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Oral microbial dysbiosis is known to increase susceptibility of an individual to develop rheumatoid arthritis (RA). Individuals at-risk of RA may undergo different phases of disease progression. In this study, we aim to investigate whether and whereby the oral microbiome communities alter prior to symptoms of RA. Seventy-nine saliva samples were collected from 29 high-risk individuals, who were positive for anti-citrullinated protein antibodies (ACPA) and have no clinical arthritis, 27 RA patients and 23 healthy controls (HCs). The salivary microbiome was examined using 16S ribosomal RNA gene sequencing. Alpha and beta diversity analysis and the linear discriminant analysis were applied to examine the bacterial diversity, community structure and discriminatory taxa between three groups, respectively. The correlation between salivary bacteria and autoantibodies were analyzed. In the "pre-clinical" stages, salivary microbial diversity was significantly reduced comparing to RA patients and HCs. In contrast to HCs, like RA patients, individuals at high-risk for RA showed a reduction in the abundance of genus Defluviitaleaceae_UCG-011 and the species Neisseria oralis , but an expansion of Prevotella _6. Unexpectedly, the relative abundance of Porphyromonas gingivalis , reported as opportunistic pathogens for RA development, was significantly decreased in high-risk individuals. Additionally, we identified four genera in the saliva from high-risk individuals positively correlated with serum ACPA titers, and the other two genera inversely displayed. In summary, we observed a characteristic compositional change of salivary microbes in individuals at high-risk for RA, suggesting that oral microbiota dysbiosis occurs in the "pre-clinical" stage of RA and are correlated with systemic autoimmune features. [ABSTRACT FROM AUTHOR]

The intestinal microbiota of piglets fed with a Control diet low in dietary fibre and modified wheat bran variants as an additional source of insoluble dietary fibre was characterised. In this context, variances in the microbiota of three different gut segments were assessed. Wheat bran was either included in its native form or modified by fermentation and extrusion before added at 150 g/kg to a basal diet for 48 piglets (12 animals per treatment). Total DNA was extracted from digesta samples from the jejunum, the end of the ileum and the colon ascendens. Samples were prepared accordingly for subsequent sequencing with the Illumina MiSeq. The obtained results revealed distinct location-specific differences in microbial composition. WhileFirmicuteswere most predominant in all three gut segments,Bacteroideteswere additionally found in the colon at high abundance. The parameters of alpha and beta diversity analysis showed significant differences (p < 0.01) between the colon and the other two gut segments. Specialised bacterial groups likePrevotellaandRuminococcaceaewere among the most predominant ones found in the colon, as they possess cellulolytic properties to degrade (at least partially) non-starch polysaccharides, while their abundance was negligible in the jejunum and the ileum. Conversely, the generaLactobacillus, BifidobacteriumandVeillonella, for example, were among the most predominant groups in the jejunum and ileum, while in the colon they were hardly found. Although statistical taxonomical evaluation, followingp-value correction, did not reveal pronounced differences in abundance related to bran modification, alpha and beta diversity analysis showed an influence regarding the various feeding strategies applied. Based on these findings, a more in-depth view on intestinal microbial composition within the gastrointestinal tract of young pigs fed with low- and high-fibre diets was generated. [ABSTRACT FROM PUBLISHER]

To understand pathogenic mechanisms and suggest molecular biomarker candidates for the disease status of edible red algae, Pyropia, we analyzed relationships between disease symptom severity, changes in microbial communities, and the metabolic dysregulation of the red algae with 16S and 18S ribosomal RNA gene amplicon sequencing and mass spectrometry-based metabolomics. Our observations of disease symptoms and microbial communities indicated that Pythium was the major pathogen. As the disease progressed, the prokaryotic diversity and composition of the microbial communities were clearly distinct from diseased thalli compared with healthy and weakly diseased thalli. The results of the microbial correlation network analysis showed the co-occurrence of known pathogenic microbes in the diseased thalli. Similarly, the results of the metabolomic analysis showed that the relative abundance of annotated metabolites differed in the diseased thalli compared with the healthy and weakly diseased thalli. In particular, three purine metabolism-related metabolites—hypoxanthine, guanine, and inosine—increased significantly in the diseased thalli. All the affected metabolites in abundance regulation, including the three metabolites, are known to be related to biotic stress and defense mechanisms. This study contributes to filling the gaps in research on molecular and microbial events, especially the links between pathogenic and non-pathogenic microbes, metabolites, and symptom severity in Pyropia. Additionally, the results indicate that the observed prokaryotic diversity reduction and co-occurrence of the known microbial pathogens are new non-target indicators that could be beneficial in cases where no known pathogens indicate pathogenicity. Dysregulated purine metabolism-related metabolites and other stress- and defense-related metabolites are potential molecular indicators of disease status of Pyropia. [ABSTRACT FROM AUTHOR]

Background: The microbiome greatly affects health and wellbeing. Evolutionarily, it is doubtful that a host would rely on chance alone to pass on microbial colonization to its offspring. However, the literature currently offers only limited evidence regarding two alternative hypotheses: active microbial shaping by host genetic factors or transmission of a microbial maternal legacy. Results: To further dissect the influence of host genetics and maternal inheritance, we collected two-cell stage embryos from two representative wild types, C57BL6/J and BALB/c, and transferred a mixture of both genotype embryos into hybrid recipient mice to be inoculated by an identical microbiome at birth. Conclusions: Observing the offspring for six generations unequivocally emphasizes the impact of host genetic factors over maternal legacy in constant environments, akin to murine laboratory experiments. Interestingly, maternal legacy solely controlled the microbiome in the first offspring generation. However, current evidence supporting maternal legacy has not extended beyond this initial generation, resolving the aforementioned debate. BvkFmArGExF4DhB6h6D8wq Video Abstract [ABSTRACT FROM AUTHOR]

Background: Studies have shown correlations between gut microbiota and neurocognitive function, but little was known about the early postnatal gut microbiota and intraventricular hemorrhage (IVH). We aimed to explore the characteristics of gut microbiota in premature infants and their relationship with IVH, further exploring potential therapeutic targets. Methods: Premature infants delivered at Peking University First Hospital from February 2023 to August 2023 were recruited as a cohort. Feces samples were collected on postnatal days 1, 3, and 5. Premature infants were divided into normal, mild IVH, and severe IVH groups based on cranial ultrasound. 16S rRNA amplicon sequencing technology was used to determine the fecal microbiota, and the results were analyzed. Results: Thirty-eight premature infants were enrolled. There was a significant difference in alpha and beta diversity among the three groups. The relative abundance of E. coli and A. muciniphila was different among the three groups. Further random forest analysis indicated that S. lutetiensis, L. mirabilis, and N. macacae can effectively distinguish premature infants with IVH. Finally, the phylogenetic investigation of communities by reconstruction of unobserved states2 (PICRUSt2) functional gene analysis predicted significant differences in energy metabolism, carbohydrate metabolism, metabolism of cofactors and vitamins, and membrane transport between normal and severe IVH groups. Conclusions: The gut microbiota in the early postnatal period of premature infants is closely associated with the IVH status. As age increases, the differences in gut microbiota of premature infants with different degrees of IVH continue to increase, and the trend of changes with severity of IVH becomes more and more obvious. E. coli, A. muciniphila, S. lutetiensis, L. mirabilis, N. macacae, G. haemolysans, and S. oralis can effectively distinguish between IVH infants and normal premature infants. The results indicate that gut microbiota is expected to provide effective therapeutic targets for the diagnosis and treatment of IVH. [ABSTRACT FROM AUTHOR]

To examine the relationship between gut microbiota and disease development in chronic heart failure patients with different nutritional risk. The study analyzed stool samples from 62 CHF patients and 21 healthy peoples using 16S rRNA gene sequencing. CHF patients were separated into risk (n = 30) and non-risk group (n = 32) based on NRS2002 scores. Analysis methods used were LEfSe, random forest regression model, ROC curves, BugBase, PICRUSt2, metagenomeSeq. Risk group includes 11 cases of HFrEF, 6 cases of HFpEF, and 13 cases of HFmrEF. LefSe analysis confirmed that the risk group had higher levels of Enterobacter and Escherichia-Shigella. Correlation analysis revealed a negative correlation between prealbumin and Escherichia-Shigella. The presence of Enterobacter and Escherichia-Shigella worsens intestinal inflammation in CHF patients, impacting lysine metabolism by influencing its degradation metabolic function. This interference further disrupts albumin and prealbumin synthesis, leading to malnutrition in CHF patients and ultimately worsening the disease. [ABSTRACT FROM AUTHOR]

The Saihanba Mechanical Forest is an artificial national forest park with a forest-steppe landscape. The flora and fauna have been extensively studied, but a comprehensive understanding of the bacterial community composition and structure of the natural rainwater lakes present in the area has rarely been reported. In this study, the structure and functional characteristics of bacterial communities in lake sediments and water samples in the Saihanba artificial forest were investigated using 16s rRNA high-throughput sequencing. Microbial diversity analyses revealed that Proteobacteria, Acidobacteria, Bacteroidota and Verrucomicrobiota microbiota dominated. The abundance of Proteobacteria and Actinobacteriota was significantly higher (p <.05) in water samples compared to sediment samples. PICRUSt2 functional analysis predicted genes associated with the degradation of xenobiotics and the execution of essential metabolic processes. Here, we report differences in the composition of native bacterial communities in sediments and water under the Saihanba artificial forest and make functional gene predictions. This study provides a reference for further exploring the structure and functional characteristics of microbial communities in water samples and sediment environments of lakes under planted forests. [ABSTRACT FROM AUTHOR]

Background: Gastrointestinal dysfunction frequently occurs following traumatic brain injury (TBI) and significantly increases posttraumatic complications. TBI can lead to alterations in gut microbiota. The neuroprotective effects of hyperbaric oxygen (HBO) have not been well recognized after TBI. The study''s aim was to investigate the impact of HBO on TBI-induced dysbiosis in the gut and the pathological changes in the brain following TBI. Methods: Anesthetized male Sprague–Dawley rats were randomly assigned to three groups: sham surgery plus normobaric air (21% oxygen at 1 atmospheres absolute), TBI (2.0 atm) plus normobaric air, and TBI (2.0 atm) plus HBO (100% oxygen at 2.0 atmospheres absolute) for 60 min immediately after TBI, 24 h later, and 48 h later. The brain injury volume, tumor necrosis factor-α expression in microglia and astrocytes, and neuronal apoptosis in the brain were subsequently determined. The V3–V4 regions of 16S ribosomal rRNA in the fecal samples were sequenced, and alterations in the gut microbiome were statistically analyzed. All parameters were evaluated on the 3rd day after TBI. Results: Our results demonstrated that HBO improved TBI-induced neuroinflammation, brain injury volume, and neuronal apoptosis. HBO appeared to increase the abundance of aerobic bacteria while inhibiting anaerobic bacteria. Intriguingly, HBO reversed the TBI-mediated decrease in Prevotella copri and Deinococcus spp., both of which were negatively correlated with neuroinflammation and brain injury volume. TBI increased the abundance of these gut bacteria in relation to NOD-lik0065 receptor signaling and the proteasome pathway, which also exhibited a positive correlation trend with neuro inflammation and apoptosis. The abundance of Prevotella copri was negatively correlated with NOD-like receptor signaling and the Proteasome pathway. Conclusions: Our study demonstrated how the neuroprotective effects of HBO after acute TBI might act through reshaping the TBI-induced gut dysbiosis and reversing the TBI-mediated decrease of Prevotella copri. [ABSTRACT FROM AUTHOR]

Bacterial, fungal, and algal communities that colonize aquatic systems on glacial ice surfaces mediate biogeochemical reactions that alter meltwater composition and affect meltwater production and storage. In this study, we sought to improve understanding of microbial communities inhabiting the shallow aquifer that forms seasonally within the ice surface of a glacier's ablation zone (i.e., the weathering crust aquifer). Using a metagenomic approach, we compared gene contents of microbial assemblages in the weathering crust aquifer (WCA) of the Matanuska Glacier (Alaska, USA) to those recovered from supraglacial features and englacial ice. High abundances of Pseudomonadota, Cyanobacteriota, Actinomycetota, and Bacteroidota were observed across all samples, while taxa in class Gammaproteobacteria were found at significantly higher abundances in the weathering crust aquifer. The weathering crust aquifer samples also contained higher abundances of Dothideomycetes and Microbotryomyetes; fungal classes commonly observed in snow and other icy ecosystems. Phylogenetic analysis of 18S rRNA and rbcL gene sequences indicated high abundances of algae in the WCA that are closely related (> 98% and > 93% identity, respectively) to taxa of Ancylonema (Streptophyta) and Ochromonas (Ochrophyta) reported from glacial ice surfaces in Svalbard and Antarctic sea ice. Many functional gene categories (e.g., homeostasis, cellular regulation, and stress responses) were enriched in samples from the weathering crust aquifer compared to those from proximal englacial and supraglacial habitats, providing evidence for ecological specialization in the communities. The identification of phagotrophic phytoflagellate taxa and genes involved in mixotrophy implies that combined phototrophic and heterotrophic production may assist with persistence in the low light, low energy, and ephemeral conditions of the weathering crust environment. The compositional and functional differences we have documented indicate distinct microbial distributions and functional processes occur in the weathering crust aquifer environment, and we discuss how deciphering these nuances is essential for developing a more complete understanding of ecosystem biogeochemistry in supraglacial hydrological systems. [ABSTRACT FROM AUTHOR]

Breast cancer (BC) is yet a significant global health challenge across various populations including Ghana, though several studies on host-genome associated with BC have been investigated molecular mechanisms of BC development and progression, and candidate therapeutic agents. However, a little attention has been given on microbial genome in this regard, although alterations in microbiota and epigenetic modifications are recognized as substantial risk factors for BC. This study focused on identifying bacterial key genes (bKGs) associated with BC infections in the Ghanaian population and exploring potential drug molecules by targeting these bKGs through in silico analyses. At first, 16S rRNA bacterial sequence data were downloaded from NCBI database comprising 520 samples from BC patients and 442 from healthy controls. Analysis of 16S rRNA-Seq data showed significant differences in bacterial abundance between BC and healthy groups and identified 26 differential genera with the threshold values at |log2FC|>2.0 and p-value≤0.05. It was observed that two genera Prevotella and Anaerovibria are significantly upregulated in BC patients and others are downregulated. Functional analysis based on all differential genera identified 19 MetaCyc signaling pathways, twelve of which were significantly enriched in BC patients by containing 165 genes Top-ranked 10 genes mdh, pykF, gapA, zwf, pgi, tpiA, pgk, pfkA, ppsA, and pykA were identified as BC-causing bacterial key genes (bKGs) through protein-protein interaction network analysis. Subsequently, the bKG-guided top ranked 10 drug molecules Digitoxin, Digoxin, Ledipasvir, Suramin, Ergotamine, Venetoclax, Nilotinib, Conivaptan, Dihydroergotamine, and Elbasvir were identified using molecular docking analysis. The stability of top-ranked three drug-target complexes (Digitoxin-pykA, Digoxin-mdh, and Ledipasvir-pgi) were confirmed through the molecular dynamics simulation studies. Therefore, these findings might be useful resources to the wet-lab researchers for further experimental validation on bacterial therapies against BC. [ABSTRACT FROM AUTHOR]

Background: Premature infants are more prone to brain injuries owing to incomplete nervous system development and poor adaptation outside the mother's body. Without timely intervention, premature infants with brain injuries often develop intellectual disabilities, causing significant burdens on families and the society. Multiple studies have shown that gut dysbiosis can affect the nervous system, and vice versa. This study aimed to explore the changes in gut microbiota of typical premature infants and those with brain injuries on the third and seventh days after birth using 16 S rRNA technology. Methods: Fecal samples from typical premature infants (non-brain injury group, n = 17) and those with brain injuries (brain injury group, n = 21) were collected on days 1, 3, and 7 after birth for 16 S rRNA sequencing. Alpha diversity analysis was used to evaluate the diversity of gut microbiome. LEfSe and DESeq2 were used to analyze of the microorganisms' characteristics and differentiate the microorganisms between the two groups. Results: At the phylum level, Firmicutes, Proteobacteria, and Actinobacteria were the dominant flora in both groups. At the genus level, the proportion of Enterococcus in fecal samples of the brain injury group was higher than that of the non-brain injury group on day three after birth; however, the opposite was observed on day seven. Rothia and Lactobacillales were characteristic bacteria of the non-brain injury group on days three and seven after birth, whereas Enterococcus and Bifidobacteria were characteristic bacteria of the brain injury group on days three and seven after birth, respectively. Three days after birth, the Shannon and Simpson indices of the non-brain injury group were significantly higher than those of the brain injury group. Conclusion: Premature infants with brain injuries have a unique gut microbiota that is different from that of typical premature infants, indicating correlation between brain injuries and gut microbiota. [ABSTRACT FROM AUTHOR]

Background: Phenylketonuria (PKU) is a metabolic disorder that necessitates dietary restrictions, potentially impacting the composition of gut and oral microbiota. This study aimed to compare the microbiota composition between children with PKU and healthy controls. Methods: Using 16S rRNA gene sequencing, we analysed microbial communities at six phylogenetic levels. Results: Our findings revealed significant differences in the gut microbiota: Euryarchaeota was more abundant in controls (p = 0.01), while Bacilli and Lactobacillales were higher in PKU children (p = 0.019). Methanobacteriales were significantly elevated in controls (p = 0.01). At the genus and species levels, PKU children had higher Streptococcus and Eubacterium dolichum (p = 0.019, p = 0.015), whereas controls had more Barnesiella, Coprococcus, and Faecalibacterium prausnitzii (p = 0.014, p = 0.019, p = 0.014). In the oral microbiota, control children exhibited significantly higher Bacteroidetes (p = 0.032), while PKU children had increased Bacilli and Betaproteobacteria (p = 0.0079, p = 0.016). Streptococcus and Neisseria were more prevalent in PKU (p = 0.0079, p = 0.016). Conclusions: These results suggest that PKU and its dietary management significantly alter the gut and oral microbiota composition. Understanding these microbial shifts could have implications for managing PKU and improving patient outcomes. [ABSTRACT FROM AUTHOR]

Background: Phenotypic age (PhenoAge), a widely used marker of biological aging, has been shown to be a robust predictor of all-cause mortality and morbidity in different populations. Existing studies on biological aging have primarily focused on individual domains, resulting in a lack of a comprehensive understanding of the multi-systemic dysregulation that occurs in aging. Methods: PhenoAge was evaluated based on a linear combination of chronological age (CA) and 9 clinical biomarkers in 952 multi-ethnic Asian women of reproductive age. Phenotypic age acceleration (PhenoAgeAccel), an aging biomarker, represents PhenoAge after adjusting for CA. This study conducts an in-depth association analysis of PhenoAgeAccel with clinical, nutritional, lipidomic, gut microbiome, and genetic factors. Results: Higher adiposity, glycaemia, plasma saturated fatty acids, kynurenine pathway metabolites, GlycA, riboflavin, nicotinamide, and insulin-like growth factor binding proteins were positively associated with PhenoAgeAccel. Conversely, a healthier diet and higher levels of pyridoxal phosphate, all-trans retinol, betaine, tryptophan, glutamine, histidine, apolipoprotein B, and insulin-like growth factors were inversely associated with PhenoAgeAccel. Lipidomic analysis found 132 lipid species linked to PhenoAgeAccel, with PC(O-36:0) showing the strongest positive association and CE(24:5) demonstrating the strongest inverse association. A genome-wide association study identified rs9864994 as the top genetic variant (P = 5.69E-07) from the ZDHHC19 gene. Gut microbiome analysis revealed that Erysipelotrichaceae UCG-003 and Bacteroides vulgatus were inversely associated with PhenoAgeAccel. Integrative network analysis of aging-related factors underscored the intricate links among clinical, nutritional and lipidomic variables, such as positive associations between kynurenine pathway metabolites, amino acids, adiposity, and insulin resistance. Furthermore, potential mediation effects of blood biomarkers related to inflammation, immune response, and nutritional and energy metabolism were observed in the associations of diet, adiposity, genetic variants, and gut microbial species with PhenoAgeAccel. Conclusions: Our findings provide a comprehensive analysis of aging-related factors across multiple platforms, delineating their complex interconnections. This study is the first to report novel signatures in lipidomics, gut microbiome and blood biomarkers specifically associated with PhenoAgeAccel. These insights are invaluable in understanding the molecular and metabolic mechanisms underlying biological aging and shed light on potential interventions to mitigate accelerated biological aging by targeting modifiable factors. [ABSTRACT FROM AUTHOR]

Background: Acute lung injury (ALI) is a serious and common complication that occurs in children with congenital heart disease after cardiopulmonary bypass (CPB) surgery, leading to higher mortality rates and poorer prognosis. Currently, there is no reliable predictive strategy for CPB-associated lung injury (CPB-ALI) in infants. Certain characteristics of the gut microbiota could potentially serve as biomarkers for predicting the development of CPB-ALI. Methods: We conducted 16S rRNA sequencing to analyze the characteristics of the intestinal microbiota in healthy controls and infants with CHD admitted to the hospital. The CHD infants were divided into CPB-ALI and non-ALI (CPB-NALI) groups based on postoperative outcomes. Bacterial functional pathway prediction analysis was performed using PIRCUSt2, and the gut microbiota composition associated with immune status was determined with heatmap. Random forest regression models and ROC curves were utilized to predict the occurrence of CPB-ALI. Results: Our study revealed significantly different microbiota compositions among three groups (CON, CPB-ALI, and CPB-NALI). The microbiota diversity was low in the CPB-ALI group with high pathogen abundance and significant decrease in Bacteroides, while the opposite was observed in the CPB-NALI group. The microbiota dysbiosis index was high in the CPB-ALI group, with its dominant microbiota significantly associated with multiple metabolic pathways. Additionally, CPB-ALI patients showed high levels of inflammatory cytokines IL-8 and HMGB1 in their serum, with high expression of IL-8 being associated with Enterobacteriaceae. Further correlation analysis showed that the differences in gut bacterial taxonomy were related to the occurrence of ALI, length of stay in the cardiac care unit, and ventilation time. It is noteworthy that Escherichia Shigella performed best in distinguishing CPB-ALI patients from non-ALI patients. Conclusions: Our study suggests that postoperative ALI patients have distinct gut microbiota upon admission compared to non-ALI patients after surgery. Dysbiosis of the gut microbiota may potentially impact the progression of ALI through metabolic pathways, quorum sensing, and the levels of inflammatory factors expressed in the serum. Escherichia Shigella represents a potential predictive factor for the occurrence of ALI in CHD infants after surgery. Acute lung injury, congenital heart disease, cardiopulmonary bypass surgery, gut microbiota, biomarker [ABSTRACT FROM AUTHOR]

This study examined the risk of intrauterine infection associated with radical trachelectomy (RT) in early‐stage cervical cancer patients. This procedure preserves fertility but is linked to increased risk of intrauterine infection due to cervical defects during pregnancy. DNA was extracted from the formalin‐fixed paraffin‐embedded (FFPE) placental specimens of 23 pregnant post‐RT patients and 16S rRNA gene sequencing was used for bacterial identification. The prevalence of Lactobacillus crispatus and Burkholderia stabilis was significantly higher in the non‐chorioamnionitis group. In contrast, alpha diversity analysis using the PD index showed significantly higher diversity in the chorioamnionitis group (P = 0.04). The demonstrated relationship between chorioamnionitis and microbial diversity affirms the importance of controlling the genital bacterial flora in pregnancies following RT. [ABSTRACT FROM AUTHOR]

Staphylea bumalda is a rare medicine and edible shrub native to the temperate regions of Asia, possessing significant medicinal potential. In this study, the components of S. bumalda tender leaves and buds extract (SBE) were analyzed and identified by HPLC and LC/MS method, and the safety of SBE was evaluated through mouse acute toxicity models. The protective effects of SBE on dextran sulfate sodium (DSS)-induced ulcerative colitis (UC) in mice were investigated in terms of inflammatory factor levels, oxidative stress, and gut microorganisms. Results showed that hyperoside, kaempferol-3-O-rutinoside, isorhoifolin, and rutin were the main components of the extract, and SBE demonstrated good safety in experimental mice. SBE could alleviate weight losing, disease activity index (DAI) raising, and colon shortening in mice. Pathological section results showed that the inflammatory cell infiltration decreased significantly, and the number of goblet cells increased significantly in the SBE group. After SBE treatment, interleukin-6 (IL-6), interleukin-1β (IL-1β), and tumor necrosis factor-α (TNF-α) levels in serum were significantly decreased, and the levels of myeloperoxidase (MPO) and nitric oxide (NO) in colon tissues were significantly decreased. SBE inhibited gut inflammation by increasing Lactobacillus. In summary, SBE played a therapeutic role in UC mice by relieving colon injury, reducing inflammatory factor levels, and maintaining gut flora homeostasis. SBE is expected to become an auxiliary means to participate in the prevention and treatment of UC. [ABSTRACT FROM AUTHOR]

Phytoremediation of oil pollution using free-floating aquatic plants is a promising method for water body cleaning. In this study, the influence of Eichhornia crassipes and Pistia stratiotes on the degradation of oil pollution was investigated. The loss of oil alkanes and the rheological characteristics of water were evaluated, and an analysis of the emerging rhizospheric microbial communities was carried out using high-throughput sequencing. The presence of E. crassipes and P. stratiotes plants in oil-contaminated tanks had no effect on the degradation of oil alkanes. However, the presence of plants promoted the development of rhizospheric bacteria capable of growing in oil-contaminated environments. Alpha diversity of microbial communities in oil-contaminated samples was higher in the presence of plants. Additionally, plants significantly reduced the water/oil interfacial tension, which facilitated the availability of hydrocarbons for biodegradation. A difference was noted in the microbiome between E. crassipes and P. stratiotes. Changes in the composition of microbial communities highlight the potential of E. crassipes and P. stratiotes as rhizospheric hosts for microorganisms in the phytoremediation of water bodies. [ABSTRACT FROM AUTHOR]

Nowadays, the enormously growing amount of kitchen waste and wasted sludge has greatly received global attention. Vermicomposting has been represented as an eco-friendly and sustainable alternative for organic waste management. This study utilized kitchen waste generated by the university canteen and excess sludge from municipal wastewater treatment to collaboratively realize waste to resource through vermicomposting with a composting control. The results indicated that the treatment utilizing an equal mass ratio of wasted sludge and kitchen waste (T3) exhibited the greatest reduction in total organic carbon and the highest increase in total nitrogen. Furthermore, the predominant phyla observed were Proteobacteria, Actinobacteriota, Bacteroidetes, and Firmicutes. Functional prediction analysis demonstrated higher relative abundances of β-glucosidase (ascF) and 6-phospho-β-glucosidase (bglA, celF) in the vermicomposting, suggesting that the earthworms essentially enhanced the cellulose degradation. More importantly, the co-occurrence network analysis demonstrated that the vermicomposting showed a stronger interaction between Gordonia and other bacteria, thereby enhancing its ability to degrade macromolecular compounds. In general, the vermicomposting can smoothly and remarkably stabilize the kitchen waste, assisted by excess sludge and sawdust. [ABSTRACT FROM AUTHOR]

Serotonergic neurons in the central nervous system control behavior and mood, but knowledge of the roles of serotonergic circuits in the regulation of immune homeostasis is limited. Here, we employ mouse genetics to investigate the functions of enteric serotonergic neurons in the control of immune responses and find that these circuits regulate IgA induction and boost host defense against oral, but not systemic Salmonella Typhimurium infection. Enteric serotonergic neurons promote gut-homing, retention and activation of intestinal plasmacytoid dendritic cells (pDC). Mechanistically, this neuro-immune crosstalk is achieved through a serotonin-5-HT receptor 7 (HTR7) signaling axis that ultimately facilitates the pDC-mediated differentiation of IgA+ B cells from IgD+ precursors in the gut. Single-cell RNA-seq data further reveal novel patterns of bidirectional communication between specific subsets of enteric neurons and lamina propria DC. Our findings thus reveal a close interplay between enteric serotonergic neurons and gut immune homeostasis that enhances mucosal defense. Roles of serotonergic neurons in immune homeostasis and host defense are largely unexplored. Here the authors show that in mice enteric serotonergic neurons regulate immune homeostasis and host defense against Salmonella infection by orchestrating gut homing and activation of plasmacytoid dendritic cell, ultimately promoting the differentiation of protective IgA+ B cells. [ABSTRACT FROM AUTHOR]

Introduction: Genistin, as a kind of natural isoflavone glycoside, has good biological activity, and its weak absorption makes it closely related to intestinal flora. However, the roleof theintestinal flora is still unclear andwhether themetabolites produced by the intestinal flora are absorbed systemically is also variable. Methods: Genistin was fermented for 24 h based on fecal bacteria fermentation technology. The components were qualitatively and quantitatively analyzed by HPLC and UHPLC-Q-Exactive Orbitrap Mass spectrometry. The composition of intestinal flora in fermentation samples from fecal bacteria was detected by 16S rRNA sequencing. Five representative probiotics were cultured in vitro and fermented with genistin to determine similarities and differences in genistin metabolites by different bacteria at different times. Finally, the absorption results of metabolites by fermentation were verified by a Caco-2 cell monolayer. Results: The HPLC results of fecal fermentation showed that genistein levels increased from 0.0139 ± 0.0057 mg/mL to 0.0426 ± 0.0251 mg/mL and two new metabolites were produced. A total of 46 metabolites following fecal fermentation were identified, resulting from various biotransformation reaction products, such as decarbonylation, hydroxylation, and methylation. Simultaneously, the 16S rRNA results showed that the intestinal flora changed significantly before and after fermentation and that the intestinal microorganisms in the control (Con) group and the fermentation (Fer) group showed a significant separation trend. Five genera, Lactobacillus, Bifidobacterium, Parabacteroides, Sutterella, and Dorea, were considered the dominant flora for genistin fermentation. The qualitative results of fermentation of genistin by five probiotics at different times showed that there were significant differences in small molecule metabolites by fermentation of different bacteria. Meanwhile, most metabolites could be identified following fecal bacteria fermentation, which verified the importance of the dominant bacteria in the feces for the biotransformation of components. Finally, the absorption results of the metabolites based on the Caco-2 cell monolayer showed that 14 metabolites could be absorbed into the circulation in vivo through the mesentery. Discussion: The small molecule metabolites of genistin by fermentation of fecal bacteria can be well absorbed systemically by the body. These studies provide a reference value for explaining the transformation and absorption of flavonoid glycosides in the intestine. [ABSTRACT FROM AUTHOR]

There is a growing interest in studying the microbiota associated with aging by integrating multiple longevity researches while minimizing the influence of confounding factors. Here, we reprocessed metagenomic sequencing data from four different aging research studies and evaluated potential confounding factors in order to minimize the batch effect. Subsequently, we detected the diversity and abundance of the gut microbiome in three different age cohorts. Out of 1053 different bacteria species, only four showed substantial depletion across different age groups: Ligilactobacillus ruminis, Turicibacter sp. H121, Blautia massiliensis, and Anaerostipes hadrus. Archaea accumulated more in young individuals compared to elderly and centenarians. Candida albicans was more prevalent in centenarians, but Nakaseomyces glabratus (also known as Candida glabrata) was more common in elderly adults. Shuimuvirus IME207 showed a significant increase in centenarians compared to both control groups. In addition, we utilized a Fisher's exact test to investigate topological properties of differentially abundant microbiota in the co-occurrence network of each age group. Microbial signatures specific to different age stages were identified based on the condition: the reads showing differential abundance were higher compared to the other age groups. Lastly, we selected Methanosarcina sp. Kolksee for the Y group, Prevotella copri for the E group and Shuimuvirus IME207 for the C group as representatives of age-related characteristics to study how their interactions change during the aging process. Our results provide crucial insights into the gut microbiome's ecological dynamics in relation to the aging process. [ABSTRACT FROM AUTHOR]

Background: Dengue is the most re-emergent infection, with approximately 100 million new cases reported annually, yet no effective treatment or vaccine exists. Here, we aim to define the microbial community structure and their functional profiles in the dengue positive patients with varying disease severity. Methodology/Principal findings: Hospital admitted 112 dengue-positive patients blood samples were analyzed by dual RNA-sequencing to simultaneously identify the transcriptionally active microbes (TAMs), their expressed genes and associated pathways. Results highlight that patients with severe dengue exhibited increased microbial diversity and presence of opportunistic species (unique and core) which includes Bacillus cereus, Burkholderia pseudomallei, Streptococcus suis, and Serratia marcescens. The functional profile analysis revealed enriched metabolic pathways such as protein degradation, nucleotide biosynthesis, ion transport, cell shape integrity, and ATP formation in severe cases, indicating the high energy demands and adaptability of these microbes. Conclusion: Our metatranscriptomic approach provides a species-level characterization of blood microbiome composition and reveals a heightened diversity of TAMs in patients with severe dengue, underscoring the need for further research into the role of blood microbiota in disease progression. Comparing the microbial signatures across the severity classes early in the disease offers unique potential for convenient and early diagnosis of dengue infection. Author summary: Dengue poses a significant public health challenge in tropical and subtropical regions. The lack of a specific treatment or broadly effective vaccine highlights the critical need for novel approaches. In this study, we investigated the transcriptionally active microbial species (TAMs) in 112 dengue-positive patients from MAX Hospital in Delhi, India, to identify their correlations with disease severity. RNA-seq analysis revealed an increased abundance of opportunistic TAMs in severe dengue patients, with some species showing significant associations with platelet counts and total leukocyte count (TLC). Our findings underscore the underappreciated importance of the blood microbiome in dengue, particularly the heightened metabolic activity of these opportunistic species in severe cases. This study offers valuable insights for early infection diagnosis for dengue management. The species-level data identified here could pave the way for systematic exploration of microbial involvement in dengue virus (DENV) infections, potentially serving as an indicator for new adjuvant treatment strategies. [ABSTRACT FROM AUTHOR]

Cape gooseberries are exquisitely flavored fruits; their rapid deterioration reduces their shelf life. Understanding the unique mycobiome of fruit peels is an essential step in identifying the taxa causing postharvest loss. The current study proposes to analyze the fungal communities of cape gooseberry peels collected from an organic orchard at unripe and ripe stages and purchased from open-air market sites, using the ITS2 region metabarcoding. According to the Kruskal–Wallis test, there were no statistically significant differences found in either the phylogenetic or non-phylogenetic alpha diversity indices. Significant differences in fungal communities were observed between the market and orchard groups based on beta diversity results. Ascomycota (85.72–96.76%), Basidiomycota (3.21–13.91%), and Chytridiomycota (0.07–9.35%) were the most common fungal phyla, their abundance varying with the ripening stage and origin. Dothideomycetes in the orchard group and Saccharomycetes in the market group were the two most prevalent classes. Furthermore, we investigate which taxa showed a significant difference in abundance between the two conditions (market vs. orchard) using the analysis of compositions of microbiomes with bias correction (ANCOM-BC) test. Regardless of the phase, the orchard samples exhibited a notable increase in the mean absolute abundance of various beneficial fungal taxa, including Tilletiopsis washingtonensis and Articulospora proliferata, whereas the market samples demonstrated a high abundance of harmful yeasts and molds such as Meyerozyma guilliermondii, Candida railenensis, and Botrytis caroliniana. Although it is unclear how these microorganisms augment at the market sites and might impact the fruit quality after harvest, from a fruit safety perspective, it is essential to comprehend the diversity and variation of the mycobiome composition at different ripening stages to further develop strategies to improve food safety postharvest. [ABSTRACT FROM AUTHOR]

Background: The presence of bacteria in the blood of healthy individuals remains controversial. This study explored the comprehensive bacterial profiles and specific biomarkers in different components of healthy Chinese blood donors. Methods: A total of 5230 whole blood (WB) specimens were collected. Among them, 5200 random samples were pooled into 26 mixed samples for bacterial profile analysis. The remaining 30 random samples were divided into 4 groups based on components: WB, plasma, red blood cells (RBCs), and buffy coat (BC). Subsequently, the amplicons of the bacterial 16S rDNA V3–V4 fragments were sequenced to measure the diversity and composition of the bacteria using next‐generation sequencing. Results: The bacterial DNAs in the blood primarily originated from the Proteobacteria phylum. A total of 301 species of bacterial DNA were found in blood specimens, with 46 species being present among all groups. A significantly higher abundance of bacterial DNA was found in the plasma and RBCs compared to those in BC and WB. However, the plasma and RBC groups showed significantly higher species diversity and richness compared to the BC and WB groups. In addition, the WB group had a significantly different community structure and composition compared to the plasma and RBC groups but was similar to the BC group. Conclusion: The presence of bacterial DNA fragments was confirmed in blood from healthy Chinese donors. The bacterial DNA fragments enriched in plasma showed the highest diversity, followed by RBC, WB, and BC. These results provide a foundation for further research on the microbiome in the blood of healthy individuals. [ABSTRACT FROM AUTHOR]

Inonotus hispidus (Bull.) P. Karst., is a medicinal fungus, which parasitizes broad-leaved tree such as Morus alba L., Fraxinus mandshurica Rupr., and Ulmus macrocarpa Hance. To elucidate the internal relationship between I. hispidus and its hosts, this study analyzed endophytic bacteria and fungi in the roots of M. alba and F. mandshurica growing I. hispidus using the 16S rDNA and ITS high-throughput sequencing technologies; and conducted widely targeted metabolomics research using UPLC-MS/MS. The results showed that Cyanobacteria and unidentified chloroplasts had the highest relative abundance at the phylum and genus levels, respectively. For endophytic fungi, Ascomycota was dominant at the phylum level, while Pleosporales gen Incertae sedis and Oncopodiella were the dominant genera in the roots of M. alba and F. mandshurica, respectively. Widely targeted metabolomics identified 562 differential metabolites and 46 metabolic pathways. Correlation analysis revealed that Xanthobacteraceae, Pseudorhodoplanes, and Bauldia were potential regulators of phenolic acids and phenylpropanoids biosynthesis. Additionally, the genus Oncopodiella was primarily associated with the enrichment of lipids, amino acids, sugars, phenolic acids, and other compounds. This result provides significant insights into the size of the fruiting body, resource development, and active ingredients of I. hispidus from different tree sources. [ABSTRACT FROM AUTHOR]

As a large agricultural country, China produces a large number of agricultural and sideline products while harvesting agricultural products every year. Crop straw is one of them. Broom sorghum is a traditional crop in China, which produces a large amount of straw resources every year. These straw resources are placed in the field and cannot be used efficiently. The purpose of this study was to solve the problem of straw utilization of Broom sorghum, one of the main food crops in arid and semi-arid areas of northern China. Broom sorghum is not only a nutritious food crop, its straw is also rich in crude fiber and mineral elements, which has high utilization value. However, due to the high content of lignocellulose in straw, the texture is hard, which limits its digestion and utilization efficiency as feed. In this study, the broom sorghum straw was used as the research object, and the straw raw materials were treated with Lactobacillus plantarum, cellulase and xylanase, respectively. After silage fermentation for 30 d and 60 d, the bags were opened to determine the nutritional quality, fermentation quality, microbial community structure and other indicators. The best fermentation time and additives for broom sorghum straw silage were comprehensively screened to improve the nutritional value of straw and animal production performance. The results showed that the nutritional quality of silage straw increased with the extension of fermentation time. Compared with silage straw after 30 days of fermentation, the nutritional quality and fermentation quality of straw were significantly improved after 60 days of fermentation. Lactobacillus plantarum, cellulase and xylanase could improve the silage performance of broom sorghum straw by improving the microbial community structure in straw, and the effect of cellulase was the best. When cellulase was used in straw at the standard of 20 U/g FM, the content of water-soluble carbohydrates could be significantly increased to 31.35 g/kg FM, and the concentration of lactic acid was also significantly increased to 23.79 g/kg FM. Therefore, in actual production, it is recommended to use cellulase at a dose of 20 U/g FM in broom sorghum silage and open the bag after 60 days of silage fermentation. The results of this study provided a scientific basis for the efficient utilization of broom sorghum straw as feed. [ABSTRACT FROM AUTHOR]

This study analyzed the effects of Trichoderma harzianum on the growth of continuous cropping Lagenaria siceraria and the physical and chemical properties of rhizosphere soil and microbial community structure, using Illumina Miseq (PE300) high-throughput sequencing technology along with physiological and biochemical detection. The results indicated that after applying T. harzianum, the growth of L. siceraria was significantly promoted, with increases in plant height, fresh weight, and dry weight of 21.42%, 24.5%, and 4.5%, respectively. The pH of the rhizosphere soil decreased from 7.78 to 7.51, while the electrical conductivity, the available phosphorus, the available potassium, and the total nitrogen were markedly higher compared to the control group and increased by 13.95%, 22.54%, 21.37%, and 16.41%, respectively. The activities of catalase and sucrase in the rhizosphere increased by 18.33% and 61.47%, and the content of soil organic carbon (SOC) increased by 27.39%, which indicated that T. harzianum could enhance soil enzyme activity and promotes the transformation of organic matter. The relative abundance of beneficial bacteria such as Pseudomonas increased, while the relative abundance of harmful fungi such as Fusarium and Podosphaera decreased significantly. [ABSTRACT FROM AUTHOR]

Low temperatures pose a critical challenge to aquaculture operations, as they can significantly affect fish health and overall productivity. The study investigated the impact of low-temperature stress on juvenile golden pompano, focusing on serum indicators, intestinal microbiome, and intestinal transcriptome. With 180 fish divided into low-temperature (18 ± 0.5) ℃ and control (28 ± 0.5) ℃ groups, the gradual temperature decrease mimicked natural seasonal changes. Each group had 3 replicates, with 30 fish per replicate. Results indicated significant effects on serum indicators, including enzyme activity and ion concentrations. While intestinal flora richness was not drastically affected, the dominant flora composition changed. Transcriptome analysis revealed 1752 differentially expressed genes, with enrichment in pathways related to circadian rhythm, proteasome, metabolism, and signaling pathways. This research enhances understanding of cold stress responses in juvenile golden pompano, offering insights for tailored aquaculture management to promote robust and stress-resistant fish stocks. The findings contribute to sustainable aquaculture practices and lay the groundwork for future studies on temperature stress and fish health. [ABSTRACT FROM AUTHOR]

Achnatherum inebrians is a perennial grass widely distributed in northwest China. Nearly all wild A. inebrians plants are infected by Epichloë endophytes. In this study, bacteria from the phyllosphere were isolated from leaves of both endophyte‐free and endophyte‐infected A. inebrians and sequenced for identification. Pseudomonas, comprising 48.12% of the culturable bacterial communities, was the most dominant bacterial genus. Thirty‐four strains from 12 Pseudomonas species were used to inoculate A. inebrians seeds and plants. Results indicated that Epichloë significantly increased the diversity and richness index of the phyllosphere. Pseudomonas Sp1, Sp3, Sp5 and Sp7 had a significantly positive effect on plant growth and photosynthesis, whereas Sp10, Sp11 and Sp12 had a significantly negative effect. Whole‐genome and pan‐genome analysis suggested that the variability in the effects of Pseudomonas on A. inebrians was related to differences in genome composition and genomic islands. [ABSTRACT FROM AUTHOR]

The oral microbiome, studied by sampling the saliva or by oral rinse, has been long thought to have diagnostic capacity for head and neck cancers (HNC). However, previous reports on the HNC oral microbiome provide inconsistent results. The aim of this study is to consolidate these datasets and determine the oral microbial composition between HNC patients to healthy and premalignant individuals. We analyzed 16 published head and neck cancer (HNC) short-read 16S rRNA sequencing datasets, specifically targeting the V3V4, V4 and V4V5 regions. These datasets included saliva and oral rinse samples from donors with HNC, as well as from healthy and premalignant donors. Differences in diversities and microbial abundance were determined. HNC saliva displayed lower alpha diversity than healthy donors. In contrast, the opposite trend was observed for oral rinse samples. Beta diversity scores were largely similar across different patient types. Similar oral phyla were detected for all samples, but proportions were largely dependent on sample type (i.e., saliva or oral rinse) and primer set utilized for 16S rRNA sequencing. Neisseria, Leptotrichia and Megasphaera were elevated in healthy saliva, while Mycoplasma was elevated in HNC saliva. Oral rinse and saliva displayed similar enrichment for Fusobacterium, while Veillonella, Alloprevotella, and Campylobacter showed conflicting results. The sparse partial least squares discriminant analysis model performed effectively in discriminating HNC from healthy or premalignant patients using V3V4 saliva (AUC = 0.888) and V3V4 oral rinse (AUC = 0.928), while poor discriminative capacity was observed for V4 saliva (AUC = 0.688). In conclusion, our meta-analysis highlighted the limitations of 16S rRNA sequencing, particularly due to variations across study batches, primer sets (i.e., V3V4, V4), and sample types. Hence, caution should be exercised when interpreting 16S rRNA sequencing results across studies, especially when different primer sets and sample types are used. [ABSTRACT FROM AUTHOR]

Background. Currently, it is known that the gut microbiota plays an important role in the functioning of the immune system, and a rebalancing of the bacterial community can arouse complex immune reactions and lead to immune-mediated responses in an organism, in particular, the development of atopic dermatitis (AD). Cytokines and chemokines are regulators of the innate and adaptive immune response and represent the most important biomarkers of the immune system. It is known that changes in cytokine profiles are a hallmark of many diseases, including atopy. However, it remains unclear how the bacterial imbalance disrupts the function of the immune response in AD. Objectives. We attempted to determine the role of gut bacteria in modulating cytokine pathways and their role in atopic inflammation. Methods. We sequenced the 16S rRNA gene from 50 stool samples of children aged 3–12 years who had confirmed atopic dermatitis, and 50 samples from healthy children to serve as a control group. To evaluate the immune status, we conducted a multiplex immunofluorescence assay and measured the levels of 41 cytokines and chemokines in the serum of all participants. Results. To find out whether changes in the composition of the gut microbiota were significantly associated with changes in the level of inflammatory cytokines, a correlation was calculated between each pair of bacterial family and cytokine. In the AD group, 191 correlations were significant (Spearman's correlation coefficient, p ≤ 0.05), 85 of which were positive and 106 which were negative. Conclusions. It has been demonstrated that intestinal dysbiosis is associated with alterations in cytokine profiles, specifically an increase in proinflammatory cytokine concentrations. This may indicate a systemic impact of these conditions, leading to an imbalance in the immune system's response to the Th2 type. As a result, atopic conditions may develop. Additionally, a correlation between known AD biomarkers (IL-5, IL-8, IL-13, CCL22, IFN-γ, TNF-α) and alterations in the abundance of bacterial families (Pasteurellaceae, Barnesiellaceae, Eubacteriaceae) was observed. [ABSTRACT FROM AUTHOR]

【Objective】 Based on the long-term positioning experiment of organic carbon source material application, the response characteristics of rice rhizosphere anaerobic microbial community diversity to organic carbon source material input in Erhai lake basin were analyzed. 【Method】 Three treatments as non-fertilizer（CK）, chemical fertilizer（T1） and corn straw combined with chemical fertilizer（T2） were set to analyze the diversity characteristics of rice rhizosphere anaerobic microbial communities based on nitrogen conversion functional genes（nifH） and carbon conversion functional genes（cbbL）. The correlation between soluble N and P contents in soil and anaerobic microbial population was analyzed using redundancy analysis（RDA）. 【Result】 The results of Alpha and Beta diversity analysis showed that the Observed species, Shannon index and Chao1 index significantly improved（P<0.05）, and the difference of anaerobic microbial community structure significantly enhanced. Moreover, long-term application of organic carbon source material significantly increased the relative abundance of Proteobacteria and Cyanobacteria（P<0.05） at the phylum level. At the genus level, the population abundance of Methylibium and Bradyrhizobium increased, while the population abundance of Paraburkholderia decreased. In addition, the relative abundance of Cupriavidus taiwanensis and Alkaliphilus oremlandii significantly increased at species level（P<0.05）,however, Azohydromonas lata and Sulfuricaulis limicola decreased（P<0.05）. The results of redundancy analysis showed that soluble N had the highest resolution to the anaerobic microbial community. 【Conclusion】 In the high carbon storage farmland of Erhai lake basin, corn straw combined with chemical fertilizer mainly affected the community structure, physiological and ecological functions of rice rhizosphere anaerobic microorganisms by regulating the content of soluble nitrogen in the soil, and then affected their carbon and nitrogen conversion process. The results of the study have a certain role in promoting the accurate prediction of the changes of carbon, nitrogen and microbial structure in rice field and their influencing pathways, and can provide a theoretical basis for the optimization of regional farmland ecosystem management measures and the reasonable protection of farmland ecosystem. [ABSTRACT FROM AUTHOR]

To investigate the oral microflora of patients with oesophageal squamous cell carcinoma (ESCC), saliva samples were collected from 20 patients with ESCC and 21 healthy controls. The V3-V4 region of 16S rDNA was amplified and sequenced by the Illumina MiSeq high-throughput sequencing platform. The final sequences were used for OTU analysis. Alpha and beta diversity analysis showed that the bacterial diversity and richness of the ESCC group were lower than those of the control group, while the variability of the ESCC group was higher than that of the control group. According to the Metastats difference analysis and LEfSe analysis, the high risk of ESCC may be related to Actinomyces and Atopobium, while the healthy control group is closely related to Fusobacterium and Porphyromonas (the analysis was performed at the genus level). The establishment of the relationship between oral microbiota and risk of ESCC may lead to significant advances in understanding the aetiology of cancer and may open a new research paradigm for cancer prevention. [ABSTRACT FROM AUTHOR]

Purpose: Fluoroquinolone-resistant (FQR) Escherichia coli causes transrectal prostate biopsy infections. In order to reduce colonization of these bacteria in carriers, we would like to understand the surrounding microbiome to determine targets for decolonization. Materials and Methods: We perform an observational study to investigate the microbiome differences in men with and without FQR organisms found on rectal culture. A rectal swab with two culturettes was performed on men before an upcoming prostate biopsy procedure as standard of care to perform "targeted prophylaxis." Detection of FQR was performed by the standard microbiology lab inoculates the swab onto MacConkey agar containing ciprofloxacin. The extra swab was sent for 16S rRNA amplicon sequencing (MiSeq paired-end) using the V1V2 primer. Alpha and beta-diversity analysis were performed using QIIME. We used PERMANOVA to evaluate the statistical significance of beta-diversity distances within and between groups of interest. Results: We collected 116 rectal swab samples before biopsy for 16S rRNA amplicon sequencing. We identified 18 isolates (15.5%, 18/116) that were positive and had relative reduced diversity profiles (p<0.05). Enterobacteriaceae were significantly over-represented in the FQR subjects (adjusted p=0.03). Conclusions: Microbiome analysis determined that men colonized with FQR bacteria have less diverse bacterial communities (dysbiosis), higher levels of Enterobacteriaceae and reduced levels of Prevotella disiens . These results may have implications in pre/ probiotic intervention studies. [ABSTRACT FROM AUTHOR]

Abstract Osteoporosis (OP) is a common metabolic bone disease characterized by low bone mass and microstructural deterioration of bone. Changes in the composition and structure of gut microbiota (GM) are related to changes of bone mass and bone microstructure. However, the relationship between GM and bone mineral density (BMD) is complex, and data are especially scarce for Chinese Han youth. Therefore, 62 Chinese Han youth participants were recruited. Furthermore, according to the T–score evaluation criteria of the World Health Organization (WHO), we divided the BMD levels of participants into three groups: osteoporosis\BDL, osteopenia\BDM, normal bone density\BDH, and the associations between GM community and BMD groups were conducted. According to alpha and beta diversity analysis, significant differences were found in the microbial richness and composition between groups. The dominant phyla of GM in a cohort of Chinese Han youth were Bacteroidota (50.6%) and Firmicutes (41.6%). Anaerobic microorganisms, such as g_Faecalibacterium and g_Megamonas, account for the largest proportion in the gut, which were mainly Firmicutes phylum. The dominant genera and species in the three BMD groups were g_Prevotella, g_Bacteroides, g_Faecalibacterium, g_Megamonas, s_Prevotella copri, s_unclassified_g_Faecalibacterium, s_unclassified_g_Prevotella, s_unclassified_g_Bacteroides and s_Bacteroides plebeius. g_Faecalibacterium, g_Bacteroides and g_Ruminococcus differed between the BDH and BDL groups as well as between the BDH and BDM groups. LEfSe showed three genus communities and eight species communities were enriched in the three BMD groups, respectively. The associations between microbial relative abundance and T–score was not statistically significant by Spearman and regression analysis. In conclusion, the alpha diversity indexes in the BDH group were higher than in the BDL group, and several taxa were identified that may be the targets for diagnosis and therapy of OP.

Abstract Background Taxol, derived from Taxus trees, is a valuable natural resource for the development of anticancer drugs. Endophytic fungi from Taxus trees are a promising alternative source of Taxol. However, the impact of plant-endophytic microbial interaction on the host’s Taxol biosynthesis is largely unknown. Results In the current study, the diversity of endophytic fungi in three different Taxus species was analyzed using Internal Transcribed Spacer sequencing. A total of 271 Operational Taxonomic Units (OTUs) were identified, grouping into 2 phyla, 8 classes, 16 orders, 19 families, and 19 genera. Alpha and beta diversity analysis indicated significant differences in endophytic fungal communities among the various Taxus trees. At the genus level, Alternaria and Davidiella were predominantly found in T. mairei and T. media, respectively. By utilizing a previously published dataset, a Pearson correlation analysis was conducted to predict the taxol biosynthesis-related fungal genera. Following screening, two isolates of Alternaria (L7 and M14) were obtained. Effect of inoculation with Alternaria isolates on the gene expression and metabolite accumulation of T. mairei was determined by transcriptomic and untargeted metabolomic studies. The co-inoculation assay suggests that the two Alternaria isolates may have a negative regulatory effect on taxol biosynthesis by influencing hormone signaling pathways. Conclusion Our findings will serve as a foundation for advancing the production and utilization of Taxus and will also aid in screening endophytic fungi related to taxol production.

Abstract This study investigates sex-specific effects in a gain-of-function model to evaluate Nfil3 function in relation to high-fat diet (HFD)-induced metabolic dysfunction-associated steatotic liver disease (MASLD) and gut microbiota (GM)-induced alterations in the bile acid (BA) profile. MASLD is induced in both wild type and Nfil3-deficient (NKO) C57BL/6 J mice through an HFD. The hepatic immune response is evaluated using flow cytometry, revealing that NKO mice exhibit lower body weight, serum triglyceride (TG) levels, tissue injury, inflammation, and fat accumulation. The Nfil3 deletion reduces macrophage counts in fibrotic liver tissues, decreases proinflammatory gene and protein expression, and diminishes gut barrier function. Alpha and beta diversity analysis reveal increased GM alpha diversity across different sexes. The Nfil3 gene deletion modifies the BA profile, suggesting that negative feedback through the Nfil3-FXR-FGF15 axis facilitates BA recycling from the liver via enterohepatic circulation. Therefore, inhibiting Nfil3 in the liver offers a viable treatment approach for MASLD.

Chemical coagulation has gained recognition as an effective technique to enhance the removal efficiency of pollutants in wastewater prior to their entry into a constructed wetland (CW) system. However, its potential impact on the chemical and microbial properties of soil and plant systems within CWs requires further research. This study investigated the impact of using ferric chloride (FeCl 3) as a pre-treatment stage for dairy wastewater (DWW) on the chemical and microbial properties of water-soil-plant systems of replicated pilot-scale CWs, comparing them to CWs treating untreated DWW. CWs treating amended DWW had better performance than CWs treating raw DWW for all water quality parameters (COD, TSS, TP, and TN), ensuring compliance with the EU wastewater discharge directives. Soil properties remained mostly unaffected except for pH, calcium and phosphorus (P), which were lower in CWs treating amended DWW. As a result of lower nitrogen (N) and P loads, the plants in CWs receiving FeCl 3 -amended DWW had lower N and P contents than the plants of raw DWW CWs. However, the lower loads of P into amended DWW CWs did not limit the growth of Phragmites australis, which were able to accumulate trace elements higher than CWs receiving raw DWW. Alpha and Beta-diversity analysis revealed minor differences in community richness and composition between both treatments, with only 3.7% (34 genera) showed significant disparities. Overall, the application of chemical coagulation produced superior effluent quality without affecting the properties of soil and plant of CWs or altering the functioning of the microbial community. [Display omitted] • Wastewater pre-treatment using FeCl 3 improved the performance of CWs. • FeCl 3 pre-treatment had no negative effects on soil and plant properties. • FeCl 3 pre-treatment did not alter microbial community diversity and composition. [ABSTRACT FROM AUTHOR]

【Objective】The microbial community diversity characteristics of alkaline tobacco planting soil in Baoshan Mountains were analyzed, and the inhibition effect of deep tillage and application of bio-organic fertilizer on soil quality degradation was investigated, so as to provide theoretical basis for the optimal management of regional tobacco planting soil. 【Method】With deep ploughing (30 cm) as the main treatment, and bio-organic fertilizer cultivation as the secondary treatment, a random block experiment was set up to analyze and test the main physical and chemical properties, enzyme activities and microbial community structure of the soil; analyze the main physical and chemical properties and enzyme activities of the soil relationship with microbial population abundance. 【Results】The treatment of deep tillage + chemical fertilizer + bio-organic fertilizer (treatment CS) significantly decreased soil bulk density and pH by 28.64% and 9.21%, respectively; significantly increased soil organic matter, total phosphorus, available phosphorus and available potassium content, as well as invertase and urease activities, 31.54%, 21.63%, 165.31%, 77.34%, 21.68, 27.95% and 238.55% respectively. The results of Alpha and Beta diversity analysis showed that there was no significant difference in bacterial Chao1 index and Shannon index among the treatments; CS treatment significantly increased the fungal Chao1 index and Shannon index (P<0.05), which promoted the enhancement of bacterial and fungal community differences, and affected the fungal community structure. The effect of composition is more pronounced. The results of community structure showed that CS treatment significantly increased the abundance of Proteobacteria and Mortierellomycota by 74.32% and 280.70%, respectively; The population abundance of Chloroflexi, Actinobacteria and Basidiomycota decreased by 12.83%, 21.88%, 36.57% and 70.04%, respectively. LEfSe analysis showed that CS treatment resulted in an increase in significantly different species of bacteria and fungi at the genus level. The results of BugBase phenotype prediction and FUNGuild functional prediction showed that CS treatment significantly affected soil microbial functional groups, among which the abundance of pathogenic bacteria and phytopathogenic fungi decreased significantly. The correlation results showed that soil bulk density and pH were the main physicochemical factors affecting soil bacterial and fungal community structure. 【Conclusion】Deep tillage and application of bio-organic fertilizer reduce soil bulk density and pH, increase organic matter and nutrient content, promote the formation of soil microbial functional diversity, and improve soil enzyme activity, which are effective measures to improve the quality of alkaline tobacco planting soil. [ABSTRACT FROM AUTHOR]

Introduction: Enterotoxigenic Escherichia coli (ETEC) is the main diarrhea-causing pathogen in children and young animals and has become a global health concern. Berberine is a type of "medicine and food homology" and has a long history of use in China, particularly in treating gastrointestinal disorders and bacterial diarrhea. Methods: In this study, we explored the effects of berberine on growth performance, intestinal inflammation, oxidative damage, and intestinal microbiota in a weaned piglet model of ETEC infection. Twenty-four piglets were randomly divided into four groups--a control group (fed a basal diet [BD] and infused with saline), a BD+ETEC group (fed a basal diet and infused with ETEC), a LB+ETEC group (fed a basal diet with 0.05% berberine and infused with ETEC infection), and a HB +ETEC group (fed a basal diet with 0.1% berberine and infused with ETEC). Results: Berberine significantly improved the final body weight (BW), average daily gain (ADG), and average daily feed intake (ADFI) (P<0.05) of piglets, and effectively decreased the incidence of diarrhea among the animals (P<0.05). Additionally, berberine significantly downregulated the expression levels of the genes encoding TNF-α, IL-1b, IL-6, IL-8, TLR4, MyD88, NF-kB, IKKa, and IKKb in the small intestine of piglets (P<0.05). ETEC infection significantly upregulated the expression of genes coding for Nrf2, CAT, SOD1, GPX1, GST, NQO1, HO-1, GCLC, and GCLM in the small intestine of the animals (P<0.05). Berberine significantly upregulated 12 functional COG categories and 7 KEGG signaling pathways. A correlation analysis showed that berberine significantly increased the relative abundance of beneficial bacteria (Gemmiger, Pediococcus, Levilactobacillus, Clostridium, Lactiplantibacillus, Weissella, Enterococcus, Blautia, and Butyricicoccus) and decreased that of pathogenic bacteria (Prevotella, Streptococcus, Parabacteroides, Flavonifractor, Alloprevotella) known to be closely related to intestinal inflammation and oxidative stress in piglets. In conclusion, ETEC infection disrupted the intestinal microbiota in weaned piglets, upregulating the TLR4/MyD88/NF-kB and Nrf2 signaling pathways, and consequently leading to intestinal inflammation and oxidative stress-induced damage. Discussion: Our data indicated that berberine can optimize intestinal microbiota balance and modulate the TLR4/MyD88/NF-kB and Nrf2 signaling pathways, thus helping to alleviate intestinal inflammation and oxidative damage caused by ETEC infection in weaned piglets. [ABSTRACT FROM AUTHOR]

Across the United States, melons are a high demand crop reaching a net production of 2.7 million tons in 2020 with an economic value of $915 million dollars. The goal of this study was to characterize the bacterial diversity of cantaloupe rinds and soil from commercial melon fields at the point of harvest from two major production regions, Arizona, and California. Cantaloupes and composite soil samples were collected from three different commercial production fields, including Imperial Valley, CA, Central Valley, CA, and Yuma Valley, AZ, at the point of harvest over a three-month period, and 16S rRNA gene amplicon sequencing was used to assess bacterial diversity and community structure. The Shannon Diversity Index showed higher diversity among soil compared to the cantaloupe rind regardless of the sampling location. Regional diversity of soil differed significantly, whereas there was no difference in diversity on cantaloupe surfaces. Bray-Curtis Principal Coordinate Analysis (PCoA) dissimilarity distance matrix found the samples clustered by soil and melon individually, and then clustered tighter by region for the soil samples compared to the cantaloupe samples. Taxonomic analysis found total families among the regions to be 52 for the soil samples and 12 among cantaloupes from all three locations, but composition and abundance did vary between the three locations. Core microbiome analysis identified two taxa shared among soil and cantaloupe which were Bacillaceae and Micrococcaceae. This study lays the foundation for characterizing the cantaloupe microbiome at the point of harvest that provides the cantaloupe industry with those bacterial families that are potentially present entering post-harvest processing, which could assist in improving cantaloupe safety, shelf-life, cantaloupe quality and other critical aspects of cantaloupe post-harvest practices. [ABSTRACT FROM AUTHOR]

The urban environmental effects can have multifaceted impacts on the orchard soil microbial community structure and function. To specifically study these effects, we investigated the soil bacterial and fungal community in the laxly managed citrus orchards using amplicon sequencing. Ascomycota demonstrated significant dominance within the citrus orchard soils. The increased presence of beneficial Trichoderma spp. (0.3%) could help suppress plant pathogens, while the elevated abundance of potential pathogenic fungi, such as Fusarium spp. (0.4%), might raise the likelihood of disorders like root rot, thereby hindering plant growth and resulting in reduced yield. Moreover, we observed significant differences in the alpha and beta diversity of bacterial communities between urban and rural soils (p < 0.001). Environmental surveys and functional prediction of bacterial communities suggested that urban transportation factors and rural waste pollution were likely contributing to these disparities. When comparing bacterial species in urban and rural soils, Bacillus spp. exhibited notable increases in urban areas. Bacillus spp. possess heavy metal tolerance attributed to the presence of chromium reductase and nitroreductase enzymes involved in the chromium (VI) reduction pathway. Our findings have shed light on the intricate interplay of urban environmental effects and root systems, both of which exert influence on the soil microbiota. Apart from the removal of specific pollutants, the application of Bacillus spp. to alleviate traffic pollution, and the use of Trichoderma spp. for plant pathogen suppression were considered viable solutions. The knowledge acquired from this study can be employed to optimize agricultural practices, augment citrus productivity, and foster sustainable agriculture. [ABSTRACT FROM AUTHOR]

Emerging research on the microbiome highlights the significant role of gut health in the development of kidney stones, indicating that an imbalance in gut bacteria or dysbiosis can influence the formation of stones by altering oxalate metabolism and urinary metabolite profiles. In particular, the overabundance of specific bacteria such as Enterococcus and Oxalobacter spp., which are known to affect oxalate absorption, is observed in patients with urolithiasis. This study investigates the effects of gut dysbiosis on urolithiasis through fecal microbiota transplantation (FMT) from patients to rats and its impact on urinary mineral excretion and stone formation. Fecal samples from eight patients with calcium oxalate stones and ten healthy volunteers were collected to assess the gut microbiome. These samples were then transplanted to antibiotic-pretreated Wistar rats for a duration of four weeks. After transplantation, we evaluated changes in the fecal gut microbiome profile, urinary mineral excretion rates, and expression levels of intestinal zonula occluden-1 (ZO-1), SLC26A6 and renal NF-κB. In humans, patients with urolithiasis exhibited increased urinary calcium and oxalate levels, along with decreased citrate excretion and increased urinary supersaturation index. The fecal microbiota showed a notable abundance of Bacteroidota. In rodents, urolithiasis-FMT rats showed urinary disturbances similar to patients, including elevated pH, oxalate level, and supersaturation index, despite negative renal pathology. In addition, a slight elevation in the expression of renal NF-κB, a significant intestinal SLC26A6, and a reduction in ZO-1 expression were observed. The gut microbiome of urolithiasis-FMT rats showed an increased abundance of Bacteroidota, particularly Muribaculaceae, compared to their healthy FMT counterparts. In conclusion, the consistent overabundance of Bacteroidota in both urolithiasis patients and urolithiasis-FMT rats is related to altered intestinal barrier function, hyperoxaluria, and renal inflammation. These findings suggest that gut dysbiosis, characterized by an overgrowth of Bacteroidota, plays a crucial role in the pathogenesis of calcium oxalate urolithiasis, underscoring the potential of targeting the gut microbiota as a therapeutic strategy. [ABSTRACT FROM AUTHOR]

Introduction: Clubroot disease is a devastating soil borne disease caused by infection with Plasmodiophora brassicae, which primarily affects cruciferous plants. The microbial diversity of the soil is an essential indicator of its quality. Methods: This study measured the physicochemical properties of the soil to study the effect of its microbial diversity on the infection of oilseed rape with P. brassicae. High-throughput sequences of the soil bacteria and fungi in the interroot soils of P. brassicae were analyzed under different treatment conditions. Results: In the study, it was found that the efficiency of strain X216 in preventing and controlling the root disease of rapeseed was positively correlated with the amount of solution used to irrigate the root system. The results of the greenhouse and field trials showed that the efficiency of strain X216 against the root disease of rapeseed was 43.16% in the field and 62.14% in the greenhouse. Proteobacteria, Chloroflexi, Rozellomycota, and Basidiomycota are critical phylum in the development of clubroot disease. The application of biocontrol increased the relative abundance of Actinobacteria, Bacillus, Mesorhizobium, Mycobacterium, Streptomyces and Filobasidium, which affected the structure and abundance of microbial communities. A principal coordinate analysis showed that the microbial structure in the soil varied substantially in the bacterial community, and there was no significant difference in soil structure in the fungal community. Discussion: The occurrence of clubroot disease affected the structure of interroot microbial community composition in the soil, which resulted in a decrease in its community diversity. The application of the biocontrol bacterium X216 increased the soil microbial diversity. It effectively reduced the occurrence of P. brassicae, and this study provides a basis to study the microbial diversity in cruciferous crops. [ABSTRACT FROM AUTHOR]

Following bowel surgery, infectious complications, including anastomotic leak (AL), remain major sources of morbidity and mortality. Bowel preparation is often administered with the assumption that gut decontamination reduces post-surgical complications. In this study, we tested this hypothesis using a murine model of colon surgery. The mice were fed either regular chow or a high-fat, high-sugar Western diet. The day before surgery, the mice received one of four interventions: water (control), mechanical bowel preparation (MBP), oral antibiotics (OA), or both MBP and OA. We found no differences in the rates of AL among the experimental groups, and diet did not appear to affect the outcomes. Exploratory analyses showed changes in the gut microbiome consistent with the different treatments, but investigations of fecal short-chain fatty acids and RNA sequencing of colonic tissue did not reveal specific effects of the treatments or the presence of AL. However, we did identify bacterial genera that may be causally associated with AL and developed a predictive index from stool samples as a marker for the presence of AL. Future research is needed to identify and validate a microbial predictive tool and to uncover the microbial-driven mechanisms that lead to AL. [ABSTRACT FROM AUTHOR]