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https://www.readbyqxmd.com/read/29058217/data-analysis-for-gut-microbiota-and-health
#1
Xingpeng Jiang, Xiaohua Hu
In recent years, data mining and analysis of high-throughput sequencing of microbiomes and metagenomic data enable researchers to discover biological knowledge by characterizing the composition and variation of species across environmental samples and to accumulate a huge amount of data, making it feasible to infer the complex principle of species interactions. The interactions of microbes in a microbial community play an important role in microbial ecological system. Data mining provides diverse approachs to identify the correlations between disease and microbes and how microbial species coexist and interact in a host-associated or natural environment...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29056887/dietary-coconut-water-vinegar-for-improvement-of-obesity-associated-inflammation-in-high-fat-diet-treated-mice
#2
Nurul Elyani Mohamad, Swee Keong Yeap, Huynh Ky, Wan Yong Ho, Sook Yee Boo, Joelle Chua, Boon-Kee Beh, Shaiful Adzni Sharifuddin, Kamariah Long, Noorjahan Banu Alitheen
Obesity has become a serious health problem worldwide. Various types of healthy food, including vinegar, have been proposed to manage obesity. However, different types of vinegar may have different bioactivities. This study was performed to evaluate the anti-obesity and anti-inflammatory effects of coconut water vinegar on high-fat-diet (HFD)-induced obese mice. Changes in the gut microbiota of the mice were also evaluated. To induce obesity, C57/BL mice were continuously fed an HFD for 33 weeks. Coconut water vinegar (0...
2017: Food & Nutrition Research
https://www.readbyqxmd.com/read/29055712/a-decade-of-rna-virus-metagenomics-is-not-enough
#3
REVIEW
Alexander L Greninger
It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win...
October 18, 2017: Virus Research
https://www.readbyqxmd.com/read/29055396/role-of-gut-microbiota-in-idiopathic-nephrotic-syndrome-in-children
#4
Kazunari Kaneko, Shoji Tsuji, Takahisa Kimata
Nephrotic syndrome characterized by heavy proteinuria and edema is the most common chronic kidney disease in children. It is classified into three categories, of which the idiopathic type accounts for the vast majority of cases. As indicated by the name, the etiology of idiopathic nephrotic syndrome remains unknown though it has been suggested that impaired T cell function is involved. Recently, evidence has mounted to suggest that dysfunction in regulatory T cells plays an important role in the development of allergic disease, a recognized comorbid condition for children with idiopathic nephrotic syndrome...
October 2017: Medical Hypotheses
https://www.readbyqxmd.com/read/29053714/atopic-asthmatic-immune-phenotypes-associated-with-airway-microbiota-and-airway-obstruction
#5
Benjamin A Turturice, Halvor S McGee, Brian Oliver, Melissa Baraket, Brian T Nguyen, Christian Ascoli, Ravi Ranjan, Asha Rani, David L Perkins, Patricia W Finn
BACKGROUND: Differences in asthma severity may be related to inflammation in the airways. The lower airway microbiota has been associated with clinical features such as airway obstruction, symptom control, and response to corticosteroids. OBJECTIVE: To assess the relationship between local airway inflammation, severity of disease, and the lower airway microbiota in atopic asthmatics. METHODS: A cohort of young adult, atopic asthmatics with intermittent or mild/moderate persistent symptoms (n = 13) were assessed via bronchoscopy, lavage, and spirometry...
2017: PloS One
https://www.readbyqxmd.com/read/29053686/empirical-metagenomic-and-computational-techniques-illuminate-the-mechanisms-by-which-fungicides-compromise-bee-health
#6
Shawn A Steffan, Prarthana S Dharampal, Luis Diaz-Garcia, Cameron R Currie, Juan Zalapa, Chris Todd Hittinger
Growers often use fungicide sprays during bloom to protect crops against disease, which exposes bees to fungicide residues. Although considered "bee-safe," there is mounting evidence that fungicide residues in pollen are associated with bee declines (for both honey and bumble bee species). While the mechanisms remain relatively unknown, researchers have speculated that bee-microbe symbioses are involved. Microbes play a pivotal role in the preservation and/or processing of pollen, which serves as nutrition for larval bees...
October 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29053261/influence-of-scale-on-biomass-growth-and-nutrient-removal-in-an-algal-bacterial-leachate-treatment-system
#7
Kaitlyn D Sniffen, Jacob Ryan Price, Christopher M Sales, Mira Olson
Data collected from experiments conducted at a flask scale are regularly used as input data for life cycle assessments and techno-economic analyses for predicting the potential productivities of large scale commercial facilities. This study measures and compares nitrogen removal and biomass growth rates in treatment systems that utilize an algae-bacteria consortium to remediate landfill leachate at three scales: small (0.25L), mid (100L) and large (1000L). The mid- and large-scale vessels were run for 52 consecutive weeks as semi-batch reactors under variable environmental conditions...
October 20, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/29052232/different-functional-genes-of-upper-airway-microbiome-associated-with-natural-course-of-childhood-asthma
#8
Bong-Soo Kim, Eun Lee, Min-Jung Lee, Mi-Jin Kang, Jisun Yoon, Hyun-Ju Cho, Jaehyun Park, Sungho Won, So Yeon Lee, Soo-Jong Hong
BACKGROUND: Microbial colonization of the airway plays a role in the pathogenesis of asthma; however, the effect of the upper airway microbiome on childhood asthma is not fully understood. We analyzed the metagenome of airway microbiome to understand the associated role of upper airway microbiome with the natural course of childhood asthma. METHODS: Nasopharyngeal swabs were collected from children with asthma, those in asthma remission, and control groups. High-throughput sequencing was used to examine the structure and functional dynamics of the airway microbiome with respect to asthma phenotypes...
October 20, 2017: Allergy
https://www.readbyqxmd.com/read/29051250/metagenome-of-the-microbial-community-of-anammox-granules-in-a-nitritation-anammox-wastewater-treatment-system
#9
Andrey V Mardanov, Alexey V Beletsky, Yury Nikolaev, Roman Y Kotlyarov, Anna Kallistova, Nikolai V Pimenov, Nikolai V Ravin
We sequenced the metagenome of a granular sludge in a nitritation/anammox bioreactor used for the treatment of ammonium-rich wastewater. Proteobacteria, Planctomycetes, Bacteroidetes, Chloroflexi, Ignavibacteriae, and Acidobacteria were the predominant phyla in the studied bioreactor. Binning of contigs yielded a near-complete genome of the dominant anammox bacterium assigned to the candidate genus Brocadia.
October 19, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29051248/metagenomic-analysis-of-microbial-diversity-in-landfill-lysimeter-soil-of-ghazipur-landfill-site-new-delhi-india
#10
Juhi Gupta, Rashmi Rathour, Madan Kumar, Indu Shekhar Thakur
We report the soil microbial diversity and functional aspects related to degradation of recalcitrant compounds, determined using a metagenomic approach, in a landfill lysimeter prepared with soil from Ghazipur landfill site, New Delhi, India. Metagenomic analysis revealed the presence and functional diversity of complex microbial communities responsible for waste degradation.
October 19, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29050374/taxonomic-structure-and-functional-association-of-foxtail-millet-root-microbiome
#11
Tao Jin, Yayu Wang, Yueying Huang, Jin Xu, Pengfan Zhang, Nian Wang, Xin Liu, Haiyan Chu, Guang Liu, Honggang Jiang, Yuzhen Li, Jing Xu, Karsten Kristiansen, Liang Xiao, Yunzeng Zhang, Gengyun Zhang, Guohua Du, Houbao Zhang, Hongfeng Zou, Haifeng Zhang, Zhuye Jie, Suisha Liang, Huijue Jia, Jingwang Wan, Dechun Lin, Jinying Li, Guangyi Fan, Huanming Yang, Jian Wang, Yang Bai, Xun Xu
The root microbes play pivotal roles in plant productivity, nutrient uptakes, and disease resistance. The root microbial community structure has been extensively investigated by 16S/18S/ITS amplicons and metagenomic sequencing in crops and model plants. However, the functional associations between root microbes and host plant growth are poorly understood. This work investigates the root bacterial community of foxtail millet (Setaria italica) and its potential effects on host plant productivity. We determined the bacterial composition of 2882 samples from foxtail millet rhizoplane, rhizosphere and corresponding bulk soils from 2 well-separated geographic locations by 16S rRNA gene amplicon sequencing...
October 1, 2017: GigaScience
https://www.readbyqxmd.com/read/29049378/immune-modulatory-genomic-properties-differentiate-gut-microbiota-of-infants-with-and-without-eczema
#12
Seungdae Oh, Gaik Chin Yap, Pei-Ying Hong, Chiung-Hui Huang, Marion M Aw, Lynette Pei-Chi Shek, Wen-Tso Liu, Bee Wah Lee
Gut microbiota play an important role in human immunological processes, potentially affecting allergic diseases such as eczema. The diversity and structure of gut microbiota in infants with eczema have been previously documented. This study aims to evaluate by comparative metagenomics differences in genetic content in gut microbiota of infants with eczema and their matched controls. Stools were collected at the age of one month old from twelve infants from an at risk birth cohort in a case control manner. Clinical follow up for atopic outcomes were carried out at the age of 12 and 24 months...
2017: PloS One
https://www.readbyqxmd.com/read/29047329/genome-sequencing-of-39-akkermansia-muciniphila-isolates-reveals-its-population-structure-genomic-and-functional-diverisity-and-global-distribution-in-mammalian-gut-microbiotas
#13
Xianfeng Guo, Shenghui Li, Jiachun Zhang, Feifan Wu, Xiangchun Li, Dan Wu, Min Zhang, Zihao Ou, Zhuye Jie, Qiulong Yan, Peng Li, Jiangfeng Yi, Yongzheng Peng
BACKGROUND: Akkermansia muciniphila is one of the most dominant bacteria that resides on the mucus layer of intestinal tract and plays key role in human health, however, little is known about its genomic content. RESULTS: Herein, we for the first time characterized the genomic architecture of A. muciniphila based on whole-genome sequencing, assembling, and annotating of 39 isolates derived from human and mouse feces. We revealed a flexible open pangenome of A. muciniphila currently consisting of 5644 unique proteins...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29045390/the-dynamics-of-molecular-evolution-over-60-000-generations
#14
Benjamin H Good, Michael J McDonald, Jeffrey E Barrick, Richard E Lenski, Michael M Desai
The outcomes of evolution are determined by a stochastic dynamical process that governs how mutations arise and spread through a population. However, it is difficult to observe these dynamics directly over long periods and across entire genomes. Here we analyse the dynamics of molecular evolution in twelve experimental populations of Escherichia coli, using whole-genome metagenomic sequencing at five hundred-generation intervals through sixty thousand generations. Although the rate of fitness gain declines over time, molecular evolution is characterized by signatures of rapid adaptation throughout the duration of the experiment, with multiple beneficial variants simultaneously competing for dominance in each population...
October 18, 2017: Nature
https://www.readbyqxmd.com/read/29043660/sera-of-peruvians-with-fever-of-unknown-origins-include-viral-nucleic-acids-from-non-vertebrate-hosts
#15
Tung Gia Phan, Juana Del Valle Mendoza, Mohammadreza Sadeghi, Eda Altan, Xutao Deng, Eric Delwart
Serum samples collected from 88 Peruvians with unexplained fever were analyzed for viral sequences using metagenomics. Nucleic acids of anelloviruses, pegivirus A (GBV-C), HIV, Dengue virus, and Oropouche virus were detected. We also characterized from two sera the RNA genomes of new species of partitivirus and dicistrovirus belonging to viral families known to infect fungi or arthropod, respectively. Genomic DNA of a putative fungal cellular host could be PCR amplified from the partitivirus-containing serum sample...
October 17, 2017: Virus Genes
https://www.readbyqxmd.com/read/29041989/links-of-gut-microbiota-composition-with-alcohol-dependence-syndrome-and-alcoholic-liver-disease
#16
Veronika B Dubinkina, Alexander V Tyakht, Vera Y Odintsova, Konstantin S Yarygin, Boris A Kovarsky, Alexander V Pavlenko, Dmitry S Ischenko, Anna S Popenko, Dmitry G Alexeev, Anastasiya Y Taraskina, Regina F Nasyrova, Evgeny M Krupitsky, Nino V Shalikiani, Igor G Bakulin, Petr L Shcherbakov, Lyubov O Skorodumova, Andrei K Larin, Elena S Kostryukova, Rustam A Abdulkhakov, Sayar R Abdulkhakov, Sergey Y Malanin, Ruzilya K Ismagilova, Tatiana V Grigoryeva, Elena N Ilina, Vadim M Govorun
BACKGROUND: Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29041965/enrichment-allows-identification-of-diverse-rare-elements-in-metagenomic-resistome-virulome-sequencing
#17
Noelle R Noyes, Maggie E Weinroth, Jennifer K Parker, Chris J Dean, Steven M Lakin, Robert A Raymond, Pablo Rovira, Enrique Doster, Zaid Abdo, Jennifer N Martin, Kenneth L Jones, Jaime Ruiz, Christina A Boucher, Keith E Belk, Paul S Morley
BACKGROUND: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29041958/towards-a-balanced-view-of-the-bacterial-tree-of-life
#18
Frederik Schulz, Emiley A Eloe-Fadrosh, Robert M Bowers, Jessica Jarett, Torben Nielsen, Natalia N Ivanova, Nikos C Kyrpides, Tanja Woyke
The bacterial tree of life has recently undergone significant expansion, chiefly from candidate phyla retrieved through genome-resolved metagenomics. Bypassing the need for genome availability, we present a snapshot of bacterial phylogenetic diversity based on the recovery of high-quality SSU rRNA gene sequences extracted from nearly 7000 metagenomes and all available reference genomes. We illuminate taxonomic richness within established bacterial phyla together with environmental distribution patterns, providing a revised framework for future phylogeny-driven sequencing efforts...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29040428/understanding-the-promises-and-hurdles-of-metagenomic-next-generation-sequencing-as-a-diagnostic-tool-for-infectious-diseases
#19
Patricia J Simner, Steven Miller, Karen C Carroll
Agnostic metagenomic next-generation sequencing (mNGS) has emerged as a promising single, universal pathogen detection method for infectious diseases diagnostics. This methodology allows for identification and genomic characterization of bacteria, fungi, parasites and viruses without the need for a priori knowledge of a specific pathogen directly from clinical specimens. Although there are increasing reports of mNGS successes, several hurdles need to be addressed, such as differentiation of colonization from infection, extraneous sources of nucleic acid, method standardization, and data storage, protection, analysis, and interpretation...
October 12, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29040406/matam-reconstruction-of-phylogenetic-marker-genes-from-short-sequencing-reads-in-metagenomes
#20
Pierre Pericard, Yoann Dufresne, Loïc Couderc, Samuel Blanquart, Hélène Touzet
Motivation: Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution...
October 11, 2017: Bioinformatics
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