Nature Medicine, Journal Year: 2019, Volume and Issue: 25(7), P. 1104 - 1109
Published: June 24, 2019
Language: Английский
Nature, Journal Year: 2020, Volume and Issue: 579(7798), P. 265 - 269
Published: Feb. 3, 2020
Abstract Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health 1–3 . Despite intense research efforts, how, when where new diseases appear are still source of considerable uncertainty. A disease was recently reported in Wuhan, Hubei province, China. As 25 January 2020, at least 1,975 cases had been since the first patient hospitalized on 12 December 2019. Epidemiological investigations have suggested that outbreak associated with seafood market Wuhan. Here we study single who worker admitted Central Hospital Wuhan 26 2019 while experiencing included fever, dizziness cough. Metagenomic RNA sequencing 4 sample bronchoalveolar lavage fluid from identified strain family Coronaviridae , which is designated here ‘WH-Human 1’ coronavirus (and has also referred ‘2019-nCoV’). Phylogenetic analysis complete viral genome (29,903 nucleotides) revealed most closely related (89.1% nucleotide similarity) group SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) previously found bats China 5 This highlights ongoing ability spill-over animals cause humans.
Language: Английский
Citations
12275
Genome Research, Journal Year: 2017, Volume and Issue: 27(5), P. 824 - 834
Published: March 15, 2017
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex populations may be composed from dozens related strains, further amplifying challenge assembly. metaSPAdes addresses various challenges by capitalizing on computational ideas proved to useful in assemblies single cells and highly polymorphic diploid genomes. We benchmark against other state-of-the-art metagenome assemblers demonstrate it results high-quality across diverse sets.
Language: Английский
Citations
3656
Bioinformatics, Journal Year: 2015, Volume and Issue: 32(4), P. 605 - 607
Published: Oct. 29, 2015
Abstract Summary: The recovery of genomes from metagenomic datasets is a critical step to defining the functional roles underlying uncultivated populations. We previously developed MaxBin, an automated binning approach for high-throughput microbial metagenomes. Here we present expanded algorithm, MaxBin 2.0, which recovers co-assembly collection datasets. Tests on simulated revealed that 2.0 highly accurate in recovering individual genomes, and application several metagenomes environmental samples demonstrated it could achieve two complementary goals: more bacterial compared single sample as well comparing community composition between different sampling environments. Availability implementation: freely available at http://sourceforge.net/projects/maxbin/ under BSD license. Contact: [email protected] Supplementary information: data are Bioinformatics online.
Language: Английский
Citations
2078
Nature, Journal Year: 2020, Volume and Issue: 583(7815), P. 282 - 285
Published: March 26, 2020
The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-21. This has been tentatively seafood market Wuhan, China, where sale wild animals may be source zoonotic infection2. Although bats are probable reservoir hosts for SARS-CoV-2, identity any intermediate host that have facilitated transfer to humans unknown. Here we report identification SARS-CoV-2-related coronaviruses Malayan pangolins (Manis javanica) seized anti-smuggling operations southern China. Metagenomic sequencing identified pangolin-associated belong two sub-lineages coronaviruses, including one exhibits strong similarity receptor-binding domain SARS-CoV-2. discovery multiple lineages pangolin coronavirus their SARS-CoV-2 suggests should considered as possible emergence removed from wet markets prevent transmission. javanica); these belonged
Language: Английский
Citations
1937
Nature Biotechnology, Journal Year: 2017, Volume and Issue: 35(8), P. 725 - 731
Published: Aug. 1, 2017
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide adoption MISAG MIMAG will facilitate more robust comparative genomic analyses diversity.
Language: Английский
Citations
1868
PeerJ, Journal Year: 2015, Volume and Issue: 3, P. e1165 - e1165
Published: Aug. 27, 2015
Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because nature these existing binning methods often miss a number species. In addition, most tools are not scalable datasets. Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances genome abundance tetranucleotide frequency for accurate binning. outperforms alternative in accuracy computational efficiency on both synthetic real It automatically forms hundreds high quality bins very assembly consisting millions contigs matter hours single node. is open source available at https://bitbucket.org/berkeleylab/metabat.
Language: Английский
Citations
1731
Science, Journal Year: 2020, Volume and Issue: 368(6494), P. 973 - 980
Published: May 28, 2020
Bacteria were first detected in human tumors more than 100 years ago, but the characterization of tumor microbiome has remained challenging because its low biomass. We undertook a comprehensive analysis microbiome, studying 1526 and their adjacent normal tissues across seven cancer types, including breast, lung, ovary, pancreas, melanoma, bone, brain tumors. found that each type distinct composition breast particularly rich diverse microbiome. The intratumor bacteria are mostly intracellular present both immune cells. also noted correlations between or predicted functions with types subtypes, patients' smoking status, response to immunotherapy.
Language: Английский
Citations
1646
Methods, Journal Year: 2016, Volume and Issue: 102, P. 3 - 11
Published: March 21, 2016
Language: Английский
Citations
1556
Nature Biotechnology, Journal Year: 2017, Volume and Issue: 35(9), P. 833 - 844
Published: Sept. 1, 2017
Language: Английский
Citations
1545
Nucleic Acids Research, Journal Year: 2016, Volume and Issue: 45(D1), P. D535 - D542
Published: Nov. 9, 2016
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of web interface and some new services that provide users with platform takes them from raw reads an integrated analysis experience. redesigned allows researchers direct access tools data, emphasis has changed user-created genome-groups, detailed summaries views data have selected. Perhaps biggest change been enhanced capability for analyze their private compare it available public data. Researchers can assemble sequence annotate contigs using RASTtk. also provides RNA-Seq, variation, model reconstruction differential expression analysis, all delivered through updated workspace. Private be compared by 'virtual integration' any PATRIC's number genomes comparison in expanded over 80 000, special on antimicrobial resistance uses this improve both subsystem annotation k-mer classification, tags as having signatures indicate susceptibility or specific antibiotics.
Language: Английский
Citations
1501