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https://www.readbyqxmd.com/read/27818083/shotgun-metagenomics-of-250-adult-twins-reveals-genetic-and-environmental-impacts-on-the-gut-microbiome
#1
Hailiang Xie, Ruijin Guo, Huanzi Zhong, Qiang Feng, Zhou Lan, Bingcai Qin, Kirsten J Ward, Matthew A Jackson, Yan Xia, Xu Chen, Bing Chen, Huihua Xia, Changlu Xu, Fei Li, Xun Xu, Jumana Yousuf Al-Aama, Huanming Yang, Jian Wang, Karsten Kristiansen, Jun Wang, Claire J Steves, Jordana T Bell, Junhua Li, Timothy D Spector, Huijue Jia
The gut microbiota has been typically viewed as an environmental factor for human health. Twins are well suited for investigating the concordance of their gut microbiomes and decomposing genetic and environmental influences. However, existing twin studies utilizing metagenomic shotgun sequencing have included only a few samples. Here, we sequenced fecal samples from 250 adult twins in the TwinsUK registry and constructed a comprehensive gut microbial reference gene catalog. We demonstrate heritability of many microbial taxa and functional modules in the gut microbiome, including those associated with diseases...
November 2, 2016: Cell Systems
https://www.readbyqxmd.com/read/27781166/the-single-species-metagenome-subtyping-staphylococcus-aureus-core-genome-sequences-from-shotgun-metagenomic-data
#2
Sandeep J Joseph, Ben Li, Robert A Petit Iii, Zhaohui S Qin, Lyndsey Darrow, Timothy D Read
In this study we developed a genome-based method for detecting Staphylococcus aureus subtypes from metagenome shotgun sequence data. We used a binomial mixture model and the coverage counts at >100,000 known S. aureus SNP (single nucleotide polymorphism) sites derived from prior comparative genomic analysis to estimate the proportion of 40 subtypes in metagenome samples. We were able to obtain >87% sensitivity and >94% specificity at 0.025X coverage for S. aureus. We found that 321 and 149 metagenome samples from the Human Microbiome Project and metaSUB analysis of the New York City subway, respectively, contained S...
2016: PeerJ
https://www.readbyqxmd.com/read/27708392/unique-features-of-ethnic-mongolian-gut-microbiome-revealed-by-metagenomic-analysis
#3
Wenjun Liu, Jiachao Zhang, Chunyan Wu, Shunfeng Cai, Weiqiang Huang, Jing Chen, Xiaoxia Xi, Zebin Liang, Qiangchuan Hou, Bing Zhou, Nan Qin, Heping Zhang
The human gut microbiota varies considerably among world populations due to a variety of factors including genetic background, diet, cultural habits and socioeconomic status. Here we characterized 110 healthy Mongolian adults gut microbiota by shotgun metagenomic sequencing and compared the intestinal microbiome among Mongolians, the Hans and European cohorts. The results showed that the taxonomic profile of intestinal microbiome among cohorts revealed the Actinobaceria and Bifidobacterium were the key microbes contributing to the differences among Mongolians, the Hans and Europeans at the phylum level and genus level, respectively...
October 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27587331/microbially-mediated-plant-salt-tolerance-and-microbiome-based-solutions-for-saline-agriculture
#4
Yuan Qin, Irina S Druzhinina, Xueyu Pan, Zhilin Yuan
Soil salinization adversely affects plant growth and has become one of the major limiting factors for crop productivity worldwide. The conventional approach, breeding salt-tolerant plant cultivars, has often failed to efficiently alleviate the situation. In contrast, the use of a diverse array of microorganisms harbored by plants has attracted increasing attention because of the remarkable beneficial effects of microorganisms on plants. Multiple advanced '-omics' technologies have enabled us to gain insights into the structure and function of plant-associated microbes...
November 15, 2016: Biotechnology Advances
https://www.readbyqxmd.com/read/27572178/specialized-microbiome-of-a-halophyte-and-its-role-in-helping-non-host-plants-to-withstand-salinity
#5
Zhilin Yuan, Irina S Druzhinina, Jessy Labbé, Regina Redman, Yuan Qin, Russell Rodriguez, Chulong Zhang, Gerald A Tuskan, Fucheng Lin
Root microbiota is a crucial determinant of plant productivity and stress tolerance. Here, we hypothesize that the superior halo-tolerance of seepweed Suaeda salsa is tightly linked to a specialized belowground microbiome. To test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16S rRNA gene and fungal nuclear rRNA internal transcribed spacer profiling. Data showed that the dominant α-proteobacteria and γ-proteobacteria communities in bulk soil and root endosphere tend to be phylogenetically clustered and at the same time exhibit phylogenetic over-dispersion in rhizosphere...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27405167/-urinary-metabolomics-study-of-the-effects-of-scutellaria-baicalensis-georgi-ethanol-extract-on-d-galactose-induced-rats
#6
Yan-fen Chang, Wen-xia Gong, Yan-hong Zheng, Jian-wei Li, Yu-zhi Zhou, Xue-mei Qin, Guan-hua Du
The purpose of this study is to evaluate the anti-aging effects and reveal the underlying mechanism of Scutellaria baicalensis Georgi ethanol extract (SBG) in D-galactose-induced rats. Fifty rats were randomly divided into five groups: vehicle control group, D-galactose group, and D-galactose combined with 50, 100, 200 mg x kg(-1) SBG. A rat aging model was induced by injecting subcutaneously D-galactose (100 mg x kg(-1)) for ten weeks. At the tenth week, the locomotor activity (in open-field test) and the learning and memory abilities (in Morris water maze test) were examined respectively...
January 2016: Yao Xue Xue Bao, Acta Pharmaceutica Sinica
https://www.readbyqxmd.com/read/27338709/a-52-week-safety-study-in-cynomolgus-macaques-for-genetically-modified-rice-expressing-cry1ab-1ac-protein
#7
Jie Mao, Xing Sun, Jian-Hua Cheng, Yong-Jie Shi, Xin-Zheng Wang, Jun-Jie Qin, Zhi-Hong Sang, Kun He, Qing Xia
A 52-week feeding study in cynomolgus macaques was carried out to evaluate the safety of Bt rice Huahui 1 (HH1), a transgenic rice line expressing Cry1Ab/1Ac protein. Monkeys were fed a diet with 20% or 60% HH1 rice, 20% or 60% parental rice (Minghui 63, MH63), normal diet, normal diet spiked with purified recombinant Cry1Ab/1Ac fusion protein or bovine serum albumin (BSA) respectively. During the feeding trail, clinical observations were conducted daily, and multiple parameters, including body weight, body temperature, electrocardiogram, hematology, blood biochemistry, serum metabolome and gut microbiome were examined at regular intervals...
September 2016: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/27135948/exploring-the-goat-rumen-microbiome-from-seven-days-to-two-years
#8
Lizhi Wang, Qin Xu, Fanli Kong, Yindong Yang, De Wu, Sudhanshu Mishra, Ying Li
Rumen microbial communities play important roles in feed conversion and the physiological development of the ruminants. Despite its significance, little is known about the rumen microbial communities at different life stages after birth. In this study, we characterized the rumen bacterial and the archaeal communities in 11 different age groups (7, 15, 30, 60, 90, 120, 150, 180, 360, 540 and 720 days old) of a crossbred F1 goats (n = 5 for each group) by using an Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene...
2016: PloS One
https://www.readbyqxmd.com/read/26961389/preliminary-analysis-of-salivary-microbiome-and-their-potential-roles-in-oral-lichen-planus
#9
Kun Wang, Wenxin Lu, Qichao Tu, Yichen Ge, Jinzhi He, Yu Zhou, Yaping Gou, Joy D Van Nostrand, Yujia Qin, Jiyao Li, Jizhong Zhou, Yan Li, Liying Xiao, Xuedong Zhou
Several studies have explored the origin and development mechanism of oral lichen planus (OLP) with limited attention to the role of bacteria in the progression of this common oral disease. Here we utilized MiSeq sequencing of 16S rRNA gene amplicons to identify complex oral microbiota associated with OLP from saliva samples of two subtypes (reticular and erosive) of OLP patients and healthy controls. Our analyses indicated that the overall structure of the salivary microbiome was not significantly affected by disease status...
2016: Scientific Reports
https://www.readbyqxmd.com/read/26834834/metagenomic-analysis-of-microbial-consortia-enriched-from-compost-new-insights-into-the-role-of-actinobacteria-in-lignocellulose-decomposition
#10
Cheng Wang, Da Dong, Haoshu Wang, Karin Müller, Yong Qin, Hailong Wang, Weixiang Wu
BACKGROUND: Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenomic analysis of the rice straw-adapted (RSA) microbial consortia enriched from compost ecosystems to decipher the systematic and functional contexts within such a distinctive microbiome...
2016: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/26603211/metagenomic-insights-into-communities-functions-of-endophytes-and-their-associates-with-infection-by-root-knot-nematode-meloidogyne-incognita-in-tomato-roots
#11
Bao-Yu Tian, Yi Cao, Ke-Qin Zhang
Endophytes are known to play important roles in plant's health and productivity. In this study, we investigated the root microbiome of tomato in association with infection by root knot nematodes. Our objectives were to observe the effects and response of the bacterial endophytes before nematode attacks and to reveal the functional attributes of microbes in plant health and nematode pathogenesis. Community analysis of root-associated microbiomes in healthy and nematode-infected tomatoes indicated that nematode infections were associated with variation and differentiation of the endophyte and rhizosphere bacterial populations in plant roots...
2015: Scientific Reports
https://www.readbyqxmd.com/read/26583008/comparative-metagenomics-reveals-impact-of-contaminants-on-groundwater-microbiomes
#12
Christopher L Hemme, Qichao Tu, Zhou Shi, Yujia Qin, Weimin Gao, Ye Deng, Joy D Van Nostrand, Liyou Wu, Zhili He, Patrick S G Chain, Susannah G Tringe, Matthew W Fields, Edward M Rubin, James M Tiedje, Terry C Hazen, Adam P Arkin, Jizhong Zhou
To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion ( >55%) of the community is composed of poorly characterized low abundance (individually <1%) lineages...
2015: Frontiers in Microbiology
https://www.readbyqxmd.com/read/26505801/microbiome-interaction-with-sugar-plays-an-important-role-in-relapse-of-childhood-caries
#13
Jing Tian, Man Qin, Wenli Ma, Bin Xia, He Xu, Qian Zhang, Feng Chen
Childhood caries have a high relapse rate after full mouth therapy. This study aimed to elucidate the relationship between the microbiome, sugar, and the relapse of childhood caries after therapy. A total of 24 children aged 2-4 years who underwent one caries treatment session participated in this study. Supragingival plaque was collected before therapy and 1 and 7 months after therapy, then sequenced using the 16S rRNA high-throughput approach. We found 11 phyla, 140 genera, and 444 species in 72 samples. The children were divided into relapse-free (n = 13) and relapse (n = 11) groups according to whether they relapsed 7 months after therapy...
December 4, 2015: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/26408641/metagenomic-analysis-of-faecal-microbiome-as-a-tool-towards-targeted-non-invasive-biomarkers-for-colorectal-cancer
#14
Jun Yu, Qiang Feng, Sunny Hei Wong, Dongya Zhang, Qiao Yi Liang, Youwen Qin, Longqing Tang, Hui Zhao, Jan Stenvang, Yanli Li, Xiaokai Wang, Xiaoqiang Xu, Ning Chen, William Ka Kei Wu, Jumana Al-Aama, Hans Jørgen Nielsen, Pia Kiilerich, Benjamin Anderschou Holbech Jensen, Tung On Yau, Zhou Lan, Huijue Jia, Junhua Li, Liang Xiao, Thomas Yuen Tung Lam, Siew Chien Ng, Alfred Sze-Lok Cheng, Vincent Wai-Sun Wong, Francis Ka Leung Chan, Xun Xu, Huanming Yang, Lise Madsen, Christian Datz, Herbert Tilg, Jian Wang, Nils Brünner, Karsten Kristiansen, Manimozhiyan Arumugam, Joseph Jao-Yiu Sung, Jun Wang
OBJECTIVE: To evaluate the potential for diagnosing colorectal cancer (CRC) from faecal metagenomes. DESIGN: We performed metagenome-wide association studies on faecal samples from 74 patients with CRC and 54 controls from China, and validated the results in 16 patients and 24 controls from Denmark. We further validated the biomarkers in two published cohorts from France and Austria. Finally, we employed targeted quantitative PCR (qPCR) assays to evaluate diagnostic potential of selected biomarkers in an independent Chinese cohort of 47 patients and 109 controls...
September 25, 2015: Gut
https://www.readbyqxmd.com/read/25911445/evaluation-of-composition-and-individual-variability-of-rumen-microbiota-in-yaks-by-16s-rrna-high-throughput-sequencing-technology
#15
Wei Guo, Ying Li, Lizhi Wang, Jiwen Wang, Qin Xu, Tianhai Yan, Bai Xue
The Yak (Bos grunniens) is a unique species of ruminant animals that is important to agriculture of the Tibetan plateau, and has a complex intestinal microbial community. The objective of the present study was to characterize the composition and individual variability of microbiota in the rumen of yaks using 16S rRNA gene high-throughput sequencing technique. Rumen samples used in the present study were obtained from grazing adult male yaks (n = 6) in a commercial farm in Ganzi Autonomous Prefecture of Sichuan Province, China...
August 2015: Anaerobe
https://www.readbyqxmd.com/read/25755571/gut-microbiome-and-liver-diseases
#16
Shalimar
Nan Qin(1,2), Fengling Yang(1), Ang Li(1), Edi Prifti(3), Yanfei Chen(1), Li Shao(1,2), Jing Guo(1), Emmanuelle Le Chatelier(3), Jian Yao(1,2), Lingjiao Wu(1), Jiawei Zhou(1), Shujun Ni(1), Lin Liu(1), Nicolas Pons(3), Jean Michel Batto(3), Sean P. Kennedy(3), Pierre Leonard(3), Chunhui Yuan(1), Wenchao Ding(1), Yuanting Chen(1), Xinjun Hu(1), Beiwen Zheng(1,2), Guirong Qian(1), Wei Xu(1), S. Dusko Ehrlich(3,4), Shusen Zheng(2,5) and Lanjuan Li(1,2) Alterations of the human gut microbiome in liver cirrhosis...
September 2014: Journal of Clinical and Experimental Hepatology
https://www.readbyqxmd.com/read/25701246/association-between-tobacco-use-and-the-upper-gastrointestinal-microbiome-among-chinese-men
#17
Emily Vogtmann, Roberto Flores, Guoqin Yu, Neal D Freedman, Jianxin Shi, Mitchell H Gail, Bruce A Dye, Guo-Qing Wang, Vanja Klepac-Ceraj, Bruce J Paster, Wen-Qiang Wei, Hui-Qin Guo, Sanford M Dawsey, You-Lin Qiao, Christian C Abnet
PURPOSE: Tobacco causes many adverse health conditions and may alter the upper gastrointestinal (UGI) microbiome. However, the few studies that studied the association between tobacco use and the microbiome were small and underpowered. Therefore, we investigated the association between tobacco use and the UGI microbiome in Chinese men. METHODS: We included 278 men who underwent esophageal cancer screening in Henan Province, China. Men were categorized as current, former, or never smokers from questionnaire data...
April 2015: Cancer Causes & Control: CCC
https://www.readbyqxmd.com/read/25658087/extensive-description-and-comparison-of-human-supra-gingival-microbiome-in-root-caries-and-health
#18
COMPARATIVE STUDY
Lin Chen, Bingcai Qin, Minquan Du, Huanzi Zhong, Qingan Xu, Yuhong Li, Ping Zhang, Mingwen Fan
Knowledge of the polymicrobial etiology of root caries is limited. To conduct a comprehensive research study on root caries, we utilized 454-pyrosequencing of 16S rRNA gene libraries and quantitative PCR to compare supra-gingival bacterial communities from healthy sites and carious sites of 21 patients with root caries (Patient-controls and Patient-cases) and the sites of 21 healthy individuals (Healthy-controls) from two nursing homes. Healthy-controls and Patient-cases showed no significant differences in terms of biomass, species richness, and species diversity...
2015: PloS One
https://www.readbyqxmd.com/read/25647155/fecal-microbial-transplant-effect-on-clinical-outcomes-and-fecal-microbiome-in-active-crohn-s-disease
#19
David L Suskind, Mitchell J Brittnacher, Ghassan Wahbeh, Michele L Shaffer, Hillary S Hayden, Xuan Qin, Namita Singh, Christopher J Damman, Kyle R Hager, Heather Nielson, Samuel I Miller
BACKGROUND: Crohn's disease (CD) is a chronic idiopathic inflammatory intestinal disorder associated with fecal dysbiosis. Fecal microbial transplant (FMT) is a potential therapeutic option for individuals with CD based on the hypothesis that changing the fecal dysbiosis could promote less intestinal inflammation. METHODS: Nine patients, aged 12 to 19 years, with mild-to-moderate symptoms defined by Pediatric Crohn's Disease Activity Index (PCDAI of 10-29) were enrolled into a prospective open-label study of FMT in CD (FDA IND 14942)...
March 2015: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/25491920/the-establishment-of-the-infant-intestinal-microbiome-is-not-affected-by-rotavirus-vaccination
#20
Li Ang, Silvia Arboleya, Guo Lihua, Yuan Chuihui, Qin Nan, Marta Suarez, Gonzalo Solís, Clara G de los Reyes-Gavilán, Miguel Gueimonde
The microbial colonization of the intestine during the first months of life constitutes the most important process for the microbiota-induced host-homeostasis. Alterations in this process may entail a high-risk for disease in later life. However, the potential factors affecting this process in the infant are not well known. Moreover, the potential impact of orally administered vaccines upon the establishing microbiome remains unknown. Here we assessed the intestinal microbiome establishment process and evaluated the impact of rotavirus vaccination upon this process...
2014: Scientific Reports
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