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Unsupervised statistical clustering of environmental shotgun sequences

Andrey Kislyuk, Srijak Bhatnagar, Jonathan Dushoff, Joshua S Weitz
2009 BMC Bioinformatics  
The development of effective environmental shotgun sequence binning methods remains an ongoing challenge in algorithmic analysis of metagenomic data.  ...  Conclusion: An unsupervised binning method based on statistical signatures of short environmental sequences is a viable stand-alone binning method for low complexity samples.  ...  The authors are grateful to Sourav Chatterji, Jonathan Eisen, and Ichitaro Yamazaki for their help in the utilization of CompostBin.  ... 
doi:10.1186/1471-2105-10-316 pmid:19799776 pmcid:PMC2765972 fatcat:mx4scjhxzjb55hcsfeqztoz4xy

A fuzzy classifier to taxonomically group DNA fragments within a metagenome

Sara Nasser, Adrienne Breland, Frederick C. Harris, Monica Nicolescu
2008 NAFIPS 2008 - 2008 Annual Meeting of the North American Fuzzy Information Processing Society  
The classification achieved an accuracy of 99% for Acid Mine Drainage a published environmental genome sample.  ...  The fuzzy classifier is used to group shotgun sequence fragments as small as 500 base pairs according to their DNA signatures, namely GC Content and oligonucleotide frequencies.  ...  Acid mine drainage environmental genome was shown to contain 5 genomes. We use shotgun sequences of two genomes of AMD, namely Leptospirillum sp.  ... 
doi:10.1109/nafips.2008.4531252 fatcat:pwufk724fngapbxdzidgkdt2ge

Shotgun metagenomics, from sampling to analysis

Christopher Quince, Alan W Walker, Jared T Simpson, Nicholas J Loman, Nicola Segata
2017 Nature Biotechnology  
Cheap, high-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology.  ...  with limited similarity to sequenced genomes, are needed.  ...  Unsupervised methods, or clustering, look for natural groups in the data.  ... 
doi:10.1038/nbt.3935 pmid:28898207 fatcat:r4sddqxi7vfh3iautypgdvlxmu

Two-stage microbial community experimental design

Timothy L Tickle, Nicola Segata, Levi Waldron, Uri Weingart, Curtis Huttenhower
2013 The ISME Journal  
Microbial community samples can be efficiently surveyed in high throughput by sequencing markers such as the 16S ribosomal RNA gene.  ...  The accuracies of each sampling technique and their influences on the characteristics of the resulting selected microbial community were evaluated using both simulated and experimental data.  ...  The Human Microbiome Project (HMP), for example, contained over 5000 16S-sequenced samples (by Roche 454), only B700 of which were selected for Illumina shotgun metagenomic sequencing.  ... 
doi:10.1038/ismej.2013.139 pmid:23949665 pmcid:PMC3834858 fatcat:5efopa6ssrgmfifko4c6kge5pi

METAGENassist: a comprehensive web server for comparative metagenomics

D. Arndt, J. Xia, Y. Liu, Y. Zhou, A. C. Guo, J. A. Cruz, I. Sinelnikov, K. Budwill, C. L. Nesbo, D. S. Wishart
2012 Nucleic Acids Research  
With recent improvements in DNA sequencing and sample extraction techniques, the quantity and quality of metagenomic data are now growing exponentially.  ...  Users can upload their bacterial census data from a wide variety of common formats, using either amplified 16S rRNA data or shotgun metagenomic data.  ...  PCA is an unsupervised clustering method for transforming a complex collection of data points such that the important properties of the sample can be more simply displayed on a two-dimensional cluster/  ... 
doi:10.1093/nar/gks497 pmid:22645318 pmcid:PMC3394294 fatcat:qettuopmnvcgddlcf24cshpy4m

Analytical Tools and Databases for Metagenomics in the Next-Generation Sequencing Era

Mincheol Kim, Ki-Hyun Lee, Seok-Whan Yoon, Bong-Soo Kim, Jongsik Chun, Hana Yi
2013 Genomics & Informatics  
of sequencing techniques.  ...  The massive data production and substantial cost reduction in next-generation sequencing have led to the rapid growth of metagenomic research both quantitatively and qualitatively.  ...  Sequence-driven targeted metagenomics is normally conducted by PCR-based directed sequencing of environmental genomic DNA.  ... 
doi:10.5808/gi.2013.11.3.102 pmid:24124405 pmcid:PMC3794082 fatcat:lotsy2zoxzgl3mn2pd2a3zkobi

Multiple Data Analyses and Statistical Approaches for Analyzing Data from Metagenomic Studies and Clinical Trials [chapter]

Suparna Mitra
2019 Msphere  
Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms (microbes) obtained from a common habitat.  ...  Thus, no matter how many hypotheses we have, we need a good understanding of genomics, bioinformatics, and statistics to work together to analyze and interpret these datasets in a meaningful way.  ...  In case readers have shotgun sequence datasets from environmental samples or from fecal samples, they do not need to perform alignment step to get rid of the host-associated sequences, unless there is  ... 
doi:10.1007/978-1-4939-9074-0_20 pmid:31278679 fatcat:7w4u45qkrbd63fkag36aoik2ia

Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma

Mykhaylo Usyk, Abhishek Pandey, Richard B. Hayes, Una Moran, Anna Pavlick, Iman Osman, Jeffrey S. Weber, Jiyoung Ahn
2021 Genome Medicine  
We completed 16S rRNA gene amplicon sequencing, DNA deep shotgun metagenomic, and RNA-seq metatranscriptomic sequencing.  ...  Using shotgun metagenomics, we further identified 37 bacterial strains differentially expressed between the risk groups, with specific dominance of Bacteroides dorei within the high-risk GMB cluster and  ...  Acknowledgements We thank all the study participants for participating in the study and the Environmental Sample Preparation and Sequencing Facility at Argonne National Laboratory that performed the sequencing  ... 
doi:10.1186/s13073-021-00974-z pmid:34641962 pmcid:PMC8513370 fatcat:cs2xt6ml2je5lbkgml7pw7lvje

MetaCompare: a computational pipeline for prioritizing environmental resistome risk

Min Oh, Amy Pruden, Chaoqi Chen, Lenwood S Heath, Kang Xia, Liqing Zhang
2018 FEMS Microbiology Ecology  
This is determined through the assembly of shotgun sequencing data and analysis of contigs containing ARGs to determine if they contain sequence similarity to MGEs or human pathogens.  ...  One sentence summary: A computational pipeline ranking resistome risk for given environmental samples based on shotgun metagenomic sequencing data was developed.  ...  Figure 1 . 1 Overview of MetaCompare pipeline for ranking resistome risk based on shotgun metagenomic sequencing data obtained from a given environmental sample.  ... 
doi:10.1093/femsec/fiy079 pmid:29718191 pmcid:PMC5995210 fatcat:6zll2wzbfzhmncy6snqubjrtlu

Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies

Anastasis Oulas, Christina Pavloudi, Paraskevi Polymenakou, Georgios A. Pavlopoulos, Nikolas Papanikolaou, Georgios Kotoulas, Christos Arvanitidis, loannis Iliopoulos
2015 Bioinformatics and Biology Insights  
Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data.  ...  This has led to the rapid expansion of research in the field and the establishment of "metagenomics", often defined as the analysis of DNA from microbial communities in environmental samples without prior  ...  Full shotgun metagenomics has the capacity to fully sequence the majority of available genomes within an environmental sample (or community).  ... 
doi:10.4137/bbi.s12462 pmid:25983555 pmcid:PMC4426941 fatcat:vsux4rgqlfcg3mtpdw27wykudm

bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes

Matthew Z. DeMaere, Aaron E. Darling
2019 Genome Biology  
Leading approaches depend upon time series or transect studies, the efficacy of which is a function of community complexity, target abundance, and sequencing depth.  ...  We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs using a single time point.  ...  We acknowledge the use of computing resources from the NeCTAR Research Cloud, the QCIF and the UTS eResearch Group.  ... 
doi:10.1186/s13059-019-1643-1 fatcat:l26i5fnubbf3ljdey3fyyyzsfi

Fuzzy Genome Sequence Assembly for Single and Environmental Genomes [chapter]

Sara Nasser, Adrienne Breland, Frederick C. Harris, Monica Nicolescu, Gregory L. Vert
2009 Studies in Fuzziness and Soft Computing  
This chapter presents fuzzy methods for multiple genome sequence assembly of cultured genomes (single organism) and environmental genomes (multiple organisms).  ...  We evaluate our method on artificially created environmental genomes to test various combinations of organisms and on an environmental genome.  ...  The acid mine drainage environmental genome was shown to contain 2 major groups. We use shotgun sequences of two genomes of AMD, namely Leptospirillum sp.  ... 
doi:10.1007/978-3-540-89968-6_2 fatcat:dhn5s7xzsnc6datdonyzb6wazy

Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities

Gongchao Jing, Zheng Sun, Honglei Wang, Yanhai Gong, Shi Huang, Kang Ning, Jian Xu, Xiaoquan Su
2017 Scientific Reports  
With the rapid development of Next Generation Sequencing technologies, metagenome datasets have been increasing explosively, both in sample number and in sequence volume.  ...  between microbiota dynamics and human health status 2 or environmental factors 3 .  ...  The β diversity evaluation includes unsupervised hierarchical clustering, supervises clustering using PCA (Principle Component Analysis), PCoA (Principle Co-ordinate Analysis) and multivariate statistical  ... 
doi:10.1038/srep40371 pmid:28079128 pmcid:PMC5227994 fatcat:q2c452avozgc7pdvq2tqv4dbga

Signatures within the esophageal microbiome are associated with host genetics, age, and disease

Nandan P. Deshpande, Stephen M. Riordan, Natalia Castaño-Rodríguez, Marc R. Wilkins, Nadeem O. Kaakoush
2018 Microbiome  
Here, the esophageal microbiomes of 106 prospectively recruited patients were assessed using 16S rRNA and 18S rRNA amplicon sequencing as well as shotgun sequencing, and associations with age, gender,  ...  The esophageal microbiome has been proposed to be involved in a range of diseases including the esophageal adenocarcinoma cascade; however, little is currently known about its function and relationship  ...  Acknowledgements The authors would like to thank all patients who participated in this study and staff of the Gastrointestinal and Liver Unit, The Prince of Wales Hospital (Sydney) for their help with  ... 
doi:10.1186/s40168-018-0611-4 pmid:30558669 pmcid:PMC6297961 fatcat:fia73qvso5djfnyvzn53rghwey

Integrating host gene expression and the microbiome to explore disease pathogenesis

Allyson L Byrd, Julia A Segre
2015 Genome Biology  
and outcomes in the context of human inflammatory disease.  ...  Clinical studies exploring the role of the microbiome in disease outcome  ...  The microbial OTUs were first filtered for abundance and then subjected to unsupervised and supervised cluster analyses.  ... 
doi:10.1186/s13059-015-0625-1 pmid:25887564 pmcid:PMC4389776 fatcat:hur7wuyvtnglpd7vdmu4xwpzsq
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