New insights from uncultivated genomes of the global human gut microbiome DOI Creative Commons
Stephen Nayfach, Zhou Jason Shi, R. Seshadri

и другие.

Nature, Год журнала: 2019, Номер 568(7753), С. 505 - 510

Опубликована: Март 13, 2019

The genome sequences of many species the human gut microbiome remain unknown, largely owing to challenges in cultivating microorganisms under laboratory conditions. Here we address this problem by reconstructing 60,664 draft prokaryotic genomes from 3,810 faecal metagenomes, geographically and phenotypically diverse humans. These provide reference points for 2,058 newly identified species-level operational taxonomic units (OTUs), which represents a 50% increase over previously known phylogenetic diversity sequenced bacteria. On average, OTUs comprise 33% richness 28% abundance per individual, are enriched humans rural populations. A meta-analysis clinical gut-microbiome studies pinpointed numerous disease associations OTUs, have potential improve predictive models. Finally, our analysis revealed that uncultured undergone reduction has resulted loss certain biosynthetic pathways, may offer clues improving cultivation strategies future. Draft metagenomes populations enrich understanding identifying two thousand new taxa associations.

Язык: Английский

A new coronavirus associated with human respiratory disease in China DOI Creative Commons
Fan Wu,

Zhao Su,

Bin Yu

и другие.

Nature, Год журнала: 2020, Номер 579(7798), С. 265 - 269

Опубликована: Фев. 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.

Язык: Английский

Процитировано

12302
metaSPAdes: a new versatile metagenomic assembler DOI Creative Commons
Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov

и другие.

Genome Research, Год журнала: 2017, Номер 27(5), С. 824 - 834

Опубликована: Март 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.

Язык: Английский

Процитировано

3690
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets DOI Open Access
Yu‐Wei Wu, Blake A. Simmons, Steven W. Singer

и другие.

Bioinformatics, Год журнала: 2015, Номер 32(4), С. 605 - 607

Опубликована: Окт. 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.

Язык: Английский

Процитировано

2096
Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins DOI Creative Commons
Tommy Tsan‐Yuk Lam, Na Jia,

Yawei Zhang

и другие.

Nature, Год журнала: 2020, Номер 583(7815), С. 282 - 285

Опубликована: Март 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

Язык: Английский

Процитировано

1942
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea DOI Creative Commons
Robert M. Bowers, Nikos C. Kyrpides, Ramūnas Stepanauskas

и другие.

Nature Biotechnology, Год журнала: 2017, Номер 35(8), С. 725 - 731

Опубликована: Авг. 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.

Язык: Английский

Процитировано

1883
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities DOI Creative Commons
Dongwan Kang, Jeff Froula, Rob Egan

и другие.

PeerJ, Год журнала: 2015, Номер 3, С. e1165 - e1165

Опубликована: Авг. 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.

Язык: Английский

Процитировано

1735
The human tumor microbiome is composed of tumor type–specific intracellular bacteria DOI
Deborah Nejman, Ilana Livyatan, Garold Fuks

и другие.

Science, Год журнала: 2020, Номер 368(6494), С. 973 - 980

Опубликована: Май 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.

Язык: Английский

Процитировано

1671
MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices DOI

Dinghua Li,

Ruibang Luo,

Chi-Man Liu

и другие.

Methods, Год журнала: 2016, Номер 102, С. 3 - 11

Опубликована: Март 21, 2016

Язык: Английский

Процитировано

1579
Shotgun metagenomics, from sampling to analysis DOI
Christopher Quince, Alan W. Walker, Jared T. Simpson

и другие.

Nature Biotechnology, Год журнала: 2017, Номер 35(9), С. 833 - 844

Опубликована: Сен. 1, 2017

Язык: Английский

Процитировано

1555
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center DOI Creative Commons
Alice R. Wattam, James J. Davis,

Rida Assaf

и другие.

Nucleic Acids Research, Год журнала: 2016, Номер 45(D1), С. D535 - D542

Опубликована: Ноя. 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.

Язык: Английский

Процитировано

1507