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https://www.readbyqxmd.com/read/29423379/identification-and-characterization-of-blood-and-neutrophil-associated-microbiomes-in-patients-with-severe-acute-pancreatitis-using-next-generation-sequencing
#1
Qiurong Li, Chenyang Wang, Chun Tang, Xiaofan Zhao, Qin He, Jieshou Li
Infectious complications are a leading cause of death for patients with severe acute pancreatitis (SAP). Yet, our knowledge about details of the blood microbial landscape in SAP patients remains limited. Recently, some studies have reported that the peripheral circulation harbors a diverse bacterial community in healthy and septic subjects. The objective of this study was to examine the presence of the blood bacterial microbiome in SAP patients and its potential role in the development of infectious complications...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29402771/micro-integral-membrane-protein-mimp-a-newly-discovered-anti-inflammatory-protein-of-lactobacillus-plantarum-enhances-the-gut-barrier-and-modulates-microbiota-and-inflammatory-cytokines
#2
Mingming Yin, Xuebing Yan, Wenhao Weng, Yongzhi Yang, Renyuan Gao, Minfeng Liu, Cheng Pan, Qi Zhu, Hao Li, Qing Wei, Tongyi Shen, Yanlei Ma, Huanlong Qin
BACKGROUND/AIMS: Recent studies have demonstrated that the manipulation of the gut microbiome represents a promising treatment for inflammatory bowel disease (IBD). We previously identified micro integral membrane protein (MIMP) as the smallest domain of surface layer protein from Lactobacillus Plantarum. However, the therapeutic relevance of MIMP in IBD remains unknown. METHODS: We initially employed a dextran sodium sulphate (DSS)-induced colitis model and evaluated the effect of MIMP on the inflammation response, intestinal barrier and gut microbiota using histological examination, Fluorescein isothiocyanate-Dextran detection and pyrosequencing analysis respectively...
January 25, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29361968/an-obesity-associated-gut-microbiome-reprograms-the-intestinal-epigenome-and-leads-to-altered-colonic-gene-expression
#3
Yufeng Qin, John D Roberts, Sara A Grimm, Fred B Lih, Leesa J Deterding, Ruifang Li, Kaliopi Chrysovergis, Paul A Wade
BACKGROUND: The gut microbiome, a key constituent of the colonic environment, has been implicated as an important modulator of human health. The eukaryotic epigenome is postulated to respond to environmental stimuli through alterations in chromatin features and, ultimately, gene expression. How the host mediates epigenomic responses to gut microbiota is an emerging area of interest. Here, we profile the gut microbiome and chromatin characteristics in colon epithelium from mice fed either an obesogenic or control diet, followed by an analysis of the resultant changes in gene expression...
January 23, 2018: Genome Biology
https://www.readbyqxmd.com/read/29291559/spatiotemporal-changes-in-bacterial-community-and-microbial-activity-in-a-full-scale-drinking-water-treatment-plant
#4
Luanfeng Hou, Qin Zhou, Qingping Wu, Qihui Gu, Ming Sun, Jumei Zhang
To gain insight into the bacterial dynamics present in drinking water treatment (DWT) systems, the microbial community and activity in a full-scale DWT plant (DWTP) in Guangzhou, South China, were investigated using Illumina Hiseq sequencing analyses combined with cultivation-based techniques during the wet and dry seasons. Illumina sequencing analysis of 16S rRNA genes revealed a large shift in the proportion of Actinobacteria, Proteobacteria and Firmicutes during the treatment process, with the proportion of Actinobacteria decreased sharply, whereas that of Proteobacteria and Firmicutes increased and predominated in treated water...
December 29, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29197739/a-meta-analysis-of-the-use-of-probiotics-to-alleviate-depressive-symptoms
#5
REVIEW
Qin Xiang Ng, Christina Peters, Collin Yih Xian Ho, Donovan Yutong Lim, Wee-Song Yeo
INTRODUCTION: Some preclinical and clinical studies have demonstrated the positive impact of probiotic supplementation on depressive symptoms. This paper aims to provide an updated meta-analysis on the topic. METHODS: Using the keywords [probiotics OR gut OR microflora OR microbiome OR bacteria OR yeast OR yoghurt OR lactobacillus OR bifidobacterium] AND [mood OR depression OR MDD OR suicide], a preliminary search on the PubMed, Ovid, Clinical Trials Register of the Cochrane Collaboration Depression, Anxiety and Neurosis Group (CCDANTR) and Cochrane Field for Complementary Medicine database yielded 917 papers published in English between 1-Jan-1960 and 1-June-2017...
November 16, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/29161429/crosstalk-between-the-microbiome-and-epigenome-messages-from-bugs
#6
Yufeng Qin, Paul A Wade
Mammals exist in a complicated symbiotic relationship with their gut microbiome, which is postulated to have broad impacts on host health and disease. As omics-based technologies have matured, the potential mechanisms by which the microbiome affects host physiology are being addressed. The gut microbiome, which provides environmental cues, can modify host cell responses to stimuli through alterations in the host epigenome and, ultimately, gene expression. Increasing evidence highlights microbial generation of bioactive compounds that impact the transcriptional machinery in host cells...
November 17, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29117868/correction-to-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
Upon publication of the original article [1], it was noted that references 11 and 22 were miscited in the reference list.
November 8, 2017: Genome Biology
https://www.readbyqxmd.com/read/29036812/altered-gut-microbiota-in-a-mouse-model-of-alzheimer-s-disease
#8
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
#9
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%C3%A2-th17-cells-induced-by-propionibacterium-acnes-strains-associated-with-healthy-and%C3%A2-acne-skin
#10
George W Agak, Stephanie Kao, Kelsey Ouyang, Min Qin, David Moon, Ahsan Butt, Jenny Kim
Studies of the human skin microbiome suggest that Propionibacterium acnes strains may contribute differently to skin health and disease. However, the immune phenotype and functions of T helper type 17 (Th17) cells induced by healthy (PH) versus acne (PA) skin-associated P. acnes strains are currently unknown. We stimulated peripheral blood mononuclear cells 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...
August 31, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28859695/learning-microbial-community-structures-with-supervised-and-unsupervised-non-negative-matrix-factorization
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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