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PubMed2026

Postpartum compositional changes in bovine calf nasal and dam vaginal microbiota and concurrent immune responses following prepartum betadine lavages.

As interest in bovine reproductive tract microbial communities increases, there remains limited information on how the insult of parturition influences postpartum dam reproductive microbiota and early-life microbial development. The objective of this study was to characterize postpartum changes in dam vaginal microbiota and neonatal calf nasal microbiota following transient prepartum disruption of the dam vaginal microbiota using betadine lavages (BLGs), and to evaluate concurrent systemic immune responses in dams and calves. Multiparous beef cows (n = 12) were randomly assigned to either BLG (n = 7) or control (CON; n = 5) 3 wk prior to the expected calving date, and dam vaginal swabs, calf nasal swabs, and blood were collected at 0 (+1), 15 (±1), 30 (±1), and 60 (±1) d postpartum. Samples from Angus cow-calf pairs (n = 12) underwent 16S rRNA gene sequencing with standard contamination controls and QIIME2 processing. Blood samples were analyzed using the D2Dx immunity assay to evaluate systemic humoral immune responses. Microbial alpha diversity (ANOVA), Bray-Curtis beta diversity (PERMANOVA), taxonomic composition (LEfSe), and D2Dx immune responses (repeated-measures mixed model) were analyzed (P < 0.05). In calves, treatment influenced nasal alpha diversity at d 0 (P = 0.03), while nasal beta diversity tended to differ at d 0 (P = 0.08); however, treatment effects were not detected at d 15, 30, or 60 for alpha diversity (P ≥ 0.76) or beta diversity (P ≥ 0.14). Calf nasal communities shifted over time (P = 0.001), with d 0 differing from d 15, 30, and 60, and beta diversity differing over time (P = 0.006). In dams, BLG did not alter vaginal alpha diversity (P ≥ 0.42) or beta diversity (P ≥ 0.14) over time, and time did not affect vaginal alpha diversity (P = 0.60) while vaginal beta diversity tended to shift over time (P = 0.06). Postpartum dam vaginal and calf nasal communities differed compositionally regardless of time (P < 0.05). Systemic immune responses, measured via D2Dx scores, fluctuated postpartum in dams (day effect: P < 0.001) and calves (day effect: P < 0.001), with BLG calves tending toward decreased immune response compared with CON (P = 0.08). Prepartum BLG minimally influenced neonatal nasal microbial diversity at birth and did not alter postpartum dam vaginal community structure, while calf nasal microbiota and D2Dx immune responses changed markedly over the first 60 d of life.

Animals↗

PubMed2026

Delayed maturation of the milk microbiome in women with type 1 diabetes.

AIMS/HYPOTHESIS: The breastmilk microbiome plays a crucial role in gut microbial colonisation and immune development, but little is known about how it is influenced by type 1 diabetes. METHODS: We conducted a longitudinal 16S rRNA gene sequencing study of milk from women with type 1 diabetes (n=69 pregnancies; 174 samples) and women who did not have type 1 diabetes (n=49 pregnancies; 123 samples), collected at seven timepoints from birth to 15 months postpartum. Alpha diversity (richness, inverse Simpson evenness) was analysed by generalised linear mixed models, beta diversity was analysed by Bray-Curtis dissimilarities and PERMANOVA, and differential abundance was analysed by limma. Additionally, we examined associations with maternal genetic risk score (GRS), maternal HLA type, glycaemic management (HbA1c) and breastmilk secretory IgA (sIgA), and performed a parallel analysis for the infant stool microbiome. RESULTS: A significant interaction between type 1 diabetes status and timepoint was observed for alpha diversity, both richness (p=0.01) and inverse Simpson diversity (p=0.003), indicating distinct temporal trajectories between women with and without type 1 diabetes. In those without type 1 diabetes, richness increased significantly between birth and 1 week postpartum, but this early increase was delayed in women with type 1 diabetes to between 1 week and 3 months postpartum (p=0.002). Beta diversity analysis revealed earlier and more extensive compositional shifts in women without type 1 diabetes compared to those with type 1 diabetes. These differences persisted after adjusting for Caesarean delivery, BMI, parity and infant sex, and were not attributable to a delay in initiating breastfeeding. Taxa with delayed enrichment in women with type 1 diabetes included Streptococcus spp. and Rothia mucilaginosa, which metabolise human milk oligosaccharides to short-chain fatty acids to promote development of the infant's gut barrier and immune system. Maternal GRS, HLA, HbA1c or sIgA were not associated with milk microbiota diversity trajectories. In infant stool samples, alpha diversity did not differ between exposure groups, and showed no evidence of delayed maturation. Beta diversity revealed an early compositional shift between birth and 1 week postpartum only in infants born to women without type 1 diabetes. Similarly, significant taxonomic changes between birth and 1 week postpartum were detected only in infants born to women without type 1 diabetes, but with some taxa differing between exposure groups at 1 week. CONCLUSIONS/INTERPRETATION: Maternal type 1 diabetes is associated with delayed early maturation of the breastmilk microbiome. Early compositional differences in microbiota restructuring were also observed in the infant gut, partially mirroring the pattern in the milk microbiome; however, sustained differences in infant gut microbiota diversity were not detected. Further investigation could determine whether these changes affect development of the infant's gut and immune system.

Humans↗

PubMed2025

Gut Colonization With Vancomycin-Resistant Enterococcus Shapes the Gut Microbiome in the Intensive Care Unit.

BACKGROUND: Gut pathogen colonization with vancomycin-resistant Enterococcus (VRE) is common in the intensive care unit (ICU) and is associated with worse clinical outcomes; however, the timing of VRE colonization and its collateral effects on the gut microbiome are incompletely understood. METHODS: Medical ICU patients admitted with sepsis and receiving broad-spectrum antibiotics were sampled via deep rectal swabs at ICU admission and on ICU day 3, 7, 14, and 30. Rectal swabs were cultured for VRE on selective media and analyzed via 16S ribosomal RNA gene sequencing. RESULTS: Ninety patients were sampled (340 longitudinal swabs). VRE positivity rose from 20% at ICU admission to a peak of 33% by ICU day 14 and then modestly declined to 31% by ICU day 30. Paralleling this, alpha diversity fell while Enterococcus relative abundance rose through ICU day 14 with both returning to baseline by ICU day 30. The median relative abundance of Enterococcus was 38% (interquartile range [IQR], 7.4%-75%) for VRE-positive samples compared to 0.01% (IQR, 0%-19%) for VRE-negative samples (rank-sum P < .01); 38 samples had ≥90% Enterococcus and 8 samples were 100% Enterococcus by sequencing. VRE was associated with lower alpha diversity (median Shannon index 1.90 [IQR, 0.89-2.66] if VRE positive versus 2.64 [IQR, 1.58-3.22] if VRE negative; P < .01). CONCLUSIONS: VRE gut colonization peaked at ICU day 14 followed by a modest decline and was associated with low alpha diversity. Improved understanding of dynamic changes in the gut microbiome may facilitate successful future ICU interventions. CLINICAL TRIALS REGISTRATION: NCT03865706.

Aged↗

PubMed1992

Mechanisms that generate junctional diversity in alpha and delta chains that use the Tcrd-V3 gene product.

The signals that dictate whether a thymocyte will express the alpha beta or gamma delta T-cell receptors are unknown. Although it is also not known if these two different cell types use identical recombinational machinery during rearrangement, the same variable (V) region genes can be used by both alpha and delta chains. By examining the products of rearrangements in alpha beta or gamma delta thymocytes that express identical V genes, we hoped to determine whether these cell types might differ in particular aspects of their recombinational activity. The polymerase chain reaction was used to show that the Tcrd-V2, Tcrd-V3, and Tcra-V3 genes are expressed as both Tcra and Tcrd transcripts in fetal and adult BALB/c mice. Sequencing of V delta 3 isolates was performed in order to compare the contribution of various mechanisms to the generation of junctional diversity. Extensive junctional diversity was present at all stages of development examined (fetal, newborn, and adult). During early development both alpha and delta chain junctional diversity is generated primarily by variability in the position of joining two gene segments (i.e., Tcrd-V3 to Tcra-J in alpha chains; Tcrd-V3 to Tcrd-D2 and Tcrd-D2 to Tcrd-J1 in delta chains). The pattern of base pair deletion from the end of the Tcrd-V3 gene was identical in alpha and delta chains and deletions occurred in fetal as well as adult T cells. In later development T cells use not only this mechanism for alpha and delta chains but also the addition of bases at gene segment junctions, presumably through the action of terminal deoxynucleotidyl transferase (TdT). Finally, a comparison of the variable domains of these alpha and delta chains shows that a notable difference is the variability in length of the CDR 3 region which can be significantly longer in delta-chains than in alpha-chains.

Amino Acid Sequence↗

PubMed2026

Blood and gut virome remodeling in gastric cancer: Anellovirus expansion and novel virus discovery.

Gastric cancer (GC) is a prevalent malignancy worldwide, yet effective early diagnostic tools remain lacking, and the role of the virome, a key component of the tumor microenvironment, in GC progression is largely unknown. This study aimed to characterize the virome landscapes in peripheral blood and feces of GC patients versus healthy controls, and to identify viral signatures associated with GC onset and metastasis. We performed viral metagenomic sequencing on pooled libraries from 100 GC patients (45 non-metastatic, 55 metastatic) and 50 healthy controls, followed by taxonomic annotation, diversity assessment, LEfSe differential abundance testing, and co-occurrence network analysis. In blood, the GC virome shifted from a bacteriophage-dominated profile in controls to one overwhelmingly dominated by Anelloviridae (> 80%), with significantly decreased alpha diversity. In contrast, the gut virome of GC patients showed increased alpha diversity and coexistence of diverse bacteriophages. LEfSe identified betatorquevirus in blood as a key discriminatory taxon for GC. Network analysis revealed negative correlations between Anelloviridae and multiple bacteriophage families, suggesting niche competition. We also discovered 67 provisional novel anellovirus species and one novel gemykibivirus in GC patient blood. Collectively, our findings indicate that GC is associated with compartment-specific virome remodeling in blood and gut, and that expansion of blood anelloviruses holds promise as a non-invasive biomarker. This study provides a foundational resource for understanding the virome's role in GC.

Humans↗

PubMed2026

Fecal immunochemical tests from population-based colorectal cancer screening programs support prospective microbiome cohorts.

BACKGROUND: Large, prospective cohorts are needed to research the gut microbiome's role in colorectal cancer (CRC) risk. We evaluated the gut microbiome leveraging residual fecal immunochemical tests (FIT) from a CRC screening program in Turin, Italy, and conducted one of the largest population-based case-control studies across the adenoma-carcinoma sequence to date. METHODS: We extracted DNA from residual FIT stool, used whole-genome shotgun sequencing, and included those with CRC (N = 44), advanced adenomas (N = 269), early adenomas (N = 134), and FIT-negative controls (N = 478). Alpha diversity, beta diversity, and species, gene, and pathway relative abundances were estimated. Multivariable logistic regression models were used to estimate associations of these metrics with colorectal neoplasms. RESULTS: Alpha diversity was mostly inversely associated with colorectal neoplasms, particularly early adenomas (OR: 0.45, 95% CI: 0.25-0.80; P = 0.01). Presence of oral pathogens, including Parvimonas micra, was associated with higher odds of CRC. Furthermore, Escherichia coli and Bacteroides fragilis were strongly associated with higher odds of all colorectal neoplasms. Several genes and pathways were associated with colorectal neoplasms. CONCLUSIONS: Our findings align with smaller studies of the gut microbiome and colorectal neoplasms, supporting that CRC screening programs provide opportunities to prospectively study the gut microbiome's association with cancer risk in large populations.

Humans↗

PubMed2026

Rumen DNA virome plasticity and viral metabolic potential are associated with seasonal adaptation in grazing yak and cattle on the Qinghai-Tibet Plateau.

BACKGROUND: As a diverse and abundant component of the rumen ecosystem, viruses interact with other microorganisms and are thought to influence microbial metabolism and host productivity. However, how the rumen virome responds to seasonal fluctuations in extreme environments remains poorly understood. Here, metagenomic analyses were used to investigate temporal dynamics of viral diversity, functional potential, and virus-host associations in the rumen virome of yak and cattle on the Qinghai-Tibet Plateau across warm and cold seasons. RESULTS: Rumen viral communities exhibited pronounced seasonal variation in both yaks and cattle, with higher alpha diversity observed during the cold season than in the warm season. Across seasons, the yak rumen virome showed greater alpha diversity and community stability than that of cattle. In total, 27,353 temperate and 31,976 virulent viral operational taxonomic units (vOTUs) were identified, predominantly belonging to the class Caudoviricetes. These viruses were linked to microbial hosts spanning 24 bacterial and 8 archaeal phyla, with Bacteroidota and Bacillota representing the dominant lineages. Virus-host associations were more numerous in the cold season and showed distinct host-specific patterns between yaks and cattle. Cold-season virome exhibited reduced diversity of anti-defense genes and enrichment of auxiliary metabolic genes (AMGs) associated with fatty acid metabolism and hemicellulose degradation. Notably, greater divergence between yaks and cattle was observed during the cold season: the yak rumen virome was enriched in pathways related to amino acid, lipid, and energy metabolism, as well as cellulose-degrading CAZyme families, whereas the cattle rumen virome showed enrichment in general carbohydrate metabolism and replication and repair processes. CONCLUSION: Seasonal plasticity of rumen DNA virome and pronounced interspecific divergence between yaks and cattle provide insight into their distinct microbial processes in the harsh environment of the Qinghai-Tibet Plateau. These findings suggest that the rumen DNA virome exhibits complex ecological and functional responses to seasonal variation and may be associated with host-microbiome interactions and nutrient utilization under environmental stress. This study highlights the ecological relevance of rumen viral genomes in understanding virus-microbiome interactions, microbial adaptation, and nutrient utilization in high-altitude ruminants.

Auxiliary metabolic genes↗

PubMed2026

Gut microbiome in advanced non-small cell lung cancer: effect of chemotherapy and impact on efficacy.

BACKGROUND: While evidence linking the gut microbiome (GM) to cancer immunotherapy is growing, data regarding its role in chemotherapy remains limited. This study aims to investigate the effect of chemotherapy on GM composition and its potential as a predictive biomarker for treatment outcomes in advanced non-small cell lung cancer (NSCLC). METHODS: Advanced NSCLC patients treated with chemotherapy at Ramathibodi Hospital were prospectively enrolled. Clinical data and stool samples were collected at three time points: baseline, post-evaluation, and at progression of disease (PD). Fecal bacterial DNA was extracted, followed by PacBio Sequel II sequencing and comprehensive bioinformatic analysis. Clinical data were summarized using descriptive statistics. Progression-free survival (PFS) and overall survival (OS) were estimated by the Kaplan-Meier method, and predictive factors were identified using Cox-regression analysis. RESULTS: This study analyzed 54 stool samples from 27 NSCLC patients treated with platinum-doublet chemotherapy. The median PFS and OS were 5.3 months [95% confidence interval (CI): 2.4-8.4] and 13.8 months (95% CI: 5.2-not reached), respectively. Post-chemotherapy changes (n=20 paired samples) showed a significant decrease in microbial richness, as evidenced by reduced abundance-based coverage estimator (ACE) (P=0.02) and Chao1 (P=0.03) alpha diversity indices. Taxonomically, the relative abundance of Enterobacter was significantly decreased post-chemotherapy (P=0.03). Regarding treatment response (n=26 evaluable patients; 13 PD, 13 clinical benefit), baseline alpha diversity was not predictive of outcome. However, the relative abundance of Akkermansia was notably higher in the clinical benefit group, approaching statistical significance (P=0.07). CONCLUSIONS: Chemotherapy significantly reduced GM by decreasing species richness (as measured by the ACE and Chao1 index), while species diversity (as measured by the Shannon and Simpson index) remained unchanged. Therefore, confirming the definitive role of the GM as a predictive biomarker in chemotherapy-treated NSCLC patients necessitates further investigation in a larger, more robustly powered cohort.

Gut microbiome (GM)↗

PubMed2024

Networks of human milk microbiota are associated with host genomics, childhood asthma, and allergic sensitization.

The human milk microbiota (HMM) is thought to influence the long-term health of offspring. However, its role in asthma and atopy and the impact of host genomics on HMM composition remain unclear. Through the CHILD Cohort Study, we followed 885 pregnant mothers and their offspring from birth to 5 years and determined that HMM was associated with maternal genomics and prevalence of childhood asthma and allergic sensitization (atopy) among human milk-fed infants. Network analysis identified modules of correlated microbes in human milk that were associated with subsequent asthma and atopy in preschool-aged children. Moreover, reduced alpha-diversity and increased Lawsonella abundance in HMM were associated with increased prevalence of childhood atopy. Genome-wide association studies (GWASs) identified maternal genetic loci (e.g., ADAMTS8, NPR1, and COTL1) associated with HMM implicated with asthma and atopy, notably Lawsonella and alpha-diversity. Thus, our study elucidates the role of host genomics on the HMM and its potential impact on childhood asthma and atopy.

Humans↗

PubMed2026

Oral bacteriome in pediatric patients with malignancies prior to chemotherapy: a pilot study using full-length 16S rRNA sequencing.

OBJECTIVE: To characterize the composition, diversity, and ecological features of the oral bacteriome in pediatric patients with malignancies prior to chemotherapy initiation. METHODS: In this prospective pilot study,supragingival plaque samples were collected from 10 pediatric cancer patients prior to the initiation of chemotherapy. Bacterial genomic DNA was extracted from each sample, and the full-length 16S rRNA gene was amplified and sequenced on the PacBio Sequel II platform using circular consensus sequencing (CCS). Raw CCS reads were quality-filtered and denoised into amplicon sequence variants (ASVs) using DADA2, and taxonomic assignment was performed against the SILVA 138 reference database. Alpha diversity was assessed using the Chao1, Shannon, Simpson, and Faith's phylogenetic diversity (PD whole tree) indices, while beta diversity was evaluated through principal coordinate analysis (PCoA), and non-metric multidimensional scaling (NMDS). Microbial co-occurrence networks were constructed to characterize bacterial interactions, and functional potential was predicted using PICRUSt2, and BugBase. RESULTS: A total of 614,473 high-quality CCS reads were generated, yielding 1,697 ASVs. Alpha diversity analysis revealed substantial inter-individual variation in microbial richness and diversity among the pediatric cancer patients. The bacterial community was dominated by the phyla Firmicutes, Proteobacteria, Bacteroidota, Actinobacteriota. At the genus level, Streptococcus, Prevotella, Neisseria, and Haemophilus were the most abundant taxa. Beta diversity analysis revealed distinct clustering patterns, indicating highly individualized microbial profiles. Co-occurrence network analysis identified several keystone taxa and potential pathogenic associations within the supragingival plaque community. Functional prediction indicated that the dominant metabolic pathways were related to amino acid metabolism, carbohydrate metabolism, and membrane transport. CONCLUSION: These preliminary findings reveal a taxonomically diverse, highly individualized pre-chemotherapy oral bacteriome, providing foundational baseline profiles to guide future longitudinal investigations of chemotherapy-induced dysbiosis and personalized interventions.

Humans↗

PubMed2024

Water source, latrine type, and rainfall are associated with detection of non-optimal and enteric bacteria in the vaginal microbiome: a prospective observational cohort study nested within a cluster randomized controlled trial.

BACKGROUND: Less than one-third of sub-Saharan Africans have access to improved water sources. In US, Indian, and African studies, Bacterial vaginosis (BV) is increased among women with poor water, sanitation, and hygiene (WASH). We examined water source, sanitation (latrine type), and rainfall in relation to the vaginal microbiome (VMB). METHODS: In a cluster randomized controlled trial of menstrual cups and cash transfer, we measured the impact of cups on VMB via 16S rRNA gene amplicon sequencing in a subset of 436 adolescent girls. We analyzed how self-reported water source and latrine type at home related to VMB over 18-months, examining community state type I (CST-I, L. crispatus dominant) vs. other CST; alpha diversity; targeted taxa (coliform and other water-related pathogens); and non-targeted taxa via machine learning approaches. Mixed effects multivariable longitudinal models were adjusted for intervention arm, age, socioeconomic status, sexual activity, and cluster-level school WASH and rainfall (in millimeters). RESULTS: Adjusting for all covariates in all models: (1) the odds of CST-I were increased among participants with piped water (vs. pond), and decreased with traditional pit latrine vs. flush toilet. (2) Alpha diversity varied by water source and latrine type without consistent trends. (3) Coliform bacteria relative abundance (RA) was higher among participants with traditional pit or ventilated improved pit latrines vs. flush toilet, and higher among participants relying on stream vs. pond water. Streptococcus agalactiae RA was higher among participants with non-flush toilets, while Bacteroides fragilis RA was lower with non-flush toilets. (4) Key taxa from non-targeted analyses associated with water source and latrine type included typical vaginal bacteria, opportunistic pathogens, and urinary tract pathobionts. (6) Increased rainfall was associated with decreased odds of CST-I. TRIAL REGISTRATION: ClinicalTrials.gov NCT03051789, February 14, 2017.

Adolescent↗

PubMed2025

Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics.

BACKGROUND: Early-life gut microbiota affects immune system development, including the lung immune response (gut-lung axis). We aimed to investigate whether gut microbiota composition in neonates in the first week of life is associated with hospital admissions for viral lower respiratory tract infections (vLRTIs). METHODS: The Baby Biome Study (BBS) is a prospective birth cohort, which enrolled mother-baby pairs between Jan 1, 2016, and Dec 31, 2017, at three UK hospitals. In the present study, we only included BBS babies with a sequenced first-week stool sample and successful data linkage. Stool was collected in the first week of life for shotgun-metagenomic sequencing. We examined the following microbiota features: alpha diversity (Chao1, Shannon, and Simpson indices) and community structures (cluster-partitioning against medoids method). The participants were followed up through linkage to the Hospital Episode Statistics-Admitted Patient Care (HES-APC) database to determine vLRTI hospital admission incidence in the first 2 years of life. We used Poisson mixed-effects models for univariable and multivariable analyses to evaluate the association between microbiota features and vLRTI hospital admission incidence, adjusting for confounders identified through direct acyclic graphs. FINDINGS: 3305 (95%) of the 3476 BBS-enrolled babies for whom consent to data linkage was obtained were included in the present study. 1111 (34%) babies had a first-week sequenced stool sample, of whom 1082 (97%; 564 born vaginally and 518 born by caesarean section) were successfully linked to HES-APC, and had median follow-up of 2·0 years (IQR 1·4-2·9). Most babies were born at term (996 [92%] ≥37 weeks gestational age and 1070 [99%] >35 weeks gestational age) and healthy (1050 [97%] had no comorbidities), and 520 (48%) were female and 562 (52%) were male. Higher first-week gut microbiota alpha diversity was associated with reduced rates of vLRTI hospital admission (Chao1 Index adjusted hazard ratio [HR] 0·92 [95% CI 0·85-0·99]; Shannon Index adjusted HR 0·57 [0·33-0·98]; and Simpson Index adjusted HR 0·36 [0·11-1·20]). Three microbiota clusters were identified. Cluster 1 had a mixed composition and cluster 2 was dominated by Bifidobacterium breve, with both clusters observed in babies born vaginally and by caesarean section. Cluster 3 was found only in vaginally born babies and was dominated by Bifidobacterium longum. Having cluster 1 (mixed) or cluster 2 (B breve dominated) was independently associated with increased rates of vLRTI hospital admission compared with cluster 3 (B longum dominated; cluster 1 [mixed] 3·05 [1·25-7·41] and cluster 2 [B breve dominated] 2·80 [1·06-7·44]). INTERPRETATION: We report observational evidence that first-week gut microbiota differences are associated with clinically severe vLRTI in young children. This study identified bacterial species that could be of interest for vLRTI prevention. This finding has important implications for the design of future research and intervention strategies. FUNDING: The Wellcome Trust and Wellcome Sanger Institute core funding.

Humans↗

PubMed2026

Characteristics and assembly mechanisms of tobacco-associated bacteria in typical tobacco-planting regions across China.

INTRODUCTION: Plant-associated microbiota critically modulates host growth and environmental adaptation, yet assembly mechanisms, niche differentiation, and ecological strategies of bacterial communities inhabiting tobacco microhabitats remain poorly elucidated across geographical gradients. METHODS: Here, we systematically characterized bacterial microbiome assembly across five tobacco-associated niches (bulk soil, rhizosphere soil, root, stem, and leaf) from seven typical tobacco-planting regions using 16S rRNA amplicon sequencing, genome annotation, and niche breadth analysis. The independent and interactive effects of geographical location and host compartment on community structure, and further compared genomic traits, functional profiles, and life-history strategies between specialist and generalist bacterial populations were quantified. RESULTS: The results revealed a deterministic soil-plant continuum stratification of bacterial communities and diversity, with progressively simplified communities and decreasing alpha diversity from bulk soil to above-ground tissues, accompanied by progressive dominance of Proteobacteria. Geographical factors predominantly structured soil microbial communities via divergent edaphic properties, while host filtering acted as a universal dominant driver shaping endophytic microbiome assembly. Niche differentiation analysis demonstrated that niche-specialized bacterial ASVs overwhelmingly dominated all microhabitats and geographical sites, whereas generalist taxa only constituted auxiliary populations. Although specialist and generalist microbes exhibited highly conserved core genomic architectures and overall functional repertoires, they displayed distinct niche-specific functional divergence in metabolic pathways, stress resistance, and secondary metabolism across host compartments. Life-history strategy analysis further revealed that Y-strategist represented the core adaptive bacterial population, especially enriched in above-ground tobacco tissues. DISCUSSION: Our study establishes a hierarchical dual-filtering assembly model for tobacco microbiota, clarifies the ecological differentiation and functional adaptation of specialist and generalist bacteria, and provides fundamental insights into the assembly rules and adaptive mechanisms of crop-associated microbiomes for future microbial resource utilization and agricultural microbiome regulation.

biogeography↗

PubMed2026

Long-term microbiome and clinical effects of a microbiome-guided personalized diet versus low-FODMAP diet in irritable bowel syndrome: A 12-month follow-up randomized controlled trial.

Dietary therapy is central to irritable bowel syndrome (IBS) management, yet the long-term durability of the low-FODMAP diet (LFD), and of microbiome-guided personalization, remains unclear. We assessed the long-term clinical and gut-microbiome effects of a microbiome-guided personalized diet (PD) compared with a standard LFD in adults meeting Rome IV criteria for IBS. In this multicenter, open-label randomized controlled trial with blinded outcome assessment, participants who completed a 6-week dietary intervention (PD or LFD) were followed at 6 and 12 months without further dietary intervention. Outcomes included the IBS Severity Scoring System (IBS-SSS), IBS Quality of Life (IBS-QOL), and the Hospital Anxiety and Depression Scale (HADS); gut microbiota were profiled by 16S rRNA sequencing. Longitudinal changes were evaluated using linear mixed-effects models, responder analyses, PERMANOVA, and PERMDISP. Both diets reduced IBS-SSS at 6 weeks. PD maintained symptom improvement at 6 and 12 months (-82.0 and -78.3 points from baseline), whereas LFD benefits regressed by 12 months (+29.3 points; between-group p = 0.001). At 12 months, IBS-SSS responder rates were higher with PD than LFD (62.5% vs 34.5%; absolute risk difference +28.0%, 95% CI 4.2-47.7; Fisher p = 0.029), and IBS-QOL, HADS-anxiety, and HADS-depression showed more favourable trajectories with PD. PD was associated with sustained Shannon alpha-diversity gains (+0.488 at 6 weeks; +0.205 at 12 months; both p < 0.01). A modest between-group beta-diversity difference at 6 months (R2 = 0.035; p = 0.011) was not significant at 12 months. This hypothesis-generating follow-up suggests more durable benefit with PD; larger trials powered for long-term clinical and microbiome outcomes are warranted.

Humans↗

PubMed2026

Gut bacteria associated with an atherogenic TMAO-dietary pattern and choline-rich foods among aging women.

BACKGROUND AND AIMS: Choline can be metabolized by gut bacteria with a choline utilization gene, CutC, as identified through genome sequencing studies. This metabolism produces trimethylamine, the precursor to the atherosclerotic metabolite trimethylamine N-oxide (TMAO). Bacterial species involved in trimethylamine production in free-living humans have been under-investigated. We previously developed the TMAO dietary pattern (TMAO-DP), which is predictive of plasma TMAO and choline. We evaluated associations between the TMAO-DP, dietary choline, and choline-rich foods (fish, red meat, eggs) with the abundance of species with CutC. We also explored associations between the TMAO-DP and microbiome diversity. METHODS AND RESULTS: This cross-sectional analysis included 287 women (mean age = 79.6 years) from the Women's Health Initiative. Diet was assessed using a food frequency questionnaire. Stool samples were collected and the V3-V4 regions of the 16S ribosomal RNA were sequenced. Adjusted linear regression models evaluated associations between the TMAO-DP with the CLR-transformed abundance of species with CutC and with alpha-diversity indices. For beta-diversity, PERMANOVA examined measures of Aitchison distance within and between quartiles of the TMAO-DP. Associations between dietary choline and choline-rich foods with the abundance of species were evaluated using linear regression. The TMAO-DP was associated with Acidaminococcus intestini [Beta (SE): 0.23 (0.09), p-value = 0.035] and Desulfovibrio desulfuricans [Beta (SE): 0.16 (0.6), p = 0.035]. The TMAO-DP was not associated with alpha- or beta-diversity. CONCLUSION: This study provides evidence that Desulfovibrio desulfuricans and Acidaminococcus intestini, two species identified as having CutC by gene sequencing, may produce trimethylamine from diet in free-living women.

Humans↗

PubMed1988

Organization and genomic distribution of "82H" alpha satellite DNA. Evidence for a low-copy or single-copy alphoid domain located on human chromosome 14.

We have investigated the organization and genomic distribution of sequences homologous to p82H, a cloned human alpha satellite sequence purported, based on previous in situ hybridization experiments, to exist at the centromere of each human chromosome. We report here that, using Southern blotting analysis under conditions of high stringency, p82H hybridizes solely to a low-copy or single-copy alphoid domain located at or near the centromeric region of human chromosome 14. In contrast, conditions of reduced hybridization stringency permit extensive cross-hybridization with non-identical, chromosome-specific alpha satellite subsets found elsewhere in the human genome. Thus, the previously described ubiquity of "82H" human centromeric sequences reflects the existence of diverse alpha satellite subsets located at the centromeric region of each human chromosome.

Animals↗

PubMed2026

Impact of Tilapinevirus tilapiae (TiLV) infection on the composition and functional dynamics of gut microbiota in Nile Tilapia (Oreochromis niloticus) (Linnaeus, 1758).

Tilapinevirus tilapiae (TiLV) (formerly Tilapia Lake Virus) is a highly prevalent pathogen capable of inducing significant mortality rates in Nile tilapia (Oreochromis niloticus). The alterations induced by Tilapia Lake Virus (TiLV) in the gut microbiota composition, diversity and functional prediction of Nile tilapia have not been thoroughly investigated. This study investigated the gut microbiota of a healthy control group and a TiLV-infected group of Nile tilapia of size 30 ± 2.45g. The alpha diversity of microbiota was hardly affected by TiLV infection, whereas species richness and beta diversity patterns explained the significant differences between control and TiLV-infected groups. The study highlighted a decline in Cetobacterium and an increase in Mycobacterium in the TiLV-infected group. The phyla, including Firmicutes, Actinobacteriota and Proteobacteria, exhibited a significant increase in the TiLV-infected group, while Bacteroidota and Fusobacteriota decreased substantially. The PICRUSt-based functional gene prediction revealed that TiLV infection had considerably changed the KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways associated with membrane transport, amino acid metabolism, transcription, carbohydrate metabolism, cellular process and signalling in the gut microbiota of Nile tilapia. The results suggest that the infection by TiLV altered the composition and functional pathways in the gut microbiota of Nile tilapia.

Animals↗

PubMed2026

Microbial allies in a cotton pest: A descriptive account of associated microbiota dynamics in Dysdercus cingulatus across development.

BACKGROUND: Hemipteran insects harbour several symbiotic partners, mainly bacteria, which play pivotal roles for hosts like dietary provision, support overall physiology, xenobiotic degradation and manipulate/regulate behaviour. Most of these symbionts usually reside and operate from the digestive tracts of the animals. Cotton is one of the major cash crops in India and Dysdercus cingulatus (D. cingulatus) though a secondary pest, is causing significant destruction of cotton bolls, poor lint quality and reduce oil content of seeds. Premature opening of cotton bolls often leads to bacterial and fungal infections, thus resulting in extensive economic loss worldwide. D. cingulatus is a hemimetabolous insect that comprises of developmental stages like egg, nymph (5 instar stages), and adult. The present work explored the ontogeny specific diversity in the associated microbiota and predicted their probable functional inputs in D. cingulatus. RESULTS: The data obtained using 16S rRNA gene sequencing (NovaSeq 6000) revealed presence of members of Proteobacteria (65.83%), Firmicutes (24%), Actinobacteria (10%) phyla throughout the ontogeny of D. cingulatus. Highest alpha diversity of these symbiotic bacteria was recorded in the third instar nymphs in contrast to rest of the developmental stages. Among all the observed genera, Stenotrophomonas, Hungatella and Glutamicibacter were predominant from egg to adult stages. MicFunPred, a tool used for predicting the probable functional inputs of these symbionts, hinted at their probable stage specific contribution in crucial biochemical pathways such as polyketide biosynthesis, ascorbate/aldarate metabolism, pentose phosphate and glyoxylate cycles, steroid hormone and peptidoglycan biosynthesis, and glycolysis/pyruvate metabolism. CONCLUSIONS: The primary investigations on the ontogenetic composition and diversity of associated microbiota, suggest dynamic shifts in D. cingulatus, concurrent with their probable functions/roles in the host development and metabolism. To the best of our knowledge, this is the first report on symbiotic microbiota variation across the developmental stages of D. cingulatus that provides preliminary descriptive observations that may guide future functional and experimental investigations into microbiota-based pest management.

Animals↗