@article {pmid42054621,
year = {2026},
author = {Doiron, RC and Cotechini, T},
title = {The 2025 AUA Guideline Update on Recurrent Urinary Tract Infections: Important New Recommendations Reflecting Progress in an Often-Ignored Disease Space.},
journal = {The Journal of urology},
volume = {216},
number = {2},
pages = {171-173},
doi = {10.1097/JU.0000000000005079},
pmid = {42054621},
issn = {1527-3792},
}

@article {pmid42333002,
year = {2026},
author = {Claus, J and McInnes, RS and Hullegie, S and Damoiseaux, RAMJ and Schilder, AGM and Top, J and Schuurman, R and Chu, ML and Bogaert, D and van Schaik, W and Venekamp, RP and van de Wijgert, JHHM},
title = {The impact of topical or oral antibiotics in children with acute otitis media on their middle ear, nasopharyngeal, and gut microbiomes.},
journal = {Epidemiology and infection},
volume = {154},
number = {},
pages = {e94},
doi = {10.1017/S0950268826101836},
pmid = {42333002},
issn = {1469-4409},
support = {84801 5006/ZONMW_/ZonMw/Netherlands ; },
mesh = {Humans ; *Otitis Media/drug therapy/microbiology ; *Ear, Middle/microbiology/drug effects ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; Administration, Oral ; *Nasopharynx/microbiology ; Female ; Male ; Administration, Topical ; Infant ; Child, Preschool ; *Gastrointestinal Microbiome/drug effects ; *Microbiota/drug effects ; Amoxicillin/administration & dosage ; Acute Disease ; Bacteria/classification/drug effects/isolation & purification ; },
abstract = {Acute otitis media (AOM) is a major driver of paediatric antibiotic prescriptions. We assessed the impact of oral and topical antibiotics on middle ear, nasopharyngeal, and gut microbiome compositions, and the gut resistome, in children with AOM and ear discharge (AOMd). Fifty-eight children with AOMd and ear pain and/or fever were randomized to oral amoxicillin suspension (n = 31) or hydrocortisone-bacitracin-colistin eardrops (n = 27) for 7 days. From 57 out of 58 children, baseline, and Week-2 middle ear fluid (MEF) and nasopharyngeal (NP) samples were sequenced, along with baseline, Week-2, and Month-3 faecal samples. At baseline, the top 5 MEF genera were Streptococcus, Haemophilus, Turicella, Staphylococcus and Alloiococcus and NP genera Moraxella, Haemophilus, Streptococcus, Corynebacterium, and Dolosigranulum. At Week-2, the ear discharge had resolved in all but four children (oral n = 3, eardrops n = 1). In NP samples, the relative and absolute abundances of Streptococcus decreased to a greater extent after oral than eardrop treatment, but Moraxella and Haemophilus increased only following oral treatment. Neither treatment significantly altered the faecal microbiome or resistome at Week-2 and Month-3. Therefore, both treatments resolved the middle ear discharge in most children, but oral amoxicillin suspension may reduce NP Streptococcus more than hydrocortisone-bacitracin-colistin eardrops at the cost of potentially increasing other NP pathobionts.},
}

Humans
*Otitis Media/drug therapy/microbiology
*Ear, Middle/microbiology/drug effects
*Anti-Bacterial Agents/administration & dosage/therapeutic use
Administration, Oral
*Nasopharynx/microbiology
Female
Male
Administration, Topical
Infant
Child, Preschool
*Gastrointestinal Microbiome/drug effects
*Microbiota/drug effects
Amoxicillin/administration & dosage
Acute Disease
Bacteria/classification/drug effects/isolation & purification

@article {pmid42420081,
year = {2026},
author = {Strobel, KM and Ortigoza, EB and Bautista, GM},
title = {The impact of gastrointestinal motility on feeding tolerance in the very preterm infant.},
journal = {Seminars in perinatology},
volume = {},
number = {},
pages = {152269},
doi = {10.1016/j.semperi.2026.152269},
pmid = {42420081},
issn = {1558-075X},
abstract = {Infants who are preterm experience developmental arrest of the gastrointestinal system, which continues to mature throughout their neonatal intensive care hospitalization. During this period of development and clinical exposures, infants frequently experience episodes of enteral feeding intolerance. Currently, definitions of feeding intolerance are vague and fail to distinguish developmental feeding patterns from pathological feeding intolerance. In this review, we disentangle these entities by examining the physiology of the fetal and neonatal gut, the development of the microbiome, and factors that compound intestinal dysmotility. We will also review clinical, imaging, and biomarker approaches to the assessment of feeding intolerance. Finally, we propose a standardized, trajectory-based definition to support more consistent clinical care and enable future trials to use uniform definitions. Notably, this review will focus on the typical preterm infant trajectory, not infants at risk of intestinal failure.},
}

@article {pmid42420265,
year = {2026},
author = {Vilar Geraldi, M and Dwibedi, C and Jaiswal, R and Gregori, G and Zhou, X and Lv, B and Zheng, Y and Wang, X and Wu, H and Axelsson, KF and Bäckhed, F and Tremaroli, V and Lorentzon, M},
title = {Gut microbiota associates with frailty in older women.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42420265},
issn = {2041-1723},
support = {2023-01976, 2023-01976, 2022-06725, 2018-05973, 2024-03723,//Vetenskapsrådet (Swedish Research Council)/ ; Lorentzon, 2023-2024//Konung Gustaf V:s och Drottning Victorias Frimurarestiftelse (King Gustaf V and Queen Victoria's Foundation of Freemasons)/ ; 2024-0104//Familjen Erling-Perssons Stiftelse (Erling-Persson Family Foundation)/ ; Lorentzon, 2016//IngaBritt och Arne Lundbergs Forskningsstiftelse (Ingabritt and Arne Lundberg Research Foundation)/ ; KAW 2020.0239//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; },
mesh = {Humans ; Female ; Aged ; *Frailty/microbiology/mortality ; Aged, 80 and over ; *Gastrointestinal Microbiome/genetics/physiology ; Sweden/epidemiology ; Frail Elderly ; Bacteria/classification/genetics/isolation & purification ; Cohort Studies ; },
abstract = {Frailty is a multifactorial geriatric condition linked to increased mortality and adverse health outcomes and is associated with gut microbiome features that differ from those observed in healthy ageing. We analyze gut metagenomic profiles in relation to estimated frailty severity and frailty-related clinical outcomes assessed with an internally developed and validated Frailty Mortality Index (FMI) in the SUPERB cohort, comprising 2,081 Swedish women aged 75-80 years. The FMI is a composite measure that integrates functional, physiological and psychological dimensions associated with frailty and mortality risk, and shows stronger associations with mortality compared to the Charlson Comorbidity Index in the SUPERB cohort. The FMI is inversely associated with microbial diversity, gene richness, and predicted functional capacity, which are linked to physical function, mortality and fall-related injuries. A total of 404 bacterial species are significantly associated with FMI, and most show concordant associations in a Chinese cohort of 1,448 older adults. Here we show microbial signatures linked to frailty and mortality across different continents.},
}

Humans
Female
Aged
*Frailty/microbiology/mortality
Aged, 80 and over
*Gastrointestinal Microbiome/genetics/physiology
Sweden/epidemiology
Frail Elderly
Bacteria/classification/genetics/isolation & purification
Cohort Studies

@article {pmid42420350,
year = {2026},
author = {Payoungkiattikun, W and Dobutr, T and Roamcharern, N and Jangpromma, N and Klaynongsruang, S and Daduang, J and Daduang, S and Patramanon, R},
title = {Alcalase-derived egg white hydrolysates exhibit ACE inhibition In silico and gut microbiota modulation In vivo.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-60508-8},
pmid = {42420350},
issn = {2045-2322},
support = {CRP6105020400//Agricultural Research Development Agency/ ; NRU581004//National Research University (NRU)/ ; },
abstract = {This study investigated the dual ACE-inhibitory and gut microbiota-modulating potential of egg white hydrolysate (EWH), obtained through Alcalase enzymatic hydrolysis. LC-ESI-MS/MS analysis of the most bioactive fraction (F2), which exhibited strong antioxidant and antibacterial activities, identified six putative bioactive peptides: VLLPDEVSGL, MANKGPAYGM, AAAAGLNPGLM, GIIQHEL, MAGFVPLLLL, and NVLQPSSVDSQ. Molecular docking revealed that EWH-2 (MANKGPAYGM) and EWH-6 (NVLQPSSVDSQ) exhibited the strongest binding to ACE, with Gibbs free energies (ΔG) of - 14.4 and - 13.8 kcal/mol and dissociation constants (Kd) of 2.7 × 10[-11] M and 8 × 10[-11] M, respectively. These interactions involved the S1, S2, and zinc-binding motifs via hydrophobic interactions and hydrogen bonds. These findings were supported by 100 ns molecular dynamics simulations, confirming stable ACE-peptide complexes with particularly favorable binding for EWH-2. In vivo administration of EWH to male rats for 14 days (n = 6 per group) significantly increased gut microbial alpha diversity and reshaped microbial community composition. EWH treatment enriched genera such as Prevotella, Paraprevotella, Sutterella, Butyricimonas, and Barnesiella, which are associated with short-chain fatty acid production and metabolic health. Collectively, these findings demonstrate that Alcalase-derived EWH exhibits dual ACE-inhibitory and gut microbiota-modulating activities, suggesting potential benefits for blood pressure regulation and metabolic health.},
}

@article {pmid42420430,
year = {2026},
author = {Ogashira, S and Kunimatsu, R and Koizumi, Y and Yoshimi, Y and Ogasawara, T and Abe, F and Okazaki, K and Kado, I and Tanimoto, K},
title = {CAMBRA caries risk stratification is associated with distinct salivary and supragingival plaque microbiomes in pre-orthodontic patients.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-61457-y},
pmid = {42420430},
issn = {2045-2322},
support = {24K20058//Japan Society for the Promotion of Science/ ; },
abstract = {Fixed orthodontic appliances impair oral hygiene and increase the risk of dental caries and white spot lesions (WSLs). Although the Caries Management by Risk Assessment (CAMBRA) tool enables multifactorial caries risk evaluation, its association with the oral microbiome remains unclear. In this cross-sectional study, we examined the relationship between CAMBRA risk classification, clinical indices, and salivary and supragingival plaque microbiomes in 149 pre-orthodontic patients. Participants were classified into Low, Moderate, High, and Extreme risk groups based on CAMBRA. We evaluated the decayed, missing, and filled (DMF) index, number of WSLs, plaque control record, stimulated salivary flow rate (SSFR), salivary pH, buffering capacity, culture-based bacterial indices, and 16 S rRNA gene sequencing profiles. The DMF index and number of WSLs were higher in the High- and Extreme-risk groups, whereas SSFR and buffering capacity were lower in the Extreme-risk group. Alpha-diversity metrics, beta-diversity analyses, and genus-level relative abundance showed group-specific differences in saliva and dental plaque, with genera including Haemophilus, Rothia, Veillonella, Treponema, Parvimonas, and Leptotrichia. These cross-sectional findings suggest that CAMBRA-based risk stratification is associated with distinct clinical characteristics and oral microbiome profiles before orthodontic treatment and may provide biological support for CAMBRA-based pretreatment assessment in this patient population.},
}

@article {pmid42420462,
year = {2026},
author = {Desharnais, L and Swaby, A and Messaoudene, M and Doré, S and Yu, MW and Fiset, B and Breton, V and Ponce, M and Hu, Y and Wilson, L and Sorin, M and Wang, Y and Dewar, K and Pollak, M and Elkrief, A and Routy, B and Walsh, LA and Quail, DF},
title = {Diet-microbiome synergy underlies obesity-associated immunotherapy efficacy.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42420462},
issn = {1476-4687},
abstract = {Physiological host factors, such as the gut microbiome and obesity, independently influence anti-tumour immunity and responses to immune checkpoint inhibitors (ICIs)[1], with high body mass index (BMI) having an unexpected link with greater ICI efficacy[2-6]. However, how these factors interact across diverse dietary contexts remains unclear. Here, using 12 mouse diet models that reflect a spectrum of obesity biology, we characterize diet-driven metabolic, immune and gut microbiota features associated with ICI sensitivity. We find that obesity-associated ICI responses are poorly correlated with metabolic dysfunction and are instead dependent on the diet-gut axis. Obesogenic diets promote a robust and persistent gut microbial ecosystem that is capable of restoring ICI sensitivity following a short-term diet switch or fecal microbiota transplants (FMTs) from non-responder models. Monocolonization of germ-free mice with favourable bacteria such as Lactobacillus johnsonii, together with an obesogenic diet, synergistically promotes tumour regression through an enrichment of microbiota-derived aromatic amino acid metabolites. Moreover, human-to-mouse FMT from donors with a high BMI enhanced ICI efficacy compared with donors with a normal BMI, and an obesogenic diet restored sensitivity following FMT from a non-responder patient. Our study provides insight on epidemiological associations between BMI and ICI efficacy, and suggests that immunomodulatory synergy between diet and the gut microbiota could be leveraged to improve ICI outcomes and FMT interventions.},
}

@article {pmid42420814,
year = {2026},
author = {Cheng, Q and Guo, S and Du, Z and Li, X and Wang, Z and Jiang, X and Zhu, L and Yang, B and Feng, Y and Wang, Y and Shen, X},
title = {Healthy wheat roots are enriched in Bacillus sp. XN303, conferring resistance to Fusarium crown rot, promoting seedling growth, and detoxifying deoxynivalenol.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.71111},
pmid = {42420814},
issn = {1526-4998},
support = {//National Natural Science Foundation of China/ ; //Shaanxi Fundamental Science Research Project for Chemistry and Biology/ ; },
abstract = {BACKGROUND: Fusarium crown rot (FCR), caused predominantly by Fusarium pseudograminearum, is a devastating soil-borne disease threatening global wheat production. Systematic discovery of keystone microbial taxa with biocontrol potential from the wheat microbiome remains poorly explored. This study aimed to identify core microbiome biomarkers associated with FCR resistance and functionally validate candidate biocontrol agents.

RESULTS: Bacterial and fungal communities across five wheat compartments (rhizosphere, root, stem, leaf, grain) were profiled under FCR challenge. Host compartment niche was the primary driver of wheat microbial community assembly. FCR infection reduced root and stem microbial α-diversity, strengthened homogeneous selection-dominated deterministic fungal assembly in stems, coincided with declined dispersal limitation in root bacterial assembly, and disrupted microbial network stability. Integrated analysis identified Bacillus ASV_2195, enriched in healthy wheat roots, as a core FCR resistance biomarker. The corresponding strain, Bacillus sp. XN303, was isolated. Whole-genome sequencing of XN303 uncovered gene clusters encoding antimicrobial compounds and plant-beneficial traits. Functionally, XN303 directly inhibited F. pseudograminearum growth by 71.64%, reduced the FCR disease index by 79.21%, and lowered pathogen density in rhizosphere soil and stems by 22.89% and 20.28%, respectively, in pot assays. In addition, XN303 demonstrated the capacity to detoxify deoxynivalenol (DON) and activate jasmonic acid-mediated defense priming in wheat.

CONCLUSION: Bacillus sp. XN303, identified through microbiome-guided screening, confers robust FCR protection via pathogen antagonism, DON detoxification, growth promotion, and defense priming, representing a potential candidate biocontrol agent for sustainable FCR management. © 2026 Society of Chemical Industry.},
}

@article {pmid42420833,
year = {2026},
author = {Luo, D and Lu, F and Yang, L and Gan, Z and Zhang, X and Zhao, Z and Dong, R},
title = {Harnessing probiotics to combat nonylphenol toxicity: a multiomics approach of gut microbiome remodelling in Silurus meridionalis.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-13161-4},
pmid = {42420833},
issn = {1471-2164},
support = {GZSTYYCYJSTX-202605//Guizhou Modern Agricultural Industry Technology System of China/ ; 2024 (No. 079//the Guizhou Provincial Key Technology R&D Program/ ; 32460918//the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: As a ubiquitous environmental endocrine disruptor, nonylphenol (NP) threatens aquatic organisms, driving the need for sustainable mitigation strategies. While probiotics represent promising eco-friendly supplements, their molecular mechanisms against NP toxicity remain unclear. In this study, S. meridionalis received 7-week of probiotic (Bacillus subtilis and Lactobacillus acidophilus) pretreatment followed by 15 days of NP exposure. Integrated metagenomics, transcriptomics, and metabolomics analyses, with Reverse transcription quantitative real-time PCR (RT‒qPCR) and Enzyme-linked immunosorbent assay (ELISA) validation, were performed to elucidate microbial, genetic and metabolic responses. Growth performance, including the specific growth rate (SGR) and weight gain rate (WGR), was concurrently assessed.

RESULTS: NP exposure significantly suppressed WGR and SGR, and induced gut microbiota dysbiosis alongside and lipid metabolism disorders in S. meridionalis. Probiotic pretreatment effectively reversed these toxic effects and restored the inhibited WGR and SGR. Multiomics integration revealed that the protective effects of probiotics were mediated by a coherent "microbe-host" co-metabolism network across 3 progressive layers: (1) Microbial Remodelling: in which beneficial taxa (e.g., Bacteroides eggerthii and Cetobacterium sp.) were enriched, and the functional capacity for short-chain fatty acid (SCFA) synthesis and ethanolamine metabolism was enhanced; (2) Host Gene Regulation: in which key lipid metabolism genes (ek1, cept1, ept1, mogat2, and abcg2a) were upregulated, and lipase activity was restored; and (3) Metabolic Pathway Activation and Physiological Repair: in which the activity of the NP-suppressed Kennedy pathway was reactivated, thereby promoting phosphatidylethanolamine (PE) and phosphatidylcholine (PC) synthesis and ultimately restoring gut barrier function. These results were further were corroborated by RT‒qPCR and ELISA.

CONCLUSION: This study systematically elucidated that probiotics alleviated NP toxicity by remodelling a "microbiota-host Kennedy pathway gene-metabolite (PE and PC)-growth performance" regulatory network. The key mechanism is the beneficial microbiota activating the host Kennedy pathway and restoring gut phospholipid homeostasis and barrier function. These findings provide a theoretical basis for developing targeted, lipid metabolism focused probiotic feed additives for use in sustainable aquaculture.},
}

@article {pmid42420920,
year = {2026},
author = {Kurtbeyoglu, E and Caferoglu Akin, Z and Ozdemir, F},
title = {Maternal chrononutrition during pregnancy and the composition of intestinal and placental microbiota.},
journal = {BMC pregnancy and childbirth},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12884-026-09584-2},
pmid = {42420920},
issn = {1471-2393},
support = {TDK-2022-11922//Bilimsel Araştırma Projeleri, Erciyes Üniversitesi/ ; },
abstract = {BACKGROUND: Disrupted feeding timing may alter microbiota profiles and contribute to metabolic disturbances. This study aimed to investigate the impact of maternal chrononutrition during pregnancy on maternal gut and placental microbiota.

METHODS: This study was conducted between April 2022 and February 2023 at Erciyes University Faculty of Medicine Hospitals and Kayseri Private Dünyam Hospital in Kayseri, Türkiye, among healthy pregnant women with predominantly daytime feeding (pDT, n = 10) or predominantly nighttime feeding (pNT, n = 10). A questionnaire was administered, and three-day food consumption diaries were recorded at both 20-26 and 32-36 weeks of gestation. Fecal samples were collected at 32-36 weeks of gestation, and placental samples were collected at birth and stored at -80 °C until analysis.

RESULTS: Although total daily energy intake at both gestational periods (20-26 and 32-36 weeks) was similar between the groups, gestational weight gain was greater in the pNT group [16.30 (5.25) kg] than in the pDT group [11.90 (3.41) kg] (p = 0.039). Compared with the pDT group, the Firmicutes: Bacteroidetes ratio was higher in the maternal gut microbiota of the pNT group. Furthermore, Bacilli, Lactobacillales, Lactobacillaceae, and Lactobacillus were significantly more abundant in the pDT group than in the pNT group (p < 0.05). The intestinal and placental microbiota of the pDT and pNT groups had similar alpha and beta diversity.

CONCLUSIONS: Our findings suggest that predominantly daytime or nighttime feeding during pregnancy may influence the composition of maternal gut and placental microbiota. These microbiome alterations may have potential implications for maternal and infant health; however, larger longitudinal studies are needed to clarify their long-term relevance, including possible links with fetal programming.},
}

@article {pmid42421159,
year = {2026},
author = {Frejlichová, L and Maldonado-González, MM and Škarpa, P and Tomšovský, M and Eichmeier, A},
title = {Beyond detection: unveiling microbial dynamics in oak seedlings using fungal isolation and amplicon sequencing.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00929-0},
pmid = {42421159},
issn = {2524-6372},
support = {LDF_VP_2021028//Internal Grant Schemes of Mendel University in Brno, Internal Grant Agency of the Faculty of Forestry and Wood Technology/ ; CZ.02.1.01/0.0/0.0/16_017/0002334//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; },
abstract = {BACKGROUND: Forest nurseries are critical for producing resilient nursery stock for reforestation and planting of ornamental trees, yet the microbial communities associated with nursery grown plants remain poorly characterized. Quercus robur L. seedlings from seven Czech forest nurseries were analyzed to assess microbial diversity, co-occurrence patterns, and environmental drivers.

RESULTS: Microbial communities were characterized using fungal ITS2 and bacterial 16S rRNA gene amplicon sequencing, fungal isolation, and comprehensive soil chemistry. HTAS revealed broader taxonomic and functional profiles compared to isolation, which selectively enriched for fast growing pathogens. Both methods were found to be complementary, emphasizing the value of methodological integration. Fungal communities exhibited pronounced site specific beta diversity and responded to inorganic soil parameters, particularly calcium, phosphorus, and pH/CaCl2. Bacterial communities were more spatially cohesive and primarily associated with humification related factors. Trends in fungal alpha diversity were observed in relation to organic matter fractions (e.g., Cox, DH). SparCC genus level association analyses revealed high magnitude compositional association patterns, but no network edges remained significant after FDR correction; these patterns are therefore interpreted as exploratory and hypothesis generating rather than as evidence of direct microbial interactions.

CONCLUSIONS: Mineral soil properties were associated with microbial community structure and fungal trophic composition. Despite standardized nursery conditions, edaphic variability exerted strong filtering effects on fungal and bacterial communities. These findings provide ecological insight into seedling microbe interactions and offer a basis for microbiome informed nursery management strategies.},
}

@article {pmid42421214,
year = {2026},
author = {Raya Tonetti, F and Han, H and Fondevila, MF and Wei, W and Özdirik, B and Bajaj, JS and Schubert, ML and Sikaroodi, M and Gillevet, PM and Lang, S and Demir, M and Rahman, IR and van der Donk, WA and Bosques-Padilla, F and Verna, EC and Abraldes, JG and Brown, RS and Vargas, V and Altamirano, J and Caballería, J and Shawcross, DL and Louvet, A and Lucey, MR and Mathurin, P and Garcia-Tsao, G and Stärkel, P and Bataller, R and Hsu, CL and Llorente, C},
title = {Non-absorbable antibiotics worsen alcohol-associated liver disease in gastric acid-suppressed mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2694797},
doi = {10.1080/19490976.2026.2694797},
pmid = {42421214},
issn = {1949-0984},
mesh = {Animals ; *Anti-Bacterial Agents/adverse effects/administration & dosage/therapeutic use ; *Proton Pump Inhibitors/adverse effects/administration & dosage ; Mice ; *Gastric Acid/metabolism ; Male ; *Gastrointestinal Microbiome/drug effects ; *Liver Diseases, Alcoholic/microbiology/pathology ; Dysbiosis/chemically induced ; Humans ; Mice, Inbred C57BL ; Disease Models, Animal ; Liver/pathology/drug effects ; },
abstract = {Gastric acid-suppressive medications, particularly proton pump inhibitors (PPIs), are commonly used in patients with alcohol-associated liver disease (ALD) to prevent and manage upper gastrointestinal bleeding, gastroesophageal reflux disease, and non-steroidal anti-inflammatory/aspirin-induced gastroesophageal damage. By inhibiting the gastric H[+]/K[+]-ATPase, PPIs suppress acid secretion and impair bacterial killing, thereby promoting gut dysbiosis that disrupts barrier integrity and enhances bacterial translocation, ultimately exacerbating liver injury. PPIs are frequently co-administered with antibiotics for indications such as gastrointestinal bleeding, Spontaneous Bacterial Peritonitis (SBP), other infections, or hepatic encephalopathy prophylaxis, but the consequences of this combined therapy on gut microbial ecology and disease outcomes remain unclear. Our study addresses this gap by showing how PPI use, alone or with antibiotics, reshapes the gut microbiome and aggravates liver disease progression. In previous studies, we showed that PPIs promote dysbiosis and ALD progression in mice and humans by facilitating intestinal expansion and hepatic translocation of Gram-positive Enterococcus. Fecal cytolysin, an Enterococcus faecalis exotoxin that induces hepatocyte death, predicts mortality in patients with alcohol-associated hepatitis (AH). In this study, we have examined the mechanism by which PPIs alone and in combination with non-absorbable antibiotics targeting Gram-positive bacteria influence ALD, as well as the disease mechanisms associated with cytolytic Enterococcus faecalis and the development of therapeutic strategies. In mice, alcohol administration during gastric acid suppression promoted expansion of Gram-positive taxa, including cytolysin-producing Enterococcus. Similarly, PPI use in patients with AH was associated with increased fecal Enterococcus and higher 30-d mortality, underscoring the translational relevance of our findings. Unexpectedly, treatment of acid-suppressed mice with non-absorbable antibiotics designed to suppress Gram-positive bacteria worsened ethanol-induced steatohepatitis: while Enterococcus abundance decreased, Streptococcus and other potentially pathogenic taxa expanded, leading to increased bacterial translocation and aggravated liver injury. In patients with cirrhosis or metabolic dysfunction-associated steatotic liver disease (MASLD), PPIs did not promote Enterococcus expansion, indicating etiology-dependent microbiome responses. Finally, we identified dipalmitoylphosphatidylcholine and Caspase-1 inhibitor as in vitro and in vivo modulators of cytolysin activity, highlighting potential therapeutic avenues. Collectively, our study demonstrates how PPIs and non-absorbable antibiotics targeting Gram-positive bacteria interact with the gut microbiome to drive ALD, underscoring the need for careful therapeutic management.},
}

Animals
*Anti-Bacterial Agents/adverse effects/administration & dosage/therapeutic use
*Proton Pump Inhibitors/adverse effects/administration & dosage
Mice
*Gastric Acid/metabolism
Male
*Gastrointestinal Microbiome/drug effects
*Liver Diseases, Alcoholic/microbiology/pathology
Dysbiosis/chemically induced
Humans
Mice, Inbred C57BL
Disease Models, Animal
Liver/pathology/drug effects

@article {pmid42421228,
year = {2026},
author = {Serrano-García, L and Martínez-Salvador, E and Belda-Marco, A and Herrero-Oliva, C and Cortés, J and Llombart-Cussac, A and Fernández-Murga, L},
title = {Modulation of the response to immunotherapy in triple-negative breast cancer: the role of the microbiota and microbial metabolites in the tumor microenvironment.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2697600},
doi = {10.1080/19490976.2026.2697600},
pmid = {42421228},
issn = {1949-0984},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Triple Negative Breast Neoplasms/therapy/immunology/microbiology ; Female ; *Immunotherapy ; *Gastrointestinal Microbiome/immunology ; Animals ; },
abstract = {Triple-negative breast cancer is an aggressive and heterogeneous breast cancer subtype for which immune checkpoint inhibitors combined with chemotherapy have improved outcomes in selected patients. However, primary and acquired resistance remain common, underscoring the need to identify extrinsic, modifiable determinants of antitumor immunity. Increasing evidence indicates that the gut and tumor-associated microbiota shape systemic and intratumoral immune tone and influence the efficacy of cancer therapies. Beyond microbial composition, microbiota-derived metabolites-including short-chain fatty acids, indole-tryptophan derivatives, bile acids, polyamines, and other small molecules-can act as functional mediators linking microbial ecology to immune-cell programming and tumor biology. These metabolites modulate dendritic cell function, T-cell priming and fitness, myeloid polarization, inflammatory set points, and metabolic pathways within the tumor microenvironment, thereby potentially enhancing or constraining responses to chemoimmunotherapy. Importantly, while some studies propose intratumoral microbial effects, most clinically actionable evidence currently supports systemic gut-derived metabolites and immune tone modulation that secondarily shapes the TNBC tumor microenvironment. In this review, we synthesize current knowledge on (i) the immunobiology of triple-negative breast cancer (TNBC) relevant to microbiota-driven modulation, (ii) mammary and gut microbiome features reported in TNBC, and (iii) mechanistic pathways through which microbial metabolites may regulate antitumor immunity and immune checkpoint inhibitors (ICI) sensitivity. We also discuss methodological considerations for integrating microbiome profiling with metabolomics and immune phenotyping and evaluate emerging opportunities to leverage microbiota-derived metabolites as biomarkers and therapeutic targets. Finally, we highlight translational strategies-including diet, pre/probiotics, antibiotic stewardship, fecal microbiota transplantation, and metabolite-centric ("postbiotic") approaches-and outline priorities for TNBC-focused, prospective multi-omics studies to move from associative signatures toward actionable interventions.},
}

Humans
*Tumor Microenvironment/immunology
*Triple Negative Breast Neoplasms/therapy/immunology/microbiology
Female
*Immunotherapy
*Gastrointestinal Microbiome/immunology
Animals

@article {pmid42421295,
year = {2026},
author = {Han, EJ and Kim, DH and Lee, JJ and Chung, HJ},
title = {The gut microbiome and mitochondrial function in metabolism, immunity, and disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2699451},
doi = {10.1080/19490976.2026.2699451},
pmid = {42421295},
issn = {1949-0984},
mesh = {Humans ; *Mitochondria/metabolism ; Animals ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; Energy Metabolism ; },
abstract = {The gut microbiome is a key regulator of host physiology, yet its effects remain difficult to predict across individuals and contexts. Similar microbial compositions frequently give rise to divergent and delayed phenotypic outcomes, indicating that models based solely on signal strength or steady-state responses are insufficient to explain microbiome-driven host function. In this review, we propose a conceptual perspective in which microbiome-associated variability is shaped by the capacity of host cells to maintain mitochondrial function under persistent metabolic and immune stress. Microbiome-derived metabolites and immune activity define the metabolic and redox environments that constrain mitochondrial performance, thereby influencing how effectively cells recover from repeated stress. When mitochondrial membrane potential, redox balance, and energy production are not fully restored, mitochondria may show increased engagement of quality-control pathways. Over repeated stress-recovery cycles, this pattern may be associated with reduced functional reserve despite preserved baseline activity. This testable perspective may help explain why microbiome-associated phenotypes are delayed, variable, and context-dependent, and it highlights mitochondrial recovery capacity as a potential determinant of disease vulnerability and host-microbiome interactions.},
}

Humans
*Mitochondria/metabolism
Animals
*Gastrointestinal Microbiome
*Host Microbial Interactions
Energy Metabolism

@article {pmid42421310,
year = {2026},
author = {Chowdhury, R and Bosire, EM and Wolverton, LR and Pavinski Bitar, PD and Bell, KE and Keresztes, I and Chien, RC and Altier, C},
title = {Salmonella exploits a quorum-sensing family signal of the gut commensal Stenotrophomonas maltophilia to facilitate its colonization.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2699455},
doi = {10.1080/19490976.2026.2699455},
pmid = {42421310},
issn = {1949-0984},
mesh = {Animals ; *Stenotrophomonas maltophilia/physiology/metabolism/genetics ; Mice ; *Quorum Sensing ; Virulence ; Colon/microbiology ; Oxidative Stress ; Signal Transduction ; *Salmonella/physiology/pathogenicity/growth & development ; Host-Pathogen Interactions ; Virulence Factors/metabolism ; Salmonella Infections/microbiology ; },
abstract = {Successful colonization by enteric pathogens requires overcoming colonization resistance of the native microbiota while tightly regulating the expression of energetically-expensive virulence factors. Here we describe a feedback mechanism by which the enteric pathogen Salmonella orchestrates this balance through environmental manipulation. We show that Salmonella-induced oxidative stress can stimulate the colonic resident Stenotrophomonas maltophilia to enhance the secretion of the diffusible signal factor cis-2-hexadecenoic acid (c2-HDA), a potent repressor of Salmonella virulence. By sensing this metabolite, Salmonella can attenuate its own virulence program to favor proliferation and colonic colonization. In murine models, Salmonella colonization was significantly enhanced in the colon, and inflammation reduced, in the presence of c2-HDA produced by S. maltophilia. Moreover, the ability of Salmonella to recognize c2-HDA within the murine colon was crucial for its successful colonization. These findings reveal a pathogen-commensal signaling axis through which pathogen-driven inflammatory cues reshape the metabolic output of the microbiota, generating regulatory signals that are co-opted to optimize pathogen fitness in the gut.},
}

Animals
*Stenotrophomonas maltophilia/physiology/metabolism/genetics
Mice
*Quorum Sensing
Virulence
Colon/microbiology
Oxidative Stress
Signal Transduction
*Salmonella/physiology/pathogenicity/growth & development
Host-Pathogen Interactions
Virulence Factors/metabolism
Salmonella Infections/microbiology

@article {pmid42421531,
year = {2026},
author = {Juhl, A and Park, SH and Simanian, M and Wang, Y},
title = {Inflammatory biomarkers and oral microbiome alterations in depression and anxiety disorders: a systematic review.},
journal = {The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/15622975.2026.2688864},
pmid = {42421531},
issn = {1814-1412},
abstract = {BACKGROUND/OBJECTIVES: Depression and anxiety are increasingly linked to systemic inflammation and microbiome alterations, yet the role of the oral microbiome remains poorly characterised. This systematic review synthesises recent human evidence examining associations between depression or anxiety and (1) peripheral or salivary inflammatory biomarkers and (2) oral microbiome alterations.

MATERIALS AND METHODS: Following PRISMA 2020 guidance, PubMed, Web of Science, and PsycINFO were searched for studies published between 2016 and 2026. Eligible studies assessed depression, depressive symptoms, anxiety, generalised anxiety disorder (GAD), or PTSD-related symptoms alongside inflammatory biomarkers in blood or saliva and/or oral microbiome profiles. Reference lists of key eligible studies were also screened. Risk of bias was assessed using the Newcastle-Ottawa Scale (NOS) or an adapted NOS framework.

RESULTS: Fifty-three primary studies met eligibility criteria, including 42 studies evaluating inflammatory or salivary biomarkers and 11 studies examining oral microbiome profiles. Depression was associated with alterations in pro-inflammatory markers, particularly CRP, IL-6-related signalling, TNF-α, and other cytokine or chemokine markers. Anxiety-related findings were more heterogeneous. Oral microbiome studies reported altered community composition and taxa associated with depression, anxiety, and trauma-related symptoms, but findings varied by population, sampling site, and adjustment for oral-health and behavioural confounders.

CONCLUSIONS: Current evidence suggests depression and anxiety-related conditions are associated with low-grade inflammatory activity and alterations in the oral microbiome. These findings support an oral-immune-brain framework for future research, but the current evidence remains largely observational.},
}

@article {pmid42421565,
year = {2026},
author = {Molajafari, A and Ebrahim-Saraie, HS and Moghadam, MT and Hasannejad-Bibalan, M},
title = {A Comprehensive Study of Bidirectional Interactions Between the Human Microbiome and Blood Malignancies and Hematologic Conditions: Focus on Novel Therapeutic Strategies.},
journal = {Journal of clinical laboratory analysis},
volume = {},
number = {},
pages = {e70306},
doi = {10.1002/jcla.70306},
pmid = {42421565},
issn = {1098-2825},
abstract = {BACKGROUND: The human microbiota plays a key role in maintaining host homeostasis by regulating immune responses, metabolism, and hematopoiesis. Microbial dysbiosis has been increasingly associated with immune dysfunction, inflammation, and bone marrow abnormalities that may contribute to hematological diseases. This review summarizes current evidence on the role of the microbiota in normal hematopoiesis and its potential involvement in benign and malignant hematological disorders.

METHODS: A narrative literature review was conducted through comprehensive searches of major scientific databases without time restrictions using the keywords Microbiome, Dysbiosis, Hematopoiesis, Anemia, Immune Thrombocytopenia, Congenital Neutropenia, Thrombosis, Lymphoma, Leukemia, and Multiple Myeloma. Relevant experimental, clinical, and review articles were screened and synthesized.

RESULTS: Available evidence suggests that the microbiota may influence hematopoietic stem cell function, immune cell development, and hematopoietic homeostasis. Microbial dysbiosis has been proposed to be associated with benign hematological disorders, including anemia, immune thrombocytopenia, congenital neutropenia, and thrombosis, as well as hematological malignancies such as leukemia, lymphoma, and multiple myeloma. Certain bacterial and viral infections may also influence disease progression and therapeutic responses. Microbiota-targeted interventions, including probiotics, prebiotics, dietary interventions, fecal microbiota transplantation, and other microbiome-based therapies, have shown potential as adjunctive therapeutic strategies.

CONCLUSIONS: Current evidence suggests that microbiota dysbiosis may contribute to the pathogenesis of various hematological disorders. A better understanding of host-microbiota interactions may support the development of novel biomarkers and microbiota-based therapeutic approaches, although further clinical studies are required to confirm their efficacy and safety.},
}

@article {pmid42421628,
year = {2026},
author = {Chen, X and Jamieson, L and Weyrich, LS and Nath, S},
title = {Global Landscape of Publicly Available Human Oral Microbiome Data.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345261456612},
doi = {10.1177/00220345261456612},
pmid = {42421628},
issn = {1544-0591},
abstract = {Despite rapid growth in oral microbiome research, it remains unclear how well publicly available data reflect the diversity of the global human population. This study systematically evaluated the geographic and sampling-type representativeness of publicly available human oral microbiome data. A global meta-research analysis of publicly available human oral microbiome records in the NCBI BioSample database released up to December 31, 2025, was conducted. Records were retrieved, harmonized, and analyzed across 4 dimensions: geographic origin, oral sampling type, temporal trends, and population-adjusted representation using a derived representation index (RI). A total of 222,454 BioSamples from 1,600 studies were identified, spanning 92 countries and 4 major oral sampling-type groups: oral fluids, oral mucosa and surfaces, dental plaque and calculus, and special or lesion-associated sites. Geographic distribution was highly concentrated; nearly half of all geographically annotated samples originated from the United States and China, while 61% of countries worldwide contributed no samples. Low- and middle-income regions, including Central and Southern Asia (RI = -12.76) and Sub-Saharan Africa (RI = -11.21), were underrepresented relative to their population sizes. Sampling-type distribution was similarly uneven, with saliva samples comprising more than half of all samples. In contrast, disease-relevant sites, including carious lesions, periapical lesions, and the dental pulp, each represented less than 0.2% of the dataset. Together, these findings underscore that publicly available human oral microbiome data remain unevenly distributed across geographic origin and sampling types, reflecting structural and practical factors that have persisted over time. Deliberate efforts to improve global representation, sampling diversity, and metadata standardization are needed to build a more scientifically robust oral microbiome evidence base.},
}

@article {pmid42421768,
year = {2026},
author = {Wu, X and Deng, Y and Li, S and Zou, K and Duan, Z and Ibrahim, N and Zhou, J and Jiang, L and Liu, X and Fu, S and Liang, Y},
title = {Compartment-Specific Variation in Bacterial Microbiome and Polyphyllin Profiles in Paris polyphylla.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {1725012},
pmid = {42421768},
issn = {1687-918X},
abstract = {Paris polyphylla (P. polyphylla) is a valuable traditional Chinese medicinal plant, yet the spatial distribution of its compartment-specific bacterial microbiomes and their correlative relationships with bioactive polyphyllins remain poorly characterized. Here, we combined 16S rRNA amplicon sequencing, metabolite analysis, and bioinformatics to investigate the distribution patterns of bacterial communities and polyphyllins across bulk soil (BS), rhizosphere soil (RS), root endospheres (REs), stem endospheres (SEs), and leaf endospheres (LEs) of P. polyphylla. A spot inoculation assay was further used to verify the interactions between the dominant genus Pseudomonas (strain Pseudomonas palleroniana P6) and key polyphyllin I and VII. The results showed that polyphyllin I and II were highly accumulated in aerial SEs and leaves, whereas polyphyllin VI, VII, and diosgenin were predominantly concentrated in REs. Bacterial diversity and richness showed a gradual decline from BS to LE, with ecological niche differentiation identified as the primary driver of bacterial community divergence across compartments, which was further modulated by polyphyllin content. Pseudomonas, the dominant genus in all compartments, displayed a decreasing relative abundance with ascending compartmental niches, and its abundance was significantly negatively correlated with polyphyllin I levels but positively correlated with polyphyllin VII levels-a trend experimentally validated by gradient polyphyllin concentration-based microbial growth assays. Redundancy analysis (RDA) indicated that polyphyllin content (especially VI, VII, and diosgenin) significantly influenced bacterial community composition. Additionally, P. polyphylla exhibited selective enrichment of beneficial microbes, with selection pressure intensifying progressively across compartments. This study clarifies the compartment-specific distribution patterns of bacterial microbiomes and polyphyllins in P. polyphylla and their correlative relationships, deepens the understanding of plant-microbiome interactions in medicinal plants, and provides a theoretical basis for optimizing P. polyphylla cultivation strategies and developing microbial inoculants for sustainable agricultural production.},
}

@article {pmid42421846,
year = {2026},
author = {Cuteri, V and Storoni, C and Cao, S and Li, Y},
title = {Artificial intelligence-driven phage therapy in veterinary medicine: an adaptive One Health strategy to mitigate antimicrobial resistance in livestock systems.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1829777},
pmid = {42421846},
issn = {2297-1769},
abstract = {Antimicrobial resistance (AMR) in animal production systems is a major structural driver of the global resistance crisis. Food-producing animals account for the majority of global antimicrobial consumption, generating sustained selective pressure across livestock, environmental, and zoonotic bacterial reservoirs. Intensive poultry, swine, cattle, and aquaculture systems amplify pathogen transmission and accelerate resistance emergence. Bacteriophage therapy offers a species-specific, microbiome-preserving alternative to conventional antibiotics; however, large-scale veterinary implementation has historically been constrained by challenges including strain-level host prediction, resistance evolution, biosafety considerations, manufacturing scalability, economic feasibility, and regulatory adaptation. Recent advances in artificial intelligence (AI) show promise for enabling precision veterinary phage therapy, though most applications remain at the computational proof-of-concept or preclinical stage. Deep learning and graph-based genomic models have demonstrated high accuracy on benchmark datasets, reinforcement learning has been explored in computational models for cocktail optimization, and AI-assisted genomic screening can enhance biosafety assessment. Integration with real-time AMR surveillance could potentially facilitate adaptive deployment strategies, subject to field validation. Economic modeling suggests that moderate reductions in metaphylactic antibiotic use could yield production and public health benefits, though these estimates remain illustrative. This review synthesizes current evidence on AI-guided phage discovery, epidemiological modeling, microbiome modulation, horizontal gene transfer risk assessment, economic evaluation, and regulatory innovation. Within a One Health framework, adaptive AI-guided phage platforms represent a high-leverage strategy for reducing antimicrobial dependence, provided that critical knowledge gaps are addressed.},
}

@article {pmid42421935,
year = {2026},
author = {Memida, T and Jaar, JC and Chen, T and Cao, G and Kuriki, N and Abdolahinia, ED and Okamoto, M and Shindo, S and Yamashita, S and He, X and Suzuki, M and Vardar, S and Kawai, T and Han, X},
title = {Hyperglycemia and systemic inflammation differentially shape immune dysregulation, tissue destruction, and microbiota in experimental periodontitis and peri-implantitis in diabetic mice.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1847456},
pmid = {42421935},
issn = {1664-3224},
mesh = {Animals ; *Peri-Implantitis/immunology/microbiology/pathology/etiology ; *Periodontitis/immunology/microbiology/pathology/etiology ; Mice ; *Hyperglycemia/immunology/microbiology ; *Microbiota/immunology ; *Diabetes Mellitus, Experimental/immunology/complications/microbiology ; *Inflammation/immunology ; Disease Models, Animal ; Cytokines/metabolism ; Male ; },
abstract = {AIM: To investigate the impact of hyperglycemia and systemic inflammation on experimental periodontitis/peri-implantitis in diabetic mice, focusing on osteoimmunological dysregulation and oral microbial alteration.

MATERIALS AND METHODS: After implant placement, diabetic db/db mice were treated with Liraglutide, Indomethacin, or both, followed by ligature-induced experimental periodontitis/peri-implantitis. Samples were analyzed for bone loss, inflammatory cytokines, osteoclast activity, RAGE expression, IL-17-associated inflammatory responses, and Treg infiltration. The periodontal/peri-implant microbiota were examined by metagenomics and tested in vitro for inflammatory cytokine induction.

RESULTS: Liraglutide, but not indomethacin, effectively reduced bone loss, immune cell infiltration, RAGE, IL-17A expression, and restored Foxp3[+] Treg presence. Post-treatment cytokine responses were slightly different between peri-implantitis sites compared to those in periodontitis sites. Oral microbiota composition from diabetic mice differed significantly from that of normoglycemic mice. Liraglutide treatment produced the greatest deviation from the ligation-only profile and shifted the microbiome toward normoglycemic control. The peri-implant microbiome was more resistant to interventions than the periodontal communities. Hyperglycemia control alleviated microbiome-induced pro-inflammatory responses in vitro.

CONCLUSIONS: Diabetic hyperglycemia is a more predominant driver than systemic inflammation in exacerbating periodontitis/peri-implantitis tissue destruction, immune dysregulation, and eliciting a pro-inflammatory oral microbial environment. The local inflammatory response and microbial alteration around the tooth and implant were similar but not identical.},
}

Animals
*Peri-Implantitis/immunology/microbiology/pathology/etiology
*Periodontitis/immunology/microbiology/pathology/etiology
Mice
*Hyperglycemia/immunology/microbiology
*Microbiota/immunology
*Diabetes Mellitus, Experimental/immunology/complications/microbiology
*Inflammation/immunology
Disease Models, Animal
Cytokines/metabolism
Male

@article {pmid42421950,
year = {2026},
author = {Lu, W and Wang, Y and Zhang, J and Li, Y and Huang, L and Yang, W and Zhou, S and Zhou, M and Chen, Y and Wu, R and Wang, Y and Zhang, H and Wan, J and Xia, F and Zhang, Z and Shen, L},
title = {Fecal microbiome and metabolome dynamics during immunotherapy-based total neoadjuvant therapy in rectal cancer: associations with treatment response and toxicity.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1871586},
pmid = {42421950},
issn = {1664-3224},
mesh = {Animals ; Female ; Humans ; Male ; Mice ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Immunotherapy/adverse effects/methods ; *Metabolome ; Metabolomics ; Multiomics ; *Neoadjuvant Therapy/adverse effects/methods ; *Rectal Neoplasms/therapy/metabolism/microbiology/immunology ; Treatment Outcome ; Clinical Trials, Phase II as Topic ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; },
abstract = {BACKGROUND: Immunotherapy-based total neoadjuvant therapy (iTNT) is a promising strategy for microsatellite-stable locally advanced rectal cancer (LARC), yet therapeutic response and treatment-related toxicity remain heterogeneous. Integrated fecal microbiome and metabolome profiling may provide non-invasive biomarkers and functional clues for optimizing iTNT.

METHODS: We conducted a longitudinal fecal multi-omics study using samples from patients with microsatellite-stable LARC enrolled in the TORCH trial (NCT04518280). A total of 102 fecal samples were collected before treatment, during treatment, and after completion of iTNT. Metagenomic sequencing and untargeted metabolomics were integrated to characterize longitudinal microbial and metabolic changes. We also examined baseline features associated with therapeutic response, and multi-omics signatures linked to hematologic and gastrointestinal toxicities. A murine tumor model treated with radiotherapy plus immunotherapy, with or without GABA supplementation, was used for functional testing of the response-associated metabolite.

RESULTS: iTNT induced longitudinal gut microbiome remodeling. This remodeling was characterized by altered community structure, increased alpha diversity, enhanced microbial network connectivity, enrichment of Firmicutes-associated taxa, and depletion of Bacteroidetes and Proteobacteria. Fecal metabolomic profiles also shifted during treatment, with prominent changes in amino acid-related pathways and significant concordance between microbial and metabolic profiles. Responders were enriched in several Firmicutes-associated genera, including Ruminococcus, Anaerostipes, and Coprobacillus. In contrast, non-responders showed enrichment of Klebsiella and response-associated metabolites including gamma-aminobutyric acid (GABA). Microbial functional and metabolomic pathway analyses showed convergent enrichment of arginine and proline metabolism, which includes an alternative GABA-related metabolic route. Functionally, GABA supplementation weakened the antitumor efficacy of radiotherapy plus immunotherapy and was accompanied by systemic T cell dysfunction. In addition, specific microbial taxa and fecal metabolic features were associated with hematologic toxicity and diarrhea severity, with baseline metabolites showing exploratory potential for toxicity stratification.

CONCLUSION: This study provides a longitudinal fecal microbiome-metabolome resource for iTNT in LARC and identifies candidate microbial and metabolic features associated with treatment response and toxicity. GABA was functionally supported as a response-associated immunomodulatory metabolite, while candidate microbial functional signals warrant further mechanistic validation.},
}

Animals
Female
Humans
Male
Mice
*Feces/microbiology
*Gastrointestinal Microbiome/drug effects
*Immunotherapy/adverse effects/methods
*Metabolome
Metabolomics
Multiomics
*Neoadjuvant Therapy/adverse effects/methods
*Rectal Neoplasms/therapy/metabolism/microbiology/immunology
Treatment Outcome
Clinical Trials, Phase II as Topic
Randomized Controlled Trials as Topic
Multicenter Studies as Topic

@article {pmid42422040,
year = {2026},
author = {Husseneder, C and Jin, T and Chen, J and Sun, Q and Ziesmann, J},
title = {Longitudinal comparison of 16S rRNA gene amplicon datasets of the Formosan subterranean termite gut microbiome: Variation across primers, colonies, time and rearing conditions.},
journal = {Data in brief},
volume = {67},
number = {},
pages = {113030},
pmid = {42422040},
issn = {2352-3409},
abstract = {The Formosan subterranean termite (FST), Coptotermes formosanus Shiraki (Blattodea: Heterotermitidae) is an aggressive and economically important invasive wood-destroying pest of national and international concern. Its efficiency in destroying lignocellulose is largely attributed to the diverse symbiotic community of microorganisms in the hind gut of the worker caste, consisting of bacteria, archaea and protists. As a global invasive species subjected to changing climate and habitat the FST has become a model for investigating the influence of environmental changes on symbiotic gut microbiota. This dataset represents a pilot analysis detecting colony variation in the gut bacteria community of FST workers from Louisiana, USA, and changes over time when termites were reared under different atmospheric conditions using 16S rRNA gene Illumina NovaSeq 6000 (2 × 250) amplicon sequencing with two different primer sets. The dataset contains 24,499,161 forward and an equal number of reverse sequence reads of the V3-4 (341F-785R) and V4-5 (515F-926R) hypervariable regions. The sequences represent the gut bacteria communities of FST workers from three different colonies, each split into two treatment groups reared in ambient air (ca. 0.04% CO2) vs. 5% CO2 and sampled at 10 time points over the course of two months. The dataset was made public through NCBI's Sequence Read Archive under BioProject ID # PRJNA1446068 [1]. Validation of the dataset is presented in form of denoising statistics (Table 1) and alpha-rarefaction curves (Fig. 1). Rarefaction was performed to show sufficient sequencing depth to capture bacterial richness and diversity and normalize for unequal number of sequences among samples. Sequences were taxonomically assigned in QIIME2 using SILVA 138 as reference database. Lists of all detected phyla and the 10 most abundant Amplicon Sequence Variants (ASVs) are included as Tables 2 and 3. The dataset will be used in follow-up publications to assess how primer bias affects the detection of certain core bacterial taxa in the guts of FST workers and how CO2 concentration in the atmosphere impacts bacterial Alpha- and Beta-diversity. In addition, the longitudinal nature of the data collected over two months enables analyses to assess the extent to which gut microbiota will change over time after termite colonies are brought to the lab and how much microbiota differ between termite colonies collected from the same region. Therefore, this dataset is expected to inform the experimental designs for future studies.},
}

@article {pmid42422252,
year = {2026},
author = {Bonato, B and Castiello, U},
title = {The metabolic layer of cognition: integrating metabolomics, breathomics, and systems neuroscience.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1842643},
pmid = {42422252},
issn = {1662-4548},
abstract = {Cognitive neuroscience has made substantial progress in mapping neural activity underlying perception, memory, and decision-making. However, widely used methods such as functional magnetic resonance imaging and electrophysiology primarily measure indirect physiological correlates of neuronal activity and provide limited access to the biochemical processes that support neural signaling. In this review, we propose that metabolism might constitutes a critical intermediate layer linking neural activity and behavior. Drawing on advances in metabolomics and breathomics, we examine how mass spectrometry-based analytical techniques enable sensitive detection of metabolites, neurotransmitters, lipids, and volatile organic compounds that could reflect metabolic processes associated with neuronal signaling and cognitive states. We synthesize emerging research at the intersection of neuroenergetics, systems neuroscience, and metabolic profiling, highlighting how these approaches can complement established neuroimaging and electrophysiological methods. In particular, we discuss the potential of volatile organic compounds in exhaled breath as non-invasive indicators of systemic metabolic responses accompanying cognitive processes. At the same time, we address key conceptual and methodological challenges in interpreting peripheral metabolic signals in relation to brain activity, including the influence of systemic physiology, microbiome metabolism, and environmental factors. Finally, we outline future directions for integrating metabolomic and breathomic measurements with neural and behavioral data in multimodal experimental frameworks. Incorporating metabolic dynamics into systems-level models may provide a new perspective on how cognition emerges from interactions between brain activity and whole-body physiology.},
}

@article {pmid42422257,
year = {2026},
author = {Tian, C and Yang, S and Zhang, X and Yan, H},
title = {Ligand-specific duality of aryl hydrocarbon receptor signaling in cognitive health: from environmental neurotoxicity to microbiome-mediated neuroprotection.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1823961},
pmid = {42422257},
issn = {1662-4548},
abstract = {The aromatic hydrocarbon receptor (AhR) is a key molecular interface integrating environmental chemical signals with host-microbiome metabolism, with profound effects on brain function. This review systematically addresses the ligand-specific duality of AhR signaling in cognitive health, comparing the predominantly neurotoxic signaling driven by environmental polycyclic aromatic hydrocarbons (PAHs) with the predominantly neuroprotective signaling mediated by gut microbiota-derived tryptophan metabolites. However, this dichotomy is context-dependent rather than absolute. PAHs activate AhR in a sustained, high-affinity manner, engaging downstream NF-κB neuroinflammation, NLRP3 inflammasome activation, oxidative stress, synaptic dysfunction, and transgenerational epigenetic alterations. In contrast, microbiota-derived metabolites such as indole-3-propionic acid (IPA) and kynurenic acid (KYNA) elicit transient, low-affinity AhR activation that engages cell-type-specific programs promoting anti-inflammatory responses, neurogenesis, blood-brain barrier integrity, and neuronal homeostasis. Critically, the outcome of AhR activation is modulated by ligand pharmacokinetics, cell-type identity, temporal dynamics of receptor engagement, and tissue-specific co-factor availability. These contextual variables determine whether AhR functions as a driver of neurodegeneration or a guardian of cognitive resilience. We further examine the divergent roles of AhR in Alzheimer's and Parkinson's diseases, where the balance between detrimental and protective ligands determines disease progression. Finally, we discuss therapeutic strategies targeting the AhR-gut-brain axis, including dietary modulation, probiotic interventions, and selective AhR modulators. Understanding the context-dependent outcomes of AhR activation provides a framework for developing precision approaches to preserve cognitive function and prevent neurodegeneration.},
}

@article {pmid42422454,
year = {2026},
author = {Wang, X and Zhang, Y and Ye, M and Kong, C and Diao, M},
title = {Clinical and stool microbiome correlates of simple post-ERCP hyperamylasemia in children undergoing therapeutic ERCP for pancreatobiliary obstructive disorders: an exploratory pilot study.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1851821},
pmid = {42422454},
issn = {2296-2360},
abstract = {BACKGROUND: Simple post-ERCP hyperamylasemia is a common biochemical finding after therapeutic endoscopic retrograde cholangiopancreatography (ERCP), but pediatric data integrating procedural characteristics with stool microbiome features remain limited.

METHODS: We performed an exploratory single-center observational pilot study of 24 successful therapeutic ERCP procedures in children younger than 18 years with pancreatobiliary obstructive disorders between January 2024 and December 2025. The primary endpoint was simple post-ERCP hyperamylasemia, defined as serum amylase >3 times the upper limit of normal within 24 h after ERCP without new or worsening abdominal pain. Baseline clinical variables, predefined stool microbiome features derived from pre-ERCP metagenomic data (Shannon diversity, Enterococcus abundance, and Bifidobacterium abundance), and intraprocedural variables were compared between groups. Exploratory signal prioritization was used only to identify candidate associations for future validation.

RESULTS: Hyperamylasemia occurred in 8/24 procedures (33.3%). Compared with non- hyperamylasemia group, the affected children had higher baseline gamma-glutamyl transferase and C-reactive protein, longer procedure time, more difficult cannulation, more inadvertent pancreatic duct cannulation, more pancreatic contrast injection, and more rescue precut access. Stool microbiome features in the hyperamylasemia group included lower Shannon diversity, higher Enterococcus abundance, and lower Bifidobacterium abundance. Procedure time and Shannon diversity emerged as the most interpretable combined signals, but all model estimates should be viewed cautiously because of the small event count.

CONCLUSION: In this pilot dataset, simple post-ERCP hyperamylasemia clustered with technically demanding procedures and a low-diversity, Enterococcus-enriched stool microbiome profile. These findings are hypothesis-generating and require prospective multicenter validation before they can inform pediatric ERCP surveillance or risk-stratification research.},
}

@article {pmid42422455,
year = {2026},
author = {Gan, H and Boyarchuk, O and Feng, A and Jiang, L and Yang, K},
title = {Editorial: Rethinking infection in pediatric atopic dermatitis: from microbial dysbiosis to precision prevention.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1905309},
pmid = {42422455},
issn = {2296-2360},
}

@article {pmid42422729,
year = {2026},
author = {Zhang, CT and Ye, YX and Huang, XX and Wei, XJ and Ji, L and Zhang, WH and Gao, J and Chen, R},
title = {Intermittent hypoxia drives lung microbiome-metabolome remodeling to create a pro-inflammatory landscape in murine OSAHS.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1797420},
pmid = {42422729},
issn = {1664-302X},
abstract = {BACKGROUND: Obstructive sleep apnea-hypopnea syndrome (OSAHS), characterized by intermittent hypoxia (IH), is associated with pulmonary complications. The specific mechanisms by which IH impacts the lung's native microbiome and its functional metabolic output, however, remains largely uncharted.

METHODS: We established an OSAHS model in C57BL/6J mice using 4 weeks of IH exposure. Lung histology and inflammatory cytokines in bronchoalveolar lavage fluid (BALF) were assessed. We performed an integrated analysis of the lung microenvironment using 16S rRNA sequencing for the microbiota and LC-MS for the metabolome.

RESULTS: IH induced significant lung inflammation, evidenced by inflammatory infiltration and a polarized cytokine profile (elevated IL-1β, IL-6, TNF-α; decreased IL-10). Microbiome analysis revealed IH-driven dysbiosis, characterized by a marked shift in community structure and enrichment of pro-inflammatory taxa (e.g., Bacillota, Mycoplasma). Concurrently, metabolomic profiling uncovered widespread disturbances, with significant alterations in 500 metabolites. Key changes included rises in pro-inflammatory molecules (e.g., stachydrine) and falls in protective mediators (e.g., prostaglandin E2, embelin). Pathway analysis indicated these metabolites were enriched in niacin metabolism, inflammatory mediator regulation of TRP channels, and neuroactive ligand-receptor interactions. Crucially, correlation analysis delineated a robust interplay between the specific IH-altered microbial taxa and the disturbed metabolic pathways, suggesting a coordinated microenvironmental response.

CONCLUSION: Our integrated analysis reveals a compelling association between the lung microbiota and metabolome, suggesting their potential role as a cooperative factor associated with pulmonary inflammation in OSAHS. This study establishes a valuable resource and outlines a framework for future mechanistic and therapeutic exploration.},
}

@article {pmid42422736,
year = {2026},
author = {Kaur, P and Rivera-Nieves, J},
title = {A standardized fecal microbiota transplantation protocol enables consistent, microbiota-driven colitis in IL-10-deficient mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1842264},
pmid = {42422736},
issn = {1664-302X},
abstract = {Gut microbiota dysbiosis is a central feature of inflammatory bowel disease (IBD), yet experimental systems that enable controlled investigation of microbiota-driven inflammation remain limited. In interleukin-10-deficient (Il10[-/-]) mice, intestinal inflammation is strictly dependent on the presence of commensal microbiota; however, disease onset and severity are highly variable, reflecting differences in microbial composition across environments. To overcome this limitation, pharmacologic approaches such as piroxicam administration have been widely used to synchronize disease, but these methods introduce epithelial injury and non-microbiota-dependent inflammatory pathways that confound mechanistic interpretation. Here, we describe a standardized fecal microbiota transplantation (FMT) protocol that enables controlled microbiota-driven induction of colitis in Il10[-/-] recipient mice without the use of chemical triggers. In this model, recipient mice aged 8-10 weeks receive fecal microbiota via oral gavage from either colitic Il10[-/-]; Itgb7[-/-] double knockout (DKO) donor mice or non-colitic young Il10[-/-] controls. The DKO donors exhibit impaired mucosal immune regulation and reduced IgA responses, features associated with the emergence of a colitogenic microbial community. Repeated FMT administration over 9 weeks promotes uniform disease induction and reduces variability in disease kinetics across experimental cohorts. Importantly, this approach preserves microbiota-driven disease mechanisms while improving experimental consistency compared with conventional spontaneous Il10[-/-] models and avoids the confounding effects of pharmacologic synchronization. The protocol is compatible with downstream histological, immunological, and microbiome analyses and provides a practical platform for investigating host-microbiota interactions and microbiome-targeted therapeutic strategies in IBD.},
}

@article {pmid42422745,
year = {2026},
author = {Aghdam, SA and Brown, AMV},
title = {Diverse banana endophytes reveal potential genotype-driven community structure affected by domestication.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1830341},
pmid = {42422745},
issn = {1664-302X},
abstract = {Plant endophytic microbiomes play critical roles in plant health, productivity, and stress tolerance, however, their relationship with host genotype remains poorly understood. This study focused on endophytic microbiomes of six banana (Musa spp.) cultivars grown under shared environmental conditions to determine how genotype influences microbial diversity and structure. We used deep amplicon sequencing to investigate the endophytic microbiomes from above- and below-ground tissues of wild diploid cultivars Musa balbisiana, M. balbisiana "Thai Black", and M. textilis, and domesticated triploid cultivars Dwarf Cavendish, Williams Hybrid, and hybrid FHIA-25, grown in sympatry. Across all samples, dominant genera included Pseudomonas, Acinetobacter, Enterobacter, Devosia, and Rhizobium, while 27.4% of ASVs were unclassified. Although many core taxa were shared, each cultivar and tissue harbored distinct low-abundance microbial taxa. Beta diversity analyses revealed that banana cultivar explained a small but significant proportion of community variation (Bray-Curtis R [2] = 2.7%, p = 0.002; Weighted UniFrac R [2] = 2.9%, p = 0.005), whereas tissue type and domestication contributed less to overall variation. PICRUSt2 predicted functional differences among endophytic communities across banana cultivars, with 49 pathways differing between wild and domesticated plants, including enrichment of lipid metabolism, biotin biosynthesis, and aromatic compound degradation in domesticated cultivars. However, because domestication status and ploidy differed among the selected cultivars, these effects could not be fully separated in the current study. Together, these results indicate that banana genotype influences endophytic microbiome composition and predicted function, although host genotype accounted for only a modest proportion of the observed variation, highlighting the importance of additional ecological and environmental factors in shaping plant-associated microbial communities.},
}

@article {pmid42422750,
year = {2026},
author = {Frías-Ordoñez, JS and Portillo-Miño, JD and Marulanda-Fernandez, H and Carlosama, Y and Otero-Parra, L and Urrego, JA and Otero-Ramos, E and Otero Regino, W},
title = {Rethinking gastric carcinogenesis: a multiscale ecological model of risk beyond Helicobacter pylori.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1823306},
pmid = {42422750},
issn = {1664-302X},
abstract = {Gastric cancer remains one of the leading causes of cancer mortality worldwide, characterized by marked geographic disparities that cannot be fully explained by the distribution of Helicobacter pylori infection alone. Although H. pylori is recognized as the principal etiological agent, reductionist models centered exclusively on infection prevalence and eradication fail to account for the complex heterogeneity of gastric cancer risk across populations. In this narrative review, we propose a multiscale ecological framework that integrates infectious, host, environmental, microbial, and socioeconomic determinants to reinterpret gastric carcinogenesis as an emergent phenomenon arising from dynamic interactions across biological and geographic scales. Drawing on current epidemiological, molecular, and systems biology evidence, we examine how H. pylori interacts with host genetic susceptibility, epigenetic alterations, microbial community dynamics, dietary exposures, environmental modifiers, and structural social determinants to shape the trajectory of the Correa precancerous cascade. This integrative perspective helps explain key epidemiological paradoxes, including the persistence of high gastric cancer incidence in regions with comparable infection prevalence and the incomplete risk reduction observed after bacterial eradication in advanced mucosal injury. We further highlight the concept of persistent molecular and microenvironmental "carcinogenic memory," whereby epigenetic alterations and dysbiotic microecological states sustain oncogenic potential even after elimination of the infectious agent. By framing gastric carcinogenesis as a complex ecological process rather than a pathogen-driven event, this model bridges mechanistic insights with population-level patterns and provides a conceptual platform for more effective prevention strategies. Ultimately, this framework supports a shift toward integrated approaches that combine early detection, targeted eradication, environmental modification, microbiome-aware strategies, and equitable health policies to reduce the global burden of gastric cancer.},
}

@article {pmid42422949,
year = {2026},
author = {Santos, JD and Elias-Oliveira, J and Cipriano, UG and Vargas-Pinilla, P and Carlos, D and Bonato, VLD and Tostes, RC},
title = {Vascular Health and Gender-Affirming Hormone Therapy: The Immune System in Motion.},
journal = {Arteriosclerosis, thrombosis, and vascular biology},
volume = {},
number = {},
pages = {},
doi = {10.1161/ATVBAHA.125.322093},
pmid = {42422949},
issn = {1524-4636},
abstract = {Given that fluctuations in sex hormone levels greatly influence cardiovascular homeostasis, this review addresses how gender-affirming hormone therapy impacts vascular function and the immune system, and how these effects may contribute to altered cardiovascular performance in transgender individuals. Gender-affirming hormone therapy alters leukocyte activation and cytokine secretion, that may impact vascular responsiveness, with distinct effects in feminizing and masculinizing regimens. Moreover, gender-affirming hormone therapy-induced changes in the gut microbiome and body composition, together with factors such as sex chromosomes, and environmental stressors may further modulate inflammatory states with potential consequences for cardiovascular health. This review also discusses factors that limit current research, contributing to inconsistent findings and persistent gaps in understanding the cardiovascular and immunologic effects of gender-affirming hormone therapy, along with directions for future studies. Although available data remain limited, understanding these interconnections is essential for optimizing therapeutic strategies, improving cardiovascular health, and fostering more inclusive clinical practices for the transgender community.},
}

@article {pmid42422999,
year = {2026},
author = {Mei, Z and Xiong, X},
title = {Immune regulatory mechanisms and potential microbiota-associated targets in Kawasaki disease: an integrative multi-omics and network pharmacology study.},
journal = {Artificial cells, nanomedicine, and biotechnology},
volume = {54},
number = {1},
pages = {305-320},
doi = {10.1080/21691401.2026.2700919},
pmid = {42422999},
issn = {2169-141X},
mesh = {*Mucocutaneous Lymph Node Syndrome/immunology/microbiology/metabolism/genetics ; Humans ; Multiomics ; *Network Pharmacology ; *Gastrointestinal Microbiome/immunology ; },
abstract = {Kawasaki disease (KD) is a systemic vasculitis in children primarily affecting the coronary arteries, and studies suggest that the gut microbiota may be involved in KD pathogenesis, inflammatory responses, and immune regulation. This study employed an integrative multi-omics strategy to systematically investigate gut microbiota-metabolite interactions in KD. Key molecular targets were identified using network-based analyses and machine learning models, with Mendelian randomization providing causal validation. Single-cell transcriptomics and molecular docking further elucidated immune cell interactions and metabolite-protein binding, highlighting critical regulatory pathways. We identified SELP as a core molecular target in KD, predominantly expressed in platelets and involved in immune and inflammatory responses. Gut microbiota-derived metabolites, including palmitoylethanolamide, pantothenic acid, and 1-O-caffeoylglycerol, may regulate immune cell interactions via the RESISTIN signalling pathway. Altered abundances of microbial taxa such as Bacteroides, Parabacteroides, and Bifidobacterium suggest their potential role in inflammation modulation. Activation of IL-17, TNF, MAPK, and PI3K-Akt pathways further contributes to disease progression, highlighting the microbiota-metabolite-SELP axis as a potential therapeutic target in KD. These findings lay the groundwork for subsequent in vitro and in vivo studies, advancing the development of microbiome-based intervention strategies.},
}

*Mucocutaneous Lymph Node Syndrome/immunology/microbiology/metabolism/genetics
Humans
Multiomics
*Network Pharmacology
*Gastrointestinal Microbiome/immunology

@article {pmid42423005,
year = {2026},
author = {Creedon, AC and Bernard, HM and Amati, F and Segata, N and Wallace, SM and Arrè, A and Smith, HA and Platts, A and Bulsiewicz, WJ and Bermingham, KM and Capdevila, J and Piperni, E and Roomans Ledo, A and Johnson, C and Caro, C and Karimjee, N and Linenberg, I and Giordano, F and Davies, R and Kim, C and Wolf, J and Asnicar, F and Spector, TD and Berry, SE},
title = {Does a diverse whole-food plant-based dietary intervention improve gut microbiome composition, gut symptoms, energy and hunger in healthy adults? A randomised controlled trial.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-19},
doi = {10.1017/S0007114526107703},
pmid = {42423005},
issn = {1475-2662},
abstract = {Diets low in diverse fibre-rich plant foods contribute to the rise of chronic disease. The BIOME study (NCT06231706; 6-week parallel randomised controlled trial) in 399 adults (35-65 years; BMI 18·5-40 kg/m[2]; fibre intake < 20 g/d) investigated a whole-food plant blend containing > 30 ingredients, rich in (poly)phenols, fibre and micronutrients. Participants were randomised (1:1:1) to the blend (30 g/d), an isoenergetic control (bread croutons, 28 g/d) or probiotic (Lactobacillus rhamnosus, 15bn CFU/d). Analysts were blinded to allocation. The primary outcome was change in 'favourable' and 'unfavourable' gut microbiome species (ZOE Microbiome Health Ranking 2025); secondary outcomes included blood metabolites, symptoms, stool output, anthropometry, hunger, sleep, energy and mood. A crossover sub-study explored postprandial glucose, hunger and mood. Of 349 participants analysed (fifty excluded), self-reported adherence was > 98 %. The 30+ plant blend resulted in more species changing relative abundance at 6 weeks v. control (57 v. 14 species-level genome bins (SGB), P < 0·001) and probiotic (57 v. 4 SGB, P < 0·001). There were no significant between-group differences in microbiome health ranks of significantly changing species (increasing or decreasing). Blend participants self-reported reduced indigestion, constipation, heartburn and flatulence and increased energy v. control (all P < 0·05). Six related but no serious adverse events occurred. In the sub-study, adding the blend to a high-carbohydrate meal (v. meal alone) reduced hunger, increased fullness and energy (3-h incremental AUC, all P < 0·05), with no effect on postprandial glucose. This 30+ plant blend represents a simple strategy to modify gut microbiome composition and benefit gastrointestinal symptoms in healthy adults.},
}

@article {pmid42423119,
year = {2026},
author = {Gilad, O and Balaguer, F and Half, EE and Monahan, KJ and Stoffel, EM and Kupfer, SS},
title = {Colorectal Cancer Screening in Hereditary and Familial High-Risk Populations: Best Practices and Future Directions.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.70615},
pmid = {42423119},
issn = {1097-0215},
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related morbidity and mortality worldwide yet is largely preventable through effective screening and surveillance. While most CRC cases are sporadic, a substantial proportion occur in individuals at increased risk due to hereditary cancer syndromes or family history who require tailored screening strategies different from population-based approaches with respect to age of initiation, surveillance intervals, and modality. This review summarizes current evidence on CRC risk across higher risk groups, including Lynch syndrome, polyposis syndromes, carriers of moderate-penetrance genes, and individuals with a family history of CRC. Efficacy of colonoscopic surveillance and the potential roles of emerging biomarker tests and artificial intelligence-assisted technologies for detection of colorectal neoplasia are discussed. Current CRC surveillance guidelines, quality metrics and adherence in higher risk groups are reviewed. As research in genomics, biomarkers, microbiome, and artificial intelligence evolves, personalized risk-based screening strategies hold promise for optimizing CRC prevention. High-quality, population-specific data will be essential to refine surveillance intensity, improve adherence, and reduce CRC burden in higher risk populations.},
}

@article {pmid42423294,
year = {2026},
author = {Staab, S and Cardenas, A and Peixoto, RS and Schreiber, F and Voolstra, CR},
title = {UniCoracle: Automated hierarchical Feature Selection via Bottom-Up Propagation and Top-Down Skimming using the UniCorP algorithm and the Coracle machine-learning framework.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag507},
pmid = {42423294},
issn = {1367-4811},
abstract = {Identifying meaningful associations between microbial communities and measured physiological or environmental variables becomes increasingly complex and computationally demanding given the continuous growth of microbiome datasets. The Coracle machine learning (ML) framework was recently developed to address this by integrating multiple data transformations, feature selection techniques, and ML models to yield condensed lists of features that align to target variables of interest. Further, we recently developed the UniCorP feature aggregation algorithm to identify uniquely correlated features (UNICORNs) based on the UniCor metric that iteratively enrich each taxonomic level in an automated bottom-up approach. Here we present UniCoracle, a fully automated analytical framework that integrates UniCorP's bottom-up propagation approach with a subsequent and newly developed top-down skimming (TDS) strategy, implemented with the Coracle ML framework. This combined approach leverages the inherent taxonomic structure of microbiome community data (e.g., ASVs derived from 16S rRNA gene amplicon sequencing) to maintain predictive stability, reduce computational runtime, and identify biologically meaningful taxonomic associations. We compare the original, non-hierarchical Coracle with the TDS Coracle method and the UniCoracle approach. Evaluations across the tested datasets show that UniCoracle achieves competitive or improved predictive performance relative to both Coracle's multi-step and the TDS-based Coracle implementations. Our results demonstrate UniCoracle's improvements in predictive accuracy over both Coracle's multi-step and the TDS Coracle methods. UniCoracle provides full control over feature set size and runtime, offering a streamlined and user-friendly framework for biological hypothesis generation. It identifies features (e.g., bacterial taxa) at the lowest (most specific) hierarchical level (e.g., ASV or species within a taxonomic hierarchy) that are associated with continuous target variables. Availability: UniCoracle is freely accessible via a dedicated web server at micportal.org. The source code is open-source and available on GitHub at github.com/SebastianStaab/UniCoracle.git and Zenodo at https://doi.org/10.5281/zenodo.19050205. Supplementary information: Example datasets and a tutorial are provided on the web server: micportal.org.},
}

@article {pmid42423304,
year = {2026},
author = {Rehman, M and Sajjad, W and Kang, S and Rafiq, M and Zhao, Y},
title = {Mobilization of the ancient resistome from thawing permafrost.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/1040841X.2026.2698958},
pmid = {42423304},
issn = {1549-7828},
abstract = {Permafrost, ground frozen for at least two consecutive years, covers nearly one-quarter of the Northern Hemisphere and hosts diverse microbial communities. Climate-driven thaw is releasing preserved microorganisms and genetic material into contemporary ecosystems, where ancient genetic elements may be reintroduced into modern microbes and participate in gene exchange processes. Among these, antibiotic resistance genes (ARGs), which confer resistance to antibiotics, represent a critical yet underrecognized threat. Many originate from ancient microbial ecosystems shaped by natural antibiotic production and resistance, encode mechanisms not yet observed in clinical settings, and are associated with mobile genetic elements (MGEs) that facilitate horizontal gene transfer across microbial domains. Here, we synthesize evolutionary, molecular, and ecological perspectives on the preservation, release, and mobilization of permafrost-derived ARGs. We highlight mineral-DNA interactions that enhance the long-term stability of extracellular DNA containing ARGs and review the roles of MGEs in redistributing resistance determinants following thaw. We discuss conceptual models of rare cross-domain gene transfer and consider ecological and evolutionary implications under thawing conditions. ARG release from permafrost represents a neglected environmental factor that may contribute to antimicrobial resistance (AMR) dynamics and warrants investigation. Finally, identify key knowledge gaps and propose interdisciplinary frameworks for surveillance, risk assessment, and mitigation.},
}

@article {pmid42423461,
year = {2026},
author = {Clear, KY and Arnone, AA and Tsai, YT and Wilson, AS and Carneiro Buchele, ML and Furdui, CM and Howard-McNatt, M and Chiba, A and Soto-Pantoja, DR and Tooze, JA and Peoples, A and Duet, ML and Katz, A and Giri, DD and Iyengar, NM and Cook, KL},
title = {Obesity and Age Elevate Tissue-Resident Microbiota Akkermansia muciniphila to Induce Oxidative Stress and Promote Breast Cancer Risk.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-25-2087},
pmid = {42423461},
issn = {1538-7445},
abstract = {Obesity is a modifiable risk factor for postmenopausal breast cancer. As obesity-gut microbiome interactions are well known, obesity might also impact tissue-resident microbiome populations as a mechanism promoting breast cancer. Using non-cancerous breast tissue samples, we demonstrated that obesity and aging interact to shift the tissue-resident microbiome in breast cancer patients. Breast tissue from postmenopausal women with obesity displayed a significantly different α-diversity and β-diversity than pre- and postmenopausal women without obesity. At the species level, breast tissue from postmenopausal women with obesity expressed elevated Akkermansia muciniphila abundance when compared with all other groups. A secondary cohort of non-cancerous breast tissue from reduction mammoplasty patients indicated participant body mass index correlates with breast A. muciniphila abundance. Elevated mammary gland A. muciniphila in female MMTV-PyMT mice fed a high-fat Western diet increased tumorigenesis, tumor multiplicity, and oxidative stress markers, and administration of antioxidant N-acetylcysteine reduced A. muciniphila-induced tumorigenesis and redox perturbations. In an orthotopic progression model, mammary gland A. muciniphila in Western diet-fed mice promoted ER+ tumor growth and lung metastases. Taken together, these results suggest obesity and aging interact to enrich breast A. muciniphila abundance, modifying tissue redox balance as a risk factor for obesity-mediated postmenopausal breast cancer.},
}

@article {pmid42423485,
year = {2026},
author = {Loi, R and Simbula, G and Caddeo, A and Pibiri, M},
title = {The Role of Gut Microbiota in Liver Regeneration After Partial Hepatectomy: New Evidence From Animal and Human Studies.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {14},
pages = {e72126},
pmid = {42423485},
issn = {1530-6860},
mesh = {*Liver Regeneration/physiology ; Humans ; Animals ; *Hepatectomy ; *Gastrointestinal Microbiome/physiology ; Fibroblast Growth Factors/metabolism ; *Liver/metabolism/surgery ; Bile Acids and Salts/metabolism ; },
abstract = {Liver regeneration is increasingly recognized as a process influenced not only by hepatocellular signaling but also by the gut-liver axis, where gut microbiota-derived metabolites, immune mediators, and extracellular vesicles modulate hepatic recovery after liver damage. In this review, we explore recent progress in understanding the gut microbiota's role in liver regeneration and discuss its therapeutic potential in the context of hepatic surgery and liver transplantation. Emerging evidence shows that beneficial microbial taxa, including Akkermansia muciniphila, Bifidobacterium longum, and Parabacteroides distasonis, enhance liver regeneration by regulating short-chain fatty acid production, bile acid metabolism, and tricarboxylic acid cycle pathways, while dysbiosis and microbial translocation can impair regenerative outcomes. Key host-microbiome interactions, particularly the Farnesoid X Receptor (FXR)-Fibroblast Growth Factor 19 (FGF19) signaling axis, play a central role in protecting hepatocytes from bile acid overload and supporting regeneration, highlighting the therapeutic potential of FXR agonists, FGF19 mimetics, probiotics, dietary interventions, and metabolite supplementation. At the same time, monitoring bile acids profiles alongside gut microbiota composition may allow early detection and prevention of complications. In addition, microbial-derived markers such as the lipopolysaccharide/lipoteichoic acid ratio may serve as predictive biomarkers for post-hepatectomy liver failure. Adjunctive approaches, including vitamin D supplementation, may further support regeneration through vitamin D receptor-mediated regulation of bile acid homeostasis and cell-cycle progression. In the context of live donor liver transplantation, the detection of occult bacteremia further underscores the complexity of host-microbiome interactions and suggests that microbiological surveillance could improve postoperative management. Collectively, these findings emphasize the importance of microbiota-targeted strategies to improve hepatic regeneration, reduce postoperative complications, and optimize outcomes following liver surgery and transplantation.},
}

*Liver Regeneration/physiology
Humans
Animals
*Hepatectomy
*Gastrointestinal Microbiome/physiology
Fibroblast Growth Factors/metabolism
*Liver/metabolism/surgery
Bile Acids and Salts/metabolism

@article {pmid42423541,
year = {2026},
author = {Tsang, J and Liu, R and Jamil, R and Galiwango, RM and Okech, B and Huibner, S and de Carvalho, MGA and Buchanan, LB and Liu, CM and Tobian, AAR and Prodger, JL and Kaul, R},
title = {HIV Transmission and Immunology of the Male Reproductive Tract.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {96},
number = {1},
pages = {e70266},
pmid = {42423541},
issn = {1600-0897},
support = {PJT-198144/CAPMC/CIHR/Canada ; PJT-180629/CAPMC/CIHR/Canada ; //University of Toronto/ ; },
mesh = {Humans ; Male ; *HIV Infections/transmission/immunology ; Microbiota/immunology ; *Penis/immunology/virology/microbiology ; *Urethra/immunology/virology/microbiology ; Animals ; Circumcision, Male ; },
abstract = {The penile epithelium, encompassing multiple anatomical sites, is the primary location of human immunodeficiency virus (HIV) acquisition in heterosexual men. Although the per-contact risk of penile HIV acquisition is generally low, substantial global discrepancies in HIV prevalence still exist, particularly in low-income regions. In uncircumcised men, the immune milieu of the subpreputial space is a key determinant of HIV risk, with inflammation-mediated epithelial disruption and target cell recruitment facilitating viral infection. Specific bacterial components of the penile microbiome cause local inflammation and enhance susceptibility, while penile circumcision reduces HIV risk by both removing susceptible foreskin tissues and reducing the abundance of these bacteria. The penile urethra is also an important site of HIV acquisition, particularly among circumcised men, but determinants of urethral susceptibility remain poorly understood. Penile-vaginal sex induces transient inflammation and epithelial damage at both the subpreputial space and urethra, likely mediated by mechanical effects and/or the sexual exchange of pro-inflammatory bacteria. This review summarizes knowledge regarding the immunological and microbial determinants of penile HIV acquisition risk, highlights biological factors and sexual practices that shape the penile immune milieu, and discusses current advances in microbiome-targeting interventions as potential HIV prevention strategies.},
}

Humans
Male
*HIV Infections/transmission/immunology
Microbiota/immunology
*Penis/immunology/virology/microbiology
*Urethra/immunology/virology/microbiology
Animals
Circumcision, Male

@article {pmid42423730,
year = {2026},
author = {Ordoñez-Arévalo, B and Zarza, E and Dunn, MF and Huerta-Lwanga, E and de Los Ángeles Calixto-Romo, M and Guillén-Navarro, K},
title = {Comparative genomic analysis of hemicellulose-degrading potential in bacterial isolates from the anterior intestine of Eisenia andrei (Bouché, 1972).},
journal = {Archives of microbiology},
volume = {208},
number = {9},
pages = {},
pmid = {42423730},
issn = {1432-072X},
mesh = {Animals ; *Polysaccharides/metabolism ; *Oligochaeta/microbiology ; *Intestines/microbiology ; *Bacteria/genetics/isolation & purification/metabolism/classification/enzymology ; Xylans/metabolism ; Genomics ; Genome, Bacterial ; Bacterial Proteins/genetics/metabolism ; Phylogeny ; },
abstract = {Earthworms and their associated microbiota can degrade various types of lignocellulosic residues, but the enzymes, carbohydrate-binding modules, and sugar transporters involved in this process remain imperfectly understood. The present study aimed to identify genes and characterize hemicellulose degradation strategies of bacterial strains with high xylanolytic activity from the earthworm gut. The strains, originally isolated from the anterior intestine of earthworms fed on a diet of palm fiber (Streptomyces thermophilus PF5-2S and Niallia circulans PF7-2S) and coffee husk (Cellulosimicrobium cellulans CH6-3S and Bacillus amyloliquefaciens CH7-2S), were selected for their high xylanolytic activity. We describe shared CAZyme (carbohydrate-active enzyme) genes between the species that encode intracellular accessory enzymes (such as GH51, GH67, and CE7), essential for the depolymerization of branched oligosaccharides, suggesting a cytoplasmic degradation mechanism. We also found that each strain possesses a unique functional repertoire of genes, suggesting a variety of hemicellulolytic strategies that can be attributed to the various isoforms or different carbohydrate-binding modules of these enzymes. Niallia circulans PF7-2S and Bacillus amyloliquefaciens CH7-2S share most of their esterase-encoding CAZyme genes, which allow them to deacetylate hemicellulose. Both Actinobacteria and Firmicutes included in this study form associations in the earthworm gut microenvironment employing different (selfish and communal) and similar mechanisms to accelerate and regulate the degradation of plant biomass. That could explain why the earthworm can efficiently degrade different types of waste. Knowing the molecular aspects involved in the degradation of hemicellulose in the intestinal environment of Eisenia andrei as a study model is essential for bioprospecting purposes in the management and utilization of plant residues.},
}

Animals
*Polysaccharides/metabolism
*Oligochaeta/microbiology
*Intestines/microbiology
*Bacteria/genetics/isolation & purification/metabolism/classification/enzymology
Xylans/metabolism
Genomics
Genome, Bacterial
Bacterial Proteins/genetics/metabolism
Phylogeny

@article {pmid42423764,
year = {2026},
author = {Righetti, D and Soliman Tamayo, BK and Lampis, S and Lens, PNL},
title = {Effects of Per- and Polyfluoroalkyl Compounds (PFASs) on Anaerobic Granular Sludge: Methane Production and Microbial Community Composition.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02793-4},
pmid = {42423764},
issn = {1432-184X},
abstract = {PFASs are a group of pollutants ubiquitous in the environment, for which their effects on the microbial community composition and activity of anaerobic granular sludge are still poorly understood. With our study, we aimed to provide insight into the impact of four PFASs on the methane yield of anaerobic granular sludge (AGS) using acetate as the substrate. Anaerobic granular sludge was exposed to different concentrations of 1H,1H,2H,2H-Tridecafluorooctan-1-ol (6:2FTOH), 1H,1H,2H,2H-Perfluoro-1-decanol (8:2FTOH), Tridecafluorohexane-1-sulfonic acid (PFHxS) and Perfluorooctanoic acid (PFOA). While the two fluorotelomers caused marginal changes in methane production, PFHxS and PFOA greatly inhibited acetoclastic methanogenesis. Depending on the concentration, the AGS could recover its activity after a certain number of hours when incubated with PFASs. The 50% Inhibitory Concentration (IC50) of the methane production was estimated to be 278.98 (± 3.2) mg/L for PFOA and 1,091.9 (± 26.78) mg/L for PFHxS. PFASs exposure also influenced the archaeal and eubacterial communities. The most significant change was observed with the eubacterial community, which showed an increase in the relative abundance of the genus Sulfurospirillum in the samples treated with 2,000 mg/L of 8:2FTOH and 600 mg/L of PFOA, whose presence grew to represent 16.65% and 45.4% of all reads in those samples. These findings provide insight into the differential impact of PFASs on methanogenic processes and highlight their potential to disrupt key microbial functions in anaerobic systems.},
}

@article {pmid42424147,
year = {2026},
author = {Ebel, ER and Kulkarni, AS and Mongad, DS and Olm, MR and Devi, SI and Mir, BA and Ozarkar, S and Sonnenburg, ED and Shouche, YS and Sonnenburg, JL and Dhotre, DP},
title = {Gut microbiomes of tribal communities in India vary with dairy and grain consumption.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2694242},
doi = {10.1080/19490976.2026.2694242},
pmid = {42424147},
issn = {1949-0984},
mesh = {Humans ; India ; Feces/microbiology ; *Diet ; *Edible Grain/metabolism ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; *Dairy Products ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Female ; Gastrointestinal Tract/microbiology ; },
abstract = {Highly diverse gut microbiomes of non-industrialized populations share similarities with ancestral states of symbiosis and are linked to low rates of chronic inflammatory diseases. Yet there is still limited understanding of the diverse array of non-industrialized gut microbiomes throughout the world, including among the tribal populations of India. In this study, we surveyed dietary and fecal microbiome variation among 76 adults from eight tribal communities in four biogeographic regions of India, including Warli on the western coast, Gond and Madia in the northeast Deccan Plateau, Kabui (or Rongmei Naga) in the northeast hills of the Himalayas, and Balti, Boto, Brokpa, and Purigpa in the northwest Trans-Himalayas. Metagenomic and 16S sequencing of fecal samples identified Segatella, Agathobacter, and Faecalibacterium as core members of the gut microbiome of all populations, with Segatella copri (formerly Prevotella copri) dominant at mean 25%-47% relative abundance. Four Trans-Himalayan populations with diets uniquely defined by dairy and diverse cereals had elevated gut alpha diversity and distinct beta diversity, driven by prevalent and abundant Bifidobacterium as well as taxa shared with the ruminant microbiome. Strains of B. adolescentis present in the dairy-consuming populations were genetically distinct from industrialized strains around the world and encoded CAZymes consistent with selection by dairy and grain consumption. The gut microbiomes of a minority of subjects shared taxonomic and functional features with a previously described sample of Californians, suggesting that the pressures posed by globalization could be impacting the microbiomes of tribal populations. These results highlight the nutritional and microbiological contribution of dairy livestock in shaping gut communities and emphasize the large effect that lifestyle can have on the diversity and function of non-industrialized gut microbiomes.},
}

Humans
India
Feces/microbiology
*Diet
*Edible Grain/metabolism
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification
*Dairy Products
Male
Adult
RNA, Ribosomal, 16S/genetics
Female
Gastrointestinal Tract/microbiology

@article {pmid42424228,
year = {2026},
author = {Bogdanova, AA and Borbón-García, A and Ley, RE and Tyakht, AV},
title = {Human gut flagellome profiling using FlaPro reveals TLR5-related phenotype-specific alterations in IBD.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2698917},
doi = {10.1080/19490976.2026.2698917},
pmid = {42424228},
issn = {1949-0984},
mesh = {Humans ; *Toll-Like Receptor 5/genetics/immunology/metabolism ; *Flagellin/genetics/immunology/metabolism ; *Inflammatory Bowel Diseases/microbiology/immunology/genetics ; *Gastrointestinal Microbiome ; Multiomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Colitis, Ulcerative/microbiology/immunology ; Phenotype ; Crohn Disease/microbiology/immunology ; Machine Learning ; Computational Biology/methods ; },
abstract = {Flagellin, the structural protein of bacterial flagella, activates the innate immune receptor Toll-like receptor 5 (TLR5). However, the ability of different flagellins to bind and stimulate TLR5 varies widely, suggesting that the composition of an individual's flagellin repertoire, defined as flagellome, may influence host-microbiome interactions and inflammation. Here, we developed FlaPro, a computational pipeline for quantification and functional annotation of human gut flagellomes. Functional categories in FlaPro are derived from a machine learning model trained on experimentally characterized flagellins with defined TLR5-binding and stimulatory activities. Application of FlaPro to a multi-omics inflammatory bowel disease (IBD) cohort revealed a marked depletion of flagellome diversity and a reduced ratio of silent to stimulatory flagellins in Crohn's disease and ulcerative colitis. These alterations were consistent across genomic and transcriptional layers, indicating a disease-associated shift toward more stimulatory flagellome profiles. Our findings suggest that specific features of the gut flagellome contribute to TLR5-mediated immune activation and may serve as functionally interpretable microbiome markers for future microbiome-wide association studies in health and disease. The workflow implemented in Snakemake is openly available at https://github.com/leylabmpi/FlaPro.},
}

Humans
*Toll-Like Receptor 5/genetics/immunology/metabolism
*Flagellin/genetics/immunology/metabolism
*Inflammatory Bowel Diseases/microbiology/immunology/genetics
*Gastrointestinal Microbiome
Multiomics
*Bacteria/classification/genetics/isolation & purification/metabolism
Colitis, Ulcerative/microbiology/immunology
Phenotype
Crohn Disease/microbiology/immunology
Machine Learning
Computational Biology/methods

@article {pmid42424326,
year = {2026},
author = {Brown, CR and Yacoub, MN and Bogan, JE and Buehler, MD and Hoffman, ML and Krumbeck, JA and Loughman, ZJ},
title = {Cloacal microbiome variation in wild and captive Eastern Indigo Snakes (Drymarchon couperi) with and without Cryptosporidium serpentis infection.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0350824},
doi = {10.1371/journal.pone.0350824},
pmid = {42424326},
issn = {1932-6203},
mesh = {Animals ; *Cloaca/microbiology/parasitology ; *Cryptosporidium/isolation & purification ; *Snakes/microbiology/parasitology ; *Microbiota ; *Cryptosporidiosis/microbiology/parasitology ; Animals, Wild/microbiology ; },
abstract = {The Eastern Indigo Snake (EIS; Drymarchon couperi), a federally threatened species native to the southeastern United States, serves as a valuable model for examining the effects of captivity and infection on gastrointestinal microbial composition in reptiles. As an alternative to direct gut sampling, we examined the cloacal microbiomes of EISs to evaluate changes in microbial community structure across our study groups. This study assessed the cloacal microbiome of wild and captive EISs using shotgun metagenomic sequencing. Samples were divided into three groups for comparative microbiome analysis: captive snakes positive for Cryptosporidium serpentis (C. serpentis), captive snakes negative for C. serpentis, and wild snakes. Alpha (Shannon index, paired Wilcoxon test) and beta diversity (Bray-Curtis dissimilarity, PERMANOVA, CAP) metrics were used to assess microbial diversity and community composition across groups. Furthermore, a linear discriminant analysis effect size (LEfSe) was used to identify microbial taxa significantly enriched in C. serpentis-positive versus C. serpentis-negative captive snakes. Bacterial, fungal, bacteriophage, nematode, and protozoan taxa were significantly enriched in C. serpentis-positive snakes compared with C. serpentis-negative captive snakes, based on a linear discriminant analysis (LDA) score ≥ 2.5 and p ≤ 0.05. Total taxa species Shannon diversity was consistent between C. serpentis-positive and negative captive snakes (p = 0.55) while wild snake samples were significantly more diverse (p = 0.026). Wild snakes also exhibited a significantly increased Shannon diversity of fungi (p = 0.044), protozoa (p = 0.012), and nematodes (p = 0.008) compared to their captive counterparts. This study offers the first in-depth characterization of the cloacal microbiome in reptiles, specifically in EISs, using shotgun metagenomic sequencing. The findings establish a foundation for exploring microbiota-host interactions with implications for reptile health, disease ecology, and conservation management.},
}

Animals
*Cloaca/microbiology/parasitology
*Cryptosporidium/isolation & purification
*Snakes/microbiology/parasitology
*Microbiota
*Cryptosporidiosis/microbiology/parasitology
Animals, Wild/microbiology

@article {pmid42424436,
year = {2026},
author = {Huang, K and Zhang, S and Wang, H and Qu, Y and Lu, Y and Li, R and Roohani, Y and Qiu, L and Cao, S and Li, G and Zhang, J and Yin, D and Wierenga, R and Kavi, D and Liu, S and She, T and Marwaha, S and Carter, JN and Zhou, X and Wheeler, MT and Bernstein, JA and Wang, M and He, P and Zhou, J and Snyder, MP and Cong, L and Regev, A and Leskovec, J},
title = {Autonomous biomedical research with an artificial intelligence agent.},
journal = {Science (New York, N.Y.)},
volume = {},
number = {},
pages = {eadz4351},
doi = {10.1126/science.adz4351},
pmid = {42424436},
issn = {1095-9203},
abstract = {Biomedical research is increasingly constrained by repetitive, fragmented workflows that slow discovery. We introduce Biomni, a general-purpose biomedical artificial intelligence agent that autonomously executes diverse research tasks. To map the biomedical action space, Biomni's action-discovery agent mines tools, databases, and protocols from thousands of publications across 25 domains, building a unified agentic environment. Its general-purpose architecture integrates large language model reasoning with retrieval-augmented planning and code-based execution, dynamically composing workflows without predefined templates. Systematic benchmarking shows strong generalization across heterogeneous tasks-causal gene prioritization, drug repurposing, rare-disease diagnosis, microbiome analysis, and molecular cloning-without task-specific tuning. Real-world case studies demonstrate Biomni interpreting multi-modal datasets, optimizing protein stability, orchestrating wet-lab instruments, and generating experimentally testable protocols. Biomni envisions artificial intelligence augmenting human scientists and accelerating discovery.},
}

@article {pmid42424776,
year = {2026},
author = {Su, W and Yi, Q and Du, M and Gong, T and Yang, M and Wang, F and Jin, M and Wang, Y and Lu, Z},
title = {Insights into the conversion of odor compounds by a novel microbial agent during swine manure storage: a multi-omics integration of microbiome, metabolome and genome.},
journal = {Waste management (New York, N.Y.)},
volume = {223},
number = {},
pages = {115724},
doi = {10.1016/j.wasman.2026.115724},
pmid = {42424776},
issn = {1879-2456},
abstract = {Deep-pit manure storage in intensive swine farming has emerged as a major source of malodorous emissions, posing significant environmental and public health concerns. This study developed a targeted microbial agent by systematic screening of malodor-degrading microorganisms (Alcaligenes faecalis A1, Bacillus velezensis B6, Pediococcus pentosaceus L4 and Meyerozyma guilliermondii Y7), and multi-omics approach was used to elucidate the mechanism of odorous compounds conversion during manure storage after inoculation with microbial agent. The agent significantly reduced emissions of NH3 (42.22%) and H2S (48.90%), concurrently decreasing key malodorous compounds (phenol, 4-ethylphenol, 3-methylindole, methyl mercaptan, putrescine). LC-MS revealed the dynamic changes of these major malodor substances, their precursors and metabolites during the treatment of microbial agent. High-throughput sequencing identified core functional taxa driving odor mitigation, including bacteria (Alcaligenes, Bacillus, Pediococcus, Rhodopseudomonas, Lysinibacillus and Sedimentibacter) and fungi Meyerozyma, Kurtzmaniella, Mucor, Rhizopus and Candida). Network correlation analysis revealed that the inoculated microbial agent was negatively associated with odor-producing microbiota, while positively associated with microbiota potentially involved in odor abatement, with the inoculated strain Alcaligenes faecalis A1 playing a particularly prominent role. Whole-genome sequencing highlighted abundant odor-metabolizing genes in Alcaligenes faecalis A1 and Bacillus velezensis B6. Notably, we identified critical pathways in Alcaligenes faecalis A1, including newly characterized functional roles of gene clusters for aromatic compound degradation (dmpLMNOP) and catechol metabolism (catAE), alongside denitrification and sulfur metabolism genes. These findings establish a mechanistic basis for microbial odor abatement, providing foundational insights for optimizing bioaugmentation strategies in manure management systems.},
}

@article {pmid42424946,
year = {2026},
author = {Tyagi, B and Tyagi, A and Vashishta, M and Tyagi, N and Chandrasekaran, B and Shukla, V and Nair, DT and Ankem, M and Cai, L and Ufondu, A and Jayaraman, A and Damodaran, C},
title = {Integrated analyses of the microbiome, metabolome, and spatial transcriptomics reveal sex-dependent bladder vulnerability to chronic inorganic arsenic.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142653},
doi = {10.1016/j.jhazmat.2026.142653},
pmid = {42424946},
issn = {1873-3336},
abstract = {Inorganic arsenic (iAs) is a widespread environmental carcinogen; however, the mechanisms by which chronic low-dose exposure promotes bladder carcinogenesis in a sex-dependent manner remain insufficiently characterized. Analyses of patient bladder tumors revealed arsenic concentrations consistent with chronic environmental exposure, even when urinary arsenic levels were within current guideline limits. To replicate physiologically relevant exposure, male and female mice received iAs in drinking water for 12 months. This exposure induced urothelial hyperplasia, hemorrhage, inflammation, early neoplastic changes in the bladder, and dose-dependent lung injury. Arsenic speciation demonstrated significant sex differences: males accumulated higher levels of monomethylated arsenic (MMA), while females exhibited increased dimethylarsinic acid (DMA) and greater methylation capacity. Arsenic exposure reduced protective commensal populations and enriched stress-tolerant, pro-inflammatory taxa across the gut, urinary, and bladder microbiomes. In males, proliferative and DNA methylation signatures were predominant, whereas in females, oxidative, endocrine, and redox stress signatures were more pronounced. Spatial transcriptomics identified sex-specific activation of carcinogenic and immune-stromal pathways in the bladder epithelium, with increased populations of cancer-epithelial cells and macrophages. Integrated analyses of the microbiome, metabolome, and spatial transcriptome indicated that chronic arsenic exposure reprograms the gut-bladder axis in both dose- and sex-dependent manners. These findings define a mechanistic, sex-dependent gut-bladder axis through which chronic low-dose arsenic toxicity promotes premalignant bladder pathology.},
}

@article {pmid42425035,
year = {2026},
author = {Li, B and Song, L and Zhang, H and Cheng, A and Fan, K and Yang, W and Fan, J and Liu, Q},
title = {Synergistic effects of Rhodopseudomonas palustris and Bacillus subtilis on cadmium accumulation in Forsythia suspensa.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120467},
doi = {10.1016/j.ecoenv.2026.120467},
pmid = {42425035},
issn = {1090-2414},
abstract = {Cadmium (Cd(II)) contamination threatens agricultural systems and the safety of traditional Chinese medicinal herbs. While beneficial microbes can alleviate Cd(II) stress in plants, the synergistic mechanisms underlying microbial co-inoculation in medicinal plant species remain unclear. This study investigated the individual and combined effects of Rhodopseudomonas palustris and Bacillus subtilis on Forsythia suspensa under Cd(II) stressed. The results showed that co-inoculation achieved markedly better effects than single-strain inoculation. Specifically, the HRB treatment enhanced plant height, belowground fresh weight, and aboveground fresh weight by 148.87%, 207.91%, and 188.81%, respectively, compared to the Cd(II) group. Furthermore, microbial inoculation enhanced chlorophyll content and strengthened the antioxidant defense system. The activities of SOD, POD, and CAT, as well as GSH content, were greatly improved: SOD activity increased by 3.2-6.3 folds, POD activity by 73.4%-173.9%, CAT activity by 66.2%-156.0%, and GSH content by 131.81% in the HRB group. Meanwhile, oxidative damage was alleviated, with MDA content decreasing by 62.61% in the HRB group. Crucially, co-inoculation modified the rhizosphere microenvironment: it improved bacterial diversity, enhanced soil enzyme activities (S-UE, S-CAT, S-ALP, and S-SC increased by 44.92%, 10.82%, 12.12%, and 10.75%, respectively, in the HRB group), and reduced Cd(II) bioavailability (acid-extractable Cd(II) decreased by 36.77% in the HRB group). Compared to the Cd(II) group, all inoculation treatments significantly increased the relative abundances of beneficial bacterial phyla including Proteobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes, while decreasing the abundances of Chloroflexi and Rokubacteria. These variations ultimately reduced Cd(II) accumulation in plant tissues. Pearson correlation analysis indicated that beneficial bacterial taxa and soil enzyme activities were positively correlated with plant physiological indices, whereas these parameters were negatively correlated with Cd(II) bioavailability and plant Cd(II) accumulation. Collectively, this study demonstrates that R. palustris and B. subtilis work synergistically to mitigate Cd(II) phytotoxicity and reduce Cd(II) accumulation in F. suspensa. The findings provide a promising bioremediation strategy for cultivating safer medicinal plants in Cd(II)-contaminated soils.},
}

@article {pmid42425294,
year = {2026},
author = {Zhang, JS and Chu, CH and Chen, Z and Yu, OY},
title = {The oral microbiome associated with early childhood caries in preschool children: A scoping review.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {106892},
doi = {10.1016/j.jdent.2026.106892},
pmid = {42425294},
issn = {1879-176X},
abstract = {OBJECTIVE: This review compares the oral microbiota profiles of preschool children with early childhood caries (ECC) to those of caries-free controls.

METHODS: PubMed, Web of Science, Embase, and Scopus were systematically searched for English-language reports published before January 1, 2026. Studies using next-generation sequencing (NGS) to compare the oral microbiota of systemically healthy preschool children (≤6 years) with and without ECC were included. Data on study characteristics, participant and sample information, study methods, and key study outcomes were extracted. Data were qualitatively synthesized, stratified by oral sample type and microbial kingdom.

RESULTS: Twenty-one studies published between 2013 and 2025 were included. Some studies include overlapping sample types and microbial kingdoms, with three examining both plaque and salivary samples, and three analyzing both bacterial and fungal microbiota. Nine studies examined plaque bacterial microbiota. Eight reported no differences in alpha diversity between ECC-affected children and caries-free controls, whereas all studies reported significant differences in beta diversity between groups. Based on replication criteria, ten bacterial species were enriched and nine were depleted in ECC. Four studies examining plaque fungal microbiota yielded no consistent findings regarding fungal diversity, reflecting heterogeneity and limited replication across studies. However, two fungal species were found to be enriched in ECC in two studies. Twelve studies assessed salivary bacterial microbiota. Ten reported similar alpha diversity between ECC and control groups, while findings on beta diversity were inconsistent across studies. Based on replication criteria, four bacterial species were enriched in ECC and one was depleted. Three studies examined salivary fungal microbiota, with no consistent findings on fungal diversity and limited concordance between studies.

CONCLUSION: This review indicates that bacterial communities exhibit similar species diversity between ECC-affected children and caries-free controls in both sample types. While plaque bacterial communities consistently differed in beta diversity and species abundance between the two groups, salivary bacterial communities show less consistent differences in beta diversity between ECC and controls. Fungal microbiota in both plaque and saliva remain understudied.

CLINICAL SIGNIFICANCE: This review provided comprehensive evidence on the microbial features associated with ECC, highlighting stronger associations between plaque-specific dysbiosis and clinical caries status in preschool children.},
}

@article {pmid42425314,
year = {2026},
author = {Patel, V and Khera, N and Singh, G and Khalid Ansari, MA},
title = {ASTHMA AT THE CROSSROADS: FROM ANTI-TNF-α SETBACKS TO NEXT-GENERATION BIOLOGICS TARGETING TYPE 1 AND TYPE 2 INFLAMMATION.},
journal = {Respiratory medicine},
volume = {},
number = {},
pages = {109033},
doi = {10.1016/j.rmed.2026.109033},
pmid = {42425314},
issn = {1532-3064},
abstract = {Severe asthma remains a major unmet clinical challenge due to its marked immunological heterogeneity and the limited efficacy of current therapies in non-Type 2 inflammatory endotypes. Although biologics targeting IL-4, IL-5, and IL-13 have significantly improved outcomes in eosinophilic asthma, therapeutic options for Type 1 and mixed inflammatory phenotypes remain inadequate. The failure of anti-TNF-α therapies highlighted critical translational barriers including cytokine redundancy, insufficient endotype stratification, and systemic safety concerns, thereby reshaping the direction of respiratory immunopharmacology toward precision-guided intervention strategies. This review critically examines the immunobiology of Type 1 and Type 2 inflammation, evaluates the mechanistic and clinical lessons derived from anti-TNF-α trials, and discusses emerging therapeutic platforms including nanobodies, RNA-based therapeutics, gene-editing technologies, cell-based immunotherapies, and advanced pulmonary delivery systems. Furthermore, the review highlights the growing role of multi-omics biomarkers, microbiome profiling, and artificial intelligence in enabling adaptive and personalized asthma management. Collectively, these advances support a transition from generalized cytokine blockade toward integrated immune-network modulation for severe asthma across diverse inflammatory endotypes.},
}

@article {pmid42425365,
year = {2026},
author = {Zhevlakova, I and Molokotina, I and Burrows, AC and Horak, AJ and Sangwan, N and Brown, JM and Podrez, EA and Byzova, TV},
title = {Gut Microbiota Shapes the Effects of Saturated and Polyunsaturated Fatty Acids on Skin and Hair Follicle Homeostasis.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2026.06.1288},
pmid = {42425365},
issn = {1523-1747},
abstract = {High-fat diets are linked to obesity and skin and hair disorders, yet the role of specific lipid classes remains unclear. Here, we show that cutaneous homeostasis is driven primarily by fatty acid composition rather than total fat content and is differentially regulated by the gut microbiota. Using omega-3 or omega-6/SFA-enriched diets under specific pathogen-free (SPF) and germ-free (GF) conditions, we demonstrate that omega-6/SFA feeding promotes weight gain, dermal white adipose tissue (dWAT) expansion, sebaceous gland enlargement, and increased hair follicle proliferation. Systemic and adipose effects occur independently of microbiota, whereas epithelial and follicular proliferation requires microbial presence. In contrast, omega-3 feeding limits adiposity and dWAT expansion regardless of microbial status but differentially regulates skin compartments in a microbiota-dependent manner. These effects are associated with selective microbiota-dependent regulation of circulating fatty acids: omega-6 species for omega-6/SFA feeding and omega-3 for omega-3 diet. Notably, circulating docosahexaenoic acid (DHA, 22:6, ω-3) levels differ between SPF and GF conditions in both diet groups, indicating microbiota-mediated control of systemic DHA bioavailability. Together, these findings identify the gut microbiome as a selective regulator of fatty acid metabolism and define a diet-microbiota-lipid axis that integrates systemic lipid availability with cutaneous homeostasis.},
}

@article {pmid42425421,
year = {2026},
author = {Moskalev, A and Veselova, O and Calabrese, V and Rashan, L and Franceschi, C},
title = {Dietary Bioactive Compounds and Inflammaging: Pro-Inflammatory Triggers and Geroprotective Countermeasures.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {103241},
doi = {10.1016/j.arr.2026.103241},
pmid = {42425421},
issn = {1872-9649},
abstract = {BACKGROUND: Chronic low-grade inflammation ("inflammaging") is a key driver of age-related pathologies including cardiovascular disease, neurodegeneration, and metabolic syndrome. Diet plays a dual role in modulating this process, acting both as a source of pro-inflammatory molecular patterns and as a delivery system for geroprotective compounds.

SCOPE AND APPROACH: This review examines the pro-inflammatory dietary components (advanced glycation end products, lipid peroxidation products, oxysterols, trans fats, and microbiome-derived metabolites) that activate pattern recognition receptors and trigger inflammatory cascades, as well as the anti-inflammatory mechanisms of bioactive dietary compounds including polyphenols, omega-3 fatty acids, carotenoids, vitamins, and essential microelements. Evidence from cellular, animal, and clinical studies is synthesized to evaluate dietary interventions for healthy aging. PubMed and Google Scholar were systematically searched from inception through November 2025, with evidence quality and translational limitations critically appraised throughout.

KEY FINDINGS AND CONCLUSIONS: Pro-inflammatory dietary components activate nuclear factor-kappa B pathways, while geroprotective compounds demonstrate potent anti-inflammatory properties through multiple mechanisms: polyphenols (quercetin, EGCG, resveratrol, curcumin) inhibit pro-inflammatory signaling and activate sirtuin and Nrf2 pathways; omega-3 fatty acids reduce pro-inflammatory eicosanoids and increase specialized pro-resolving mediators; carotenoids, vitamins, and microelements (selenium, zinc, magnesium) suppress oxidative stress and modulate immune function. These dietary geroprotectors reduce inflammatory biomarkers in cellular and animal models, while clinical evidence in humans remains largely restricted to biomarker and healthspan-related endpoints rather than demonstrated lifespan extension. Optimized nutrition-emphasizing fruits, vegetables, legumes, nuts, whole grains, and omega-3-rich foods while limiting refined sugars and trans fats-represents a cornerstone intervention for mitigating inflammaging and promoting healthy longevity, with the Dietary Inflammatory Index providing a translational framework for implementation.},
}

@article {pmid42425523,
year = {2026},
author = {Post, SE and Ceisler, HS and Lal, RG and Singh, A and Deen, MA and Bonomo, LE and Cunic, LM and Brito, IL},
title = {Discovery of Novel Glycosidase-Derived Cell-Penetrating Peptides Encoded by Human Gut Commensals.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.6c00031},
pmid = {42425523},
issn = {2161-5063},
abstract = {Intracellular delivery of therapeutics remains a major challenge for modern medicine. To enhance intracellular uptake, therapeutics can be delivered with carrier proteins possessing an inherent cell-penetrating activity. There is an increasing need for new cell-penetrating carriers with diverse biophysical properties and mechanisms of action to transport a wide range of therapeutic cargo. As many cell-penetrating proteins and peptides derive from natural proteins, we sought to mine a previously unexplored community, the human gut microbiome, for cell-penetrating sequences. Here, we performed a high-throughput functional metagenomic screen to identify cell-penetrating protein fragments from the human gut microbiome. We identified protein fragments encoded within glycosidase enzymes from members of the Bacteroidetes phylum that mediate internalization into human cell lines when displayed on the surface of nonpathogenic, noninvasive Escherichia coli. We investigate one fragment, dubbed Gh_112, that adheres to human fibronectin, activates multiple endocytic pathways, and specifically promotes uptake of E. coli into multiple cancerous epithelial cell lines rather than healthy epithelial tissue in vitro. Overall, this work demonstrates that the human gut microbiome is a source of cell-penetrating sequences and expands the known repertoire of cell-penetrating carrier systems.},
}

@article {pmid42425679,
year = {2026},
author = {Liu, J and Wang, Z and Sui, Y and Chen, J and Liao, Q},
title = {Biological control of fungal spoilage in fruit: Mechanisms, microbial interactions, and implications for food quality.},
journal = {Food microbiology},
volume = {140},
number = {},
pages = {105208},
doi = {10.1016/j.fm.2026.105208},
pmid = {42425679},
issn = {1095-9998},
abstract = {Fungal spoilage is a leading cause of postharvest losses in fruit, resulting in quality deterioration, economic losses, and food waste throughout the supply chain. Conventional control using synthetic fungicides faces increasing challenges from resistance development, environmental concerns, and regulatory restrictions. Biological control agents (BCAs) offer a sustainable alternative, but their commercial adoption requires deeper understanding of their mechanisms and reliable integration into postharvest systems. This review synthesizes recent advances in next-generation BCAs, emphasizing the science-based selection of antagonistic yeasts, bacteria, and microbiome-derived isolates. Beyond nutrient and space competition, we examine complementary mechanisms including antibiosis mediated by antimicrobial metabolites and volatile organic compounds, mycoparasitism involving cell wall-degrading enzymes, and host defense priming through jasmonate, salicylate, and ethylene signaling pathways. To address performance variability in commercial settings, we evaluate integrated strategies combining BCAs with physical treatments (heat, UV-C, modified atmospheres), food-grade additives, and advanced formulation technologies such as microencapsulation and nanotechnology-enabled delivery that enhance viability, stress tolerance, and controlled release. Finally, we discuss the need for validation under supply-chain conditions, microbiome-informed design of stable bioactive consortia, and integration of BCAs into a preharvest-to-postharvest management framework. By connecting fundamental microbial mechanisms to practical applications, this review provides a framework for developing sustainable, residue-free strategies to reduce postharvest spoilage and maintain fruit quality.},
}

@article {pmid42425689,
year = {2026},
author = {Bokulich, NA and Flörl, L and Beauchemin, E and Masarweh, C and Sitepu, IR and Kalanetra, K and Boulton, R and Mills, DA and Boundy-Mills, K},
title = {Indoor environmental conditions correlate with the microbial landscape of food production facilities across space and time.},
journal = {Food microbiology},
volume = {140},
number = {},
pages = {105219},
doi = {10.1016/j.fm.2026.105219},
pmid = {42425689},
issn = {1095-9998},
abstract = {The microbial communities inhabiting food production environments are distinguished from those of other built environments in their capacity to influence food quality and safety, impacting consumer health. However, the degree to which indoor environmental conditions influence the composition of the bacterial and fungal communities throughout food production facilities remains insufficiently explored. In this study of five commercial food production facilities, we employed remote wireless sensors paired with marker-gene amplicon sequencing (bacterial 16S rRNA genes and fungal internal transcribed spacer sequences) of processing equipment and non-processing built environment surfaces (N = 2329) to profile spatial and longitudinal changes in bacterial and fungal communities, and their association with indoor climate. Indoor sensor data only explained a small proportion of overall variance in microbiota composition, suggesting that other latent and stochastic factors predominate. Nevertheless, we identify multiple associations between indoor environmental conditions and microbial community structure, including CO2 levels with overall microbial diversity in creameries, and higher temperature and relative humidity with lower bacterial diversity in wineries, demonstrating the possible role of the indoor environment in shaping microbial communities on food processing and non-processing surfaces. This highlights indoor climate as a modifiable factor for manipulating microbial surface communities to enhance food quality and safety.},
}

@article {pmid42426003,
year = {2026},
author = {Lei, Z and Liu, H and Zhang, Y and Li, X and Xiao, C and Xing, G and Guo, R and Zhang, Y and Xu, J and Yang, W and Chen, H and Li, M and Lu, T and Li, S and Lu, Y and Yan, Q},
title = {The Cat Gut Microbial Genome Collection reveals global structure of the feline gut microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01088-3},
pmid = {42426003},
issn = {2055-5008},
support = {32202857//National Natural Science Foundation of China/ ; 2024BBB073//Hubei Key Research and Development Project/ ; YXYX2506//Open Research Project of Sichuan Provincial Clinical Research Center for Imaging Medicine/ ; XN202402//Open Project of Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education/ ; 2022CXRC9555//Ganzhou Science and Technology Innovation Talent Project - Youth Talent Project/ ; },
abstract = {The gut microbiome is a critical determinant of mammalian health, yet our understanding is largely derived from humans and laboratory models. The ecological principles governing the microbiome of globally important companion animals, such as cats, remain poorly defined. We generated the Cat Gut Microbial Genome Collection (CGMGC), a comprehensive resource encompassing over 40,000 microbial genomes. This collection spans 874 prokaryotic species, 6 fungal species, and 5543 viral operational taxonomic units, derived from feline gut samples across diverse geographical regions. Our analysis reveals that the cat gut microbiome is a highly host-specific ecosystem whose structure is primarily driven by geography rather than host genetics or diet. Over 50% of the identified prokaryotic species are unique to felines and contain novel taxonomic lineages. Functionally, the virome encodes a vast repertoire of auxiliary metabolic genes, indicating pervasive inter-kingdom control over bacterial hosts. Surprisingly, the feline gut shares significantly more microbial species with humans than with laboratory mice, suggesting convergent evolution in cohabiting species. The core ecological principles of the feline gut are profound host-specificity, geographic structuring, and pervasive viral modulation of bacterial function. This work redefines the feline microbiome as a unique model for host-microbe co-evolution and establishes a genomic foundation for a new era of evidence-based veterinary medicine.},
}

@article {pmid42414431,
year = {2026},
author = {Jeong, HG and Ryu, KJ and Joo, M and Park, S and Park, HT},
title = {Longitudinal vaginal microbiomes and quality-of-life patterns during tamoxifen therapy in breast cancer: a pilot study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-59886-w},
pmid = {42414431},
issn = {2045-2322},
support = {O2412321//Korea University Anam Hospital/ ; K2513591//Korea University Anam Hospital/ ; RS-2025-02243104//Korea Health Industry Development Institute/Republic of Korea ; },
abstract = {Tamoxifen is widely used in breast cancer treatment, but its effects on vaginal microbiome remain poorly understood. This prospective longitudinal pilot study explored vaginal microbiota profiles and quality-of-life parameters in women receiving tamoxifen for breast cancer in Seoul, South Korea (2023-2024). Eleven women initiating tamoxifen therapy were enrolled. Vaginal swabs were collected at baseline (V0) and 6 months (V6). Microbiota was profiled using 16 S rRNA gene sequencing. Quality of life was assessed using the 11-item Menopause Rating Scale. Participants were stratified by baseline colonization patterns. Overall community composition did not show a significant shift between baseline and 6 months. In the full-cohort taxa-level paired analysis, Gardnerella vaginalis (G. vaginalis) showed a nominal, non-FDR-significant increase from baseline to 6 months, and no taxon remained significant after multiple-comparison correction. A negative correlation was observed between G. vaginalis and Lactobacillus iners (L. iners) (ρ = -0.6, raw P < 0.01, FDR q < 0.05). Among participants with baseline G. vaginalis detection, 4 of 5 showed increased relative abundance at 6 months, although the confidence interval was wide. G. vaginalis abundance was associated with worse sexual-function-related quality-of-life scores in exploratory analyses, but item-level MRS comparisons did not remain significant after correction for multiple testing. In this small hypothesis-generating pilot cohort, women receiving tamoxifen showed largely stable overall vaginal community composition over 6 months, with an exploratory signal of G. vaginalis expansion among participants colonized at baseline. These findings should be interpreted cautiously given the small sample size, absence of a control group, treatment heterogeneity, and post hoc subgroup analysis, and require validation in larger controlled cohorts.},
}

@article {pmid42415063,
year = {2026},
author = {Shoup, J and Sadle, C and Buckley, A and Song, ZH and Nagarajan, N and Barnes, G},
title = {Oxytocin and RAGE signaling at the intersection of social neurodevelopment and inflammation.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08395-5},
pmid = {42415063},
issn = {1479-5876},
support = {P30ES030283/ES/NIEHS NIH HHS/United States ; AR230178P1//U.S. Department of Defense/ ; },
abstract = {BACKGROUND: Autism spectrum disorder (ASD) prevalence continues to rise despite no recent changes to screening or diagnostic criteria. A complete understanding of the pathophysiology of ASD remains elusive. Gestational and postnatal inflammation correlate strongly with ASD prevalence, which is supported by maternal immune activation prevalence studies, maternal immunoglobulin found in fetal brains with ASD and altered T-cell populations in ASD children. Elevated TNF-α, interleukins, nuclear factors, and toll-like receptor levels reported in subgroups of ASD children provide evidence of a chronic inflammatory process posited to be a consequence of a cellular danger response impacting T-cells, neutrophils, macrophages, and microglia.

MAIN BODY: The RAGE system is a multi-ligand receptor within the immunoglobulin (Ig) superfamily that plays a role in inflammatory gene signaling and may help explain how early prenatal and ongoing inflammatory insults are linked to the autistic phenotype. ASD patients demonstrate differences in RAGE signaling; elevations in inflammatory gene expression ligands (AGEs, HMGB1, S100 family), decreases in esRAGE, regionally altered C1q, and impaired APP metabolism. Each of these ligands serves a role as either increasing inflammatory gene expression, modulating transport of biomolecules, or mediating immune cell migration and phagocytosis. Additionally, the RAGE system has been demonstrated to be involved in gut-blood and blood-brain oxytocin transport. In the mouse model, chronic inflammation is associated with impaired oxytocin transport across these barriers. Young children with ASD have lower serum oxytocin levels than age-matched controls, and serum OXT levels correlate with social communication testing across all groups of children. ASD patients have an increased prevalence of asthma, atopic dermatitis, allergic rhinitis, and irritable bowel syndrome, indicating an ongoing inflammatory hyperactivity in some ASD subgroups that may disturb oxytocin transport, predisposing ASD symptomology. Furthermore, the gut microbiome and its metabolites influence RAGE signaling and may partially explain the differences in microbiome composition in ASD patients.

CONCLUSION: Altered RAGE signaling is the proposed mechanistic link between ongoing inflammation and impaired oxytocinergic signaling contributing to ASD pathogenesis in certain subgroups. Further research into the biomarkers involved could identify subpopulations of ASD patients that would benefit from early modulation of the RAGE system.},
}

@article {pmid42415118,
year = {2026},
author = {Mercado-Rodriguez, C and Chitre, S and Park, PH and Yang, Y and Pompetti, A and Gharaibeh, RZ and Brant, JO and Issa, JJ and Jobin, C},
title = {Defined bacterial consortium highlights the impact of intestinal bacteria on DNA methylation and tumorigenesis.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {},
pmid = {42415118},
issn = {1474-760X},
support = {NCI R01CA214005/NH/NIH HHS/United States ; },
mesh = {Animals ; *DNA Methylation ; Mice ; *Carcinogenesis/genetics ; Cell Proliferation ; *Colorectal Neoplasms/microbiology/genetics/pathology ; Colitis/microbiology/chemically induced/genetics ; *Gastrointestinal Microbiome ; Promoter Regions, Genetic ; Escherichia coli ; DNA Damage ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is the second leading cause of cancer-related mortality in the United States. While the gut microbiota has been shown to influence CRC development, the specific contribution of bacteria to DNA methylation and carcinogenesis remains underexplored.

RESULTS: We colonize two groups of GF Apc[Min/+] mice with two consortia, one harboring a pks[+] E. coli strain with "low-pks" activity (DSMZ) and the second with a clinical isolate exhibiting "high-pks" activity (UM149). These colonized mice are exposed to DSS-induced colitis, and analyzed for tumor burden, DNA methylation, and transcriptional changes. We find that colonization with C13-UM149 leads to more tumors, increased cell proliferation, and higher DNA damage compared to C13-DSMZ (p < 0.05). Methylation analyses show that C13-DSMZ causes extensive promoter hypermethylation and altered gene expression. Differential DNA methylation in mice colonized with either C13-DSMZ or C13-UM149 is associated with changes in pathways controlling tumor suppression, cell proliferation, inflammation, and Wnt signaling. In C13-DSMZ mice, hypermethylation is associated with gene expression involved in tumor suppression in both tumors and normal tissue, whereas hypomethylation is linked to expression of genes promoting Wnt signaling. In C13-UM149 mice, methylation changes were connected to genes involved in epithelial proliferation, extracellular matrix remodeling, and inflammatory responses.

CONCLUSIONS: These findings demonstrate that intestinal bacteria with distinct pks activities differentially modulate DNA methylation thereby influencing gene expression and tumor development. This highlights bacterial modulation of epigenetic responses as a potential mechanism underlying CRC progression.},
}

Animals
*DNA Methylation
Mice
*Carcinogenesis/genetics
Cell Proliferation
*Colorectal Neoplasms/microbiology/genetics/pathology
Colitis/microbiology/chemically induced/genetics
*Gastrointestinal Microbiome
Promoter Regions, Genetic
Escherichia coli
DNA Damage
Mice, Inbred C57BL

@article {pmid42415152,
year = {2026},
author = {Lamont, RF and Bartolomaeus, TUP and Borum, LS and Forslund-Startceva, SK and Jørgensen, JS},
title = {The role of the vaginal microbiome in pregnancy loss and preterm birth: a commentary.},
journal = {Maternal health, neonatology and perinatology},
volume = {12},
number = {1},
pages = {},
pmid = {42415152},
issn = {2054-958X},
abstract = {BACKGROUND: Eubiosis or dysbiosis of the vaginal microbiome may influence the rate of pregnancy loss and preterm birth, the major cause of neonatal and perinatal mortality worldwide.

METHODS: This was a comparison of two vaginal microbiome studies; one a cohort study and the other a multinational randomised controlled feasibility study. Both studies used cultivation-independent molecular microbiological techniques that together have implications on the risk of pregnancy loss and preterm birth in association with vaginal dysbiosis.

RESULTS: The cohort study identified a risk-associated vaginal microbiome signature in association with early pregnancy-loss that comprised an increase in the relative abundance of potentially dysbiotic organisms such as Lactobacillus iners, Sneathia and Prevotella spp and a concomitant decrease in the abundance of eubiotic microorganisms such as Lactobacillus crispatus. Convergent evidence across the two studies demonstrated that a synbiotic intervention was able to shift the vaginal microbiome from the signature demonstrated by Skafte-Holm et al., to a decrease in the abundance of Prevotella, Gardnerella and Atopobium spp, while simultaneously increasing the abundance of eubiotic vaginal Lactobacillus spp.

CONCLUSIONS: We concluded that there is convergent evidence across the two studies which might otherwise have gone unnoticed. While neither study was powered to demonstrate clinical endpoints and did not establish causal relationships between microbiome modulation and pregnancy outcomes, when administered regularly, vaginal commensal probiotics in ice-cream were effective in optimizing both the vaginal and intestinal microbiota in pregnant women at increased risk of pregnancy loss, particularly preterm birth. This emphasises the need for adequately powered trials to test whether early pregnancy vaginal microbiome modulation can improve clinical outcomes.},
}

@article {pmid42415156,
year = {2026},
author = {Houvessou, GM and Antonieta Alfane, NW and Mahoche, M},
title = {Dynamic, transition and variation of cervicovaginal microbiome and HPV infection and cervical dysplasia and cancer: a systematic review.},
journal = {Infectious agents and cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13027-026-00777-0},
pmid = {42415156},
issn = {1750-9378},
abstract = {BACKGROUND: Cervical cancer is the fourth most common malignancy in women worldwide, with approximately 660,000 new cases and 350,000 deaths annually. The burden falls disproportionately on low- and middle-income countries. Although persistent infection with high-risk HPV (hrHPV) is the necessary cause, most infected women clear the virus spontaneously, implicating additional cofactors, including the cervicovaginal microbiome in determining oncogenic outcomes.

METHODS: PubMed was searched through September 10, 2024, to identify longitudinal studies assessing cervicovaginal microbiota in relation to HPV infection or cervical lesion outcomes at two or more time points. Methodological quality was evaluated using the Newcastle-Ottawa Scale (NOS). Given the substantial heterogeneity, a structured thematic synthesis was performed across three predefined domains: (a) baseline microbiome composition and clinical outcomes; (b) community state type (CST) dynamics and temporal stability; and (c) microbiome changes following treatment.

RESULTS: Twelve studies enrolling 1,663 women across 11 countries met inclusion criteria. NOS scores ranged from 4 to 9. Lactobacillus-dominated CSTs at baseline were consistently associated with HPV clearance and CIN regression, while Lactobacillus-depleted states showed higher transition rates and unfavourable outcomes. Prior L.iners (CST III) dominance was repeatedly linked to favourable outcomes, although evidence on this species remains conflicting. Cervicovaginal dysbiosis frequently preceded HPV persistence or lesion progression.

CONCLUSION: Sustained Lactobacillus-dominated CST stability, rather than dominance by any single species, is the most consistent microbiome factor associated with favourable HPV and cervical lesion outcomes. Standardized longitudinal designs incorporating metagenomic sequencing, frequent sampling intervals, and rigorous confounder adjustment are needed to advance mechanistic understanding.

Not applicable.},
}

@article {pmid42415234,
year = {2026},
author = {Shahin, K and Wang, L and He, Z and Lv, B and Van Alin, A and Lo-Man, R and Wu, H and Sansonetti, P and Collard, JM},
title = {A metabolite-dependent mechanism by which Bifidobacterium animalis subsp. lactis promotes Bacteroides colonization.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2696647},
doi = {10.1080/19490976.2026.2696647},
pmid = {42415234},
issn = {1949-0984},
mesh = {Animals ; *Bacteroides/growth & development/metabolism ; Humans ; Mice ; Feces/microbiology ; *Bifidobacterium animalis/metabolism/growth & development ; *Gastrointestinal Microbiome ; Symbiosis ; Bifidobacterium/metabolism ; Metabolome ; Coculture Techniques ; Bacteroides fragilis/growth & development/metabolism ; },
abstract = {Prokaryote-prokaryote symbiotic relationships influence interactions within microbial communities, affecting colonization, survival, and organization. Unlike competition, consortium species facilitate growth via metabolite cross-feeding. This study explored interactions between two early human gut colonizers: partially aerotolerant Bifidobacterium spp. and strict anaerobic Bacteroides spp., using omics techniques. Promotion of Bacteroides spp. growth by Bifidobacterium animalis subsp. lactis was demonstrated through co-culture experiments in anaerobic conditions. Metabolomic analysis revealed over 150 unique metabolites present in B. animalis subsp. lactis supernatants are absent in other Bifidobacterium species, including 3-hydroxycapric acid, D-alanyl-D-alanine, 2-isopropylmalic acid, and D-glucose 2-phosphate. These compounds served as nutritional substrates, including carbon and nitrogen sources, significantly enhancing Bacteroides spp. growth. In murine models, early colonization by B. animalis subsp. lactis consolidated Bacteroides fragilis colonization (1.7 × 10[4] to 9.7 × 10[6] copy number/g fecal sample) by providing these metabolites as a niche. These findings highlight B. animalis subsp. lactis plays a critical role in gut colonization of Bacteroides spp. via its exclusive metabolic profile, offering insights into partitioned metabolic activity within gut communities and emphasizing the importance of specific metabolites in early microbial establishment.},
}

Animals
*Bacteroides/growth & development/metabolism
Humans
Mice
Feces/microbiology
*Bifidobacterium animalis/metabolism/growth & development
*Gastrointestinal Microbiome
Symbiosis
Bifidobacterium/metabolism
Metabolome
Coculture Techniques
Bacteroides fragilis/growth & development/metabolism

@article {pmid42415406,
year = {2026},
author = {Han, J and Zhang, W and Zhang, Y and Ding, J},
title = {Targeting the Organ-Brain Axis: The Modulatory Role of Peripheral Organs in Depression.},
journal = {Comprehensive Physiology},
volume = {16},
number = {4},
pages = {e70216},
doi = {10.1002/cph4.70216},
pmid = {42415406},
issn = {2040-4603},
support = {32300731//National Natural Science Foundation of China/ ; 82473431//National Natural Science Foundation of China/ ; 2023ZKZD44//Innovation Program of Shanghai Municipal Education Commission/ ; },
mesh = {Humans ; *Brain/physiopathology/metabolism ; Animals ; *Major Depressive Disorder/physiopathology ; *Depression/physiopathology ; },
abstract = {Major Depressive Disorder (MDD) is a highly prevalent mental illness whose pathophysiology remains incompletely understood. Although MDD has traditionally been conceptualized primarily as a disorder of central nervous system dysfunction, accumulating evidence supports a broader brain-body framework, particularly in biologically defined subgroups characterized by inflammatory, metabolic, endocrine, autonomic, or microbiome-related abnormalities. This review summarizes how selected peripheral organs, including the gut, liver, heart, spleen, skeletal muscle, adipose tissue, bone marrow, and endocrine glands, may communicate with the brain through neural, metabolic, immune, endocrine, and microbial pathways. Emerging preclinical and clinical evidence suggests that these peripheral signals may participate in neuroinflammation and physiological alterations associated with depressive phenotypes. However, their causal status in humans remains incompletely established, and peripheral alterations may represent contributors to, correlates of, or consequences of central pathological states. We further discuss how multi-organ communication networks may converge on shared central pathways and provide a conceptual framework for understanding selected MDD phenotypes. Finally, we evaluate therapeutic strategies targeting systemic inflammation, metabolic homeostasis, and endocrine regulation, while emphasizing current translational limitations.},
}

Humans
*Brain/physiopathology/metabolism
Animals
*Major Depressive Disorder/physiopathology
*Depression/physiopathology

@article {pmid42415599,
year = {2026},
author = {Wang, Y and Li, R and Tang, Z and Ma, Z and Dong, X and Shu, W and Cui, J and Wei, M and Liu, Z and Shen, D and Li, L and Pang, Y},
title = {Integrative profiling of oral fungal communities across Mycobacterium Tuberculosis burden groups in Xpert-positive patients.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2698284},
doi = {10.1080/07853890.2026.2698284},
pmid = {42415599},
issn = {1365-2060},
mesh = {Humans ; *Mycobacterium tuberculosis/isolation & purification ; Prospective Studies ; Female ; *Mouth/microbiology ; Male ; Sputum/microbiology ; Adult ; Middle Aged ; China/epidemiology ; *Fungi/isolation & purification/classification/genetics ; *Mycobiome ; *Microbiota ; *Tuberculosis, Pulmonary/microbiology/diagnosis ; Bacterial Load ; },
abstract = {BACKGROUND: Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a major global health burden. A growing body of evidence suggests that mucosal microbial communities may reflect or modulate host responses during infection. However, the oral microbiome in TB patients with different bacterial loads remains poorly characterized. This study aimed to investigate alterations in oral fungal communities among Xpert-positive patients, stratified by Mtb burden based on Xpert MTB/RIF testing.

METHODS: In this prospective multicenter cohort study (May-August 2024), 278 Xpert-positive TB patients were enrolled across five hospitals in China. Participants were stratified into high, medium, low, and very low Mtb burden groups according to Xpert MTB/RIF cycle threshold values. Paired sputum and tongue swab samples were collected. Oral fungal profiles were characterized via ITS sequencing, followed by taxonomic assignment, diversity analysis, and multivariable association testing (MaAsLin 2) to identify robust biomarkers.

RESULTS: Oral fungal community structure varied significantly across Mtb burden strata. Beta-diversity analysis revealed distinct clustering between the very low burden group and higher burden groups (high, medium, low). High-burden patients were enriched with environmental taxa such as Blumeria and Toxicocladosporium, whereas low-burden groups exhibited higher abundances of Candida, Aspergillus, and Penicillium. Notably, MaAsLin 2 analysis confirmed that Penicillium and Podosphaera were independently associated with lower Mtb burden after adjusting for confounders. Neutral model analysis indicated that stochastic processes predominantly drive the assembly of these oral fungal communities. Functional prediction suggested enhanced aerobic respiration and metabolic enzyme activity in high-burden groups.

CONCLUSIONS: This study analyzed the oral fungal microbiome stratified by Mtb burden strata in Xpert-positive patients, revealing distinct shifts in fungal composition and functional potential. Fungal dysbiosis and altered microbial metabolic capacity may offer insight into host-microbe interactions in pulmonary TB (PTB). These findings underscore the potential value of fungal microbiome profiling for assessing Mtb burden, beyond its application in TB diagnosis alone.},
}

Humans
*Mycobacterium tuberculosis/isolation & purification
Prospective Studies
Female
*Mouth/microbiology
Male
Sputum/microbiology
Adult
Middle Aged
China/epidemiology
*Fungi/isolation & purification/classification/genetics
*Mycobiome
*Microbiota
*Tuberculosis, Pulmonary/microbiology/diagnosis
Bacterial Load

@article {pmid42415676,
year = {2026},
author = {Brand, HS and Boukema, IC and Oldenburg, L and Opperman, RCM and de Boer, NKH},
title = {[Series: Important medical-dental interactions. Oral manifestations in patients with intestinal diseases].},
journal = {Nederlands tijdschrift voor tandheelkunde},
volume = {133},
number = {7-08},
pages = {336-344},
doi = {10.5177/ntvt.07/08.26020},
pmid = {42415676},
issn = {0028-2200},
mesh = {Humans ; *Intestinal Diseases/complications/immunology ; *Intestinal Mucosa/microbiology ; },
abstract = {The intestine, consisting of the small and large intestines, is a functional and immunologically active organ in which digestion, absorption, and defence are closely intertwined. Immediately following the stomach is the duodenum, where the food chyme comes into contact with pancreatic digestive juices and bile, enabling further nutrient breakdown. The primary function of the small intestine is the absorption of nutrients through the intestinal mucosa. The large intestine is responsible for the reabsorption of water and electrolytes and is home to a diverse microbiome, consisting of various microorganisms involved in the digestion of complex carbohydrates. This microbiome is constantly interacting with the intestinal immune system, maintaining a delicate balance between tolerance and immune activation. Disruption of this balance can lead to or contribute to various conditions, some of which are discussed in this overview.},
}

Humans
*Intestinal Diseases/complications/immunology
*Intestinal Mucosa/microbiology

@article {pmid42416090,
year = {2026},
author = {He, L and Ye, Y},
title = {Effects of metabolic syndrome on pulmonary infection in pediatric bronchial asthma: a narrative review.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1770376},
pmid = {42416090},
issn = {2296-2360},
abstract = {Bronchial asthma is a heterogeneous disease characterized by chronic airway inflammation and airway hyperresponsiveness. It is the most common chronic airway inflammatory disease in children and severely affects their physical and mental health. The exacerbation of asthma in children often involves interactions among environmental triggers, the airway microbiome, and the innate immune response. Studies have confirmed that asthma in children is closely associated with lung infections. On the one hand, asthma in children increases the likelihood of lung infections; on the other hand, lung infections can significantly increase the likelihood of acute asthma attacks in children. Metabolic syndrome in children and adolescents is considered a risk factor for chronic diseases such as diabetes and cardiovascular and cerebrovascular diseases. Recent studies have shown that metabolic abnormalities in children are significantly associated with pulmonary infections and asthma in children. This review aims to review and analyze the specific effects of metabolic abnormalities on pulmonary infections and asthma exacerbations in children with asthma. Metabolic abnormalities in children cause chronic inflammation and alterations in the intestinal flora, which affect lung function, promote lung infection, and aggravate bronchial asthma in children.},
}

@article {pmid42416278,
year = {2026},
author = {Dutton, CL and Follis, M and Munaweera, J and Maisha, FM and Mulligan, CJ and Moore, JM},
title = {The gut microbiome in early life predicts malaria susceptibility.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1769376},
pmid = {42416278},
issn = {2235-2988},
mesh = {Humans ; Infant ; Female ; Feces/microbiology ; *Gastrointestinal Microbiome ; Democratic Republic of the Congo/epidemiology ; RNA, Ribosomal, 16S/genetics ; *Malaria/epidemiology ; Disease Susceptibility ; *Bacteria/classification/genetics/isolation & purification ; Male ; Infant, Newborn ; DNA, Ribosomal/genetics/chemistry ; Dysbiosis ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Despite intensive international efforts and broad implementation of control and prevention efforts, malaria continues to take a devastating toll on the most vulnerable populations, especially infants and young children. Emerging data support an important role for gut microbiome disruption in exacerbating, and potentially contributing to, adverse outcomes in malaria in young children. Less well understood are the role of the gut microbiome in early infancy in determining malaria susceptibility and how malaria exposure may impact gut microbial communities during this highly dynamic and sensitive period of microbiome development.

METHODS: To address these gaps, we recruited mother-infant dyads at birth in malaria-endemic eastern Democratic Republic of Congo. Infant fecal samples collected at six weeks, and at three, six and 12 months of age, as well as at passive malaria sick and post-treatment visits, were subjected to full length 16S rRNA sequencing.

RESULTS: Significant differences in relative abundance of a number of bacterial species distinguished those infants who never had a malaria visit from those who did, and those malaria episodes resulted in gut dysbiosis. Classifier analysis with Boruta selection revealed preliminary predictive capacity of the six-week fecal microbiome for malaria susceptibility through the first year of life, with a modest signal partially intertwined with bednet use. Healthy gut-associated Bifidobacterium breve and its metabolic partner Cutibacterium avidum, along with Megasphaera micronuciformis were associated with malaria resistance, whereas bacteria previously associated with pathogenic processes, including Streptococcus salivarius, Klebsiella pneumoniae, and Rothia mucilaginosa, associated with malaria susceptibility.

CONCLUSIONS: These results provide the first evidence that gut microbial composition in early infancy is associated with subsequent malaria susceptibility. These associations, if confirmed in larger cohorts, may inform future investigation of microbiome-targeted strategies to support resistance to malaria in early life.},
}

Humans
Infant
Female
Feces/microbiology
*Gastrointestinal Microbiome
Democratic Republic of the Congo/epidemiology
RNA, Ribosomal, 16S/genetics
*Malaria/epidemiology
Disease Susceptibility
*Bacteria/classification/genetics/isolation & purification
Male
Infant, Newborn
DNA, Ribosomal/genetics/chemistry
Dysbiosis
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA

@article {pmid42416280,
year = {2026},
author = {Zhang, A and Yang, J and Wang, X and Xehesbek, B and Zhang, J and Hu, X and Zhang, B and Huang, R},
title = {Mechanisms of caries induced by sugars: a narratives review from microbial metabolism to oral ecological imbalance and public health strategies for caries prevention.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1834886},
pmid = {42416280},
issn = {2235-2988},
mesh = {*Dental Caries/prevention & control/microbiology/etiology ; Humans ; Microbiota ; Biofilms/growth & development ; Streptococcus mutans/metabolism ; Lactobacillus/metabolism ; *Mouth/microbiology ; *Sugars/metabolism/adverse effects ; Candida albicans/metabolism ; Microbial Interactions ; Actinomyces/metabolism ; *Dietary Sugars/adverse effects/metabolism ; Probiotics ; },
abstract = {Dental caries is defined as a chronic, multifactorial disease characterized by the demineralization of dental hard tissues resulting from the acid production by oral microbial communities metabolizing dietary sugars. The ingestion of sugars is a pivotal ecological factor in the progression of caries, with mechanisms that extend beyond merely providing substrates for cariogenic bacteria. This review explores the influence of sugars on the metabolism, adhesion, biofilm formation, and interspecies interactions of oral microorganisms, with a particular focus on species such as Streptococcus mutans, Lactobacilli, Actinomyces, and Candida albicans. The disruption of the oral microbiome balance by these sugars initiates and promotes the process of caries. The review comprehensively summarizes contemporary public health strategies for caries prevention based on microbial ecological theories, including the limitations of sugar intake, fluoride application, probiotics, and ecological management, assessing their effectiveness and challenges. The objective of this study is to establish a theoretical framework and practical guidelines for the precise prevention of dental caries.},
}

*Dental Caries/prevention & control/microbiology/etiology
Humans
Microbiota
Biofilms/growth & development
Streptococcus mutans/metabolism
Lactobacillus/metabolism
*Mouth/microbiology
*Sugars/metabolism/adverse effects
Candida albicans/metabolism
Microbial Interactions
Actinomyces/metabolism
*Dietary Sugars/adverse effects/metabolism
Probiotics

@article {pmid42416294,
year = {2026},
author = {Szőke, Z and Fehér, P and Ferenczi, S and Lakatos, I and Stéger, V and Sükösd, Á and Sükösd, F and Sára, L},
title = {Uterine leiomyoma, retained fetal cranial bones, and reproductive microbiome analysis in a fallow deer (Dama dama): a case report.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1872878},
pmid = {42416294},
issn = {2297-1769},
abstract = {Pathological and microbiological surveillance of wildlife can reveal clinically silent but biologically important reproductive disorders. This case report describes a middle-aged (6-7 years) fallow deer hind (Dama dama) in good body condition, legally culled in Hungary, in which post-mortem examination identified a uterine leiomyoma in the left uterine horn and retained fetal cranial bones in the cranial vagina. To the best of our knowledge, this is the first published description of uterine leiomyoma in this species. Gross pathology, histopathology, and desmin immunohistochemistry supported the diagnosis of leiomyoma, and 16S rRNA amplicon sequencing was used to compare the microbiomes of the unaffected uterine horn, affected uterine tissue, and feces. The affected uterine sample showed a microbial profile more similar to that of feces than the unaffected uterine sample, with an increased relative abundance of genera, including Bacteroides, Escherichia-Shigella, and Turicibacter. As this was a single post-mortem case, no treatment was administered. These findings suggest a possible association between chronic mechanical obstruction, retained fetal material, and marked local microbial alteration, while also illustrating the limitations of causal inference from single-animal microbiome data. This case expands the differential diagnosis of reproductive tract lesions in wild ruminants and highlights the value of integrating pathology with careful microbiome interpretation in wildlife case reports.},
}

@article {pmid42416328,
year = {2026},
author = {Sadia, RT and Cheng, Q},
title = {DepMicroDiff: Diffusion-Based Dependency-Aware Multimodal Imputation for Microbiome Data.},
journal = {Computational and structural biotechnology journal},
volume = {35},
number = {1},
pages = {0150},
pmid = {42416328},
issn = {2001-0370},
abstract = {Microbiome data analysis is essential for understanding host health and disease, yet its inherent sparsity and noise pose major challenges for accurate imputation, hindering downstream tasks such as biomarker discovery. Existing imputation methods, including recent diffusion-based models, often fail to capture the complex interdependencies between microbial taxa and overlook contextual metadata that can inform imputation. We introduce DepMicroDiff, a novel framework that combines diffusion-based generative modeling with a Dependency-Aware Transformer (DAT) to explicitly capture both mutual pairwise dependencies and autoregressive relationships. DepMicroDiff is further enhanced by variational autoencoder-based pretraining across diverse cancer datasets and conditioning on patient metadata encoded via a pretrained Transformer-based encoder (Bidirectional Encoder Representations from Transformers). Experiments on The Cancer Genome Atlas microbiome datasets show that DepMicroDiff substantially outperforms state-of-the-art baselines, achieving higher Pearson correlation coefficient (up to 0.788), cosine similarity (up to 0.812), and lower root mean square error and mean absolute error across multiple cancer types, demonstrating its robustness and generalizability for microbiome imputation.},
}

@article {pmid42416386,
year = {2026},
author = {Wicaksono, WA and Köberl, M and White, RA and Jansson, JK and Jansson, C and Cernava, T and Berg, G},
title = {Plant-specific microbial diversity facilitates functional redundancy at the soil-root interface.},
journal = {Plant and soil},
volume = {523},
number = {2},
pages = {811-825},
pmid = {42416386},
issn = {0032-079X},
abstract = {AIMS: Plant-specific microbial diversity reflecting host-microbe coevolution was frequently shown at the structural level but less on the functional scale. We studied the microbiome of three compartments at the soil root interface (root endosphere, rhizosphere, bulk soil) of medicinal plants cultivated under organic management in Egypt. The study aimed to examine the impact of the rhizosphere on microbial community composition and diversity in desert agricultural soil, as well as to identify specific functions associated with the rhizosphere.

METHODS: The microbiome community structure, diversity, and microbial functioning were evaluated through the utilization of 16S rRNA gene amplicon and shotgun metagenome sequencing.

RESULTS: We found the typical rhizosphere effect and plant-species-specific enrichment of bacterial diversity. The annual plants Calendula officinalis and Matricaria chamomilla (Asteraceae) were more similar than the perennial Solanum distichum (Solanaceae). Altogether, plant species explained 50.5% of the variation in bacterial community structures in the rhizosphere. Our results indicate a stronger effect of the plant species in terms of modulating bacterial community structures in the rhizosphere than in root endosphere samples. The plant-driven rhizosphere effect could be linked to redundant plant beneficial functions in the microbiome, while enrichment of specific genes related to amino acid ion transport and metabolism, carbohydrate transport and metabolism, defense mechanisms, and secondary metabolites biosynthesis were more specific.

CONCLUSIONS: The study explores the microbiome continuum at the soil-root interface of medicinal plant species, revealing significant bacterial community structure shifts and plant specificity. The study provides insights into the essential microbiome components contributing to rhizosphere functionality.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-024-07097-5.},
}

@article {pmid42416499,
year = {2026},
author = {Grunsted, P and Xu, C and Janitz, A and Reese, J and Campbell, J and Santiago-Rodriguez, TM and Cregeen, SJJ and Petrosino, JF and Hwang, J},
title = {Nasal cavity microbial makeup and the influence on psychiatric symptoms following fire exposure in firefighters.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1832151},
pmid = {42416499},
issn = {2813-4338},
abstract = {BACKGROUND: Firefighters experience high levels of occupational stress and trauma, increasing their risk of depression, anxiety, and post-traumatic stress disorder (PTSD). Although microbial communities may influence brain function and behavior through neural pathways, the nasal microbiome remains understudied. This study examined associations between nasal microbiome characteristics and psychiatric symptoms among firefighters.

METHODS: We conducted a cross-sectional study of 34 firefighters recruited from Texas fire stations. Participants completed validated questionnaires assessing depression, anxiety, and PTSD. Nasal swabs were collected before and after fire suppression and 16S rRNA sequencing was used to characterize microbial communities. Alpha and beta diversity, relative abundance, and differential microbial associations with psychiatric outcomes were assessed using logistic, linear, and linear mixed regression methods.

RESULTS: Sixteen participants (47%) met criteria for depression, six (18%) for anxiety, and four (12%) for PTSD. Alpha diversity was significantly lower in individuals with anxiety (adjusted p = 0.04) while there were no differences in beta diversity or differences in either diversity for PTSD or depression. Increased abundance of the genus Ruminococcus was associated with increased odds of anxiety, while Hydrotalea was associated with PTSD. Depression scores were positively associated with several genera including Aerococcus (1.22; 95%CI: 0.43-2.02) and Dermabacter (1.50; 95% CI: 0.37-2.63). Fire suppression was associated with increased Enhydrobacter (2.08; 95% CI: 0.80 to 3.46) and decreased Hymenobacter (-1.25; 95% CI: -2.22 to -0.27) abundance.

CONCLUSIONS: This study identifies preliminary links between nasal microbiome composition and psychiatric symptoms in firefighters and suggests that fire suppression may alter nasal microbial communities.},
}

@article {pmid42416500,
year = {2026},
author = {Cui, C and Xie, Y and Yuan, J and Ni, J and Wang, Y and Wei, A and Tao, R},
title = {Contact sensitization to hair care allergens in scalp seborrheic dermatitis: associations with disease severity and microbiota profiles.},
journal = {Frontiers in allergy},
volume = {7},
number = {},
pages = {1862176},
pmid = {42416500},
issn = {2673-6101},
abstract = {BACKGROUND: Scalp seborrheic dermatitis (SSD) is a chronic inflammatory skin disorder characterized by impaired barrier function and intolerance to topical products. However, the relationship between contact sensitization and scalp microbiota in SSD remains unclear.

METHODS: A total of 63 participants underwent patch testing with 62 allergens and were grouped according to the presence or absence of scalp involvement. Clinical assessments included symptom severity, transepidermal water loss, and stratum corneum hydration. Bacterial 16S rRNA V3-V4 sequencing and fungal ITS1 sequencing were performed in a subset of 36 patients with SSD to evaluate associations between allergen sensitization and scalp microbiota.

RESULTS: The most frequent sensitizers in patients with SSD were cobalt chloride, cetrimonium bromide, p-methylaminophenol, nickel sulfate, decyl glucoside, and minoxidil, although overall sensitization rates did not differ significantly between SSD and control groups. Specific allergens were associated with age, sex, disease duration, and disease severity. Increased transepidermal water loss was correlated with fragrance and preservative allergens. Minoxidil sensitization was negatively associated with Malassezia, whereas several fragrance and preservative allergens were correlated with Candida, Staphylococcus, and Corynebacterium.

CONCLUSION: Patients with SSD showed distinct sensitization patterns associated with clinical characteristics, barrier dysfunction, and scalp microbiota alterations. These findings suggest that patch test reactivity in SSD should be interpreted in the broader context of allergen exposure, skin barrier status, and microbial imbalance.},
}

@article {pmid42417008,
year = {2026},
author = {Wang, X and Wang, Q and Jiang, W and Wang, B and Zhang, X and Wang, T},
title = {Enterohepatic Circulation of Polystyrene Nanoplastics Promotes Intestinal Inflammation by Impairing Enteric Neurons.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.6c00685},
pmid = {42417008},
issn = {1936-086X},
abstract = {Microplastics (MPs) are emerging contaminants of increasing concern, yet their in vivo fate and mechanisms of intestinal toxicity remain poorly defined. Here, we demonstrate that polystyrene nanoplastics (PS-NPs) undergo a previously overlooked enterohepatic recirculation pathway that markedly enhances their intestinal retention. Using oral exposure and a Zombie mouse model with intravenous PS-NPs delivery, we show that systemically absorbed PS-NPs are efficiently captured by the liver, concentrated in the gallbladder, and subsequently reintroduced into the intestine via bile. Chronic PS-NPs exposure caused pronounced epithelial injury, including goblet cell loss, tight-junction disruption, and robust cytokine-mediated inflammation. Multiomics analyses revealed gut microbial dysbiosis, extensive shifts in metabolite profiles, and enrichment of neuroactive signaling pathways, suggesting microbiome-metabolite contributions to toxicity. We further identified significant enteric neurotoxicity characterized by reduced expression of vasoactive intestinal peptide, increased expression of tyrosine hydroxylase, and downregulation of the mechanosensitive PIEZO1 channel. Together, these findings establish hepatobiliary recycling as a key driver of intestinal PS-NPs accumulation and demonstrate that epithelial damage, microbiome-metabolite imbalance, and enteric nervous system dysfunction collectively mediate PS-NPs-induced gut pathology. This work provides mechanistic insights essential for evaluating the health risks of environmental PS-NPs exposure.},
}

@article {pmid42417102,
year = {2026},
author = {Bibi, A and Zhou, L and You, M and Niu, H and Tasleem, MW and Wu, H and Zhang, H},
title = {Management of Type 2 Diabetes Mellitus: Targeting Gut Microbiome Therapy.},
journal = {The American journal of Chinese medicine},
volume = {},
number = {},
pages = {1-26},
doi = {10.1142/S0192415X26500497},
pmid = {42417102},
issn = {1793-6853},
abstract = {Marked by high blood glucose and systemic metabolic dysfunction, type 2 diabetes mellitus (T2DM) is a significant health issue with a rapidly increasing worldwide prevalence. Recent studies have highlighted the gut microbiota as a key determinant of host metabolism, and identified that the composition and metabolic activity are closely linked to the development and progression of T2DM. This review comprehensively explores the intricate connection between T2DM and the gut microbiota, with a particular focus on how traditional Chinese medicine (TCM) can influence intestinal microbiota composition to manage disease. It also discusses the therapeutic potential of TCM, which includes natural medicinal extracts like baicalin, berberine, tetrahydrocurcumin, ginsenoside Rb1, ophiopogonin D, and resveratrol, compound formulations, and acupuncture, in regulating the intestinal microbiota ecosystem to manage T2DM. Although the current evidence suggests that these interventions may slow T2DM progression, most studies have been confined to animal models and early clinical trials which lack adequate clinical evidence to confirm their efficacy. This discrepancy has created an imbalance between theoretical and validated clinical applications. Building on existing research, future research should focus on large-scale clinical trials and advanced multi-omics studies to uncover the potential of TCM in managing T2DM through the gut microbiota.},
}

@article {pmid42417340,
year = {2025},
author = {Perepanova T, S and Kozlov R, S and Pushkar D, Y and Apolikhin O, I and Kaprin A, D},
title = {[Updated international guidelines for the diagnosis and management of patients with urinary tract infection: an analytical review].},
journal = {Urologiia (Moscow, Russia : 1999)},
volume = {},
number = {6},
pages = {164-172},
pmid = {42417340},
issn = {1728-2985},
mesh = {Humans ; *Urinary Tract Infections/diagnosis/therapy/drug therapy ; Female ; *Practice Guidelines as Topic ; Cystitis/diagnosis ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {The latest 2025 guidelines of the European Association of Urology (EAU), the American Urological Association, the Canadian Urological Association, and the Society of Urodynamics, Female Pelvic Medicine & Urogenital Reconstruction (AUA/CUA/SUFU) introduce a new classification system for urinary tract infections (UTIs) and update sections on cystitis and asymptomatic bacteriuria (ABU). Current approaches to the management of patients with UTIs, ABU, and even symptomatic bacteriuria are being reconsidered. In the era of increasing antimicrobial resistance among uropathogens, advances in researching of human microbiome and urobiome have changed the long-standing assumption that any bacteriuria necessarily requires antimicrobial treatment. At present, even in patients with a confirmed diagnosis of acute bacterial cystitis, international recommendations consider symptomatic treatment and a watchful waiting strategy as acceptable options for selected patient groups. The new UTI classification, diagnostic features and symptoms of UTIs and ABU, non-antibiotic treatment options for cystitis, and age-related characteristics of UTI presentation are discussed in this review. Key aspects of the pathogenesis of recurrent UTIs are briefly addressed. Various urine sampling approaches are discussed, along with a differentiated strategy for prescribing antimicrobial therapy to women with acute and recurrent cystitis and non-antibiotic measures for recurrence prevention. The diagnostic value of urinalysis has also expanded to include new indicators of microbial load and assessment of urine contamination. The role of modern molecular diagnostic methods, beyond standard urine culture, in the diagnosis and treatment of UTIs is analyzed. The need to adhere to principles of rational antibiotic use to avoid collateral damage associated with antimicrobial therapy for UTIs is emphasized.},
}

Humans
*Urinary Tract Infections/diagnosis/therapy/drug therapy
Female
*Practice Guidelines as Topic
Cystitis/diagnosis
Anti-Bacterial Agents/therapeutic use

@article {pmid42417540,
year = {2026},
author = {Wimmer, MI and Reichel, M and Thiele, A and Yarritu, A and Matz-Rauch, A and Anandakumar, H and Hernandez Götz, L and Lesker, TR and Potapenko, O and Gebremedhin, N and Anders, W and Liévano Contreras, SV and Wang, R and Behrens, F and Hoppe, B and Nonn, O and Schiattarella, GG and Schaefer, F and Holle, J and Strowig, T and Zernecke, A and Eckardt, KU and Knauf, F and Wilck, N and Bartolomaeus, H},
title = {Interleukin-17A mediates cardiorenal injury in oxalate nephropathy.},
journal = {Cardiovascular research},
volume = {},
number = {},
pages = {},
doi = {10.1093/cvr/cvag158},
pmid = {42417540},
issn = {1755-3245},
abstract = {AIMS: Cardiovascular disease (CVD) is the leading cause of mortality in chronic kidney disease (CKD). While CKD is known to give rise to systemic inflammation, its inciting factors remain poorly defined. Oxalate, long implicated in rare genetic kidney disorders, accumulates with decreased kidney function and has emerged as a driver of inflammation and independent risk factor for CVD. Here, we investigate the immunological mechanisms linking oxalate nephropathy to systemic inflammation, cardiac damage and kidney injury.

METHODS AND RESULTS: Oxalate nephropathy was induced in C57Bl6/N mice through an oxalate-enriched diet. Oxalate induced systemic immune activation, renal fibrosis, and adverse cardiac remodeling, including pulmonary congestion with systolic and diastolic dysfunction. Flow cytometry analysis identified interleukin (IL)-17A as a dominant inflammatory effector, with expansion of Th17 and Th17-like Treg in the kidney, intestine, and spleen. Bulk mRNA sequencing confirmed these findings in kidney and heart. In line, plasma IL-17A was increased in oxalate-fed mice. Confirming the oxalate-IL-17A relationship, plasma IL-17A was elevated in patients with primary hyperoxaluria. Gut microbiome analysis by 16S amplicon sequencing showed only mild oxalate-induced alterations in mice. However, soluble oxalate directly enhanced Th17 polarization and disrupted mitochondrial respiration in vitro. In vivo, antibody-mediated IL-17A blockade improved kidney function, cardiac fibrosis, reduced neutrophil infiltration, and partially restored cardiac function in oxalate-fed mice.

CONCLUSIONS: Our study identifies oxalate as a systemic immunometabolic stressor and IL-17A as a central mediator of oxalate-induced cardiorenal injury. These findings establish the oxalate-IL-17A axis as a mechanistic link between CKD and CVD and suggest IL-17A inhibition as a potential therapeutic strategy to reduce cardiovascular damage in CKD.},
}

@article {pmid42417706,
year = {2026},
author = {Oliveira, MEAS and Lucino, D and Garcia, GJY and Bertozzi, BG and Bassinello, PZ and Colombari Filho, JM and Piler de Carvalho, CW and Góes-Neto, A and Rocha, LO and Kabuki, DY and Freitas Silva, O and Takeiti, CY},
title = {Germination and Polishing Reshape Microbial Communities in Japonica and Indica Rice.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c02819},
pmid = {42417706},
issn = {1520-5118},
abstract = {Germination is a process used to improve the nutritional quality of rice. However, its impact on rice microbiomes remains poorly understood. This study evaluated the microbiota of two rice ecotypes, low-amylose (Mochi) and high-amylose (BRS Formoso), after germination and polishing using 16S rRNA and ITS amplicon sequencing. Bacterial alpha diversity was highest in commercial brown rice (Shannon index 3.21) and lowest in commercial polished rice (1.50). Beta diversity indicated that germination exerted a similar effect on bacterial community composition in both ecotypes. Principal Coordinate Analysis suggested that polishing did not markedly influence microbiome composition relative to germination. The microbial profiles of Mochi and BRS Formoso were dominated by Pantoea, Pseudomonas, Rhizopus, and Moesziomyces. Overall, germination strongly influenced bacterial and fungal communities, emerging as the main factor shaping microbial structure and dynamics. These findings provide new insights into how processing affects the rice microbiome, with implications for food quality and safety.},
}

@article {pmid42417710,
year = {2026},
author = {LePage, J and Wetherelt, H and Addis, E and Dizney, L and Beck, AE},
title = {Investigating short-term dynamics of gut microbiome composition in the Western deer mouse.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icag094},
pmid = {42417710},
issn = {1557-7023},
abstract = {The gut microbiome plays an important role in mammalian host health and ability to adapt to environmental conditions. While the gut microbiome is often considered fairly stable over short periods of time in the absence of a dramatic stressor, relatively little is known about the actual time scale of microbiome shifts, particularly in wildlife species. Most existing temporal studies utilize captive subjects, while here we employ the Western deer mouse, Peromyscus sonoriensis, in a field-based study to assess short-term microbiome dynamics (less than two days) in the wild. Mice were live-trapped at several urban and rural parks over a two-night trapping period in and around Spokane, Washington, USA in May of 2024. We collected fecal samples from 43 different individuals, capturing two to four time points per individual, and bacterial community composition was determined via 16S profiling with Nanopore sequencing. Genus-level profiles were compared across time points for each individual, showing relative consistency in types of taxa present for most mice, but some marked shifts in Ligilactobacillus in some mice. Calculation of intraclass correlation coefficients, however, showed low stability in alpha diversity (Shannon index) over time, suggesting greater variability than initially anticipated. Analysis with respect to site urbanization, sex, and age showed a significant effect of age when accounting for homogeneity of variance, with additional exploration of urbanization and sex needed in future work. These results provide important insight into the understudied area of host microbiome dynamics and highlight the complex relationships between microbiome, health, and environment.},
}

@article {pmid42417728,
year = {2026},
author = {Välikangas, T and Fritze, H and Pitkänen, JM and Peltoniemi, K and Järvi-Laturi, E and Christensen, TR and Väisänen, M and Lämsä, J and Paavola, R and Hultman, J},
title = {Environmental variation structures northern peatland soil microbiome composition and function in a reindeer herding area exclosure experiment.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag072},
pmid = {42417728},
issn = {1574-6941},
abstract = {Northern peatlands store large carbon stocks but are sensitive to disturbance. Hydrology, vegetation, herbivory and snow conditions may affect soil microorganisms involved in methane (CH4) cycling and nitrous oxide (N2O) production/reduction. We investigated how reindeer exclusion and snow depth (increased and reduced relative to ambient) manipulations (ongoing for three seasons) influenced archaeal and bacterial communities in a boreal rich fen. Metagenomic (MG) and metatranscriptomic (MT) sequencing were combined with pore-water chemistry and CH4 flux measurements to link the microbiome to ecosystem processes. Microbial communities differed between outside and inside the exclosure. However, these patterns primarily reflected underlying hydrological variation. Slightly wetter inside plots showed higher expression of denitrification genes (norB, nosZ) and lower (nirS+nirK)/nosZ ratios, indicating greater potential for complete denitrification to N2 instead of N2O. Methane dynamics were mainly associated with vegetation: plots associated with Carex rostrata exhibited lower pmoA/mcrA ratios and elevated CH4 fluxes. Snow manipulations had subtle effects: reduced snow depth decreased the expression of taxa dependent on microbial interactions, while effect to the investigated metabolic marker genes was small. Overall hydrology, leading to variations in redox conditions and nutrient availability, together with vegetation appeared as the primary drivers on microbial greenhouse gas processes in this peatland.},
}

@article {pmid42417977,
year = {2026},
author = {Yu, SJ and Stanley, D and Van, TTH and Steel, JC and Bajagai, YS},
title = {Metagenomics comparison identifies shared pathogenic microbiome in humans, pigs and chickens.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-026-13948-1},
pmid = {42417977},
issn = {1432-0614},
support = {PRO-017656//AgriFutures Australia/ ; PRO-017656//AgriFutures Australia/ ; },
abstract = {Integrating human, animal, and environmental health is crucial for combating infectious diseases, as an estimated 60 to 75% of emerging infectious diseases originate from zoonotic sources globally. In this study, we analysed 1274 shotgun metagenomic faecal samples of humans, pigs, and chickens collected across multiple countries to estimate levels of microbial sharing at the species-level genome bins (SGBs) resolution. We confirm that host species, rather than geography, significantly structures the gut microbial community, as shown by alpha and beta diversity analyses. Despite this high host specificity, we identified substantial cross-host sharing of SGBs, including taxa recognised as pathogens such as Escherichia coli, Clostridium perfringens, Clostridium innocuum, Clostridium disporicum, Enterococcus species, and Streptococcus alactolyticus. Core taxa were predominantly host-specific, while non-core taxa were more frequently shared across humans, pigs, and chickens. LEfSe analysis identified distinctive microbial signatures for each host, further supporting differences in community composition. These findings demonstrate that unrelated and geographically distant humans and livestock can harbour highly similar microbial populations with pathogenic potential. This work provides molecular evidence supporting the need for integrated One Health surveillance to better detect, manage, and prevent zoonotic and reverse zoonotic transmission events across interconnected human, animal, and environmental systems. KEY POINTS: • There is substantial cross-host sharing of species-level genome bins, including potential pathogens • Core taxa are predominantly host-specific • Non-core taxa are more likely to be shared across humans, pigs, and chickens.},
}

@article {pmid42418003,
year = {2026},
author = {Yin, L and Wu, J and Wang, X and Mou, Z and Gan, J and Xiao, Q},
title = {Rhizome differentiation is associated with metabolic specialization and rhizosphere microbial assembly in Rheum officinale Baill.},
journal = {Plant cell reports},
volume = {45},
number = {8},
pages = {},
pmid = {42418003},
issn = {1432-203X},
support = {MYK2026013//Hubei Minzu University/ ; 31260057//National Natural Science Foundation of China/ ; 2023BCB066//Key Research and Development Program of Hubei Province/ ; 2024BSB013//Central Government Guided Local Science and Technology Development Fund of Hubei Province/ ; E [2025] TG31//Central Financial Forestry Science and Technology Promotion Demonstration Project/ ; 2019ACA120//Major Technical Innovation Special Project of the Hubei Provincial Department of Science and Technology/ ; },
mesh = {*Rhizome/metabolism/microbiology/genetics ; *Rhizosphere ; *Rheum/metabolism/microbiology/genetics ; Metabolomics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Anthraquinones/metabolism ; Microbiota ; Metabolome ; Transcriptome ; },
abstract = {Distinct rhizome architectures are associated with differences in metabolic profiles and rhizosphere microbial composition within a single plant. Rhizome differentiation is a common developmental feature in perennial medicinal plants, yet its association with secondary metabolism and rhizosphere microbial assembly remains poorly understood. Here, we investigated the functional divergence between main rhizome (DH) and lateral rhizome (DC) of Rheum officinale Baill. using integrated metabolomic and transcriptomic analyses, quantitative real-time PCR (qRT-PCR) validation, and rhizosphere microbiome analyses. Metabolomic profiling revealed distinct patterns in anthraquinone allocation among rhizome types. DC exhibited a higher relative abundance of total detected anthraquinones and was enriched in both free anthraquinones (e.g., rhein) and selected glycosylated anthraquinones (e.g., chrysophanol 1-tetraglucoside), whereas DH preferentially accumulated other glycosylated metabolites such as cassiaside B2. Transcriptomic analysis identified 484 differentially expressed genes (DEGs) associated with these metabolic differences. Genes involved in anthraquinone biosynthesis and modification, including polyketide synthase (PKS), cytochrome P450 (CYP450), O-methyltransferase (OMT), and UDP-glycosyltransferase (UGT) family members, exhibited differential expression patterns associated with rhizome type, which were further validated by qRT-PCR. Although overall rhizosphere microbial diversity showed no significant differences between rhizome types, specific taxonomic shifts were observed, with Stenotrophomonas enriched in DC and Bacilli enriched in DH. Integrated analysis indicated correlation patterns among rhizome architecture, anthraquinone metabolism, transcriptional variation, and rhizosphere microbial composition. However, the directionality and underlying mechanisms of these relationships remain unresolved and warrant further mechanistic investigation. This study provides new insights into the biological basis of rhizome differentiation in Rheum officinale Baill.},
}

*Rhizome/metabolism/microbiology/genetics
*Rhizosphere
*Rheum/metabolism/microbiology/genetics
Metabolomics
Gene Expression Profiling
Gene Expression Regulation, Plant
Anthraquinones/metabolism
Microbiota
Metabolome
Transcriptome

@article {pmid42418044,
year = {2026},
author = {Zela, CI and Castellar, C and de Oliveira Franco, D and Graf, AL and Calegario, RF and De Mio, LLM},
title = {Endophytic microorganisms from 'Bordô' grapes as biological control agents against Colletotrichum and Botrytis.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {42418044},
issn = {1678-4405},
mesh = {*Vitis/microbiology ; *Botrytis/growth & development/physiology ; *Colletotrichum/growth & development/physiology ; *Biological Control Agents ; *Plant Diseases/microbiology/prevention & control ; *Endophytes/isolation & purification/genetics/physiology/classification ; Antibiosis ; Phylogeny ; Brazil ; },
abstract = {Colletotrichum spp. and Botrytis cinerea are the main causal agents of grape bunch rot in Brazil. Although chemical control is widely used, it has limitations, such as the selection of resistant pathogen populations and environmental concerns. Biological control emerges as a promising alternative; however, commercial products for viticulture remain limited. We hypothesized that by prospecting endophytic microorganisms from berries of Vitis hosts more resistant to rots, it would be possible to identify isolates with greater biocontrol potential. In this study, 52 endophytic isolates from berries of V. labrusca cv. 'Bordô' were evaluated. In vitro assays showed mycelial growth inhibition of C. nymphaeae and B. cinerea of up to 33% and 60%, respectively. Three isolates antagonistic to both pathogens were molecularly identified as AvCaPR20-VA4L (Clavispora asparagi), AvZmPR20-VB5B (Zygoascus meyerae), and AvTmPR20-PA1N (Tatumella sp.). In postharvest assays, the isolates achieved 31.5-73.5% control of grape ripe rot (C. nymphaeae) and 39.1-59.4% control of gray mold (B. cinerea), with AvTmPR20-PA1N showing the highest efficacy, comparable to chlorothalonil. In untreated berries, disease incidence reached 53.1% for grape ripe rot and 100% for gray mold. Next-generation sequencing of the natural berry microbiota revealed the recurrent presence of Clavispora and Tatumella in non-inoculated 'Bordô' vines, confirming their natural association with grape berry tissues. These findings highlight the potential of exploring microbial diversity from naturally resistant plants as a sustainable strategy for biological disease management in viticulture.},
}

*Vitis/microbiology
*Botrytis/growth & development/physiology
*Colletotrichum/growth & development/physiology
*Biological Control Agents
*Plant Diseases/microbiology/prevention & control
*Endophytes/isolation & purification/genetics/physiology/classification
Antibiosis
Phylogeny
Brazil

@article {pmid42418110,
year = {2026},
author = {Adeosun, WB and Poswayo, SKL and Parihar, SP and Loots, DT},
title = {The functionality of the cysteinyl leukotriene receptor 1 (CysLTR1) in the lung by metabolomics analysis of bronchoalveolar lavage fluid.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {4},
pages = {},
pmid = {42418110},
issn = {1573-3890},
mesh = {Animals ; *Receptors, Leukotriene/metabolism/genetics ; *Bronchoalveolar Lavage Fluid/chemistry ; *Metabolomics/methods ; Mice ; *Lung/metabolism ; Mice, Knockout ; Gas Chromatography-Mass Spectrometry ; Male ; Mice, Inbred C57BL ; },
abstract = {INTRODUCTION: The cysteinyl leukotriene receptor 1 (CysLTR1) is known as a potent lipid mediator with a well-established role in inflammatory regulation and lung disease. While its involvement in immune cell recruitment has been previously reported, its broader impact on pulmonary metabolism remains poorly understood.

OBJECTIVES: The study aims to investigate the metabolic consequences of a CysLTR1 deletion in mice to elucidate its role in pulmonary metabolic homeostasis.

METHODS: Bronchoalveolar lavage fluid (BALF) was collected from CysLTR1 knockout (KO) and wild-type (WT) mice (n = 4 per group), and analysed using standardized untargeted gas chromatography-time-of-flight mass spectrometry (GC-TOFMS) metabolomics.

RESULTS: Metabolomics analyses of the BALF collected from the CysLTR1 KO mice presented significantly reduced levels of glucose, glucosamine, and glyceric acid, indicating the role of the CysLTR in lung glucose uptake and consequently lung glycolysis and gluconeogenesis. This is further supported by reductions in myo-inositol and D-chiro-inositol, also supporting previous findings that this occurs due to insulin resistance. Consequential disruption of various glucose-dependent pathways, including the pentose phosphate pathway (reduced gluconic acid, sedoheptulose and xylose) and purine metabolism (reduced 1-methylinosine) indicates a consequential altered nucleotide turnover, and the significantly reduced concentrations of butanoic acid, decan-2-ol, and 1-hexadecanol, indicate changes to fatty acid metabolism in the lung, as a compensatory response to the initial glucose deficiency induced by the CysLTR1 KO. Lastly, the changes to mandelic acid, glutaric acid, tricarballylic acid, and decan-2-ol, furthermore, indicate the role of CysLTR1 in the composition/metabolism of the microbiome.

CONCLUSION: This study expands our knowledge on the role of CysLTR1 beyond its role in immune regulation, which may contribute to a better understanding of CysLTR1 associated lung diseases and in the development of improved therapeutic strategies.},
}

Animals
*Receptors, Leukotriene/metabolism/genetics
*Bronchoalveolar Lavage Fluid/chemistry
*Metabolomics/methods
Mice
*Lung/metabolism
Mice, Knockout
Gas Chromatography-Mass Spectrometry
Male
Mice, Inbred C57BL

@article {pmid42418242,
year = {2026},
author = {Robinson, JM and Guentas, L and Breed, MF},
title = {A microbial mirage: when microbiome metrics may obscure ecological meaning.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001777},
pmid = {42418242},
issn = {2057-5858},
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Ecology ; },
abstract = {Metrics such as alpha diversity, inferred functional potential and network complexity have become standard metrics in microbiome research. While they offer convenient ways to summarize complex data, these metrics may sometimes obscure more than they reveal. Alpha diversity, for example, measures richness and evenness. However, two samples may exhibit identical diversity scores, yet one could be dominated by beneficial taxa and the other by pathogens. Similarly, the presence of genes associated with particular functions does not guarantee that those functions are expressed or ecologically relevant under given conditions. Functional inference is also limited by database bias and often lacks empirical validation. Likewise, correlation-based network analyses can produce spurious associations driven by shared environmental covariates, sequencing depth or batch effects. These issues are routinely encountered in genomic workflows - from 16S/ITS amplicon surveys to shotgun metagenomics, genome-resolved metagenomics and gene-centric network analyses - where apparently 'clean' summary metrics can mask very different ecological realities. Here, we use simple, domain-relevant examples to illustrate how over-reliance on these metrics can lead to misinterpretation. Rather than rejecting these approaches, we outline when they are most informative, when they require caution and what complementary analyses can strengthen ecological inference. We propose a practical framework based on four questions: what exactly is being summarized, at what biological level, under which ecological conditions and with what form of validation? While acknowledging their value, we argue for greater critical scrutiny in their application and interpretation, and advocate for approaches that prioritize functional validation, temporal resolution and systems thinking to support more meaningful ecological insight.},
}

*Microbiota/genetics
*Metagenomics/methods
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
Ecology

@article {pmid42418267,
year = {2026},
author = {Jaitner, JF and Gambardella, N and Afonso, L and Valente, R and Tomasino, MP and Correia, AM and Rosso, M and Alves, F and Magalhães, C},
title = {Mapping potential pathogen profiling in cetacean blow: comparative insights from sequencing technologies.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001773},
pmid = {42418267},
issn = {2057-5858},
mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/pathogenicity ; *Microbiota/genetics ; *Cetacea/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Cetaceans play a critical role in marine ecosystems and function as sentinel species for detecting environmental perturbations, underscoring the importance of assessing their health for effective marine conservation. This study employed 16S rRNA gene sequencing to characterize the prokaryotic communities present in exhaled breath condensate (EBC) samples from cetaceans, utilizing both short-read (Illumina) and long-read (PacBio) sequencing platforms. Putative pathogenic taxa were identified using the Multiple Bacterial Pathogen Detection (MBPD) database. Substantial differences in microbial community composition were observed between sequencing approaches. The PacBio platform yielded 2,373 amplicon sequence variants (ASVs) spanning 30 bacterial phyla, with 614 ASVs identified as potential pathogens. In contrast, the Illumina dataset generated 350 ASVs across 17 phyla, of which 46 were flagged as potentially pathogenic. Discrepancies were also evident in diversity metrics: PacBio-derived profiles exhibited higher alpha diversity and produced beta diversity clustering patterns that corresponded with sample metadata, while Illumina-based profiles did not reveal meaningful clustering. Distinct EBC microbial signatures were identified for Globicephala macrorhynchus and Delphinus delphis, with clear differences from the surrounding seawater microbiota. These findings support the use of EBC as a non-invasive and informative tool for respiratory microbiome analysis in marine mammals. Notably, this study provides the first characterization of the respiratory microbiota in D. delphis, offering a valuable methodological baseline for future research into host-microbiome interactions, health assessment and putative pathogen monitoring in free-ranging cetacean populations, using non-invasive approaches.},
}

Animals
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification/pathogenicity
*Microbiota/genetics
*Cetacea/microbiology
High-Throughput Nucleotide Sequencing/methods
Phylogeny
Sequence Analysis, DNA/methods

@article {pmid42418460,
year = {2026},
author = {Chen, K and Travanty, NV and Garshong, RA and Wasserberg, G and Apperson, CS and Roe, RM and Ponnusamy, L},
title = {Geographic and Orientia infection status influence on the bacterial microbiome of free-living chiggers in North Carolina, USA.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0353174},
doi = {10.1371/journal.pone.0353174},
pmid = {42418460},
issn = {1932-6203},
mesh = {Animals ; North Carolina/epidemiology ; *Microbiota ; *Trombiculidae/microbiology ; RNA, Ribosomal, 16S/genetics ; *Scrub Typhus/microbiology/transmission/epidemiology ; *Orientia tsutsugamushi ; Phylogeny ; Geography ; },
abstract = {Chiggers (larval Trombiculid mites) serve as vectors for Orientia species that cause scrub typhus, a potentially serious illness in humans with a broadening global distribution. To date, there is limited research on the chigger microbiome in the United States (US) compared to some other parts of the world. Investigating chigger bacterial communities is essential for understanding the potential role they play in pathogen transmission dynamics within these arthropods. This study investigated the bacterial communities of free-living chiggers collected from sites across the three ecoregions in North Carolina using 16S rDNA gene targeted next-generation sequencing. Molecular identification of the chigger revealed three species: Eutrombicula splendens, Eutrombicula tinami, and Pseudoschoengastia sp. All three trombiculid mite species occurred at least once in the Mountains and Piedmont, except for E. tinami, which was absent from the Coastal Plain ecoregion. Microbiome analysis revealed significant differences in alpha and beta diversity among the collection sites for E. splendens. No significant differences in overall microbiome diversity were observed between E. splendens and Pseudoschoengastia sp., the two dominant chigger species. However, the microbiome of E. splendens alone exhibited significant differences in both Shannon diversity and beta diversity between Orientia-infected and uninfected individuals. Within E. splendens, genera like Brevibacillus and Telluria were more abundant in Orientia-positive chiggers, while Methylobacterium was more abundant in Orientia-negative chiggers. We also found potentially pathogenic bacterial genera, including Rickettsia, Listeria, Legionella, Staphylococcus, and Streptococcus sequences. These findings suggest that geography and Orientia infection influence chigger-associated bacterial communities, potentially affecting their vector competence.},
}

Animals
North Carolina/epidemiology
*Microbiota
*Trombiculidae/microbiology
RNA, Ribosomal, 16S/genetics
*Scrub Typhus/microbiology/transmission/epidemiology
*Orientia tsutsugamushi
Phylogeny
Geography

@article {pmid42418560,
year = {2026},
author = {Jackson, K and Galipeau, HJ and Hann, A and Constante, M and Zangara, MT and Bording-Jorgensen, M and Fuentes, A and Ho, H and Wang, J and Shimbori, C and Moayyedi, P and Surette, M and Bercik, P and Coombes, BK and Hosseinidoust, Z and Verdu, EF},
title = {Phage intervention improves colitis and response to corticosteroids by attenuating virulence of Crohn's disease-associated bacteria.},
journal = {Science translational medicine},
volume = {18},
number = {857},
pages = {eadz4589},
doi = {10.1126/scitranslmed.adz4589},
pmid = {42418560},
issn = {1946-6242},
mesh = {*Crohn Disease/microbiology/drug therapy ; Animals ; *Colitis/microbiology/drug therapy/complications/therapy ; Virulence/drug effects ; Escherichia coli/pathogenicity/drug effects ; *Bacteriophages/physiology ; *Adrenal Cortex Hormones/therapeutic use/pharmacology ; Humans ; *Phage Therapy ; Budesonide/therapeutic use/pharmacology ; Female ; Promoter Regions, Genetic/genetics ; },
abstract = {Adherent-invasive Escherichia coli (AIEC) exhibits proinflammatory properties and has been implicated in the pathogenesis of Crohn's disease (CD), a form of inflammatory bowel disease (IBD). Antibiotic use in CD lacks specificity and may worsen microbiome disruption, prompting interest in bacteriophages (phages) for targeted microbiome editing. Here, we identified HER259, a phage active against clinical AIEC isolates. HER259 ameliorated colitis in gnotobiotic models and attenuated the virulence of AIEC strain NRG857c, including suppression of the FimH adhesin through inversion of the fimS promoter to its "off" orientation. The effects were confirmed in CD-microbiota colitis models. Withdrawal of HER259 treatment led to reversion of the fimS promoter and reactivated colitis. The HER259 phage also enhanced the therapeutic effect of subtherapeutic budesonide independent of microbial drug metabolism. These findings support targeted phage therapy as an adjunct treatment approach in IBD, demonstrating modulation of bacterial virulence and improved response to conventional treatments that may reduce drug-related side effects.},
}

*Crohn Disease/microbiology/drug therapy
Animals
*Colitis/microbiology/drug therapy/complications/therapy
Virulence/drug effects
Escherichia coli/pathogenicity/drug effects
*Bacteriophages/physiology
*Adrenal Cortex Hormones/therapeutic use/pharmacology
Humans
*Phage Therapy
Budesonide/therapeutic use/pharmacology
Female
Promoter Regions, Genetic/genetics

@article {pmid42418776,
year = {2026},
author = {Patel, JJ and McClave, SA},
title = {Nutrition Therapy in Critically Ill Adults.},
journal = {The New England journal of medicine},
volume = {395},
number = {2},
pages = {162-174},
doi = {10.1056/NEJMra2506111},
pmid = {42418776},
issn = {1533-4406},
mesh = {Humans ; *Critical Illness/therapy ; *Enteral Nutrition/adverse effects ; *Parenteral Nutrition/adverse effects ; Refeeding Syndrome/prevention & control ; Nutritional Requirements ; Energy Intake ; },
abstract = {In the acute phase of critical illness, adults have severe catabolism, inflammation, muscle loss, and gut dysfunction, all of which shape nutritional requirements. Early enteral nutrition supports gut integrity and microbiome health, but trials have shown that early short-term parenteral nutrition is a safe alternative when enteral feeding is not possible. Large trials have shown that early full-dose energy delivery offers no benefit over restrictive dosing and may increase gastrointestinal and metabolic complications, findings that support a restrictive nutrition strategy, especially in patients who have circulatory shock or are at risk for refeeding syndrome. Similarly, large trials have shown no advantage of high-dose over standard-dose protein and suggest harm in patients with acute kidney injury. Because adverse events are common with enteral nutrition, safe nutrition delivery requires gradual advancement, strategies for prevention of refeeding syndrome, glycemic control, and avoidance of routine gastric residual volume monitoring. Patient heterogeneity underscores the need for precise, biomarker-guided, phase-specific nutrition to preserve lean muscle mass and improve recovery.},
}

Humans
*Critical Illness/therapy
*Enteral Nutrition/adverse effects
*Parenteral Nutrition/adverse effects
Refeeding Syndrome/prevention & control
Nutritional Requirements
Energy Intake

@article {pmid42418792,
year = {2026},
author = {Tao, J and Yu, S and Lu, P and Gu, M and Kong, M and Guo, J and Zhao, Z and Su, H and Li, H and Zhang, J and Jin, J and Cao, P},
title = {Rhizoplane microbiome: niche-specific recruitment and plant defense priming against bacterial wilt disease.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiag483},
pmid = {42418792},
issn = {1532-2548},
abstract = {The plant microbiome plays a pivotal role in host adaptation and disease suppression, yet niche-specific microbial responses to biotic stress, particularly within distinct plant compartments, remain poorly understood. Here, we revealed that bacterial wilt disease (BWD) induced pronounced niche-specific microbiome alterations in tobacco, with the rhizoplane emerging as a critical hub for beneficial microbial recruitment and defense coordination. Utilizing 16S and ITS amplicon sequencing across six distinct plant niches, we observed significantly enhanced bacterial diversity and a striking enrichment of potentially beneficial microbes in the rhizoplane under BWD stress. Eight potent antagonistic bacterial strains were isolated from this key niche, with Stenotrophomonas sp. ASV61 and Chryseobacterium sp. ASV172 demonstrating robust in vitro biocontrol potential and confirming in vivo plant resistance and growth promotion. We further elucidated the superior biocontrol mechanisms of Chryseobacterium sp. ASV172, attributing its superior efficacy to enhanced colonization and flexirubin-mediated antagonism. Crucially, plant transcriptomic profiling unveiled that these beneficial microbes engaged in a signaling dialogue with host plants, dynamically modulating defense hormone pathways. While Ralstonia alone manipulated host defenses by sustaining salicylic acid (SA) responses, antagonistic strains re-directed the plant towards robust jasmonic acid (JA) signaling, thereby restoring a more effective defense posture. Collectively, our findings underscore the disproportionate importance of the rhizoplane over the rhizosphere in assembling a resilient microbiome against soil-borne diseases, paving the way for targeted rhizoplane microbiome engineering strategies for sustainable disease management.},
}

@article {pmid42418807,
year = {2026},
author = {Tahmasebi, H and Bahar, A and Khazaei, M and Arabestani, MR},
title = {The Dual Role of the Gut Microbiota in Cancer Chemoresistance.},
journal = {MicrobiologyOpen},
volume = {15},
number = {4},
pages = {e70357},
doi = {10.1002/mbo3.70357},
pmid = {42418807},
issn = {2045-8827},
mesh = {Humans ; *Drug Resistance, Neoplasm ; *Neoplasms/drug therapy/microbiology ; *Gastrointestinal Microbiome ; *Antineoplastic Agents/therapeutic use/metabolism/pharmacology ; Probiotics ; Fecal Microbiota Transplantation ; Animals ; },
abstract = {Chemoresistance is one of the primary reasons that cancer chemotherapy fails to deliver successful treatment outcomes and contributes to poor overall survival rates for patients with cancer. New research has begun to shed light on the effects of the gut microbiome (GM). This new research will examine how certain microorganisms (referred to as "bad bacteria") can contribute to cancer treatment failure, as well as how others (such as Bifidobacterium, Akkermansia, and Lactobacillus) can enhance treatment success. This review will focus on the molecular mechanisms underlying these effects, including drug metabolism by microorganisms, modulation of the immune system by microorganisms, regulation of cellular apoptosis by microorganisms, and metabolic crosstalk between tumor tissue and the microbiome. Finally, we will look at new therapies under development that leverage knowledge of the microbiome to combat chemoresistance, including fecal microbiota transplantation, targeted probiotic and prebiotic supplementation, and dietary modifications. By studying the complex interactions among the host, the microbiome, and chemotherapeutic agents, we hope to demonstrate how microbiome-centered approaches can tailor and enhance an individual's cancer treatment while transforming the GM from a passive participant to an active target in cancer therapy.},
}

Humans
*Drug Resistance, Neoplasm
*Neoplasms/drug therapy/microbiology
*Gastrointestinal Microbiome
*Antineoplastic Agents/therapeutic use/metabolism/pharmacology
Probiotics
Fecal Microbiota Transplantation
Animals

@article {pmid42418876,
year = {2026},
author = {Aveta, EF and Vougioukas, P and Qi, F and Mehler, J and Behringer, KI and Gericke, N and Walczak, M and Vallejo-Janeta, AP and Blank, T and Hellwig, M and Lassak, J},
title = {Deciphering underground decarboxylase activity towards Nε-modified lysine derivatives in enterobacteria.},
journal = {Food chemistry},
volume = {524},
number = {},
pages = {150234},
doi = {10.1016/j.foodchem.2026.150234},
pmid = {42418876},
issn = {1873-7072},
abstract = {Thermal food processing generates diverse compounds interacting with the gut microbiota. Despite their abundance, the microbial turnover of diet-borne Nε-modified lysine derivatives remains largely unexplored. We demonstrate that the enterobacterial ornithine decarboxylase SpeC degrades the prevalent advanced glycation end product Nε-carboxymethyllysine (CML) to carboxymethylcadaverine via an underground activity (∼4 molecules/enzyme/min). This promiscuity extends to additional Nε-modified lysine derivatives - namely formylated (FmL), monomethylated (MML) and dimethylated (DML) lysine - yielding previously unknown biogenic amines (mono- and dimethylcadaverine, formylcadaverine). Functionally, SpeC enables Escherichia coli to utilize CML as a sole nitrogen source. In specific strains, this metabolism reinforces pH-stress responses, supporting survival under mild acidic conditions typical for the colon. Furthermore, SpeC orthologs are widespread across human gut genomes, correlating with geography, diet, and disease. Together, these findings suggest a potential diet-microbiome communication axis, linking the intake of modified dietary chemicals to microbial physiology and hypothesized host impacts.},
}

@article {pmid42419211,
year = {2026},
author = {Ma, Y and Gao, Q and Lu, J and Liu, X},
title = {The composite detoxification agent alleviates the toxicity induced by mycotoxins in Hy-Line Brown laying hens by regulating antioxidant capacity and gut bacterial communities.},
journal = {Poultry science},
volume = {105},
number = {10},
pages = {107347},
doi = {10.1016/j.psj.2026.107347},
pmid = {42419211},
issn = {1525-3171},
abstract = {This study evaluated the efficacy of a composite detoxification agent in mitigating the adverse effects of naturally mold-contaminated feed in laying hens. A total of 800 Hy-Line Brown hens (156 days old) were randomly allocated to five dietary treatments (8 replicates with 20 birds per replicate), following a 7-d adaptation and a 113-d experimental period. The basal diet served as the control (CON group). Experimental treatments were structured as follows: ZH group (5% of normal corn in the feed replaced with moldy corn); ZJ group (5% of normal corn replaced with moldy corn + 0.1 g/kg composite detoxification agent); DH group (5% of normal soybean meal replaced with moldy cottonseed meal); DJ group (5% of normal soybean meal replaced with moldy cottonseed meal + 0.1 g/kg composite detoxification agent). Compared with CON, hens fed the ZH diet exhibited decreased (P < 0.05) egg production, average daily feed intake, egg weight, egg mass, and albumen quality, deteriorated feed conversion ratio. Serum biochemistry in ZH hens revealed lower total protein and alkaline phosphatase levels but higher blood urea nitrogen. Additionally, hens fed ZH diet displayed oxidative stress, characterized by elevated malondialdehyde (MDA) and reduced activities of total antioxidant capacity (T-AOC), catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), glutathione S-transferase (GST), and nitric oxide (NO) (P < 0.05). Although less pronounced, similar alterations were observed in DH hens. Supplementation with the composite detoxifier restored laying performance and improved antioxidant status in both ZJ and DJ groups. Notably, the detoxifier enhanced gut microbiota diversity, enriched beneficial taxa including Lactobacillus and Limosilactobacillus, and correlated with alterations in the microbiota-host axis. These results indicate that the composite detoxifier alleviates mycotoxin-induced impairments and supports its application for managing feed mycotoxicosis in commercial layer production.},
}

@article {pmid42419242,
year = {2026},
author = {Liu, H and Yan, Y and Guo, Z and Gao, Y and An, Y and Zhou, J and Li, X and Wang, S and Feng, G and Gao, Q and Gou, Z},
title = {Biodegradable microplastics disrupt root exudate driven plant-microbe interactions, compromising plant growth and rhizosphere microenvironment health.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142930},
doi = {10.1016/j.jhazmat.2026.142930},
pmid = {42419242},
issn = {1873-3336},
abstract = {Microplastics (MPs) pollution already posed a serious threat to human health. Biodegradable (bio) plastics serve as alternatives to traditional plastics. However, the ecological impact of bio-MPs has not been adequately assessed. This study evaluates the effects of two types of bio-MPs (poly (butylene adipate-co-terephthalate) (PBAT) and polylactic acid (PLA)) on plant growth and the rhizosphere soil microenvironment. Exposure to bio-MPs significantly decreased tomato growth, soil enzyme activities, and rhizosphere microbial diversity. In addition, bio-MPs significantly reduced the abundance of beneficial microorganisms (growth-promoting, nutrient cycling, stress resistance) in the rhizosphere soil. The secretion levels of several root exudates decreased significantly, including citric acid, quinic acid, indole, p‑coumaric acid, and flavone. This decrease led to alterations in multiple metabolic pathways: the TCA cycle, the biosynthesis of phenylalanine, tyrosine, and tryptophan, and the phenylpropanoid biosynthesis pathway. Meanwhile, these specific metabolites showed a significant positive correlation with beneficial rhizosphere microorganisms. Compared with traditional MPs, these findings suggests that the presence of bio‑MPs may interfere with normal plant-microbe interactions, which is further associated with an imbalance in the rhizosphere ecological microenvironment and may ultimately contribute to impaired plant growth. In the meantime, the beneficial effects of root exudates on plant resistance against bio‑MP toxicity have also received preliminary confirmation. This finding provides valuable evidence for evaluating the impact of bio-plastics on plant rhizosphere soil health.},
}

@article {pmid42419245,
year = {2026},
author = {Han, Z and Zhang, Y and Luan, X and Feng, H and Wang, Y and Deng, Y and Hu, C and Yang, M},
title = {Clinically prevalent transposons contribute to erm gene dissemination in the field soil under pseudo-persistent erythromycin contamination.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142927},
doi = {10.1016/j.jhazmat.2026.142927},
pmid = {42419245},
issn = {1873-3336},
abstract = {Clinically relevant antibiotic resistance genes (ARGs) or their ancestral genes are widespread in natural soil microbiome at ultralow abundance. Whether and how long-term antibiotic pressure in soil accelerate dissemination of these ARGs remain unclear. Here, annual cycle of erythromycin exposure at levels around 5-20 μg∙kg[-1] was conducted in previously undisturbed field soil for consecutive five years, to simulate the pseudo-persistent characteristic of antibiotic contamination in soil environment. The primary clinically relevant macrolide resistance genes, rRNA methyltransferase genes (erm genes), were initially rare but gradually enriched, exhibiting a 37.8-fold increase after five years, which was greatly higher than macrolide efflux pump genes and inactivation genes (less than 2.3-fold). Among diverse mobile genetic elements, transposase gene tnpA exhibited potential association with the horizontal transfer of erm genes during long-term erythromycin exposure. From genetic and statistical evidence, enriched erm genes were presumed to locate on Bacilli with mobile transposable elements Tn554 and Tn551, which were clinically prevalent gene clusters in pathogens-Enterococcus and Staphylococcus. Thus, there may be a historical contribution of long-term erythromycin contamination to erm-carrying clinical transposable elements in soil microbiome. Our findings also demonstrated soil erythromycin exposure at levels much lower than laboratory-determined minimal selective concentrations (MSCs) still exhibits long-term effects on erm genes. Taking pseudo-persistent characteristic of antibiotic contamination, we further proposed long-term in-situ assessment with endpoint of clinically relevant ARGs to obtain a real-world MSC in the future studies.},
}

@article {pmid42419261,
year = {2026},
author = {Valles-Colomer, M and Foster, JA},
title = {Decoding the microbiome: Insights into FMT for depression.},
journal = {Cell host & microbe},
volume = {34},
number = {7},
pages = {1154-1156},
doi = {10.1016/j.chom.2026.06.004},
pmid = {42419261},
issn = {1934-6069},
mesh = {*Fecal Microbiota Transplantation ; Humans ; *Major Depressive Disorder/therapy/microbiology ; *Microbiota ; Animals ; },
abstract = {While fecal microbiota transplantation (FMT) emerges as a promising microbiome-targeted treatment approach, its application in major depressive disorder (MDD) remains investigational. In this issue of Cell Host & Microbe, Wang et al. provide insights into the potential underpinnings of FMT in MDD and offer a step toward decoding the molecular pathways accompanying clinical response.},
}

*Fecal Microbiota Transplantation
Humans
*Major Depressive Disorder/therapy/microbiology
*Microbiota
Animals

@article {pmid42419262,
year = {2026},
author = {Gelsinger, DR and Wang, HH},
title = {Toward precision microbiome therapeutics: From black box to blueprint.},
journal = {Cell host & microbe},
volume = {34},
number = {7},
pages = {1157-1161},
doi = {10.1016/j.chom.2026.06.014},
pmid = {42419262},
issn = {1934-6069},
mesh = {Humans ; Metagenomics ; *Gastrointestinal Microbiome/physiology/genetics ; Bacteria/genetics ; Animals ; Gene Editing ; *Precision Medicine/methods ; Microbiota ; },
abstract = {The gut microbiome influences human health, yet microbiome-mediated therapies have lagged as metagenomics identifies gut-colonizing microbes without clarifying functional networks. Prior microbiome "reset" approaches improved clinical outcomes despite limited mechanistic understanding. We argue a critical field inflection point: in situ genome editing of native bacteria enables mechanism-driven, programmable, species-specific therapeutics.},
}

Humans
Metagenomics
*Gastrointestinal Microbiome/physiology/genetics
Bacteria/genetics
Animals
Gene Editing
*Precision Medicine/methods
Microbiota

@article {pmid42419263,
year = {2026},
author = {Zuo, W and Liu, YY and Shen, J and Dai, L},
title = {Understanding ripple effects in the gut microbiome.},
journal = {Cell host & microbe},
volume = {34},
number = {7},
pages = {1162-1166},
doi = {10.1016/j.chom.2026.06.002},
pmid = {42419263},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; },
abstract = {Targeted perturbations of individual microbial taxa can propagate through complex ecological networks and generate ripple effects that reshape gut microbiota structure and function. Here, we discuss the need for predictive ecological and data-driven frameworks that enable precise and controllable microbiome engineering to minimize or leverage ripple effects.},
}

*Gastrointestinal Microbiome/physiology
Humans
Animals

@article {pmid42419264,
year = {2026},
author = {Xavier, JB},
title = {Operationalizing microbiome ecology in cancer care.},
journal = {Cell host & microbe},
volume = {34},
number = {7},
pages = {1167-1169},
doi = {10.1016/j.chom.2026.05.022},
pmid = {42419264},
issn = {1934-6069},
mesh = {Humans ; *Neoplasms/therapy/microbiology ; *Microbiota/drug effects ; *Dysbiosis/therapy ; Ecology ; },
abstract = {Cancer treatment can disrupt the microbiome, worsening outcomes for cancer patients. Ecology frames these changes as transitions between measurable states, enabling the prediction of microbiome trajectories to support clinical decision making. Longitudinal monitoring and microbial restoration can translate microbiome ecology into strategies that improve cancer care.},
}

Humans
*Neoplasms/therapy/microbiology
*Microbiota/drug effects
*Dysbiosis/therapy
Ecology