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Shotgun metagenomics

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https://www.readbyqxmd.com/read/28530140/associations-of-nasopharyngeal-metabolome-and-microbiome-with-severity-among-infants-with-bronchiolitis-a-multi-omic-analysis
#1
Christopher J Stewart, Jonathan M Mansbach, Matthew C Wong, Nadim J Ajami, Joseph F Petrosino, Carlos A Camargo, Kohei Hasegawa
RATIONALE: Bronchiolitis is the most common lower respiratory infection in infants; however, it remains unclear which infants with bronchiolitis will develop severe illness. In addition, while emerging evidence indicates associations of the upper-airway microbiome with bronchiolitis severity, little is known about the mechanisms linking airway microbes and host response to disease severity. OBJECTIVES: To determine the relations among the nasopharyngeal airway metabolome profiles, microbiome profiles, and severity in infants with bronchiolitis...
May 21, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28473000/tracking-microbial-colonization-in-fecal-microbiota-transplantation-experiments-via-genome-resolved-metagenomics
#2
Sonny T M Lee, Stacy A Kahn, Tom O Delmont, Alon Shaiber, Özcan C Esen, Nathaniel A Hubert, Hilary G Morrison, Dionysios A Antonopoulos, David T Rubin, A Murat Eren
BACKGROUND: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits...
May 4, 2017: Microbiome
https://www.readbyqxmd.com/read/28472388/cafe-accelerated-alignment-free-sequence-analysis
#3
Yang Young Lu, Kujin Tang, Jie Ren, Jed A Fuhrman, Michael S Waterman, Fengzhu Sun
Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures...
May 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28472118/effect-of-dietary-supplementation-with-lactobacillus-acidophilus-d2-csl-cect-4529-on-caecum-microbioma-and-productive-performance-in-broiler-chickens
#4
Alessandra De Cesare, Federico Sirri, Gerardo Manfreda, Paola Moniaci, Alberto Giardini, Marco Zampiga, Adele Meluzzi
This study examines the effects of the dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) (LA) on productive performances, incidence of foot pad dermatitis and caecum microbioma in broiler chickens. A total of 1,100 one-day old male Ross 308 chicks were divided into 2 groups of 16 replicates with 25 birds each and reared from 1-41 d. One group was fed a basal diet (CON) and the other group the same diet supplemented with LA. Caecum contents were collected from 4 selected birds at day one and 5 selected birds at the end of the rearing period...
2017: PloS One
https://www.readbyqxmd.com/read/28469608/genome-centric-analysis-of-a-thermophilic-and-cellulolytic-bacterial-consortium-derived-from-composting
#5
Leandro N Lemos, Roberta V Pereira, Ronaldo B Quaggio, Layla F Martins, Livia M S Moura, Amanda R da Silva, Luciana P Antunes, Aline M da Silva, João C Setubal
Microbial consortia selected from complex lignocellulolytic microbial communities are promising alternatives to deconstruct plant waste, since synergistic action of different enzymes is required for full degradation of plant biomass in biorefining applications. Culture enrichment also facilitates the study of interactions among consortium members, and can be a good source of novel microbial species. Here, we used a sample from a plant waste composting operation in the São Paulo Zoo (Brazil) as inoculum to obtain a thermophilic aerobic consortium enriched through multiple passages at 60°C in carboxymethylcellulose as sole carbon source...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28467925/gut-microbiome-based-metagenomic-signature-for-non-invasive-detection-of-advanced-fibrosis-in-human-nonalcoholic-fatty-liver-disease
#6
Rohit Loomba, Victor Seguritan, Weizhong Li, Tao Long, Niels Klitgord, Archana Bhatt, Parambir Singh Dulai, Cyrielle Caussy, Richele Bettencourt, Sarah K Highlander, Marcus B Jones, Claude B Sirlin, Bernd Schnabl, Lauren Brinkac, Nicholas Schork, Chi-Hua Chen, David A Brenner, William Biggs, Shibu Yooseph, J Craig Venter, Karen E Nelson
The presence of advanced fibrosis in nonalcoholic fatty liver disease (NAFLD) is the most important predictor of liver mortality. There are limited data on the diagnostic accuracy of gut microbiota-derived signature for predicting the presence of advanced fibrosis. In this prospective study, we characterized the gut microbiome compositions using whole-genome shotgun sequencing of DNA extracted from stool samples. This study included 86 uniquely well-characterized patients with biopsy-proven NAFLD, of which 72 had mild/moderate (stage 0-2 fibrosis) NAFLD, and 14 had advanced fibrosis (stage 3 or 4 fibrosis)...
May 2, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28453677/afs-identification-and-quantification-of-species-composition-by-metagenomic-sequencing
#7
Yongchao Liu, Fabian Ripp, Rene Koeppel, Hanno Schmidt, Sören Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt, Thomas Hankeln
Summary: DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28452176/microbial-acceleration-of-aerobic-pyrite-oxidation-at-circumneutral-ph
#8
E Percak-Dennett, S He, B Converse, H Konishi, H Xu, A Corcoran, D Noguera, C Chan, A Bhayyacharyya, T Borch, E Boyd, E E Roden
Pyrite (FeS2 ) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro-organisms in pyrite oxidation under acidic-pH conditions is well known, to date there is very little known about the capacity for aerobic micro-organisms to oxidize pyrite at circumneutral pH...
April 27, 2017: Geobiology
https://www.readbyqxmd.com/read/28451970/an-agile-functional-analysis-of-metagenomic-data-using-super-focus
#9
Genivaldo Gueiros Z Silva, Fabyano A C Lopes, Robert A Edwards
One of the main goals in metagenomics is to identify the functional profile of a microbial community from unannotated shotgun sequencing reads. Functional annotation is important in biological research because it enables researchers to identify the abundance of functional genes of the organisms present in the sample, answering the question, "What can the organisms in the sample do?" Most currently available approaches do not scale with increasing data volumes, which is important because both the number and lengths of the reads provided by sequencing platforms keep increasing...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28451968/ghostx-a-fast-sequence-homology-search-tool-for-functional-annotation-of-metagenomic-data
#10
Shuji Suzuki, Takashi Ishida, Masahito Ohue, Masanori Kakuta, Yutaka Akiyama
Metagenomic analysis based on whole genome shotgun sequencing data requires fast protein sequence homology searches for predicting the function of proteins coded on metagenome short reads. However, huge amounts of sequence data cause even general homology search analyses using BLASTX to become difficult in terms of computational cost. GHOSTX is a sequence homology search tool specifically developed for functional annotation of metagenome sequences. The tool is more than 160 times faster than BLASTX and has sufficient search sensitivity for metagenomic analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28449715/functional-implications-of-microbial-and-viral-gut-metagenome-changes-in-early-stage-l-dopa-na%C3%A3-ve-parkinson-s-disease-patients
#11
J R Bedarf, F Hildebrand, L P Coelho, S Sunagawa, M Bahram, F Goeser, P Bork, U Wüllner
BACKGROUND: Parkinson's disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naïve PD patients might also serve as a biomarker...
April 28, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28449106/microbiomeanalyst-a-web-based-tool-for-comprehensive-statistical-visual-and-meta-analysis-of-microbiome-data
#12
Achal Dhariwal, Jasmine Chong, Salam Habib, Irah L King, Luis B Agellon, Jianguo Xia
The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28448616/abundance-profiling-of-specific-gene-groups-using-precomputed-gut-metagenomes-yields-novel-biological-hypotheses
#13
Konstantin Yarygin, Alexander Tyakht, Andrey Larin, Elena Kostryukova, Sergei Kolchenko, Vilgelm Bitner, Dmitry Alexeev
The gut microbiota is essentially a multifunctional bioreactor within a human being. The exploration of its enormous metabolic potential provides insights into the mechanisms underlying microbial ecology and interactions with the host. The data obtained using "shotgun" metagenomics capture information about the whole spectrum of microbial functions. However, each new study presenting new sequencing data tends to extract only a little of the information concerning the metabolic potential and often omits specific functions...
2017: PloS One
https://www.readbyqxmd.com/read/28443069/long-term-enrichment-of-stress-tolerant-cellulolytic-soil-populations-following-timber-harvesting-evidenced-by-multi-omic-stable-isotope-probing
#14
Roland C Wilhelm, Erick Cardenas, Hilary Leung, András Szeitz, Lionel D Jensen, William W Mohn
Soil management is vital for maintaining the productivity of commercial forests, yet the long-term impact of timber harvesting on soil microbial communities remains largely a matter of conjecture. Decomposition of plant biomass, comprised mainly of lignocellulose, has a broad impact on nutrient cycling, microbial activity and physicochemical characteristics of soil. At "Long-term Soil Productivity Study" sites in California dominated by Ponderosa pine, we tested whether clear-cut timber harvesting, accompanied by varying degrees of organic matter (OM) removal, affected the activity and structure of the cellulose-degrading microbial populations 16 years after harvesting...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28424662/untangling-genomes-of-novel-planctomycetal-and-verrucomicrobial-species-from-monterey-bay-kelp-forest-metagenomes-by-refined-binning
#15
John Vollmers, Martinique Frentrup, Patrick Rast, Christian Jogler, Anne-Kristin Kaster
The kelp forest of the Pacific temperate rocky marine coastline of Monterey Bay in California is a dominant habitat for large brown macro-algae in the order of Laminariales. It is probably one of the most species-rich, structurally complex and productive ecosystems in temperate waters and well-studied in terms of trophic ecology. However, still little is known about the microorganisms thriving in this habitat. A growing body of evidence suggests that bacteria associated with macro-algae represent a huge and largely untapped resource of natural products with chemical structures that have been optimized by evolution for biological and ecological purposes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28421041/metagenome-wide-association-study-and-machine-learning-prediction-of-bulk-soil-microbiome-and-crop-productivity
#16
Hao-Xun Chang, James S Haudenshield, Charles R Bowen, Glen L Hartman
Areas within an agricultural field in the same season often differ in crop productivity despite having the same cropping history, crop genotype, and management practices. One hypothesis is that abiotic or biotic factors in the soils differ between areas resulting in these productivity differences. In this study, bulk soil samples collected from a high and a low productivity area from within six agronomic fields in Illinois were quantified for abiotic and biotic characteristics. Extracted DNA from these bulk soil samples were shotgun sequenced...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28394451/ancient-dna-analysis-identifies-marine-mollusc-shells-as-new-metagenomic-archives-of-the-past
#17
Clio Der Sarkissian, Vianney Pichereau, Catherine Dupont, Peter C Ilsøe, Mickael Perrigault, Paul Butler, Laurent Chauvaud, Jón Eiríksson, James Scourse, Christine Paillard, Ludovic Orlando
Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity, and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories...
April 10, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28389755/soda-pans-of-the-pannonian-steppe-harbor-unique-bacterial-communities-adapted-to-multiple-extreme-conditions
#18
Attila Szabó, Kristóf Korponai, Csaba Kerepesi, Boglárka Somogyi, Lajos Vörös, Dániel Bartha, Károly Márialigeti, Tamás Felföldi
Soda pans of the Pannonian steppe are unique environments regarding their physical and chemical characteristics: shallowness, high turbidity, intermittent character, alkaline pH, polyhumic organic carbon concentration, hypertrophic condition, moderately high salinity, sodium and carbonate ion dominance. The pans are highly productive environments with picophytoplankton predominance. Little is known about the planktonic bacterial communities inhabiting these aquatic habitats; therefore, amplicon sequencing and shotgun metagenomics were applied to reveal their composition and functional properties...
April 7, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28384336/filthy-lucre-a-metagenomic-pilot-study-of-microbes-found-on-circulating-currency-in-new-york-city
#19
Julia M Maritz, Steven A Sullivan, Robert J Prill, Emre Aksoy, Paul Scheid, Jane M Carlton
BACKGROUND: Paper currency by its very nature is frequently transferred from one person to another and represents an important medium for human contact with-and potential exchange of-microbes. In this pilot study, we swabbed circulating $1 bills obtained from a New York City bank in February (Winter) and June (Summer) 2013 and used shotgun metagenomic sequencing to profile the communities found on their surface. Using basic culture conditions, we also tested whether viable microbes could be recovered from bills...
2017: PloS One
https://www.readbyqxmd.com/read/28384184/assessing-biosynthetic-potential-of-agricultural-groundwater-through-metagenomic-sequencing-a-diverse-anammox-community-dominates-nitrate-rich-groundwater
#20
William B Ludington, Thaddeus D Seher, Olin Applegate, Xunde Li, Joseph I Kliegman, Charles Langelier, Edward R Atwill, Thomas Harter, Joseph L DeRisi
BACKGROUND: Climate change produces extremes in both temperature and precipitation causing increased drought severity and increased reliance on groundwater resources. Agricultural practices, which rely on groundwater, are sensitive to but also sources of contaminants, including nitrate. How agricultural contamination drives groundwater geochemistry through microbial metabolism is poorly understood. METHODS: On an active cow dairy in the Central Valley of California, we sampled groundwater from three wells at depths of 4...
2017: PloS One
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