The oral microbiota plays an important role in the development of various diseases,whereas its association with gestational diabetes mellitus (GDM) remains largely unclear.The aim of this study is to identify biomarke...The oral microbiota plays an important role in the development of various diseases,whereas its association with gestational diabetes mellitus (GDM) remains largely unclear.The aim of this study is to identify biomarkers from the oral microbiota of GDM patients by analyzing the microbiome of the saliva and dental plaque samples of 111 pregnant women.We find that the microbiota of both types of oral samples in GDM patients exhibits differences and significantly varies from that of patients with periodontitis or dental caries.Using bacterial biomarkers from the oral microbiota,GDM classification models based on support vector machine and random forest algorithms are constructed.The area under curve (AUC) value of the classification model constructed by combination of Lautropia and Neisseria in dental plaque and Streptococcus in saliva reaches 0.83,and the value achieves a maximum value of 0.89 by adding clinical features.These findings suggest that certain bacteria in either saliva or dental plaque can effectively distinguish women with GDM from healthy pregnant women,which provides evidence of oral microbiome as an informative source for developing noninvasive biomarkers of GDM.展开更多
With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simul- taneously le...With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simul- taneously leveraging of single-cell genomics and metagenomics, researchers can greatly improve the efficiency and accuracy of obtaining whole genome information from complex microbial communities, which not only allow us to identify microbes but also link function to species, identify subspecies variations, study host-virus interactions and etc. Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and annotation. With the development of sequencing and computational methods, single-cell metagenomics will undoubtedly broaden its application in various microbiome studies.展开更多
Microbes have played a fundamental role in the natural his- tory of our planet, and have done so for billions of years. They have adapted to Earth＇s many environments from the mild to the very extreme. Studying their...Microbes have played a fundamental role in the natural his- tory of our planet, and have done so for billions of years. They have adapted to Earth＇s many environments from the mild to the very extreme. Studying their diversity and their way of life is critical for understanding their full impact on the global ecology. Although the field of metagenomics is still young, it has unravelled a wider microbial diversity that had otherwise been completely overlooked by the traditional methods of microbiology. There are three major metagenomic themes： （a） marker metagenomics that surveys microbial community structure by targeting the highly-conserved 16S rRNA gene, （b） functional metagenomics that takes the total environmental DNA, from which it infers the metabolic potential of the microbial community, and （c） identification of novel enzymes.展开更多
A comprehensive profiling of the vaginal microbial communities and their variability enables an accurate description of the microbiome in women.However,there is a lack of studies available on Chinese women.In the pres...A comprehensive profiling of the vaginal microbial communities and their variability enables an accurate description of the microbiome in women.However,there is a lack of studies available on Chinese women.In the present study,the composition of the vaginal microbiota during pregnancy and the 6-week postpartum period of 454 Chinese women was characterized by sequencing the V3-V4 region of the 16S ribosomal RNA(rRNA)gene.The vaginal microbiome showed variations during pregnancy and the postpartum period based on the abortion history,hypertensive disorders,delivery mode,and maternal age.Co-variation of 22 bacterial taxa,including the Lactobacillus genus and two of its species,may account for the common characteristics of the vaginal microbiome under scenarios of different medical histories and pregnancy outcomes.In contrast,discriminant bacterial species were significantly different between women who had preterm birth(PTB)with and without premature rupture of membranes(PROM),and the community state type(CST)IV-A without any predominant Lactobacillus species in the microbiota was more prevalent during pregnancy in the PROM-PTB cases,suggesting that specific bacterial species could be considered to distinguish between different types of PTB.By providing data on Chinese women,this study will enrich the knowledge of the human microbiome and contribute to a better understanding of the association between the vaginal microbiome and reproductive health.展开更多
Dear Editor,Clustered regularly interspaced short palindromic repeats （CRISPR）, which are widely present in prokaryotic genomes （Grissa et al., 2007）, belong to a family of DNA sequences characterized as short dir...Dear Editor,Clustered regularly interspaced short palindromic repeats （CRISPR）, which are widely present in prokaryotic genomes （Grissa et al., 2007）, belong to a family of DNA sequences characterized as short direct repeats （DR） separated by spacers （Jansen et al., 2002）. CRISPR and CRISPR-asso- ciated （cas） genes are involved in resistance against exogenous sequences, and recognition of infected bacte- riophages depends on the sequence similarity between spacers and targeted phage DNA segments （Barrangou et al., 2007）. CRISPRs exhibited diversity in different microbial communities, and that may be the response to different phaqe infections （Tyson and Banfield, 2008）.展开更多
基金supported by the National Natural Science Foundation of China (31722031, 31670119, 31870107 and 32070122)the Key Research Program of the Chinese Academy of Sciences (KFZDSW-219)the Medical Health Science and Technology Project of Zhejiang Provincial (2019ZD048, 2018275012)。
文摘The oral microbiota plays an important role in the development of various diseases,whereas its association with gestational diabetes mellitus (GDM) remains largely unclear.The aim of this study is to identify biomarkers from the oral microbiota of GDM patients by analyzing the microbiome of the saliva and dental plaque samples of 111 pregnant women.We find that the microbiota of both types of oral samples in GDM patients exhibits differences and significantly varies from that of patients with periodontitis or dental caries.Using bacterial biomarkers from the oral microbiota,GDM classification models based on support vector machine and random forest algorithms are constructed.The area under curve (AUC) value of the classification model constructed by combination of Lautropia and Neisseria in dental plaque and Streptococcus in saliva reaches 0.83,and the value achieves a maximum value of 0.89 by adding clinical features.These findings suggest that certain bacteria in either saliva or dental plaque can effectively distinguish women with GDM from healthy pregnant women,which provides evidence of oral microbiome as an informative source for developing noninvasive biomarkers of GDM.
文摘With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simul- taneously leveraging of single-cell genomics and metagenomics, researchers can greatly improve the efficiency and accuracy of obtaining whole genome information from complex microbial communities, which not only allow us to identify microbes but also link function to species, identify subspecies variations, study host-virus interactions and etc. Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and annotation. With the development of sequencing and computational methods, single-cell metagenomics will undoubtedly broaden its application in various microbiome studies.
基金supported by the Training Program of the Major Research Plan of the National Natural Science Foundation of China (NSFC,Grant No.91131013)the ‘‘100-Talent Program" of the Chinese Academy of Sciencessupported by competitive research funding from King Abdullah University of Science and Technology (KAUST) in Saudi Arabia
文摘Microbes have played a fundamental role in the natural his- tory of our planet, and have done so for billions of years. They have adapted to Earth＇s many environments from the mild to the very extreme. Studying their diversity and their way of life is critical for understanding their full impact on the global ecology. Although the field of metagenomics is still young, it has unravelled a wider microbial diversity that had otherwise been completely overlooked by the traditional methods of microbiology. There are three major metagenomic themes： （a） marker metagenomics that surveys microbial community structure by targeting the highly-conserved 16S rRNA gene, （b） functional metagenomics that takes the total environmental DNA, from which it infers the metabolic potential of the microbial community, and （c） identification of novel enzymes.
基金supported by the National Natural Science Foundation of China(Grant Nos.81825019,31722031,31670119,and 31870107)the Beijing Leading Talents in Science and Technology(Grant No.Z181100006318008)+1 种基金the China Mega-Project on Infectious Disease Prevention(Grant Nos.2018ZX10713002-002,2018ZX10101003-002,and 2018ZX10301401)the National Key R&D Program of China(Grant No.2016YFC1000705).
文摘A comprehensive profiling of the vaginal microbial communities and their variability enables an accurate description of the microbiome in women.However,there is a lack of studies available on Chinese women.In the present study,the composition of the vaginal microbiota during pregnancy and the 6-week postpartum period of 454 Chinese women was characterized by sequencing the V3-V4 region of the 16S ribosomal RNA(rRNA)gene.The vaginal microbiome showed variations during pregnancy and the postpartum period based on the abortion history,hypertensive disorders,delivery mode,and maternal age.Co-variation of 22 bacterial taxa,including the Lactobacillus genus and two of its species,may account for the common characteristics of the vaginal microbiome under scenarios of different medical histories and pregnancy outcomes.In contrast,discriminant bacterial species were significantly different between women who had preterm birth(PTB)with and without premature rupture of membranes(PROM),and the community state type(CST)IV-A without any predominant Lactobacillus species in the microbiota was more prevalent during pregnancy in the PROM-PTB cases,suggesting that specific bacterial species could be considered to distinguish between different types of PTB.By providing data on Chinese women,this study will enrich the knowledge of the human microbiome and contribute to a better understanding of the association between the vaginal microbiome and reproductive health.
文摘Dear Editor,Clustered regularly interspaced short palindromic repeats （CRISPR）, which are widely present in prokaryotic genomes （Grissa et al., 2007）, belong to a family of DNA sequences characterized as short direct repeats （DR） separated by spacers （Jansen et al., 2002）. CRISPR and CRISPR-asso- ciated （cas） genes are involved in resistance against exogenous sequences, and recognition of infected bacte- riophages depends on the sequence similarity between spacers and targeted phage DNA segments （Barrangou et al., 2007）. CRISPRs exhibited diversity in different microbial communities, and that may be the response to different phaqe infections （Tyson and Banfield, 2008）.
