16S rDNA Sequence Research Articles

Integrating fecal metabolomics and gut microbiome to reveal the mechanism of Schisandra chinensis-Acorus tatarinowii Schott treatment in Alzheimer’s disease rats

BackgroundSchisandra chinensis (Turcz.) Baill (Schisandraceae) and Acorus tatarinowii Schott (Araceae Juss) (Sc-At) are two traditional Chinese medicinal herbs that are widely used in the treatment of neurological disorders such as insomnia. In our previous study, we found that Sc-At could improve the therapeutic efficacy of Alzheimer’s disease by affecting aromatase activity and estrogen levels, among other pathways. Material and methodsIn this study, first, the ameliorative effect of Sc-At on cognitive dysfunction in Alzheimer’s disease model rats was verified by Y-maze test together with Elisa assay. Second, fecal untargeted metabolomics analysis was performed using a UPLC-Q-TOF/MS-based metabolomics approach. 16S rDNA sequencing was utilized to screen the differential flora between groups, and linear discriminantan alysis effect size (LEfSe) was used to find the target flora. Finally, Spearman correlation analysis was combined to find the relationship between differential flora and differential metabolites in feces. Results(1) The results of Y-maze test and Elisa assay indicated that Sc-At could improve the cognitive dysfunction of AD model rats. (2) Metabolomics results showed that fecal metabolite levels were significantly different from those of rats in the blank group, and 18 potential biomarkers in feces were screened, mainly affecting linoleic acid metabolism, steroid hormone biosynthesis, sphingomyelin metabolism, riboflavin metabolism, etc. The 16S rDNA results showed that the abundance and diversity of intestinal flora in AD rats were destroyed, and the Sc-At treatment was able to reverse these changes. (3) Spearman’s correlation analysis showed a significant correlation between differential metabolites in feces and intestinal flora, further suggesting that Sc-At treats Alzheimer’s disease through the gut-brain axis. ConclusionsIn this study, we explored the mechanism of Sc-At in the treatment of Alzheimer’s disease by integrating fecal untargeted metabolomics and 16S rDNA gene sequencing, and the results showed that Sc-At exerts therapeutic effects on Alzheimer’s disease by improving the intestinal flora and related metabolic pathways.

Clinical formulation Zhigan Oral Liquid intervenes in alcoholic liver injury by regulating the intestinal flora and PI3K\\AKT\\NF-κB pathway

Introduction: Zhigan Oral Liquid (ZOL) was developed from the empirical formulation of Professor Zhao Wenxia, a nationally renowned practitioner of Chinese medicine, and it has been used in Chinese medicine for many years for the effective treatment of alcoholic liver damage (ALD). However, the interventional mechanism of action of the dosage indications for different stages of ALD pathogenesis is not clear. Methods: The main chemical components of ZOL were qualitatively analyzed by ultra-high performance liquid chromatography (UHPLC-Q-Orbitrap HRMS) in tandem with quadrupole electrostatic field orbital well high resolution mass spectrometry and quantitatively analyzed by high-performance liquid chromatography (HPLC). Network pharmacological analysis was performed to predict the targets and pathways of the potential pharmacodynamic components. The pharmacodynamic effects and potential target mechanisms were verified in a murine model of ALD. To observe the effect of ZOL on the intestinal flora, 16s rDNA sequencing was performed on ALD mice. Results: ZOL can achieve alcohol detoxification by increasing the activity of ALDH and other detoxification enzymes and can intervene in the process of alcoholic liver injury and liver fibrosis by regulating the alcohol-induced bacterial dysbiosis, increasing the level of antioxidants, and inhibiting the activation of the PI3K\\AKT\\NF-κB signaling pathway. Kakkalide, Luteolin, Puerarin, tectoridin, and dihydromyricetin are related to the flavonoids that may be the main pharmacodynamic components that exert their medicinal effects. Conclusions: The findings have significant implications for the development of Empirical treatments for alcoholic liver injury. Furthermore, the study contributes to promoting development and utilization of new dosage forms of hospital preparations by emphasizing the composition identification and animal experimental efficacy of ZOL. Overall, this study provides valuable insights into establishing an alcohol-induced liver injury model, and demonstrates the potential of ZOL as a common treatment for alcoholic liver injury a rich source.

Lithium affects sodium balance but not intestinal microbiota - studies in Drosophila melanogaster

BackgroundThe trace element lithium (Li) is known for its therapeutic mood-stabilizing application in humans, but also for its various bioactivities, which have been uncovered in model organisms. According to the literature, Li may interfere with the homeostasis of other minerals in mammals, namely sodium, calcium and magnesium. In addition, Li was found to influence the composition and diversity of the intestinal microbiota in vertebrates, an observation that may be related to the many bioactivities of Li. MethodsBased on these previous findings, we employed the model organism Drosophila melanogaster to decipher whether Li exhibits similar bioactivities in invertebrates. First, we examined the influence of increasing dietary Li supply (0 -100 mM LiCl) on the status of Li and ten other minerals via Inductively coupled plasma - mass spectrometry (ICP-MS) in heads and remaining body parts of the three wildtype strains w1118, Oregon-R-C and Canton-S. In addition, we investigated the potential impact of Li feeding (0, 0.1, 1mM LiCl) on the total bacterial load, α- and β-diversity via real-time quantitative polymerase chain reaction (RT q-PCR) and 16S rDNA sequencing in the intestines of female w1118. ResultsOur observations revealed that Li accumulates linearly in both sexes and all body parts of the three Drosophila strains as the dietary Li supply increases. While the status of most elements remained unchanged, the sodium levels of the fly also correlated positively with the Li content of the diet. The intestinal microbiota, however, remained largely unaffected by Li feeding in terms of both, bacterial load and diversity. ConclusionThese findings support the hypothesis that elevating the Li supply affects sodium homeostasis in Drosophila, a finding coherent with observations in mammals. Furthermore, our data opposes a possible involvement of the bacterial intestinal colonization in the bioactivity of Li in Drosophila.

Desmodium styracifolium (Osb.) Merr. Extracts alleviate cholestatic liver disease by FXR pathway

Ethnopharmacological relevanceCholestatic liver disease (CLD) is a disease characterized by cholestasis. Farnesoid X receptor (FXR) is a nuclear receptor that maintains homeostasis in bile acid metabolism. Studies have shown that gut microbiota interfered with the FXR pathway. Modulation of FXR to inhibit cholestasis has become a key measure in the treatment of CLD. In traditional folk medicine, Desmodium styracifolium (Osb.) Merr. was used as a primary treatment for gallstones, gonorrhea, jaundice, cholecystitis and other diseases. Modern pharmacological studies had also found that the herb has anti-calculus, anti-inflammatory, antioxidant, diuretic and liver damage. Therefore, we speculated that Desmodium styracifolium (Osb.) Merr. extracts (DME) could alleviate CLD through the FXR pathway and might be associated with the gut microbiota. However, studies of DME alleviating CLD through the FXR pathway have not been reported. Aim of studyTo study the effect and mechanism of DME in relieving CLD through in vivo and in vitro experiments. Materials and methodsFirst, mice were administrated with alpha-naphthyl isothiocyanate (ANIT) to establish a CLD model in vivo. Meanwhile, HepG2 cells were induced by lithocholic acid (LCA) to establish the CLD model in vitro. To evaluate the therapeutic effect of DME on CLD mice, hematoxylin-eosin (HE) staining, and biochemical indicators were performed. The prototype of the blood components in mice serum was detected by ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). 16S rDNA sequencing was used to analyze the gut microbiota. Finally, the protein and mRNA expression of the FXR pathway in mice liver tissues or HepG2 cells were detected by Western blot, qRT-PCR, or immunofluorescence. ResultsPathological testing and biochemical indexes showed that DME significantly reduced serum ALT, AST, ALP, TBIL, DBIL, TBA and liver TBA levels, and attenuated liver tissue injury, necrosis and jaundice in CLD mice. In addition, MetagenomeSeq analysis of gut microbiota showed that DME significantly up-regulated the abundance of Parvibacter, down-regulated the abundance of Paenalcaligenes, and regulated bile acid homeostasis. In terms of mRNA expression, DME significantly upregulated the mRNA levels of Nr1h4, Abcb11, Cyp7a1 and Slc10a1. Meanwhile, in terms of protein expression, DME significantly up-regulated the protein expression levels of FXR, BSEP, CYP7A1 and NTCP, which regulated bile acid homeostasis. Finally, the molecular docking results showed that the components of DME, such as Lumichrome, Daidzein and Folic acid, all had good binding ability with FXR, and the surface plasmon resonance (SPR) results also showed that both Lumichrome and Daidzein had a relatively high affinity with FXR. ConclusionDME alleviated CLD through the FXR pathway, and the mechanisms might be associated with the gut microbiota.

Isolation and evaluation of Pediococcus acidilactici YH-15 from cat milk: Potential probiotic effects and antimicrobial properties

The study aimed to screen for the possible presence of lactic acid bacteria (LAB) in cat milk in order to evaluate their probiotic properties. The isolates were characterized by biochemical identification, morphological tests and 16S rDNA sequencing. Afterward, gastrointestinal passage, in vitro safety and probiotic properties were evaluated. The results showed that the isolates had 10 strains of Pediococcus acidilactici permitted in the feed additive catalog. The high survival rate in the acid and bile salt resistance test reflected the good strain tolerance of the isolates to the simulated gastrointestinal conditions of the host in vitro. The mean inhibitory diameters of the 10 strains against chloramphenicol and tetracycline were 23.6 mm and 17.4 mm, respectively; none of the hemolytic tests showed α/β hemolytic ring. The bacteriostatic test showed that P. acidilactici YH-9, YH-14 and YH-15 had inhibitory effects on four common pathogenic bacteria, including Escherichia coli, Salmonella typhimurium, Staphylococcus aureus and Streptococcus. The adhesion test showed that P. acidilactici YH-15 had good adhesion to HT-29 cells. Based on these results, we concluded that P. acidilactici YH-15 extracted from cat milk has potential application as a clinical probiotic therapy and health care product.

Multi-omics and bioinformatics for the investigation of therapeutic mechanism of roucongrong pill against postmenopausal osteoporosis

Ethnopharmacological relevanceThe Roucongrong Pill (RCRP), originating from the historical General Medical Collection of Royal Benevolence, is frequently used to treat postmenopausal osteoporosis (PMOP). Despite its prevalent application, the specific anti-osteoporotic mechanisms of RCRP remain to be elucidated. Aim of the studyThis study aims to elucidate the therapeutic mechanism of RCRP in the context of ovariectomy (OVX)-induced PMOP in rats. By employing an integrative approach, the research combines medicinal chemistry, gut microbiota (GM) profiling, metabolomics, MetOrigin traceability, network pharmacology, molecular docking, and molecular dynamics simulations to deliver a comprehensive analysis. Materials and methodsSprague-Dawley (SD) rats underwent bilateral OVX to establish a PMOP model. The therapeutic efficacy of RCRP was evaluated through bone metrics (BMD, bone strength, BV/TV, Tb.Sp), hematoxylin and eosin (H&E) histological assessment, and bone metabolism markers (OPG, BALP, TRACP-5b, β-CTX, RANKL). Fecal metabolomics and 16S rDNA sequencing were employed to assess the influence of RCRP on GM and metabolite profiles. Furthermore, MetOrigin facilitated the traceability analysis of relevant metabolites. Molecular docking identified potential RCRP compounds with anti-PMOP activity, while their stability and protein interactions were assessed through molecular dynamics simulations. Network pharmacology further confirms the targets of action. ResultsRCRP alleviated PMOP in rats, enhancing bone strength, cortical and trabecular BMD, BV/TV, and serum OPG levels, while reducing Tb.Sp, serum BALP, TRACP-5b, β-CTX, and RANKL concentrations. A total of twenty-six distinct metabolites were identified, of which ten—tribufos, sulfoacetic acid, betamethasone dipropionate, 9-oxooctadeca-10,12,15-trienoic acid, menatetrenone, piperlongumine, maltopentaose, enol-phenylpyruvate, catechol, pentaacetate, and (+)-2-methylpropanoic acid—exhibited correlations with six GM species: Turicibacter, Roseburia, Colidextribacter, Helicobacter, Odoribacter, and Lachnoclostridium, as determined by Spearman's correlation analysis. Notably, MetOrigin revealed the microbial metabolism of taurine and hypotaurine, along with host-specific steroid hormone synthesis. Computational docking studies demonstrated robust interactions between five RCRP-derived steroids (hydroxyecdysone, corticosterone, trilostane, 5α-androstan-3,6,17-trione, and cortisol) and key enzymes (estradiol 17α-dehydrogenase and UDP-glucuronosyltransferase), suggesting a potential enhancement of therapeutic efficacy against PMOP. Furthermore, molecular dynamics simulations indicated stable interactions between hydroxyecdysone and two proteins, with binding free energies of −67.427 kJ/mol and −156.948 kJ/mol, respectively. Through network pharmacology and molecular docking approaches, potential targets of these metabolites were identified, including estrogen receptors ESR1 and ESR2, dual specificity phosphatase 6 (DUSP6), sex hormone-binding globulin (SHBG), prostaglandin E receptor 4 (PTGER4), cannabinoid receptor 2 (CNR2), cathepsin K (CTSK), and androgen receptor (AR). ConclusionsRCRP effectively mitigates OVX-induced bone loss in PMOP rats by modulating GM and associated metabolites, along with their potential targets and key metabolic pathways, including taurine and hypotaurine metabolism, as well as steroid hormone biosynthesis. These findings offer new insights into the therapeutic mechanisms by which RCRP may alleviate PMOP.

A new species of the Trichia botrytis complex from the cloud forest in Ecuador

The paper describes a new myxomycete species, Trichia tuberculata, from the Ecuadorian cloud forest. The phylogeny constructed with nuclear 18S rDNA and mitochondrial 17S rDNA sequences indicates that the taxon is closely related to the recently described species T. acetocorticola, T. nubila, and T. pinicola, all within the T. botrytis complex. The morphology of the inner peridium surface and capillitium also aligns T. tuberculata with these species. However, the distinctive tuberculate peridium, short elater tips, and perhaps the distribution range (so far found in the equatorial zone only) distinguish T. tuberculata from related taxa.

Identification and characterisation of dextran produced by a novel high yielding Weissella cibaria Fiplydextran strain

An exopolysaccharide (EPS)-producing bacterial strain was isolated from fermented soy milk and identified as Weissella cibaria strain Fiplydextran through morphological, biochemical and 16S rDNA sequence analysis. Here, we report the optimisation of cultural conditions for the organism to achieve maximum EPS production, along with its molecular characterisation, functional properties, and prebiotic potential. The exceptionally high EPS yield (0.61 g per g of sucrose) was obtained from the optimised medium (200 g/L of sucrose, 15 g/L of yeast extract) at 30 °C after 48 h. HPAEC-PAD analysis revealed that the EPS is homopolymer of glucose having Mw as 3.23 × 107 Da determined using viscosity method. Methylation analysis and NMR results confirmed the EPS as dextran with α (1 → 6)-linkage (96.5 %) as main chain and α (1 → 3)- as branch chain linkage (3.5 %). Thermogravimetric analysis exhibited higher thermal stability of EPS. The EPS was observed to support the growth of Bacteroides spp. in pure culture form but not that of Lactobacillus or Bifidobacterium spp. However, a low level of bifidogenic activity was observed upon use of mixed culture of B. fragilis and B. longum. The research implies industrial applications of W. cibaria Fiplydextran for the production of high molecular weight dextran with better yield.

Light-driven differences in bacterial networks and organic matter decomposition: Insights from an analysis of the harmful cyanobacterium Microcystis aeruginosa PCC 7806

Freshwater systems are critical yet often underestimated components of global carbon cycling, functioning both as carbon sinks and sources. Cyanobacteria play a key role in this cycle by capturing atmospheric carbon dioxide through photosynthesis. The captured carbon is either released back into the atmosphere or sequestered in sediments following organismal decay. This study examines the pivotal role of cyanobacteria, specifically Microcystis aeruginosa PCC 7806, in the biogeochemical cycling of carbon in freshwater ecosystems, with a focus on how light influences the degradation of cyanobacteria-derived organic matter. Using a combination of 16S rDNA sequencing and excitation-emission matrix coupled with parallel factor (EEM-PARAFAC) analysis, we conducted a 50-day experiment to investigate the dynamics of dissolved organic matter (DOM) and lysate organic matter (LOM) derived from M. aeruginosa PCC 7806 under light and dark conditions. Our results demonstrate that light significantly impacts bacterial community composition, gene functionality, and the decomposition of organic matter. The findings emphasize the crucial role of light in facilitating microbial adaptation, stabilizing microbial networks and driving organic substrate transformation. These insights underscore the influence of light on microbial community dynamics and organic matter degradation, revealing shifts in microbial populations under varying light conditions. This suggests a strong link between photochemical processes and microbial activity, with significant ecological implications.

Weitiao No. 3 (3) enhances the efficacy of anti-programmed cell death protein-1 immunotherapy by modulating the intestinal microbiota in an orthotopic model of gastric cancer mice.

To explore the effects of Weitiao No. 3 (3, WD-3) on anti-programmed cell death protein-1 (PD-1) immunotherapy in gastric cancer (GC). The intestinal microbiota was analyzed by 16S rDNA sequencing of fecal samples from three groups: healthy people (Health), GC patients (GC), and WD-3-treated GC patients (WD-3). Next, we established an orthotopic model of GC mice, which were treated with anti-PD-1, WD-3, or an inoculation of intestinal bacteria. Immune markers CD3, CD4, CD8, and forkhead box protein P3 (FOXP3), and the cell proliferation marker Ki67, were evaluated by immunohistochemistry. Cell apoptosis in GC tumors was assessed by terminal-deoxynucleotidyl-transferase-mediated deoxyuridine triphosphate nick end labeling staining. Enzyme-linked immunosorbent assays (ELISAs) were performed to analyze the serum levels of the following cytokines in GC mice: tumor necrosis factor (TNF)-α, interleukin (IL)-2, IL-6, IL-10, interferon (IFN)-γ, and transforming growth factor (TGF)-β. Sequencing data showed that there were significant differences in the composition of the gut microbial community among the three human groups. The gut bacteria in the three groups mainly comprised the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. At the genus level, the relative abundances of Bifidobacterium and Coprococcus showed significant decreases in the GC group, and an obvious increase in the WD-3 group, compared with the Health group. Interestingly, the relative abundance of Saccharopolyspora was only detected in the WD-3 group. The results of in vivo experiments in GC mice showed that WD-3 or anti-PD-1 treatment increased the levels of CD3+, CD4+, and CD8+ T cells, but decreased the levels of FOXP3+ regulatory T cells. Furthermore, WD-3 or PD-1 antibody treatment inhibited proliferation and promoted apoptosis of GC tumor cells. ELISA analysis showed that WD-3 or PD-1 antibody treatment facilitated TNF-α, IL-2, and IFN-γ expression, while suppressing IL-6, IL-10, and TGF-β expression. Combination therapy with WD-3 and anti-PD-1 intensified all of these effects. WD-3 enhanced the immunotherapeutic efficacy of anti-PD-1 by modulating the intestinal microbiota in an orthotopic model of GC mice.

The gut microbiotas with metabolites regulate the protective role of miR-30a-5p in myocardial infarction

IntroductionGut microbial homeostasis is closely associated with myocardial infarction (MI). However, little is known about how gut microbiota influences miRNAs-regulated MI. ObjectivesThis study aims to elucidate the connections between miR-30a-5p, MI, gut microbiota, and gut microbial metabolite-related pathways, to explore potential strategy for preventing and treating MI. MethodsWe evaluated the effects of knocking out (KO) or overexpressing (OE) miR-30a-5p on MI by assessing cardiac structure and function, myocardial enzyme levels, and apoptosis. Then, we applied 16S rDNA sequencing and metabolomics to explore how intestinal microecology and its microorganisms affect miR-30a-5p-regulated MI. ResultsThe results showed that KO exacerbated MI, whereas OE improved MI damage, compared to the wild-type (WT) mice. KO exacerbated intestinal barrier structure deterioration and further downregulated the expression of Cloudin-1, Occludin, and ZO-1 in MI mice. 16S rDNA sequencing-analyzed gut microbiome of KO and WT mice found that KO mainly reduced g_Lactobacillus. Transplanting fecal microorganisms from KO mice aggravated MI damage in WT mice. However, administering probiotics (mainly containing Lactobacillus) helped neutralize these damages. Intriguingly, fecal microbiota transplantation from OE mice reduced MI damage. Analysis of intestinal microbial metabolites in KO and WT mice found that KO may mainly affect ABC transporters. ABCC1 was identified as the target of KO-aggravated MI. Furthermore, fecal transplantation microorganisms of MI patients aggravated MI injury in mice and miR-30a-5p and ABCC1 were involved in the process. ConclusionsOur findings demonstrate that miR-30a-5p regulates MI by affecting intestinal microbiota homeostasis and targeting ABCC1. This highlights the critical importance of maintaining a healthy gut microbiota homeostasis in MI management.

Xiaobugan decoction prevents CCl4-induced acute liver injury by modulating gut microbiota and hepatic metabolism

BackgroundThe liver plays a crucial role in detoxification and metabolism. When its capacity to metabolize foreign substances is exceeded, it can lead to acute liver injury (ALI). Therefore, preventing liver disease and maintaining daily liver health are of utmost importance. Xiaobugan Decoction (XBGD), a traditional Chinese medicine (TCM) formula, is recorded in ‘Fuxingjue’, is used in folk practice to promote liver health and regulate respiration. However, the hepatoprotective mechanisms of XBGD remained unclear. PurposeWe investigated the prophylactic and hepatoprotective effects of XBGD and explored its related molecular mechanisms using a mouse model of carbon tetrachloride (CCl4)-induced ALI. Study design and methodsXBGD composition was determined using analytical methods, and the main compounds were identified using ultra-high-performance liquid chromatography coupled with Q-Exactive focus mass spectrum (UHPLC-QE-MS) and high-performance liquid chromatography (HPLC). A CCl4-induced L02 cell injury model was employed to explore the protective effects of XBGD on liver cells, and a CCl4-induced ALI mouse model was used to investigate the hepatoprotective effects of XBGD. ResultsCellular experiments demonstrated that XBGD had a protective function against L02 cell damage by increasing cell viability, restoring alanine aminotransferase (ALT), aspartate aminotransferase (AST), and superoxide dismutase (SOD) levels, reducing malondialdehyde (MDA) content, and improving mitochondrial membrane potential (ΔΨm). In the mouse ALI model, XBGD prevented ALI by reducing ALT, AST, and alkaline phosphatase (ALP) levels and inhibiting oxidative stress. Quantitative real-time polymerase chain reaction (qPCR), immumohistochemical staining and western blotting results revealed that XBGD exerted hepatoprotective effects by reducing inflammatory responses and inhibiting cell apoptosis. Furthermore, 1H-NMR metabolomics indicated that XBGD regulates hepatic and intestinal metabolism, whereas 16S rDNA sequencing demonstrated the regulatory effects of XBGD on the gut microbiota. Correlation analysis highlighted the close relationship among gut microbiota, metabolites, and ALI indicators. ConclusionsXBGD is a promising TCM for the prevention of CCl4-induced ALI via regulation of microbiota and metabolism. This study provides a new perspective on the development of hepatoprotective measures and the prevention of liver disease in daily life.

Existence and Distribution of the Microbiome in Tumour Tissues of Children with Hepatoblastoma

Cancer microbiota have recently been demonstrated in several cancer types. The microbiota enhances inflammation in the cancer microenvironment and affects the disease pathology by regulating tumourigenesis, cancer progression, and chemotherapy resistance. Hepatoblastoma (HB), the most common childhood malignant tumour, is a malignant embryonic tumour. However, the pathogenesis and molecular basis of HB remain poorly understood. In this study, to explore the existence and distribution of the microbiome in tumour tissues and adjacent non-tumour tissues of children with HB, we mainly performed 16S rDNA sequencing, and the results showed that the diversity and abundance of the microbiome in children with HB were significantly different between HB tumours and adjacent non-tumour tissues (p < 0.01). At the phylum level, the dominant microbiomes in the tumour tissues were Proteobacteria, Bacteroidetes, and Firmicutes. At the genus level, Ruminococcus was more abundant in HB tumours than in the adjacent non-tumour tissues. Simultaneously, the abundances of Bacteroides, Parabacteroides, Lachnospiracea-NK4A136, and Alistipes in HB tumours were lower than those in the adjacent non-tumour tissues. In addition, Romboutsia strongly correlated with alpha-fetoprotein, an important indicator of HB. Sphingomonas was abundant in primary HB tumours, whereas Oscillibacter and Pandoraea were abundant in metastatic HB tumours. However, whether these bacteria are associated with HB needs further evaluation. Therefore, we identified the microbiome that correlated with the occurrence and development of HB. Ruminococcus and Romboutsia were identified as potential bacterial markers of HB tumours. To conclude, we found that HB also contains cancer microbiota, and it is necessary to shed light on the microbiome characteristics of HB in the future.

The role of Ni- and Cd-resistant rhizobacteria in promoting the growth of rice seedlings and alleviating the combined phytotoxicity of Ni and Cd

The problem of potentially toxic metal pollution is increasingly acute with the development of human society. In this study, we investigated the remediation of nickel (Ni) and cadmium (Cd) co-contamination through inoculating rice with three new-isolated Ni- and Cd-resistant plant growth-promoting rhizobacteria (PGPR) Y3, Y4, and Y5. These three strains possessed growth-promoting properties, including 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, the ability of indoleacetic acid (IAA) production, phosphate solubilization, siderophores production, and exopolysaccharide (EPS) development. According to 16S rDNA sequence homology, strains Y3, Y4, and Y5 were identified as Pseudomonas sp., Chryseobacterium sp., and Enterobacter sp., respectively. Based on the results of rice germination experiments conducted under combined toxicity, we set the contamination concentrations for Ni2+ at 20 μg mL−1 and Cd2+ at 40 μg mL−1. Then we conducted potting experiments at these concentration levels to study the effects of strains Y3, Y4, and Y5 on rice growth under synergistic Ni and Cd stress. The results indicated that the inoculated strains Y3, Y4, and Y5 were effective in promoting the growth of rice seedlings under the combined stress of Ni and Cd, and conferring tolerance to Ni and Cd by increasing the antioxidant enzyme activities of the seedlings. Among them, strain Y3 exhibited stronger ACC deaminase activity, IAA production capacity, and EPS production capacity, showing the most pronounced growth-promoting effect on rice. It was demonstrated that after inoculation with strain Y3, the germination rate of rice seeds increased by 43 %, the fresh weight of stems improved by 35 %, and the chlorophyll content enhanced by 70 % and other growth-promoting phenomena. Additionally, under Ni and Cd stress, strain Y5 performed better than strain Y4 in terms of IAA production capacity and its influence on rice root growth, suggesting that IAA production might play a specifically essential role in root growth under Ni and Cd stress.

Comparative Analysis of Intestinal TLR4 Gene Expression and Functional Verification in Lepus yarkandensis and Oryctolagus cuniculus.

Lepus yarkandensis live year-round in harsh desert environments and are less susceptible to enteritis. The living conditions of Oryctolagus cuniculus in captivity were suitable, but they were highly susceptible to death by Gram-negative bacteria infected with inflammatory bowel disease complex.TLR4 is closely related to the occurrence of enteritis, and the neighbor-joining topology based on the 12S rDNA sequences showed that the relationship between O. cuniculus and L. yarkandensis is as high as 98%.Therefore, we chose O. cuniculus and L. yarkandensis for comparative study.The purpose of this study was to investigate the role of Toll-like receptor 4 (TLR4) in the regulation of immunity and inflammation in the intestinal tract of L. yarkandensis. In this study, the TLR4 gene was cloned for the first time in the colon of L. yarkandensis. The expression of TLR4 in the intestinal tissues of L. yarkandensis and O. cuniculus was detected by histological observation, real-time fluorescence quantification PCR(qRT-PCR), and protein blotting (Western blot).An LPS-induced cell inflammation model was constructed in vitro, and ELISA was used to examine the effect of pEGFP-N1-TLR4 and siRNA knockout on the anti-inflammatory ability of the TLR4 gene. The results showed that the open reading frame of the L. yarkandensis TLR4 gene was 2520bp in length. Compared with the sequence of O. cuniculus, there were 15 differences in the TLR4 amino acid sequence of L. yarkandensis, 12 of which occurred in the LRR domain and 2 in the TIR domain, and the sequence changed from G to D at position 298. Immunohistochemistry showed that TLR4 was mainly expressed in the epithelial cells of the colon L. yarkandensis, and the expression level of TLR4 in the cecum and colon was significantly lower compared with that of O. cuniculus. qRT-PCR and Western blot results showed that the expression level of TLR4 in the colon of L. yarkandensis was significantly lower than that of O. cuniculus. At the cellular level, ELISA showed that overexpression of the TLR4 protein in L. yarkandensis could reduce the LPS-induced inflammatory response. Therefore, according to the above results, the protein structure and function of L. yarkandensis TLR4 may be different due to the change of nucleotide, which affects its binding with LPS and the activation of downstream molecules, so that L. yarkandensis is not prone to enteritis and can adapt to the harsh desert environment for a long time. This study also laid the foundation for improving the disease resistance of O. cuniculus and promoting the development and utilization of genes in L. yarkandensis.

Network Analysis of Gut Microbial Communities Reveals Key Reason for Quercetin Protects against Colitis

As one of the most representative natural products among flavonoids, quercetin (QUE) has been reported to exhibit beneficial effects on gut health in recent years. In this study, we utilized a dextran sulfate sodium (DSS)-induced colitis mice model to explore the protective effects and underlying mechanisms of QUE on colitis. Our data demonstrated that QUE oral gavage administration significantly ameliorates the symptoms and histopathological changes associated with colitis. Additionally, the concentration of mucin-2, the number of goblet cells, and the expression of tight junction proteins (such as ZO-1, Occludin, and Claudin-1) were all found to be increased. Furthermore, QUE treatment regulated the levels of inflammatory cytokines and macrophage polarization, as well as the oxidative stress-related pathway (Nrf2/HO-1) and associated enzymes. Additionally, 16S rDNA sequencing revealed that QUE treatment rebalances the alterations in colon microbiota composition (inlcuding Bacteroidaceae, Bacteroides, and Odoribacter) in DSS-induced colitis mice. The analysis of network dynamics reveals a significant correlation between gut microbial communities and microenvironmental factors associated with inflammation and oxidative stress, in conjunction with the previously mentioned findings. Collectively, our results suggest that QUE has the potential to treat colitis by maintaining the mucosal barrier, modulating inflammation, and reducing oxidation stress, which may depend on the reversal of gut microbiota dysbiosis.

Metabolomics and 16S rDNA sequencing of intestinal flora reveal the regulation of Sparassis latifolia polysaccharides on splenic immune function in lead-exposed mice

Sparassis latifolia polysaccharides (SLPs) have immunomodulatory activity and lead excretion ability, but its regulatory mechanism through the gut microbiota-spleen axis has not been elucidated. In this study, spleen metabolomics and intestinal flora sequencing were combined to explore the regulatory mechanism of SLPs on spleen immune function in lead-exposed mice. The results showed that SLPs effectively reduced spleen lead content, alleviated spleen enlargement and oxidative stress. SLPs changed glycerophospholipid metabolism, increased lysophosphatidylcholine content and inhibited the expression of G2A, ERK2 and NF-kB genes and the phosphorylation of ERK2 and NF-kB in lead-exposed mice. Furthermore, SLPs inhibited potential intestinal pathogens such as Clostridium_sensu_stricto_1, Lachnospiraceae, Oscillospiraceae and Alistipes_indistinctus, which were positively correlated with phosphatidylethanolamine metabolites. In addition, SLPs reduced the spleen tissue damage of lead-exposed mice by co-housing, and reduced the relative abundance of Clostridium_sensu_stricto_1, Prevotellaceae, and RF39, which were positively correlated with spleen enlargement, and inhibited the expression of ERK2/NF-κB signaling pathway-related genes such as G2A, ERK2 and Fas. In summary, SLPs can reduce the relative abundance of pathogenic microorganisms by regulating the structure of intestinal flora, regulate the glycerophospholipid metabolism of spleen in lead-exposed mice, alleviate oxidative damage and inflammatory response, and restore spleen immune function.

Impact of Glycine Powder Air-Abrasive Debridement on Peri-Implant Mucositis: A Randomized Control Trial of Clinical, Microbial, and Immunological Changes.

Peri-implant mucositis, a dysbiosis-driven inflammatory disease, is a precursor to peri-implantitis, underscoring the need for early disease management. Therefore, we investigated the efficacy of glycine powder in resolving clinical inflammation and restoring host-microbial homeostasis. Thirty subjects were randomized to receive either glycine powder air-abrasive debridement or ultrasonic instrumentation. Clinical parameters (probe depth [PD], modified Sulcular Bleeding Index [mSBI], modified Plaque Index [mPlI]), biofilm and peri-implant crevicular fluid were collected at baseline and at 1-day, 1-, 3-, 6-weeks and 3- and 6-months post-therapy. Microbial recolonization was examined using 16S rDNA sequencing and immune response was semi-quantified using a bead-based 17-plex microarray. At 6-months, both groups demonstrated non-significant reductions in mSBI when compared to baseline (p > 0.05, Wald test, mixed model for repeated measures). However, mSBI and PD decreased in the test group from week-1 to 3-months, while control group decreased at 1- and 3-weeks only. mSBI was lower in the test group when compared to controls from Week-1 to 3-months, while PD differed between groups at 6 weeks and 3-months. Glycine group demonstrated significant microbial shifts after 24-h, increases in species richness and health-compatible species, and loss of pathobionts (p < 0.001, Dunn test). Pro-inflammatory cytokines decreased from 1- to 6-weeks or 3-months (p < 0.05, Wald test). Comparable results were obtained in the ultrasonic group at 3-weeks and sustained over 6-weeks post-therapy. Glycine therapy leads to early and sustained change in host-microbial interactions when compared to ultrasonics, however, the changes wrought by both therapies were sustained for a maximum of 3 months. ClinicalTrials.gov identifier: NCT05810558.

Endogenous ethanol- and thermo-tolerant strain from Malaysia pineapple peel: Screening and molecular characterisation

The current study aims to identify an endogenous acetic acid bacterial strain isolated from a Malaysian pineapple capable of tolerating high ethanol and temperatures. A total of 23 strains of presumed acetic acid bacteria were isolated from the pineapple peel waste. Subsequently, three isolates with the highest acid yield were subjected to 16S rDNA sequencing; Acetobacter tropicalis (A. tropicalis), Staphylococcus haemolyticus, and Staphylococcus ureilyticus. Tolerance evaluations against pH, temperature, ethanol, sugar, and acetic acid demonstrated that all three strains tolerated significant temperatures, ethanol, and sugar levels. Based on the results, A. tropicalis possesses the potential to reduce cooling system load during acetic acid manufacture in hot climate regions with a notable acetic acid yield.

Antibacterial periodontal ligament stem cells enhance periodontal regeneration and regulate the oral microbiome

BackgroundThe transplantation of periodontal ligament stem cells (PDLSCs) has been shown to enhance periodontal regeneration in animal models and clinical trials. However, it is not known whether PDLSCs are antibacterial and whether this affects oral microbiota and periodontal regeneration.MethodsWe isolated human PDLSCs from periodontal ligament of extracted teeth. Rats’ periodontal fenestration defects were prepared, and treated with PDLSC injections (Cell group), using saline injections (Saline group) as the control. The oral microbiota was explored by 16 S rDNA sequencing and compared with that before surgery (PRE group). The antibacterial property of PDLSCs and its underlying mechanism were tested in vitro.ResultsMicrobiome analyses reveal a decreased biodiversity, a changed community structure, and downregulated community functions of the oral microbiome in the Saline group. PDLSCs injections enhance periodontal regeneration, reverse the decrease in diversity, and increase the abundance of non-pathogenic bacterial Bifidobacterium sp. and Lactobacillus sp., making the oral microbiome similar to that of the PRE group. In vitro, PDLSCs inhibit the growth of Staphylococcus aureus, Escherichia coli, and Fusobacterium nucleatum. The main mechanism of action is postulated to involve production of the cationic antimicrobial peptide LL-37.ConclusionsOur findings reveal that PDLSC injections enhance periodontal regeneration and regulate the oral microbiome to foster an oral cavity microenvironment conducive to symbiotic microbiota associated with health.