@article {pmid41964220,
year = {2026},
author = {Huang, S and Zou, H and Yi, S and Tang, X and Hu, L and Dan, J and Wang, C and Wang, H and Zhang, J and Yang, J and Li, X and Xiao, T and Bai, W and Chen, X and Lin, X and Li, Y and Hao, T and Zhao, Y and Fan, Z and Cai, J and Hu, J and Zhu, W and Jiang, D and Yan, G and Lin, Y and Liang, J},
title = {Identification of YBX1 as an essential host RNA binding protein governing tumor-selective replication of oncolytic virus M1.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymthe.2026.04.013},
pmid = {41964220},
issn = {1525-0024},
abstract = {Oncolytic virus M1 (OVM), currently in phase I/II clinical trial, is a single-stranded, positive-sense RNA virus. However, the host factors that engage its viral RNA to govern viral replication and oncolytic efficacy remain largely unknown. Here, by using RNA affinity purification coupled with mass spectrometry (RAP-MS) and CRISPR-Cas9 screening, we identify Y-box binding protein 1 (YBX1) as a predominant proviral RNA-binding protein. Functional dissection reveals that the cold shock domain of YBX1, specifically its aromatic residues W65, F74, and F85, are essential for binding OVM RNA and sustaining viral replication. PAR-CLIP sequencing maps that YBX1 binds to conserved sequence elements at the NSP4-capsid junction and 3'UTR regions that function as promoters for viral RNA synthesis. Consequently, loss of YBX1 severely impairs viral RNA synthesis. This molecular dependency translates to a profound functional effect: across multiple tumor models, YBX1 deficiency abrogates OVM replication and oncolytic activity, while re-expression restores both. Importantly, YBX1 expression levels not only correlate with cellular susceptibility to OVM in cancer cell lines and ex vivo tumors but are also elevated in several human malignancies. Collectively, these findings establish YBX1 as a master regulator of OVM replication and a predictive biomarker for its therapeutic efficacy.},
}

@article {pmid41960430,
year = {2026},
author = {Khelfaoui, I and Wang, W and Shehata, AI and Meskher, H and El Basuini, MF and Mohamed, AMA and Abouelenein, MF and Degha, HE and Alhoshy, M and Teiba, II and Mahmoud, O and Mahmoud, SS},
title = {STROBE-causal machine learning for the human microbiome: systematic review on methodological innovations and validation frameworks.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1705116},
pmid = {41960430},
issn = {1664-302X},
abstract = {The reproducibility crisis in causal microbiome research necessitates robust validation frameworks. Current studies often face inconsistent validation methods, limited interpretability, and a lack of standardized reporting, creating a gap in reliable causal inference. This systematic review evaluates over 60 peer-reviewed studies published between 2015 and 2024 to: (1) establish benchmarking standards leveraging synthetic data and biological plausibility assessments; (2) compare advanced causal machine learning (ML) methodologies, including Double/Debiased ML, Deep Instrumental Variables (Deep IV), and Directed Acyclic Graphs (DAGs), in their application to microbiome-host systems; and (3) propose the STROBE-CML (Strengthening the Reporting of Observational Studies in Epidemiology-Causal Machine Learning) guidelines to standardize reporting practices. We emphasize critical innovations such as federated validation pipelines and time-series causal discovery frameworks that address these gaps by facilitating scalable, privacy-preserving, and reproducible inference across heterogeneous cohorts. A decision support tool is introduced to guide researchers in selecting appropriate causal ML approaches based on data structure, research question, and computational constraints. By synthesizing methodological advances with rigorous validation paradigms, this review provides a roadmap for generating reliable, biologically interpretable, and clinically translatable causal claims in microbiome science.},
}

@article {pmid41775773,
year = {2026},
author = {Chowdhury, SF and Sarkar, MMH and Al Sium, SM and Naser, SR and Hossain, MS and Habib, MA and Akter, S and Banu, TA and Goswami, B and Jahan, I and Chakrovarty, T and Molla, MMA and Nafisa, T and Yeasmin, M and Ghosh, AK and Khan, MS},
title = {Metatranscriptomic insights into host-microbiome interactions underlying asymptomatic COVID-19 cases.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41775773},
issn = {2045-2322},
support = {GOB 224125200//Ministry of Science and Technology, Government of the People's Republic of Bangladesh/ ; },
abstract = {UNLABELLED: Coronavirus disease 2019 (COVID-19) remains a major global health concern, with emerging evidence highlighting the role of the human microbiome in influencing disease severity. While extensive research has been conducted on COVID-19, studies examining host-pathogen interactions at the transcriptomic level remain limited. In this study, we investigated the metatranscriptomic profiles of forty nasopharyngeal samples collected from COVID-19 patients across different Bangladeshi cohorts. Sequencing data were processed to analyze taxonomic composition, microbial diversity, and antimicrobial resistance gene (ARG) patterns using multiple bioinformatic pipelines. COVID-19 positive and asymptomatic patients exhibited a higher abundance of pathogenic and multidrug-resistant bacteria, whereas COVID-19 negative individuals showed increased fungal diversity. Differential gene expression analysis revealed significant upregulation of immune response related genes, including pro-inflammatory cytokines, in COVID-19 positive cases. Notably, asymptomatic patients demonstrated reduced TLR4 expression, suggesting a potential reducing of innate immune activation, which may contribute to asymptomatic clinical outcomes. Additionally, functional enrichment highlighted active ARG expression in positive cases, indicating potential links between the respiratory microbiome and host immune modulation. These findings provide insights into the host-microbiome interplay underlying COVID-19 severity and highlight the need for further validation in larger, ethnically diverse cohorts with comprehensive clinical metadata.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-40563-x.},
}

@article {pmid41959668,
year = {2026},
author = {Chung, HA and Fralish, Z and Tu, T and Reker, D},
title = {Profiling biological effects of microbiome metabolites via machine learning.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115282},
pmid = {41959668},
issn = {2589-0042},
abstract = {Human microbiome-derived metabolites are key mediators of host physiology. However, their biological effects remain largely uncharacterized due to limitations of current low-throughput and untargeted experimental approaches that are time intensive and costly. This has hindered the systematic biological characterization of microbiome metabolites. To address this gap and accelerate the identification of biological effects of microbiome metabolites, we developed and experimentally validated a machine learning platform trained on publicly available drug development data to rapidly predict a wide array of chemical and biological properties of microbiome metabolites. Prospective experimental validation confirmed the accuracy of our models and uncovered previously unknown effects of several metabolites. For example, we identified previously unknown interleukin 8 secretion stimulation by the metabolites spermine and spermidine, which have been regarded anti-inflammatory thus far. Our findings demonstrate the potential power of machine learning to accelerate the functional annotations of microbiome-derived metabolites, paving the way for biomarker and therapeutic discovery.},
}

@article {pmid41957416,
year = {2026},
author = {Hunter, AK and Adair, K and Horgan, A and Jordan, J and Stadler, DD and Bohannan, BJM},
title = {Impact of dietary protein quantity on the non-dysbiotic human microbiome: a controlled feeding study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46663-y},
pmid = {41957416},
issn = {2045-2322},
}

@article {pmid41957628,
year = {2026},
author = {Yang, W and Wu, J and Zhou, Y and Yu, Z and Shang, X and Huang, J},
title = {PfVPS4, an ESCRT AAA-ATPase, is essential for asexual proliferation and gametocyte sexual conversion in Plasmodium falciparum.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07362-9},
pmid = {41957628},
issn = {1756-3305},
support = {32170071//National Natural Science Foundation of China/ ; 32200450//National Natural Science Foundation of China/ ; 32300051//National Natural Science Foundation of China/ ; 2023JJ40798//Natural Science Foundation of Hunan Province/ ; 2023JJ30651//Natural Science Foundation of Hunan Province/ ; },
abstract = {BACKGROUND: Malaria, caused by Plasmodium spp., remains a major global health threat. Among them, Plasmodium falciparum is the most pathogenic, and its asexual intraerythrocytic proliferation is the pathological basis. This process has enormous biosynthetic demands and highly relies on the coordinated function of the endomembrane and vesicular transport systems. The transition from asexual proliferation to sexual differentiation similarly involves remodeling of internal membrane complexes, membrane reshaping, and precise protein sorting. In eukaryotic cells, the Endosomal Sorting Complexes Required for Transport (ESCRT) complex is a core machinery for membrane remodeling and endosomal development. However, how the ESCRT system regulates the complex life cycle of Plasmodium, particularly during intraerythrocytic proliferation and sexual conversion, remains an important unresolved question.

METHODS: In this study, using Plasmodium falciparum as a model system, we applied CRISPR-Cas9-mediated homologous recombination to achieve conditional knockdown of PfVPS4, the core ATPase of the ESCRT complex - vacuolar protein sorting-associated protein 4 (PfVPS4). Western blotting and immunofluorescence assays were used to assess PfVPS4 abundance and subcellular localization. Tightly synchronized cultures were used to evaluate its effects on parasite growth, merozoite numbers, and gametocyte conversion rate. In vitro protein purification, enzyme kinetics, and site-directed mutagenesis were performed to identify the impact of key residues on PfVPS4 ATPase activity and to validate the synergistic activation by its cofactor PfVta1. In addition, multiple sequence alignment and AlphaFold3 modeling were used to predict and display structural features before and after mutation of key sites.

RESULTS: We successfully generated conditional knockdown lines in both Pf3D7 and PfNF54 parasite strains, enabling effective knockdown at different stages of the intraerythrocytic cycle and during gametocytogenesis. Knockdown of PfVPS4 led to an 84% reduction in asexual progeny parasite numbers, decreased merozoite numbers, and a 46% reduction in gametocyte conversion rate, without affecting subsequent gametocyte maturation. Biochemical assays showed that PfVPS4 ATPase activity is optimal at pH 7.5 and 37°C, and is dependent on Mg²⁺, with a Vmax of 2.23 ± 0.053 U/mg and a Km of 0.086 mM. Site-directed mutagenesis validated the essential role of the canonical catalytic residues (D213, E214) and the species-specific key residues (T161, I288) in maintaining enzymatic activity, and confirmed that the cofactor PfVta1 significantly enhances PfVPS4 activity.

CONCLUSION: PfVPS4 is essential for normal asexual blood-stage replication and efficient sexual conversion in Plasmodium falciparum. Its knockdown severely disrupts intraerythrocytic proliferative homeostasis and reduces gametocyte conversion, indicating that this protein has a broader role in coordinating parasite proliferation and transmission. Given its essentiality, species‑specific residues, and regulation by PfVta1, PfVPS4 and its complex are attractive antimalarial drug targets.},
}

@article {pmid41947255,
year = {2026},
author = {Van Daele, W and Tito Tadeo, RY and Perera, J and Tshokey, T and Iversen, PO and Jayasinghe, S and Raffaetà, R and Wangmo, N and Fjeld, HE and R, SC and Thoradeniya, T and Raes, J},
title = {Toward ethical human microbiome research: improving health through radical interdisciplinary and intercultural co-laboration.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41947255},
issn = {2049-2618},
support = {Project no. 324158//Norwegian Research Council/ ; grant G0B7320N//Fonds Wetenschappelijk Onderzoek/ ; GA n. 949742 ERC-HealthXCross//European Union's Horizon 2020 Research and Innovation Programme/ ; },
mesh = {Humans ; *Microbiota ; *Biomedical Research/ethics ; Global Health ; Europe ; North America ; },
abstract = {As human microbiome research is globalizing, it raises ethical concerns regarding the European and North American dominance in the field, which may reproduce a colonial bias and perpetuate inequities in global health research and outcomes. We suggest disentangling this ethical quandary into three main concerns: 1) scientific bias toward European and North American populations; 2) limited meaningful community inclusion, participation, and ownership, and 3) scant significant inclusion of diverse global researchers. We then formulate three recommendations for their resolution, deploying co-laboration-joint labor of diverse partners in generating synergies between diverse disciplines, cultures, and knowledges around shared concerns-and co-laborative science-a form of citizen science based on such synergies between diverse partners-to guide meaningful inclusive, participatory, and ethical human microbiome research. To conclude, we promote a programmatic list for putting co-laborative ethical science into practice, benefiting global communities, individuals, and researchers alike and decolonizing and improving health worldwide.},
}

Humans
*Microbiota
*Biomedical Research/ethics
Global Health
Europe
North America

@article {pmid41949699,
year = {2026},
author = {Shen, H and Zhang, L and Ma, X and Yin, Y and Wang, J and Tan, B},
title = {Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41949699},
issn = {1869-1889},
abstract = {The human microbiome is a dynamic ecosystem that profoundly influences host physiology through complex molecular interactions. Advances in high-throughput profiling now enable multi-omics measurements at scale, yet integration remains difficult due to biological complexity, technical variability, sparsity, and small cohorts. This review targets bioinformatics practitioners and clinical microbiology researchers applying machine learning to host-microbiome studies. Here, we survey state-of-the-art methods for integrating heterogeneous data types and highlight algorithmic innovations for high dimensionality and small cohorts. We also examine approaches for interpretability that translate mechanistic insight into clinically actionable models. Finally, we outline a standardized benchmarking framework emphasizing open data, rigorous evaluation, and biologically informed architectures. By synthesizing multi-omics measurements with advanced analytics, we chart a pathway toward personalized, microbiome-based therapies while deepening our understanding of host-microbiome crosstalk.},
}

@article {pmid41952172,
year = {2026},
author = {Zhang, J and Jiang, C and Zhou, X and Gao, P and Wong, S and Snyder, M and Shen, X},
title = {Cross-body site microbial interactions influence the human plasma metabolome.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02405-w},
pmid = {41952172},
issn = {2049-2618},
support = {#025402-00001//Ministry of Education - Singapore/ ; },
abstract = {BACKGROUND: The human microbiome profoundly influences the host plasma metabolome and health, but most studies have focused on the gut microbiome in isolation. A comprehensive assessment of how microbiomes from multiple body sites jointly shape host metabolism has been lacking.

RESULTS: Using data from three independent human cohorts (n = 435), we systematically analyzed the selective and joint influences of microbiomes from multiple body sites on the human plasma metabolome (814 annotated metabolites). Microbiomes from all body sites contributed to plasma metabolome variation, collectively explaining 30.13% of the inter-individual variation. The gut microbiome showed the largest contribution (18.44%), followed by oral (14.70%), skin (11.5%), and nasal (5.88%) microbiomes. Microbial composition did not necessarily predict metabolic function for example, despite distinct compositions, oral and gut microbiomes exhibited similar associations with circulating metabolites. Machine learning and mediation analyses revealed widespread cooperative and synergistic microbial interactions across body sites, particularly along the oral-gut axis. Over half of the metabolites were jointly influenced by multiple body-site microbiomes. This axis showed cross-site microbial crosstalk and sequential metabolic processing, regulating metabolites such as indole derivatives and carboxylic acids. The oral-gut microbiome-metabolome axis was further amplified in insulin resistance (IR), linking enhanced microbial cooperation to metabolic dysregulation.

CONCLUSION: Our findings reveal the systemic and interactive nature of microbiome-metabolome relationships and highlight the need to integrate spatially distributed microbial ecosystems to fully understand host metabolic regulation and disease mechanisms. Video Abstract.},
}

@article {pmid41957184,
year = {2026},
author = {Ye, Y and Liu, C and Jia, L and Tang, X and Li, Z},
title = {Efficacy and safety of ustekinumab biosimilars for treating moderate-to-severe plaque psoriasis: a systematic review and network meta-analysis.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41957184},
issn = {1432-1912},
support = {82404633//National Natural Science Foundation of China/ ; },
abstract = {To compare the efficacy and safety of different ustekinumab biosimilars for treating moderate-to-severe plaque psoriasis (PP), providing an evidence-based basis for clinical medication. We systematically searched randomized controlled trials on ustekinumab biosimilars for treating moderate-to-severe PP in adults from Embase, PubMed, Cochrane Library, and Web of Science. Stata 18.0 was utilized for data analysis. Nine studies were included, involving 4293 moderate-to-severe PP patients. 1) Ustekinumab biosimilars and the reference listed drug (RLD) ustekinumab-RP had no significant difference in the psoriasis area and severity index (PASI) improvement (P > 0.05), and the biosimilar CT-P43 was most effective in improving PASI at different time points. 2) For the dermatology life quality index, Bmab1200, AVT04 and CT-P43, had statistically significant differences from the RLD (P < 0.05). 3) The biosimilar CT-P43 was most effective in improving the Physician Global Assessment score, with the highest SUCRA value (99.8%). 4) The reduction of the body surface area and the treatment-emergent adverse event rate had no statistically significant difference from the RLD (P > 0.05). 5) The biosimilar CT-P43 and Bmab1200 demonstrated a lower probability of generating anti-drug antibodies, showing statistically significant differences from other biosimilars (P < 0.05). Ustekinumab biosimilars demonstrate comparable efficacy and safety to ustekinumab-RP for treating moderate-to-severe PP in adults. The biosimilar CT-P43 is more effective in improving short-term PASI. Due to limitations in the number and quality of included studies, more high-quality studies are required to validate these findings.},
}

@article {pmid41946245,
year = {2026},
author = {Rana, C and Vikas, V and Narwal, N and Korpela, K and De, S},
title = {Dynamics of extended spectrum cephalosporin and carbapenem resistance genes in Escherichia coli: An emerging environmental hazard.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141955},
doi = {10.1016/j.jhazmat.2026.141955},
pmid = {41946245},
issn = {1873-3336},
abstract = {Carbapenem- and cephalosporin-resistant Escherichia coli (CCREC) represent a growing global hazard, disseminating across human, animal and environmental reservoirs. We analysed 81,718 E. coli genomes, carrying key cephalosporin and carbapenem resistance genes, to characterise the global trends in resistance determinants and phylogenetic lineages. Further, spatiotemporal trends and international transmission dynamics, with time-scaled phylogenetic and ancestral state reconstruction was performed on a globally representative subset. The dataset spanned 1905 till 2024, covering 3169 Sequence Types (STs) and 84 countries. Three STs dominated globally: ST131 (phylogroup B2), ST10 (phylogroup A/B1), and ST410 (phylogroup C). ST131 expanded rapidly after 2008, peaking around 2020, and was strongly associated with human infections, while ST10 was enriched in animals and birds (χ[2] tests, p < 0.0001). Extended-Spectrum β-lactamase (ESBL) and carbapenemase trajectories showed steep rises, with blaCTX-M-15 significantly more prevalent in ST131 (χ[2] test, p < 0.0001). The blaCTX-M-15 was the most prevalent globally, while blaNDM-5 surpassed blaNDM-1 after 2010. The blaNDM-5 was majorly associated with ST167. Asia was dominant in blaNDM-5 and blaCTX-M-15/14/27/55, Europe exhibited high blaCTX-M-15/blaOXA-1/blaOXA-48 frequencies, and North America carried blaKPC and blaCMY-2. The ST131/B2 harboured higher virulence scores (median 31.0 [29.0-34.0]) than in ST10 (median 18.0 [14.0-26.0]). The E. coli lineage originated around 1263, with early dispersal from the USA to Europe. We identified 1482 transmission routes among 863 ST131 E. coli genomes, dominated by USA-Japan and USA-Canada links. This emphasizes the urgent need for One Health containment strategies to limit the spread of CCREC.},
}

@article {pmid41947254,
year = {2026},
author = {Passmore, JS and Nieves Delgado, A and Happel, AU},
title = {Ethical design as a prerequisite for translational microbiome science.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41947254},
issn = {2049-2618},
support = {INV-037612/GATES/Gates Foundation/United States ; VI.Vidi.221F.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; K43TW012864/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Translational Research, Biomedical/ethics ; *Translational Science, Biomedical/ethics ; Research Design ; },
abstract = {Human microbiome research is expanding globally, yet remains dominated by samples, institutions, and leadership from the Global North. This imbalance undermines scientific validity, as microbiomes are shaped by socio-ecological context and temporal dynamics, and risks producing diagnostics and therapeutics that are not applicable across diverse populations. In this comment, we engage with van Daele et al.'s framework of co-laboration and argue for ethical, interdisciplinary, and locally led research models that center community participation, context-rich metadata, and equitable authorship. We outline structural requirements-governance tools, funding mechanisms, and accountability systems-needed to ensure these frameworks are implemented and advance both scientific integrity and global health equity. Video Abstract.},
}

Humans
*Microbiota
*Translational Research, Biomedical/ethics
*Translational Science, Biomedical/ethics
Research Design

@article {pmid41940156,
year = {2026},
author = {Ma, J and Qiao, J and Cao, Y and Cheng, Z},
title = {Harnessing artificial intelligence to decode the rhizosphere microbiome.},
journal = {aBIOTECH},
volume = {7},
number = {1},
pages = {100005},
pmid = {41940156},
issn = {2662-1738},
abstract = {The rhizosphere microbiome plays crucial roles in plant health by regulating nutrient cycling and enhancing stress resilience. However, due to its complexity, the rhizosphere microbiome is quite challenging to analyze using conventional approaches. Recent advances in artificial intelligence (AI) offer unprecedented opportunities to decipher intricate microbial interactions and leverage their potential for crop breeding. In this review, we assess AI methodologies derived from human microbiome studies that address foundational data challenges, including high dimensionality, compositionality, and sparsity. Next, we examine the uses of these methods for the functional prediction of microbial traits. We then shift our focus to the rhizosphere, exploring AI-driven approaches for predictive modeling of rhizosphere dynamics, integrating plant phenotypic and microbiome data, and designing synthetic microbial communities (SynComs). Finally, we discuss the major challenges and future prospects of using AI in rhizosphere microbiome research. Specifically, we propose an emerging AI paradigm that integrates complementary inside-out (hologenome-based genomic selection) and outside-in (SynCom design) strategies, powered by transformative technologies such as federated learning, large language models, digital twins, and autonomous AI agents. This review underscores the potential for AI to revolutionize microbiome science and crop improvement.},
}

@article {pmid41943876,
year = {2026},
author = {Šunić, I and Šarac, J and Havaš Auguštin, D and Pozdniakova, S and Ferguson, RMW and Jergović, M and Visentin, D and Borràs, S and Archer, E and Henderson, DK and Vitko, S and Ašić, A and Bošnjaković, A and Maglica, Ž and Viegas, C and Novokmet, N and Karlović, N and Marjanović, D and Muszyński, A and Liu, Y and Karisola, P and Alenius, H and Krych, L and Lovrić, M},
title = {The Indoor Microbiome: Sampling, Analysis and Emerging Trends.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70272},
doi = {10.1111/1758-2229.70272},
pmid = {41943876},
issn = {1758-2229},
support = {101057497//European Union's Horizon Europe research and innovation programme/ ; 101057779//European Union's Horizon Europe research and innovation programme/ ; 101056883//the European Union/ ; 22.00324//Swiss State Secretariat for Education, Research and Innovation/ ; 10040524//United Kingdom Research and Innovation/ ; APP2017786//Australian National Health and Medical Research Council/ ; APP2008813//Australian National Health and Medical Research Council/ ; 101057693//European Union's Call on Environment and Health (HORIZON-HLTH-2021-ENVHLTH-02)/ ; /AMS_/Academy of Medical Sciences/United Kingdom ; },
mesh = {*Microbiota ; *Fungi/isolation & purification/genetics/classification ; *Air Pollution, Indoor/analysis ; *Bacteria/genetics/classification/isolation & purification ; *Air Microbiology ; Humans ; Dust/analysis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Indoor spaces contain diverse microbial communities that shape human health. These microorganisms are particularly relevant to respiratory diseases, including asthma and allergies. Despite growing recognition of the importance of indoor microbial exposures, research in this field is slowed by differences in methods. These inconsistencies make it difficult to compare results and draw conclusions. This systematic review analyses 106 studies published between 2000 and 2025 that investigated indoor microbiomes in dust, air, and other matrices across homes, schools, and other built environments. We assessed sampling strategies, DNA extraction protocols, sequencing technologies, and bioinformatic pipelines, identifying trends, inconsistencies, and areas requiring harmonisation. Passive sampling, particularly dust collection, was the most common approach, while Illumina-based 16S rRNA and ITS amplicon sequencing dominated molecular analyses. However, variations in targeted gene regions, extraction kits, and analytical tools limited cross-study comparability. Ecological findings revealed consistent detection of bacterial taxa such as Staphylococcus, Streptococcus, and Corynebacterium, and fungal taxa including Cladosporium, Aspergillus, and Penicillium, with diversity shaped by building characteristics, ventilation, humidity, occupancy, and presence of pets. This review highlights the need for standardised protocols in indoor microbiome research to facilitate reproducibility, enable meta-analyses, and inform health-related guidelines for indoor environments.},
}

*Microbiota
*Fungi/isolation & purification/genetics/classification
*Air Pollution, Indoor/analysis
*Bacteria/genetics/classification/isolation & purification
*Air Microbiology
Humans
Dust/analysis
RNA, Ribosomal, 16S/genetics

@article {pmid41930951,
year = {2026},
author = {Everett, BA and Prindle, A},
title = {AexB is an aromatic amino acid exporter that functions as a metabolic safety valve.},
journal = {mBio},
volume = {},
number = {},
pages = {e0023126},
doi = {10.1128/mbio.00231-26},
pmid = {41930951},
issn = {2150-7511},
abstract = {UNLABELLED: Aromatic amino acids-tryptophan, tyrosine, phenylalanine, and histidine-are essential for bacterial growth and are among the most energetically expensive metabolites to synthesize. Despite this cost, it has been recently shown that bacteria possess exporters for these amino acids. Here, we identify aexB (formerly yvjA) as a gene encoding a novel aromatic amino acid exporter in Bacillus subtilis. Using a transposon-based screen, we found that aexB overexpression confers resistance to the toxic tryptophan analog 5-fluorotryptophan. Additional analog screens revealed that AexB also promotes tolerance to toxic derivatives of tyrosine, phenylalanine, and histidine but not non-aromatic amino acids. LC-MS analysis showed that AexB specifically exports aromatic amino acids, and co-culture assays confirmed that overexpression of aexB can support the growth of aromatic amino acid auxotrophs. Furthermore, overexpression of aexB impaired growth when intracellular tryptophan was limiting. On the other hand, deletion of aexB exacerbated growth defects under excess tryptophan conditions, likely due to feedback inhibition of aromatic amino acid synthesis pathways. Our findings reveal that AexB is an aromatic amino acid exporter that functions as a metabolic safety valve.

IMPORTANCE: Identification and characterization of amino acid exporters is a broadly relevant topic. Amino acid synthesis is energetically costly, and thus functional relevance for their export is unintuitive. Identification of the molecular components that allow export may offer new engineering opportunities to improve biomanufacturing and metabolic engineering. Characterization of these exporters may also provide a more complete understanding of the human microbiome where amino acids, especially tryptophan, have been established as nodes of crosstalk between host and microbiota.},
}

@article {pmid41926667,
year = {2026},
author = {Chen, Y and Duan, R and Zhang, C and Li, G and Ji, X and Zhang, Q and Pei, F and Wang, K and Duan, L},
title = {Maternal Preconception Antibiotic Exposure Disrupts Microbial Succession: A Transgenerational Risk for Offspring Gut Mucosal Immaturity and Colitis Susceptibility.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e16931},
doi = {10.1002/advs.202516931},
pmid = {41926667},
issn = {2198-3844},
support = {2021YFA1301300//National Key R&D Program of China/ ; 82470578//National Natural Science Foundation of China/ ; 7254451//Beijing Natural Science Foundation/ ; },
abstract = {The early-life microbiome plays a pivotal role in host development and lifelong health. Maternal factors are increasingly recognized as crucial in shaping offspring microbiome. However, how maternal preconception perturbations affects offspring health remain unclear. Thus, we combined animal and clinical data to elucidate whether preconception microbial perturbations disrupt microbial succession and increase offspring susceptibility to colitis. In animals, preconception antibiotic exposure induced long-lasting disruptions in offspring microbial ecology, through enhanced maternal-offspring microbial transmission, altered microbial developmental trajectories, and increased selective pressures during microbial community assembly. Ultimately, these alterations resulted in persistent gut mucosal immaturity and heightened susceptibility to colitis in adulthood. Complementary clinical studies revealed concordant alterations in gut microbiome and metabolome of children with inflammatory bowel disease (IBD) and their seemingly healthy mothers, characterized by pro-inflammatory taxa and metabolites. Notably, mothers of IBD children reported significantly higher antibiotic exposure than controls, which was also associated with enhanced maternal-offspring microbial transmission and increased selective pressures during microbial community assembly. Our findings reveal a potential intergenerational mechanism in which preconception perturbations are associated with disrupted microbial succession, transgenerational propagation of gut mucosal immaturity, and susceptibility to colitis. These results underscore the importance of judicious antibiotic use during the often-overlooked preconception period.},
}

@article {pmid41928970,
year = {2026},
author = {Rock, RR and Alexander, M and Noecker, C and Trepka, KR and Upadhyay, V and Ortega, EF and Ramirez, L and Siewert, L and Olson, CA and Halsey, T and Pröbstel, AK and Baranzini, SE and Turnbaugh, PJ},
title = {Female-enriched Eggerthella lenta drives neuroinflammation and IFN-γ via host receptor TLR2.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.16.711194},
pmid = {41928970},
issn = {2692-8205},
abstract = {UNLABELLED: Women are at increased risk of autoimmune diseases, including multiple sclerosis (MS); however, the degree to which sex differences in the gut microbiota impact autoimmunity remains largely unexplored. Our 27-cohort meta-analysis revealed 60 sex-associated gut bacterial species. Leveraging an independent clinical cohort, we demonstrate that female-enriched species significantly associate with MS status and clinical disability (EDSS). Top female-enriched species Eggerthella lenta drove disease in the experimental autoimmune encephalomyelitis (EAE) MS model, consistent with brain and gut lamina propria T cell infiltration and MS-associated T helper (Th) signatures. E. lenta induced intestinal Th1 and Th17 in healthy mice, independent of bacterial viability. Mechanistically, we demonstrate that TLR2 directly drives E. lenta -induced IFN-γ production in Th cells and is necessary for exacerbation of EAE. Together, we identify a causal host-microbe axis contributing to sex differences in autoimmunity and provide a framework for evaluating sex as a biological variable in human microbiome research.

HIGHLIGHTS: 27-cohort meta-analysis identifies a robust sex-signature in human gut microbiota.Female-enriched species are associated with MS risk and severity. Female-enriched Eggerthella lenta exacerbates the EAE model. E. lenta impacts neuroinflammation via toll-like receptor 2.},
}

@article {pmid41915473,
year = {2026},
author = {Zhao, Y and Li, J and Han, K and Chen, L and Zhuang, Q and Li, S and Hua, M and Li, N and Yue, J and Gu, C and Rong, C and Yang, D and Deng, Z and Huang, J and He, L and Zeng, H and Yu, Z and Chen, C},
title = {Phage-related symbiosis and antagonism shape gut ecosystem dynamics in Lachnospiraceae and Bacteroidaceae.},
journal = {Cell reports},
volume = {45},
number = {4},
pages = {117166},
doi = {10.1016/j.celrep.2026.117166},
pmid = {41915473},
issn = {2211-1247},
abstract = {The human gut microbiota is shaped by intricate, yet poorly resolved interactions among bacteria, as well as their relationship to bacteriophages. However, resolving this complex interaction and dynamics has been limited by the challenges in genome recovery and functional characterization. We develop culture-enriched metagenomic co-barcoding sequencing (cMECOS), obtain 5,006 high- or medium-quality (HMQ) metagenome-assembled genomes (MAGs) and reconstruct bacteria-phage interaction networks via CRISPR spacer mapping. This framework uncovers two ecologically distinct, inter-specific bacterial networks: a Lachnospiraceae-dominated community associates with temperate phages and is characterized by metabolic cross-feeding and a Bacteroidaceae-dominated community linked to virulent phages and marked by resource competition. Both network architectures are disrupted in both inflammatory bowel disease (IBD) and obesity (OB), underscoring their role in ecosystem stability. Our work establishes cMECOS as a powerful platform for deciphering complex microbiome interactions and identifies phage-related bacterial networks as critical regulators of gut homeostasis, providing a foundation for phage-informed therapeutic development.},
}

@article {pmid41924306,
year = {2026},
author = {Batacan, R and Rao, A and Bajagai, YS and Stanley, D and Briskey, D},
title = {Oleoylethanolamide supplementation enriches Akkermansia muciniphila and modulates intestinal barrier function in adults with obesity: A randomized, double-blind, placebo-controlled trial.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2622259},
pmid = {41924306},
issn = {2993-3935},
abstract = {Targeted modulation of the gut microbiome represents a promising nutritional strategy to support metabolic and intestinal health in overweight and obese adults. Oleoylethanolamide (OEA) is an endogenous lipid mediator that regulates satiety, lipid metabolism, and inflammation, but its effects on the human microbiome are not well defined. In this randomized, double-blind, placebo-controlled trial, 57 adults with obesity (BMI 30-40 kg/m[2]) received either 300 mg of TRPTI, providing 250 mg/day of OEA (n = 28), or placebo (n = 29) for 12 weeks. Outcomes included shotgun metagenomics, microbiome profiling, intestinal barrier and inflammatory biomarkers, and safety measures. OEA was safe and well-tolerated with no adverse changes in clinical biomarkers. Although overall microbial diversity remained stable, OEA induced selective, health-relevant compositional shifts. Notably, Faecalibacterium prausnitzii and Akkermansia muciniphila were enriched. These changes coincided with functional host benefits, including increased occludin at Week 12 and interleukin-2 at Week 6, while reducing interleukin-1β, consistent with improved epithelial barrier dynamics and reduced inflammation. Functional pathway analysis suggested enhanced microbial metabolic and redox capacity. These findings indicate OEA supplementation selectively enriches beneficial gut bacteria - particularly A. muciniphila, while improving gut barrier biomarkers and immune function without disrupting microbiome stability. These findings position OEA as a safe, targeted microbiome-modulating ingredient with potential applications for supporting gut and metabolic health.},
}

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

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

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

@article {pmid41905546,
year = {2026},
author = {Pietilä, TK and Cantini, E and Itkonen, ST and Salonen, A and Pajari, AM},
title = {Replacing red meat with non-soy legumes alters choline metabolites but not systemic inflammation or proxies of gut barrier function in healthy males in a 6-week RCT.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110355},
doi = {10.1016/j.jnutbio.2026.110355},
pmid = {41905546},
issn = {1873-4847},
abstract = {While the health burden of high red and processed meat intake has been acknowledged in observational studies, studying the effects and mechanisms in controlled settings with healthy participants have generated mixed findings. We aimed to investigate whether a partial replacement of unprocessed and processed red meat (from 760 g/week to 200 g/week) with non-soy legume foods in apparently healthy men (age 37.9 y, BMI 25.5 ± 3.3 kg/m[2], mean±SD) yields beneficial effects on low-grade inflammation through changes in proxies of gut barrier function and choline metabolites. This study was a randomised, 6-week parallel trial with groups (allocation ratio 1:1) following their habitual diet with a reference red meat intake (Meat, n = 51) or with partial substitution with legumes (Bean, n = 51). We report no major differences in high-sensitivity-CRP or glycoprotein acetyls, Olink cytokines and immune modulators between the groups at 6-wk using one-way baseline-adjusted analysis of covariance. Lower concentration of plasma cholines, and higher urine dimethylamine excretion were observed in the Bean group (all P < 0.05), while no differences in urine trimethylamine-N-Oxide (TMAO) or gut barrier function occurred. We found BMI, TMAO, and gut barrier function explaining the variance within the Olink biomarkers, and linked some to diet, TMAO and/or gut barrier function. Partial replacement of red meat with non-soy legumes for 6-weeks altered choline metabolites but did not lead to significant changes in low-grade inflammation. Our results highlight the robustness of the inflammatory markers to changes in healthy individuals with an intact gut barrier.},
}

@article {pmid41906659,
year = {2026},
author = {Zheng, NZ and Yuan, JW and Zhou, JW and Li, XJ and Huang, GL and Gao, WX and Xie, XY and Wen, WP and Li, J},
title = {Efficacy Evaluation of Ultrasound Fusion-Guided Core Needle Biopsy for Infratemporal Fossa Lesions.},
journal = {Head & neck},
volume = {},
number = {},
pages = {},
doi = {10.1002/hed.70247},
pmid = {41906659},
issn = {1097-0347},
support = {GuikeAB24010081//Guangxi Key Research and Development Program/ ; 2023B1111040004//Natural Science Foundation of Guangdong Province/ ; 2022A1515010506//Natural Science Foundation of Guangdong Province/ ; GuikeAA24206008//Guangxi Science and Technology Major Program/ ; 2023P-ZD06//Key Clinical Technique of Guangzhou/ ; 23ptpy107//Fundamental Research Funds for the Central Universities/ ; 2023WST01//Key laboratory start-up project/ ; 2025ZD01903901//National Science and Technology Major Project on Prevention and Control of Emerging and Major Infectious Diseases/ ; 82020108009//National Natural Science Foundation of China/ ; S2024116//Guangxi Medical and Health Appropriate Technology Development and Promotion Application Project/ ; },
abstract = {BACKGROUND: Lesions of infratemporal fossa (ITF) represent a group of pathologically heterogeneous diseases. Endoscopic biopsy has been the primary diagnostic method. To facilitate precise treatment, we introduced ultrasound fusion-guided core needle (UFCN) biopsy, which offers accuracy, minimal invasiveness, and real-time capability. This study aimed to evaluate the efficacy of UFCN biopsy for ITF lesions.

METHODS: This retrospective cohort study compared patients with ITF lesions who underwent UFCN biopsy or not. Using logistic Poisson regression analysis, we evaluated the efficacy of UFCN biopsy by assessing the rate of general anesthesia endoscope biopsy, the time cost to final pathological diagnosis, and the rate of diagnosis-matched treatment.

RESULTS: Thirteen patients who underwent UFCN biopsy were included in the US group, and 24 patients who did not undergo UFCN biopsy were included in the ES group. Patients in the US group had a significantly lower risk of undergoing endoscopic biopsy under general anesthesia (OR of 0.04 95% CI 0.00-0.25) and a reduced time to diagnosis (OR of 0.68 95% CI 0.54-0.86). Additionally, UFCN biopsy was associated with a higher rate of diagnosis-matched treatment (OR of 47.23 95% CI 4.18-2043.94).

CONCLUSIONS: UFCN biopsy was an effective solution for ITF lesion pathological diagnosis. It can reduce the need for endoscope biopsy under general anesthesia, increase the rate of diagnosis-matched treatment, and shorten the time to pathology confirmation.},
}

@article {pmid41907522,
year = {2026},
author = {Hickman, B and Salonen, A and Kolho, KL and De Vos, WM and Korpela, K},
title = {Associations between the infant gut microbiota and the living environment.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2603823},
pmid = {41907522},
issn = {2993-3935},
abstract = {The human gut microbiota is central to the health and development of the host, and the early-life microbiota is affected by a range of factors that can alter the infant's development for years to come. The role of the external, natural environment in shaping the gut microbiota is still largely unknown. We examined how the environment surrounding the home postnatally is associated with the infant gut microbiota in the first 2 y of life. The study utilized 16 s rRNA data from 893 children's fecal samples from the longitudinal birth cohort HELMi. We show that the environment has a minimal overall association with microbiota development (R[2] < 1%). Air quality explained the greatest degree of variation in microbiota composition, while only forests, agriculture and inland wetlands near the home had any significant association with bacterial genera. The results suggest that the infant gut microbiota is not strongly dependent on the external natural environment, and that the impact of the environment is mostly due to exposure to air pollution that may affect the host's immune system and indirectly the gut microbiota.},
}

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

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

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

@article {pmid41902199,
year = {2026},
author = {Skurnik, M and Tetik, R and Qasim, MS and Sachsenröder, J and Dieckmann, R and Leon-Velarde, CG and Widmalm, G and Strauch, E and Bhattacharjee, A},
title = {Identification of Receptor Binding Proteins of Yersinia Phage φR1-37 and Enterocoliticin That Use the Same Bacterial Surface Receptor.},
journal = {Viruses},
volume = {18},
number = {3},
pages = {},
pmid = {41902199},
issn = {1999-4915},
support = {288701//Research Council of Finland/ ; BfR_45-002//German Federal Institute for Risk Assessment project/ ; 2022 03014//Swedish Research Council/ ; },
mesh = {*Bacteriophages/genetics/metabolism ; *Yersinia enterocolitica/virology/metabolism/genetics ; Protein Binding ; *Bacteriocins/metabolism/genetics ; Multigene Family ; *Receptors, Cell Surface/metabolism ; *Receptors, Virus/metabolism ; },
abstract = {The bacterium Yersinia enterocolitica serotype O:3 is targeted by two distinct agents, the bacteriophage φR1-37 and the bacteriocin-like enterocoliticin (a tailocin), which both utilize the lipopolysaccharide (LPS) outer core (OC) hexasaccharide as their primary host receptor. In order to understand this convergent recognition mechanism, we first characterized the enterocoliticin system, reporting the complete sequence of its large, biosynthetic gene cluster. Most of the 42 predicted gene products were functionally annotated by homology to known gene products. We then focused on identifying the receptor-binding proteins (RBPs) responsible for host attachment of both agents in order to elucidate a possible shared mechanism of binding. For phage φR1-37, the receptor binding complex was identified as the inseparable Gp298 tail fiber protein and its Gp297 trimerization chaperone, confirming its function as the RBP. Based on sequence identity with Gp298, the Orf39 gene product of the enterocoliticin cluster was predicted to be its corresponding RBP. An analytical comparison of the predicted RBPs revealed a highly conserved homologous region spanning 80-85 amino acid residues, which presents the only structural explanation for their identical receptor specificity. To resolve the binding mechanism, we generated high-confidence trimeric structural models for the Gp298 and Orf39 proteins using AlphaFold3-multimer. These models validated the high structural similarity of the RBP domains, despite global dissimilarity of the complete trimeric structures. Further docking simulations with a pentasaccharide ligand (generated by CarbBuilder) provided suggestive molecular models for the protein-carbohydrate interactions within the OC region. Intriguingly, a database search using the identified binding site motif revealed their wide and diverse presence in various phage tail proteins, suggesting that this motif is a specialized, common structure for carbohydrate recognition. This work identifies a conserved, novel sugar-binding motif as the molecular basis of host recognition for these key anti-Yersinia biologics.},
}

*Bacteriophages/genetics/metabolism
*Yersinia enterocolitica/virology/metabolism/genetics
Protein Binding
*Bacteriocins/metabolism/genetics
Multigene Family
*Receptors, Cell Surface/metabolism
*Receptors, Virus/metabolism

@article {pmid41903990,
year = {2026},
author = {Gorji, L and Seldomridge, AN and Holder, AM},
title = {Leveraging the Human Microbiome to Improve Immunotherapy Sensitivity.},
journal = {Surgical oncology clinics of North America},
volume = {35},
number = {2},
pages = {285-298},
doi = {10.1016/j.soc.2025.10.007},
pmid = {41903990},
issn = {1558-5042},
mesh = {Humans ; *Immunotherapy/methods ; *Neoplasms/therapy/immunology/microbiology ; *Microbiota/immunology ; *Precision Medicine/methods ; Tumor Microenvironment/immunology ; },
abstract = {The human microbiome is composed of distinct microbial communities or ecosystems found throughout the human body, including within unique tumor microenvironments. In this review, we discuss the microbiome's influence on solid tumors, how the microbiome can be modulated to improve response to immunotherapy, and how emerging evidence suggests that microbiome modulation can add to the repertoire of personalized medicine.},
}

Humans
*Immunotherapy/methods
*Neoplasms/therapy/immunology/microbiology
*Microbiota/immunology
*Precision Medicine/methods
Tumor Microenvironment/immunology

@article {pmid41904117,
year = {2026},
author = {Chouhan, D and Grossman, AS and Kerns, KA and Stocke, KS and Kim, M and Dong, PT and Kumar, A and Lei, L and Lamont, RJ and McLean, JS and He, X and Bor, B},
title = {Ultrasmall oral Saccharibacteria modulate gingival immunoactivation through type IV pili and TLR2-dependent endocytosis.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-70546-5},
pmid = {41904117},
issn = {2041-1723},
support = {1R01DE031274//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; T90 DE026110-07//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; 1S10OD034405-01//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; T90 DE026110-07//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
abstract = {Saccharibacteria are ultrasmall episymbionts that require host-bacteria to grow. They are positively associated with inflammatory diseases within the human microbiome, yet their mechanisms for interacting with the human host and contributing to diseases remain unknown. This study investigated the tripartite interactions between Saccharibacteria (Nanosynbacter lyticus strain TM7x and other strains), their host/non-host-bacteria, and human oral gingival epithelial cells. Both host and non-host-bacteria strongly induce proinflammatory cytokines in epithelial cells, while Saccharibacteria alone elicits limited immune activation. Remarkably, Saccharibacteria dampened proinflammatory cytokine responses to host/non-host-bacteria during coinfection. Mechanistically, this effect results from Saccharibacteria-mediated clustering and endocytosis of surface TLR2 receptor, ultimately leading to reduce TLR2-mediated cytokine signalling. Sacchribacteria type IV pili appendages facilitate epithelial cell binding and subsequent immune dampening via direct interaction between pili adhesins and TLR2. High resolution imaging shows that Saccharibacteria are internalized by epithelial cells through caveolin-mediated endocytosis, subsequently colocalize with endosome markers, and eventually are trafficked to lysosomes for degradation. Moreover, a subset of the Saccharibacteria survives lysosomal degradation and retains the ability to reinfect host-bacteria, highlighting a mechanism for transient persistence in the oral microbiome and a vital role in human immune and microbiome modulation.},
}

@article {pmid41895287,
year = {2026},
author = {Gubatan, J and Sojwal, RS and Ye, J and Boye, TL and Hoang, JN and Fardeen, T and Temby, M and Rubin, SJS and Spencer, SP and Kotagiri, P and Rogalla, S and Rosen, MJ and Nielsen, OH and Boyd, S and Sonnenburg, J and Sinha, SR},
title = {Multi-omics reveal vitamin D regulation of immune-gut microbiome interactions and tolerogenic pathways in inflammatory bowel disease.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102703},
doi = {10.1016/j.xcrm.2026.102703},
pmid = {41895287},
issn = {2666-3791},
abstract = {Loss of immune tolerance to the gut microbiome plays a pathogenic role in inflammatory bowel disease (IBD). How dietary factors alter host immune-gut microbiome interactions in IBD is unclear. Here, we apply multi-omics (immunoglobulin A or G and 16S rRNA sequencing [IgA-seq, IgG-seq], blood single-cell RNA sequencing [scRNA-seq], and immune repertoire sequencing) to investigate the effects of 12 weeks of vitamin D on host immune microbe interactions in patients with IBD. Vitamin D treatment associates with decreased disease activity and inflammatory markers and increased IgA-bound and decreased IgG-bound gut microbiota. Vitamin D alters the profiles of IgA-bound (increased Lachnospiraceae, Blautia) and IgG-bound (decreased Proteobacteria, Enterococcaceae) gut bacteria. Vitamin D increases B cell activating factor (BAFF) signaling between plasmacytoid dendritic cells and B cells, alters BCR and TCR clonotypes that associate with Ig-bound gut microbiota, and increases α4β7+ B and T regulatory cells. Our results demonstrate that vitamin D promotes immune tolerance to gut microbiota in patients with IBD. Clinical trial is registered under NCT04828031.},
}

@article {pmid41898386,
year = {2026},
author = {Tahtouh Zaatar, M and Othman, R and Abushawish, M and Akl, M and Alachkar, MT and Almatboona, G and Alriyami, F and Alshaibani, A and Ashkanani, D and Basharova, M and Imam, M and Khassay, N and Mikhael, MS and Naderi Far, R and Shaqra, S and Verwey, K and Suleimanova, A and Yousafzada, M and Burmagina, Y},
title = {The Women's Microbiome: Molecular Insights, Clinical Gaps, and Future Frontiers in Precision Health with Implications for Gulf Cooperation Council Populations.},
journal = {International journal of molecular sciences},
volume = {27},
number = {6},
pages = {},
doi = {10.3390/ijms27062521},
pmid = {41898386},
issn = {1422-0067},
mesh = {Humans ; Female ; *Microbiota ; *Women's Health ; *Precision Medicine ; Probiotics ; Pregnancy ; Vagina/microbiology ; Gastrointestinal Microbiome ; },
abstract = {The human microbiome has emerged as a central regulator of health and disease; however, women-specific microbiome research has only recently gained focused scientific attention. Accumulating evidence demonstrates that microbial ecosystems across the gut, vagina, skin, breast tissue, and reproductive tract are dynamically shaped by female hormones, life-stage transitions, and environmental exposures. These interactions influence immune regulation, metabolic homeostasis, reproductive outcomes, mental health, and cancer risk, in part through microbiome-mediated endocrine pathways such as the estrobolome. Advances in high-resolution molecular technologies-including metagenomics, metabolomics, spatial and single-cell profiling, and artificial intelligence-driven modeling-have shifted microbiome research from descriptive taxonomy toward functional, mechanistic, and predictive science. These approaches highlight microbial function and metabolite production as stronger determinants of health outcomes than taxonomic composition alone. Nonetheless, major gaps persist, including limited causal evidence, methodological heterogeneity, underrepresentation of non-Western populations, and barriers to clinical translation. Microbiome-targeted interventions, including probiotics, prebiotics, postbiotics, and emerging microbiota-based therapies, have garnered increasing interest in women's health. Select Lactobacillus and Bifidobacterium strains show potential in modulating vaginal and gastrointestinal health, pregnancy outcomes, and immune function; however, clinical effects remain highly strain-specific and context-dependent. Discrepancies between experimental findings, commercial claims, and validated clinical use underscore the need for rigorous, women-centered trials and standardized outcome measures. This narrative review synthesizes current molecular insights into the women's microbiome across endocrine interactions, pregnancy, reproductive and metabolic health, lifestyle influences, and microbiome-based therapeutic strategies. We integrate clinical perspectives to identify diagnostic and translational challenges and propose future directions emphasizing precision microbiome medicine, validated biomarkers, careful evaluation of microbiome-targeted interventions, and inclusive research frameworks, including populations from the Gulf Cooperation Council (GCC). Collectively, this review positions the microbiome as a critical yet underutilized axis in women's health and outlines a roadmap toward personalized, evidence-based care across the female lifespan.},
}

Humans
Female
*Microbiota
*Women's Health
*Precision Medicine
Probiotics
Pregnancy
Vagina/microbiology
Gastrointestinal Microbiome

@article {pmid41900479,
year = {2026},
author = {Park, H and Kim, JS and Kim, DJ and Suk, KT},
title = {Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030720},
pmid = {41900479},
issn = {2076-2607},
support = {NRF-2020R1I1A3073530//National Research Foundation of Korea/ ; NRF-2020R1A6A1A03043026//National Research Foundation of Korea/ ; },
abstract = {Advances in sequencing technologies have transformed human microbiome research, yet most analyses still rely on species-level profiles. However, strains rather than species represent the true ecological and functional units of the microbiome. Individual strains can vary substantially in gene content, metabolic capacity, virulence factors, antimicrobial resistance, and host-interaction properties. These differences critically influence immune responses, epithelial barrier integrity, disease susceptibility, and therapeutic outcomes. Here, we synthesize recent human microbiome studies that provide robust strain-resolved evidence, focusing on three major themes: (i) the emergence and long-term persistence of personalized strain repertoires, (ii) strain-specific pathobiont traits that drive host pathology, and (iii) the implications of strain-level ecology for the development of next-generation microbiome therapeutics. We also highlight key methodological innovations including high-resolution amplicon profiling, advanced metagenomic and single-cell genomics, and culture-based functional approaches that collectively enable strain-level resolution and are reshaping the field.},
}

@article {pmid41889649,
year = {2026},
author = {Su, R and Ma, J and Li, J and Liu, Y and Ma, T and Wang, J and Mai, Q and Ma, Q and Wang, J and Wang, H and Yang, S and Zhang, X},
title = {Fecal microbiota transplantation ameliorates alcohol-associated liver disease through coordinated restoration of short-chain fatty acid and α-linolenic acid signaling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1744446},
pmid = {41889649},
issn = {1664-302X},
abstract = {BACKGROUND: Alcohol-associated liver disease (ALD) is closely linked to gut microbiota dysbiosis. However, the specific microbial metabolic functions that drive the transition from microbial imbalance to hepatic inflammation and metabolic injury remain unclear, limiting the development of mechanism-based therapeutic strategies.

METHODS: This study integrated human microbiome analysis with fecal microbiota transplantation (FMT) experiments in an ALD mouse model. Multi-omics approaches, including 16S rRNA gene sequencing, untargeted metabolomics, and immunological profiling, were employed to systematically characterize the interactions among gut microbiota composition, microbial-derived metabolites, and host immune responses.

RESULTS: We observed that ALD progression was characterized by an early shift in microbial composition followed by a marked decline in microbial diversity, culminating in an ecological collapse of the gut microbiota. FMT from healthy donors significantly improved liver histopathology and serum biochemical parameters, accompanied by restoration of gut microbial diversity and key metabolic functions. Metabolomic analyses revealed enhanced short-chain fatty acid (SCFA) production and activation of α-linolenic acid (ALA)-related metabolic pathways following FMT. These metabolic improvements were associated with reduced inflammatory responses and improved immune homeostasis.

CONCLUSION: Our findings demonstrate that FMT from healthy donors ameliorates ALD by restoring critical microbial metabolic functions, particularly SCFA production and ALA-related pathways. These results highlight microbial metabolic function as a promising therapeutic target for microbiome-based interventions in ALD.},
}

@article {pmid41892691,
year = {2026},
author = {Li, L and Smardz, M and Soh, D and Marsh, PD and Hoare, A and Diaz, PI},
title = {Nutritional Pressure from Serum Amplifies Dysbiotic Features in an Oral Microbiome Synthetic Community.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag070},
pmid = {41892691},
issn = {1751-7370},
abstract = {Despite rapid advances in characterizing the human microbiome, the ecological pressures shaping its transitions from healthy to diseased states remain poorly resolved. This is particularly true for periodontitis, a slow-progressing chronic inflammatory disease associated with well-defined shifts in the subgingival microbiome. Here, we report the development of a complex synthetic community model of the subgingival microbiome, designed for systematic interrogation of ecological factors that drive community restructuring. The model includes 22 prevalent and abundant subgingival species maintained in mucin-rich medium under microaerophilic, continuous culture conditions, in a chemostat. Using this system, we interrogated the impact of serum, as a surrogate for the inflammatory exudate produced by the host in response to biofilm accumulation, on community structure and function. Through integrated 16S rRNA gene sequencing, metatranscriptomics, and metabolomics, we found that serum was not required for a community with a periodontitis-like configuration to establish, but its presence intensified features of dysbiosis. Serum increased total biomass, promoted polymicrobial aggregate formation, promoted nitrogen and protein metabolism thereby modifying the environmental pH towards alkalinity, and introduced nitrosative stress. Serum also modified the community metatranscriptome in ways that paralleled microbiome activities in human periodontitis. Serum, however, decreased community diversity by disproportionally conferring a competitive advantage to the pathogen Porphyromonas gingivalis. This synthetic community model has revealed serum as a key nutritional pressure that modulates subgingival microbiome ecology and may perpetuate dysbiosis.},
}

@article {pmid41894083,
year = {2026},
author = {Li, Y and Jiang, M and Pang, J and Ma, C and Zhang, H and Yin, F and Jia, Y and Zou, X and Zuo, T and Zhang, H},
title = {High-altitude exposure remodels the gut microbiota: health and disease.},
journal = {MedScience},
volume = {},
number = {},
pages = {},
pmid = {41894083},
issn = {3091-4981},
abstract = {With the increasing number of individuals travelling to or residing in high-altitude regions, understanding the physiological and pathological consequences of such environments has become increasingly important. High-altitude exposure poses significant challenges to human health, primarily due to hypobaric hypoxia, which triggers a cascade of responses, including energy deficiency, oxidative stress, and inflammation. One of the critical consequences is the disruption of the gut barrier, which facilitates the translocation of the gut microbiota and further exacerbates local and systemic inflammation. Notably, the gut microbiota, a dynamic environmental sensor, undergoes significant remodelling in high-altitude environments. The modified production of microbial metabolites such as bile acids influences gut homeostasis as well as glucose and lipid metabolism, and ultimately contributes to individual variability in high-altitude acclimatization. These changes have been implicated in the pathogenesis of altitude-related illnesses such as acute and chronic mountain sickness, as well as in metabolic and gastrointestinal disorders such as diabetes, obesity, irritable bowel syndrome, colorectal cancer, cholelithiasis, and osteoporosis. Preliminary explorations have demonstrated the therapeutic potential of microbiome-based interventions such as faecal microbiota transplantation in acute and chronic mountain sickness. Further research into gut microbiota modulation may provide applicable options for promoting high-altitude acclimatization and preventing high-altitude illness.},
}

@article {pmid41882398,
year = {2026},
author = {Addington, E and Gannon, A and Larcombe, DE and Lawaetz, AC and McHugh, RE and Vahtokari, S and Munnoch, JT},
title = {Microbial Biotechnology in Medicine.},
journal = {Progress in molecular and subcellular biology},
volume = {62},
number = {},
pages = {217-250},
pmid = {41882398},
issn = {0079-6484},
mesh = {Humans ; *Biotechnology/methods ; Synthetic Biology/methods ; Microbiota ; Probiotics/therapeutic use ; Animals ; Precision Medicine ; },
abstract = {The convergence of biology, technology, and medicine has revolutionised healthcare, with microbial biotechnology at the forefront. While many microbes are often considered solely for their infectious properties, many are major producers of natural products, including antimicrobials. Now, not only sources of clinically relevant drugs, they are also being directly engineered for advanced applications such as targeted drug delivery, immune modulation, and precision therapeutics. Microorganisms are key sources of novel antimicrobials, immunomodulatory, and anticancer agents, which synthetic biology and genomics mining can exploit. Bioengineering and exploration of underused microbial taxa offer promising solutions to the problem of rising antimicrobial resistance. Microbes also play crucial roles in modern vaccine development, from live attenuated to recombinant antigen production. The human microbiome has emerged as an interesting player in health, driving innovations in diagnostics and therapies that include next-generation probiotics and microbiota transplants. Furthermore, synthetic biology further empowers the design of 'smart' microbes for in situ therapeutic functions like imaging, biosensing, and targeted treatment. While transformative, these innovations also raise critical ethical and regulatory concerns, including biosafety, ecological impact, data privacy, and equitable access. This chapter explores the multifaceted roles of microbes in medical biotechnology-spanning therapeutics, vaccines, microbiome-based interventions, and engineered systems-underscoring their importance in the evolution of sustainable, personalised healthcare.},
}

Humans
*Biotechnology/methods
Synthetic Biology/methods
Microbiota
Probiotics/therapeutic use
Animals
Precision Medicine

@article {pmid41882400,
year = {2026},
author = {Hacioglu, O},
title = {Microbiota and Microbiome.},
journal = {Progress in molecular and subcellular biology},
volume = {62},
number = {},
pages = {307-331},
pmid = {41882400},
issn = {0079-6484},
mesh = {Humans ; *Microbiota ; Dysbiosis/microbiology ; Animals ; Bacteria/genetics ; Host Microbial Interactions ; },
abstract = {The human microbiota represents a complex and dynamic ecosystem composed of microorganisms from various taxonomic groups, including bacteria, viruses, fungi, archaea, and protozoa. These microorganisms inhabit different anatomical regions of the human body, such as the genitourinary system, the gastrointestinal tract, the oral cavity, the skin, and the respiratory tract, exhibiting distinct densities, compositions, and functional characteristics, and interact reciprocally with the host organism. The term microbiota not only defines the diversity and abundance of microorganisms but also encompasses their functional influence on host physiology. At this point, the concept of the microbiome becomes relevant. The microbiome refers to the collective genomic content of all microorganisms comprising the microbiota, that is, their genetic material and the potential biological functions encoded by their genes. Therefore, microbiome analysis enables not only the assessment of microbial diversity, but also of metabolic capacity, signal transduction, immune regulation, and other host-microbe interactions. The microbiota and microbiome play important roles in preserving human health and homeostatic balance. A healthy microbial composition promotes immune system development, aids digestion and nutrient absorption, reduces pathogenic microorganism colonization, and contributes to the integrity of the mucosal barrier. In contrast, dysbiosis, or disruption of microbial equilibrium, has been linked to a variety of pathophysiological illnesses, including inflammatory diseases, metabolic disorders, neurodegenerative diseases, and some neoplasms. Today, microbiome research is not only essential for understanding health and disease mechanisms but also forms the foundation for innovative future medical applications.},
}

Humans
*Microbiota
Dysbiosis/microbiology
Animals
Bacteria/genetics
Host Microbial Interactions

@article {pmid41884244,
year = {2026},
author = {Salvadori, M and Rosso, G},
title = {Gut-kidney axis: Dysbiosis and renal disease.},
journal = {World journal of nephrology},
volume = {15},
number = {1},
pages = {115357},
pmid = {41884244},
issn = {2220-6124},
abstract = {According United States renal data system the morbidity rate for chronic kidney disease (CKD) is 2.5 times than patients not affected by CKD and the mortality rate is 144.9 per 1000 persons-years. The gut microbiota is involved in uremic toxins (UTs) production. This fact was demonstrated by experiments in rats, which revealed better survival in CKD rats that were deprived of the gut microbiota. In men, UT levels are low in CKD patients without a colon. Diet may affect the gut microbiota through food additives such as prebiotics, probiotics and post biotics. Conservation processes and food processing may also affect the gut microbiota. Other factors are food quantity and composition. The gut microbiota may be the cause of UTs production and accumulation in the blood. Additionally, there is interplay among different organs such as liver, kidney and gut. Several theories have been formulated to justify the interplay between the metabolic dysfunctions. In particular, the increase of species such as Eggerthelia lenta, Fusobacterium nucleatum and Alistipes shahii leads to an increase of the aromatic amino acids degradation, and secondary bile acids and trimethyamine oxide biosynthesis in the intestine. This fact determines an increase of the levels of UT precursors such as indole, p-cresol, phenol, phenylacetaleyde, benzoic acid and trimethylamine. Recent studies document the following. The human microbiome project revealed that the gut microbiota may play an important role in both human health and diseases, including kidney disease. Recently, several studies have shown a strict correlation between the gut microbiota and CKD. Probiotics, prebiotics and synbiotics are possible therapies. Probiotics are living microorganisms that, consumed in adequate quantities, are beneficial for the patient, and act on the intestinal microbiome equilibrium. Lactobacilli and Bifidobacteria are common examples of probiotics. Prebiotics are generally fibers not absorbed by the gut, representing a selective nutrient for the microbiome already present in the gut, which favors their growth and activity. Inulin, fructo-oligosaccharides and other fibers are examples of prebiotics. The association and synergism between probiotics and prebiotics is symbiotic.},
}

@article {pmid41877507,
year = {2026},
author = {Lee, JG and Lim, J and Cho, NJ and Park, S and Gil, HW and Seo, H and Song, HY and Park, SH and Oh, KH and Kim, YL and Bieber, BA and Pisoni, RL and Lee, EY and , },
title = {Xerosis elevates the risk of catheter-related infections in peritoneal dialysis patients.},
journal = {Kidney research and clinical practice},
volume = {},
number = {},
pages = {},
doi = {10.23876/j.krcp.24.275},
pmid = {41877507},
issn = {2211-9132},
abstract = {BACKGROUND: Catheter-related infections, such as exit-site infection and tunnel infection, are major complications in peritoneal dialysis (PD) patients, affecting their prognosis. This study investigates the association between skin conditions and catheter-related infections.

METHODS: Data from two distinct sources were analyzed: (1) 626 PD patients in the Korean arm of the Peritoneal Dialysis Outcomes and Practice Patterns Study (PDOPPS) and (2) skin microbiome data from 76 dialysis patients at Soonchunhyang University Cheonan Hospital. The relationship between catheter-related infection and self-reported xerosis and pruritus severity was assessed by Cox regression. Risk factors for xerosis and pruritus were evaluated by logistic regression. Furthermore, we discovered the relationship between the severity of pruritus and the relative abundance of Staphylococcus aureus on the skin.

RESULTS: The risk of catheter-related infections in PD patients increased with xerosis (hazard ratio [HR], 2.71; 95% confidence interval [CI], 1.19-6.18) and pruritus (HR, 2.57; 95% CI, 1.27-5.22), particularly increasing the risk of S. aureus-associated catheter-related infections (xerosis: HR, 5.66; 95% CI, 1.97-16.30; pruritus: HR, 5.93; 95% CI, 2.18-16.15). The relative abundance of S. aureus was notably higher in patients with severe pruritus. Moreover, patients were more likely to exhibit severe xerosis if they owned pets, had higher serum creatinine levels, and elevated calcium-phosphorus product levels.

CONCLUSION: Xerosis and pruritus significantly increase the risk of catheter-related infections, especially those caused by S. aureus. Instead of relying solely on prophylactic antibiotics for infection prevention, this study highlights the need for new preventive strategies in PD patients, focusing specifically on effective skin management.},
}

@article {pmid41879296,
year = {2026},
author = {Penney, R and Buchanan, LB and Rojas-Vargas, J and Lin, J and Khan, Y and Davidson, J and Wilson, CA and Tai, V and Russo, TA and Hope, TJ and Wilcox, H and Monari, B and Ravel, J and Al, KF and Dave, S and Wang, PZT and Burton, JP and Prodger, JL},
title = {Pathological phimosis is associated with foreskin immune cell infiltration but not microbiota composition.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0072525},
doi = {10.1128/msphere.00725-25},
pmid = {41879296},
issn = {2379-5042},
abstract = {UNLABELLED: The penile microbiota has been implicated in genital inflammation and increased risk of HIV, HPV, HSV-2, and female-partner bacterial vaginosis in adult males, yet its development during childhood and potential role in pediatric foreskin pathologies remain unknown. We characterized the coronal sulcus microbiota of 75 pediatric males (median age 8.5 years; 43% with pathological phimosis) before and after circumcision and compared these profiles to 56 uncircumcised adult men. Pediatric penile microbiota were highly diverse, dominated by strict and facultative anaerobes, and loosely structured compared to adults, who exhibited two distinct, ecologically organized communities. Circumcision markedly reduced anaerobic taxa and increased Corynebacterium and Staphylococcus. Pathological phimosis (the inability to retract the foreskin due to scarring) was associated with increased densities of CD3+ T cells, CD4+ cells, and CD11c+ dendritic cells, suggesting an adaptive immune mechanism; however, pathological phimosis was not associated with microbiota composition. Nonetheless, Mobiluncus was negatively correlated with CD11c+ dendritic cells, while Campylobacter and Peptoniphilus were negatively correlated with CD56+ NK cells, suggesting microbe-immune interactions. Our data suggest pathologic phimosis is driven by adaptive immune responses but not by specific bacteria; the pathology may be driven by differences in host responses to bacteria or by other stimuli, such as fungal antigens. Our data also demonstrate that the transition to adulthood is accompanied by reorganization of penile communities into structured types previously linked to infection risk, highlighting puberty as a potential window for interventions that promote protective adult microbiota and improve lifelong sexual and reproductive health.

IMPORTANCE: The human penis hosts complex bacterial communities that can influence inflammation, infection risk, and sexual health, but little is known about how these communities form early in life or whether they contribute to childhood foreskin inflammatory disorders. We combined 16S rRNA sequencing with quantitative microscopy to investigate the penile microbiota in boys and its relationship to pathological phimosis, a common condition marked by foreskin scarring. We found that phimosis is associated with infiltration of T cells and dendritic cells, indicating an adaptive immune process, but with no associations with specific bacteria. We also show that penile microbiota reorganize during puberty into structured community types previously linked to HIV and sexually transmitted infection risk. These findings suggest that childhood pathologic phimosis is mediated by adaptive immune responses rather than driven by specific bacterial communities and identify puberty as a critical period for shaping adult penile microbiota, with implications for lifelong genital health.},
}

@article {pmid41872622,
year = {2026},
author = {Lee, H and Oh, Y and Seo, TW and Choi, YB and Kim, S and Cheon, S and Lee, DG and Kang, S and Han, K and Heo, YM and Mun, S},
title = {Exploring Cyclo (-Gly-Pro) for inflammation modulation in atopic dermatitis: a study on streptococcal postbiotics.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {41872622},
issn = {2092-9293},
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by intense itching and eczematous lesions, significantly affecting quality of life. Complex interactions involving genetic predispositions, environmental factors, and immune dysregulation contribute to AD pathogenesis, with impaired skin barriers and Staphylococcus aureus playing critical roles. Recent interest in postbiotics, beneficial compounds derived from probiotics, has opened potential therapeutic avenues.

OBJECTIVE: This study investigates the postbiotic solution derived from three human skin-derived Streptococcus isolates, to identify a core bioactive compound and its therapeutic role in AD.

METHODS: Using GC-MS and GC-FID, we quantified Cyclo (-Gly-Pro) and assessed its impact on inflammatory biomarkers in an AD-like keratinocyte cell model. The effect of different incubation temperatures on the compound's production was also analyzed. Furthermore, 16S V3-V4 amplicon sequencing was performed to analyze changes in the skin microbiome of AD patients following treatment.

RESULTS: Cyclo (-Gly-Pro) was consistently present across all strains, with production inversely related to incubation temperature, peaking at 25 °C. Our findings suggest that optimized production conditions and potential synergistic effects with other postbiotic components could enhance therapeutic efficacy.

CONCLUSION: These results support further in vivo research to elucidate the mechanisms and validate the compound's role in AD treatment strategies, potentially leading to novel dermatological therapies.},
}

@article {pmid41873970,
year = {2026},
author = {Valenzuela-Diaz, S and Dikareva, E and Hickman, B and Kiljunen, S and Kolho, K-L and de Vos, W and Salonen, A and Korpela, K},
title = {Impact of phage enrichment on the observed infant gut phageome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0215325},
doi = {10.1128/spectrum.02153-25},
pmid = {41873970},
issn = {2165-0497},
abstract = {The human gut microbiota, particularly during infancy, plays a pivotal role in shaping long-term health outcomes. While research on the bacterial microbiota has advanced rapidly, the infant gut virome-dominated by bacteriophages-remains underexplored due to technical challenges in viral DNA detection and recovery. To address this, we optimized a polyethylene glycol (PEG)-based protocol for phage DNA enrichment tailored to the constraints of infant fecal samples, focusing on maximizing viral yield from minimal input material. We validated the optimized protocol on fecal samples from 41 infants at 1, 6, and 12 months of age and assessed the impact of phage enrichment on the observed gut phageome. The results demonstrate that the optimized protocol improves viral DNA recovery and significantly alters the observed virome composition, especially in older infants. Without appropriate enrichment, key features of the gut virome may be underrepresented or missed entirely. These findings underscore the importance of protocol optimization in virome studies and provide a scalable, cost-effective method for robust infant gut virome profiling.IMPORTANCEUnderstanding the viral component of the infant gut microbiome is essential for uncovering its role in early-life health, yet technical limitations have hindered its study. This work presents a systematically optimized and validated protocol for enriching viral DNA from infant stool samples, designed specifically for low-input material typical of early life. By adapting polyethylene glycol-based precipitation methods, we achieved consistent and scalable recovery of viral DNA across infants of different ages. Application of this protocol revealed key age- and delivery mode-specific differences in phage diversity and replication strategies that were undetectable using standard approaches. Our findings demonstrate that careful protocol optimization is critical for accurate virome profiling in infants and offer a practical solution to overcome longstanding methodological challenges in the field.},
}

@article {pmid41874246,
year = {2026},
author = {Koh, H},
title = {Phylogeny-informed random forests for human microbiome studies.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0345125},
doi = {10.1128/spectrum.03451-25},
pmid = {41874246},
issn = {2165-0497},
abstract = {UNLABELLED: Random Forest is a widely used tree-based ensemble learning algorithm that efficiently captures complex nonlinear relationships and higher-order feature interactions with no distributional assumptions to be satisfied. It is also well-suited to human microbiome studies, where the data are highly skewed, overdispersed, discrete, and irregular. Here, I pay particular attention to the phylogenetic tree information that reflects evolutionary ancestry and functional relatedness among microbial features. Proper incorporation of phylogenetic tree information into microbiome data analysis has provided new insights and improved analytical performance. In this paper, I introduce an extension of the Random Forest algorithm that incorporates phylogenetic tree information, named Phylogeny-Informed Random Forests (PIRF), to improve predictive accuracy in human microbiome studies. The core mechanism of PIRF lies in its localized approach; rather than treating all features as competing globally to be selected or weighted, PIRF identifies informative features within each phylogenetic cluster (i.e., a localized group of microbial features that are evolutionarily and functionally related), thereby enriching functional representations while reducing tree-to-tree correlation. I demonstrate the high predictive accuracy of PIRF, compared with other off-the-shelf tools, across seven benchmark tasks: four classification problems (gingival inflammation, immunotherapy response, type 1 diabetes, and obesity) and three regression problems (cytokine level, age based on oral microbiome, and age based on gut microbiome).

IMPORTANCE: PIRF is an extension of the Random Forest algorithm that incorporates phylogenetic tree information to improve predictive accuracy in human microbiome studies. PIRF can serve as a useful tool for microbiome-based disease diagnostics and personalized medicine. The software and tutorials are freely available as an R package, named PIRF, at https://github.com/hk1785/PIRF.},
}

@article {pmid41867523,
year = {2026},
author = {Kanno, N and Ohtani, T and Oda, N and Kato, S and Ohkuma, M and Shigeto, S},
title = {Domain-Level Classification of Archaea and Bacteria Using AI-Assisted Single-Cell Raman Spectroscopy.},
journal = {ACS omega},
volume = {11},
number = {10},
pages = {16913-16921},
pmid = {41867523},
issn = {2470-1343},
abstract = {Archaea and Bacteria are two fundamentally distinct domains of life that share prokaryotic traits, yet differ markedly in molecular and cellular architecture. While many archaeal species identified thus far have been found in extreme environments, recent metagenomic studies have revealed their widespread presence in moderate habitats, including soils, oceans, and even the human microbiome. However, archaea remain less well characterized than bacteria, largely due to the technical challenges associated with culturing and identifying these microorganisms. In this study, we present a culture-independent method for discriminating archaea from bacteria at the single-cell level using Raman spectroscopy combined with machine learning. We constructed a Raman spectral data set comprising 22 prokaryotic species (11 archaea and 11 bacteria) and developed a domain-level Archaea-Bacteria (AB) classifier using the LightGBM tree-based machine learning algorithm. Our AB classification model achieved an average classification accuracy of 89.1% and a sensitivity of 98.1% on eight representative species (including two independent held-out test species) with minimal data size and preprocessing. We also compared its performance to convolutional neural networks with transfer learning, a widely used deep learning approach. Our method provides a robust analytical framework for archaeal detection and represents a valuable addition to the microbiological toolkit, particularly for studying unculturable or low-abundance archaeal populations in complex microbial communities.},
}

@article {pmid41869825,
year = {2026},
author = {Mehta, A and Stebliankin, V and Mathee, K and Narasimhan, G},
title = {MEditome: Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {15578666261428562},
doi = {10.1177/15578666261428562},
pmid = {41869825},
issn = {1557-8666},
abstract = {RNA editing is a post-transcriptional modification that alters single-nucleotide sites within RNA strands, thus diversifying transcriptomes and proteomes and modulating gene expression. While better characterized in eukaryotes and in a few microbes, the study of RNA editing in entire microbiomes remains unexplored. Recent studies have demonstrated that A-to-I RNA editing contributes to bacterial adaptation and pathogenicity. Previously, we developed MetaEdit, a reference-based computational pipeline to detect RNA edit sites in microbiomes. While MetaEdit successfully identified RNA edit sites in Escherichia coli within the context of the human gut microbiome, including previously reported loci, it relied primarily on aligning reads to reference genomes of target bacteria. This dependence on reference genomes introduced potential biases, as editing can only be identified in reference genomes, while editing in novel microbial strains missing from the reference databases could be overlooked. Even for reference genomes, the search for edit sites is inefficient since it would have to be conducted one reference genome at a time.Here, we introduce MEditome, employing de novo assembly to overcome these limitations. This crucial change enables the detection of RNA edit sites across all microbial organisms in the microbiome, including novel bacterial strains for which comprehensive reference genomes are unavailable. Using sequencing data from the Integrative Human Microbiome Project, MEditome identified 2,295 unique RNA editing sites across diverse bacterial taxa. Several of these overlaps with previously identified edits in E. coli detected by MetaEdit in hok/gef gene family and arginine-associated genes, providing in silico validation of accuracy. We observed taxon-specific editing patterns and gene-level differential editing associated with inflammatory bowel disease, highlighting RNA editing as a potential regulatory mechanism influencing microbial adaptation and host-microbe interactions.},
}

@article {pmid41870192,
year = {2026},
author = {Ranga, A and Malhotra, AG and Singh, J and Pandey, KM},
title = {Genomic Sequencing from Sanger to Next-Generation Sequencing: Historical Context, Comparative Advances, and Prospects for Next-Generation Phenomics.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261433762},
doi = {10.1177/15578100261433762},
pmid = {41870192},
issn = {1557-8100},
abstract = {DNA sequencing has revolutionized biological and biomedical research, offering profound insights into genome organization, function, and variability. From the pioneering Sanger capillary electrophoresis method to the advent of next-generation sequencing, the field has evolved toward unprecedented speed, scalability, and cost decreases over the years. These advancements have enabled diverse applications across genomics, transcriptomics, metagenomics, epigenomics, and precision medicine, powering global initiatives such as the Human Genome Project, the Human Microbiome Project, and the 1000 Genomes Project. Bioinformatics has also advanced in data processing, variant detection, and functional annotation, helping transform raw sequencing data into biologically meaningful insights and knowledge. Although highly advanced, sequencing technologies still encounter challenges, including accuracy trade-offs and the need for efficient management of rapidly increasing volumes of data. Leveraging the genomic revolution, this review explores the shifts toward next-generation phenomics (NGP), an archetype that uses artificial intelligence that integrates multi-omics data with digital phenotyping, the Internet of Things, and real-time analytics. The goal of NGP is to integrate genotypic and phenotypic data to support predictive modeling of health, disease, and environmental interactions. By tracing history, advances in sequencing technologies, and future perspectives on NGP, this article offers a comprehensive overview for researchers and clinicians, highlighting how the integration of omics and digital data will drive the generation of personalized and systems-level biology.},
}

@article {pmid41859029,
year = {2026},
author = {Darby, P and Kilgour, E and Then, CK and Bromiley, A and McLellan, J and Kiltie, AE},
title = {Inter-observer variability in radiotherapy contouring with the use of autocontouring software: A systematic review.},
journal = {Clinical and translational radiation oncology},
volume = {58},
number = {},
pages = {101144},
pmid = {41859029},
issn = {2405-6308},
abstract = {Inter-observer variability (IOV) in radiotherapy contouring remains a significant source of uncertainty, especially for complex anatomical regions. Autocontouring software, including both atlas-based and deep-learning-based models, aims to improve contouring consistency and reduce workload. A systematic review was conducted in accordance with PRISMA guidelines to evaluate the impact of autocontouring software on IOV. Twenty-five eligible studies were identified that quantitatively assessed IOV using these tools. Extracted data included anatomical site, observer and case numbers, contouring method and evaluation metrics. Most studies reported significant reductions in IOV with the use of autocontouring. Edited autocontours frequently achieved mean Dice Similarity Coefficient (DSC) values above 0.85 for clinical and planning target volumes and 0.90 for organs at risk (OARs) with well-defined anatomy, using deep learning methods. Deep-learning-based models demonstrated greater consistency compared to atlas-based methods. Structures such as the lungs, heart and bladder showed the most substantial improvements, while anatomically indistinct targets such as the prostate bed and pelvic lymph nodes showed limited benefit. However, discrepancies remained between observers for certain structures despite the use of automation. Overall, autocontouring tools, particularly deep-learning models, improve contouring consistency in radiotherapy planning. However, performance is strongly influenced by anatomical complexity and segmentation method. Larger multi-institutional studies and standardised evaluation protocols are needed to support widespread clinical adoption and strengthen quality assurance.},
}

@article {pmid41861247,
year = {2026},
author = {Allen, WJ and Williams, S and Collinson, I},
title = {The Great Escape: Protein Trafficking from the Bacterial Cytosol to the Outer Membrane.},
journal = {Annual review of biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biochem-051024-011856},
pmid = {41861247},
issn = {1545-4509},
abstract = {To protect their delicate, carefully curated contents from the world, bacteria encase themselves within a protective envelope made up of sugars, lipids, and proteins. Cell envelopes give bacteria their characteristic shapes, provide rigidity and mechanical stability, and form a selective antechamber-granting access only to a desirable subset of environmental substances. Yet this protective layer is a double-edged sword: Its effectiveness at keeping things out also makes it difficult for things to leave, including the proteins required to interface with the outside world and form the envelope itself. Bacteria have solved this problem by constructing an array of proteinaceous nanomachines that expend energy to selectively shuttle proteins and other building blocks to their intended destinations. Here, we present an overview of our current understanding of how these transporters work, focusing on the major, conserved machines that ferry proteins across the cell envelope throughout the domain Bacteria. The emphasis is on recent discoveries and open questions, with the hope that answering these will provide new avenues to help combat the rising threat of antimicrobial resistance and the rapidly expanding list of diseases linked to human microbiome composition.},
}

@article {pmid41862100,
year = {2026},
author = {Cordeiro, J and Macela, C and Kleiner, R and Vaskovich-Koubi, D and Moura, LIF and Satchi-Fainaro, R and Florindo, HF},
title = {Harnessing the power of microbiome, nanotechnology, and immunity against cancer.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114839},
doi = {10.1016/j.jconrel.2026.114839},
pmid = {41862100},
issn = {1873-4995},
abstract = {The human microbiome has emerged as a key player in health and disease, including cancer, which remains one of the leading causes of mortality worldwide. Although advances in understanding the tumor immune microenvironment and the development of immunotherapies have transformed cancer treatment, clinical efficacy remains limited by suboptimal response rates and severe side effects. Recent integrative research in cancer biology, immune-oncology, and cancer microbiome research, enabled by omics technologies and advanced bioinformatics, has begun to reveal intricate links between the microbiome, cancer progression, and immune modulation. These findings underscore the microbiome's pivotal role in shaping both therapeutic efficacy and resistance mechanisms. Currently, nanotechnology, propelled into mainstream success through the development of COVID-19 mRNA vaccines, is offering new tools for precision oncology. Nanomaterials are now being explored not only for targeted drug delivery but also for monitoring and modulating the microbiome, with significant potential for biomarker discovery and personalized medicine. In this article, we explore the role of the microbiota in tumorigenesis and cancer therapy, with a particular focus on its crosstalk with the immune system. We highlight emerging microbiota-targeted therapeutic strategies and discuss how nanotechnology-based systems are being designed to modulate the microbiome-immune-cancer axis. Finally, we discuss future directions in leveraging the convergence of microbiome science, nanotechnology, and immunotherapy to advance cancer treatment.},
}

@article {pmid41862195,
year = {2026},
author = {Raithel, M and Zlatou, V and Kremenevski, I and Hagel, AF and Konturek, P},
title = {[Endogenous Alcohol Production in the Human Micro- and Mycobiome: Auto-Brewery Syndrome].},
journal = {Zeitschrift fur Gastroenterologie},
volume = {64},
number = {3},
pages = {270-276},
doi = {10.1055/a-2772-7942},
pmid = {41862195},
issn = {1439-7803},
mesh = {Humans ; *Ethanol/metabolism ; *Dysbiosis/diagnosis ; *Gastrointestinal Microbiome/physiology ; *Mycobiome/physiology ; Syndrome ; Dietary Carbohydrates/adverse effects/metabolism ; },
abstract = {Pathological changes in the human microbiome and mycobiome can lead to endogenous production of toxic metabolites, including alcohol. Auto-brewery syndrome (ABS) is characterized by endogenous alcohol formation after high-carbohydrate intake in cases of dysbiosis or underlying disease.Cases described since 1948 were analyzed up to May 2025 via selective literature review regarding symptoms, pathophysiology, diagnostics, and therapy. Syndromes not clearly attributable to endogenous alcohol (e.g., autointoxication, intestinal fermentation syndrome) were excluded.Around 30 cases show variable clinical features with neuropsychiatric, gastrointestinal, and hepatological symptoms, sometimes causing emergencies or accidents. Alcohol is produced by microbial or mycotic overgrowth (e.g., E. coli, Klebsiella, Saccharomyces, Candida) following carbohydrate intake. Diagnosis requires detailed personal and external history, exclusion of other causes, and, if needed, monitored carbohydrate challenge with alcohol measurement. Treatment focuses on carbohydrate reduction, antibiotics or antifungals, and management of underlying conditions.ABS is rare but causes endogenous alcohol-related symptoms that must be considered in medical and legal evaluation of unexplained symptoms or incidents.},
}

Humans
*Ethanol/metabolism
*Dysbiosis/diagnosis
*Gastrointestinal Microbiome/physiology
*Mycobiome/physiology
Syndrome
Dietary Carbohydrates/adverse effects/metabolism

@article {pmid41852409,
year = {2025},
author = {Bailey, A and Leuther, KK and Robinson, LA},
title = {The microbiome and lung cancer: microbial effects on host immune responses and treatment outcomes.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1606551},
pmid = {41852409},
issn = {2813-4338},
abstract = {The human microbiome plays a critical role in shaping physiological processes, immune system function, metabolism, and disease development. Recent research has highlighted the microbiome's profound cancer impact, particularly on lung cancer. This review explores how microbial communities in lung and gut influence tumor progression, immune responses, and treatment outcomes as well as describing the interactions between the microbiome and the host immune system in modulating the efficacy of cancer therapies. Emerging evidence from preclinical and clinical studies investigating the role of the lung and gut microbiome in lung cancer focus on alterations in the microbiota that influence the tumor microenvironment, modulate immune responses, and potentially enhance/hinder treatment effectiveness such as chemotherapy, targeted therapies, and immunotherapy. Microbial diversity plays a significant role in immune regulation, and specific microbial species may activate/suppress immune cells such as T-cells, dendritic cells, and macrophages. Furthermore, this review examines the therapeutic implications of microbiome modulation, including the use of probiotics, antibiotics, and fecal microbiota transplantation in enhancing cancer therapies. Alterations in the lung and gut microbiome and their interaction in the recently described gut-lung axis with its bidirectional communication significantly influence the tumor microenvironment and systemic immune responses. These findings suggest that microbial diversity can regulate immune functions, with specific species capable of activating or suppressing immune cell activity. Furthermore, microbiome-targeted interventions show potential in improving the effectiveness of treatments including chemotherapy, targeted therapies, and immunotherapy, underscoring the importance of the microbiome as a key factor in lung cancer pathogenesis and treatment.},
}

@article {pmid41852434,
year = {2025},
author = {Chen, XD},
title = {Understanding of the effect of microbiome on human health: a chemical process engineering perspective.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1605814},
pmid = {41852434},
issn = {2813-4338},
abstract = {Aspects about the straightforward linking of gut health or the gut microbiota with existing diseases are critically explored. While there is a popular notion that gut health directly influences overall health and can cause or alleviate diseases, the mechanisms behind these effects are not fully understood. Chemical process engineering (CPE) concepts bring new insights into the effects of human microbiome, which may clarify the fundamental influences. The discussions presented here suggest the future directions of research, which need to be pursued for the benefit of human health.},
}

@article {pmid41852694,
year = {2026},
author = {Jablonska, S and Kula, A and Putonti, C},
title = {Shared taxa but distinct communities: within-individual comparisons of oral, nasal, and urinary microbiomes in asymptomatic "healthy" females.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1691965},
pmid = {41852694},
issn = {2813-4338},
abstract = {Although microbial community compositions vary throughout the healthy human body, some taxa can be found to reside in multiple anatomical sites. Moreover, some microbiota that have been found to be interconnected, e.g., the gastrointestinal tract and the oral cavity, the female urinary tract and the vagina, the nose (specifically the nares) and the skin. Previously, the urinary microbiome has only been compared to proximal sites; however, several species that inhabit the asymptomatic female urinary tract are also found in distant communities, e.g., Streptococcus mitis, also found in the oral cavity, and Staphylococcus epidermidis, also found in the nares. This prompted our investigation of communities of the oral cavity, nares, and urinary tract, collected from the same individual. In this study, we profiled the oral, nasal, and urinary microbiomes of 26 self-identified "healthy" female participants using 16S rRNA amplicon sequencing. The urinary microbiome was found to be distinct from the oral and nasal communities. Nevertheless, Actinomyces, Corynebacterium, Escherichia + Shigella, Lawsonella, Staphylococcus, and Streptococcus were found to be present within communities of all three anatomical sites. Genera predominant within the oral and nasal communities were often low-abundant taxa within the urinary microbiome. To date, comparisons of the urinary microbiome to microbiomes of other anatomical sites is limited. The distinction between the urinary microbiome and that of the more distant oral and nasal site highlights the role that the environment plays in shaping these communities.},
}

@article {pmid41852816,
year = {2022},
author = {Tadmor, AD and Mahmoudabadi, G and Foley, HB and Phillips, R},
title = {Identification and spatio-temporal tracking of ubiquitous phage families in the human microbiome.},
journal = {Frontiers in microbiomes},
volume = {1},
number = {},
pages = {1097124},
pmid = {41852816},
issn = {2813-4338},
abstract = {Viruses are a major component of the human microbiome, yet their diversity, lifestyles, spatiotemporal dynamics, and functional impact are not well understood. Elucidating the ecology of human associated phages may have a major impact on human health due to the potential ability of phages to modulate the abundance and phenotype of commensal bacteria. Analyzing 690 Human Microbiome Project metagenomes from 103 subjects sampled across up to 18 habitats, we found that despite the great interpersonal diversity observed among human viromes, humans harbor distinct phage families characterized by their shared conserved hallmark genes known as large terminase subunit (TerL) genes. Phylogenetic analysis of these phage families revealed that different habitats in the oral cavity and gut have unique phage community structures. Over a ~7-month timescale most of these phage families persisted in the oral cavity and gut, however, presence in certain oral habitats appeared to be transitory, possibly due to host migration within the oral cavity. Interestingly, certain phage families were found to be highly correlated with pathogenic, carriage and disease-related isolates, and may potentially serve as novel biomarkers for disease. Our findings shed new light on the core human virome and offer a metagenomic-independent way to probe the core virome using widely shared conserved phage markers.},
}

@article {pmid41853366,
year = {2023},
author = {Scaturro, M and Del Chierico, F and Motro, Y and Chaldoupi, A and Flountzi, A and Moran-Gilad, J and Girolamo, A and Koutsiomani, T and Krogulska, B and Lindsay, D and Matuszewska, R and Papageorgiou, G and Pancer, K and Panoussis, N and Rota, MC and Uldum, SA and Velonakis, E and Chaput, DL and Ricci, ML},
title = {Premise plumbing bacterial communities in four European cities and their association with Legionella.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1170824},
pmid = {41853366},
issn = {2813-4338},
abstract = {INTRODUCTION: Legionella species are Gram negative, facultative, intracellular bacteria found in natural and engineered water systems. Understanding the bacterial interactions underlying the success of Legionella in aquatic environments could be beneficial for control.

MATERIALS AND METHODS: We aimed to profile, by 16S rRNA gene amplicon sequencing (V3-V4), the bacterial communities in premise plumbing systems of buildings in four European cities (Copenhagen, Warsaw, Rome, Athens), and identify positive and negative associations of specific community members to culturable Legionella.

RESULTS: The coarse taxonomic composition was similar across the four cities, but Copenhagen and Warsaw had richer, more diverse communities than Athens and Rome, with a greater number of city-specific amplicon sequence variants (ASVs). The cities had statistically significant differences in bacterial communities at the ASV level, with relatively few shared ASVs. Out of 5,128 ASVs, 73 were classified as Legionella, and one or more of these were detected in most samples from each city (88.1% overall). Interestingly, the relative abundance of Legionella ASVs did not correlate with Legionella culture status. Overall, 44.2% of samples were Legionella culture positive: 71.4% in Warsaw, 62.2% in Athens, 22.2% in Rome, and 15.2% in Copenhagen. 54 specific ASVs and 42 genera had significant positive or negative associations with culturable Legionella. Negative associations included Staphylococcus, Pseudomonas, and Acinetobacter. Positive associations included several Nitrospira ASVs and one classified as Nitrosomodaceae oc32, ASVs in the amoeba-associated genera Craurococcus-Caldovatus and Reyranella, and the predatory genus Bdellovibrio.

DISCUSSION: Some of these associations are well supported by laboratory studies, but others are the opposite of what was expected. This highlights the difficulties in translating pure culture results to in complex real-life scenarios. However, these positive and negative associations held across the four cities, across multiple buildings and plumbing compartments. This is important because developing better control measures, including probiotic approaches, will require an understanding of ecological relationships that can be generalised across different engineered water systems.},
}

@article {pmid41853368,
year = {2023},
author = {Paulo, LS and Msema Bwire, G and Klipstein-Grobusch, K and Kamuhabwa, A and Kwesigabo, G and Chillo, P and Asselbergs, FW and Lenters, VC},
title = {Urbanization gradient, diet, and gut microbiota in Sub-Saharan Africa: a systematic review.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1208166},
pmid = {41853368},
issn = {2813-4338},
abstract = {INTRODUCTION: As Sub-Saharan Africa (SSA) undergoes rapid urbanization changes in diet and lifestyle have contributed to a rise in non-communicable diseases (NCDs) across the region. Changes in gut microbiota which play an important role in human health may be an underlying driving factor. While evidence suggests that the gut microbiota differs between the extreme levels of economic development (least vs highly developed), it is not well-established which factors along the urbanization gradient are most influential, especially for SSA. This systematic review analyzed published articles from SSA countries that examined the differences in the composition and diversity of gut microbiota along the urbanization gradient. The findings of this review have important implications for understanding the impact of urbanization on human health in the SSA.

METHODS: Peer-reviewed articles that examined the link between the urbanization gradient, dietary patterns, and gut microbiota using culture-independent techniques were included in the review.

RESULTS: A total of 3,265 studies were identified and screened. Eighty-nine (89) studies underwent full-text review, and 23 studies were extracted and included for final analysis. Among these studies, it was observed that hunter-gatherers had high alpha diversity (within-person variation) and beta diversity (between-person variation) in their gut microbiota compared to rural and urban residents in SSA. However, there were inconsistent differences between rural and urban at the individual taxa levels, potentially due to limited statistical power and large variability in the study techniques and designs. Similarly, there were no clear differences in the relative abundance of genera across the urbanization gradient. Additionally, both diet and intestinal parasites were associated with the composition and diversity of the gut microbiota.

CONCLUSION: The review revealed there are variations in both alpha and beta diversity of the gut microbiota across the urbanization gradient with a higher diversity observed in rural areas. However, we did not observe significant differences in the relative abundance at phyla or genus levels consistently across the urbanization gradient. Moreover, our findings suggest that the mode of subsistence, diet, and intestinal parasites play a role in shaping the composition and diversity of the gut microbiota in SSA.

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021251006, identifier CRD42021251006.},
}

@article {pmid41853371,
year = {2023},
author = {Campbell, PM and Willmott, T and Humphreys, GJ and Piscoran, O and Chea, H and Summers, AM and Konkel, JE and Knight, CG and Augustine, T and McBain, AJ},
title = {Transplantation impacts on the oral microbiome of kidney recipients and donors.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1258290},
pmid = {41853371},
issn = {2813-4338},
abstract = {INTRODUCTION: Chronic kidney disease (CKD) may affect the human microbiome via increased concentrations of uremic toxins such as urea and creatinine.

METHODS: We have profiled the oral microbiota in patients with CKD before and one week after kidney transplantation. Living kidney donors were also longitudinally tracked over a similar period, allowing direct comparison between a group undergoing transplant surgery alone (donors) (n=13) and a group additionally undergoing the introduction of immunosuppressive agents and the resolution of CKD (recipients) (n=45).

RESULTS: Transplantation was associated with a similar pattern of decreasing alpha diversity in the oral microbiome in recipients and donors via Kruskal-Wallis testing, within one week of transplantation. Amplicon sequence variants (ASVs) associated with Haemophilus parainfluenzae, Aggregatibacteria segnis, Peptostreptococcus and Actinobacillus were significantly decreased in recipients within a week of transplantation.

DISCUSSION: A reduction in ASVs in these genera could influence the risk of bacterial endocarditis, a rare but high-mortality kidney transplantation complication. A range of factors may drive the observed changes in oral microbiome including both factors associated with surgery itself and the decreases in salivary urea, administration of macrolide antibiotic immunosuppressants, and disruption to immune function that characterise kidney transplant.},
}

@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 {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 {pmid41856432,
year = {2026},
author = {Patel, S and Wagner, MS and Bay, O and Wong Valencia, CE and Zgarbova, E and Rodriguez, CI and Leal, DN and Yamashita, M and Devkota, S and Michelsen, KS and Targan, SR and Barrett, RJ},
title = {A method to enrich functional human Paneth cells in iPSC-derived intestinal organoids.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101769},
doi = {10.1016/j.jcmgh.2026.101769},
pmid = {41856432},
issn = {2352-345X},
}

@article {pmid41856651,
year = {2026},
author = {Zhang, B and Lan, P and He, XS},
title = {[Interpretation of the guidelines for the full-course management of early colorectal cancer (2025 version)].},
journal = {Zhonghua wei chang wai ke za zhi = Chinese journal of gastrointestinal surgery},
volume = {29},
number = {3},
pages = {382-385},
doi = {10.3760/cma.j.cn441530-20260104-00008},
pmid = {41856651},
issn = {1671-0274},
support = {2023YFC2507401//National Key Research and Development Program of China/ ; 2024A04J4088//Science and Technology Program of Guangzhou/ ; },
mesh = {Humans ; *Colorectal Neoplasms/therapy/diagnosis ; Practice Guidelines as Topic ; Early Detection of Cancer ; China ; },
abstract = {Colorectal cancer is a highly prevalent malignant tumor in China, for which early detection and standardized management are crucial for improving prognosis. To establish systematic, full-cycle diagnosis and treatment standards, the working group for the development of guidelines for the full-course management of early colorectal cancer has formulated the guidelines for the full-course management of early colorectal cancer (2025 version) based on the latest evidence. This guideline is the first to comprehensively cover the entire process of screening, diagnosis, treatment, and follow-up for early colorectal cancer. Its core innovations include: establishing a precise screening stratification system based on the "modified Asia-Pacific risk score"; formulating quantitative quality control standards for endoscopic and pathological diagnosis; constructed a stepped treatment pathway prioritizing endoscopic therapy, with supplemental surgery guided by high-risk pathological features; and routinely integrating the multidisciplinary team (MDT) approach into the decision-making process. This article aims to provide an integrated interpretation of the guideline's core updated concepts and practical points, offering clear guidance for the standardization and homogenization of clinical practice.},
}

Humans
*Colorectal Neoplasms/therapy/diagnosis
Practice Guidelines as Topic
Early Detection of Cancer
China

@article {pmid41846931,
year = {2026},
author = {Ren, Q and Sun, T and Shen, S and Cao, Y and Wei, L and Zhao, Y and Wan, F and Sui, P and Xiao, K and Bai, H and Guo, D and He, Q and Zhi, M and Yang, J and Jiang, J and Zhang, W and Ding, X},
title = {Macrophage-derived CCL20 promotes abdominal aortic aneurysm progression via lymphocytes CCR6.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1780720},
pmid = {41846931},
issn = {1664-3224},
mesh = {*Aortic Aneurysm, Abdominal/immunology/pathology/metabolism/etiology ; *Receptors, CCR6/metabolism/genetics/immunology ; *Chemokine CCL20/metabolism/genetics/immunology ; Animals ; Mice ; Humans ; Disease Progression ; *Macrophages/immunology/metabolism ; Male ; Disease Models, Animal ; *Lymphocytes/immunology/metabolism ; Mice, Inbred C57BL ; Single-Cell Analysis ; },
abstract = {INTRODUCTION: Abdominal aortic aneurysm (AAA) is a chronic vascular disease marked by chronic inflammation and immune dysregulation. The C-C motif chemokine ligand 20 (CCL20) - C-C motif chemokine receptor type 6 (CCR6) axis modulates immune responses in vascular diseases, but its role in AAA remains unclear. This study investigates the involvement of the CCL20-CCR6 axis in AAA formation.

METHODS: Single-cell RNA sequencing datasets and bulk RNA sequencing datasets were analyzed to assess cellular composition and transcriptional changes. Transcriptomic analysis, enzyme-linked immunosorbent assay, UK Biobank database analysis, CellChat analysis, immunofluorescence staining, and mouse models were employed to explore the CCL20-CCR6 axis in AAA.

RESULTS: Substantial immune cell infiltration (T lymphocytes & B lymphocytes) and loss of structural cells (fibroblasts, endothelial cells and smooth muscle cells) were identified using single-cell RNA sequencing datasets. Macrophage polarization was imbalanced, with enriched M1-like macrophages and elevated CCL20 secretion. Macrophages could promote the formation of AAA by recruiting a large number of immune cells via the CCL20-CCR6 axis. In vitro, CCL20 neutralization reduced immune cell recruitment; in vivo, the knockdown of this axis inhibited AAA progression.

CONCLUSIONS: Macrophage-derived CCL20 aggravates lymphocyte recruitment via the CCR6, promoting AAA progression. CCL20 may serve as a biomarker for AAA. Targeting the CCL20-CCR6 axis could inhibit immune recruitment and AAA progression.},
}

*Aortic Aneurysm, Abdominal/immunology/pathology/metabolism/etiology
*Receptors, CCR6/metabolism/genetics/immunology
*Chemokine CCL20/metabolism/genetics/immunology
Animals
Mice
Humans
Disease Progression
*Macrophages/immunology/metabolism
Male
Disease Models, Animal
*Lymphocytes/immunology/metabolism
Mice, Inbred C57BL
Single-Cell Analysis

@article {pmid41026105,
year = {2026},
author = {Fleres, G and Cheng, S and Badrane, H and Dupont, CL and Espinoza, JL and Abbey, D and Driscoll, E and Newbrough, A and Hao, B and Mansour, A and Nguyen, MH and Clancy, CJ},
title = {Blood Cultures Contain Populations of Genetically Diverse Candida albicans Strains that May Differ in Echinocandin Tolerance and Fitness.},
journal = {The Journal of infectious diseases},
volume = {233},
number = {3},
pages = {560-572},
doi = {10.1093/infdis/jiaf495},
pmid = {41026105},
issn = {1537-6613},
support = {R21 AI160098/AI/NIAID NIH HHS/United States ; 1IO1BX001955//VA Merit Review/ ; R21 AI160098/NH/NIH HHS/United States ; },
mesh = {*Candida albicans/genetics/drug effects/isolation & purification/classification ; Animals ; *Antifungal Agents/pharmacology ; Humans ; Mice ; *Echinocandins/pharmacology ; Microbial Sensitivity Tests ; Blood Culture ; *Genetic Variation ; Candidiasis/microbiology ; *Candidemia/microbiology ; Biofilms/growth & development ; Female ; Drug Resistance, Fungal ; Micafungin/pharmacology ; Male ; },
abstract = {BACKGROUND: It is unknown whether within-patient Candida albicans diversity is common during bloodstream infections (BSIs).

METHODS: We determined whole genome sequences of 10 C. albicans strains from blood cultures (BCs) in each of 4 patients. We performed detailed phenotypic studies on strains from 1 patient.

RESULTS: BCs in 3 patients contained mixed populations of strains that differed by large-scale genetic variants, including chromosome (Chr) 5 or 7 aneuploidy and Chr1 loss of heterozygosity (n = 1 each). In patient M, Chr7 trisomy (Tri7) strains were attenuated for hyphal and biofilm formation in vitro, due at least in part to NRG1 over-expression. Nevertheless, representative Tri7 strain M1 underwent filamentation during disseminated candidiasis (DC) in mice. M1 was more fit than euploid strain M2 during DC and mouse gastrointestinal colonization, and in blood ex vivo. M1 and M2 exhibited identical echinocandin minimum inhibitory concentrations, but M2 was more tolerant to micafungin in vitro. Furthermore, M2 was more competitive with M1 in mouse kidneys following micafungin treatment than it was in absence of micafungin. Tri7 strains represented 74% of patient M's baseline BC population, but euploid strains were 98% of the population after 3d of echinocandin treatment. Findings suggest that echinocandin tolerant, euploid strains were a subpopulation to more fit Tri7 strains at baseline and then were selected upon echinocandin exposure.

CONCLUSIONS: BCs in some patients are comprised of diverse C. albicans populations not recognized by the clinical lab, rather than single strains. Clinical relevance of C. albicans diversity and echinocandin tolerance merits further investigation.},
}

*Candida albicans/genetics/drug effects/isolation & purification/classification
Animals
*Antifungal Agents/pharmacology
Humans
Mice
*Echinocandins/pharmacology
Microbial Sensitivity Tests
Blood Culture
*Genetic Variation
Candidiasis/microbiology
*Candidemia/microbiology
Biofilms/growth & development
Female
Drug Resistance, Fungal
Micafungin/pharmacology
Male

@article {pmid41844111,
year = {2026},
author = {Wang, Y and Jian, C},
title = {How in situ produced dextrans with distinct molecular structures modulate texture and in vitro digestive behavior of mycelium-based high-fiber bread.},
journal = {Food chemistry},
volume = {511},
number = {},
pages = {148838},
doi = {10.1016/j.foodchem.2026.148838},
pmid = {41844111},
issn = {1873-7072},
abstract = {This study investigated the effects of structurally distinct dextrans produced in-situ by Weissella confusa VIII40 and Pediococcus beninensis DSM 22752 on high-fiber bread containing 50% Cordyceps sinensis mycelium. Fermentation with W. confusa VIII40 yielded 4.86% dextran, significantly improving loaf volume (19%) and reducing crumb hardness (52%) and staling rate (83%), effects not observed with P. beninensis DSM 22752 dextran (2.22%). These improvements were associated with partial solubilization of mycelial fibers and reduced dough stiffness. Fermentation increased soluble phenolics (29%), antioxidant activity (16%), and protein digestibility, while lowering starch hydrolysis and estimated glycemic index. W. confusa VIII40 dextran resulted in the lowest starch hydrolysis and highest bile acid binding, likely through increased digesta viscosity (2.6-fold) and particle size (1.6-fold) during simulated intestinal digestion. Ex-situ dextran addition confirmed concentration-dependent reductions in starch and protein hydrolysis, though less effectively than in-situ synthesis. Overall, in-situ dextran presents a promising strategy for developing high-fiber bread.},
}

@article {pmid41827072,
year = {2026},
author = {Takkar, B and Maddheshiya, A and Adhikary, P and Reddy, VA and Majumder, PP and Mukherjee, S and Das, T and , },
title = {Gut microbiome changes in people with diabetic retinopathy in India. DRMS-India report # 1: operational protocol and trends from first 100 participants.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00821-9},
pmid = {41827072},
issn = {1757-4749},
abstract = {BACKGROUND: Diabetic retinopathy (DR) is a common microvascular complication of diabetes mellitus (DM), and the leading cause of vision impairment and blindness. India is among the top three countries in DM prevalence, and both DM and DR are projected to rise sharply in the future. There is no accepted strategy for the prevention of DR other than DM control. Recent studies suggest that DM is associated with alterations in a core group of gut microbiota, and progression to DR may be influenced by changes within this core group, highlighting a potential link between DR and gut microbiome. We studied these changes in a protocol-driven large case-control study, the Diabetic Retinopathy Microbiome Study-India (DRMS-India: CTRI/2024/02/062511), analysed the results of the first 100 individuals, and evaluated variations in gut microbiome in DR.

METHODS: The DRMS is designed to recruit 462 people aged ≥ 30 years into three cohorts: healthy controls (HCs), DM, and DR, at 17 independent sites in India. Shotgun metagenomic sequencing of first-pass morning fecal samples is performed at a centralized laboratory and correlated with disease status, lifestyle, dietary, and systemic factors.

RESULTS: The first 100 participants included 26 HC, 33 DM, and 41 DR. The trends showed the DR group had 1, 6, and 10 unique core phyla, genera, and species, respectively. Alpha diversity was highest in the DR group; Beta diversity plots showed separate clusters of HCs and DR, with DM overlapping both. Firmicutes (highest in DR), Proteobacteria (highest in DM), Bacteroidetes, and Actinobacteria (highest in HC) were common phyla. Segatella was the most common genus, and Segatella copri was the most common species across all groups to date. Most microbial gene families were annotated to Molecular Functions (MF), and the pathways attributed to carbohydrate, amino acid, lipid, and nucleotide metabolism, indicating distinct functional adaptations in their gut microbiome.

CONCLUSION: Trends from the first 100 individuals indicate that the gut microbiome of Indians with DR exhibits discriminatory features in microbial diversity and abundance, as well as in gene families and pathways that impact host gut metabolism. Data trends from DRMS-India indicate a region-specific non-invasive biomarker that may guide preventive therapy for DR.},
}

@article {pmid41822125,
year = {2026},
author = {Berg, G and Antonietti, M and Egamberdieva, D and Korsten, L and Wicaksono, WA},
title = {Microbiome-inspired solutions to save human and planetary health.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1744452},
pmid = {41822125},
issn = {1664-302X},
abstract = {Microbial communities are dynamic networks that regulate nutrient cycling, energy flow, and ecosystem stability, making microbial diversity essential to the health and resilience of all living organisms and ecosystems. However, Anthropocene-driven human activities have led to substantial losses of microbial diversity in environmental and host-associated microbiomes. Despite their critical role, microbiome is underrepresented in conservation and public health strategies, creating a knowledge and intervention gap. Emerging strategies based on microbiome approach offer promising avenues for restoring microbial diversity and enhancing Planetary Health. Achieving these goals requires coordinated global policies, interdisciplinary collaboration, and recognition of microbes as essential partners in sustaining life on Earth.},
}

@article {pmid41774188,
year = {2026},
author = {Yadav, A and Melkani, GC},
title = {Microbes, mood, and metabolism/obesity: Pharmacological insights into the gut-obesity-depression triad.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {83},
number = {1},
pages = {},
pmid = {41774188},
issn = {1420-9071},
support = {AG065992//National Institute of Aging/ ; },
abstract = {The global rise in obesity and depression, two highly prevalent and often comorbid disorders has intensified interest in the gut–brain axis as a shared biological link. Mounting evidence indicates that the gut microbiota profoundly influences both metabolic and neuropsychiatric regulation, positioning it as a promising therapeutic target for these interconnected conditions. This review explores the complex interactions among microbial dysbiosis, host metabolism, and mood regulation, emphasizing pharmacological strategies that harness this triad for treatment. Gut-derived hormones such as glucagon-like peptide-1 (GLP-1) and microbiome-produced metabolites, including short-chain fatty acids (SCFAs) and bile acids, have demonstrated potential to modulate appetite, insulin sensitivity, inflammation, and brain function. GLP-1 receptor agonists like semaglutide originally developed for diabetes and obesity also exhibit antidepressant properties, highlighting their dual therapeutic promise. Emerging microbiome-based interventions, such as precision probiotics, engineered psychobiotics, and fecal microbiota transplantation (FMT), are being investigated to restore microbial balance and improve both metabolic and mood outcomes. Furthermore, combination therapies pairing microbiota-targeted agents with conventional antidepressants or anti-obesity drugs may offer synergistic benefits, enhance efficacy while minimize adverse effects. Despite this promise, significant challenges remain, including ensuring safety, understanding long-term impacts, navigating regulatory hurdles for live biotherapeutics, and addressing ethical concerns about altering the human microbiome. A deeper understanding of the gut–microbiome–brain axis may ultimately enable personalized, microbiota-guided therapies that treat both the physiological and psychological dimensions of obesity and depression, marking a major step toward holistic and precision medicine.},
}

@article {pmid41808145,
year = {2026},
author = {Bu, D and Yan, J and Yang, W and Zhang, X and Li, Q},
title = {Ensemble test for microbiome data.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02367-z},
pmid = {41808145},
issn = {2049-2618},
support = {12401359//National Natural Science Foundation of China/ ; 12325110//National Natural Science Foundation of China/ ; QNTD202303//Youth Academic Innovation Team Construction Project of Capital University of Economics and Business/ ; GZC20241867//Postdoctoral Fellowship Program of CPSF/ ; YSBR-034//CAS Project for Young Scientists in Basic Research/ ; },
abstract = {MOTIVATION: Recent research has revealed strong correlations between the human microbiome and various diseases. However, statistical analysis of microbiome data remains challenging due to its inherent sparsity and high dimensionality. PERMANOVA (Permutational multivariate analysis of variance using distance matrices) has been extensively employed to test the association between microbiome data and biological features. Its non-parametric nature makes it appealing, as it does not impose restrictions on data dimension or distribution. Despite its merits, several limitations have restricted its further application.

RESULTS: This paper introduces E-MANOVA (Ensemble multivariate analysis of variance using distance matrices), a method designed to address these limitations. Traditional PERMANOVA lacks consistent robustness across different distance metrics and association signals, which can lead to power reduction in specific scenarios. Leveraging the idea of ensemble learning, we construct base tests by taking the similarity matrix to the rth power and then combine these tests to build a final ensemble test. Our resulting test statistic exhibits high power and robustness compared to other existing methods. Furthermore, we employ direct moment approximation and the Pearson type III distribution to approximate the permutation null distribution, completely avoiding the computationally intensive permutation procedure. Finally, we utilize the Cauchy combination method to aggregate p-values from multiple distances, eliminating the need to pre-specify a single distance measure before analysis.

CONCLUSIONS: Our extensive simulations demonstrate that the proposed method outperforms existing methods across various situations. Further analysis of real data from cigarette smokers and curated microbiome data shows that our proposed method identifies the highest number of significant associations among all competing methods. Video Abstract.},
}

@article {pmid41807298,
year = {2026},
author = {Huang, J and Qin, Q and Li, X and Jiang, K and Xu, J and Mao, Y and Kang, W and Gao, R and Cheng, Y and Zhao, W and Ke, J and Mou, X},
title = {Bacteroides-associated NAD[+] depletion correlates with exacerbated radiation-induced colorectal injury and impaired mucosal proliferative capacity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2641260},
doi = {10.1080/19490976.2026.2641260},
pmid = {41807298},
issn = {1949-0984},
abstract = {Radiation proctitis (RP) is a frequent complication of pelvic radiotherapy that compromises treatment delivery and patient quality of life, yet the factors shaping injury severity remain incompletely defined. We prospectively profiled pretreatment fecal microbiomes and metabolomes from 55 patients and stratified them by outcome into mild versus severe RP. Baseline microbial composition showed Bacteroidales enriched in severe RP and Firmicutes enriched in mild cases. Multi-omics integration highlighted nicotinate/nicotinamide pathways; severe RP was characterized by concomitant reductions in both fecal and tissue NAD[+] levels, along with an enrichment of microbial nicotinate/nicotinamide metabolism genes, primarily contributed by Bacteroides ovatus, B. xylanisolvens, and B. fragilis. In mice, fecal microbiota transplantation from severe-RP donors exacerbated radiation-induced colorectal injury and decreased colorectal NAD[+], supporting a causal role for the microbiota. Gavage with Bacteroides similarly worsened pathology and lowered NAD[+], whereas nicotinamide mononucleotide (NMN) supplementation attenuated the injury. Mechanistically, Bacteroides gavage reduced mitochondrial membrane potential, decreased the Lgr5[+] stem-cell proportion and proliferative indices, associated with Wnt pathway modulation. NMN reversed these effects in parallel with NAD[+] restoration. Together, these results identify a microbiota‒metabolite association wherein Bacteroidales enrichment is associated with NAD[+] depletion, reduced mucosal proliferative capacity, and exacerbated radiation-induced colorectal injury. The work deepens insight into RP pathogenesis and suggests a potential basis for microbiome- and metabolite-targeted approaches to attenuate severe RP.},
}

@article {pmid41805175,
year = {2026},
author = {Ligthart, K and Elzinga, J and Segers, A and Smidt, H and de Vos, WM},
title = {High stability of the genome of Akkermansia muciniphila Muc[T] under long-term culturing conditions.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0240025},
doi = {10.1128/spectrum.02400-25},
pmid = {41805175},
issn = {2165-0497},
abstract = {UNLABELLED: To advance our understanding of the genomic stability of Akkermansia muciniphila, its type strain Muc[T] was grown for over 1,000 generations at five different culturing conditions, followed by the isolation of single colonies and their subsequent genomic DNA sequencing, physiological, and functional analysis. Notably, not a single mutation was found in the genomes using our sequencing approach of the dozen strains isolated after growth for 1,000 generations in media containing porcine gastric mucin, either grown with or without shaking. Similarly, strains isolated from cultures grown in minimal medium containing high or low N-acetylglucosamine, or low N-acetylglucosamine containing 1% ox bile, exhibited very low mutation rates between 2.1 × 10[-10] and 8.6 × 10[-11] per nucleotide per generation. From these, a total of five unique strains were obtained that contained one or more nucleotide variations. Subsequent analysis and characterization revealed that two of the five strains included a G duplication in a nonanucleotide homopolymer G region in the gene with the locus tag Amuc_1413, resulting in a frameshift and a subsequent loss of mucin binding capacity. Analysis of published genomes of Akkermansia spp. confirmed the instability of this nonanucleotide G region in this Amuc_1413 gene, predicted to be involved in exopolysaccharide export. These findings provide valuable insight into the stability of the A. muciniphila genome and identify phase variation as a mechanism that can explain some of the earlier reported heterogeneity. We conclude that A. muciniphila Muc[T] has large genomic stability under long-term culturing conditions and identified the Amuc_1413 protein as essential for mucus binding.

IMPORTANCE: Akkermansia muciniphila Muc[T] has emerged as a next-generation beneficial microbe due to its capacity to improve gut barrier function in mouse models and humans. To assess the potential of A. muciniphila Muc[T] for industrial applications, we studied the genomic stability by cultivating different growth conditions for over 1,000 generations. We found that the genome of A. muciniphila Muc[T] is highly stable when grown on mucin medium and relatively stable when grown in industrial media. Additionally, we characterized the obtained mutants that identified phase variation as a mechanism operating in A. muciniphila, which allowed us to identify the gene with the locus tag Amuc_1413, encoding a protein involved in exopolysaccharide production, to be involved in mucus binding.},
}

@article {pmid41803883,
year = {2026},
author = {Wei, Z and Xu, T and Gu, X and He, Q and Feng, Q and Li, M},
title = {Single-cell RNA-seq and in vitro study reveal Fusobacterium nucleatum impairs β-cell identity in type 2 diabetes via the NF-κB-CDKN1C axis.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-07981-x},
pmid = {41803883},
issn = {1479-5876},
}

@article {pmid41803692,
year = {2026},
author = {Dhar, GA and Koster, H and van Beek, N and Korpela, K},
title = {Infant gut microbiota coverage by different culture media.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04854-7},
pmid = {41803692},
issn = {1471-2180},
}

@article {pmid41802201,
year = {2026},
author = {Pettersen, VK and Ponsero, AJ and Jian, C and Riumin, A and Kurilshikov, A and Moyo, SJ and Justine, M and Klingenberg, C and Debelius, J and Valles-Colomer, M and Noordzij, HT and Zhernakova, A and Korpela, K and Esteban-Torres, M and Brusselaers, N},
title = {Off to a good start: Current gaps and priorities in early-life microbiome research.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuag010},
pmid = {41802201},
issn = {1574-6976},
abstract = {Early-life microbial exposures are essential for optimal development of human physiology. Yet, understanding of the human microbiome during pregnancy and childhood is still far from being complete. To identify knowledge gaps and establish research priorities, a multidisciplinary expert panel used the Delphi method for consensus development and conducted a literature search on early-life microbiome determinants. Responses from 55 researchers from an online survey were analyzed alongside keyword frequency from 20 501 publications. This approach enabled us to categorize existing evidence and highlight areas requiring investigation. While the main routes for mother-to-child bacterial transmission and their contributions to the newborn microbiome have been studied, many gaps remain. Priority areas include non-bacterial microbes, ecological principles of colonization, environmental and social influences, body sites beyond the gut, and factors affecting the maternal microbiome and its effects on the child's microbiome. Significance of factors such as hygiene habits, non-antibiotic medications, and pollution remains to be uncovered. Knowledge is also limited on postnatal microbial sharing via household contacts and shared environments (e.g. family members, peers) and the contribution of these pathways to microbiome assembly. We hope this report will guide and inspire future research into the early-life microbiome as a modifiable factor in reducing disease risk.},
}

@article {pmid41801038,
year = {2026},
author = {Manninen, J and Korhonen, A and Johnson, KL and Tahvonen, O and Luukkonen, A and Saarenpää, M and Puhakka, R and Uimonen, L and Kummola, L and Skevaki, C and Renz, H and Rajaniemi, J and Laitinen, OH and Roslund, MI},
title = {Playgrounds as microbial interfaces: strategies to enhance soil microbiomes and support healthy childhoods.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0166225},
doi = {10.1128/msystems.01662-25},
pmid = {41801038},
issn = {2379-5077},
abstract = {Emerging evidence suggests that reduced exposure to biodiversity, including rich environmental microbiota, is associated with negative outcomes in the health and well-being of children. Biodiversity loss not only impacts individual health but also poses significant threats to planetary health. It destabilizes systems that regulate climate, purify air and water, maintain soil fertility, and support plant and microbial life essential for environmental health. Here, we review the scientific evidence on microbiome-supportive strategies in eco-centric, child-friendly playground environments. Investigating how environmental features influence soil microbiomes and exposure pathways could provide insights into how playgrounds function as living interfaces. These are places where environmental microbes shape children's microbial colonization patterns, immune and endocrine regulatory systems, while also contributing to ecosystem services such as biodiversity support and pollutant mitigation-particularly relevant given that many pollutants are known to disrupt immune and endocrine functions in children. These dynamics have far-reaching implications for child well-being, preventive health strategies, physical activity, environmental literacy, and broader sustainability. A multi-omic systems approach offers a critical pathway to uncover the ecological and health-related impacts of nature-associated microbial exposure and characterize host-microbiome interactions underlying immune and endocrine regulation, brain development, cognition, and stress-related disorders. Our review highlights a lack of such integrative studies, underscoring the need to advance this line of research to inform evidence-based, sustainable, and health-promoting urban design.},
}

@article {pmid41797849,
year = {2026},
author = {Jalalifar, S and Bajelan, B and Mohammadi, R and Ghafoury, R and Kalhori, Z and Pooshang-Bagheri, K and Nekouian, R and Faranoush, M},
title = {The impact of gut microbiota on leukemia and prospects for novel therapies.},
journal = {Infectious medicine},
volume = {5},
number = {1},
pages = {100239},
pmid = {41797849},
issn = {2772-431X},
abstract = {The Human Microbiome Project has underscored the pivotal role of the gut microbiome in human health, revealing its potential influence on leukemia development, progression, and treatment response. This review summarizes evidence on microbiome-targeted therapies such as probiotics, fecal microbiota transplantation, antimicrobial peptides, and nanoparticles. These approaches may improve leukemia treatment outcomes through immune and metabolic modulation and reduced toxicity. Although emerging data suggest beneficial effects, most findings remain correlative and limited by small, heterogeneous studies. Further mechanistic and clinical research is required to clarify causal pathways, standardize interventions, and evaluate long-term safety. Personalized microbiome-based strategies that integrate molecular and immunologic profiling may ultimately refine leukemia management and improve survival.},
}

@article {pmid40920071,
year = {2025},
author = {Dallon, E and Moran, HM and Chidambaran, SR and Kian, A and Huang, BYH and Fried, SD and DiRuggiero, J},
title = {Investigation of the global translational response to oxidative stress in the model archaeon Haloferax volcanii reveals untranslated small RNAs with ribosome occupancy.},
journal = {mSphere},
volume = {10},
number = {9},
pages = {e0034325},
pmid = {40920071},
issn = {2379-5042},
support = {T32 GM080189/GM/NIGMS NIH HHS/United States ; T32 GM149382/GM/NIGMS NIH HHS/United States ; DP2-GM140926/GM/NIGMS NIH HHS/United States ; DP2 GM140926/GM/NIGMS NIH HHS/United States ; MCB-2034271 and,MCB-57951//National Science Foundation/ ; 2045844//National Science Foundation/ ; },
mesh = {*Oxidative Stress/genetics ; *Haloferax volcanii/genetics/metabolism ; *Ribosomes/metabolism/genetics ; *RNA, Small Untranslated/genetics ; *Protein Biosynthesis ; *RNA, Archaeal/genetics ; Gene Expression Regulation, Archaeal ; },
abstract = {Oxidative stress induces a wide range of cellular damage, often causing disease and cell death. While many organisms are susceptible to the effects of oxidative stress, haloarchaea have adapted to be highly resistant. Several aspects of the haloarchaeal oxidative stress response have been characterized; however, little is known about the impacts of oxidative stress at the translation level. Using the model archaeon Haloferax volcanii, we performed RNA-seq and ribosome profiling (Ribo-seq) to characterize the global translation landscape during oxidative stress. We identified 281 genes with differential translation efficiency (TE). Downregulated genes were enriched in ribosomal and translation proteins, in addition to peroxidases and genes involved in the TCA cycle. We also identified 42 small noncoding RNAs (sRNAs) with ribosome occupancy. Size distributions of ribosome footprints revealed distinct patterns for coding and noncoding genes, with 12 sRNAs matching the pattern of coding genes, and mass spectrometry confirming the presence of seven small proteins encoded by these sRNAs. However, the majority of sRNAs with ribosome occupancy had no evidence of coding potential. Of these ribosome-associated sRNAs, 12 had differential ribosome occupancy or TE during oxidative stress, suggesting that they may play a regulatory role during the oxidative stress response. Our findings on ribosomal regulation during oxidative stress, coupled with potential roles for ribosome-associated noncoding sRNAs and sRNA-derived small proteins in H. volcanii, revealed additional regulatory layers and underscored the multifaceted architecture of stress-responsive regulatory networks.IMPORTANCEArchaea are found in diverse environments, including as members of the human microbiome, and are known to play essential ecological roles in major geochemical cycles. The study of archaeal biology has expanded our understanding of the evolution of eukaryotes, uncovered novel biological systems, and revealed new opportunities for applications in biotechnology and bioremediation. Many archaeal systems, however, remain poorly characterized. Using Haloferax volcanii as a model, we investigated the global translation landscape during oxidative stress. Our findings expand current knowledge of translational regulation in archaea and further illustrate the complexity of stress-responsive gene regulation.},
}

*Oxidative Stress/genetics
*Haloferax volcanii/genetics/metabolism
*Ribosomes/metabolism/genetics
*RNA, Small Untranslated/genetics
*Protein Biosynthesis
*RNA, Archaeal/genetics
Gene Expression Regulation, Archaeal

@article {pmid39596404,
year = {2024},
author = {Wang, Z and Kaplan, RC and Burk, RD and Qi, Q},
title = {The Oral Microbiota, Microbial Metabolites, and Immuno-Inflammatory Mechanisms in Cardiovascular Disease.},
journal = {International journal of molecular sciences},
volume = {25},
number = {22},
pages = {},
pmid = {39596404},
issn = {1422-0067},
support = {K01 HL169019/HL/NHLBI NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; R01 HL170904/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Cardiovascular Diseases/microbiology/immunology/metabolism ; *Mouth/microbiology ; Inflammation/microbiology/metabolism/immunology ; Gastrointestinal Microbiome ; Microbiota ; Animals ; },
abstract = {Cardiovascular diseases (CVDs) remain a leading cause of global morbidity and mortality. Recent advancements in high-throughput omics techniques have enhanced our understanding of the human microbiome's role in the development of CVDs. Although the relationship between the gut microbiome and CVDs has attracted considerable research attention and has been rapidly evolving in recent years, the role of the oral microbiome remains less understood, with most prior studies focusing on periodontitis-related pathogens. In this review, we summarized previously reported associations between the oral microbiome and CVD, highlighting known CVD-associated taxa such as Porphyromonas gingivalis, Fusobacterium nucleatum, and Aggregatibacter actinomycetemcomitans. We also discussed the interactions between the oral and gut microbes. The potential mechanisms by which the oral microbiota can influence CVD development include oral and systemic inflammation, immune responses, cytokine release, translocation of oral bacteria into the bloodstream, and the impact of microbial-related products such as microbial metabolites (e.g., short-chain fatty acids [SCFAs], trimethylamine oxide [TMAO], hydrogen sulfide [H2S], nitric oxide [NO]) and specific toxins (e.g., lipopolysaccharide [LPS], leukotoxin [LtxA]). The processes driven by these mechanisms may contribute to atherosclerosis, endothelial dysfunction, and other cardiovascular pathologies. Integrated multi-omics methodologies, along with large-scale longitudinal population studies and intervention studies, will facilitate a deeper understanding of the metabolic and functional roles of the oral microbiome in cardiovascular health. This fundamental knowledge will support the development of targeted interventions and effective therapies to prevent or reduce the progression from cardiovascular risk to clinical CVD events.},
}

Humans
*Cardiovascular Diseases/microbiology/immunology/metabolism
*Mouth/microbiology
Inflammation/microbiology/metabolism/immunology
Gastrointestinal Microbiome
Microbiota
Animals

@article {pmid30240894,
year = {2019},
author = {Allaband, C and McDonald, D and Vázquez-Baeza, Y and Minich, JJ and Tripathi, A and Brenner, DA and Loomba, R and Smarr, L and Sandborn, WJ and Schnabl, B and Dorrestein, P and Zarrinpar, A and Knight, R},
title = {Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {17},
number = {2},
pages = {218-230},
pmid = {30240894},
issn = {1542-7714},
support = {K08 DK102902/DK/NIDDK NIH HHS/United States ; T32 OD017863/OD/NIH HHS/United States ; },
mesh = {Computational Biology/*methods ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Individuality ; Metabolomics/*methods ; Metagenomics/*methods ; *Microbiota ; },
abstract = {Advances in technical capabilities for reading complex human microbiomes are leading to an explosion of microbiome research, leading in turn to intense interest among clinicians in applying these techniques to their patients. In this review, we discuss the content of the human microbiome, including intersubject and intrasubject variability, considerations of study design including important confounding factors, and different methods in the laboratory and on the computer to read the microbiome and its resulting gene products and metabolites. We highlight several common pitfalls for clinicians, including the expectation that an individual's microbiome will be stable, that diet can induce rapid changes that are large compared with the differences among subjects, that everyone has essentially the same core stool microbiome, and that different laboratory and computational methods will yield essentially the same results. We also highlight the current limitations and future promise of these techniques, with the expectation that an understanding of these considerations will help accelerate the path toward routine clinical application of these techniques developed in research settings.},
}

Computational Biology/*methods
*Gastrointestinal Microbiome
Gastrointestinal Tract/*microbiology
Humans
Individuality
Metabolomics/*methods
Metagenomics/*methods
*Microbiota

@article {pmid41777539,
year = {2026},
author = {Wang, M and Li, X and Liu, X and Ye, Y and Zhou, P and Liu, Y and Zhu, L and Wei, W and Li, Z and Li, Z and Wu, R and Peng, Y and Liu, Z and Lu, X and Zhao, J and Kan, B},
title = {Restaurant occupational exposure affects the profiles of oral and gut pathobiomes and resistomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771459},
pmid = {41777539},
issn = {1664-302X},
abstract = {INTRODUCTION: Restaurant occupational exposure refers to contact with food-processing environments, raw materials, and customers, which may influence the composition of the human microbiome. Differences and associations between human oral and gut pathobiome and their resistomes under restaurant occupational exposure remain unclear. We conducted a comprehensive metagenomic analysis of paired oral and fecal samples from Front-of-House (FOH) workers and Back-of-House (BOH) workers to elucidate the effects of occupational exposure in the restaurant environment on oral and gut pathobiome, antimicrobial resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs).

METHODS: We collected the oral and fecal samples from 35 FOH and 37 BOH workers across 24 Chinese restaurants in Zhengzhou, Henan, China. The diversity and relative abundances of microbial species, ARGs, VFs, and MGEs were compared. Clonal strains from paired oral and fecal samples were analyzed. The serovars of Salmonella were determined using the ucgMLST. Finally, we used the O2PLS method to explore relationships among ARG subtypes, bacterial communities (species-level), MGEs (subtype-level), and plasmids.

RESULTS: The gut microbiome acts as the primary reservoir, exhibiting greater alpha diversity and a higher burden of pathogens/resistomes (including high-risk Rank_I genes). In contrast, the oral microbiome was more sensitive to occupational differences. Significant beta diversity variations in microbiomes, antimicrobial resistance genes (ARGs), and virulence factors were observed exclusively in oral samples. Notably, Salmonella Typhimurium was significantly more prevalent in the oral cavity of BOH workers (R [2] = 0.032, p = 0.047), indicating their potential role as intermediaries in foodborne pathogen transmission. Strain-level analysis confirmed that clonal strains of the opportunistic pathogen and probiotics were shared between the oral cavity and the gut. O2PLS analysis identified plasmids as the main correlates of ARGs.

DISCUSSION: While the gut serves as the primary reservoir for pathogens/resistomes, restaurant occupational exposure distinctly shapes oral microbial/resistome profiles, underscoring the critical need for reinforced hygiene management, particularly for BOH workers, to mitigate pathogen and resistance transmission.},
}

@article {pmid41046872,
year = {2025},
author = {Yang, S and Yang, M and Jennings, M and Timek, H and Haley, AE and Romee, R and Li, J},
title = {Repurposing the bacterial surface display technology for drug delivery.},
journal = {Advanced drug delivery reviews},
volume = {227},
number = {},
pages = {115701},
doi = {10.1016/j.addr.2025.115701},
pmid = {41046872},
issn = {1872-8294},
support = {DP2 GM154019/GM/NIGMS NIH HHS/United States ; R01 CA299955/CA/NCI NIH HHS/United States ; R01 CA303150/CA/NCI NIH HHS/United States ; },
mesh = {*Drug Delivery Systems ; Humans ; Animals ; *Bacteria/metabolism/genetics ; },
abstract = {Bacteria have emerged as versatile platforms for therapeutic delivery, owing to their inherent adaptability, genetic tractability, and ability to interface with the human microbiome and immune system. This review explores the evolution of bacterial engineering for medical applications, emphasizing drug delivery strategies enabled by bacterial surface display technologies. We outline the advantages of surface display, such as enhanced localization, prolonged therapeutic activity, and reduced systemic toxicity, over conventional bacterial secretion and lysis-based delivery methods. The review details key biological mechanisms of surface display in both Gram-negative and Gram-positive bacteria, including outer membrane proteins, sortase-mediated anchoring, and spore-based systems. We also highlight emerging applications of surface-displayed cytokines, nanobodies, and immunomodulatory proteins in cancer therapy, vaccine development, microbiome engineering, and animal health. Innovative approaches combining bacterial display with conjugation systems and biosensors expand the potential of these living therapeutics for precise, responsive, and programmable interventions. Furthermore, we propose a future roadmap that leverages computational tools such as AlphaFold and in silico screening to rationally identify optimal outer membrane anchors, accelerating the design of next-generation surface display platforms. While challenges remain, including regulatory hurdles and microbial stability, continued interdisciplinary innovation with synthetic biology promises to transform engineered bacteria into clinically viable therapeutic agents. This review positions bacterial surface display as a powerful and underexplored modality for targeted drug delivery, bridging synthetic biology, immune engineering, and translational medicine.},
}

*Drug Delivery Systems
Humans
Animals
*Bacteria/metabolism/genetics

@article {pmid41791702,
year = {2026},
author = {Wong, WH and Yu, Y and Hu, Y and Shen, Y and Chen, J and Jarvis, K and Sanford, N and Knudson, KA and Gersh, R and Ye, CY and Bastow, B and Kashi, PK and Palmer, M and Azeze, GG and Wang, RCC and Segars, J and Bischoff, FZ},
title = {Non-invasive blood-based detection of endometriosis can improve standard-of-care by facilitating early diagnosis and clinical management among symptomatic women.},
journal = {Journal of minimally invasive gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmig.2026.02.042},
pmid = {41791702},
issn = {1553-4669},
abstract = {STUDY OBJECTIVE: To develop and validate a non-invasive, blood-based diagnostic assay for endometriosis that performs accurately across menstrual cycl phases and complements existing imaging modalities.

DESIGN: Multi-center case-control study with machine learning classification and independent cohort validation.

SETTING: Clinical and search settings involving symptomatic women evaluated for suspected endometriosis.

PATIENTS: A total of 298 reproductive-age women were included. The training cohort comprised 218 participants (137 endometriosis-positive and 81 controls). A modest, independent and retrospective validation cohort included 80 participants (40 endometriosis-positive and 40 controls).

INTERVENTIONS: Peripheral blood sampling with quantification of three microRNAs via qPCR, three protein biomarkers, one steroid hormone using immunoassay, as well as the participant's age and body mass index. Biomarker data were integrated using a random forest machine learning model to classify disease status.

MEASUREMENTS AND MAIN RESULTS: In the independent validation cohort, the assay achieved an area under the curve (AUC) of 0.944, sensitivity of 0.80, and specificity of 0.975. Subgroup analysis by menstrual cycle phase demonstrated consistent performance: proliferative-phase samples achieved an AUC of 0.935, sensitivity of 0.767, and specificity of 0.962, while secretory-phase samples achieved an AUC of 0.993, sensitivity of 0.90, and specificity of 1.00. Compared with transvaginal ultrasound and/or MRI, the blood-based assay identified 61.5% histologically confirmed endometriosis cases that were missed by the imaging modalities.

CONCLUSION: A minimally invasive, multi-omic blood-based assay integrating molecular biomarkers with machine learning can accurately detect endometriosis across menstrual cycle phases and provides complementary diagnostic values. This approach has the potential to improve early detection, and guide timely clinical intervention. A prospective validation is ongoing in geographically and ethnically diverse populations to further assess its broad clinical utility.},
}

@article {pmid41790992,
year = {2026},
author = {Berendse, R and Verkleij, M and Daams, J and Hemmings, S and Lindauer, R and Korosi, A and Zantvoord, JB and Lok, A},
title = {The microbiome and PTSD: a scoping review across preclinical and clinical studies.},
journal = {European journal of psychotraumatology},
volume = {17},
number = {1},
pages = {2627060},
doi = {10.1080/20008066.2026.2627060},
pmid = {41790992},
issn = {2000-8066},
abstract = {BACKGROUND: Posttraumatic Stress Disorder (PTSD) is a psychiatric condition that substantially impairs quality of life and global health. Emerging evidence implicates that the human microbiome contributes to PTSD pathophysiology via gut-brain-immune interactions, although the underlying mechanisms and therapeutic implications remain unclear.

OBJECTIVE: This review aimed to systematically map the evidence linking microbiome alterations to PTSD, with a focus on mechanistic pathways, therapeutic potential, and research gaps.

METHODS: This scoping review was conducted in Medline, Embase, and PsychINFO from inception to 18-03-2025. Eligible studies included human participants with PTSD and preclinical rodent models employing validated PTSD paradigms. Outcomes of interest included microbiome diversity and composition, gut-brain axis biomarkers, and effects of microbiome-targeted interventions.

RESULTS: Fifty studies were included, comprising 20 human, 29 preclinical and one cross-species study. Human observational studies frequently observed reduced overall microbial diversity, along with a loss of short-chain fatty acid (SCFA)-producing bacteria, such as Ruminococcaceae and Lachnospiraceae, and an increased abundance of Veillonella, Odoribacter, and Catenibacterium linked to gut permeability and inflammation. Human intervention studies testing probiotics, prebiotics, fermented soy, and dietary fibre showed preliminary evidence for symptom and related metabolic and inflammatory marker improvements; however, microbiome effects were inconsistent. Preclinical models revealed stress-induced reductions in Bifidobacteria, Verrucomicrobia, and Parabacteroides, and increases in Coprobacillus and Anaeroplasma. Functional consequences included impaired barrier integrity, altered SCFA levels, and heightened immune activation. Preclinical interventions, particularly Mycobacterium vaccae, as well as probiotics, synbiotics, acetate, and MDMA, mitigated microbial alterations, reduced anxiety-like behaviours, and modulated neuroimmune pathways.

CONCLUSION: Current evidence supports an association between PTSD and microbiome alterations, with convergent human and preclinical findings. However, human research remains limited by small, cross-sectional designs, which preclude causal inferences. Rigorous longitudinal and interventional studies are required to establish causality and assess microbiome-targeted therapies as adjuncts in PTSD treatment.},
}

@article {pmid41787261,
year = {2026},
author = {Dühr, H and Pärnänen, K and Kucháriková, N and Werner, P and Pershagen, G and Lahti, L and Alenius, H and Bergström, A and Ruuskanen, MO and Fyhrquist, N},
title = {Lifestyle associates with unique resistome and microbiome signatures in children.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04665-2},
pmid = {41787261},
issn = {1471-2180},
}

@article {pmid41786702,
year = {2026},
author = {Kiran, S and Cruz, AR and Daniau, A and Ma, B and Marbouty, M and Pipoli Da Fonseca, J and Legrand, A and Baudry, L and Cokelaer, T and Bensussan, M and Moya-Nilges, M and Garneau, J and Monot, M and Ochieng, JB and Antonio, M and Tamboura, B and de Vos, WM and Salonen, A and Hossain, J and Omore, R and Sow, SO and Sansonetti, PJ and Ravel, J and Cerf-Bensussan, N and Schnupf, P},
title = {Segmented filamentous bacteria are worldwide human gut commensals.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-70010-4},
pmid = {41786702},
issn = {2041-1723},
support = {OPP1141338//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; Coups d'élan//Fondation Bettencourt Schueller (Bettencourt Schueller Foundation)/ ; 866222//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 260822//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 260822//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; JCJC MicroEducation//Agence Nationale de la Recherche (French National Research Agency)/ ; 339407//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; },
abstract = {Segmented filamentous bacteria (SFB) describe morphologically similar gut commensals found in mammals, fish and birds. In mice, SFB intimately colonizes the ileal epithelium at the time of weaning and elicits a strong pleiotropic immune activation that fosters colonization resistance while augmenting disease severity in various disease models. SFB is therefore critical in both health and disease but information regarding SFB in humans remains limited. Here, we first identify and characterize a human SFB species with SFB-specific morphology, including the hook-like tip structure that mediates attachment, and unique genome features, including a starch and glycogen degradation module. This species, which we name Anisomitus miae and establish as the nomenclature type for the SFB genus, is common across Africa. We then bioinformatically identify, based on the 16S rRNA gene V3-V4 variable region sequence, four major, and two minor, human SFB lineages in forty-four countries distributed across all six inhabited continents. We provide evidence towards the co-colonization potential of the SFB lineages and their colonization dynamics, including a potent but short-lived colonization peak in children between one to five years of age. This study establishes the presence of multiple SFB species in the human population and SFB as a minor but wide-spread group of commensals in humans.},
}

@article {pmid41784952,
year = {2026},
author = {Typpö, L and Solasaari, T and Korpela, K and de Vos, WM and Salonen, A and Kolho, KL},
title = {Green Stool Predominance in Babies and Subsequent Bowel Function at 1-2 Years of Age.},
journal = {Acta paediatrica (Oslo, Norway : 1992)},
volume = {},
number = {},
pages = {},
doi = {10.1111/apa.70483},
pmid = {41784952},
issn = {1651-2227},
support = {//Lastentautien Tutkimussäätiö/ ; 202010020//Mary ja Georg C. Ehrnrooth Foundation/ ; 00210976//Finnish Cultural Foundation/ ; 329/31/2015//Tekes/Business Finland/ ; },
abstract = {AIM: To study the relationship between bowel function after birth and at 1-2 years of age in the prospective HELMi cohort of term infants.

METHODS: We focused on infants with predominantly green stools (n = 152) for three consecutive weeks in early life and their sex, age, and delivery mode-matched controls (n = 300), and evaluated bowel function at 1-2 years. We also evaluated bowel function in babies who had cried the most (n = 179) and compared the findings with the rest of the cohort (n = 689).

RESULTS: There were no alarming signs of gastrointestinal dysfunction in any of the infants. Infants with green stools in early life had 1.5-2 times more reports of abdominal symptoms at 1-2 years compared to controls (p < 0.005), and stool-mucus was twice as frequent at 1 year (p < 0.05). Compared to controls, 1-year-old infants who cried most as babies had a higher frequency of defecation (a median of 14 per week [IQR 8-17] vs. 12 [IQR 7-15]; p < 0.05) and showed twice as frequent stool-mucus at 1 year (p < 0.05).

CONCLUSION: In healthy term babies, occasional abdominal pain or predominantly green stools were associated with benign gastrointestinal symptoms in later infancy. This functional variation may reflect altered microbiota, warranting further research.},
}

@article {pmid41784399,
year = {2026},
author = {Nurmi, V and Hedman, L and Vapalahti, K and Hepojoki, J and Uğurlu, H and Iheozor-Ejiofor, R and Knight, C and Saksela, K and Kantele, A and Hedman, K and Vapalahti, O},
title = {Anti-spike IgG Avidity Enhances Neutralization of Severe Acute Respiratory Syndrome Coronavirus 2: A Prospective Study of Primary Infections and Immunizations.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag068},
pmid = {41784399},
issn = {1537-6613},
support = {//The Medical Society of Finland/ ; //Finnish Society for Study of Infectious Diseases/ ; //Finnish Foundation for Research on Viral Diseases/ ; //Sigrid Jusélius Foundation/ ; //Magnus Ehrnrooth Foundation/ ; //Finnish Society of Sciences and Letters/ ; //Research Council of Finland/ ; //VTR-State Funding for/ ; //Medical Research in University Hospitals/ ; //EU Horizon VEO and DURABLE/ ; //Sakari Alhopuro Foundation/ ; //Jane and Aatos Erkko Foundation/ ; //Helsinki University Hospital Research and Education Fund/ ; },
abstract = {BACKGROUND: Immune protection against coronavirus disease 2019 (COVID-19) relies, along with cellular immunity, on anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. We studied the effect of IgG avidity, the average antibody binding strength, on anti-SARS-CoV-2 neutralizing antibodies (nAbs), often considered the hallmark of effective immunity. Prior studies estimating the significance of avidity for nAb-mediated immunity have been complicated by the fact that not only the quality but also the quantity of antibodies impacts the results. Here we provide means for quantifying the impact of IgG avidity on neutralization, irrespective of antibody titer.

METHODS: We introduce for anti-SARS-CoV-2 spike protein (S) and nucleoprotein (N) antibodies, IgG avidity assays shown to be unaffected by the IgG concentration. Hospitalized (n = 14) and nonhospitalized (n = 14) COVID-19 patients and vaccinees (n = 20) of early 2020 were assayed for Wuhan S-IgM, S-IgA, S-IgG, and S-IgG avidity; Wuhan N-IgG and N-IgG avidity; and Wuhan, Beta, and Delta nAbs, to identify the factors contributing to neutralization efficiency.

RESULTS: N-IgG avidity was superior to S-avidity in pinpointing the time of SARS-CoV-2 primary infection. Both Wuhan nAb and Delta nAb correlated, expectedly, with Wuhan S-IgG level (P < .0001 each). Wuhan S-IgG avidity intensified homologous (Wuhan; P = .001) but not significantly heterologous (Delta; P = .053) neutralization. Accordingly, along with postinfection time, the average neutralization efficiency of S-IgG molecules increased while their concentration decreased. Quantitatively, doubling of Wuhan S-IgG avidity, at constant S-IgG quantity, augmented Wuhan neutralization 1.58- to 1.68-fold.

CONCLUSIONS: Comprehensive serological profiles of early SARS-CoV-2 primary infections and immunizations provided a model showing that the antiviral neutralization potency is enhanced by anti-spike IgG avidity. The methodology presented is applicable widely beyond COVID-19.},
}

@article {pmid41778780,
year = {2026},
author = {Mambuque, E and Del Amo-de Palacios, A and Huete, SG and Marsh, CC and Theron, G and García-Basteiro, AL and Serrano-Villar, S},
title = {Beyond bacilli: integrating the microbiome into the TB research agenda.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638004},
pmid = {41778780},
issn = {1949-0984},
mesh = {Humans ; *Tuberculosis/microbiology/diagnosis/therapy ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Animals ; Antitubercular Agents/therapeutic use ; Metabolomics ; Lung/microbiology ; },
abstract = {Tuberculosis (TB) remains a leading infectious killer, with growing evidence that the human microbiome-particularly in the gut and lungs-shapes susceptibility, progression, and treatment outcomes. Over the past decade, studies have reported that TB-associated dysbiosis, which is more common in the gut than in the lung, is often marked by the loss of short-chain fatty acid-producing taxa and the expansion of opportunistic microbes. However, findings are frequently confounded by diet, antibiotic exposure, comorbidities, geography, and methodological variability. Most research has relied on compositional profiling, offering limited insight into functional mechanisms. This narrative review synthesizes recent evidence, emphasizing the need to integrate multiomics approaches-metagenomics, metatranscriptomics, and metabolomics-and experimental validation to uncover causal links between microbiome alterations and TB pathogenesis or therapy response. We discuss potential clinical applications, including microbiome-based diagnostics (such as stool-based microbial or metabolite signatures for TB risk stratification), prognostic indicators (such as gut microbiome recovery predicting immune normalization during therapy), and adjunctive interventions (including microbiome-derived products to reduce drug-induced liver injury or fecal microbiota transplantation, which has been shown to be safe in people with HIV on stable ART) to mitigate drug toxicity or enhance immune recovery. Key priorities include methodological standardization, confounder control, mechanistic studies, and the inclusion of high-burden settings. By moving beyond descriptive surveys toward functional, translational research, integrating insights from different microbiome methods into TB prevention, diagnosis, and treatment could redefine the clinical research agenda and open new avenues for precision medicine in this global disease.},
}

Humans
*Tuberculosis/microbiology/diagnosis/therapy
*Gastrointestinal Microbiome
*Dysbiosis/microbiology
Animals
Antitubercular Agents/therapeutic use
Metabolomics
Lung/microbiology

@article {pmid41767369,
year = {2026},
author = {He, Y and Jin, Y and Gao, M and Jin, J and Chen, K and Zhou, L and Shi, J and Luo, B and Liang, Y},
title = {Nonlinear association of serum uric acid and C-peptide with arterial stiffness in patients with type 2 diabetes: a real-world study.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1700359},
pmid = {41767369},
issn = {1664-2392},
mesh = {Humans ; *Diabetes Mellitus, Type 2/blood/physiopathology/complications ; *Uric Acid/blood ; Male ; Female ; Middle Aged ; *Vascular Stiffness/physiology ; *C-Peptide/blood ; Cross-Sectional Studies ; Aged ; Pulse Wave Analysis ; Biomarkers/blood ; },
abstract = {BACKGROUND: Diabetes has become one of the most serious and prevalent chronic diseases, and its cardiovascular complications are responsible for over 50% of diabetes-related deaths. However, the relationships between uric acid (UA) and C-peptide on arterial stiffness (AS) in patients with type 2 diabetes mellitus (T2DM) are still poorly understood. This study aimed to evaluate the associations between UA and C-peptide with AS in T2DM patients.

METHODS: In this cross-sectional study of 1,715 participants with T2DM, we recorded levels of fasting UA, C-peptide, and other characteristics. Elevated AS was defined as a brachial-ankle pulse wave velocity (baPWV) of ≥1,400 cm/s. Logistic regression and a restricted cubic spline (RCS) model were employed to assess the associations of UA and C-peptide with AS.

RESULTS: Fasting UA and C-peptide levels were independently and significantly associated with elevated AS in patients with T2DM, as determined by multivariate analyses (P < 0.05). Notably, RCS analyses revealed nonlinear relationships with threshold effects between fasting UA, C-peptide, and elevated AS (P for nonlinearity < 0.05). Compared to patients with C-peptide levels < 0.580 μg/L, those with levels ≥ 0.580 μg/L had an approximately 87% relatively higher odds of elevated AS (OR = 1.87, 95% CI: 1.32, 2.65).

CONCLUSION: The elevated AS odds in patients with T2DM were nonlinearly associated with the levels of serum fasting UA and C-peptide.},
}

Humans
*Diabetes Mellitus, Type 2/blood/physiopathology/complications
*Uric Acid/blood
Male
Female
Middle Aged
*Vascular Stiffness/physiology
*C-Peptide/blood
Cross-Sectional Studies
Aged
Pulse Wave Analysis
Biomarkers/blood

@article {pmid41760847,
year = {2026},
author = {Eilers, T and Delanghe, L and De Boeck, I and Van Rillaer, T and Van Malderen, J and Bakelants, S and Van Beeck, W and Wittouck, S and Lebeer, S},
title = {Pangenome-based design of strain-specific primers enables precise monitoring of bacteria in human microbiome intervention trials.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41449-8},
pmid = {41760847},
issn = {2045-2322},
support = {HBC.2022.1000//Agentschap Innoveren en Ondernemen/ ; HBC.2020.2873//Agentschap Innoveren en Ondernemen/ ; 12S4222N//Fonds Wetenschappelijk Onderzoek/ ; 1S08523N//Fonds Wetenschappelijk Onderzoek/ ; 1224923N//Fonds Wetenschappelijk Onderzoek/ ; 12AZ624N//Fonds Wetenschappelijk Onderzoek/ ; 852600//Horizon 2020 Framework Programme/ ; },
}

@article {pmid41757006,
year = {2026},
author = {Tran, HN and Kirven, KJ and Davenport, ER},
title = {SCiMS: Sex Calling in Metagenomic Sequences.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.17.705110},
pmid = {41757006},
issn = {2692-8205},
abstract = {BACKGROUND: Host sex is a critical determinant of microbial community structure, influenced by hormonal profiles, physiology, and sex-stratified behaviors. Despite its importance, sex metadata is frequently missing or mislabeled in microbiome studies. Existing genomic sex-calling tools often fail in low-host-biomass samples (e.g., stool) because they require high read depths to achieve reliability.

RESULTS: Here, we present SCiMS (Sex Calling in Metagenomic Sequences), a bioinformatic tool that leverages host-derived DNA within metagenomic datasets to accurately predict host sex, even at low host coverage. SCiMS uses sex-chromosome read density ratios within a Bayesian classifier to provide high-accuracy sex calls. In simulations, SCiMS achieves >85% accuracy with as few as 450 host reads. When applied to 1,339 samples from the Human Microbiome Project, SCiMS outperforms existing tools, showing higher accuracy and more balanced precision-recall tradeoffs across body sites. SCiMS also generalizes effectively to non-human hosts, achieving 100% accuracy in a murine dataset and outperforming alternatives in a chicken dataset with a ZW sex determination system.

CONCLUSIONS: SCiMS provides an accurate, scalable, and cross-species generalizable solution for host sex classification in metagenomic datasets, even when host DNA is minimal. By enabling the recovery of missing sex metadata, it serves as a quality-control tool for ensuring the integrity of analyses in microbiome research. SCiMS is freely available at http://github.com/davenport-lab/SCiMS .},
}

@article {pmid41753674,
year = {2026},
author = {Ece, G and Aktaş, A and Koyuncu Özyurt, Ö and Demirbakan, H and Alışkan, HE and Sağlık, İ and Zorbozan, O and Çetin Duran, A and Uğur, AR and Öcal, D and Uzunoğlu, E and Kaya, E and Mutlu Sarıgüzel, F and Bayındır, F and Yetkin, G and Altındiş, M and Yenice Aktaş, S and Kula Atik, T},
title = {Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753674},
issn = {2076-2607},
abstract = {The human microbiome is increasingly recognized as a key determinant of health and disease, yet methodological variability continues to limit reproducibility and clinical translation of findings. This review synthesizes current approaches in microbiome research, critically evaluating each step from sampling to sequencing and downstream bioinformatics. Pre-analytical factors such as sample type, collection method, preservation, and storage conditions profoundly affect microbial community profiles and remain a major source of bias. Nucleic acid extraction protocols and quality assessment strategies are discussed with emphasis on optimized lysis techniques, contamination controls, and DNA yield evaluation. Advances in sequencing technologies are highlighted, including 16S rRNA amplicon sequencing, shotgun metagenomics, third-generation long-read platforms, and emerging single-cell and minimal-input methods, each with specific advantages and limitations in taxonomic and functional resolution. Bioinformatics pipelines for taxonomic profiling, variant detection, phylogenetic inference, and functional annotation are compared, with attention to widely used reference databases such as RefSeq, GTDB, and SILVA. Integrative multi-omics approaches, including metatranscriptomics, metabolomics, and genome-scale metabolic modeling, are presented as powerful tools for linking microbial community structure to host physiology and disease mechanisms. Despite these advances, the lack of standardized workflows across pre-analytical, sequencing, and computational steps continues to hinder inter-study comparability and biomarker validation. This review aims to provide a methodological framework that highlights both strengths and limitations of current technologies while underlining the need for harmonized protocols to ensure reproducibility and accelerate the translation of microbiome research into clinical practice.},
}

@article {pmid41750603,
year = {2026},
author = {Herrera-Quintana, L and Iturbe-Sanz, P and Olivares-Arancibia, J and Vázquez-Lorente, H and Plaza-Diaz, J},
title = {Interplay of Microbiome, Oxidative Stress and Inflammation in Health and Disease.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41750603},
issn = {2076-3921},
abstract = {The human microbiome plays a crucial role in health, being involved in both physiological and pathological processes. The highly dynamic microbiome composition is shaped by different factors, which also may affect host-microbe interactions. Although this relationship is complex and incompletely understood, the interplay between the microbiome, oxidative stress and inflammation is increasingly recognized. Microbial metabolites and specific probiotic strains contribute to maintaining redox homeostasis through multiple pathways, such as regulating the immune system and inflammatory processes or influencing mitochondrial reactive oxygen species production and antioxidant signaling pathways. Oxidative stress and inflammation, in turn, may affect the microbiome by altering microbial diversity and function. These disturbances are believed to create a vicious cycle that further disrupts homeostasis and promotes the appearance of different diseases. This review synthesizes current evidence on the interplay between the microbiome, oxidative stress, and inflammation, highlighting its relevance to both physiological and pathological states.},
}

@article {pmid41750436,
year = {2026},
author = {Napier, BA and Allegretti, JR and Feuerstadt, P and Kelly, CR and Van Hise, NW and Jäger, R and Stuivenberg, GA and Kassam, Z and Reid, G},
title = {Multi-Species Synbiotic Supplementation After Antibiotics Promotes Recovery of Microbial Diversity and Function, and Increases Gut Barrier Integrity: A Randomized, Placebo-Controlled Trial.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41750436},
issn = {2079-6382},
support = {N/A//Seed Health, Inc./ ; },
abstract = {Background: Antibiotics are essential for treating infections; however, they disrupt the microbiome and key microbiome-dependent functions. Clinical evidence is mixed for probiotic supplementation following antibiotics due to product heterogeneity and inconsistencies in evaluating biological mechanisms that drive clinical consequences. Accordingly, this study investigates the effects of a multi-species synbiotic on gut microbiome composition and function, and gut barrier integrity, during and following antibiotics. Methods: In a randomized, placebo-controlled trial designed to assess proof-of-mechanism, healthy adult participants received a daily synbiotic (53.6 billion AFU multi-species probiotic and 400 mg Indian pomegranate extract; DS-01) or matching placebo for 91 days. All participants also received ciprofloxacin (500 mg orally twice daily) and metronidazole (500 mg orally three times daily) for the first 7 days. Samples were collected at baseline and Days 7, 14, 49, and 91. Endpoints included fecal microbiome composition, fecal acetate and butyrate levels, urinary Urolithin A (UroA), serum p-cresol sulfate (pCS), gut barrier integrity, and safety. Results: The multi-species synbiotic significantly increased the alpha-diversity of Bifidobacterium and Lactobacillus at all timepoints compared to placebo, including short-term (Day 7, p < 0.0001) and end-of-study (Day 91, p < 0.001). The multi-species synbiotic enhanced recovery of native beneficial microbes, including butyrate-producing species and a novel Oscillospiraceae species (UMGS1312 sp900550625, p < 0.001). Beneficial microbiome-dependent metabolites increased, including fecal butyrate (119%, p < 0.05), fecal acetate (62%, p < 0.01), and UroA (13,008%, p < 0.05), whereas detrimental metabolite pCS decreased (68%, p < 0.05) compared to placebo. Functionally, the multi-species synbiotic improved gut barrier integrity rapidly (Day 7; 305%, p < 0.05) and over the long-term (Day 91; 161%, p < 0.05) compared to placebo. Conclusions: During and after antibiotics, this multi-species synbiotic promotes recovery of gut microbiome diversity and native beneficial microbes, microbiome metabolite recovery, and gut barrier function, all of which underpin antibiotic-associated gastrointestinal symptoms.},
}

@article {pmid41748043,
year = {2026},
author = {Alvaro-Fuss, M and DeClercq, V and Blodgett, JM and Theou, O and Langille, MGI and Beiko, RG},
title = {Effect of bedrest on the human gut and oral microbiome: implications for frailty.},
journal = {Experimental gerontology},
volume = {216},
number = {},
pages = {113079},
doi = {10.1016/j.exger.2026.113079},
pmid = {41748043},
issn = {1873-6815},
abstract = {The physiological effects of spaceflight resemble those of ageing and prolonged inactivity, and ground-based microgravity analogs have emerged as promising models for studying frailty. The human microbiome is increasingly recognised for its role in age-associated decline, although precise mechanisms remain unclear. Here, we evaluate the gut and oral microbiomes of twenty-two participants, aged 55-65, who were enrolled in a head-down tilt bedrest (HDBR) study, the first Canadian HDBR study conducted in an older cohort. Participants were randomly assigned to an inactivity or multi-modality exercise intervention group for fourteen days of HDBR, followed by seven days of rehabilitation and additional follow-up appointments. Gut (n = 343) and oral (n = 344) taxonomic profiles were generated using V4-V5 16S rRNA gene sequencing from fecal and salivary samples collected throughout the study. Gut functional profiles were generated using metagenomic (n = 86) data, used for pathway inference, and metabolomic (n = 83) data. Frailty was measured using a 36-item frailty index. Inactivity-associated changes to the gut microbiome during HDBR included decreasing α-diversity, decreasing Akkermansia and Lactobacillus, and increasing Bacteroides. Exercise-associated changes included increasing gut Roseburia. Both gut and oral β-diversity were associated with frailty scores and individual frailty components. We conclude that inactivity-associated changes to the human microbiome are associated with the early stages of frailty development, and that exercise may serve as an effective countermeasure against these effects. These results may inform strategies to preserve the health of both older adults facing prolonged periods of inactivity, as well as astronauts during longer space exploration missions.},
}

@article {pmid41748019,
year = {2026},
author = {Piccinno, G and Asnicar, F},
title = {Advanced computational analysis in metagenomic studies to support precision medicine.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2026.02.018},
pmid = {41748019},
issn = {1469-0691},
abstract = {BACKGROUND: The human microbiome has been linked to host health and is suggested to play a direct role in the onset of certain human diseases, as well as in impacting treatment efficacy. Characterizing the microbiome composition and its interaction with the host is now supported by an established, continuously improving set of bioinformatic and statistical resources that enable reproducible answers to fundamental questions about microbiome sample composition and its association with sample and host information. Extensive evidence highlighted that, in a non-diseased state, the microbiome composition is determined by multiple factors, including the acquisition of microbes at birth, lifestyle, dietary patterns, social interactions, antibiotic use, or probiotic intake, among others. In disease states, the microbiome may alter its composition and, in some cases, present specific biomarkers, as in colorectal cancer. Some microbiome components have also been associated with improved immunotherapy response in clinical oncology, suggesting a potential beneficial role for certain species and supporting the use of the microbiome as an additional therapeutic tool in these scenarios.

OBJECTIVES: This review summarizes computational approaches for microbiome characterization, highlights key findings on microbiome-disease associations, and provides a perspective on directions and open questions relevant to address in the future.

SOURCES: We selected scientific studies and reviews, published in peer-reviewed journals, based on their impact in the field and relevance to the topic of this manuscript. Literature selection was conducted by reviewing scientific publications retrieved from major scientific databases, such as PubMed, and by combining with the authors' knowledge of the literature.

CONTENT: Here we review computational approaches to characterize and model the microbiome's structure in health and disease and discuss multi-cohort data analysis, integration, and validation methods.

IMPLICATIONS: Improved microbiome characterization supports precision medicine by informing prevention or treatment, leveraging refined microbiome signature and modulation strategies.},
}

@article {pmid41743807,
year = {2026},
author = {Zhou, H and Jiang, S and Zhang, L and Zhao, J and Zhou, T and Zhang, L and Ma, Y and Liu, S and You, Z and Li, F and Chen, S and Chen, L and Wang, Q and Xing, X and Chen, W and Li, D},
title = {Impact of Ozone Exposure on Oral Microbiome: A Controlled, Randomized, Crossover Trial.},
journal = {Environment & health (Washington, D.C.)},
volume = {4},
number = {2},
pages = {236-245},
pmid = {41743807},
issn = {2833-8278},
abstract = {Environmental ozone pollution may adversely impact human health, while dysbiosis is implicated in various health outcomes. However, the effects of ozone exposure on the human microbiome remain unclear. This study conducted a controlled, randomized, crossover ozone exposure trial with 29 participants exposed to filtered air and ozone. Oral microbiome samples were collected for 16S rRNA sequencing. A mixed-effects model was used to analyze the impact of ozone exposure on the diversity and composition of the oral microbiome, as well as their association with lung functions. The results showed that the ozone concentration remained stable at 5 ± 5.1 parts per billion (ppb) under filtered air and 282.2 ± 44 ppb during ozone exposure. Acute ozone exposure significantly impaired lung function and reduced oral microbiome diversity, with forced vital capacity (FVC) decreasing by 0.41 L, expiratory volume in one second (FEV1) by 0.36 L, and peak expiratory flow (PEF) by 0.81 L, while observed species richness (Sobs), abundance-based coverage estimator (Ace), and chao indices (Chao) decreased by 21.83, 22.24, and 21.87%, respectively. Males exhibited greater sensitivity to ozone exposure than females, reflected in both reduced lung function and alterations in the oral microbiome. The altered microbiome was mainly enriched in metabolic pathways. Among the microbiome, Treponema medium exhibited a significant correlation and mediating effect on ozone-induced lung function impairment, which may serve as a sensitive indicator of changes in lung function. These findings provide new insights into the health effects caused by ozone exposure.},
}

@article {pmid41740230,
year = {2026},
author = {Li, Z and Wang, P and Gao, H and Zhi, M and Gu, X and Sun, T and Wang, Y and Shen, S and Ma, X and Ji, X and Zhang, X and Liu, D and Feng, Q},
title = {Parvimonas micra exacerbates periodontitis by infiltrating host cells through TmpC and circumventing lysosomal elimination via AppA.},
journal = {EBioMedicine},
volume = {125},
number = {},
pages = {106187},
doi = {10.1016/j.ebiom.2026.106187},
pmid = {41740230},
issn = {2352-3964},
abstract = {BACKGROUND: Periodontitis poses a significant threat to human oral health, and microorganisms serving as the initiating factor in its pathogenesis. Parvimonas micra (P. micra), a Gram-positive anaerobic bacterium prevalent within the oral cavities of patients with periodontitis, remains underexplored in terms of its full contribution to periodontitis pathogenesis.

METHODS: 16S rRNA sequencing was performed on human gingival crevicular fluid samples, whilst micro-CT was used in experimental rat models to assess the impact of P. micra on periodontitis progression. Single-cell RNA sequencing was employed to examine dynamic alterations in rat periodontal cell composition and the enrichment of gene pathways during P. micra infection. Finally, His pull-down assay combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to identify key virulence factors of P. micra and host cell receptors.

FINDINGS: In this study, we examined the abundance of P. micra in gingival crevicular fluid and validated its pathogenic potential in vivo. Single-cell RNA sequencing revealed that P. micra disrupted the periodontal immune and mineralisation microenvironment. Further investigation showed that P. micra manipulated its surface adhesins to bind receptors on periodontal ligament stem cells, activating the intracellular NF-κB and ERK1/2 signalling pathways and impairing osteogenic activity. Finally, we identified a mechanism by which P. micra employed a surface protein to evade autophagic clearance, thereby facilitating immune escape.

INTERPRETATION: This study identifies P. micra as a pivotal periodontal pathogen, and the elucidation of its molecular mechanisms provides potential therapeutic targets for periodontitis and related systemic conditions.

FUNDING: This work was supported by the National Natural Science Foundation of China (No. 82270980, 82071122), Noncommunicable Chronic Diseases-National Science and Technology Major Project (2023ZD0501400), Taishan TePin Scientist Project of Shandong Province (tstp20250546), the Natural Science Foundation of Jiangsu Province (No. BK20240268), High-Level Hospital Construction Project of Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University (No. 0024C035), Shandong Provincial Key Research and Development Program (Competitive Innovation Platform, 2025CXPT042), the Major Innovation Projects in Shandong Province (No. 2021SFGC0502), and the Shandong Province Key Research and Development Program (No. 2021ZDSYS18).},
}

@article {pmid41737300,
year = {2026},
author = {Shi, W and Wang, M and Jin, Z and Chen, X and Li, J and Lai, H and Li, X and Zhong, Q and Chen, Y and Chen, S},
title = {Metabolomics Analysis Reveals Gut Microbiota-Associated Sakuranin Modulates Endometrial Stem Cell Differentiation and Inflammation to Alleviate Pain in Endometriosis.},
journal = {Journal of pain research},
volume = {19},
number = {},
pages = {557430},
pmid = {41737300},
issn = {1178-7090},
abstract = {BACKGROUND: Endometriosis (EMS) is characterized by pain symptoms that seriously affect patients' quality of life. Gut microbiome-related metabolites (GMRM) play an important role in the process of EMS. However, the role of GMRM in endometrial stem cells and EMS-related pain remains unclear.

METHODS: An untargeted metabolomics approach was employed to analyze the fecal samples of 10 healthy individuals (heal), 11 EMS patients without dysmenorrhea (pless), and 14 EMS patients with dysmenorrhea (pain). The impact of potential key metabolite sakuranin on EMS-related pain was further investigated in vitro and in vivo.

RESULTS: We identified 33 metabolites that were commonly changed in the painful group compared to the health and pless groups, and these metabolites were associated with differential microorganisms. Among them, sakuranin was downregulated in the painful group and exhibited a notably inverse correlation with the degree of pain. ROC curve revealed that sakuranin had a relatively high predictive value for EMS-related pain (AUC=0.8027). Functionally, sakuranin inhibited differentiation, migration, and inflammatory cytokine production, and decreased the expression of VEGF and ALCAM in SUSD2-positive primary endometrial cells. In EMS mice, sakuranin suppressed ectopic lesion growth, reduced inflammation, modulated angiogenesis and proliferation markers (VEGF, ALCAM, Ki-67), and regulated sympathetic and sensory nerve markers, resulting in alleviated pain behaviors.

CONCLUSION: We delineated the metabolic landscape related to EMS-related pain and uncovered that sakuranin has the potential to inhibit the growth of EMS and alleviate EMS-related pain. This finding offers therapeutic strategies of sakuranin in alleviating the pain symptoms associated with EMS.},
}

@article {pmid41734518,
year = {2026},
author = {Dhillon, A and Yadav, P and Gupta, S and Singh, SV and Sohal, JS and Rawat, KD},
title = {Microbiome alterations and host-pathogen interactions in paratuberculosis: A one health perspective.},
journal = {Veterinary microbiology},
volume = {315},
number = {},
pages = {110940},
doi = {10.1016/j.vetmic.2026.110940},
pmid = {41734518},
issn = {1873-2542},
abstract = {Paratuberculosis is a chronic ruminal-enteric infection caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has significant economic, trade, and public health implications. In addition to evading host immunity, MAP modulates the gut microbiome, resulting in dysbiosis that exacerbates disease progression. A conceptual framework is proposed in which Johne's disease (JD) can serve as the paradigm of chronic infection, based on dysbiosis in microbial imbalance, immune escape, and pathogen survival in a self-sustaining loop, as in human tuberculosis and Crohn's disease. This review evaluates the evidence on MAP-induced microbiome alterations and their impact on host-pathogen relations, immune responses, and metabolic processes in cattle, sheep, goats, and other ruminants. JD-associated dysbiosis is characterized by reduced microbial diversity, depletion of butyrate-producing taxa (e.g., Ruminococcaceae and Lachnospiraceae), enrichment of pro-inflammatory Enterobacteriaceae, and disruption of short-chain fatty acid (SCFA) metabolic pathways. Recent studies suggest that such alterations in microbes can be the initial signs of diagnosis and pre-treatment components, such as probiotics, prebiotics, dietary modifications, and microbiome-based vaccinations. This summary bridges the research on the veterinary and human microbiome, revealing that MAP-Microbiome interactions reflect immunological evasion and microbial persistence schemes observed with other intracellular pathogens. Evidence across species and disciplines highlights the interdependence between host microbiome stability, pathogen persistence, and disease progression. However, variances between studies show the need to adopt standardized methodologies, longitudinal studies, and multi-omics designs to establish whether dysbiosis precedes or follows MAP infection. The review is the first to combine molecular, immunological, and microbiome-level data into the One Health concept of MAP persistence. Moreover, this review takes a One Health approach where the investigation of MAP-induced dysbiosis offers an understanding of chronic inflammation, microbial ecology, and persistence strategies applicable to veterinary as well as human health. This way, we can emphasize the diagnostic, therapeutic, and translational opportunities of microbiome-based interventions in JD using a One Health model that connects ruminant disease to human inflammatory bowel diseases, including Crohn's disease.},
}