@article {pmid41853378,
year = {2023},
author = {Zimmermann, P},
title = {Exploring the microbial landscape of the nasopharynx in children: a systematic review of studies using next generation sequencing.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1231271},
pmid = {41853378},
issn = {2813-4338},
abstract = {INTRODUCTION: The nasopharynx harbours a diverse and dynamic microbial community, which plays an important role in maintaining the health and homeostasis of the respiratory tract, as well as in immune system development. Understanding factors that influence the composition of the nasopharyngeal microbiome in children and its association with diseases is of particular importance, as children are at a heightened risk for respiratory infections and other adverse health outcomes.

OBJECTIVES: This review systematically summarises studies which investigated the nasopharyngeal microbiome in children, including its dynamics, stability over time, and the influence of intrinsic and extrinsic factors on its composition.

METHODS: MEDLINE was searched using the OVID interface. Original studies which investigated the nasopharyngeal microbiome using next generation sequencing in children were summarised.

RESULTS: The search identified 736 studies, of which 77 were included. The studies show that the nasopharyngeal microbiome in children is dynamic and influenced by many external factors. A high abundance of Haemophilus, Moraxella, and Streptococcus and a low abundance of Corynebacterium and Dolosigranlum are associated with adverse health outcomes such as respiratory tract infections, wheezing and asthma exacerbations. Factors which have been identified as risk factors for these adverse health outcomes, such as being born by Caesarean section, not being breast-fed, having siblings, day-care attendance, and antibiotic exposure have been shown to be associated with the aforementioned features in the nasopharyngeal microbiome.

CONCLUSION: The association between specific nasopharyngeal microbial profiles and adverse health outcomes highlights the potential of the nasopharyngeal microbiome as a marker for identifying children at risk for disease and even more importantly, as an avenue for targeted interventions and preventive strategies.},
}

@article {pmid41853380,
year = {2023},
author = {Galeeva, JS and Starikova, EV and Fedorov, DE and Manolov, AI and Pavlenko, AV and Konanov, DN and Krivonos, DV and Babenko, VV and Klimina, KM and Veselovsky, VA and Morozov, MD and Gafurov, IR and Gaifullina, RF and Govorun, VM and Ilina, EN},
title = {Microbial communities of the upper respiratory tract in mild and severe COVID-19 patients: a possible link with the disease course.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1067019},
pmid = {41853380},
issn = {2813-4338},
abstract = {The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, it is involved in modulating the immune response to infectious agents in the host organism, just like the intestinal microbiota. A relationship between the composition of the respiratory microbiota and the likelihood of development and the severity of COVID-19 may be assumed. In this study, we applied the 16S rRNA metagenomic sequencing to analyze the oropharyngeal swabs from 120 COVID-19 patients collected during the first and the second waves of the COVID-19 epidemic in Russia. Differential abundance analysis with respect to comorbidities suggested association of Neisseria oralis, Neisseria mucosa, unidentified Veillonella spp., Lautropia mirabilis species with more severe lung damage, and Streptococcus salivarius, Capnocytophaga sputigena and Haemophilus parahaemolyticus with a milder course of the disease. We hypothesize that the latter bacteria (or some of them) might be beneficial for the respiratory tract and might be able to alleviate the course of the COVID-19 disease.},
}

@article {pmid41853381,
year = {2023},
author = {Li, L and Yan, Y and Wang, X and Hou, Y and Ding, L and Wang, Z and Song, Q and Ding, W and Zhang, X},
title = {Allicin modulates the intestinal microbiota to attenuate blood glucose and systemic inflammation in type 2 diabetic rats.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1102694},
pmid = {41853381},
issn = {2813-4338},
abstract = {INTRODUCTION: Allicin is a wide spectrum prebiotic for human health, but whether it can attenuate blood in diabetes patients is rarely reported. In this study, we built a rat model and investigated the effect of allicin on diabetes mellitus type 2 (T2DM). We found that allicin could effectively reduce blood glucose levels, regulate intestinal microbiota, reduce lipid and body weight accumulation, and systemic inflammation in T2DM rats.

METHODS: The rat model of type 2 diabetes was made by streptozotocin, and different doses of allicin were given orally by gavage. The intestinal contents of diabetes rats were sequenced and analyzed by 16S technology, and the clinical indicators of rats were detected for joint analysis.

RESULTS: Allicin can improve the intestinal flora of type 2 diabetes rats, enrich beneficial metabolites, reduce blood glucose, improve blood lipids, reduce systemic inflammation, and improve type 2 diabetes.

DISCUSSION: Intestinal microbiome analysis showed that allicin gavage significantly regulated the structure and main components of the intestinal microbiota in T2DM rats. Allicin increased the abundance of probiotic microbes, such as Lactobacillus, Clostridium and Akkermansia, while it reduced pathogenic microbes, such as Enterobacter, Erysipelatoclostridium and Colidextribacter. Allicin gavage increased the abundance of intestinal short-chain fatty acids, such as acetic acid and propionic acid. Correlation analysis showed that the increased gut microbes by allicin gavage were significantly associated with health physiological parameters but negatively related to serum inflammatory factors such as interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-a), and hypersensitive C-reactive protein (hs-CRP). In addition, our study also suggests that allicin may have prebiotic effects on chronic liver injury. This study shows that allicin can regulate various clinical symptoms of T2DM and is a potential therapeutic drug for T2DM.},
}

@article {pmid41853384,
year = {2023},
author = {Walusimbi, B and Lawson, MAE and Nassuuna, J and Kateete, DP and Webb, EL and Grencis, RK and Elliott, AM},
title = {The effects of helminth infections on the human gut microbiome: a systematic review and meta-analysis.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1174034},
pmid = {41853384},
issn = {2813-4338},
abstract = {UNLABELLED: The gut microbiome is important in shaping human health. One key factor that has been proposed to affect the gut microbiome is helminth infection. Unravelling the association and/or interaction between helminth infections and the gut microbiome may reveal new insights into the mechanisms through which parasitic worms impact the prognosis of infections and diseases. While considerable work has gone into reviewing data on the effect of helminth infection on gut microbiome in animal studies, less attention has been given to this area of research in human studies. This study set out to address this through an exhaustive systematic review of literature. Articles were identified through EMBASE, MEDLINE, Web of Science and Science Direct following a registered protocol (PROSPERO). After assessing methodological quality (ICROMS) and publication bias, a random effects meta-analysis was performed to investigate the overall effect that intestinal parasites can have on the human gut microbiome using alpha- and beta-diversity metrics and adjusting for age, sex and antihelminthic treatment taken by individuals. A total of 19 out of 3466 articles were included in the final meta-analysis. Our results show that helminth infection increases the host bacterial diversity, as well as microbial richness. This work further contributes to the understanding of how the gut microbiome structure changes depends on whether one is infected with helminths or not. It also lays the foundation for future research aimed at establishing how these interactions could explain the disparity in phenotypes such as infection, disease and vaccine responses reported in different regions worldwide.

https://www.crd.york.ac.uk/prospero/, identifier CRD42020192182.},
}

@article {pmid41853385,
year = {2023},
author = {Leo, S and Cetiner, OF and Pittet, LF and Messina, NL and Jakob, W and Falquet, L and Curtis, N and Zimmermann, P},
title = {The association between the composition of the early-life intestinal microbiome and eczema in the first year of life.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1147082},
pmid = {41853385},
issn = {2813-4338},
abstract = {INTRODUCTION: The early-life intestinal microbiome plays a crucial role in the development and regulation of the immune system. Perturbations in its composition during this critical period have been linked to the development of allergic diseases.

OBJECTIVE: This study aimed to investigate the association between the composition of the early-life intestinal microbiome and the presence of eczema in the first year of life using shotgun metagenomic sequencing and functional analyses (metabolic pathways).

METHODS: Stool samples from 393 healthy term infants collected at 1 week of age were analyzed with shotgun metagenomic sequencing. Environmental and clinical data were prospectively collected using 3-monthly validated questionnaires. Participants were clinically assessed during study visits at 12 months of age. Eczema was diagnosed by the UK diagnostic tool and by a research nurse. Data analysis was stratified by delivery mode.

RESULTS: Eczema was diagnosed in 16.4% (60/366) of participants by nurse diagnosis. Infants born by cesarean section (CS) with nurse-diagnosed eczema had a higher relative abundance of Escherichia, Shigella, Enterobacter, and Citrobacter and a lower relative abundance of Veillonella than CS-born infants without eczema. In addition, CS-born infants without eczema had a higher abundance of genes involved in lactic fermentation. Vaginally born infants with eczema had a higher relative abundance of Bacteroides and a lower abundance of Streptococcus.

CONCLUSION: There is an association between the bacterial composition of the intestinal microbiome at 1 week of age and the presence of eczema in the first 12 months of life.},
}

@article {pmid41853386,
year = {2023},
author = {Goemann, HM and Ulrich, DEM and Peyton, BM and Gallegos-Graves, V and Mueller, RC},
title = {Severe and mild drought cause distinct phylogenetically linked shifts in the blue grama (Bouteloua gracilis) rhizobiome.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1310790},
pmid = {41853386},
issn = {2813-4338},
abstract = {Plants rely on a diverse rhizobiome to regulate nutrient acquisition and plant health. With increasing severity and frequency of droughts worldwide due to climate change, untangling the relationships between plants and their rhizobiomes is vital to maintaining agricultural productivity and protecting ecosystem diversity. While some plant physiological responses to drought are generally conserved, patterns of root exudation (release of small metabolites shown to influence microbes) and the consequential effects on the plant rhizobiome can differ widely across plant species under drought. To address this knowledge gap, we conducted a greenhouse study using blue grama (Bouteloua gracilis), a drought-tolerant C4 grass native to shortgrass prairie across North American plains, as a model organism to study the effect of increasing drought severity (ambient, mild drought, severe drought) on root exudation and the rhizobiome. Our previous results demonstrated physiological effects of increasing drought severity including an increase in belowground carbon allocation through root exudation and shifts in root exudate composition concurrent with the gradient of drought severity. This work is focused on the rhizobiome community structure using targeted sequencing and found that mild and severe drought resulted in unique shifts in the bacterial + archaeal and fungal communities relative to ambient, non-droughted controls. Specifically, using the change in relative abundance between ambient and drought conditions for each ZOTU as a surrogate for population-scale drought tolerance (e.g., as a response trait), we found that rhizobiome response to drought was non-randomly distributed across the phylogenies of both communities, suggesting that Planctomycetota, Thermoproteota (formerly Thaumarchaeota), and the Glomeromycota were the primary clades driving these changes. Correlation analyses indicated weak correlations between droughted community composition and a select few root exudate compounds previously implicated in plant drought responses including pyruvic acid, D-glucose, and myoinositol. This study demonstrates the variable impacts of drought severity on the composition of the blue grama rhizobiome and provides a platform for hypothesis generation for targeted functional studies of specific taxa involved in plant-microbe drought responses.},
}

@article {pmid41853387,
year = {2023},
author = {Rodríguez-Ramos, J and Oliverio, A and Borton, MA and Danczak, R and Mueller, BM and Schulz, H and Ellenbogen, J and Flynn, RM and Daly, RA and Schopflin, L and Shaffer, M and Goldman, A and Lewandowski, J and Stegen, JC and Wrighton, KC},
title = {Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1199766},
pmid = {41853387},
issn = {2813-4338},
abstract = {Although river ecosystems constitute a small fraction of Earth's total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.},
}

@article {pmid41853500,
year = {2024},
author = {Wang, G and Menon, S and Wilsack, L and Rehak, R and Lou, L and Turbide, C and Auger, J and Tremblay, A and Mathieu, O and Binda, S and Tompkins, TA and Bruehlmann, S and Andrews, CN},
title = {Spatially and temporally precise microbiome profiling in the small intestine using the SIMBA capsule with X-ray tracking.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1321624},
pmid = {41853500},
issn = {2813-4338},
abstract = {INTRODUCTION: Few minimally invasive options for sampling the small intestinal (SI) luminal fluid exist to study the SI microbiota in health and disease. To address the lack of tools and methods to study GI regions that are difficult to access, Nimble Science developed a fully autonomous and passive sampling method, the Small Intestine MicroBiome Aspiration (SIMBA™) capsule, for convenient, high-quality, and reliable sampling to study the diet-microbiota interactions in the SI.

METHODS: The sealing efficacy and microbial DNA preservation capacity of the SIMBA capsules was first validated through in vitro simulation assays. Then, a clinical study was conducted with 20 healthy participants to validate the in vivo use of SIMBA capsules to reliably capture samples for SI microbiome analysis before and after an intervention (NCT04489329). Briefly, participants ingested the capsules at baseline and 7 days later, with a probiotic capsule containing a blend of L. rhamnosus R0011 and B. longum R0175. Following baseline SIMBA capsule ingestion, multiple low-dosage x-ray scans were performed to track the sampling location. Fecal samples corresponding with the baseline and intervention capsule were analyzed for comparison.

RESULTS: The SIMBA capsules' performance in vitro demonstrated the potential for contamination-free sampling with preservation of the microbial communities. Within the clinical study, the capsules performed safely and reliably for collection of SI content. X-ray tracking confirmed that 97.2% of the capsules completed sample collection in the SI regions before reaching the colon. Importantly, our data showed that the capsules sampled in the right area of the intestines and that baseline SIMBA microbiome profile is significantly different from fecal microbiome profile. SIMBA successfully detected a concurrent probiotic intervention in the small intestine, which was not detectable using stool samples.

DISCUSSIONS: The high accuracy of sampling location and sealing efficacy of the SIMBA capsules makes them potentially useful research tools in clinical trials for studying diet-microbiota interactions in health and disease, and perhaps eventually for the clinical diagnosis of GI tract conditions affecting the SI such as SIBO.},
}

@article {pmid41853502,
year = {2024},
author = {Tarrant, I and Finlay, BB},
title = {The potential of live biotherapeutic products in allergic disease: current findings and future directions.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1418633},
pmid = {41853502},
issn = {2813-4338},
abstract = {With the global prevalence of allergic disease continuing to rise at an alarming rate, the need for effective and safe therapeutics is paramount. Given the critical role of the early-life microbiota on immune development, emerging research suggests the potential use of live biotherapeutic products (LBP) for the prevention and treatment of childhood allergy. However, findings are limited and inconsistent. Therefore, the present review critically evaluates the current animal and human data on the therapeutic value of LBPs in allergy, the underlying immunological mechanisms by which LBPs may mediate allergy susceptibility, limitations of the current research that need to be addressed, and future research directions. Accordingly, LBPs may protect against allergic disease through several immunological and physiological mechanisms during early-life, including regulation of Th1/Th2 balance, SCFA-induced activation of GPR41/43 and HDAC inhibition, and maturation of epithelial barrier integrity. Taken together, current findings indicate powerful immunomodulatory properties of LBPs on allergic immune response, with LBPs offering exciting potential as a novel therapeutic tool for childhood allergy. However, the efficacy of LBPs in allergy is complex and influenced by many population and methodological factors, resulting in varied therapeutic benefits. While research thus far has focused on traditional probiotic strains, greater investigation into microbial consortiums selected from the microbiota of non-allergic infants may provide greater promise as a therapeutic tool for allergic disease. Further investigation, particularly into long-term efficacy, strain-specific effects, optimal supplementation regimes, and use of multi-strain consortiums, is necessary before findings can be translated into clinical applications to tackle childhood allergic disease.},
}

@article {pmid41853503,
year = {2024},
author = {Greenman, N and Abdelli, LS and Hassouneh, SA and Ali, S and Johnston, C and Naser, SA and Azarian, T},
title = {Impact of propionic acid-rich diets on microbial composition of the murine gut microbiome.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1451735},
pmid = {41853503},
issn = {2813-4338},
abstract = {Propionic acid (PPA), an anti-fungal agent and common food additive, has been shown to induce atypical neurodevelopment in mice, accompanied by gastrointestinal dysfunction potentially resulting from gut dysbiosis. A putative association between dietary PPA exposure and gut dysbiosis is suggested but has not been explored directly. Here, we investigated PPA-associated alteration in gut microbial composition that may result in dysbiosis. Using long-read metagenomic sequencing, gut microbiomes of mice fed an untreated (n=9) or PPA-rich (n=13) diet were sequenced to assess differences in microbial composition and bacterial metabolic pathways. Dietary PPA was associated with an increased abundance of notable taxa, including several species of Bacteroides, Prevotella, and Ruminococcus, whose member species have previously been associated with PPA production. Microbiomes of PPA exposed mice also possessed a greater abundance of pathways related to lipid metabolism and steroid hormone biosynthesis. Our findings demonstrate PPA's effect in altering the gut microbiota and associated metabolic pathways. These observed changes highlight how preservatives listed as safe for consumption may affect gut microbiome composition with implications for one's health.},
}

@article {pmid41853505,
year = {2024},
author = {Rusling, MR and DeMar, JC and Chakraborty, N and Hoke, AV and Miller, SA and Rosenberger, JG and Batuure, AB and Wilder, DM and Sajja, VS and Long, JB and Hammamieh, R and Gautam, A},
title = {The effect of dietary omega-6 fatty acid enrichment in rodent models of military-relevant acute traumatic psychological stress and traumatic brain injury.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1430340},
pmid = {41853505},
issn = {2813-4338},
abstract = {INTRODUCTION: Sequelae from traumatic brain injuries (TBIs) and post-traumatic stress disorder (PTSD) are major career-limiting factors for combat soldiers. Overlap between TBI and PTSD symptoms alongside other common comorbidities complicate the diagnosis and treatment. Systems-level and high-throughput approaches are key in understanding the underlying biomolecular mechanisms and differentiating these conditions.

METHODS: The present study identifies dietary factors and proposes mechanisms behind psychological stress and TBI, using established preclinical animal models and a multi-omics approach. Here, we used microbiome characterizations of rats exposed to simulations of blast-induced TBI and underwater trauma (UWT)-induced psychological stress. We further studied the effect of dietary omega-6 versus omega-3 polyunsaturated fatty acid (n-6, n-3 PUFA) enrichment on the insult responses. The use of excess n-6 PUFA was chosen due to its high prevalence in the Western diet and pro-inflammatory nature. Prior to TBI or UWT, animals were maintained for 6 weeks and continued thereafter on either a standard diet or two customized chows imbalanced and diminished in omega-3 content. Corresponding shams were carried out for all groups. Fecal bacterial microbiome populations were assessed using 16S rRNA gene sequencing.

RESULTS: Physiologic outcome modeling identified that dietary status affected post-TBI lactate dehydrogenase (LDH) and triglyceride levels, with n-3 PUFA having a large attenuating influence. The UWT model showed similar trends, with diet significantly altering LDH, terminal corticosterone (14 days post-exposure), and a fear behavior susceptibility. Fecal microbiome alpha diversity was significantly reduced by high levels of n-3 PUFA. Likewise, beta diversity of the microbiome was significantly affected by both diet and time but not exposure to TBI or UWT. Compositionally, temporal effects on the microbiome were more likely to be observed with the diets. The most affected features fell within the Proteobacteria phyla, in which n-3 PUFA enrichment significantly reduced Alphaproteobacteria in the TBI model and increased Gammaproteobacteria in the UWT group.

DISCUSSION: All these observations can influence the vulnerability or resilience of the warfighter to blast-induced TBI and acute psychological stress. The microbiome mechanisms facilitate and provide a knowledge-driven unbiased panel of signatures to discriminate between the two insults and is an essential tool for designing precise care management.},
}

@article {pmid41853506,
year = {2024},
author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S},
title = {Corrigendum: A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1484878},
doi = {10.3389/frmbi.2024.1484878},
pmid = {41853506},
issn = {2813-4338},
abstract = {[This corrects the article DOI: 10.3389/frmbi.2024.1359580.].},
}

@article {pmid41853507,
year = {2024},
author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S},
title = {A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1359580},
pmid = {41853507},
issn = {2813-4338},
abstract = {The human gut microbiome, crucial for health, can be disrupted by antibiotic treatment, leading to various health issues and the rise of antimicrobial resistance (AMR). This study investigates the impact of a probiotic on the gut microbiome's composition and antimicrobial resistance genes (ARGs) content following antibiotic treatment. Conducted as a single-centre, double-blind, randomized, placebo-controlled trial, adults taking oral antibiotics were allocated into a probiotic or placebo group. Evaluations included viable cell enumeration and shotgun metagenomic sequencing for microbiome analysis, along with ARG assessment. The probiotic maintained the numbers of lactobacilli, significantly increased the Bacteroides population and decreased numbers of enterobacteria. The lactobacilli and enterococci numbers decreased in the placebo. The alpha diversity remained stable in the probiotic group throughout the study, but significant reductions were observed in the placebo group post antibiotic treatment. There was significant spatial separation in beta diversities between groups at the end of the study. Compared to baseline levels, there was a significant reduction in the abundance of ARGs in the probiotic group at the end of the study, while ARG abundance in the placebo group was comparable with baseline levels at the end of the study. Co-occurrence network analysis observed consistent betweenness centrality and node degree within group in the probiotic group whereas scores decreased in the placebo group. This study suggests that the probiotic may minimize the disruption of antibiotic treatment on the gut microbiome by preserving microbial diversity and reducing ARG abundance.},
}

@article {pmid41853509,
year = {2024},
author = {Fu, X and Shama, A and Norbäck, D and Chen, Q and Xia, Y and Zhang, X and Sun, Y},
title = {Exploring the role of indoor microbiome and environmental characteristics in rhinitis symptoms among university students.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1277177},
pmid = {41853509},
issn = {2813-4338},
abstract = {INTRODUCTION: Rhinitis is one of the most prevalent chronic respiratory diseases worldwide. There is emerging evidence suggesting that the indoor microbiome may contribute the onset and exacerbation of rhinitis symptoms, but comprehensive studies on this topic remain scarce.

METHODS: In this study, we assessed the microbiome assemblage of settled air dust collected in Petri dishes in 86 dormitory rooms of Shanxi University, China using 16s rRNA sequencing. A self-administered questionnaire, including questions about rhinitis symptoms and personal information, was completed by 357 students residing in these dormitories. Logistic and linear regression model was applied to examine the associations between environmental characteristics, indoor microbiome, and rhinitis.

RESULTS: The most abundant genera in the dormitories were Ralstonia (15.6%), Pelomonas (11.3%), Anoxybacillus (9.3%) and Ochrobactrum (6.2%). Taxa richness in the class of Actinobacteria and Fusobacteriia was negatively/protectively associated with rhinitis (p<0.05). Six bacterial genera, including those from Actinobacteria (Actinomyces), Fusobacteriia (Fusobacterium), and Bacteroidetes (Prevotella and Capnocytophaga), were negatively/protectively associated with rhinitis. Conversely, seven genera, predominantly from Alphaproteobacteria and Betaproteobacteria (Sphingomonas, Caulobacter, uncharacterized Caulobacteraceae and Comamonadaceae), were positively associated with rhinitis. Living in higher floor level and higher indoor PM2.5 concentrations were associated with a higher abundance of taxa potentially protective against rhinitis and a lower abundance of taxa potentially increasing the risk of rhinitis (P<0.01). However, having curtain indoor and higher indoor CO2 concentrations were associated with a lower abundance of taxa potentially protective against rhinitis and a higher abundance of taxa potentially increasing the risk of rhinitis (P<0.01).

DISCUSSION: This study enhances our understanding of the complex interactions between environmental characteristics, indoor microbiomes, and rhinitis, shedding light on potential strategies to manipulate indoor microbiome for disease prevention and control.},
}

@article {pmid41853510,
year = {2024},
author = {Kim, H and Lee, K and Lee, JY and Kwon, BE and Kim, HJ and Park, H and Kim, T and Kwak, JG and Choi, JE and Hong, KH and Chun, J and Shin, C},
title = {Distinct Cutibacterium acnes subspecies defendens strains classified by multi-omics dissection alleviate inflammatory skin lesions of a rosacea-like mouse model.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1362408},
pmid = {41853510},
issn = {2813-4338},
abstract = {INTRODUCTION: Cutibacterium acnes (C. acnes) resides in various organs such as the skin, prostate, eye, nose, stomach, and intestine, indicating the possibility of extensive crosstalk between this bacterium and the human body. C. acnes strains are classified into three subspecies based on phylogenetics and distinguishable phenotypes. Among them, C. acnes subsp. defendens strains are characterized by anti-inflammatory features, raising expectations for their potential as future microbiome therapeutics. However, the heterogeneity of C. acnes subsp. defendens and its corresponding immunological functions have not been clearly addressed.

METHODS: The genetic diversity of the strains was assessed using single- and multi-locus sequence typing. Their immune-modulatory functions were evaluated in vitro using 2D and 3D assays with immune and epithelial cells. The anti-inflammatory effects were further confirmed in vivo using a rosacea-like mouse model. Comparative genomic and transcriptomic analyses were conducted to uncover mechanisms underlying the immunosuppressive activity of the strains.

RESULTS: We demonstrated that the newly isolated C. acnes subsp. defendens strains, exhibiting phenotypic heterogeneity, are distinctly clustered using single- and multi-locus sequence typing methods. These strains showed strong immune-regulatory functions in immune and epithelial cell-based 2D and 3D in vitro assays. Furthermore, their anti-inflammatory role was functionally confirmed in vivo using a rosacea-like mouse model, where they alleviated skin lesions characterized by hyperplasia and dermal inflammation. Comparative transcriptomics revealed that these strains may exert their immunosuppressive effects through the enhanced expression of acnecins and transcriptional variation in envelope stress regulators (specifically the two-component systems, CesSR homologs). Additionally, we propose that these C. acnes type II strains produce anti-inflammatory metabolites or peptides smaller than 3 kDa, which are associated with elevated pyrimidine and reduced L-arginine biosynthesis.

DISCUSSION: The newly isolated C. acnes subsp. defendens strains demonstrate significant anti-inflammatory properties both in vitro and in vivo, suggesting their potential as microbiome-based therapeutics. Their unique genomic and transcriptomic profiles, including the production of small bioactive compounds and specific transcriptomic patterns, underpin their immunosuppressive capabilities. These findings provide a foundation for developing novel treatments for inflammatory skin conditions, such as rosacea.},
}

@article {pmid41853511,
year = {2024},
author = {Pitell, S and Woo, C and Trump, E and Haig, SJ},
title = {Balancing water conservation and health: do water-saving showerheads impact the microbes we breathe in during showering?.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1416055},
pmid = {41853511},
issn = {2813-4338},
abstract = {Low-flow showerheads offer consumers economic and water-saving benefits, yet their use may inadvertently affect the microbial content of produced water and water-associated aerosols. This study aimed to compare the abundance and microbial composition of bacteria in shower water and associated respirable aerosols produced by various low flow rate (1, 1.5, and 1.8 gpm) showerheads. Our findings indicate that the lowest-flow showerhead produces water with lower total microbial and opportunistic bacterial pathogen densities compared to higher low flow rate counterparts. However, microbiome analysis revealed that 1.8 gpm flow rate showerheads exhibit reduced abundance of Gram-negative organisms and common biofilm-forming organisms, suggesting potentially lower pathogenicity compared to 1 and 1.5 gpm low-flow showerheads. Additionally, the number of respirable aerosols produced by showerheads as well as the partitioning of certain microorganisms from the water to aerosol phases was negatively correlated with flow rate, suggesting that there may be increasing exposure potential to pathogenic bioaerosols when using a 1gpm showerhead compared to a 1.8 gpm showerhead. However, the 1.5 gpm showerhead seemed to balance microbial partitioning, aerosol generation, and water conservation. Moreover, the microbial composition of aerosols produced from shower water was more influenced by the age of the showerhead than the flow rate, highlighting the significance of biofilm formation on the microbial community. Overall, our findings underscore the importance of evaluating the microbial risk associated with low-flow showerheads using multiple metrics in both water and aerosols, and dynamically assessing this over time, to ensure accurate future risk assessment.},
}

@article {pmid41853512,
year = {2024},
author = {Beilig, S and Pannekens, M and Voskuhl, L and Meckenstock, RU},
title = {Assessing anaerobic microbial degradation rates of crude light oil with reverse stable isotope labelling and community analysis.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1324967},
pmid = {41853512},
issn = {2813-4338},
abstract = {Oil reservoirs represent extreme environments where anaerobic degradation profoundly influences oil composition and quality. Despite the common observation of biodegraded oil, the microbial degradation rates remain largely unknown. To address this knowledge gap, we conducted microcosm incubations with light oil as carbon source, original formation water and sulfate as electron acceptor, closely mimicking in situ conditions to assess oil degradation rates. Samples were taken from a newly drilled oil well to exclude contamination with injection water and allochthonous microorganisms. At the end of the incubations, microbial community analyses with 16S rRNA gene amplicon sequencing revealed the most prominent phyla as Desulfobacterota, Thermotogota, Bacteroidota, Bacillota (formerly Firmicutes), and Synergistota, collectively accounting for up to 44% of relative abundance. Ion chromatography and reverse stable isotope labeling were used to monitor sulfate reduction and CO2 evolution respectively. We calculated an average degradation rate of 0.35 mmol CO2 per year corresponding to 15.2 mmol CO2/mol CH2(oil) per year. This resembles to approximately 200 years to degrade one gram of oil under the applied, presumably ideal conditions. Factoring in the available oil-water-contact (OWC) zone within the incubations yielded a degradation rate of 120 g CH2 m[-2] OWC per year, closely aligning with the modeled degradation rates typically observed in oil reservoirs. Moreover, our study highlighted the utility of the reverse stable isotope labeling (RSIL) approach for measuring complex substrate degradation at minute rates.},
}

@article {pmid41853514,
year = {2024},
author = {Asumang, P and Ntumi, R and Dwomoh, F},
title = {Unveiling microbial dynamics: a review of health and immune enhancement in school settings.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1488702},
pmid = {41853514},
issn = {2813-4338},
abstract = {This review focuses on the role of microorganisms in promoting health and immune function within school environments. Microbes, including bacteria, viruses, fungi, and other microorganisms, constitute the human microbiome and play a crucial role in various bodily functions and immune system development. The complex interactions between microorganisms and the immune system in schools, where children spend a significant amount of time, are not fully understood. While schools have traditionally emphasized hygiene practices to prevent the spread of infectious diseases, recent research has highlighted the potential consequences of reduced microbial exposure during early life. The "hygiene hypothesis" suggests that limited exposure to microbes in infancy may increase the risk of allergies, asthma, and autoimmune diseases in adulthood. This paper explores the microbial diversity found in schools, the benefits of exposure to different microorganisms, and the implications of hygiene practices on immune system development. It also examines current research on microbial intervention strategies and their potential to influence overall health in schools. Understanding the role of microbes in school environments has implications for public health policies and educational practices, aiming to create healthier and more conducive learning environments for the younger generation. By comprehensively exploring this topic, this review contributes to a broader understanding of the significance of microbes in promoting health and immune function in school settings and its relevance to future health research.},
}

@article {pmid41853515,
year = {2024},
author = {, and Barberio, D},
title = {Navigating regulatory and analytical challenges in live biotherapeutic product development and manufacturing.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1441290},
pmid = {41853515},
issn = {2813-4338},
abstract = {The recent FDA approvals of Rebyota™ and Vowst™ represent landmark milestones within the burgeoning field of live microbiota-based products. Future microbiota-based treatment approaches also hold significant promise for treating patients with a myriad of diseases and disorders, yet substantial hurdles hinder their development and utilization. Foremost, existing regulatory frameworks governing live biotherapeutic product (LBP) manufacturing development have notable gaps, requiring comprehensive expansion and refinement. Along with regulatory challenges, hurdles remain in the optimization and validation of analytical methodologies essential for characterizing LBPs, including for microbial identification, potency, and bioburden. To address these challenges, Microbiome Therapeutics Innovation Group (MTIG) spearheaded collaborative efforts, engaging industry leaders and the FDA in discussions aimed at catalyzing improvements in LBP analytics and refining the current regulatory landscape. Extrapolating on feedback from these discussions, this review highlights challenges and identifies critical gaps. Specific recommendations for future regulatory guidance are proposed, as are recommendations for interactions that developers can take now with regulatory agencies to support the development of maturing guidance. Key analytical factors to consider in LBP development are reviewed, highlighting strengths and weaknesses of various methodologies. Collaboration among regulatory and government agencies, industry, and academia, facilitated by coalitions like MTIG, will be instrumental in ushering the microbiota-based therapeutics field into the next phase of approvals and advancements, ultimately benefiting patients.},
}

@article {pmid41853517,
year = {2024},
author = {Dalman, MR and Simison, WB and Nielsen, D and Bhatta, S and Ramahi, N and Yee, C and Thapaliya, D and Kadariya, J and Cheatham, S and Olson, H and Smith, TC},
title = {Staphylococcus aureus carriage is associated with microbiome composition in the nares and oropharynx, not the hand, of monozygotic twins.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1457940},
pmid = {41853517},
issn = {2813-4338},
abstract = {BACKGROUND: Staphylococcus aureus is a gram-positive bacterium commonly found in the nares and oropharynx of one in three individuals and has the potential to cause significant health problems. With antibiotic-resistant strains causing 11,000 deaths yearly and ~2% of the population nasally colonized with methicillin-resistant S. aureus, a search for predictive markers and associative relationships between carriage have been long-sought goals. Within our study, we leveraged monozygotic twin participants in concert with multi-site microbiome analyses to characterize the impacts of S. aureus on composition.

RESULTS: We recruited 147 monozygotic twin pairs and characterized three sites, i.e., the nares, oropharynx, and hand microbiomes, using 16S rRNA v3-v4 sequencing in addition to S. aureus carriage status. The prevalence of S. aureus was highest in the oropharynx followed by nares and hand with concordance between twin pairs highest in the nares, followed by oropharynx. The detection of S. aureus was statistically correlated with differences in microbiome composition across sites, as indicated by beta diversity and DESeq2 analyses. Microbiome composition was most similar in twins' nares that were S. aureus culture-positive concordant, whereas twins that were culture-negative concordant had the most similarity in the oropharynx. Of significance, Moraxella nonliquefacians and Capnocytophaga were inversely associated with S. aureus in the nares and oropharynx, respectively.

CONCLUSIONS: This improved understanding of S. aureus colonization in nares, oropharynx, and hand microbiomes in monozygotic twin pairs is a further step towards unraveling the degree to which the microbiome is influenced by host genetics and S. aureus carriage.},
}

@article {pmid41853520,
year = {2024},
author = {Fu, X and Norbäck, D and Sun, Y},
title = {Editorial: Environmental microbiomes, metabolites, and respiratory diseases.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1388525},
doi = {10.3389/frmbi.2024.1388525},
pmid = {41853520},
issn = {2813-4338},
}

@article {pmid41853521,
year = {2024},
author = {Curtis-Joseph, N and Peterson, R and Brown, CE and Beekman, C and Belenky, P},
title = {Mouse diet and vendor impact microbiome perturbation and recovery from early-life pulses of amoxicillin.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1432202},
pmid = {41853521},
issn = {2813-4338},
abstract = {The gut microbiome is a dynamic ecosystem shaped by various factors, including diet, sex, and environment. This system plays a crucial role in host health, such that perturbation in the form of antibiotics can lead to a vast array of negative outcomes. Accordingly, a growing body of work seeks to develop interventions to protect the microbiome during antibiotic exposure. While it is well established that antibiotics can disrupt the microbiome in the short term, how the impact of antibiotics is modulated by factors such as diet, sex, and environment is poorly understood. In this study, we analyzed how sex, diet and early life environment (vendor of origin) modulate the impact and recovery of the microbiome in mice treated with oral amoxicillin. Utilizing 16S rRNA gene sequencing and bioinformatic analyses, we looked at the microbiome response to antibiotics under high-sugar and high-fat (Western) and standard high-fiber mouse (Chow) diets in male and female C57BL/6 from Jackson Laboratory, and female mice from Charles River Laboratories. The microbiome composition of each set of mice had a distinct pre-antibiotic starting point, depending on vendor, sex, and diet. These differences were further exacerbated by antibiotic exposure and revealed that each group responded differently to this perturbation. In particular, we found that the Western diet microbiome had an exacerbated response to antibiotics with greater changes in alpha, and beta diversity, and microbial composition when compared to the antibiotic-treated Chow diet cohort. In particular, we detected blooms in Enterobacteriaceae, Streptococcaceae, and Peptostreptococcaceae that were not found in the Chow diet. The response to antibiotics on each diet also appeared to be vendor and sex dependent. Charles River female mice had less Bifidobacteriaceae, Clostridia_UCG.014, and Clostridiaceae compared to Jackson Laboratory females in a Western diet, while female mice had more Bacteroides, Bilophila, and Parasutterella compared to male mice. In a narrow sense, these findings underscore the importance of considering vendor source, diet, and sex when examining antibiotics' impact on mice. The broader implications suggest that we will likely need to utilize patient-specific microbiome-informed approaches in the development of human therapeutics to safeguard the microbiome during antibiotic exposure.},
}

@article {pmid41853522,
year = {2024},
author = {Rusling, M and Karim, A and Kaye, A and Lee, CJ and Wegman Points, L and Mathis, V and Lampeter, T and Yuan, LL},
title = {Influences of Ruminococcus bromii and Peptostreptococcaceae on voluntary exercise behavior in a rodent model.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1389103},
pmid = {41853522},
issn = {2813-4338},
abstract = {INTRODUCTION: This study investigates the relationship between the gut microbiome and voluntary exercise, focusing on wheel running activity in a rat model. The gut microbiome plays a crucial role in host physiology, homeostasis, and behavior. Alterations in the gut microbiome have been linked to various pathological states and health conditions, including obesity.

METHODS: Given the strong association between physical inactivity and obesity development, our study aimed to identify microbiome factors associated with elevated levels of voluntary exercise. Male Sprague Dawley rats were used in the 4-week exercise paradigm in which voluntary wheel running behavior was monitored alongside weekly microbiome sampling from fecal pellets.

RESULTS: We observed individual differences in running activity among the cohort. Significant positive correlations in running distance were identified across the 4-week time course, suggesting that running activity ranking was largely preserved. Furthermore, earlier running activity emerged as a potential predictor for subsequent running behaviors. Analysis of gut microbiome revealed that alpha diversity was positively correlated with daily running distances, with significant differences in beta diversity observed between high and low running groups. Taxonomic analysis showed distinct abundance differences between running and sedentary conditions, particularly in the Ruminococcaceae and Peptostreptococcaceae families.

DISCUSSION: Our results suggest that the microbiome composition changes significantly early in exercise exposure, potentially influencing exercise behavior. Ruminococcaceae, particularly R. bromii, was identified as a significant contributor to exercise adaptation, while Peptostreptococcaceae was inversely related to running performance as well as alpha diversity. This study underscores the potential of the gut microbiome as a modulator of exercise behavior. Future research should focus on the biological mechanisms linking microbiome changes to exercise adaptation, with R. bromii and Peptostreptococcus as promising candidates for influencing exercise behaviors through future interventional studies.},
}

@article {pmid41853523,
year = {2024},
author = {Kirsch, MR and Smith, SN and Becker, DJ and Watters, JL and Marske, KA and Siler, CD and Lanier, HC},
title = {Family shapes microbiome differences in Oklahoma salamanders.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1277645},
pmid = {41853523},
issn = {2813-4338},
abstract = {INTRODUCTION: Given the role of microbiomes in promoting host health and homeostasis, understanding the factors shaping skin microbial communities in wild vertebrates has become increasingly important in conservation. This goal is even more pressing for amphibians, for which the skin has multiple critical functions, and pathogens currently decimating populations are linked to significant changes in skin microbiomes. However, because microbiomes are also shaped by environmental and ecological influences, as well as by host phylogeny, it is important to quantify these contributions to microbiome structure in the presence of infection.

METHODS: To understand the joint influence of these diverse factors shaping microbiomes, we used 16S rRNA sequencing to characterize the skin microbial communities of six salamander species (families Plethodontidae and Salamandridae) found in Oklahoma and contrasted the effects of infection status, phylogeny, host ecology, and host environment (i.e., climate) on skin microbiomes.

RESULTS: Differences at the level of host family were the main factor influencing microbiome diversity; however, we did not detect a substantial phylogenetic signal. Instead, host ecology and environment were more important in driving microbiome differences among species and genera. Salamanders that tested positive for the skin fungal parasite Batrachochytrium dendrobatidis (Bd) also had slightly less diverse microbiomes than Bd-free animals, but no such differences were associated with the systemic pathogen ranavirus (RV).

DISCUSSION: Together, these results indicate a nuanced relationship between the number and type of microbes present on salamander skin and the factors influencing them. By developing a baseline assessment of the microbiome diversity and richness present on the skin of these focal species, this work also provides a foundation for monitoring and evaluating changes in skin microbiomes as populations continue to experience stressors and diseases.},
}

@article {pmid41853525,
year = {2024},
author = {Gaber, M and Arnone, AA and Vidi, PA and Cook, KL},
title = {The microbiome: a link between obesity and breast cancer risk.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1394719},
pmid = {41853525},
issn = {2813-4338},
abstract = {Globally, breast cancer is the leading cause of cancer incidence and mortality among all female cancers. Hereditary factors only account for 5-10% of breast cancers, highlighting the importance of non-hereditary factors, such as obesity. The increasing prevalence of obesity underscores the need to understand its contribution to breast cancer risk. Multiple mechanisms may mediate pro-carcinogenic effects of obesity, including altered adipokine levels, local and systemic inflammation, disruption of insulin and insulin-like growth factor signaling, increased estrogen levels, and alterations of the microbiome. In this review, we focus on the link between gut microbiome alterations and breast cancer risk in the context of obesity. First, we discuss how obesity influences the gut microbiome. Next, we describe the effect of such microbiome alterations on breast carcinogenesis, highlighting underlying molecular mechanisms. Finally, we review preclinical data on the interactions between host and bacteria, current challenges to study the obesity-microbiome connection, and future perspectives in this field.},
}

@article {pmid41853527,
year = {2024},
author = {Zorgani, A and Das, BC},
title = {Exploring the memory of the gut microbiome: a multifaceted perspective.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1363961},
pmid = {41853527},
issn = {2813-4338},
}

@article {pmid41853528,
year = {2024},
author = {Kane, LP and Van Bonn, WG and Oliaro, FJ and Edwardson, CF and Smith, M and Pinnell, LJ},
title = {Transport from the wild rapidly alters the diversity and composition of skin microbial communities and antifungal taxa in spring peeper frogs.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1368538},
pmid = {41853528},
issn = {2813-4338},
abstract = {Amphibians are routinely collected from the wild and added into managed care and public display facilities; however, there is a gap in understanding how these practices might alter the diversity and composition of skin microbial communities on these animals. The aim of this study was to evaluate and compare skin microbial communities of spring peeper frogs (Pseudacris crucifer) from acquisition in the wild through the end of their quarantine period and identify microbial taxa with antifungal properties. From an original group of seventy-six frogs, cohorts of ten were swabbed when acquired in the wild, upon transport from the wild, and swabbed throughout a 9-week quarantine period while under managed care. An immediate loss of microbial richness and diversity was evident upon transfer of the frogs from their original environment and continued throughout subsequent sampling time-points during quarantine. Importantly, antifungal taxa comprised significantly more of the overall skin community after the frogs were moved from the wild, largely due to members of the family Moraxellaceae. Overall, our findings demonstrate that amphibian skin microbiome changes immediately on removal from the wild, and that these changes persist throughout quarantine while being housed under managed care. This may play a pivotal role in the development of dermatological disease and have implications in the health and immune function of amphibians.},
}

@article {pmid41853529,
year = {2024},
author = {Huttelmaier, S and Shuai, W and Sumner, JT and Hartmann, EM},
title = {Phage communities in household-related biofilms correlate with bacterial hosts.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1396560},
pmid = {41853529},
issn = {2813-4338},
abstract = {The average American spends 93% of their time in built environments, almost 70% of that is in their place of residence. Human health and well-being are intrinsically tied to the quality of our personal environments and the microbiomes that populate them. Conversely, the built environment microbiome is seeded, formed, and re-shaped by occupant behavior, cleaning, personal hygiene and food choices, as well as geographic location and variability in infrastructure. Here, we focus on the presence of viruses in household biofilms, specifically in showerheads and on toothbrushes. Bacteriophage, viruses that infect bacteria with high host specificity, have been shown to drive microbial community structure and function through host infection and horizontal gene transfer in environmental systems. Due to the dynamic environment, with extreme temperature changes, periods of wetting/drying and exposure to hygiene/cleaning products, in addition to low biomass and transient nature of indoor microbiomes, we hypothesize that phage host infection in these unique built environments are different from environmental biofilm interactions. We approach the hypothesis using metagenomics, querying 34 toothbrush and 92 showerhead metagenomes. Representative of biofilms in the built environment, these interfaces demonstrate distinct levels of occupant interaction. We identified 22 complete, 232 high quality, and 362 medium quality viral OTUs. Viral community richness correlated with bacterial richness but not Shannon or Simpson indices. Of quality viral OTUs with sufficient coverage (614), 532 were connected with 32 bacterial families, of which only Sphingomonadaceae, Burkholderiaceae, and Caulobacteraceae are found in both toothbrushes and showerheads. Low average nucleotide identity to reference sequences and a high proportion of open reading frames annotated as hypothetical or unknown indicate that these environments harbor many novel and uncharacterized phage. The results of this study reveal the paucity of information available on bacteriophage in indoor environments and indicate a need for more virus-focused methods for DNA extraction and specific sequencing aimed at understanding viral impact on the microbiome in the built environment.},
}

@article {pmid41853531,
year = {2024},
author = {Smith, A and Ghori, NU and Foster, R and Nicol, MP and Barnett, T and Pickering, J and Whelan, A and Strunk, T and Wood, F and Raby, E and Fear, M and Weston, S and Campbell, AJ and Hoyne, GF and Bowen, AC},
title = {Optimisation of the sampling method for skin microbiome studies in healthy children: a pilot cohort study.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1446394},
pmid = {41853531},
issn = {2813-4338},
abstract = {INTRODUCTION: Recent interest in the diverse ecosystem of bacteria, fungi and viruses that make up the skin microbiome has led to numerous studies investigating the skin microbiome in healthy skin and in dermatological conditions. However, skin microbiome analysis is challenging due to relatively low numbers of skin microorganisms compared to mucosal sites, such as the respiratory or gastrointestinal tracts. Microbiome results are heavily influenced by sampling methods. Previous sampling methods include that of cotton swabs, tape stripping, patch sampling and punch biopsies. It is essential to have a standardised sampling method for microbiome studies to have comparable results between studies. Two non-invasive methods of sampling the skin microbiome; a skin scraping versus a flocked swab were chosen as methodologies likely to be efficient, effective, and easy to access for future skin microbiome studies in children. Here we compare the two sampling methods to describe the composition of the skin microbiome in healthy children.

METHOD: Samples were collected from six healthy children aged three to nine years from the skin overlying the cubital fossa, cheek and axilla using (i) flocked swabs and (ii) skin scrapings with a glass slide. Samples were collected from the left and right sides of the body at two separate time points, one week apart. Quantitative PCR of the gene encoding 16S ribosomal ribonucleic acid (rRNA) was performed to compare the bacterial load collected by each sampling method. Full-length 16S rRNA gene amplicon sequencing was performed to compare the relationship of sampling method and time with the diversity and ecology of bacteria between different body sites.

RESULTS: From six children, 78 flocked swabs and 78 skin scraping samples were collected, along with details of their overall health and skin care practices. qPCR results indicated higher total bacterial load from flocked swabs compared with skin scrapings. Flocked swabs and skin scraping methods had very similar bacterial compositional profiles. The skin microbiome was diverse between individuals and remained relatively stable within individuals over time.

DISCUSSION: Overall, results were similar between sample types, however bacterial DNA yield was higher for flocked swab samples (compared to skin scraping methods) and with a simpler protocol is the preferred sampling method for future studies.},
}

@article {pmid41853532,
year = {2024},
author = {Wei, Y and Zhou, C},
title = {Bacteriophages: a double-edged sword in the gastrointestinal tract.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1450523},
pmid = {41853532},
issn = {2813-4338},
abstract = {The symbiotic relationship between the gut microbiome and the human body is a concept that has grown in popularity in recent years. Bacteriophages (phages) are components of the gut microbiota and their imbalance plays a role in the pathogenesis of numerous intestinal disorders. Meanwhile, as a new antimicrobial agent, phage therapy (PT) offers unique advantages when compared with antibiotics and brings a new dawn for treatment of multidrug-resistant bacteria in intestinal and extraintestinal disorders. In this review, we provide a brief introduction to the characterization of phages, particularly focusing on newly discovered phages. Additionally, we outline the involvement of gut phages in disease pathogenesis and discuss the status and challenges of utilizing phages as therapeutic targets for treatment of enteric infection.},
}

@article {pmid41853533,
year = {2024},
author = {Liu, Z and Shen, Y and Fu, Y and Sun, D and Li, L and Lv, Z},
title = {Association of resistome abundance with hyperuricaemia in elderly individuals: a metagenomics study.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1384703},
pmid = {41853533},
issn = {2813-4338},
abstract = {INTRODUCTION: Hyperuricaemia (HUA), one of chronic diseases, has an increased prevalence and is related to diseases such as gout, arthritis, infectious diseases, etc. Antimicrobial resistance (AMR) in the gut is considered as an atypical chronic disease, and poses risk to human health. The gut microbiome has been proved to be a reservoir for AMR and play an important role in HUA patients. The microbial characteristics of the gut in individuals with HUA have been previously explored, however, the characteristics of the resistome in individuals with HUA have remained largely unexplored.

METHODS: Thus, we investigated the landscape of the AMR in individuals with HUA and without HUA, and the potentially influential factors in a case-control study using metagenomics-based approaches.

RESULTS: We found that drinking juice and abnormal stool were risk factors associated with HUA. The taxonomic diversity of gut microbiota in individuals with HUA was lower than that in non-HUA individuals. Notably, a higher abundance and diversity of the resistome (entire antimicrobial resistance genes) was observed in individuals with HUA (median: 1.10 vs. 0.76, P = 0.039, U-test), especially in tetracycline resistance genes (median: 0.46 vs. 0.20, P < 0.001, U-test), which are associated with more complex mobile genetic elements (MGEs) in individuals with HUA. Furthermore, we found that a higher abundance of the resistome was positively correlated with uric acid (UA) levels and affected by several host-associated factors (mainly dietary habits). Specifically, pork consumption and the consumption of root and tuber vegetables were identified as contributing factors. We also found a higher abundance of virulence genes (VGs), mostly related to adherence, antimicrobial activity, competitive advantage, and exoenzymes, in the gut microbial community of individuals with HUA.

DISCUSSION: All findings revealed higher activity of the resistome and pathogenicity of the microbiota in individuals with HUA, indicating a higher health risk in the elderly HUA population.},
}

@article {pmid41853538,
year = {2024},
author = {Valeriano, VD and Lahtinen, E and Hwang, IC and Zhang, Y and Du, J and Schuppe-Koistinen, I},
title = {Vaginal dysbiosis and the potential of vaginal microbiome-directed therapeutics.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1363089},
pmid = {41853538},
issn = {2813-4338},
abstract = {A healthy vaginal microbiome (VMB) is dominated by Lactobacillus spp. and provides the first line of defense against invading pathogens. Vaginal dysbiosis, characterized by the loss of Lactobacillus dominance and increase of microbial diversity, has been linked to an increased risk of adverse genital tract diseases, including bacterial vaginosis, aerobic vaginitis, vulvovaginal candidiasis, sexually transmitted infections, and pregnancy complications such as preterm birth. Currently, antibiotics and antifungals are recommended first-line treatments with high cure rates, but they also can lead to high recurrence and resistance development. As an alternative, lactobacilli have been utilized to restore the vaginal microbiota. In this review article, we discuss vaginal dysbiosis in various gynecological infections and potential interventions based on Live Biotherapeutic Products (LBPs) with a focus on those that use intravaginal treatment modalities to modulate the VMB. Based on these, we provide insights on key factors to consider in designing phenotypic and genotypic screens for selecting bacterial strains for use as vaginally administered microbiome-directed therapeutics. Lastly, to highlight current progress within this field, we provide an overview of LBPs currently being developed with published clinical trial completion for recurrent BV, VVC, and UTI. We also discuss regulatory challenges in the drug development process to harmonize future research efforts in VMB therapy.},
}

@article {pmid41853539,
year = {2024},
author = {Chandel, N and Gorremuchu, JP and Thakur, V},
title = {Antimicrobial resistance burden, and mechanisms of its emergence in gut microbiomes of Indian population.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1432646},
pmid = {41853539},
issn = {2813-4338},
abstract = {INTRODUCTION: The human gut microbiome harbors millions of bacterial species, including opportunistic pathogens, and this microbial community is exposed to antimicrobial agents present in food, the external environment, or drugs. Thus, it increases the risk of commensals being enriched with resistant genes, which may get even transmitted to opportunistic pathogens often with the help of mobile genetic elements. There is limited information about the current burden of resistant genes in the healthy gut microbiome of the Indian population, the latter is not only the largest in the world but is also periodically monitored for the prevalence of antibiotic resistance in clinical samples.

METHODS: We analyzed publicly available fecal whole-metagenome shotgun sequencing data from 141 samples from three healthy Indian cohorts for antimicrobial-resistance burden, and their likely transmission modes.

RESULTS: The overall resistance profile showed a higher number of resistance genes against tetracycline, glycopeptide, and aminoglycoside. Out of a total of 188 antimicrobial resistance genes identified in all cohorts, moderately to highly prevalent ones could potentially target seven of the 'reserve' group antibiotics (colistin, fosfomycin, Polymyxin). We also observed that geographical location affected the prevalence/abundance of some of the resistance genes. The higher abundance of several tetracycline and vancomycin resistance genes in tribal cohorts compared to the other two urban locations was intriguing. Species E. coli had the highest number of resistant genes, and given its relatively modest abundance in gut microbiomes can pose a risk of becoming a hub for the horizontal transfer of resistance genes to others. Lastly, a subset of the resistance genes showed association with several types of mobile genetic elements, which potentially could facilitate their transmission within the gut community.

DISCUSSION: This is a first systematic report on AMR genes in healthy gut microbiome samples from multiple locations of India. While trends for several of the prevalent AMR genes showed similarity with global data, but a few population specific trends need further attention by policy-makers. The association of AMR genes with mobile elements may pose a risk for transmission to other gut bacteria.},
}

@article {pmid41853540,
year = {2024},
author = {Kaye, A and Rusling, M and Dhopeshwarkar, A and Kumar, P and Wagment-Points, L and Mackie, K and Yuan, LL},
title = {Microbiome variations induced by delta9-tetrahydrocannabinol predict weight reduction in obese mice.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1412468},
pmid = {41853540},
issn = {2813-4338},
abstract = {INTRODUCTION: Obesity and high-fat diets induce consistent alterations in gut microbiota composition. Observations from epidemiological reviews and experiments also illustrate weight regulation effects of delta9-tetrahydrocannabinol (THC) with microbiome shifts. Therefore, we investigated the weight-loss potential of THC in obese mice models and to elucidate the contribution of specific gut microbiome changes in THC-induced weight loss.

METHODS: High-fat diet induced obese mice were treated with oral THC supplementation for two weeks and compared with controls. In addition to measuring weight, fecal samples were obtained at various timepoints, sequenced for bacterial 16s rRNA content and analyzed using QIIME2. Alpha and beta diversity were computed followed by linear mixed effects (LME) modeling of bacterial relative abundance relationship to THC treatment and weight change.

RESULTS: In both male and female mice, the THC group had significantly greater average weight loss than controls (-17.8% vs. -0.22%, p<0.001 and -13.8% vs. +2.9%, p<0.001 respectively). Male mice had 8 bacterial taxonomic features that were both significantly different in relative abundance change over time with THC and correlated with weight change. An LME model using three bacterial features explained 76% of the variance in weight change with 24% of variation explained by fixed effects of feature relative abundance alone. The model also accurately predicted weight change in a second male mouse cohort (R=0.64, R[2]=0.41, p=<0.001). Female mice had fewer significant predictive features and were difficult to model, but the male-produced 3-feature model still accurately predicted weight change in the females (R=0.66, R[2]=0.44, p<0.001).

CONCLUSION: Using a stepwise feature selection approach, our results indicate that sex-specific gut microbiome composition changes play some role in THC-induced weight loss. Additionally, we illustrated the concept of microbiome feature-based modeling to predict weight changes.},
}

@article {pmid41853542,
year = {2024},
author = {Daharsh, L and Lohani, SC and Ramer-Tait, AE and Li, Q},
title = {Characterization of double humanized BLT-mice with stable engraftment of a human gut bacterial microbiome.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1404353},
pmid = {41853542},
issn = {2813-4338},
abstract = {Humanized mice with human-like immune systems are commonly used to study immune responses to human-specific pathogens. However, one limitation of using humanized mice is their native murine gut microbiota, which significantly differs from that in humans. Given the importance of the gut microbiome to human health, these differences may profoundly impact the ability to translate results from humanized mouse studies to humans. Further, there is a critical need for improved pre-clinical models to study the complex in vivo relationships of the gut microbiome, immune system, and human disease. We previously created double humanized mice with a functional human immune system and a stable, human-like gut microbiome. Here, we characterized the engrafted human gut bacterial microbiome in our double humanized mouse model generated by transplanting fecal material from healthy human donors into the gut of humanized mice. Analysis of bacterial microbiomes in fecal samples from double humanized mice revealed they had unique 16S rRNA gene profiles consistent with those of the individual human donor samples. Importantly, transplanted human-like gut microbiomes were stable in mice for the duration of the study, extending up to 14.5 weeks post-transplant. Microbiomes of double humanized mice also harbored predicted functional capacities that more closely resembled those of the human donors than humanized mice. In conclusion, our study highlights the successful engraftment of human fecal microbiota in BLT humanized mice and underscores the stability of this model, offering a valuable platform for investigating the intricate interplay among the human gut microbiome, immune system, and various diseases in vivo.},
}

@article {pmid41853546,
year = {2024},
author = {Bailey, A and Hogue, S and Pierce, CM and Paul, S and La Fuente, N and Thapa, R and Kim, Y and Robinson, LA},
title = {Metagenomic characterization of the tracheobronchial microbiome in lung cancer.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1457537},
pmid = {41853546},
issn = {2813-4338},
abstract = {BACKGROUND: The tracheobronchial and oral microbiome may be associated with lung cancer, potentially acting as predictive biomarkers. Therefore, we studied the lung and oral bacteriome and virome in non-small cell lung cancer (NSCLC) patients compared to melanoma controls to discover distinguishable features that may suggest lung cancer microbial biomarkers.

METHODS: In this pilot case-control study, we recruited ten patients with early-stage NSCLC (cases) and ten age-matched melanoma patients (controls) who both underwent tumor resection. Preoperative oral gargles were collected from both groups, who then underwent transbronchoscopic tracheal lavage after intubation. Lung tumor and adjacent non-neoplastic lung were sterilely collected after resection. Microbial DNA from all lung specimens underwent 16S rRNA gene sequencing. Lavage and gargle specimens underwent whole-genome shotgun sequencing. Microbiome metrics were calculated to compare both cohorts. T-tests and Wilcoxon rank sum tests were used to test for significant differences in alpha diversity between cohorts. PERMANOVA was used to compare beta diversity.

RESULTS: No clear differences were found in the microbial community structure of case and control gargles, but beta diversity of case and control lavages significantly differed. Two species, Granulicatella adiacens and Neisseria subflava, which are both common oral commensal organisms, appeared in much higher abundance in case versus control lavages. Case lavages also maintained higher relative abundances of other oral commensals compared to controls.

CONCLUSIONS: Lung lavages demonstrated oral microbiota enrichment in cases compared to controls, suggesting microaspiration and resultant inflammation. The oral commensals Granulicatella adiacens and Neisseria subflava were more abundant in the tracheobronchial lavages of lung cancer versus melanoma patients, implicating these microorganisms as potential lung cancer biomarkers, warranting further validation studies.},
}

@article {pmid41853547,
year = {2024},
author = {Giongo, A and Arnhold, J and Grunwald, D and Smalla, K and Braun-Kiewnick, A},
title = {Soil depths and microhabitats shape soil and root-associated bacterial and archaeal communities more than crop rotation in wheat.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1335791},
pmid = {41853547},
issn = {2813-4338},
abstract = {The plethora of microorganisms inhabiting the immediate vicinity of healthy root systems plays a pivotal role in facilitating optimal nutrient and water acquisition by plants. In this study, we investigated the soil microbial communities associated with wheat roots within distinct microhabitats, root-affected soil (RA), rhizosphere (RH), and rhizoplane (RP). These microhabitats were explored at five soil depths, and our investigation focused on wheat cultivated in a monoculture (WM) and wheat crop rotation (WR). Overall, there were significant differences in microbiota composition between WM and WR, although no difference in bacterial diversity was observed. Differentially abundant taxa between WM and WR were observed in all three microhabitats, emphasizing important insights on the localization of commonly associated bacteria to wheat roots. Comparing the microhabitats, RP exhibited the most dissimilar microbial composition between WM and WR. Taxa that were differentially abundant between WM and WR were observed in the three microhabitats. The high relative abundance of taxa belonging to the phylum Proteobacteria in the rhizoplane, such as Devosia, Pseudomonas, Shinella, and Sphingomonas, along with other genera, such as Pedobacter (Bacteroidota), Agromyces and Streptomyces (Actinobacteriota) highlight the recruitment of potentially beneficial bacterial taxa to the vicinity of the roots. Interestingly, these taxa were observed along the entire length of wheat roots, even at depths of up to 120 cm. The presence of specific taxa associated with wheat roots at all soil depths may be beneficial for coping with nutrient and water shortages, particularly under upcoming climate scenarios, where water may be a limiting factor for plant growth. This study provides valuable insights for designing management strategies to promote a diverse and healthy microbial community in wheat cropping systems, considering soil depth and microhabitats as key factors. Although, at this time, we cannot link specific bacterial taxa to yield reductions commonly observed in monocultural fields, we propose that some genera may enhance plant nutrient or water acquisition in rotation compared with monoculture. Advanced technologies, including functional analyses and culturomics, may further enhance our understanding of the ecological roles played by these microbes and their potential applications in sustainable agriculture.},
}

@article {pmid41853549,
year = {2024},
author = {Mahmoudabadi, G and Homyk, K and Catching, AB and Mahmoudabadi, A and Foley, HB and Tadmor, AD and Phillips, R},
title = {Machine learning models can identify individuals based on a resident oral bacteriophage family.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1408203},
pmid = {41853549},
issn = {2813-4338},
abstract = {Metagenomic studies have revolutionized the study of novel phages. However these studies trade depth of coverage for breadth. We show that the targeted sequencing of a small region of a phage terminase family can provide sufficient sequence diversity to serve as an individual-specific barcode or a "phageprint'', defined as the relative abundance profile of the variants within a terminase family. By collecting ~700 oral samples from ~100 individuals living on multiple continents, we found a consistent trend wherein each individual harbors one or two dominant variants that coexist with numerous low-abundance variants. By tracking phageprints over the span of a month across ten individuals, we observed that phageprints were generally stable, and found instances of concordant temporal fluctuations of variants shared between partners. To quantify these patterns further, we built machine learning models that, with high precision and recall, distinguished individuals even when we eliminated the most abundant variants and further downsampled phageprints to 2% of the remaining variants. Except between partners, phageprints are dissimilar between individuals, and neither country-of-residence, genetics, diet nor cohabitation seem to play a role in the relatedness of phageprints across individuals. By sampling from six different oral sites, we were able to study the impact of millimeters to a few centimeters of separation on an individual's phageprint and found that such limited spatial separation results in site-specific phageprints.},
}

@article {pmid41853551,
year = {2024},
author = {Uzoigwe, CE},
title = {Gut eutrophication.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1481250},
pmid = {41853551},
issn = {2813-4338},
abstract = {"Classical eutrophication" occurs when raw unfixed nutrients enter an aquatic environment. This causes the deleterious proliferation in fauna most adept at exploiting this abundance of nutrition. The net effect is de-diversification. We propose an analogous process in the gut: "gut eutrophication". Evidence shows that consumption of processed food, high in unfixed disaccharides, causes an expansion of bacteria in the gut habitat with a metabolic proclivity for these nutrients. This is at the expense of microbiota with a predilection for complex macromolecule macronutrients. There is a loss of diversity and the effect is exacerbated by a sedentary lifestyle. Gut luminal low oxygen tension favors salubrious gut commensals. This effect is potentiated by exercise but thwarted by inactivity. Antibiotics cause an obvious gut dysbiosis. So too can diet in a more insidious manner. The transition in microbial composition, seen in "gut eutrophication", may be an aetiological component of metabolic disease-associated gut dysbiosis.},
}

@article {pmid41853553,
year = {2024},
author = {Gupta, D and Sarkar, A and Pal, Y and Suthar, V and Chawade, A and Kushwaha, SK},
title = {Bovine reproductive tract and microbiome dynamics: current knowledge, challenges, and its potential to enhance fertility in dairy cows.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1473076},
pmid = {41853553},
issn = {2813-4338},
abstract = {The cattle production system focuses on maintaining an animal-based food supply with a lower number of cattle. However, the fecundity of dairy cows has declined worldwide. The reproductive tract microbiome is one of the important factors which can influence bovine fecundity. Therefore, reproductive tract microbiomes have been explored during the estrus cycle, artificial insemination, gestation, and postpartum to establish a link between the micro-communities and reproductive performance. These investigations suggested that microbial dysbiosis in the reproductive tract may be associated with declined fertility. However, there is a scarcity of comprehensive investigations to understand microbial diversity, abundance, shift, and host-microbiome interplay for bovine infertility cases such as repeat breeding syndrome (RBS). This review summarizes the occurrence and persistence of microbial taxa to gain a better understanding of reproductive performance and its implications. Further, we also discuss the possibilities of microbiome manipulation strategies to enhance bovine fecundity.},
}

@article {pmid41853555,
year = {2024},
author = {Ferro, LE and Bittinger, K and Trudo, SP and Beane, KE and Polson, SW and Kim, JK and Trabulsi, JC},
title = {A short-term, randomized, controlled, feasibility study of the effects of different vegetables on the gut microbiota and microRNA expression in infants.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1342464},
pmid = {41853555},
issn = {2813-4338},
abstract = {The complementary diet influences the gastrointestinal (gut) microbiota composition and, in turn, host health and, potentially, microRNA (miRNA) expression. This study aimed to assess the feasibility of altering the gut microbial communities with short-term food introduction and to determine the effects of different vegetables on the gut microbiota and miRNA expression in infants. A total of 11 infants were randomized to one of the following intervention arms: control, broccoli, or carrot. The control group maintained the milk diet only, while the other groups consumed either a broccoli puree or a carrot puree on days 1-3 along with their milk diet (human milk or infant formula). Genomic DNA and total RNA were extracted from fecal samples to determine the microbiota composition and miRNA expression. Short-term feeding of both broccoli and carrots resulted in changes in the microbiota and miRNA expression. Compared to the control, a trend toward a decrease in Shannon index was observed in the carrot group on days 2 and 4. The carrot and broccoli groups differed by weighted UniFrac. Streptococcus was increased on day 4 in the carrot group compared to the control. The expression of two miRNAs (i.e., miR-217 and miR-590-5p) trended towards decrease in both the broccoli and carrot groups compared to the control, whereas increases in eight and two different miRNAs were observed in the carrot and broccoli groups, respectively. Vegetable interventions differentially impacted the gut microbiota and miRNA expression, which may be a mechanism by which total vegetable intake and variety are associated with reduced disease risk.},
}

@article {pmid41853558,
year = {2024},
author = {Pannoni, SB and Holben, WE},
title = {Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1274277},
pmid = {41853558},
issn = {2813-4338},
abstract = {Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA-simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.},
}

@article {pmid41853703,
year = {2024},
author = {Ellis, JR and Powell, EJ and Tomasovic, LM and Marcheskie, RL and Girish, V and Warman, A and Sivaloganathan, D},
title = {Changes in the Skin Microbiome Following Dermatological Procedures: A Scoping Review.},
journal = {Applied microbiology (Basel, Switzerland)},
volume = {4},
number = {2},
pages = {972-985},
pmid = {41853703},
issn = {2673-8007},
support = {T32 GM136577/GM/NIGMS NIH HHS/United States ; },
abstract = {The skin microbiome consists of bacteria, fungi, viruses, and mites, which play a crucial role in maintaining skin health and immune function. Imbalances in this microbial community, known as dysbiosis, are implicated in various dermatological conditions. While skincare products are known to influence the skin microbiome, the effects of dermatological procedures have not been extensively studied. Here, we perform a scoping review to outline the studies investigating the impacts of dermatological interventions on the skin microbiome. Phototherapy emerged as the most studied intervention, encompassing UV phototherapy, light therapy, laser therapy, and photodynamic therapy. Chemical interventions, such as chemical peels, micropigmentation, and debridement, have comparatively limited studies describing their impacts on the skin microbiome. To date, no studies have been done on a wide variety of common dermatological procedures such as cryotherapy, skin grafts, and dermabrasion, which may have stronger likelihoods of affecting the skin microbiome. This underscores the need for further research on the influences of dermatological procedures, especially chemical and physical interventions, on the skin microbiome. More comprehensive pre-clinical and clinical studies are essential not only for understanding the long-term consequences of these procedures, but also for optimizing patient outcomes in dermatological care.},
}

@article {pmid41853869,
year = {2026},
author = {Abedin, ZU and Shah, A and Mazhar, S and Khan, SM and Aamir, AB and Yousaf, S and Fnu, D and Mahato, RK and Ansari, A},
title = {Lactobacillus-Based Microbiome Therapy for Acne Vulgaris: A GRADE Systematic Review and Meta-Analysis of Randomized Controlled Trials.},
journal = {Journal of cosmetic dermatology},
volume = {25},
number = {3},
pages = {e70792},
pmid = {41853869},
issn = {1473-2165},
mesh = {Humans ; *Acne Vulgaris/therapy/microbiology ; *Probiotics/administration & dosage/adverse effects/therapeutic use ; Randomized Controlled Trials as Topic ; *Lactobacillus ; Treatment Outcome ; Benzoyl Peroxide/therapeutic use/administration & dosage ; *Microbiota ; Administration, Oral ; },
abstract = {BACKGROUND: Acne vulgaris is one of the most prevalent disorders affecting 9%-10% of the global population, representing as papules, pustules, and comedones, with a pathogenesis involving increased sebum production, C. acnes colonization, and inflammation. Conventional treatments like retinoids and antibiotics often cause side effects, thus diverting attention toward probiotics as an alternative therapy. Lactobacillus probiotics, having their immunomodulatory, anti-inflammatory, and antimicrobial properties, are useful in managing acne by reducing inflammation and oxidative stress with proved safety profile and the potential to reduce antibiotic reliance. This systematic review and meta-analysis evaluate the efficacy of Lactobacillus-based probiotics compared to placebo and benzoyl peroxide in reducing inflammatory lesions, non-inflammatory lesions, and total acne lesion counts. The findings aim to clarify their therapeutic role and provide evidence on their effectiveness and safety.

OBJECTIVES: This systematic review and meta-analysis investigated the effectiveness of oral and topical Lactobacillus-based probiotics or postbiotics, compared with placebo or benzoyl peroxide, in patients with acne vulgaris.

METHODS: A systematic review and meta-analysis of randomized controlled trials (RCTs) was conducted, including studies evaluating oral or topical Lactobacillus-based probiotic or postbiotic interventions in patients with acne vulgaris. Primary outcomes were changes in inflammatory lesion counts, while secondary outcomes included non-inflammatory and total lesion counts, skin hydration, and sebum concentration. All analyses were performed using random-effects models with 95% confidence intervals (CI), and heterogeneity was quantified using the I[2] statistic.

RESULTS: A total of five RCTs involving 332 participants were included. The pooled mean difference for non-inflammatory lesions was -1.39 (95% CI -5.10 to 2.32, p = 0.46), for inflammatory lesions was -0.08 (95% CI -1.28 to 1.11, p = 0.89), and for total lesion counts was -9.07 (95% CI -20.71 to 2.57, p = 0.13). These results concluded that there was no significant reduction in lesion counts with Lactobacillus-based probiotics as compared to placebo or benzoyl peroxide. Heterogeneity was moderate to low across studies.

CONCLUSION: This meta-analysis indicates that Lactobacillus-based probiotics do not provide significant clinical benefits in reducing inflammatory lesions, non-inflammatory lesions, and total acne lesion counts in Acne vulgaris patients compared to placebo or benzoyl peroxide.},
}

Humans
*Acne Vulgaris/therapy/microbiology
*Probiotics/administration & dosage/adverse effects/therapeutic use
Randomized Controlled Trials as Topic
*Lactobacillus
Treatment Outcome
Benzoyl Peroxide/therapeutic use/administration & dosage
*Microbiota
Administration, Oral

@article {pmid41853881,
year = {2026},
author = {Picariello, E and De Nicola, F},
title = {Unveiling the Hidden Drivers: How Vegetation Cover, Season and Forest Management Shape the Soil Microbial Community in Two Mediterranean Forest Ecosystems.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70255},
doi = {10.1111/1758-2229.70255},
pmid = {41853881},
issn = {1758-2229},
support = {//Fondo di Ricerca di Ateneo FRA 2023/ ; },
mesh = {*Soil Microbiology ; *Forests ; Seasons ; *Bacteria/classification/genetics/isolation & purification ; Fungi/classification/isolation & purification/genetics ; Biodiversity ; Ecosystem ; Quercus/growth & development ; *Microbiota ; Fagus/growth & development ; Mediterranean Region ; Turkey ; Soil/chemistry ; },
abstract = {Soil provides essential ecosystem services and serves as a habitat for biodiversity, but it is often affected by disturbances from management practices and seasonal changes, which can alter its microbial communities. This study investigated the combined effects of dominant vegetation, forest management, and seasonal variation on soil microbial communities and enzyme activity over one year in turkey oak and beech forests managed as high forest or coppice. Results showed that the dominant vegetation type had a greater influence on microbial communities than seasonal changes. While forest management did not significantly affect microbial activity, it altered microbial community composition. In beech forests, bacterial communities (at the order level) showed relative abundances higher in soil under high forest with respect to coppice, whereas the fungal community showed orders most abundant under coppice management with respect to the high forest. Forest management changed the relative abundances of microbial communities, but it did not remarkably affect microbial community functions and, thus, the associated ecosystem services. Our results highlight that the forest type should be considered when evaluating forest management. This study offers new insights into the factors influencing the composition of soil microbial communities and their associated ecosystem functions.},
}

*Soil Microbiology
*Forests
Seasons
*Bacteria/classification/genetics/isolation & purification
Fungi/classification/isolation & purification/genetics
Biodiversity
Ecosystem
Quercus/growth & development
*Microbiota
Fagus/growth & development
Mediterranean Region
Turkey
Soil/chemistry

@article {pmid41853994,
year = {2026},
author = {Yang, Q and Aghdam, R and Tran, PQ and Anantharaman, K and Solís-Lemus, C},
title = {Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70245},
doi = {10.1111/1758-2229.70245},
pmid = {41853994},
issn = {1758-2229},
support = {506328//A Community Science Program New Investigator award/ ; //Natural Science and Engineering Research Council of Canada (NSERC)/ ; DBI-2047598//National Science Foundation/ ; DEB-2144367//National Science Foundation/ ; Hatch 1025641//USDA National Institute of Food and Agriculture/ ; //University of Wisconsin-Madison/ ; //Joint Genome Institute/ ; //Office of Science/ ; },
mesh = {*Ecosystem ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Metagenome ; *Lakes/microbiology ; *Fresh Water/microbiology ; Metagenomics ; Transcriptome ; },
abstract = {Freshwater lakes are dynamic ecosystems, with varying oxygen dynamics that influence microbiome structure, composition, and transcriptomic activity. In many freshwater studies, ecological function and abundance metrics are used to discover keystone species; however, it is well established that abundance does not equal activity. Despite the existence of long-term time series spanning multiple years, no previous study has looked at how microbial community and activity (metatranscriptomics) are influenced by shifting oxygen conditions across depths at the microbial network level. In this study, we leverage metagenome-assembled genomes and transcriptomic activity to identify keystone taxa in the ecosystem. Using the SPIEC-EASI and CARlasso methods, we mapped key microbial associations and used permutation-based analyses to assess the robustness of keystone identification. Our results reveal that a taxon's ecological centrality is context-dependent and that many species identified as keystone by abundance alone do not exhibit corresponding transcriptional activity. Notably, members of Bacteroidota and other lineages emerged as keystone taxa only when both abundance and activity were considered. Our study underscores the importance of combining metagenomic and metatranscriptomic approaches for accurate identification of functionally relevant keystone species in freshwater ecosystems, providing a framework for future microbial ecology studies.},
}

*Ecosystem
*Bacteria/genetics/classification/isolation & purification/metabolism
*Microbiota/genetics
Metagenome
*Lakes/microbiology
*Fresh Water/microbiology
Metagenomics
Transcriptome

@article {pmid41854082,
year = {2026},
author = {Park, N and Lee, B and Jeon, HJ and Yeon Kim, J and Park, S and Kim, SE and Lee, DK and Lee, Y},
title = {Inulin-Butyrate Nanogel for Modulation of Gut Microbiome, Intestinal Barrier, and Regulatory T-Cells in Colitis.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e13252},
doi = {10.1002/smll.202513252},
pmid = {41854082},
issn = {1613-6829},
support = {//National Research Foundation of Korea/ ; RS-2023-00265981//Ministry of Health & Welfare, Republic of Korea/ ; },
abstract = {Inflammatory bowel diseases (IBD) arise from a vicious cycle of intestinal barrier dysfunction, gut microbiome dysbiosis, and dysregulated immune responses. Current therapies predominantly suppress immunity but fail to address root causes or break this cycle. While inulin, a prebiotic, restores microbial diversity and enables colon-targeted drug delivery, they lack specificity for inflamed tissue. On the other hand, even though butyrate, a microbial metabolite, is a potent enhancer of intestinal barrier integrity and anti-inflammatory Treg cell differentiation, their clinical applications are limited by rapid systemic absorption, impractical dosing, and unpleasant odor. To address these limitations, we have developed an inulin-butyrate conjugate-based nanogel (IBN) which is capable of targeted modulation of gut microbiome, intestinal barrier, and immune systems in colitis. In dextran sodium sulfate (DSS)-induced colitis mice, IBN specifically accumulates in the inflamed colon and released high amounts of butyrate via gut microbial enzymes (inulinase/esterase). The inulin shell improved the gut microbiome, while the released butyrate enhances intestinal barrier functions and promotes Treg differentiation, yielding robust therapeutic activity. Taken together, IBN addresses the multifactorial nature of IBD, offering a biocompatible, transformative strategy to disrupt the disease cycle and restore gut homeostasis.},
}

@article {pmid41854140,
year = {2026},
author = {Adamová, Z and Filová, M and Tisančinová, J and Chrostek, M and Slováček, R},
title = {Probiotics and synbiotics in perioperative care for colorectal surgery - a future component of the ERAS protocol?.},
journal = {Rozhledy v chirurgii : mesicnik Ceskoslovenske chirurgicke spolecnosti},
volume = {105},
number = {2},
pages = {75-79},
doi = {10.48095/ccrvch202675},
pmid = {41854140},
issn = {0035-9351},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Synbiotics/administration & dosage ; *Perioperative Care/methods ; *Postoperative Complications/prevention & control ; Digestive System Surgical Procedures ; *Colorectal Surgery ; },
abstract = {INTRODUCTION: Colorectal surgery is associated with a high risk of postoperative complications, particularly infections. In recent years, the role of the microbiome in this context has been increasingly discussed. Probiotics and synbiotics are being investigated as potential tools for modulating the microbial environment and improving surgical outcomes.

AIM: This review article summarizes the available evidence from randomized con-trolled trials, meta-analyses, and systematic reviews evaluating the effects of probiotics and synbiotics on the incidence of complications and postoperative recovery in patients undergoing colorectal surgery. Current studies indicate that the administration of probiotics and synbiotics may reduce the risk of infectious complications, modulate systemic inflammatory responses, accelerate the restoration of bowel function, and shorten the duration of antibiotic therapy. Data regarding their impact on anastomotic leakage remain limited. The intervention appears to be well tolerated and safe.

CONCLUSION: Perioperative administration of probiotics or synbiotics represents a promising and cost-effective intervention in colorectal surgery. However, larger and more standardized trials are required to prove the effect, determine the optimal composition, dosage, and duration of therapy before routine clinical implementation.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
*Synbiotics/administration & dosage
*Perioperative Care/methods
*Postoperative Complications/prevention & control
Digestive System Surgical Procedures
*Colorectal Surgery

@article {pmid41854146,
year = {2026},
author = {Guo, X and Zhao, J},
title = {Multidisciplinary advances in oral health management in patients with systemic lupus erythematosus: a comprehensive review.},
journal = {Quintessence international (Berlin, Germany : 1985)},
volume = {0},
number = {0},
pages = {0},
doi = {10.3290/j.qi.b6961709},
pmid = {41854146},
issn = {1936-7163},
abstract = {Systemic lupus erythematosus (SLE) is a complex chronic autoimmune disease that can affect multiple organ systems, including the skin, joints, kidneys and oral cavity. In recent years, there has been growing interest in the oral health of patients with SLE, with studies showing that the incidence of dental caries, periodontal disease, oral mucosal lesions and salivary dysfunction is significantly higher in patients with SLE than in the general population. Factors such as immune system abnormalities, long-term use of glucocorticoids and immunosuppressants, and dysbiosis of the oral microbiome all contribute to an increased oral disease burden in patients with SLE. Oral health problems affect not only patients' nutritional intake, social interactions and self-esteem but may also create an inflammatory feedback loop exacerbating the underlying systemic condition. A multidisciplinary management approach involving rheumatology, dentistry and psychological support - with more refined and individualised strategies for prevention, treatment and follow-up - is crucial for patients with SLE. This review distinguishes itself from prior syntheses by systematically integrating the pivotal role of nursing teams within the multidisciplinary framework, and proposing actionable, structured protocols for assessment, referral, and long-term follow-up. Future research should focus on exploring the interaction between the oral microbiome and immune response mechanisms and strive to develop more effective interventions and standardised diagnostic and treatment protocols to improve the oral health and overall quality of life of patients with SLE.},
}

@article {pmid41854347,
year = {2026},
author = {Perry, EK and Hasnain, A and Cole, BJ and Carlson, HK and Deutschbauer, AM and Chiniquy, D},
title = {Methane-fed microbial communities enriched from field-grown rice support diverse heterotrophic bacteria.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag023},
pmid = {41854347},
issn = {1574-6941},
abstract = {Rice paddies naturally host methane-oxidizing bacteria known as methanotrophs, due to the production of methane in flooded soils. Enhancing the activity of native methanotrophs could improve the sustainability of rice cultivation, but knowledge of how this could impact other members of the rice microbiome remains incomplete. To gain insight into which members of the rice microbiome might benefit from increased methanotrophic activity, we passaged 51 aerobic microbial enrichment cultures from rice rhizosphere and tissue samples in a chemically-defined medium with methane as the primary carbon source and electron donor. We profiled the cultures over time by 16S rRNA gene amplicon sequencing and sequenced the genomes of 44 isolates to gain functional insights. Taxa whose relative abundance increased during community growth on methane represented more than a dozen families, many of which are not known to utilize one-carbon substrates. Several of the enriched genera have not previously been linked to methane cycling in rice fields, and genomic analysis of the sequenced isolates revealed considerable variation in predicted carbon source utilization and nitrogen cycling capabilities. Together, these findings broaden the understanding of how aerobic methanotrophs may impact microbiome assembly and nutrient cycling in rice paddies.},
}

@article {pmid41854352,
year = {2026},
author = {Joseph, J and Patnaik, SK and Abraham, D and Mathew, J and Alexander, J},
title = {Gut and oral microbiota characterized in systemic lupus erythematosus patients from India: A pilot study.},
journal = {Lupus},
volume = {},
number = {},
pages = {9612033261432163},
doi = {10.1177/09612033261432163},
pmid = {41854352},
issn = {1477-0962},
abstract = {Introduction: Systemic lupus erythematosus (SLE) is a multifaceted autoimmune disorder influenced both intrinsically by immune cell alterations, genetic factors, and the microbiome, as well as extrinsically by environmental factors. Methods: In this pilot study, we investigated the role of various peripheral immune cells (CD3[+], CD4[+], CD8[+], CD4[+]/CD8[+], CD4-/CD8-, NK cells (CD16[+]CD56[+]), and CD19[+]) and the gut and salivary microbiota in patients with SLE, comparing these factors to healthy controls. Results and Discussion: Results showed significant alterations in the proportions of CD4[+] and CD8[+] T cells in SLE patients, with an inverse correlation between these subsets. Additionally, the CD4[+] ratio was found to be elevated in SLE. CD4[+] T cells were strongly correlated with double-negative T cells, while CD8[+] T cells correlated with NK cells. Metagenomic shotgun sequencing of fecal and salivary samples revealed a disruption in the microbiome, particularly the taxa Pasteurellaceae and Veillonella, which were altered in both the gut and oral microbiomes of SLE patients. These changes suggest that there may be overlap in the composition and function of these microbial populations across different body sites. Dysbiosis was observed in both the gut and oral microbiomes of individuals with SLE, distinguishing them from healthy controls. Conclusion: Our findings highlight specific microbiome alterations in SLE patients and suggest that microbiome composition could serve as a potential exploratory tool for diagnosing and prognosticating the disease in larger, adequately powered cohorts.},
}

@article {pmid41854449,
year = {2026},
author = {Xing, N and Hu, J and Bao, G and Zhang, X and Huo, X and Wen, Y and Li, X and Tang, Y and Liu, W},
title = {Toxicity of Polystyrene Nanoplastics and Tributyl Phosphate to Rye under Freeze-Thaw Cycles: Implications for Crop Safety and Mechanistic Insights from Transcriptome and Root Microbiome.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14574},
pmid = {41854449},
issn = {1520-5118},
abstract = {Climate-driven freeze-thaw (FT) cycles amplify the combined toxicity of polystyrene nanoplastics (PS) and tributyl phosphate (TBP) in crops. TBP is a common plasticizer. Our multiomics study reveals that PS and TBP form complexes via van der Waals forces, enhancing PS uptake in rye roots. Coexposure induces severe oxidative stress (H2O2: 1.35-, 4.71-fold → 9.04-fold), suppresses photosynthesis, and activates antioxidant defenses, with FT conditions intensifying these effects. TBP restructures the root endophytic microbiome, enriching TBP-degrading bacteria (Acidovorax, Massilia). Transcriptomic analysis identifies jasmonic and abscisic acid (ABA) signaling pathways as central coordinators of plant defense through reactive oxygen species (ROS) scavenging and metabolic reprogramming. These findings demonstrate that FT cycles exacerbate NPs-plasticizer toxicity through three interconnected mechanisms: physicochemical complex formation, root microbiome remodeling, and hormonal signaling crosstalk. The study provides crucial mechanistic insights for assessing climate-pollution risks in cold-region agriculture, highlighting the need to consider pollutant interactions under dynamic environmental conditions.},
}

@article {pmid41854509,
year = {2026},
author = {Jayamanna Mohottige, MW and Peel, E and Juhász, A and Nye-Wood, MG and Belov, K and Colgrave, ML and Hogg, CJ},
title = {Characterisation of pouch secretions from breeding Tasmanian devils.},
journal = {Reproduction (Cambridge, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/reprod/xaag024},
pmid = {41854509},
issn = {1741-7899},
abstract = {Tasmanian devils (Sarcophilus harrisii), like all marsupials, give birth to altricial young. Here we employ proteomic analysis to identify components of devil pouch secretions that may contribute to offspring survival and development. Proteins were extracted from five samples and analysed by liquid chromatography-tandem mass spectrometry. Peptide-level evidence revealed proteins involved in a diverse set of immune pathways, including those mediating iron-ion transport, defence responses to bacteria, innate immune responses, and antigen processing. A core set of 200 proteins was identified across at least three samples, 63 of which were associated with antimicrobial or immunoregulatory functions. These included immunoglobulins, components of complement and coagulation cascade, and antimicrobial proteins and peptides. These findings provide preliminary evidence that the Tasmanian devil's pouch secretions could be involved in microbiome restructuring during lactation through their immune protein content. Moreover, the data indicate that these proteins may act synergistically in pathways triggered by immune challenges or physiological stress.},
}

@article {pmid41854749,
year = {2026},
author = {Balafif, F and Wardhana, DW and Nazwar, TA and Balafif, F and Panjaitan, C and Kholipah, AN and Mustofa, },
title = {Gut microbiota modulation as an adjuvant therapy to improve treatment response and survival in brain tumor patients: a systematic review.},
journal = {Neurosurgical review},
volume = {49},
number = {1},
pages = {},
pmid = {41854749},
issn = {1437-2320},
}

@article {pmid41855162,
year = {2026},
author = {Armijos Briones, M and Ayala Aguirre, PE and Benitez Sellan, PL and Lanata-Flores, A and Marcillo-Toala, O and Rumbea, DA and Mera, RM and Del Brutto, OH},
title = {Study protocol: Dental and periodontal characteristics of older adults in Atahualpa, Ecuador within the Atahualpa Project cohort.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0337166},
pmid = {41855162},
issn = {1932-6203},
mesh = {Humans ; Ecuador/epidemiology ; Aged ; Male ; Cross-Sectional Studies ; Female ; Middle Aged ; *Oral Health ; *Periodontal Diseases/epidemiology ; Aged, 80 and over ; Gingival Crevicular Fluid ; Cohort Studies ; Cone-Beam Computed Tomography ; },
abstract = {This study protocol describes an observational, cross-sectional investigation of oral health in community-dwelling older adults from Atahualpa, a rural village in Ecuador, embedded within the long-standing Atahualpa Project cohort. Using a door-to-door survey approach, all registered residents aged ≥60 years (n = 410) will be invited to participate. Participants will attend twice weekly at the School of Dentistry of University through six coordinated stations: The first station will include a general oral diagnosis and the collection of general participant data using the unique Atahualpa project identifier. The second station will record the periodontal clinical examination according to the AAP/EFP 2018 clinical guidelines. In addition, subgingival biofilm sampling will be performed for 16S rRNA sequencing and gingival crevicular fluid for multiplex cytokine profiling. The third station will obtain high-resolution digital models through an intra-oral scanning (IOS) for dental morphometrics. The fourth station will record a cone-beam computed tomography (CBCT) to support periodontal charting, and complementary structural findings. The fifth station will indicate dental treatments: restorations, root canals, extractions, and prosthesis using computer-aided design and computer-aided manufacturing (CAD/CAM). Finally, the last station will perform an oral health education: oral health promotion and structured questionnaires such as the Geriatric Oral Health Assessment Index (GOHAI), the European Health Literacy Survey-16 (HLS-EU-Q16) (in its Spanish version) and the Short Health Literacy Screen (BHLS). Primary objectives are to quantify associations between periodontitis severity, microbial composition, and local inflammatory profiles with neurocognitive and neuroimaging outcomes already available in the cohort (total MoCA and a composite cerebral small vessel disease score), controlling. Therefore, this protocol addresses the research question of whether, in older adults residing in the Atahualpa community, greater periodontitis severity is associated with lower neurocognitive performance and a higher burden of cerebral small vessel disease on neuroimaging within the existing cohort. It also examines whether the composition of the subgingival microbiome and cytokine profiles in gingival crevicular fluid correlate with periodontal severity and are related to these cerebral outcomes. Furthermore, it describes three-dimensional dental morphology (including features derived from ASUDAS for comparison with published Pima frequencies) to clarify whether there is similarity between the two ethnic groups.},
}

Humans
Ecuador/epidemiology
Aged
Male
Cross-Sectional Studies
Female
Middle Aged
*Oral Health
*Periodontal Diseases/epidemiology
Aged, 80 and over
Gingival Crevicular Fluid
Cohort Studies
Cone-Beam Computed Tomography

@article {pmid41855263,
year = {2026},
author = {Dutta, S and Mahen, KK and Massey, WJ and Varadharajan, V and Burrows, AC and Horak, AJ and Mrdjen, M and Mouannes, N and Orabi, D and Osborn, LJ and Grubb, T and Hohe, RC and Banerjee, R and Uppin, V and Laungani, D and Hamilton, GE and Ye, X and Sangwan, N and Dwidar, M and Hajjar, AM and Willard, B and Martin, M and Guetschow, E and Westcott, P and McMullen, MR and Nagy, LE and Wang, Z and Hazen, SL and Brown, JM},
title = {Gut microbe-derived N-acyl serinol lipids shape host postprandial metabolic homeostasis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {12},
pages = {e2517314123},
doi = {10.1073/pnas.2517314123},
pmid = {41855263},
issn = {1091-6490},
support = {R01 DK130227/DK/NIDDK NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; P50 AA024333/AA/NIAAA NIH HHS/United States ; RF1 NS133812/NS/NINDS NIH HHS/United States ; 24POST1178494//American Heart Association (AHA)/ ; N/A//Cleveland Clinic (CC)/ ; S10 OD030398/CD/ODCDC CDC HHS/United States ; R01 HL179780/HL/NHLBI NIH HHS/United States ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Postprandial Period/physiology ; *Homeostasis ; Animals ; Humans ; Mice ; Male ; *Lipids/chemistry ; Amides/metabolism ; Lipid Metabolism ; Mice, Inbred C57BL ; Bacteria/metabolism ; },
abstract = {Although strong evidence links the gut microbiome to metabolic disease, the mechanisms linking microbiota to hormonal and metabolic responses to food are not well understood. After a meal, gut bacteria produce a wide array of small molecule, protein, and lipid metabolites originating from bacterial sources. Attributing physiological function to select gut microbe-derived metabolites is critical to understanding diet-microbe-host interactions, and to developing microbiome-inspired therapies to improve human health. Here, we have investigated the role of a poorly annotated class of gut microbiome-derived lipids called N-acyl amides in postprandial metabolic physiology. Here, we show that both bacterial production and provision of exogenous N-acyl amides reorganize host hormone-driven metabolic transition after a meal. Moreover, N-acyl amides exert broad effects on the meal- and circadian-related reorganization of gene expression, metabolic hormones, and gut microbiome composition. Collectively, these results demonstrate that microbiota-derived N-acyl amides play a physiologic role in postprandial metabolic homeostasis in the host.},
}

*Gastrointestinal Microbiome/physiology
*Postprandial Period/physiology
*Homeostasis
Animals
Humans
Mice
Male
*Lipids/chemistry
Amides/metabolism
Lipid Metabolism
Mice, Inbred C57BL
Bacteria/metabolism

@article {pmid41855730,
year = {2026},
author = {Mudiyanselage, HH and Ali, A and Farooq, M and Ghaffar, A and Waduge, LW and Gomis, SM and Niu, YD and Abdul-Careem, MF},
title = {Probiotic-driven microbiota shifts confer the resistance to infectious bronchitis virus infection in poultry.},
journal = {Veterinary microbiology},
volume = {316},
number = {},
pages = {110986},
doi = {10.1016/j.vetmic.2026.110986},
pmid = {41855730},
issn = {1873-2542},
abstract = {Infectious bronchitis virus (IBV) is an economically significant viral infection in commercial broilers. Despite vaccination, outbreaks are still reported due to the emergence of new IBV variants. Probiotics, particularly strains of Lactobacillus, have been shown to help mitigate various disease outbreaks and exhibit strong immunomodulatory effects, especially in the respiratory tract. A study was conducted to understand the effect of a cocktail of Lactobacillus and a commercial probiotic on respiratory and gastrointestinal microbiome shifts in 6, 9 and 15 days post-infection (dpi) following IBV infection in commercial broilers. In general the virus-challenged group without any probiotics showed significantly higher (p = 0.0488) histopathological lesion scores compared to both probiotics treated groups prior to the IBV challenge. Cecum alpha diversity in Lactobacillus supplemented group prior to infection showed significantly higher (p < 0.05) diversity and evenness compared to the group supplemented with Lactobacillus only in all the considered time points, whereas the group supplemented with commercial probiotics prior to viral challenge showed significantly lower (p < 0.05) diversity compared to commercial probiotics only group at 15 dpi. Beta diversity analysis in cecum indicated both Lactobacillus supplemented and commercial probiotics supplemented prior to infection developed a significantly different (p < 0.05) and distinct microbial composition compared to all the other groups. According to differential abundance analysis, IBV infection was shown to favor the abundance of Lactobacillus in cecum. Commercial probiotics supplemented prior to the infection showed despite initial dysbiosis, dominant bacteria were able to get restored at 15 dpi in both cecum and trachea. Functional analysis in the cecum and trachea depicted that although Lactobacillus supplemented prior to infection showed more stress and proliferation in the initial time point, all the groups have more similar pathways at the later stage in the cecum but in the trachea, the group supplemented with Lactobacillus prior to infection was still showing transition to more colonization focused state. The study outcome adds to the understanding of respiratory and gastrointestinal microbiome shifts in a lengthier time period in probiotics supplemented broilers prior to IBV infection.},
}

@article {pmid41855966,
year = {2026},
author = {Zhang, J and Ip, JC and Hamed, M and Lee, JS and Mo, J},
title = {A review on antibiotic use in tilapia farming: Pharmacokinetics, impacts, and potential health risks.},
journal = {Marine pollution bulletin},
volume = {228},
number = {},
pages = {119582},
doi = {10.1016/j.marpolbul.2026.119582},
pmid = {41855966},
issn = {1879-3363},
abstract = {The rapid expansion of global aquaculture has propelled tilapia to become the third most widely farmed freshwater fish species worldwide, valued for its rapid growth, remarkable adaptability and economic value. However, the improper use of antibiotics, including misuse, overuse, and prophylactic application has posted multi-scale risks to health and ecological security, underscoring the urgent need for a comprehensive evaluation. This review aims to: (1) clarify the current status of antibiotic use in tilapia farming, covering major categories, administration methods, practical dose ranges, and international regulatory disparities, with emphasis on overuse and irrational drug combinations; (2) elucidate the pharmacokinetic behavior of antibiotics in tilapia (e.g., absorption, distribution, metabolism, and excretion), focusing on tissue-specific residue patterns and bioaccumulation; (3) systematically assess the direct toxicological impacts of antibiotics on tilapia, encompassing physiological disturbances, metabolic toxicity, immune suppression, gut microbiota dysbiosis and mechanisms of antimicrobial resistance induction; (4) reveal the ecological perturbations caused by antibiotics in aquaculture environments, including disruptions to microbial communities, degradation of essential ecological functions and the emergence and transmission of antibiotic resistance genes; (5) investigate the potential human health risks associated with food-chain bioaccumulation, including dietary exposure, allergic responses, gut microbiome imbalance, and promotion of resistant pathogens in humans. Overall, this review provides evidence to support rational antibiotic-use guidelines, improved residue monitoring and antimicrobial resistance surveillance, and the development of safer alternatives to promote sustainable aquaculture.},
}

@article {pmid41856032,
year = {2026},
author = {Caetta, A and Aasen, D and Adamcyzk, P and Yuan, H and Zhou, Y and Roberts, D and Grindle, C and Schoem, S and Hughes, A},
title = {Characterizing the microbiome of the middle ear using 16S RNA sequencing in pediatric patients with and without middle ear effusions requiring ventilation tubes.},
journal = {International journal of pediatric otorhinolaryngology},
volume = {204},
number = {},
pages = {112798},
doi = {10.1016/j.ijporl.2026.112798},
pmid = {41856032},
issn = {1872-8464},
}

@article {pmid41856106,
year = {2026},
author = {Yuan, S and Zhu, H and Yu, M and Jia, H and Peng, S and Ma, Y},
title = {Discovery of human gut phage-encoded anti-CRISPR proteins unveils diverse mechanisms for phages to evade type II CRISPR immunity.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.02.017},
pmid = {41856106},
issn = {1934-6069},
abstract = {Phages encode diverse anti-CRISPR (Acr) proteins to counteract bacterial CRISPR-Cas systems. However, gut phage Acrs remain poorly characterized. Using an integrated bioinformatics and high-throughput functional screening approach, we identify 651 phage-encoded positive Acr candidates that target type II CRISPR systems, which predominate in the human gut. Among these, a subset of Acrs is verified through plasmid interference assays, with plaque assays confirming CRISPR-Cas inhibitory activity for 36 Acr candidates. Mechanistic characterization of five Acrs, including the Acr against subtype II-B systems (AcrIIB-1), reveals distinct inhibition strategies. Remarkably, 213 positive Acr candidates, designated here as GutAcraca, exhibit structural convergence by adopting similar folds and exhibit dual functionality: transcription regulation to support their production and inhibition of CRISPR-Cas systems. These GutAcraca are widely distributed across microbial species (detected in 26% of species). Our work uncovers the extensive diversity of phage-encoded Acrs in the human gut and highlights their potential as biotechnology tools.},
}

@article {pmid41856107,
year = {2026},
author = {Potloane, D and Symul, L and Ngcapu, S and Lewis, L and France, M and Vermeren, L and Elsherbini, J and Chetty, C and Mafunda, NA and Polliah, AM and Mtshali, A and Kama, A and Magini, N and Mitchev, N and Mzobe, G and Khan, A and Demidkina, BC and Goldenberg, M and Xu, J and Rutt, L and Shirtliff, B and Cook, S and Murthy, M and Hussain, F and Passmore, JS and Jaspan, HB and Kullin, B and Happel, AU and Liebenberg, L and Relman, DA and Holmes, S and Kwon, DS and Ravel, J and Mitchell, CM},
title = {VIBRANT: A phase 1 randomized trial of multi-strain vaginal L. crispatus live biotherapeutic products in people with bacterial vaginosis.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.02.016},
pmid = {41856107},
issn = {1934-6069},
abstract = {Bacterial vaginosis (BV) is characterized by high microbial diversity. High recurrence rates following antibiotics may stem from poor recolonization by protective Lactobacillus species. This phase 1 randomized trial in the United States and South Africa evaluated two vaginally delivered live biotherapeutic products (LBPs) containing multiple Lactobacillus crispatus strains. After metronidazole treatment for BV, participants received either a placebo or 3 or 7 days of active LBPs. LBP strains were detected by metagenomics in 66.1% (47/71) of participants in the active arms in the first 5 weeks. Among those, nearly half (49%, 23/47) remained colonized at 12 weeks despite the short initial treatment course. Participants were most often colonized by one of three component strains, with no geographic differences in strain colonization observed. LBPs were safe, acceptable, and well tolerated, with no serious adverse events (AEs) reported. These results provide a foundation for the development of transformational interventions aimed at optimizing the vaginal microbiome.},
}

@article {pmid41856218,
year = {2026},
author = {Wu, YH and Wang, LC},
title = {Establishment and utilization of striped catfish skin epithelial cell line to study host-pathogen interaction.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {111280},
doi = {10.1016/j.fsi.2026.111280},
pmid = {41856218},
issn = {1095-9947},
abstract = {The scaleless striped catfish (Pangasianodon hypophthalmus) is an economically important aquaculture species but is frequently infected by Aeromonas hydrophila (AH), causing substantial economic losses. Fish skin mucosa plays a protective role by initiating inflammatory responses to AH challenge. However, how the skin epithelial cells, the outermost defensive layer of skin tissue, respond and interact with AH remains unknown. This study aims to establish a skin epithelial cell line from striped catfish and investigate the response of skin epithelial cells under AH challenge. Skin epithelial cells were isolated and subcultured at optimal temperature and serum concentration, and epithelial properties were confirmed by the epithelial marker cytokeratin. The established skin epithelial cell line was inoculated with or without AH to evaluate survival and immune responses. We found cells survived at a tissue-damaging concentration of AH and showed an extremely higher immune response. Moreover, the presence of mucus and its microbiome may regulate AH-induced immune response, suggesting a complexity of skin-AH interaction in vivo. In conclusion, this study successfully established a striped catfish skin epithelial cell line and utilized it to characterize the outermost skin epithelial responses to AH in the presence of the mucus microbiome. By employing this cell line, new insights into epithelial-level immune interactions with pathogens were provided.},
}

@article {pmid41856288,
year = {2026},
author = {Pudlo, NA and Pereira, GV and Schaus, SR and Yang, Q and Fuentes, JJ and Jin, C and Hein, R and Zhang, L and Terrapon, N and Lyssiotis, CA and Schmidt, TM and Hansson, GC and Luis, AS and Martens, EC},
title = {The butyrate-producing Gram-positive human gut bacterium, Hoskinsella mucinilytica, selectively targets host mucin N-acetylhexosamines.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {111371},
doi = {10.1016/j.jbc.2026.111371},
pmid = {41856288},
issn = {1083-351X},
abstract = {The personalized microbial communities (micobiota) that inhabit the distal guts of humans have evolved to process a variety of complex carbohydrates. Many gut bacteria depolymerize and ferment dietary fiber polysaccharides, mutualistically providing short-chain fatty-acids and other metabolites to their host. Some human gut bacteria have evolved to utilize components of host mucin glycoproteins-the major component of secreted mucus that protects the gut. Recent studies have implicated certain mucin-degrading bacteria in the development of intestinal inflammation, making identification of new gut bacteria that possess the ability to degrade mucins an important goal. We used gastric mucin to isolate a novel bacterium, Hoskinsella mucinilytica, that is largely restricted to using the N-acetylglucosamine and N-acetylgalactosamine sugars found in the O-linked glycans appended to secreted mucin. This butyrate-producing bacterium accesses these sugars from both polymeric gastric mucin and chemically released oligosaccharides. It also has a genome with correspondingly restricted carbohydrate-active enzyme content with only three demonstrated mucin-degrading glycoside hydrolase enzymes belonging to families GH31, 36 and 89. Surprisingly, strains with identical 16S rRNA V4 region to this isolate appear to be rare in the now numerous sequence-based microbiota surveys with only 30/7390 (0.41%) human subjects harboring detectable levels of this bacterium in their stool with an overall relative abundance ranging from 0.0004-0.013% when it is detected. This combination of low prevalence and low abundance suggests that this species could occupy an unknown niche for which access to mucin is important but otherwise renders it difficult to detect in stool-based microbiota surveys.},
}

@article {pmid41856524,
year = {2026},
author = {Janssen, KP and Basic, M and Bolsega, S and Metwaly, A and Jokisch, F and von Gamm, S and Scheiber, J and Burkhardt, R and Liebisch, G and Neuhaus, K and Brunner, S and Clavel, T and Wortmann, E and Coleman, OI and Haller, D and Bleich, A and Krautbauer, S and Ecker, J},
title = {Extrinsic lipids are absorbed and accumulate in colorectal cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336377},
pmid = {41856524},
issn = {1468-3288},
abstract = {BACKGROUND: Colorectal cancer (CRC) exhibits increased levels of arachidonic acid-derived pro-inflammatory derivatives indicating an uptake of dietary polyunsaturated fatty acids (PUFAs).

OBJECTIVE: We aimed to investigate uptake of extrinsic fatty acids (FAs) in tumours and their relevance for CRC lipid metabolism and progression.

DESIGN: Total FAs were quantified using gas chromatography-mass spectrometry in non-diseased mucosa and tumour tissue from patients with CRC of a discovery cohort (n=152), validated in an independent cohort (n=28) and associated with clinical, genomic and microbiome data. The genetic mouse tumour model Apc[1638N] was used to track the flux of stable isotope-labelled FAs in tumours from the intestinal lumen. The relationship between FA uptake and tumour progression was investigated in 2D and 3D cell models.

RESULTS: Extrinsic long chain PUFAs, including arachidonic acid, accumulate in CRC, particularly in right-sided tumours, and in tumours of Apc[1638N] mice. The CRC-specific FA profiles were independent of sex, molecular subtypes, early-disease or late-disease onset. The absorption of FAs from the intestinal lumen in tumours was confirmed in specific pathogen-free Apc[1638N] mice. In the absence of the microbiome, in germ-free Apc[1638N] mice, fewer tumours were developed, and survival was increased. Inhibition of FA import or β-oxidation reduces cancer cell proliferation.

CONCLUSION: Extrinsic FAs accumulate in CRC, verifying a central role of arachidonic acid-derived inflammatory mediators, but also suggesting a relevance of dietary FAs for cancer cell proliferation. It will be intriguing to explore to what extent targeting this flux pathway together with the interrelated microbiome opens new therapeutic avenues for CRC in humans.},
}

@article {pmid41856839,
year = {2026},
author = {Suchodolski, JS and Toresson, L},
title = {Microbiome Modulation in Veterinary Medicine: From Diet to Fecal Microbiota Transplantation.},
journal = {The Veterinary clinics of North America. Small animal practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cvsm.2026.01.009},
pmid = {41856839},
issn = {1878-1306},
abstract = {The intestinal microbiome plays a crucial role in host health. As intestinal dysbiosis can have different underlying causes, multimodal therapeutic approaches are often necessary. Dietary modulation potentially combined with fibers should be the first-line approaches in all patients with acute or chronic enteropathy and help modulate the microbiome. A subset of animals with chronic intestinal disease have marked dysbiosis that results in abnormal microbial function and reflects underlying mucosal pathology, which often persists in chronic inflammatory enteropathy. Fecal microbiota transplantation can be a useful adjunct treatment of chronic disorders, but in patients with severe dysbiosis, repeated treatments are likely needed.},
}

@article {pmid41843084,
year = {2026},
author = {Madhusoodhanan, R and Raman, K and Akbar, R and Pambayan Ulagan, M and Mariadoss Arokia, VA and P, T},
title = {Modulating gut microbiota in type 2 diabetes mellitus: advances and challenges in precision medicine.},
journal = {Acta diabetologica},
volume = {},
number = {},
pages = {},
pmid = {41843084},
issn = {1432-5233},
}

@article {pmid41843114,
year = {2026},
author = {Jabeen, M and Hameed, H and Razzaq, AA and Jamshaid, M and Shakeel, MA and Mushtaq, T},
title = {Dental caries beyond eradication: microbiome centered and equilibrium driven therapeutic strategies.},
journal = {Archives of microbiology},
volume = {208},
number = {6},
pages = {},
pmid = {41843114},
issn = {1432-072X},
}

@article {pmid41843167,
year = {2026},
author = {Shamsuzzaman, M and Dahal, RH and Kim, J},
title = {Probiotic and immune-modulatory capacities of three human gut-derived strains of Parabacteroides distasonis.},
journal = {Archives of microbiology},
volume = {208},
number = {6},
pages = {},
pmid = {41843167},
issn = {1432-072X},
mesh = {*Probiotics/pharmacology ; Humans ; Animals ; *Gastrointestinal Microbiome ; Mice ; RNA, Ribosomal, 16S/genetics ; *Bacteroidetes/genetics/isolation & purification/classification/physiology/immunology ; Macrophages/immunology ; Cytokines/metabolism ; RAW 264.7 Cells ; Phylogeny ; Antioxidants/pharmacology ; Nitric Oxide/metabolism ; },
abstract = {The human gut microbiome harbors diverse beneficial bacteria with potential roles in supporting host health. Parabacteroides distasonis has recently attracted interest as a next-generation probiotic (NGP) candidate; however, functional evidence for human-derived strains remains limited. Here, three human gut-derived P. distasonis strains (B2-S-102, B2-Q-110, and Y3-G-102) were isolated from healthy individuals and characterized using comparative genomics and in vitro functional assays. Species-level identity was supported by 16S rRNA gene analysis and whole-genome relatedness metrics (ANI > 97% and dDDH > 70%), consistent with established species delineation thresholds. Under controlled laboratory conditions, the strains showed tolerance to acidic pH (pH 2.0), bile salts (0.3%), and simulated gastric and intestinal fluids. Functionally, the strains exhibited measurable antioxidant activity (35.03 ± 7.76% to 51.22 ± 5.60% DPPH inhibition) and α-amylase inhibitory activity (51.03 ± 32.12% to 69.23 ± 4.26%) in vitro. Cell-free supernatants inhibited albumin denaturation (47.65 ± 3.56% to 65.26 ± 4.15%), while live bacteria reduced nitric oxide production and pro-inflammatory cytokines (IL-6, TNF-α, IFN-γ, and IL-1β) in LPS-stimulated RAW 264.7 macrophages (p < 0.05). The strains also displayed in vitro growth-inhibitory activity against Escherichia coli, Acinetobacter baumannii, and Salmonella enteritidis. Genome mining identified multiple biosynthetic gene clusters, indicating genetic potential for secondary metabolite production; however, expression and metabolite identity were not experimentally validated. No haemolytic activity was observed, supporting a favorable preliminary safety profile. Overall, these findings provide preliminary in vitro evidence supporting the potential of human-derived P. distasonis strains as NGP candidates for further evaluation.},
}

*Probiotics/pharmacology
Humans
Animals
*Gastrointestinal Microbiome
Mice
RNA, Ribosomal, 16S/genetics
*Bacteroidetes/genetics/isolation & purification/classification/physiology/immunology
Macrophages/immunology
Cytokines/metabolism
RAW 264.7 Cells
Phylogeny
Antioxidants/pharmacology
Nitric Oxide/metabolism

@article {pmid41843355,
year = {2026},
author = {Alum, EU and Nwachoko, N and Tufail, T and Govindarajan, RK and Alum, BN and Nwuruku, OA and Aja, PM},
title = {Gut Microbiota Resilience and Environmental Stressors: A Hidden Key to Lifespan Optimization?.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41843355},
issn = {1867-1314},
abstract = {Gut microbiota resilience, the capacity of intestinal microbial communities to resist, adapt, and recover from perturbations has emerged as a critical determinant of human health and longevity. Environmental stressors such as antibiotics, pollutants, poor diet, infections, and psychosocial stress challenge this resilience, often leading to dysbiosis (a sustained disruption of microbial community structure and/or function), impaired metabolism, chronic inflammation, and increased disease susceptibility across the lifespan. While dysbiosis has been extensively studied, the resilience dimension remains underexplored, particularly in the context of cumulative and repeated stress exposures. This narrative review explores microbial resilience, identifying environmental disruptors, and their manifestation at life stages, highlighting its hidden yet crucial role in optimizing lifespan. We critically evaluate the consequences of reduced resilience for chronic disease, frailty, and therapeutic response, while emphasizing the protective roles of diversity, functional redundancy, and host-microbe feedback loops. Translational strategies including dietary modulation, microbial therapeutics, behavioral interventions, and precision tools such as multi-omics and biosensors, are assessed for their potential to strengthen resilience and promote healthy aging. By reframing gut microbiota resilience as both a biological property and a public health target, this work advances a novel perspective: that fostering resilience may mitigate environmental insults, personalize interventions, and extend healthspan.},
}

@article {pmid41843611,
year = {2026},
author = {Zhang, WX and Du, J and Dong, L and Zhang, SS and Song, G and Ao, L and Wang, Y and Ma, L and Sun, W and Ma, J and Tian, X and Qu, B and Long, T and Chen, L and Huang, Z and Qiao, J and Zhang, Y and Li, J and Lu, X and Cui, F and Ren, X and Lu, QB},
title = {Comprehensive profiling of skin microbiome diversity and major determinants in a multi-regional Chinese population.},
journal = {Cell reports},
volume = {45},
number = {3},
pages = {117097},
doi = {10.1016/j.celrep.2026.117097},
pmid = {41843611},
issn = {2211-1247},
abstract = {The human skin microbiome is essential for health and is shaped by both host and environmental factors. To establish a nationwide baseline, we profile the skin microbiome of 1,029 Chinese individuals across three body sites (hand, axilla, and foot), four geographic regions, and four ethnic groups using 16S rRNA gene sequencing. Within each skin site, we identify two cutotypes, one of which is consistently dominated by Staphylococcus. Microbial diversity and community composition vary across body sites, geography, ethnicity, gender, and age, with geographic location emerging as the strongest source of variation and enabling accurate classification by Random Forest models. Notably, Han and minority populations within the same region exhibit greater similarity than the same ethnic group across different regions. Aging-related shifts differ by both body site and geography, reflecting interactions between physiological and environmental influences. This population-scale study provides a comprehensive reference for the Chinese skin microbiome and reveals how host and environmental factors jointly structure skin microbial communities.},
}

@article {pmid41843697,
year = {2026},
author = {Dilrukshi, N and Kottahachchi, J and Dissanayake, T and Muneeswaran, K and Fernando, N},
title = {Group B Streptococcus and Vaginal Microbiome Dynamics in Pregnancy.},
journal = {Medical principles and practice : international journal of the Kuwait University, Health Science Centre},
volume = {},
number = {},
pages = {1-23},
doi = {10.1159/000551477},
pmid = {41843697},
issn = {1423-0151},
abstract = {OBJECTIVE: This study aims to compare the vaginal microbiome of Group B Streptococcus (GBS) positive and negative pregnant women in selected tertiary care hospitals in Sri Lanka.

METHOD: Fifteen GBS-positive and fifteen GBS-negative women were included in the study. The composition of vaginal microbiome was profiled by sequencing 16S rRNA V3-V4 region. Microbiome diversity and variation were evaluated.

RESULTS: Alpha diversity measured by Shannon diversity and Chao1 index differed significantly between GBS-positive and GBS-negative groups (Chao1 p=0.0003, Shannon p=0.0003), while beta diversity Pairwise Permutational Multivariate Analysis of Variance (PERMANOVA) p=0.435) showed no significant difference, indicating similar overall bacterial compositions. Gardnerella and Prevotella were more abundant in GBS-positive group, while majority of the GBS-negative group was dominated by Lactobacillus (87.9%). Lactobacillus iners was the most abundant species in both groups. Lactobacillus gallinarum, reported for the first time in Sri Lanka, was the second most common Lactobacillus species. Linear Discriminant Analysis effect size (LEfSe) identified no taxa enriched in GBS-negative group, whereas GBS-positive group showed significantly higher relative abundance with several taxa with Bifidobacterium showed the highest linear discriminant analysis (LDA) score (4.459). Methylocystis, though of low biological relevance, was significantly abundant in GBS-positive group (p=0.025).

CONCLUSIONS: Lactobacillus spp. were reduced in GBS-positive women, with higher abundance of other bacterial taxa suggesting that disruption of a Lactobacillus dominant vaginal microbiome may facilitate GBS colonization and potentially increase the risk of neonatal infection.  .},
}

@article {pmid41843749,
year = {2026},
author = {Ribeiro, MM and Liu, C and Xu, JF and Liang, S and Goldman, GH},
title = {Pseudomonas aeruginosa adaptation and persistence in the aspergilloma microbiome revealed by integrated multi-omics.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkag063},
pmid = {41843749},
issn = {2160-1836},
abstract = {Chronic pulmonary aspergillosis involves the formation of a fungal ball (aspergilloma) in lung cavities. Pseudomonas aeruginosa commonly co-colonizes these lesions; however, the in vivo mechanisms underlying its persistence are unknown. Using a multi-omics approach on resected aspergillomas, we defined the genomic, transcriptional, and metabolic adaptations of P. aeruginosa within this polymicrobial niche. We reconstructed high-quality P. aeruginosa genomes and identified a conserved core genome, along with accessory genes for secondary metabolism, virulence, and antimicrobial resistance. Phylogenomics revealed heterogeneous evolutionary paths among co-colonizing strains. Metatranscriptomics showed stark physiological heterogeneity, from metabolically aggressive to stress-adapted states. High expression of phenazine, quorum-sensing (PQS), siderophore, and secretion-system operons was corroborated by metabolomic detection of phenazine-1-carboxylic acid and 2-heptylquinolin-4(1H)-one, confirming active bacterial antagonism in vivo. Concurrent Aspergillus fumigatus transcriptomics revealed the activation of oxidative stress responses, secondary metabolism (e.g., fumagillin), and iron scavenging, demonstrating reciprocal competition. Host transcriptomics revealed patient-specific immune signatures that correlated with the metabolic activity of the co-colonizers. This work provides an integrated systems-level analysis of the tri-kingdom aspergilloma ecosystem. P. aeruginosa persistence is driven by genomic plasticity and context-dependent expression of competitive pathways, shaped within a chronic inflammatory environment. These findings redefine aspergillomas as active polymicrobial consortia, establishing a framework for targeting resilient microbial communities in chronic lung disease.},
}

@article {pmid41844212,
year = {2026},
author = {O'Connell, KA and Celdran-Bonafonte, D},
title = {Beyond Comfort: A Review of the Critical Role of Bedding Selection in Rodent Welfare, Microenvironment, and Research Reproducibility.},
journal = {Journal of the American Association for Laboratory Animal Science : JAALAS},
volume = {},
number = {},
pages = {1-13},
doi = {10.30802/AALAS-JAALAS-25-182},
pmid = {41844212},
issn = {2769-6677},
abstract = {This review addresses the critical but often underappreciated influence of bedding selection on rodent welfare, cage microenvironment, occupational health, and research outcomes in biomedical studies. Although contact bedding is widely preferred by mice and rats and is the current industry standard, there is considerable variation in bedding type, volume, sterility, and manufacturer practices, with no established universal protocols. We synthesize over 150 publications, evaluating corncob, wood, and cellulose-based beddings with respect to their physical attributes, absorbency, ammonia management, dust and contaminant control, and support of species-typical behaviors. The review highlights methodological challenges and inconsistent results across studies, with absorbency and ammonia accumulation particularly affected by bedding mass, volume, and microbial contamination, rather than material type alone. Occupational health risks, including ergonomic strain and allergen exposure, are impacted by bedding handling frequency and composition. Animal health is generally not strongly influenced by bedding type, although pine shavings and certain corncob products present toxicity and reproductive risks in some studies. Bedding also has documented impacts on hepatic enzyme induction, neurobehavioral development, pain sensitivity assays, and gut microbiome composition, posing substantial risks for experimental confounding and compromised reproducibility. Based on the evidence, cellulose bedding is recommended for minimizing negative outcomes, but the complexity and variability inherent in bedding selection necessitate careful documentation and transparent reporting. We advocate for standardized detail in publications to ensure comparability and rigor across rodent-based research.},
}

@article {pmid41844223,
year = {2026},
author = {Graziano, M and Garbini, GL and Devigili, A and Pinzoni, L and Quagliariello, A and Bosi, E and Gasparini, C and Fondi, M and Martino, ME},
title = {From microbiome to sperm motility traits: an inside-out perspective.},
journal = {Biology letters},
volume = {22},
number = {3},
pages = {},
doi = {10.1098/rsbl.2025.0759},
pmid = {41844223},
issn = {1744-957X},
support = {//Italian Ministry of University and Research/ ; //University of Padova/ ; },
mesh = {Animals ; Male ; *Poecilia/microbiology/physiology ; *Sperm Motility/physiology ; *Microbiota ; Skin/microbiology ; Spermatozoa/physiology ; Bacteria/classification ; },
abstract = {Growing interest in the relationship between microbiome composition and host biology has revealed the many ways host-associated microbes influence physiology, ecology and evolution. However, microbial communities associated with reproductive organs-and their roles in reproduction-remain poorly understood. Here, we characterized the skin- and ejaculate-associated microbiomes in an internally fertilizing fish and tested whether microbial diversity and specific bacterial taxa correlate with sperm motility traits key for reproductive success. We used the guppy (Poecilia reticulata), a well-established model in ecology and evolutionary biology with well-characterized reproductive physiology. In guppies, sperm velocity is a validated predictor of male reproductive performance, making them a powerful system for exploring microbiome-fertility interactions. Our analyses reveal a correlation between skin microbiome diversity and sperm performance. Notably, increased skin microbiome total richness is associated with reduced sperm velocity, whereas no significant associations were detected for ejaculate-associated microbiomes. We also identified bacterial taxa across both tissues that were positively or negatively linked with sperm performance. These findings suggest that, while the ejaculate-associated microbiome may directly influence sperm traits, the skin microbiome could serve as a proxy for reproductive potential by reflecting systemic physiological and immunological states associated with fertility.},
}

Animals
Male
*Poecilia/microbiology/physiology
*Sperm Motility/physiology
*Microbiota
Skin/microbiology
Spermatozoa/physiology
Bacteria/classification

@article {pmid41844930,
year = {2026},
author = {Kumari, N and Pal, G and Chawak, K and Arbi, SH and Anand, S},
title = {Current trends and updates on the emerging role of fecal microbiota transplantation in the treatment of neurodegenerative diseases.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {4},
pages = {},
pmid = {41844930},
issn = {1572-9699},
mesh = {*Fecal Microbiota Transplantation/trends/methods ; Humans ; *Neurodegenerative Diseases/therapy/microbiology ; Gastrointestinal Microbiome ; Animals ; Feces/microbiology ; },
abstract = {Fecal microbiota consists of a consortium of bacterial populations that reside in the human body, particularly in the gastrointestinal system, and are crucial to numerous physiological processes. Due to its promising clinical potential and acceptable safety profile, FMT has been the subject of numerous investigations as a possible therapeutic method for curing diverse disorders. Neurodegenerative diseases (NDs) are one among them and warrant immediate attention. There is a lack of efficient treatments for many ailments, and despite decades of research, we still don't fully understand their mechanisms and causes. The lack of advancement has prompted the research community to focus more on investigating novel or different elements that may impact the etiology or management of these disorders. The gut-brain axis, which embraces the two-way communication between the gut and brain via immunological, neurological, endocrine, and metabolic pathways, is one such element. Since NDs are frequently linked to aberrant gut microbiome compositions, it is not surprising that altering the gut microbiome can be a promising strategy in the treatment and management of neurological disorders. Fecal microbiota transplantation (FMT) is a technique employed for modulating microbiome composition and is becoming more and more common. FMT or recolonizing the ''diseased'' gut with a normal microbiome is one way to restore a dysbiotic gut. Traditionally used to treat Clostridium difficile-linked infections, FMT has lately been investigated as a probable treatment strategy for NDs. This review aims to systematically tap the current trends and updates on the employment of FMT in neurodegenerative research, whether as a treatment regimen or to look into the role of the microbiota in pathogenesis.},
}

*Fecal Microbiota Transplantation/trends/methods
Humans
*Neurodegenerative Diseases/therapy/microbiology
Gastrointestinal Microbiome
Animals
Feces/microbiology

@article {pmid41844942,
year = {2026},
author = {Thu, MS and Le, HBC and Duc, NP and Mai, VH and Walker, N and Hirankarn, N},
title = {Impact of microbiome-modulating strategies in cancer patients receiving immunotherapy (MSIT): A systematic review and meta-analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44743-7},
pmid = {41844942},
issn = {2045-2322},
support = {N42A680423//National Research Council of Thailand/ ; },
abstract = {The gut microbiota influences immune checkpoint inhibitors (ICIs) efficacy. Microbiome-modulating strategies (MMSs), including probiotics, synbiotics, and faecal microbiota transplantation (FMT), have emerged as promising adjuncts, but their clinical impact remains uncertain. We systematically reviewed PubMed, Embase, and CENTRAL to February 2025 for clinical cohorts evaluating MMS in cancer patients receiving ICIs. Thirty-six studies (25 trials/cohorts; n = 2,746) were included. Meta-analyses, and subgroup analyses were performed for efficacy along with microbiome shifts and safety. MMS plus ICIs achieved a pooled objective response rate (ORR) of 40% (95% CI: 31%-49%; I[2] = 63.4%; p = 0.0003; 95% PI: 15%-72%). Descriptive proportions showed ORR of 45% (95% CI: 32%-58%; I[2] = 72.5%; p = 0.0058) for probiotics and 33% (95% CI: 22%-48%; I[2] = 60.7%; p = 0.0064) for FMT; however, these findings are non-comparative and confounded by study differences. Exploratory subgroup signals were noted for probiotics in NSCLC (ORR 55%; 95%CI: 45%-64%; I[2] = 0%; p = 0.3683) and FMT in melanoma (ORR 39%; 95% CI: 15%-69%; I[2] = 72.5%; p = 0.0262). Dual ICI regimens showed the highest point estimate for ORR (43%; 95% CI: 17%-73%; I[2] = 68.5%; p = 0.0747) but increased toxicity. Microbiome analyses revealed enrichment of short-chain fatty acid-producing taxa and Bifidobacterium spp. among responders. Based on a limited pooled sample size (n = 143), MMS-related adverse events were mostly grade 1-2 (42%; 95% CI: 14%-77%, I[2] = 53.8%, p = 0.0210), with rare severe events (1%). Overall, MMS show promising, though preliminary, hypothesis-generating signals for modulating ICI response. Given high heterogeneity and reliance on early-phase, single-arm trials, the findings underscore urgent need for large, biomarker-driven randomized controlled trials to define optimal interventions and cautiously integrate microbiome modulation into immuno-oncology care.},
}

@article {pmid41845058,
year = {2026},
author = {Doan, T and Yan, D and Arzika, AM and Abdou, A and Maliki, R and Aichatou, B and Bello, IM and Beidi, D and Galo, N and Harouna, N and Karamba, AM and Mahamadou, S and Abarchi, M and Ibrahim, A and Zhong, L and Chen, C and Liu, Y and Yu, D and Abraham, T and Cheng, AS and Peterson, B and Oldenburg, CE and Porco, TC and Arnold, BF and Hinterwirth, A and Lebas, E and O'Brien, KS and Lietman, TM},
title = {Mass azithromycin distribution and antibiotic resistance in the gut and nasopharynx: a cluster-randomized trial.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41845058},
issn = {1546-170X},
abstract = {Repeated semiannual azithromycin mass drug administration (MDA) to children has been shown to reduce all-cause childhood mortality. However, antibiotic resistance is a major public health concern as the program is being implemented in sub-Saharan Africa. In the double-blind, cluster-randomized, placebo-controlled trial (AVENIR) in Niger, we evaluated the impact of azithromycin MDA targeting different age groups on mortality and on the gut and nasopharyngeal microbiome and resistome of children in participating communities. A total of 3,000 communities were randomized in a 1:1:1 allocation to 3 arms: 2 years of semiannual MDA of (1: child-azithromycin) azithromycin to 1-59-month olds, (2: infant-azithromycin) azithromycin to 1-11-month olds and placebo to 12-59-month olds or (3: placebo) placebo to 1-59-month olds. Mortality (co-primary endpoint) and safety data have previously been published. Here we report on resistance (the co-primary endpoint). One hundred fifty communities (50 per arm) were selected for this analysis. A total of 4,382 rectal and 4,402 nasopharyngeal samples were included. The co-primary outcomes included changes in gut and nasopharynx macrolide AMR. The trial met its primary AMR endpoint for the gut but not for the nasopharynx. The gut macrolide AMR burden in fold change between arms was highest in child-azithromycin compared with placebo (1.16, 95% confidence interval (CI): 1.06-1.28; P < 0.01), followed by child-azithromycin compared with infant-azithromycin (1.13, 95% CI: 1.02-1.23; P = 0.01), and infant-azithromycin compared with placebo (1.04×, 95% CI: 0.94-1.15×; P = 0.66). There were no statistically significant differences in macrolide AMR selection fold change in the nasopharynx between arms: 2.14 (95% CI: 0.93-4.99) for child-azithromycin versus placebo, 2.08 (95% CI: 0.93-4.69) for infant-azithromycin versus placebo, and 1.03 (95% CI: 0.46-2.30) for child-azithromycin versus infant-azithromycin. Close monitoring of AMR should be an essential component of MDA for childhood mortality. ClinicalTrials.gov registration: NCT04224987.},
}

@article {pmid41845406,
year = {2026},
author = {Zong, Y and Kong, J and Yang, F and Wang, M and Wang, J and Wang, Q},
title = {Guominkang formula alleviates airway inflammation in HDM-induced asthma mice by regulating Wnt/β-Catenin pathway.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {},
pmid = {41845406},
issn = {1749-8546},
support = {No. 82174243//the General program of National Natural Science Foundation of China/ ; No. 7242227//the General project of Beijing Natural Science Foundation/ ; No.zyyzdxk-2023251//the High level Key Discipline of National Administration of Traditional Chinese Medicine - Traditional Chinese constitutional medicine/ ; No.2023-JYB-JBZD-009//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: The Guominkang formula (GMK), formulated according to the principle of "treatment based on constitution differentiation," comprises Prunus mume (Siebold) Siebold & Zucc. (Wumei), Saposhnikovia divaricata (Turcz. ex Ledeb.) Schischk. (Fangfeng), Ganoderma lucidum (Curtis) P. Karst. (Lingzhi), and Periostracum Cicadae (Chantui). Clinically, GMK has been shown to modulate allergic constitution, effectively treating allergic asthma (AA) and various other allergic conditions, with a favorable safety profile and substantial therapeutic benefits. However, the precise mechanisms underlying its immune-modulatory effects, particularly in the context of AA, remain inadequately defined.

AIMS: This study aimed to investigate the therapeutic effects and underlying mechanisms of GMK in a mouse model of AA.

METHODS: The components of GMK were analyzed via LC-MS/MS. AA was induced in female mice through nasal instillation of house dust mites (HDM). Therapeutic efficacy was assessed through histopathological examination of lung tissue, measurement of airway hyperresponsiveness (AHR), and analysis of inflammatory cell infiltration, including eosinophils, neutrophils, macrophages, and subsets of T cells (Th1, Th2, Th17, and Treg). Serum levels of total IgE, HDM-specific IgE (HDM-sIgE), and cytokines (IL-1β, IL-4, IL-5, IL-6, IL-10, IL-13, IL-17, and IFN-γ) were quantified. Additionally, gut microbiome composition and differences between experimental groups were analyzed. Lung tissue transcriptomics identified differentially expressed genes (DEGs) and related signaling pathways. Western blot analysis was performed to evaluate protein expression levels of the Wnt/β-Catenin signaling pathways, contributing to the understanding of GMK's anti-asthma effects. Molecular docking studies were conducted to explore the binding interactions between GMK and the Wnt3a protein.

RESULTS: Fourteen compounds were identified in GMK. The formula exhibited significant therapeutic effects in an AA mouse model, evidenced by a reduction in Th2 and Th17 cell populations, restoration of the Th1/Th2 and Th17/Treg immune balance, alleviation of eosinophilic airway inflammation, and a decrease in total IgE and HDM-sIgE levels in serum. GMK also downregulated the expression of IL-1β, IL-4, IL-5, IL-6, IL-10, IL-13, and IL-17, while upregulating IFN-γ expression. Among the various doses, the medium dose proved most effective in mitigating airway inflammation, reducing airway remodeling, and decreasing AHR. Microbiome analysis revealed that GMK treatment reversed the reduced abundance of Firmicutes and Dubosiella in asthma mice, while increasing the abundance of Bacteroidetes and Norank_f_Muribaculaceae. Transcriptomic analysis demonstrated that, compared to asthma mice, DEGs in the lung tissue of GMK-treated mice were primarily enriched in the Wnt and related pathways. Furthermore, GMK modulated the Wnt/β-catenin signaling pathway to treat AA. Molecular docking studies confirmed predicted strong binding interactions between multiple bioactive compounds in GMK and the Wnt3a protein.

CONCLUSIONS: GMK regulates Th immune balance by modulating the Wnt/β-catenin signaling pathway, thereby reducing airway inflammation in HDM-induced asthma mice. Targeting the Wnt/β-catenin signaling pathway in the lungs may offer a novel therapeutic approach for allergic asthma treatment.},
}

@article {pmid41845494,
year = {2026},
author = {Huang, Q and Du, D and Guo, J and Liu, J and Sun, P},
title = {Heat stress suppresses lactation through potential rumen-mammary communication mediated by extracellular vesicles: integrated analysis of microbiome, metabolome, and miRNA profiles.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02363-3},
pmid = {41845494},
issn = {2049-2618},
support = {2022YFD1301101//National Key Research and Development Program of China/ ; CARS-37//Earmarked Fund for China Agriculture Research System/ ; Y2025YC52//Central Public-interest Scientific Institution Basal Research Fund/ ; ASTIP-IAS07//Agricultural Science and Technology Innovation Program/ ; },
abstract = {BACKGROUND: Heat stress (HS) imposes significant physiological and economic challenges to dairy production, yet the integrative mechanisms linking rumen microbial dysbiosis, host metabolic disruption, and lactation suppression remain not yet fully understood. Emerging evidence suggests that extracellular vesicles (EVs) and their cargo, particularly microRNAs (miRNAs), may participate in systemic inter-organ communication under stress. This study aimed to elucidate how HS suppresses lactation through potential rumen-mammary communication mediated by EVs, using a comprehensive multi-omics approach.

RESULTS: Dairy cows exposed to HS exhibited elevated rectal temperatures and respiratory rates, accompanied by significant reductions in the yield of milk, milk fat and protein. Rumen fermentation was markedly impaired, with decreased pH, butyrate, and valerate proportions, and systemic inflammation was evidenced by increased pro-inflammatory cytokines and barrier dysfunction. Metagenomic profiling revealed that HS reshaped the rumen microbiome, significantly reducing the relative abundances of Prevotella, Bifidobacterium, and Lactobacillus species while enriching methanogenic and low-efficiency fermentative taxa. Functionally, HS enhanced microbial methane metabolism and suppressed carbohydrate degradation pathways, reducing the host's energy supply for milk synthesis. Metabolomic analyses supported this shift, with distinct metabolites significantly correlated with lactation performance. Notably, extracellular vesicle (EV)-derived miRNAs from both plasma and milk showed significant expression changes under HS conditions, predominantly targeting signaling pathways related to stress and immune responses, hormone regulation, and mammary gland development and function.

CONCLUSIONS: This study demonstrates that HS suppresses lactation through multi-level alterations in the rumen microbiome, metabolic homeostasis, and EV-derived miRNA signaling, collectively supporting the existence of a potential rumen-mammary communication axis. These findings offer novel insights into the pathogenesis of HS responses.},
}

@article {pmid41845517,
year = {2026},
author = {Lin, L and Popova, M and Tapio, I and Guan, LL and Seifert, J},
title = {Harnessing the early-life gut microbiome for sustainable ruminant production.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00549-6},
pmid = {41845517},
issn = {2524-4671},
}

@article {pmid41845563,
year = {2026},
author = {Liu, S and Schlicht, K and Beckmann, A and Hartmann, K and Wang, W and Kruse, L and Wietzke-Braun, P and Hollstein, T and Becker, U and Ziegenbruch, U and Baumgartner, F and Diederich, W and Laudes, A and Muchaier, J and Stobbe, M and Homeister, L and Remy, S and Dornstauder, N and Vogel, M and Schindler, C and Türk, K and Geisler, C and Rohmann, N and Laudes, M},
title = {Parasutterella excrementihominis is associated with attenuated metabolic improvements during obesity therapy in humans.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2644687},
doi = {10.1080/19490976.2026.2644687},
pmid = {41845563},
issn = {1949-0984},
mesh = {Humans ; *Obesity/microbiology/therapy/metabolism ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; Cross-Sectional Studies ; Weight Loss ; Insulin Resistance ; C-Reactive Protein/metabolism ; Diabetes Mellitus, Type 2/microbiology/metabolism ; },
abstract = {Alterations in the composition and function of the gut microbiome are important in obesity and type 2 diabetes development. Using our cross-sectional FoCus cohort, we recently found Parasutterella species were increased in human obesity and type 2 diabetes and linked to abnormalities in triglyceride metabolism and L-cysteine homeostasis, the latter being important for beta-cell function. To gain further insights, we now quantified gut Parasutterella excrementihominis by qPCR in n = 215 human subjects during an interdisciplinary non-surgical obesity therapy program consisting of an initial weight-reduction phase (weeks 1-12) followed by a weight-maintenance phase (weeks 13-26). P. excrementihominis abundance was significantly reduced during the weight reduction phase. While baseline abundance levels did not predict the success of weight-reduction, they were inversely associated with C-reactive-protein improvements. Interestingly, the decrease in P. excrementihominis abundance during the weight reduction phase was positively correlated with improvements in insulin sensitivity throughout the overall obesity intervention. Regarding the weight maintenance phase, a re-increase of P. excrementihominis abundance was significantly associated with weight regain. In summary, our data suggest that P. excrementihominis attenuates metabolic and inflammatory improvements in obese human subjects under therapy and highlight a potential role of this bacterial species in metabolic adaptation during weight loss interventions.},
}

Humans
*Obesity/microbiology/therapy/metabolism
Male
Female
*Gastrointestinal Microbiome
Middle Aged
Adult
Cross-Sectional Studies
Weight Loss
Insulin Resistance
C-Reactive Protein/metabolism
Diabetes Mellitus, Type 2/microbiology/metabolism

@article {pmid41845564,
year = {2026},
author = {Zhang, Y and Wang, DD},
title = {Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2644682},
doi = {10.1080/19490976.2026.2644682},
pmid = {41845564},
issn = {1949-0984},
mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; Metagenomics ; Animals ; *Diet ; Metabolomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Proteomics ; Multiomics ; },
abstract = {Type 2 diabetes (T2D) is a heterogeneous metabolic disorder in which environmental exposures interact with host biology to drive insulin resistance and progressive β-cell dysfunction. This review synthesizes recent advances showing how the gut microbiome mediates these processes across multiple levels of resolution. First, large-scale shotgun metagenomic studies consistently identify a reproducible T2D-associated signature characterized by depletion of short-chain fatty acid-producing taxa and enrichment of opportunistic, pro-inflammatory microorganisms, while highlighting the importance of controlling for major confounders such as adiposity and glucose-lowering medications. Second, functional profiling and metabolomics link microbial community shifts to coordinated pathway changes-including reduced short-chain fatty acid and secondary bile acid production and increased endotoxin- and branched-chain amino acid-related metabolism-that influence gut barrier integrity, inflammatory tone, insulin sensitivity, and pancreatic β-cell function. Third, we discuss how integrative multi-omics (metagenomics, metatranscriptomics, proteomics, and metabolomics) can connect microbial genetic potential to in vivo activity and circulating metabolites, while introducing key challenges such as temporal variability, anatomical heterogeneity, and "dark matter" in gene and metabolite annotation. Fourth, strain-resolved analyses reveal that many disease-associated functions are carried by specific lineages within species, refining microbial targets and helping explain inconsistent species-level associations. Fifth, we summarize how diet shapes microbial ecology and function-supporting microbiome-informed precision nutrition-and highlight emerging evidence beyond bacteria, including viral and fungal community components. Finally, we outline translational opportunities and evidence gaps, emphasizing the need for diverse longitudinal cohorts, mechanistic validation, and well-controlled interventional trials to evaluate microbiome-directed strategies for T2D prevention and treatment.},
}

*Diabetes Mellitus, Type 2/microbiology/metabolism
Humans
*Gastrointestinal Microbiome
Metagenomics
Animals
*Diet
Metabolomics
Bacteria/classification/genetics/metabolism/isolation & purification
Proteomics
Multiomics

@article {pmid41845903,
year = {2026},
author = {Cao, H and Sun, J and Lv, Y and Ye, J and Wang, Y and Jiang, H},
title = {Targeting the gut-kidney axis to improve kidney transplantation prognosis: from mechanisms to clinical intervention strategies.},
journal = {Renal failure},
volume = {48},
number = {1},
pages = {2642487},
doi = {10.1080/0886022X.2026.2642487},
pmid = {41845903},
issn = {1525-6049},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Gastrointestinal Microbiome/immunology ; *Graft Rejection/prevention & control/immunology ; Prognosis ; Fecal Microbiota Transplantation ; *Kidney/immunology ; *Kidney Failure, Chronic/surgery/immunology ; Intestinal Mucosa/immunology ; Immune Tolerance ; },
abstract = {Kidney transplantation is an important treatment for end-stage renal disease, but lifelong immunosuppression is needed to prevent immune rejection, but the immunosuppressive therapy increases the risk of post-transplant complications. Therefore, how to improve the long-term survival of transplanted kidneys and reduce rejection has become a hot spot in current research. Recently, the 'gut-kidney axis' has received widespread attention as an important pathway for immune regulation. It refers to the fact that changes in either side of the gastrointestinal tract and kidney will affect the other side through energy metabolism, immuno-inflammation, intestinal mucosa, intestinal flora, among others, up and including to adverse consequences, which can be mutually causative. With the theory of 'gut-kidney axis', more and more studies have found that intestinal immune cells and microbiota play an important role in maintaining immune homeostasis and regulating the immune microenvironment of renal transplant recipients. Some studies have found that intestinal immune cells and microbiota not only influence the systemic immune status, but also may regulate the immune response of transplanted kidneys through metabolites and inflammatory mediators. In this review, we summarize the potential mechanisms of intestinal immune cells and microbiota in immune tolerance and rejection after renal transplantation based on the theory of 'gut-kidney axis'. In addition, we highlight microbiome modulation strategies, particularly dietary interventions and fecal microbiota transplantation, as emerging approaches with potential to improve transplant outcomes. A deeper understanding of the mechanism of action of the gut-kidney axis will provide new ideas and therapeutic targets for immunomodulation after renal transplantation.},
}

Humans
*Kidney Transplantation/adverse effects
*Gastrointestinal Microbiome/immunology
*Graft Rejection/prevention & control/immunology
Prognosis
Fecal Microbiota Transplantation
*Kidney/immunology
*Kidney Failure, Chronic/surgery/immunology
Intestinal Mucosa/immunology
Immune Tolerance

@article {pmid41845908,
year = {2026},
author = {Yao, R and Qian, F and Zhao, H and Shen, X and Zhu, Y and Wang, L},
title = {Microbiome Landscapes in Squamous Cell Carcinoma Tissue Microenvironments: A Comparative Analysis.},
journal = {Immunity, inflammation and disease},
volume = {14},
number = {3},
pages = {e70406},
doi = {10.1002/iid3.70406},
pmid = {41845908},
issn = {2050-4527},
support = {2022MS009//Basic scientific research project of Naval Medical University/ ; XTCX-KJ-2023-44//Shanghai Collaborative Innovation Project/ ; },
mesh = {Humans ; *Carcinoma, Squamous Cell/microbiology/pathology ; *Tumor Microenvironment ; *Microbiota/genetics ; Female ; Male ; Middle Aged ; },
abstract = {INTRODUCTION: Squamous cell carcinoma (SCC) is one of the most prevalent human cancers. While anatomically distinct, SCCs exhibit diverse similarities in etiology and molecular. The extent to which different SCCs share microbial landscapes within the tumor tissue microenvironment remains unclear.

METHODS: We analyzed RNA sequencing data from 419 SCC samples across five anatomical sites: cutaneous (CuSCC), esophageal (ESCC), lung (LSCC), head and neck (HNSCC), and cervical (CeSCC). Differential microbial abundance between tumor and adjacent normal tissue was assessed using multivariable linear models implemented in MaAsLin2. For each anatomical site, an independent external validation cohort was included (totaling 156 samples) to validate key microbial findings using the area under the receiver operating characteristic curve (AUROC).

RESULTS: The five SCC cohorts shared 28 shared core bacterial genera, with Staphylococcus was widespread and had the highest relative abundance (mean 13.74%) in all cohorts. ESCC, HNSCC, and LSCC exhibited more similar dysregulated microbiota, with Clostridioides showing the most significant up-regulation in tumor relative to adjacent tissue (the mean model coefficient value, coef = 3.26). Notably, Bradyrhizobium (CeSCC, CuSCC, LSCC, mean coef = -2.58), Massilia (in CeSCC, ESCC, HNSCC, mean coef = -1.99), Providencia (in CeSCC, HNSCC, LSCC, mean coef = 0.93), and Ralstonia (in CuSCC, ESCC, HNSCC, mean coef = -0.52) displayed significant differential expression across multiple cohorts, as confirmed in the validation cohorts (AUROC > 0.6).

CONCLUSIONS: Despite the absence of a common dysbiotic microbiota among SCCs due to anatomical differences, potential similarities in adjacent sites suggest a unified disease perspective and may pave the way for novel preventive and therapeutic strategies.},
}

Humans
*Carcinoma, Squamous Cell/microbiology/pathology
*Tumor Microenvironment
*Microbiota/genetics
Female
Male
Middle Aged

@article {pmid41846072,
year = {2026},
author = {Oladokun, S and Grenier, B and Oakley, B and Bortoluzzi, C and Ramkumar, M},
title = {Gut check: Exploring tools, techniques, and future directions in microbiome research.},
journal = {Poultry science},
volume = {105},
number = {6},
pages = {106713},
doi = {10.1016/j.psj.2026.106713},
pmid = {41846072},
issn = {1525-3171},
abstract = {Poultry microbial communities are now recognized as key contributors to host nutrition, immune function, disease resilience, and overall health and performance, driving growing interest in this research field. This symposium brought together leading experts to discuss the latest advancements in analytical tools and technologies for investigating the poultry microbiome. Presentations highlighted current progress in microbiome profiling techniques, next-generation sequencing technologies, advanced data analysis methods such as machine learning, and the integration of cutting-edge approaches in microbiome research. A roundtable discussion further engaged participants in identifying key challenges in the field, including method standardization, reproducibility, and data interpretation, while emphasizing emerging opportunities to translate microbiome insights into practical strategies for disease control, antibiotic alternatives, and sustainable poultry production. The knowledge shared in this symposium is highly relevant to poultry researchers and the industry, as they work to enhance bird health, welfare, and productivity.},
}

@article {pmid41846103,
year = {2026},
author = {Trzos, K and Hutsch, T and Koval, A and Śmierciak, D and Machaj, G and Molano, LG and Rehner, J and Rahman, MM and Förster, MO and Bednarek, M and Yilmaz, B and Pilarczyk-Zurek, M and Surma, S and Koziel, J and Krawczyk, M and Keller, A and Becker, SL and Ylla, G and Jura, J and Kotlinowski, J},
title = {Probiotic Lactobacillus rhamnosus mitigates PBC-like features in Mcpip1-deficient mice via modulation of gut-liver crosstalk.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {1872},
number = {5},
pages = {168216},
doi = {10.1016/j.bbadis.2026.168216},
pmid = {41846103},
issn = {1879-260X},
abstract = {BACKGROUND: Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease characterized by progressive biliary destruction and cholestasis. Current therapies, including ursodeoxycholic acid (UDCA), exhibit limited efficacy in advanced disease. In this study, we investigate the therapeutic potential of microbial intervention using Lactobacillus rhamnosus (Lbr) in the Mcpip1[fl/fl]Alb[Cre] knockout mouse model of PBC, which we described previously. Knockout mice develop human PBC-like features such as bile acid dysregulation, autoantibodies, cholangiocyte hyperplasia and fibrosis.

METHODS: Six-week-old Mcpip1[fl/fl] (wild-type) and Mcpip1[fl/fl]Alb[Cre] (knockout) mice were treated with Lactobacillus rhamnosus supplementation, UDCA (15 mg/kg/day), UDCA + Lbr, and UDCA + OCA (obeticholic acid, 10 mg/kg/day) for six weeks. Treatment response was characterized by liver and gut pathology, serum biomarkers, transcriptomic profiles, and microbiome composition.

RESULTS: Treatment of Mcpip1[fl/fl]Alb[Cre] animals with Lbr decreased serum bile acids and reduced pathological cholangiocyte dysplasia in the liver, decreased leukocyte infiltration and fibrosis. RNAseq of liver tissue revealed enrichment of humoral immune responses and T cell activation pathways in knockouts, all of which were significantly attenuated by Lbr monotherapy. Gut pathology marked by increased intraepithelial lymphocyte infiltration and mucosal hypertrophy, was also normalized upon Lbr administration. Finally, probiotic treatment modulated the microbiome by increasing the Firmicutes/Bacteroidetes ratio and enriching butyrate-producing Lachnospiraceae. Administration of UDCA and UDCA+OCA had less pronounced effects: only decreased serum bile acids was detected in both groups.

CONCLUSIONS: Probiotic intervention with Lbr represents a feasible strategy to attenuate fibrotic progression in a mouse model of autoimmune cholestatic disease by modulation of the gut-microbiome-immune crosstalk.},
}

@article {pmid41846126,
year = {2026},
author = {Wang, X and Zhao, L and Teng, Y and Hu, W and Xu, Y and Ma, J and Song, J and Ren, W and Zhang, J and Zhu, H and Wang, X and Wang, Y and Luo, Y and Kuramae, EE},
title = {Decoding the adaptive strategies of versatile diazotrophs to multi-metal(loid) stress in mercury-mining impacted farmland soils.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141760},
doi = {10.1016/j.jhazmat.2026.141760},
pmid = {41846126},
issn = {1873-3336},
abstract = {Diazotrophs are crucial for Earth's nitrogen cycle via biological nitrogen fixation, while also modulating other elemental cycles and exhibiting bioremediation potential. However, their responses to co-occurring heavy metal(loid) (HM) contaminants in polluted soils remain poorly understood. Using combined nifH (encoding nitrogenase) amplicon and metagenomic sequencing, we characterized the taxonomic structure and metabolic potential of diazotrophic community across multi-HM contamination gradients in mercury-mining impacted farmlands (paddy vs. upland). Results identified selenium (upland soils: 0-3.08 mg kg[-1]) and arsenic (paddy soils: 5.38-17.1 mg kg[-1]) as the primary HMs shaping diazotrophic diversity, whereas mercury (0.067-99.6 mg kg[-1]) showed a significant but weak correlation. Selenium and mercury correlated positively with diversity in upland soils (arsenic negatively), whereas all three HMs correlated negatively in paddy soils. Diazotrophic indicator taxa varied by HM type, yet certain taxa tolerated all three HMs simultaneously-notably Chromatiaceae/Pseudomonadaceae in upland soils and Xanthobacteraceae in paddy soils. Moreover, diazotrophs in upland soils exhibited synergistic associations with functional guilds involved in HM resistance and element cycling (e.g., carbon fixation and hydrogen metabolism), contrasting with the negative correlations in paddy soils. Metagenomic binning indicated that dominant diazotrophs were primarily aerobic heterotrophs with versatile metabolic potentials, including multi-HM resistance (e.g., arsenic/mercury reduction, efflux, and antioxidation) and energy acquisition via trace gas (CO, H2), manganese, and sulfide oxidation. These findings provide novel insights into diazotrophic adaptive strategies under multi-HM stress, advancing our understanding of their ecological and environmental functions.},
}

@article {pmid41846268,
year = {2026},
author = {Stengele, K and Stauber, L and Thoenen, L and Janse van Rensburg, H and D'Adda, V and Schlaeppi, K},
title = {Benzoxazinoid-mediated microbiome feedbacks enhance Arabidopsis growth and defence.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71098},
pmid = {41846268},
issn = {1469-8137},
support = {189249//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; //University of Bern Interfaculty Research Collaboration "One Health"/ ; },
abstract = {Plants modulate their surrounding microbiome via root exudates and such conditioned soil microbiomes feed back on the performance of the next generation of plants. How plants perceive altered soil microbiomes and modulate their performance in response to such microbiome feedbacks, however, remains largely unknown. As tool to condition contrasting microbiomes in soil, we made use of two maize lines, which differ in their ability to exude benzoxazinoids (BXs). Based on these differentially conditioned soil microbiomes we have established a model system with Arabidopsis thaliana (Arabidopsis) to investigate the mechanisms of microbiome feedbacks. Arabidopsis plants responding to the BX-conditioned soil microbiome grew better and were developmentally more advanced. Further, these plants harboured differential root bacterial communities, showed enhanced defence signatures in transcriptomes of their shoots, and they were more resistant to the fungal pathogen Botrytis cinerea. Intriguingly, Arabidopsis responded with both improved growth and enhanced defence to the BX-conditioned soil microbiome, and we found that this simultaneous increase of growth and defence was mediated by priming of the defences. Further advancing our basic understanding of how plants respond to soil microbiomes and mediate their feedbacks is particularly important for the goal to improve crops so they can benefit from their soil microbiome.},
}

@article {pmid41846281,
year = {2026},
author = {Clarke, C and Banasik, M and Juodeikis, R and Warren, MJ and Pickersgill, RW},
title = {Evolutionarily divergent DUF4465 domains have a common vitamin B12-binding function.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.70231},
pmid = {41846281},
issn = {2211-5463},
support = {Grant BB/X001946/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {The DUF4465 family (DUF, domain of unknown function) contains more than 1000 members distributed across eight bacterial clades with species from diverse microenvironments including various gut microbiomes, hydrothermal vents, and soil. In the gut commensal Bacteroides thetaiotaomicron (B. theta), DUF4465 containing proteins act as high-affinity B12-binding proteins that scavenge this cofactor to ensure bacterial survival. Such B12 capture is essential for bacteria that have lost the ability to synthesize B12 de novo. This raises the question of whether B12-binding is ubiquitous across this family of proteins. Here, we show that B12-binding is a recurrent function of eight distantly related members of the DUF4465 family. It is reasonable to conclude that B12-binding is a common function of most DUF4465 proteins. These results establish DUF4465 as a structurally conserved family of augmented β-jellyroll B12-binding proteins with widespread roles in microbial competition for this essential cofactor. Impact statement DUF4465 defines a widespread, structurally conserved bacterial cobalamin-binding domain and provides a promising scaffold for protein-based B12 capture and purification.},
}

@article {pmid41846394,
year = {2026},
author = {Müller, T and Kohlhepp, W},
title = {Advances in the pharmacological management of early motor manifestations of Parkinson's disease (PD).},
journal = {Expert review of neurotherapeutics},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/14737175.2026.2645845},
pmid = {41846394},
issn = {1744-8360},
abstract = {INTRODUCTION: Parkinson's disease (PD) is a heterogeneous, chronic neurodegenerative disorder. Once the diagnosis is made, symptomatic dopamine substituting therapy is initiated.

AREAS COVERED: This narrative review discusses exemplary past and recent failed attempts.

EXPERT OPINION: The diagnosis of PD at the onset of motor symptoms is already late in terms of disease progression. An easy-to apply, reliable, sensitive diagnostic biomarker for predictive screening is currently outstanding. Nevertheless, the ability to delay progression and/or cure of the disease is currently the greatest unmet need. Chronic neurodegenerative processes arise from various distinct yet interconnected metabolic and pathological cascade sequences that work together. The translation of promising treatments concepts for beneficial disease modification has failed once they were tested in levodopa-naive patients. Microbiome alteration with short fatty acids or acetyl-DL-leucine supplementation, only enhance levodopa efficacy, But do not modify disease progression in a benefical way. Presently, there is also a lack of real innovation in terms of dopamine substitution.},
}

@article {pmid41846613,
year = {2026},
author = {Mura, JD and Kaundal, A and Vashisth, T and Nimmakayala, P},
title = {Editorial: Isolation, identification, characterization, and utilization of beneficial microbes for crop improvement.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1792485},
doi = {10.3389/fpls.2026.1792485},
pmid = {41846613},
issn = {1664-462X},
}

@article {pmid41846864,
year = {2026},
author = {Váradi, M and Magyar, B and Széles, Á and Korda, S and Németh, B and Simon, B and Reis, H and Oláh, C and Horváth, O and Dér, B and Nyirády, P and Szarvas, T},
title = {Prognostic and predictive factors of immune checkpoint inhibitor therapy in urinary bladder cancer.},
journal = {Pathology oncology research : POR},
volume = {32},
number = {},
pages = {1612333},
pmid = {41846864},
issn = {1532-2807},
mesh = {Humans ; *Urinary Bladder Neoplasms/drug therapy/pathology/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; Prognosis ; *Biomarkers, Tumor ; Immunotherapy/methods ; B7-H1 Antigen ; },
abstract = {Immune checkpoint inhibitor (ICI) therapy has become a firmly integrated component of the systemic treatment repertoire for locally advanced and metastatic urothelial bladder cancer (UBC). Over the past decade, multiple ICIs have demonstrated meaningful clinical activity, and their indications have expanded across treatment lines, including second-line therapy after platinum, first-line therapy for cisplatin-ineligible disease, avelumab maintenance following chemotherapy, and, more recently, combination strategies such as pembrolizumab plus enfortumab vedotin. Despite these advances, patient responses to ICIs remain highly heterogeneous. While a subset of patients achieves substantial tumor regression and long-term survival, a considerable proportion derives little or no benefit. The rapidly evolving therapeutic landscape - encompassing antibody-drug conjugates, targeted agents, and perioperative ICI approvals - further emphasizes the need to identify which patients are most likely to respond to immunotherapy. Given the marked variability in therapeutic sensitivity and the increasing availability of alternative effective treatments, accurate prediction of ICI efficacy is becoming increasingly crucial for personalized treatment selection. In this review, we provide a comprehensive overview of currently established and emerging biomarkers of ICI response in UBC, including PD-L1 immunohistochemistry, serum inflammatory markers, tumor mutational burden, histology and molecular subtypes, gene expression patterns and microbiome features. We discuss their strengths, limitations, and potential translational relevance, highlighting ongoing challenges and future directions.},
}

Humans
*Urinary Bladder Neoplasms/drug therapy/pathology/immunology
*Immune Checkpoint Inhibitors/therapeutic use
Prognosis
*Biomarkers, Tumor
Immunotherapy/methods
B7-H1 Antigen

@article {pmid41846867,
year = {2025},
author = {Hu, C and Wang, S and Gao, Z and Qing, M and Tan, L and Yang, L and Li, F},
title = {Curcumin in oral health: mechanisms, clinical evidence, and delivery strategies.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1661443},
pmid = {41846867},
issn = {1663-9812},
abstract = {Curcumin, a polyphenolic compound derived from the turmeric rhizome (Curcuma longa), has attracted significant interest in dentistry and oral medicine because of its multifaceted therapeutic properties. In particular, curcumin exhibits potent anti-inflammatory, antioxidant, and antimicrobial activities that are relevant to a wide spectrum of oral diseases. We conducted a narrative search of PubMed (2000-2025) using iterative keyword combinations related to curcumin and oral diseases/mechanisms, screened reference lists, and selected studies on the basis of their relevance to oral pathobiology, delivery systems, and clinical/translational outcomes. This narrative review summarized the current knowledge concerning the molecular mechanisms of curcumin and its clinical applications in oral health. We outlined how curcumin modulates key inflammatory pathways and oxidative stress responses, and how it exerts broad-spectrum antimicrobial effects against oral pathogens. We detailed the efficacy of curcumin in specific oral conditions, including periodontal diseases, dental caries, recurrent aphthous stomatitis, oral lichen planus, oral submucous fibrosis, oral candidiasis, radiation/chemotherapy-induced oral mucositis, and oral cancers. In each context, we highlighted evidence from in vitro studies, animal models, and clinical trials, and noted the benefits of curcumin, such as reduced inflammation, enhanced healing, microbial inhibition, and in some cases outcomes comparable to those of standard therapies. Across conditions, curcumin shows adjunctive benefit: In periodontal disease, it reduces plaque and gingival inflammation comparable to chlorhexidine and improves probing outcomes when added to scaling and root planing; in recurrent aphthous stomatitis, it reduces pain and ulcer size with steroid-like efficacy; in radiotherapy/chemotherapy-induced oral mucositis, it delays onset and decreases severity; in oral candidiasis, it decreases fungal burden and enhances photodynamic therapy; and in oral squamous cell carcinoma early clinical studies show modulation of inflammatory cytokines and the oral microbiome. Various delivery systems developed to overcome the poor bioavailability of curcumin-from mouthwashes and gels to nanocarriers and mucoadhesive formulations-are reviewed. Although many studies reported promising results with minimal toxicity or side effects, there were study limitations such as small sample sizes, variability in formulations, and the pharmacokinetic properties of curcumin. Overall, the reviewed data support the role of curcumin as a safe, formulation-dependent adjunct-not a stand-alone therapy-in oral medicine.},
}

@article {pmid41846893,
year = {2026},
author = {Bautista, J and Cortiñas Sardi, P and Paguay-Caisabanda, I and Gancino-Guevara, K and López-Cortés, A},
title = {Integrating microbiome insights into cervical cancer.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1766052},
pmid = {41846893},
issn = {2296-858X},
abstract = {Cervical cancer is largely preventable, yet it continues to cause substantial morbidity and mortality worldwide, particularly in regions with limited access to human papillomavirus (HPV) vaccination and screening. Persistent infection with high-risk HPV genotypes, especially HPV-16 and HPV-18, represents the primary initiating event in cervical carcinogenesis. However, viral infection alone does not fully explain why only a subset of infected individuals develop high-grade lesions or invasive disease. Recent longitudinal and mechanistic studies indicate that the cervicovaginal microbiome plays an important modulatory role by influencing epithelial barrier integrity, local immune responses, and inflammatory homeostasis. This review synthesizes current evidence from multi-omics and translational studies linking cervicovaginal microbial composition and function to HPV persistence, cervical intraepithelial neoplasia (CIN), and cervical cancer progression. Communities dominated by Lactobacillus crispatus are frequently associated with antiviral conditions and mucosal stability, whereas anaerobe-enriched microbial profiles, commonly referred to as community state type IV (CST IV), are associated with chronic inflammation, metabolic dysregulation, and increased lesion severity. Microbial metabolites and inflammatory mediators may interact with HPV oncogene activity and host epigenetic regulation, supporting a microbiome-metabolome-epigenome axis in cervical carcinogenesis. The review also discusses emerging clinical implications, including microbiome-based biomarkers and microbiota-targeted interventions. While early studies suggest potential benefits of probiotics and postbiotics for HPV clearance and immune modulation, current evidence remains limited. Methodological heterogeneity, low-biomass sampling, and population variability continue to restrict causal inference and clinical translation. Addressing these challenges will be essential for integrating microbiome-informed strategies into cervical cancer prevention and management.},
}

@article {pmid41846999,
year = {2026},
author = {Mechan-Llontop, ME and Nauta, KM and Gates, DR and Wang, X and Cooper, J and Burton, NO},
title = {Bacterial pyruvate metabolism regulates host insulin sensitivity in C. elegans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.04.709558},
pmid = {41846999},
issn = {2692-8205},
abstract = {Two different individuals can consume an identical diet but experience different physiological outcomes. While there are many potential mechanistic reasons for this, one increasingly recognized reason is that differences in an animal's microbiome can lead to differences in the processing of dietary nutrients. Thus, though a diet might start out the same, how it is experienced by a host is dependent on their microbiome. While exciting, mechanistic studies of diet-microbiome-host effects are often limited by the lack of high throughput laboratory techniques to identify and define interactions between dietary metabolites, microbial metabolism, and host biology. We hypothesized that the model organism Caenorhabditis elegans is an advantageous animal model for rapidly identifying and genetically dissecting interactions between dietary nutrients, microbial metabolism, and host physiology. Here, we used an established model of the effects of dietary glucose on insulin resistant mutant animals (daf-2 /IR mutants) to study how differences in bacterial metabolism influence the consequences of dietary sugars on animal physiology. We found that the effect of dietary sugars on daf-2 mutant physiology is dependent on how the microbiome metabolizes dietary sugars. We found dietary sugar suppresses multiple daf-2 mutant phenotypes in the presence of some bacteria but has no effect in the presence of others. To determine how bacteria mediate the effects of dietary sugars on host physiology we screened 5,000 transposon mutations in the canonical C. elegans dietary bacteria, E. coli OP50 for effects on animal insulin signaling. From this, we found that the effects of exogenous sugars on the phenotype of daf-2 mutant animals is dependent on the function of pyruvate dehydrogenase in bacteria and that the loss of bacterial pyruvate dehydrogenase genes (ex. aceE) is sufficient to mimic the effects of dietary sugars on dauer formation, longevity, and gene expression in insulin signaling deficient animals. Collectively, our findings further support the growing body of evidence that the effects of dietary nutrients on animal physiology can be influenced by the gut microbiome. In addition, these studies demonstrate the advantages of the C. elegans model system for studying 3-way diet-microbiome-host interactions that are difficult to dissect in other model systems.},
}

@article {pmid41847005,
year = {2026},
author = {Azamar, KMM and Rajesh, K and Downing, B and Javith, M and Yamhure, I and Porras, AM},
title = {Comparative Genomic and Functional Profiling of ECM-Targeting Enzymes in Bacteroides , a Key Genus of the Human Gut Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.04.709643},
pmid = {41847005},
issn = {2692-8205},
abstract = {UNLABELLED: Purpose The human extracellular matrix (ECM) provides essential cues for intestinal homeostasis. While most studies focus on ECM degradation by host cells, our prior work suggests that commensal gut microbes may also contribute to these remodeling processes. Here, we continue exploring this novel dimension of host-microbe interactions by profiling the proteolytic diversity and substrate-specific activity of ECM-targeting enzymes across species of Bacteroides, a dominant and metabolically versatile gut genus.

METHODS: We curated a custom ECM-specific enzyme database from the BRENDA repository and used it to perform comparative genomic analyses across 11 Bacteroides species, mapping the diversity and abundance of candidate ECM-degrading proteases and carbohydrate active enzymes (CAZymes). Functional activity was evaluated via in vitro degradation assays using purified substrates. Family-specific protease inhibitors were used to confirm the major catalytic classes involved.

RESULTS: ECM-targeting CAZymes and proteases were broadly encoded across all 11 genomes, with gene counts positively correlated with genome size and GAG-associated genes comprising the largest substrate category. Experimental degradation assays revealed species- and substrate-specific activity patterns, including elastin degradation restricted to a subset of species, a capacity previously undocumented in intestinal Bacteroides . Genomic predictions showed limited concordance with measured enzymatic activity, suggesting context-dependent regulation of ECM-degrading enzymes. Inhibitor experiments confirmed that collagen degradation is driven primarily by metalloproteases and secondarily by serine proteases across representative species.

CONCLUSIONS: Our findings position commensal Bacteroides as a rich, yet underappreciated, source of ECM-degrading enzymes. This work underscores the need to consider microbiota as key modulators of host tissue homeostasis and potential targets for therapeutic modulation.

BIOGRAPHY: Dr. Ana Maria Porras is an Assistant Professor of Biomedical Engineering at the University of Florida, where she leads the Tissue-Microbe Interactions lab. Her group leverages cell and tissue engineering, bioinformatics, and statistical modeling to understand how microorganisms regulate human extracellular matrix remodeling. Her work centers primarily on the gut microbiome, cardiovascular health, and tropical infectious diseases. Dr. Porras is also a science artist, and a science communicator, particularly in interested in evidence-based, culturally informed, and multilingual practices to improve public engagement with science. She is the co-founder and Senior Advisor of the Latinx in Biomedical Engineering community, and the recipient of multiple awards, including the UF Excellence Award for Assistant Professors, the NSF Faculty Early Career Development (CAREER) Award, the NIH Maximizing Investigators Research Award (MIRA), the AAAS Early Career Award for Public Engagement with Science, and and the Rising Star Award from the Academy of Science, Engineering, and Medicine of Florida. Prior to arriving in Florida, Dr. Porras was a Presidential Postdoctoral Fellow at Cornell University. She holds a B.S. in biomedical engineering from the University of Texas at Austin, and a Ph.D. from the University of Wisconsin-Madison, where she was an American Heart Association Predoctoral Fellow.},
}

@article {pmid41847008,
year = {2026},
author = {Yancey, CE and Brumfield, KD and Ettwiller, L and Colwell, RR},
title = {Microbial Community multi-omic analysis of marsh sediment post crustacean shell compost enrichment: pathogen emergence and community response.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.06.710096},
pmid = {41847008},
issn = {2692-8205},
abstract = {Changes in nutrient availability can rapidly alter microbial processes in natural environments, with implications in biogeochemical cycling and pathogen emergence. Short-term, functional responses of microbial communities to nutrient amendment in coastal communities remain poorly understood, particularly in temperate environments. A 48-hour microcosm pulse experiment was completed in which paired metagenomic and metatranscriptomic sequencing were employed to examine how the decomposition of chitin rich substrates, namely crab and lobster shell compost, alters salt marsh microbiome structure and function. Within 48 hours of amendment, pronounced shifts in community metabolism were observed, including increased chitin degradation and utilization, stress-response, and sporulation. These responses coincided with marked decreases in genes associated with key biogeochemical processes, including carbon fixation, sulfur oxidation and reduction, and other metabolic pathways. Shell compost addition also enriched putative pathogens and virulence-associated genes, accompanied by modest transcriptional activation, notably aerolysin A (aerA) , which encodes the pore-forming exotoxin aerolysin. These results demonstrate temperate salt marsh sediment microbiomes can undergo shifts in community composition and function that is associated with chitin-rich nutrient perturbation. The sensitivity of temperate coastal systems to organic matter input and the potential for ecological and public-health relevant outcomes are underscored, notably given that chitin is among the most abundant and readily available bionutrients in aquatic ecosystems globally.},
}

@article {pmid41847165,
year = {2026},
author = {Khanna, S},
title = {Specialty grand challenge in gastrointestinal infections.},
journal = {Frontiers in gastroenterology (Lausanne, Switzerland)},
volume = {5},
number = {},
pages = {1808344},
pmid = {41847165},
issn = {2813-1169},
}

@article {pmid41847176,
year = {2026},
author = {Gu, Z and Zhang, M and Shen, F and Chen, J and Gu, Y and Gong, Y and Xue, Q and Zhou, H and Liu, Y and Shao, S and Zhang, Y and Bai, J and Hua, K and Zhou, G and Ding, J},
title = {The Role of Bacterial Outer Membrane Vesicles in Tumor Development: Facts, Potential Applications and Future Perspectives.},
journal = {International journal of nanomedicine},
volume = {21},
number = {},
pages = {582600},
pmid = {41847176},
issn = {1178-2013},
mesh = {Humans ; *Neoplasms/therapy/pathology/immunology ; *Bacterial Outer Membrane/chemistry/metabolism ; Animals ; Tumor Microenvironment ; Antineoplastic Agents ; Epithelial-Mesenchymal Transition ; },
abstract = {Bacterial outer membrane vesicles (OMVs), nanosized lipid bilayer particles released by both Gram-negative and Gram-positive bacteria, are emerging as crucial mediators of host-microbe interactions in cancer biology. This review synthesizes current evidence on how OMVs modulate tumor initiation, progression, and therapeutic responses through multifaceted mechanisms aligned with the 14 hallmarks of cancer. Studies demonstrate that OMVs can either promote or inhibit neoplastic processes depending on their bacterial origin and cargo composition. Tumor-promoting OMVs enhance proliferative signaling, drive epithelial-mesenchymal transition, facilitate metastatic dissemination via barrier disruption and angiogenesis, and weaken antitumor immunity. Conversely, other OMVs exert antineoplastic effects by triggering intrinsic apoptosis, cell-cycle arrest, immunogenic cell death, and remodeling of the tumor immune microenvironment. Pre-clinical studies further highlight the translational potential of engineered OMVs as precision nano-vaccines, immunotherapeutic agents, and adjuvants that synergize with immune checkpoint blockade, chemotherapy, or photothermal therapy while minimizing systemic toxicity. Future directions could focus on mapping of OMV cargo-pathway-phenotype networks by multidisciplinary methods, programmable vesicle design using synthetic biology, and real-time microbiome-OMV monitoring in early-phase clinical trials to enable individualized onco-therapeutics. Collectively, OMVs represent a versatile platform to bidirectionally regulate oncogenesis and therapeutic responses. Exploiting their molecular plasticity through rational engineering and precision medicine frameworks would bring transformative potential for cancer prevention, diagnosis, and treatment.},
}

Humans
*Neoplasms/therapy/pathology/immunology
*Bacterial Outer Membrane/chemistry/metabolism
Animals
Tumor Microenvironment
Antineoplastic Agents
Epithelial-Mesenchymal Transition

@article {pmid41847216,
year = {2026},
author = {Shi, H and Huang, L and Zhang, JH and Shen, C and Zhang, N and Lv, C and Shao, L and Li, M and Sun, Z and Shi, L and Yu, G and Chen, Y},
title = {Gut Microbiota Regulates Brain-Bone Axis to Influence Osteoporosis Pathogenesis and Treatment.},
journal = {Research (Washington, D.C.)},
volume = {9},
number = {},
pages = {1178},
pmid = {41847216},
issn = {2639-5274},
abstract = {Osteoporosis is a systemic skeletal disorder characterized by reduced bone mass, impaired microarchitecture, and increased fracture risk, primarily resulting from dysregulated bone remodeling. Increasing evidence highlights a close interaction between bone metabolism and the gut microbiota. Alterations in bone mineral density can influence gut microbial composition. Conversely, microbial dysbiosis disrupts bone homeostasis through multiple pathways, including microbial metabolites, immune regulation, and neuroendocrine signaling. Short-chain fatty acids suppress osteoclast differentiation and enhance intestinal calcium absorption, while gut dysbiosis promotes bone loss by impairing intestinal barrier integrity and increasing proinflammatory cytokines such as tumor necrosis factor-α and interleukin-6. The gut-brain-bone axis represents an important regulatory network linking the central nervous system, gut-derived signals, and skeletal remodeling. Chronic stress and neurodegenerative conditions activate the hypothalamic-pituitary-adrenal axis and bone-derived extracellular vesicle signaling, thereby favoring bone resorption. Estrogen deficiency further disrupts the receptor activator of nuclear factor κΒ ligand/osteoprotegerin signaling pathway and alters gut microbial composition, contributing to postmenopausal bone loss. Therapeutic strategies targeting this axis, including probiotics, prebiotics, fecal microbiota transplantation, dietary fiber supplementation, and pharmacological or natural compounds, show potential in restoring microbial balance and improving bone metabolism. Future studies integrating multiomics approaches and well-designed clinical trials are needed to clarify microbiome-bone interactions and support the development of targeted interventions for osteoporosis.},
}