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Shotgun sequence microbes

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https://www.readbyqxmd.com/read/27917166/temporal-metagenomic-and-metabolomic-characterization-of-fresh-perennial-ryegrass-degradation-by-rumen-bacteria
#1
Olga L Mayorga, Alison H Kingston-Smith, Eun J Kim, Gordon G Allison, Toby J Wilkinson, Matthew J Hegarty, Michael K Theodorou, Charles J Newbold, Sharon A Huws
Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached bacteria. In this study, we investigated temporal niche specialization of primary and secondary populations of attached rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27889153/metagenomics-reveals-flavour-metabolic-network-of-cereal-vinegar-microbiota
#2
Lin-Huan Wu, Zhen-Ming Lu, Xiao-Juan Zhang, Zong-Min Wang, Yong-Jian Yu, Jin-Song Shi, Zheng-Hong Xu
Multispecies microbial community formed through centuries of repeated batch acetic acid fermentation (AAF) is crucial for the flavour quality of traditional vinegar produced from cereals. However, the metabolism to generate and/or formulate the essential flavours by the multispecies microbial community is hardly understood. Here we used metagenomic approach to clarify in situ metabolic network of key microbes responsible for flavour synthesis of a typical cereal vinegar, Zhenjiang aromatic vinegar, produced by solid-state fermentation...
April 2017: Food Microbiology
https://www.readbyqxmd.com/read/27822529/thermus-and-the-pink-discoloration-defect-in-cheese
#3
Lisa Quigley, Daniel J O'Sullivan, David Daly, Orla O'Sullivan, Zuzana Burdikova, Rostislav Vana, Tom P Beresford, R Paul Ross, Gerald F Fitzgerald, Paul L H McSweeney, Linda Giblin, Jeremiah J Sheehan, Paul D Cotter
A DNA sequencing-based strategy was applied to study the microbiology of Continental-type cheeses with a pink discoloration defect. The basis for this phenomenon has remained elusive, despite decades of research. The bacterial composition of cheese containing the defect was compared to that of control cheese using 16S rRNA gene and shotgun metagenomic sequencing as well as quantitative PCR (qPCR). Throughout, it was apparent that Thermus, a carotenoid-producing genus, was present at higher levels in defect-associated cheeses than in control cheeses...
May 2016: MSystems
https://www.readbyqxmd.com/read/27822528/urban-transit-system-microbial-communities-differ-by-surface-type-and-interaction-with-humans-and-the-environment
#4
Tiffany Hsu, Regina Joice, Jose Vallarino, Galeb Abu-Ali, Erica M Hartmann, Afrah Shafquat, Casey DuLong, Catherine Baranowski, Dirk Gevers, Jessica L Green, Xochitl C Morgan, John D Spengler, Curtis Huttenhower
Public transit systems are ideal for studying the urban microbiome and interindividual community transfer. In this study, we used 16S amplicon and shotgun metagenomic sequencing to profile microbial communities on multiple transit surfaces across train lines and stations in the Boston metropolitan transit system. The greatest determinant of microbial community structure was the transit surface type. In contrast, little variation was observed between geographically distinct train lines and stations serving different demographics...
May 2016: MSystems
https://www.readbyqxmd.com/read/27708392/unique-features-of-ethnic-mongolian-gut-microbiome-revealed-by-metagenomic-analysis
#5
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/27669488/urinary-microbiome-of-kidney-transplant-patients-reveals-dysbiosis-with-potential-for-antibiotic-resistance
#6
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
https://www.readbyqxmd.com/read/27583441/diversity-of-gut-microbiota-metabolic-pathways-in-10-pairs-of-chinese-infant-twins
#7
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
https://www.readbyqxmd.com/read/27573830/captivity-humanizes-the-primate-microbiome
#8
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
https://www.readbyqxmd.com/read/27570522/species-divergence-vs-functional-convergence-characterizes-crude-oil-microbial-community-assembly
#9
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
https://www.readbyqxmd.com/read/27446035/plants-rather-than-mineral-fertilization-shape-microbial-community-structure-and-functional-potential-in-legacy-contaminated-soil
#10
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
https://www.readbyqxmd.com/read/27353502/dynamic-functional-characterization-and-phylogenetic-changes-due-to-long-chain-fatty-acids-pulses-in-biogas-reactors
#11
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
https://www.readbyqxmd.com/read/27243603/deeper-insight-into-the-structure-of-the-anaerobic-digestion-microbial-community-the-biogas-microbiome-database-is-expanded-with-157-new-genomes
#12
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
https://www.readbyqxmd.com/read/27196065/metagenomic-analysis-of-the-indian-ocean-picocyanobacterial-community-structure-potential-function-and-evolution
#13
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
https://www.readbyqxmd.com/read/27126080/biocathodes-reducing-oxygen-at-high-potential-select-biofilms-dominated-by-ectothiorhodospiraceae-populations-harboring-a-specific-association-of-genes
#14
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
https://www.readbyqxmd.com/read/27107375/details-matter-designing-skin-microbiome-studies
#15
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
https://www.readbyqxmd.com/read/26994316/the-impact-of-tropical-forest-logging-and-oil-palm-agriculture-on-the-soil-microbiome
#16
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
https://www.readbyqxmd.com/read/26935422/cervical-microbiota-associated-with-higher-grade-cervical-intraepithelial-neoplasia-in-women-infected-with-high-risk-human-papillomaviruses
#17
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
https://www.readbyqxmd.com/read/26924912/proteome-dynamics-of-the-specialist-oxalate-degrader-oxalobacter-formigenes
#18
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
https://www.readbyqxmd.com/read/26849217/comparing-apples-and-oranges-next-generation-sequencing-and-its-impact-on-microbiome-analysis
#19
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
https://www.readbyqxmd.com/read/26791506/mg-rast-a-metagenomics-service-for-analysis-of-microbial-community-structure-and-function
#20
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
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