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Shotgun sequence microbes

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
Asha Rani, Ravi Ranjan, Halvor S McGee, Kalista E Andropolis, Dipti V Panchal, Zahraa Hajjiri, Daniel C Brennan, Patricia W Finn, David L Perkins
Recent studies have established that a complex community of microbes colonize the human urinary tract; however, their role in kidney transplant patients treated with prophylactic antibiotics remains poorly investigated. Our aim was to investigate the urinary microbiome of kidney transplant recipients. Urine samples from 21 patients after kidney transplantation and 8 healthy controls were collected. All patients received prophylactic treatment with the antibiotic combination trimethoprim-sulfamethoxazole. Metagenomic DNA was isolated from urine samples, sequenced using shotgun sequencing approach on Illumina HiSeq 2000 platform, and analyzed for microbial taxonomic and functional annotations...
September 9, 2016: Translational Research: the Journal of Laboratory and Clinical Medicine
Shaoming Zhou, Ruihuan Xu, Fusheng He, Jiaxiu Zhou, Yan Wang, Jianli Zhou, Mingbang Wang, Wenhao Zhou
Early colonization of gut microbiota in human gut is a complex process. It remains unclear when gut microbiota colonization occurs and how it proceeds. In order to study gut microbiota composition in human early life, the present study recruited 10 healthy pairs of twins, including five monozygotic (MZ) and five dizygotic (DZ) twin pairs, whose age ranged from 0 to 6 years old. 20 fecal samples from these twins were processed by shotgun metagenomic sequencing, and their averaged data outputs were generated as 2G per sample...
2016: PloS One
Jonathan B Clayton, Pajau Vangay, Hu Huang, Tonya Ward, Benjamin M Hillmann, Gabriel A Al-Ghalith, Dominic A Travis, Ha Thang Long, Bui Van Tuan, Vo Van Minh, Francis Cabana, Tilo Nadler, Barbara Toddes, Tami Murphy, Kenneth E Glander, Timothy J Johnson, Dan Knights
The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome...
September 13, 2016: Proceedings of the National Academy of Sciences of the United States of America
Yong Nie, Jie-Yu Zhao, Yue-Qin Tang, Peng Guo, Yunfeng Yang, Xiao-Lei Wu, Fangqing Zhao
Oil reservoirs exhibit extreme environmental conditions such as high salinity and high temperature. Insights into microbial community assemblages in oil reservoirs and their functional potentials are important for understanding biogeochemical cycles in the subterranean biosphere. In this study, we performed shotgun metagenomic sequencing of crude oil samples from two geographically distant oil reservoirs in China, and compared them with all the 948 available environmental metagenomes deposited in IMG database (until October 2013)...
2016: Frontiers in Microbiology
Jakub Ridl, Michal Kolar, Michal Strejcek, Hynek Strnad, Petr Stursa, Jan Paces, Tomas Macek, Ondrej Uhlik
Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq...
2016: Frontiers in Microbiology
Panagiotis G Kougias, Laura Treu, Stefano Campanaro, Xinyu Zhu, Irini Angelidaki
The process stability of biogas plants is often deteriorated by the accumulation of Long Chain Fatty Acids (LCFA). The microbial community shifts due to LCFA disturbances have been poorly understood as the molecular techniques used were not able to identify the genome characteristics of uncultured microorganisms, and additionally, the presence of limited number of reference genomes in public databases prevented the comprehension of specific functional roles characterizing these microorganisms. The present study is the first research which deciphers by means of high throughput shotgun sequencing the dynamics of the microbial community during an inhibitory shock load induced by single pulses of unsaturated LCFA at two different concentrations (i...
2016: Scientific Reports
Laura Treu, Panagiotis G Kougias, Stefano Campanaro, Ilaria Bassani, Irini Angelidaki
This research aimed to better characterize the biogas microbiome by means of high throughput metagenomic sequencing and to elucidate the core microbial consortium existing in biogas reactors independently from the operational conditions. Assembly of shotgun reads followed by an established binning strategy resulted in the highest, up to now, extraction of microbial genomes involved in biogas producing systems. From the 236 extracted genome bins, it was remarkably found that the vast majority of them could only be characterized at high taxonomic levels...
September 2016: Bioresource Technology
Beatriz Díez, Johan A A Nylander, Karolina Ininbergs, Christopher L Dupont, Andrew E Allen, Shibu Yooseph, Douglas B Rusch, Birgitta Bergman
Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context...
2016: PloS One
Elie Desmond-Le Quéméner, Mickaël Rimboud, Arnaud Bridier, Céline Madigou, Benjamin Erable, Alain Bergel, Théodore Bouchez
Biocathodes polarized at high potential are promising for enhancing Microbial Fuel Cell performances but the microbes and genes involved remain poorly documented. Here, two sets of five oxygen-reducing biocathodes were formed at two potentials (-0.4V and +0.1V vs. saturated calomel electrode) and analyzed combining electrochemical and metagenomic approaches. Slower start-up but higher current densities were observed at high potential and a distinctive peak increasing over time was recorded on cyclic voltamogramms, suggesting the growth of oxygen reducing microbes...
August 2016: Bioresource Technology
Heidi H Kong
The use of genomic sequencing to investigate microbes has expanded, yet it has also raised questions regarding optimal approaches to studying the skin microbiome. Meisel et al. show that while whole genome shotgun metagenomic sequences were most similar to expected microbial profiles, sequencing of the hypervariable regions V1-V3 of the 16S ribosomal RNA gene had greater accuracy than sequencing of the hypervariable region V4 in determining genus and species level classifications of prominent skin bacteria...
May 2016: Journal of Investigative Dermatology
Binu M Tripathi, David P Edwards, Lucas William Mendes, Mincheol Kim, Ke Dong, Hyoki Kim, Jonathan M Adams
Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm...
May 2016: Molecular Ecology
Chandrika J Piyathilake, Nicholas J Ollberding, Ranjit Kumar, Maurizio Macaluso, Ronald D Alvarez, Casey D Morrow
It is increasingly recognized that microbes that reside in and on human body sites play major roles in modifying the pathogenesis of several diseases, including cancer. However, specific microbes or microbial communities that can be mechanistically linked to cervical carcinogenesis remain largely unexplored. The purpose of the study was to examine the association between cervical microbiota and high-grade cervical intraepithelial neoplasia (CIN 2+) in women infected with high-risk (HR) human papillomaviruses (HPV) and to assess whether the cervical microbiota are associated with oxidative DNA damage as indicated by the presence of cervical cells positive for 8-hydroxy-2'-deoxyguanosine...
May 2016: Cancer Prevention Research
Melissa E Ellis, James A Mobley, Ross P Holmes, John Knight
Oxalobacter formigenes is a unique intestinal organism that relies on oxalate degradation to meet most of its energy and carbon needs. A lack of colonization is a risk factor for calcium oxalate kidney stone disease. The release of the genome sequence of O. formigenes has provided an opportunity to increase our understanding of the biology of O. formigenes. This study used mass spectrometry based shotgun proteomics to examine changes in protein levels associated with the transition of growth from log to stationary phase...
2016: Journal of Proteomics & Bioinformatics
Adam G Clooney, Fiona Fouhy, Roy D Sleator, Aisling O' Driscoll, Catherine Stanton, Paul D Cotter, Marcus J Claesson
Rapid advancements in sequencing technologies along with falling costs present widespread opportunities for microbiome studies across a vast and diverse array of environments. These impressive technological developments have been accompanied by a considerable growth in the number of methodological variables, including sampling, storage, DNA extraction, primer pairs, sequencing technology, chemistry version, read length, insert size, and analysis pipelines, amongst others. This increase in variability threatens to compromise both the reproducibility and the comparability of studies conducted...
2016: PloS One
Kevin P Keegan, Elizabeth M Glass, Folker Meyer
Approaches in molecular biology, particularly those that deal with high-throughput sequencing of entire microbial communities (the field of metagenomics), are rapidly advancing our understanding of the composition and functional content of microbial communities involved in climate change, environmental pollution, human health, biotechnology, etc. Metagenomics provides researchers with the most complete picture of the taxonomic (i.e., what organisms are there) and functional (i.e., what are those organisms doing) composition of natively sampled microbial communities, making it possible to perform investigations that include organisms that were previously intractable to laboratory-controlled culturing; currently, these constitute the vast majority of all microbes on the planet...
2016: Methods in Molecular Biology
Emiko Matsunaga, Yujiro Higuchi, Kazuki Mori, Kosuke Tashiro, Satoru Kuhara, Kaoru Takegawa
By screening for microbes that exhibit β-d-galactofuranosidase (Galf-ase) activity, a Streptomyces sp. strain, named JHA19, was isolated from a soil sample from Kagawa University, Japan, in 2010. Here, we report the results of whole-genome shotgun sequencing and found that the strain has four predicted Galf-ase genes.
2015: Genome Announcements
Eduardo Castro-Nallar, Ying Shen, Robert J Freishtat, Marcos Pérez-Losada, Solaiappan Manimaran, Gang Liu, W Evan Johnson, Keith A Crandall
BACKGROUND: The relationships between infections in early life and asthma are not completely understood. Likewise, the clinical relevance of microbial communities present in the respiratory tract is only partially known. A number of microbiome studies analyzing respiratory tract samples have found increased proportions of gamma-Proteobacteria including Haemophilus influenzae, Moraxella catarrhalis, and Firmicutes such as Streptococcus pneumoniae. The aim of this study was to present a new approach that combines RNA microbial identification with host gene expression to characterize and validate metagenomic taxonomic profiling in individuals with asthma...
2015: BMC Medical Genomics
Andreas Bremges, Irena Maus, Peter Belmann, Felix Eikmeyer, Anika Winkler, Andreas Albersmeier, Alfred Pühler, Andreas Schlüter, Alexander Sczyrba
BACKGROUND: The production of biogas takes place under anaerobic conditions and involves microbial decomposition of organic matter. Most of the participating microbes are still unknown and non-cultivable. Accordingly, shotgun metagenome sequencing currently is the method of choice to obtain insights into community composition and the genetic repertoire. FINDINGS: Here, we report on the deeply sequenced metagenome and metatranscriptome of a complex biogas-producing microbial community from an agricultural production-scale biogas plant...
2015: GigaScience
Diana H Taft, Namasivayam Ambalavanan, Kurt R Schibler, Zhuoteng Yu, David S Newburg, Hitesh Deshmukh, Doyle V Ward, Ardythe L Morrow
OBJECTIVE: Late onset sepsis (LOS) contributes to mortality and morbidity in preterm infants. We tested the hypotheses that microbes causing LOS originate from the gut, and that distortions in the gut microbial community increases subsequent risk of LOS. STUDY DESIGN: We examined the gut microbial community in prospectively collected stool samples from preterm infants with LOS and an equal number of age-matched controls at two sites (Cincinnati, OH and Birmingham, AL), by sequencing the bacterial 16S rDNA...
2015: PloS One
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