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https://www.readbyqxmd.com/read/28569210/bacteriophage-prokaryote-dynamics-and-interaction-within-anaerobic-digestion-processes-across-time-and-space
#1
Junyu Zhang, Qun Gao, Qiuting Zhang, Tengxu Wang, Haowei Yue, Linwei Wu, Jason Shi, Ziyan Qin, Jizhong Zhou, Jiane Zuo, Yunfeng Yang
BACKGROUND: Bacteriophage-prokaryote dynamics and interaction are believed to be important in governing microbiome composition and ecosystem functions, yet our limited knowledge of the spatial and temporal variation in phage and prokaryotic community compositions precludes accurate assessment of their roles and impacts. Anaerobic digesters are ideal model systems to examine phage-host interaction, owing to easy access, stable operation, nutrient-rich environment, and consequently enormous numbers of phages and prokaryotic cells...
May 31, 2017: Microbiome
https://www.readbyqxmd.com/read/28491055/metagenomic-sequencing-of-diamondback-moth-gut-microbiome-unveils-key-holobiont-adaptations-for-herbivory
#2
Xiaofeng Xia, Geoff M Gurr, Liette Vasseur, Dandan Zheng, Huanzi Zhong, Bingcai Qin, Junhan Lin, Yue Wang, FengQin Song, Yong Li, Hailan Lin, Minsheng You
Herbivore specialists adapt to feed on a specific group of host plants by evolving various mechanisms to respond to plant defenses. Insects also possess complex gut microbiotas but their potential role in adaptation is poorly understood. Our previous study of the genome of diamondback moth, Plutella xylostella, revealed an intrinsic capacity to detoxify plant defense compounds, which is an important factor in its success as a pest. Here we expand on that work with a complete taxonomic and functional profile of the P...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28481971/bioinformatics-tools-for-quantitative-and-functional-metagenome-and-metatranscriptome-data-analysis-in-microbes
#3
Sheng-Yong Niu, Jinyu Yang, Adam McDermaid, Jing Zhao, Yu Kang, Qin Ma
Metagenomic and metatranscriptomic sequencing approaches are more frequently being used to link microbiota to important diseases and ecological changes. Many analyses have been used to compare the taxonomic and functional profiles of microbiota across habitats or individuals. While a large portion of metagenomic analyses focus on species-level profiling, some studies use strain-level metagenomic analyses to investigate the relationship between specific strains and certain circumstances. Metatranscriptomic analysis provides another important insight into activities of genes by examining gene expression levels of microbiota...
May 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28469109/comparison-of-composition-and-diversity-of-bacterial-microbiome-in-human-upper-and-lower-respiratory-tract
#4
Zhi-Hong Feng, Qin Li, Si-Ran Liu, Xiao-Nan Du, Chen Wang, Xiu-Hong Nie, Wei Wang, Sun Ying
No abstract text is available yet for this article.
May 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28240162/effects-of-dietary-non-fiber-carbohydrates-on-composition-and-function-of-gut-microbiome-in-monogastrics-a-review
#5
Hailong Jiang, Dongsheng Che, Guixin Qin, Xiangjie Kong, Mohammed Hamdy Farouk
Non-fiber carbohydrates (NFC) have a crucial function on the gut health of monogastrics. This paper aims to review the relevant published materials on the influence of NFC's on the gut's microbial population and composition in monogastrics, and points out the areas of the required research. Total bacteria count and Lactobacillus sp. were decreased with an increase in composition of dietary NFC intake, as well as accompanied by a decrease in the short-chain fatty acids (SCFAs) levels. Consequently, some metabolites were affected by the accumulation of the bile acids, including molecules which control different gene expression levels, as regulators involved in glucose (FXR and TGR5) and fat metabolism (cholesterol)...
February 23, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28213609/gut-microbial-profile-is-altered-in-primary-biliary-cholangitis-and-partially-restored-after-udca-therapy
#6
Ruqi Tang, Yiran Wei, Yanmei Li, Weihua Chen, Haoyan Chen, Qixia Wang, Fan Yang, Qi Miao, Xiao Xiao, Haiyan Zhang, Min Lian, Xiang Jiang, Jun Zhang, Qin Cao, Zhuping Fan, Maoying Wu, Dekai Qiu, Jing-Yuan Fang, Aftab Ansari, M Eric Gershwin, Xiong Ma
OBJECTIVE: A close relationship between gut microbiota and some chronic liver disorders has recently been described. Herein, we systematically performed a comparative analysis of the gut microbiome in primary biliary cholangitis (PBC) and healthy controls. DESIGN: We first conducted a cross-sectional study of 60 ursodeoxycholic acid (UDCA) treatment-naïve patients with PBC and 80 matched healthy controls. Second, an independent cohort composed of 19 treatment-naïve patients and 34 controls was used to validate the results...
February 17, 2017: Gut
https://www.readbyqxmd.com/read/28120199/a-comprehensive-profiling-of-supragingival-bacterial-composition-in-chinese-twin-children-and-their-mothers
#7
COMPARATIVE STUDY
Qin Du, Mingyun Li, Xuedong Zhou, Kun Tian
To investigate the factors influencing the oral microbiome, 16 twin pairs and their mothers were enrolled in this study. There were 7 monozygotic (MZ) twins and 9 dizygotic (DZ) twins, with an average age of 6.18 ± 3.5. Supragingival plaques and caries tissues were collected and the 16S rDNA was analyzed by 454 pyrosequencing. A total of 18 phyla and 179 genuses were found. Caries children harbored a higher portion of Actinobacteria than caries-free ones, and one lineage was found to be less abundant in the caries tissues compared to the supragingival plaque at each level from the phylum down to the genus level, which was Fusobacteria at Phylum, Fusobacteriia at Class, Fusobacteriales at Order, Leptotrichiaceae at Family and Leptotrichia at genus level...
May 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28051107/corrigendum-unique-features-of-ethnic-mongolian-gut-microbiome-revealed-by-metagenomic-analysis
#8
Wenjun Liu, Jiachao Zhang, Chunyan Wu, Shunfeng Cai, Weiqiang Huang, Jing Chen, Xiaoxia Xi, Zebin Liang, Qiangchuan Hou, Bin Zhou, Nan Qin, Heping Zhang
No abstract text is available yet for this article.
January 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/27818083/shotgun-metagenomics-of-250-adult-twins-reveals-genetic-and-environmental-impacts-on-the-gut-microbiome
#9
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...
December 21, 2016: Cell Systems
https://www.readbyqxmd.com/read/27781166/the-single-species-metagenome-subtyping-staphylococcus-aureus-core-genome-sequences-from-shotgun-metagenomic-data
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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...
March 10, 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
#18
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
#19
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
#20
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
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