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Shotgun sequence microbes

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https://www.readbyqxmd.com/read/28337070/genomic-methods-and-microbiological-technologies-for-profiling-novel-and-extreme-environments-for-the-extreme-microbiome-project-xmp
#1
Scott Tighe, Ebrahim Afshinnekoo, Tara M Rock, Ken McGrath, Noah Alexander, Alexa McIntyre, Sofia Ahsanuddin, Daniela Bezdan, Stefan J Green, Samantha Joye, Sarah Stewart Johnson, Don A Baldwin, Nathan Bivens, Nadim Ajami, Joseph R Carmical, Ian Charold Herriott, Rita Colwell, Mohamed Donia, Jonathan Foox, Nick Greenfield, Tim Hunter, Jessica Hoffman, Joshua Hyman, Ellen Jorgensen, Diana Krawczyk, Jodie Lee, Shawn Levy, Natàlia Garcia-Reyero, Matthew Settles, Kelley Thomas, Felipe Gómez, Lynn Schriml, Nikos Kyrpides, Elena Zaikova, Jon Penterman, Christopher E Mason
The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines...
March 10, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28198672/integrated-metagenomic-data-analysis-demonstrates-that-a-loss-of-diversity-in-oral-microbiota-is-associated-with-periodontitis
#2
Dongmei Ai, Ruocheng Huang, Jin Wen, Chao Li, Jiangping Zhu, Li Charlie Xia
BACKGROUND: Periodontitis is an inflammatory disease affecting the tissues supporting teeth (periodontium). Integrative analysis of metagenomic samples from multiple periodontitis studies is a powerful way to examine microbiota diversity and interactions within host oral cavity. METHODS: A total of 43 subjects were recruited to participate in two previous studies profiling the microbial community of human subgingival plaque samples using shotgun metagenomic sequencing...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28176851/comparative-study-of-the-gut-microbiome-potentially-related-to-milk-protein-in-murrah-buffaloes-bubalus-bubalis-and-chinese-holstein-cattle
#3
Jiachao Zhang, Chuanbiao Xu, Dongxue Huo, Qisong Hu, Qiannan Peng
Previous studies suggested a close relationship between ruminant gut microbes and the mammary gland. In this study, shotgun metagenomic sequencing was used to reveal the differences in the intestinal microbiome potentially related to milk components in Murrah buffaloes and Chinese Holstein cattle. A PCoA based on the weighted Unifrac distances showed an apparent clustering pattern in the structure of intestinal microbiota between buffalo and cattle. We could attribute the structural difference to the genera of Sutterella, Coprococcus and Dorea...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28144631/studying-vertical-microbiome-transmission-from-mothers-to-infants-by-strain-level-metagenomic-profiling
#4
Francesco Asnicar, Serena Manara, Moreno Zolfo, Duy Tin Truong, Matthias Scholz, Federica Armanini, Pamela Ferretti, Valentina Gorfer, Anna Pedrotti, Adrian Tett, Nicola Segata
The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling...
January 2017: MSystems
https://www.readbyqxmd.com/read/28004480/a-metagenomic-study-of-the-preventive-effect-of-lactobacillus-rhamnosus-gg-on-intestinal-polyp-formation-in-apc-min-mice
#5
Y Ni, V H Y Wong, W C S Tai, J Li, W Y Wong, M M L Lee, F L Y Fong, H El-Nezami, G Panagiotou
AIMS: To investigate the in vivo effects of Lactobacillus rhamnosus GG (LGG) on intestinal polyp development and the interaction between this single-organism probiotic and the gut microbiota therein. METHODS AND RESULTS: The Apc(Min/+) mouse model was used to study the potential preventive effect of LGG on intestinal polyposis, while shotgun metagenomic sequencing was employed to characterize both taxonomic and functional changes within the gut microbial community...
December 22, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27976685/disentangling-the-influence-of-earthworms-in-sugarcane-rhizosphere
#6
Lucas P P Braga, Caio A Yoshiura, Clovis D Borges, Marcus A Horn, George G Brown, Harold L Drake, Siu M Tsai
For the last 150 years many studies have shown the importance of earthworms for plant growth, but the exact mechanisms involved in the process are still poorly understood. Many important functions required for plant growth can be performed by soil microbes in the rhizosphere. To investigate earthworm influence on the rhizosphere microbial community, we performed a macrocosm experiment with and without Pontoscolex corethrurus (EW+ and EW-, respectively) and followed various soil and rhizosphere processes for 217 days with sugarcane...
December 15, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27933318/global-analysis-and-comparison-of-the-transcriptomes-and-proteomes-of-group-a-streptococcus-biofilms
#7
Jeffrey A Freiberg, Yoann Le Breton, Bao Q Tran, Alison J Scott, Janette M Harro, Robert K Ernst, Young Ah Goo, Emmanuel F Mongodin, David R Goodlett, Kevin S McIver, Mark E Shirtliff
To gain a better understanding of the genes and proteins involved in group A Streptococcus (GAS; Streptococcus pyogenes) biofilm growth, we analyzed the transcriptome, cellular proteome, and cell wall proteome from biofilms at different stages and compared them to those of plankton-stage GAS. Using high-throughput RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) shotgun proteomics, we found distinct expression profiles in the transcriptome and proteome. A total of 46 genes and 41 proteins showed expression across the majority of biofilm time points that was consistently higher or consistently lower than that seen across the majority of planktonic time points...
November 2016: MSystems
https://www.readbyqxmd.com/read/27917166/temporal-metagenomic-and-metabolomic-characterization-of-fresh-perennial-ryegrass-degradation-by-rumen-bacteria
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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...
March 2017: 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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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