Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches...Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches.While the study represents a valuable methodological step forward,it remains limited by singlecenter design,lack of quantitative calibration,and insufficient control for contamination and inter-laboratory variability.This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized,consensus-driven workflows to ensure reproducibility and clinical reliability.The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration,particularly for recurrence prediction,treatment-response monitoring,and perioperative complication risk assessment.By addressing these methodological,economic,and ethical challenges,the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.展开更多
Wantong Jingu Tablet(WJT),a mixture of traditional Chinese medicine,was reported to relieve the symptoms of rheumatoid arthritis(RA),but its pharmacological mechanism was not completely understood.The aim of this stud...Wantong Jingu Tablet(WJT),a mixture of traditional Chinese medicine,was reported to relieve the symptoms of rheumatoid arthritis(RA),but its pharmacological mechanism was not completely understood.The aim of this study was to investigate the therapeutic mechanisms of WJT for RA in vivo.The effects of WJT on joint pathology,as well as the levels of Bax,Bcl-2,caspase-3,cleaved-caspase-3,ERK1/2,pERK1/2,TNF-α,IL-1β,and IL-6 were measured using collagen-induced arthritis(CIA)rats.The intestinal flora composition and the metabolites alteration were analyzed by 16S rDNA sequencing and metabolomics method,respectively.We found that WJT ameliorated the severity of the CIA rats which might be mediated by inducing apoptosis,inactivating the MEK/ERK signals and reducing the production of pro-inflammatory cytokines.WJT,in part,relieved the gut microbiota dysbiosis,especially bacterial phylum Bacteroidetes,Tenericutes and Deferribacteres,as well as bacterial genus Vibrio,Macrococcus and Vagococcus.3’-N-debenzoyl-2’-deoxytaxol,tubulysin B,and magnoline were significantly associated with the specific genera.We identified serotonin,glutathione disulfide,N-acetylneuraminic acid,naphthalene and thromboxane B2 as targeted molecules via metabolomics.Our findings contributed to the understanding of RA pathogenesis,and WJT played essential roles in gut microbiota health and metabolite modulation in the CIA rats.展开更多
BACKGROUND Gallstone(GS),a prevalent biliary disorder,is associated with bile stasis,infection,and cholesterol metabolism.Recent research highlights the potential role of bile microbiota in GS pathogenesis.This is a c...BACKGROUND Gallstone(GS),a prevalent biliary disorder,is associated with bile stasis,infection,and cholesterol metabolism.Recent research highlights the potential role of bile microbiota in GS pathogenesis.This is a case control study conducted at Jinshan Hospital between 2022 and 2023.AIM To investigate the relationship between bile microbiota dysbiosis and GS formation,and analyze bile microbiota composition in GS patients.METHODS This is a retrospective analysis conducted at Jinshan Hospital between 2022 and 2023.A total of 40 patients were analyzed,including 25 with GS and 15 with GSfree(GSF).Bile samples from 27 patients were analyzed using 16S rRNA gene sequencing to assess microbial composition.RESULTS Significant differences were found in bile acid profiles between GS and GSF groups,with lower microbial diversity in GS patients,indicated by reduced Shannon,Chao,Ace,and Sobs indices,and a higher Simpson index.At the phylum level,the most abundant taxa in GS patients were Proteobacteria(91.59%),Firmicutes(2.90%),and Actinobacteria(1.70%),while Proteobacteria(79.81%),Firmicutes(9.67%),and Bacteroidota(3.80%)were predominated in the GSF group.Notably,Achromobacter was more abundant in GS patients,while Acinetobacter,Lactobacillus,and Prevotella were enriched in the GSF group,suggesting their potential protective role against GS formation.CONCLUSION Dysbiosis,particularly overgrowth of Proteobacteria,may contribute to gallstone formation,while Lactobacillus could play a protective role.Further research is needed to validate these findings.展开更多
This study establishes and validates a method for the precise quantification of aquatic microbial loads using microbial diversity absolute quantitative sequencing.By adding synthetic spike-in DNA to water samples from...This study establishes and validates a method for the precise quantification of aquatic microbial loads using microbial diversity absolute quantitative sequencing.By adding synthetic spike-in DNA to water samples from the Dahei River prior to DNA extraction and 16S rRNA gene sequencing,it generates standard curves to convert sequencing data into absolute microbial copy numbers.The method,which is proved highly accurate(R^(2)>0.99),reveals a clear contrast between the river sites:the upstream community has not only a significantly higher total microbial load but also a completely different makeup of species compared to the downstream site.This approach effectively overcomes the limitations of relative abundance analysis,providing a powerful tool for environmental monitoring,and proposes key steps for future standardization to ensure data comparability and integration.展开更多
BACKGROUND This study aimed to identify characteristic gut genera in obese and normal-weight children(8-12 years old)using 16S rDNA sequencing.The research aimed to provide insights for mechanistic studies and prevent...BACKGROUND This study aimed to identify characteristic gut genera in obese and normal-weight children(8-12 years old)using 16S rDNA sequencing.The research aimed to provide insights for mechanistic studies and prevention strategies for childhood obesity.Thirty normal-weight and thirty age-and sex-matched obese children were included.Questionnaires and body measurements were collected,and fecal samples underwent 16S rDNA sequencing.Significant differences in body mass index(BMI)and body-fat percentage were observed between the groups.Analysis of gut microbiota diversity revealed lowerα-diversity in obese children.Differences in gut microbiota composition were found between the two groups.Prevotella and Firmicutes were more abundant in the obese group,while Bacteroides and Sanguibacteroides were more prevalent in the control group.AIM To identify the characteristic gut genera in obese and normal-weight children(8-12-year-old)using 16S rDNA sequencing,and provide a basis for subsequent mechanistic studies and prevention strategies for childhood obesity.METHODS Thirty each normal-weight,1:1 matched for age and sex,and obese children,with an obese status from 2020 to 2022,were included in the control and obese groups,respectively.Basic information was collected through questionnaires and body measurements were obtained from both obese and normal-weight children.Fecal samples were collected from both groups and subjected to 16S rDNA sequencing using an Illumina MiSeq sequencing platform for gut microbiota diversity analysis.RESULTS Significant differences in BMI and body-fat percentage were observed between the two groups.The Ace and Chao1 indices were significantly lower in the obese group than those in the control group,whereas differences were not significant in the Shannon and Simpson indices.Kruskal-Wallis tests indicated significant differences in unweighted and weighted UniFrac distances between the gut microbiota of normal-weight and obese children(P<0.01),suggesting substantial disparities in both the species and quantity of gut microbiota between the two groups.Prevotella,Firmicutes,Bacteroides,and Sanguibacteroides were more abundant in the obese and control groups,respectively.Heatmap results demonstrated significant differences in the gut microbiota composition between obese and normal-weight children.CONCLUSION Obese children exhibited lowerα-diversity in their gut microbiota than did the normal-weight children.Significant differences were observed in the composition of gut microbiota between obese and normal-weight children.展开更多
Background:Osteoporosis(OP)has become a major public health issue,threatening the bone health of middle-aged and elderly people from all around the world.Changes in the gut microbiota(GM)are correlated with the mainte...Background:Osteoporosis(OP)has become a major public health issue,threatening the bone health of middle-aged and elderly people from all around the world.Changes in the gut microbiota(GM)are correlated with the maintenance of bone mass and bone quality.However,research results in this field remain highly controversial,and no systematic review or meta-analysis of the relationship between GM and OP has been conducted.This paper addresses this shortcoming,focusing on the difference in the GM abundance between OP patients and healthy controls based on previous 16S ribosomal RNA(rRNA)gene sequencing results,in order to provide new clinical reference information for future customized prevention and treatment options of OP.Methods:According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses(PRISMA),we comprehensively searched the databases of Pub Med,Web of Science,Embase,Cochrane Library,and China National Knowledge Infrastructure(CNKI).In addition,we applied the R programming language version 4.0.3 and Stata 15.1 software for data analysis.We also implemented the Newcastle-Ottawa Scale(NOS),funnel plot analysis,sensitivity analysis,Egger’s test,and Begg’s test to assess the risk of bias.Results:This research ultimately considered 12 studies,which included the fecal GM data of 2033 people(604 with OP and 1429 healthy controls).In the included research papers,it was observed that the relative abundance of Lactobacillus and Ruminococcus increased in the OP group,while the relative abundance for Bacteroides of Bacteroidetes increased(except for Ireland).Meanwhile,Firmicutes,Blautia,Alistipes,Megamonas,and Anaerostipes showed reduced relative abundance in Chinese studies.In the linear discriminant analysis Effect Size(LEfSe)analysis,certain bacteria showed statistically significant results consistently across different studies.Conclusions:This observational meta-analysis revealed that changes in the GM were correlated with OP,and variations in some advantageous GM might involve regional differences.展开更多
Objective To investigate the effects of Qingguang'anⅡFormula(QGAⅡ)on the gut micro-biota of mice with chronic high intraocular pressure(IOP)model,and explore its key micro-biota for protecting the optic nerve.Me...Objective To investigate the effects of Qingguang'anⅡFormula(QGAⅡ)on the gut micro-biota of mice with chronic high intraocular pressure(IOP)model,and explore its key micro-biota for protecting the optic nerve.Methods A total of 10 specific pathogen free(SPF)grade female DBA/2J mice were random-ly divided into model group and QGAⅡgroup(n=5 for each group),while additional 5 SPF-grade female C57BL/6J mice were assigned to control group.Mice presented spontaneous high IOP and showed elevated approximately at the age of seven months.The high IOP was maintained until week 38,when gavage was initiated.Mice in control group underwent the same intragastric treatment,while those in QGAⅡgroup were gavaged with QGAⅡ(9.67 g/kg),once a day for four weeks.Retinal morphology was examined using hematoxylin and eosin(HE)staining,with the number of retinal ganglion cells(RGCs)counted.The expression level of Brn3a protein,a specific marker for RGCs,was detected by immunofluorescence,with the mean optical density(OD)measured for quantitative analysis.In addition,16S rDNA se-quencing was leveraged to analyze changes in the diversity of gut microbiota,including theirα-diversity(Chao1,Shannon,Pielou’s evenness,and observed species index)andβ-diversity.Venn diagrams and linear discriminant analysis effect size(LEfSe)analysis was employed to investigate the number of amplicon sequence variants(ASVs),the abundance of differential gut microbiota species,and the classification of species at both the phylum and genus levels within the three groups of mice.Results HE staining revealed that compared with control group,model group showed signif-icant reduction in the number of RGCs(P<0.01),with intracellular vacuolar degeneration and nuclear pyknosis.After QGAⅡtreatment,the number of RGCs was significantly in-creased compared with model group(P<0.01),with notable improvements in intracellular vacuolar degeneration.Immunofluorescence analysis showed that the mean OD of Brn3a protein was significantly decreased in model group compared with control group(P<0.01),while QGAⅡtreatment significantly elevated its expression level(P<0.01).Analysis ofα-diversity showed that after QGAⅡintervention,the Chao1,Shannon,and Pielou’s evenness indices were significantly increased(P<0.01),and the observed species index was elevated(P<0.05).β-Diversity analysis demonstrated distinct clustering among the three groups,indicating relatively low similarity in bacterial community structures.ASV clustering identi-fied a total of 14061 ASVs across all groups,with 9514 ASVs shared between model and QGAⅡgroups.At the phylum level,the abundance of Bacteroidetes was significantly decreased in model group compared with control group(P<0.01),while Firmicutes and the Firmicutes/Bacteroidetes(F/B)ratio were significantly increased(P<0.01).QGAⅡtreatment significantly reduced both Firmicutes abundance and the F/B ratio(P<0.01).At the genus level,Lactobacillus was dominant across all groups,with its abundance significantly in-creased in model group(P<0.01)and subsequently decreased following QGAⅡintervention(P<0.05).Conclusion QGAⅡrestructured the gut microbiota of DBA/2J mice with chronic high IOP,bringing changes in their diversity and abundance of components.Firmicutes,Bacteroidetes,Lactobacillus,along with their associated microorganisms,are likely critical components of the gut microbiota that contribute to the optic neuroprotective effects of QGAⅡon chronic high IOP mice.展开更多
Ma-Mu-Ran Antidiarrheal Capsules(MMRAC)is traditional Chinese medicine that has been used to treat diarrhea caused by acute enteritis(AE)and bacillary dysentery in Xinjiang(China)for many years.However,the potential t...Ma-Mu-Ran Antidiarrheal Capsules(MMRAC)is traditional Chinese medicine that has been used to treat diarrhea caused by acute enteritis(AE)and bacillary dysentery in Xinjiang(China)for many years.However,the potential therapeutic mechanism of MMRAC for AE and its regulatory mechanism on host metabolism is unclear.This study used fecal metabolomics profiling with GC/MS and 16S rRNA gene sequencing analysis to explore the potential regulatory mechanisms of MMRAC on a dextran sulfate sodium salt(DSS)-induced mouse model of AE.Fecal metabolomics-based analyses were performed to detect the differentially expressed metabolites and metabolic pathways.The 16S rRNA gene sequencing analysis was used to assess the altered gut microbes at the genus level and for functional prediction.Moreover,Pearson correlation analysis was used to integrate differentially expressed metabolites and altered bacterial genera.The results revealed that six intestinal bacteria and seven metabolites mediated metabolic disorders(i.e.,metabolism of amino acid,carbohydrate,cofactors and vitamins,and lipid)in AE mice.Besides,ten altered microbes mediated the differential expression of eight metabolites and regulated these metabolisms after MMRAC administration.Overall,these findings demonstrate that AE is associated with metabolic disorders and microbial dysbiosis.Further,we present that MMRAC exerts protective effects against AE by improving host metabolism through the intestinal flora.展开更多
<b>Objective:</b> 120 patients with severe pneumonia who were kept in the comprehensive ICU of our hospital in 2018 were selected, and 16s rDNA sequencing was performed to analyze the composition of pathog...<b>Objective:</b> 120 patients with severe pneumonia who were kept in the comprehensive ICU of our hospital in 2018 were selected, and 16s rDNA sequencing was performed to analyze the composition of pathogenic bacteria in the sputum of severe pneumonia. <b>Methods:</b> The sputum samples of patients with severe bacterial pneumonia were collected, and the diversity of pathogens in the samples was analyzed by polymerase chain reaction (PCR) amplification and high-throughput sequencing (16s rDNA PCR-DGGE). <b>Results:</b> Sequence showed that sputum samples contained a relatively large number of species, and there were many species that were not detected by sequencing. The dominant bacteria were <i>Streptococcus, Sphingomonas, Corynebacterium, Denatobacteria, Aquobacteria, Acinetobacteria, Prevotella, Klebsiella, Pseudomonas</i>, etc. <b>Conclusion:</b> Bacteria caused by sputum of severe bacterial pneumonia are complex and diverse, which provides new methods and ideas for individualized treatment of patients with severe pneumonia.展开更多
The diagnosis of pathogenic bacteria in severe pneumonia is difficult and the prognosis is poor. Its outcome is closely related to bacterial pathogenicity and the timeliness and pertinence of antibiotic treatment. The...The diagnosis of pathogenic bacteria in severe pneumonia is difficult and the prognosis is poor. Its outcome is closely related to bacterial pathogenicity and the timeliness and pertinence of antibiotic treatment. Therefore, early diagnosis is of great significance to the prognosis of patients. Sputum examination and culture is the gold standard for the diagnosis of pathogens of severe pneumonia. However, due to the long time of bacterial culture, the early use of antibiotics, the change of bacteria species, mixed infection and other problems, the results of bacterial culture in sputum are often false negative. With the continuous application of new molecular biology techniques in clinical detection, the classification of bacteria and microorganisms has deepened from the identification of phenotypic characteristics to the classification of gene characteristics. Sequencing analysis with 16S rDNA sequencing technology has the characteristics of high sequencing flux, large amount of data obtained, short cycle, and can more comprehensively reflect the species composition of microbial community, real species distribution and abundance information. In this paper, 16S rDNA sequencing technology was used to analyze the bacterial population composition in the sputum of severe pneumonia, and to explore a new method of etiological diagnosis.展开更多
Objective: to explore the value of 16S rRNA sequencing in analyzing the microbial community of diabetic foot skin. Methods: 26 cases of diabetic foot patients admitted to our hospital (March 2019-April 2021) were sele...Objective: to explore the value of 16S rRNA sequencing in analyzing the microbial community of diabetic foot skin. Methods: 26 cases of diabetic foot patients admitted to our hospital (March 2019-April 2021) were selected by random sample sampling method, and their foot skin samples were collected. 16S rRNA sequencing technology was used to identify microbial species and analyze the flora characteristics and the correlation between skin micro-ecological groups and the occurrence of diabetic foot disease was analyzed. Results: the course of diabetes in 17 patients was long and the level of glycosylated hemoglobin was high. The difference between the two methods was significant (P>0.05). Wagner level of diabetic foot patients was positively correlated with the risk of skin microecology imbalance (r=8.256, P<0.001). Conclusion: compared with the culture results, 16S rRNA sequencing analysis of pathogenic bacteria has higher accuracy, simple operation and significant application value, which can be further popularized.展开更多
Intensive fish farming systems in Brazil have increased the disease incidence, mainly of bacterial origin, due to higher stocking density, high organic matter levels and poor quality of the aquatic environment that ca...Intensive fish farming systems in Brazil have increased the disease incidence, mainly of bacterial origin, due to higher stocking density, high organic matter levels and poor quality of the aquatic environment that causes high mortality rates during outbreaks. The identification of pathogenic species using a fast and reliable method of diagnosis is essential for successful epidemiological studies and disease control. The present study evaluated the use of direct colony PCR in combination with 16S rRNA gene sequencing to diagnose fish bacterial diseases, with the goal of reducing the costs and time necessary for bacterial identification. The method was successful for all 178 isolates tested and produced bands with the same intensity as the standard PCR performed using pure DNA. In conclusion, the genetics methods allowed detecting the most common and important pathogens in Aquaculture, including 12 species of occurrence in Brazilian fish farms. The results of the present study constitute an advance in the available diagnostic methods for bacterial pathogens in fish farms.展开更多
BACKGROUND Distant metastasis causes most colorectal cancer(CRC)deaths.Gut microbiota(GM)dysbiosis and altered metabolites drive metastasis progression,serving as potential diagnostic biomarkers.AIM To investigate alt...BACKGROUND Distant metastasis causes most colorectal cancer(CRC)deaths.Gut microbiota(GM)dysbiosis and altered metabolites drive metastasis progression,serving as potential diagnostic biomarkers.AIM To investigate alterations in GM and metabolites between patients with nonmetastatic and distant metastatic CRC.METHODS According to the inclusion criteria,fresh fecal samples were collected from 14 non-metastatic CRC patients and 15 distant metastatic CRC patients.We performed 16S rRNA sequencing to analyze the composition,diversity,and differential abundance of GM,along with predictive functional profiling of microbial communities.Additionally,all samples underwent liquid chromatography-mass spectrometry(LC-MS)-based untargeted metabolomic sequencing to identify metabolic changes and predict their biological functions.RESULTS The cohort comprised 16 non-metastatic CRC patients(designated as the S group)and 16 distant metastatic CRC patients(designated as the DZ group).Sequence analysis(16S rRNA)identified a total of 35016 operational taxonomic units(OTUs)across both groups(16886 OTUs in the S group;16270 in the DZ group;1860 shared between groups).Inter-group microbial diversity analysis revealed notable differences in theβ-diversity group(P<0.05).Comparative analysis of GM revealed significant taxonomic composition differences between groups(P<0.05),with higher relative abundances of Butyricicoccus,Ruminococcus_1,Coprococcus_2 in the S group,Pyramidobacter,Christensenellaceae_R-7_group,and Romboutsia in the DZ group(all P<0.05).Functional analysis of differential microbiota revealed predominant enrichment in metabolic pathways.LC-MS-based untargeted metabolomics detected 91 differential metabolites in both positive and negative ionization modes.GM-derived metabolites showed significant alterations in the DZ group.Kyoto Encyclopedia of Genes and Genomes and Human Metabolome Database analyses revealed associated pathways involving nucleic acids,organic heterocyclic compounds,alkaloids,lipids/lipid-like molecules,and nucleotides.These metabolites may function synergistically,as evidenced by positive correlations between diazoxide,hydroquinidine,aurapten,and triptophenolide.Differential metabolites were primarily involved in aminoacyl-tRNA biosynthesis,central carbon metabolism in cancer,phenylalanine metabolism,vitamin B6 metabolism,and protein digestion and absorption pathways.CONCLUSION GM and microbial metabolites differ significantly between CRC patients with distant metastasis and those without metastasis.Metabolites involved in nucleic acid,alkaloid,and lipid metabolism pathways potentially contribute to distant metastasis in CRC.展开更多
Catalpa bungei,a fast-growing timber tree,is threatened by the lepidopteran pest Omphisa plagialis.Previous studies in our laboratory successfully generated transgenic C.bungei lines overexpressing Cry genes(Cry1Ab,Cr...Catalpa bungei,a fast-growing timber tree,is threatened by the lepidopteran pest Omphisa plagialis.Previous studies in our laboratory successfully generated transgenic C.bungei lines overexpressing Cry genes(Cry1Ab,Cry2A,and Cry9-2)that exhibited resistance to O.plagialis,but their potential impact on soil bacterial communities remains unclear.In this study,we analyzed nine transgenic C.bungei lines(three independent lines for each Cry gene)to characterize their rhizosphere bacterial communities using high-throughput sequencing of the 16S ribosomal DNA(rDNA)V4-V5 regions.A total of 628 amplicon sequence variants(ASVs)were shared among all transgenic and wild-type(WT)lines,forming a stable core microbiome dominated by Proteobacteria,Bacteroidota,Acidobacteriota,and Actinobacteriota.Alpha diversity showed no significant differences,while beta diversity revealed minor but distinct compositional shifts.Cry1Ab lines exhibited higher abundances of fast-growing taxa,particularly Proteobacteria and Bacteroidota;Cry2A lines displayed intermediate profiles,whereas Cry9-2 lines were nearly indistinguishable from WT communities.Linear discriminant analysis of the effect size revealed significant enrichment of taxa such as Burkholderiaceae and Ralstonia in the Cry1Ab rhizosphere,in contrast to the higher abundance of Chloroflexi in the WT.Functional predictions indicated consistent metabolic pathways across all treatments,suggesting strong ecological redundancy.This study demonstrates minimal impact on rhizosphere microbial communities in transgenic C.bungei plants.The Cry9-2 construct exhibited superior environmental stability,whereas the Cry1Ab construct caused only slight but ecologically acceptable shifts.These findings support the ecological safety of Bt-transgenic C.bungei and identify Cry9-2 as a particularly favorable candidate for forestry applications.This comparative evaluation of three Cry genes in a tree species provides a framework for future gene-specific biosafety assessments in woody plants.展开更多
Earthworms exhibit distinct biological traits contributing to ecosystem resilience.As a keystone species of terrestrial ecosystem,they influence soil health.This study investigates the transformation of bacterial popu...Earthworms exhibit distinct biological traits contributing to ecosystem resilience.As a keystone species of terrestrial ecosystem,they influence soil health.This study investigates the transformation of bacterial population as they pass through the gut of Metaphire birmanica,with a focus on knowing its role in shaping microbial diversity,directing to understand its influence on soil fertility and ecosystem restoration.We used advance high-throughput 16S rRNA sequencing to assess surrounding soil,earthworm gut,and cast samples.Following DNA extraction,the process of amplification,and sequencing,bacterial taxonomy was compared across various levels using bioinformatics.Findings revealed that M.birmanica gut acted as a selective environment,leading a distinct microbial composition that predominantly favored anaerobic bacteria like Firmicutes.The observed microbial patterns suggest potential ecological implications,including possible roles of families like Sphingomonadaceae and Pseudomonadaceae in nutrient cycling and Bacillus and Pseudomonas in plant growth promotion,increased nutrient availability,and enhanced soil structure.These results highlight M.birmanica's significant role in influencing soil microbial ecology,offering significant implications for sustainable agriculture and soil restoration.展开更多
A 605 bp section of mitochondrial 16S rRNA gene from Paralichthys olivaceus, Pseudorhombus cinnamomeus, Psetta maxima and Kareius bicoloratus, which represent 3 families of Order Pleuronectiformes was amplified by PCR...A 605 bp section of mitochondrial 16S rRNA gene from Paralichthys olivaceus, Pseudorhombus cinnamomeus, Psetta maxima and Kareius bicoloratus, which represent 3 families of Order Pleuronectiformes was amplified by PCR and sequenced to show the molecular systematics of Pleuronectiformes for comparison with related gene sequences of other 6 flatfish downloaded from GenBank. Phylogenetic analysis based on ge- netic distance from related gene sequences of 10 flatfish showed that this method was ideal to explore the rela- tionship between species, genera and families. Phylogenetic trees set-up is based on neighbor-joining, maximum parsimony and maximum likelihood methods that accords to the general rule of Pleuronectiformes evolution. But they also resulted in some confusion. Unlike data from morphological characters, P. olivaceus clustered with K. bicoloratus, but P. cinnamomeus did not cluster with P. olivaceus, which is worth further studying.展开更多
Objective:To determine the effects of a high-fat diet(HFD)on the gut microbiome in rats,to explore the relationship between the intestinal flora and blood lipid profile.Methods:SpragueeDawley rats were fed an HFD for ...Objective:To determine the effects of a high-fat diet(HFD)on the gut microbiome in rats,to explore the relationship between the intestinal flora and blood lipid profile.Methods:SpragueeDawley rats were fed an HFD for four weeks to induce hyperlipidemia,then 16S rRNA sequencing was used to compare the intestinal flora between hyperlipidemic and control diet-fed rats.Results:The microbiome of rats fed an HFD for four weeks differed from that of control diet-fed rats.Bacterial species that were less abundant were most affected by HFD feeding,among which were many pathogenic species,which became significantly more abundant.Eighteen genera were present in significantly different numbers in hyperlipidemic and control rats,more than half of which have been linked to infection and inflammation,or energy intake and obesity.The results indicated a type of stress response of the flora to a high-fat environment.In addition,the age of the rats tended to influence the gut microbial composition.Conclusion:These findings suggest that HFD may induce hyperlipidemia by affecting the gut microbial composition.Changes in the abundance of pro-inflammatory and pathogenic bacteria,and those that influence energy intake and obesity,may be important mediators of this.展开更多
AIM To investigate the material basis and mechanism underlying the therapeutic effect of DLC in T2DM.METHODS T2DM was triggered in rats using a high-sugar,high-fat diet alongside 35 mg/kg streptozotocin.The effect of ...AIM To investigate the material basis and mechanism underlying the therapeutic effect of DLC in T2DM.METHODS T2DM was triggered in rats using a high-sugar,high-fat diet alongside 35 mg/kg streptozotocin.The effect of DLC on the intestinal microbiota in T2DM rats was analyzed via 16S rDNA sequencing.Targeted metabolomics was conducted to evaluate the impact of DLC on the levels of nine short-chain fatty acids(SCFAs).Untargeted metabolomics examined DLC-induced alterations in fecal metabolites and associated metabolic pathways.Additionally,Spearman’s correlation analysis assessed gut microbiota and fecal metabolite relationships.RESULTS DLC significantly attenuated pathological weight loss,reduced fasting blood glucose levels,restored blood sugar homeostasis,and ameliorated dyslipidemia in T2DM rats.The 16S rDNA sequencing revealed that DLC enhanced microbial diversity and reversed intestinal dysbiosis.Targeted metabolomics indicated decreased acetic acid and propionic acid levels and increased butyric acid,isobutyric acid,and 2-methylbutyric acid levels after DLC treatment.Untargeted metabolomics revealed 57 metabolites with altered expression associated with amino acid,carbohydrate,purine,and biotin pathways.The Spearman analysis demonstrated significant links between specific gut microbiota taxa and fecal metabolites.CONCLUSION DLC may exert hypoglycemic effects by modulating intestinal flora genera,SCFA levels,and fecal metabolites.展开更多
Recently,the gut microbiota has been identified as a significant risk factor associated with metabolic disorders related to obesity.Advances in high-throu-ghput sequencing technology have clarified the relationship be...Recently,the gut microbiota has been identified as a significant risk factor associated with metabolic disorders related to obesity.Advances in high-throu-ghput sequencing technology have clarified the relationship between childhood obesity and changes in the gut microbiota.This commentary focuses on analyzing the study by Li et al,which utilized 16S rRNA molecular markers to compare differences in gut microbiota between obese and normal-weight children.Additionally,the review by Pan et al is referenced to supplement perspectives and evaluate the findings of this study.We also analyze the strengths and limitations of the original study and suggest potential research directions to elucidate the complex relationship between gut microbiota and childhood obesity,thereby providing a scientific basis for developing effective prevention and treatment strategies.展开更多
Objective Recent studies have overturned the traditional concept of the lung as a “sterile organ” revealing that pulmonary microbiota dysbiosis and abnormal surfactant proteins(SPs) expression are involved in the pr...Objective Recent studies have overturned the traditional concept of the lung as a “sterile organ” revealing that pulmonary microbiota dysbiosis and abnormal surfactant proteins(SPs) expression are involved in the progression of silicosis. This study aimed to investigate the relationship between abnormal SPs expression and dysbiosis of lung microbiota in silica-induced lung fibrosis, providing insights into mechanisms of silicosis.Methods Lung pathology, SPs expression, and microbiota composition were evaluated in silicaexposed mice. A mouse model of antibiotic-induced microbiota depletion was established, and alveolar structure and SPs expression were assessed. The roles of the lung microbiota and SPs in silicosis progression were further evaluated in mice with antibiotic-induced microbiota depletion, both with and without silica exposure.Results Silica exposure induced lung inflammation and fibrosis, along with increased expression of SPA expression. Antibiotics(Abx)-induced microbiota depletion elevated SP-A and SP-D expression.Furthermore, silica exposure altered lung microbiota composition, enriching potentially pathogenic taxa.However, antibiotic-induced microbiota depletion prior to silica exposure reduced silica-mediated lung fibrosis and inflammation.Conclusion Lung microbiota is associated with silica-induced lung injury. Overproduction of SP-A and SP-D, induced by Abx-induced microbiota depletion, may enhance the resistance of mouse lung tissue to silica-induced injury.展开更多
文摘Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches.While the study represents a valuable methodological step forward,it remains limited by singlecenter design,lack of quantitative calibration,and insufficient control for contamination and inter-laboratory variability.This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized,consensus-driven workflows to ensure reproducibility and clinical reliability.The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration,particularly for recurrence prediction,treatment-response monitoring,and perioperative complication risk assessment.By addressing these methodological,economic,and ethical challenges,the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.
文摘Wantong Jingu Tablet(WJT),a mixture of traditional Chinese medicine,was reported to relieve the symptoms of rheumatoid arthritis(RA),but its pharmacological mechanism was not completely understood.The aim of this study was to investigate the therapeutic mechanisms of WJT for RA in vivo.The effects of WJT on joint pathology,as well as the levels of Bax,Bcl-2,caspase-3,cleaved-caspase-3,ERK1/2,pERK1/2,TNF-α,IL-1β,and IL-6 were measured using collagen-induced arthritis(CIA)rats.The intestinal flora composition and the metabolites alteration were analyzed by 16S rDNA sequencing and metabolomics method,respectively.We found that WJT ameliorated the severity of the CIA rats which might be mediated by inducing apoptosis,inactivating the MEK/ERK signals and reducing the production of pro-inflammatory cytokines.WJT,in part,relieved the gut microbiota dysbiosis,especially bacterial phylum Bacteroidetes,Tenericutes and Deferribacteres,as well as bacterial genus Vibrio,Macrococcus and Vagococcus.3’-N-debenzoyl-2’-deoxytaxol,tubulysin B,and magnoline were significantly associated with the specific genera.We identified serotonin,glutathione disulfide,N-acetylneuraminic acid,naphthalene and thromboxane B2 as targeted molecules via metabolomics.Our findings contributed to the understanding of RA pathogenesis,and WJT played essential roles in gut microbiota health and metabolite modulation in the CIA rats.
基金Supported by the Youth Scientific Research Launch Fund Project of Jinshan Hospital,Affiliated with Fudan University,No.JYQN-LC-202214.
文摘BACKGROUND Gallstone(GS),a prevalent biliary disorder,is associated with bile stasis,infection,and cholesterol metabolism.Recent research highlights the potential role of bile microbiota in GS pathogenesis.This is a case control study conducted at Jinshan Hospital between 2022 and 2023.AIM To investigate the relationship between bile microbiota dysbiosis and GS formation,and analyze bile microbiota composition in GS patients.METHODS This is a retrospective analysis conducted at Jinshan Hospital between 2022 and 2023.A total of 40 patients were analyzed,including 25 with GS and 15 with GSfree(GSF).Bile samples from 27 patients were analyzed using 16S rRNA gene sequencing to assess microbial composition.RESULTS Significant differences were found in bile acid profiles between GS and GSF groups,with lower microbial diversity in GS patients,indicated by reduced Shannon,Chao,Ace,and Sobs indices,and a higher Simpson index.At the phylum level,the most abundant taxa in GS patients were Proteobacteria(91.59%),Firmicutes(2.90%),and Actinobacteria(1.70%),while Proteobacteria(79.81%),Firmicutes(9.67%),and Bacteroidota(3.80%)were predominated in the GSF group.Notably,Achromobacter was more abundant in GS patients,while Acinetobacter,Lactobacillus,and Prevotella were enriched in the GSF group,suggesting their potential protective role against GS formation.CONCLUSION Dysbiosis,particularly overgrowth of Proteobacteria,may contribute to gallstone formation,while Lactobacillus could play a protective role.Further research is needed to validate these findings.
基金supported by the National Natural Science Foundation of China(Grant No.32160172)the Key Science-Technology Project of Inner Mongolia(2023KYPT0010)+1 种基金the Natural Science Foundation of Inner Mongolia Autonomous Region of China(Grant No.2025QN03006)the 2023 Inner Mongolia Public Institution High-level Talent Introduction Scientific Research Support Project.
文摘This study establishes and validates a method for the precise quantification of aquatic microbial loads using microbial diversity absolute quantitative sequencing.By adding synthetic spike-in DNA to water samples from the Dahei River prior to DNA extraction and 16S rRNA gene sequencing,it generates standard curves to convert sequencing data into absolute microbial copy numbers.The method,which is proved highly accurate(R^(2)>0.99),reveals a clear contrast between the river sites:the upstream community has not only a significantly higher total microbial load but also a completely different makeup of species compared to the downstream site.This approach effectively overcomes the limitations of relative abundance analysis,providing a powerful tool for environmental monitoring,and proposes key steps for future standardization to ensure data comparability and integration.
文摘BACKGROUND This study aimed to identify characteristic gut genera in obese and normal-weight children(8-12 years old)using 16S rDNA sequencing.The research aimed to provide insights for mechanistic studies and prevention strategies for childhood obesity.Thirty normal-weight and thirty age-and sex-matched obese children were included.Questionnaires and body measurements were collected,and fecal samples underwent 16S rDNA sequencing.Significant differences in body mass index(BMI)and body-fat percentage were observed between the groups.Analysis of gut microbiota diversity revealed lowerα-diversity in obese children.Differences in gut microbiota composition were found between the two groups.Prevotella and Firmicutes were more abundant in the obese group,while Bacteroides and Sanguibacteroides were more prevalent in the control group.AIM To identify the characteristic gut genera in obese and normal-weight children(8-12-year-old)using 16S rDNA sequencing,and provide a basis for subsequent mechanistic studies and prevention strategies for childhood obesity.METHODS Thirty each normal-weight,1:1 matched for age and sex,and obese children,with an obese status from 2020 to 2022,were included in the control and obese groups,respectively.Basic information was collected through questionnaires and body measurements were obtained from both obese and normal-weight children.Fecal samples were collected from both groups and subjected to 16S rDNA sequencing using an Illumina MiSeq sequencing platform for gut microbiota diversity analysis.RESULTS Significant differences in BMI and body-fat percentage were observed between the two groups.The Ace and Chao1 indices were significantly lower in the obese group than those in the control group,whereas differences were not significant in the Shannon and Simpson indices.Kruskal-Wallis tests indicated significant differences in unweighted and weighted UniFrac distances between the gut microbiota of normal-weight and obese children(P<0.01),suggesting substantial disparities in both the species and quantity of gut microbiota between the two groups.Prevotella,Firmicutes,Bacteroides,and Sanguibacteroides were more abundant in the obese and control groups,respectively.Heatmap results demonstrated significant differences in the gut microbiota composition between obese and normal-weight children.CONCLUSION Obese children exhibited lowerα-diversity in their gut microbiota than did the normal-weight children.Significant differences were observed in the composition of gut microbiota between obese and normal-weight children.
基金supported by the National Natural Science Foundation of China(No.81860391)the Guangxi Medical High-level Backbone Talents Training“139”Program Training Project(No.[2020]15)the Guangxi Hundred Thousand Talents Project(No.[2019]32),China.
文摘Background:Osteoporosis(OP)has become a major public health issue,threatening the bone health of middle-aged and elderly people from all around the world.Changes in the gut microbiota(GM)are correlated with the maintenance of bone mass and bone quality.However,research results in this field remain highly controversial,and no systematic review or meta-analysis of the relationship between GM and OP has been conducted.This paper addresses this shortcoming,focusing on the difference in the GM abundance between OP patients and healthy controls based on previous 16S ribosomal RNA(rRNA)gene sequencing results,in order to provide new clinical reference information for future customized prevention and treatment options of OP.Methods:According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses(PRISMA),we comprehensively searched the databases of Pub Med,Web of Science,Embase,Cochrane Library,and China National Knowledge Infrastructure(CNKI).In addition,we applied the R programming language version 4.0.3 and Stata 15.1 software for data analysis.We also implemented the Newcastle-Ottawa Scale(NOS),funnel plot analysis,sensitivity analysis,Egger’s test,and Begg’s test to assess the risk of bias.Results:This research ultimately considered 12 studies,which included the fecal GM data of 2033 people(604 with OP and 1429 healthy controls).In the included research papers,it was observed that the relative abundance of Lactobacillus and Ruminococcus increased in the OP group,while the relative abundance for Bacteroides of Bacteroidetes increased(except for Ireland).Meanwhile,Firmicutes,Blautia,Alistipes,Megamonas,and Anaerostipes showed reduced relative abundance in Chinese studies.In the linear discriminant analysis Effect Size(LEfSe)analysis,certain bacteria showed statistically significant results consistently across different studies.Conclusions:This observational meta-analysis revealed that changes in the GM were correlated with OP,and variations in some advantageous GM might involve regional differences.
基金National Natural Science Foundation of China(81904260)Scientific Research Project of Hunan Province Department of Education(22B0398)Scientific Research Project of Traditional Chinese Medicine of Hunan Province(D2022045).
文摘Objective To investigate the effects of Qingguang'anⅡFormula(QGAⅡ)on the gut micro-biota of mice with chronic high intraocular pressure(IOP)model,and explore its key micro-biota for protecting the optic nerve.Methods A total of 10 specific pathogen free(SPF)grade female DBA/2J mice were random-ly divided into model group and QGAⅡgroup(n=5 for each group),while additional 5 SPF-grade female C57BL/6J mice were assigned to control group.Mice presented spontaneous high IOP and showed elevated approximately at the age of seven months.The high IOP was maintained until week 38,when gavage was initiated.Mice in control group underwent the same intragastric treatment,while those in QGAⅡgroup were gavaged with QGAⅡ(9.67 g/kg),once a day for four weeks.Retinal morphology was examined using hematoxylin and eosin(HE)staining,with the number of retinal ganglion cells(RGCs)counted.The expression level of Brn3a protein,a specific marker for RGCs,was detected by immunofluorescence,with the mean optical density(OD)measured for quantitative analysis.In addition,16S rDNA se-quencing was leveraged to analyze changes in the diversity of gut microbiota,including theirα-diversity(Chao1,Shannon,Pielou’s evenness,and observed species index)andβ-diversity.Venn diagrams and linear discriminant analysis effect size(LEfSe)analysis was employed to investigate the number of amplicon sequence variants(ASVs),the abundance of differential gut microbiota species,and the classification of species at both the phylum and genus levels within the three groups of mice.Results HE staining revealed that compared with control group,model group showed signif-icant reduction in the number of RGCs(P<0.01),with intracellular vacuolar degeneration and nuclear pyknosis.After QGAⅡtreatment,the number of RGCs was significantly in-creased compared with model group(P<0.01),with notable improvements in intracellular vacuolar degeneration.Immunofluorescence analysis showed that the mean OD of Brn3a protein was significantly decreased in model group compared with control group(P<0.01),while QGAⅡtreatment significantly elevated its expression level(P<0.01).Analysis ofα-diversity showed that after QGAⅡintervention,the Chao1,Shannon,and Pielou’s evenness indices were significantly increased(P<0.01),and the observed species index was elevated(P<0.05).β-Diversity analysis demonstrated distinct clustering among the three groups,indicating relatively low similarity in bacterial community structures.ASV clustering identi-fied a total of 14061 ASVs across all groups,with 9514 ASVs shared between model and QGAⅡgroups.At the phylum level,the abundance of Bacteroidetes was significantly decreased in model group compared with control group(P<0.01),while Firmicutes and the Firmicutes/Bacteroidetes(F/B)ratio were significantly increased(P<0.01).QGAⅡtreatment significantly reduced both Firmicutes abundance and the F/B ratio(P<0.01).At the genus level,Lactobacillus was dominant across all groups,with its abundance significantly in-creased in model group(P<0.01)and subsequently decreased following QGAⅡintervention(P<0.05).Conclusion QGAⅡrestructured the gut microbiota of DBA/2J mice with chronic high IOP,bringing changes in their diversity and abundance of components.Firmicutes,Bacteroidetes,Lactobacillus,along with their associated microorganisms,are likely critical components of the gut microbiota that contribute to the optic neuroprotective effects of QGAⅡon chronic high IOP mice.
基金supported by Tianchi plan of introducing high-level talents in the Xinjiang Uygur Autonomous Region(2019-39)Major projects of Xinjiang Uygur Autonomous Region“Research and development of new ethnic drugs and large varieties”(2016A03005-2).
文摘Ma-Mu-Ran Antidiarrheal Capsules(MMRAC)is traditional Chinese medicine that has been used to treat diarrhea caused by acute enteritis(AE)and bacillary dysentery in Xinjiang(China)for many years.However,the potential therapeutic mechanism of MMRAC for AE and its regulatory mechanism on host metabolism is unclear.This study used fecal metabolomics profiling with GC/MS and 16S rRNA gene sequencing analysis to explore the potential regulatory mechanisms of MMRAC on a dextran sulfate sodium salt(DSS)-induced mouse model of AE.Fecal metabolomics-based analyses were performed to detect the differentially expressed metabolites and metabolic pathways.The 16S rRNA gene sequencing analysis was used to assess the altered gut microbes at the genus level and for functional prediction.Moreover,Pearson correlation analysis was used to integrate differentially expressed metabolites and altered bacterial genera.The results revealed that six intestinal bacteria and seven metabolites mediated metabolic disorders(i.e.,metabolism of amino acid,carbohydrate,cofactors and vitamins,and lipid)in AE mice.Besides,ten altered microbes mediated the differential expression of eight metabolites and regulated these metabolisms after MMRAC administration.Overall,these findings demonstrate that AE is associated with metabolic disorders and microbial dysbiosis.Further,we present that MMRAC exerts protective effects against AE by improving host metabolism through the intestinal flora.
文摘<b>Objective:</b> 120 patients with severe pneumonia who were kept in the comprehensive ICU of our hospital in 2018 were selected, and 16s rDNA sequencing was performed to analyze the composition of pathogenic bacteria in the sputum of severe pneumonia. <b>Methods:</b> The sputum samples of patients with severe bacterial pneumonia were collected, and the diversity of pathogens in the samples was analyzed by polymerase chain reaction (PCR) amplification and high-throughput sequencing (16s rDNA PCR-DGGE). <b>Results:</b> Sequence showed that sputum samples contained a relatively large number of species, and there were many species that were not detected by sequencing. The dominant bacteria were <i>Streptococcus, Sphingomonas, Corynebacterium, Denatobacteria, Aquobacteria, Acinetobacteria, Prevotella, Klebsiella, Pseudomonas</i>, etc. <b>Conclusion:</b> Bacteria caused by sputum of severe bacterial pneumonia are complex and diverse, which provides new methods and ideas for individualized treatment of patients with severe pneumonia.
文摘The diagnosis of pathogenic bacteria in severe pneumonia is difficult and the prognosis is poor. Its outcome is closely related to bacterial pathogenicity and the timeliness and pertinence of antibiotic treatment. Therefore, early diagnosis is of great significance to the prognosis of patients. Sputum examination and culture is the gold standard for the diagnosis of pathogens of severe pneumonia. However, due to the long time of bacterial culture, the early use of antibiotics, the change of bacteria species, mixed infection and other problems, the results of bacterial culture in sputum are often false negative. With the continuous application of new molecular biology techniques in clinical detection, the classification of bacteria and microorganisms has deepened from the identification of phenotypic characteristics to the classification of gene characteristics. Sequencing analysis with 16S rDNA sequencing technology has the characteristics of high sequencing flux, large amount of data obtained, short cycle, and can more comprehensively reflect the species composition of microbial community, real species distribution and abundance information. In this paper, 16S rDNA sequencing technology was used to analyze the bacterial population composition in the sputum of severe pneumonia, and to explore a new method of etiological diagnosis.
文摘Objective: to explore the value of 16S rRNA sequencing in analyzing the microbial community of diabetic foot skin. Methods: 26 cases of diabetic foot patients admitted to our hospital (March 2019-April 2021) were selected by random sample sampling method, and their foot skin samples were collected. 16S rRNA sequencing technology was used to identify microbial species and analyze the flora characteristics and the correlation between skin micro-ecological groups and the occurrence of diabetic foot disease was analyzed. Results: the course of diabetes in 17 patients was long and the level of glycosylated hemoglobin was high. The difference between the two methods was significant (P>0.05). Wagner level of diabetic foot patients was positively correlated with the risk of skin microecology imbalance (r=8.256, P<0.001). Conclusion: compared with the culture results, 16S rRNA sequencing analysis of pathogenic bacteria has higher accuracy, simple operation and significant application value, which can be further popularized.
基金thank the State of Sao Paulo Research Foundation(FAPESP-Process 2011/07951-5)for the financial support.
文摘Intensive fish farming systems in Brazil have increased the disease incidence, mainly of bacterial origin, due to higher stocking density, high organic matter levels and poor quality of the aquatic environment that causes high mortality rates during outbreaks. The identification of pathogenic species using a fast and reliable method of diagnosis is essential for successful epidemiological studies and disease control. The present study evaluated the use of direct colony PCR in combination with 16S rRNA gene sequencing to diagnose fish bacterial diseases, with the goal of reducing the costs and time necessary for bacterial identification. The method was successful for all 178 isolates tested and produced bands with the same intensity as the standard PCR performed using pure DNA. In conclusion, the genetics methods allowed detecting the most common and important pathogens in Aquaculture, including 12 species of occurrence in Brazilian fish farms. The results of the present study constitute an advance in the available diagnostic methods for bacterial pathogens in fish farms.
文摘BACKGROUND Distant metastasis causes most colorectal cancer(CRC)deaths.Gut microbiota(GM)dysbiosis and altered metabolites drive metastasis progression,serving as potential diagnostic biomarkers.AIM To investigate alterations in GM and metabolites between patients with nonmetastatic and distant metastatic CRC.METHODS According to the inclusion criteria,fresh fecal samples were collected from 14 non-metastatic CRC patients and 15 distant metastatic CRC patients.We performed 16S rRNA sequencing to analyze the composition,diversity,and differential abundance of GM,along with predictive functional profiling of microbial communities.Additionally,all samples underwent liquid chromatography-mass spectrometry(LC-MS)-based untargeted metabolomic sequencing to identify metabolic changes and predict their biological functions.RESULTS The cohort comprised 16 non-metastatic CRC patients(designated as the S group)and 16 distant metastatic CRC patients(designated as the DZ group).Sequence analysis(16S rRNA)identified a total of 35016 operational taxonomic units(OTUs)across both groups(16886 OTUs in the S group;16270 in the DZ group;1860 shared between groups).Inter-group microbial diversity analysis revealed notable differences in theβ-diversity group(P<0.05).Comparative analysis of GM revealed significant taxonomic composition differences between groups(P<0.05),with higher relative abundances of Butyricicoccus,Ruminococcus_1,Coprococcus_2 in the S group,Pyramidobacter,Christensenellaceae_R-7_group,and Romboutsia in the DZ group(all P<0.05).Functional analysis of differential microbiota revealed predominant enrichment in metabolic pathways.LC-MS-based untargeted metabolomics detected 91 differential metabolites in both positive and negative ionization modes.GM-derived metabolites showed significant alterations in the DZ group.Kyoto Encyclopedia of Genes and Genomes and Human Metabolome Database analyses revealed associated pathways involving nucleic acids,organic heterocyclic compounds,alkaloids,lipids/lipid-like molecules,and nucleotides.These metabolites may function synergistically,as evidenced by positive correlations between diazoxide,hydroquinidine,aurapten,and triptophenolide.Differential metabolites were primarily involved in aminoacyl-tRNA biosynthesis,central carbon metabolism in cancer,phenylalanine metabolism,vitamin B6 metabolism,and protein digestion and absorption pathways.CONCLUSION GM and microbial metabolites differ significantly between CRC patients with distant metastasis and those without metastasis.Metabolites involved in nucleic acid,alkaloid,and lipid metabolism pathways potentially contribute to distant metastasis in CRC.
基金funded by the Chinese Academy of Forestry-Special funds for basic scientific research service expenses of the central level public welfare research institutes(Grant No.CAFYBB2020QD001)the National Natural Science Foundation of China(Grant Nos.32101550,32271917)+1 种基金Jiangsu Agricultural Science and Technology Innovation Fund(Grant No.CX(24)3052)National Forestry and Grassland Administration’s Center for Science and Technology Development Projects(Grant No.KJZXSA202202).
文摘Catalpa bungei,a fast-growing timber tree,is threatened by the lepidopteran pest Omphisa plagialis.Previous studies in our laboratory successfully generated transgenic C.bungei lines overexpressing Cry genes(Cry1Ab,Cry2A,and Cry9-2)that exhibited resistance to O.plagialis,but their potential impact on soil bacterial communities remains unclear.In this study,we analyzed nine transgenic C.bungei lines(three independent lines for each Cry gene)to characterize their rhizosphere bacterial communities using high-throughput sequencing of the 16S ribosomal DNA(rDNA)V4-V5 regions.A total of 628 amplicon sequence variants(ASVs)were shared among all transgenic and wild-type(WT)lines,forming a stable core microbiome dominated by Proteobacteria,Bacteroidota,Acidobacteriota,and Actinobacteriota.Alpha diversity showed no significant differences,while beta diversity revealed minor but distinct compositional shifts.Cry1Ab lines exhibited higher abundances of fast-growing taxa,particularly Proteobacteria and Bacteroidota;Cry2A lines displayed intermediate profiles,whereas Cry9-2 lines were nearly indistinguishable from WT communities.Linear discriminant analysis of the effect size revealed significant enrichment of taxa such as Burkholderiaceae and Ralstonia in the Cry1Ab rhizosphere,in contrast to the higher abundance of Chloroflexi in the WT.Functional predictions indicated consistent metabolic pathways across all treatments,suggesting strong ecological redundancy.This study demonstrates minimal impact on rhizosphere microbial communities in transgenic C.bungei plants.The Cry9-2 construct exhibited superior environmental stability,whereas the Cry1Ab construct caused only slight but ecologically acceptable shifts.These findings support the ecological safety of Bt-transgenic C.bungei and identify Cry9-2 as a particularly favorable candidate for forestry applications.This comparative evaluation of three Cry genes in a tree species provides a framework for future gene-specific biosafety assessments in woody plants.
文摘Earthworms exhibit distinct biological traits contributing to ecosystem resilience.As a keystone species of terrestrial ecosystem,they influence soil health.This study investigates the transformation of bacterial population as they pass through the gut of Metaphire birmanica,with a focus on knowing its role in shaping microbial diversity,directing to understand its influence on soil fertility and ecosystem restoration.We used advance high-throughput 16S rRNA sequencing to assess surrounding soil,earthworm gut,and cast samples.Following DNA extraction,the process of amplification,and sequencing,bacterial taxonomy was compared across various levels using bioinformatics.Findings revealed that M.birmanica gut acted as a selective environment,leading a distinct microbial composition that predominantly favored anaerobic bacteria like Firmicutes.The observed microbial patterns suggest potential ecological implications,including possible roles of families like Sphingomonadaceae and Pseudomonadaceae in nutrient cycling and Bacillus and Pseudomonas in plant growth promotion,increased nutrient availability,and enhanced soil structure.These results highlight M.birmanica's significant role in influencing soil microbial ecology,offering significant implications for sustainable agriculture and soil restoration.
基金Supported by Natural Science Fund of China (No. 30271036) and Natural Science Fund of Shandong Province of China
文摘A 605 bp section of mitochondrial 16S rRNA gene from Paralichthys olivaceus, Pseudorhombus cinnamomeus, Psetta maxima and Kareius bicoloratus, which represent 3 families of Order Pleuronectiformes was amplified by PCR and sequenced to show the molecular systematics of Pleuronectiformes for comparison with related gene sequences of other 6 flatfish downloaded from GenBank. Phylogenetic analysis based on ge- netic distance from related gene sequences of 10 flatfish showed that this method was ideal to explore the rela- tionship between species, genera and families. Phylogenetic trees set-up is based on neighbor-joining, maximum parsimony and maximum likelihood methods that accords to the general rule of Pleuronectiformes evolution. But they also resulted in some confusion. Unlike data from morphological characters, P. olivaceus clustered with K. bicoloratus, but P. cinnamomeus did not cluster with P. olivaceus, which is worth further studying.
基金the National Natural Science Foundation of China(81773960 and 81973535)the National Science and Technology Major Projects for“Major New Drugs Innovation and Development”(2017ZX09301011).
文摘Objective:To determine the effects of a high-fat diet(HFD)on the gut microbiome in rats,to explore the relationship between the intestinal flora and blood lipid profile.Methods:SpragueeDawley rats were fed an HFD for four weeks to induce hyperlipidemia,then 16S rRNA sequencing was used to compare the intestinal flora between hyperlipidemic and control diet-fed rats.Results:The microbiome of rats fed an HFD for four weeks differed from that of control diet-fed rats.Bacterial species that were less abundant were most affected by HFD feeding,among which were many pathogenic species,which became significantly more abundant.Eighteen genera were present in significantly different numbers in hyperlipidemic and control rats,more than half of which have been linked to infection and inflammation,or energy intake and obesity.The results indicated a type of stress response of the flora to a high-fat environment.In addition,the age of the rats tended to influence the gut microbial composition.Conclusion:These findings suggest that HFD may induce hyperlipidemia by affecting the gut microbial composition.Changes in the abundance of pro-inflammatory and pathogenic bacteria,and those that influence energy intake and obesity,may be important mediators of this.
基金Supported by the National Natural Science Foundation of China,No.82160771NATCM's Project of High-Level Construction of Key TCM Disciplines:Traditional Medicine of Chinese Minority(Zhuang Medicine),No.zyyzdxk-2023165+7 种基金Guangxi One Thousand Young and Middle-Aged College and University Backbones Teachers Cultivation Program,No.[2019]5Guangxi Traditional Chinese Medicine Multidisciplinary Cross Innovation Team Project,No.GZKJ2309Guangxi Key R&D Plan Project,No.AB21196016Guangxi Key Discipline of Traditional Chinese Medicine Zhuang Pharmacy,No.GZXK-Z-20-64The First-Class Subject of Traditional Chinese Medicine(Ethnic Pharmacy)in Guangxi,No.[2018]12Guangxi Science and Technology Base and Talent Special Project,No.AD20238058 and No.AD21238031the Third Batch of Cultivating High-level Talent Teams in the“Qi Huang Project”of the Guangxi University of Chinese Medicine,No.202406and Huang Danian Style Teacher Team From Universities in Guangxi Zhuang Autonomous Region“Traditional Chinese Medicine Inheritance and Innovation Teacher Team”,No.[2023]31.
文摘AIM To investigate the material basis and mechanism underlying the therapeutic effect of DLC in T2DM.METHODS T2DM was triggered in rats using a high-sugar,high-fat diet alongside 35 mg/kg streptozotocin.The effect of DLC on the intestinal microbiota in T2DM rats was analyzed via 16S rDNA sequencing.Targeted metabolomics was conducted to evaluate the impact of DLC on the levels of nine short-chain fatty acids(SCFAs).Untargeted metabolomics examined DLC-induced alterations in fecal metabolites and associated metabolic pathways.Additionally,Spearman’s correlation analysis assessed gut microbiota and fecal metabolite relationships.RESULTS DLC significantly attenuated pathological weight loss,reduced fasting blood glucose levels,restored blood sugar homeostasis,and ameliorated dyslipidemia in T2DM rats.The 16S rDNA sequencing revealed that DLC enhanced microbial diversity and reversed intestinal dysbiosis.Targeted metabolomics indicated decreased acetic acid and propionic acid levels and increased butyric acid,isobutyric acid,and 2-methylbutyric acid levels after DLC treatment.Untargeted metabolomics revealed 57 metabolites with altered expression associated with amino acid,carbohydrate,purine,and biotin pathways.The Spearman analysis demonstrated significant links between specific gut microbiota taxa and fecal metabolites.CONCLUSION DLC may exert hypoglycemic effects by modulating intestinal flora genera,SCFA levels,and fecal metabolites.
文摘Recently,the gut microbiota has been identified as a significant risk factor associated with metabolic disorders related to obesity.Advances in high-throu-ghput sequencing technology have clarified the relationship between childhood obesity and changes in the gut microbiota.This commentary focuses on analyzing the study by Li et al,which utilized 16S rRNA molecular markers to compare differences in gut microbiota between obese and normal-weight children.Additionally,the review by Pan et al is referenced to supplement perspectives and evaluate the findings of this study.We also analyze the strengths and limitations of the original study and suggest potential research directions to elucidate the complex relationship between gut microbiota and childhood obesity,thereby providing a scientific basis for developing effective prevention and treatment strategies.
基金supported by the National Natural Science Foundation of China Joint Fund for Regional Innovation and Development(Grant numbers [U21A20334])the Postgraduate Innovation Funding Project of Hebei Province(Grant numbers [CXZZBS2022116])。
文摘Objective Recent studies have overturned the traditional concept of the lung as a “sterile organ” revealing that pulmonary microbiota dysbiosis and abnormal surfactant proteins(SPs) expression are involved in the progression of silicosis. This study aimed to investigate the relationship between abnormal SPs expression and dysbiosis of lung microbiota in silica-induced lung fibrosis, providing insights into mechanisms of silicosis.Methods Lung pathology, SPs expression, and microbiota composition were evaluated in silicaexposed mice. A mouse model of antibiotic-induced microbiota depletion was established, and alveolar structure and SPs expression were assessed. The roles of the lung microbiota and SPs in silicosis progression were further evaluated in mice with antibiotic-induced microbiota depletion, both with and without silica exposure.Results Silica exposure induced lung inflammation and fibrosis, along with increased expression of SPA expression. Antibiotics(Abx)-induced microbiota depletion elevated SP-A and SP-D expression.Furthermore, silica exposure altered lung microbiota composition, enriching potentially pathogenic taxa.However, antibiotic-induced microbiota depletion prior to silica exposure reduced silica-mediated lung fibrosis and inflammation.Conclusion Lung microbiota is associated with silica-induced lung injury. Overproduction of SP-A and SP-D, induced by Abx-induced microbiota depletion, may enhance the resistance of mouse lung tissue to silica-induced injury.
