Helicobacter pylori infection (HPI) is a prevalent infectious disease associated with gastric ulcer, gastric cancer, and many nongastrointestinal disorders. To identify genes that may serve as microbial markers for HPI, we performed shotgun metagenomic sequencing of fecal samples from 313 Chinese volunteers who had undergone a C14 breath test. Through comparing differences in intestinal microbial community structure between H. pylori-positive and H. pylori-negative individuals, we identified 58 HPI-associated microbial species (P < 0.05, Wilcoxon test). A classifier based on microbial species markers showed high diagnostic ability for HPI (AUC = 0.84). Furthermore, levels of gut microbial vitamin B12 (VB12) biosynthesis and plasma VB12 were significantly lower in H. pylori-positive individuals compared with H. pylori-negative individuals (P < 0.05, Wilcoxon test). This study reveals that certain alterations in gut microbial species and functions are associated with HPI and shows that gut microbial shift in HPI patients may indirectly elevate the risk of VB12 deficiency.

Daoming Wang;Yan Li;Huanzi Zhong;Qiuxia Ding;Yuxiang Lin;Shanmei Tang;Yang Zong;Qi Wang;Xiuqing Zhang;焕明 杨;Rong Wang;Xiao Liu

FEBS Open Bio

2019-9-1

Background: The gut microbiota evolves from birth and is in early life influenced by events such as birth mode, type of infant feeding, and maternal and infant antibiotics use. However, we still have a gap in our understanding of gut microbiota development in older children, and to what extent early events and pre-school lifestyle modulate the composition of the gut microbiota, and how this impinges on whole body metabolic regulation in school-age children. Results: Taking advantage of the KOALA Birth Cohort Study, a long-term prospective birth cohort in the Netherlands with extensive collection of high-quality host metadata, we applied shotgun metagenomics sequencing and systematically investigated the gut microbiota of children at 6-9 years of age. We demonstrated an overall adult-like gut microbiota in the 281 Dutch school-age children and identified 3 enterotypes dominated by the genera Bacteroides, Prevotella, and Bifidobacterium, respectively. Importantly, we found that breastfeeding duration in early life and pre-school dietary lifestyle correlated with the composition and functional competences of the gut microbiota in the children at school age. The correlations between pre-school dietary lifestyle and metabolic phenotypes exhibited a striking enterotype dependency. Thus, an inverse correlation between high dietary fiber consumption and low plasma insulin levels was only observed in individuals with the Bacteroides and Prevotella enterotypes, but not in Bifidobacterium enterotype individuals in whom the gut microbiota displayed overall lower microbial gene richness, alpha-diversity, functional potential for complex carbohydrate fermentation, and butyrate and succinate production. High total fat consumption and elevated plasma free fatty acid levels in the Bifidobacterium enterotype are associated with the co-occurrence of Streptococcus. Conclusions: Our work highlights the persistent effects of breastfeeding duration and pre-school dietary lifestyle in affecting the gut microbiota in school-age children and reveals distinct compositional and functional potential in children according to enterotypes. The findings underscore enterotype-specific links between the host metabolic phenotypes and dietary patterns, emphasizing the importance of microbiome-based stratification when investigating metabolic responses to diets. Future diet intervention studies are clearly warranted to examine gut microbe-diet-host relationships to promote knowledge-based recommendations in relation to improving metabolic health in children.

Huanzi Zhong;John Penders;Zhun Shi;Huahui Ren;Kaiye Cai;Chao Fang;Qiuxia Ding;Carel Thijs;Ellen E. Blaak;Coen D.A. Stehouwer;Xun Xu;焕明 杨;Jian Wang;Jun Wang;Daisy M.A.E. Jonkers;Ad A.M. Masclee;Susanne Brix;Junhua Li;Ilja C.W. Arts;Karsten Kristiansen

Microbiome

2019-1-4

High specificity of trypsin is a prerequisite for accurate identification and quantification of proteins in shotgun proteomics. It is important to minimize nonspecific enzymatic cleavages during proteomic sample preparation. Methods: In this study, protein extraction and trypsin digestion conditions were extensively evaluated using the less-complex Escherichia coli lysates to improve the sensitivity of detecting low-abundance nonspecific peptides by liquid chromatography/tandem mass spectrometry. Results: Trypsin digestion buffers and digestion times were proved to have a significant effect on nonspecific cleavages. The triethylammonium bicarbonate buffer induces significantly lower nonspecific cleavages than the other two buffers, but a freshly prepared urea solution does not induce more than sodium dodecyl sulfate. Because prolonged trypsin digestion resulted in a considerable number of nonspecific cleavages, an optimized 2-h protocol was developed with 45.2% less semispecific tryptic peptides but 18.5% more unmodified peptides identified than the commonly used 16-h protocol. Conclusions: The significant decrease in nonspecific cleavages and artificial modifications improves the accuracy of protein quantification and the identification of low-abundance proteins, and it is especially useful for studying protein posttranslational modifications. For trypsin digestion, the proposed 2-h protocol can potentially be a replacement for the traditional 16-h protocol.

Zhilong Lin;Yan Ren;Zhaomei Shi;Keren Zhang;焕明 杨;Siqi Liu;Piliang Hao

Rapid Communications in Mass Spectrometry

2020-5-30

Background: Viral infection causes multiple forms of human cancer, and HPV infection is the primary factor in cervical carcinomas Recent single-cell RNA-seq studies highlight the tumor heterogeneity present in most cancers, but virally induced tumors have not been studied HeLa is a well characterized HPV+ cervical cancer cell line Result: We developed a new high throughput platform to prepare single-cell RNA on a nanoliter scale based on a customized microwell chip Using this method, we successfully amplified full-length transcripts of 669 single HeLa S3 cells and 40 of them were randomly selected to perform single-cell RNA sequencing Based on these data, we obtained a comprehensive understanding of the heterogeneity of HeLa S3 cells in gene expression, alternative splicing and fusions Furthermore, we identified a high diversity of HPV-18 expression and splicing at the single-cell level By co-expression analysis we identified 283 E6, E7 co-regulated genes, including CDC25, PCNA, PLK4, BUB1B and IRF1 known to interact with HPV viral proteins Conclusion: Our results reveal the heterogeneity of a virus-infected cell line It not only provides a transcriptome characterization of HeLa S3 cells at the single cell level, but is a demonstration of the power of single cell RNA-seq analysis of virally infected cells and cancers.

Liang Wu;Xiaolong Zhang;Zhikun Zhao;Ling Wang;Bo Li;Guibo Li;Michael Dean;Qichao Yu;Yanhui Wang;Xinxin Lin;Weijian Rao;Zhanlong Mei;Yang Li;Runze Jiang;Huan Yang;Fuqiang Li;Guoyun Xie;Liqin Xu;Kui Wu;Jie Zhang;Jianghao Chen;Ting Wang;Karsten Kristiansen;Xiuqing Zhang;Yingrui Li;焕明 杨;Jian Wang;Yong Hou;Xun Xu

GigaScience

2015

Bacterial pathogens typically infect only a limited range of hosts; however, the genetic mechanisms governing host-specificity are poorly understood. The a-proteobacterial genus Bartonella comprises 21 species that cause host-specific intraerythrocytic bacteremia as hallmark of infection in their respective mammalian reservoirs, including the human-specific pathogens Bartonella quintana and Bartonella bacilliformis that cause trench fever and Oroya fever, respectively. Here, we have identified bacterial factors that mediate host-specific erythrocyte colonization in the mammalian reservoirs. Using mouse-specific Bartonella birtlesii, human-specific Bartonella quintana, cat-specific Bartonella henselae and rat-specific Bartonella tribocorum, we established in vitro adhesion and invasion assays with isolated erythrocytes that fully reproduce the host-specificity of erythrocyte infection as observed in vivo. By signature-tagged mutagenesis of B. birtlesii and mutant selection in a mouse infection model we identified mutants impaired in establishing intraerythrocytic bacteremia. Among 45 abacteremic mutants, five failed to adhere to and invade mouse erythrocytes in vitro. The corresponding genes encode components of the type IV secretion system (T4SS) Trw, demonstrating that this virulence factor laterally acquired by the Bartonella lineage is directly involved in adherence to erythrocytes. Strikingly, ectopic expression of Trw of rat-specific B. tribocorum in cat-specific B. henselae or human-specific B. quintana expanded their host range for erythrocyte infection to rat, demonstrating that Trw mediates host-specific erythrocyte infection. A molecular evolutionary analysis of the trw locus further indicated that the variable, surface-located TrwL and TrwJ might represent the T4SS components that determine host-specificity of erythrocyte parasitism. In conclusion, we show that the laterally acquired Trw T4SS diversified in the Bartonella lineage to facilitate host-restricted adhesion to erythrocytes in a wide range of mammals.

Muriel Vayssier-Taussat;Danielle Le Rhun;Hong Kuan Deng;Francis Biville;Sandra Cescau;Antoine Danchin;Geneviève Marignac;Evelyne Lenaour;Henri Jean Boulouis;Maria Mavris;Lionel Arnaud;焕明 杨;Jing Wang;Maxime Quebatte;Philipp Engel;Henri Saenz;Christoph Dehio

PLoS Pathogens

2010-6

[This corrects the article DOI: 10.3389/fimmu.2018.02194.].

Longlong Wang;Wei Zhang;Liya Lin;Xiao Li;Nitin K. Saksena;Jinghua Wu;Shiyu Wang;Joseph G. Joyce;Xiuqing Zhang;焕明 杨;Jian Wang;I. Ming Wang;Xiao Liu

Frontiers in Immunology

2018

Background The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays an important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis characterizing the diverse microbial communities has been lacking. Results We performed shotgun-sequencing of 52 samples from the cervical canal and the peritoneal fluid of Chinese women of reproductive age using the Illumina platform. Direct annotation of sequencing reads identified the taxonomy of bacteria, archaea, fungi and viruses, confirming and extending the results from our previous study. We replicated our previous findings in another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid using the BGISEQ-500 platform revealing that microorganisms in the samples from the same individuals were largely shared in the entire reproductive tract. Human sequences made up more than 99% of the 20GB raw data. After filtering, vaginal microorganisms were well covered in the generated reproductive tract gene catalogue, while the more diverse upper reproductive tract microbiota would require greater depth of sequencing and more samples to meet the full coverage scale. Conclusions We provide novel detailed data on the microbial composition of a largely unchartered body site, the female reproductive tract. Our results indicated the presence of an intra-individual continuum of microorganisms that gradually changed from the vagina to the peritoneal fluid. This study also provides a framework for understanding the implications of the composition and functional potential of the distinct microbial ecosystems of the female reproductive tract in relation to health and disease.

Fei Li;Chen Chen;Weixia Wei;Zirong Wang;Juanjuan Dai;Lilan Hao;Liju Song;Xiaowei Zhang;Liping Zeng;Hui Du;Huiru Tang;Na Liu;焕明 杨;Jian Wang;Lise Madsen;Susanne Brix;Karsten Kristiansen;Xun Xu;Junhua Li;Ruifang Wu;Huijue Jia

GigaScience

2018-10-1

Many studies have suggested that adenosine diphosphate ribosyl transferase (ADPRT), X-ray repair cross-complementing 1 (XRCC1), and xeroderma pigmentosum complementary group D (XPD) are three major DNA base excision repair (BER) genes and that they act interactively in stimulating and executing BER processes. Polymorphisms of these genes may influence the rate of gene transcription, the stability of the messenger RNA, or the quantity and activity of the resulting protein. Thus, the susceptibility or severity of several disorders is influenced by possession of specific alleles of polymorphic genes. So, it is plausible that variations and mutations in these genes affect DNA repair capacity in normal populations, and thus facilitate cancer development in normal or exposed individuals. To promote translation of scientific findings for potential clinical application of DNA repair function, we have searched publications relevant to molecular epidemiology studies of associations between single-nucleotide polymorphisms (SNPs) in the genes, and several frequent human cancer. We have focused on five particular polymorphisms as our starting point: the T→C polymorphism (Val762Ala) in exon 17 of ADPRT, the novel transition at the promoter region (-77T→C) of XRCC1, two common nonsynonymous polymorphisms (Arg194Trp and Arg399Gln), and the C→A silent polymorphism (Arg156Arg) in exon 6 of XPD. We review here the case-control studies examining whether these polymorphisms are correlated with reduced DNA repair efficiency, their influence on the development of different solid tumors, and their possible interactions with other genetic factors and environmental exposures.

Jun Jiang;Xiuqing Zhang;焕明 杨;Wendy Wang

2009

Background: Structural variants (SVs) are less common than single nucleotide polymorphisms and indels in the population, but collectively account for a significant fraction of genetic polymorphism and diseases. Base pair differences arising from SVs are on a much higher order (>100 fold) than point mutations; however, none of the current detection methods are comprehensive, and currently available methodologies are incapable of providing sufficient resolution and unambiguous information across complex regions in the human genome. To address these challenges, we applied a high-throughput, cost-effective genome mapping technology to comprehensively discover genome-wide SVs and characterize complex regions of the YH genome using long single molecules (>150 kb) in a global fashion.Results: Utilizing nanochannel-based genome mapping technology, we obtained 708 insertions/deletions and 17 inversions larger than 1 kb. Excluding the 59 SVs (54 insertions/deletions, 5 inversions) that overlap with N-base gaps in the reference assembly hg19, 666 non-gap SVs remained, and 396 of them (60%) were verified by paired-end data from whole-genome sequencing-based re-sequencing or de novo assembly sequence from fosmid data. Of the remaining 270 SVs, 260 are insertions and 213 overlap known SVs in the Database of Genomic Variants. Overall, 609 out of 666 (90%) variants were supported by experimental orthogonal methods or historical evidence in public databases. At the same time, genome mapping also provides valuable information for complex regions with haplotypes in a straightforward fashion. In addition, with long single-molecule labeling patterns, exogenous viral sequences were mapped on a whole-genome scale, and sample heterogeneity was analyzed at a new level.Conclusion: Our study highlights genome mapping technology as a comprehensive and cost-effective method for detecting structural variation and studying complex regions in the human genome, as well as deciphering viral integration into the host genome.

Hongzhi Cao;Alex R. Hastie;Dandan Cao;Ernest T. Lam;Yuhui Sun;Haodong Huang;Xiao Liu;Liya Lin;Warren Andrews;Saki Chan;Shujia Huang;Xin Tong;Michael Requa;Thomas Anantharaman;Anders Krogh;焕明 杨;Han Cao;Xun Xu

GigaScience

2014-12-30

The root nodule symbiosis of plants with nitrogen-fixing bacteria affects global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of 10 plant species covering the diversity of nodule morphotypes, bacterial symbionts, and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator NODULE INCEPTION in 10 of 13 genomes of nonnodulating species within this clade. The discovery that multiple independent losses shaped the present-day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so-far-underestimated selection pressure against this symbiosis.

Maximilian Griesmann;Yue Chang;Xin Liu;Yue Song;Georg Haberer;Matthew B. Crook;Benjamin Billault-Penneteau;Dominique Lauressergues;Jean Keller;Leandro Imanishi;Yuda Purwana Roswanjaya;Wouter Kohlen;Petar Pujic;Kai Battenberg;Nicole Alloisio;Yuhu Liang;Henk Hilhorst;Marco G. Salgado;Valerie Hocher;Hassen Gherbi;Sergio Svistoonoff;Jeff J. Doyle;Shixu He;Yan Xu;Shanyun Xu;Jing Qu;Qiang Gao;Xiaodong Fang;Yuan Fu;Philippe Normand;Alison M. Berry;Luis G. Wall;Jean Michel Ané;Katharina Pawlowski;Xun Xu;焕明 杨;Manuel Spannagl;Klaus F.X. Mayer;Gane Ka Shu Wong;Martin Parniske;Pierre Marc Delaux;Shifeng Cheng

Science

2018-7-13