Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin

Assembly Mechanisms and Functional Adaptations of Soil Fungal Communities of Different Plant Rhizospheres in Ilmenite Mining Area

This study investigated the mechanisms of structural assembly and functional adaptations of fungal communities in the rhizosphere soils of seven different plants grown in the ilmenite zone. We analyzed changes in the rhizosphere soil fungal communities using ITS sequencing. The results revealed that different plants affected the properties of the rhizosphere soil. The contents of organic matter, total nitrogen, and total potassium in the rhizosphere soil exhibited significant variations compared to the soil that was not occupied by plants. Soil fungal composition analysis revealed that Ascomycota and Basidiomycota were the dominant phyla in the soil of this mining area. At the genus level, compared to the mineral soil without plants, the proportion of Epicoccum increased in the rhizosphere soils of different plants, while the proportion of Fusarium decreased. Alpha diversity studies revealed that fungal diversity in the rhizospheres of different plants changed significantly. Beta diversity studies showed a significant differentiation in the fungal community structure of different plant rhizosphere soils compared to the KB group. The FunGuild predictions indicated that different plant rhizosphere soils are enriched with different guilds and trophic patterns of fungi. In addition, we found that soil physical and chemical properties were significantly correlated with the abundance and diversity of fungal communities. The above results indicate that plant species and soil physicochemical properties are important factors influencing the assembly of soil fungal communities in the rhizosphere. This research provides insights into the assembly mechanisms and functional adaptations of fungal community structures in the rhizosphere soils of seven plant species in ilmenite iron mining areas. This helps us to screen plant and fungal community assemblages that can promote soil restoration in ilmenite mining areas and provide a theoretical basis for future ecological restoration in ilmenite areas.

Effects of Live and Peptide-Based Antimicrobiota Vaccines on Ixodes ricinus Fitness, Microbiota, and Acquisition of Tick-Borne Pathogens

This study explored the effects of antimicrobiota vaccines on the acquisition of Borrelia and Rickettsia, and on the microbiota composition of Ixodes ricinus ticks. Using a murine model, we investigated the immunological responses to live Staphylococcus epidermidis and multi-antigenic peptide (MAP) vaccines. Immunized mice were infected with either Borrelia afzelii or Rickettsia helvetica, and subsequently infested with pathogen-free I. ricinus nymphs. We monitored the tick feeding behavior, survival rates, and infection levels. Additionally, we employed comprehensive microbiota analyses, including the alpha and beta diversity assessments and microbial co-occurrence network construction. Our results indicate that both live S. epidermidis and MAP vaccines elicited significant antibody responses in mice, with notable bactericidal effects against S. epidermidis. The vaccination altered the feeding patterns and fitness of the ticks, with the Live vaccine group showing a higher weight and faster feeding time. Microbiota analysis revealed significant shifts in the beta diversity between vaccine groups, with distinct microbial networks and taxa abundances observed. Notably, the MAP vaccine group exhibited a more robust and complex network structure, while the Live vaccine group demonstrated resilience to microbial perturbations. However, the effects of antimicrobiota vaccination on Borrelia acquisition appeared taxon-dependent, as inferred from our results and previous findings on microbiota-driven pathogen refractoriness. Staphylococcus-based vaccines altered the microbiota composition but had no effect on B. afzelii infection, and yielded inconclusive results for R. helvetica. In contrast, previous studies suggest that E. coli-based microbiota modulation can induce a pathogen-refractory state, highlighting the importance of both bacterial species and peptide selection in shaping microbiota-driven pathogen susceptibility. However, a direct comparison under identical experimental conditions across multiple taxa is required to confirm this taxon-specific effect. These findings suggest that antimicrobiota vaccination influences tick fitness and microbiota assembly, but its effects on pathogen transmission depend on the bacterial taxon targeted and the selected peptide epitopes. This research provides insights into the need for strategic bacterial taxon selection to enhance vaccine efficacy in controlling tick-borne diseases.

Bacteria invade the brain following intracortical microelectrode implantation, inducing gut-brain axis disruption and contributing to reduced microelectrode performance

Brain-machine interface performance can be affected by neuroinflammatory responses due to blood-brain barrier (BBB) damage following intracortical microelectrode implantation. Recent findings suggest that certain gut bacterial constituents might enter the brain through damaged BBB. Therefore, we hypothesized that damage to the BBB caused by microelectrode implantation could facilitate microbiome entry into the brain. In our study, we found bacterial sequences, including gut-related ones, in the brains of mice with implanted microelectrodes. These sequences changed over time. Mice treated with antibiotics showed a reduced presence of these bacteria and had a different inflammatory response, which temporarily improved microelectrode recording performance. However, long-term antibiotic use worsened performance and disrupted neurodegenerative pathways. Many bacterial sequences found were not present in the gut or in unimplanted brains. Together, the current study established a paradigm-shifting mechanism that may contribute to chronic intracortical microelectrode recording performance and affect overall brain health following intracortical microelectrode implantation.

Orally Administrated Precision Nanomedicine for Restoring the Intestinal Barrier and Alleviating Inflammation in Treatment of Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) presents a significant challenge in healthcare, characterized by its chronicity and complex pathogenesis involving genetic, immune, and environmental factors. Current treatment modalities, including anti-inflammatory drugs, immunomodulators, and biologics, often lack sufficient efficacy and are accompanied by adverse effects, necessitating the urgent search for therapeutic approaches targeting mucosal barrier restoration and inflammation modulation. Precision nanomedicine emerges as a promising solution to directly address these challenges. This study introduces the development of a targeted sequential nanomedicine for precise IBD treatment. This innovative formulation combines a prodrug carrier containing quercetin to restore intestinal barrier integrity through the regulation of tight junctions and an anti-inflammatory agent dexamethasone acetate to alleviate inflammation. Surface modification with pectin enables colon-specific drug delivery, facilitated by degradation by colon-specific microbiota. Responsive drug release, controlled by reactive oxygen species-sensitive chemical bonds within the carrier, ensures both spatial and temporal accuracy. In vitro and in vivo investigations confirm the nanomedicine's favorable physicochemical properties, release kinetics, and therapeutic efficacy, elucidating potential underlying mechanisms. Oral administration of the nanomedicine shows promising results in restoring intestinal barrier function, reducing inflammation, and modulating the gut microbiota. Consequently, this study presents a promising nanomedicine candidate for advancing IBD treatment paradigms.

The Impact of Human Salivary Amylase Gene Copy Number and Starch on Oral Biofilms

The copy number (CN) variant AMY1 encodes the salivary amylase enzyme which promotes starch digestion. Although this gene has been associated with dental caries and periodontal disease susceptibility, the impact of the interaction between AMY1 CN and starch on oral biofilms is unclear. We explored how oral microbiota communities shaped by AMY1 CN respond to starch by employing an in vitro model of biofilm formation. We cultured biofilms using saliva samples from 31 donors with a range of AMY1 CNs (between 2 and 20 copies) and self-reported gum disease states; we used media with and without starch. Many of the most prevalent genera in saliva were also prevalent in the derived biofilms. The presence of starch in the media was associated with lower biofilm alpha diversity. We found a significant interaction between AMY1 CN and the media carbohydrate content that influenced the proportions of Atopobium and Veillonella. Members of these genera have been associated with dental caries and periodontitis. These findings suggest that the effects of carbohydrates on oral microbiome composition depend on AMY1 CN and that human oral bacteria evolved in response to expansion of this host gene locus.

The Response Microbial of the Cucumber Rhizosphere Network Keystone Taxa of the Cucumber Rhizosphere to Continuous Fertilization

Fertilization is a common agricultural practice used to modify the physicochemical properties of soil, which in turn affects plant growth and the rhizosphere microbial community. However, the mechanisms underlying the variation in the cucumber rhizosphere microecosystem have not been thoroughly investigated. In this study, we conducted three rounds of continuous plant growth experiments in pots to test different fertilizers and reveal the evolutionary features of the rhizosphere microecosystem. Through topological analysis of the microbial co-occurrence networks, we identified putative taxa associated with fertilization disturbances. Structural equation models (SEMs) predict plausible mechanistic links between soil physicochemical properties, plant growth and the rhizosphere microbiome. The results suggest that continuous fertilization with single fertilizers reduces microbial diversity and may disrupt the structure of the microbial network. Furthermore, it was found that the predicted distribution of keystone taxa (Bacteroidetes, Ascomycota, etc.) was significantly sensitive to the application of certain fertilizers. Moreover, it was modeled by the SEMs that the accumulation of NO3- and Na+ in fertilized soil was one of the putative principal causes of rhizosphere microbial network deterioration. This study provides new insights into the dynamic changes in the cucumber rhizosphere microbial community under continuous fertilization and highlights the potential utility of SEMs in analyzing causal relationships in agroecosystem studies before experimental validation.

Gut microbiota dysbiosis and associated immune response in systemic lupus erythematosus: impact of disease and treatment

BACKGROUND

Gut microbial dysbiosis and leaky gut play a role in systemic lupus erythematosus (SLE). Geographical location and dietary habits affect the microbiome composition in diverse populations. This study explored the gut microbiome dysbiosis, leaky gut, and systemic immune response to gut bacterial consortium in patients with SLE exhibiting mild/moderate and severe disease activity.

METHODS

Fecal and blood samples were collected from patients with SLE and healthy volunteers. Genomic DNA was extracted from the stool samples and subjected to 16S rRNA amplicon sequencing and microbiome profiling. Additionally, enzyme-linked immunosorbent assays were employed to determine the serum lipopolysaccharide level, as an assessment of gut permeability, and the systemic immune response against gut bacteria.

RESULTS

Patients with SLE showed significantly lower gut bacterial richness and diversity, indicated by observed OTUs (56.6 vs. 74.44; p = 0.0289), Shannon (3.05 vs. 3.45; p = 0.017) and Simpson indices (0.91 vs. 0.94; p = 0.033). A lower Firmicutes-to-Bacteroidetes ratio (1.07 vs. 1.69; p = 0.01) was observed, with reduced genera such as Ruminococcus 2 (0.003 vs. 0.026; p = 0.0009) and Agathobacter (0.003 vs. 0.012; p < 0.0001) and elevated Escherichia-Shigella (0.04 vs. 0.006; p < 0.0001) and Bacteroides (0.206 vs. 0.094; p = 0.033). Disease severity was associated with a higher relative abundance of Prevotella (0.001 vs. 0.0001; p = 0.04). Medication effects included lower Romboutsia (0.0009 vs. 0.011; p = 0.005) with azathioprine and higher Prevotella (0.003 vs. 0.0002; p = 0.038) with cyclophosphamide. Furthermore, categorization by prednisolone dosage revealed significantly higher relative abundances of Slackia (0.0007 vs. 0.00002; p = 0.0088), Romboutsia (0.009 vs. 0.002; p = 0.0366), and Comamonas (0.002 vs. 0.00007; p = 0.0249) in patients receiving high-dose prednisolone (> 10 mg/day). No differences in serum lipopolysaccharide levels were found, but SLE patients exhibited elevated serum gut bacterial antibody levels, suggesting a systemic immune response.

CONCLUSION

This study confirms the gut microbiome dysbiosis in patients with SLE, influenced by disease severity and specific medication usage.

Gut Microbiota Alteration with Moderate-to-Vigorous-Intensity Exercise in Middle School Female Football Athletes

BACKGROUND

The gut microbiota significantly influences health and metabolic processes. This study aimed to investigate the impact of exercise intensity on the gut microbiota of middle school female football athletes.

METHODS

In this four-week controlled comparative study, twenty-nine participants were divided into three groups: non-exercise group (NEG), moderate-intensity exercise group (MIEG), and vigorous-intensity exercise group (VIEG). They followed their respective exercise regimens for four weeks. Fecal samples were collected for 16S rRNA gene sequencing to evaluate microbiota composition.

RESULTS

The MIEG exhibited significantly greater microbial diversity compared to the NEG, while the VIEG showed lower diversity than the MIEG. Various microbiota profiles were identified, with the MIEG having higher levels of beneficial bacteria such as Bacteroides.

CONCLUSIONS

Moderate-intensity exercise promotes a healthier gut microbiota compared to vigorous exercise in young female athletes. These findings underscore the potential of moderate exercise to enhance gut health and may inform training strategies for adolescent athletes.

Significant Enrichment of Potential Pathogenic Fungi in Soil Mediated by Flavonoids, Phenolic Acids, and Organic Acids

It is well established that root exudates play a crucial role in shaping the assembly of plant rhizosphere microbial communities. Nonetheless, our understanding of how different types of exudates influence the abundance of potential pathogens in soil remains insufficient. Investigating the effects of root exudates on soil-dwelling pathogenic fungi is imperative for a comprehensive understanding of plant-fungal interactions within soil ecosystems and for maintaining soil health. This study aimed to elucidate the effects of the principal components of root exudates-flavonoids (FLA), phenolic acids (PA), and organic acids (OA)-on soil microbial communities and soil properties, as well as to investigate their mechanisms of action on soil potential pathogenic fungi. The results demonstrated that the addition of these components significantly modified the composition and diversity of soil microbial communities, with OA treatment notably altering the composition of dominant microbial taxa. Furthermore, the introduction of these substances facilitated the proliferation of saprophytic fungi. Additionally, the incorporation of flavonoids, phenolic acids, and organic acids led to an increased abundance of potential pathogenic fungi in the soil, particularly in the FLA and PA treatments. It was observed that the addition of these substances enhanced soil fertility, pH, and antioxidant enzyme activity. Specifically, FLA and PA treatments reduced the abundance of dominant microbial taxa, whereas OA treatment altered the composition of these taxa. These findings suggest that the inclusion of flavonoids, phenolic acids, and organic acids could potentially augment the enrichment of soil potential pathogenic fungi by modulating soil properties and enzymatic activities. These results offer valuable insights into the interactions between plants and fungal communities in soil ecosystems and provide a scientific foundation for the management and maintenance of soil health.

Identification of the saccharifying microbiota based on the absolute quantitative analysis in the batch solid-state fermentation system

The fermentation process of Chinese baijiu, a distinctive example of batch solid-state fermentation (BSSF), involves the recurrent use of the same raw material to optimize starch utilization. However, it is unclear which microorganisms are able to metabolize low concentration starch effectively. In this study, we successfully identified the key saccharifying microbiota that degraded low-concentration starch in the BSSF system by absolute quantification techniques. The results indicated a 61.93 % enhancement in the efficient utilization of starch, absolute quantification combined with correlation analysis revealed that Geotrichum, Aspergillus, Bacillus, Candida, and Kroppenstedtia were the saccharifying microbiota, with relative abundances exceeding 10 % during fermentation. In the KEGG metabolic pathway, these five saccharifying microbiota had a complete metabolic pathway for degrading starch to d-glucose-1p and d-glucose, including eight related enzymes: maltose phosphorylase, α-amylase, glucoamylase, oligo-1,6-glucosidase, α-glucosidase, pullulanase, α-glucosidase, and maltogenic α-amylase. These studies showed that the saccharifying microbiota can co-degrade starch by multiple saccharifying enzymes, thus improving the utilization of starch substrates.

Gut Microbiota and Neurotransmitter Regulation: Functional Effects of Four Traditional Chinese Fermented Soybean (Sojae Semen Praeparatum)

This study aims to evaluate the potential disease prevention and treatment functions of four types of traditional Chinese fermented Sojae Semen Praeparatum (SSP) by analyzing their nutritional active components and their effects on the gut microbiota. Raw soybeans and the four SSPs were administered as dietary supplements to normal SD rats for 6 weeks. Fecal samples were collected at weeks 0, 2, and 6 to assess changes in the gut microbiota. Our results revealed that different fermentation methods resulted in variations in soybean isoflavone content. Fermented soybeans promoted the growth of beneficial microorganisms associated with short-chain fatty acid production in the gut microbiota, such as Christensenellaceae_R_7_group, compared to unfermented soybeans. Supplementation with SSPs fermented with different processes increased the diversity of the rat gut microbiota, except for the fermented group of qingwenjiedu decoction (QW). The dominant gut microbiota in the fermented group of Artemisia Annuae Herba and Mori Folium (QS) exhibited anti-inflammatory effects, while the dominant gut microbiota in the fermented group of Ephedrae Herba and Perillae Folium (MZ) showed antidepressant effects. In the neurotransmitter analysis, MZ reduced gamma-aminobutyric acid (GABA) levels, the fermented group without Chinese medicine (DD) decreased dopamine levels, and both QS and QW increased norepinephrine levels. Correlation analysis highlighted connections between gut microbiota, neurotransmitters, and chemical levels. The results indicate that SSPs may contribute uniquely to health by maintaining intestinal balance and improving neurological disorders while predicting a potential association between neurotransmitters and gut microbiota by correlation analysis.

A dataset of prokaryotic diversity in the surface layer of the China Seas

Coastal and nearshore zones, severing as a connection between the land and the open ocean, are some of the most productive and complex ecosystems, where prokaryotes are abundant and highly diverse. However, the systematic study of the diversity of prokaryotes on a large-scale range in coastal and nearshore zones is limited due to scattered sampling sites, various sampling collection methods, and different data processing methods across various studies. Here, we provide a dataset of 16S rRNA gene sequences obtained from the surface water samples across the China Seas, including the Bohai Sea, the Yellow Sea, the East China Sea, and the South China Sea. The dataset comprises 1,194 samples collected through field sampling and literature search. A total of 30,308 operational taxonomic units clustered at 97% sequence identity were obtained. Sixty-five bacterial and nine archaeal phyla were identified. This dataset offers a basic understanding of prokaryotic diversity in the China Seas, also provides a foundation for in-depth investigations into prokaryotic distribution across different regions and their interactions in various environments.

Bacterial community in the hyphosphere of an arbuscular mycorrhizal fungus differs from that in the surrounding environment and is influenced by hyphal disruption

Bacterial composition and functions in the hyphosphere of arbuscular mycorrhizal (AM) fungi are complex because AM fungal hyphae transport carbon compounds from plant photosynthesis which feed bacteria and act as signaling molecules. This function is lost when hyphae separate from roots, a common occurrence in soil. However, the impact of such disturbances on hyphal surface bacteria remains unclear. We used in vitro bi-compartmented Petri plates with carrot roots and the AM fungus Rhizophagus irregularis MUCL 43194, separating root and hyphal compartments. Treatments included hyphae connected to roots (+ AM), no hyphae (-AM), and hyphae cut at different times (C3D and C0D, where C3D indicates hyphae cut 3 days before inoculation and C0D indicates hyphae cut on the day of inoculation) subjected to a bacterial suspension extracted from a field soil. Thirteen bacterial phyla were identified, with Streptomyces, Pseudomonas, Rhodococcus, and Cellulomonas dominating. Hyphae increased bacterial ASV relative abundance, notably enriching Actinobacteria ASVs. After 14 days, α-diversity decreased from -AM to C3D, C0D, and + AM, with fewer Bacteroidetes species in + AM compared to -AM. Root-connected hyphae led to deterministic bacterial assembly, while cut hyphae resulted in stochastic assembly. Our findings show that physical disruption of hyphae significantly affects bacterial diversity and may influence ecological functions.

The biodegradable polymer poly(butylene succinate-co-adipate) modulates the community structures of actively growing bacteria in rotifer culture water

The production efficiency of rotifers, representing a crucial feed for fish larvae, is a key factor determining fish production in aquaculture. Poly(butylene succinate-co-adipate) (PBSA) is a biodegradable polymer that enhances rotifer growth, but its effect on bacterial composition remains unknown. This study was aimed to investigate changes in the structure and function of actively growing bacterial communities in rotifer culture water after PBSA treatment. PBSA induced rapid changes in water quality, including elevated organic carbon levels, decreased pH, and increased in bacterial abundance and respiration, suggesting the elution of oligomers and monomers. Consequently, these conditions led to the increased prevalence of certain actively growing bacterial families, notably Alteromonadaceae and Hyphomonadaceae, compared with that in water without PBSA, which persisted throughout the experiment. Moreover, a decrease in ammonium concentrations was observed after PBSA treatment. As functions predicted using PICRUSt2 indicated that bacteria influenced by PBSA were unlikely to directly contribute to nitrogen conversion processes such as nitrification, denitrification, and nitrogen fixation, this observation was attributed to enhanced bacterial assimilation. These findings help elucidate how PBSA enhances rotifer production, highlighting the importance of considering the functional roles of the potential microbial consortium created by PBSA to optimize its use in seed production.

The influence of carbon dioxide on fermentation products, microbial community, and functional gene in food waste fermentation with uncontrol pH

Food waste is a major problem faced by human beings. Acidogenic fermentation is an effective and feasible technology for resource recovery from food waste. The mixture of volatile fatty acids (VFAs) hinders the utilization of fermentation products. In this study, we constructed fermentation reactors for food waste treatment. The operation period was separated to three stages: Stage 1 (from day 1-102), Stage 2 (from day 103-208), and Stage 3 (from day 209-304). CO2 was sparged to the reactors to promote the acetate enrichment at Stage 3. Bioinformatics analysis were performed to analyze the microbial community, genes, and pathways. Results showed that the highest average concentration of acetate was 6044 mg-COD/L (R1) and 5000 mg-COD/L (R2) at Stage 3, which was corresponded to the stage with highest acetate ratio (63% and 66% in R1 and R2). But the highest total VFAs concentration was 39424 mg-COD/L at Stage 2. Aeriscardovia belonging to Actinobacteria had an average relative abundance of 85.7% after CO2 sparging. Compared with Stage 1 and Stage 2, the number of down-regulated genes and pathways at Stage 3 were much higher than the number of up-regulated genes and pathways. The significant down-regulated genes were wcaB and ttrC, and the significant down-regulated pathways were pyruvate fermentation to acetone and acetyl-CoA fermentation to butanoate II pathway. This study demonstrated that CO2 can promote the acetate enrichment during food waste fermentation. The main mechanism was enriching acetate fermentation microorganisms and inhibiting the interfere genes and pathways.

Effects of Monascus pilosus SWM 008-Fermented Red Mold Rice and Its Functional Components on Gut Microbiota and Metabolic Health in Rats

Red mold rice, fermented by Monascus spp., has been reported to modulate gut microbiota composition and improve metabolic health. Previous studies indicate that red mold rice can reduce cholesterol, inhibit hepatic lipid accumulation, and enhance bile acid excretion, while also altering gut microbiota under high-fat dietary conditions. However, it remains unclear whether these effects are directly due to Monascus-derived products modulating gut microbiota or are a consequence of improved metabolic health conditions, which indirectly influence gut microbiota. This study aimed to evaluate the effects of Monascus pilosus SWM 008 fermented red mold rice and its components-monascin, monascinol, ankaflavin, and polysaccharides-on gut microbiota and metabolic health in rats fed a normal diet. Over eight weeks, physiological, biochemical, and gut microbiota parameters were assessed. Results showed no significant changes in body weight or liver/kidney function, confirming safety. Gut microbiota analysis revealed that red mold rice, monascin, monascinol, and polysaccharides significantly altered gut microbiota composition by increasing the relative abundance of beneficial bacteria, such as Akkermansia muciniphila, Ligilactobacillus murinus, and Duncaniella dubosii. Functional predictions indicated enhanced vitamin K2 biosynthesis, nucleotide metabolism, and other metabolic pathways linked to improved gut health. In conclusion, Monascus pilosus SWM 008 fermented red mold rice demonstrated safety and beneficial effects, suggesting its potential as a functional food to maintain gut microbiota balance under normal dietary conditions.

Gut Microbiota Metabolites Sensed by Host GPR41/43 Protect Against Hypertension

BACKGROUND

Fermentation of dietary fiber by the gut microbiota leads to the production of metabolites called short-chain fatty acids, which lower blood pressure and exert cardioprotective effects. Short-chain fatty acids activate host signaling responses via the functionally redundant receptors GPR41 (G-protein-coupled receptor 41) and GPR43 (G-protein-coupled receptor 43), which are highly expressed by immune cells. Whether and how these receptors protect against hypertension or mediate the cardioprotective effects of dietary fiber remains unknown.

METHODS

Cardiovascular phenotype was assessed in untreated and Ang II (angiotensin II) treated hypertensive wild-type and GPR41/43 knockout (KO) double knockout male mice fed diets with different levels of fiber content. Some mice received TLR4 (toll-like receptor 4)-antagonist treatment and bone marrow chimeras. SNPs (single-nucleotide polymorphisms) associated with GPR41 and GPR43 expression were assessed in UK Biobank participants.

RESULTS

Untreated GPR41/43KO mice had unaltered blood pressure but had greater cardiac and renal collagen deposition with higher macrophage numbers in the kidney compared with wild-type mice. Ang II-treated GPR41/43KO mice showed higher systolic blood pressure, cardiorenal weights and collagen deposition, and increased gut permeability, which allows the translocation of gastrointestinal bacterial components such as lipopolysaccharides into the circulation. The use of an antagonist to the lipopolysaccharide receptor, TLR4, a potent proinflammatory signaling molecule, restored the cardiovascular phenotype in GPR41/43KO mice. The lack of GPR41/43 expression in the immune compartment was sufficient to lead to a worsened hypertensive phenotype. We also demonstrate that GPR41/43 is, at least partially, responsible for the blood pressure-lowering and cardioprotective effects of a high-fiber diet. Finally, using the UK Biobank, we provide translational evidence that variants associated with lower expression of both GPR41 and GPR43 are more prevalent in participants with hypertension.

CONCLUSIONS

Our findings highlight that lack of short-chain fatty acid-receptor signaling via both GPR41 and GPR43 increases risk of high blood pressure, suggesting treatments that target these receptors could be a novel strategy to prevent or treat hypertension.

Bacterial profiles of the oral, vaginal, and rectal mucosa and colostrum of periparturient sows

The commensal microbiota influences the health, feeding efficiency, and reproductive performance of sows. The microbiota composition in the alimentary and genitourinary tracts and in colostrum/milk during pregnancy and lactation also impacts the microbiota and immune system, growth, and health of the piglets. Knowledge of the microbial compositions is important for evaluation of these effects and for discovering ways to improve the health and productivity of the sows. Oral, vaginal, and rectal mucosa and colostrum were sampled from 32 sows of variable parity in late pregnancy, and colostrum within 6 hours of delivery of the first piglet, on four commercial piglet-producing farms in Finland. Microbial compositions were analyzed by 16S rRNA gene amplicon sequencing. The most abundant genera of the oral microbiota were Rothia, Moraxella, and Streptococcus. The rectal microbiota was dominated by Clostridium sensu stricto 1. Streptococcus was the most abundant genus in the vagina and colostrum. Moderate differences in diversity and composition were observed between farms. The relative abundances of the genera Neisseria (MaAsLin 2 q = 0.002, ANCOMBC q = 0.005), Fusobacterium (MaAsLin 2 q = 0.008, ANCOMBC q = 0.04) and Bacteroides (MaAsLin 2 q < 0.005, ANCOMBC q = 0.06) were lower in oral samples and Romboutsia (MaAsLin 2 q = 0.07, ANCOMBC q = 0.05), Turicibacter (MaAsLin 2 q = 0.08, ANCOMBC q = 0.02) and Lachnospiraceae_UCG_007 (MaAsLin 2 q = 0.1, ANCOMBC q = 0.05) were higher in rectal samples of multiparous compared to primiparous sows. In vaginal samples there was a tendency of higher relative abundances of the genera Fusobacterium and Streptococcus in multiparous than primiparous sows. Among the differentially abundant taxa, F. necrophorum and F. nucleatum were identified in oral samples, F. gastrosuis and F. necrophorum in vaginal samples, and S. dysgalactiae in colostrum samples. This study provides a comprehensive overview of the mucosal and colostrum microbiota of periparturient sows during normal production conditions on Finnish commercial farms.

Psychobiotic Protection of Nutritional Supplements and Probiotics in Patients Undergoing Hemodialysis: A Randomized Trial

BACKGROUND/OBJECTIVES

The prevalence of depression and anxiety symptoms is remarkably high in malnourished individuals undergoing hemodialysis. The goal of this project was to evaluate the impact of administering an oral nutritional supplement combined with a probiotic blend on the microbiota, intestinal permeability, and depression symptoms in malnourished hemodialysis patients.

METHODS

With this aim, a randomized trial was conducted with three parallel groups: a control group with individualized diet, a supplement-placebo (SU-PL) group with oral nutritional supplementation (ONS), and a supplement-probiotic (SU-PR) group with ONS in conjunction with a probiotic blend. Blood and fecal samples were collected at basal time, and at 3 and 6 months. Several blood biomarkers, like zonulin, lipopolysaccharide-binding protein (LBP), lipopolysaccharide (LPS), and brain-derived neurotrophic factor (BDNF), were measured, and the fecal microbiome was sequenced with the Illumina platform. The Hospital Anxiety and Depression Scale (HADS) was used for the estimation of depression (HADS-D) and anxiety (HADS-A) symptoms, along with the standardized mental health index SF12-MH from the general health questionnaire SF-12.

RESULTS

The results showed that patients who consumed the probiotic blend maintained the LPS levels from their baseline readings and decreased their BDNF levels compared to the SU-PL or control groups. Moreover, a significant decrease in HADS-D scores (less depressive symptoms) and an increase in SF12-MH scores (higher quality of life) were found in that group in comparison to the other groups. The intervention produced an impact on the microbiome population, where the SU-PR group had reduced Akkermansia abundance with respect to the other groups, while their Acidaminococcus abundance decreased and their Barnesiella abundance increased with respect to the SU-PL group.

CONCLUSIONS

Overall, the results indicate that the probiotic with the nutritional supplement could reduce the intestinal permeability biomarkers and improve depressive symptoms and quality of life in malnourished hemodialysis patients.

phylotypr: an R package for classifying DNA sequences

The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.

The role of gut microbiota at different developmental stages in the adaptation of the Etiella zinckenella to a plant host

Insect gut symbiotic microbiota play a crucial role in the nutritional, physiological, and behavioral aspects of their hosts, providing valuable insights for investigating the co-evolution of insects and plants. Sophora alopecuroides L. serves as an important windbreak plant, while Etiella zinckenella is a major pest that infests its seeds. However, the structure of the gut microbiota community in E. zinckenella remains poorly understood. In this study, we analyzed the gut microbiota of E. zinckenella across different developmental stages-larvae (1st-5th instars), pupae, and adults-infesting S. alopecuroides using 16 S rRNA high-throughput sequencing. The results revealed that the dominant phyla throughout the development of E. zinckenella were Proteobacteria and Bacteroidota, although the dominant genera varied significantly across stages. Diversity analysis of gut microbiota at different developmental stages indicated that microbial diversity was significantly higher in the larval stage compared to the pupal and adult stages. Functional predictions further highlighted the richness of metabolic pathways within the gut microbiota of E. zinckenella. Notably, carbohydrate metabolism functions were significantly more abundant during the larval stage, while lipid metabolism functions were substantially lower. Our findings demonstrate dynamic changes in the composition and diversity of the gut microbiota across the developmental stages of E. zinckenella, underscoring the critical roles of these bacteria during specific stages of the insect's life cycle. This study lays the groundwork for future strategies aimed at controlling E. zinckenella through modulation of its gut microbiota, offering significant theoretical implications.

The Promoting Effects of Fermented Bile Acid on Growth Performance and Intestinal Health of Litopenaeus vannamei Through the Modulation of Lipid Metabolism and Gut Microbiota

Two types of bile acids (BAs), named fermented bile acids (FBAs) and 170HDa, were produced by a biological approach to assess their effects on growth performance, metabolism, and intestinal health in white shrimp. In this study, five experimental diets were prepared with varying levels of FBAs (0.02% for A1, 0.03% for A2, 0.04% for A3, 0.05% for A4, and 0.06% for A5) and five diets containing different concentrations of 170HDa (0.02% for B1, 0.03% for B2, 0.04% for B3, 0.05% for B4, and 0.06% for B5). Additionally, positive diets (P) with commercial BAs at a level of 0.04%, along with and negative diet (N) without BA supplementation, were included as controls. FBAs and 170HDa were found to improve the growth performance including final weight, weight gain, and specific growth rate and reduce the activities of aspartate aminotransferase and alanine aminotransferase in hemolymph. The alkaline phosphatase (AKP) activity of hemolymph in shrimp treated with FBAs was generally higher than in groups treated with 170HDa and the control groups. However, the acid phosphatase (ACP) activity of hemolymph in shrimp treated with FBAs showed similar levels to those treated with 170HDa and the control groups. The gene expression levels of antilipopolysaccharride factor (ALF) and proPO were significantly lower in most FBAs and 170HDa-treated groups compared to the control groups (p < 0.05). Additionally, the gene expression levels of α2M in hepatopancreas were significantly higher in the 170HDa-treated groups compared to those in the FBAs-treated group (p < 0.05). The FBAs and 170HDa significantly enhanced the intestinal health by boosting the proinflammatory capacity and increasing the diversity of the intestinal microbiota, thereby combating pathogenic microorganisms. Notably, there was a significant increase (p < 0.05) in the abundance of Proteobacteria, Firmicutes, Tenericutes, and Cyanobacteria at the phylum level, as well as Vibrio, Rhodobacter, and Shewanella at the genus level, respectively. These findings indicate that dietary FBAs and 170HDa have positive effects on growth performance and intestinal health by modulating lipid metabolic profiles, immune responses, the integrity of intestinal wall, and the diversity of intestinal microbes in white shrimp. This study suggests that FBAs and 170HDa could serve as effective dietary supplements to enhance shrimp production and health management in aquaculture, providing a promising strategy for sustainable aquaculture practices.

Gut microbiome and immune checkpoint inhibitor toxicity

BACKGROUND

Multiple studies have suggested that gut microbiome may influence immune checkpoint inhibitor (ICI) efficacy, but its association with immune-related adverse events (irAEs) is less well studied. In this prospective cohort study, we assessed whether gut microbiome composition at start, or changes during ICI, are associated with severe irAEs.

METHODS

Stool samples of cancer patients treated with anti-PD-1 ± anti-CTLA-4 were analyzed using 16S rRNA gene sequencing and metagenomic shotgun sequencing. Differences in alpha and beta diversity between patients with and without severe irAE were assessed, as well as differential relative abundance (RA) of taxa, MetaCyc pathways, and seven prespecified literature-based bacterial groups including pathobionts and Ruminococcaceae.

FINDINGS

We analyzed 497 samples of 195 patients before and soon after starting ICI, at severe irAE onset and after starting immunosuppression. Mean RA of the pathobionts group was significantly higher in patients who developed a severe irAE (8.2 %) compared to those who did not (4.8 %; odds ratio 1.40; 95 %CI 1.07-1.87) at baseline, and also early during ICI treatment and at severe irAE onset. A significantly stronger decrease in RA of Ruminococcaceae after starting ICI was observed in patients who developed a severe irAE compared to those who did not. RAs of Ruminococcaceae, the genus Ruminococcus, and the species R. bromii and R. callidus were significantly lower at severe irAE onset compared to other time points.

INTERPRETATION

Gut microbiome dysbiosis signaled by higher RA of pathobionts and decrease in RA of Ruminococcaceae may predispose to severe irAEs.

Multi-level analysis of gut microbiome extracellular vesicles-host interaction reveals a connection to gut-brain axis signaling

Microbiota-released extracellular vesicles (MEVs) have emerged as a key player in intercellular signaling. However, their involvement in the gut-brain axis has been poorly investigated. We hypothesize that MEVs cross host cellular barriers and deliver their cargoes of bioactive compounds to the brain. In this study, we aimed to investigate the cargo capacity of MEVs for bioactive metabolites and their interactions with the host cellular barriers. First, we conducted a multi-omics profiling of MEVs' contents from ex vivo and stool samples. Metabolomics analysis identified various neuro-related compounds encapsulated within MEVs, such as arachidonyl-dopamine, gabapentin, glutamate, and N-acylethanolamines. Metaproteomics unveiled an enrichment of enzymes involved in neuronal metabolism, primarily in the glutamine/glutamate/gamma-aminobutyric acid (GABA) pathway. These neuro-related proteins and metabolites were correlated with Bacteroides spp. We isolated 18 Bacteroides strains and assessed their GABA production capacity in extracellular vesicles (EVs) and culture supernatant. A GABA-producing Bacteroides finegoldii, released EVs with a high GABA content (4 µM) compared to Phocaeicola massiliensis. Upon testing the capacity of MEVs to cross host barriers, MEVs exhibited a dose-dependent paracellular transport and were endocytosed by Caco-2 and hCMEC/D3 cells. Exposure of Caco-2 cells to MEVs did not alter expression of genes related to intestinal barrier integrity, while affected immune pathways and cell apoptosis process as revealed by RNA-seq analyses. In vivo, MEVs biodistributed across mice organs, including the brain, liver, stomach, and spleen. Our results highlight the ability of MEVs to cross the intestinal and blood-brain barriers to deliver their cargoes to distant organs, with potential implication for the gut-brain axis.

IMPORTANCE

Microbiota-released extracellular vesicles (MEVs) have emerged as a key player in intercellular signaling. In this study, a multi-level analysis revealed presence of a diverse array of biologically active molecules encapsulated within MEVs, including neuroactive metabolites, such as arachidonyl-dopamine, gabapentin, glutamate, and N-acylethanolamines, and gamma-aminobutyric acid (GABA). Metaproteomics also unveiled an enrichment of neural-related proteins, mainly the glutamine/glutamate/GABA pathway. MEVs were able to cross epithelial and blood-brain barriers in vitro. RNA-seq analyses showed that MEVs stimulate several immune pathways while suppressing cell apoptosis process. Furthermore, MEVs were able to traverse the intestinal barriers and reach distal organs, including the brain, thereby potentially influencing brain functionality and contributing to mental and behavior.

Quantitative profiling of the vaginal microbiota improves resolution of the microbiota-immune axis

BACKGROUND

The composition of the vaginal microbiota is closely linked to adverse sexual and reproductive health outcomes, due in part to effects on genital immunology. Compositional approaches such as metagenomic sequencing provide a snapshot of all bacteria in a sample and have become the standard for characterizing the vaginal microbiota, but only provide microbial relative abundances. We hypothesized that the addition of absolute abundance data would provide a more complete picture of host-microbe interactions in the female genital tract.

RESULTS

We analyzed cervicovaginal secretions from 196 female sex workers in Kenya and found that bacterial load was elevated among women with diverse, bacterial vaginosis (BV)-type microbiota and lower among women with Lactobacillus predominance. Bacterial load was also positively associated with proinflammatory cytokines, such as IL-1α, and negatively associated with chemokines, such as IP-10. The associations between bacterial load and immune factors differed across bacterial community states, but L. crispatus predominance was the only microbial community where higher bacterial load was not associated with higher proinflammatory cytokines. Total vaginal bacterial load was also a stronger predictor of the genital immune environment than BV by Nugent score, the current clinical standard, in the Kenya-based cohort and in a Uganda-based confirmatory cohort.

CONCLUSIONS

Our results suggest that total vaginal bacterial load is at least as strong a predictor of the genital immune milieu as current BV clinical diagnostic tools, supporting exploration of the vaginal bacterial load as a predictor of adverse reproductive and sexual health outcomes. Video Abstract.

Metabarcoding expands knowledge on diversity and ecology of rare actinobacteria in the Brazilian Cerrado

Rare and unknown actinobacteria from unexplored environments have the potential to produce new bioactive molecules. This study aimed to use 16 s rRNA metabarcoding to determine the composition of the actinobacterial community, particularly focusing on rare and undescribed species, in a nature reserve within the Brazilian Cerrado called Sete Cidades National Park. Since this is an inaccessible area without due legal authorization, it is understudied, and, therefore, its diversity and biotechnological potential are not yet fully understood, and it may harbor species with groundbreaking genetic potential. In total, 543 operational taxonomic units (OTUs) across 14 phyla were detected, with Actinobacteria (41.2%), Proteobacteria (26.5%), and Acidobacteria (14.3%) being the most abundant. Within Actinobacteria, 107 OTUs were found, primarily from the families Mycobacteriaceae, Pseudonocardiaceae, and Streptomycetaceae. Mycobacterium and Streptomyces were the predominant genera across all samples. Seventeen rare OTUs with relative abundance < 0.1% were identified, with 82.3% found in only one sample yet 25.5% detected in all units. Notable rare and transient genera included Salinibacterium, Nocardia, Actinomycetospora_01, Saccharopolyspora, Sporichthya, and Nonomuraea. The high diversity and distribution of Actinobacteria OTUs indicate the area's potential for discovering new rare species. Intensified prospection on underexplored environments and characterization of their actinobacterial diversity could lead to the discovery of new species capable of generating innovative natural products.

Isolation, characterization of Bacillus subtilis and Bacillus amyloliquefaciens and validation of the potential probiotic efficacy on growth, immunity, and gut microbiota in hybrid sturgeon (Acipenser baerii ♀ × Acipenser schrenckii ♂)

Probiotics are increasingly considered as an alternative to antibiotics in developing environmentally sustainable aquaculture practices. Hybrid sturgeon (Acipenser baerii ♀ × Acipenser schrenckii ♂), a globally popular species valued for its nutritional content and caviar, has limited research on host-associated probiotics. In this study, we isolated and identified Bacillus subtilis and Bacillus amyloliquefaciens from healthy hybrid sturgeon and assessed their impact on growth, immunity, gut microbiota, and transcriptome following an 8-week feeding trial. The isolated strains demonstrated strong production of protease, amylase, lipase, and cellulase, along with broad-spectrum pathogen inhibition, including Aeromonas veronii, Aeromonas sobria, and Yersinia ruckeri. Supplementation with B. subtilis and B. amyloliquefaciens significantly improved growth performance and increased survival rates against A. veronii infection. Mechanistically, probiotics altered gut microbiota composition, enhancing digestive functions. Transcriptome analysis further revealed that probiotic supplementation boosted immune response and protein digestion and absorption. These findings suggest that B. subtilis and B. amyloliquefaciens are promising probiotic candidates for the hybrid sturgeon industry, offering effective protection against A. veronii infection.

Physicochemical and isotopic similarity between well water and intruding surface water is not synonymous with similarity in prokaryotic diversity and community composition

Intruding surface water can impact the physicochemical and microbiological quality of groundwater. Understanding these impacts is important because groundwater provides much of the world's potable water, and reduced quality is a potential public health risk. In this study, we monitored six shallow groundwater wells and three surface water bodies in the North Ostrobothnia region of Finland twice monthly for 12 months (October 2021-October 2022) via (i) on-site and off-site measurements of physicochemical water quality parameters, (ii) determination of stable water isotope compositions, and (iii) analysis of microbial communities (via amplicon sequencing of the V3-V4 16S rRNA gene sub-regions). Water from one well showed clear overall physicochemical and isotopic similarity with a nearby pond, as well as temporal fluctuations in water temperature and isotopes that mirrored those of the pond. Isotope mixing analyses suggested that about 80-95 % of the well water comes from the pond. Such large-scale intrusion might be expected to reduce prokaryotic diversity and composition in the aquifer, either by strong influx of surface water taxa or changes to aquifer physicochemistry. Compared to the pond, however, prokaryotic communities from the well showed significantly higher alpha diversity and a composition more similar to a nearby well unaffected by intrusion. The finding that physicochemical and isotopic similarity between well water and intruding surface water is not synonymous with similarity in prokaryotic diversity and community composition makes clear the need for a multi-method approach when studying the impact of surface water intrusion on shallow wells.

The spatiotemporal variations of marine nematode populations may serve as indicators of changes in marine ecosystems

The volcanic island, Kueishan Island, harbors two unique shallow-water ecosystems: hydrothermal vents and coral communities. The unique geologic features render the island an ideal place as a spectrum for studying two different ecosystems and mimicking the impacts of climate change on coral reef biota in the future. However, little is known about the meiofauna community there. Hence, we investigated the diversity and composition of free-living marine nematodes over two years by collecting individuals from sediments sampled across a gradient of habitats, including hydrothermal vents, buffering sites, and coral reefs. During the first year, we also monitored abiotic factors, such as sediment and water properties, along with biotic factors, including bacterial diversity assessed through amplicon sequencing, to evaluate their influence on the nematode community. Our findings revealed markedly low nematode abundance and diversity at sulfide-rich vent sites (abundance < 5 ind./L; Shannon index < 1) throughout the study period, contrasting with the highest levels observed at the coral community site (<165.4 ind./L, Shannon index = 1.65). The food supply seemed to be the main factor that drove the difference, as nematode abundance and diversity increased with sedimentary total organic carbon and bacterial diversity. In addition, significant differences in nematode composition were observed between the different sampling sites. Combined with nematode and microbiome data, the buffering site that endured more stress from vent activities was recognized. Our results suggest that the dynamics of nematode communities could be incorporated into projects assessing environmental impacts on coral reef ecosystems.

Fecal Microbiota Transplantation (FMT) From a Human at Low Risk for Alzheimer's Disease Improves Short-Term Recognition Memory and Increases Neuroinflammation in a 3xTg AD Mouse Model

Human microbiota-associated murine models, using fecal microbiota transplantation (FMT) from human donors, help explore the microbiome's role in diseases like Alzheimer's disease (AD). This study examines how gut bacteria from donors with protective factors against AD influence behavior and brain pathology in an AD mouse model. Female 3xTgAD mice received weekly FMT for 2 months from (i) an 80-year-old AD patient (AD-FMT), (ii) a cognitively healthy 73-year-old with the protective APOEe2 allele (APOEe2-FMT), (iii) a 22-year-old healthy donor (Young-FMT), and (iv) untreated mice (Mice-FMT). Behavioral assessments included novel object recognition (NOR), Y-maze, open-field, and elevated plus maze tests; brain pathology (amyloid and tau), neuroinflammation (in situ autoradiography of the 18 kDa translocator protein in the hippocampus); and gut microbiota were analyzed. APOEe2-FMT improved short-term memory in the NOR test compared to AD-FMT, without significant changes in other behavioral tests. This was associated with increased neuroinflammation in the hippocampus, but no effect was detected on brain amyloidosis and tauopathy. Specific genera, such as Parabacteroides and Prevotellaceae_UGC001, were enriched in the APOEe2-FMT group and associated with neuroinflammation, while genera like Desulfovibrio were reduced and linked to decreased neuroinflammation. Gut microbiota from a donor with a protective factor against AD improved short-term memory and induced neuroinflammation in regions strategic to AD. The association of several genera with neuroinflammation in the APOEe2-FMT group suggests a collegial effect of the transplanted microbiome rather than a single-microbe driver effect. These data support an association between gut bacteria, glial cell activation, and cognitive function in AD.

A Pilot Study Characterization of the Scalp Microbiome in Central Centrifugal Cicatricial Alopecia Shows Shift in Corynebacterium

Introduction

Aberrant fibrosis in central centrifugal cicatricial alopecia (CCCA) is thought to be driven by persistent low-grade inflammation, but the source of inflammation is unclear. Alterations in the scalp microbiota may contribute to inflammation and thus provide a target for therapeutic intervention. We sought to compare the bacterial and fungal cutaneous scalp microbiota in patients with CCCA versus controls.

Methods

Six patients with CCCA and seven controls were sampled at the vertex scalp. 16S rRNA sequencing of V3-V4 region and internal transcribed spacer amplicon sequencing was used to compare bacterial and fungal microbiomes.

Results

A significantly higher relative abundance of Corynebacterium was noted in patients with CCCA versus controls. No significant difference in scalp fungal or bacterial microbiota composition was observed.

Limitations

V3-V4 sequencing can be limited in detection of major skin bacterial species.

Conclusion

CCCA is characterized by a distinct bacterial microbiome community and high relative abundances of Corynebacterium. Future studies should characterize the relationship between Corynebacterium and scalp inflammation and the role it may play in the progression of CCCA.

Nonselective beta blockade enhances gut microbiome diversity in a rodent model of trauma, hemorrhage, and chronic stress

BACKGROUND

Traumatic injury leads to gut dysbiosis with changes in microbiome diversity and conversion toward a "pathobiome" signature characterized by a selective overabundance of pathogenic bacteria. The use of non-selective beta antagonism in trauma patients has been established as a useful adjunct to reduce systemic inflammation. We sought to investigate whether beta-adrenergic blockade following trauma would prevent the conversion of microbiome to a "pathobiome" phenotype.

METHODS

Sprague-Dawley rats (n = 6-8/group) were subjected to routine daily handling (naïve), lung contusion with hemorrhagic shock (LCHS), or LCHS with daily chronic stress (LCHS/CS), each with or without administration of intraperitoneal propranolol (BB) (10 mg/kg/day). Fecal microbiome was measured on Days 0, 7, and 14 using high-throughput 16S rRNA sequencing and QIIME2 bioinformatics analyses. Alpha- and beta-diversity and microbiome composition were assessed with significance defined as * p < 0.05.

RESULTS

Use of propranolol following LCHS or LCHS/CS demonstrated a significant increase in the number of bacterial species (Chao1 index), as well as overall richness and evenness (Shannon index) compared with their untreated counterparts at Day 7. By Day 14, these differences were no longer apparent between BB and untreated groups subjected to LCHS/CS. There was an abundance of commensal bacteria such as Oscillospiraceae and Clostridia in LCHS and LCHS/CS treated with BB after 7 days which persisted at 14 days.

CONCLUSION

These findings suggest a role for beta-antagonism in altering the diversity of the gut microbiome and the need for further studies to elucidate the cellular and molecular mechanisms underlying this intriguing connection of microbiome with trauma and beta-blockade.

Levofloxacin Prophylaxis in Pediatric and Young Adult Allogeneic Hematopoietic Stem Cell Transplantation Recipients Does not Prevent Infective Complications and Infections-related Deaths

Background

The prophylactic use of quinolones in the setting of allogeneic hematopoietic stem cell transplantation (allo-HCT) is controversial and solid evidence is missing, particularly in children.

Methods

In this single-center retrospective study, we compared outcomes in patients receiving (n = 74) or not receiving (n = 70) levofloxacin (LVX) prophylaxis, assessing overall survival, event-free survival, acute graft-versus-host disease (aGvHD) and bloodstream infection incidence, and infection-related mortality. Gut microbiota composition was analyzed in a subgroup using 16S rRNA sequencing of stool samples collected pre-HCT and at engraftment.

Results

We analyzed 144 allo-HCT in 143 patients performed for any indication. No differences were found in the 2 groups regarding main HCT outcomes, namely, cumulative incidence of aGvHD (37.9% vs 43.5%; P = .733), grade III-IV aGvHD (12.2% vs 8.7%; P = .469), gut aGVHD (12.2% vs 17.5%; P = .451), bloodstream infections (25.6% vs 34.1%; P = .236) and death from bacterial infection (9.5% vs 4.3%; P = 0.179). In patients experiencing bacterial infections, those receiving prophylaxis showed higher incidence of quinolone-resistant strains (P = .001). On a subgroup of 50 patients, we analyzed the gut microbiota composition, showing a lower abundance of Blautia (P = .015), Enterococcus (P = .011), and Actinomyces (P = .07) at neutrophil engraftment in patients receiving LVX prophylaxis.

Conclusions

LVX prophylaxis in the setting of allo-HCT does not prevent infective complications and increases the prevalence of antibiotic-resistant strains.

The relative importance of host phylogeny and dietary convergence in shaping the bacterial communities hosted by several Sonoran Desert Drosophila species

Complex eukaryotes vary greatly in the mode and extent that their evolutionary histories have been shaped by the microbial communities that they host. A general understanding of the evolutionary consequences of host-microbe symbioses requires that we understand the relative importance of host phylogenetic divergence and other ecological processes in shaping variation in host-associated microbial communities. To contribute to this understanding, we described the bacterial communities hosted by several Drosophila species native to the Sonoran Desert of North America. Our sampling consisted of four species that span multiple dietary shifts to cactophily, as well as the dietary generalist D. melanogaster, allowing us to partition the influences of host phylogeny and extant ecology. We found that bacterial communities were compositionally indistinguishable when considering incidence only but varied when considering the relative abundances of bacterial taxa. Variation in community composition was not explained by host phylogenetic divergence but could be partially explained by dietary variation. In support of the important role of diet as a source of ecological selection, we found that specialist cactophilic Drosophila deviated more from neutral predictions than dietary generalists. Overall, our findings provide insight into the evolutionary and ecological factors that shape host-associated microbial communities in a natural context.

The microbial co-infection interaction network in apical periodontitis with sinus tracts

OBJECTIVES

This study aims to characterize the bacterial co-occurrence features and potential interactions associated with the presence of sinus tracts in apical periodontitis in a Chinese population by using 16S rRNA next-generation sequencing (NGS).

METHODS

Thirty-one samples from twenty-six patients were collected from root canals. Following the extraction of the bacterial DNA, the V3-V4 hypervariable regions of the 16S rRNA gene were sequenced. Compositional diversity, prominent taxa and co-occurrence network analysis were compared according to the presence or absence of sinus tracts.

RESULTS

The overall microbiota in two groups exhibited distinguished patterns. Actinomyces dominated in samples with sinus tracts while Prevotella was the most abundant in samples without sinus tracts. The major pathogens in sinus tracts exhibited a complex co-occurrence network, in which Pseudomonas formed a distinctive cluster with enriched abundance, and the extensive correlations centered on Desulfovibrio and Pseudoramibacter may suggest novel dependencies. In the network without sinus tracts, the Bacteroidetes and Firmicutes taxa presented close internal associations.

CONCLUSIONS

The sequencing results confirmed the complexity of the microbiota in AP. The presence of sinus tracts was associated with distinctive infective patterns and complicated microbial co-infection interaction networks. Further investigations should be adopted to elucidate the relationship between the novel interactions and disease progression.

CLINICAL SIGNIFICANCE

Exploring the microbial interactions leads to a better understanding of etiology of apical periodontitis. Utilizing next generation sequencing techniques, our research uncovered the bacterial community structure and observed co-infection networks associated with sinus tracts, providing potential insights for prognosis prediction and targeted therapeutics of persistent inflammation.

Parent-child microbiota relationships involved in childhood obesity: A CORALS ancillary study

OBJECTIVES

Childhood obesity continues to rise worldwide. Family gut microorganisms may be associated with childhood obesity. The aim of the study was to analyze bacterial similarities in fecal microbiota composition between parent-offspring pairs as linked to body weight.

METHODS

A total of 146 father/mother and offspring pairs were categorized into four groups according to the weight status of the parent-child pair as follows: group 1, parent and child with normal weight; group 2, parent and child with overweight/obesity; group 3, parent with normal weight and child with overweight/obesity; group 4, parent with overweight/obesity and child with normal weight. Anthropometric measurements and lifestyle assessments were performed in all participants. Microbiota characteristics were determined by 16S ribosomal RNA gene sequencing. Logistic regression models were performed to determine whether the abundance of any bacteria was able to predict childhood obesity. Moreover, receiver operating characteristic curves were fitted to define the relative diagnostic strength of bacterial taxa for the correct identification of childhood obesity.

RESULTS

The absence/abundance of Catenibacterium mitsuokai, Prevotella stercorea, Desulfovibrio piger, Massiliprevotella massiliensis, and Phascolarctobacterium succinatutens was involved in body weight family associations. A positive relationship between P. succinatutens richness from parents and M. massiliensis from children was observed with regard to body weight status (odds ratio, 1.14, P = 0.013).

CONCLUSIONS

This study describes five potential gut bacteria that may be putatively involved in family weight status relationships and appear to be useful for predicting obesity.

Net cage aquaculture alters the co-occurrence network and functions of bacterial communities in offshore areas

A better understanding of bacterial communities and the factors that drive them is essential to maintain their functions and services. As an ecosystem closely linked to human activities, the health of offshore aquaculture depends on the diversity and functions of bacteria in its environment. However, little attention has been paid to the vertical interface of the offshore aquaculture areas with shellfish net cages. In this study, high-throughput sequencing was used to analyze bacterial communities in different water layers of a net cage scallop farm in the offshore area of Northeast of China. Based on the results, an increased richness of bacterial communities was observed in the water adjacent to the net cages. Meanwhile, apparently different bacterial community compositions were observed among the water layers, with an enrichment of Cyanobacteria, Bacteroidota, and Firmicutes in the water layers above, parallel to, and below the net cages, respectively. According to the predicted functions, the bacterial communities of the water layers above, parallel to, and below the net cages were identified as phototrophy-, chemoheterotrophy-, and nitrogen respiration-dominated. Furthermore, network analysis revealed a complex but unstable bacterial community in the water layer containing the net cage. Finally, partial least squares path modelling revealed that the net cage aquaculture directly influenced the environmental variables and bacterial richness, which further induced the variations in bacterial community composition, and ultimately affected their ecological functions. These results provide a basic understanding of bacterial communities in net cage scallop farms and highlight the effects of offshore aquaculture on variations in ecological functions.

High-dose dual therapy for Helicobacter pylori eradication inducing less impact on the gut microbiota

BACKGROUND

Helicobacter pylori (H. pylori) eradication regimens may have different effects on the gut microbiota. Few studies have analyzed the safety of high-dose dual therapy (HDDT) from a micro-ecological perspective. This study aimed to compare the impact of H. pylori eradication with HDDT and bismuth quadruple therapy (BQT) on gut microbiota.

PATIENTS AND METHODS

H. Pylori-infected treatment-naive patients were recruited and screened from September 2023 to April 2024 and randomly assigned to the HDDT group (esomeprazole 20 mg, amoxicillin 750 mg, qid, 14 days) or BQT group (esomeprazole 20 mg, amoxicillin 1000 mg, clarithromycin 500 mg, and bismuth potassium citrate 600 mg, bid, 14 days). Fresh stool specimens were collected and stored before treatment and at week 2 and week 8 after treatment. The diversity and composition of the gut microbiota were compared and analyzed in both groups using 16 S rRNA gene sequencing.

RESULTS

Forty-nine H. pylori positive patients were enrolled and randomly assigned to either the HDDT (n = 24) or the BQT group (n = 25) group. Compared with baseline, alpha and beta diversities significantly changed at week 2 after receiving BQT and did not recover fully at week 8. However, in the HDDT group, the diversities at week 2 changed mildly without statistical significance, compared to baseline. Additionally, a greater number of species had alterations in their abundances in the BQT group compared to the HDDT group at week 2. However, the abundances of these species were restored to their previous levels at week 8 in both the HDDT and BQT groups.

CONCLUSIONS

Compared to BQT, HDDT exerted less impact on the diversity and composition of the gut microbiota.

CLINICAL TRIAL REGISTRATION

ChiCTR2100053268.

Effects of Limosilactobacillus fermentum KBL375 on Immune Enhancement and Gut Microbiota Composition in Cyclophosphamide-Induced Immunosuppressed Mice

This study evaluated the immune-enhancing efficacy of Limosilactobacillus fermentum KBL375 isolated from the feces of healthy Koreans. KBL375-treated splenocytes showed enhancement of cytotoxicity against YAC-1 cells, the target of natural killer (NK) cells, with an increase in CD335, granzyme B, perforin, and interferon-gamma (IFN-γ). Oral administration of KBL375 in mice with cyclophosphamide (CP)-induced immunosuppression improved body weight and immune functions, including immune organ indices, lymphocyte proliferations, and immunoglobulin (Ig) A levels. Notably, KBL375 increased NK cell cytotoxicity and proportion in immunosuppressed mice. Perforin/IFN-γ expression levels, which indicated NK cell activation, were also increased in KBL375-treated mice. Furthermore, KBL375 led to an increase in beneficial microbes, such as Bifidobacterium, in the gut microbiome of immunosuppressed mice, fostering a favorable intestinal microbial environment. These comprehensive results suggest that KBL375 exhibits potent immune regulatory functions and positively influences the gut microbiota, implying its potential as a probiotic agent for immune enhancement.

Spinach seed microbiome characteristics linked to suppressiveness against Globisporangium ultimum damping-off

Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.

Use of a Novel Passive E-Nose to Monitor Fermentable Prebiotic Fiber Consumption

We developed a home-based electronic nose (E-Nose) to passively monitor volatile organic compounds (VOCs) emitted following bowel movements and assessed its validity by correlating the output with prebiotic fiber intake. Healthy, non-overweight participants followed a three-week protocol which included the following: (1) installing the E-Nose in their bathroom; (2) activating the device following each bowel movement; (3) recording their dietary intake; (4) consuming a fiber bar (RiteCarbs) containing a blend of 10 g of prebiotic fiber daily during weeks two and three; and (5) submit stool specimens at the beginning and end of the study for 16S rRNA gene sequencing and analysis. Participants' fecal microbiome displayed significantly increased relative abundance of putative total SCFA-producing genera (p = 0.0323) [total acetate-producing genera (p = 0.0214), total butyrate-producing genera (p = 0.0131)] and decreased Gram-negative proinflammatory genera (p = 0.0468). Prebiotic intervention significantly increased the participants' fiber intake (p = 0.0152), E-Nose Min/Max (p = 0.0339), and area over the curve in VOC-to-fiber output (p = 0.0044). Increased fiber intake was negatively associated (R2 = 0.53, p = 0.026) with decreased relative abundance of putative Gram-negative proinflammatory genera. This proof-of-concept study demonstrates that a prototype E-Nose can noninvasively detect a direct connection between fiber intake and VOC outputs in a home-based environment.

Distinct bacteria display genus and species-specific associations with mycobionts in paramo lichens in Colombia

Lichens are complex symbiotic systems where fungi interact with an extracellular arrangement of one or more photosynthetic partners and an indeterminate number of other microbes. Recently, specific lichen-microbial community associations have been proposed. In this study, we aimed to characterize the differences in bacteria associated with closely related lichens, under a defined set of environmental conditions in Colombian paramos. Our goal was to determine if there is a correlation between microbiota and host divergence in lichen species belonging to the genus Sticta. We found that specific microbiota are defined by their mycobiont at the genus level. Further, distinct bacterial families show differences among the three studied genera, and specific amplicon sequence variants further discriminate among lichen species within each genus. A geographic component also determines the composition of these microbial communities among lichen species. Our functional analysis revealed that fungal partners play a key role in synthesizing complex polysaccharides, while bacterial-derived antioxidants and photoprotective mechanisms contribute to desiccation tolerance in lichens. These insights highlight the complex interactions within lichen symbioses that could be relevant in environments such as the paramo ecosystem.

Feasibility and Tolerability of Daily Microgreen Consumption in Healthy Middle-Aged/Older Adults: A Randomized, Open-Label, Controlled Crossover Trial

Background/Objectives: Microgreens are rich in nutrients and phytochemicals that can support healthy aging, including attenuation of cardiovascular disease risk. The nutrient and phytochemical contents of red beet (i.e., bull's blood' beet, Beta vulgaris) and red cabbage (Brassica oleracea var capitate) microgreens, as well as existing preclinical evidence suggest their cardioprotective effects, but the feasibility, gastrointestinal tolerability, and human health effects of daily microgreen consumption are unknown. This study aimed to evaluate the feasibility and gastrointestinal tolerability of 2 weeks of daily microgreen consumption in healthy middle-aged/older (MA/O) adults. A secondary aim was to characterize potential health effects. Methods: Healthy MA/O adults (initial n = 26) were randomized to consume either 2 cups of 'bull's blood' beet or red cabbage microgreens daily for 2 weeks in a crossover design, with each treatment period separated by 2 weeks. Feasibility was determined through participant retention and intervention compliance (i.e., total doses consumed divided by 14 days), while gastrointestinal tolerability was determined by a gastrointestinal health questionnaire and bowel movement log. Impacts of microgreen consumption on brachial and aortic hemodynamic parameters, and gut microbiota composition were evaluated. Results: Daily consumption for 2 weeks of 'bull's blood' beet and red cabbage microgreens was found to be feasible as indicated by high participant retention (final n = 24) and overall treatment compliance of 95.6%. Gastrointestinal symptom severity was not impacted overall, though an improvement in gastrointestinal inflammation-associated symptom severity scores following the red cabbage microgreen intervention (p = 0.047) was observed. There were no changes in bowel movement quality, hemodynamic parameters, or on alpha or beta diversity of the gut microbiota. Conclusions: Daily consumption of 'bull's blood' beet and red cabbage microgreens is feasible and tolerable in healthy MA/O adults. Future studies designed to evaluate their health impacts are needed.

Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition

BACKGROUND

In recent years, juicing has often been promoted as a convenient way to increase fruit and vegetable intake, with juice-only diets marketed for digestive cleansing and overall health improvement. However, juicing removes most insoluble fiber, which may diminish the health benefits of whole fruits and vegetables. Lower fiber intake can alter the microbiota, affecting metabolism, immunity, and mental health, though little is known about juicing's specific effects on the microbiota. This study addresses this gap by exploring how juicing impacts gut and oral microbiome composition in an intervention study.

METHODS

Fourteen participants followed one of three diets-exclusive juice, juice plus food, or plant-based food-for three days. Microbiota samples (stool, saliva, and inner cheek swabs) were collected at baseline, after a pre-intervention elimination diet, immediately after juice intervention, and 14 days after intervention. Moreover, 16S rRNA gene amplicon sequencing was used to analyze microbiota taxonomic composition.

RESULTS

The saliva microbiome differed significantly in response to the elimination diet (unweighted UniFrac: F = 1.72, R = 0.06, p < 0.005; weighted UniFrac: F = 7.62, R = 0.23, p-value = 0.0025) with a significant reduction in Firmicutes (p = 0.004) and a significant increase in Proteobacteria (p = 0.005). The juice intervention diets were also associated with changes in the saliva and cheek microbiota, particularly in the relative abundances of pro-inflammatory bacterial families, potentially due to the high sugar and low fiber intake of the juice-related products. Although no significant shifts in overall gut microbiota composition were observed, with either the elimination diet or the juice intervention diets, bacterial taxa associated with gut permeability, inflammation, and cognitive decline increased in relative abundance.

CONCLUSIONS

These findings suggest that short-term juice consumption may negatively affect the microbiota.

A Multimarker Approach to Identify Microbial Bioindicators for Coral Reef Health Monitoring-Case Study in La Réunion Island

The marine microbiome arouses an increasing interest, aimed at better understanding coral reef biodiversity, coral resilience, and identifying bioindicators of ecosystem health. The present study is a microbiome mining of three environmentally contrasted sites along the Hermitage fringing reef of La Réunion Island (Western Indian Ocean). This mining aims to identify bioindicators of reef health to assist managers in preserving the fringing reefs of La Réunion. The watersheds of the fringing reefs are small, steeply sloped, and are impacted by human activities with significant land use changes and hydrological modifications along the coast and up to mid-altitudes. Sediment, seawater, and coral rubble were sampled in austral summer and winter at each site. For each compartment, bacterial, fungal, microalgal, and protist communities were characterized by high throughput DNA sequencing methodology. Results show that the reef microbiome composition varied greatly with seasons and reef compartments, but variations were different among targeted markers. No significant variation among sites was observed. Relevant bioindicators were highlighted per taxonomic groups such as the Firmicutes:Bacteroidota ratio (8.4%:7.0%), the genera Vibrio (25.2%) and Photobacterium (12.5%) dominating bacteria; the Ascomycota:Basidiomycota ratio (63.1%:36.1%), the genera Aspergillus (40.9%) and Cladosporium (16.2%) dominating fungi; the genus Ostreobium (81.5%) in Chlorophyta taxon for microalgae; and the groups of Dinoflagellata (63.3%) and Diatomea (22.6%) within the protista comprising two dominant genera: Symbiodinium (41.7%) and Pelagodinium (27.8%). This study highlights that the identified bioindicators, mainly in seawater and sediment reef compartments, could be targeted by reef conservation stakeholders to better monitor La Réunion Island's reef state of health and to improve management plans.

Metabarcoding for the Monitoring of the Microbiome and Parasitome of Medically Important Mosquito Species in Two Urban and Semi-urban Areas of South Korea

Interactions between microbial communities and the host can modulate mosquito biology, including vector competence. Therefore, future vector biocontrol measures will utilize these interactions and require extensive monitoring of the mosquito microbiome. Metabarcoding strategies will be useful for conducting vector monitoring on a large scale. We used 16S and 18S rRNA gene metabarcoding through iSeq100 sequencing to characterize the microbiome and eukaryome of Aedes albopictus (Skuse 1894) and Culex pipiens (Linnaeus 1758), two globally important vectors present in South Korea. Mosquitoes were collected from an urban and a semi-urban location in South Korea. Bacterial alpha and beta diversities varied by population. Pseudomonadota dominated the microbiomes of both species. The microbiome composition varied by population and was dominated by different taxa. At the genus level, Wolbachia sp. was the most enriched genus in Cx. pipiens, followed by Aeromonas sp. In Ae. Albopictus, the most abundant group was Enterococcus sp. The gregarine parasite Ascogregarina taiwanensis was highly prevalent in Ae. Albopictus and its absence was marked by the presence of seven bacterial taxa. To our knowledge, this is the first characterization of the microbiome of Ae. albopictus and Cx. pipiens in these regions of South Korea and contributes to the current information on the microbiome of mosquito species, which can be used in further studies to assess pathogen-microbiome and microbiome-microbiome interactions.

Microbiota Involved in the Degradation of Tremella fuciformis Polysaccharide and Microbial Enzymatic Potential Revealed by Microbiome and Metagenome

Tremella fuciformis, as a traditional edible fungus in Asian countries, is rich in polysaccharides with a variety of bioactivities. Nevertheless, its high molecular weight and complex structure have caused limitations in its application and structural analysis. In this study, we successfully screened a Tremella fuciformis polysaccharide-degrading bacterium from the soil by enriching and screening. The mixed bacterium consisted mainly of Verrucomicrobium (55.4%) and Lysobacter (43.8%), which released extracellular enzymes that enabled the degradation of Tremella fuciformis polysaccharides. The functional annotation using microbiome and metagenome combined with bioinformatics revealed its active carbohydrate metabolism, binding, and catalysis. It exposed the enzymatic potential of the bacterium and provided a basis for the exploration of hydrolytic enzymes for hardly degradable polysaccharides in fungi.

Non-native PGPB consortium consisting of Pseudomonas sp. G31 and Azotobacter sp. PBC2 promoted winter wheat growth and slightly altered the native bacterial community

Plant growth-promoting bacteria (PGPB) are considered an effective eco-friendly biostimulator. However, relatively few studies have examined how PGPB affect the native bacterial community of major crops. Thus, this study investigates the impact of a PGPB consortium, comprising Pseudomonas sp. G31 and Azotobacter sp. PBC2 (P1A), on the soil bacterial community of wheat under field conditions. As a result of PGPB application, we observed a significant increase in seed yield, as well as in nitrate content (1st and 3rd time points) and available phosphorus (2nd time point) in the rhizosphere compared to control. For the metataxonomic study, Next-Generation Sequencing was performed using the Illumina NovaSeq 6000 system. The consortium used did not have a significant impact on the diversity of native soil bacteria and slightly affected the taxonomic composition of bacteria with no significant changes in bacterial dominants at the phylum and genus level. Nevertheless, 3 weeks after application, P1A increased the relative abundance of Nitrospira which could have influenced the increase in nitrates in the rhizosphere, and also decreased Bdellovibrio. The results indicate that the P1A consortium, due to its ability to promote plant growth without detrimental alternations in the bacterial community of the soil, may be a potential candidate for commercialization.

Dynamic soil columns simulate Arctic redox biogeochemistry and carbon release during changes in water saturation

Thawing Arctic permafrost can induce hydrologic change and alter redox conditions, shifting the balance of soil organic matter (SOM) decomposition. There remains uncertainty about how soil saturation and redox transitions impact dissolved and gas phase carbon fluxes, and efforts to link hydrobiogeochemical processes to ecosystem-scale models are limited. This study evaluates SOM decomposition of Arctic tundra soils using column experiments, water chemistry measurements, microbial community analysis, and a PFLOTRAN reactive transport model. Soil columns from a thermokarst channel (TC) and an upland tundra (UC) were exposed to cycles of saturation and drainage, which controlled carbon emissions. During saturation, an outflow of dissolved organic carbon from the UC soil correlated with elevated reduced iron and decreased pH; during drainage, UC carbon dioxide fluxes were 70% higher than TC fluxes. Intermittent methane release was observed for TC, consistent with higher methanogen abundance. Slower drainage in the TC soil correlated with more subtle biogeochemical changes. PFLOTRAN simulations captured experimental trends in soil carbon fluxes, oxygen concentrations, and water contents. The model was then used to evaluate additional soil water drainage rates. This study emphasizes the importance of considering hydrologic change when evaluating and simulating SOM decomposition in dynamic Arctic tundra environments.

Insights into the representativeness of biodiversity assessment in large reservoir through eDNA metabarcoding

Monitoring biodiversity on a large scale, such as in hydropower reservoirs, poses scientific challenges. Conventional methods such as passive fishing gear are prone to various biases, while the utilization of environmental DNA (eDNA) metabarcoding has been restricted. Most eDNA studies have primarily focused on replicating results from traditional methods, which themselves have limitations regarding representativeness and bias. In our study, we employed eDNA metabarcoding with three markers (12SrRNA, COI, and 16SrRNA) to evaluate the biodiversity of an 800 km2 reservoir. We utilized hydrodynamic modeling to determine water flow velocity and the water renewal ratio throughout the study area. Additionally, we conducted statistical comparisons-rarefaction curves and multivariate methods-among samples as an alternative approach to assess biodiversity representation. The eDNA identified taxa previously documented in the reservoir by traditional monitoring methods, as well as revealed 29 -nine fishes and 20 non-fish-previously unreported species. These results highlight the robustness of eDNA as a biodiversity monitoring technique. Our findings also indicated that by randomly sampling 30% of the original number of samples, we could effectively capture the same biodiversity. This approach enabled us to comprehend the reservoir's biodiversity profile and propose a straightforward, cost-effective monitoring protocol for the future based on eDNA.