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Search Results: 1 - 10 of 6420 matches for " Zhiheng Pei "
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Oral Microbiome Profiles: 16S rRNA Pyrosequencing and Microarray Assay Comparison
Jiyoung Ahn, Liying Yang, Bruce J. Paster, Ian Ganly, Luc Morris, Zhiheng Pei, Richard B. Hayes
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0022788
Abstract: Objectives The human oral microbiome is potentially related to diverse health conditions and high-throughput technology provides the possibility of surveying microbial community structure at high resolution. We compared two oral microbiome survey methods: broad-based microbiome identification by 16S rRNA gene sequencing and targeted characterization of microbes by custom DNA microarray. Methods Oral wash samples were collected from 20 individuals at Memorial Sloan-Kettering Cancer Center. 16S rRNA gene survey was performed by 454 pyrosequencing of the V3–V5 region (450 bp). Targeted identification by DNA microarray was carried out with the Human Oral Microbe Identification Microarray (HOMIM). Correlations and relative abundance were compared at phylum and genus level, between 16S rRNA sequence read ratio and HOMIM hybridization intensity. Results The major phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were identified with high correlation by the two methods (r = 0.70~0.86). 16S rRNA gene pyrosequencing identified 77 genera and HOMIM identified 49, with 37 genera detected by both methods; more than 98% of classified bacteria were assigned in these 37 genera. Concordance by the two assays (presence/absence) and correlations were high for common genera (Streptococcus, Veillonella, Leptotrichia, Prevotella, and Haemophilus; Correlation = 0.70–0.84). Conclusion Microbiome community profiles assessed by 16S rRNA pyrosequencing and HOMIM were highly correlated at the phylum level and, when comparing the more commonly detected taxa, also at the genus level. Both methods are currently suitable for high-throughput epidemiologic investigations relating identified and more common oral microbial taxa to disease risk; yet, pyrosequencing may provide a broader spectrum of taxa identification, a distinct sequence-read record, and greater detection sensitivity.
Substantial Alterations of the Cutaneous Bacterial Biota in Psoriatic Lesions
Zhan Gao, Chi-hong Tseng, Bruce E. Strober, Zhiheng Pei, Martin J. Blaser
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002719
Abstract: For psoriasis, an idiopathic inflammatory disorder of the skin, the microbial biota has not been defined using cultivation-independent methods. We used broad-range 16S rDNA PCR for archaea and bacteria to examine the microbiota of normal and psoriatic skin. From 6 patients, 19 cutaneous samples (13 from diseased skin and 6 from normal skin) were obtained. Extracted DNA was subjected to the broad range PCR, and 1,925 cloned products were compared with 2,038 products previously reported from healthy persons. Using 98% sequence identity as a species boundary, 1,841 (95.6%) clones were similar to known bacterial 16S rDNA, representing 6 phyla, 86 genera, or 189 species-level operational taxonomic unit (SLOTU); 84 (4.4%) clones with <98% identity probably represented novel species. The most abundant and diverse phylum populating the psoriatic lesions was Firmicutes (46.2%), significantly (P<0.001) overrepresented, compared to the samples from uninvolved skin of the patients (39.0%) and healthy persons (24.4%). In contrast, Actinobacteria, the most prevalent and diverse phylum in normal skin samples from both healthy persons (47.6%) and the patients (47.8%), was significantly (P<0.01) underrepresented in the psoriatic lesion samples (37.3%). Representation of Propionibacterium species were lower in the psoriatic lesions (2.9±5.5%) than from normal persons (21.1±18.2%; P<0.001), whereas normal skin from the psoriatic patients showed intermediate levels (12.3±21.6%). We conclude that psoriasis is associated with substantial alteration in the composition and representation of the cutaneous bacterial biota.
Diversity of 23S rRNA Genes within Individual Prokaryotic Genomes
Anna Pei, Carlos W. Nossa, Pooja Chokshi, Martin J. Blaser, Liying Yang, David M. Rosmarin, Zhiheng Pei
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0005437
Abstract: Background The concept of ribosomal constraints on rRNA genes is deduced primarily based on the comparison of consensus rRNA sequences between closely related species, but recent advances in whole-genome sequencing allow evaluation of this concept within organisms with multiple rRNA operons. Methodology/Principal Findings Using the 23S rRNA gene as an example, we analyzed the diversity among individual rRNA genes within a genome. Of 184 prokaryotic species containing multiple 23S rRNA genes, diversity was observed in 113 (61.4%) genomes (mean 0.40%, range 0.01%–4.04%). Significant (1.17%–4.04%) intragenomic variation was found in 8 species. In 5 of the 8 species, the diversity in the primary structure had only minimal effect on the secondary structure (stem versus loop transition). In the remaining 3 species, the diversity significantly altered local secondary structure, but the alteration appears minimized through complex rearrangement. Intervening sequences (IVS), ranging between 9 and 1471 nt in size, were found in 7 species. IVS in Deinococcus radiodurans and Nostoc sp. encode transposases. T. tengcongensis was the only species in which intragenomic diversity >3% was observed among 4 paralogous 23S rRNA genes. Conclusions/Significance These findings indicate tight ribosomal constraints on individual 23S rRNA genes within a genome. Although classification using primary 23S rRNA sequences could be erroneous, significant diversity among paralogous 23S rRNA genes was observed only once in the 184 species analyzed, indicating little overall impact on the mainstream of 23S rRNA gene-based prokaryotic taxonomy.
diversityofactinomycetesatmolecularandgenelevel
liu,zhiheng
生物多样性 , 1993,
Abstract: ?chemosystematicsandgeneticsystematicsofthepracticallyimportantactinomycetesarediscussed.useofnewtaxonomictechniquestorecognizethediversityof?actionmycetesatmolecularandgenelevelisalsostatedbasedonthecurrentreaserchofactionmycetessystematics.
Diversified Microbiota of Meconium Is Affected by Maternal Diabetes Status
Jianzhong Hu, Yoko Nomura, Ali Bashir, Heriberto Fernandez-Hernandez, Steven Itzkowitz, Zhiheng Pei, Joanne Stone, Holly Loudon, Inga Peter
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0078257
Abstract: Objectives This study was aimed to assess the diversity of the meconium microbiome and determine if the bacterial community is affected by maternal diabetes status. Methods The first intestinal discharge (meconium) was collected from 23 newborns stratified by maternal diabetes status: 4 mothers had pre-gestational type 2 diabetes mellitus (DM) including one mother with dizygotic twins, 5 developed gestational diabetes mellitus (GDM) and 13 had no diabetes. The meconium microbiome was profiled using multi-barcode 16S rRNA sequencing followed by taxonomic assignment and diversity analysis. Results All meconium samples were not sterile and contained diversified microbiota. Compared with adult feces, the meconium showed a lower species diversity, higher sample-to-sample variation, and enrichment of Proteobacteria and reduction of Bacteroidetes. Among the meconium samples, the taxonomy analyses suggested that the overall bacterial content significantly differed by maternal diabetes status, with the microbiome of the DM group showing higher alpha-diversity than that of no-diabetes or GDM groups. No global difference was found between babies delivered vaginally versus via Cesarean-section. Regression analysis showed that the most robust predictor for the meconium microbiota composition was the maternal diabetes status that preceded pregnancy. Specifically, Bacteroidetes (phyla) and Parabacteriodes (genus) were enriched in the meconium in the DM group compared to the no-diabetes group. Conclusions Our study provides evidence that meconium contains diversified microbiota and is not affected by the mode of delivery. It also suggests that the meconium microbiome of infants born to mothers with DM is enriched for the same bacterial taxa as those reported in the fecal microbiome of adult DM patients.
The effect of H. pylori eradication on meal-associated changes in plasma ghrelin and leptin
Fritz Francois, Jatin Roper, Neal Joseph, Zhiheng Pei, Aditi Chhada, Joshua R Shak, Asalia de Perez, Guillermo I Perez-Perez, Martin J Blaser
BMC Gastroenterology , 2011, DOI: 10.1186/1471-230x-11-37
Abstract: Veterans referred for upper GI endoscopy were evaluated at baseline and ≥8 weeks after endoscopy, and H. pylori status and body weight were ascertained. During the first visit in all subjects, and during subsequent visits in the initially H. pylori-positive subjects and controls, blood was collected after an overnight fast and 1 h after a standard high protein meal, and levels of eight hormones determined.Of 92 enrolled subjects, 38 were H. pylori-negative, 44 H. pylori-positive, and 10 were indeterminate. Among 23 H. pylori-positive subjects who completed evaluation after treatment, 21 were eradicated, and 2 failed eradication. After a median of seven months following eradication, six hormones related to energy homeostasis showed no significant differences, but post-prandial acylated ghrelin levels were nearly six-fold higher than pre-eradication (p = 0.005), and median integrated leptin levels also increased (20%) significantly (p < 0.001). BMI significantly increased (5 ± 2%; p = 0.008) over 18 months in the initially H. pylori-positive individuals, but was not significantly changed in those who were H. pylori-negative or indeterminant at baseline.Circulating meal-associated leptin and ghrelin levels and BMI changed significantly after H. pylori eradication, providing direct evidence that H. pylori colonization is involved in ghrelin and leptin regulation, with consequent effects on body morphometry.The healthful regulation of energy homeostasis in humans, depends on centrally-acting hormones such as ghrelin and leptin [1,2]. Serum ghrelin concentrations increase during fasting, and decrease after eating [3]; ghrelin decreases energy expenditure and promotes weight gain [4]. In contrast, leptin produced primarily by adipocytes, reduces appetite and increases energy utilization [5]. The gastric epithelium expresses both ghrelin and leptin (and their receptors) [6,7]; inflammation can modify their production [8,9].Helicobacter pylori, which colonizes the human stom
Simrank: Rapid and sensitive general-purpose k-mer search tool
Todd Z DeSantis, Keith Keller, Ulas Karaoz, Alexander V Alekseyenko, Navjeet NS Singh, Eoin L Brodie, Zhiheng Pei, Gary L Andersen, Niels Larsen
BMC Ecology , 2011, DOI: 10.1186/1472-6785-11-11
Abstract: Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset.Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity.Molecular ecology methods often require the collection of thousands of polymer sequences (DNA, RNA or proteins) extracted from biological specimens (isolates or communities) followed by a similarity search of those sequences against one or more reference databases. The match results enable the deduction of community composition [1] or inference of functional capacity [2,3] within organisms or across populations. The most popular method for sequence comparison has been to find local alignment pairings using BLAST [4] but due to speed limitations, other software has emerged to bypass the time-consuming alignment step by simply counting the number of short sub-sequences shared between a subject and query. Sub-sequence oligomers are referred to as k-mers and are the set of possible fragments of a given length (2-mer, 3-mer, 4-mer, etc.) from a polymer. K-mer matching has been employed for diverse objectives in genomics including bacterial gene discovery [5], identifying DNA signatures of pathogenic bacterial genomes [6], delineating plant genome polyadenylation sites [7], spotting genetic engineering in bacteria [8], assembling shotgun DNA sequences [9], human genome re-sequencing [10], protein superfamily recognition [11], and sequence clustering [12]. Rapid k-mer similarity searches have become the foundation for high-throughput phylogenetic classification of DNA [13-15]. Surprisingly, a general-purpose open-source software tool to aid biologists in performing all the aforementioned tasks is not readily available. MICA [16] can match DNA k-mers again
Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome
Carlos W Nossa, William E Oberdorf, Liying Yang, J?rn A Aas, Bruce J Paster, Todd Z DeSantis, Eoin L Brodie, Daniel Malamud, Michael A Poles, Zhiheng Pei
World Journal of Gastroenterology , 2010,
Abstract: AIM: To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to classify bacteria isolated from the human foregut microbiome.METHODS: A foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral, esophageal, and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial species. Candidate primers evaluated were from the European rRNA database. To assess the effect of sequence length on accuracy of classification, 16S rRNA genes of various lengths were created by trimming the full length sequences. Sequences spanning various hypervariable regions were selected to simulate the amplicons that would be obtained using possible primer pairs. The sequences were compared with full length 16S rRNA genes for accuracy in taxonomic classification using online software at the Ribosomal Database Project (RDP). The universality of the primer set was evaluated using the RDP 16S rRNA database which is comprised of 433 306 16S rRNA genes, represented by 36 phyla.RESULTS: Truncation to 100 nucleotides (nt) downstream from the position corresponding to base 28 in the Escherichia coli 16S rRNA gene caused misclassification of 87 (39.7%) of the 219 sequences, compared with misclassification of only 29 (13.2%) sequences with truncation to 350 nt. Among 350-nt sequence reads within various regions of the 16S rRNA gene, the reverse read of an amplicon generated using the 343F/798R primers had the least (8.2%) effect on classification. In comparison, truncation to 900 nt mimicking single pass Sanger reads misclassified 5.0% of the 219 sequences. The 343F/798R amplicon accurately assigned 91.8% of the 219 sequences at the species level. Weighted by abundance of the species in the esophageal dataset, the 343F/798R amplicon yielded similar classification accuracy without a significant loss in species coverage (92%). Modification of the 343F/798R primers to 347F/803R increased their universality among foregut species. Assuming that a typical polymerase chain reaction can tolerate 2 mismatches between a primer and a template, the modified 347F and 803R primers should be able to anneal 98% and 99.6% of all 16S rRNA genes in the RDP database.CONCLUSION: 347F/803R is the most suitable pair of primers for classification of foregut 16S rRNA genes but also possess universality suitable for analyses of other complex microbiomes.
Low-Dose Prospectively Electrocardiogram-Gated Axial Dual-Source CT Angiography in Patients with Pulsatile Bilateral Bidirectional Glenn Shunt: An Alternative Noninvasive Method for Postoperative Morphological Estimation
Xiaopeng Ji, Bin Zhao, Zhaoping Cheng, Biao Si, Zhiheng Wang, Yanhua Duan, Pei Nie, Haiou Li, Shifeng Yang, Hui Jiao, Ximing Wang
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0094425
Abstract: Objective To explore the clinical value of low-dose prospectively electrocardiogram-gated axial dual-source CT angiography (low-dose PGA scanning, CTA) in patients with pulsatile bilateral bidirectional Glenn shunt (bBDG) as an alternative noninvasive method for postoperative morphological estimation. Methods Twenty patients with pulsatile bBDG (mean age 4.2±1.6 years) underwent both low-dose PGA scanning and conventional cardiac angiography (CCA) for the morphological changes. The morphological evaluation included the anatomy of superior vena cava (SVC) and pulmonary artery (PA), the anastomotic location, thrombosis, aorto-pulmonary collateral circulation, pulmonary arteriovenous malformations, etc. Objective and subjective image quality was assessed. Bland–Altman analysis and linear regression analyses were used to evaluate the correlation on measurements between CTA and CCA. Effective radiation dose of both modalities was calculated. Results The CT attenuation value of bilateral SVC and PA was higher than 300 HU. The average subjective image quality score was 4.05±0.69. The morphology of bilateral SVC and PA was displayed completely and intuitively by CTA images. There were 24 SVC above PA and 15 SVC beside PA. Thrombosis was found in 1 patient. Collateral vessels were detected in 13 patients. No pulmonary arteriovenous malformation was found in our study. A strong correlation (R2>0.8, P<0.001) was observed between the measurements on CTA images and on CCA images. Bland–Altman analysis demonstrated a systematic overestimation of the measurements by CTA (the mean value of bias>0).The mean effective dose of CTA and CCA was 0.50±0.17 mSv and 4.85±1.34 mSv respectively. Conclusion CT angiography with a low-dose PGA scanning is an accurate and reliable noninvasive examination in the assessment of morphological changes in patients with pulsatile bBDG.
Association between Selected Oral Pathogens and Gastric Precancerous Lesions
Christian R. Salazar, Jinghua Sun, Yihong Li, Fritz Francois, Patricia Corby, Guillermo Perez-Perez, Ananda Dasanayake, Zhiheng Pei, Yu Chen
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0051604
Abstract: We examined whether colonization of selected oral pathogens is associated with gastric precancerous lesions in a cross-sectional study. A total of 119 participants were included, of which 37 were cases of chronic atrophic gastritis, intestinal metaplasia, or dysplasia. An oral examination was performed to measure periodontal indices. Plaque and saliva samples were tested with real-time quantitative PCR for DNA levels of pathogens related to periodontal disease (Porphyromonas gingivalis, Tannerella forsythensis, Treponema denticola, Actinobacillus actinomycetemcomitans) and dental caries (Streptococcus mutans and S. sobrinus). There were no consistent associations between DNA levels of selected bacterial species and gastric precancerous lesions, although an elevated but non-significant odds ratio (OR) for gastric precancerous lesions was observed in relation to increasing colonization of A. actinomycetemcomitans (OR = 1.36 for one standard deviation increase, 95% Confidence Interval = 0.87–2.12), P. gingivalis (OR = 1.12, 0.67–1.88) and T. denticola (OR = 1.34, 0.83–2.12) measured in plaque. To assess the influence of specific long-term infection, stratified analyses by levels of periodontal indices were conducted. A. actinomycetemcomitans was significantly associated with gastric precancerous lesions (OR = 2.51, 1.13–5.56) among those with ≥ median of percent tooth sites with PD≥3 mm, compared with no association among those below the median (OR = 0.86, 0.43–1.72). A significantly stronger relationship was observed between the cumulative bacterial burden score of periodontal disease-related pathogens and gastric precancerous lesions among those with higher versus lower levels of periodontal disease indices (p-values for interactions: 0.03–0.06). Among individuals with periodontal disease, high levels of colonization of periodontal pathogens are associated with an increased risk of gastric precancerous lesions.
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