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https://www.readbyqxmd.com/read/29036812/altered-gut-microbiota-in-a-mouse-model-of-alzheimer-s-disease
#1
Ling Zhang, Ying Wang, Xia Xiayu, Changhua Shi, Wei Chen, Nan Song, Xinjing Fu, Rui Zhou, Yan-Feng Xu, Lan Huang, Hua Zhu, Yunlin Han, Chuan Qin
The topic of gut microbiota is currently attracting considerable interest as a potential factor in Alzheimer's disease (AD). However, the extent and time course of alterations in the gut microbiota, and their effects on AD pathology remain uncertain. Herein, we compared the fecal microbiomes and fecal short chain fatty acid composition (SCFAs) between wild-type and AD model mice at different ages under strictly controlled specific pathogen free conditions, and also conducted microscopic investigations of intestinal structures...
October 7, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28932895/taxonomic-and-functional-analyses-of-the-supragingival-microbiome-from-caries-affected-and-caries-free-hosts
#2
Jinzhi He, Qichao Tu, Yichen Ge, Yujia Qin, Bomiao Cui, Xiaoyu Hu, Yuxia Wang, Ye Deng, Kun Wang, Joy D Van Nostrand, Jiyao Li, Jizhong Zhou, Yan Li, Xuedong Zhou
Caries is one of the most prevalent and costly infectious diseases affecting humans of all ages. It is initiated by cariogenic supragingival dental plaques forming on saliva-coated tooth surfaces, yet the etiology remains elusive. To determine which microbial populations may predispose a patient to caries, we report here an in-depth and comprehensive view of the microbial community associated with supragingival dental plaque collected from the healthy teeth of caries patients and healthy adults. We found that microbial communities from caries patients had a higher evenness and inter-individual variations but simpler ecological networks compared to healthy controls despite the overall taxonomic structure being similar...
September 20, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28864077/phenotype-and-antimicrobial-activity-of-th17-cells-induced-by-propionibacterium-acnes-strains-associated-with-healthy-and-acne-skin
#3
George W Agak, Stephanie Kao, Kelsey Ouyang, Min Qin, David Moon, Ahsan Butt, Jenny Kim
Studies of human skin microbiome suggest that Propionibacterium acnes strains may contribute differently to skin health and disease. However, the immune phenotype and functions of Th17 cells induced by healthy (PH) vs. acne (PA) skin-associated P. acnes strains are currently unknown. We stimulated PBMCs from healthy donors and observed that PA strains induce higher IL-17 levels than PH strains. We next generated PH and PA strain-specific Th17 clones and show that P. acnes strains induce Th17 cells of varied phenotype and function that are stable in the presence of IL-2 and IL-23...
August 29, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28859695/learning-microbial-community-structures-with-supervised-and-unsupervised-non-negative-matrix-factorization
#4
Yun Cai, Hong Gu, Toby Kenney
BACKGROUND: Learning the structure of microbial communities is critical in understanding the different community structures and functions of microbes in distinct individuals. We view microbial communities as consisting of many subcommunities which are formed by certain groups of microbes functionally dependent on each other. The focus of this paper is on methods for extracting the subcommunities from the data, in particular Non-Negative Matrix Factorization (NMF). Our methods can be applied to both OTU data and functional metagenomic data...
August 31, 2017: Microbiome
https://www.readbyqxmd.com/read/28814344/microbial-phylogeny-determines-transcriptional-response-of-resistome-to-dynamic-composting-processes
#5
Cheng Wang, Da Dong, P J Strong, Weijing Zhu, Zhuang Ma, Yong Qin, Weixiang Wu
BACKGROUND: Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases...
August 16, 2017: Microbiome
https://www.readbyqxmd.com/read/28802277/microbiome-in-lung-explants-of-idiopathic-pulmonary-fibrosis-a-case-control-study-in-patients-with-end-stage-fibrosis
#6
Georgios D Kitsios, Mauricio Rojas, Daniel J Kass, Adam Fitch, John C Sembrat, Shulin Qin, Kristen L Veraldi, Kevin F Gibson, Kathleen Lindell, Joseph M Pilewski, Barbara Methe, Kelvin Li, John McDyer, Bryan J McVerry, Alison Morris
The microbiome has been proposed to play a role in the progression of idiopathic pulmonary fibrosis (IPF) based on bronchoalveolar lavage analyses, but the microbiome of lung tissue in IPF has not been explored. In a case-control study of lung explants analysed by 16S rRNA gene sequencing, we could not reliably detect bacterial DNA in basilar tissue samples from patients with either chronic or acute exacerbations of IPF, in contrast to control candidate-donor lungs or cystic fibrosis explants. Thus, our data do not indicate microbiome alterations in regions of IPF lung with advanced fibrosis...
August 11, 2017: Thorax
https://www.readbyqxmd.com/read/28750650/quantitative-metagenomics-reveals-unique-gut-microbiome-biomarkers-in-ankylosing-spondylitis
#7
Chengping Wen, Zhijun Zheng, Tiejuan Shao, Lin Liu, Zhijun Xie, Emmanuelle Le Chatelier, Zhixing He, Wendi Zhong, Yongsheng Fan, Linshuang Zhang, Haichang Li, Chunyan Wu, Changfeng Hu, Qian Xu, Jia Zhou, Shunfeng Cai, Dawei Wang, Yun Huang, Maxime Breban, Nan Qin, Stanislav Dusko Ehrlich
BACKGROUND: The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease. RESULTS: To investigate the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study based on deep shotgun sequencing was performed, using gut microbial DNA from 211 Chinese individuals...
July 27, 2017: Genome Biology
https://www.readbyqxmd.com/read/28727425/database-and-bioinformatics-studies-of-probiotics
#8
REVIEW
Lin Tao, Bohua Wang, Yafen Zhong, Siok Hoon Pow, Xian Zeng, Chu Qin, Peng Zhang, Shangying Chen, Weidong He, Ying Tan, Hongxia Liu, Yuyang Jiang, Weiping Chen, Yu Zong Chen
Probiotics have been widely explored for health benefits, animal cares, and agricultural applications. Recent advances in microbiome, microbiota, and microbial dark matter research have fueled greater interests in and paved ways for the study of the mechanisms of probiotics and the discovery of new probiotics from uncharacterized microbial sources. A probiotics database named PROBIO was developed to facilitate these efforts and the need for the information on the known probiotics, which provides the comprehensive information about the probiotic functions of 448 marketed, 167 clinical trial/field trial, and 382 research probiotics for use or being studied for use in humans, animals, and plants...
September 6, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28714965/a-wellness-study-of-108-individuals-using-personal-dense-dynamic-data-clouds
#9
Nathan D Price, Andrew T Magis, John C Earls, Gustavo Glusman, Roie Levy, Christopher Lausted, Daniel T McDonald, Ulrike Kusebauch, Christopher L Moss, Yong Zhou, Shizhen Qin, Robert L Moritz, Kristin Brogaard, Gilbert S Omenn, Jennifer C Lovejoy, Leroy Hood
Personal data for 108 individuals were collected during a 9-month period, including whole genome sequences; clinical tests, metabolomes, proteomes, and microbiomes at three time points; and daily activity tracking. Using all of these data, we generated a correlation network that revealed communities of related analytes associated with physiology and disease. Connectivity within analyte communities enabled the identification of known and candidate biomarkers (e.g., gamma-glutamyltyrosine was densely interconnected with clinical analytes for cardiometabolic disease)...
August 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28569210/bacteriophage-prokaryote-dynamics-and-interaction-within-anaerobic-digestion-processes-across-time-and-space
#10
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
#11
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
#12
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
#13
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
#14
REVIEW
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 NFCs 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)...
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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