@article {pmid43000596,
year = {2026},
author = {Su, Z and Zhang, Y and Li, S and Liu, G and Wang, S},
title = {Panax notoginseng alleviates obesity and insulin resistance involving the Enterocloster clostridioformis-IRS-PI3K-AKT axis.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {43000596},
issn = {1869-1889},
abstract = {In this study, supplementation with Panax notoginseng (PN) in obese mice reversed excessive weight gain, improved glucose homeostasis and insulin sensitivity, and significantly reversed hepatic steatosis. Concurrently, PN treatment normalized the intestinal microecosystem, reflected in a decreased Firmicutes-to-Bacteroidetes ratio (F/B ratio) and an enrichment of the commensal species Enterocloster clostridioformis (EC). Of particular note, oral administration of EC alone largely reproduced the major beneficial phenotypes observed with PN-namely, reduced fat mass, improved glycaemic regulation, and attenuated hepatic triglyceride deposition. Mechanistically, EC intervention suppressed the pathological overactivation of the hepatic insulin receptor substrate (IRS)-phosphatidylinositol-3 kinase (PI3K)-AKT kinase (AKT) pathway and inhibited the phosphorylation of IRS. This recalibration of the insulin signaling cascade improved insulin sensitivity and effectively counteracted the metabolic disturbances provoked by the high-fat diet (HFD). Taken together, these results suggest that the anti-obesity effects of PN are at least partially mediated by gut microbiota-driven EC enrichment, with consequent modulation of the IRS-PI3K-AKT pathway. Collectively, our findings identify EC as a potential candidate commensal bacterium and highlight the importance of the PN-EC-IRS-PI3K-AKT regulatory axis in counteracting obesity and its associated comorbidities.},
}

@article {pmid43000727,
year = {2026},
author = {Steenkamp, I and Pillay, L},
title = {Hidradenitis suppurativa in primary care: From early recognition to modern management.},
journal = {South African family practice : official journal of the South African Academy of Family Practice/Primary Care},
volume = {68},
number = {1},
pages = {e1-e6},
doi = {10.4102/safp.v68i1.6318},
pmid = {43000727},
issn = {2078-6204},
mesh = {Humans ; *Hidradenitis Suppurativa/diagnosis/therapy/epidemiology ; *Primary Health Care ; Early Diagnosis ; },
abstract = {Hidradenitis suppurativa (HS), also known as acne inversa, is a heterogeneous, chronic, relapsing inflammatory disease of the pilo-sebaceous unit, primarily affecting intertriginous areas such as the axillae, groin and anogenital region. Despite its relatively low global prevalence, HS remains underdiagnosed, especially in primary care settings, where it is often mistaken for recurrent boils. The pathogenesis is multifactorial, involving follicular occlusion, immune dysregulation, genetic susceptibility, microbiome imbalance, hormonal influences and lifestyle factors. Hidradenitis suppurativa typically presents after puberty with a peak incidence during the second and third decades of life. The condition is characterised by painful nodules, abscesses and in advanced stages of the disease, forms sinus tracts and scars that greatly impair quality of life. Early recognition and a multidisciplinary management approach, including lifestyle modification, long-term medical therapy and surgical intervention when indicated, are essential to prevent disease progression and complications. This article provides an evidence-based overview of HS and practical guidance for family practitioners on its recognition, classification and management within the South African context.},
}

Humans
*Hidradenitis Suppurativa/diagnosis/therapy/epidemiology
*Primary Health Care
Early Diagnosis

@article {pmid43000839,
year = {2026},
author = {Xie, YS and Wu, ZL and Wei, FQ and Zheng, SG},
title = {[Characterization of the caries-associated oral microbiome across age groups based on global metagenomic species-level genome bins data].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {61},
number = {11},
pages = {1622-1632},
doi = {10.3760/cma.j.cn112144-20260122-00038},
pmid = {43000839},
issn = {1002-0098},
support = {82501126//National Natural Science Foundation of China/ ; },
abstract = {Objective: Based on the analysis of global multicenter metagenomic species-level genome bin (SGB), this study aims to identify core cariogenic SGBs across all age groups and provide a basis for the precise diagnosis and age-stratified prevention and treatment of dental caries. Methods: Eight published studies available in the National Center for Biotechnology Information database before August 2024 were included, with a total of 496 oral metagenomic samples enrolled. Samples were stratified into saliva and dental plaque groups across three age segments (<6, 6 to<13, and≥13 years). Taxonomic profiling, core microbiota identification, and differential analysis of strains were conducted. Results: Analysis at the SGB level revealed that 652 SGBs were detected in plaque samples and 931 SGBs in saliva samples. Specific core SGB clusters were identified in each age group (<6, 6 to<13, and≥13 years), with 13 SGBs consistently detected across all groups (detection rate>50%). Differential analysis indicated that caries was accompanied by marked ecological dysbiosis. These differential patterns were highly age-and sample-specific. Saliva samples in the group aged<6 years identified the most numerous differential SGBs (227). In plaque samples of aged 6 to<13 years, the caries group was characterized by Streptococcus enrichment versus Capnocytophaga in the healthy group. Notably, in the≥13-year-old group, the caries-associated microbiome shifted to anaerobic Prevotella species alongside Streptococcus. Heatmap analysis confirmed clear ecological turnovers across all ages, with the sharpest demarcation found in the youngest age group. Conclusions: Analysis at the SGB level unveils microbial dysbiosis patterns with greater precision than traditional species-level profiling, providing a novel theoretical basis for the precision diagnosis and age-specific management of dental caries.},
}

@article {pmid43000952,
year = {2026},
author = {Ha, S and Lv, C and Cui, J and Yu, H and Sun, L},
title = {A validated low-abundance uterine microbial signature associated with chronic endometritis.},
journal = {Zygote (Cambridge, England)},
volume = {},
number = {},
pages = {1-15},
doi = {10.1017/S0967199426100677},
pmid = {43000952},
issn = {1469-8730},
abstract = {BACKGROUND: Chronic endometritis (CE) is a persistent inflammatory endometrial disorder associated with infertility, recurrent implantation failure, and pregnancy loss. While previous microbiome studies have focused on Lactobacillus depletion and common genital tract bacteria, low-abundance microbial lineages remain poorly characterised.

OBJECTIVE: To identify reproducible low-abundance microbial signatures associated with CE and evaluate their robustness through external validation and complementary analyses.

METHODS: Uterine lavage specimens from infertile women with CE (n = 29) and non-CE controls (n = 16) were analysed by 16S rRNA sequencing in a discovery cohort. An independent cohort of 58 participants was used for external validation. CE was diagnosed by hysteroscopy and CD138 immunohistochemistry (≥5 stromal plasma cells/10 high-power fields). Multiple negative controls were included, and contaminants were assessed using decontam. Prespecified analyses included cervicovaginal source tracking, shotgun metagenomics in a subset, cytokine profiling, and post-treatment follow-up.

RESULTS: CE samples exhibited increased richness and modestly higher diversity. Presence/absence-based beta diversity demonstrated clearer separation between CE and controls. CE was associated with enrichment of Patescibacteria, Planctomycetota, Bdellovibrionota, and selected archaeal-lineage signals. After contaminant filtering, major rare-lineage features remained enriched. Patescibacteria and Bdellovibrio-related signals correlated with CD138-positive plasma-cell counts and inflammatory cytokines. A nested discovery model achieved an area under the receiver operating characteristic curve (AUC) of 0.84, and the locked marker panel achieved an AUC of 0.81 in external validation.

CONCLUSIONS: CE is associated with a reproducible low-abundance microbial signature in uterine lavage samples. These findings highlight candidate microbial lineages for further investigation but do not establish causality or uterine residency.},
}

@article {pmid43000968,
year = {2026},
author = {Jia, J and Zhang, J and Zhang, W and Zhang, F and Yun, K and Yan, J},
title = {[Microbiomics‑Based Prediction of Postmortem Interval in Rats with Ethanol Exposure Combined with CO Poisoning].},
journal = {Fa yi xue za zhi},
volume = {42},
number = {4},
pages = {295-301},
doi = {10.12116/j.issn.1004-5619.2024.440903},
pmid = {43000968},
issn = {1004-5619},
mesh = {Animals ; *Postmortem Changes ; *Ethanol/toxicity ; Rats ; *Carbon Monoxide Poisoning/microbiology ; RNA, Ribosomal, 16S/genetics ; Male ; Rats, Sprague-Dawley ; *Bacteria/genetics/classification/isolation & purification ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Time Factors ; },
abstract = {OBJECTIVES: To investigate the temporal changes of intestinal bacterial communities in rats that died from combined ethanol and carbon monoxide (CO) poisoning using microbiome analysis techniques, and to explore potential correlations between these changes and the postmortem interval (PMI).

METHODS: Four experimental groups were established：fatal CO poisoning, fatal CO poisoning following ethanol exposure, ethanol exposure, and blank controls. Rectal specimens were collected at 0, 1, 3, 7, and 14 days postmortem. High-throughput sequencing of the 16S rRNA gene was employed to analyze bacterial communities. Bacterial diversity, relative abundance, and community differences were analyzed. A predictive model for PMI estimation using bacterial community succession patterns was constructed using a random forest algorithm.

RESULTS: The intestinal bacterial community structure of rats changed at both the phylum and genus levels within 14 days postmortem in the experimental groups. The PMI estimation model based on bacterial characteristics demonstrated good predictive performance across different experimental groups, with model fitting accuracies of 0.60, 0.59, 0.61 and 0.60 for each of the four groups. The average prediction error across all groups was approximately 1 day.

CONCLUSIONS: Ethanol exposure, CO poisoning, and the combined effects of ethanol exposure and CO poisoning all affect postmortem bacterial succession in rat cadavers. In forensic practice, it is recommended to adopt a predictive model specifically developed for the corresponding poisoning condition to improve the accuracy of PMI estimation.},
}

Animals
*Postmortem Changes
*Ethanol/toxicity
Rats
*Carbon Monoxide Poisoning/microbiology
RNA, Ribosomal, 16S/genetics
Male
Rats, Sprague-Dawley
*Bacteria/genetics/classification/isolation & purification
Disease Models, Animal
*Gastrointestinal Microbiome
Time Factors

@article {pmid43001270,
year = {2026},
author = {Kallapura, G and Prakash, AS and Prasad, R and Josphine, I and Maurya, M and Dhar, D},
title = {Gut microbiota composition of India's Baiga tribe: Insights from an indigenous particularly vulnerable tribal group.},
journal = {iScience},
volume = {29},
number = {11},
pages = {118082},
pmid = {43001270},
issn = {2589-0042},
abstract = {The transition from traditional foraging lifestyles to modernized urban environments is associated with reduced human gut microbiome diversity. To examine this shift within the Indian subcontinent, we used shotgun metagenomics to compare the gut microbiota of 50 adults: 25 from the indigenous, foraging, and particularly vulnerable Baiga tribe and 25 from an urban population in Bhopal, Central India. The Baiga maintained a diverse ecosystem enriched with fiber-degrading bacteria such as Roseburia and Faecalibacterium, forming networks suited to complex carbohydrate fermentation. The urban microbiome showed lower phylogenetic diversity and evenness, with higher relative abundance of Prevotella copri and dairy-adapted taxa. Functionally, the tribal gut retained pathways for environmental sensing and complex plant metabolism, whereas the urban gut was enriched in pathways associated with potential inflammation. These findings identify the Baiga as a reservoir of preserved human microbial diversity relevant to metabolic health.},
}

@article {pmid43001315,
year = {2026},
author = {Zhou, X and Zhao, C and Jia, R and He, Z and Lin, Z and Cao, J and Luo, Y and Yang, S and Liu, D and Li, Y},
title = {Effects of andrographolide on growth performance, serum indices, and multi-site microbial communities in weaned calves.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {27},
number = {},
pages = {474-492},
pmid = {43001315},
issn = {2405-6383},
abstract = {Weaning stress frequently induces systemic inflammation and oxidative stress in calves, thereby impairing growth performance and increasing susceptibility to gastrointestinal and respiratory diseases. Andrographolide (AG) is a natural active compound extracted from the medicinal plant Andrographis paniculata. It exhibits potent anti-inflammatory and antioxidant properties, but its impacts on calf physiological health and multi-site microbial ecosystems remain poorly understood. This study aimed to evaluate the effects of AG supplementation on growth performance, serum anti-inflammatory and antioxidant levels, and microbial communities across multiple sites (rumen, rectum, and nasal cavity) in weaned calves. Eighteen healthy Angus calves (age 90 ± 3 d, initial body weight 88.25 ± 4.98 kg) were randomly assigned to three groups (n = 6 per group): 0 mg/kg AG group (CON), 8 mg/kg AG group (L-AG), and 16 mg/kg AG group (H-AG). The trial lasted for 42 d. Results indicated that AG supplementation linearly increased calf average daily gain (ADG; P = 0.011); however, the L-AG group exhibited the most significant weight gain advantage during the latter phase (22-42 d) (P = 0.026). Serum analysis revealed that AG supplementation significantly enhanced calves' antioxidant (e.g., superoxide dismutase [SOD] and glutathione peroxidase [GSH-Px]) and anti-inflammatory (e.g., interleukin [IL]-4 and IL-10) capacities (P < 0.05), while markedly reducing pro-inflammatory factors (e.g., IL-1β, IL-2, and IL-6) and the oxidative stress marker (malondialdehyde) (P < 0.05); the H-AG group exhibited the most pronounced anti-inflammatory and antioxidant effects. Microbiome analysis revealed that AG treatment consistently remodeled microbial communities across all sites (P < 0.05). In the rumen, the L-AG group specifically enriched beneficial genera associated with volatile fatty acid (VFA) synthesis, including Pseudoscardovia, CAG-238, CAG-127, and CAG-793 (P adj < 0.05). In the nasal cavity, AG significantly reduced the abundance of multiple potential pathogenic microorganisms, including Pasteurella, Moraxella_C, Brevundimonas, and Exiguobacterium_A (P adj < 0.05). Furthermore, AG enhanced cross-site microbial interactions, with a numerical increase in cross-site edges (CON = 529, L-AG = 741, H-AG = 866). The AG treatments significantly altered the network topological structure (P < 0.05), suggesting a strengthening of the gut-lung axis. In summary, AG supplementation during calf weaning effectively suppressed inflammation and oxidative stress responses while improving growth performance and health status through multi-site microbial regulation. Based on the observed phenotypic and microbiome differences, L-AG appears to favor long-term growth benefits by optimizing rumen microbial communities, whereas H-AG maximizes short-term improvements through more potent anti-inflammatory and antioxidant effects.},
}

@article {pmid43001780,
year = {2026},
author = {Fang, H and Shu, Y and Zhou, Z and Li, Y and Gong, T and Yang, M and Zhang, B and Jin, Y and Liu, Y and Wang, C and Zhao, L and Liu, Y and Chen, P},
title = {Identification of ebastine and ceritinib as effective inhibitors of Fusobacterium nucleatum FtsZ.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0132626},
doi = {10.1128/spectrum.01326-26},
pmid = {43001780},
issn = {2165-0497},
abstract = {UNLABELLED: The role of microorganisms in cancer is not a new concept-bacteria, parasites, and viruses have all been implicated in cancer development. Fusobacterium nucleatum, a member of the oral microbiota, has emerged as an important cancer-associated bacterium. Unbiased global genomic analyses have demonstrated that F. nucleatum is enriched in human colorectal cancer (CRC) tissues compared with noncancerous colorectal tissues, underscoring the urgent need for specific antimicrobial agents targeting F. nucleatum for CRC prevention and treatment. In this study, structure-based virtual screening successfully identified ebastine and ceritinib as antimicrobial agents targeting Fusobacterium nucleatum FtsZ (FnFtsZ). Their potent anti-F. nucleatum activity was confirmed through in vitro assays, including minimum inhibitory concentration determination and microscopic observation of filamentous morphology. Both ebastine and ceritinib exhibited significant antibacterial effects. Enzyme activity and polymerization assays demonstrated that their mechanism of action involves inhibition of FnFtsZ GTPase activity and disruption of FnFtsZ polymerization. Scanning electron microscopy (SEM) and light microscopy further confirmed that these compounds effectively disrupt cell division, leading to abnormal or halted division and inhibiting F. nucleatum proliferation. Overall, our findings identified ebastine and ceritinib as potential drugs against F. nucleatum proliferation, although further structural optimization is required. Additionally, our results demonstrate the effectiveness of an integrated computational-experimental approach targeting bacterial cell division in microbiome-associated pathologies.

IMPORTANCE: Colorectal cancer (CRC) is strongly driven by the enrichment of the oncogenic bacterium Fusobacterium nucleatum in gut lesions. However, the lack of targeted anti-F. nucleatum drugs significantly limits microbe-related interventions for CRC. In this study, we repurposed two clinically approved drugs, ebastine and ceritinib, as highly effective inhibitors of FnFtsZ, the key protein responsible for bacterial cell division. We demonstrated that both drugs inhibit bacterial proliferation by suppressing FnFtsZ function and disrupting the cell division process. Our work offers safe, readily available candidate agents for controlling CRC-associated pathogenic bacteria and establishes a reliable computational-experimental workflow to screen division-targeted antimicrobials for microbiome-related cancers.},
}

@article {pmid43001783,
year = {2026},
author = {Paris, ER and Salcedo, RSR and Buessecker, S and Pozarycki, C and Desmarais, M and Sephus, CD and Schartup, AT and Bartlett, DH and Ingall, ED and Doran, PT and Andersson, A and Glass, JB and Quartini, E and Schmidt, BE and Bowman, JS and Dekas, AE},
title = {Free-living autotrophs drive a carbon fixation peak within the Orca Basin chemocline while heterotrophs dominate total activity from seawater to brine.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag279},
pmid = {43001783},
issn = {1751-7370},
abstract = {Deep hypersaline anoxic basins (DHABs) are stratified, polyextreme environments found within enclosed and semi-enclosed seas worldwide. Here, we quantified microbial activity in Orca Basin, the largest known DHAB, to investigate carbon cycling across its steep chemical and salinity gradients. We measured total anabolic activity and dissolved inorganic carbon (DIC) fixation as a function of metabolic lifestyle (autotroph or heterotroph) and spatial niche (free-living or particle-associated) using dual-isotope labeling experiments and single-cell analysis by nanoscale secondary ion mass spectrometry (nanoSIMS). Activity was detected within all ten depths investigated from seawater to hypersaline brine, including by most cells within the brine. DIC fixation and total anabolic activity peaked within the oxic-anoxic interface, notably separate from the peak in cell and particle density deeper in the halocline. Autotrophs drove the peak in DIC fixation, but heterotrophs drove that of total activity; autotrophs were more abundant than heterotrophs at this depth but on average smaller and slower growing. Particle-associated heterotrophs, but not autotrophs, were significantly more active than their free-living counterparts within the interface. Heterotrophic communities derived an average of 4% to 10% of their biomass from DIC across the vertical transect, contributing just 2% of total DIC fixation within the peak but the majority within overlying seawater. Metagenomic analysis of catabolically active, sorted cells indicated members of at least five phyla were active within the oxic-anoxic interface, including putatively autotrophic Thermoproteota. These data provide high-sensitivity microbial activity measurements in Orca Basin and highlight the widespread viability of the resident microbiome.},
}

@article {pmid43001800,
year = {2026},
author = {Tang, Y and Sun, Y},
title = {Benchmarking gut microbiome health indices by their sensitivity to subclinical risk in 12,561 adults.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0331626},
doi = {10.1128/spectrum.03316-26},
pmid = {43001800},
issn = {2165-0497},
abstract = {A growing number of indices claim to summarize gut "microbiome health," yet they are routinely treated as interchangeable, even though their relative sensitivity to host risk remains undefined. In 12,561 adults from the American Gut Project (16S rRNA gene profiles), we benchmarked five indices spanning distinct constructs-taxonomic composition (Gut Microbiome Wellness Index 2 [GMWI2] and ZOE), diversity (Shannon), functional redundancy index (FRI), and reference-based structural deviation (microbiome deviation index [MDI])-along a cumulative lifestyle-risk gradient and against four chronic disease clusters. Shannon diversity, abundance-weighted ZOE, and MDI each shifted dose-dependently from the earliest risk increments (Jonckheere-Terpstra P < 0.001), and pathway-level composites moved in the expected directions; FRI and GMWI2 did not. Disease associations were index specific and cluster specific: Shannon (protective direction) and ZOE (risk direction) were associated with all four clusters, MDI with metabolic/systemic disease, and FRI with gastrointestinal disease, whereas GMWI2 showed no association throughout. The five indices were only moderately intercorrelated (Spearman |ρ| ≤0.52). Shannon and ZOE-the most consistent performers-showed only modest effects (per standard deviation, odds ratios 0.84-0.94 and 1.08-1.22, respectively), and neither captured the structural-deviation signal indexed by MDI. Associations between environmental stressors (including PM10, heptachlor, and ozone) and microbiome outcomes were concentrated in higher-risk hosts, consistent with host vulnerability gating the microbiome's environmental stress response. Together, these results show that widely used microbiome health indices are not interchangeable: they detect overlapping but non-identical facets of dysbiosis, and their sensitivity to subclinical risk depends on index formulation and data resolution. An interpretable, complementary panel rather than any single score may therefore best support early stratification.IMPORTANCEGut microbiome "health" is increasingly summarized using single numerical scores, yet these scores are often treated as equivalent despite measuring different biological features. By comparing five widely used indices in 12,561 adults, we show that they differ substantially in their ability to detect early, subclinical changes associated with cumulative lifestyle risk. Measures of microbial diversity, abundance-weighted taxonomic composition, and deviation from a healthy reference changed progressively from the earliest risk increments, whereas a functional redundancy measure and a presence/absence-based taxonomic index were comparatively insensitive, and pairwise correlations between indices were only moderate (|ρ| ≤0.52). We also found that associations between environmental pollutants and microbiome disruption were strongest among individuals with higher baseline lifestyle risk. These findings argue against relying on a single universal microbiome health score and support the use of complementary indices for early risk stratification and future microbiome-based prevention research.},
}

@article {pmid43001898,
year = {2026},
author = {Mazzoni, C and Yassour, M},
title = {IBD is associated with species-specific changes in gut microbial gene diversity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0082726},
doi = {10.1128/msystems.00827-26},
pmid = {43001898},
issn = {2379-5077},
abstract = {UNLABELLED: Intra-species genomic variation provides the raw material for natural selection and can reflect the recent diversification history of microbial populations. Environmental stress may be regarded as the ultimate accelerator of the evolutionary process, especially for microorganisms, which can alter their DNA if presented with nutrient limitation, toxins, or pathogen attack. Chronic intestinal inflammation, as in inflammatory bowel disease (IBD), represents prolonged environmental stress for gut commensal bacteria, bringing many enteric species down to undetectable levels. However, it remains unclear how microbes that colonize IBD patients actually respond to IBD-associated stressors and whether stress-driven bacterial dynamics may be identified at the population level from the bacterial gut metagenome. To investigate IBD-associated strain-level population dynamics, we performed metagenomic analyses focusing on measuring within-individual bacterial diversity for a panel of gut commensals present across IBD patients and Controls. First, we found species-specific differences in genome-level bacterial diversity. Then, we found that certain genes and functions may harbor different levels and kinds of genetic divergence within the same species across IBD patients and Controls. Functions that were enriched in IBD with both neutral divergence and functional divergence were associated with motility and iron-scavenging, among others. These results may point toward functions that are under selection in the context of IBD stress and could inform future mechanistic work, exploring previously unknown routes of bacterial diversification and adaptation to stress in the gut microbiome.

IMPORTANCE: Inflammatory bowel disease (IBD) is characterized by profound alterations in the gut microbiome composition, and most research so far has focused on changes in species-level abundance to understand gut microbiome contributions to disease dynamics. However, investigating strain-level variation has the potential to uncover previously unknown factors underlying bacterial persistence during gut inflammation, hence revealing key aspects driving gut dysbiosis. Here, we showed that IBD is associated with species-specific changes in gut microbial population-level genetic diversity and identified individual genes and functions that seem to harbor differential genetic diversity within IBD-associated strains. More broadly, our results highlight how intra-species population- and gene-level diversity could be used as sensors of environmental stress in the gut microbiome, and further studies could follow up on the functions highlighted in this work to establish causal links between gut inflammatory conditions and processes of bacterial adaptation to stress.},
}

@article {pmid43002042,
year = {2026},
author = {Liu, S and Chen, W and Chen, L and Wang, Y and Zhou, L and Yin, Q and Wang, Z and Wang, D and Lu, Z},
title = {Targeted Dual-Responsive Probiotic Microspheres for Sequential Protection, Adhesion, and On-Demand Release in Ulcerative Colitis Therapy.},
journal = {Biomacromolecules},
volume = {27},
number = {11},
pages = {7377-7387},
doi = {10.1021/acs.biomac.6c01432},
pmid = {43002042},
issn = {1526-4602},
support = {52273060//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Probiotics/administration & dosage/chemistry/pharmacology ; Animals ; *Microspheres ; *Colitis, Ulcerative/drug therapy/chemically induced/microbiology/pathology ; Mice ; Dextran Sulfate/toxicity ; Mice, Inbred C57BL ; Humans ; },
abstract = {Oral probiotics show promise for inflammatory bowel disease but are limited by poor gastrointestinal viability, targeting, and colonization. We developed a multi-targeting probiotic composite microsphere (PCM) via scalable solution blow-spinning, with >20-fold higher throughput than electrospinning. PCMs provide three key functions: (1) pH-triggered probiotic protection: PCMs contract in gastric acid, shielding probiotics and increasing survival 2162-fold over free probiotics; (2) charge-mediated adhesion: negatively charged microspheres adhere to positively charged mucin overexpressed at inflamed colonic lesions; and (3) enzyme-triggered release: overexpressed hyaluronidase degrades hyaluronic acid, releasing viable bacteria via the "Trojan horse" mechanism. This sequential mechanism ensures high local probiotic density at inflamed sites. In DSS-induced mouse colitis, PCMs outperformed 5-aminosalicylic acid in alleviating inflammation, repairing the mucosal barrier, and restoring microbial homeostasis. 16S rRNA sequencing showed selective enrichment of beneficial genera and suppression of inflammation-associated pathobionts. This scalable, multi-responsive platform offers next-generation oral therapy for IBD and microbiome-associated gastrointestinal diseases.},
}

*Probiotics/administration & dosage/chemistry/pharmacology
Animals
*Microspheres
*Colitis, Ulcerative/drug therapy/chemically induced/microbiology/pathology
Mice
Dextran Sulfate/toxicity
Mice, Inbred C57BL
Humans

@article {pmid43002081,
year = {2026},
author = {Irfan, B and Ghafarian, AM and Salahie, A and Shihabi, K and Ewidat, O and Riyad, N and Kamel, M and Khan, I and Tesfaye, B},
title = {Nutrition's Impact on Recovery in Craniofacial and Otorhinolaryngological Injuries: Considering Areas of Armed Conflict and Humanitarian Emergencies.},
journal = {The Journal of craniofacial surgery},
volume = {37},
number = {1-2},
pages = {383-388},
pmid = {43002081},
issn = {1536-3732},
mesh = {Humans ; *Armed Conflicts ; *Craniocerebral Trauma/physiopathology ; *Facial Injuries ; *Malnutrition/physiopathology/complications ; Emergencies ; *Neck Injuries ; Wound Healing/physiology ; *Nutritional Status ; Recovery of Function ; },
abstract = {Head-and-neck trauma can often create a double burden wherein metabolic demand surges just as oral intake is curtailed by pain, dysphagia, fixation, airway protection, and procedure-related restrictions. This article argues that nutrition often becomes the rate-limiting step of recovery in craniofacial and otorhinolaryngological injuries. We synthesize how the neuroendocrine stress-metabolic response drives hypercatabolism and immune activation, and how malnutrition can derail these adaptive programs by impairing collagen deposition, angiogenesis, leukocyte function, and the oral microbiome, and thereby raising the risk of infection and potentially delaying wound closure, speech, mastication, swallowing, and psychosocial reintegration. We then map some of the compounding effects of armed conflict and humanitarian crises, wherein the absence of robust medical and humanitarian aid and coupled with resource shortages, patients may be pushed into states of poorer health outcomes.},
}

Humans
*Armed Conflicts
*Craniocerebral Trauma/physiopathology
*Facial Injuries
*Malnutrition/physiopathology/complications
Emergencies
*Neck Injuries
Wound Healing/physiology
*Nutritional Status
Recovery of Function

@article {pmid43002096,
year = {2026},
author = {Radlinski, LC and Bäumler, AJ},
title = {Beyond association: pathogenesis models reveal ecological drivers of vaginal dysbiosis.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0028726},
doi = {10.1128/iai.00287-26},
pmid = {43002096},
issn = {1098-5522},
abstract = {Despite its critical importance to health, our understanding of the vaginal microbiome lags far behind other mucosal sites, reflecting both the distinct biology of the human vaginal microenvironment and the historic neglect of women's reproductive health in biomedical research. Recent investment in this area, coupled with the widespread use of high-throughput omics technologies, has greatly expanded our understanding of vaginal microbiota states and their associations with health and disease. However, associative studies that correlate community composition with clinical outcomes are limited in their ability to define causal, modifiable host-microbe relationships that support a protective microbiota. Consequently, broad probiotic strategies based on descriptive findings show limited success in restoring lasting homeostasis in the female reproductive tract. Murine infection models provide tractable systems for identifying evolutionarily conserved physiological processes that influence microbial growth. Here, we highlight studies across pathogenesis fields that leverage murine models to identify ecological factors controlling infection susceptibility in the vaginal microenvironment. Rather than treating pathogen colonization as an endpoint alone, we emphasize how genetically tractable microbes reveal the resources, barriers, and immune responses mediating microbial persistence, ascension, and inflammation. Where possible, we integrate these findings with clinical observations to assess their relevance to human reproductive health. Together, these studies illustrate how imperfect but tractable models reveal causal drivers of vaginal dysbiosis in women and help ground large-scale associative studies in a more clinically relevant way.},
}

@article {pmid43002309,
year = {2026},
author = {Jasur, R and Abdujalilovich, BS and Bakhodirjon, S and Narziyev, Z and Kamol, K},
title = {Microbiome-associated metabolites as emerging biomarkers of cancer immunotherapy response: from mechanistic networks to clinical validation.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {43002309},
issn = {1874-9356},
abstract = {Immune checkpoint blockade has improved outcomes across several cancers, yet many patients experience primary or acquired resistance. The gut microbiome may contribute to this variation through metabolic activities that influence systemic and tumor-associated immunity. This narrative review examines microbiome-associated metabolites as potential markers of immunotherapy response, with particular attention to their biological origins, immune effects, and clinical validation. We distinguish metabolites produced directly by microorganisms, such as fermentation-derived short-chain fatty acids and bacterial indoles, from host substrates transformed by microbial enzymes, including secondary bile acids. We also consider host-microbial co-metabolites and predominantly host- or tumor-derived mediators, such as kynurenine and CD39/CD73-generated adenosine, whose regulation may be influenced by the microbiome. Evidence concerning inosine, polyamines, and lipid mediators is interpreted according to their specific metabolic sources. These compounds have been linked to epithelial barrier function, antigen presentation, T-cell activity, and immunosuppressive signaling, although their effects vary across biological compartments and clinical settings. We examine the limitations of stool and circulating measurements, pre-analytical variability, metabolomic assays, and the distinction between mechanistic findings and clinically validated associations. Current evidence supports further investigation of selected metabolite signatures, but few have undergone independent clinical validation. Reliable biomarker development will require source-aware interpretation, standardized quantitative methods, longitudinal clinical studies, and evidence that metabolite measurements improve decisions about immunotherapy.},
}

@article {pmid43002367,
year = {2026},
author = {Tiwari, S and Bhattacharya, S},
title = {Sodium Butyrate: A Microbiota-Derived Short-Chain Fatty Acid Regulating Inflammation, Gut Barrier Function, and Colorectal Cancer Progression.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {43002367},
issn = {1867-1314},
abstract = {Colorectal cancer (CRC) is a polyetiologic disease related to genetic changes, chronic inflammation, dysregulation of the intestinal barrier, diet and gut microbiota dysbiosis. Butyrate is a short-chain fatty acid (SCFA) produced by the microbiota that plays a crucial role in energy metabolism, epithelial homeostasis and mucosal immunity. Sodium butyrate (NaB), the sodium salt of butyric acid, has therefore been the subject of experimental investigation and appears to be a therapeutic option of potential interest. This review critically explores the biological, pharmacological and translational significance of butyrate and NaB in CRC. It details the origins and physicochemical properties, pharmacokinetics, effects on the intestinal barrier, and interactions with the intestinal microbiota, alongside immunomodulatory actions, molecular pathways underlying anti-cancer efficacy, clinical evidence, and patent holdings, and further explores prospective formulation and delivery methods. Butyrate/NaB exerts pleiotropic effects via inhibition of HDAC and activation of free fatty acid receptors (FFARs), such as GPR41/FFAR3, GPR43/FFAR2 and GPR109A/HCAR2.These processes regulate various inflammatory and oncogenic signaling pathways, including NF-κB, NLRP3, Wnt/β-catenin, PI3K/Akt, MAPK, and STAT3, as well as mitochondrial metabolism, oxidative stress, cell-cycle progression, apoptosis, epithelial-mesenchymal transition, and immune-cell function. Additionally, butyrate helps preserve gut barrier function and can influence CRC biology by interacting with the tumour microenvironment, microbial metabolism, and epithelial cells. There is extensive preclinical evidence of the barrier-protective, anti-inflammatory, immunomodulatory, and anticancer properties of butyrate/NaB in cell- and animal-based models. The strength of evidence, however, depends on the model, concentration/dose, duration of treatment and endpoint. The mechanistic and preclinical results should therefore not be interpreted as being equivalent to actual clinical efficacy. There is limited available human evidence for specific therapeutic uses of CRC. Various factors limit its translational application, including rapid metabolism, a short biological half-life, and low systemic exposure, as well as inherent butyrate fluctuations, formulation challenges, and a scarcity of stringent clinical trials tailored to CRC. Colon-targeted delivery systems, microencapsulation, nanotechnology-based delivery systems, microbiome-directed interventions, patient selection by biomarkers, and rational combination strategies may overcome these limitations. Butyrate/NaB offers a promising multitarget strategy for CRC research; however, further investigation into its mechanisms, pharmacokinetics, dosing, formulation, and large-scale clinical trials is necessary to validate its therapeutic efficacy and define its translational potential.},
}

@article {pmid43002368,
year = {2026},
author = {Kshirsagar, S and Narwal, N and Rajendran, V and Vinchurkar, RV and Kelkar, S and Kadyan, S and Vishweswaraiah, RH and Vij, S and Pradhan, D},
title = {From Phenotype to Phylogenomics: Evolution of Lactobacillaceae Taxonomy, the 2020 Reclassification and its Technological and Regulatory Implications.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {43002368},
issn = {1867-1314},
abstract = {Lactic acid bacteria (LAB) are a diverse group of microorganisms with major importance in food fermentation, biopreservation, probiotic development, and biotechnology. Advances in molecular biology and whole-genome sequencing have revealed limitations of traditional phenotype-based classification, driving a transition toward genome-based taxonomy and fundamentally reshaping the classification of the family Lactobacillaceae. This review traces the evolution of LAB taxonomy from classical phenotypic classification through the molecular era to contemporary phylogenomic approaches. It examines the genomic methodologies underpinning modern bacterial systematics, including whole-genome sequencing, Average Nucleotide Identity (principally a species-level measure), Average Amino Acid Identity, and core-genome phylogenetics, which culminated in the landmark 2020 reclassification of the former genus Lactobacillus into 25 phylogenetically coherent genera. The review further evaluates the scientific evidence supporting this reclassification and its validation through subsequent phylogenomic, pangenomic, and ecological studies. Genome-based taxonomy has established a more evolutionarily coherent and biologically informative classification of Lactobacillaceae, improving our understanding of ecological adaptation, metabolic diversity, and functional potential. Genus-level taxonomy provides a useful framework for comparative research, but its predictive value is limited by the strain-specific nature of many functional and safety traits. The revised taxonomy has nevertheless strengthened comparative genomics, microbiome research, strain selection, and communication across scientific, industrial, and regulatory domains. Although the nomenclatural transition has created challenges for product labeling, regulatory documentation, database harmonization, and scientific communication, it provides a more robust evolutionary framework for future research and industrial innovation. Remaining challenges, including limitations of 16 S rRNA-based identification, uncertainty surrounding genomic thresholds, and incorporation of uncultured diversity through metagenomics and pangenomics, indicate that Lactobacillaceae taxonomy will continue to evolve as genomic resources and analytical approaches advance.},
}

@article {pmid43002640,
year = {2026},
author = {da Silva Santos, A and Teixeira, JP and Boiago, MM and Brancalion, CA and da Silva, AS and de Lima Neto, DF and da Rosa, JG and Bajay, MM},
title = {Temporal Dynamics of the Faecal Microbiota and Physiological Responses to Phytobiotics and Organic Acids in Broiler Chickens.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.70126},
pmid = {43002640},
issn = {1439-0396},
support = {//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil (CAPES)/ ; },
abstract = {This study compared three alternative feed-additive blends with an antibiotic control to assess growth performance, physiological responses and age-related variation in the faecal microbiota of broiler chickens. A total of 240 male Cobb 500 broilers were allocated to four treatments with four replicate pens each: antibiotic control, organic acids (OA), plant extracts and essential oils (PE+EO), and essential oils combined with prebiotic/probiotic components and minerals (EO+PRE/PRO). Faecal bacterial profiles were assessed by 16S ribosomal RNA gene sequencing in 16 pooled libraries representing the four treatments at 7, 21, 35 and 42 days. Microbiome analyses were exploratory because only one library was available per treatment-age combination. Alpha diversity did not differ significantly by treatment or age. Permutational multivariate analysis of variance identified an age effect on Bray-Curtis community composition (R[2] = 0.312, p = 0.0139), but no treatment effect (R[2] = 0.201, p = 0.221). No genus showed a treatment effect after false-discovery-rate correction. Predicted functional analysis identified 31 pathways with a global age effect and no robust treatment effect. The PE + EO blend improved feed conversion relative to the antibiotic control during Days 1-21 and 1-35. Physiological, meat-quality and intestinal-morphometry responses varied among treatments. Thus, host responses to these additives occurred alongside predominantly age-associated faecal microbial variation; the data do not establish that microbiota changes mediated the host responses.},
}

@article {pmid43002692,
year = {2026},
author = {Margalida, A and Castellano-Hinojosa, A and Oliva-Vidal, P and Boutin, S and María Martínez, J and Braun, M and Sauer-Gürth, H and Schulze-Hagen, K and Wink, M},
title = {Host and anatomical filters prevent microbiome convergence in avian scavengers.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {47},
pages = {e2626358123},
doi = {10.1073/pnas.2626358123},
pmid = {43002692},
issn = {1091-6490},
support = {PID2022-142328OB-I00//Ministry of Science and Innovation/ ; },
mesh = {Animals ; *Microbiota ; Bacteria/classification/genetics ; *Falconiformes/microbiology ; Male ; Female ; Cloaca/microbiology ; *Host Microbial Interactions ; },
abstract = {How host-associated microbiomes assemble under intense environmental microbial exposure remains a central question in microbial ecology. Vultures represent a unique natural system because these species differ markedly in feeding ecology and carcass use. We characterized bacterial communities across four anatomical niches (facial, buccal, tracheal, and cloacal) in 155 individuals spanning all four European obligate vulture species (subfamily Gypaetinae: Gypaetus barbatus, Neophron percnopterus, and Aegypiinae: Aegypius monachus and Gyps fulvus) and the facultative scavenger Milvus milvus. Microbiome composition was jointly structured by host species and anatomical niche, with host identity explaining more variation than anatomical compartment and a significant interaction indicating that interspecific differentiation depended on body site. Each niche supported distinct bacterial assemblages and core microbiomes: Cloacal communities were enriched in anaerobic gut-associated taxa, whereas facial and tracheal communities contained more environmental and respiratory-associated bacteria. Host-specific taxonomic signatures persisted within anatomical niches despite recurrent exposure to the same carrion-associated microbial pool. Age further influenced community composition, whereas sex had little detectable effect. The facultative scavenger showed the same broad anatomical compartmentalization observed in obligate scavengers, although taxonomic signatures differed among species. Thus, sustained exposure to a shared, microbially rich resource was insufficient to produce a common scavenger microbiome. Instead, microbiome assembly reflected hierarchical filtering by host identity, anatomical environment, and ontogeny. These findings distinguish microbial exposure from microbial persistence, establishing avian scavengers as a natural model for understanding how host-associated communities remain differentiated, despite recurrent exposure to shared environmental microbial reservoirs across ecological and anatomical scales in vertebrate hosts.},
}

Animals
*Microbiota
Bacteria/classification/genetics
*Falconiformes/microbiology
Male
Female
Cloaca/microbiology
*Host Microbial Interactions

@article {pmid43002898,
year = {2026},
author = {Yu, X and He, J and Liu, M},
title = {Critical advances and translational bottlenecks of gut microbiota-gut-brain axis targeted therapy for neurodegenerative and neurodevelopmental disorders.},
journal = {Journal of neuroimmunology},
volume = {423},
number = {},
pages = {579117},
doi = {10.1016/j.jneuroim.2026.579117},
pmid = {43002898},
issn = {1872-8421},
abstract = {Neurological diseases have become a major global public health burden. Existing central nervous system-targeted therapies can only alleviate clinical symptoms but fail to halt the progression of neurodegenerative diseases, presenting mechanistic limitations and therapeutic bottlenecks. The gut microbiota participates in the regulation of central nervous system (CNS) homeostasis and neuropathological processes via the microbiota-gut-brain axis (MGBA). Notably, dysbiosis may induce damage to the blood-brain barrier, neurotransmitter dysregulation, and immune imbalance, thereby mediating the onset and progression of various neurological diseases, including Parkinson's disease, Alzheimer's disease (AD), autism spectrum disorder (ASD), and multiple sclerosis (MS). This article provides a systematic review of the core mechanisms by which the gut microbiome regulates neurological diseases, including inflammation regulation, oxidative stress responses, and neuroendocrine remodeling mediated by microbial metabolites. It also comprehensively summarizes the research progress, application advantages, and existing limitations of novel gut-targeted interventions, such as probiotics, prebiotics, fecal microbiota transplantation (FMT), dietary interventions, and live biological therapies. At the same time, the article critically examines key bottlenecks prevalent in the field: the causal relationship between the microbiota and disease remains unclear; there is a significant translational gap between animal and human studies; there is a lack of unified standards for multi-omics analysis systems; and interference from confounding factors such as age, diet, and medications is significant. Existing research indicates that gut microbiota interventions complement traditional symptomatic treatments and hold promising prospects for early disease intervention and adjunctive therapy for refractory patients. Future efforts should integrate multi-omics and artificial intelligence technologies to decipher the causal networks governing gut-central nervous system regulation, establish standardized research frameworks, advance the clinical translation of precision gut microbiota therapies, and provide new approaches for the comprehensive prevention, control, and personalized treatment of neurological disorders.},
}

@article {pmid43003072,
year = {2026},
author = {Kotlarova, A and Vlasak, J and Wald, M and Stolz, A},
title = {Skin Microbiome in Lymphatic Insufficiency And Lymphedema: A Systematic Review of Clinical Sequencing Studies.},
journal = {Lymphology},
volume = {59},
number = {3},
pages = {153-160},
pmid = {43003072},
issn = {2522-7963},
mesh = {Humans ; *Skin Microbiome ; *Lymphedema/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Lymphatic insufficiency predisposes to chronic edema, barrier dysfunction, and recurrent cellulitis/erysipelas. Because the skin microbiome interacts with cutaneous immunity, dysbiosis may contribute to infectious complications and lymphatic insufficiency progression. We performed a PRISMA 2020-guided systematic review of studies indexed in PubMed/MEDLINE, Scopus, and Web of Science from inception to 31 December 2025. Studies included adult clinical studies that profiled the skin microbiome in lymphatic insufficiency/lymphedema using molecular methods (primarily 16S rRNA sequencing) and compared affected skin with contralateral sites and/or healthy controls. Four studies with 292 subjects met inclusion criteria and encompassed cancer‑related upper‑limb lymphedema and endemic lower‑limb lymph-edema (filarial lymphedema and podoconiosis). Methodological quality assessment using the Newcastle-Ottawa Scale demonstrated moderate-to-high quality across the included studies. All studies reported differences between affected and control skin, but no consistent taxonomic "signature" emerged. Reported changes included greater microbial heterogeneity, relative enrichment of potentially pathogenic taxa (notably Staphylococcus and Streptococcus), depletion of common commensals (Corynebacterium and Cutibacterium), and greater representation of anaerobes with increasing clinical severity. Standardized longitudinal studies are needed to establish causality and clinical utility.},
}

Humans
*Skin Microbiome
*Lymphedema/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid43003155,
year = {2026},
author = {Levin, G and Peláez-Vico, MÁ and Fichman, Y and Schuster, G and Mittler, R},
title = {H2O2 as a universal interspecies signaling molecule.},
journal = {Free radical biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2026.11.015},
pmid = {43003155},
issn = {1873-4596},
abstract = {Hydrogen peroxide (H2O2) plays a central role in cells, serving as important signal transduction molecule but also potentially causing oxidative stress, leading to cell death. Recent studies reveal that in addition to its many intracellular redox-driven signaling roles, H2O2 can mediate different cell-to-cell, organism-to-organism, and even interspecies communication, with major consequences for the health, symbiosis, and/or survival of the involved organisms. While new research has revealed some of the mechanisms and outcomes of interspecies H2O2 signaling, the effects of H2O2-driven interspecies communication routes on entire communities and ecosystems remain largely unknown. Here, we summarize current research on interspecies H2O2 signaling. We present examples from multiple biological systems to demonstrate the universality of H2O2/redox-driven communication mechanisms and discuss their effects on participating organisms. Finally, we highlight the potential contributions interspecies H2O2 signaling may have to communities and ecosystems and how studying interspecies H2O2 signaling can help us prevent long-term agricultural, ecological, and human health damages.},
}

@article {pmid43003303,
year = {2026},
author = {Ovaskainen, O and Łukasik, P and Roslin, T},
title = {Joint species distribution modelling of insect microbiota: Time to jump onto a new opportunity.},
journal = {Current opinion in insect science},
volume = {},
number = {},
pages = {101650},
doi = {10.1016/j.cois.2026.101650},
pmid = {43003303},
issn = {2214-5753},
abstract = {How microbes and insects influence each other is a topical question in insect science. With this contribution, we highlight joint species distribution models (JSDMs) - which model all microbial taxa in a community jointly rather than one at a time - as a statistical framework particularly well suited for resolving the drivers of host-microbe associations. While JSDM has been widely applied to microbiota of organisms other than insects, only a handful of studies have applied them thus far to insect systems. To encourage insect microbiota researchers to catch up with the benefits of JSDM, we outline the statistical and ecological basics of JSDM and give flesh to the modelling framework by reviewing how it has so far been applied to insect microbiota. We highlight the power of JSDMs in separating host, environmental and microbial drivers of community assembly, and in generating hypotheses about how different microbes influence each other. We further propose a predictive framework for identifying and characterizing five ecological categories of insect-associated microbes: (1) obligate nutritional symbionts; (2) facultative endosymbionts; (3) specialized gut associates; (4) transient microbes; and (5) pathogens and parasites. In particular, we hypothesize how the ecological characteristics of these different microbial categories are reflected in the statistical signatures recovered by JSDMs. We further suggest how JSDM can be applied to address the phylogenetic and ecological scales at which microbiome patterns are structured and to uncover how global environmental changes may reshape insect microbiota.},
}

@article {pmid43003314,
year = {2026},
author = {Xiang, J and Lian, B and Li, H and Bai, W and Wang, J},
title = {Valorization of livestock biogas slurry through indigenous Oocystis sp. cultivation for nutrient recovery and production of plant-beneficial biomass.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136214},
doi = {10.1016/j.biortech.2026.136214},
pmid = {43003314},
issn = {1873-2976},
abstract = {Livestock biogas slurry contains abundant nitrogen and phosphorus resources, but requires effective strategies for nutrient recovery and high-value utilization. This study isolated an indigenous Oocystis sp. strain from livestock biogas slurry and evaluated its potential for coupling wastewater treatment with the production of value-added algal biomass. The nutrient-removal performance of Oocystis sp. in the sequential bacteria-microalgae coupling system was evaluated, while its growth, biochemical composition, and IAA-equivalent content were compared among different cultivation backgrounds. The sequential bacteria-Oocystis sp. coupling system achieved overall removal efficiencies of 96.68 %, 84.72 %, 72.07 %, and 87.13 % for PO4[3-]-P, total phosphorus, NH4[+]-N, and NO3[-]-N, respectively. Compared to BG11 cultivation, cultivation in microbially treated slurry increased soluble protein and IAA-equivalent contents of Oocystis sp. biomass by 57.60 % and 142.57 %, respectively. Furthermore, application of the Oocystis sp. culture produced in microbially treated slurry increased plant dry weight, root length, and root activity by 53.84 %, 44.13 %, and 154.18 %, respectively. Moreover, within the microbially treated slurry background, the WBO treatment was associated with altered rhizosphere bacterial community composition, and several WBO-enriched taxa showed positive correlations with plant growth traits. Therefore, indigenous Oocystis sp. cultivation provides a promising route for nutrient recovery from livestock biogas slurry and subsequent agricultural utilization of the resulting microalgal culture.},
}

@article {pmid43003693,
year = {2026},
author = {Niedobová, J and Wijacki, T and Faltýnková, A},
title = {Predator-associated microbiomes as hidden modulators of pesticide-compatible biological control in agroecosystems.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.71483},
pmid = {43003693},
issn = {1526-4998},
support = {RO1526//Ministerstvo Zemědělství/ ; },
abstract = {Beneficial arthropod predators are central components of integrated pest management, yet their performance in crop systems is often variable because predator efficacy depends on interactions among host traits, prey availability, intraspecific and interspecific interactions, pesticide exposure and environmental stressors. Predator-associated microbiomes, including gut microbiota, tissue-resident bacteria and facultative or obligate endosymbionts, represent an overlooked functional layer that may influence predator nutrition, stress physiology, reproduction, behaviour, dispersal and pesticide tolerance. This review synthesizes evidence from spiders, ladybird beetles, green lacewings, earwigs and predatory Heteroptera, with emphasis on traits that determine biological pest control under agroecosystem pressure. A central contribution is an evidence hierarchy that distinguishes descriptive, associative, experimental, mechanistic and field-level evidence. The strongest predator-specific associations currently come from spiders, where tissue-resident microbial assemblages have been linked to the spider insecticide survival, predicted detoxification pathways and physiological resilience under chemical stress; however, causal microbial mechanisms remain insufficiently tested. In other predator groups, microbiome-associated patterns suggest plausible microbial contributions to predator performance, but experimentally validated microbiome-mediated effects remain limited and are often inferred from symbiont surveys, diet-induced shifts in predator-associated microbiomes, reproductive manipulation and functional prediction. We argue that pest management research should move from descriptive microbiome profiling toward causal tests linking microbial taxa and functions to predator performance, pesticide compatibility and field-scale pest suppression. Incorporating microbiome information and experimentally validated microbial traits into ecotoxicology, mass rearing and conservation biological control could improve the reliability and resilience of predator-based pest suppression in agricultural landscapes. © 2026 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.},
}

@article {pmid43003811,
year = {2026},
author = {Kayongo, A and Bartolomaeus, TUP and Hecker, J and Birkner, T and Vila, E and Ntayi, ML and Markó, L and Löber, U and Olweny, G and Kyalo, E and Kyamulabi, D and Ndawula, J and Ssengooba, W and Nabatanzi, R and Kyobe, S and Nassali, F and Kigozi, E and Kalyesubula, R and Munana, R and Namaganda, J and Musiime, CJ and Sekibira, R and Bagaya, BS and Kateete, DP and Joloba, ML and Jjingo, D and Lusiba, J and Worodria, W and Mayanja-Kizza, H and Lalitha, R and Ham, W and Sanyu, I and Zawedde, J and Robertson, NM and Obondo, JS and Weidinger, C and Kunkel, D and Kirenga, BJ and Siddharthan, T and Hurst, JR and Checkley, W and Cookson, WB and Moffatt, MF and Forslund-Startceva, SK},
title = {Microbial ecological instability and non-linear host interactions shape airway inflammation in HIV-associated COPD.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {43003811},
issn = {2041-1723},
support = {R21TW012354//U.S. Department of Health & Human Services | NIH | Fogarty International Center (FIC)/ ; 3R21TW012354-S1/S2//U.S. Department of Health & Human Services | NIH | Fogarty International Center (FIC)/ ; K43TW013092//U.S. Department of Health & Human Services | NIH | Fogarty International Center (FIC)/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/immunology/complications ; *HIV Infections/complications/microbiology/immunology ; Sputum/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Inflammation/microbiology ; Female ; Male ; Adult ; *Host Microbial Interactions/immunology ; Middle Aged ; Longitudinal Studies ; Cytokines/metabolism ; Multiomics ; Bronchoalveolar Lavage Fluid ; },
abstract = {Chronic obstructive pulmonary disease (COPD) is increasingly recognized among people living with HIV in sub-Saharan Africa, yet the mechanisms linking airway microbial ecology to chronic inflammation remain poorly understood. Here, we study 200 adults stratified by HIV and COPD status, including 160 participants with two-year longitudinal follow-up, using an integrated multi-omics framework combining sputum 16S rRNA profiling, bacterial outer membrane vesicle quantification, airway cytokine profiling, CyTOF immune phenotyping, bulk transcriptomics of induced sputum, bronchoalveolar lavage and peripheral blood, and bronchoalveolar lavage single-cell RNA sequencing-guided deconvolution. We find that sputum microbial communities are shaped predominantly by temporal ecological turnover rather than HIV or COPD status. Although microbial diversity, microbiome instability, outer membrane vesicle burden and inferred airway cellular composition remain largely preserved, HIV-associated COPD exhibits disease-specific microbial signatures together with inflammatory transcriptional remodeling concentrated in induced sputum. Integrated analyses identify selective host-microbe interaction networks linking discrete microbial taxa with inflammatory, immune and transcriptional programmes.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/immunology/complications
*HIV Infections/complications/microbiology/immunology
Sputum/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Inflammation/microbiology
Female
Male
Adult
*Host Microbial Interactions/immunology
Middle Aged
Longitudinal Studies
Cytokines/metabolism
Multiomics
Bronchoalveolar Lavage Fluid

@article {pmid43003812,
year = {2026},
author = {Kong, L and Wenyue, M and Tingting, L and Jiani, W and Ziyi, L and Yongfang, L and Jingqi, Y and Qinmiao, Y and Yingting, L},
title = {The gut microbiota dietary index reveals a modifiable diet-depression association varying by BMI and possibly linked to inflammation: a hypothesis-generating modified diet for future intervention research.},
journal = {Translational psychiatry},
volume = {16},
number = {1},
pages = {},
pmid = {43003812},
issn = {2158-3188},
mesh = {Humans ; Female ; *Inflammation ; *Gastrointestinal Microbiome/physiology ; Male ; *Diet ; Cross-Sectional Studies ; *Depression/microbiology ; *Body Mass Index ; Adult ; Middle Aged ; },
abstract = {In the context of the microbiota-gut-brain axis, diet represents a critical yet still debated component of translational psychiatry. However, population-based evidence linking microbiota-supportive dietary patterns to depressive symptoms remains limited. This research leverages the Dietary Index for Gut Microbiota (DI-GM) to examine the associations between a gut-microbiota-friendly diet and depression, providing a theoretical framework for future research on practical applications. Using data from 28,884 adults, this cross-sectional study evaluated the association between DI-GM and PHQ-9 using survey-compatible descriptive and conventional regression analyses, ordinary-weighted generalized additive models (GAMs), XGBoost with SHAP for exploratory feature ranking, and an exploratory mediation-type analysis of systemic inflammation. Participants with depression had lower DI-GM scores than those without depression. Model-based analyses suggested an inverse predicted pattern between DI-GM and PHQ-9, especially with the interaction GAM indicating significant BMI-related heterogeneity (a more pronounced inverse association at higher BMI). XGBoost with SHAP analyses identified fiber, refined grains, percent energy from fat and whole grains as dietary features with relatively larger contributions to model predictions. Exploratory mediation-type analysis suggested that inflammation may partially explain the DI-GM-PHQ-9 association. However, a high DI-GM diet lacks depression-related nutrients like vitamin D, omega-3 fatty acids, and zinc. Based on these hypothesis-generating findings, we propose a conceptual framework for a Modified Gut Microbiota-Friendly Diet (MGFD) with high DI-GM score, caloric control, and targeted nutrient supplementation, requiring validation via prospective cohorts, randomized trials, and gut microbiome/metabolomic studies.},
}

Humans
Female
*Inflammation
*Gastrointestinal Microbiome/physiology
Male
*Diet
Cross-Sectional Studies
*Depression/microbiology
*Body Mass Index
Adult
Middle Aged

@article {pmid43003844,
year = {2026},
author = {Wang, Y and Xu, X and Chen, X and Zhang, Y and Zheng, W and Zhang, T},
title = {Scellmate enables contamination aware curation and host mobilome linkage analysis of large SAG datasets.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {43003844},
issn = {2041-1723},
support = {17212124//Research Grants Council, University Grants Committee (RGC, UGC)/ ; },
mesh = {*Genome, Bacterial/genetics ; *Microbiota/genetics ; Single-Cell Analysis/methods ; Metagenome/genetics ; *Bacteria/genetics/classification ; *Data Curation/methods ; Biocuration ; Metagenomics/methods ; Phylogeny ; },
abstract = {Single-cell genomics enables cell-resolved insights into in-situ microbial communities, yet single amplified genomes (SAGs) are often fragmented, taxonomically ambiguous, and prone to contamination, limiting their biological interpretation. Here, we present Scellmate, a scalable, semi-supervised framework that integrates whole-SAG curation, species-level taxonomic anchoring and SAG-mobilome linkage analysis for large-scale SAG datasets. Following benchmarking of its SAG curation and SAG-eMGE linkage modules using in silico and four-strain mock SAG datasets, respectively, Scellmate was applied to 11,976 sewage-derived SAGs. This approach yielded 4,198 SAGs passing Scellmate's whole-SAG curation, which captured pronounced heterogeneity masked by bulk methods. At the species level, we resolved extensive hidden diversity within abundant taxa such as Aliarcobacter that was unresolved by matched metagenome-assembled genomes; at the strain level, we pinpointed a distinct Agathobacter rectalis cluster carrying specialized carbon-utilization pathways, suggesting niche differentiation. Leveraging these curated SAGs, we identified 6,474 host-mobilome linkages across 2,378 SAGs; these linkages not only showed high concordance with host-association data within the Integrated Microbial Genomes (IMG) system but also significantly expanded species-level host assignments. Furthermore, we detected frequent inter-species sharing patterns of diverse cryptic plasmids within the order Bacteroidales. Together, this work demonstrates that high-throughput single-cell genomics, empowered by the robust framework, resolves fine-scale heterogeneity and host-mobilome dynamics, advancing culture-independent microbiome research.},
}

*Genome, Bacterial/genetics
*Microbiota/genetics
Single-Cell Analysis/methods
Metagenome/genetics
*Bacteria/genetics/classification
*Data Curation/methods
Biocuration
Metagenomics/methods
Phylogeny

@article {pmid43003899,
year = {2026},
author = {Kumpitsch, C and Bauer, E and Arora, B and Schmitz, RA and Moissl-Eichinger, C},
title = {The mammalian archaeome: diversity, function and emerging roles in health and disease.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {43003899},
issn = {1740-1534},
abstract = {Archaea are a fundamental yet historically overlooked part of the mammalian microbiome. Once thought to be limited to extreme environments, archaea, particularly methanogenic archaea, are now recognized as widespread colonizers of mammalian hosts, with key roles in gut metabolism, microbial syntrophy and host interaction. In this Review, we summarize current knowledge on the distribution, diversity and function of the mammalian archaeome, with a focus on humans and ruminants. We explore the ecological and physiological roles of Methanobrevibacter spp. as key gastrointestinal colonizers, archaeal interactions with bacterial communities and the host, and the impact of external factors such as diet, age and health status on the archaeome. We further highlight the translational potential of archaeome research, including methane mitigation strategies in cattle and emerging associations between the archaeome and human disease. By integrating insights across host species, we argue that understanding the archaeome is essential to fully comprehend mammalian microbiome function, evolution and its relevance to health and disease.},
}

@article {pmid43003900,
year = {2026},
author = {Javaid, N and Mateeva, T},
title = {The microbiome's voyage beyond Earth.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {43003900},
issn = {1740-1534},
}

@article {pmid43004013,
year = {2026},
author = {Scholten, J and El Aater, K and Bakker, CMD and Stockmann, HBAC and van Egmond, M and Kazemier, G and Tuynman, JB and Oosterling, SJ},
title = {Oral antibiotic prophylaxis in colorectal surgery and perioperative microbiota composition: a systematic review.},
journal = {International journal of colorectal disease},
volume = {41},
number = {1},
pages = {},
pmid = {43004013},
issn = {1432-1262},
support = {Uit2023/ad/2023.10//Spaarne Gasthuis Academie/ ; },
mesh = {Humans ; *Antibiotic Prophylaxis ; Colorectal Surgical Procedures ; Administration, Oral ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/administration & dosage ; Surgical Wound Infection/prevention & control/microbiology ; },
abstract = {PURPOSE: Oral antibiotic bowel prophylaxis (OAP) is used to reduce infectious complications in colorectal surgery, but its effects on perioperative gut microbiota composition remain unclear. This systematic review evaluated the impact of OAP on intestinal microbiota composition in adults undergoing colorectal surgery.

METHODS: A systematic search of PubMed, Cochrane Library, and Google Scholar was conducted up to November 18th, 2025, following PRISMA guidelines. Studies were eligible if they included adult colorectal surgery patients receiving OAP and reported microbiota composition using 16S rRNA sequencing and/or qPCR. Primary outcomes were changes in microbial diversity and taxonomic composition. Secondary outcomes were surgical site infection (SSI) and anastomotic leakage (AL).

RESULTS: Eleven studies involving over 1500 microbiota samples met inclusion criteria. OAP regimens varied widely in agents, duration, and combination with mechanical bowel preparation (MBP) or probiotics. Across studies, OAP consistently reduced microbial diversity and altered taxonomic composition, some shifts, such as increased Enterococcus or decreased Bacteroides, persisted postoperatively. Only a minority of studies assessed microbiota recovery beyond the early postoperative phase. Clinical outcomes such as SSI and anastomotic leakage were inconsistently reported, with limited direct correlations to microbiota data.

CONCLUSION: OAP substantially alters perioperative gut microbiota composition in colorectal surgery patients. Heterogeneity in sampling, analysis, and clinical correlation limits definitive conclusions. Standardized study designs are needed to clarify the relationship between OAP and microbiota composition changes.},
}

Humans
*Antibiotic Prophylaxis
Colorectal Surgical Procedures
Administration, Oral
*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/administration & dosage
Surgical Wound Infection/prevention & control/microbiology

@article {pmid43004014,
year = {2026},
author = {Unno, T and Choi, G and Hwang, H and Cheon, NJ and Jeong, SE and Lee, TW and Kim, K and Park, S and Seo, J and Kang, JY and Choi, YS and Ahn, US and Kim, L and Han, D and Kim, SS and Jang, J},
title = {Ecological Variation in Bacterial Community Composition and Zoonotic Genus Distribution Across Body Sites, Host Species, and Seasonal Life-History Stages in Insectivorous Bats.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {43004014},
issn = {1432-184X},
support = {NIE-B-2024-38//National Institute of Ecology/ ; No. 2022R1C1C1003384//National Research Foundation of Korea/ ; },
mesh = {Animals ; *Chiroptera/microbiology/physiology ; *Bacteria/classification/isolation & purification/genetics ; Seasons ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Phylogeny ; Skin Microbiome ; Republic of Korea ; Zoonoses/microbiology ; Feces/microbiology ; },
abstract = {Bats harbour diverse genera containing zoonotic species, yet whether colonisation by these genera reflects stable host-microbe associations or transient environmental exposure remains unresolved. We propose that bat bacterial communities are shaped by three axes of variation: body site defines the microbial niche, host species imposes ecological and phylogenetic constraints, and seasonal life-history transitions alter exposure regimes. We tested four predictions: (1) each body site would (2) host species would show different bacterial profiles associated with differences in roosting ecology, colony density, and foraging behavior; (3) active and hibernation periods would differ in community structure and predicted metabolic function; and (4) zoonotic genera would show predominantly transient detection across years within individuals. Using 16 S rRNA gene amplicon sequencing of 2,747 oral, skin, and gut (stool) samples from eight insectivorous bat species across four seasons (2021-2024) in South Korea, all four predictions were supported. Body site was the strongest determinant of community structure: mean zoonotic genus relative abundance was 10-fold higher in gut (6.91%) than in oral samples (0.69%), dominated by Helicobacter and Chlamydia, while skin carried Rickettsia and Bartonella. Host species structured oral communities most strongly (PERMANOVA R[2] = 0.295), with interspecific variation in zoonotic genus composition. PICRUSt2 predicted that hibernation-associated oral taxa were enriched in fatty acid β-oxidation pathway genes, paralleling the host's metabolic switch from carbohydrate to lipid catabolism during torpor. Longitudinal tracking of 80 recaptured individuals over 2-3 years confirmed predominantly transient carriage, supporting seasonal environmental acquisition rather than chronic colonisation.},
}

Animals
*Chiroptera/microbiology/physiology
*Bacteria/classification/isolation & purification/genetics
Seasons
RNA, Ribosomal, 16S/genetics
*Microbiota
Phylogeny
Skin Microbiome
Republic of Korea
Zoonoses/microbiology
Feces/microbiology

@article {pmid43004160,
year = {2026},
author = {Ndiaye, PA and Saidi, R and Sellami, W and Ibnyasser, A and Kadmiri, IM and Idbella, M and Houasli, C and Daoui, K and Bargaz, A},
title = {Chickpea responsiveness to contrasting P fertilization reveals agro-physiological and genotypic variability in P use efficiency and rhizosphere microbial communities.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {43004160},
issn = {1471-2229},
mesh = {*Cicer/genetics/microbiology/growth & development/metabolism/physiology ; *Rhizosphere ; *Phosphorus/metabolism ; Genotype ; Soil Microbiology ; *Fertilizers ; *Microbiota ; },
abstract = {BACKGROUND: Phosphorus (P) is crucial for grain legumes including chickpea, however P use efficiency (PUE) for both chickpea symbiosis and plant growth strongly relies on chickpea genotypic variability and responsiveness to contrasting P conditions including source, availability and application rate. In this study, three winter Moroccan chickpea (Cicer arientinum L.) varieties (Arifi, Bochra and Taounate) were assessed for plant growth, PUE and rhizosphere soil-associated microbiome composition under both available "ortho-P" and unavailable P sources (rock-P) at increasing rates (0, 40, 80 and 120 kg P2O5 ha[- 1]).

RESULTS: Chickpea growth traits related to shoot dry weight (SDW), leaf area index (LAI), branches number and plant height were significantly enhanced under ortho-P (120 kg ha[- 1]). The highest pod DW (PDW) (108%) and Harvest Index (HI) (55%) were obtained under rock-P (120 kg ha[- 1]) as compared to unfertilized treatment, which is the case of Taounate variety that exhibited the highest PDW (2.33 g plant[- 1]), pod number (9.5 per plant), LAI (321), high PUE and P harvest index (PHI) as a consequence of improved root traits (biomass, length and surface-area). Meanwhile, Bochra variety responded more favorably to rock-P (40, 80 and 120 kg ha[- 1]) showing a higher PUE concomitantly to a lower root traits. Furthermore, chickpea varieties and P sources influenced the rhizosphere-associated microbial community with a notable abundance of Actinobacteria under rock-P in Bochra variety and Chytridiomycota phylum in Taounate variety under ortho-P, while Bochra and Arifi varieties had more Basidiomycota and Mortierellomycota under ortho-P.

CONCLUSIONS: Findings revealed that ortho-P-fertilized Taounate and rock-P-fertilized Bochra exhibited high PUE and yielded superior agro-physiological performance concomitantly with specific rhizosphere microbial modifications. Such a genotype-P specific pattern indicates a differential responsiveness to P fertilization suggesting tight relationships between chickpea genotypic diversity, responsiveness to P and modulation of the rhizosphere microbiota that needs to be deciphered.},
}

*Cicer/genetics/microbiology/growth & development/metabolism/physiology
*Rhizosphere
*Phosphorus/metabolism
Genotype
Soil Microbiology
*Fertilizers
*Microbiota

@article {pmid43004180,
year = {2026},
author = {Aldeyarbi, S and Elhanafy, E and Saber-Ayad, M and Abu Almaaty, AH and Sagheer, A and Hassan, MK},
title = {Molecular mechanisms of colorectal cancer: from carcinogenesis and molecular classification to targeted therapy.},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {32},
number = {1},
pages = {},
pmid = {43004180},
issn = {1528-3658},
support = {23_828//ARICA/ ; },
mesh = {Humans ; *Colorectal Neoplasms/etiology/metabolism/genetics/diagnosis/therapy/pathology/drug therapy ; Molecular Targeted Therapy ; Tumor Microenvironment ; Animals ; *Carcinogenesis/genetics ; Biomarkers, Tumor ; Chromosomal Instability ; Microsatellite Instability ; Cell Transformation, Neoplastic/genetics/metabolism ; Gene Expression Regulation, Neoplastic ; DNA Methylation ; },
abstract = {Colorectal cancer (CRC) is a heterogeneous disease that results from the progressive accumulation and interactions at multiple levels of genetic alterations, which lead to the transformation of normal colonic epithelium into malignant colorectal tumors. Understanding the molecular basis of CRC pathogenesis, together with the interactions between genetic alterations, epigenetic modifications, environmental and lifestyle factors, is essential for improving prevention, diagnosis, prognosis, and treatment strategies. This review aims to provide a critical reference point for understanding the temporal dynamics of colorectal carcinogenesis, the evolution of molecular classification systems, including their computational and machine-learning foundations and emerging image-based prediction approaches, molecular drivers and the tumor microenvironment (TME) of CRC by summarizing the most investigated molecular pathways involved in CRC pathogenesis and their role as biomarkers for early CRC diagnosis based on the three main molecular mechanisms of colorectal carcinogenesis: chromosomal instability (CIN), microsatellite instability (MSI), and CpG island methylator phenotype (CIMP). Importantly, emerging evidence reveals that the TME acts as an important factor in driving CRC progression by regulating the immune system through dynamic cellular and molecular interactions. In particular, tumor metabolic reprogramming and microbiota-driven alterations act as major drivers of therapy resistance and immune escape. Combining these mechanisms will enhance biomarker discovery and aid in developing precision medicine for patients with CRC. This review also highlights the regulatory roles of key signaling pathways, including Wnt/β-catenin, epidermal growth factor receptor (EGFR), tumor protein p53 (TP53), and transforming growth factor-beta (TGF-β) signaling, during CRC initiation and progression, while further addressing current targeted therapies and emerging precision-based and experimental therapeutic strategies.},
}

Humans
*Colorectal Neoplasms/etiology/metabolism/genetics/diagnosis/therapy/pathology/drug therapy
Molecular Targeted Therapy
Tumor Microenvironment
Animals
*Carcinogenesis/genetics
Biomarkers, Tumor
Chromosomal Instability
Microsatellite Instability
Cell Transformation, Neoplastic/genetics/metabolism
Gene Expression Regulation, Neoplastic
DNA Methylation

@article {pmid43004182,
year = {2026},
author = {Luo, G and Pan, Z and Yu, T and Xie, Y and Liu, Q and Yang, X and Yan, Z and Xia, C and Su, J},
title = {Altered circulating blood microbiota in unexplained recurrent spontaneous abortion.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43004182},
issn = {1471-2180},
support = {2220001004427//Foshan Self-funded Science and Technology Innovation Projects/ ; 2024LZ-B1001//Guangdong Provincial Medical Association Clinical Research Fund/ ; },
mesh = {Humans ; Female ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Pregnancy ; *Abortion, Habitual/microbiology/blood ; Adult ; Cytokines/blood ; *Dysbiosis/microbiology/blood ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: The etiology of unexplained recurrent spontaneous abortion (URSA) remains poorly understood. Emerging evidence implies that URSA is closely related to dysbiosis of the symbiotic microbiota, while the characteristics of blood microbiome in URSA remain unclear.

METHODS: In the present preliminary exploratory study, 20 patients with URSA and 11 healthy postpartum controls were enrolled for blood microbiome analysis by full-length 16 S rRNA gene sequencing and cytokines profiling by Luminex assay.

RESULTS: It was found that although alpha diversity was similar between the two groups, beta diversity analysis revealed a significantly distinct overall microbiota structure in URSA patients. It was found that Blautia wexlerae was remarkably enriched in URSA, while Hydrogenophaga sp. HaHa333 and Zoogloea resiniphila were significantly depleted. Co-occurrence network analysis by topological properties suggested a more pronounced compartmentalized structure with stronger intra‑module associations within the blood microbiome of URSA as indicated by the higher modularity index, which exhibited a predominantly positive and monotonous correlation pattern. Concurrently, the decreased IL-1β and IL-8 in serum co-existed with enrichment of B. wexlerae in URSA. However, IL-27 and IL-13 was elevated, and the level of IL-27 was negatively associated with the URSA-depleted H. sp. HaHa333.

CONCLUSIONS: In this proof-of-concept investigation, it is the first time to systematically characterize the blood microbiome in URSA patients with cross-sectional clinical observation. These hypothesis-generating findings suggested that URSA is associated with a distinct blood microbiota and an altered cytokine profile, which requires future large-scale validation.},
}

Humans
Female
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Pregnancy
*Abortion, Habitual/microbiology/blood
Adult
Cytokines/blood
*Dysbiosis/microbiology/blood
*Bacteria/classification/genetics/isolation & purification

@article {pmid43004363,
year = {2026},
author = {Trivett, H and Dalby, MJ and Peel, N and Heavens, D and Kiu, R and Acuna-Gonzalez, A and Mohamad, M and Humayun, G and Leggett, RM and Patel, VC and Hall, LJ},
title = {Decoding the microbiome and resistome of advanced chronic liver disease through long-read metagenomics.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {43004363},
issn = {1756-994X},
support = {BBX011089/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 220876/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Metagenomics/methods ; Metagenome ; *Gastrointestinal Microbiome ; *Microbiota ; Liver Cirrhosis/microbiology ; Chronic Disease ; Male ; Female ; Enterococcus faecium/genetics ; Acute-On-Chronic Liver Failure/microbiology ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; *Liver Diseases/microbiology ; Middle Aged ; },
abstract = {BACKGROUND: Patients with advanced chronic liver disease (ACLD) and underlying cirrhosis frequently require repeated courses of antimicrobial therapy, with both the frequency and spectrum of antimicrobial exposure increasing alongside disease progression. In this population, impaired immune function and increased intestinal barrier dysfunction contribute to a heightened susceptibility of multidrug-resistant bacterial infections.

METHODS: To comprehensively characterise the gastrointestinal microbiome and antimicrobial resistance gene (ARG) landscape across the clinical spectrum of ACLD, and to identify microbial and resistome signatures associated with disease severity, we employed long-read metagenomic sequencing (Oxford Nanopore Technologies) to profile the gastrointestinal microbiome and resistome in patients with acute-on-chronic liver failure (ACLF), decompensated cirrhosis (DC), and stable cirrhosis (SC), compared to healthy controls (HC).

RESULTS: ACLF patients showed marked enrichment of Enterococcus faecium, with six of 28 samples showing >95% relative abundance, highlighting its potential as a bacterial biomarker of advanced cirrhosis. We reconstructed 28 high-quality metagenome-assembled genomes (MAGs) of E. faecium from cirrhosis patients, 17 from ACLF cases. E. faecium dominance was associated with substantially reduced microbial diversity and a marked depletion of key commensal taxa, including Blautia, Akkermansia, Faecalibacterium, and Bifidobacterium. Consistent with these compositional shifts, resistome analysis revealed significant enrichment of clinically relevant antimicrobial resistance genes (ARGs) in DC and ACLF, including determinants conferring resistance to aminoglycosides, beta-lactams, and glycopeptides, consistent with prior antimicrobial exposure.

CONCLUSION: Long-read metagenomics enables high-resolution characterisation of microbial and resistome dynamics across ACLD severities. By capturing taxonomic shifts, functional potential, and ARG enrichment, this approach provides valuable insights into microbiome trajectories linked with disease severity, informing mechanistic research and potential clinical interventions.},
}

Humans
*Metagenomics/methods
Metagenome
*Gastrointestinal Microbiome
*Microbiota
Liver Cirrhosis/microbiology
Chronic Disease
Male
Female
Enterococcus faecium/genetics
Acute-On-Chronic Liver Failure/microbiology
Drug Resistance, Bacterial/genetics
Bacteria/genetics
*Liver Diseases/microbiology
Middle Aged

@article {pmid43004378,
year = {2026},
author = {Liu, W and Zhang, H and Zhang, L and Wang, W and Liu, B and Li, R and Yao, Y and Xie, L},
title = {Bacterial lipopolysaccharide mediates the interplay between tumor microbiome and immune microenvironment in breast cancer: development of a prognostic risk score.},
journal = {Breast cancer research : BCR},
volume = {28},
number = {1},
pages = {},
pmid = {43004378},
issn = {1465-542X},
support = {ZDXK202233//Jiangsu Provincial Medical Key Discipline/ ; 2022-LCYJ-DBZ-07//Nanjing Drum Tower Hospital/ ; NDYGN2023030//Project of Chinese Hospital Reform and Development Institute, Nanjing University/ ; },
mesh = {*Tumor Microenvironment/immunology ; *Lipopolysaccharides/metabolism/immunology ; Female ; *Breast Neoplasms/immunology/microbiology/pathology/genetics/mortality ; Humans ; Prognosis ; Animals ; *Microbiota/immunology ; Mice ; Biomarkers, Tumor/genetics ; Gene Expression Regulation, Neoplastic ; },
abstract = {BACKGROUND: The immunosuppressive microenvironment of breast cancer drives a 'cold' tumor phenotype characterized by limited immune cell infiltration and poor response to immunotherapy. While intratumoral microbiota and circulating lipopolysaccharide (LPS) have the potential to remodel immunity, the specific mechanisms and prognostic impact of LPS-driven immunomodulation in breast cancer remain unclear.

METHODS: We utilized the Comparative Toxicogenomics Database (CTD) to systematically identify LPS-related genes. Prognosis-associated LPS-related genes (PALRGs) were identified via Cox regression analyses. Subsequently, we applied LASSO-Cox regression to construct an LPS-related risk score (LPSRS) and evaluated its predictive performance and associations with immune microenvironment characteristics in TCGA-BRCA (n = 1,196) and GEO (n = 525) cohorts. For further validation, we recruited an independent clinical cohort of 56 breast cancer patients and confirmed differential expression of LPSRS genes and tumor microenvironment (TME) heterogeneity between high- and low-risk groups. We integrated RNA sequencing with 2bRAD-M sequencing to explore potential interactions between the tumor microbiome and host gene expression. Finally, we conducted mechanistic validation using 4T1 tumor-bearing mice, with treatment groups receiving either Pseudomonas. putida or purified LPS.

RESULTS: We identified 26 PALRGs and constructed an 8-gene LPSRS signature as Risk Score which demonstrated strong prognostic performance (C-index = 0.750, 95% CI 0.712-0.788) across multiple independent cohorts and our clinical cohort. Notably, low-risk patients exhibited significant Pseudomonas enrichment (median abundance: 4.3% vs. 2.4%, P = 0.04). Correlation analysis revealed significant associations between Pseudomonas abundance and transcriptome (P = 6.36 × 10[-6]). In mechanistic validation experiments, Pseudomonas-treated mice showed an significant reduction in tumor volume (P = 0.0009), accompanied by a 2- fold increase in M1 macrophage polarization (P < 0.0001), confirming the beneficial remodeling of the TME.

CONCLUSIONS: Intratumoral microbiota-related LPS is associated with microbiome-immunity crosstalk in breast cancer. LPSRS serves as a promising prognostic marker with therapeutic insights.},
}

*Tumor Microenvironment/immunology
*Lipopolysaccharides/metabolism/immunology
Female
*Breast Neoplasms/immunology/microbiology/pathology/genetics/mortality
Humans
Prognosis
Animals
*Microbiota/immunology
Mice
Biomarkers, Tumor/genetics
Gene Expression Regulation, Neoplastic

@article {pmid43004464,
year = {2026},
author = {Fan, Y and Liu, G and Liang, G and Yang, X and Zhang, J and Sun, P and Liu, L and Ye, L and Xia, X and Feng, Y},
title = {A cross-border comparison reveals expanded microbial diversity and zoonotic risk in Rhipicephalus microplus ticks of Yunnan, China.},
journal = {Parasites & vectors},
volume = {19},
number = {1},
pages = {},
pmid = {43004464},
issn = {1756-3305},
support = {202502AA310014//Major Science and Technology Projects in Yunnan Province/ ; 202202AG050013//Major Science and Technology Projects in Yunnan Province/ ; },
mesh = {Animals ; *Rhipicephalus/microbiology/virology ; China/epidemiology ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Zoonoses/microbiology/epidemiology/transmission ; Female ; Virome ; Humans ; Tick-Borne Diseases/microbiology/transmission/epidemiology ; *Microbiota ; Viruses/genetics/classification/isolation & purification ; Salivary Glands/microbiology/virology ; Biodiversity ; },
abstract = {BACKGROUND: Rhipicephalus microplus is a critical vector for numerous agents of livestock and human diseases. Border regions are potential hotspots for pathogen exchange and emerging tick-borne diseases, yet comprehensive surveys of the total pathogen community (virome and microbiome) in ticks from these areas are limited. This study aimed to characterize the microbial diversity within R. microplus across different geographical locations (local vs. imported) and tissue types in Yunnan, China, to understand ecological drivers and assess associated zoonotic risks.

METHODS: We performed meta-transcriptomic sequencing to profile the RNA virome and 16S rRNA gene sequencing to analyze the bacterial microbiome of R. microplus samples. Ticks were dissected into three key tissues: midgut, salivary glands, and ovaries. Bioinformatic and statistical analyses included taxonomic assignment, diversity metrics (alpha and beta diversity), co-occurrence network analysis, and tests for assessing the impact of geographic origin and tissue type on community structure.

RESULTS: Our analysis revealed a highly diverse community of virome and bacterial microbiome. The virome comprised 63 viral families, including 28 with known animal hosts, such as the clinically significant families Flaviviridae, Phenuiviridae, and Peribunyaviridae. The bacterial microbiome included 167 bacterial genera, dominated by known pathogenic genera (Coxiella, Rickettsia, Anaplasma, Ehrlichia). We identified three novel viruses. Viral diversity was significantly richer in cross-border than in local samples, and the midgut exhibited the highest viral diversity among tissues. Network analysis indicated potential interactions between specific viral (e.g., Chuviridae) and bacterial taxa.

CONCLUSIONS: This study reveals that R. microplus in border areas harbors a high diversity of pathogens with zoonotic potential. The composition of this pathogen community is fundamentally shaped by both geographic origin and vector tissue tropism. The elevated diversity at cross-border sites identifies them as key surveillance targets. These findings provide crucial data for informing surveillance strategies and early warning systems against tick-borne diseases in high-risk border regions.},
}

Animals
*Rhipicephalus/microbiology/virology
China/epidemiology
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Zoonoses/microbiology/epidemiology/transmission
Female
Virome
Humans
Tick-Borne Diseases/microbiology/transmission/epidemiology
*Microbiota
Viruses/genetics/classification/isolation & purification
Salivary Glands/microbiology/virology
Biodiversity

@article {pmid43004628,
year = {2026},
author = {Xin, W and Zhang, J and Tian, W and Ren, L and Zhu, Z and Chen, Z and Ye, M and Yang, L and Liu, Y and Zhou, J and Zheng, C and Tang, W},
title = {Root Microbiota Reprogram Aboveground Metabolite Allocation Across Tea Plant Tissues.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.71041},
pmid = {43004628},
issn = {1365-3040},
support = {FKLBDAITI202301//Open Project Program of Fujian Key Laboratory of Big Data Application and Intellectualization for Tea Industry/ ; 2025W02//China Oolong Tea Industry Collaborative Innovation Center Open Research Fund/ ; N2023Z010//Joint Funding Project for Technological Innovation in the Resource Chemistry Industry of Nanping/ ; },
abstract = {Tea quality is determined by the composition and spatial distribution of specialized metabolites, such as amino acids, catechins, and caffeine, which vary across tissues and developmental stages. However, the mechanisms underlying metabolite allocation among tissues remain unclear. Plant-associated microbiota, particularly root communities, play important roles in regulating plant metabolism, yet their coordinated effects across plant compartments are poorly understood. Here, we combined metabolomic and microbiome analyses to investigate metabolic-microbial interactions in the white tea cultivar Zhenghe Dabai. Metabolite-associated microbial taxa identified from leaves were linked to root-derived isolates, and two synthetic communities (SynCom1 and SynCom2) were constructed and applied to the rhizosphere. Both SynComs enhanced flavan metabolite accumulation, especially proanthocyanidins, but exhibited distinct regulatory patterns. SynCom1 increased stem-enriched proanthocyanidins and multiple amino acids, including theanine, while SynCom2 promoted specific flavan derivatives and amino acids such as glutamate and tryptophan. Transcriptomic analysis revealed differential activation of flavonoid biosynthesis and amino acid transport pathways, with SynCom1 upregulating the transporter gene CsCAT1. Overall, our results demonstrate that root microbiota can differentially regulate host metabolism and metabolite allocation, providing new insights into microbiome-mediated quality formation in tea and highlighting the potential of synthetic microbial communities for crop improvement.},
}

@article {pmid43004850,
year = {2026},
author = {Zhao, J and Wang, Y and Yan, G and Chen, H and Xie, Y and Wang, W and Liu, H},
title = {Synthetic Community Driven by a Keystone Rhizosphere Bacterium Suppresses Whitefly-Mediated Begomovirus Transmission via the Jasmonate Signaling Pathway in Tomato.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.71032},
pmid = {43004850},
issn = {1365-3040},
support = {2023YFD1400600//National Key Research and Development Program of China/ ; XZNKY-2026ZF001//Talent Resource Development Special Project of Xizang Autonomous Region: Innovation Capability and Key Technology R&D for Plant Protection and Utilization of Resource Insects/ ; },
abstract = {Tomato production is threatened by the combined stress of whiteflies and the whitefly-transmitted Tomato yellow leaf curl virus (TYLCV). Although the rhizosphere microbiome plays a critical role in plant defense, the rational assembly strategy and underlying mechanisms of a synthetic microbial community (SynCom) targeting this insect-virus complex remain unclear. Here, leveraging the beneficial soil legacy induced by Beauveria bassiana, we constructed an eight-strain synthetic community through multi-omics analysis, soil incubation, and root exudate chemotaxis assays. One-strain knockout experiments confirmed that strain N2 is the keystone species driving the biocontrol function. Through supernatant cross-culture assays, we further refined this consortium into an optimized synthetic community (OptSynM) consisting of the single keystone strain and four helper strains. Bioassays demonstrated that OptSynM significantly reduced whitefly fitness and suppressed TYLCV accumulation in tomato plants. Within the consortium, the helper strains enhanced the rhizosphere colonization of N2 by promoting its growth and biofilm formation. Mechanistically, OptSynM activated host systemic immunity via the jasmonic acid signaling pathway. Furthermore, OptSynM maintained robust biocontrol efficacy in pot trials conducted with natural agricultural soil. Our findings highlight the practical promise of microbiome-based interventions and provide a strategic framework for using synthetic microbial communities to facilitate sustainable agricultural practices.},
}

@article {pmid43004864,
year = {2026},
author = {Nachman, EJ and Neilson, T and White, MG},
title = {Therapeutic Targeting of the Cancer Microbiome and Metabolome: Ongoing Trials and Future Directions for the Surgical Oncologist.},
journal = {Journal of surgical oncology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jso.70451},
pmid = {43004864},
issn = {1096-9098},
support = {K12TR004908/NH/NIH HHS/United States ; },
abstract = {The role of the human microbiome in cancer development, progression, and response to therapy has moved from correlative curiosity to demonstrated impact on tumor biology. This represents a critical factor for surgical oncologists as they not only resect these tumors, but also direct perioperative antimicrobial exposure and increasingly co-manage neoadjuvant and surveillance pathways in which microbial state may predict and modify response. This review summarizes the basis for therapeutic modulation of the cancer microbiome and metabolome in a contemporary clinical-trial landscape across four broad strategies: additive (fecal microbiota transplantation, defined consortia, and live biotherapeutic products), subtractive (targeted antimicrobials), dietary and metabolome-directed interventions, and engineered or next-generation platforms. Particular attention is given to subtractive approaches in colon and rectal cancer and to the underexplored perioperative interface between the microbiome and surgical outcomes such as anastomotic leak. We outline the principal methodological and translational obstacles, including low-biomass contamination, causal inference, unintended antibiotic effects, and product standardization. Looking ahead, we propose roles for surgeons across the care continuum, from biospecimen stewardship and trial referral to integration of microbiome and circulating tumor DNA signals in surveillance.},
}

@article {pmid43004956,
year = {2026},
author = {Qiu, J and Chen, Z and Chen, T and Cao, L},
title = {Probiotic Lactobacillus reuteri mitigates 5-fluorouracil-induced oral mucositis via suppression of the FTO/CMPK2/NLRP3 pathway.},
journal = {Histology and histopathology},
volume = {},
number = {},
pages = {25172},
doi = {10.14670/HH-25-172},
pmid = {43004956},
issn = {1699-5848},
support = {2025KY433//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; },
abstract = {BACKGROUND: 5-Fluorouracil (5-FU)-induced oral mucositis (OM) is associated with the fat-tissue-associated protein (FTO)/cytidine monophosphate kinase 2 (CMPK2)/NOD-like receptor protein 3 (NLRP3) inflammatory axis. Lactobacillus reuteri (LR) may protect against 5-FU-induced OM through this pathway, yet the precise mechanism requires clarification. We aimed to investigate whether LR alleviates 5-FU-induced OM by suppressing the FTO/CMPK2/NLRP3 inflammasome pathway.

METHODS: A hamster OM model was established using 5-FU injections and mechanical irritation, with LR administered in drinking water. Macroscopic scoring, histopathology, serum ELISA, and tissue oxidative markers were assessed. Protein expression of FTO, CMPK2, NLRP3, apoptosis-associated speck-like protein containing a CARD (ASC), and pro-caspase-1 was analyzed by western blot. In vitro, human oral keratinocytes (HOKs) were treated with 5-FU, LR, FTO-overexpression transfection (oe-FTO), and/or lipopolysaccharides (LPS). Cell viability, migration, proliferation, ROS, cytokines, and mRNA/protein levels of FTO/CMPK2/NLRP3 were evaluated. LR alone and LPS alone controls were included to rule out direct effects.

RESULTS: In hamsters, LR significantly reduced mucosal ulceration (injury score from 3.67 ± 0.52 to 2.50 ± 0.84, p<0.05), inflammatory cell infiltration, mast cell numbers (p<0.01), and serum IL-8, TNF-α, and IL-1β (all p<0.01). LR also ameliorated oxidative stress (decreased MDA, increased SOD) and downregulated FTO, CMPK2, and NLRP3 protein expression (all p<0.01). qPCR confirmed successful LR colonization in the OM of LR-treated hamsters. In HOKs, LR (10[9] CFU/mL) restored 5-FU+oe-FTO-impaired cell viability (from 45.3±3.8% to 71.5±4.6% at 24h, p<0.01), migration (from 40.2±3.3% to 70.4±3.4%, p<0.01), and proliferation (EdU-positive cells from 29.8±3.0% to 39.9±1.9%, p<0.01). Baseline assessment showed that LR alone enhanced HOK viability and reduced ROS/IL-8/TNF-α (p<0.05), whereas LPS alone reduced viability and elevated ROS/IL-8/TNF-α/IL-1β (p<0.05). FTO overexpression exacerbated 5-FU damage and pathway activation, while FTO knockdown reversed these deficits (migration: from 45.24±4.49% to 62.52±5.59%, p<0.01; EdU: from 32.42±3.08% to 47.44±2.98%, p<0.01). LR suppressed FTO/CMPK2/NLRP3 expression at mRNA and protein levels, and these effects were abolished by the NLRP3 agonist LPS.

CONCLUSION: LR alleviates 5-FU-induced OM by inhibiting the FTO/CMPK2/NLRP3 inflammasome axis, reducing inflammation and oxidative stress. These findings are supported by both overexpression and knockdown experiments, as well as by human-relevant insights into LR-microbiome interactions.},
}

@article {pmid43005165,
year = {2026},
author = {Sun, T and Mei, G and Li, M and Mo, J and Zhang, C and Ma, Y and Zhao, J and Peng, S and Lin, F and Chen, JL and Li, Z},
title = {Compound microbial intelligent membrane fermentation reshapes the bacterial community and reduces antibiotic, metal, and biocide resistance genes and virulence factors in duck litter.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1997145},
pmid = {43005165},
issn = {1664-302X},
abstract = {BACKGROUND: Contaminated duck litter is a leading cause of flock disease and a bottleneck for the sustainable development of large-scale dry-rearing systems.

METHODS: We applied shotgun metagenomics to litter from four positions within each of three independent compound microbial intelligent membrane fermentation beds, with unfermented litter from the same three batches as the control. We investigated the bacterial community alongside the abundance of antibiotic, metal and biocide resistance genes (ARGs, MRGs and BRGs) and of virulence factor genes (VFGs).

RESULTS: Fermented litter was consistently enriched in thermophilic and thermotolerant taxa and in beneficial genera such as Paenibacillus and Bacillus, while opportunistic pathogens including Streptococcus, Mycobacterium and Escherichia were clearly reduced. The total burden of the ARG and VFG classes fell in every fermented position, and representative determinants were consistently depleted: floR, qacEdelta1 and sul2 among the ARGs, ruvB among the MRGs, mexF, ideR and sodA among the BRGs, and htpB, clpV and katA among the VFGs. A small number of genes, tet(L), fexA and bacA among them, rose in the most active zones, indicating structural remodeling of the resistance reservoir rather than uniform removal. Fermentation was not spatially uniform: the upper and edge layers were more active, and the center-lower layer remained closest to the unfermented control.

CONCLUSION: Intelligent membrane fermentation reduced the overall abundance of resistance and virulence determinants in the litter microbiome, and spatial uniformity is important for the process. Because these data are DNA-based, they describe the abundance of resistance and virulence determinants and not resistance or virulence phenotypes.},
}

@article {pmid43005206,
year = {2026},
author = {Ageel, AM and Subbaram, K and Ali, S and Arul, QA},
title = {Gut Microbiome Influences the Efficacy of Neuropsychiatric Drugs.},
journal = {Advanced pharmaceutical bulletin},
volume = {16},
number = {3},
pages = {448-450},
pmid = {43005206},
issn = {2228-5881},
}

@article {pmid43005250,
year = {2026},
author = {Gao, G and Wei, J and Gan, L and Wang, H and Zhang, H and Yu, X and Bi, B},
title = {Intestinal adaptation of crayfish to pond and rice paddy farming: a microbiome-enzyme perspective.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1989196},
pmid = {43005250},
issn = {1664-302X},
abstract = {The red swamp crayfish (Procambarus clarkii) is a globally significant aquaculture species, yet the biological trade-offs between intensive pond monoculture and integrated rice-crayfish co-culture systems remain poorly understood at the intestinal level. This study investigated the intestinal physiological and microbial adaptations of P. clarkii reared in pond (high-input formulated feed) and rice paddy (low-input natural diet) systems for 60 days. We integrated analyses of intestinal digestive, antioxidant, immune barrier, and energy metabolism enzymes with 16S rRNA sequencing of the gut content-associated microbiota. Rice paddy-cultured crayfish exhibited significantly higher amylase activity, enhanced antioxidant enzyme activities (SOD, CAT, GSH-Px), and lower oxidative damage (MDA), alongside higher immune barrier enzyme activities (AKP, ACP) and reduced Na[+]/K[+]-ATPase activity compared to pond-cultured crayfish. Conversely, pond-cultured crayfish showed elevated lipase and total protease activities, lower immune barrier enzyme activities, and greater energy transport workload. Microbial analysis of intestinal lumen contents revealed higher lumen-associated microbial diversity in the rice paddy group, with enrichment of Bacteroidota and taxa commonly associated with polysaccharide degradation, whereas the pond group showed enrichment of Pseudomonadota (formerly Proteobacteria) and taxa that include potential opportunistic pathogens such as Citrobacter and Acinetobacter. BugBase phenotype prediction indicated higher abundance of "Potentially pathogenic" phenotypes in the pond group. These findings suggest that the two aquaculture systems are associated with distinct, coordinated intestinal adaptation patterns: a "stress-resistance-oriented" phenotype in rice paddies characterized by enhanced antioxidant defense, efficient carbohydrate utilization, lower physiological burden, and a more diverse lumen-associated microbiota with greater abundance of potentially beneficial taxa, versus a "growth-oriented" phenotype in ponds characterized by elevated metabolic load, oxidative stress, altered immune status, and opportunistic pathogen enrichment. This study provides a basis for further hypothesis-driven research and may help inform sustainable aquaculture practices, balancing productivity with animal health and welfare.},
}

@article {pmid43005270,
year = {2026},
author = {Thangamani, RA and Jayachandran, J and Jayavel, A and Ponnaiya, SKM and Mitra, A and Shanmugam, P and Radhakrishnan, A and Banerjee, A and Duttaroy, AK},
title = {Comparative analysis of gut and skin microbiota from the coastal and non-coastal populations in Tamil Nadu using 16S rRNA gene sequencing: a pilot study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1849751},
pmid = {43005270},
issn = {1664-302X},
abstract = {BACKGROUND: The human gut and skin microbiota play a vital role in maintaining physiological balance and immune function. Factors such as age, diet, geography, and genetic factors influence their composition, and disruptions can contribute to metabolic alterations and chronic diseases. Coastal populations are exposed to environmental pollutants and experience disrupted gut microbial balance, impaired epithelial barrier integrity, and possibly dysbiosis-associated inflammatory responses. In this study, we aim to analyze microbiome diversity in coastal and non-coastal populations of Tamil Nadu, India, using 16S rRNA sequencing.

METHODS: Fecal and skin swab samples were collected from 75 participants, 57 from coastal regions and 18 from non-coastal regions. DNA was extracted, and using the Illumina MiSeq platform, the 16S rRNA sequencing was performed. The alpha and beta diversity analyses compared the fecal and skin microbiota diversity and composition.

RESULTS: The study revealed that Firmicutes dominated the gut microbiota in both coastal and non-coastal groups, with higher abundances of Bacilli and Clostridia in the coastal group. In skin swabs, Firmicutes and Proteobacteria were predominant, with different clustering patterns observed in coastal samples. Beta diversity analyses revealed overlapping but distinct microbial communities between the two groups.

CONCLUSION: This pilot study highlights differences in gut and skin microbiota between coastal and non-coastal populations. However, further study with a larger sample size is required to better understand the impact of environmental exposures on human health.},
}

@article {pmid43005284,
year = {2026},
author = {Olafusi, CO and Tebamifor, ME and Bejapade, TI and Afolabi, IS and Ogunlana, OO},
title = {Microbiota-mediated blocking of plasmodium falciparum sporozoites in Anopheles: a systematic review.},
journal = {Frontiers in insect science},
volume = {6},
number = {},
pages = {1958166},
pmid = {43005284},
issn = {2673-8600},
abstract = {INTRODUCTION: The development of Plasmodium falciparum sporozoites in the mosquito, Anopheles, is essential for malaria transmission. Despite the unsurprising fact that the mosquito microbiota has become a major factor in the modulation of the competence of mosquitoes, the specific types of microbial taxa and mechanisms affecting the development of the sporozoite are not well synthesized. This systematic review brings together and critically evaluates the available evidence to understand the role of microbiota in the development of P. falciparum sporozoites in Anopheles mosquitoes with a specific focus on the salivary gland microbiome.

METHODS: A systematic search of PubMed, Scopus, and Google Scholar databases (2000-2026) was conducted, and 41 studies met the inclusion criteria. Extraction and synthesis of data were conducted in the form of a narrative in accordance with the PRISMA guidelines. Risk of bias was assessed using SYRCLE's tool for animal studies.

RESULTS: The Wolbachia effects varied by strain and species: wAlbB caused a 3.4- to 3.7-fold decrease in sporozoites, wAnga-Mali had a negative correlation with 95% presence, and there was no correlation for wAnmo in An. moucheti. All African countries (1-57% prevalence) were consistently affected by Microsporidia MB, with no fitness costs. Serratia ureilytica Su_YN1 inhibited ~98% of parasites using outer membrane vesicles loaded with AmLip, which targets parasites via the phosphatidylcholine scavenging pathway. 93% transmission blocking was obtained in mouse models with engineered symbionts (transgenesis + paratransgenesis).

DISCUSSION: The mosquito microbiota plays a significant, but strain-, species-, and context-dependent role in the development of P. falciparum sporozoites. The Microsporidia and Serratia species are promising candidates for field deployment, offering sustainable, environmentally friendly complements to chemical insecticides for malaria vector control.},
}

@article {pmid43005329,
year = {2026},
author = {Naeem, M},
title = {Microbial communication networks governing the ecosystem dynamics of Salmonella in poultry environments: ecological interactions, colonization resistance, and emerging control strategies.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1908527},
pmid = {43005329},
issn = {2673-7647},
abstract = {Salmonella remains one of the leading foodborne pathogens associated with poultry, posing significant challenges to animal health, food safety, and public health worldwide. Conventional control strategies have largely focused on pathogen elimination through antimicrobials, biosecurity, and vaccination; however, increasing evidence suggests that Salmonella persistence is strongly influenced by interactions within complex microbial ecosystems. This review synthesizes current knowledge on how microbial communication networks regulate the colonization, persistence, and transmission of Salmonella throughout poultry production systems. Particular emphasis is placed on quorum sensing, metabolic cross-feeding, competitive exclusion, interkingdom signaling, biofilm-associated interactions, and ecological communication occurring within the gut, litter, water systems, and other environmental reservoirs. Recent studies demonstrate that microbial community structure and function influence pathogen behavior through coordinated signaling pathways and indirect ecological interactions that collectively determine colonization resistance and ecosystem resilience. Emerging microbiome engineering approaches, including defined microbial consortia, prebiotics, probiotics, quorum-sensing inhibitors, and ecological network manipulation, offer promising alternatives to conventional pathogen-directed interventions. Integrating microbial ecology with multi-omics technologies and systems biology is expected to facilitate precision microbiome-based strategies for sustainable Salmonella control. Viewing Salmonella as a participant in interconnected microbial communication networks rather than an isolated pathogen provides a conceptual framework for developing innovative interventions that improve poultry health, enhance food safety, and support One Health objectives.},
}

@article {pmid43005355,
year = {2026},
author = {Zhang, L and Zhou, L},
title = {Higher Adherence to a Sulfur Microbial Diet is Associated with Reduced Osteoarthritis Risk in Women.},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {638511},
pmid = {43005355},
issn = {1179-1411},
abstract = {INTRODUCTION: Osteoarthritis ranks among the top contributors to disability among women, and accumulating research suggests that dietary factors and the gut microbiota play a role in its development. The sulfur microbial diet (SMD), a dietary pattern originally derived from its association with sulfur-metabolizing gut bacteria, has been associated with inflammatory bowel disorders, yet whether it correlates with osteoarthritis remains unclear.

MATERIAL AND METHODS: We performed a prospective cohort study enrolling 114,831 female participants who were free of osteoarthritis at study baseline. SMD scores were calculated using online 24-hour dietary recall data and categorized into quartiles for statistical analysis. New-onset osteoarthritis was identified through linked health records. Progressive-adjusted Cox proportional-hazards models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs); we also carried out restricted cubic splines, sensitivity analyses, qualitative exploratory biomarker analysis, and subgroup analyses.

RESULTS: Relative to women in the lowest SMD quartile, those in the top SMD quartile exhibited a markedly reduced risk of developing new-onset osteoarthritis in the fully adjusted model (HR 0.75, 95% CI 0.60-0.95; P = 0.018), with a significant linear trend (P for trend = 0.019). In the original cohort, this relationship remained stable after removing early events and individuals with metabolic disorders. Although inverse associations appeared stronger among younger women, never-smokers, and women consuming alcohol fewer than three times per week, none of the corresponding interaction tests was statistically significant, providing no formal evidence of effect modification. The exploratory biomarker analysis was hypothesis-generating and did not quantify a causal pathway. Additional reviewer-requested analyses in a separate sample did not reproduce the significant highest-versus-lowest quartile association and showed a shallow U-shaped spline pattern.

CONCLUSIONS: Higher adherence to the sulfur microbial diet was associated with a moderately lower risk of new-onset osteoarthritis among women. This unexpected inverse association differs from previous findings concerning gastrointestinal outcomes. Given the observational design, these findings do not establish causality and should be considered hypothesis-generating. The SMD may represent a modifiable dietary feature worthy of further investigation for female OA primary prevention, but the present findings do not support specific dietary recommendations.},
}

@article {pmid43005451,
year = {2026},
author = {Karadimova-Watts, MVM and Philippou, E and Nikiphorou, E},
title = {Can nutrition prevent the onset of Rheumatoid Arthritis? A mini review of dietary risk and progression from pre-clinical autoimmunity.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1864271},
pmid = {43005451},
issn = {2296-861X},
abstract = {Rheumatic and musculoskeletal diseases are major causes of disability worldwide, and many have inflammation at their core. Rheumatoid Arthritis (RA), in particular, is preceded by a prolonged "pre-clinical" phase in which genetic susceptibility and modifiable exposures, including diet, interact. Nutrition is thought to play an important role as an 'external' but modifiable factor in inflammatory diseases. The existing literature suggests that it may act as a lever for prevention and risk modification through direct or indirect effects on adiposity, systemic inflammation, mucosal immunity, the gut microbiome, and cardiometabolic comorbidity. In this mini review, we synthesize and critically appraise the evidence linking dietary patterns and targeted nutritional interventions with RA risk.},
}

@article {pmid43005463,
year = {2026},
author = {Bluszcz, G and Roszkowska, Z and Domański, J and Sharabi, A and Rapiejko, J and Małek, J and Ambroziak, U and Bobrowicz, M},
title = {MACS: mild by definition, challenging by nature.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1957127},
pmid = {43005463},
issn = {1664-2392},
mesh = {Humans ; *Hydrocortisone/metabolism ; *Adrenal Gland Neoplasms/metabolism/complications/diagnosis ; *Cushing Syndrome/diagnosis/metabolism ; },
abstract = {Mild autonomous cortisol secretion (MACS) is the most frequent form of cortisol excess in patients with adrenal incidentalomas. Although it lacks the classical phenotype of overt Cushing's syndrome, MACS is increasingly recognized as a clinically relevant condition associated with multisystem complications rather than a benign biochemical finding. This narrative review summarizes current evidence on the pathophysiology, clinical manifestations, diagnostic limitations, and management of MACS, with particular focus on cardiometabolic, skeletal, muscular, neuropsychiatric, frailty-related, reproductive, and emerging microbiome-related consequences. Chronic exposure to low-grade cortisol excess is being recognized as a factor associated with hypertension, disorders of glucose metabolism, dyslipidemia, increased cardiovascular risk, metabolic dysfunction-associated steatotic liver disease, skeletal fragility, impaired muscle function, frailty, sleep and circadian disturbances, cognitive and mood alterations, hypogonadism, and possible changes in gut microbiota. The 1 mg overnight dexamethasone suppression test remains the cornerstone of diagnosis, but its interpretation is limited by assay variability, medication interference, comorbidities, and imperfect reflection of long-term tissue glucocorticoid exposure. Emerging approaches, including steroid profiling, hair cortisol/cortisone, salivary cortisone, inflammatory indices, metabolomic tools, and exploratory biomarkers related to microbial metabolites, may improve risk stratification in the future but remain investigational. Management should be individualized. Adrenalectomy may benefit selected patients with unilateral disease and clinically relevant cortisol-related comorbidities, whereas evidence supporting pharmacological therapy remains limited. MACS should be regarded as a heterogeneous multisystem condition requiring structured clinical assessment and individualized management. Prospective studies are needed to define clinically meaningful endpoints, refine diagnostic thresholds, and identify patients most likely to benefit from intervention.},
}

Humans
*Hydrocortisone/metabolism
*Adrenal Gland Neoplasms/metabolism/complications/diagnosis
*Cushing Syndrome/diagnosis/metabolism

@article {pmid43005468,
year = {2026},
author = {Nie, S and Li, Z and Zhang, Z and Song, B and Ouyang, J and Xu, Y and Zhang, H and Chen, Z and Gu, Z and Gu, W},
title = {Gut-on-a-Chip for Infectious Diseases: A Pathogen-Centric Review of Model Selection and Validation.},
journal = {BME frontiers},
volume = {7},
number = {},
pages = {0336},
pmid = {43005468},
issn = {2765-8031},
abstract = {Gut-on-a-chip systems are microfluidic, 3-dimensional (3D) in vitro platforms designed to recapitulate selected intestinal features, including epithelial polarity, fluid flow, peristalsis-like deformation, mucus formation, oxygen gradients, and, in some designs, epithelial-endothelial or host-microbiome interactions. Rather than treating increasing structural complexity as an inherent surrogate for biological fidelity, this review evaluates gut-on-a-chip models according to the infectious-disease question being addressed, the specific biological functions reproduced, the measurable infection endpoints, and the level of experimental or translational validation. We synthesize evidence across bacterial, viral, and parasitic infections and compare the relative maturity of these applications. Bacterial models currently represent the most mature evidence base, whereas fungal infections are considered where direct gut-on-a-chip evidence remains limited. We further examine host-microbiome interactions and gut-organ-axis platforms only when they provide a mechanistic or translational perspective relevant to infection. Four major evidence gaps are identified: limited head-to-head benchmarking against established models or clinical observations, incomplete standardization of chip and infection parameters, limited culture duration and microbial complexity in many systems, and relatively sparse infection-specific applications of artificial intelligence. Finally, we propose a validation-oriented framework linking pathogen, biological question, required chip feature, measurable endpoint, and evidence level, and we clarify the current regulatory position of new approach methodologies (NAMs).},
}

@article {pmid43005483,
year = {2026},
author = {Wu, M and Chen, L and Zhou, J and Huang, H and Chen, X and Wan, S and Xie, X and Zhou, M and Zhang, Z},
title = {Intermittent hypoxia-driven gut microbial and metabolic remodeling in obstructive sleep apnea: mechanisms and evidence across target organs.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1965973},
pmid = {43005483},
issn = {2235-2988},
mesh = {Humans ; *Sleep Apnea, Obstructive/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; *Hypoxia/metabolism ; Animals ; Intestinal Barrier Function ; Fatty Acids, Volatile/metabolism ; },
abstract = {Obstructive sleep apnea (OSA) exposes tissues to recurrent intermittent hypoxia (IH) and is associated with multisystem morbidity. Growing evidence implicates the gut microbiota and microbial metabolism in these consequences, but their contribution to target-organ injury remains uncertain. This narrative review examines how IH remodels the intestinal environment and evaluates the evidence linking these changes to systemic injury, distinguishing preclinical experimental findings from human clinical observations. IH can disturb intestinal oxygen homeostasis, impair epithelial barrier function, and alter microbial and host-microbial metabolic pathways involving short-chain fatty acids, bile acids, and trimethylamine N-oxide. These changes may influence distant tissues through metabolic signaling and immune activation. Preclinical studies support a functional microbial contribution to selected cardiovascular, metabolic, and neurocognitive phenotypes, but mechanistic resolution and applicability vary with exposure conditions, diet, and host background. Human studies remain predominantly observational and do not establish microbial mediation of OSA-related organ injury. Overall, the gut microbiota is best regarded as a context-dependent contributor and amplifier of IH-related injury, rather than a universal mediator. A focus on microbial function and host-microbial co-metabolism may be more informative than inconsistent taxonomic signatures. Longitudinal studies and targeted interventions are needed to establish clinical relevance and determine whether microbiome-directed approaches can complement established OSA treatment.},
}

Humans
*Sleep Apnea, Obstructive/metabolism/microbiology
*Gastrointestinal Microbiome/physiology
*Hypoxia/metabolism
Animals
Intestinal Barrier Function
Fatty Acids, Volatile/metabolism

@article {pmid42998020,
year = {2026},
author = {Saedi, N and Zhang, S and Lund, MS and Cai, Z and Karaman, E},
title = {Microbiome-Informed Genomic Prediction of CH4:CO2 Ratio in Holstein Dairy Cattle Using 16S rRNA Profiles and SNP Markers.},
journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie},
volume = {},
number = {},
pages = {},
doi = {10.1111/jbg.70086},
pmid = {42998020},
issn = {1439-0388},
support = {1115-00023B//Innovationsfonden/ ; },
abstract = {Ruminant animals produce methane as a by-product of microbial fermentation in the rumen, with cattle being the largest contributors among ruminants. Methane emissions may be influenced directly by the host's genetics and indirectly through host-mediated effects on rumen microbiome composition. In this study, we investigated whether modelling both direct and indirect genetic effects could improve the genomic prediction of breeding values for methane emissions. We used genotype, methane CH4:CO2 ratio and 16S rRNA gene amplicon sequencing data (16S), including 16S genus (16S-G), 16S species (16S-S) from Danish Holstein cows. A conventional genomic best linear unbiased prediction (GBLUP) model was used as a benchmark and compared with a microbiome-informed GBLUP approach based on three linked linear mixed models for the prediction of breeding values. In GMBLUP, the first model regresses methane emissions on three random animal effects (archaeal 16S, bacterial 16S and polygenic effects) using corresponding microbiome and genomic relationship matrices. The second and third models separately regress archaeal and bacterial 16S on random animal effects defined by the genomic relationship matrix. We evaluated prediction accuracy using five-fold cross-validation. The GBLUP model, which used only genomic marker information, achieved a mean accuracy of 0.20 across the five folds when evaluated in the animal subsets corresponding to the 16S-G and 16S-S datasets, while GMBLUP showed higher accuracy, particularly for the 16S-G dataset, with a mean accuracy of 0.48. These results highlight that incorporating microbiome information into genomic prediction models may improve predictive performance for the CH4:CO2 ratio, although further validation in larger and independent populations is required before practical implementation in breeding programmes.},
}

@article {pmid42998127,
year = {2026},
author = {Psyllia, D and Stylianakis, D and Denaro, N and Pistis, M and Lambertini, M and Lai, E and Molozzu, D and Psyllia, MM and Stylianakis, I and Stochino, ME and Chillotti, C and Scartozzi, M and Petrelli, F and Solinas, C},
title = {Antibiotic Exposure and Treatment Outcomes in Head and Neck Squamous Cell Carcinoma and Nasopharyngeal Carcinoma: A Systematic Review and Meta-Analysis.},
journal = {Current oncology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42998127},
issn = {1534-6269},
mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; *Squamous Cell Carcinoma of Head and Neck/drug therapy/therapy/mortality ; *Nasopharyngeal Carcinoma/drug therapy/mortality/therapy ; Treatment Outcome ; *Nasopharyngeal Neoplasms/drug therapy ; Immune Checkpoint Inhibitors/therapeutic use ; Chemoradiotherapy ; },
abstract = {PURPOSE OF REVIEW: Systemic antibiotics may disrupt the gut and oral microbiome, potentially affecting anticancer treatment efficacy. Their prognostic relevance in head and neck squamous cell carcinoma (HNSCC) and nasopharyngeal carcinoma (NPC), particularly during immune checkpoint inhibitor (ICI)-based therapy or definitive chemoradiotherapy (CRT), remains uncertain. This systematic review and meta-analysis evaluated associations between systemic antibiotic exposure around treatment initiation and oncologic outcomes.

METHODS: PubMed/MEDLINE, Embase, and Scopus were searched from January 2015 to March 28, 2026. Eligible studies included patients with HNSCC or NPC receiving ICI, definitive CRT, or chemo-immunotherapy and reporting overall survival (OS), progression-free survival (PFS), or objective response rate (ORR). Random-effects models pooled hazard ratios (HRs) and 95% confidence intervals (CIs) for OS and PFS; ORR was synthesized descriptively. Risk of bias was assessed, as appropriate, using ROBINS-I, ROBINS-E, RoB 2, or the Newcastle-Ottawa Scale.

RESULTS: Eleven studies involving 6,293 patients were included; nine studies (4,507 patients) contributed to survival meta-analyses. Antibiotic exposure was associated with worse OS (HR 1.78, 95% CI 1.52-2.08) and PFS (HR 1.58, 95% CI 1.28-1.96). Associations were consistent in ICI-treated cohorts (OS HR 1.80, 95% CI 1.53-2.13; PFS HR 1.67, 95% CI 1.24-2.25) and CRT cohorts (OS HR 1.73, 95% CI 1.29-2.32; PFS HR 1.53, 95% CI 1.11-2.11). Heterogeneity was low-to-moderate for OS (I2=28.6%) and negligible for PFS (I2=0%). Leave-one-out analyses showed stable OS (HR range 1.76-1.86) and PFS estimates (1.58-1.63). Worse OS was observed for both 30-60-day pre-ICI exposure (HR 2.04, 95% CI 1.43-2.90) and concurrent/peri-treatment exposure (HR 1.74, 95% CI 1.49-2.04). ORR was descriptively lower in antibiotic-exposed patients. Most studies had serious/high risk of bias, primarily due to confounding by indication.

CONCLUSIONS: Systemic antibiotic exposure around treatment initiation is associated with inferior survival and response in HNSCC and NPC. However, predominantly observational evidence and substantial confounding preclude causal inference. Prospective microbiome-informed studies are needed.},
}

Humans
*Anti-Bacterial Agents/therapeutic use/adverse effects
*Squamous Cell Carcinoma of Head and Neck/drug therapy/therapy/mortality
*Nasopharyngeal Carcinoma/drug therapy/mortality/therapy
Treatment Outcome
*Nasopharyngeal Neoplasms/drug therapy
Immune Checkpoint Inhibitors/therapeutic use
Chemoradiotherapy

@article {pmid42998368,
year = {2026},
author = {Dall, SM and Møllekær, AH and Kousgaard, SJ and Jakobsen, SS and Larsen, L and Sørensen, B and Thorlacius-Ussing, O and Albertsen, M},
title = {Microbial and antimicrobial resistance signatures differentiate healthy and inflamed ileal pouches in patients with ulcerative colitis.},
journal = {Journal of Crohn's & colitis},
volume = {20},
number = {11},
pages = {},
pmid = {42998368},
issn = {1876-4479},
support = {81-A.21//Svend Andersen Fonden/ ; 10.46540/4308-00176B//Independent Research Fund Denmark/ ; 101078234//European Union/ ; },
mesh = {Humans ; *Colitis, Ulcerative/microbiology/surgery ; *Pouchitis/microbiology ; Female ; *Colonic Pouches/microbiology ; Male ; Feces/microbiology ; Adult ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; Fecal Microbiota Transplantation ; },
abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation (FMT) from healthy donors with a normally functioning colon has limited clinical effect in the treatment of chronic pouchitis. However, a normally functioning ileal pouch-anal anastomosis (IPAA) physiology differs from individuals with a healthy intact colon. We aimed to investigate the microbial characteristics of patients with a normally functioning IPAA (HealthyPouch) compared with chronic pouchitis (SickPouch), ulcerative colitis (UC), and a healthy intact colon microbiome (NormalGut). Furthermore, we investigated how repeated antibiotic use influences antimicrobial resistance on a bacterial genome level.

METHODS: Fecal samples from 190 participants were collected; HealthyPouch (n = 38), SickPouch (n = 37), UC (n = 23), and NormalGut (n = 92) and sequenced with Illumina and taxonomically profiled. Samples from HealthyPouch, SickPouch, and NormalGut were also long-read sequenced using Oxford Nanopore Technologies for reconstruction of 12 282 metagenome-assembled genomes (MAGs). DNA methylation motifs were used for plasmid-host association.

RESULTS: The HealthyPouch microbiome is distinct from both the UC, NormalGut, and SickPouch microbiome. Escherichia coli MAGs in the SickPouch (n = 21) microbiome had significantly higher co-occurring ciprofloxacin resistance mutations in the gyrA and parC genes, compared to both HealthyPouch (n = 26; BH adjusted P < .05) and NormalGut (n = 40; BH adjusted P < .05). Based on DNA methylation pattern, three plasmids were associated with E. coli carrying extended-spectrum beta lactamase genes.

CONCLUSIONS: HealthyPouch microbiota differs from NormalGut microbiota, and could therefore be more appropriate for FMT treatment of chronic pouchitis. The association between E. coli and resistance gene-carrying plasmids underscores the importance of integrating plasmid analysis into metagenome-based approaches for personalized antibiotic treatment and resistance monitoring.},
}

Humans
*Colitis, Ulcerative/microbiology/surgery
*Pouchitis/microbiology
Female
*Colonic Pouches/microbiology
Male
Feces/microbiology
Adult
Middle Aged
Anti-Bacterial Agents/therapeutic use
*Gastrointestinal Microbiome/genetics
*Drug Resistance, Bacterial/genetics
Escherichia coli/genetics
Fecal Microbiota Transplantation

@article {pmid42998537,
year = {2026},
author = {Chu, Y and Qian, Y and Shi, J and Hu, M and Ling, R and Wu, Y and Dai, H and Yan, Z and Xian, Q and Chen, H and Jiang, H and Zhu, W},
title = {Fecal microbiota capsule transplantation plus immunotherapy as first-line maintenance therapy for patients with malignant solid tumors: A single-arm, dose-escalation, exploratory phase I study.},
journal = {Translational oncology},
volume = {75},
number = {},
pages = {103106},
doi = {10.1016/j.tranon.2026.103106},
pmid = {42998537},
issn = {1936-5233},
abstract = {BACKGROUND: Chemotherapy combined with programmed cell death protein-1 (PD-1) antibody immunotherapy has become the standard first-line treatment for most patients with malignant solid tumors. However, data from multiple phase III trials indicate that even with first-line induction followed by immunotherapy maintenance, median progression-free survival (PFS) remains less than one year.

METHODS: In this phase I dose-escalation trial (3 + 3 design), 12 patients who completed six cycles of first-line chemoimmunotherapy received oral fecal microbiota transplantation (FMT) capsules plus anti-PD-1 maintenance immunotherapy at escalating dose levels (i to i + 3). The primary endpoint was safety; secondary endpoints included the recommended phase II dose (RP2D), PFS, and disease control rate (DCR). Fecal and blood samples were collected for exploratory microbiome and metabolomic analyses.

RESULTS: No grade ≥3 FMT-related toxicities occurred. With a median follow-up of 36.9 months, median PFS was 19.8 months (95% CI 11.2-28.4); maintenance-phase PFS was 11.7 months (95% CI 4.1-19.3). 4 patients remained progression-free on continued immunotherapy. Four patients (33.3%) experienced grade 1-2 gastrointestinal events. Microbiomic analyses showed post-FMT expansion of Blautia and Faecalibacterium, with dose level i + 1 demonstrating the greatest α-diversity shift and engraftment rate. Metabolomic analysis showed that serum arachidonic acid levels increased after FMT.

CONCLUSION: Oral FMT combined with immunotherapy as first-line maintenance therapy for solid tumors was safe and well tolerated, showed promising preliminary efficacy, and induced favorable compositional changes in the gut microbiota. This study was registered with the Chinese Clinical Trial Registry (Registration No.: ChiCTR2100054928).},
}

@article {pmid42998587,
year = {2026},
author = {Leone, L and Papale, M and Appolloni, L and Cattaneo, A and Abbamondi, GR and Tommonaro, G and Lo Giudice, A and Chianese, E and Poli, A and Finore, I and Di Donato, P},
title = {From community profiling to functional insights: bacterial populations in marine sediments from an Antarctic Specially Protected Area (Terra Nova Bay, Ross Sea, Antarctica).},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128811},
doi = {10.1016/j.micres.2026.128811},
pmid = {42998587},
issn = {1618-0623},
abstract = {Marine sediments remain among the least characterised components of the Antarctic microbial landscape. Here, bacterial communities were investigated in sediments from three sites within the Antarctic Specially Protected Area No. 161, in Terra Nova Bay (Ross Sea, Antarctica). Samples were collected during the XXXIII Italian Antarctic Expedition. The sites differed in their local environmental context, including proximity to the Adélie penguin colony and Mario Zucchelli Station. Bacterial communities were characterised by 16S rRNA gene sequencing (V3-V4 region), with amplicon sequence variants resolved using DADA2, and complemented by PICRUSt2 predicted functional potential, bacterial isolation, and quorum-sensing bioassays. Bacteroidota and Proteobacteria dominated all sites, but community composition and diversity differed significantly among sampling sites. AC showed the highest alpha diversity, while ASPA2 showed the lowest. Of the 5423 amplicon sequence variants detected across the nine samples (three per site), 680 were shared across all samples and defined a core microbiome dominated by Bacteroidota and Proteobacteria. Despite marked differences in community composition, broad predicted functional profiles were relatively conserved, whereas finer-scale KEGG Orthology profiles showed site-associated variation. Seventeen psychrophilic strains were isolated, predominantly Psychrobacter, and most displayed hydrolytic activity towards olive oil, tributyrin, or both substrates. Biosensor-responsive activity was detected exclusively in enrichment cultures and not in extracts from individual isolates, providing preliminary evidence of putative quorum-sensing-related activity associated with mixed microbial consortia. These findings provide a baseline for investigating environmental drivers of Antarctic sediment microbiomes and microbial interactions in future studies.},
}

@article {pmid42998756,
year = {2026},
author = {Farhadi, L and Khalil, N and Kowalczyk, W and Lio, P and Yosipovitch, G},
title = {Bacteriophage-Derived Endolysins in Atopic Dermatitis and Other Pruritic Dermatoses: Mechanistic Rationale, Clinical Evidence, and Limitations.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2026.10.037},
pmid = {42998756},
issn = {1523-1747},
abstract = {Chronic pruritus in atopic dermatitis (AD) is associated with cutaneous dysbiosis, including loss of protective commensals and expansion of Staphylococcus aureus. S. aureus can promote itch through secreted proteases and toxins that activate sensory neurons and amplify type 2 inflammation. Because broad-spectrum antimicrobials may disrupt commensal communities, bacteriophage-derived endolysins have been proposed as a more targeted approach. These enzymes cleave bacterial peptidoglycan and can rapidly lyse susceptible bacteria without requiring active growth, although their antimicrobial spectrum varies by enzyme. Preclinical studies support selective antistaphylococcal activity, but early clinical findings in AD are mixed. Therefore, endolysins should be considered alongside other microbiome-directed approaches, including topical bacteriotherapy with protective commensals. This review evaluates how endolysins work, the available clinical evidence, and the remaining questions about formulation, patient selection, inflammation caused by rapid bacterial breakdown, and toxins that may remain active after the bacteria are killed.},
}

@article {pmid42998821,
year = {2026},
author = {Bai, Y and Li, ZB and Dong, PY and Feng, YN and Zhang, XF and Zhang, BQ and You, W},
title = {Multi-omics studies show that naringin improves cyclophosphamide-induced testicular and intestinal damage by enhancing energy metabolism.},
journal = {The Journal of steroid biochemistry and molecular biology},
volume = {},
number = {},
pages = {107142},
doi = {10.1016/j.jsbmb.2026.107142},
pmid = {42998821},
issn = {1879-1220},
abstract = {Cyclophosphamide (CTX) is an anticancer agent that severely impairs male reproductive health. Naringin (NAR), a flavonoid compound, has the potential to ameliorate CTX-induced damage; however, the underlying mechanisms remain unclear. In this study, an integrative approach combining transcriptomics, microbiome analysis, and serum metabolomics was employed to comprehensively evaluate the protective effects of NAR on reproductive function in CTX-treated mice. Microbiome analysis revealed that NAR restored CTX-induced alterations in gut microbial composition. Metabolomic profiling demonstrated that NAR stabilised cholesterol metabolism and primary bile acid biosynthesis, increased serum choline levels, and alleviated reproductive dysfunction in CTX-exposed mice. Transcriptomic analyses of the testes and intestine indicated that NAR modulated glycolysis and the MAPK signalling pathway in CTX-treated mice. Validation of serum metabolites further supported their role in promoting intestinal and testicular development. Research indicates that naringin ameliorates cyclophosphamide-induced reproductive risks in males, partly due to its enhancement of energy metabolism.},
}

@article {pmid42998838,
year = {2026},
author = {Bongers, KS},
title = {The impact of the gut microbiome on skeletal muscle in health and disease.},
journal = {The American journal of the medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.amjms.2026.11.009},
pmid = {42998838},
issn = {1538-2990},
abstract = {The gut microbiome, the community of bacteria residing the lower gastrointestinal tract, is increasingly recognized as an important influence on skeletal muscle physiology, with critical implications for muscle disorders such as sarcopenia and muscular dystrophy. Researchers have uncovered multiple microbiome-derived metabolites that alter skeletal muscle protein synthesis, mitochondrial biogenesis, protein degradation, and glucose transport. Moreover, the microbiome mediates systemic cytokine release of interleukin-6 and tumor necrosis factor alpha, which can drive muscle loss. These studies have led to the identification of gut bacterial species (such as Veillonella atypica and Roseburia inulinivorans) that improve muscle endurance and strength when administered as probiotics in animal models. Several clinical trials of microbiome-focused therapies have also been conducted, with suggestion of benefits as well as potential harms. Taken together, the gut microbiome plays a key role in modulating skeletal muscle physiology, and may serve as the basis for novel therapeutics targeting muscle disease.},
}

@article {pmid42999037,
year = {2026},
author = {Madamanchi, K and Gurrala, S and Watson, J and Melkani, G},
title = {Gut microbiome depletion aggravates glial-mediated Alzheimer's disease pathology through inflammatory, metabolic, and proteostatic dysregulation.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2753247},
doi = {10.1080/19490976.2026.2753247},
pmid = {42999037},
issn = {1949-0984},
mesh = {Animals ; *Alzheimer Disease/microbiology/metabolism/pathology/physiopathology ; *Neuroglia/metabolism/pathology ; Humans ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Amyloid beta-Peptides/metabolism ; Proteostasis ; Brain/metabolism/pathology ; Drosophila ; Drosophila melanogaster ; Bacteria/classification/isolation & purification/genetics ; Inflammation ; },
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by chronic neuroinflammation, metabolic dysfunction, and impaired proteostasis. Emerging evidence suggests that the gut microbiome influences brain function through the gut-brain axis; however, the mechanisms by which this communication affects AD pathology remain poorly understood. In this study, we used humanized Drosophila AD models expressing human AD-related transgenes in glial cells to investigate how glial AD pathology influences the gut microbiome and how microbiome depletion affects behavior and disease progression. Our findings revealed significant alterations in the abundance of several gut microbial taxa, including Lactobacillus, Acetobacter, Enterococcus, Enterobacter, Pseudomonas, Leuconostoc, Providencia, and Gluconobacter, suggesting a potential interaction between the gut microbiome and AD progression. To further define the role of the gut microbiome in AD progression, we treated Drosophila with antibiotics to achieve substantial microbiome depletion (SMD) and evaluated the resulting behavioral, physiological, and molecular changes. Compared with conventional controls, flies with SMD exhibited enhanced inflammatory signaling and cell death, impaired autophagy, lipid dysregulation, and increased accumulation of amyloid β-42 (aβ42) and phospho-tau (pTau), with the extent of these changes varying among the different humanized AD models. These molecular alterations further exacerbated sleepcircadian disruption, altered locomotor performance, and worsened learning and memory deficits. Furthermore, we demonstrated a link between enhanced neuroinflammation and the accumulation of aβ42, pTau, and amyloid precursor protein (APP) proteins. Collectively, our findings demonstrate that gut microbiome depletion aggravates glial-mediated AD pathology through the coordinated disruption of inflammatory, metabolic, and proteostatic pathways, ultimately leading to behavioral dysfunction. These results identify the gut microbiome as a critical regulator of glial homeostasis and provide new insights into its contribution to the progression of neurodegenerative disorders.},
}

Animals
*Alzheimer Disease/microbiology/metabolism/pathology/physiopathology
*Neuroglia/metabolism/pathology
Humans
*Gastrointestinal Microbiome/drug effects
Disease Models, Animal
Amyloid beta-Peptides/metabolism
Proteostasis
Brain/metabolism/pathology
Drosophila
Drosophila melanogaster
Bacteria/classification/isolation & purification/genetics
Inflammation

@article {pmid42999040,
year = {2026},
author = {Sadegi, M and Johnson, BB and Sanches, TM and Ang, G and Cao, J and Ambre, M and Brennan, M and George, O and Knight, R and Baud, A and Palmer, AA and Polesskaya, O},
title = {Replication of Host St6galnac1 -Microbiome Association Across Distinct Experimental Conditions in Heterogeneous Stock Rats.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.09.758003},
pmid = {42999040},
issn = {2692-8205},
abstract = {The gut microbiome is shaped by both environmental and host genetic factors. Identifying specific host loci is essential for understanding the heritability of microbiome-associated traits. The gene St6galnac1 encodes a sialyltransferase involved in mucin O-glycosylation. Tonnelé et al. (2025) identified significant associations between a locus containing St6galnac1 gene, and the abundance of genus Paraprevotella using cecal samples collected from fasted animals. This association was replicated across three cohorts, and paralleled with association found in humans between a functionally related sialyltransferase gene ST6GAL1 and Paraprevotella . Given the sensitivity of microbiome analyses to factors including sampling site, feeding status, and analytical framework, independent replication of these findings is important and it is also important to know if the association generalizes across other conditions or is highly specific to certain environments. Here, we performed a replication analysis using stool (not cecal) samples from 174 HS rats that were not fasted prior to collection. Stool samples underwent 16S rRNA gene sequencing, and microbial community structure was analyzed using compositionally aware methods. The rats were genotyped at the top SNP that was associated with Paraprevotella in the Tonnelé et al. (2025) study. The association between genotype and Paraprevotella abundance was tested using a linear mixed model accounting for sex, cohort, and genetic relatedness. We successfully replicated (p=0.015) St6galnac1 - Paraprevotella association. These findings support the robustness of the St6galnac1 - Paraprevotella association across different sampling strategies and experimental conditions.},
}

@article {pmid42999093,
year = {2026},
author = {Doty, CM and Brady, DJ and Barb, JJ and Thompson, SL and Rincon, N and Browning, B and Kelly, DL and Bennett, ME and Elmer, G and Leggio, L and Brandler, BJ and Roche, DJO},
title = {The effect of minocycline on the gut microbiome in individuals with alcohol use disorder and healthy controls.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.09.758026},
pmid = {42999093},
issn = {2692-8205},
abstract = {Alcohol Use Disorder (AUD) is associated with altered gut microbial composition. Yet, many microbiome studies have included AUD populations with co-occurring conditions (e.g., alcohol associated liver disease; ALD), limiting insight into unique contributions of AUD to gut dysbiosis. Further, preclinical studies show that gut microbiome composition can mediate the behavioral effects of minocycline, including alcohol-related and affective behaviors, but no studies have tested these effects in humans with AUD. This study aimed to 1) compare gut microbiome features between healthy controls (HCs) and individuals with AUD, without ALD, and 2) determine the effects of minocycline on the human gut microbiome. We conducted a four-week randomized, double-blind, placebo-controlled trial of minocycline (100-200 mg/day) in adults with AUD (n=31) and HCs (n=26). We collected fecal samples (n=244) at baseline and each weekly visit for 16S rRNA gene sequencing. Alpha diversity (richness and evenness of taxa within a sample) did not differ by diagnostic group, treatment, or time. In contrast, beta diversity (microbiome composition differences between samples) differed between AUD and controls and was shifted by minocycline over time. AUD, vs. controls, was associated with differences in several taxa prevalences, including reduced Dialister and Subdoligranulum and increased Collinsella , Streptococcus , and Phascolarctobacterium . Minocycline, vs. placebo, rapidly and robustly restructured the microbiome, altering numerous taxa, including Lachnospira , Ruminococcaceae , Clostridium sensu stricto , and Christensenellaceae, and metabolic pathways (e.g., ubiquinol biosynthesis and methylphosphonate degradation). AUD is associated with a distinct gut microbial composition, whereas minocycline produces rapid, sustained, diagnosis-independent gut microbiome restructuring, without altering alpha diversity.},
}

@article {pmid42999116,
year = {2026},
author = {Veerus, L and Sun, H and Almet, AA and Levin, ER and Battaje, RR and Dam, VS and Shah, D and Clerk, R and Chang, B and Woortman, MA and Stuckey, JE and Shumaker, MJ and Yin, YS and Kundu, A and Talaue-Weeast, M and Gao, Z and Cardenas, V and Zhang, XS and Nyangahu, DD and Jaspan, HB and Manhart, M and Nie, Q and Barrett, E and Nejsum, LN and Dominguez-Bello, MG and Blaser, MJ and , },
title = {Urea is a dynamic and functional component of mammalian breast milk.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.28.755206},
pmid = {42999116},
issn = {2692-8205},
abstract = {Urea is a constituent of human milk, yet its regulation and interactions with the infant gut microbiome have not been established. Combining three human cohorts, a mouse model, and microbiome analyses, we show that milk urea increases across lactation, is conserved across mammals, and is not explained by maternal serum urea or diet. Instead, we identify lactation-dependent remodeling of mammary urea metabolism and transport, including dynamic epithelial AQP3 localization consistent with regulated urea transfer into milk. Alongside urea, maternal milk and stool provide reservoirs of urea-metabolizing bacteria that help establish the infant "ureabiome", with encoded urea-utilization capacity. This maternal-infant axis is context-dependent: infant formulas provide higher urea levels than human milk, while functional assays show that urea supports both commensal and opportunistic bacteria in a concentration-dependent manner. Together, these findings define a maternal nitrogen axis linking milk urea to infant gut microbiome assembly and function.},
}

@article {pmid42999133,
year = {2026},
author = {Mifflin, KA and Kigerl, KA and Manrique, P and Cyr, A and Medipally, AK and Guan, Z and Gowdy, KM and Popovich, PG},
title = {Oral Bacterial Translocation Promotes Lung Dysbiosis and Infection Risk after Spinal Cord Injury.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.09.758070},
pmid = {42999133},
issn = {2692-8205},
abstract = {Spinal cord injury (SCI) causes systemic pathophysiology that extends beyond the injured spinal cord. Respiratory infections remain a leading cause of death after SCI and can impair neurological recovery, yet the microbial source of these infections remains poorly defined. This study defined the onset and origin of pulmonary dysbiosis after SCI by testing whether commensal bacteria move to the lung from the gut or oral cavity. In a murine model, bacterial culture, 16S rRNA sequencing and source-tracking analyses showed that SCI rapidly increased lung bacterial burden and shifted the pulmonary microbiome toward an oral-like community. Gut-associated bacteria did not measurably reach the lung through lymphatic or vascular routes. Systemic antibiotics commonly used to treat infection failed to reliably reduce post-SCI lung bacterial burden. In contrast, oral and lung-directed antibiotic delivery reduced bacteria linked to post-injury dysbiosis more effectively. These findings identify the oral cavity as a proximal source of lung dysbiosis after SCI, and support route-specific strategies to prevent respiratory infection after SCI.},
}

@article {pmid42999137,
year = {2026},
author = {Nien, TS and Grathwohl, K and Koenig, A and Borries, C and Lu, A and Mallott, EK},
title = {Shifts in the Maternal Gut Microbiome Across Pregnancy are Associated with Energetic Status in Phayre's Leaf Monkeys.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.15.759161},
pmid = {42999137},
issn = {2692-8205},
abstract = {BACKGROUND: During pregnancy, mothers experience physiological changes that support fetal development, including shifts in energy utilization and increasing insulin resistance during late gestation. While these changes benefit the fetus, they can also impose energetic costs that affect the mother's physical condition and metabolic phenotype. Previous studies suggest that the gut microbiome, a key regulator of female metabolism and energy harvest, may play a critical role in mediating these physiological challenges.

RESULTS: In this study, metagenomic sequencing of the gut microbiome of 120 samples revealed dramatic shifts in gut bacterial composition and function associated with pregnancy and lactation in 14 wild Phayre's leaf monkeys, Trachypithecus phayrei crepusculus , from two groups at the Phu Khieo Wildlife Sanctuary, Thailand. Alpha diversity, beta diversity, and taxonomic composition all differed between cycling and the 3 [rd] trimester. Furthermore, bacterial dissimilarity between these states was negatively correlated with postpartum physical condition; that is, mothers whose gut microbiota remained more stable during pregnancy recovered sooner after giving birth. Functional profiling revealed a depletion of pathways involved in purine salvage and glutamate degradation during the 3 [rd] trimester.

CONCLUSION: Overall, our study demonstrates that the gut microbiome undergoes substantial changes during pregnancy, and the stability of these microbial communities predicts postpartum maternal health and potentially influence lifetime reproductive output.},
}

@article {pmid42999170,
year = {2026},
author = {Comrie, JMC and Tan, X and Le, HH and Lee, MT and Richter, A and Thompson, SC and Besler, KR and Johnson, EL},
title = {Dietary omega-3 polyunsaturated fatty acids interact with select gut microbes to produce bioactive metabolites found in infant gut microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.10.756005},
pmid = {42999170},
issn = {2692-8205},
abstract = {Gut microbes metabolize nutrients in infant diets, producing compounds that play roles in host health. Long-chain polyunsaturated fatty acids (LCPUFAs) are an important component of infant diets, supporting neurological development and immune regulation. Emerging evidence demonstrates that gut microbes, alongside the host, participate in the metabolism of dietary lipids, highlighting an underexplored avenue for LCPUFA biology. In this work, alkyne-tagged eicosapentaenoic acid (EPA [Alk]) was used to investigate interactions between LCPUFAs and the gut microbiota. Flow cytometry and comparative metabolomics identified gut microbial EPA interactors in the ileum of mice. Further comparative metabolomics analysis identified the conversion of EPA to N -acyl amino acids, including attachment to phenylalanine (EP-Phe) and leucine (EP-Leu). Targeted analysis of ex vivo stool cultures determined that EP-Phe and EP-Leu are produced by gut bacteria. A survey of lipid-relevant infant gut bacteria determined various flow cytometry-confirmed EPA-microbe interactions and identified Enterococcus faecalis, Bacteroides thetaiotaomicron, and Clostridium bifermentans as competent producers of EP-Phe or EP-Leu. Thus, both novel metabolites from diet-derived inputs and microbial producers of these metabolites were identified. Together, this highlights important microbiome-centric consequences of LCPUFA consumption and emphasizes that the gut microbiome may be an important consideration in targeted supplementation strategies.},
}

@article {pmid42999235,
year = {2026},
author = {Niraula, S and Jang, JW and Jung, J and Stirewalt, SL and Alagna, M and Du, J and Staley, C and Seed, P and Green, SJ and Ho, KJ},
title = {Shotgun metagenomic and untargeted metabolomic analysis of gut microbiome associated with peripheral artery disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.16.757428},
pmid = {42999235},
issn = {2692-8205},
abstract = {BACKGROUND: While the human gut microbiome is a potentially important and modifiable risk factor for cardiovascular diseases, the links between the gut microbiome and peripheral artery disease (PAD) and its clinical subgroups (claudication and chronic limb-threatening ischemia; CLTI) are not well understood.

METHODS: We used shotgun metagenomics and untargeted metabolomics to analyze the fecal samples of people with PAD and age- and sex-matched non-PAD controls collected in a cross-sectional manner. We used functional prediction pathways, a network analysis, and weighted gene co-expression network analysis of metagenomic, metabolomics, and clinical data to better understand PAD-associated dysbiosis.

RESULTS: Alpha and beta diversity were similar between the PAD (n=78) and non-PAD (n=20) groups. Differentially abundant species were dominated by those belonging to the Lachnospiraceae, Ruminococcaceae and Enterobacteriaceae families. Fecal butyrate levels were reduced between the non-PAD and PAD groups, but differences were not statistically significant. There was significantly reduced alpha diversity in the samples of the CLTI compared to claudication subgroup. Abundance of multiple butyrate producers were greater in the claudication group compared to CLTI. Network analysis revealed 5 meta-modules, each with specific associations to PAD presentation and metabolomic profiles, and species that are both top module hubs and differentially abundant between groups. Community interconnectedness appears to increase in claudication, followed by community disintegration in CLTI.

CONCLUSIONS: This metagenomic-metabolomic analysis of the gut microbiome of individuals with PAD, highlights the importance of studying functional capacity, diversity, and connectivity between species. Microbial modules may allow an integrative view of the microbial ecology relevant to presence and progression of PAD.},
}

@article {pmid42999269,
year = {2026},
author = {Mannochio-Russo, H and Nelson, MR and Charria-Girón, E and Torres-Ortega, LR and Agongo, J and Gonçalves Nunes, WD and Patan, A and Strobel, M and David, LC and Panitchpakdi, M and Gentry, EC and Caraballo-Rodríguez, AM and Zemlin, J and Kamenik, Z and Acebo, N and Montoya Giraldo, YA and Bauermeister, A and Wang, M and van der Hooft, JJJ and Hagey, LR and Mohanty, I and Dorrestein, PC},
title = {The Evolving Bileome: A Pan-Repository Landscape of Expanded Bile Acid and Related Steroidal Signatures.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.10.758218},
pmid = {42999269},
issn = {2692-8205},
abstract = {Bile acids and related steroidal metabolites are among the most studied biomolecules, yet recent work has revealed far greater structural diversity than previously recognized, much of it shaped by the microbiome. We previously introduced a repository-scale bile acid MS/MS library built from queries targeting C24 bile acid fragmentation, limited to Orbitrap Q Exactive datasets within GNPS/MassIVE. Here we announce a major expansion of this library: a bile acid and steroidal MS/MS spectral library assembled across three major metabolomics repositories, now capturing C23, C24 (including alkamine), C26 (C-C bonded aceto derivatives), and C27 bile acids, as well as C28 bile alcohols. The expanded libraries comprise 640,141 unique MS/MS spectra, of which 120,293 (18.8%) match 2,529 reference spectra, leaving most of this steroidal chemical space structurally unassigned. Linked to harmonized pan-repository metadata, the library provides a starting point for classifying MS/MS spectra as likely bile acids or related steroids, with two example analyses illustrated here. This resource allows researchers to flag candidate bile acid and steroidal signatures in their own data for further characterization.},
}

@article {pmid42999290,
year = {2026},
author = {Mitchell, MK and Carty, MA and Snow, NL and Archambault, MT and Budsberg, AE and Carrillo, EV and Vignieri, EE and Older, EA and Rometo, OL and Van de Wal, LE and Floyd, KJ and Baker, LR and Kunkle, CA and Li, J and Ellermann, M},
title = {Cannabinoid receptor 1 activity promotes microbial dysbiosis by stimulating the oxygen-dependent expansion of Enterobacteriaceae.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.10.758071},
pmid = {42999290},
issn = {2692-8205},
abstract = {The endocannabinoid system is comprised of bioactive lipids that signal via cannabinoid receptors, which can modulate barrier and immune functions along the gastrointestinal tract. Clinical studies indicate that endocannabinoid activity is dysregulated in inflammatory bowel diseases. Moreover, an increase in gut endocannabinoids is correlated with microbial dysbiosis in Crohn's disease. Here, we show that endocannabinoid activity promotes metabolic dysfunction within the colonic mucosa, resulting in microbial dysbiosis and exacerbated colitis. Stimulation of the cannabinoid receptor CB1 resulted in the expansion of Enterobacteriaceae within the gut microbiome, a common feature of inflammation-associated dysbiosis. Preceding this microbial change, CB1 activity induced transcriptional signatures of mitochondrial stress and immune activation within the colonic mucosa. This was followed by a reduction in mucosal ATP production and the induction of aerobic respiration genes in luminal Escherichia coli . Genetic inactivation of aerobic respiration in E. coli limited its proliferation, indicating that CB1 activity stimulates oxygen-dependent Enterobacteriaceae growth. In IBD susceptible mice, endocannabinoid activity promoted mucosal infection by an E. coli pathobiont, which corresponded with elevated pro-inflammatory markers. In inflammation resistant mice, acute CB1 stimulation was sufficient to accelerate the infection dynamics of an Enterobacteriaceae pathogen, resulting in exacerbated colitis. Taken together, our data support a model in which endocannabinoid signaling at the CB1 receptor disrupts respiratory metabolism in the colon, compromising the anoxic environment of the lumen that is critical for maintaining aerobically respiring pathogens at low abundance. More broadly, our findings highlight a proinflammatory effect of endocannabinoid activity that can contribute to intestinal disease development.},
}

@article {pmid42999300,
year = {2026},
author = {Krishnavajhala, A and Gingras, MC and Santiago-Rodriguez, TM and Chen, Y and Bandaranaike, D and Bhamidipati, S and Qin, X and Kottapalli, K and Momin, Z and Santhanam, A and Walker, K and Wang, Q and Griffin, SM and Masternak, MM and Ross, MC and Muzny, D and Wu, J and Urquieta, E and Gibbs, RA and Doddapaneni, H},
title = {Microbial Dynamics Across Commercial Spaceflights of Varying Duration.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.29.728784},
pmid = {42999300},
issn = {2692-8205},
abstract = {Spaceflight introduces environmental stressors that can alter human microbiomes and immune responses. We analyzed 259 and 17 biospecimens for microbiome and single-cell studies from n=6 astronauts across two commercial ISS missions: Axiom 2 (10-day mission) and Axiom 3 (21-day mission). Samples included saliva, stool, urine, and body swabs from 10 anatomical sites, profiled via 16S ribosomal RNA (rRNA) gene amplicon sequencing. Gut and oral microbiomes remained stable, while skin-associated communities exhibited transient diversity shifts post-flight. Taxonomic analysis revealed individual and site-specific patterns, as well as from the spaceflight/ISS environment. Cytokine profiling from single-cell data indicated immune activation, with IL-32 and IL-16 transcripts elevated in Axiom 2 and Axiom 3. Microbiome and interleukin correlation analyses found 14 significant associations in Axiom 2 data. These findings provide an integrated view of microbiome individuality. Our study represents a descriptive comparison of two missions, informing strategies for crew health on future long-duration missions.},
}

@article {pmid42999392,
year = {2026},
author = {An, Y and Xia, Y and Sun, J},
title = {Disrupted microbial queuosine biosynthesis contributes to dysbiosis in human inflammatory bowel disease.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.12.26365231},
pmid = {42999392},
abstract = {BACKGROUND AND AIMS: As a microbiome/diet-derived vitamin, queuine (q) is a micronutrient that eukaryotes acquire from microbiota or diet. Vitamin q, the free base form of queuosine (Q), is used for Q-modification of transfer RNA (tRNA). Although tRNA-Q-modification in regulating eukaryotic cell physiology is recognized, the relationship between Q-tRNA-modification and the human microbiome in health and inflammatory bowel diseases (IBD) remains unknown. Which bacteria produce q and how the q-producing bacteria contributing to human health and IBD are not explored. Here, we hypothesize that disrupted microbial Q-biosynthesis contributes to the dysbiosis of human IBD. We performed comprehensive multi-omics integrative analyses using publicly available datasets. Specifically, we re-analyzed publicly available shotgun metagenomic, single-cell RNA sequencing (scRNA-seq), metabolic datasets, and completed meta-analysis.

METHODS: To systematically investigate microbial Q-biosynthesis in healthy individuals and IBD patients, we performed a systematic secondary analysis by integrating 9 publicly available metagenomic datasets, 15 scRNA-seq datasets and one metabolic dataset published prior to 2026. We present a novel secondary bioinformatic reanalysis of sequence outputs mapped to the latest microbial taxonomy, functional pathways and microbial Q-related genes. Longitudinal study of shotgun metagenomics across the human lifespan (3146 samples) enabled taxonomic and functional profiling.

RESULTS: We first identified key q-producing bacteria (e.g., Bacteroides and Alistipes) in healthy populations. We then found that patients with IBD had significantly reducation of q-producing bacteria and a coordinated downregulation of the Q-related pathways, including Q, preQ 0 , de novo guanosine ribonucleotide biosynthesis and de novo guanosine deoxyribonucleotide biosynthesis pathways. This functional impairment was primarily driven by reduced contributions from Bacteroides , Alistipes and Akkermansia . The longitudinal stability of the q-producing bacteria community across the human lifespan (1638 samples). We observed a significant negative correlation between host age and the abundance of q-producing bacteria in patients with UC. Moreover, Queuine tRNA-ribosyltransferase 1 (QTRT1) expression in human intestinal epithelial cells was significantly reduced in patients with IBD compared to healthy controls.

CONCLUSIONS: Our study used multi-omics datasets to define a novel functional dysbiosis characterized by a reduction of microbial Q-biosynthesis in patients with IBD. Vitamin q and its tRNA modification is lesser-recognized in human IBD. Understanding the cellular and organismal mechanisms of this microbiome-dependent micronutrient will advance the prevention of IBD and improve the quality of life of patients with IBD.

Queuine, vitamin q, is a highly conserved hypermodified nucleoside micronutrition could only be acquired from microbiota or diet. It is used for modification of transfer RNA to protein transitional fidelity, but the specific microbial pathways evolved and the relationship with IBD are unclear.

WHAT THIS STUDY ADDS: This study identifies a novel functional dysbiosis in IBD patients characterized by the depletion of q-producing gut bacteria (e.g., Bacteroides and Alistipes) and the downregulated microbial Q biosynthesis pathways, which correlates with host QTRT1 deficiency to potentially drive IBD pathogenesis.

1. Identifies the altered Q-biosynthesis pathway in human IBD. Establishes the "Microbial Q-synthesis-Host tRNA modification" axis as a novel mechanistic link, shifting human IBD microbiome research from taxonomic description to functional epitranscriptomics.Overcomes the inherent biases of traditional meta-analyses through a unified secondary bioinformatic reanalysis, leveraging HMP unified metabolic analysis network 3 (HUMAnN3)-based modeling of 3,000+ samples, to reveal a universal breakdown of the microbial Q-biosynthetic supply chain across all IBD subtypes.Recognize vitamin q as a critical gut-health micronutrient, influencing dietary guidelines and the regulation of functional medical foods for IBD management.},
}

@article {pmid42999460,
year = {2026},
author = {Omeir, K and Ancira, J and Gabrilska, R and Tipton, C and Phillips, N and Wolcott, J and Phillips, CD},
title = {The Structural Genome Shapes the Chronic Wound Microbiome.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.13.26365461},
pmid = {42999460},
abstract = {Recent studies report associations between the patient genome and the chronic wound microbiome, suggesting a causal relationship. Guided by the expectation that larger genomic perturbations are less likely to be neutral, here we study the association of genomic copy number variants (CNVs) with abundances of wound species. Genomic and metagenomic data were collected from 597 patients with chronic wounds at initial clinical visit. Association studies included 831 CNVs and 68 species, implementing a two-cohort design and study-wide significance threshold. There were 47 CNVs (5.7%) associated with 25 species (36.8%); an additional 1,730 associations achieved study-wide significance in one cohort. Associations with haplotype dosage variation dominated significant associations (69.4%) indicating haplotype dosage is important beyond simply locus copy count. Significant co-occurrences between associated and non-associated species, all involving anaerobes, support a model in which the genome selects for certain species that in turn shape the broader microbiome through ecological interactions. Significant CNVs encompassed 66 genes which were functionally overrepresented for several terms, with extracellular matrix (ECM) and ECM-cell interaction terms emphasized. Four collagen and collagen remodeling genes were distributed across four unlinked significant CNVs, a result that strikingly aligns with the previous studies reporting other collagen or ECM component associations. Related, cytoskeletal dynamics are also strongly implicated. Heritability estimates drawing on all available data and controlling for species correlation and patient factors yielded 30 species with significant heritabilities, 24 of which were greater than 20%. These findings extend the genomic basis of the chronic wound microbiome by emphasizing importance of genomic structural variation and suggest a prominent role for variation across ECM-cellular connections as mechanisms defining microbial selection.},
}

@article {pmid42999727,
year = {2026},
author = {Amin, MN},
title = {Microbiome-Derived Metabolites in Multiple Sclerosis: Mechanisms of Immune Regulation and Therapeutic Potential: A Literature Review.},
journal = {Cureus},
volume = {18},
number = {10},
pages = {e117645},
pmid = {42999727},
issn = {2168-8184},
abstract = {Multiple sclerosis (MS) is a chronic autoimmune neuroinflammatory disease characterized by immune dysregulation, demyelination, and neurodegeneration of the central nervous system (CNS). Increasing evidence suggests that gut microbiota and microbiome-derived metabolites play important roles in the pathogenesis and progression of MS by modulating the gut-brain-immune axis. This narrative review examines the possible immunomodulatory effects of microbiome-derived metabolites in MS, with particular emphasis on short-chain fatty acids (SCFAs), tryptophan-derived metabolites, and polyamines, and evaluates their potential therapeutic implications. This review was conducted using the most recent available studies relevant to the topic. The search included PubMed, Google Scholar, and PMC databases. Eligible studies focused on randomized controlled trials, systematic reviews, meta-analyses, observational studies, reviews, and other publications that examined the role of microbiota and its metabolites in MS. The reviewed evidence indicates that MS-associated dysbiosis is accompanied by altered microbial metabolite production, disruption of regulatory T cell (Treg)/T helper 17 (Th17) balance, impaired barrier integrity, and increased neuroinflammation. SCFAs, tryptophan-derived metabolites, and polyamines demonstrate immunoregulatory effects through modulation of T-cell responses, cytokine signaling, and inflammatory pathways. Microbiota-targeted interventions, including probiotics, prebiotics, dietary modulation, and metabolite supplementation, have shown promising immunological and clinical effects. However, methodological heterogeneity, small cohorts, variable interventions, and insufficient long-term clinical validation limit definitive conclusions regarding therapeutic efficacy. Future large-scale longitudinal and multi-omics studies are crucial for clarifying the underlying mechanisms and unlocking microbiota-targeted strategies to manage MS more effectively.},
}

@article {pmid43000087,
year = {2026},
author = {Mei, Z and Dai, DLY and Sifuentes, E and Petersen, C and Turvey, SE},
title = {Microbiome-Targeted Interventions for Pediatric Asthma and Allergic Diseases: Current and Emerging Approaches.},
journal = {Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2026.10.038},
pmid = {43000087},
issn = {1534-4436},
abstract = {Allergic diseases are among the most common chronic diseases of childhood and remain a major public health challenge. Increasing evidence indicates that the early-life gut microbiome plays a central role in immune maturation, making it an attractive target for allergy prevention. During the first 1000 days of life, interactions between the developing microbiome and the immune system help establish immune tolerance, while disruptions to this process increase the risk of asthma and allergic diseases. Current microbiome-targeted strategies largely focus on optimizing early-life microbial exposures through interventions such as mode of delivery, antibiotic stewardship, breastfeeding, and exposure to diverse environmental microorganisms. These approaches are already incorporated into public health recommendations and promote healthy microbiome development without directly manipulating microbial communities. Newer approaches seek to intervene more precisely through microbial transfer therapies, live biotherapeutic products, prebiotics, postbiotics, and microbial metabolite-based therapies. Although several have shown encouraging preclinical and early clinical results, evidence supporting routine clinical use remains limited. The next generation of microbiome therapeutics is likely to be defined less by changing which microbes are present than by restoring the microbial functions that establish immune tolerance. This conceptual advance is driving the development of increasingly targeted microbiome-based interventions and provides a framework for the next generation of allergy prevention strategies. Translating these mechanistic insights into safe, effective therapies that complement established public health measures represents the next major challenge in preventing asthma and allergic diseases.},
}

@article {pmid43000106,
year = {2026},
author = {Zhao, Y and Chen, Y and Tan, J and Fang, L and Jiang, L},
title = {AI-enabled rumen microbiome engineering for methane mitigation in ruminants.},
journal = {Biotechnology advances},
volume = {94},
number = {},
pages = {109094},
doi = {10.1016/j.biotechadv.2026.109094},
pmid = {43000106},
issn = {1873-1899},
abstract = {Enteric methane from ruminants is a major agricultural source of greenhouse gas emissions, yet durable mitigation remains difficult because methane arises from host-regulated, cross-kingdom microbial networks rather than from methanogens alone. Artificial intelligence (AI) offers a means to integrate methane phenotypes with rumen multi-omics, host genetics, diet, fermentation traits, and environmental data. However, predictive accuracy does not by itself identify causal or controllable targets. Here, rumen methane is framed as a constrained engineering problem in which carbon and reducing equivalents must be redirected while digestibility, animal health, and productivity are preserved. We examine the construction of AI-ready datasets, multimodal prediction, interpretable learning, causal target discovery, and the transition from computational hypotheses to deployable interventions. Particular attention is given to methanogenic pathways, interspecies hydrogen transfer, alternative electron sinks, and context-dependent treatment responses. Demonstrated interventions and prospective engineering strategies include structure-guided inhibitor discovery, redox-routing combinations, live microbial consortia, phage- and enzyme-based control, early-life programming, and adaptive precision deployment. Across these approaches, a complete design-build-test-learn cycle is still needed to connect model outputs with mechanistic assays, rumen simulation, controlled animal studies, and external multi-farm validation. Progress also depends on harmonized phenotypes, leakage-resistant evaluation, transparent uncertainty, standardized reporting, and early consideration of manufacturing, regulation, economics, and life-cycle impacts. AI-enabled rumen microbiome engineering can therefore accelerate methane mitigation only when prediction is linked to causal biology and measurable, persistent performance across diverse ruminant systems.},
}

@article {pmid43000189,
year = {2026},
author = {Morioka, T and Miyaoka, D and Nakatani, S and Kakutani, Y and Miyamoto, S and Nagakura, Y and Uematsu, M and Hirano, T and Yae, H and Yamamoto, M and Sato, N and Fujimoto, K and Emoto, M and Imoto, S and Uematsu, S},
title = {Longitudinal Taxonomic and Predicted Functional Gut Microbiome Responses to Tirzepatide and Semaglutide: An Exploratory Secondary Analysis of the OMDOT-1 Randomized Controlled Trial.},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.71533},
pmid = {43000189},
issn = {1463-1326},
support = {23K15232//Japan Society for the Promotion of Science/ ; JP25K02682//Japan Society for the Promotion of Science/ ; JP25K22560//Japan Society for the Promotion of Science/ ; JP26H02419//Japan Society for the Promotion of Science/ ; JP26K19344//Japan Society for the Promotion of Science/ ; JP26ae0121040//Japan Agency for Medical Research and Development/ ; JP26ae0121048//Japan Agency for Medical Research and Development/ ; },
abstract = {AIMS: Glucagon-like peptide-1-based therapies improve metabolic outcomes, but longitudinal gut microbiome dynamics remain poorly characterized. We compared taxonomic and predicted functional microbiome responses to tirzepatide and semaglutide in Type 2 diabetes.

MATERIALS AND METHODS: This exploratory secondary analysis included 36 participants from a randomized controlled trial comparing tirzepatide, semaglutide and conventional treatment. Faecal samples were collected at five time points over 16 weeks and analyzed by 16S rRNA gene sequencing. Genus-level features were screened using MaAsLin2, and candidate genera were further evaluated using longitudinal mixed-effects models. Predicted microbial functions were inferred using PICRUSt2 and analyzed using MaAsLin2. Primary analyses were adjusted for baseline body mass index, with exploratory sensitivity analyses additionally adjusted for changes in body weight and haemoglobin A1c.

RESULTS: No significant between-group differences in beta diversity were observed. Alpha diversity increased predominantly in the tirzepatide group, with a significant time-by-treatment interaction versus control. Longitudinal trajectories relative to the control group differed for several genera, including Romboutsia_B, Barnesiella and Ruminococcus_E with both treatments and Vescimonas with tirzepatide (q < 0.05). Across 2106 predicted EC features, longitudinal effects were positively correlated between tirzepatide and semaglutide (67.1% concordant direction; Pearson r = 0.450, p < 0.001). Treatment-versus-control analyses identified predicted functional changes involving energy and carbohydrate metabolism.

CONCLUSIONS: Tirzepatide and semaglutide were associated with partially distinct taxonomic changes, accompanied by broadly similar predicted functional patterns. These longitudinal findings complement, while remaining distinct from, Week-16 shotgun metagenomic endpoint analyses.

TRIAL REGISTRATION: Japan Registry of Clinical Trials (jRCT), jRCT1051240017.},
}

@article {pmid43000446,
year = {2026},
author = {Zhuo, Q and Fu, K and Liu, Z and Zhang, H},
title = {Bacillus subtilis attenuates acetaminophen-induced liver injury and preserves gut-liver homeostasis in mice.},
journal = {Cell communication and signaling : CCS},
volume = {24},
number = {1},
pages = {},
pmid = {43000446},
issn = {1478-811X},
support = {81802964//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Bacillus subtilis/physiology ; *Acetaminophen/adverse effects ; *Chemical and Drug Induced Liver Injury/pathology/metabolism/microbiology ; *Liver/pathology/metabolism/drug effects ; Mice ; Male ; *Homeostasis/drug effects ; *Probiotics/pharmacology ; Mice, Inbred C57BL ; Intestines ; },
abstract = {Acetaminophen (APAP) overdose produces an early oxidative insult followed by sterile inflammation and tissue repair, but whether probiotic interventions can influence these distinct phases remains unclear. Here, we evaluated the effects of Bacillus subtilis on APAP-induced liver injury in mice. B. subtilis pretreatment reduced serum aminotransferases and hepatic necrosis, restored the hepatic GSH/GSSG ratio, and decreased cellular ROS and p-JNK level at 24 h. When B. subtilis treatment was initiated after APAP and continued daily, it did not significantly reduce liver injury at 48 h but lowered serum aminotransferases and residual hepatic necrosis at days 5 and 7, consistent with a later recovery-associated benefit. B. subtilis pretreatment reduced the frequencies of Ly-6G[+] neutrophils and total myeloid cells during acute injury, increased the proportion of TIM4[+] Kupffer cells during recovery, and shifted serum cytokines toward a less inflammatory profile. In parallel, B. subtilis preserved colonic morphology and occludin/ZO-1 expression and lowered circulating LPS. Recovery-stage transcriptomic and microbiome analyses associated B. subtilis with antioxidant and metabolic programs and altered microbial community structure. Metabolomic analysis identified candidate metabolites elevated in B. subtilis-treated mice; among these, histidine and acetyl-L-carnitine were selected for functional testing and provided partial biochemical protection, whereas only live B. subtilis reproduced the combined hepatic and intestinal effects. These findings show that viable B. subtilis limits acute APAP hepatotoxicity and supports recovery while preserving intestinal barrier integrity.},
}

Animals
*Bacillus subtilis/physiology
*Acetaminophen/adverse effects
*Chemical and Drug Induced Liver Injury/pathology/metabolism/microbiology
*Liver/pathology/metabolism/drug effects
Mice
Male
*Homeostasis/drug effects
*Probiotics/pharmacology
Mice, Inbred C57BL
Intestines

@article {pmid42996360,
year = {2026},
author = {Holsinger, RMD},
title = {Editorial: Decoding the gut-brain axis: implications for neurodegenerative disease therapies.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {2015896},
doi = {10.3389/fnagi.2026.2015896},
pmid = {42996360},
issn = {1663-4365},
}

@article {pmid42996471,
year = {2026},
author = {Shao, H and Li, X and Miao, X and Tang, L and Gu, Y and Qin, Z and Han, J and Li, J and Wang, Q and Yang, W and Chen, H and Wu, J},
title = {Characterization of lower-airway microbial communities in pulmonary tuberculosis by BALF metagenomic sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1938581},
pmid = {42996471},
issn = {2235-2988},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Tuberculosis, Pulmonary/microbiology ; *Metagenomics/methods ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Female ; Mycobacterium tuberculosis/genetics/isolation & purification ; Male ; Middle Aged ; Bronchoscopy ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Adult ; },
abstract = {OBJECTIVE: Pulmonary tuberculosis (PTB) is an infectious disease caused by the Mycobacterium tuberculosis complex (MTBC). This study aimed to characterize the lower-airway microbiome in patients with PTB and compare it with that of patients without PTB (Non-PTB) undergoing bronchoscopy for pulmonary disease, in order to describe differences in microbial composition between the two groups and improve our understanding of pulmonary microbial ecology in tuberculosis.

METHODS: We performed metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) from 75 patients (38 PTB, 37 Non-PTB). Microbial diversity, composition, and differential taxa were analyzed using standard bioinformatics tools.

RESULTS: PTB samples showed higher Shannon and Simpson indices, whereas Richness did not differ significantly between groups. Beta diversity analyses revealed modest but statistically detectable differences in microbial community composition between PTB and Non-PTB samples. The PTB group showed higher relative abundances of MTBC and several oral-associated taxa (e.g., Prevotella and Fusobacterium), whereas Non-PTB samples showed higher relative abundances of taxa including Pseudomonas aeruginosa and Aspergillus fumigatus.

CONCLUSION: This BALF metagenomic study characterized lower-airway microbial features in patients with PTB and identified differences in microbial community composition and structure between PTB and patients with heterogeneous Non-PTB pulmonary diseases.},
}

Humans
*Bronchoalveolar Lavage Fluid/microbiology
*Tuberculosis, Pulmonary/microbiology
*Metagenomics/methods
*Microbiota
High-Throughput Nucleotide Sequencing
Female
Mycobacterium tuberculosis/genetics/isolation & purification
Male
Middle Aged
Bronchoscopy
*Bacteria/classification/genetics/isolation & purification
Metagenome
Adult

@article {pmid42996472,
year = {2026},
author = {Zhang, X and Wang, H and Xing, J and Zhao, H and Liu, Y and Jiao, J},
title = {Microecological-metabolic links along the brain-gut-muscle axis in Tuina analgesia from the perspectives of gut metagenomics and untargeted metabolomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1957609},
pmid = {42996472},
issn = {1664-302X},
abstract = {Chronic pain involves multilevel processes including central sensitization, peripheral tissue abnormalities, neuroimmune responses, metabolic alterations, and changes in gut microecology. Tuina and related manual therapies can influence local soft-tissue status, peripheral sensory input, autonomic activity, inflammatory responses, and muscle metabolism, whereas the links between their distal systemic effects and gut microecology remain insufficiently characterized. The brain, gut, and skeletal muscle can interact through autonomic pathways, immune-inflammatory signaling, circulating metabolites, myokines, and other distal signals, providing a biological context for analyzing cross-organ changes related to Tuina analgesia. A limited number of studies have reported changes in gut microbiota after Tuina, massage, or combined manual interventions; however, direct evidence continuously linking mechanical stimulation, microbial function, metabolic signaling, and pain improvement remains limited. Gut metagenomics extends analysis beyond species composition to strains, functional genes, and metabolic pathway potential, whereas untargeted metabolomics captures metabolic changes jointly shaped by the host and microbiota. Short-chain fatty acids, bile acids, tryptophan derivatives, and molecules related to lipid and energy metabolism have shown functional associations with neuroimmune regulation, sensory neural activity, and pain sensitization in different pain models. Myokines, metabolites, and extracellular vesicle signals derived from skeletal muscle also provide a possible biological basis for bidirectional gut-muscle communication. Nevertheless, most of these mechanisms originate from studies of pain, the microbiome, or exercise physiology and cannot be directly equated with mechanisms of Tuina analgesia. Integrated metagenomic and metabolomic analyses can identify candidate links involving microbial functions, metabolic alterations, host responses, and pain phenotypes, thereby narrowing the scope of subsequent functional validation. Their interpretation remains influenced by Tuina stimulation parameters, diet, gut transit, medication use, circadian rhythms, and other host factors. Standardization of the intervention, longitudinal multi-omics observation, targeted quantification, functional experiments, and cross-center replication will help clarify the temporal relationships and functional significance of these changes. Microecological-metabolic links across the brain, gut, and skeletal muscle can therefore serve as a cross-organ framework for investigating the systemic effects of Tuina analgesia, although specific pathways and their clinical predictive value still require direct experimental and prospective validation.},
}

@article {pmid42996507,
year = {2026},
author = {Zhang, P and Zhang, X and Ji, C and Hu, W},
title = {Chinese herbal medicine for recurrent urinary tract infection: formulation-specific clinical evidence, experimental pharmacology, and unresolved recurrence mechanisms.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1950004},
pmid = {42996507},
issn = {1663-9812},
abstract = {Chinese herbal medicine (CHM) is used for recurrent or chronic urinary symptoms within the traditional category of dysuria, often through stage-specific treatment during symptomatic and remission phases. Whether defined CHM preparations prevent recurrent bacterial cystitis or modify recurrence biology remains uncertain. The aim of this study is to critically evaluate formulation-specific clinical evidence for CHM in women with recurrent urinary tract infection (rUTI) and determine whether reported benefits are connected to recurrence biology.

MATERIALS AND METHODS: Structured searches of PubMed, China National Knowledge Infrastructure, and Wanfang Data were closed on 13 July 2026. After within-batch screening and cross-source reconciliation, 103 reports were linked into 96 study or unresolved-report clusters. Clusters were classified by directness, and clinical confidence was appraised using allocation, participant flow, recurrence ascertainment, denominator integrity, comparator, intervention identity, safety reporting, internal consistency, and report independence.

RESULTS: Ten core clusters directly addressed prospective recurrence or suppressive treatment, but every comparative estimate was of very low confidence. Reported signals were formulation-specific and were limited by attrition, responder-conditioned denominators, active comparators, co-interventions, poorly defined recurrence, internal numerical inconsistencies, or report linkage. Botanical identity and study-batch chemistry were usually inadequate. Experimental studies supported anti-adhesion, virulence-modulating, anti-inflammatory, immune, and urothelial plausibility, including chemically characterized Persicaria capitata extract and more specific Caveolin-1 evidence for purified cynaroside, but predominantly used acute or pretreatment models. No microbiome or biomarker study evaluated clinical mediation.

CONCLUSION: Current evidence is inconclusive rather than uniformly negative and supports cautious hypothesis generation for specific preparations, not a class-wide efficacy or safety claim. No clinical study demonstrates that CHM reduces recurrence by clearing persistent uropathogens, interrupting gut-bladder or vaginal transmission, restoring microbial ecology, or repairing the urothelial barrier. Reproducible products, intention-to-treat recurrence trials, longitudinal strain-resolved sampling, and prespecified mediation analyses are required.},
}

@article {pmid42996510,
year = {2026},
author = {Zhong, X and Wu, H and Na, HK},
title = {Dietary Regulation of the Tumor Immune Microenvironment in Cancer Immunotherapy.},
journal = {Journal of cancer prevention},
volume = {31},
number = {4},
pages = {195-213},
pmid = {42996510},
issn = {2288-3649},
abstract = {Cancer progression is driven by complex interaction among malignant cells, stromal components, and tumor-infiltrating immune cells, which together define the tumor immune microenvironment (TIME). Tumor cells evade immune surveillance by impairing the cytotoxic CD8[+] T-cell function and promoting immunosuppressive cell populations including regulatory T cells, tumor-associated macrophages, and myeloid-derived suppressor cells. Although immune checkpoint blockade and adoptive T-cell therapy have advanced cancer treatment, their clinical efficacy remains limited by therapeutic resistance, heterogenous responses, and treatment-related toxicities. Dietary factors have emerged as potential modulators of antitumor immunity through their effects on immune cell metabolism, inflammatory signaling, and the gut microbiota. In this review, we summarize the mechanisms underlying immunosuppression within the TIME and discuss how macronutrients, micronutrients, food-derived bioactive compounds, and dietary patterns regulate immune cell function and antitumor immune responses. We further highlight the potential of dietary modulation to improve immunotherapy outcomes while critically evaluating current preclinical and clinical evidence. Finally, we discuss the challenges associated with translating these findings into clinical practice, including bioavailability, context-dependent effects, and the need for well-designed clinical trials. A better understanding of diet-mediated immune regulation may provide new opportunities for developing complementary strategies to enhance cancer immunotherapy.},
}

@article {pmid42996652,
year = {2026},
author = {Rowe, JC and Winston, JA},
title = {Bile acid dysmetabolism and microbial dysbiosis coincide with Clostridioides difficile infection in pediatric inflammatory bowel disease.},
journal = {Npj gut and liver},
volume = {3},
number = {1},
pages = {35},
pmid = {42996652},
issn = {3004-9806},
support = {K08 AI153550/AI/NIAID NIH HHS/United States ; },
abstract = {Pediatric inflammatory bowel disease (IBD) patients are at increased risk for Clostridioides difficile infection. This review highlights bile acid dysmetabolism, driven by gut microbiota dysbiosis and reduced microbial production of secondary bile acids, as a key factor linking pediatric IBD to increased CDI susceptibility. We examine interactions among IBD, dysbiosis, bile acid metabolism, and C. difficile, and discuss emerging microbiome-based interventions aimed at restoring bile acid homeostasis.},
}

@article {pmid42996672,
year = {2026},
author = {Adamu Bukari, AR and Opulente, DA and Hittinger, CT and d'Enfert, C and Cuomo, CA and Gerstein, AC},
title = {Linking geography, isolation source, and genomic diversity in a global Candida albicans phylogeny.},
journal = {Npj fungal science},
volume = {1},
number = {1},
pages = {7},
pmid = {42996672},
issn = {3091-3896},
support = {U19 AI110818/AI/NIAID NIH HHS/United States ; },
abstract = {Candida albicans is a common commensal species in the human microbiome at multiple sites and an opportunistic pathogen. Previous phylogenomic analyses identified major clades but often relied on imprecise genomic methods, limited geographic and ecological sampling, and non-standardized strategies for phylogenetic resolution. Here, we address these gaps by reconstructing a whole-genome phylogeny to examine how geography and site of isolation contribute to phylogenetic structure in C. albicans. We analyzed phased genomes from 945 global isolates obtained across diverse clinical and ecological contexts and applied an agnostic, threshold-based clustering approach to systematically define cluster boundaries and quantify intraspecific genomic features. Our analyses preserved previously defined major clusters while identifying six novel clusters, predominantly composed of highly admixed Asian isolates. Although geographic origin and isolation source were each significantly associated with cluster membership, these associations were confounded because isolates from specific regions were disproportionately derived from particular sources. However, an analysis of environmental isolates alongside a diverse strain collection from Winnipeg, Canada, highlights the potential for frequent local transmission. More than 95% of isolates were heterozygous at the mating-type locus, while aneuploidy was present in 8% of isolates distributed across the phylogeny. Analysis of the AGO1 PAZ domain involved in RNAi interference identified both known and novel RNAi variants, predominantly in a heterozygous state. Intra-host analysis of isolates from 95 individuals revealed predominantly clonal colonization, though fourteen individuals harbored isolates from different clusters. Together, these findings refine the phylogenetic structure of C. albicans and provide insights into genomic plasticity and strain transmission in this common fungal species.},
}

@article {pmid42996839,
year = {2026},
author = {Zaniboni, A},
title = {Management of diarrhea in patients receiving liposomal irinotecan-based regimens: a narrative review of mechanisms, clinical impact, and evidence-based strategies.},
journal = {Journal of gastrointestinal oncology},
volume = {17},
number = {5},
pages = {325},
pmid = {42996839},
issn = {2078-6891},
abstract = {BACKGROUND AND OBJECTIVE: Liposomal irinotecan (nal-IRI) in combination with 5-fluorouracil and leucovorin (5-FU/LV) represents the standard second-line treatment for metastatic pancreatic ductal adenocarcinoma (mPDAC) following progression on gemcitabine-based therapy. Despite its demonstrated survival benefit, diarrhea remains a clinically significant toxicity that can compromise dose intensity, treatment adherence, and quality of life. This review provides a comprehensive and updated overview of the pathophysiology, incidence, and evidence-based management of diarrhea associated with nal-IRI-based regimens.

METHODS: A structured narrative review of the available literature was performed, including prospective randomized trials, supportive care guidelines, pharmacogenomic data, and emerging translational evidence. Given the heterogeneity of study designs and the limited number of nal-IRI-specific supportive care trials, a formal meta-analysis was not feasible.

KEY CONTENT AND FINDINGS: Diarrhea associated with nal-IRI is mechanistically complex, encompassing acute cholinergic and delayed secretory components mediated by SN-38-induced mucosal injury and enterohepatic recirculation. Grade 3-4 diarrhea occurs in approximately 13-20% of patients across major pancreatic cancer trials. Evidence-based management strategies are presented, including pharmacologic interventions (atropine, loperamide, octreotide, fluoroquinolones), supportive care, and dose modification protocols. Emerging approaches-including gut microbiome modulation, beta-glucuronidase inhibitors, and novel antisecretory agents-are also reviewed.

CONCLUSIONS: A multidisciplinary, proactive management approach-beginning before the first nal-IRI dose-is essential to minimize diarrhea-related morbidity and optimize treatment outcomes. Integration of pharmacogenomic data and emerging biomarkers-particularly UGT1A1*28 genotyping and gut microbiome β-glucuronidase activity profiling-may further individualize risk stratification and management in this patient population.},
}

@article {pmid42996978,
year = {2026},
author = {Sun, Y and Hong, Z and Guo, Y and Cui, H and Jiang, Y and Yu, Q},
title = {The mucosal immune microenvironment in chronic pharyngitis: epithelial barrier dysfunction, inflammatory persistence, and therapeutic perspectives.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {2000898},
pmid = {42996978},
issn = {1664-3224},
mesh = {Humans ; *Pharyngitis/immunology/therapy/microbiology ; Chronic Disease ; Animals ; *Immunity, Mucosal ; *Cellular Microenvironment/immunology ; Inflammation/immunology ; Immunity, Innate ; Adaptive Immunity ; Microbiota ; },
abstract = {Chronic pharyngitis is a clinically heterogeneous condition in which persistent throat symptoms, visible mucosal abnormalities, and underlying biological processes do not necessarily coincide. This critical narrative review synthesizes evidence from human chronic pharyngitis, experimental injury models, adjacent upper-airway disorders, and other mucosal systems to examine how epithelial barrier function, innate and adaptive immunity, microbial ecology, sensory signaling, and tissue repair may contribute to disease persistence. Experimental studies identify epithelial injury and activation of shared inflammatory and stress-response pathways, while human observations highlight substantial variation in anatomical site, microbial findings, immune organization, and treatment response. Adaptive immune responses appear strongly context dependent; microbial community changes are most informative when linked to organism viability, metabolite production, host sensing, or colonization resistance; and sensory pathways may contribute to symptoms partly independently of measurable inflammation. We propose that persistent disease can arise through three overlapping routes: continued exposure, durable alteration of tissue responsiveness, and incomplete resolution or repair, with microbial and sensory processes acting as modifiers. This framework separates symptom improvement, biological target engagement, and durable restoration of tissue function as distinct therapeutic outcomes. Future studies should prioritize anatomically precise longitudinal cohorts, site-resolved single-cell and spatial profiling, functional perturbation in primary pharyngeal systems, and mechanism-informed trials with follow-up after treatment withdrawal. By linking clinical presentation to local biological function and recovery trajectories, chronic pharyngitis may be reclassified into reproducible biological subgroups that support more precise mechanistic investigation and treatment.},
}

Humans
*Pharyngitis/immunology/therapy/microbiology
Chronic Disease
Animals
*Immunity, Mucosal
*Cellular Microenvironment/immunology
Inflammation/immunology
Immunity, Innate
Adaptive Immunity
Microbiota

@article {pmid42997004,
year = {2026},
author = {Cheng, YJ and Tao, MP and Qian, K and Ye, W},
title = {Reprogramming the gut-brain axis in neurodegeneration: comparative microbiome, metabolite, immunometabolic, polyphenol, probiotic, and epigenetic mechanisms in Alzheimer's and Parkinson's diseases.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1865514},
pmid = {42997004},
issn = {1663-4365},
abstract = {The gut-brain axis has emerged as a central mechanistic framework linking dietary bioactives, microbial ecology, and neurodegenerative disease progression. Similar microbiome-related mechanisms have also been implicated in colorectal cancer, suggesting potential shared links between microbial dysbiosis, inflammation, and disease progression. This study synthesizes preclinical evidence examining how polyphenols, polyphenol-derived compounds, and advanced delivery systems, including nanoparticles and synbiotics, modulate Alzheimer's disease (AD) and Parkinson's disease (PD) through microbiome-dependent mechanisms. Evidence from transgenic mice, toxin-induced rodent models, and Drosophila systems was compared across microbiome alterations, microbial metabolites, signaling pathways, epigenetic regulation, and functional outcomes. Across AD and PD models, dietary bioactives consistently promoted restoration of gut microbial homeostasis, characterized by enrichment of beneficial taxa and reduction of dysbiosis-associated microorganisms. These changes were accompanied by alterations in microbial metabolites, particularly short-chain fatty acids (SCFAs), tryptophan-derived metabolites, and lipid-associated signaling molecules. These metabolites provide functional links between microbial ecology and CNS physiology and may regulate epigenetic processes, including histone acetylation, DNA methylation, chromatin remodeling, and non-coding RNA activity. Despite substantial upstream convergence, downstream effects showed disease-specific patterns. In AD models, microbiome modulation predominantly influenced metabolic, amyloidogenic, and neurotrophic pathways, including AKT/GSK3β, NRF2, NF-κB, and BDNF-associated signaling, contributing to reduced amyloid-β deposition, attenuated tau pathology, and improved cognitive outcomes. In PD models, greater emphasis was placed on inflammatory, oxidative, and mitochondrial pathways involving SIRT1/NRF2, TLR4/MyD88/NF-κB, inflammasome signaling, and neuronal survival mechanisms, resulting in reduced neuroinflammation and preservation of dopaminergic neurons and motor function. Epigenetic regulation represents an additional convergence layer through which microbial metabolites and polyphenols may influence inflammatory, metabolic, mitochondrial, and neuronal gene programs in both disorders. Nanoparticle-based delivery systems enhanced bioavailability, tissue targeting, and microbiome-related effects, whereas synbiotic strategies reinforced microbial and metabolic homeostasis. Collectively, these findings support a microbiome-metabolite-epigenome-brain framework in which dietary bioactives modulate neurodegeneration through interconnected microbial, metabolic, immune, redox, mitochondrial, and epigenetic pathways. This framework provides a mechanistic basis for developing disease-tailored and precision-oriented gut-brain interventions for AD and PD.},
}

@article {pmid42997201,
year = {2026},
author = {Li, Z and Yang, Y and Liu, B and Sun, J and Tang, X and Yang, Y},
title = {Clear aligner interface properties, oral microbial ecology, and strategies for biofilm control and caries-risk mitigation: a scoping review.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1951083},
pmid = {42997201},
issn = {2235-2988},
mesh = {*Biofilms/growth & development ; Humans ; *Dental Caries/prevention & control/microbiology ; *Microbiota ; *Mouth/microbiology ; Saliva/microbiology ; Bacterial Adhesion ; },
abstract = {BACKGROUND: Clear aligners create an aligner-tooth interface that may retain saliva, microorganisms, and dietary substrates. Evidence linking interface properties, oral microecological responses, and preventive interventions remains fragmented.

OBJECTIVE: To map and synthesize evidence on clear aligner interface properties and microbial adhesion, oral microbial ecology during clear aligner wear, and strategies for biofilm control and caries-risk mitigation.

METHODS: Following Joanna Briggs Institute methodology and PRISMA-ScR guidance, PubMed, Embase, and Web of Science Core Collection were searched from inception to August 31, 2026, without language restrictions. Backward and forward citation searching supplemented database searches. Original clinical, in vitro, and ex vivo studies involving active clear aligner treatment, associated materials or interfaces, or clear-aligner-specific interventions were eligible when they reported microbial, biofilm, microbiome, metabolomic, caries-related, or mineral outcomes. Two reviewers independently screened records; two authors charted and verified data. Findings were synthesized descriptively within three evidence domains.

RESULTS: Of 988 records, 132 reports were included. Because reports could contribute to more than one domain, 62 informed interface properties and microbial adhesion, 47 oral microbial ecology during wear, and 76 biofilm control and caries-risk mitigation. No single polymer, manufacturing method, or surface parameter consistently predicted microbial adhesion or biofilm formation. Outcomes reflected interactions among material characteristics, local topography, salivary conditioning, aging and exposure, microbial species, and experimental models. Clinical microbial responses were compartment- and time-dependent. Salivary and tooth-associated communities often remained relatively stable at the community level, whereas the inner aligner surface sometimes exhibited localized taxonomic, functional, metabolic, and pH-related changes. Investigated interventions included cleaning, antimicrobial and antifouling interface modifications, anticaries and remineralizing approaches, probiotics, and environment-responsive systems. Although many strategies reduced microbial burden, biofilm-related outcomes, acidogenicity, or mineral loss under tested conditions, evidence was predominantly short-term and preclinical. Assessments of durability, material performance, and safety were heterogeneous.

CONCLUSIONS: Clear aligner-microbiota interactions appear context-dependent rather than uniformly favorable or unfavorable. Evidence neither establishes causal relationships between interface or microecological changes and clinical disease nor identifies a universally superior intervention. More standardized, clinically representative evidence may clarify their clinical relevance and inform preventive management during clear aligner treatment.},
}

*Biofilms/growth & development
Humans
*Dental Caries/prevention & control/microbiology
*Microbiota
*Mouth/microbiology
Saliva/microbiology
Bacterial Adhesion

@article {pmid42997212,
year = {2026},
author = {Khan, FZA and Ali, SA},
title = {Maternal iron deficiency, preterm birth, and disrupted microbial inheritance: a proposed double-hit hypothesis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1953925},
pmid = {42997212},
issn = {2235-2988},
mesh = {Humans ; Female ; *Premature Birth/microbiology/etiology ; Vagina/microbiology ; Infant, Newborn ; Pregnancy ; Dysbiosis/microbiology ; Milk, Human/microbiology ; *Microbiota ; *Iron Deficiencies ; Iron ; Gastrointestinal Microbiome ; *Anemia, Iron-Deficiency/complications ; },
abstract = {The maternal microbiome is the infant's primary microbial inheritance, transmitted mainly through the maternal gut, vaginal delivery, breast milk, and skin-to-skin contact. Maternal iron deficiency (ID), with anemia, is a common and modifiable nutritional condition associated with impaired immune function and increased preterm birth (PTB) risk, whereas evidence for ID without anemia remains limited. It may influence maternal microbial ecology; however, its potential effect on maternal-to-infant microbial transmission remains unexplored. This review, conducted across PubMed, Embase, and Web of Science (January 2000-June 2026), proposes a double-hit hypothesis defined by the source and biological context of disruption rather than by a strictly temporal sequence. The first hit comprises potentially altered maternal-origin microbial and immunologic inputs from the vaginal, gut, and breast milk ecosystems; the second hit comprises PTB and neonatal intensive care (NICU)-associated disruption of early microbial succession. Human evidence directly linking ID to vaginal dysbiosis is limited to a single study, evidence relating maternal iron status to milk lactoferrin is inconsistent, and the contribution of vaginal communities to persistent infant gut colonization remains uncertain whereas vaginal exposure may have transient ecological or immunologic effects. No study has simultaneously evaluated maternal iron biomarkers, vaginal community state type (CST), breast milk composition, maternal gut microbiome and longitudinal infant gut microbiota. The proposed framework is therefore hypothesis-generating and identifies testable pathways through which maternal ID may alter maternal microbial and immunologic inputs, while also being associated with an increased risk of PTB. PTB, together with the resulting prematurity-related vulnerability and subsequent postnatal exposures, may further disrupt early infant microbiome development.},
}

Humans
Female
*Premature Birth/microbiology/etiology
Vagina/microbiology
Infant, Newborn
Pregnancy
Dysbiosis/microbiology
Milk, Human/microbiology
*Microbiota
*Iron Deficiencies
Iron
Gastrointestinal Microbiome
*Anemia, Iron-Deficiency/complications

@article {pmid42997231,
year = {2026},
author = {He, X and Zhang, B and Zhao, E and Fang, Y and Liu, J and Zhu, Y and Xu, H and Zhao, Q and Song, X and Wang, T and Xu, H and Huang, W},
title = {Exposure to Size-Fractioned Ambient Particles Associated with Alterations in Gut Microbiome and Pro-Atherosclerotic Biomarkers in Young Adults.},
journal = {Environmental health perspectives},
volume = {134},
number = {7},
pages = {904-922},
pmid = {42997231},
issn = {1552-9924},
mesh = {Humans ; Biomarkers ; *Gastrointestinal Microbiome/drug effects ; *Particulate Matter/adverse effects ; Particle Size ; Young Adult ; Male ; Female ; *Air Pollutants/adverse effects ; *Environmental Exposure/adverse effects ; Longitudinal Studies ; Beijing ; Adult ; *Atherosclerosis/epidemiology ; Feces ; },
abstract = {Background: Ambient fine and ultrafine particles are linked to the progression of atherosclerotic cardiovascular diseases, wherein gut microbiome may play a critical role. However, the underlying mechanisms and relevant metabolic pathways are not yet fully understood. Objectives: To identify the features and metabolic pathways of gut microbiome, and to explore their potential roles in the pro-inflammatory and pro-atherosclerotic effects of particles in size ranges of 5-560 nm (measured as number concentration, PNC5-560). Methods: We conducted a longitudinal panel study of 152 young adults in Beijing, China, with four monthly clinical examinations between September 2019 and January 2020. Gut microbiome, fecal metabolome, and circulating pro-inflammatory and pro-atherosclerotic biomarkers were measured. Linear mixed-effects models were used to examine the associations linking short-term PNC5-560 exposure to health indicators. We further evaluated whether gut microbiota could mediate changes in these biomarkers and identified the underlying metabolic pathways. Results: Major sources of PNC5-560 in the study area were identified as diesel vehicle emissions (37.9%), gasoline vehicle emissions (39.4%), nucleation (9.2%), and secondary aerosols (11.9%). Per interquartile range increment in PNC5-560 over the preceding 7 days was associated with significant elevations in circulating pro-inflammatory and pro-atherosclerotic biomarkers, with effect estimates ranging from 2.1% (95% CI: 0.4%, 3.8%) to 198.6% (95% CI: 29.3%, 365.8%). PNC5-560 exposure was also associated with decreased gut microbial α-diversity (e.g., Shannon, Simpson, and Chao1) and altered taxonomic composition. Several microbial species (e.g., Solibaculum mannosilyticum, Bacteroides stercoris, and Bifidobacterium longum) were identified as potential mediators of the effects of PNC5-560 on pro-inflammatory and pro-atherosclerotic responses, with mediation proportions up to 9.8% (95% CI: 0.8, 38.3) and 4.8% (95% CI: 0.09, 22.5), respectively. Functional analyses further revealed that these mediating effects involved perturbations in nucleotide and amino acid metabolism pathways. Conclusions: This study provides evidence suggesting that gut microbiome may regulate nucleotide and amino acid metabolism, thereby partially mediating the detrimental cardiovascular effects of size-fractioned ambient particles.},
}

Humans
Biomarkers
*Gastrointestinal Microbiome/drug effects
*Particulate Matter/adverse effects
Particle Size
Young Adult
Male
Female
*Air Pollutants/adverse effects
*Environmental Exposure/adverse effects
Longitudinal Studies
Beijing
Adult
*Atherosclerosis/epidemiology
Feces

@article {pmid42997375,
year = {2026},
author = {Bai, Y and Yu, Y and Huang, X and Yang, X and Yu, R and Xiang, Q},
title = {Effects of probiotic or synbiotic supplementation on glycolipid metabolism in patients with coronary heart disease: a systematic review and meta-analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1877366},
pmid = {42997375},
issn = {1664-302X},
abstract = {OBJECTIVE: This systematic review and meta-analysis, combined with trial sequential analysis (TSA), evaluated the effects of probiotic/synbiotic supplementation on glycolipid metabolism in patients with coronary heart disease (CHD).

METHODS: Randomized controlled trials published up to May 1, 2026, were systematically searched across major databases, including PubMed, Embase, Cochrane Library, Web of Science, MEDLINE, and ClinicalTrials.gov. Pooled analyses were performed using Review Manager 5.3, and TSA was conducted to assess the conclusiveness of evidence. Mean difference (MD) and risk ratio (RR) were calculated for continuous and dichotomous outcomes, respectively.

RESULTS: Six trials involving 296 participants were included. Probiotic/synbiotic supplementation was associated with a reduction in fasting blood glucose (FBG) (MD - 19.25 mg/dL, 95% CI -32.28 to -6.22, p = 0.004) and an increase in high-density lipoprotein cholesterol (HDL-C) (MD 3.70 mg/dL, 95% CI 1.65 to 5.74, p = 0.0004) based on four studies involving 192 participants. No significant effects were observed on low-density lipoprotein cholesterol, very low-density lipoprotein cholesterol, total cholesterol, triglycerides, insulin, homeostasis model assessment of insulin resistance, quantitative insulin sensitivity check index, systolic blood pressure, or diastolic blood pressure (p ≥ 0.05). Although adverse event rates did not differ significantly (p ≥ 0.05), safety evidence was limited by few events and a wide confidence interval. TSA showed that the cumulative evidence for both HDL-C and FBG did not cross the prespecified monitoring boundaries or reach the required information sizes. The certainty of evidence for all outcomes was rated as low or very low.

CONCLUSION: Probiotic/synbiotic supplementation may be associated with increased HDL-C and reduced FBG levels in patients with CHD. However, given the negative TSA findings, low certainty of evidence, and lack of hard cardiovascular outcomes, changes in HDL-C and FBG cannot be regarded as direct evidence of cardiovascular benefit. Furthermore, generalizability is limited, as five of the six studies were conducted in Iran and only one in China, which may limit applicability to populations with different dietary patterns, microbiome profiles, ethnic backgrounds, or healthcare systems. The substantial heterogeneity in probiotic strains, formulations, doses, and treatment durations also limits generalization to probiotics or synbiotics as a whole.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420251178187; identifier: CRD420251178187.},
}

@article {pmid42997464,
year = {2026},
author = {Liu, X and Yang, W and Wang, Y and Peng, S and Zhou, J and Qiu, Q},
title = {Nasopharyngeal microbiota as a diagnostic biomarker for chronic rhinosinusitis with nasal polyps.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1865473},
pmid = {42997464},
issn = {2235-2988},
mesh = {Humans ; *Rhinosinusitis/diagnosis/microbiology ; *Nasal Polyps/diagnosis/microbiology/complications ; *Microbiota ; *Biomarkers/analysis ; *Nasopharynx/microbiology ; Chronic Disease ; RNA, Ribosomal, 16S/genetics ; Male ; Female ; Bacteria/classification/genetics/isolation & purification ; Adult ; Middle Aged ; Recurrence ; DNA, Bacterial/genetics/chemistry ; *Sinusitis/diagnosis/microbiology ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Chronic rhinosinusitis with nasal polyps (CRSwNP) is a common inflammatory disorder with high postoperative recurrence rates. The nasopharyngeal microbiome may play a role in disease pathogenesis, but its diagnostic and prognostic utility remains unclear. This study characterized the nasopharyngeal microbiota in CRSwNP patients and evaluated its potential as a biomarker.

METHODS: 32 nasopharyngeal swab samples from CRSwNP patients and 11 from controls were collected and subjected to 16S rRNA gene sequencing. Microbial diversity, species composition, and differential abundance were analyzed. A diagnostic model was constructed using LASSO regression, with feature selection performed entirely within a 10-fold cross-validation framework, and model stability was validated via 100 Bootstrap resampling iterations. For recurrence prediction, due to the limited number of events (n=10), only exploratory univariate screening was conducted, and the stability of candidate biomarkers was evaluated using Bootstrap validation with internal feature selection (300 iterations).

RESULTS: CRSwNP patients exhibited significantly altered microbial composition at phylum and genus levels, as well as higher Shannon and Chao1 indices compared with controls, although the clinical and biological significance of this diversity increase requires further investigation. The three-genus combined diagnostic panel consisting of Fibrobacter, Ruminococcaceae_UCG-002, and Staphylococcus demonstrated favorable diagnostic performance. For recurrence prediction, Helicobacter and Parabacteroides were identified as stable candidate biomarkers, with Bootstrap selection frequencies of 24.0% and 27.3%, respectively. The recurrence-related findings are exploratory hypothesis-generating results and do not possess clinical predictive capability; they require validation in an independent large-cohort study.

CONCLUSIONS: The nasopharyngeal microbiota of CRSwNP patients exhibited significant alterations. The three-genus combined diagnostic panel demonstrated good discriminatory ability, supporting its potential as a non-invasive diagnostic biomarker. The identification of recurrence-related markers provides candidate targets for future research; however, due to the limited sample size, they currently lack clinical predictive capability. This study provides foundational data for microbiome research and clinical translation in CRSwNP.},
}

Humans
*Rhinosinusitis/diagnosis/microbiology
*Nasal Polyps/diagnosis/microbiology/complications
*Microbiota
*Biomarkers/analysis
*Nasopharynx/microbiology
Chronic Disease
RNA, Ribosomal, 16S/genetics
Male
Female
Bacteria/classification/genetics/isolation & purification
Adult
Middle Aged
Recurrence
DNA, Bacterial/genetics/chemistry
*Sinusitis/diagnosis/microbiology
Sequence Analysis, DNA

@article {pmid42997684,
year = {2026},
author = {Aggarwal, S and Grond, K and Miller, T and Kabir, F and Hasan, I and Matson, S and Dev, S and Drown, DM},
title = {Microbial and Water Quality Dynamics in a Utilidor-Housed Subsurface Drinking Water Distribution System Under Low-Use Conditions.},
journal = {ACS ES&T water},
volume = {},
number = {},
pages = {},
pmid = {42997684},
issn = {2690-0637},
abstract = {Cold-region utilidor-based drinking water distribution systems (DWDSs) are considered climate-resilient infrastructure but remain poorly characterized. Elevated temperatures and water age in such systems may accelerate disinfectant decay and microbial growth. We investigated water chemistry and microbiomes in a utilidor-housed subsurface DWDS serving a mixed-use sub-Arctic community during low demand following partial closure. Main and premise plumbing samples were collected over eight events spanning 14 months. Physicochemical measurements accompanied 16S rRNA gene amplicon sequencing. Temperatures increased from 7.2°C at the inlet to 31.9°C distally, while free chlorine residual declined significantly. Alpha diversity increased with distance and correlated negatively with disinfectant residual and dissolved oxygen. Microbial community composition differed significantly by location and time; Proteobacteria dominated most sites. Genera containing opportunistic pathogens included Legionella (80.7%), Mycobacterium (24.7%), and Pseudomonas (32.5%), with significant associations with total dissolved solids, nitrate, and dissolved organic carbon. These findings demonstrate that elevated temperatures and disinfectant decay may influence microbial communities and favor pathogen-associated taxa under low use. Utilidor-based DWDSs may, therefore, indicate vulnerabilities in buried systems under climate-driven warming and reduced demand. Results highlight the need for design and operational strategies addressing thermal control, water age, and disinfectant stability to protect drinking water quality in climate-stressed systems.},
}

@article {pmid42997884,
year = {2026},
author = {Siang, SC and Shan, CY and Fazhan, H and Waiho, K},
title = {Mud Crab Genus Scylla Broodstock Culture: Current Challenges and the Potential of a Hybrid Specific Pathogen Free Approach.},
journal = {Tropical life sciences research},
volume = {37},
number = {3},
pages = {1-14},
pmid = {42997884},
issn = {1985-3718},
abstract = {Mud crab (genus Scylla) farming forms an integral part of coastal aquaculture in Asia region, with their cultivation supporting coastal livelihoods, driving economic growth through their high market demand and promoting mangrove forest conservation and environmental sustainability via mangrove ecosystem integration. However, instability in the production chain, especially the early stages from broodstock cultivation to larval rearing and crablet, promoted the continued reliance on wild-caught broodstock. Such reliance on wild-caught broodstock introduces significant biosecurity risks, particularly through pathogen transmission and inconsistent reproductive performance. Current management selects mature females based on size and ovarian development, followed by acclimation and prophylactic formalin baths to mitigate bacterial and fungal infections. This review examines the biosecurity risks of relying on wild broodstock and proposes a practical "hybrid" approach that combines the innate immune resilience of wild populations with Specific Pathogen Free (SPF)-like conditions to enhance disease resistance, reproductive success and overall production sustainability. Nutritional strategies employ high-protein feeds, such as fish and bivalves, to enhance ovarian maturation, but untreated wild-caught feeds heighten pathogen transmission risks. By quarantine, disinfection and microbiome management protocol, pathogen load can be reduced while innate immunity can be improved.},
}

@article {pmid42992837,
year = {2026},
author = {El-Dougdoug, NK and Magistrado, D and Perry, KI and Short, SM},
title = {Microbiota modulation impacts life history traits and mating success in male Aedes aegypti mosquitoes.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0046526},
doi = {10.1128/msphere.00465-26},
pmid = {42992837},
issn = {2379-5042},
abstract = {UNLABELLED: Aedes aegypti mosquitoes transmit multiple arboviruses, but population suppression through the mass release of sterile or incompatible male mosquitoes can effectively reduce populations. These methods depend on the reliable mass-rearing of healthy, robust males that can successfully mate with wild females. The microbiota is a critical component of the larval diet, and its modulation can dramatically influence life history traits relevant to mass-rearing and male quality. Here, we used axenic (microbe-free), monoxenic (inoculated with Escherichia coli), and "laboratory community" mosquitoes (inoculated with an undefined microbiota derived from laboratory mosquitoes) to show that longevity was significantly enhanced in axenic and monoxenic males compared to laboratory community males. Moreover, monoxenic males more efficiently obtained mates in non-competitive mating scenarios compared to laboratory community males. However, microbiota treatment had no effect on mating success when males from different treatments competed for a mate. Our findings suggest that the microbiota is a key determinant of male mosquito life history, with direct implications for optimizing production of males for control programs.

IMPORTANCE: The microbes found in association with mosquitoes are crucial to mosquito development and have the capacity to influence multiple life history traits. In the current study, we comprehensively and functionally evaluate the role of the microbiota in mating success and other life history traits of male mosquitoes. Males are crucial to disease transmission, via their role in mating, and via their use in mosquito population control. By focusing on males, the understudied sex in mosquito research, we provide novel and foundational insight into how microbial communities influence male life history traits and mating success. Moreover, our findings establish a critical framework for understanding how the microbiota may affect male quality, production efficiency, and performance in vector control programs that involve mass production of adult male mosquitoes.},
}

@article {pmid42992852,
year = {2026},
author = {Morabbi, SM and Bhowmik, N and Sutherland, S and Wylie, EA and Decker, RS and Al Daerwish, A and Pérez Pérez, M and Pascual, E and Lutter, EI and Philmus, B and Stubbendieck, RM},
title = {Differential metabolite production underlies disruption of the cystic fibrosis airway microbiota by pathogens.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0115726},
doi = {10.1128/msystems.01157-26},
pmid = {42992852},
issn = {2379-5077},
abstract = {Cystic fibrosis (CF) results in accumulation of mucus in the airways that promotes pathogen colonization, leading to respiratory exacerbations, lung failure, and death. The CF airway harbors a complex microbiota, including pathogens and oropharyngeal bacteria. Here, we reanalyzed 5,260 16S rRNA gene microbiota data sets to infer associations between members of the CF microbiota. We determined that pathogens are more likely to proliferate and dominate when present, while oropharyngeal bacteria are generally present at lower abundances. We found that higher diversity and increasing numbers of pairwise associations between bacteria were positively correlated with lung function. In contrast, dominance of the microbiota by pathogens was associated with loss of lung function. We determined that pathogens are largely negatively associated with each other and oropharyngeal bacteria, suggesting they are antagonistic toward other bacteria. As a first test of this hypothesis, we cultured 1,597 isolates from 96 people with CF and performed 12,542 coculture assays against eight representative pathogens and oropharyngeal bacteria, finding 23% of interactions resulted in inhibition. Among our isolates, Pseudomonas were the most inhibitory, but we observed variable activity between different isolates. We further found Pseudomonas aeruginosa isolates, even those from the same donor and time point, exhibited significant differences in their metabolome and bioactivity profiles that correlated with acquisition of mutations. Together, our results suggest that pathogens may disrupt the CF microbiota and proliferate in part through bioactive metabolite production. Furthermore, these data highlight that characterizing multiple isolates is necessary to capture the full landscape of chemically mediated interactions within microbiomes.IMPORTANCEThe cystic fibrosis (CF) airway harbors a complex microbiota, including oropharyngeal bacteria and opportunistic pathogens that establish chronic infections. We found that microbiota diversity is correlated with health and that a pathogen-dominated microbiota is associated with low lung function. We then inferred potential microbial interactions by determining abundance associations between CF genera, which suggested that pathogens antagonize other bacteria. To test this prediction, we cultured bacteria from people with CF and performed thousands of coculture assays, finding that approximately one-quarter of interactions resulted in growth inhibition. Pseudomonas broadly inhibited other members of the CF airway microbiota. However, we observed marked variability in bioactivity and metabolite profiles of Pseudomonas aeruginosa isolates, even from the same donor at the same time. Our results suggest that pathogens disrupt the CF microbiota, possibly through bioactive metabolite production, and that characterizing multiple isolates is necessary to capture the complete picture of interactions in these communities.},
}

@article {pmid42992936,
year = {2026},
author = {Hu, Y and Sun, L and Huang, Y and Jiang, F and Tong, X and Yang, J and Ju, Y and Yang, Z and Liufu, S and Hu, Y and Ma, W and Guo, R and Li, W and Zhang, T and Zhu, X and Zhang, Z},
title = {Integrated optimization of experimental and computational workflows improves genome recovery in long-read gut metagenomics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0113826},
doi = {10.1128/msystems.01138-26},
pmid = {42992936},
issn = {2379-5077},
abstract = {Short-read metagenomic sequencing has been widely applied in microbial research due to its high quality and decreasing cost. However, short reads are inherently fragmented, which limits assembly contiguity and the recovery of complete microbial genomes. In contrast, long-read sequencing, with significantly longer read lengths, helps overcome these limitations. Achieving complete and accurate genome recovery is the core goal of metagenomics. To address this challenge, we systematically evaluated and optimized the long-read metagenomic workflow, from sample processing to computational assembly, using the CycloneSEQ platform.IMPORTANCEOur results suggest that upstream experimental protocols are important contributors to long-read metagenomic performance within the evaluated framework. In particular, magnetic-plate DNA extraction, together with pretreatment, was associated with more favorable input and downstream sequencing-related characteristics for long-read analysis. These changes were also associated with broader microbial recovery in the evaluated data sets. Assembly benchmarking further showed that integrating matched long-read (CycloneSEQ) and short-read (DNBSEQ) data sets provided a favorable balance across multiple evaluation dimensions. In our fecal metagenomic data set, long-read-first assembly followed by short-read polishing showed strong overall performance when recovery, contiguity, and sequence accuracy were considered together, although workflow performance remained metric dependent.},
}

@article {pmid42992937,
year = {2026},
author = {Paulsen, AA and Roghair Stroud, MN and Halverson, LJ},
title = {Physiological, behavioral, and genetic factors that shape interactions in the plant growth-promoting maize rhizosphere synthetic community.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0088826},
doi = {10.1128/msystems.00888-26},
pmid = {42992937},
issn = {2379-5077},
abstract = {Profiling microbiomes is an important way to understand the function and composition of communities in the wild, but natural microbiomes are often highly complex and often unamenable to experimentation to reveal cause-and-effect relationships. By using a small group of cultivable strains to represent those found in the wild, synthetic communities are one solution to this problem. Here we describe the maize rhizosphere synthetic community (MARSc), a genome-enabled 31-member bacterial community representative of the diversity found on the roots of maize grown in Iowa soils. This community is built around Pseudomonas putida KT2440, a model maize rhizosphere colonist and synthetic biology chassis. We characterized microbe-microbe interactions and biofilm formation of MARSc members in a variety of environmental contexts, finding that both behaviors are broadly controlled by nutrient levels. Genomic analysis and microbiome profiling of these organisms revealed that annotated biofilm genes (such as surface attachment and exopolysaccharide production) were significantly correlated with rhizosphere abundance, but neither trait correlated to in vitro biofilm formation. In vitro interaction assay findings were surprisingly consistent with co-correlations of rhizosphere abundance among MARSc members on roots. Finally, we found that when applied to the roots, MARSc can increase maize biomass (dry weight) by up to 40%-50% under varying nitrogen fertilization levels. Altogether, MARSc is a useful tool for identifying some of the factors influencing rhizosphere microbiome assembly and will be a strong foundation for further work in this area.IMPORTANCEThe microbiome surrounding the roots of plants can play an integral role in plant health and growth, and it is composed of thousands of species of microbes that are specific to the plant and environment it is grown in. However, due to this complexity, little is known about the means by which microbiomes form. In this study, we developed the maize rhizosphere synthetic community (MARSc) to gain a better understanding of the formation and function of microbiomes on the roots of plants. This consortium consists of 30 bacterial isolates plus Pseudomonas putida KT2440, a model maize root colonist. In this study, we investigated the interactions between these organisms, their genomes, cultural characteristics, and growth on the roots of maize. We show that MARSc increases maize growth under low nitrogen fertilizer, suggesting it will be a useful tool for identifying the mechanisms behind microbiome formation and plant growth promotion.},
}