and neck region, it can still disrupt gut homeostasis. Mice subjected to head and neck irradiation developed marked epithelial damage in both the oral and intestinal mucosa, as evidenced by pronounced RIOM and diminished barrier integrity. Histological examination revealed substantial mucosal thinning and leukocyte infiltration in the tongue, along with reduced occludin and ZO-1 expression in colonic tissues. Supplementation with hydrogen-rich water (HW) markedly decreased the severity of oral lesions and preserved epithelial thickness, while restoring the expression of tight junction proteins in the colon. Fecal 16S rRNA sequencing showed that radiation alone provoked expansions of Streptococcus and Helicobacter, coupled with a decline in short-chain fatty acid-producing families (Lachnospiraceae, Ruminococcaceae). In contrast, HW supplementation partially reversed these microbial shifts, which correlated with reduced oral inflammatory markers. Collectively, these findings underscore an oral-gut axis whereby HW fosters mucosal healing through microbiome stabilization and decreased inflammatory stress, suggesting that HW as a promising adjunct for managing head and neck irradiation-related complications.},
}

@article {pmid41909890,
year = {2025},
author = {Park, G and Oh, S and Kim, M and Jeong, Y and Kim, G},
title = {Common microbial signatures in blood and their amplification in clinical disorders.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2473450},
pmid = {41909890},
issn = {2993-3935},
abstract = {Blood microbiome research has emerged as a significant area of study, exploring microbial signatures within the bloodstream and their potential implications for various clinical disorders. This study aimed to identify common microbial signatures in blood across cohorts and investigate how these signatures are altered in clinical conditions. We conducted a meta-analysis of 15 publicly available studies utilizing amplicon sequencing, including 687 control and 651 case individuals with various disorders from diverse geographic locations to compare their blood microbiome profiles. The results revealed that most microbes detected in the blood originated from the gut, oral cavity, and skin, with several genera such as Corynebacterium, Streptococcus, and Lactobacillus consistently identified across studies. Furthermore, we observed a significant increase in microbial diversity and abundance in individuals with clinical disorders compared to the control group. Notably, microbial genera originating from the gut and oral cavity, including Acinetobacter, Prevotella, and Clostridium sensu stricto-1, were more prevalent in disease cohorts, suggesting a potential link between the translocation of microbial signatures and disease pathology. The study underscores the importance of considering microbial signatures as potential biomarkers in clinical settings and calls for further investigation into the role of circulating microbial DNA in immune response and disease progression.},
}

@article {pmid41909891,
year = {2025},
author = {Manzoor, H and Kayani, MUR},
title = {Insights into the gut microbiome-metabolite dynamics in breast cancer.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2483446},
pmid = {41909891},
issn = {2993-3935},
abstract = {In recent years, understanding the intricate connection between gut microbiome and cancer development has gained significant attention. The gut microbiome has a key role in maintaining overall human health and modulating the body's defense mechanism against various diseases. This review examines the multifaceted association between the gut microbiome and breast cancer, providing a comprehensive overview of studies from the last two decades that investigate both anti-cancer and pro-cancer properties of gut metabolites. Compounds such as nisin, inosine, acetate, propionate, and conjugated linoleic acids have demonstrated potential as therapeutic agents against breast cancer, while others, including butyrate, lactate, certain bile acids, and secondary metabolites, exhibit dual roles, showing both anti-cancer and pro-cancer properties under different conditions, with some implicated in tumor progression. Moreover, emerging research highlights the dual roles of these metabolites in influencing the efficacy of conventional breast cancer therapies. Despite promising evidence, the molecular mechanisms underlying these opposing actions remain unclear and require further investigation. To advance our understanding, future research should prioritize elucidating these mechanisms, establishing dose-response relationships, and conducting animal and clinical studies to validate in vitro findings. This review also identifies key gaps and highlights potential directions for future research in this field.},
}

@article {pmid41909893,
year = {2025},
author = {Jorgensen, JA and Choo-Kang, C and Wang, L and Issa, L and Gilbert, JA and Ecklu-Mensah, G and Luke, A and Bedu-Addo, K and Forrester, T and Bovet, P and Lambert, EV and Rae, D and Argos, M and Kelly, TN and Sargis, RM and Dugas, LR and Dai, Y and Layden, BT},
title = {Toxic metals impact gut microbiota and metabolic risk in five African-origin populations.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2481442},
pmid = {41909893},
issn = {2993-3935},
abstract = {Underlying mechanisms by which exposures to toxic metals/metalloids impact obesity and type 2 diabetes (T2DM) risk remain largely unknown. Gut microbiota have been strongly associated with cardiometabolic risk. To assess relationships between high metal exposures, gut dysbiosis, and metabolic dysregulation, we analyzed associations among gut microbiome taxa, dichotomized metal levels (arsenic, lead, mercury, cadmium), clinical measures (BMI, fasting blood glucose, blood pressure), and diagnoses (hypertension, obesity, diabetes) in 178 African-origin adults (52% female, mean age = 43.0 ± 6.4 years) from Ghana, South Africa, Jamaica, Seychelles, and USA. High vs. low lead and arsenic levels had a significant effect on beta diversity (p < 0.05). Seventy-one taxa were associated with high lead levels: 30 with elevated BMI, 22 with T2DM, and 23 with elevated fasting blood glucose (p < 0.05); 115 taxa were associated with high arsenic levels: 32 with elevated BMI, 33 with T2DM, and 26 with elevated blood glucose (p < 0.05). Porphyrin metabolism was the most enriched metabolic pathway in taxa associated with higher lead and arsenic exposure. These data provide the first findings from African-origin adults that demonstrate the association between the gut microbiome with lead and arsenic exposure and obesity and T2DM risk.},
}

@article {pmid41900768,
year = {2026},
author = {Zhou, S and Xu, Z and Shen, J},
title = {Female Reproductive Tract Organ-on-Chips: Modeling Barrier Function and Drug Transport.},
journal = {Pharmaceutics},
volume = {18},
number = {3},
pages = {},
pmid = {41900768},
issn = {1999-4923},
support = {1U01FD007656//United States Food and Drug Administration/ ; 33040//Massachusetts Life Sciences Center/ ; },
abstract = {Female reproductive tract (FRT) disorders such as maternal conditions and gynecological cancers represent a significant global health burden. However, women's health, and particularly locally acting therapies targeting the FRT, has historically been underprioritized in drug development and translational research. Developing safe and effective therapies requires a clear understanding of drug transport across FRT barriers. Conventional in vitro culture systems and animal studies fail to recapitulate the physiological complexity of the human FRT, including stratified mucosal architecture, functional mucus barriers, microbiome interactions, as well as dynamic hormonal regulation. Recently, organ-on-chip (OoC) microfluidic platforms, integrating human cells with precisely controlled perfusion, have emerged as advanced in vitro systems capable of recreating dynamic physiological microenvironments. This review summarizes the major anatomical and physiological barriers of the FRT, including the vagina, cervix, endometrium, and placenta, and discusses critical design considerations for the development of FRT-on-chip models. We highlight the advanced OoC developed to study infection, drug permeation, hormonal responses, and maternal-fetal interface dynamics. Finally, future perspectives are outlined, including the integration of immune components, vascularization strategies, and multi-organ systems to better simulate inter-organ communication. Collectively, these advances underscore the potential of FRT-on-chip models as predictive platforms for preclinical drug screening, toxicity evaluation, and personalized medicine.},
}

@article {pmid41900770,
year = {2026},
author = {Vadlapatla, R and Shirazi, AN and Koomer, A and Weng, J and Ghilarducci, ME and Qudus, A and Parang, K},
title = {Microbiome-Responsive Hydrogels: From Biological Cues to Smart Biomaterials.},
journal = {Pharmaceutics},
volume = {18},
number = {3},
pages = {},
pmid = {41900770},
issn = {1999-4923},
abstract = {Background: Stimuli-responsive hydrogels (SRHs) are smart polymeric materials that undergo reversible physicochemical changes in response to abiotic cues and externally applied fields, enabling applications in drug delivery, wound healing, and tissue engineering. However, they exhibit limited biological specificity and do not adequately reflect the dynamic, disease-relevant complexity of native tissue microenvironments. Microbe-colonized tissues display distinctive biochemical features driven, shaped by microbial metabolism, including localized pH gradients, short-chain fatty acid production, secretion of quorum-sensing molecules, biofilm formation, and expression of specialized enzymes. These endogenous, spatiotemporally regulated signals are closely linked to host physiology and pathology but remain underutilized in hydrogel design. This review aims to highlight microbiome-responsive hydrogels (MRHs) as a strategy to address this gap. Methods: This study summarizes current engineering approaches, key microbial stimuli, and emerging biomedical applications of MRHs, with emphasis on translational and regulatory challenges. Results: Microbiome-responsive hydrogels (MRHs) address this gap by leveraging microbial metabolic and biochemical cues to induce swelling, degradation, drug release, antibacterial activity, or structural transformation. By directly coupling to microbe-derived stimuli, MRHs offer improved physiological relevance, enhanced local specificity, and new opportunities for precision therapy targeting disease-associated microbial niches. Conclusions: Despite their promise, MRHs remain an early and fragmented field, lacking standardized biological triggers, material design frameworks, and performance evaluation strategies. This review summarizes current engineering approaches, key microbial stimuli, and emerging biomedical applications, with emphasis on translational and regulatory challenges, positioning MRHs as an underexplored platform for next-generation smart biomaterials.},
}

@article {pmid41900857,
year = {2026},
author = {Shah, IM and Lebrilla, CB and German, JB and Mills, DA},
title = {Selective Human-Milk-Inspired Antimicrobial Peptides for the Treatment of Bacterial Vaginosis.},
journal = {Pharmaceutics},
volume = {18},
number = {3},
pages = {},
pmid = {41900857},
issn = {1999-4923},
support = {R43AI165105/GF/NIH HHS/United States ; },
abstract = {Background: Antimicrobial resistance (AMR) is a global healthcare threat. Traditional largely non-selective antibiotics produce side effects due to the natural host microbiome being modified creating a loss in homeostasis. In women, AMR is a cause of acute generational impact. For example, bacterial vaginosis (BV), the most common gynecological infection in reproductive-age women, is a serious public health concern due to its high rates of recurrence, secondary infections, and reproductive issues; and two currently prescribed antibiotics for BV do not fully resolve the symptoms. Objective: The strong need for innovative, potent, safe, and selective therapeutics has prompted a search for such bioactive molecules in milk. Resulting from 200 million years of evolutionary pressure, mammalian lactation not only nourishes infants, but it has also been under relentless Darwinian selective pressure to provide protection from a variety of infections. Methods: Computationally designed human-milk-inspired peptides (AMPs) were tested in standard microbicidal assays for activity against BV pathogens, and evaluated for stability and safety. Results: Several AMPs are bactericidal towards Gardnerella vaginalis, a major BV-associated pathogen, and other BV-associated pathogens. Some novel AMPs do not impact the viability of key lactobacilli linked to a healthy vaginal microbiome. These stable, membrane-acting cationic AMPs reduce inflammation during an infection assay and are safe in EpiVag organoid tissues. Conclusions: AMPs can address concerns like non-selectivity and antibiotic resistance-thereby addressing AMR. Lead AMPs from this study offer a promising solution for the development of novel therapeutics for the treatment of BV, which may reduce the burden of AMR.},
}

@article {pmid41900935,
year = {2026},
author = {Santaniello, U and Mastorino, L and Pala, V and Rosset, F and Crespi, O and Quaglino, P and Ribero, S},
title = {Pharmacomicrobiomics in Psoriasis: Microbiome-Drug Interactions Across Systemic Treatments.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {3},
pages = {},
pmid = {41900935},
issn = {2075-1729},
abstract = {Psoriasis is a chronic immune-mediated skin disease with highly variable responses to systemic therapies. Emerging evidence highlights the microbiome as a potential modulator of drug efficacy and toxicity. Gut bacteria can enzymatically metabolize drugs, such as methotrexate, altering bioavailability and therapeutic outcomes, while microbial metabolites-including short-chain fatty acids, branched-chain amino acids, and tryptophan derivatives-shape host immunity and barrier integrity, influencing drug action. Baseline microbial signatures have been linked to treatment response, potentially predicting anti-TNF or IL-17 inhibitor efficacy. Systemic therapies themselves reshape microbial communities: IL-17 blockade induces broad shifts in gut and skin microbiota, whereas cyclosporine and anti-TNF agents exert subtler effects. Small molecules such as apremilast and fumarates may reduce fungal overgrowth and influence microbial composition, whereas data on JAK/TYK2 inhibitors remain limited. Notably, current evidence exhibits a literature bias toward the gut microbiota, while the roles of the oral and skin axes remain understudied. Adjunctive microbiome-directed interventions, including probiotics and fecal microbiota transplantation, have demonstrated potential to enhance treatment outcomes by promoting anti-inflammatory taxa and restoring barrier function. Despite these promising findings, current evidence is heterogeneous, often limited by small sample sizes, short follow-up, and variable methodology. Integrating pharmacomicrobiomics data with clinical, genetic, and multi-omics profiling could enable precision medicine approaches in psoriasis, allowing therapy selection tailored to individual microbial and metabolic signatures. Future research should focus on longitudinal, multicenter studies to identify actionable microbial biomarkers, clarify mechanistic interactions between drugs, microbes, and host immunity, and evaluate microbiome-targeted adjuncts in randomized trials. Understanding the bidirectional crosstalk between systemic therapies and the microbiome may transform psoriasis management, improving efficacy, reducing adverse events, and enabling durable, personalized responses.},
}

@article {pmid41901063,
year = {2026},
author = {Nunna Sai Venkata, L and Mishra, AK and Mohanta, YK and Rustagi, S and Bahuguna, A and Tomar, A and Baek, KH and Mishra, B},
title = {The Gut Gambit: A Review of How Microbial Imbalance Fuels Metabolic Mayhem.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901063},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology/metabolism ; Oxidative Stress ; *Metabolic Diseases/microbiology/metabolism ; Epigenesis, Genetic ; Probiotics ; Inflammation/microbiology ; Animals ; },
abstract = {BACKGROUND/OBJECTIVES: An imbalance in gut microbiota, known as gut dysbiosis, results in reactive oxygen species overproduction, which can cause inflammatory conditions, damage DNA, trigger immunity, and induce epigenetic modifications of crucial genes that regulate metabolic pathways. Such a condition can also weaken the resilience of the protective gut wall and elevate colon permeability, allowing toxins from the gut to reach the liver and bloodstream, contributing to oxidative damage, autoimmune diseases, and epigenetic changes linked to metabolic disorders.

METHODS: The Scopus database was exclusively searched for the literature. Relevant articles were identified using predefined keywords, including gut dysbiosis, microbiota, microbiome, oxidative stress, metabolic disorders, inflammation, and epigenetics or combinations. Gut microbiota- and diet-induced metabolic disorders, particularly obesity, insulin resistance, dyslipidemia, and hypertension, may be inherited through epigenetic pathways.

RESULTS: The evidence analyzed suggests that the gut microbiota serves as a diverse metabolic and immunological organ. Its disruption affects the production of short-chain fatty acids, bile acid metabolism, immune signaling, and the redox balance, which contributes to the development of obesity, insulin resistance, and metabolic syndrome.

CONCLUSIONS: This review highlights key epigenetic mechanisms underlying metabolic disorders and oxidative stress in the context of gut dysbiosis. Furthermore, therapeutic strategies targeting the gut microbiota, such as dietary interventions, prebiotics, probiotics, postbiotics, and fecal microbiota transplantation, hold promise for mitigating oxidative stress and inflammation associated with metabolic syndrome.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology/metabolism
Oxidative Stress
*Metabolic Diseases/microbiology/metabolism
Epigenesis, Genetic
Probiotics
Inflammation/microbiology
Animals

@article {pmid41901066,
year = {2026},
author = {Thomas, EG and Ortutu, BF and Watson, JC and Ong, E and Blankley, KE and Meaurio Martin, A and Shankar, S and Zhang, D and Boland, DJ and Wu, CS},
title = {Purified Diets Lacking Fermentable Fiber Reduce Microbial Diversity, Alter Epithelial Transcriptome, and Exacerbate Colitis.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901066},
issn = {2072-6643},
support = {R21ES036683/ES/NIEHS NIH HHS/United States ; RP230204//Texas A&M Health-Center of Excellence in Cancer Research/ ; 58-3091-1-018//Texas A&M AgriLife Institute for Advancing Health Through Agriculture/ ; },
mesh = {Animals ; *Dietary Fiber/administration & dosage ; Mice, Inbred C57BL ; Male ; *Gastrointestinal Microbiome ; *Transcriptome ; *Colitis/microbiology/chemically induced ; Mice ; *Intestinal Mucosa/metabolism/microbiology ; Fermentation ; Fatty Acids, Volatile/metabolism ; Colon/metabolism/microbiology ; Dextran Sulfate ; Feces/microbiology ; *Diet ; Disease Models, Animal ; },
abstract = {Background/Objectives: Dietary fibers play key roles in shaping gut microbiome and intestinal homeostasis. While purified diets offer experimental precision and reproducibility in rodent models, they omit the complex mixture of fermentable and non-fermentable fibers found in grain-based chow diets. We hypothesized that excluding fermentable fiber impairs intestinal homeostasis by reducing microbial metabolites and altering the colonic epithelial transcriptome, thereby increasing susceptibility to inflammation. Methods: Wildtype male C57BL/6 mice were maintained on either a standard grain-based chow diet or a purified low-fat diet (LFD) containing 5% non-fermentable cellulose for ten weeks. Fecal microbiomes, short-chain fatty acid (SCFA) profiles, and colonic epithelial transcriptomes were analyzed. A separate group was challenged with dextran sodium sulfate (DSS) following a five-week dietary intervention to compare colitis severity between the two diet groups. Results: Relative to mice fed the grain-based chow, those consuming the purified LFD (containing only non-fermentable cellulose) showed decreased gut microbial diversity and significantly lower SCFA levels. These changes were accompanied by marked differences in colonic epithelial cell transcriptomes. In LFD-fed mice, the top upregulated gene networks included ribosomal pathways and MHC complex protein binding, suggesting increased growth and gut inflammation. The most downregulated pathways included mineral absorption, actin and tubulin binding, and membrane organelle assembly, indicating major alterations in cellular structure and transport. LFD-fed mice also exhibited increased colonic expression of S100a9, a gut inflammation biomarker, and more severe disease symptoms when challenged with DSS compared to chow-fed mice. Conclusions: Fermentable fibers are one of the factors contributing to intestinal homeostasis and mitigating the severity of ulcerative colitis.},
}

Animals
*Dietary Fiber/administration & dosage
Mice, Inbred C57BL
Male
*Gastrointestinal Microbiome
*Transcriptome
*Colitis/microbiology/chemically induced
Mice
*Intestinal Mucosa/metabolism/microbiology
Fermentation
Fatty Acids, Volatile/metabolism
Colon/metabolism/microbiology
Dextran Sulfate
Feces/microbiology
*Diet
Disease Models, Animal

@article {pmid41901079,
year = {2026},
author = {Cirio, S and Mantegazza, G and Salerno, C and Guglielmetti, S and Allam, A and Campus, G and Cagetti, MG},
title = {Assessing the Impact of Heyndrickxia coagulans Administered Through Sugar-Free Chewing Gum on Dental Biofilm: A Double-Blind Randomized Controlled Trial.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901079},
issn = {2072-6643},
mesh = {Humans ; *Chewing Gum ; Double-Blind Method ; *Biofilms/drug effects ; Male ; Female ; Adult ; *Dental Plaque/microbiology ; *Probiotics/administration & dosage ; Middle Aged ; Young Adult ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background:Heyndrickxia coagulans has emerged as a candidate for oral health applications, and chewing gum offers a promising delivery method. This study evaluates whether H. coagulans delivered via sugar-free chewing gum can induce detectable changes in plaque microbial ecology. Methods: A randomized, double-blind, placebo-controlled clinical trial was conducted on 52 healthy adults. Participants consumed probiotic or control gum for 4 weeks. Dental plaque was collected at baseline (T0), mid-intervention (T1), end of intervention (T2), and one week post-intervention (T3). qPCR quantified H. coagulans, while 16S rRNA gene profiling assessed microbial diversity and taxonomic composition. Statistical analyses included rank-based difference-in-differences models, Wilcoxon and Mann-Whitney tests, and differential abundance inference based on negative binomial modeling. Results: Forty-four subjects completed the study. In the Intervention group, the strain was detected in 71.4% of participants at T1 and 61.9% at T2, and it persisted in 9.5% at T3. Differential abundance analysis revealed a broad depletion of taxa linked to oral dysbiosis at T2 with partial persistence at T3, along with selective enrichment of beneficial strains. Conclusions:H. coagulans delivered via chewing gum can reach the dental biofilm and induce modest, transient shifts in microbial composition. However, these biofilm ecology findings should be interpreted in the context of clinical outcomes.},
}

Humans
*Chewing Gum
Double-Blind Method
*Biofilms/drug effects
Male
Female
Adult
*Dental Plaque/microbiology
*Probiotics/administration & dosage
Middle Aged
Young Adult
RNA, Ribosomal, 16S/genetics

@article {pmid41901112,
year = {2026},
author = {Solano-Aguilar, G and Lakshman, S and Chen, C and Beshah, E and Molokin, A and Vinyard, B and Dawson, HD and Santin-Duran, M and Bruna, G and Smith, A and Urban, JF},
title = {Fruit and Vegetable Supplemented-Diet Ameliorates Dextran Sodium Sulfate (DSS)-Induced Colitis by Modulating Host Transcriptome and Gut Metagenome Response.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901112},
issn = {2072-6643},
support = {Cris 8040-51000-058-00D//United States Department of Agriculture/ ; },
mesh = {Animals ; Dextran Sulfate ; *Fruit ; *Colitis/chemically induced/prevention & control/microbiology/diet therapy ; *Transcriptome ; *Gastrointestinal Microbiome ; *Dietary Supplements ; *Vegetables ; Swine ; *Metagenome ; Disease Models, Animal ; *Diet ; Colon/pathology ; },
abstract = {Background/Objectives: Dietary intake of fruits and vegetables (FVs) has been inversely associated with a lower risk of ulcerative colitis. Using a pig model, we evaluated the effect of FV supplementation on dextran sulfate sodium (DSS)-induced colitis. Methods: Six-week-old pigs were fed a grower diet (negative control), grower diet + 4% DSS (positive control), half-FV diet + DSS, or full-FV diet + DSS. FV levels matched half or full daily recommendations from the Dietary Guidelines for Americans (DGA). Clinical signs were monitored; proximal colon contents (PCs) and mucosa (PCM) were analyzed for metagenome, transcriptome and histopathology. Results: Full-FV pigs showed no diarrhea, less fecal occult blood (FOB), crypt hyperplasia, but no changes in gene expression or microbiome diversity (p < 0.05). Half-FV pigs had increased FOB, differentially expressed genes (DEGs) linked to tissue remodeling, crypt/goblet cell hyperplasia and two cases of diarrhea (p < 0.05). DSS controls showed reduced immune-related DEGs, altered microbiome, PCM erosion, FOB, and persistent diarrhea in one pig (p < 0.05). Conclusions: A three-week full-FV diet conferred protection against DSS-induced colitis, with a dose-dependent protection of intestinal tissue and gut metagenome under inflammatory challenge.},
}

Animals
Dextran Sulfate
*Fruit
*Colitis/chemically induced/prevention & control/microbiology/diet therapy
*Transcriptome
*Gastrointestinal Microbiome
*Dietary Supplements
*Vegetables
Swine
*Metagenome
Disease Models, Animal
*Diet
Colon/pathology

@article {pmid41901128,
year = {2026},
author = {Lupu, VV and Nedelcu, AH and Borka-Balas, R and Anton, CR and Tarnita, I and Azoicai, A and Forna, L and Munteanu, D and Anton, SC and Shawais, SK and Badescu, MC and Salaru, DL and Morariu, ID and Anton, E and Petrariu, F and Lupu, A},
title = {The Gut Microbiota: An Essential Component in Understanding Pediatric Obesity: A Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
pmid = {41901128},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Pediatric Obesity/microbiology ; Child ; Dysbiosis/microbiology ; Probiotics ; },
abstract = {Background: Childhood obesity has become a major public health concern worldwide. Increasing evidence suggests that alterations in the gut microbiome may play a significant role in the development and progression of pediatric obesity. This narrative review synthesizes and analyzes recent studies investigating microbiome alterations in children with obesity, highlighting emerging insights and their potential implications for disease management. Understanding the relationship between gut microbial composition and obesity may provide new perspectives for prevention and therapeutic strategies in overweight pediatric populations. This narrative review was conducted through a search of major biomedical databases, including PubMed and Web of Science, complemented by manual screening of reference lists of relevant articles. Key findings: Children affected by obesity exhibit significant changes in gut microbiome composition, characterized by reduced microbial diversity and predominance of the Firmicutes and Bacteroidetes phyla. The balance between these two bacterial groups appears critical for maintaining gut homeostasis. Studies consistently report an increased Firmicutes-to-Bacteroidetes ratio in children with elevated body weight, suggesting that disruption of this balance may contribute to metabolic dysregulation and obesity-related pathologies. Given the essential role of the gut microbiota in nutrient metabolism and energy extraction, dysbiosis in obesity is associated with enhanced energy harvest and lipid absorption. Certain bacterial populations may promote increased caloric uptake, thereby contributing to weight gain and adiposity. Multidimensional interventions, including dietary modification and physical activity, have demonstrated the potential to reduce obesogenic microbiota patterns and restore microbial diversity. Additionally, probiotic supplementation is being investigated as a strategy to reestablish microbial homeostasis and potentially support body mass index reduction. Despite promising findings, further research is required to clarify mechanisms, establish causality, and determine the clinical effectiveness of microbiome-targeted therapies before they can be fully integrated into the management of pediatric obesity.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Pediatric Obesity/microbiology
Child
Dysbiosis/microbiology
Probiotics