Fecal microbiota transplantation (FMT) is increasingly recognized as an alternative to antibiotics for treating recurrent Clostridioides difficile infection. The success of FMT heavily depends on the appropriate selection of donors, encompassing factors such as diet patterns, lifestyle, environmental exposures, and intestinal microbiota diversity. A potential super donor was identified from 5 healthy adults and provided stool samples periodically over 2 years (2021-2022). The samples underwent 16S rRNA sequencing via the Illumina MiSeq platform, and microbial diversity was analyzed using QIIME 2 in comparison with 152 healthy individuals. The stool microbiome composition of the potential super donor remained stable without significant changes over a 2-year period. Both alpha and beta diversity analyses revealed significant differences between the super donor and the 152 healthy individuals. The super donor exhibited significantly higher microbial diversity based on alpha diversity metrics (P< 0.0001) and distinct compositional profiles as shown by beta diversity. Linear discriminant analysis effect size (LEfSe) analysis indicated that Faecalibacterium and Prevotella strains comprised a significant proportion, with notable differences in relative abundance patterns (P< 0.05). Furthermore, 7 bacterial species were isolated from the super donor, all of which demonstrated inhibitory effects on the growth of C. difficile in vitro. These findings suggest that selecting donors with specific microbiota profiles, particularly those exhibiting higher microbial diversity, may potentially contribute to the inhibition of C. difficile, and further clinical studies are warranted to validate these findings.

Morphological adaptations play a key role in shaping the feeding behavior and microbiome associations of Cephalobidae nematodes. To investigate how morphology influences nematode-associated microbiomes, we selected two widely distributed species: Acrobeles complexus, exhibiting elaborated oral structures, and Zeldia punctata, with simpler oral morphology. Unlike earlier studies that reported the microbiomes of A. complexus and Z. punctata independently, this study is the first to directly compare the two species. By integrating in silico re-analysis of our previously published microbiome datasets with new light microscopy and scanning electron microscopy (SEM) observations, we demonstrate how morphological adaptations, such as labial probolae and cuticle structures, shape associated bacterial communities. Our results revealed that A. complexus harbored a more diverse bacterial community than Z. punctata. Morphology showed that the complex oral structures of A. complexus facilitated selective bacterial capture, supporting greater microbial diversity compared to the simpler morphology of Z. punctata. Although statistical significance was not observed, the two species showed distinct patterns of microbial richness and diversity. Principal Coordinate Analysis (PCoA) revealed clearly separated bacterial community structures between the species. Linear discriminant analysis effect size identified potential microbial biomarkers at the genus level, including Firmicutes and Clostridium in A. complexus and Actinobacteria and Pseudomonas in Z. punctata. Predicted functional pathway analysis revealed notable differences in microbial metabolism, such as enrichment of bacterial secretion systems in A. complexus and amoebiasis and lipid metabolism pathways in Z. punctata. This study highlights the role of morphological adaptations in shaping microbiome composition in Cephalobidae nematodes and provides insights into the contribution of free-living bacterivorous nematodes to soil microbial balance. These findings lay the groundwork for further studies on nematode-mediated microbial interactions in soil ecosystems.

Irritable bowel syndrome (IBS) is a chronic functional gastrointestinal disorder influenced by stress, microbial dysbiosis, and immune activation. Microbiota-directed therapies, including fecal microbiota transplantation and probiotics, show promise, but their sex-specific effects remain unclear. We compared the therapeutic effects of lyophilized fecal microbiota (LFM) with Bifidobacterium longum BBH016 in male and female Wistar rats subjected to repeated water avoidance stress. Fecal pellet output (FPO), colonic mast cell infiltration, and fecal short-chain fatty acids were measured. Gut microbial composition and function were analyzed by 16S rRNA sequencing and Kyoto Encyclopedia of Genes and Genomes pathway prediction. Both interventions significantly reduced FPO and mast cell infiltration in males but had less pronounced effects in females. Microbiota analyses revealed sex-dependent responses, with distinct microbial trajectories in each treatment group. Using linear discriminant analysis effect size, we identified seven key taxa with treatment- or sex-specific enrichment. Alistipes onderdonkii and Bacteroides uniformis consistently increased in both LFM- and B. longum-treated groups, regardless of sex. Bacteroides finegoldii and Barnesiella intestinihominis were specifically enriched in the LFM group. In males, Blautia faecis and Fusicatenibacter saccharivorans were enriched following the interventions, whereas Parabacteroides goldsteinii appeared exclusively in stressed males. Functional predictions revealed the enrichment of estrogen signaling and bile acid pathways in males and the attenuation of proinflammatory pathways in females following LFM. Correlations between microbial taxa and host outcomes were predominantly observed in male rats. These findings highlight sex-specific microbial and host responses to microbiota-targeted therapies in a stress-induced IBS model, emphasizing sex as a biological variable in designing personalized microbiome-based treatments.

ABSTRACT This study aimed to investigate the effects of cellulase and Lactobacillus plantarum on the fermentation characteristics, in situ digestibility, and microbial communities of apple pomace (AP) silage. Fresh AP was selected as the silage raw material, and four treatments were designed: no additive (CON), cellulase supplementation (CE), Lactobacillus plantarum inoculation (LP), and their combination (LPCE). Silage samples were collected on days 20, 40, and 80 during fermentation to analyze relevant indices. The results showed that during the ensiling of AP, cellulase supplementation reduced the pH, neutral detergent fiber (NDF), and acid detergent fiber (ADF) contents, while increasing the rumen effective degradability of dry matter (DM) ( p &lt; 0.05). Lactobacillus plantarum inoculation enhanced lactic acid (LA) production, lowered the pH, reduced DM loss, and improved the antioxidant activity and rumen effective degradability of NDF and ADF ( p &lt; 0.05). The combined addition of Lactobacillus plantarum and cellulase increased LA and acetic acid production, further reduced the pH, decreased NDF and ADF content, as well as increased antioxidant activity and effective degradability of DM, NDF and ADF ( p &lt; 0.05). The linear discriminant analysis effect size coupled with linear discriminant analysis showed that compared with the CON treatment, there was a higher relative abundance of Pseudomonadales in the CE treatment. Compared with the CON treatment, the LP treatment showed higher abundance of Lactiplantibacillus, etc., but lower abundance of Peptostreptococcales_Tissierellales , etc. In conclusion, the combined supplementation of cellulase and Lactobacillus plantarum in AP silage improved fermentation quality, reduced DM loss, and enhanced rumen utilization efficiency. This synergistic strategy provides a promising approach for valorizing AP through silage technology.

BackgroundZearalenone (ZEN), a common mycotoxin in ruminant diets, could disturb the rumen ecosystem and impair rumen fermentation. Noticeably, ZEN has been shown to reduce the relative abundances of specific bacterial taxa that potentially possess quorum sensing (QS) functions, which are deemed essential for the microbial interactions and adaptations during rumen fermentation. Nonetheless, whether QS communications participate in the responses of rumen microbial fermentation to ZEN remains unknown. Therefore, the present trial was performed to explore the potential roles of QS during the alterations of rumen microbial fermentation by ZEN through a rumen simulation technique (RUSITEC) system, in a replicated 4 × 4 Latin square design.ResultsZEN significantly (P < 0.05) reduced QS signal autoinducer-2 (AI-2), and tended to (P = 0.051) downregulate QS signal C4-homoserine lactone (HSL). ZEN also significantly (P < 0.05) decreased total volatile fatty acid (TVFA), acetate, propionate, isobutyrate, isovalerate, organic matter disappearance (OMD), neutral detergent fiber disappearance (NDFD), and acid detergent fiber disappearance (ADFD) in different manners. The linear discriminant analysis effect size (LEfSe) analysis indicated significantly (P < 0.05) differential enrichments of a series of bacterial taxa such as Butyrivibrio_sp_X503, Rhizobium daejeonense, Hoylesella buccalis, Ezakiella coagulans, Enterococcus cecorum, Ruminococcus_sp_zg-924, Polystyrenella longa, and Methylacidimicrobium fagopyrum across different treatments. The phylogenetic investigation of communities by reconstruction of unobserved states 2 (PICRUSt2) analysis suggested that QS were predicted to be significantly (P < 0.05) affected by ZEN. The metabolomics analysis detected considerable significantly (P < 0.05) differing metabolites and implied that ZEN challenge significantly (P < 0.05) influenced the indole alkaloid biosynthesis, biosynthesis of alkaloids derived from shikimate pathway, and sesquiterpenoid and triterpenoid biosynthesis. Significant (P < 0.05) interconnections of QS molecules with the differential rumen fermentation traits, differential bacterial taxa, and differential metabolites were exhibited by Spearman analysis.ConclusionsZEN negatively affected the QS signals of AI-2 and C4-HSL, which was found to correlate with the fluctuations in specific rumen fermentation characteristics, ruminal bacterial populations, and ruminal metabolisms. These interrelationships implied the potential involvement of QS in the reactions of rumen microbiota to ZEN contamination, and probably contributed to the inhibition of rumen fermentation.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40104-025-01337-z.

The Leizhou goat is a vital indigenous breed, yet its disease resilience can complicate early health monitoring. The white blood cell (WBC) count is a key indicator of immune status, but its relationship with the gut microbiota remains uncharacterized in this breed. This study aimed to characterize the fecal microbiota of Hainan black goats stratified based on their WBC counts. The goats were stratified into Lower, Middle, and High WBC groups based on peripheral WBC counts to compare their fecal microbiota and identify potential associations with systemic immunity. Significant differences in microbial alpha- and be-ta-diversity were observed among the groups, with the High WBC group showing the greatest richness. The microbiota was dominated by Bacillota and Bacteroidota at the phylum level. Linear discriminant analysis Effect Size (LEfSe) identified specific taxa en-riched in each group, such as Ruminococcusin the High WBC group. Critically, Spearman correlation analysis demonstrated significant positive correlations between WBC counts and the relative abundance of genera like unclassified_f_Oscillospiraceae and unclassi-fied_c_Clostridia. These findings demonstrate that WBC counts are significantly associated with distinct shifts in the gut microbial community structure of Hainan black goats. The identified WBC-associated microbial biomarkers suggest a link between the gut microbi-ome and host immune regulation, providing a foundation for future research on microbi-ota-mediated health assessment in goats.

The lung-targeting characteristic of Hantavirus infection and the unclear mechanism underlying its interaction with the lung microbiome hampers the development of effective prevention and control strategies. In this study, lung tissues from Apodemus agrarius and Rattus norvegicus were collected at Hantavirus surveillance sites in Hunan Province. Metagenomic sequencing was subsequently applied to compare microbiome diversity, community structure, and function between infected and uninfected groups. Then the linear discriminant analysis effect size (LEfSe) was employed to identify key biomarkers. The results indicated that after infection with Hantaan virus (HTNV), Apodemus agrarius exhibited significantly increased evenness but markedly decreased richness of lung microbial communities, as reflected by consistent reductions in the number of observed species, Abundance-based Coverage Estimator (ACE) index, and Chao1 index. In contrast, Rattus norvegicus infected with Seoul virus (SEOV) showed no significant difference in microbial richness compared with uninfected controls, and even a slight increase was observed. These findings suggest that host species and virus type may play an important role in shaping microbial community responses. Furthermore, β-diversity analysis showed that the community structure was clearly separated by the host rodent species, as well as by their virus infection status. LEfSe analysis identified taxa with discriminatory power associated with infection status. Streptococcus agalactiae and Streptococcus were associated with SEOV-infected Rattus norvegicus, while Chlamydia and Chlamydia abortus were relatively enriched in uninfected Apodemus agrarius. This exploratory study reveals preliminary association between specific host-Hantavirus pairings (HTNV-Apodemus agrarius and SEOV-Rattus norvegicus) and the rodent lung microbiome, offering potential insights for future research into viral pathogenesis.

As the relationship between oral microbiota and treatment efficacy in esophageal cancer remains unexplored, we aimed to clarify it using metagenomic analysis. Of the 140 consecutive patients with esophageal squamous cell carcinoma (ESCC) who underwent esophagectomy with R0 resection at Hiroshima University Hospital between April 2020 and May 2024, 74 who received neoadjuvant therapy were included in this study. 16S rRNA gene from oral tongue coating samples was amplified using polymerase chain reaction and subjected to next-generation sequencing. The oral microbiome data were analyzed using QIIME2 and linear discriminant analysis effect size, and the relationship between the oral microbiota and treatment efficacy and prognosis was assessed. Alpha diversity of the oral microbiota was significantly correlated with the pathological response. Univariate and multivariate analyses showed that the alpha diversity of the oral microbiome (high versus low) was a significant predictor of a good pathological response. Patients with high alpha diversity had significantly improved recurrence-free survival and overall survival compared with those with low alpha diversity. Furthermore, eight bacterial groups (Lactobacillales, Peptostreptococcales-Tissierellales, Bifidobacteriaceae, Erysipelotrichaceae, Lactobacillaceae, Anaerovoracaceae, Staphylococcaceae, and Aerococcaceae) were significantly more abundant in individuals who responded well to neoadjuvant therapy and two bacterial groups (Streptococcaceae and Corynebacteriaceae) were significantly more abundant in poor responders. Our results demonstrate a correlation between the oral microbiome and ESCC treatment efficacy, suggesting that it is a significant prognostic factor. Our findings may also help predict the efficacy of esophageal cancer treatment.

Diversity of Gut Microbiota and Metabolites in Benign Prostatic Hyperplasia with Different Prostate Volumes

Analyzing the composition and structure of the gut bacterial community in Antheraea pernyi is essential for improving its economic traits, as well as for understanding gut bacteria-host interactions in lepidopteran insects. This study utilized the Illumina MiSeq PE 300 platform to conduct 16S rRNA gene sequencing for a comparative analysis of gut bacterial community in laboratory-reared and field-released (spring and autumn) Antheraea pernyi larvae of the same strain. The study revealed the specific effects of rearing environment and seasonal variation on the structural and functional dynamics of the larval gut bacterial communities. The composition of the dominant gut bacteria varied significantly with rearing environment and season. Laboratory-reared and spring field-released groups exhibited similar bacterial community structures, whereas the autumn field-released group showed a significant trend toward specialization, characterized by enrichment of specific bacterial taxa. Linear discriminant analysis effect size identified statistically significant biomarkers across samples. Taxonomic analysis revealed that Actinomycetota, Actinobacteria, Mycobacteriales, Dietziaceae, and Dietzia were characteristic of the gut bacteria profile in spring field-released, Lactobacillales, Enterococcaceae, and Enterococcus were enriched in the autumn field-released group, and the laboratory-reared group exhibited a relative dominance of Alphaproteobacteria. Functional prediction indicated that gut bacterial community structure likely influences its metabolic potential, which may suggest an adaptive response of the Antheraea pernyi to distinct ecological environments. This study provides important insights into the highly complex nature of insect-microbe interactions.

PurposeTo identify the basic genomic profile of Acanthamoeba, obtain information on Acanthamoeba endosymbionts, and analyze the correlation between these endosymbionts and the prognosis of Acanthamoeba keratitis (AK) patients.MethodsWhole-genome sequencing was conducted on 30 cornea-derived Acanthamoeba strains. Pan-genome analysis was performed, and endosymbionts were identified by metagenomic analysis. Gimenez staining, fluorescence in situ hybridization, and transmission electron microscopy were used to prove the existence of endosymbionts. Linear discriminant analysis effect size was used to associate endosymbiont species with AK clinical prognosis. The correlation between the endosymbiont Ralstonia and pathogenicity was experimentally validated by assessing the biological characteristics of Acanthamoeba and by performing clinical and histopathological evaluations in AK mouse models.ResultsWhole genome sequencing revealed that the Acanthamoeba genome size was 37.1–105.0 Mb and GC content was 53.9%–60.5%. Pan-genomic analysis indicated an open state of the Acanthamoeba genome. Metagenomic analysis identified the presence of endosymbionts within Acanthamoeba, notably the endosymbiont Ralstonia, which was associated with poor prognosis at the genus level (P = 0.047). Acanthamoeba harboring the endosymbiont Ralstonia exhibited an increased migration area, enhanced adhesion, and had a more pronounced cytopathic effect. The size of clinical scores and corneal ulcers showed a significant increase in mouse models induced by Acanthamoeba with endosymbiont Ralstonia.ConclusionsWhole-genome sequencing highlighted the symbiotic relationship between Acanthamoeba and associated microorganisms. The presence of the endosymbiont Ralstonia influenced the biological characteristics of Acanthamoeba and was correlated with clinical poor prognosis in AK, suggesting its potential as a target for clinical intervention.

Natural exogenous additives (EA) suitable for the tobacco fermentation need to be developed to enhance the fermentation quality and economic value of low-grade cigar tobacco leaves (CTLs). This study analyzed the impacts of three compound Chinese herbal medicine (CHM) on metabolites and microorganisms during CTLs fermentation. The results manifested that EA facilitated the degradation of total sugar, starch and protein, while enhancing the accumulation of reducing sugar in CTLs. Furthermore, EA raised contents of free amino acids (FAAs), while Asp, Glu, Ser and His were found to be key differential FAAs of CTLs. During fermentation, the total contents of volatile flavor components (VFCs) initially increased and then declined. Furthermore, EA contributed to more harmonious compositions of VFCs by promoting the formation of neophytadiene, ketones, esters and aldehydes, as well as facilitating nicotine degradation. According to variable importance in the projection (VIP) > 1 and odor activity value (OAV) > 1, 7 key differential VFCs were identified. EA enhanced positive microbial interactions and led to a more stable and coordinated symbiotic network. Linear discriminant analysis effect size (LEfSe) identified 9 genera as differentially dominant microorganisms in CTLs, which were closely associated with chemical compositions and key differential flavor metabolites. In addition, EA promoted cigar tobacco characteristics (CTCs) by altering bacterial alpha diversity and influencing the assembly of dominant microbial communities. Overall, this study offered theoretical insights into the innovative applications of CHM in CTLs fermentation, and presented new perspectives for enhancing CTLs quality and customizing flavor profiles.Graphical abstractSupplementary InformationThe online version contains supplementary material available at 10.1186/s40643-025-00998-y.

Structural and functional responses of microbial communities in coastal sediments towards anthropogenic pollution caused by ship breaking activities.

Arginine Requirements for WOD188 Broilers on a Low-Protein Diet: Insights from Growth Performance and Intestine Health.

Composition and concentration of road salts alter amphibian microbial ecosystems: Insights from Ranadybowskii.

Synergistic partnership between Serratia marcescens 2G5 and Amorpha fruticosa L. for enhanced phytoremediation of lead and cadmium contaminated soil.

The role of gut microbiota in adolescent depression: Insights from adverse childhood experiences.

This study investigated the effects of dietary garlic powder supplementation on growth performance, nutrient digestibility, carcase traits and caecal microbiome of meat-type ducks. A total of 288 day-old-duck (initial body weight (BW) 41 ± 2.1 g) were randomly allocated into four groups of control diet (0% garlic powder; T0) and garlic powder supplemented diets at 0.8% (T1), 1.6% (T2) and 2.4% (T3). Each group had eight replicates (pens) with nine ducks in each pen. Quadratic response (p < .001) was found on performance parameters, whereas ducks fed T1 and T2 diets had higher (p < .01) feed intake, final BW and average daily gain compared to T0 and T3 (p < .01), but FCR was unaffected. Ducks on T1 and T2 also exhibited greater carcase yield and lower non-carcase weight (p < .001), showing a quadratic pattern (p < .001). Thymus, heart, bursa of Fabricius, and ventriculus were influenced (p < .01) by garlic levels, with T2 and T3 showing increased values. Garlic powder increased (p < .001) the HDL and decreased (p < .01) the LDL content. Caecal microbiota profiling via 16S rRNA sequencing showed significant microbial diversity and community composition shifts. Alpha diversity was highest in T1, and beta diversity analysis confirmed treatment-specific clustering (PERMANOVA R 2 = 0.15, p < .01). Linear discriminant analysis effect size (LEfSe) analysis identified distinct microbial biomarkers for each group, correlating with performance and digestibility traits. Functional KEGG prediction analysis revealed amino acid and vitamin metabolism in response to garlic supplementation. Overall, 0.8–1.6% garlic improved duck performance by positively altering the composition of the caecal microbiome, while excessive inclusion (2.4%) diminished these benefits.

This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91). Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups. Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced α-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases. This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.

ABSTRACT This study investigated the water quality of swimming pools in Thailand, examining the impact of chlorine (Cl), pH, and bather load on pathogenic bacterial growth. Thirty-eight water samples were collected from various swimming pools across Thailand. The water was collected 20 cm below the surface and above the pool floor, at both the pool entrance and the pool rim, between 11:00 and 13:00 h, with pH, number of bathers, and Cl levels were recorded. The water, collected in eight sterilized 250 ml centrifuge bottles with 0.25 mg sodium thiosulfate, was filtered through a 0.22 μm PES sterile disposable filter and transferred to sterile 50 ml conical tubes for DNA extraction and 16S rDNA sequencing, followed by bioinformatic analysis. Linear discriminant analysis effect size identified two bacterial species, such as Gardnerella vaginalis and Sphingomonas koreensis, which were significantly associated with high Cl (p.0.05). The analysis of relative abundance revealed that Blastomonas natatoria was present in 38.6% of commercial pools, while Rickettsia typhi was found in 63% of commercial pools. The study highlights the potential health risks associated with swimming pools, particularly for immunocompromised individuals. Precautions, e.g., maintaining hygiene and avoiding pool water ingestion are recommended to minimize the risk of infection.