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BACKGROUND The Amazon Region hosts invaluable and unique biodiversity as well as mineral resources. Consequently, large illegal and artisanal gold mining areas exist in indigenous territories. Mercury has been used in gold mining, and some has been released into the environment and atmosphere, primarily affecting indigenous people such as the Yanomami. In addition, other heavy metals have been associated with gold mining and other metal-dispersing activities in the region. OBJECTIVE Investigate the gut microbiome of two semi-isolated groups from the Amazon, focusing on metal resistance. METHODS Metagenomic data from the Yanomami and Tunapuco gut microbiome were assembled into contigs, and their putative proteins were searched against a database of metal resistance proteins. FINDINGS Proteins associated with mercury resistance were exclusive in the Yanomami, while proteins associated with silver resistance were exclusive in the Tunapuco. Both groups share 77 non-redundant metal resistance (MR) proteins, mostly associated with multi-MR and operons with potential resistance to arsenic, nickel, zinc, copper, copper/silver, and cobalt/nickel. Although both groups harbour operons related to copper resistance, only the Tunapuco group had the pco operon. CONCLUSION The Yanomami and Tunapuco gut microbiome shows that these people have been exposed directly or indirectly to distinct scenarios concerning heavy metals.
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Objective:To explore the profile and gene functional changes of gut microbiota (GM) in women with postmenopausal osteoporosis (PMOP) in Northwest China, and the correlations between GM and bone mineral density (BMD).Methods:From November 2018 to October 2019, postmenopausal women were screened on their initial visits to our hospital, and 24 new osteoporosis (OP) patients, 30 new osteopenia patients and nine negative controls were recruited. Fecal samples were collected for GM DNA extraction, and Illumina platforms were used for high-throughput sequencing of 16S rRNA and metagenome. Species annotation, GM profile and gene functions were viewed and analyzed.Results:GM profiles were significatly different in different groups, and the LDA scores of Peptostreptococcaceae, Romboutsia, unidentified Clostridiales, Megamonas, Erysipelatoclostridium, Klebsiella and Erysipelatoclostridium ramosum were more than 3 in OP group. Metagenomic sequencing analysis indicated that gene numbers were positively correlated with BMD, and metabolism, carbohydrate metabolism, starch and sucrose metabolism and oxidative phosphorylation were negatively correlated with BMD. Receiver operating characteristic curve(ROC) showed that carbohydrate metabolism, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, oxidative phosphorylation, respectively, could identify OP with preferable sensitivity and specificity (areas under curve were 0.70, 0.72, 0.73 and 0.75, respectively). Conclusions:High-throughput sequencing had great potential for GM analysis of postmenopausal women with OP, providing evidence of the correlations between GM and BMD.
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Objective To analyze the correlation between intestinal flora changes and neonatal necrotizing enterocolitis (NEC)through 16S rRNA metagenomic sequencing and bacterial culture. Methods From September 2018 to March 2019, 10 NEC cases and 6 controls were randomly selected in the neonatal ICU ward of Nanjing maternal and child health care hospital to analyze the 16S rRNA metagenomic diversity of the for intestinal flora. The fecal samples and corresponding environmental samples were corrected from 51 cases of NEC children and their case controls to isolate and culture Clostridium. Results The dispersion of samples within the case group was smaller than that of the control group, and the sample diversity was higher than that of the control group. In the isolation and culture of Clostridium, the overall detection rate of Clostridium in the case group was 43.14% (22/51), and the detection rate of Clostridium butyricum was the highest (19.61%, 10/51). There was a statistical difference between the two groups (χ2=5.85, P=0.015 58). All Clostridium strains did not carry the A, B and E type neurotoxin genes. Conclusion: Increased intestinal flora diversity, intestinal flora abundance and changes in the abundance of Clostridium may be closely related to the intestinal environment of children with NEC; Clostridium, especially Clostridium butyricum, may be related to the occurrence of NEC.
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Infectious disease is still one of the leading causes of death nowadays .More than half of pathogens causing infections are still unclear through conventional microbiological diagnostics in clinical laboratory.Recently, the metagenomic sequencing is being applied in the pathogenic diagnosis with full coverage, high efficiency and few bias.Though metagenomic sequencing has shown good performance in pathogenic diagnosis for respiratory tract infection , central nervous system infection and bloodstream infection, it still cannot replace the conventional microbiological tests ; however, this state-of-the-art tool should be considered as an effective supplement to pathogen diagnosis .This article reviews the current application of metagenomic sequencing in clinical scenarios and related pitfalls , with the aim of promoting better utilization of the tool.
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Objective@#To detect pathogens in clinical cerebrospinal fluid samples from 5 suspected encephalitis cases.@*Methods@#Five cerebrospinal samples were treated with both random and virus sequence independent targeted amplification(VSITA) method , followed by next-generation sequencing. Host trascriptome profiling combined with quantitative PCR were conducted to verify the detected pathogen.@*Results@#Cytomegalovirus(CMV) was detected in 3 cases. Quantitative PCR showed weakly positive result (Ct value: 30.23, 32.83, 34.08). The enhancement result of host infection pathway indicated CMV infection (P=0.213). Sequencing reads analysis showed better result in VSITA (P=0.096).@*Conclusions@#This is the first application of VSITA for cerebrospinal fluid samples. This enrichment method showed great potential while it needs further improvement. Consistency in gene expression detection between VSITA and random method makes it possible for host transcriptome profiling. Analysis result detected increase of CMV infection pathway in 3 positive cases, which further identified CMV infection in the 3 cases.
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OBJECTIVE@#To explore the change of intestinal microecology in patients with primary Sjogren's syndrome (pSS) and correlation with disease activity, and also discuss the therapy effect of Yangyin Yiqi Huoxue Recipe (, YYHD).@*METHODS@#Sixteen pSS patients were enrolled in the present study, who received 3-month treatment of YYHR, 200 mL orally twice daily. Their pre-and post-test ESSDAI scores, erythrocyte sedimentation rate (ESR) and serum immunoglobulin G (IgG) levels were measured respectively. The 16SrDNA metagenomic sequencing was used to detect and analyze the abundance and diversity of intestinal bacteria flora and the proportion of bacteria at the levels of phylum, family, and genus, in comparision with those of 6 healthy subjects in the control group.@*RESULTS@#The abundance and diversity of intestinal bacteria flora in pSS patients were lower than those of healthy subjects (P0.05).@*CONCLUSIONS@#There exists an imbalance of intestinal microecology in pSS patients, which can be improved through the treatment with YYHD. Besides, such treatment can also improve the disease activity and adjust the diversity of intestinal bacteria flora, the composition and the abundance of intestinal flora.