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Shotgun metagenomics

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https://www.readbyqxmd.com/read/28900024/metabolic-roles-of-uncultivated-bacterioplankton-lineages-in-the-northern-gulf-of-mexico-dead-zone
#1
J Cameron Thrash, Kiley W Seitz, Brett J Baker, Ben Temperton, Lauren E Gillies, Nancy N Rabalais, Bernard Henrissat, Olivia U Mason
Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called "dead zones," are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown...
September 12, 2017: MBio
https://www.readbyqxmd.com/read/28898207/shotgun-metagenomics-from-sampling-to-analysis
#2
Christopher Quince, Alan W Walker, Jared T Simpson, Nicholas J Loman, Nicola Segata
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and in human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging of members and understanding of how communities function. High-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology. Still, computational approaches to overcome the challenges that affect both assembly-based and mapping-based metagenomic profiling, particularly of high-complexity samples or environments containing organisms with limited similarity to sequenced genomes, are needed...
September 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28893308/more-than-2500%C3%A2-years-of-oil-exposure-shape-sediment-microbiomes-with-the-potential-for-syntrophic-degradation-of-hydrocarbons-linked-to-methanogenesis
#3
Antonios Michas, Gisle Vestergaard, Kathleen Trautwein, Pavlos Avramidis, Dimitris G Hatzinikolaou, Constantinos E Vorgias, Heinz Wilkes, Ralf Rabus, Michael Schloter, Anne Schöler
BACKGROUND: Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods...
September 11, 2017: Microbiome
https://www.readbyqxmd.com/read/28884091/alterations-of-the-gut-microbiome-in-hypertension
#4
Qiulong Yan, Yifang Gu, Xiangchun Li, Wei Yang, Liqiu Jia, Changming Chen, Xiuyan Han, Yukun Huang, Lizhe Zhao, Peng Li, Zhiwei Fang, Junpeng Zhou, Xiuru Guan, Yanchun Ding, Shaopeng Wang, Muhammad Khan, Yi Xin, Shenghui Li, Yufang Ma
Introduction: Human gut microbiota is believed to be directly or indirectly involved in cardiovascular diseases and hypertension. However, the identification and functional status of the hypertension-related gut microbe(s) have not yet been surveyed in a comprehensive manner. Methods: Here we characterized the gut microbiome in hypertension status by comparing fecal samples of 60 patients with primary hypertension and 60 gender-, age-, and body weight-matched healthy controls based on whole-metagenome shotgun sequencing...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28873967/connections-between-the-human-gut-microbiome-and-gestational-diabetes-mellitus
#5
Ya-Shu Kuang, Jin-Hua Lu, Sheng-Hui Li, Jun-Hua Li, Ming-Yang Yuan, Jian-Rong He, Nian-Nian Chen, Wan-Qing Xiao, Song-Ying Shen, Lan Qiu, Ying-Fang Wu, Cui-Yue Hu, Yan-Yan Wu, Wei-Dong Li, Qiao-Zhu Chen, Hong-Wen Deng, Christopher J Papasian, Hui-Min Xia, Xiu Qiu
The human gut microbiome can modulate metabolic health and affect insulin resistance, and it may play an important role in the etiology of gestational diabetes mellitus (GDM). Here, we compared the gut microbial composition of 43 GDM patients and 81 healthy pregnant women via whole-metagenome shotgun sequencing of their fecal samples, collected at 21-29 weeks, to explore associations between GDM and the composition of microbial taxonomic units and functional genes. A metagenome-wide association study identified 154 837 genes, which clustered into 129 metagenome linkage groups (MLGs) for species description, with significant relative abundance differences between the 2 cohorts...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28865481/members-of-the-candidate-phyla-radiation-are-functionally-differentiated-by-carbon-and-nitrogen-cycling-capabilities
#6
R E Danczak, M D Johnston, C Kenah, M Slattery, K C Wrighton, M J Wilkins
BACKGROUND: The Candidate Phyla Radiation (CPR) is a recently described expansion of the tree of life that represents more than 15% of all bacterial diversity and potentially contains over 70 different phyla. Despite this broad phylogenetic variation, these microorganisms appear to feature little functional diversity, with members generally characterized as obligate fermenters. Additionally, much of the data describing CPR phyla has been generated from a limited number of environments, constraining our knowledge of their functional roles and biogeographical distribution...
September 2, 2017: Microbiome
https://www.readbyqxmd.com/read/28852182/unveiling-the-gut-microbiota-composition-and-functionality-associated-with-constipation-through-metagenomic-analyses
#7
Leonardo Mancabelli, Christian Milani, Gabriele Andrea Lugli, Francesca Turroni, Marta Mangifesta, Alice Viappiani, Andrea Ticinesi, Antonio Nouvenne, Tiziana Meschi, Douwe van Sinderen, Marco Ventura
Functional constipation (FC) is a gastrointestinal disorder with a high prevalence among the general population. The precise causes of FC are still unknown and are most likely multifactorial. Growing evidence indicates that alterations of gut microbiota composition contribute to constipation symptoms. Nevertheless, many discrepancies exist in literature and no clear link between FC and gut microbiota composition has as yet been identified. In this study, we performed 16 S rRNA-based microbial profiling analysis of 147 stool samples from 68 FC individuals and compared their microbial profiles with those of 79 healthy subjects (HS)...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28846439/microbial-lineages-in-sarcoidosis-a-metagenomic-analysis-tailored-for-low-microbial-content-samples
#8
Erik L Clarke, Abigail P Lauder, Casey E Hofstaedter, Young Hwang, Ayannah S Fitzgerald, Ize Imai, Wojciech Biernat, Bartłomiej Rękawiecki, Hanna Majewska, Anna Dubaniewicz, Leslie A Litzky, Michael D Feldman, Kyle Bittinger, Milton D Rossman, Karen C Patterson, Frederic D Bushman, Ronald G Collman
RATIONALE: The etiology of sarcoidosis is unknown, but microbial agents are suspected as triggers. OBJECTIVE: We sought to identify bacterial, fungal or viral lineages in specimens from sarcoidosis patients enriched relative to controls using metagenomic DNA sequencing. Since DNA from environmental contamination contributes disproportionately to samples with low authentic microbial content, we developed improved methods for filtering environmental contamination...
August 28, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28837129/large-scale-comparative-metagenomics-of-blastocystis-a-common-member-of-the-human-gut-microbiome
#9
Francesco Beghini, Edoardo Pasolli, Tin Duy Truong, Lorenza Putignani, Simone M Cacciò, Nicola Segata
The influence of unicellular eukaryotic microorganisms on human gut health and disease is still largely unexplored. Blastocystis spp. commonly colonize the gut, but its clinical significance and ecological role are currently unsettled. We have developed a high-sensitivity bioinformatic pipeline to detect Blastocystis subtypes (STs) from shotgun metagenomics, and applied it to 12 large data sets, comprising 1689 subjects of different geographic origin, disease status and lifestyle. We confirmed and extended previous observations on the high prevalence the microrganism in the population (14...
August 22, 2017: ISME Journal
https://www.readbyqxmd.com/read/28831604/distinct-taxonomic-and-functional-composition-of-soil-microbiomes-along-the-gradient-forest-restinga-mangrove-in-southeastern-brazil
#10
Lucas William Mendes, Siu Mui Tsai
Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters...
August 22, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28831408/shotgun-metagenomic-data-on-the-human-stool-samples-to-characterize-shifts-of-the-gut-microbial-profile-after-the-helicobacter-pylori-eradication-therapy
#11
Eugenia A Boulygina, Maria I Markelova, Dilyara R Khusnutdinova, Maria N Siniagina, Sergey Yu Malanin, Rustam A Abdulkhakov, Sayar R Abdulkhakov, Vladislav M Chernov, Tatiana V Grigoryeva
The shotgun sequencing data presented in this report are related to the research article named "Gut microbiome shotgun sequencing in assessment of microbial community changes associated with H. pylori eradication therapy" (Khusnutdinova et al., 2016) [1]. Typically, the H. pylori eradication protocol includes a prolonged two-week use of the broad-spectrum antibiotics. The presented data on the whole-genome sequencing of the total DNA from stool samples of patients before the start of the eradication, immediately after eradication and several weeks after the end of treatment could help to profile the gut microbiota both taxonomically and functionally...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28811246/microbial-metagenomics-mock-scenario-based-sample-simulation-m3s3
#12
Yair Motro, Jacob Moran-Gilad
OBJECTIVES: Shotgun sequencing in increasingly applied in clinical microbiology for unbiased culture-independent diagnosis. While software solutions for metagenomics proliferate, integration of metagenomics in clinical care, requires method standardisation and validation. Virtual metagenomics samples could underpin validation by substituting real samples and thus we sought to develop a novel solution for simulation of metagenomics samples based on user-defined clinical scenarios. METHODS: We designed the Microbial Metagenomics Mock Scenario-based Sample Simulation (M3S3) workflow, which allows users to generate virtual samples from raw reads or assemblies...
August 12, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28808691/fluoride-depletes-acidogenic-taxa-in-oral-but-not-gut-microbial-communities-in-mice
#13
Koji Yasuda, Tiffany Hsu, Carey A Gallini, Lauren J Mclver, Emma Schwager, Andy Shi, Casey R DuLong, Randall N Schwager, Galeb S Abu-Ali, Eric A Franzosa, Wendy S Garrett, Curtis Huttenhower, Xochitl C Morgan
Fluoridation of drinking water and dental products prevents dental caries primarily by inhibiting energy harvest in oral cariogenic bacteria (such as Streptococcus mutans and Streptococcus sanguinis), thus leading to their depletion. However, the extent to which oral and gut microbial communities are affected by host fluoride exposure has been underexplored. In this study, we modeled human fluoride exposures to municipal water and dental products by treating mice with low or high levels of fluoride over a 12-week period...
July 2017: MSystems
https://www.readbyqxmd.com/read/28797298/community-characteristics-of-the-gut-microbiomes-of-competitive-cyclists
#14
Lauren M Petersen, Eddy J Bautista, Hoan Nguyen, Blake M Hanson, Lei Chen, Sai H Lek, Erica Sodergren, George M Weinstock
BACKGROUND: Changes in diet and exercise can alter the gut microbiome of humans and mice; however, few studies to date have assessed the microbiomes of highly fit athletes. In this pilot study, we used metagenomic whole genome shotgun (mWGS) and metatranscriptomic (RNA-Seq) sequencing to show what organisms are both present and active in the gut microbiomes of both professional and amateur level competitive cyclists and to determine if any significant differences exist between these two groups...
August 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28780361/untreated-urban-waste-contaminates-indian-river-sediments-with-resistance-genes-to-last-resort-antibiotics
#15
Nachiket P Marathe, Chandan Pal, Swapnil S Gaikwad, Viktor Jonsson, Erik Kristiansson, D G Joakim Larsson
Efficient sewage treatment is critical for limiting environmental transmission of antibiotic-resistant bacteria. In many low and middle income countries, however, large proportions of sewage are still released untreated into receiving water bodies. In-depth knowledge of how such discharges of untreated urban waste influences the environmental resistome is largely lacking. Here, we highlight the impact of uncontrolled discharge of partially treated and/or untreated wastewater on the structure of bacterial communities and resistome of sediments collected from Mutha river flowing through Pune city in India...
July 25, 2017: Water Research
https://www.readbyqxmd.com/read/28771537/a-spirochaete-is-suggested-as-the-causative-agent-of-akoya-oyster-disease-by-metagenomic-analysis
#16
Tomomasa Matsuyama, Motoshige Yasuike, Atushi Fujiwara, Yoji Nakamura, Tomokazu Takano, Takeshi Takeuchi, Noriyuki Satoh, Yoshikazu Adachi, Yasushi Tsuchihashi, Hideo Aoki, Kazushi Odawara, Shunsuke Iwanaga, Jun Kurita, Takashi Kamaishi, Chihaya Nakayasu
Mass mortality that is acompanied by reddish browning of the soft tissues has been occurring in cultured pearl oyster, Pinctada fucata martensii. The disease is called Akoya oyster disease (AOD). Although spreading pattern of the disease and transmission experiments suggest that the disease is infectious, the causative agent has not yet been identified. We used shotgun and 16S rRNA-based metagenomic analysis to identify genes that are present specifically in affected oysters. The genes found only in diseased oysters were mostly bacterial origin, suggesting that the causative agent was a bacterial pathogen...
2017: PloS One
https://www.readbyqxmd.com/read/28769920/unraveling-the-microbial-interactions-and-metabolic-potentials-in-pre-and-post-treated-sludge-from-a-wastewater-treatment-plant-using-metagenomic-studies
#17
Chandni Sidhu, Surendra Vikram, Anil Kumar Pinnaka
Sewage waste represents an ecosystem of complex and interactive microbial consortia which proliferate with different kinetics according to their individual genetic as well as metabolic potential. We performed metagenomic shotgun sequencing on Ion-Torrent platform, to explore the microbial community structure, their biological interactions and associated functional capacity of pre-treated/raw sludge (RS) and post-treated/dried sludge (DS) of wastewater treatment plant. Bacterial phylotypes belonging to Epsilonproteobacteria (∼45...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28765786/a-metagenomic-survey-of-forest-soil-microbial-communities-more-than-a-decade-after-timber-harvesting
#18
Roland C Wilhelm, Erick Cardenas, Hilary Leung, Kendra Maas, Martin Hartmann, Aria Hahn, Steven Hallam, William W Mohn
The scarcity of long-term data on soil microbial communities in the decades following timber harvesting limits current understanding of the ecological problems associated with maintaining the productivity of managed forests. The high complexity of soil communities and the heterogeneity of forest and soil necessitates a comprehensive approach to understand the role of microbial processes in managed forest ecosystems. Here, we describe a curated collection of well replicated, multi-faceted data from eighteen reforested sites in six different North American ecozones within the Long-term Soil Productivity (LTSP) Study, without detailed analysis of results or discussion...
2017: Scientific Data
https://www.readbyqxmd.com/read/28761145/large-scale-differences-in-microbial-biodiversity-discovery-between-16s-amplicon-and-shotgun-sequencing
#19
Michael Tessler, Johannes S Neumann, Ebrahim Afshinnekoo, Michael Pineda, Rebecca Hersch, Luiz Felipe M Velho, Bianca T Segovia, Fabio A Lansac-Toha, Michael Lemke, Rob DeSalle, Christopher E Mason, Mercer R Brugler
Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques - amplicon and shotgun - on water samples across four of Brazil's major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches...
July 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28758937/a-different-microbiome-gene-repertoire-in-the-airways-of-cystic-fibrosis-patients-with-severe-lung-disease
#20
Giovanni Bacci, Alessio Mengoni, Ersilia Fiscarelli, Nicola Segata, Giovanni Taccetti, Daniela Dolce, Patrizia Paganin, Patrizia Morelli, Vanessa Tuccio, Alessandra De Alessandri, Vincenzina Lucidi, Annamaria Bevivino
In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing...
July 29, 2017: International Journal of Molecular Sciences
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