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A method for achieving complete microbial genomes and improving bins from metagenomics data

Lauren M. Lui, Torben N. Nielsen, Adam P. Arkin, Morgan Langille
2021 PLoS Computational Biology  
Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity.  ...  Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities.  ...  We would like to thank Sean Jungbluth and Lily Momper for giving us access to their datasets, and Alicia Clum for providing access to sequencing data of the ZymoBIONICS mock community by the Joint Genome  ... 
doi:10.1371/journal.pcbi.1008972 pmid:33961626 fatcat:vdlclckqwndfzbekzcznaoj75a

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets

Yi Yue, Hao Huang, Zhao Qi, Hui-Min Dou, Xin-Yi Liu, Tian-Fei Han, Yue Chen, Xiang-Jun Song, You-Hua Zhang, Jian Tu
2020 BMC Bioinformatics  
Binning assembled sequences into individual groups, which represent microbial genomes, is the key step and a major challenge in metagenomic research.  ...  For CAMI datasets, Groopm2 achieved the highest purity (> 0.9) with good completeness (> 0.8), and reconstructed the most high-quality genome bins among original genome binners.  ...  Acknowledgments The authors would like to thank doctors, nurses and other health care workers, who were risking their lives to protect us against the COVID-19.  ... 
doi:10.1186/s12859-020-03667-3 pmid:32723290 fatcat:rai46vk3obegpb23qcoiw2v5yu

Recovering complete and draft population genomes from metagenome datasets

Naseer Sangwan, Fangfang Xia, Jack A. Gilbert
2016 Microbiome  
Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture  ...  We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species.  ...  Recently, Rodriguez and Konstantinidis highlighted methods for estimating metagenome coverage using real microbial metagenomic data [42] .  ... 
doi:10.1186/s40168-016-0154-5 pmid:26951112 pmcid:PMC4782286 fatcat:j3cdxxmq4beiddgbcinmafh5xe

Metagenomic tools in microbial ecology research

Neslihan Taş, Anniek Ee de Jong, Yaoming Li, Gareth Trubl, Yaxin Xue, Nicholas C Dove
2021 Current Opinion in Biotechnology  
While metagenomics is shaping our understanding of microbial functions in ecosystems via gene-centric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous  ...  Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function  ...  Acknowledgements Funding for this work was provided to Neslihan Taş The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States  ... 
doi:10.1016/j.copbio.2021.01.019 pmid:33592536 fatcat:bjbwezen7zghnmew55gb6ux2d4

Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes

Ankit Gupta, Sanjiv Kumar, Vishnu P. K. Prasoodanan, K. Harish, Ashok K. Sharma, Vineet K. Sharma
2016 Frontiers in Microbiology  
In this work, Binning-Assembly approach has been proposed and demonstrated for the reconstruction of bacterial and viral genomes from 72 human gut metagenomic datasets.  ...  More than 80% complete draft genome sequences could be reconstructed for a total of 126 bacterial and 11 viral genomes.  ...  AG is a recipient of DST-INSPIRE Fellowship and thanks the Department of Science and Technology for the fellowship.  ... 
doi:10.3389/fmicb.2016.00469 pmid:27148174 pmcid:PMC4828583 fatcat:5fxi53qbobcnlaxfbgd5tza2h4

Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome

Gherman Uritskiy, Jocelyne DiRuggiero
2019 Genes  
However, there still remain pitfalls and limitations from conventional metagenomic analysis being applied to halophilic microbial communities.  ...  , and novel genome discoveries.  ...  Acknowledgments: This work was supported by grants NNX15AP18G from NASA and DEB1556574 from the NSF. We thank Sarah Preheim for useful suggestions in the writing of this manuscript.  ... 
doi:10.3390/genes10030220 pmid:30875864 pmcid:PMC6471235 fatcat:xcbkgajgfjgc7ldzhowkamku2u

Implications of error-prone long-read whole-genome shotgun sequencing on characterizing reference microbiomes

Yu Hu, Li Fang, Christopher Nicholson, Kai Wang
2020 iScience  
Our results not only demonstrate the feasibility of characterizing complete microbial genomes and populations from error-prone Nanopore sequencing data but also highlight necessary bioinformatics improvements  ...  We showed that assembly programs consistently achieved high accuracy (∼99%) and completeness (∼99%) for bacterial strains with adequate coverage.  ...  Overall, our results have demonstrated the technical feasibility to characterize complete microbial genomes and populations from Nanopore sequencing data with metagenomic software.  ... 
doi:10.1016/j.isci.2020.101223 pmid:32563152 pmcid:PMC7305381 fatcat:gaa4id6tezdb7kj5ctjy7qqcxe

Exploring high-quality microbial genomes by assembly of linked-reads with high barcode specificity using deep learning [article]

Zhenmiao Zhang, Hongbo Wang, Chao Yang, Huang Yufen, Zhen Yue, Yang Chen, Lijuan Han, Aiping Lu, Xiaodong Fang, Lu Zhang
2022 bioRxiv   pre-print
For the human gut microbiomes, Pangaea still achieved the highest contiguity and considerably more near-complete metagenome-assembled genomes (NCMAGs) than the other assemblers.  ...  Linked-reads, in which short-reads are linked together by barcodes that mark a long original DNA fragment, are a promising method for cost-effective metagenome assembly.  ...  Acknowledgements We thank Tom Chen and Yong Wang from Universal Sequencing Technology for providing the TELL-Seq sequencing data of the ATCC-MSA-1003 mock community.  ... 
doi:10.1101/2022.09.07.506963 fatcat:nn7shc3y2nhchejegyaho4a4vq

Generation and application of pseudo–long reads for metagenome assembly

Mikang Sim, Jongin Lee, Suyeon Wy, Nayoung Park, Daehwan Lee, Daehong Kwon, Jaebum Kim
2022 GigaScience  
Background Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation.  ...  However, metagenomic assembly, especially when only short reads are available, is a complex and challenging task because mixed genomes of multiple microorganisms constitute the metagenome.  ...  PLRs improve reconstructing microbial genomes and binning metagenomic assembly Metagenomic assemblies can be used to reconstruct original microbial chromosome sequences, which can be further used for various  ... 
doi:10.1093/gigascience/giac044 pmid:35579554 pmcid:PMC9112764 fatcat:hfgntsyzfrhubca7tzw5izwn2m

Genomes from Metagenomics

I. Sharon, J. F. Banfield
2013 Science  
This copy is for your personal, non-commercial use only. clicking here. colleagues, clients, or customers by , you can order high-quality copies for your If you wish to distribute this article to others  ...  A genome derived from metagenomic data represents a population.  ...  For the many genomes from metagenomic data that are initially incomplete (typically because of undersampling), completeness can be improved by additional sequencing.  ... 
doi:10.1126/science.1247023 pmid:24288324 fatcat:iiy4fk6pl5hezbdtnc6ewi46jq

Genome-resolved metagenomics using environmental and clinical samples

Masood Ur Rehman Kayani, Wanqiu Huang, Ru Feng, Lei Chen
2021 Briefings in Bioinformatics  
Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics.  ...  In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and  ...  Samina Shaheen and Dr. Syed Shujaat Ali Zaidi for their feedback on the manuscript. Funding The Shanghai Jiao Tong University, School of Medicine New PI Startup Fund (No. 17X100040046).  ... 
doi:10.1093/bib/bbab030 pmid:33758906 pmcid:PMC8425419 fatcat:rc7cu36xing5dlew4g55wlob2y

HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps

Yuxuan Du, Fengzhu Sun
2022 Genome Biology  
AbstractRecovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging.  ...  HiCBin employs the HiCzin normalization method and the Leiden clustering algorithm and includes the spurious contact detection into binning pipelines for the first time.  ...  Ziye Wang from Fudan University for her kind help with processing the raw data.  ... 
doi:10.1186/s13059-022-02626-w pmid:35227283 pmcid:PMC8883645 fatcat:zsixcpntvzbbfduvmdzj7j5srm

A comprehensive investigation of metagenome assembly by linked-read sequencing

Lu Zhang, Xiaodong Fang, Herui Liao, Zhenmiao Zhang, Xin Zhou, Lijuan Han, Yang Chen, Qinwei Qiu, Shuai Cheng Li
2020 Microbiome  
Results We first examined the effects of read depth (C) on metagenome assembly from linked-reads in simulated data and a mock community.  ...  However, these results are in ambiguity during genome assembly, leading to unsatisfactory microbial genome completeness and contig continuity.  ...  Acknowledgements We would first thank Arend Sidow for his informative comments and revision for the paper.  ... 
doi:10.1186/s40168-020-00929-3 pmid:33176883 fatcat:enyf5m2pgjagthl54rb53ltjvy

Reads Binning Improves Alignment-Free Metagenome Comparison

Kai Song, Jie Ren, Fengzhu Sun
2019 Frontiers in Genetics  
Recently, next-generation sequencing (NGS) technologies have produced a massive amount of short reads data for microbial communities from different environments.  ...  In contrast, alignment-free methods for metagenome comparison do not depend on the completeness of genome or pathway databases.  ...  AUThOR CONTRIBUTIONs KS and FS conceived of the project and developed the methods. KS and JR performed the computations. All authors discussed the results and contributed to the final manuscript.  ... 
doi:10.3389/fgene.2019.01156 pmid:31824565 pmcid:PMC6881972 fatcat:d25fktgvdvg4lbmz7xya6ir72i


Shrikant Sharma, Shashank Rana, Raghvendar Singh
2012 International Journal of Biomedical Research  
In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable.  ...  In metagenomics, the data come from heterogeneous microbial communities, sometimes containing more than 10,000 species, with the sequence data being noisy and partial.  ...  Shotgun metagenomics also is capable of sequencing nearly complete microbial genomes directly from the environment 29 .  ... 
doi:10.7439/ijbr.v3i4.396 fatcat:4zi3csejz5g3rnjxk56cm4wp4u
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