@article {pmid41857155,
year = {2026},
author = {Wang, Z and Tan, W and Zhang, P and Xiong, H and Zhu, L and Cui, J and Li, L and Guo, C and He, L and Huang, J and Wei, H and Liu, H},
title = {Potential subtype-specific alterations in gut microbiota and branched-chain amino acid metabolism in hydrogen- and methane-predominant small intestinal bacterial overgrowth.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41857155},
issn = {2045-2322},
abstract = {We aimed to investigate the clinical, microbiome, and metabolomic characteristics of hydrogen (H2)- and methane (CH4)-predominant small intestinal bacterial overgrowth (SIBO) subtypes. We retrospectively enrolled adults who underwent standardized lactulose hydrogen–methane breath testing between February 2021 and July 2025. Participants were categorized as Normal, H2–SIBO, CH4–SIBO, or mixed H2/CH4–SIBO. Clinical characteristics were compared using Kruskal–Wallis tests and chi-square tests. Multivariable logistic regression was used to identify factors independently associated with each SIBO subtype. Expiratory gas profiles (AUC, peak, and mean values) were quantified, and correlations with age and body mass index (BMI) were assessed using Spearman analysis. In a subset of participants, stool samples underwent 16S rRNA gene sequencing and untargeted metabolomic profiling, followed by integrative analyses of microbiota composition, diversity, and metabolic signatures across SIBO subtypes. Among 503 participants, higher serum albumin levels were independently associated with H2–SIBO, whereas higher fasting glucose was independently associated with CH4–SIBO. Breath-test profiling indicated that methane parameters, rather than hydrogen, better differentiated SIBO subtypes, and total (H2 + CH4) gas output was modestly correlated with age but not BMI. In the exploratory multi-omics subset, fecal microbiota composition and metabolomic signatures differed by subtype; LEfSe identified Bacteroidaceae as a CH4-SIBO signature and Alcaligenaceae/Acidaminococcaceae as H2–SIBO signatures. Differential metabolites were enriched in pathways related to branched-chain amino acid biosynthesis, lipid metabolism, and mineral absorption. H2- and CH4-predominant SIBO subtypes exhibit distinct clinical correlates and stool microbiome–metabolome profiles. Methane exhalation appears more informative for differentiating subtypes, and age is modestly associated with total expiratory gas volumes. These findings support potential subtype-specific host–microbe metabolic interactions, although the multi-omics results should be interpreted as exploratory.},
}

@article {pmid42078608,
year = {2026},
author = {Ullah, T and Khan, AM and Mustafa, A and Fatima, M},
title = {Gut microbiome dysbiosis as a trigger for area postrema syndrome exacerbation in AQP4+ NMOSD with HBV co-exposure.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {5},
pages = {3002-3003},
pmid = {42078608},
issn = {2049-0801},
}

@article {pmid42078675,
year = {2026},
author = {Yang, X and Dong, LL and Jin, XX and Liu, XJ and Gao, M and Fang, J},
title = {Composition and Diversity Characteristics of Gut Microbiota during the Development of Telchinia issoria (Lepidoptera: Nymphalidae).},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73596},
pmid = {42078675},
issn = {2045-7758},
abstract = {Ramie (Boehmeria nivea) was a traditional economic crop of high commercial value, whose cultivation was threatened by the leaf-feeding pest Telchinia issoria. This study investigated how the gut microbiota of T. issoria shifted across its larval, pupal, and adult stages using 16S rRNA amplicon sequencing. We found that Pseudomonadota and Bacillota dominated across all stages, with stage-specific enrichments of key genera: Burkholderia-Caballeronia-Paraburkholderia in early larvae, Acinetobacter and Culicoidibacter in mid-instars, Serratia in late larvae, Enterococcus in pupae, and Pseudomonas in adults. Alpha diversity exhibited a U-shaped pattern during larval development, decreasing initially before rising again, with the lowest overall diversity observed in the pupal stage. Beta diversity confirmed distinct community structures in pupae and adults. Functionally, as predicted by PICRUSt2 based on 16S rRNA gene sequencing data, carbohydrate metabolism was enriched in pupae, whereas pathways associated with amino acid, cofactor, and vitamin metabolism were significantly decreased relative to other developmental stages. Correlation analysis suggested that elevated temperature may contribute to the decreased diversity observed in this study, which warranted further verification under controlled temperature gradients. This work establishes a foundational understanding of stage-specific microbial symbiosis in T. issoria and offers insights for future research into lepidopteran gut microbial ecology and potential biocontrol applications.},
}

@article {pmid42078837,
year = {2026},
author = {Pang, Y and Wang, Y and Deng, Q and Wang, X and Wang, J and Xue, W},
title = {Integrative transcriptomic and microbiome analyses reveal thermal adaptation mechanisms in green and red color morphs of Myzus persicae (Hemiptera: Aphididae).},
journal = {Frontiers in insect science},
volume = {6},
number = {},
pages = {1780864},
pmid = {42078837},
issn = {2673-8600},
abstract = {Under global warming, the frequency and severity of agricultural pest outbreaks have intensified, posing serious threats to agriculture. The green peach aphid (Myzus persicae (Hemiptera: Aphididae)), an important agricultural pest, exhibits green and red color morphs and differentiated thermal tolerance, yet the underlying molecular mechanisms remain unclear. In this study, based on transcriptome and 16S rDNA amplicon sequencing, we analyzed the gene expression patterns and microbial community dynamics of green and red morphs of M. persicae under high-temperature stresses (30 °C and 35 °C) and across different exposure durations, comparing their similarities and differences in heat-response processes. Principal component analysis of transcriptomic data indicated that temperature had a greater influence on the physiological responses of M. persicae than body color, with a more pronounced effect observed at 35 °C. Differential gene expression analysis revealed overlap in temperature-responsive genes but different response patterns between the two morphs, suggesting activation of divergent molecular response mechanisms. Genes encoding heat shock proteins, detoxification-related enzymes, ribosomal protein family and so on were significantly up-regulated under high temperature, with a more pronounced induction in the green morph, indicating morph-specific regulatory strategies in response to thermal stress. Moreover, 16S rDNA sequencing revealed that the primary symbiont Buchnera displayed different relative abundance trends in the green and red morphs, remaining relatively stable in the red morph but declining markedly in the green morph under heat stress, potentially associated with their variation in thermal tolerance. Collectively, this study elucidates the molecular responses and microbe-mediated regulatory mechanisms underlying thermal tolerance in green and red morphs of M. persicae, providing novel insights into the thermal adaptation of aphids and a theoretical basis for developing pest management strategies under global warming.},
}

@article {pmid42078866,
year = {2026},
author = {Ghura, S and Jmii, H and Griffith, J and Schaeffer, AJ and Klumpp, DJ},
title = {Gut Microbiome-Driven Microglial Activation Links Dysbiosis to Pain in Interstitial Cystitis/Bladder Pain Syndrome.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9087060/v1},
pmid = {42078866},
issn = {2693-5015},
abstract = {Background Interstitial cystitis/bladder pain syndrome (IC/BPS) is a debilitating condition of chronic pelvic pain associated with urinary frequency and comorbid anxiety and depression. Recent studies in IC/BPS patients and rodent models implicate fecal dysbiosis and increased systemic exposure to endotoxin. These changes potentially elicit innate immune responses via the activation of microglial cells in the central nervous system, key mediators of pain. Microglial ablation and inactivation have previously been associated with analgesia in preclinical studies, underscoring the role of microglia in IC/BPS pain. Here, we investigated whether IC/BPS-associated fecal microbiota differentially activate microglia and whether activation correlates with patient symptoms. Methods Microbiome-microglia interactions were assessed using three complementary in vitro culture models: BV2 cells, enriched primary microglia (~ 95% microglia), and mixed glial cultures (microglia and astrocytes). Microglial cultures were exposed to heat-killed, stool-derived microbiota, and the pro-inflammatory cytokines tumor necrosis factor-α (TNF-α), RANTES/CCL5, and interleukin-6 (IL-6) were quantified by ELISA. Cytokine levels were evaluated for patients and controls and correlated with patient-reported genitourinary pain index (GUPI) scores. Results In all culture models, microglia exhibited significantly increased proinflammatory responses to fecal microbiota of IC/BPS patients relative to controls. Mixed glial cultures, incorporating astrocyte-microglia interactions, exhibited the most robust cytokine responses. Cytokine levels positively correlated with GUPI pain scores. Conclusions Together, these findings further support a role for gut dysbiosis in IC/BPS symptoms and suggest microglial activation and glial-glial interactions as a contributing mechanism. Understanding gut-brain axis interactions in IC/BPS will thus enable development of novel microbiome-based therapies for treating IC/BPS patients.},
}

@article {pmid42079003,
year = {2026},
author = {Comerford, KB},
title = {The impacts of ready-to-eat-cereals and cereal fibers on gut health, body weight, and cardiometabolic health.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1717345},
pmid = {42079003},
issn = {2296-861X},
abstract = {Ready-to-eat breakfast cereals are a major source of dietary fiber, and their intake is associated with better diet quality and reduced incidence of chronic disease. However, dietary fiber intake remains significantly lower than recommended levels, particularly in North America. This fiber gap is one of the most important issues facing public health nutrition and deserves continued attention. This extensive analysis summarizes the body of research from the last decade on whole grain/high-fiber breakfast cereals, cereal fibers, and/or selected fiber sources commonly found in, or added to, breakfast cereals (e.g., wheat bran, psyllium). The primary health outcomes of interest for this review are digestive function, gut microbial effects, satiety signaling, body weight management, cardiovascular disease and blood glucose control. The evidence indicates that the fiber amount, fiber type, processing techniques, and numerous associated nutrients and phytochemicals in ready-to-eat breakfast cereals are all critical factors impacting health outcomes. Therefore, in addition to dietary guidance on total daily intake levels, guidance targeting specific health outcomes should also emphasize the unique mechanisms of action (e.g., gel-forming, digestion slowing, fecal-bulking, laxative, toxin binding, prebiotic) for the predominant types of fibers in ready-to-eat cereals and other fiber-rich foods. In particular, a growing body of research indicates that wheat bran, the predominant source of fiber in the U.S. and Canada, contains a novel array of fibers and phytonutrients that support bowel function and influence gut microbiota composition, and may help lower the risk for cardiometabolic disease. Notably, the research shows that individuals with low-cereal fiber consumption are most likely to benefit from an increase in their daily intake. While there is still much to discover regarding the mechanistic effects of different types of cereal fibers, continued encouragement to increase daily consumption of wheat fiber-rich foods, including ready-to-eat cereals, could help to close the fiber gap and reduce the incidence of multiple diet-related chronic diseases.},
}

@article {pmid42079098,
year = {2026},
author = {Wucher, BR and Pardo-De la Hoz, CJ and Stamper, I and Sharma, S and Kaune, D and Bendale, P and Peled, J and Xavier, JB},
title = {Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.20.716137},
pmid = {42079098},
issn = {2692-8205},
abstract = {The gut microbiota contains trillions of bacteria essential to health, but also harbors potential pathogens. The phylum Pseudomonadota, which includes Escherichia coli , Klebsiella pneumoniae , and Pseudomonas aeruginosa , typically composes <1% of the microbiota but causes disproportionate numbers of gut-borne bloodstream infections. Identifying the ecological dependencies that enable Pseudomonadota to cause gut-borne disease is important for human health. Here, we studied microbiota dynamics in patients undergoing allogeneic hematopoietic cell transplantation (allo-HCT) to find that microbiota compositions permissive to Pseudomonadota had, following antibiotic prophylaxis, high levels of Bacteroides- a major reservoir of polysaccharide utilization loci (PULs). We tested the causality of this clinical association in a mouse co-colonization model and discovered that Bacteroides fragilis promotes Pseudomonas gut colonization and survival to ciprofloxacin, a drug commonly used as prophylactic in allo-HCT. In vitro experiments revealed a general mechanism by which diverse Pseudomonadota species depend on Bacteroides polysaccharide breakdown to grow better, form more biofilm, and survive ciprofloxacin treatment under anaerobic conditions, a type of ecological dependency termed metabiosis . Guided by this insight, we used metagenomics to identify the PUL-encoded functions underlying the metabiotic potential of a patient's microbiota and establish a link to gut-derived Gram-negative bacteremia in allo-HCT. Together, our findings translate mechanistically based microbiome ecology into a clinically actionable framework for early risk stratification and intervention.},
}

@article {pmid42079116,
year = {2026},
author = {Bar, O and Murthy, M and Cosgrove, K and Saidi, Y and El-Arar, W and Goldenberg, M and Sauvage, G and Bergerat, A and Cooley Demidkina, B and Laliberte, K and Xu, J and Pierson, G and Kwon, DS and Niles, J and Yassour, M and Mitchell, CM},
title = {An Observational Study of the Impact of Systemic B-cell Depletion on Cervicovaginal Mucosal Environment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.16.718227},
pmid = {42079116},
issn = {2692-8205},
abstract = {IMPORTANCE: Emerging data show that B-cell depleting chemotherapies, which are increasingly used to treat autoimmune disorders and multiple sclerosis, can be associated with mucosal side effects such as inflammatory vaginitis.

OBJECTIVE: Evaluate the impact of rituximab treatment on vaginal mucosal immune markers, endocervical immune cell populations and vaginal microbiome.

DESIGN: Cross-sectional observational study conducted between 2022 - 2024.

SETTING: Academic medical center, Boston Massachusetts.

PARTICIPANTS: We enrolled women aged >18 years who were either 1) receiving rituximab for autoimmune renal disease or were 2) healthy controls.

EXPOSURE: Treatment with rituximab, an anti CD20 monoclonal antibody.

MAIN OUTCOME AND MEASURE: We compared endocervical immune cell populations, vaginal fluid immune markers, vaginal fluid immunoglobulins and vaginal microbiome composition between individuals being treated with rituximab and healthy controls.

RESULTS: We enrolled 26 women treated with rituximab for autoimmune renal disease and 26 healthy controls. Median circulating and endocervical B-cell and plasma cell proportions were significantly lower in treated participants compared to controls. Median vaginal fluid IgA concentrations were significantly lower in participants treated with rituximab, while ILE, IgM, IgG1, IgG2, IgG3 and IgG4 were not different between groups. Total T cell frequencies were similar between groups, but the proportion of activated T cells (CD4+CD38+HLADR+) was significantly lower in people treated with rituximab. Concentrations of IL10, IL13, IL17, IL21, IL23, IL4, ITAC and TNFa were elevated in vaginal fluid from the rituximab group, while IL-8 was lower. A CST-IV-C, low- Lactobacillus pattern of vaginal microbiota was more common in the rituximab group.

CONCLUSIONS AND RELEVANCE: Systemic B-cell depletion is associated with reduced vaginal fluid IgA, a more diverse microbiome composition, and increases in many vaginal fluid immune markers compared to healthy controls. The reduction in vaginal fluid IgA may provide opportunities for vaginal bacteria to induce inflammation.

KEY POINTS: Question: How does circulating B-cell depletion impact the vaginal microenvironment?Findings: In this cross-sectional study of 52 women, B cell and plasma cell proportions were significantly lower in both blood and vaginal mucosa among rituximab-treated participants compared to healthy controls. Vaginal IgA concentrations, but not other immunoglobulins, were significantly lower in rituximab treated participants. In treated participants, vaginal cytokine concentrations were elevated, and microbiome composition shifted toward non- Lactobacillus -dominant communities. In six people with inflammatory vaginitis, both circulating and endocervical B cells were lowest in people with the most severe symptoms. Meaning: Systemic B cell depletion is associated with alterations in vaginal mucosal immune markers and microbiome composition which increase local inflammation.},
}

@article {pmid42079144,
year = {2026},
author = {Nkera-Gutabara, C and Olubayo, LAI and Oduaran, OO and Kisiangani, I and Khoza, S and Gama, K and Maritze, M and Mabunda, C and Keya, D and Adetunji, KE and Tollman, S and Micklesfield, LK and Mohamed, SF and Gómez-Olivé, FX and Tluway, F and Ramsay, M and Bhatt, AS and Hazelhurst, S and Maghini, DG and , },
title = {Participant engagement and feedback in microbiome projects: a case of AWI-Gen 2.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.20.718838},
pmid = {42079144},
issn = {2692-8205},
abstract = {UNLABELLED: Returning individualized microbiome results in ways that are ethical, comprehensible, and useful remains under-explored in African settings. We nested a multi-site, mixed-methods study within the AWI-Gen Wave 2 gut microbiome sub-study of 1,801 women aged 42 - 86 years to engage the participants and provide feedback. All (1,001) participants from Agincourt and Soweto (South Africa) and Nairobi (Kenya) were invited to feedback meetings: 496 from Agincourt, 87 from Soweto, and 195 from Nairobi responded. Engagement strategies were tailored by site (small-group and home-based sessions, visual metaphors, Foldscopes, and local-language delivery). Using semi-structured discussions and structured observations analysed thematically in MAXQDA under COREQ, five cross-cutting themes emerged: (1) understanding of microbiome reports, (2) emotional responses to feedback, (3) perceived health relevance, (4) trust in research institutions, and (5) suggestions for improving engagement. Culturally grounded explanations and local-language facilitation enhanced comprehension and perceived relevance; English-heavy sessions were associated with more confusion. Most participants expressed satisfaction and described planned or enacted dietary and lifestyle changes, while frustration centred on long delays between sampling and feedback. Trust increased with transparency and individualized return of results but was often conditional on minimizing burdensome procedures such as repeat blood sampling (phlebotomy) and ensuring timely feedback. Engagement was feasible and low-cost (approximately USD 29-59 per participant) with site-specific resource needs. Limitations included constrained generalizability beyond the three study sites. Returning individualized microbiome findings in community settings in Africa is acceptable, feasible, and can motivate health-promoting behaviours when delivered promptly and in culturally and linguistically appropriate ways.

IMPORTANCE: Microbiome studies rarely return individualized results in low-resource settings due to concerns about appropriate feedback and associated costs. This gap risks eroding trust and diminishing research impact. In three African communities, tailored feedback on gut microbiome profiles was provided to 778 women. By documenting a costed, multi-site engagement model and the themes influencing acceptance and actionability, this work offers a practical framework for ethically returning complex -omics results at scale in underrepresented populations - advancing scientific equity and strengthening community trust in microbiome research.},
}

@article {pmid42079178,
year = {2026},
author = {Zhang, S and Buttimer, C and Trepka, KR and Lam, KN and Hernandez, LAR and Soto-Perez, P and Noecker, C and Canigiula, P and Ortega, EF and Lee, J and Ramirez, L and Partipilo, G and Lawrence, HB and Bottacini, F and Draper, LA and Ross, RP and Coffey, A and Shkoporov, A and Hill, C and Turnbaugh, PJ},
title = {Eggerthella lenta evades bacteriophage through reversible megabase-scale inversions of capsular polysaccharide gene clusters.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.24.720693},
pmid = {42079178},
issn = {2692-8205},
abstract = {Bacteriophages are a promising tool for microbiome editing, yet their development has been constrained by limited insights into bacteriophage-host interactions within their shared mammalian body habitat. We isolated a lytic phage ΦKL11 that efficiently targets a disease-associated member of the human gut microbiota, Eggerthella lenta , during in vitro growth. However, ΦKL11 selects for a pre-existing and reversible bacteriophage-resistant sub-population in mice. Long-read sequencing revealed a massive genomic inversion event, representing >50% of the E. lenta genome, enriched in response to bacteriophage infection. Transcriptomics linked this inversion to the altered expression of three capsular polysaccharide synthesis (CPS) gene clusters and transmission electron microscopy confirmed differential capsule production. Finally, we show that ΦKL11 has a broad host range attributable to CPS and other strain-variable genes. These findings suggest a previously unrecognized strategy for phage evasion in the gut, involving megabase-scale genomic inversions and reversible capsule variation driving phage resistance.},
}

@article {pmid42079212,
year = {2026},
author = {Mills, T and Vinzelj, JM and Cook, ER and Mills, E and Rurik, AJ and Dallas, JW and Walker, DM and Stone, PA and Siler, CD and Elshahed, MS and Youssef, NH},
title = {Exploring the diversity and community structure of the Testudines fecal mycobiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.22.720109},
pmid = {42079212},
issn = {2692-8205},
abstract = {UNLABELLED: Most gut microbiome studies have focused on bacteria, leaving a knowledge gap regarding gut associated fungi. We assessed fungal diversity in the gastrointestinal tract of the reptilian order Testudines (turtles and tortoises) using samples from 6 families, 19 genera, and 27 species. A highly diverse community affiliated with 17 phyla and 157 orders was encountered, with four phyla (Neocallimastigomycota, Chytridiomycota, Ascomycota, and Basidiomycota) representing 89.13% of the community. Neocallimastigomycota was identified in host families Testudinidae (land tortoises), Chelidae , Chelydridae , Emydidae , Geoemydidae , and Kinosternidae , with higher relative abundances in Testudinidae (40.18±37.97%) compared to all other families combined (2.71±4.04%). Neocallimastigomycota sequences were mostly affiliated with orders Testudinimycetales in the host family Testudinidae and Neocallimastigales in other host families. Chytridiomycota was identified in all host families, but was more ubiquitous and abundant in Kinosternidiae (45.17±34.12%), and exhibited a high level of variability across samples. Dikarya communities were highly diverse, with 108 orders identified, and, similar to Chytridiomoycota, exhibited a highly stochastic distribution pattern. Representatives of multiple yet-uncultured phyla (Candidatus "Algovoracomycota", "Sedimentomastigomycota", "Tartumycota" and "Cantoromastigomycota") were identified, as well as eight novel orders in Chytridiomycota and Rozellomycota. Deterministic selection shaped community assembly in the host family Testudinidae , while the process was more stochastic in other host families. Distinct community structure was driven by differences in abundance and identity of the Neocallimastigomycota when comparing Testudinidae to. Our results describe a diverse and dynamic fungal community, shaped by the co-occurrence of autochthonous (resident) and transient (allochthonous) members of the gut microbiome.

IMPORTANCE: Fungi are known to inhabit the gastrointestinal tract (GIT) of humans and mammals. However, information on the fungal community in the GIT of reptiles is relatively sparse. We investigated the diversity and community structure of fungi in the reptilian order Testudines. We conducted a culture-independent diversity survey on fecal samples obtained from 27 different host species. We identify representatives of 17 fungal phyla. As well, we demonstrate that the anaerobic gut fungi (phylum Neocallimastigomycota) are not restricted to the family Testudinidae (land tortoises) as previously suggested, but could successfully colonize and inhabit all other testudines families, including those exhibiting a predominantly omnivorous or carnivorous lifestyles. In addition, we expand on the known fungal diversity by identifying additional representatives of multiple recently described yet-uncultured phyla, and describe multiple novel orders and classes within existing phyla. Collectively, this effort adds to the growing body of knowledge of mycobiomes in underexplored animal hosts.},
}

@article {pmid42079297,
year = {2026},
author = {Cornman-Homonoff, J and Rajendran, KM and Kolandaivelu, S and Coon, SD and Kupec, JT and Wang, L and Hu, G and Jala, VR and Sandle, GI and Rajendran, VM},
title = {Dietary Sodium Restriction Reprograms Gut Microbial Fermentation and Reduces Host Energy Harvest.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.20.719706},
pmid = {42079297},
issn = {2692-8205},
abstract = {Diet is a major determinant of gut microbiome structure and function, yet the role of dietary electrolytes-particularly sodium-remains poorly defined. Here, we identify dietary sodium availability as a key regulator of gut microbial fermentation and host energy harvest. Using a controlled sodium-sufficient versus sodium-deprived dietary intervention in rats, we integrated shotgun metagenomic sequencing, functional pathway analysis, targeted short-chain fatty acid (SCFA) quantification, and host physiological phenotyping. Sodium deprivation induced a coordinated restructuring of the gut microbiome, characterized by depletion of classical saccharolytic Firmicutes, including multiple Lactobacillus species, and enrichment of stress-tolerant, metabolically flexible taxa. Functional profiling revealed a shift away from growth-associated metabolic programs toward stress-adaptive and nutrient-scavenging pathways. Consistent with these changes, fecal concentrations of key SCFAs-including acetate, butyrate, hexanoate, and valerate-were significantly reduced, indicating impaired microbial fermentative capacity. These microbiome-level alterations translated into measurable host phenotypes, including reduced cecal mass and attenuated weight gain, consistent with decreased microbial energy harvest. Together, these findings establish a functional link between luminal sodium availability, microbial metabolic efficiency, and host energy balance, extending the framework of diet-microbiome interactions beyond macronutrients to include dietary electrolytes. This work identifies sodium as a previously underappreciated ecological constraint shaping gut microbial metabolism and suggests that modulation of dietary sodium intake may influence host metabolic outcomes through microbiome-mediated mechanisms.},
}

@article {pmid42079325,
year = {2026},
author = {Akif, A and Munami, JW and Das, R and Shawon, NJ},
title = {Dietary Polyphenols in Non-Communicable Chronic Diseases: Neuro-Enteric Mechanisms, Multi-Omics Biomarkers and Translational Opportunities.},
journal = {Food science & nutrition},
volume = {14},
number = {},
pages = {e71856},
pmid = {42079325},
issn = {2048-7177},
abstract = {Polyphenols from plant foods (tea, cocoa, berries, grapes, and extra-virgin olive oil) modulate oxidative stress, inflammation, vascular function, and the gut microbiome-axes central to non-communicable chronic diseases (NCCDs) that involve the brain and enteric nervous system (ENS). Recent randomized trials and longitudinal studies report modest but reproducible benefits on cognitive domains and vascular/endothelial function with berry/grape extracts, matcha/green tea, and high-polyphenol extra-virgin olive oil; effects appear stronger in older adults or those with metabolic risk. Complementary evidence in irritable bowel syndrome (IBS)-a prototypical gut-brain disorder-suggests polyphenol-based combinations (often with probiotics/fiber) can improve quality of life and inflammatory markers, supporting enteric-central crosstalk. Emerging genetics (Mendelian randomization) and multi-omics readouts strengthen causal inferences for tea polyphenols in neurodegeneration-adjacent outcomes and outline mechanistic mediators (endothelial/BBB function, cytokine tone, microbiome-derived metabolites). Key gaps remain: heterogeneous formulations/doses, limited head-to-head trials, sparse target engagement biomarkers, and uncertain durability after discontinuation. We synthesize clinical and mechanistic advances, propose a standardized biomarker set (neurocognitive, endothelial, immune, and microbiome-metabolome), and outline designs for mechanism-anchored RCTs that integrate ENS endpoints with brain outcomes to translate associative signals into precision nutrition strategies for NCCDs.},
}

@article {pmid42079427,
year = {2026},
author = {Xolalpa-Aroche, A and Contreras-Peruyero, H and Delgado-Suárez, EJ and Hernández-Mena, DI and Moguel-Chin, WI and Rivero-Cruz, JF and Velarde, RA and Ortiz-Vázquez, E and Rivero-Cruz, BE and Lovaco-Flores, JA and Rodríguez Orduña, L and Licona-Cassani, C and Barona-Gómez, F and Sélem-Mojica, N},
title = {Genome-resolved metagenomics reveals a phylogenetically cohesive Acetilactobacillus-like species complex dominating stingless bee pot honey.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag063},
pmid = {42079427},
issn = {2730-6151},
abstract = {Pot honey, the honey produced by stingless bees, is valued for its antimicrobial capacity, which may be influenced by its microbial content. While Lactobacillaceae species are commonly associated with honeybees and honey microbiomes, most studies have focused on Apis mellifera, leaving pot honey microbial diversity largely unexplored. We present the first pot honey shotgun metagenomic analysis from bee species Melipona beecheii and Scaptotrigona mexicana. We reconstructed 24 metagenome-assembled genomes (MAGs), 15 of which lacked close matches to any described species, showing [Formula: see text]81% Average Nucleotide Identity (ANI) to available reference genomes. Phylogenetic analyses resolved these MAGs into four well-defined clades (intraclade ANI [Formula: see text], interclade ANI [Formula: see text]), consistent with four novel species within the family Lactobacillaceae. GTDB-Tk classification placed MAG clades 1 and 2 closest to Nicoliella, and clades 3 and 4 closest to Acetilactobacillus. We validated the presence of these lineages in honey by sequencing three isolates that clustered within MAG clade 2. Aminoacid similarity (AAI/cAAI) indicates the presence of two genus-level lineages: one occupying a transitional genomic space near Nicoliella, and a second representing an undescribed genus. The genomic similarity of our MAGs and isolates to those from pot honey or larval food in Malaysia, Brazil, and Australia suggests these taxa are closely associated with stingless bees and may contribute to honey properties. By reducing the genomic underrepresentation of evolutionarily divergent sister clades related to Nicoliella and Acetilactobacillus, our genome-resolved analyses reveal a globally distributed, phylogenetically cohesive Lactobacillaceae species complex dominating pot honey.},
}

@article {pmid42079428,
year = {2026},
author = {Griggs, RG and Mills, DA and Bokulich, NA},
title = {Spatial heterogeneity and microbial terroir: balancing dispersal limitation and cultivar as drivers of microbial diversity in viticulture.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag074},
pmid = {42079428},
issn = {2730-6151},
abstract = {The microbial communities inhabiting grapevines and wines exhibit spatiotemporal patterns linked to region, climate, and cultivar. However, the degree of spatial heterogeneity within and between vineyards and its relationship to cultivar-associated biodiversity selection has not been studied previously. We combined high-density sampling of grapevine microbiota (N = 230) with spatial modeling and satellite imagery in two experiments: (i) two monoclonal Chardonnay vineyards to examine spatial heterogeneity in a genetically homogenous population and (ii) three old-vine vineyards interplanted with mixed cultivars to investigate the relative effects of spatial distance and cultivar on the microbiota. Contrary to expectations based on monoclonal vineyards, cultivar effects were not apparent in mixed-cultivar vineyards. Instead, we demonstrate extensive spatial variation in the bacterial and fungal communities inhabiting individual grapevines and vineyards, and that community similarity is correlated with spatial distance within and between vineyards. This suggests that dispersal limitation may play an important role in shaping grapevine microbiota, as well as cumulative diversity within the vineyard ecosystem (gamma diversity), with implications for both plant health and wine quality. Spatial models may identify abnormalities in microbial communities, such as contaminant sources within vineyards, and future studies examining microbiota in agricultural settings should account for spatial variation within the study design, e.g. by sufficiently dense spatial sampling or collection of aggregate samples (e.g. grape musts) to avoid undersampling bias. Overall, this study adds to the complicated story of microbial biogeography associated with winegrowing and wine quality (microbial 'terroir'), highlighting the roles of dispersal and potential microclimate effects in agricultural settings.},
}

@article {pmid42079429,
year = {2026},
author = {Christensen, R and Wang, YHD and Arnoldini, M and Cremer, J},
title = {Abundance-weighted pathway mapping demonstrates family-level structure of butyrate and propionate production across the human gut microbiome.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag075},
pmid = {42079429},
issn = {2730-6151},
abstract = {Fermentation products released by bacteria in the large intestine, such as butyrate and propionate, play central roles in host physiology and health. While the metabolic pathways producing these short-chain fatty acids (SCFAs) are well-characterized, less is known about their relative prevalence across hosts and gut conditions. Here, we introduce a genome-resolved, abundance-weighted bioinformatics framework that integrates pathway-based gene identification with extensive literature validation to systematically quantify the potential for butyrate and propionate production across bacterial species and human gut microbiomes. By comparing pathway predictions against over 700 experimentally characterized strains, we demonstrate high concordance with reported metabolic phenotypes, validating our approach beyond prior purely computational studies. Weighted by species abundance across ~18 000 metagenomic samples, we find that dominant gut taxa disproportionately drive SCFA production, with butyrate pathways enriched in Bacillota and propionate pathways in Bacteroidota. This abundance-weighted analysis reveals that pathway presence is well conserved at the family level, highlighting the ecological relevance of dominant taxa for community-level fermentation potential. Our results further show pronounced inter-individual variation and associations with age, birthing method, and inflammatory bowel disease, emphasizing how shifts in microbiota composition influence SCFA availability. By combining pathway-level resolution, abundance-weighted inference, and literature-based validation, our framework provides a robust, scalable approach to link microbial functional potential with host-relevant outcomes.},
}

@article {pmid42079430,
year = {2026},
author = {Scott, WT and Nataya, ED and Belzer, C and Schaap, PJ},
title = {Metabolic modeling unveils potential probiotic roles of Flavonifractor plautii in reshaping the Western gut microbiota landscape.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag077},
pmid = {42079430},
issn = {2730-6151},
abstract = {Flavonifractor plautii, a prevalent gut commensal, uniquely combines flavonoid degradation with the capacity to produce health-promoting short-chain fatty acids (SCFAs), notably butyrate and propionate. However, its metabolic pathways, ecological roles, and health impacts remain poorly characterized. To explore its probiotic potential and ecological functions, we developed a genome-scale metabolic model, iFP655, using automated reconstruction, deep-learning-based gap-filling, thermodynamic constraints, and transcriptomics. The iFP655 model substantially improved the predictions of growth rates and SCFA profiles compared to previous models. Simulations identified acetyl-CoA pathways as the preferred route for butyrate production, whereas the energetically costly lysine pathway remained inactive despite robust gene expression. Propionate synthesis occurred primarily via the methylmalonyl-CoA pathway. Community metabolic modeling with representative species of a Western minimal gut microbiota highlighted F. plautii's contributions to enhanced SCFA production, especially butyrate, amino acid metabolism, and syntrophic interactions driven by dietary substrates. Our findings indicate that diet-driven syntrophy significantly shapes microbial community structure and function, underscoring the ecological importance of F. plautii in gut microbial interactions and highlighting its potential as a probiotic candidate to beneficially modulate gut microbiota through dietary interventions.},
}

@article {pmid42079440,
year = {2026},
author = {Yang, L and Luo, R and Zhou, W and Yin, P and Feng, Y and Zhang, Y},
title = {Recent advances in noncanonical inhibition mechanisms of anti-CRISPR proteins.},
journal = {mLife},
volume = {5},
number = {2},
pages = {133-147},
pmid = {42079440},
issn = {2770-100X},
abstract = {The CRISPR-Cas system constitutes an adaptive immune mechanism in prokaryotes that defends against mobile genetic elements. Within the perpetual co-evolutionary arms race between bacteria and their viral predators, bacteriophages encode anti-CRISPR (Acr) proteins that use sophisticated molecular strategies to sabotage CRISPR-Cas function. While canonical Acr proteins rely on steric blockade of Cas effectors, recent discoveries reveal unprecedented noncanonical mechanisms spanning CRISPR immunity stages. This review synthesizes recent mechanistic advances in this field since 2023, highlighting the expansion of noncanonical inhibition mechanisms beyond type I to include types II, V, and VI, as well as novel Acr interventions targeting multiple functional stages, such as spacer acquisition, translation-coupled inhibition, complex assembly/disassembly, and R-loop DNA binding. Structural insights demonstrate how Acr proteins achieve substoichiometric inhibition via conformational hijacking, catalytic repurposing, and molecular mimicry. Forged by the intense selective pressure of the phage-host conflict, these molecular innovations represent both remarkable evolutionary adaptations and versatile precision tools. They enable spatiotemporal control of CRISPR technologies, from engineered off-switches to diagnostic reset mechanisms, while posing critical challenges for therapeutic safety and microbiome management.},
}

@article {pmid42079634,
year = {2026},
author = {Li, L and Cai, F and Liu, S and Peng, P and Liang, J and Liu, Z and Xu, H and Mo, W and Qin, J and Tang, S and Ruan, H and Zhang, J and Liang, C and Liu, S and Qin, M and Qin, R and Luo, F and Xiong, G and Yang, C and Geng, Y and Zou, J and Huang, J},
title = {Worldwide research trends on the Helicobacter pylori-gut microbiome nexus: a bibliometric analysis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1794021},
pmid = {42079634},
issn = {1664-3224},
mesh = {Humans ; *Helicobacter pylori/immunology ; *Gastrointestinal Microbiome/immunology ; *Helicobacter Infections/microbiology/immunology ; Bibliometrics ; Dysbiosis/microbiology ; *Biomedical Research/trends ; },
abstract = {INTRODUCTION: The impact of Helicobacter pylori (H. pylori) on the gastrointestinal tract ecosystem has been widely investigated beyond the stomach. Researchers have made considerable progress in understanding the relationship between H. pylori infection, gut microbiome dysbiosis, and systemic effects in recent years. This study aimed to explore the prospects and developing trends in the field of the H. pylori-gut microbiome nexus from a bibliometric perspective.

METHODS: Articles were collected from the Web of Science Core Collection, Scopus, and PubMed (2000-2025) and analyzed using bibliometrix, VOSviewer, and CiteSpace. Analysis of 1,592 publications reveals a distinct three-phase evolutionary structure in the field.

RESULTS AND DISCUSSION: Geographically led by China and the USA, the research focus has undergone a paradigm shift: evolving from an initial "infection and eradication" phase, through a transitional "dysbiosis and ecological intervention" phase, to the current "tumor-immunity axis" hotspot. Recent high-strength citation bursts for terms like "Fusobacterium nucleatum" and "immunity" underscore this transformation, indicating that academic attention has moved beyond local gastric pathogen control to understanding H. pylori's systemic role in modulating tumor microenvironments and therapeutic responses. This bibliometric analysis maps the field's rapid growth trajectory, highlighting its value for guiding future precision oncology and microecological strategies.},
}

Humans
*Helicobacter pylori/immunology
*Gastrointestinal Microbiome/immunology
*Helicobacter Infections/microbiology/immunology
Bibliometrics
Dysbiosis/microbiology
*Biomedical Research/trends

@article {pmid42079661,
year = {2026},
author = {Yu, J and Zhuang, WW and Lei, B and Shan, RY and Wang, XM and Qu, P and Hannig, M and Liu, Y},
title = {The oral-vascular axis: immune mechanisms linking periodontal dysbiosis to systemic vascular pathology.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1793621},
pmid = {42079661},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology ; *Periodontitis/immunology/microbiology ; Animals ; *Atherosclerosis/immunology ; *Mouth/immunology/microbiology ; *Cardiovascular Diseases/immunology ; },
abstract = {Periodontitis is among the most prevalent chronic inflammatory diseases worldwide and may affect vascular health beyond the oral cavity. Framed within the concept of an oral-vascular axis, this review synthesizes clinical and mechanistic evidence linking periodontal disease with atherosclerotic cardiovascular disease (ASCVD). Epidemiological studies and meta analyses consistently associate periodontitis with higher risks of coronary heart disease (CHD), stroke, and cardiovascular mortality, with modest but reproducible effect sizes that persist after adjustment for traditional risk factors. However, heterogeneous study designs and residual confounding preclude definitive causal inference. Interventional evidence is currently dominated by surrogate endpoints, and event-level cardiovascular benefit from periodontal therapy remains unproven. Mechanistically, chronic periodontal inflammation may influence endothelial function and atherogenesis through interlocking pathways that can be viewed as a spatiotemporal, dual-regulatory network of immunity and metabolism: local dysbiosis and barrier disruption increase systemic access to microbial ligands and vesicular cargo, while systemic immune activation interacts with metabolic remodeling to shape inflammatory set-points and vascular susceptibility. Microbe-derived and host-microbe co-metabolites may further modulate redox balance, inflammatory tone, and vascular homeostasis within this network. We highlight limitations of existing interventional trials, methodological challenges in microbiome- and genetics-based causal inference, and priorities for translational research. Clinically, the oral-vascular axis motivates interdisciplinary exchange and research-facing collaboration that integrates oral health assessment with immune and vascular phenotyping, while recognizing that cardiovascular benefit from periodontal interventions remains investigational and requires event-driven validation.},
}

Humans
*Dysbiosis/immunology
*Periodontitis/immunology/microbiology
Animals
*Atherosclerosis/immunology
*Mouth/immunology/microbiology
*Cardiovascular Diseases/immunology

@article {pmid42079714,
year = {2026},
author = {Guima, SES and Bischain, B and Morais Gama, LC and Faria, AC and Lourenço, T and Bueno, DF and Heller, D and Passos-Bueno, MR and Setubal, JC},
title = {The oral maternal microbiome plays a role in the development of cleft lip and palate condition in children.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21128},
pmid = {42079714},
issn = {2167-8359},
mesh = {Humans ; *Cleft Lip/microbiology ; *Cleft Palate/microbiology ; Female ; *Microbiota ; Male ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Infant ; Mothers ; Adult ; Case-Control Studies ; },
abstract = {Non-syndromic cleft lip or palate (NS-CL/P) is an oral birth defect with complex aetiology. We compared the microbial diversity and composition of the oral microbiome of mothers of babies with NS-CL/P (CLP group) and mothers of babies without NS-CL/P (control group). Oral microbiome composition was determined by sequencing the V3-V4 regions of the 16S rRNA gene. CLP and control groups had overall similar microbial compositions, but significant differences were observed. The most significant microbial genus related to these differences was Cutibacterium, which was more abundant in the CLP group. Based on the literature, we hypothesize that a member of the Cutibacterium genus present in the oral microbiota may have a role in inflammation processes that could be related to NS-CL/P development. We found additional differences in terms of differential abundance when subsetting the dataset for mothers with a male child; in this case, depletion of Limosilactobacillus and an unknown taxon, in the CLP group, was a significant result. We conclude that the maternal oral microbiome likely plays a role in the development of the NS-CL/P condition.},
}

Humans
*Cleft Lip/microbiology
*Cleft Palate/microbiology
Female
*Microbiota
Male
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Infant
Mothers
Adult
Case-Control Studies

@article {pmid42079748,
year = {2026},
author = {Zheng, L and Jia, T and Li, Y and Zhang, Z and Su, H and Zhang, R},
title = {The interplay between gastrointestinal dysfunction and gut microbiota dynamics in sepsis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1761536},
pmid = {42079748},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Sepsis/microbiology/physiopathology/complications/immunology ; *Dysbiosis/microbiology ; Animals ; *Gastrointestinal Diseases/microbiology ; *Gastrointestinal Tract/microbiology/physiopathology ; Intestinal Mucosa/microbiology ; Multiple Organ Failure ; },
abstract = {Sepsis frequently involves early gastrointestinal dysfunction, in which intestinal barrier breakdown and microbiota dysbiosis amplify systemic inflammation and contribute to multi-organ failure. Emerging evidence indicates that the gut is not merely a bystander in sepsis but an active driver of pathogenic cascades through epithelial injury, mucosal immune dysregulation, ischemia-reperfusion stress, and impaired motility, collectively promoting microbial translocation and immune deviation. In parallel, sepsis is associated with profound remodeling of the gut microbiome, characterized by reduced commensal diversity, expansion of pathobionts, and functional shifts in key microbial metabolites, including short-chain fatty acids, bile acids, and tryptophan-derived products, which further compromise mucosal integrity and host immune tone. This narrative review synthesizes experimental, translational, and clinical findings to elucidate the bidirectional interaction gut barrier-microbiota interplay in sepsis and to summarize mechanistic links across epithelial, immune, and metabolic signaling pathways, including gut-liver and gut-brain axes relevant to sepsis-associated organ dysfunction. dysfunctional microbial community leads to systemic immune deviation, multi-organ dysfunction and sepsis-associated encephalopathy, a common and severe neurological complication of sepsis. We also discuss emerging therapeutic strategies targeting the gut-microbiota axis-such as early enteral nutrition, prebiotics/postbiotics, defined microbial consortia, fecal microbiota transplantation, and metabolite-based supplementation-and evaluate their potential and limitations in septic populations. Finally, we highlight key challenges, including unresolved causality, inter-individual variability, context-dependent responses, and safety concerns, underscoring the need for longitudinal multi-omic profiling, host-microbiome phenotyping, and mechanism-informed interventional trials to enable precision microbiome-based approaches for sepsis.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Sepsis/microbiology/physiopathology/complications/immunology
*Dysbiosis/microbiology
Animals
*Gastrointestinal Diseases/microbiology
*Gastrointestinal Tract/microbiology/physiopathology
Intestinal Mucosa/microbiology
Multiple Organ Failure

@article {pmid42079749,
year = {2026},
author = {Pi, H and Lin, H and Zhou, J and Liu, H and Liang, S and Zhu, R and Li, D and Lu, X and Yang, M and Chen, H and Li, Y},
title = {Targeted next-generation sequencing analysis of pathogens and microecology in pediatric lower respiratory tract infections identifies risk factors for severe community-acquired pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1796357},
pmid = {42079749},
issn = {2235-2988},
mesh = {Humans ; *Community-Acquired Infections/microbiology/epidemiology ; Female ; Male ; Retrospective Studies ; Child, Preschool ; Risk Factors ; *High-Throughput Nucleotide Sequencing ; Child ; *Respiratory Tract Infections/microbiology/epidemiology ; Infant ; Severity of Illness Index ; *Bacteria/genetics/classification/isolation & purification ; Microbiota/genetics ; *Pneumonia/microbiology ; Mycoplasma pneumoniae/genetics/isolation & purification ; Haemophilus influenzae/genetics/isolation & purification ; Community-Acquired Pneumonia ; },
abstract = {BACKGROUND: Traditional diagnostic methods have inherent limitations in the comprehensive assessment of the etiological spectrum and microecological characteristics of pediatric lower respiratory tract infections (LRTIs), particularly community-acquired pneumonia (CAP). Against this backdrop, the present study seeks to delineate the pathogen profile of children with LRTIs via targeted next-generation sequencing (tNGS), and further explore the associations between clinical manifestations, upper respiratory microbiome signatures and disease severity in pediatric CAP cases.

METHODS: A retrospective, single-center study was conducted on 2299 children with suspected lower respiratory tract infections. Throat swab samples from all patients underwent tNGS for pathogen detection. For 1845 CAP patients (293 SCAP, 1552 non-severe CAP [nsCAP]), clinical data and tNGS results were analyzed. Statistical comparisons, correlation analyses, and multivariate logistic regression were performed to identify factors associated with SCAP. Microbial diversity (Shannon/Simpson indices) and relative abundance of detected species were also analyzed.

RESULTS: Mycoplasma pneumoniae was the dominant atypical pathogen, with an outbreak peaking in July 2024. M. pneumoniae detection rate (35.8% vs. 8.9%, P<0.001) and relative abundance (RA) were significantly higher in SCAP than nsCAP patients and correlated positively with severity markers. Multivariate analysis identified M. pneumoniae positivity, older age, female sex, circulatory and metabolic diseases as independent risk factors for SCAP. In M. pneumoniae-negative patients, pathogens like Streptococcus pneumoniae and Haemophilus influenzae were more common in nsCAP. Upper respiratory microbial diversity was lower in SCAP patients. Increased RA of specific commensals like Schaalia odontolytica was a protective factor, while increased abundance of Stenotrophomonas maltophilia was a risk factor for SCAP. Compared to bronchoalveolar lavage fluid (BALF), throat swab tNGS showed high agreement for M. pneumoniae but higher detection of potential colonizers like H. influenzae.

CONCLUSIONS: During the study period, M. pneumoniae was a key driver of SCAP in children. Beyond single-pathogen detection, decreased upper respiratory microbial diversity and shifts in colonizing bacteria abundances were associated with pneumonia severity, offering a new ecological perspective. Throat swab tNGS is valuable for pathogen screening. The associations between upper respiratory microbial features and severity highlight a potential ecological dimension of pneumonia pathogenesis.},
}

Humans
*Community-Acquired Infections/microbiology/epidemiology
Female
Male
Retrospective Studies
Child, Preschool
Risk Factors
*High-Throughput Nucleotide Sequencing
Child
*Respiratory Tract Infections/microbiology/epidemiology
Infant
Severity of Illness Index
*Bacteria/genetics/classification/isolation & purification
Microbiota/genetics
*Pneumonia/microbiology
Mycoplasma pneumoniae/genetics/isolation & purification
Haemophilus influenzae/genetics/isolation & purification
Community-Acquired Pneumonia

@article {pmid42080299,
year = {2026},
author = {Li, Z and Ren, M and Hu, A and Meng, F and Wang, J},
title = {Depth Stratification Shapes Viral Diversity, Interactions, and Metabolic Potential in a Deep Freshwater Lake.},
journal = {Molecular ecology},
volume = {35},
number = {9},
pages = {e70367},
doi = {10.1111/mec.70367},
pmid = {42080299},
issn = {1365-294X},
support = {U24A20578//National Natural Science Foundation of China/ ; 42507557//National Natural Science Foundation of China/ ; 42372353//National Natural Science Foundation of China/ ; BK20240111//Basic Research Program of Jiangsu Province/ ; },
mesh = {*Lakes/virology/microbiology ; *Viruses/genetics/classification ; Metagenomics ; Fresh Water/virology ; Microbiota/genetics ; Ecosystem ; Geologic Sediments/virology ; Biodiversity ; Metagenome ; },
abstract = {Deep freshwater lakes exhibit distinct microbial community stratification across depth gradients, which plays important roles in biogeochemical cycling and ecosystem stability. As crucial regulators of microbiome composition and function, viruses may play key ecological roles in these stratified systems, yet their distribution patterns and ecological significance in deep-lake surface sediments remain poorly understood. Here, we assessed viral community dynamics and functional potential across the entire water depth gradient (0-155 m) of Fuxian Lake using metagenomics from 44 surface sediment samples. A total of 11,523 viral OTUs were recovered, with only 18% annotated to the family level and approximately 93% classified as putatively lytic. Viral communities showed systematic depth-related shifts across multiple dimensions. Specifically, alpha diversity, community turnover, and stochastic assembly processes increased significantly with water depth, accompanied by enhanced lytic virus dominance and larger genome sizes. Predicted virus-host association networks transitioned from highly connected and generalized at shallow depths to increasingly sparse and specialized at greater depths. Virus-encoded auxiliary metabolic genes showed significantly increasing abundance with water depth, along with functional shifts from host defense to enhanced biosynthesis and energy metabolism, especially regarding carbon fixation and organic matter degradation. Collectively, these results highlight the importance of water depth gradients in structuring viral communities within surface sediments and expand our understanding of viral ecological functions in deep lake ecosystems.},
}

*Lakes/virology/microbiology
*Viruses/genetics/classification
Metagenomics
Fresh Water/virology
Microbiota/genetics
Ecosystem
Geologic Sediments/virology
Biodiversity
Metagenome

@article {pmid42080579,
year = {2026},
author = {Sidi Mabrouk, A and Depelteau, JS and Foini, C and Kempff, A and Jonker, S and Brenzinger, S and Limpens, R and Majrouh, M and Meijer, AH and Briegel, A},
title = {ICP1 bacteriophage treatment antagonizes colonization of the zebrafish larval intestine by Vibrio cholerae.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0356525},
doi = {10.1128/spectrum.03565-25},
pmid = {42080579},
issn = {2165-0497},
abstract = {UNLABELLED: Outbreaks of cholera pose a major threat to human health. Currently, antibiotics are the most effective treatment against the causative agent, the bacterium Vibrio cholerae. However, the use of antibiotics eventually leads to the emergence of resistant strains, which necessitates the need for alternative approaches. The use of bacteriophages to target the infection by antibiotic-resistant bacteria is one promising alternative. While clearance of Vibrio cholerae with the use of phages has been performed on several animal models, none of these models are naturalistic hosts of V. cholerae. Therefore, we set out to investigate the interaction between V. cholerae and bacteriophage ICP1 both in vitro and in vivo in a naturalistic host, the zebrafish model, Danio rerio. To study the interplay between host, bacteria, and phages, we used a combination of light and ultrastructural imaging techniques, including confocal fluorescence microscopy, serial block face scanning electron microscopy (EM) imaging, and cryogenic EM, which allowed us to investigate both the colonization process by V. cholerae and clearance by the ICP1 bacteriophage. In addition, we determined the effects of the microbiome on this treatment by using germ-free, conventionalized, and monoassociated zebrafish larvae as a host. Independent of the presence and composition of microbiomes used here, V. cholerae efficiently colonized the larval intestine. Finally, we demonstrate significant in vivo clearance of V. cholerae N16961-dsRED by ICP1, underscoring the role of phage-bacteria dynamics in shaping pathogen colonization within the zebrafish larval host.

IMPORTANCE: Cholera remains a life-threatening disease that causes recurring outbreaks and significant mortality, particularly in developing and conflict-affected regions. As antimicrobial resistance continues to rise, there is an urgent need to better understand the ecological and microbial dynamics that govern Vibrio cholerae colonization and persistence. This research investigates how V. cholerae interacts with bacteriophages, the host environment, and the resident microbiota within a natural vertebrate host, offering new insights into the factors that influence pathogen clearance and shaping of the gut ecosystem during infection. The powerful combination of serial block-face scanning and cryogenic electron microscopy, fluorescence microscopy, and traditional colony/plaque counting methods revealed previously unobserved aspects of the interplay between host, pathogen, phages, and selected microsymbionts, highlighting phage-driven clearance of V. cholerae during colonization.},
}

@article {pmid42081026,
year = {2026},
author = {Zomorodimanesh, S and Razavi, SH and Zomorodimanesh, P},
title = {Exploring the Role of Probiotics in the Prevention and Treatment of Gastrointestinal Cancer.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42081026},
issn = {1867-1314},
abstract = {Probiotics, live microorganisms with health-promoting properties, play a vital role in modulating the gut microbiota and enhancing immune responses. Their potential for regulating key signaling pathways, including NF-κB, PI3K/AKT, and Wnt/β-Catenin, suggests promise in cancer prevention as they can mitigate inflammation, strengthen intestinal barriers, and influence cytokine production, offering multiple therapeutic benefits. This review highlights the mechanisms by which probiotics may contribute to gastrointestinal cancer prevention and treatment, discussing their capacity to regulate inflammatory cytokines, enhance epithelial integrity, and balance gut microbiota. Evidence from preclinical and a growing number of clinical studies is summarized. Additionally, challenges such as strain specificity, dose optimization, and safety evaluations are analyzed alongside potential integration into conventional cancer therapies. Current data indicate that probiotics hold potential as complementary agents in oncology, possibly capable of inhibiting tumor growth, enhancing immune surveillance, and improving the efficacy of existing treatments. Future research should prioritize robust, long-term clinical trials and molecular studies to optimize their application in cancer management.},
}

@article {pmid42081130,
year = {2026},
author = {Bak, NK and Østergaard, SK and Schacksen, PS and Nielsen, JL and Rohde, PD and Kristensen, TN},
title = {Host genetics and diet jointly shape the microbiome of Drosophila melanogaster but do not predict lifespan or age-related traits.},
journal = {Biogerontology},
volume = {27},
number = {3},
pages = {},
pmid = {42081130},
issn = {1573-6768},
support = {DFF-2032-00205A//Danmarks Frie Forskningsfond/ ; },
mesh = {Animals ; *Drosophila melanogaster/microbiology/genetics/physiology ; *Longevity/genetics ; *Microbiota/genetics ; *Diet ; *Aging/genetics ; Genetic Variation ; Male ; Female ; },
abstract = {The microbiome is a key determinant of organismal health, yet inter-individual variability and heterogeneous responses to environmental conditions complicates the understanding of its effects on hosts. Here, we present a comprehensive analysis using the Drosophila Genetic Reference Panel (DGRP) to investigate how the interplay between host genetic variation and diet influences microbiome composition, and to assess whether microbiome features in young flies can be used to predict lifespan and age-related traits. Our findings show that adult flies reared on a nutritionally rich control diet exhibited higher microbial richness but lower evenness compared to those on a nutritionally poor restricted diet. Principal component analysis (PCA) highlighted substantial diversity among lines reared on the same diet, and this variation was evidenced by high heritability estimates for all measured α-diversity metrics, including Unique OTU counts, Shannon and Simpson indices, as well as the relative abundances of genera and species with relative abundances exceeding 1%. These results underscore the critical roles of both environmental factors and genetic variation in shaping microbiome composition under different dietary conditions. Moreover, we identified widespread genotype-by-diet interactions, suggesting that the genetic regulation of the microbiome is highly complex. Finally, we found that the microbiome features of young flies including diversity indices, taxonomic abundances, or ordination scores cannot predict age-associated phenotypes (lifespan, locomotor activity, dry weight, and heat knockdown time). Our findings offer valuable insights into the genetic architecture that governs microbiome composition, dietary responses, and aging in Drosophila melanogaster.},
}

Animals
*Drosophila melanogaster/microbiology/genetics/physiology
*Longevity/genetics
*Microbiota/genetics
*Diet
*Aging/genetics
Genetic Variation
Male
Female

@article {pmid42081188,
year = {2026},
author = {Pollock, J and Liu, R and Rwenji, E and Orobi, E and Udayakumar, S and Huibner, S and Kung'u, M and Kabuti, R and Babu, H and , and Irungu, E and Ngurukiri, P and Muthoga, P and Adhiambo, W and Weiss, HA and Seeley, J and Abramsky, T and Kimani, J and Beattie, TS and Kaul, R},
title = {Assessing the Impact of Female Genital Mutilation/Cutting on Genital Inflammation and Microbiota Among Kenyan Female Sex Workers.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {95},
number = {5},
pages = {e70250},
pmid = {42081188},
issn = {1600-0897},
support = {MR/R023182/1//Medical Research Council (MRC) and the UK Department of International Development (DFID)/ ; //EDCTP2 supported by the European Union/ ; PJT-156123//Canadian Institute of Health Research (CIHR)/ ; PJT-180629//Canadian Institute of Health Research (CIHR)/ ; },
mesh = {Humans ; Female ; Kenya/epidemiology ; *Sex Workers ; Adult ; *Microbiota/immunology ; *Circumcision, Female/adverse effects ; *HIV Infections/epidemiology/immunology ; *Inflammation/immunology ; Young Adult ; Cytokines/metabolism ; *Vagina/microbiology/immunology ; *Genitalia, Female/microbiology/immunology ; },
abstract = {PROBLEM: Female genital mutilation/cutting (FGM/C) is harmful to physical, mental, and reproductive health, though the effect of this practice on a woman's HIV susceptibility is poorly understood. Despite the known associations of FGM/C with short-term vaginal epithelial damage, neither genital inflammation nor the genital microbiome have been explored in women who have undergone FGM/C. In this study we compare the genital immune milieu and microbiome among female sex workers (FSWs) by FGM/C status, hypothesizing that these biological factors are dysregulated in women who have undergone FGM/C, heightening their risk of HIV acquisition.

METHOD OF STUDY: 1003 FSWs in Nairobi, Kenya, were enrolled in the Maisha Fiti study and visited a study clinic up to three times from June 2019 to March 2021. Participants self-reported any previous exposure to FGM/C as well as other relevant sociodemographic factors. Levels of proinflammatory cytokines and soluble E-cadherin (sE-cad), a biomarker of epithelial barrier disruption, were measured by multiplex immunoassay using self-collected cervicovaginal secretion samples provided by HIV-uninfected participants. Genital inflammation was defined using a composite score of inflammatory cytokines previously associated with HIV acquisition. The presence of inflammation was compared longitudinally between groups using mixed models to control for potential confounders including age, bacterial vaginosis (BV) status as defined by Nugent score, and others. Vaginal bacterial abundance, Shannon diversity, and total levels of key vaginal bacteria were measured by qPCR and compared by FGM/C status in an exploratory analysis.

RESULTS: 44 of 1003 (4%) participants had undergone Type I or II FGM/C. These participants were older (p < 0.001) and more likely to test positive for herpes simplex virus-2 (HSV-2; p = 0.04), and less likely to have completed primary education (p = 0.03). Among HIV-uninfected participants, there was no evidence that genital inflammation was associated with FGM/C status after controlling for potential confounders (aOR = 0.70; 95% CI: 0.31-1.59; p = 0.40). There was no evidence of a difference in BV prevalence (p > 0.99), total bacterial abundance (p = 0.96), or Shannon diversity (p = 0.15) by FGM/C status.

CONCLUSIONS: Type I or II FGM/C was not associated with genital inflammation or microbial dysregulation in the long-term among HIV-negative FSWs in this cohort. This may be due to the duration elapsed since FGM/C occurred or the lowered mucosal immune activation previously observed in FSWs.},
}

Humans
Female
Kenya/epidemiology
*Sex Workers
Adult
*Microbiota/immunology
*Circumcision, Female/adverse effects
*HIV Infections/epidemiology/immunology
*Inflammation/immunology
Young Adult
Cytokines/metabolism
*Vagina/microbiology/immunology
*Genitalia, Female/microbiology/immunology

@article {pmid42081950,
year = {2026},
author = {Garvey, MI and Moran, RA and Wilkinson, MAC and Sanches Ferreira, AD and Gardiner, A and Holden, E and McNally, A},
title = {What grows in the sink splash zone.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2026.04.010},
pmid = {42081950},
issn = {1532-2939},
abstract = {BACKGROUND: The hospital sink drain microbiome can harbour opportunistic pathogens and antimicrobial resistance genes. Patients may be exposed to waterborne pathogens via water outlets and sink drains. We have previously shown water from a clinical hand wash basin can splash up to two metres away from the sink/tap. Here we wanted to identify which organisms could be cultured from environmental sampling within the splash zone.

METHODS: Queen Elizabeth Hospital Birmingham (QEHB) is a large UK tertiary centre. We placed an SAS Super 180 air sampler within the splash zone at approximately one metre distance of a tap on a clinical hand wash basin in the critical care unit and undertook sampling both with and without the tap running. All Gram-negative organisms were cultured and any carbapenemase producing Enterobacterales (CPE) isolated were sequenced.

RESULTS: Environmental sampling undertaken when the tap was running yielded a variety of organisms, with Gram-negative isolates including Citrobacter freundii, Enterobacter kobei, Enterobacter cloacae, Enterobacter asburiae, Pseudomonas aeruginosa and Sphingobacterium multivorum. Amongst these, we identified one CPE, C. freundii isolate QE-SINK-CF1, which carried a plasmid bearing the blaKPC-2 gene. Structural variants of this plasmid have been involved in clinical infections at QEHB. Control sampling without the tap running yielded no Gram-negative organisms.

CONCLUSIONS: Here we show a variety of Gram-negative microorganisms, including CPE, can be cultured from within the 2-metre sink splash zone. This latest work provides further evidence healthcare settings should consider splash zones and waterborne pathogen transmission risk.},
}

@article {pmid42082045,
year = {2026},
author = {Zhang, Y and Wang, Y and Yang, Q and Yang, L and Yang, X and Zhao, X and Zhao, S},
title = {Unveiling the interactions of 8:2 fluorotelomer sulfonic acid (8:2 FTSA) with the earthworm-microbe symbiosis in soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {400},
number = {},
pages = {128247},
doi = {10.1016/j.envpol.2026.128247},
pmid = {42082045},
issn = {1873-6424},
abstract = {8:2 fluorotelomer sulfonic acid (8:2 FTSA), an important per- and polyfluoroalkyl substance (PFAS) found in aqueous film-forming foams (AFFFs), is frequently detected in soil. However, the interactions of 8:2 FTSA with soil-terrestrial invertebrate systems are poorly understood. This study investigated the biotransformation, toxicity, microbiome shifts, and microbial degradation of 8:2 FTSA in a soil-earthworm system through in vivo, in vitro, and multi-omics analyses. Earthworms efficiently accumulated 8:2 FTSA and biotransformed it into 11 distinct PFAS via α/β-oxidation mediated by metabolic enzymes, with trifluoroacetic acid (TFA) as the predominant metabolite. 8:2 FTSA induced significant oxidative stress, activated metabolic detoxification, and caused potential neurotoxic effects in earthworms. Furthermore, 8:2 FTSA exposure disrupted the microbial communities in the earthworm-soil system, with greater sensitivity observed in communities on the earthworm skin and in the soil compared to those in the gut. Predicted functional profiling further suggested that the gut microbiota may have greater potential for xenobiotic transformation, whereas the skin microbiota exhibited a host-dependent and low-activity phenotype. Raoultella ornithinolytica, isolated from earthworm gut and skin, transformed over 68% of 8:2 FTSA in 6 days via α/β-oxidation. Our findings advance the understanding of 8:2 FTSA interactions with the soil-earthworm system and provide a critical foundation for assessing its ecological risk in terrestrial environments.},
}

@article {pmid42082125,
year = {2026},
author = {Marzec-Grządziel, A and Borsuk, G},
title = {Between Host and Parasite: The Microbiome of Varroa destructor and Its Relationship with Honey Bees.},
journal = {Developmental and comparative immunology},
volume = {},
number = {},
pages = {105617},
doi = {10.1016/j.dci.2026.105617},
pmid = {42082125},
issn = {1879-0089},
abstract = {The study of the microbiome of the mite Varroa destructor is crucial for understanding parasite-host interactions and their potential health implications for honey bees (Apis mellifera). The aim of this research was to characterize the microbial diversity of Varroa destructor populations collected from the body surface of honey bees and compare it with microbiome of Apis mellifera. DNA isolation was performed using standard methods, followed by next-generation sequencing (NGS) of the V3-V4 region of the 16S rRNA gene. The obtained bioinformatic data underwent taxonomic analysis, enabling the identification of dominant bacterial genera present in the Varroa and Apis mellifera microbiome. Results revealed significant microbial diversity, with dominance primarily by bacteria belonging to the families Acetobacteraceae, Morganellaceae, and Segniliparaceae. The identified bacteria may play a critical role in the pathogenicity of Varroa destructor, directly or indirectly affecting the health and condition of bees. These findings provide new insights into potential therapeutic and preventive targets for protecting bee colonies against the detrimental effects of Varroa mites.},
}

@article {pmid42082515,
year = {2026},
author = {Geng, Y and Zhang, J and Hu, Y and Tong, Q and Ye, Z and Yu, J and Tu, J and Wang, N and Zhang, HY and Liu, S and Jiang, Q and Yan, X and Wang, Y and Feng, Z},
title = {A manually curated pig gut microbiome dataset for precision feeding.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07238-8},
pmid = {42082515},
issn = {2052-4463},
support = {203-61022300002//the National Digital Animal Husbandry (Pig) Innovation Center Project/ ; },
abstract = {The gut microbiome of pigs is a complex microbial ecosystem critical to host health and agricultural productivity. While amplicon sequencing studies have expanded our understanding of this community, a lack of standardized data and metadata often hinders comparative analysis and data reuse. To address this challenge, we present the Pig Gut Microbiome Dataset (PGMD, version 1.0), a comprehensive resource developed through the systematic selection of publications, extensive manual curation of associated metadata, and standardized reprocessing of raw amplicon sequencing data. This initial release integrates 202 publications (encompassing 207 16S rRNA gene sequencing data BioProjects), comprising 12,336 samples, collected from 22 countries. The dataset encompasses 52 host species and 3,028 taxonomic groups. Samples are systematically categorized by research topics and host phenotypes, enabling users to explore microbial community composition, identify differentially abundant taxa across experimental conditions and phenotypes, investigate six core phenotype-associated microbial clades, and determine dominant taxa across four key growth stages. PGMD significantly enhances the standardization and integration of pig gut microbiome data, serving as a valuable resource for research towards precision feeding and improved animal health. All data in the dataset are hosted and available in figshare https://doi.org/10.6084/m9.figshare.25911745.v1.},
}

@article {pmid42082522,
year = {2026},
author = {Motger-Albertí, A and Gallardo-Nuell, L and Rosell-Díaz, M and Stefoglo, M and Pons, J and Garre-Olmo, J and Pérez-Brocal, V and Moya, A and Puig, J and Ramos, R and Mayneris-Perxachs, J and Fernández-Real, JM},
title = {Sex-specific microbial and tryptophan signatures of depression implicate archaeal methanogens and indole-3-acetic acid only in women.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00983-z},
pmid = {42082522},
issn = {2055-5008},
support = {PI20/01090//Instituto de Salud Carlos III/ ; PI15/01934//Instituto de Salud Carlos III/ ; CNS2023-144218//Ministerio de Ciencia, Innovación y Universidades/ ; 2021 SGR 01263//Generalitat de Catalunya/ ; },
abstract = {Sex differences in mental health are often overlooked, yet gut microbiota-host metabolite interactions may contribute to sexual dimorphism in depression. In a population-based cohort, we investigated sex-specific links among plasma tryptophan metabolites, depressive symptoms (PHQ-9), and the gut microbiome, controlling for smoking, diet, alcohol, and physical activity. Women (N = 419) exhibited higher plasma indole-3-acetic acid (IAA) and picolinic acid (PA) concentrations, but lower trigonelline (TRIG) than men (N = 383). Machine learning models with SHAP explanations revealed that IAA and TRIG were positively associated, whereas PA was negatively associated with depression severity in women, whereas only kynurenic acid (KA) was inversely associated in men. In women, depression severity strongly correlated with methanogenic archaea, including Methanobrevibacter smithii, and microbial methane-production pathways. Methanobrevibacter and specifically M. smithii were negatively linked to genes for tryptophan, PA, and KA biosynthesis, but positively to genes for IAA and nicotinate/nicotinamide metabolism. Most microbial species associated with depression severity in women were predicted to produce IAA. These findings reveal pronounced sex-specific microbiome-metabolite interactions, highlighting potentially distinct microbial mechanisms shaping depression in men and women.},
}

@article {pmid42082767,
year = {2026},
author = {Lebeer, S and Goormachtig, S},
title = {Practical lessons from microbiome citizen-science projects.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42082767},
issn = {2058-5276},
support = {852600//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G049022N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; S006424N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; VR 2016 2312 Doc.1521/4//Vlaams Instituut voor Biotechnologie (Flanders Institute for Biotechnology)/ ; },
}

@article {pmid42082772,
year = {2026},
author = {Alshareedah, I and Brunner, JD and Chain, PSG and Kumar, A},
title = {Significance and challenges in dissecting cancer-bacteriome interactions.},
journal = {BJC reports},
volume = {4},
number = {1},
pages = {},
pmid = {42082772},
issn = {2731-9377},
support = {20251143PRD1//Los Alamos National Laboratory/ ; },
abstract = {Cancer is the leading cause of death around the world. While some types of cancer have become manageable due to advancements in medicine, most cancers still lack available cures and treatments. Recent studies have shown that changes in the human microbiome, especially in the bacteriome, are associated with some cancers. Certain bacterial strains have been reported to promote the initiation and progression of cancer in humans. Other studies have used sequencing to observe changes in the bacteriome of healthy and cancer patients. However, studies that investigate the interactions between cancer cells and the complex bacteriome as a whole remain scarce. This is due to the absence of experimental methods to study the interactions between cancer cells and complex bacterial populations, which has delayed the progress in identifying cancer-causing and cancer-inhibiting bacteria, and in understanding the bacterial interactions and their influence on host cells. Here, we review approaches to studying cancer cell interactions with complex bacteriomes and suggest possible routes to overcome this problem, highlighting the need for interdisciplinary studies that may help advance this field. We speculate that a good understanding of cancer-bacteriome interactions may open the door to new lines of holistic bacteriotherapy for cancer that is otherwise unavailable.},
}

@article {pmid42083021,
year = {2026},
author = {Han, Y and Cui, J and Huang, X and Guo, P and Yang, S},
title = {Microbial inoculants with straw mediate degradation-level-specific changes in soil carbon cycling genes and microbial community.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00898-4},
pmid = {42083021},
issn = {2524-6372},
support = {2022YFD1500600//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Enhancing soil organic carbon (SOC) sequestration in degraded lands is critical for climate mitigation and sustainable agriculture. While straw amendment combined with microbial inoculants holds great promise, the underlying mechanisms governing its impact on soil microbiome and carbon cycling genes remain poorly understood.

RESULTS: Here, we employed metagenomic sequencing to analyze responses in soil carbon (C) cycling genes, microbial community structure, and functional profiles across three degradation levels (severely, moderately, and non-degraded) of cinnamon soils under straw application alone or in combination with microbial inoculants. Results showed that both straw and straw-microbial inoculants treatments significantly improved soil properties, with improvements in available nitrogen and microbial biomass carbon (severe degradation), SOC (moderate degradation), and available nutrients (non-degradation). The combined application notably reshaped microbial communities by enhancing bacterial alpha diversity while reducing fungal diversity, and strengthened the relationship of relevant key soil C genes in severely degraded soils. Soil pH exhibited significant positive correlations with soil C cycling genes. Key bacterial genera (Sphingomonas, Bradyrhizobium) showed strong associations with ABC transporters and glycoside hydrolases, and fungal genus (Chaetomium) linked to pyruvate and purine metabolism. Importantly, we observed degradation-level specificity: straw addition significantly increased the abundance of the amylase gene K01214 (encoding α-amylase for starch hydrolysis) in severely degraded soils, whereas the straw-inoculant combination enriched the chitinase gene K01207 (encoding chitinase for chitin hydrolysis) in moderately degraded soils.

CONCLUSIONS: Accordingly, we propose targeted application of straw with a customized chitinolytic-cellulolytic synthetic microbial community (1-5% of straw mass) to restore carbon cycling functions in degraded soils, while adopting optimized agronomic management to preserve microbiome stability in non-degraded soils. Our findings provide novel insights into microbial-mediated carbon cycling and a foundation for targeted soil restoration.},
}

@article {pmid42083054,
year = {2026},
author = {Todd, C and Rolshausen, PE},
title = {Microbial succession from nursery to vineyard highlights the role of beneficial and pathogenic microbes in young vineyard yield.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00905-8},
pmid = {42083054},
issn = {2524-6372},
abstract = {BACKGROUND: The grapevine microbiome plays a central role in shaping vineyard performance, yet the influence of nursery inherited microbes on vineyard establishment and early productivity remains poorly understood. Our goals were to study the endosphere and rhizosphere microbiome succession as grapevine transition from nursery to vineyard and determine in what capacity the endogenous microbiome from the nursery shapes vineyard outcomes.

RESULTS: We profiled, using amplicon-based sequencing, the fungal and bacterial communities across five bio-compartments (scion graft union, rootstock graft union, crown, roots, and rhizosphere) from two sets of grafted vines (Cabernet Sauvignon and Chardonnay grafted on 1103P rootstock) originating from two nurseries and followed their succession over three years after planting in a commercial vineyard. Nurseries produced vines with distinct endospheric microbiomes that converged overtime but that remained significantly different after three years. Microbial turnover occurred at a much faster pace in belowground (root and rhizosphere) compared to trunk compartments post-planting, with 15% of the initial microbes persisting in three-year-old vineyard. The fungal pathobiome partially inherited from nurseries and associated with vascular diseases of the trunk and root was also clearly distinct after three years. Yet, we did not observe typical disease symptoms development or vine death as we would expect, likely because vines were not under stress during the experimental timeframe. Vineyard yield was highly variable among clonal vines, and statistical modeling revealed that a narrow subset of amplicon sequence variants (ASVs) explained a large portion of this variance. Regression models using the top ten high-impact ASVs accounted for 51% and 60% of yield variation in trunk and belowground compartments, respectively. Notably, 16 of the 19 yield-associated ASVs originated from nurseries, underscoring the long-term influence of nursery-derived microbes on vineyard success.

CONCLUSION: These findings highlight the dual role of beneficial and pathogenic nursery microbiota in shaping grapevine performance. It also suggests that the nursery life stage could be leveraged to engineer the grapevine microbiome and improve vineyard resilience.},
}

@article {pmid42083059,
year = {2026},
author = {Diop, K and Benlaïfaoui, M and Hunter, S and Méndez-Salazar, EO and Hakozaki, T and Richard, C and Prifti, DK and Kourtian, S and Proulx-Rocray, F and Naimi, S and Ponce, M and Messaoudene, M and Cauchois, F and Belkaid, W and Bataille, V and Lee, K and Mihalcioiu, C and Watson, IR and Elkrief, A and Routy, B},
title = {Metagenomics and culturomics reveal the dual role of the gut microbiome in the development of immune-related toxicities and the efficacy of immune checkpoint inhibitors in cancer.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02419-4},
pmid = {42083059},
issn = {2049-2618},
support = {284894//Fonds de recherche du Québec/ ; },
abstract = {BACKGROUND: Despite their major impact on cancer treatment, immune checkpoint inhibitors (ICI) are frequently associated with immune-related adverse events (irAE). Growing evidence suggests that the occurrence of irAE may be correlated with enhanced ICI efficacy, although the underlying mechanisms remain unknown. Most studies investigating the role of the gut microbiome in oncology have relied on sequencing approaches, particularly shotgun metagenomics. Although microbiome profiling revealed strong associations between specific bacterial taxa and clinical outcomes, it has limitations, including an inability to detect low-abundance bacteria and to recover live cultivable bacteria. To overcome these limitations, we combined shotgun metagenomics and culturomics on fecal samples collected from patients with melanoma and non-small cell lung cancer (NSCLC), at baseline and at the onset of immune related (ir)-colitis.

RESULTS: We first validated across three independent cohorts of 589 patients with melanoma or NSCLC treated with ICI that grade ≥ 2 irAE were associated with significantly longer overall survival (OS) and progression-free survival (PFS). Complementary analysis using shotgun metagenomics and culturomics revealed that patients who developed grade ≥ 2 irAE had a lower alpha diversity compared to those who did not develop grade ≥ 2 irAE. Metagenomics results showed enrichment of Ruminococcus gnavus and Streptococcus vestibularis at baseline in grade ≥ 2 irAE patients, while Clostridium paraputrificum and Streptococcus spp. were isolated by culturomics from baseline stool samples from ir-colitis patients. Longitudinal analysis of paired stool samples revealed a shift in microbiome composition with enrichment of Paraclostridium bifermentans and Clostridium paraputrificum, lower lipopolysaccharide and higher flagellin concentrations at baseline compared with the time of ir-colitis. Fecal microbiome transplantation from a patient with ir-colitis into mice induced surrogate markers of colonic inflammation and enhanced the anti-tumor activity of combined anti-PD-1/CTLA-4. P. bifermentans isolated from this patient sample demonstrated direct epithelial barrier disruption in Caco-2 monolayers, characterized by decreased ZO-1 and Occludin immunofluorescence signal and increased TNF-α and IL-1β expression. Moreover, in the dextran sodium sulfate (DSS) colitis model, P. bifermentans worsened weight loss. In a separate tumor model, it amplified the anti-tumor effect of dual ICI. This beneficial effect was also maintained after treatment with P. bifermentans < 3 kDa filtered supernatant.

CONCLUSION: Altogether, our results suggest that P. bifermentans promotes subclinical colitis while increasing the efficacy of dual ICI. This provides a potential microbiome-derived link between irAE and improved anti-tumor responses. Video Abstract.},
}

@article {pmid42083117,
year = {2026},
author = {Helliwell, JA and Sciberras, P and Dosis, A and Burke, J and Chilton, CH and Wood, HM and Jayne, DG},
title = {Modulation of the gut microbiota as a novel strategy to prevent anastomotic leak after colorectal surgery: Systematic scoping review.},
journal = {Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland},
volume = {28},
number = {5},
pages = {e70472},
pmid = {42083117},
issn = {1463-1318},
mesh = {Humans ; *Anastomotic Leak/prevention & control/microbiology ; *Gastrointestinal Microbiome/physiology/drug effects ; Probiotics/therapeutic use ; *Colorectal Surgery/adverse effects ; Fecal Microbiota Transplantation ; Animals ; Female ; Male ; },
abstract = {BACKGROUND: Anastomotic leak (AL) remains a major source of morbidity following colorectal surgery. Increasing evidence implicates the gut microbiome in the pathogenesis of AL, with certain microbial species disrupting tissue repair through collagen degradation. Perioperative modulation of the microbiome may offer a novel strategy to improve anastomotic healing. This scoping review aimed to map available evidence on microbiome-targeted interventions, synthesise mechanistic insights, and identify translation gaps in relation to anastomotic outcomes.

METHODS: A systematic scoping review was performed. MEDLINE, Embase and Cochrane Central Registry of Controlled Trials databases were searched from database inception to 5th August 2025. Studies were eligible if they investigated perioperative interventions that modulated the gut microbiome and evaluated anastomotic healing or leak rates. Both clinical and preclinical studies were included. A narrative synthesis was performed by charting key findings.

RESULTS: Of 4209 records screened, 27 studies met the inclusion criteria: 9 clinical and 18 preclinical. Interventions included bowel preparation, probiotics, synbiotics, arginine/omega-3 supplementation, dietary modification, faecal microbiota transplantation (FMT), phosphate, tranexamic acid, morphine and infliximab. Among clinical studies, only oral antibiotics combined with mechanical bowel preparation were associated with a significant reduction in leak rates. Preclinical studies showed interventions such as high-fibre diets, FMT, rectal tranexamic acid and phosphate supplementation improved anastomotic healing via enhanced microbial diversity, suppression of pathogenic organisms, or inhibition of collagenolytic activity.

CONCLUSION: This review highlights a range of microbiome-targeted interventions with potential to reduce AL. While clinical evidence remains limited, several preclinical strategies demonstrate promise and warrant evaluation in early-phase human trials.},
}

Humans
*Anastomotic Leak/prevention & control/microbiology
*Gastrointestinal Microbiome/physiology/drug effects
Probiotics/therapeutic use
*Colorectal Surgery/adverse effects
Fecal Microbiota Transplantation
Animals
Female
Male

@article {pmid42083126,
year = {2026},
author = {Wu, F and Zhang, M and Wu, J and Wang, Z and Ma, Y and Dong, L and Cheng, L and Ji, T and Zheng, C and Ren, F and Fang, B},
title = {Aged Gut Microbiota Induces Mucosal Transcriptional Dysregulation, Impairing Immune Surveillance.},
journal = {Aging cell},
volume = {25},
number = {5},
pages = {e70533},
pmid = {42083126},
issn = {1474-9726},
support = {20240484606//Beijing Nova Program/ ; 241110110200//the Key Project of Henan Science and Technology Research and Development Plan/ ; FFHCI-2025061//the Cross-Innovation Open Project of Food Flavor and Health, Beijing Technology & Business University/ ; //the 2115 Talent Development Program of China Agricultural University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/immunology/genetics ; Mice ; *Intestinal Mucosa/immunology/microbiology/metabolism ; *Aging/immunology ; Mice, Inbred C57BL ; *Immunologic Surveillance ; Male ; },
abstract = {Aging is associated with systemic immune remodeling and disease susceptibility, but its impact on intestinal mucosal immunity, particularly changes in M cells, remains largely unknown. This study aimed to investigate how aging alters intestinal mucosal immune phenotypes, specifically follicle-associated epithelial cells (FAE) and the gut microbiota, and to identify interconnected pathways that may be exploited to maintain intestinal immune function in the elderly. Using intestinal tissue from young and aged mice, this study assessed manifestations of intestinal epithelial aging, changes in immune cells in the lamina propria, and microbial composition. Aging was associated with increased expression of senescence-associated secretory phenotype (SASP) markers (IL-1β, TNF-α, p16) and decreased levels of tight junction proteins (Occludin, Tricellulin), suggesting epithelial barrier dysfunction. Aged mice exhibited decreased Naïve Th cells, increased Effector Th and Th17 subsets, and decreased fecal IgA. Microbiome analysis revealed enrichment of inflammatory bacteria, such as Desulfovibrio and Candidatus_Saccharimonas, and elevated dysbiosis indices. RNA sequencing of FAEs revealed 578 differentially expressed genes, including downregulation of Gp2 and Ccl28, indicating impaired M cell function. Association analysis between microbiome changes and mucosal immune aging revealed that enrichment of key inflammatory bacteria may contribute to impaired M cell function and dysregulated intestinal mucosal immunity. These findings reveal a multi-layered disruption of intestinal homeostasis during aging-comprising barrier function, immune imbalance, FAEs dysfunction, and shifts in specific microbial taxa -leading to increased susceptibility to pathogens. Targeting these age-related pathways may provide strategies for maintaining intestinal immunity in the elderly.},
}

Animals
*Gastrointestinal Microbiome/immunology/genetics
Mice
*Intestinal Mucosa/immunology/microbiology/metabolism
*Aging/immunology
Mice, Inbred C57BL
*Immunologic Surveillance
Male

@article {pmid42083308,
year = {2026},
author = {Thakur, BK and Choudhury, SR and Turpin, W and Martin, A},
title = {Gut microbiota and diet in colorectal cancer: Converging determinants of carcinogenesis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2664684},
doi = {10.1080/19490976.2026.2664684},
pmid = {42083308},
issn = {1949-0984},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/etiology/pathology/prevention & control ; *Diet/adverse effects ; *Carcinogenesis ; *Gastrointestinal Microbiome ; Animals ; *Gastrointestinal Tract/microbiology ; *Bacteria/metabolism/genetics/classification ; },
abstract = {Diet and the gut microbiome are major, interdependent determinants of colorectal cancer (CRC) risk. This review discusses current evidence on how dietary patterns reshape microbial ecology, modulate microbial virulence, and alter host metabolic, inflammatory, and oncogenic pathways to influence colorectal carcinogenesis. We highlight key CRC-associated microbes, including pks[+] Escherichia coli, Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and Streptococcus gallolyticus, and discuss how diet governs their abundance, toxin production, and oncogenic potential. Mechanistic investigations into diet-microbe interactions reveal how pro-inflammatory, low-fiber Western-style diets foster mucosal inflammation, generation of reactive oxygen and nitrogen species, and genotoxic microbial niches, whereas fiber- and polyphenol-rich diets support protective commensals and production of anti-inflammatory metabolites. We also outline major challenges, including interindividual microbiome variability and limited translational models, and propose future directions for integrating dietary, microbial, and host-targeted strategies for CRC prevention and therapy.},
}

Humans
*Colorectal Neoplasms/microbiology/etiology/pathology/prevention & control
*Diet/adverse effects
*Carcinogenesis
*Gastrointestinal Microbiome
Animals
*Gastrointestinal Tract/microbiology
*Bacteria/metabolism/genetics/classification

@article {pmid41851157,
year = {2026},
author = {Serventi, L and Huang, C and Hofmann, R},
title = {Exploring pea soaking water as alternative to synthetic fertilizer: growth and microbial analysis of pea and tomato plants.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41851157},
issn = {2045-2322},
abstract = {Synthetic fertilizers deplete soil microbiome. Organic fertilizers lack specific nutrients for plant growth. A fertilizer that delivers essential nutrients to plants without deteriorating soil is lacking. This study investigated the viability of using pea soaking water (PSW) as substitute for synthetic fertilizers to enhance the growth of pea and tomato plants. Traits included plant growth stages, shoot and root weight, estimated chlorophyll content, and soil microbial populations. Pea plants exhibited consistent growth stages and rates of development across treatments, whereas tomato plants displayed treatment-dependent growth variations and differences in rates of development. Synthetic fertilizer (NPK) and PSW treatments increased shoot weight and chlorophyll content in both pea and tomato plants, compared with their controls. Interestingly, PSW produced comparable shoot growth to synthetic fertilizer in both crops. Root weights were similar in response to both fertilizer treatments in tomato but only increased in response to synthetic fertilizer in pea plants. Soil microbial analysis highlighted differences in Lactobacillus amount with soil supporting pea plants having higher bacteria counts. Notably, Lactobacillus amounts were reduced by 48% in the synthetic fertilizer treatment, but not by PSW, compared with the control, for tomatoes only. These findings suggest that PSW is a potential alternative to synthetic fertilizer to sustainably support plant growth. Replacement of synthetic fertilizer with PSW could reduce the environmental impact of agriculture by promoting healthy soil microbiota and preventing eutrophication, as well as reducing reliance on fertilizers. Further research is needed to explore its effect on crop yield, and applicability across crop species, field, and environmental conditions.},
}

@article {pmid41851187,
year = {2026},
author = {Su, X and Jin, J and Huang, Y and Hou, H and Li, Z and Cao, C and Wang, X and Li, F and Deng, Z and Zhang, M},
title = {Tumor-suppressing multi-enterobacteria enhance the anti-PD-1/PD-L1 efficacy in microsatellite stable colorectal cancer.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41851187},
issn = {2045-2322},
support = {Y-HR2019-0295//Beijing Xisike Clinical Oncology Research Foundation/ ; 2024AFD426//Joint Fund Project for Innovation and Development of Hubei Provincial Natural Science Foundation/ ; },
abstract = {UNLABELLED: Gut microbiome plays a pivotal role in modulating immunotherapy responses in colorectal cancer (CRC) treatment. While individual enterobacteria have been identified as enhancers of anti-PD-1/anti-PD-L1 therapy, the synergistic effects of multiple probiotic strains remain insufficiently explored. In this study, we investigated the therapeutic potential of Tumor-Suppressing Multi-Enterobacteria (TSME), a consortium of nine beneficial intestinal probiotic strains, in enhancing anti-PD-1/anti-PD-L1 therapy for microsatellite stable (MSS) CRC. Using a tumor-bearing mouse and employing techniques including flow cytometry, immunohistochemistry, ELISA, and genomic sequencing, we found that TSME significantly improved the efficacy of immune checkpoint inhibitors (ICIs) by optimizing tumor immune and microbe microenvironment. Specifically, the addition of TSME increased CD8[+] T cell infiltration and reshaped cytokine profiles, including reducing pro-inflammatory cytokines (IL-17, IL-1β, IL-6, and TNF-α) while elevating anti-inflammatory factors (IFN-γ). Moreover, TSME significantly up-regulated key immune pathways, including TNF signaling, cytokine-cytokine receptor interaction, and JAK-STAT signaling. In addition, TSME restructured the gut microbiome, increasing the abundance of beneficial bacteria such as Akkermansia and Alistipes. These findings highlight the synergistic effect of the multi-strain probiotics in enhancing ICI efficacy. Well-formulated probiotic consortia offer a promising strategy for enhancing immunotherapy outcomes in MSS CRC and advancing broader implementation of microbiome-assisted precision oncology.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-44494-5.},
}

@article {pmid41877288,
year = {2026},
author = {Wei, G and Liu, M and Huang, L and Chen, C},
title = {Metagenomic sequencing reveals the dynamic changes of pig gut fungal composition following the ages and identifies fungal species associated with diarrhea in piglets.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41877288},
issn = {2524-4671},
support = {32272831//National Natural Science Foundation of China/ ; },
abstract = {UNLABELLED: Fungi are crucial components of the pig gut microbiome, influencing host immunity and metabolism. However, the investigation about gut fungi via metagenomic sequencing remains challenging due to analytical complexity. Here, we characterized pig gut fungal profiles using 750 metagenomes collected from public repositories and our previous datasets based on a comprehensive collection of fungal reference genomes, and revealed dynamic compositional changes of pig gut fungi from birth to market (7d, 14d, 21d, 28d, 35d, 70d, and 140d). Weaning significantly shaped the gut fungal community, affecting key fungi like Lachancea kluyveri and Kazachstania slooffiae. Inter-kingdom interaction analysis revealed significant correlations between fungi and bacteria, such as between L. kluyveri and Lactobacillus amylovorus (r = -0.48) and between K. slooffiae and Lactobacillus johnsonii (r = 0.75). We identified 87 diarrhea-associated fungal species at the significance threshold of LDA > 2.0 in three experimental piglet cohorts. In antibiotic-free piglets, fungal species from Saccharomyces and Aspergillus, some of which have been considered as potential probiotics, were enriched in healthy individuals, whereas in antibiotic-treated groups, Saccharomyces spp. and K. slooffiae were higher in diarrheal piglets. Notably, K. slooffiae were negatively correlated with the pathogen M. circinelloides, suggesting a protective role during gut dysbiosis. This study provides a foundation for developing fungal-based interventions to improve pig health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00551-y.},
}

@article {pmid42071032,
year = {2026},
author = {Wang, H and Wang, F and Guo, Q and Zou, B and Li, P and Xu, X and He, J and Jiang, S and Yue, J},
title = {Dynamic changes in gut microbiota and discovery of prognostic biomarkers in locally advanced pancreatic cancer during chemoradiotherapy.},
journal = {Clinical and experimental medicine},
volume = {26},
number = {1},
pages = {},
pmid = {42071032},
issn = {1591-9528},
support = {82272753//National Natural Science Foundation of China/ ; ZF004//Collaborative Academic Innovation Project of Shandong Cancer Hospital/ ; },
abstract = {UNLABELLED: Pancreatic cancer has an exceptionally poor prognosis, with the majority of cases diagnosed at an advanced stage. Concurrent chemoradiotherapy (CCRT) remains the standard of care for locally advanced pancreatic cancer (LAPC); however, its therapeutic efficacy is limited. Emerging evidence suggests that the gut microbiota is an important modulator of cancer progression and treatment response. Nevertheless, the dynamic changes in the gut microbial ecosystem in LAPC patients undergoing CCRT remain poorly understood. This study aimed to characterize longitudinal alterations in the gut microbiota during CCRT, identify candidate microbiome-based prognostic markers, and explore their potential associations with host responses. This longitudinal study included 16 patients with LAPC. Fecal and peripheral blood samples were collected at three predefined time points: before CCRT initiation, during CCRT, and after CCRT completion. Gut microbiota composition and community structure were analyzed using 16 S rRNA sequencing targeting the V3–V4 region. Bioinformatic analyses were performed to assess taxonomic distribution, alpha and beta diversity, and microbial co-occurrence patterns. The prognostic relevance of microbial features was further evaluated using machine learning models integrating clinical parameters to predict overall survival. CCRT was associated with dynamic changes in specific microbial taxa across multiple taxonomic levels, with marked inter-individual heterogeneity in microbiota responses. In addition, microbial co-occurrence network complexity was reduced during treatment. Certain microbial taxa during CCRT showed associations with tumor-related serum biomarkers. Using integrated machine learning models, we identified candidate microbiota-based prognostic markers. In particular, Bifidobacterium and Bacteroides were associated with survival prediction, achieving areas under the receiver operating characteristic curve (AUC) of 0.833 and 0.722, respectively. CCRT is associated with longitudinal alterations in the gut microbiome of patients with LAPC, involving both compositional and structural changes. These findings suggest that microbiome dynamics may have potential value as exploratory prognostic indicators. However, given the limited sample size and observational design, further validation in larger cohorts and mechanistic studies are required before clinical application.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10238-026-02158-8.},
}

@article {pmid42075347,
year = {2026},
author = {Núñez-Muñoz, LA and Vargas-Hernández, BY and García-Sierra, MC and Calderón-Pérez, B and Xoconostle-Cázares, B and Ruiz-Medrano, R},
title = {Bacterial and Fungal Communities Associated with the Ectomycorrhizospheric Soil and Stem Endosphere of the Mycoheterotrophic Plant Monotropa uniflora.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081145},
pmid = {42075347},
issn = {2223-7747},
support = {CBF-2025-3383//Secretaría de Ciencia Tecnología e Innovación/ ; CF-2023-G-731//Secretaría de Ciencia Tecnología e Innovación/ ; },
abstract = {The mycoheterotrophic plant Monotropa uniflora relies on fungal symbionts for carbon and nutrient acquisition. However, its interactions with other microbial groups, beyond ectomycorrhizal fungi, remain unexplored. Here, we characterized bacterial and fungal communities associated with M. uniflora across two compartments: ectomycorrhizospheric soil linked to the mycorrhizal network and the surface-sterilized lower stem endosphere. Microbial community composition was assessed using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. Fungal richness was consistently higher in ectomycorrhizospheric soil than in the stem endosphere, whereas bacterial alpha diversity showed no consistent differences between compartments. Multivariate analyses suggested compartment-associated patterns in both bacterial and fungal community composition. Ectomycorrhizospheric soil was dominated by saprotrophic fungal taxa and bacterial groups with predicted metabolic potential, including taxa associated with iron, sulfur and nitrogen cycling. In contrast, the lower stem endosphere was enriched in bacterial taxa commonly associated with anaerobic and nitrogen-related metabolisms. Functional predictions further suggested an increase of carbon fixation-related pathways in rhizosphere-associated bacterial communities. Together, these results indicate that M. uniflora is associated with distinct and structured microbial assemblages across soil and internal plant compartments, highlighting the predicted functional potential of bacterial communities in nutrient- and carbon-related processes in mycoheterotrophic plant-soil systems alongside fungal partners.},
}

@article {pmid42075353,
year = {2026},
author = {Aleynova, OA and Ananev, AA and Nityagovsky, NN and Suprun, AR and Beresh, AA and Dubrovina, AS and Kiselev, KV},
title = {Ability of Different Bacteria from Grapevine to Colonize Arabidopsis thaliana Plants.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081151},
pmid = {42075353},
issn = {2223-7747},
support = {22-74-10001-П//the Russian Science Foundation/ ; },
abstract = {This study investigates the impact of inoculating seeds with bacterial endophytes isolated from Vitis amurensis Rupr. on endophytic community composition in Arabidopsis thaliana (L.) Heynh. Ten bacterial isolates of the genera Agrobacterium, Bacillus, Curtobacterium, Erwinia, Frondihabitans, Gordonia, Pantoea, Pseudomonas, Sphingomonas, and Xanthomonas were applied to seeds and some visible phenotypic effects were observed on plant growth after two weeks. High-throughput sequencing of 16S rRNA revealed that the native endophytic microbiome of A. thaliana was dominated by Gammaproteobacteria, Actinomycetes, Bacteroidia, and Alphaproteobacteria. The key families were Microscillaceae, Chitinophagaceae, Rhizobiaceae, Rhodanobacteraceae, Nocardioi-daceae, Nocardiaceae, Xanthomonadaceae, Devosiaceae, Microbacteriaceae, Crocinitomi-caceae, Pseudomonadaceae, Solimonadaceae, Comamonadaceae, Caulobacteraceae, and Micrococcaceae. Arabidopsis seed inoculation with Agrobacterium sp. R8SCh-B12, Curtobacterium sp. P7SA-B3, and Gordonia aichiensis P6PL2 significantly reduced alpha diversity (Shannon index) and altered beta diversity relative to controls, indicating strong community restructuring. These three isolates, along with Pseudomonas sp. R8SCh-B2, Sphingomonas sp. RA62c-B5, Xanthomonas sp. R7SCh-B6, and Bacillus velezensis AMR25, successfully colonized the plant tissues, as evidenced by significant increases in genus-specific amplicon sequence variants, ASVs (up to 17,820-fold for Curtobacterium sp. ASV33). In contrast, Pantoea sp. P7SCH-B5, Erwinia sp. R8SCh-B3, and Frondihabitans sp. RA62c-B2 failed to colonize A. thaliana, despite being applied to the seeds, suggesting the existence of mechanisms restraining colonization. These findings demonstrate that only a subset of grapevine-derived endophytes can effectively colonize A. thaliana, and that successful colonization correlates with significant shifts in the native microbiome, even in the absence of overt phenotypic changes. This emphasizes the importance of strain-specific compatibility in plant-endophyte interactions. Thus, we report the first descriptions of several novel endophytes that colonized Arabidopsis plants and establish a convenient model to investigate plant-bacterial interactions.},
}

@article {pmid42075357,
year = {2026},
author = {Sun, C and Ge, Z and Yang, X and Xie, X and Liang, X and Shen, L and Ren, J and Zhang, Y},
title = {Silicon Combined with Activated Carbon Enhances Salt Tolerance in Strawberry (Fragaria × ananassa) by Reinforcing Ion-Redox Homeostasis and Reshaping the Rhizosphere Microbiome.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081154},
pmid = {42075357},
issn = {2223-7747},
support = {2021C02066-7//Crop New Variety Breeding of Zhejiang Province/ ; SY202304//the Local Science and Technology Cooperation Project of Zhejiang Academy of Agricultural Sciences/ ; 2025SNJF029//the Zhejiang "Sannong Jiufang" Science and Technology Collaboration Program/ ; 2023Z112//the Ningbo Municipal Major Special Project/ ; },
abstract = {Soil salinity severely constrains strawberry production by disrupting ion homeostasis and provoking oxidative injury. This study investigated whether soluble silicon (Si) and activated carbon (AC) act to enhance salt tolerance in strawberry (Fragaria × ananassa). Under NaCl stress, plants showed pronounced growth inhibition, increased Na[+] accumulation and a deteriorated K[+]/Na[+] balance, accompanied by elevated reactive oxygen species (ROS) and lipid peroxidation. In contrast, combined AC + Si treatment consistently provided the strongest protection, improving seedling vigor and survival. Relative to NaCl alone, AC + Si increased shoot and root fresh weight by 67.5% and 78.5%, reduced shoot Na[+] by 59.1%, and lowered shoot H2O2 and MDA by 62.6% and 66.5%, respectively, indicating marked improvement in ion-redox homeostasis. Beyond plant responses, AC-containing treatments alleviated salt-induced increases in soil electrical conductivity, coinciding with a clear restructuring of the rhizosphere bacterial community and enrichment of putatively beneficial taxa. Transcriptome profiling further supported coordinated reprogramming of ion transport, redox control and stress-responsive signaling pathways under the AC + Si regime. Collectively, the results indicated that Si and AC co-application enhances strawberry salt tolerance through an integrated soil-plant-microbiome mechanism that stabilizes ion homeostasis and reinforces redox homeostasis.},
}

@article {pmid42075461,
year = {2026},
author = {Rueda Foronda, JA and Ríos López, JS and Múnera Porras, LM and Pino Rodriguez, NJ},
title = {Climate Variability Under ENSO Reshapes the Coffea arabica Rhizosphere Microbiome While Preserving a Conserved Bacterial Core.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081259},
pmid = {42075461},
issn = {2223-7747},
support = {202143210//Universidad de Antioquia/ ; },
abstract = {Climate variability is a major driver of belowground microbial assembly, yet its effects on rhizosphere microbiomes in perennial crops remain insufficiently resolved. We investigated how macroclimatic oscillations associated with the El Niño-Southern Oscillation (ENSO) influence bacterial communities in the rhizosphere of Coffea arabica. Using 16S rRNA amplicon sequencing across five sampling campaigns covering El Niño, La Niña, and Neutral phases in the Colombian Andes, together with multivariate and variance-partitioning analyses, we quantified the relative contributions of climatic and edaphic factors to rhizosphere community structure. PERMANOVA across three dissimilarity metrics showed that the ENSO explained 11-17% of β-diversity, exceeding the contribution of intra-annual seasonality (6-12%). Ordination analyses indicated moderate compositional differentiation with considerable overlap among ENSO groups, consistent with gradual community turnover under contrasting hydroclimatic conditions. Rainfall and soil pH emerged as the main edaphic correlates of community composition, although their independent effects were no longer significant after accounting for the ENSO phase and season. Despite these shifts, the rhizosphere remained dominated by Acidobacteriota, Actinobacteriota, and Proteobacteria, and a prevalence-defined core microbiome (genera detected in ≥85% of samples) was maintained across climatic phases and seasons. These results indicate that, within the explained fraction of variation, macroclimatic variability contributed more to rhizosphere bacterial turnover than local edaphic heterogeneity, while a conserved prevalence-defined bacterial core may contribute to taxonomic stability in climate-sensitive coffee systems.},
}

@article {pmid42075467,
year = {2026},
author = {Tiwari, P and Park, KI},
title = {Plant-Associated Microbiomes: Crosstalk and Engineering to Improve Nutrient Use Efficiency (NUE) in Crops of Global Importance.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081265},
pmid = {42075467},
issn = {2223-7747},
abstract = {Global climate change is rapid and poses an alarming threat to agricultural production, significantly impacting economies. Modern agriculture has strongly emphasized improving nutrient availability in crops to address rising malnutrition and contribute to global food security. However, abiotic stresses, including warmer temperatures, drought, waterlogging stress, and elevated CO2, have critical direct and indirect effects on nutrient availability in plants. This systematic review was conducted in accordance with the PRISMA guidelines. The literature survey followed a time period of 2-5 months, during which the conceptualization, analysis, writing, and editing of the article were conducted. In the present era, it is essential to adopt measures to improve the nutritional value [enhance Nutrient Use Efficiency (NUE)] and nutrient management of plant-based foods. Plant-associated microbiomes have co-evolved with their plant counterparts and perform essential functions in nutrient acquisition, including microbial sensing and cross-talk with the plant host, nutrient uptake and sharing, and signaling mechanisms. In natural and agricultural ecosystems, plant microbiomes offer major opportunities and can be harnessed to sustainably supply essential plant nutrients and improve NUE in crops of global importance. Crop-associated microbiomes can be precisely tailored to achieve targeted outcomes, enhancing nutrient acquisition and utilization via microbiome engineering. However, bridging knowledge gaps, understanding microbial colonization, plant-microbiome dynamics, and adopting precise editing approaches are crucial to boost sustainable outcomes and crop productivity. By elucidating plant microbiome crosstalk and microbe-microbe signaling, a better understanding of microbe-mediated nutrient acquisition in plants can be achieved, defining key implications in global food security.},
}

@article {pmid42075560,
year = {2026},
author = {Cho, WS and Thillaichidambaram, M and Jeon, S and Kim, GR and Lee, SU and Lee, SH and Kim, YJ and Lee, ES and Kim, Y and Kang, D and Kim, SY},
title = {Lung Microbiome Dysbiosis in Pulmonary Fibrosis Induced by Multi-Walled Carbon Nanotubes and Bleomycin in Rats.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {4},
pages = {},
doi = {10.3390/medicina62040688},
pmid = {42075560},
issn = {1648-9144},
support = {This study was supported by the 2023 overseas training grant from Pusan National University Yangsan Hospital.//Pusan National University Yangsan Hospital./ ; },
mesh = {Animals ; *Pulmonary Fibrosis/microbiology/chemically induced/physiopathology/etiology ; *Bleomycin/adverse effects ; Rats, Wistar ; Rats ; *Dysbiosis/microbiology/etiology/physiopathology ; *Nanotubes, Carbon/adverse effects ; Female ; *Microbiota/drug effects ; *Lung/microbiology/physiopathology ; Bronchoalveolar Lavage Fluid/microbiology ; Disease Models, Animal ; RNA, Ribosomal, 16S ; },
abstract = {Background and objectives: Occupational and environmental inhalation exposures, including high-aspect-ratio carbon nanotubes, can trigger pulmonary fibrosis (PF). The relationship between exposure-specific fibrogenic pathways (granulomatous inflammation versus diffuse epithelial injury) and lung microbiome dysbiosis remains incompletely understood. We therefore compared lung microbiome alterations in rat PF models induced by multi-walled carbon nanotubes (MWCNTs) and bleomycin. Materials and Methods: Female Wistar rats received a single intratracheal instillation of vehicle, MWCNTs (750 μg/rat), or bleomycin (1 mg/rat). At day 28, fibrosis and inflammation were evaluated by histopathology and bronchoalveolar lavage fluid (BALF) profiling. Lung microbial communities were characterized by 16S rRNA gene sequencing (V3-V4). Seventeen lung samples passed stringent quality control and were analyzed (control n = 5; bleomycin n = 7; MWCNT n = 5). Results: Both agents induced PF with increased profibrotic signaling, but with distinct pathological signatures: MWCNTs produced localized granulomatous lesions and a robust neutrophilic response (25% of BALF cells), whereas bleomycin caused diffuse interstitial remodeling. Bleomycin increased microbial richness (alpha diversity; p < 0.05) and significantly shifted community structure (beta diversity; p < 0.05), while MWCNT exposure showed comparatively limited changes in global diversity. The relative abundance of Pseudogracilibacillus (including P. marinus) was higher in the bleomycin group than in controls, whereas Facklamia tabacinasalis and Corynebacterium maris were more abundant in the MWCNT group. Across samples, Proteobacteria abundance was inversely correlated with BALF TGF-β, MCP-1, and neutrophil proportion. At the species level, Pseudogracilibacillus marinus was positively correlated with BALF TGF-β, while Facklamia tabacinasalis and Corynebacterium maris were positively correlated with MCP-1, CINC-3, and neutrophil proportion (Spearman; p < 0.05). Conclusions: Mechanistically distinct fibrogenic exposures generate exposure-linked lung microbiome signatures that track with host inflammatory and profibrotic responses. These signatures may support biomarker development for environmentally and occupationally relevant PF and motivate longitudinal and functional studies to clarify causality.},
}

Animals
*Pulmonary Fibrosis/microbiology/chemically induced/physiopathology/etiology
*Bleomycin/adverse effects
Rats, Wistar
Rats
*Dysbiosis/microbiology/etiology/physiopathology
*Nanotubes, Carbon/adverse effects
Female
*Microbiota/drug effects
*Lung/microbiology/physiopathology
Bronchoalveolar Lavage Fluid/microbiology
Disease Models, Animal
RNA, Ribosomal, 16S

@article {pmid42075665,
year = {2026},
author = {Cazacu, SM and Streba, CT and Constantin, C and Ionele, CM and Rogoveanu, I and Popescu, AV and Florescu, MM},
title = {The Overlap Between Crohn's Disease and Intestinal Tuberculosis: A Never-Ending Story.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {4},
pages = {},
doi = {10.3390/medicina62040794},
pmid = {42075665},
issn = {1648-9144},
mesh = {Humans ; *Crohn Disease/diagnosis/physiopathology ; *Tuberculosis, Gastrointestinal/diagnosis/physiopathology ; Diagnosis, Differential ; },
abstract = {The prevalence of Crohn's disease has increased over the last few decades, even in developing countries, whereas that of intestinal tuberculosis has decreased, which places both diseases at an epidemiological crossroads. Crohn's disease and intestinal tuberculosis share many clinical, endoscopic, imaging, and pathological features, which sometimes make differential diagnosis very difficult; an accurate diagnosis is, however, very important since an erroneous treatment can worsen the evolution or delay proper therapy. The association between past TB infection and Crohn's disease can make the diagnosis especially hard. This review summarizes current data on specific features that allow differentiation between Crohn's disease and intestinal tuberculosis, paying particular attention to the microbiome, clinical signs, endoscopy, cross-sectional imaging, bacteriological, and immunological findings detailed. The importance of computerized models and scores for the differentiation is also detailed, because common features may make the differentiation based on a single criterion difficult.},
}

Humans
*Crohn Disease/diagnosis/physiopathology
*Tuberculosis, Gastrointestinal/diagnosis/physiopathology
Diagnosis, Differential

@article {pmid42075741,
year = {2026},
author = {Raut, N and Chaudhary, AA and Patil, H and Shidhaye, S and Khobragade, R and Umekar, M and Ali, MAM and Trivedi, R},
title = {Antimicrobial Consumption and Resistance Dynamics Across Healthcare Level: Global Evidence and Stewardship Implications.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/pathogens15040414},
pmid = {42075741},
issn = {2076-0817},
support = {DDRSP-2601//Imam Mohammad ibn Saud Islamic University/ ; },
mesh = {Humans ; *Antimicrobial Stewardship ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Drug Resistance, Bacterial ; Global Health ; Delivery of Health Care ; },
abstract = {BACKGROUND/OBJECTIVES: Antimicrobial resistance (AMR) is a critical global public health challenge driven by inappropriate and excessive antimicrobial use (AMU) across human, animal, and environmental sectors.

METHOD: This narrative review synthesizes recent evidence on antimicrobial utilization and resistance patterns. A structured search of PubMed, Scopus, and Web of Science was conducted for studies published between 2015 and 2025. Eligible sources included surveillance reports, registry-based analyses, and clinical studies. Data were qualitatively analyzed to identify key trends and regional variations.

RESULT: Marked geographical variation in AMR was observed. Carbapenem resistance in Escherichia coli remains low globally (2-3%) but is higher in Southeast Asia (17-18%) and India (~40%). Klebsiella pneumoniae shows consistently high resistance (>40% globally; ~54% in India), while Pseudomonas aeruginosa exhibits stable resistance levels (35-45%). Resistance prevalence increases from primary to tertiary care settings, reflecting greater antimicrobial exposure. Vulnerable populations-including pediatric, elderly, pregnant, and immunocompromised patients-face higher risks of antimicrobial exposure and adverse outcomes, including nephrotoxicity, hepatotoxicity, and microbiome disruption. WHO AWaRe data indicate a global shift toward increased use of Watch-category antibiotics. Stewardship interventions, such as audit and feedback, prescribing restrictions, rapid diagnostics, and decision support systems, effectively reduce inappropriate AMU.

CONCLUSIONS: Integrated, data-driven antimicrobial stewardship and robust surveillance systems are essential to mitigate the global burden of AMR.},
}

Humans
*Antimicrobial Stewardship
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Drug Resistance, Bacterial
Global Health
Delivery of Health Care

@article {pmid42075766,
year = {2026},
author = {Piloto-Sardiñas, E and Rodríguez, I and Santos, HA and Paulino, PG and Corona-González, B and Cabezas-Cruz, A},
title = {Ecological Frameworks of Pathogen-Pathogen and Pathogen-Microbiome Interactions Within the Tick Holobiont.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/pathogens15040440},
pmid = {42075766},
issn = {2076-0817},
mesh = {Animals ; *Ticks/microbiology ; *Microbiota ; *Host-Pathogen Interactions ; Symbiosis ; *Tick-Borne Diseases/microbiology ; },
abstract = {Ticks harbor complex microbial communities composed of symbionts, commensals, and tick-borne pathogens (TBPs). Together, these microorganisms form the tick holobiont. Within this system, the tick's physiological architecture structures microbial communities by distributing microorganisms across distinct tissues. This compartmentalization creates spatially distinct ecological niches, which in turn shape how microbial communities assemble and interact. In this review, we integrate ecological theory with current knowledge of tick microbiome research to examine how pathogen-pathogen and pathogen-microbiome interactions emerge within these tissue-structured microbial communities. We first outline how baseline ecological filters, including tick species, developmental stage, tissue identity, vertical transmission, and environmental context, shape the microbiome configuration through community assembly processes. We then examined how TBPs, as high-impact colonizers, can further modify microbial networks by altering host-mediated selective pressures, influencing interaction topology, and reshaping community stability. Based on these observations, we propose a dual selective pressure framework in which (i) baseline ecological structuring processes and (ii) pathogen-associated selective pressures interact to determine the microbial network configuration and functional outcomes within the tick holobiont. These interacting forces may drive shifts in diversity, modularity, keystone taxa emergence, and network resilience, ultimately influencing vector competence. This review frames the microbial communities within the tick holobiont as spatially structured ecological systems shaped by multilevel selective pressures. This conceptual foundation provides a coherent framework for understanding microbial interactions in arthropod vectors and highlights avenues for mechanistic research and microbiome-based strategies to mitigate tick-borne diseases.},
}

Animals
*Ticks/microbiology
*Microbiota
*Host-Pathogen Interactions
Symbiosis
*Tick-Borne Diseases/microbiology

@article {pmid42075777,
year = {2026},
author = {Lagos, I and Pérez de Arce, E and Faggiani, I and D'Amico, F and Zilli, A and Furfaro, F and Massironi, S and Cicerone, C and Solitano, V and Parigi, TL and Peyrin-Biroulet, L and Danese, S and Allocca, M},
title = {The Role of Microbiota and Fecal Transplantation in Inflammatory Bowel Disease.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/pathogens15040451},
pmid = {42075777},
issn = {2076-0817},
mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/therapy/microbiology ; Crohn Disease/therapy/microbiology ; Colitis, Ulcerative/therapy/microbiology ; Feces/microbiology ; Treatment Outcome ; },
abstract = {Inflammatory bowel diseases (IBDs), including ulcerative colitis (UC) and Crohn's disease (CD), are consistently associated with alterations in gut microbial communities, although the extent and characteristics of these alterations vary across studies, supporting a potential role of the microbiota in disease pathogenesis and therapeutic modulation. We conducted a systematic review to synthesize current evidence on microbiota alterations in IBD and the clinical application of fecal microbiota transplantation (FMT). A total of 118 studies were included (76 focused on microbiota profiling and 42 evaluated FMT as therapy). Across heterogeneous study designs and microbial characterization methods, reduced microbial diversity was the most consistently reported alteration, generally more pronounced in CD than in UC. Depletion of Faecalibacterium prausnitzii-a key butyrate producer with anti-inflammatory properties-was commonly reported, often accompanied by functional impairment in short-chain fatty acid production. Microbial patterns were frequently associated with mucosal inflammation and varied across disease phenotypes; these patterns have been increasingly explored as predictors of treatment response and relapse, although mechanistic interpretation remains limited and causal relationships are difficult to establish. Evidence from randomized controlled trials suggests potential efficacy of FMT in UC, particularly with intensive or repeated protocols, whereas data in CD remain limited and heterogeneous, with signals of benefit often appearing transient. FMT was generally well tolerated, but long-term safety data remain scarce. Emerging multi-omic approaches are reshaping the field by integrating taxonomic and functional insights, with potential implications for risk stratification, diagnosis, prognosis, and therapeutic optimization. Further standardized, longitudinal, and mechanistically oriented studies are required to translate microbiome research into clinically actionable strategies in IBD.},
}

*Fecal Microbiota Transplantation/methods
Humans
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/therapy/microbiology
Crohn Disease/therapy/microbiology
Colitis, Ulcerative/therapy/microbiology
Feces/microbiology
Treatment Outcome

@article {pmid42075987,
year = {2026},
author = {Choińska, R and Nasiłowska, J and Wojtczak, A and Lewandowski, W and Świsłocka, R},
title = {Isoxanthohumol and Its Derivatives: Antioxidant Activity and Effects on the Gut Microbiota.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {8},
pages = {},
doi = {10.3390/molecules31081311},
pmid = {42075987},
issn = {1420-3049},
support = {2020/39/B/NZ9/01894//National Science Centre/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; *Xanthones/pharmacology/chemistry ; Humans ; *Antioxidants/pharmacology/chemistry ; Humulus/chemistry ; Animals ; Flavonoids/pharmacology/chemistry ; Propiophenones/chemistry/pharmacology ; Flavanones/chemistry/pharmacology/metabolism ; },
abstract = {Isoxanthohumol (IX) is a prenylated flavonoid derived from hop cones (Humulus lupulus) that is gaining increasing recognition for its potential biological effects. Despite numerous studies on its precursor, xanthohumol, studies on IX remain limited. Of particular interest is its metabolism, particularly its biotransformation by gut microbiota to 8-prenylnaringenin (8-PN), a potent phytoestrogen, which indicates the complex nature of its biological activity and potential health implications. This review summarizes the current state of knowledge on IX and its derivatives, covering their microbial metabolism, their impact on the gut microbiome, and the metabolic consequences of this conversion. Furthermore, it examines the relationship between the molecular structure of IX and its derivatives and their biological activity, highlighting existing research gaps and the need for further research on the safety and therapeutic potential of these compounds.},
}

*Gastrointestinal Microbiome/drug effects
*Xanthones/pharmacology/chemistry
Humans
*Antioxidants/pharmacology/chemistry
Humulus/chemistry
Animals
Flavonoids/pharmacology/chemistry
Propiophenones/chemistry/pharmacology
Flavanones/chemistry/pharmacology/metabolism

@article {pmid42076028,
year = {2026},
author = {Karczmarzyk, A and Wojcieszyńska, D and Nowak, A and Smułek, W and Guzik, U},
title = {Berberine Toxicity Profile in Experimental Models as a Basis for Assessing Its Biological Safety.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {8},
pages = {},
doi = {10.3390/molecules31081350},
pmid = {42076028},
issn = {1420-3049},
mesh = {*Berberine/toxicity/pharmacology ; Oxidative Stress/drug effects ; Animals ; },
abstract = {Berberine, a natural alkaloid, is a substance widely used in natural medicine. However, there is a significant knowledge gap regarding the potential negative effects of higher environmental concentrations of berberine resulting from its use as a supplement. Therefore, the aim of this study was to assess its toxicity towards microorganisms and organisms from various trophic levels. The results indicate that berberine may influence the reorganization of bacterial membranes, thereby negatively impacting the environmental microbiome. However, oxidative cell damage, a phenomenon commonly described in the literature, was not demonstrated. At the concentrations used, berberine may even have a protective effect. The analysis of toxicity towards Tetrahymena, Selenastrum, and Heterocypris indicated a similar level of berberine toxicity across these organisms, suggesting that the toxic effect is not species-dependent and that the mechanism of toxicity is probably based on universal cellular mechanisms.},
}

*Berberine/toxicity/pharmacology
Oxidative Stress/drug effects
Animals

@article {pmid42076046,
year = {2026},
author = {Toydemir, S and Merey, G},
title = {Biochemistry of Human Gut Microbiota: Related Diseases and Dietary Interactions.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {8},
pages = {},
doi = {10.3390/molecules31081369},
pmid = {42076046},
issn = {1420-3049},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology/metabolism ; *Diet ; Inflammatory Bowel Diseases/microbiology/metabolism ; Obesity/microbiology/metabolism ; },
abstract = {The human gut microbiota represents a complex and dynamic ecosystem of trillions of microorganisms that play a fundamental role in maintaining physiological homeostasis, regulating metabolism, and modulating the immune system. This narrative review explores the biochemical intricacies of the gut microbiome, focusing on the dominant phyla (Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, Fusobacteria) and their specific contributions to host health. A critical emphasis is placed on the metabolic outputs of these microorganisms, such as short-chain fatty acids (SCFAs) like butyrate, which serve as vital energy sources and anti-inflammatory signaling molecules. Conversely, the review examines how dysbiosis, the disruption of microbial balance, is mechanistically linked to the pathogenesis of diverse conditions, including obesity, diabetes mellitus, inflammatory bowel disease (IBD), and gout. Furthermore, it highlights the profound impact of dietary interventions on microbial architecture, notably, how non-digestible carbohydrates promote beneficial taxa and eubiosis, while high-fat and high-sugar diets drive metabolic endotoxemia and systemic inflammation. By synthesizing current knowledge on microbial biotransformations of proteins and polyphenols, this work underscores the bidirectional relationship between nutrition and the microbiome. Ultimately, understanding these biochemical interactions is essential for developing targeted probiotic, prebiotic, and nutritional strategies to prevent and manage chronic metabolic and inflammatory disorders.},
}

Humans
*Gastrointestinal Microbiome/physiology
Dysbiosis/microbiology/metabolism
*Diet
Inflammatory Bowel Diseases/microbiology/metabolism
Obesity/microbiology/metabolism

@article {pmid42076109,
year = {2026},
author = {Bharadwaj, R and Gaspar, C and Moeller, TD and Ward, D and Klempner, MS and Wang, Y and Cavacini, LA},
title = {Impact of Oral Pre-Exposure Secretory IgA Prophylactic Produced in Rice on Gut Microbiome Homeostasis.},
journal = {Pharmaceutics},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/pharmaceutics18040457},
pmid = {42076109},
issn = {1999-4923},
support = {MT21010.006//Naval Medical Research Command's Naval Advanced Medical Development Program/ ; W81XWH-21-2-0018//Combat Readiness - Medical Research Program/ ; INV-010709/GATES/Gates Foundation/United States ; },
abstract = {Background/Objectives: Enterotoxigenic Escherichia coli (ETEC) is a leading cause of diarrheal illness worldwide, resulting in approximately 380,000 deaths annually, with significant morbidity in children and travelers to endemic regions. ETEC infection begins with the attachment of the bacterium to the small intestine via filamentous colonization factors (CF), followed by the production of heat-labile (LT) and heat-stable (ST) toxins that induce watery diarrhea. Targeting CF to prevent ETEC attachment is challenging due to strain heterogeneity. Methods: In previous studies, we developed a class-switched human monoclonal antibody, 68-90, expressed as secretory IgA (SIgA) in rice for cost-effective and stable storage. Rice-produced SIgA exhibited comparable binding efficiency to CfaE, a component of CF, compared to CHO-produced SIgA in vitro. Results: In this work, we showed that oral administration of 68-90 SIgA to Aotus nancymaae did not alter gut microbiome distribution or show signs of systemic exposure. Conclusions: These findings suggest that oral delivery of ETEC-specific SIgA is safe and does not disrupt the gut microbial population, highlighting its potential as an effective and targeted therapeutic strategy.},
}

@article {pmid42076694,
year = {2026},
author = {Sahatsanon, K and Chaweewan, K and Sringarm, K and Arjin, C and Hnokaew, P and Satsook, A and Saman, P and Kim, HW and Patthararangsarith, P and Busayakanit, P and Adeyemi, KD and Sivapirunthep, P and Chaosap, C},
title = {Effects of Host-Specific Multi-Lactic Acid Bacterial Probiotics on Performance, Carcass Traits, Meat Quality, and Gut Microbiome in Fattening Pigs.},
journal = {Veterinary sciences},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/vetsci13040322},
pmid = {42076694},
issn = {2306-7381},
support = {KDS 2022/010//King Mongkut's Institute of Technology Ladkrabang/ ; No. 65-17 Sub Project No. 1//Thailand Institute of Scientific and Technological Research/ ; },
abstract = {This study evaluated the effects of a host-specific multi-lactic acid bacterial (MLAB) probiotic and sex on performance, carcass traits, meat quality, and gut microbiota in fattening pigs. Thirty-two crossbred pigs (10 ± 0.80 weeks; 23.43 ± 0.17 kg) were assigned to a 2 × 2 factorial design with diet (control or MLAB probiotics) and sex (barrow or female). The MLAB supplement consisted of seven lactic acid bacterial strains mixed in equal proportions (≈14.3% each)-Lactobacillus brevis, Lactobacillus reuteri, Weissella cibaria, Lactobacillus paraplantarum, Lactococcus lactis, Lactobacillus pentosus, and Pediococcus pentosaceus-administered at 1 × 10[9] CFU/kg feed for 12 weeks. MLAB probiotic supplementation reduced bone proportion while increasing skin and fat content (p < 0.05), with a treatment × sex interaction for loin eye area (p < 0.05). Meat quality improved in the MLAB group, showing higher ultimate pH and lower cooking loss (p < 0.05), indicating improved water-holding capacity. Female pigs exhibited higher early postmortem pH and protein content (p < 0.05). Microbiome analysis revealed increased abundances of Oxalobacteraceae and Paludibacteraceae and reduced Clostridium sensu stricto 6 (p < 0.05). These results suggest that host-adapted probiotics may support gut microbial balance and improve certain pork quality traits.},
}

@article {pmid42076708,
year = {2026},
author = {Yu, J and Dou, Z and Wang, C and Zhou, S and Shi, H and Zhang, H and Wang, H and Ma, N and Shen, X and Chang, G},
title = {Yeast Culture Enhances Production Performance in Late-Lactation Dairy Cows by Reshaping Rumen Microbiota and Metabolic Pathways.},
journal = {Veterinary sciences},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/vetsci13040336},
pmid = {42076708},
issn = {2306-7381},
support = {2022AAC02072//Natural Science Foundation of Ningxia Hui Autonomous Region/ ; KYT2023004//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Yeast culture (YC), a complex functional feed additive containing fermentation metabolites, has demonstrated potential in dairy production systems. However, its mechanistic effects on rumen function and host metabolism in lactating dairy cattle warrant further investigation. This study evaluated the impacts of YC supplementation on production performance, systemic antioxidant status, and rumen function in late-lactation Holstein cows. Fourteen multiparous Holstein cows (body weight 655 ± 28 kg; days in milk 270.4 ± 1.6 d) were randomly allocated into two groups, a control group (CON, basal diet) and a YC-supplemented group (YC, basal diet + 50 g/d YC), in a 28-day feeding trial. YC supplementation significantly increased dry matter intake (p < 0.01), nutrient digestibility (p < 0.01 for DM, CP, EE, NDF, and ADF), and milk yield (p < 0.05) compared to CON. Systemic antioxidant capacity was enhanced, as evidenced by elevated serum superoxide dismutase activity (p < 0.01) and total antioxidant capacity (p < 0.05). Rumen fermentation was improved with higher concentrations of total volatile fatty acids (p < 0.01) and microbial protein (p < 0.01) and reduced ammonia nitrogen levels (p < 0.01). Macrogenomic analysis revealed a YC-mediated restructuring of the rumen microbiota, characterized by an increased relative abundance of Firmicutes and decreased Bacteroidota. Untargeted metabolomic profiling identified significant alterations in rumen metabolite profiles, with differential metabolites enriched in pyrimidine metabolism and vitamin digestion and absorption pathways. These results indicate that YC supplementation improves production performance in late-lactation dairy cows through multi-faceted mechanisms involving rumen microbial community modulation and metabolic pathway activation, ultimately enhancing nutrient utilization and metabolic efficiency.},
}

@article {pmid42076832,
year = {2026},
author = {Carracedo Lorenzo, Z and Rizaludin, MS and Wang, J and Berdaguer, R and Brito-López, C and Sánchez-Arcos, C and Garbeva, P and Pieterse, CMJ and Dicke, M and Testerink, C and Kloth, KJ and Karlova, R},
title = {Pseudomonas volatiles shape the root transcriptome and microbiome to promote plant growth under drought.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71203},
pmid = {42076832},
issn = {1469-8137},
support = {024.004.014//NWO Dutch Research Council (NWO/OCW)/ ; },
abstract = {Volatile organic compounds (VOCs) emitted by soil bacteria influence interactions with other soil microbes and plants. While their potential as plant growth promoters is well recognized, their role in promoting plant resilience to abiotic stress and the underlying molecular mechanisms remain poorly understood. Here, we investigate the role of Pseudomonas VOCs in enhancing plant resilience to drought stress Arabidopsis seedlings were exposed to VOCs emitted by Pseudomonas strains under control and osmotic stress conditions. Plant biomass and root architecture were evaluated. Root transcriptomics analysis was performed and validated using Arabidopsis mutants and metabolomics. Volatile organic compounds effects were also tested on soil-grown Brassica oleracea and on its rhizosphere microbiome. Pseudomonas VOCs promoted plant growth under both axenic and soil conditions in A. thaliana and in B. oleracea, and under control and drought conditions. Transcriptomics, metabolomics, and functional analysis revealed interactions between Pseudomonas VOCs, glucosinolates, and ABA signalling, as well as a positive association between VOC exposure and coumarin biosynthesis. VOC treatment also reshaped the rhizosphere microbiome under drought, leading to a community composition more similar to that of well-watered plants. Overall, Pseudomonas VOCs promote plant growth under drought conditions, linked to root transcriptional reprogramming and direct or indirect microbiome modulation.},
}

@article {pmid42076857,
year = {2026},
author = {Yang, Z and Zhou, W and Chen, P and Dai, Z and Feng, G and Limpens, E and Zhang, L},
title = {Phosphorus fertilizer forms orchestrate contrasting plant-microbe recruitment strategies in the rhizosphere of field grown wheat.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71231},
pmid = {42076857},
issn = {1469-8137},
support = {ZR2021MC042//Natural Science Foundation of Shandong Province/ ; 2024YFE0105000//National Key Research and Development Program of China/ ; PC2024B02003//Pinduoduo-China Agricultural University Research Fund/ ; 32130094//National Natural Science Foundation of China/ ; 42277112//National Natural Science Foundation of China/ ; },
abstract = {Plants engage in intricate interactions with rhizosphere microbes. These interactions are crucial for plant nutrient acquisition and productivity, but the mechanisms by which different nutrient forms shape rhizosphere microbes to enhance nutrient utilization under field conditions remain unclear. We investigated the rhizosphere bacterial communities of wheat and their functions across key growth stages in response to different phosphorus (P) fertilizer forms in a 4-yr field experiment, integrating 16S rRNA gene sequencing, metatranscriptomic sequencing, and soil chemical analyses. In the field, the three P fertilizer forms showed comparable P use efficiency (PUE) over 4 years. At the three-leaf stage, insoluble P fertilizer increased root-associated citrate concentrations, enriched carboxylate-associated bacteria (e.g. Bacillus, Solirubrobacter, and Nitrospira), and resulted in higher transcript abundance of genes involved in citrate metabolism and P acquisition. Polymeric P fertilizer enhanced soil phosphatase activity, increased root-associated succinate concentrations, and had higher transcript abundance of genes involved in succinate metabolism and complex polysaccharide degradation. Soluble P fertilizer increased soil available P and enriched Devosia, favored glycoprotein degradation, while showing a limited response to P mobilization processes. This study suggests that, under field conditions, different P fertilizer forms shape distinct rhizosphere bacterial communities to improve PUE by altering root-associated carboxylate release.},
}

@article {pmid42076882,
year = {2026},
author = {Hayashi, I and Sánchez-Pinillos, M and Toju, H},
title = {Stochastic Forces in Microbial Community Assembly: Founding Community Size Governs Divergent Ecological Trajectories.},
journal = {Ecology letters},
volume = {29},
number = {5},
pages = {e70388},
doi = {10.1111/ele.70388},
pmid = {42076882},
issn = {1461-0248},
support = {202302//Kyoto University CeLiSIS Program (23CeLiSIS-02)/ ; JPMJCR23N5//Core Research for Evolutional Science and Technology/ ; 24KJ1454//Japan Society for the Promotion of Science/ ; 202302//New Energy and Industrial Technology Development Organization/ ; JPMJFR2048//Fusion Oriented REsearch for disruptive Science and Technology/ ; },
mesh = {Stochastic Processes ; *Microbiota ; Ecosystem ; },
abstract = {Biological community dynamics arise from both deterministic and stochastic processes. While species' responses to environmental factors define attractors of community structure, stochasticity, particularly during early assembly, can redirect ecological trajectories. However, quantifying such roles of stochasticity in community assembly has remained challenging. We tracked community assembly in two multi-replicated experimental systems, each with four levels of founding community size, analysing > 3000 samples across four time points. Stronger initial stochasticity led to greater divergence of both population- and community-level consequences. Strikingly, conspicuous differentiation into alternative trajectories of community assembly occurred when the absolute number of founding prokaryotic cells was less than the order of 10[4]. Thus, quantitative differences in stochasticity produced qualitative differences in community fate. These results demonstrate that early stochastic events can have enduring impacts on ecological dynamics. Deeper quantitative insights into stochasticity will reorganise our views on biological invasions, agroecosystem microbiome management, and therapeutics of human-associated microbiomes.},
}

Stochastic Processes
*Microbiota
Ecosystem

@article {pmid42077003,
year = {2026},
author = {Bukovac, J and Husain, M and Sapper, T and O'Dell, A and Bittoni, M and Gastier, H and Chebbi, A and Hockenhull, V and Dohar, Z and Moon, J and Tabung, F and Verschraegen, C and Wu, R and Kendra, K and Yang, Y and Volek, J and Spakowicz, D},
title = {How the Ketogenic Diet Shapes the Microbiome to Influence Cancer Immunotherapy Outcomes: An Exploration of Clinical Trials and Their Results.},
journal = {Nutrition and cancer},
volume = {},
number = {},
pages = {1-30},
doi = {10.1080/01635581.2026.2658807},
pmid = {42077003},
issn = {1532-7914},
abstract = {Ketogenic dietary interventions (KDIs) are increasingly explored as adjuncts in oncology due to their metabolic and immunomodulatory effects. One mechanism by which KDIs are expected to modulate the immune system is by altering the gut microbiome, which has been shown to affect treatment outcomes, particularly in the context of immunotherapies. This review synthesized findings from 43 clinical trials to evaluate the current landscape of KDIs in cancer care, with a focus on the gut microbiota and immunotherapy. Although 47% of identified trials are completed, none have yet published results combining KDIs with immunotherapy. Since 2020, however, there has been a significant increase in ongoing studies investigating this combination and incorporating microbiome endpoints. While KDIs may help shape an immunotherapy-permissive environment, further clinical evaluation is necessary to determine the full extent of KDIs on the microbiome. Future research should prioritize longitudinal microbiome profiling and standardized adherence reporting to clarify the therapeutic potential of KDIs as a metabolic adjuvant to immune checkpoint inhibitors.},
}

@article {pmid42077151,
year = {2026},
author = {Horner, KM and Corish, CA and Quinn, AM},
title = {Addressing Undernutrition in Older Adults with Plant-Based Products.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-31},
doi = {10.1017/S0029665126103000},
pmid = {42077151},
issn = {1475-2719},
abstract = {The aim of this review is to provide an overview of the evidence to date and several key considerations regarding addressing undernutrition in older adults with plant-based products. Undernutrition, resulting from inadequate protein and energy intake is common among older adults, and is associated with poor health and quality of life. Ensuring adequate protein and energy intake is a key component of strategies aiming to prevent and/or treat undernutrition. Increasing diversity of protein intake to include more sustainable plant-based sources is encouraged in the general population. However, to support healthy ageing, it is important to consider factors such as the impact of greater consumption of plant-based products on appetite and nutritional status, muscle protein synthesis and skeletal muscle mass. Although the literature in older adults is limited, the current evidence suggests no significant differences when comparing effects of plant to animal-based products/diets on a range of outcomes including appetite, nutritional status, longer-term muscle protein synthesis and muscle mass. Furthermore, there is evidence of improvements in nutritional status and muscle protein synthesis following plant protein supplementation compared to before supplementation or lower protein intakes. Therefore, greater intake of certain plant-based products could assist in enhancing sustainability of food systems and meeting nutritional requirements to prevent undernutrition. Among other factors, the plant protein source, the food matrix and presence of other nutrients need consideration. Further studies are needed in several areas, including investigating the effects of greater intake of plant-based products on the gut microbiome, and in the treatment of undernutrition.},
}

@article {pmid42077290,
year = {2026},
author = {Logan, AC and Mishra, P and Berryessa, CM and Caruso, GD and Hagenbeek, FA and Denson, TF and Robinson, JM and Prescott, SL},
title = {Challenging the prescientific frameworks of criminal justice: neurobiology and criminolytic interventions in the legalome era.},
journal = {Frontiers in psychology},
volume = {17},
number = {},
pages = {1791262},
pmid = {42077290},
issn = {1664-1078},
abstract = {Contemporary systems of criminal justice are rooted in prescientific folk psychology assumptions related to moral fiber, free will, agency, and near-universal levels of willpower. For instance, people often believe that morally "defective" people make voluntary choices, failing to utilize their own self-control capacities. Given the wide acceptance of such beliefs, they are considered "normative" within law, serving to underpin retributive punishment. However, rapid advances in biological sciences-aided by multi-omics technologies-have illuminated the ways in which brain architecture and current metabolic conditions can constrain agency and shape here-and-now decision-making. Here in this perspective article, we examine how these advances are placing the prescientific foundations of criminal justice systems under duress. Older single-gene and single neuroimage attempts at explaining criminal behavior are giving way to the legalome era. This describes a more holistic epoch in which the simultaneous integration of mass biological data (e.g., polygenetic, metabolic, microbiome, metabolomic, lipidomic, and other omics-derived information) can provide explanatory power to criminal behavior and vulnerability, and guide personalized approaches to prevention and treatment. Advances in behavioral epigenetics are revealing how genetic predispositions interact with the exposome to shape human behavior through dynamic, potentially modifiable mechanisms. Moreover, evidence suggests that the human microbiome acts as a dynamic interface between environment and brain, influencing behavior in ways that are relevant to vulnerability, impulse control, and decision-making. Promising criminolytic interventions range from nutritional and pharmaceutical approaches to cognitive-behavioral therapy and contemplative practices. The integration of biological evidence and science education, along with ethically guided neurointerventions, will be critical to more humane systems of judgement.},
}

@article {pmid42077435,
year = {2026},
author = {DiTulio, M and Navarro-Torres, CA},
title = {Clearance of multiple antibiotic-resistant coagulase-negative staphylococci is selectively associated with higher circulating α-melanocyte stimulating hormone in patients evaluated for chronic inflammatory response syndrome.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1728408},
pmid = {42077435},
issn = {1664-2392},
mesh = {Humans ; *alpha-MSH/blood ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Staphylococcus/drug effects/isolation & purification ; Adult ; Biomarkers/blood ; *Staphylococcal Infections/blood/microbiology ; Coagulase/metabolism ; Aged ; Matrix Metalloproteinase 9/blood ; Anti-Bacterial Agents/therapeutic use ; Vasoactive Intestinal Peptide/blood ; Chronic Disease ; Drug Resistance, Bacterial ; },
abstract = {INTRODUCTION: Neuroimmune regulatory peptides play central roles in coordinating inflammatory, metabolic, and mucosal immune processes in humans. Among these, α-melanocyte stimulating hormone (α-MSH), a proopiomelanocortin-derived peptide, has been implicated in modulation of cytokine signaling, epithelial barrier function, and pain processing. However, determinants of circulating α-MSH levels in chronic inflammatory states remain incompletely characterized in human clinical populations. Persistent sinonasal colonization with multiple antibiotic-resistant coagulase-negative staphylococci (MARCoNS) has been reported in some cohorts presenting with environmentally associated multisystem illness, described in some clinical settings as Chronic Inflammatory Response Syndrome (CIRS). Yet its relationship to systemic neuroendocrine biomarkers has not been quantitatively examined.

METHODS: This retrospective observational cohort study examined whether follow-up MARCoNS culture status was associated with longitudinal trajectories of α-MSH, compared with two additional biomarkers commonly assessed in this population: matrix metallopeptidase-9 (MMP-9) and vasoactive intestinal polypeptide (VIP). A total of 188 adult patients evaluated within a CIRS-informed clinical framework at a single clinical site were included. Each participant contributed two timepoints of laboratory data for α-MSH, MMP-9, and VIP, along with MARCoNS culture results.

RESULTS: Across the full cohort, α-MSH increased by an estimated 10 pg/mL, MMP-9 decreased by 398 ng/mL, and VIP increased by 20 pg/mL between baseline and follow-up. Mixed-effects modeling revealed a significant timepoint-by-MARCoNS interaction for α-MSH, such that patients who were MARCoNS-negative at follow-up exhibited higher circulating α-MSH levels compared with those who remained positive. In contrast, no corresponding MARCoNS interaction was observed for VIP or MMP-9.

DISCUSSION: These findings provide quantitative evidence that follow-up MARCoNS culture status is selectively associated with α-MSH trajectories in this retrospective cohort, supporting further prospective investigation into potential links between persistent bacterial nasal colonization and neuroendocrine-immune biomarkers in multisystem chronic illness.},
}

Humans
*alpha-MSH/blood
Male
Female
Retrospective Studies
Middle Aged
*Staphylococcus/drug effects/isolation & purification
Adult
Biomarkers/blood
*Staphylococcal Infections/blood/microbiology
Coagulase/metabolism
Aged
Matrix Metalloproteinase 9/blood
Anti-Bacterial Agents/therapeutic use
Vasoactive Intestinal Peptide/blood
Chronic Disease
Drug Resistance, Bacterial

@article {pmid42077489,
year = {2026},
author = {Islam, MZ and Pitta, DW and Niu, M},
title = {Breed-specific microbiomes drive differential responses to 3-nitrooxypropanol and Acacia mearnsii in dairy cows.},
journal = {JDS communications},
volume = {7},
number = {3},
pages = {332-338},
pmid = {42077489},
issn = {2666-9102},
abstract = {Methane (CH4) inhibitor 3-nitrooxypropanol (3-NOP) shows variable efficacy in Brown Swiss (BS) and Holstein (HF) cows, but the underlying mechanisms remain unclear. Rumination bolus, a proxy for rumen microbiota, combined with exhalomics (analysis of exhaled volatiles), offered a noninvasive approach to differentiate breed responses to CH4 mitigation strategies. We investigated whether differences in rumination bolus microbiota and exhaled VFA (eVFA) between BS and HF cows contribute to their responses to 3-NOP. Sixteen multiparous cows (8 BS, 8 HF) were studied in a replicated 4 × 4 Latin square design with a 2 × 2 factorial arrangement of 3-NOP (0 or 60 mg/kg of DM) and Acacia mearnsii tannin extract (TAN; 0% or 3% of DM). Rumination bolus samples collected 6 h postfeeding during the fourth period of the experiment were sequenced for full-length 16S rRNA sequences (PacBio Revio platform) to assess bacterial diversity, while exhaled samples from all 4 periods were analyzed for VFA using secondary electrospray ionization-MS. Microbial community shifts were analyzed using Bray-Curtis, unweighted, and weighted unique fraction metric (UniFrac) distances. Spearman correlations were performed between genus-level information and eVFA, CH4, hydrogen (H2), carbon dioxide (CO2), DMI, and milk yield between breeds. Supplementation of 3-NOP induced a modest but consistent shift in microbial composition, whereas TAN effects were minimal and inconsistent. Breed-specific differences were evident: BS harbored more Prevotella and Rikenellaceae, and HF were enriched in Succinivibrionaceae and Acetitomaculum. Under 3-NOP, HF genera aligned more strongly with propionate-producing pathways and showed stronger negative correlations with CH4, and BS genera remained more associated with acetate and butyrate proportions. Correlations with feed intake and milk yield were generally weak and inconsistent across genera. Overall, our results indicate that HF cows are more responsive to 3-NOP, likely redirecting spared H2 toward propionate-producing bacteria, and BS are more resilient to H2 fluxes and consequently less responsive to 3-NOP. Findings from this pilot study highlight the importance of host-microbiome interactions in evaluating and implementing enteric CH4 mitigation strategies in dairy cattle.},
}

@article {pmid42077491,
year = {2026},
author = {Navarro Marcos, C and de Evan, T and Gonzalez Recio, Ó and Gutiérrez Rivas, M and Dolores Carro, M},
title = {Effects of feeding agroindustrial byproducts on rumen fermentation and microbiome of sheep.},
journal = {JDS communications},
volume = {7},
number = {3},
pages = {315-320},
pmid = {42077491},
issn = {2666-9102},
abstract = {The use of agroindustrial byproducts in ruminant nutrition is gaining increased attention because of economic and environmental benefits and their potential to enhance ruminal function and animal performance. However, the effect of these byproducts on ruminal microbiome and fermentation has been scarcely investigated. This study aimed to evaluate the effects of replacing conventional feeds with agroindustrial byproducts (18:18:8 mixture of corn dried distillers grains with solubles, dry citrus pulp, and exhausted olive cake) on the ruminal microbiome and fermentation parameters of sheep. Four rumen-fistulated Lacaune sheep were used in 2 experimental periods, receiving mixed diets composed of 50% alfalfa hay and 50% of either a control concentrate (CON diet) or a concentrate with agroindustrial byproducts (BYP diet). Ruminal samples were collected at 0, 3, and 6 h postfeeding to assess microbial composition and fermentation parameters. Diet significantly influenced the ruminal microbiome, but the effect of individual sheep was more pronounced than that of the diet. Sampling time also influenced the ruminal microbiome. The inclusion of agroindustrial byproducts in the concentrate did not significantly alter ruminal fermentation parameters. However, the BYP diet led to more steady ruminal fermentation, preventing large fluctuations in total VFA and ammonia concentrations, likely the result of a broader range of fermentable substrates present in the BYP concentrate and changes in ruminal microbiome. These results may indicate improved synchronization of nutrient availability for ruminal microorganisms. Overall, replacing conventional feed ingredients with agroindustrial byproducts promoted microbial diversity and improved ruminal fermentation, potentially leading to increased dairy ruminant performance.},
}

@article {pmid42077790,
year = {2026},
author = {Fan, X and Zhou, X and Wang, L and Zhang, X and Shen, Y and Xiao, Y and Wang, H and Deng, L and Xie, Y},
title = {Comparative Analysis of Gut Microbiomes in Parasitic Roundworms Reveals Phylogeny-Associated Community Structure and Functional Adaptation.},
journal = {Transboundary and emerging diseases},
volume = {2026},
number = {},
pages = {2764696},
pmid = {42077790},
issn = {1865-1682},
mesh = {Animals ; *Gastrointestinal Microbiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Toxocara/microbiology ; Female ; Male ; *Ascaris/microbiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Roundworm nematodes are globally distributed zoonotic parasites that inhabit the intestinal tract of various mammals. Although these parasites reside in the host's guts, their own intestinal ecosystems remain poorly understood. Recent evidence suggests that helminths may harbor distinct gut microbiomes that contribute to their physiology and host interactions, yet cross-species comparisons are lacking. Here, we performed full-length 16S rRNA sequencing to characterize and compare the gut microbiomes of four major roundworm species-Ascaris suum (As), Baylisascaris schroederi (Bs), Toxocara cati (Tc), and Toxocara vitulorum (Tv). Across 38 individual worms, we identified 359 bacterial taxa dominated by Enterobacteriaceae, with Escherichia coli, Salmonella enterica, and Klebsiella pneumoniae forming a conserved core community. Despite this compositional similarity, beta-diversity and hierarchical clustering analyses revealed that microbial community structure was primarily determined by parasite phylogeny and roundworm sex, not host diet. Functional prediction using PICRUSt2 indicated clear species-specific enrichment in metabolic pathways, such as carbohydrate metabolism in Bs and xenobiotic metabolism in As, reflecting adaptive divergence of microbial functions. Collectively, these findings demonstrated that roundworm gut microbiomes exhibited taxonomic conservation but functional specialization, shaped by the evolutionary history of the parasites themselves. This study established a conceptual framework viewing the parasite as the primary host of its microbiome and provided new insights into the co-evolutionary relationships between helminths and their symbiotic bacteria.},
}

Animals
*Gastrointestinal Microbiome
Phylogeny
RNA, Ribosomal, 16S/genetics
*Toxocara/microbiology
Female
Male
*Ascaris/microbiology
Bacteria/classification/genetics/isolation & purification

@article {pmid42077846,
year = {2026},
author = {Pinheiro, GL and Lin, NJ and Parratt, KH and Hines, I and Hack, HR and Servetas, SL and Iyer, H and Da Silva, SM},
title = {The Integration of Focused Ultrasonication, ddPCR, and Flow Cytometry Effectively Estimates Genome Copies per Cell and Enhances DNA Extraction Efficiency in Escherichia coli Samples.},
journal = {ACS omega},
volume = {11},
number = {16},
pages = {23885-23899},
pmid = {42077846},
issn = {2470-1343},
abstract = {Microbiology researchers rely on nucleic acid measurement techniques, such as the quantitative polymerase chain reaction (qPCR) and DNA sequencing, to address diverse scientific and practical challenges. These applications range from detecting microbial contaminants in regenerative medicine and biotherapeutic products to advancing waste remediation, pathogen detection, biosurveillance, and microbiome studies. A critical step in these techniques is DNA extraction, which involves breaking cells to release their DNA as the required input for downstream analyses. The efficiency of this process, known as DNA extraction efficiency (DEE), directly impacts the accuracy of quantitative measurements and, therefore, the interpretation of results. Unfortunately, most DNA extraction methods suffer from suboptimal efficiency that varies across microbial strains, potentially leading to inaccurate results. In this paper, we present a highly efficient DNA extraction protocol leveraging adaptive focused acoustics (AFA) technology to achieve a balance between cell lysis and DNA integrity. Using Escherichia coli as the model organism, the protocol delivers nearly 100% DEE, setting a benchmark for performance. A key innovation in this protocol is the integration of focused ultrasonication, droplet digital polymerase chain reaction (ddPCR), and flow cytometry to estimate genome copies and the corrected DNA extraction efficiency (cDEE), which accounts for the number of genome copies. The proposed protocol addresses the need for an accurate assessment of DEE and DNA quantification, as demonstrated here with E. coli, for various DNA-based techniques, including metagenomic analysis of complex microbial communities and the development of new DNA extraction protocols. This novel protocol addresses a longstanding limitation in microbiological research and has the potential to significantly enhance accuracy and reproducibility across various applications. While there is significant potential for applying this approach, the authors acknowledge that further studies using microorganisms with thicker cell walls will enhance the utility of this framework. However, the knowledge generated in this study can be readily applied and tailored to the specific objectives of individual research groups.},
}

@article {pmid42077904,
year = {2026},
author = {Nigam, AK and Falah, K and Momper, JD and Nigam, SK},
title = {Selectivity of OATs and OATPs for Endogenous Metabolites and Signaling Molecules In Vivo.},
journal = {ACS omega},
volume = {11},
number = {16},
pages = {24714-24724},
pmid = {42077904},
issn = {2470-1343},
abstract = {Organic anion transporters (OATs, SLC22) in the kidney and organic anion-transporting polypeptides (OATPs, SLCO) in the liver play crucial roles in the disposition of small molecule drugs that are organic anions. According to the Remote Sensing and Signaling Theory, these multispecific "drug" transporters are also central to crosstalk between the liver, kidney, and other organs via endogenous small molecules (e.g., metabolites, signaling molecules, gut microbiome products). These multispecific drug transporters govern access of small molecules with high informational content across multiple scales (organism to organelle). Previous chemoinformatic and machine learning methods have proven useful for identifying molecular properties of organic anion drugs that predispose them to handling by the OAT (renal) and the OATP (hepatic) transporters. This is important for understanding pharmacokinetics (ADME) in the context of chronic kidney disease (CKD) and liver disease. Given that OATs and OATPs are involved in many metabolic diseases, we sought to determine whether molecular properties could be identified for distinguishing OAT- versus OATP-interacting endogenous metabolites in vivo. This is essential for understanding endogenous small molecule communication between the kidney proximal tubule and hepatocytes in a larger Remote Sensing and Signaling System. We analyzed in vivo metabolomics data from OAT and OATP knockout mice, focusing on endogenous metabolites selective for OATs (e.g., OAT1 or SLC22A6; OAT3 or SLC22A8) vs OATPs (including the locus containing Oatp1b2, the closest homologue of human OATP1B1 or SLCO1B1 and OATP1B3 or SLCO1B3). Applying chemoinformatic methods to a data set of 210 metabolites based on knockout mouse metabolomics (92 OAT-selective, 118 OATP-selective), we identified a set of distinguishing molecular properties (e.g., MolLogP, RingCount, NumRotatableBonds). We then used machine learning approaches (e.g., Random Forest, Naive Bayes, Logistic Regression) to classify OAT vs OATP metabolites, achieving over 75% accuracy. These results support the view that transporter knockout mouse metabolomics can help define selectivity of SLC drug transporters for endogenous metabolites, signaling molecules, antioxidants, nutrients, and gut microbiome products. In the context of the Remote Sensing and Signaling Theory, we discuss the implications for understanding organ crosstalk and interorganismal communication as well as drug disposition, drug-metabolite interactions, and metabolite-based drug design.},
}

@article {pmid42077990,
year = {2026},
author = {Kijpornyongpan, T and Krasaesin, A and Chongcharoenkit, T and Rattanapornsompong, K and Truntipakorn, A and Bhuridej, P and Rodthongkum, N and Cho, SD and Porntaveetus, T},
title = {Microbial signatures of dental caries in the incarcerated elderly: a salivary microbiota study in a restricted environment.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2662787},
pmid = {42077990},
issn = {2000-2297},
abstract = {BACKGROUND: Dental caries is driven by microbial dysbiosis and influenced by diet and lifestyle. Incarcerated populations living under regulated regimens offer a unique model to study the oral microbiota in older adults by minimising environmental confounding variables.

OBJECTIVES: This study aimed to characterise the salivary microbiota of older incarcerated adults and identify bacterial taxa associated with caries status and severity.

DESIGN: Twenty-eight incarcerated men (aged ≥ 50 years) were stratified into caries-active (CA) and caries-free (CF) groups (n = 14 each). The salivary microbiota was profiled using 16S rRNA gene sequencing to assess diversity and differential taxonomic abundance.

RESULTS: CA subjects exhibited higher genus richness and beta-dispersion compared to CF controls. The CF group was enriched with Haemophilus parainfluenzae, Aggregatibacter sp. HMT-949 and Riemerella sp. HMT-322. Conversely, the CA group harboured elevated levels of Dialister invisus, Megasphaera micronuciformis, Prevotella intermedia, Selenomonas sputigena, Capnocytophaga ochracea and Gemella haemolysans. Furthermore, G. haemolysans, Solobacterium moorei and Streptococcus were positively correlated with caries severity, whereas Veillonella rogosae and Streptococcus koreensis and Peptostreptococcusexhibited negative correlation.

CONCLUSION: This study elucidates salivary dysbiotic signatures in older adults within a controlled environment. The identified bacterial profiles provide biomarkers for caries risk, underscoring the need for targeted oral health surveillance and preventative strategies in institutionalised populations.},
}

@article {pmid42078142,
year = {2026},
author = {Fu, M and Kang, Y and Zhou, J and Zhu, L and Wang, W and Lyu, T and Lin, L},
title = {Contrasting elevational patterns of soil and root-associated fungal communities highlight host-driven filtering in Quercus wutaishansea forests.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1825787},
pmid = {42078142},
issn = {1664-462X},
abstract = {The role of plant hosts in shaping root-associated microbial communities remains a central question in ecology, particularly in the face of changing environmental conditions. While considerable attention has been paid to soil microbial diversity, the interactive dynamics between plant individuals and soil microbial pool during root-associated fungi establishment across environmental gradients remain poorly understood. In this study, we explored the elevational variation in the diversity of soil and root-associated fungal communities of Quercus wutaishansea across ten elevational belts (1020 m-1770 m above sea level (asl)) on Dongling Mountain, Beijing, China. We found that root-associated fungal communities exhibited significantly increased alpha diversity with elevation (P < 0.05), whereas soil fungal communities showed no clear elevational trends (P > 0.05). Despite substantial variation in the soil fungal pool, the composition of root-associated fungal communities remained notably stable, suggesting a strong host filtering effect (P < 0.05). Compared with hump-shaped Sim and decreasing Morisita β-diversity of soil fungi as elevation increased (P < 0.05), the β-diversity of root-associated fungi did not exhibit a consistent elevational pattern nor mirror soil fungal β-diversity. These results suggest that, beyond environmental filtering, Q. wutaishansea plays an active role in shaping its root fungal community by selecting compatible fungal partners according to its physiological needs across altitudes. The findings reveal a significant and variable plant selectivity in the recruitment of microbiomes across different elevations, offering novel insights into plant-microbiome interactions within forest ecosystems in response to climate change.},
}

@article {pmid42078328,
year = {2026},
author = {Li, M and Wong, W and Xiong, H and Chen, K},
title = {16S rRNA gene sequencing-based preliminary study on the differences in the microbiota between children with rampant caries and those with arrested caries.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1693174},
pmid = {42078328},
issn = {2673-4842},
abstract = {OBJECTIVE: In clinical practice, arrested caries (AC) poses less harm to children than rampant caries (RC), as the development of caries is arrested. However, there is limited research on the microbiology of the two types of caries. This research study the differences in microbial profiles among AC, caries-free (CF)and RC patients.

METHODS: Thirty-six children aged 3-5 years were selected, grouped into AC, CF, and RC groups, with 12 children in each group. A total of 72 samples, including non-stimulated saliva and dental plaque, were collected. Microbial DNA was extracted, and the V3-V4 region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. Bioinformatics analysis was performed with QIIME2, and taxonomic classification was based on the SILVA database. Alpha and beta diversity were assessed, and the Kruskal-Wallis test (with Benjamini-Hochberg correction) was used to identify taxonomic abundance differences.

RESULTS: The α-diversity in plaque was significantly lower than in saliva. While the salivary microbiome showed minimal variation across different caries states, the plaque microbiome displayed distinct structural differences. At the taxonomic level, Bacteroidota and Prevotella were enriched in the RCP group, while Fusobacteriota and Leptotrichia were more abundant in the ACP and CFP groups, with Corynebacterium being most abundant in the arrested caries group. Differential abundance analysis identified five putative species-level biomarkers associated with specific clinical states in dental plaque.

CONCLUSION: This study suggests that different caries statuses are linked to distinct microbial profiles in dental plaque. The analysis revealed clear differences in microbial community structures across the three clinical groups, highlighting a potential connection between caries activity and plaque dysbiosis.},
}

@article {pmid42078366,
year = {2026},
author = {Sy, M and Ndiaye, T and Thakur, R and Gaye, A and Levine, ZC and Ngom, B and Bellavia, KL and Firer, D and Toure, M and Ndiaye, IM and Diedhiou, Y and Mbaye, AM and Gomis, JF and DeRuff, KC and Deme, AB and Ndiaye, M and Badiane, AS and Paye, MF and Sabeti, PC and Ndiaye, D and Siddle, KJ},
title = {Oral and plasma microbiome in the context of acute febrile illness.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.16.26351042},
pmid = {42078366},
abstract = {Emerging infectious diseases and antimicrobial resistance (AMR) have surfaced as two major public health threats over the past two decades. Consequently, integrative surveillance systems capable of detecting both emerging pathogens and resistance-carrying bacteria are crucial. With advances in next-generation sequencing, simultaneous detection of pathogens and AMR is increasingly feasible. In this study, we used short-read metatranscriptomics complemented by total 16S rRNA metagenomic long-read sequencing to analyze paired oral and plasma samples from a cohort of febrile individuals at two locations in Senegal. Oral microbiomes differed in community composition between locations, and reduced diversity and richness were significantly associated with high fever. We identified at least one known pathogen in 15.33 % (23/150) of samples, with Borrelia crocidurae as the most frequently detected pathogen. We detected both pathogenic and non-pathogenic viruses in oral (10/72) and plasma (09/78) samples. Finally, we observed a high frequency of genes associated with resistance and virulence: 10% of samples expressed at least one AMR gene (ARG), and 24% expressed virulence factor genes. Resistance to widely used beta-lactam antibiotics was the most prevalent. Our findings provide critical data on oral and plasma microbiomes in the context of acute febrile illness in Senegal while expanding understanding of circulating ARGs.},
}

@article {pmid42078518,
year = {2026},
author = {Batistel, F},
title = {Using gnotobiotic ruminants to dissect host-microbe interactions for sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771182},
pmid = {42078518},
issn = {1664-302X},
abstract = {Ruminant animals host one of the most complex gut microbial ecosystems, enabling the conversion of fibrous plant biomass into nutrient-dense foods such as meat and milk, which are essential for global food security. Over time, successive waves of research-from the initial recognition of microbes in the rumen, through anaerobic cultivation, to more recent multi-omics approaches-have progressively expanded our understanding of rumen microbial composition and its links to animal production and greenhouse gas emissions. Despite these advances, most insights into rumen microbial composition and traits of interest are based on associative or correlative evidence, and the host-derived mechanisms that actively shape rumen microbial composition and function remain poorly defined. Early gnotobiotic studies in ruminants demonstrated the value of maintaining animals under defined microbial conditions to dissect host-microbe interactions; however, this experimental capability has largely been lost from contemporary rumen research. This Perspective argues that revisiting gnotobiotic ruminant models is both timely and necessary for establishing causal mechanisms that govern host-microbe interactions in the rumen. Integrating gnotobiotic ruminant models is essential for establishing causal relationships between host biology and rumen microbial composition, thereby providing a foundation for biologically informed strategies that can enhance the sustainability of ruminant production systems.},
}

@article {pmid42078524,
year = {2026},
author = {Najnine, F and Guo, X and Cai, J},
title = {Lactobacillus salivarius GZPH2 reshapes hepatopancreatic microbiome structure and enhances immunometabolism in Litopenaeus vannamei under farm conditions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1762396},
pmid = {42078524},
issn = {1664-302X},
abstract = {INTRODUCTION: The hepatopancreas of Litopenaeus vannamei plays a central role in digestion, metabolism, mineral homeostasis, and immune defense; however, its strain-specific responsiveness to probiotics remains insufficiently characterized. This study aimed to elucidate the comparative effects of a single-strain probiotic (Lactobacillus salivarius GZPH2; HH) and a mixed-strain consortium (EM; TH) on hepatopancreatic function under tropical semi-intensive culture conditions.

METHODS: An integrated multi-omics approach, combining histology, mineral profiling, 16S/18S rRNA sequencing, and 4D data-independent acquisition (4D-DIA) proteomics, was applied to evaluate probiotic-induced changes after 90 days of feeding, with a non-supplemented group (WH) as control.

RESULTS: Both probiotics significantly improved growth, survival, and feed efficiency, increasing biomass by 26-27% relative to the control; however, distinct mechanistic responses were observed. HH enhanced hepatopancreatic regeneration by increasing embryonic (E) and fibrillar (F) cells while reducing blister-like (B) and resorptive (R) cells, alongside greater accumulation of Mg, Fe, Ca, and Se. It also promoted microbial evenness and enriched beneficial Alphaproteobacteria (e.g., Labrenzia, Tropicibacter) and fungal taxa (Candida-Lodderomyces clade). Proteomic analysis revealed upregulation of carbohydrate metabolism, calcium regulation, immune-related proteins, and antioxidant enzymes, including hemocyanin, crustin-like proteins, chitinase, and catalase. In contrast, TH maintained a storage-oriented morphology, exhibited lower mineral deposition and microbial diversity, was dominated by Bacillus, and preferentially enriched proteolytic enzymes and redox-related pathways.

DISCUSSION: These findings demonstrate that the single-strain probiotic GZPH2 induced a more regenerative, metabolically efficient, and immunologically robust hepatopancreatic state than the mixed consortium. These findings provide multi-omics evidence supporting strain-specific probiotic selection as a precision strategy to enhance shrimp health and sustainability in aquaculture.},
}

@article {pmid42078525,
year = {2026},
author = {Brahmbhatt, HD and Chavda, P and Vadee, D and Patel, AK and Bagatharia, S},
title = {Genome characterization and comparative genomics of Limosilactobacillus reuteri HDB isolated from the gut of an Indian infant.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1780782},
pmid = {42078525},
issn = {1664-302X},
abstract = {Limosilactobacillus reuteri, formerly Lactobacillus reuteri, is a rod-shaped, Gram-positive, facultative anaerobe that colonizes the gastrointestinal tract of most vertebrates, including humans. We report the first isolation of L. reuteri strain HDB from the stool of a healthy Indian infant. Species assignment using the Type (Strain) Genome Server (TYGS) placed HDB within the L. reuteri clade, showing closest affinity to L. reuteri subspecies porcinus (dDDH 69.7%) yet clustering phylogenomically with L. reuteri DSM 17938. Hybrid de novo assembly (Illumina + Oxford Nanopore GridION MK1) generated a single circular 2,226,956 bp chromosome (GC 39.04%) encoding 2,160 CDS. Functional annotation identified genes involved in vitamin B12 biosynthesis, reuterin production, and probiotic functions, along with enriched carbohydrate and cofactor metabolic pathways. Comparative analysis with 59 L. reuteri genomes revealed a pangenome of 11,725 gene families, including 944 core gene families, 171 soft-core gene families, 1912 shell gene families, and 8698 cloud gene families, highlighting notable diversity. Core-genome phylogeny aligns HDB closely with the reference strain DSM 17938, confirming its identity as a human-associated lineage. dN/dS analysis indicated strong purifying selection across host niches, with no evidence of widespread positive selection. Genome-scale modeling predicts expanded carbohydrate flux in HDB against global references. The genetic background, along with its conserved metabolic features, suggests that HDB carries genomic characteristics commonly associated with human-derived L. reuteri strains. These observations support its consideration for further evaluation as a regionally sourced probiotic candidate. These conclusions are based on genomic and computational predictions and require experimental validation through adhesion, colonization, and safety studies.},
}

@article {pmid42078528,
year = {2026},
author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R and Han, Y},
title = {Identification of novel CRESS-DNA viruses in the human vaginal microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1790643},
pmid = {42078528},
issn = {1664-302X},
abstract = {INTRODUCTION: Circular replication-associated protein (Rep)-encoding single-stranded DNA (CRESS-DNA) viruses are widely distributed across diverse hosts and environments, yet their diversity within the human vaginal virome remains poorly characterized. This study aimed to investigate the presence, diversity, and evolutionary relationships of CRESS-DNA viruses in the human vaginal niche.

METHODS: Viral metagenomic sequencing was performed on 24 pooled vaginal swab libraries derived from women with and without vaginitis. After host sequence removal and quality control, de novo assembly and viral identification were conducted. Candidate viral genomes were curated based on genomic features, followed by functional annotation, phylogenetic analysis using Rep protein sequences, and genome-wide pairwise nucleotide identity comparisons.

RESULTS: A total of five CRESS-DNA viral genomes were identified, including four complete and one nearly complete circular genomes. All genomes exhibited canonical architectures, encoding Rep and Cap proteins and containing conserved HUH endonuclease and superfamily 3 helicase motifs. Phylogenetic analysis placed these viruses within the orders Rohanvirales, Ringavirales, Cirlivirales, and Cremevirales, representing multiple distinct evolutionary lineages. Genome-wide pairwise identity analysis showed that all identified viruses fell below established species- and genus-level thresholds, indicating that they represent novel taxa. Comparative analyses further revealed substantial divergence from known environmental and vertebrate-associated viruses.

DISCUSSION: These findings expand the known diversity of CRESS-DNA viruses in the human vaginal virome and highlight their broad evolutionary diversity. The detected viruses likely represent diverse ecological origins rather than stable host-specific infections, and no clear association with vaginitis was observed. This study provides new insights into the evolutionary landscape of CRESS-DNA viruses in the human reproductive tract and underscores the need for further investigation into their biological roles and potential health implications.},
}

@article {pmid42078532,
year = {2026},
author = {Padmanabhan, C and Puig, A},
title = {Editorial: Metagenomic insights into microbial communities in fruits and vegetable plants.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1844864},
pmid = {42078532},
issn = {1664-302X},
}

@article {pmid42078537,
year = {2026},
author = {Shen, T and Zhou, Y and Gao, J and Xiong, X and Chen, C},
title = {Gut microbiota regulates growth retardation in pigs through their metabolites of taurine and butyric acids.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1811659},
pmid = {42078537},
issn = {1664-302X},
abstract = {Growth retardation of piglets has always been observed in current pig production system. Here we defined these pigs as stunted pigs. Stunted pigs show normal feed intake, but exhibit extremely slow growth speed. This brings a big economic loss to pig industry. Many factors can lead to growth retardation, including gut microbiota which has been reported to play important roles in growth retardation of children. However, whether and which gut microbial taxa are associated with growth retardation of piglets are largely unknown. Here we used 16S rRNA gene and shotgun metagenomic sequencing to identify bacterial taxa associated with growth retardation in 126 pigs including stunted pigs and their pairwise littermates showing normal growth. We identified several Clostridium spp. significantly enriched in the gut of normal growing pigs, including Clostridium symbiosum which was the key biomarker distinguishing stunted pigs and normal growing pigs, while several Bacteroides spp. had higher abundances in stunted pigs. Clostridium spp. was significantly associated with the shifts of functional capacities of the gut microbiome between normal and stunted pigs, e.g., biosynthesis of unsaturated fatty acids. Untargeted serum metabolome analysis found that normal growing pigs had higher concentration of taurine in serum. Increased concentration of serum taurine was associated with increased abundance of Clostridium symbiosum. Furthermore, all metabolites having higher abundances in normal growing pigs were enriched in the pathway of taurine and hypotaurine metabolism. Short-chain fatty acids (SCFAs) analysis identified butyric acid having higher concentration in feces of normal growing pigs in both discovery and validation cohorts, and the changes in the abundances of Clostridium symbiosum was correlated with the shifts of the concentrations of fecal SCFAs. These results suggested that Clostridium spp., especially Clostridium symbiosum improved pig growth by increasing the concentrations of serum taurine and fecal butyric acid, and was an important biomarker associated with pig growth. This study provided important insights into the effect of the gut microbiome on pig growth retardation.},
}

@article {pmid42078551,
year = {2026},
author = {Yang, W and Ren, Q and Li, B},
title = {Case Report: Washed microbiota transplantation for the treatment of malnutrition with multidrug-resistant Klebsiella pneumoniae and Candida tropicalis coinfection in a child.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1809311},
pmid = {42078551},
issn = {2296-2360},
abstract = {BACKGROUND: Multidrug-resistant (MDR) Klebsiella pneumoniae and fungal coinfection in children with severe malnutrition are difficult to control with antibiotics alone. This report describes an 8-year-old boy whose pulmonary infection remained uncontrolled and whose nutritional status progressively deteriorated. Washed microbiota transplantation (WMT) was introduced as part of a multimodal salvage treatment strategy, after which the patient showed gradual improvement during continued antimicrobial therapy, respiratory support, and nutritional rehabilitation.

CASE PRESENTATION: We report the case of an 8-year-old boy with chronic malnutrition and recurrent severe pneumonia associated with an underlying central nervous system disorder. He developed recurrent respiratory failure and a persistent pulmonary infection caused by ESBL-producing MDR K. pneumoniae and Candida tropicalis. Despite broad-spectrum antimicrobial therapy, respiratory support, bronchoscopy/bronchoalveolar lavage, and enteral nutrition through a nasojejunal tube, infection control remained poor and nutritional status continued to deteriorate, complicated by sepsis and antibiotic-associated diarrhea. In this context, WMT was introduced through a nasojejunal tube as part of a multimodal salvage treatment strategy and was administered in two treatment courses. Thereafter, during continued antimicrobial treatment, respiratory support, and nutritional rehabilitation, the patient showed progressive clinical improvement, with subsequent negative sputum culture results, gradual radiographic resolution of pulmonary inflammation, weight gain from 14.0 to 22.5 kg, and marked functional recovery.

CONCLUSION: This case suggests that, in severely malnourished children with refractory multidrug-resistant pulmonary bacterial and fungal infections, WMT may have potential adjunctive value as part of comprehensive management. However, because multiple interventions were implemented concurrently and no pre- and post-WMT microbiome sequencing was performed, the observed clinical improvement could not be attributed exclusively to WMT. Therefore, this case should be interpreted only as an exploratory clinical observation rather than confirmatory evidence, and future prospective studies under strict ethical oversight need to be conducted.},
}

@article {pmid42078569,
year = {2026},
author = {Oliveira, JS and Keim, KS and Evans, R and Kurasch, J and Jahansouz, C and Teigen, LM and Lin, AW},
title = {Capturing static and dynamic dietary patterns for human gut microbiome research: a conceptual framework.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2665578},
pmid = {42078569},
issn = {2993-3935},
abstract = {There is inconsistency in the evidence regarding the effects of food on the gut microbiome. These inconsistencies arise, in part, from substantial inter- and intraindividual variations in diet. The wide range of foods consumed directly influences substrate availability for the microbiota. By categorizing foods into broad groups and overlooking interactions among food constituents within individual foods, current dietary pattern approaches can obscure food-specific differences needed to understand dietary effects. Differences in habitual and occasional intake further complicate analyses since frequency of food consumption can produce different gut microbiota responses within the same individual. Flexible analytical approaches are needed to capture within-individual food intake frequency and food-specific effects. To address these challenges, this narrative review presents dietary pattern concepts that distinguish static (stable or consistent) and dynamic (fluctuating or episodic) intake of specific foods at the individual level. We performed a literature search in three databases, including Medline, CINAHL, and PsycINFO, to retrieve relevant articles that distinguish the concepts of "core foods" and "secondary foods" in population-level studies. We adapt these concepts to a microbiome context at the individual level and propose future directions for studies investigating the impact of diet on the gut microbiome.},
}

@article {pmid42078571,
year = {2026},
author = {Nakato, G and Inoue, H and Onawa, S and Furukawa, R and Obana, N and Tanaka, K and Agematu, H and Song, I and Inoue, J and Fukuda, S},
title = {Development of a monoclonal antibody-based approach for selective enrichment of target Bifidobacterium longum from a complex fecal community.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2663732},
pmid = {42078571},
issn = {2993-3935},
abstract = {Individual differences in gut microbiota composition highlight the need for methods capable of selectively enriching host-associated bacteria from complex microbial communities. Conventional cultivation approaches lack the precision required for targeted enrichment, limiting progress in personalized microbiome research. Here, we established a proof-of-concept monoclonal antibody-based strategy for the selective enrichment of a target gut bacterium. We generated a monoclonal antibody (8H2) exhibiting preferential reactivity toward the human-derived Bifidobacterium longum Jih1 and demonstrated that it selectively enriched viable Jih1 cells from a defined bacterial consortium and a human fecal sample. Proteomic and genetic analyses suggested that 8H2 recognizes glutamine synthetase (GS), an enzyme typically localized intracellularly, but detected on the surface of Jih1 cells. This surface association enables antibody binding and facilitates selective enrichment within complex microbial communities. These data support the feasibility of antibody-based, selective enrichment of viable bacteria and suggest potential applications for monitoring individual-associated bacteria in personalized nutrition and microbiome-based interventions.},
}

@article {pmid42064212,
year = {2026},
author = {Anshory, M and Strepis, N and Rosandy, MG and Pawestri, AR and Iskandar, A and Wulanda, IA and Setyowatie, L and David, NI and Malem, NR and Kalim, H and Nijsten, TEC and Nouwen, JL and Thio, HB},
title = {Skin microbiome variation in people living with HIV: associations with antiretroviral therapy and host factors.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1794878},
pmid = {42064212},
issn = {2235-2988},
mesh = {Humans ; *HIV Infections/drug therapy/microbiology ; *Skin/microbiology ; Male ; *Microbiota/drug effects ; Female ; Adult ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Indonesia ; *Anti-Retroviral Agents/therapeutic use ; DNA, Bacterial/genetics ; Skin Microbiome ; },
abstract = {INTRODUCTION: The skin microbiome plays a key role in cutaneous immunity and is shaped by host immune status. HIV infection is associated with immune dysfunction and dermatological disease, yet its impact on the skin microbiome and the modifying effect of antiretroviral therapy (ART) remain incompletely defined. This prospective observational study conducted in Indonesia aimed to characterize differences in skin microbiome composition across HIV status and ART exposure and relate these profiles to clinical parameters.

METHODS: Skin swabs were obtained from sebaceous (posterior neck) and dry (dorsal forearm) sites in HIV-ART-naïve individuals, people living with HIV on ART, and HIV-negative controls, and analyzed using 16S rRNA gene sequencing. Microbial diversity and community structure were assessed using Bray-Curtis dissimilarity, PERMANOVA, and differential abundance testing with ANCOM-BC2, with multivariable models adjusting for demographic, clinical, behavioral, and anatomical factors and subgroup analyses by body mass index, skincare habits, and sampling site.

RESULTS: In total, 488 samples from 244 participants were analyzed. Both HIV groups showed significantly reduced alpha diversity compared with controls, and overall community composition differed by HIV status, although sampling site explained a larger proportion of variation. Across groups, the microbiome was dominated by Corynebacterium, Cutibacterium, Staphylococcus, and Streptococcus. Differential abundance analyses indicated targeted genus-level shifts rather than global dysbiosis, with ART-naïve individuals showing the most consistent deviations, including increased Staphylococcus and reduced Streptococcus relative to controls, and partial attenuation among participants receiving ART. HIV-associated differences were observed within both sebaceous and dry sites, and HIV status remained independently associated with microbiome composition after adjustment.

CONCLUSIONS: These findings suggest that HIV infection is associated with subtle but consistent alterations in the skin microbiome within the context of strong site-specific skin microenvironments. Longitudinal studies integrating functional profiling and host markers of cutaneous barrier integrity and inflammation are needed to clarify their clinical implications.},
}

Humans
*HIV Infections/drug therapy/microbiology
*Skin/microbiology
Male
*Microbiota/drug effects
Female
Adult
Prospective Studies
RNA, Ribosomal, 16S/genetics
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Indonesia
*Anti-Retroviral Agents/therapeutic use
DNA, Bacterial/genetics
Skin Microbiome

@article {pmid42064216,
year = {2026},
author = {Pang, S and Zhang, Z and Ma, Q and Liu, Y and Wang, S and Wang, J and Bi, Y},
title = {The gut-kidney microbiome-oxalate axis in calcium oxalate nephrolithiasis: mechanisms and microbiome-based interventions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1804800},
pmid = {42064216},
issn = {2235-2988},
mesh = {Humans ; *Nephrolithiasis/microbiology/therapy/metabolism ; *Gastrointestinal Microbiome/physiology ; *Calcium Oxalate/metabolism ; *Kidney/microbiology/metabolism ; Dysbiosis ; *Oxalates/metabolism ; Animals ; Hyperoxaluria ; },
abstract = {INTRODUCTION: Calcium oxalate nephrolithiasis is increasingly recognized as a disorder influencednot only by diet and host oxalate handling, but also by the gut-kidneymicrobiome axis. Emerging multi-omics studies suggest that disturbances inintestinal and urinary microbiota, together with altered microbial metabolites,may contribute to disrupted oxalate homeostasis, inflammatory signaling, epithelialinjury, and crystal retention.

METHODS: We performed a narrative, semi-structuredreview of PubMed, Embase, and Web of Science (2010-2025), focusing onoxalate metabolism, gut and urinary microbiota, and microbiome-targeted interventionsin nephrolithiasis, with emphasis on calcium oxalate stones. Human andexperimental studies examining microbial composition, microbial metabolites,host transport and genetic determinants, and nutritional or microbial therapieswere qualitatively synthesized.

RESULTS: Current evidence indicates that loss of oxalatedegradinggut bacteria and broader dysbiosis are associated with hyperoxaluriaand increased calcium oxalate stone risk, whereas microbiome-supportive dietarypatterns may be protective. Multi-omics analyses reveal coordinated alterationsacross stool, urine, and stone-associated microbiota, implicating pathways involvingshort-chain fatty acids, bile acids, and unconjugated bilirubin in oxalatehandling, inflammation, and lithogenesis. Nutritional modulation may favorablyinfluence this axis, while probiotics, synbiotics, and engineered livebiotherapeutics show encouraging preclinical results.

DISCUSSION: Fecal microbiota transplantationremains highly preliminary in this field, and overall human data remainlimited and heterogeneous. The gut-kidney microbiome-oxalate axis providesan integrative framework linking diet, host pathways, microbial metabolites, andmulti-site microbial communities to calcium oxalate nephrolithiasis, and may helpinform future microbiome-based prevention and adjunctive managementstrategies.},
}

Humans
*Nephrolithiasis/microbiology/therapy/metabolism
*Gastrointestinal Microbiome/physiology
*Calcium Oxalate/metabolism
*Kidney/microbiology/metabolism
Dysbiosis
*Oxalates/metabolism
Animals
Hyperoxaluria

@article {pmid42064333,
year = {2026},
author = {Reider, KE and Fannin, C and Hannah, KA and Gelona, AR and Anderson, C and Barnard-Kubow, K and Enke, RA},
title = {16S rRNA amplicon metabarcoding dataset from a retreating glacier forefield in the high tropical andes.},
journal = {Data in brief},
volume = {66},
number = {},
pages = {112758},
pmid = {42064333},
issn = {2352-3409},
abstract = {Glaciers are retreating rapidly worldwide, particularly at high elevations, changing the environments and habitats of microorganisms, plants, and animals drastically and leaving behind nutrient-poor sediment. We sought to explore seasonal, elevational, and soil age differences in microbial community diversity found in moraine deposits exposed by recent deglaciation and previously exposed during the Little Ice Age in the Cordillera Vilcanota of southeastern Peru. In the wet and dry seasons of 2023, JMU students and other researchers collected soil samples from 35 sites across a 2.5 square kilometer range in the Andes mountains. Each sample was assigned to the season collected, elevation of collection, and age of exposure. Total DNA was extracted from samples and the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq platform. The data were then processed and analyzed using the QIIME2 bioinformatics pipeline. This dataset will be useful to the field for studying ecological community and ecosystem formation in glacier forefields emerging from climate change.},
}

@article {pmid42064368,
year = {2026},
author = {Berbudi, A and Riswari, SF and Kwarteng, A},
title = {Helminth Infection, Gut Microbiome Alterations, and Their Impact on Pulmonary Tuberculosis Susceptibility.},
journal = {Journal of tropical medicine},
volume = {2026},
number = {},
pages = {3767562},
pmid = {42064368},
issn = {1687-9686},
abstract = {BACKGROUND: Helminth infections and pulmonary tuberculosis (TB) frequently coexist in low- and middle-income countries and interact through immune-mediated mechanisms that influence host susceptibility to Mycobacterium tuberculosis (Mtb). Beyond direct immunomodulation, increasing evidence indicates that helminth infections alter gut microbiome composition and microbial metabolite production, thereby shaping systemic and pulmonary immune responses through the gut-lung axis. Given the central role of the gut microbiome in regulating T-cell polarization, macrophage function, and inflammatory balance, microbiome-mediated pathways have emerged as a potential link between helminth infection and impaired host defense against pulmonary TB.

OBJECTIVES: This narrative review examines current evidence on how helminth-induced immunological changes and gut microbiome alterations, within the context of the gut-lung axis, may influence susceptibility to pulmonary TB.

METHODS: A narrative review approach was used to synthesize findings from experimental, observational, and clinical studies addressing helminth infection, gut microbiome dynamics, immune regulation, and TB.

RESULTS: Helminth infections are associated with Th2-skewed immune responses characterized by increased regulatory T-cell activity and anti-inflammatory cytokine production, which may attenuate Th1-mediated immunity essential for Mtb control. Helminths also modulate gut microbiome composition, with effects ranging from increased microbial diversity to dysbiosis, depending on helminth species and host context. These microbiome alterations may influence systemic immunity through microbial metabolites such as short-chain fatty acids (SCFAs). Importantly, SCFAs exhibit context-dependent effects, potentially supporting immune homeostasis while, under certain conditions, promoting regulatory pathways that may dampen protective antimycobacterial responses.

CONCLUSIONS: Current evidence suggests that helminth-associated immune modulation and gut microbiome alterations may influence pulmonary TB susceptibility, although most findings remain associative rather than causal. Further mechanistic and clinical studies are needed to clarify the role of the gut-lung axis in helminth-TB coinfection and to inform integrated disease management strategies in endemic regions.},
}

@article {pmid42064411,
year = {2026},
author = {Weiss, G and Voroshilina, E and Koranda, M and Blauensteiner, J and Schenk, M},
title = {Microbial signatures in follicular fluid and their association with fertilization success.},
journal = {Frontiers in reproductive health},
volume = {8},
number = {},
pages = {1773092},
pmid = {42064411},
issn = {2673-3153},
abstract = {BACKGROUND: Emerging evidence suggests that the upper female reproductive tract is not sterile and that microbial signals within follicular fluid (FF) may influence oocyte competence. However, previous studies have largely relied on pooled FF samples or dominant follicles, limiting insight into follicle-specific associations with fertilization outcomes.

METHODS: In this exploratory paired study, follicular fluid samples were collected from 24 women undergoing IVF/ICSI treatment. For each patient, two FF samples were analyzed individually: one associated with a fertilized oocyte, and one associated with an oocyte that failed fertilization. Bacterial DNA and total bacterial load (TBL) were assessed using quantitative real-time PCR targeting predefined microbial taxa.

RESULTS: Bacterial DNA above the predefined detection threshold was identified in 39.6% of all FF samples. Notably, within this exploratory cohort, FF samples associated with fertilization failure were more frequently TBL-positive compared with FF samples linked to successful fertilization (70.8% vs. 8.3%). Follicles from the same patient often differed in bacterial DNA presence, indicating substantial intra-individual variability. Several bacterial taxa, including Fannyhessea vaginae, Ureaplasma spp., and Lactobacillus spp., were more frequently detected in FF samples associated with failed fertilization; however, no individual taxon showed a consistent association with outcome across all samples.

CONCLUSION: In this paired follicle-level analysis, the absence of detectable bacterial DNA in follicular fluid was associated with fertilization outcome. These findings highlight follicle-level heterogeneity in microbial DNA detection and underscore the importance of follicle-specific analyses in reproductive microbiome research. Larger prospective studies are required to validate these observations and to clarify the biological mechanisms underlying follicular microbial signals.},
}

@article {pmid42064742,
year = {2026},
author = {Gordon, S and Evans, S and Kirven, K and Whisonant, M},
title = {Increased dietary iron alters taxonomic composition and function of zebrafish gut microbiome.},
journal = {microPublication biology},
volume = {2026},
number = {},
pages = {},
pmid = {42064742},
issn = {2578-9430},
abstract = {Gut microbiota are crucial to both gastrointestinal tract health and host well-being. Oral iron supplementation is commonly used, but knowledge of iron's impact on the gut microbiome is limited. Using Zebrafish (Danio rerio) as a model organism, we tested effects of increased dietary iron on gut taxonomic composition and function. Increased dietary iron significantly altered the zebrafish microbiome taxonomic composition and enriched physiological conditions of aerobic respiration. Mass spectrometry (GCMS and LCMS), utilized to measure primary metabolite and lipid levels, pointed to significant increases in amino acids under increased iron supplementation, but no significant change in lipid metabolite levels.},
}

@article {pmid42064815,
year = {2026},
author = {Li, J and Zhang, S and Zhang, Y and Wang, X and Zhuge, Y and Wu, Q and Zhao, Y and Gao, Q and Chen, R and Wang, Y and Jin, Q and Zhang, Y},
title = {Harnessing the gut microbiome for precision therapeutics in heart failure.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1781470},
pmid = {42064815},
issn = {1663-9812},
abstract = {Heart failure (HF) management remains challenging because patients often show large differences in how well treatments work and in how often adverse drug reactions occur. Traditional pharmacogenomics cannot fully explain these differences. Emerging evidence from pharmacomicrobiomics shows that the gut microbiome represents a previously underappreciated factor influencing drug responses. This review summarizes the two-way interactions between the gut microbiota and key HF drugs, including digoxin, angiotensin receptor-neprilysin inhibitors (ARNIs), ACE inhibitors (ACEIs), angiotensin receptor blockers (ARBs), β-blockers, sodium-glucose cotransporter 2 (SGLT2) inhibitors, mineralocorticoid receptor antagonists (MRAs), and diuretics. On the one hand, gut microbes can change drug effects because they can metabolize drugs and affect host physiological pathways. On the other hand, HF drugs can change the structure and function of the gut microbial community. This review also discusses how microbiome-related features may serve as biomarkers to support personalized treatment and how strategies such as dietary changes and microbiota-targeted therapies may improve clinical outcomes. Although evidence remains limited, and certain methods require further refinement, integrating microbiome insights into HF treatment may support more precise and individualized treatment strategies and help address current therapeutic limitations.},
}

@article {pmid42064906,
year = {2026},
author = {Nguyen, T and Woods, C and Liu, J and Wang, C and Lin, AL and Cheng, J},
title = {A multimodal AI model for modeling the genetic risk factor of Alzheimer's disease.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.13.26350803},
pmid = {42064906},
abstract = {The apolipoprotein E ε 4 (APOE4) allele is the strongest genetic risk factor for late-onset Alzheimer's disease (AD), the most common form of dementia. APOE4 carriers exhibit cerebrovascular and metabolic dysfunction, structural brain alterations, and gut microbiome changes decades before the onset of clinical symptoms. Better understanding of the early manifestion of these physiological changes is critical for development of timely AD interventions and risk reduction protocols. Multi-modal datasets encompassing a wide range of APOE ε 4 and AD associated biomarkers provide a valuable opportunity to gain insight into the APOE4 phenotype; however, these datasets often present analytical challenges due to small sample sizes and high heterogeneity. Here, we propose a two-stage multimodal AI model (APOEFormer) that integrates blood metabolites, brain vascular and structural MRI, microbiome profiles, and other clinical and demographic data to predict APOE4 allele status. In the first stage, modality-specific encoders are used to generate initial representa-tions of input data modalities, which are aligned in a shared latent space via self-supervised contrastive learning during pretraining. The contrastive learning objective encourages learning of informative and consistent representations across modalities through leveraging cross-modality relationships. In the second stage, the pretrained representations are used as inputs to a multimodal transformer that integrates information across modalities to predict a key AD-risk genetic variant (APOE4). Across 10 independent experimental runs with different train-validation-test splits, APOEFormer predicts whether an individual carries an APOE4 allele with an average prediction accuracy of 75%, demonstrating robust performance under limited sample sizes. Post hoc perturbation analysis of the predictive model revealed valuable insights into the driving components of the APOE4 phenotype- including key blood biomarkers and brain regions strongly associated with APOE4.},
}

@article {pmid42065024,
year = {2026},
author = {Bharat, AA and Ali, O and Sahadeo, UM and Ramsubhag, A and Jayaraman, J},
title = {Preparation of a fermented Sargassum extract, microbial dynamics involved, and its effect on Capsicum annuum.},
journal = {3 Biotech},
volume = {16},
number = {5},
pages = {170},
pmid = {42065024},
issn = {2190-572X},
abstract = {UNLABELLED: The study explored Sargassum valorization through the production of a fermented extract for its application as a crop biostimulant. The dried and ground Sargassum (S. natans and S. fluitans) was subjected to anaerobic fermentation utilizing the endogenous microorganisms already present in the seaweed. During the fermentation process, samples were periodically taken (5, 15, 20, 27, 30, and 35) for 16S rRNA and ITS paired-end amplicon metataxonomics. Microbiome profiling revealed distinct temporal microbiome shifts over the 35 days of fermentation, with Firmicutes, Bacteroidota, and Nectriaceae emerging as the core microbiome. Furthermore, microbial network analysis identified Clostridiaceae, Sporolactobacillaceae, and Pirellulaceae as dominant bacterial families, while Gibberella and Aspergillus showed up as prevalent fungal genera. Beta-diversity analyses showed a significant shift in microbial composition on Day 35. Extracts were screened for their antimicrobial properties against plant pathogens (Xanthomonas campestris pv. vesicatoria and Alternaria solani), however results indicated no antimicrobial effect. Plant growth trials were conducted using Capsicum annuum L. plants and the extracts were applied as foliar application sprays at 0.5-1% v/v concentrations under greenhouse conditions. All parameters measured (chlorophyll content, root and shoot length, and root and shoot weights were all significantly greater than Control-treated plants. Chlorophyll content, root length, shoot length, fresh root and shoot weight, and dry root and shoot weight all had significant increases of up to 28.82%, 60.13%, 15.95%, 67.95%, 53.90%, 82.05%, and 95.86% respectively. The result of the study promotes the usage of fermented Sargassum extracts as an organic biostimulant and aligns with sustainable agricultural practices.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04811-1.},
}

@article {pmid42065141,
year = {2026},
author = {Talbott, S and Stephens, B and Talbott, J and Oddou, M and Fumiki, A},
title = {Effects of Lactiplantibacillus Plantarum KABP051 Probiotic on Body Composition, Microbiome and Mood in Healthy Overweight Adults.},
journal = {Journal of medicinal food},
volume = {},
number = {},
pages = {1096620X261448041},
doi = {10.1177/1096620X261448041},
pmid = {42065141},
issn = {1557-7600},
abstract = {Obesity and mental health disorders are among the greatest public health challenges of the 21st century. Interestingly, an altered microbiome profile has been associated with both conditions. The aim of this randomized, double-blind, placebo-controlled clinical trial was to evaluate the effects of dietary supplementation with a specific probiotic strain (Lactiplantibacillus plantarum KABP051) on body composition and gut microbiome balance, together with measures of mood state, in a population of healthy overweight subjects. Sixty healthy, moderately stressed, nondepressed and overweight or obese volunteers were supplemented for 12 weeks with probiotic (L. plantarum KABP051; 1 billion colony forming units/day) or placebo (microcrystalline cellulose). The KABP051 group experienced significantly greater improvements compared with placebo on body composition measurements, including a reduction in body weight and waist circumference, which decreased in 1.97 ± 0.77 (mean ± SE) kg and 2.15 ± 0.81 (mean ± SE) cm versus placebo at the end of the intervention (both P < .05, mixed model for repeated measures [MMRM] and post-hoc analysis). Microbiome composition improved in KABP051 group, with significant increase in the relative abundance of Lactiplantibacillus spp. versus placebo. Body fat percentage, profile of mood states fatigue, and confusion sub-scores showed a global trend toward improvement compared with placebo, with the change at 12 weeks being significant in the three measurements in post-hoc analysis (P = .015, P = .014, and P = .016, respectively). No serious adverse events were registered during the intervention period. These results suggest that a specific strain of probiotic bacteria (L. plantarum KABP051) may have both metabolic and psychobiotic effects and may be beneficial for enhancing weight loss and body composition, improving energy (less fatigue) and mood levels while embarking on a healthy lifestyle regimen. ClinicalTrials.gov identifier: NCT06808061.},
}

@article {pmid42065212,
year = {2026},
author = {Shen, Y and Wang, Z and Cheng, X and Tang, F and Rao, S and Zhang, D},
title = {Cluster analysis of research hotspots and trends in probiotics for constipation: A comprehensive bibliometric analysis (1977-2024).},
journal = {Medicine},
volume = {105},
number = {18},
pages = {e48338},
doi = {10.1097/MD.0000000000048338},
pmid = {42065212},
issn = {1536-5964},
support = {KS2201//Kunshan key R & D program/ ; },
mesh = {*Probiotics/therapeutic use ; *Bibliometrics ; *Constipation/therapy/microbiology ; Humans ; Cluster Analysis ; *Biomedical Research/trends ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Probiotics are increasingly recognized as a promising therapeutic approach for managing constipation, sparking widespread interest in their effects on gastrointestinal health. This study conducts a cluster analysis to systematically map global research trends and hotspots in probiotics for constipation from 1977 to 2024.

METHODS: Relevant publications were retrieved from the Web of Science Core Collection. Bibliometric tools, including VOSviewer, CiteSpace, and R, were applied for cluster analysis, network visualization, and trend mapping.

RESULTS: A total of 519 publications were included in the analysis. China led in publication volume, while the United States demonstrated the highest academic influence. Key institutions, such as the University of California System and Harvard University, were identified as major contributors. High-impact journals, including Nutrients, World Journal of Gastroenterology, and Digestive Diseases and Sciences, played central roles in disseminating research. Quigley Eamonn M. M. indicated significant influence in the field. Cluster analysis of keywords revealed 6 principal research hotspots: microbial diversity and mechanisms, gut microbiota-host interaction and pathophysiology, dietary factors and microbiome analysis techniques, epidemiology, prevalence, and population health, clinical management and therapeutic efficacy, and clinical trials and study design. Citation burst analysis indicated a recent research focus shift toward mechanisms, personalized interventions, and gut microbiome modulation.

CONCLUSION: This bibliometric study based on cluster analysis identified 6 major research hotspots in probiotics for constipation, reflecting the evolving trends and collaborative networks of the field. These findings provide a comprehensive perspective on current research priorities and can guide future studies toward innovative and evidence-based clinical applications.},
}

*Probiotics/therapeutic use
*Bibliometrics
*Constipation/therapy/microbiology
Humans
Cluster Analysis
*Biomedical Research/trends
Gastrointestinal Microbiome

@article {pmid42065376,
year = {2026},
author = {Bullard, BM and VanderVeen, BN and Cardaci, TD and McDonald, SJ and Bastian, AV and Willis, NB and Xu, M and Li, J and Pierre, JF and Hofseth, LJ and Fan, D and Murphy, EA},
title = {Panaxynol mitigates chemotherapy-induced intestinal mucositis by improving the colonic microenvironment in murine models.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00035.2026},
pmid = {42065376},
issn = {1522-1547},
support = {R01CA246809//HHS | NIH | National Cancer Institute (NCI)/ ; U01CA272977//HHS | NIH | National Cancer Institute (NCI)/ ; F31AT012589//HHS | NIH | National Center for Complementary and Integrative Health (OAM)/ ; R00CA27689//HHS | NIH | National Cancer Institute (NCI)/ ; F99CA294251//HHS | NIH | National Cancer Institute (NCI)/ ; P20GM155896//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32DK007665//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; T32CA244125//HHS | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Chemotherapy-induced mucositis (CIM) is a debilitating side-effect impacting as many as 90% of cancer patients undergoing treatment. Patients receiving 5-Fluorouracil (5FU), a first-line chemotherapeutic in colorectal cancer, experience significant gastrointestinal distress that perpetuates poor patient quality of life and reduces treatment tolerance, efficacy, and survival. Natural compounds have shown promise in improving CIM through their pleiotropic actions, including immune and mucosal regulation. We examined whether panaxynol, a bioactive compound isolated from American ginseng, can alleviate murine CIM symptomology and severity. Intestinal mucositis was induced in C57BL/6J male and female mice by 5 consecutive intraperitoneal injections of 5FU (35 mg/kg/day); PBS was used as the control. Vehicle or panaxynol (2.5 mg/kg/day) was administered via oral gavage every other day, starting on Day -1, for a total of 4 treatments. Panaxynol significantly improved overall mucositis symptomology, attenuated 5FU-induced cytopenia and anemia, ameliorated the 5FU-induced loss of goblet cells per crypt, suppressed pro-inflammatory immune cells in the colonic lamina propria, and altered microbial diversity and taxonomy. Sex differences were observed, with panaxynol exerting a stronger effect in males, significantly reducing the relative percentage of colonic macrophages and neutrophils. Panaxynol treatment was associated with sex-dependent alterations in gut microbial community structure and modulation of specific taxa, including Dubosiella and Bifidobacterium, alongside male-specific increases in Romboutsia and Alistipes; Akkermansia abundance was primarily influenced by 5FU treatment. These preclinical findings support the potential of panaxynol as a therapeutic candidate for the treatment of CIM and highlight the importance of considering sex as a biological variable.},
}

@article {pmid42065459,
year = {2026},
author = {Liu, M and Yang, Z and Liu, B and Cheng, H and Qin, J and Zhang, P and Tang, T and Peng, F and Yang, J and Wei, P and Su, H},
title = {Correction: Multi-omics reveals gut microbiome- and metabolome-specific responses to sugar alcohols.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo90033j},
pmid = {42065459},
issn = {2042-650X},
abstract = {Correction for 'Multi-omics reveals gut microbiome- and metabolome-specific responses to sugar alcohols' by Mengling Liu et al., Food Funct., 2026, https://doi.org/10.1039/D6FO00282J.},
}

@article {pmid42065740,
year = {2026},
author = {Mohsenzadeh, A and Mohammadi, A and Mohsenzadeh, H and Kamali, K and Moradi, M and Ebrahimi, N and Sheikhy, M and Zabet, AH and Mirheidari, H and Bavari, S and Elahi, R},
title = {The gut microbiota and kawasaki disease: exploring the role of microbial dysbiosis and metabolites in pathogenesis and therapeutics.},
journal = {European journal of pediatrics},
volume = {185},
number = {5},
pages = {},
pmid = {42065740},
issn = {1432-1076},
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/therapy ; *Gastrointestinal Microbiome ; *Dysbiosis/complications/therapy/microbiology ; Child ; },
abstract = {Kawasaki disease (KD) is an acute, immune-mediated medium-vessel vasculitis and the leading cause of acquired heart disease in children, yet its underlying etiology remains only partially defined. Emerging evidence implicates the gut microbiota as a key modulator of KD susceptibility, immune dysregulation, and therapeutic response. This narrative review aims to synthesise current insights linking gut microbial dysbiosis and microbial metabolites to the pathogenesis, clinical expression, and treatment of KD, and to explore microbiome-informed strategies with diagnostic and therapeutic potential. We conducted a comprehensive search of PubMed, Embase, Web of Science, and Google Scholar from database inception to April 2025 for English-language studies on Kawasaki disease and the gut microbiota, including terms related to microbiome, microbial dysbiosis, metabolites, pathogenesis, immunity, inflammation, and therapy. Reference lists of relevant articles and key reviews were also screened. Children with acute KD exhibit characteristic alterations in gut microbial composition, including an overrepresentation of Streptococcus species, depletion of short-chain fatty acid (SCFA)-producing taxa such as Faecalibacterium, Ruminococcus, and Roseburia, and a significant reduction in fecal butyrate. These changes have been associated with impaired intestinal barrier integrity, heightened NLRP3 inflammasome activation, and dysregulated cytokine signalling, contributing to systemic inflammation and vascular injury. Additional factors, such as antibiotic exposure and concurrent respiratory or oropharyngeal infections, can intensify dysbiosis and have been linked to resistance to intravenous immunoglobulin (IVIG) and an increased risk of coronary artery aneurysms. Conclusions: Gut microbial imbalance and metabolite disruption are likely associated with KD, potentially through interaction with host genetics and immune pathways. Microbiome-targeted approaches, including probiotics, dietary modulation, and metabolite-based therapies, hold promise for improving diagnostic precision, predicting treatment response, and guiding the development of targeted interventions in KD.},
}

Humans
*Mucocutaneous Lymph Node Syndrome/microbiology/therapy
*Gastrointestinal Microbiome
*Dysbiosis/complications/therapy/microbiology
Child