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A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

Patrick D Schloss, Jo Handelsman
2008 BMC Bioinformatics  
In this study, we developed and applied a suite of tools to describe and compare the richness, membership, and structure of microbial communities using peptide fragment sequences extracted from metagenomic  ...  The 99% of bacteria in the environment that are recalcitrant to culturing have spurred the development of metagenomics, a culture-independent approach to sample and characterize microbial genomes.  ...  We are grateful to Gene Tyson for providing the 16S rRNA sequences from the AMD community.  ... 
doi:10.1186/1471-2105-9-34 pmid:18215273 pmcid:PMC2238731 fatcat:wpuanhfbsfexrovhaoz3npcif4

Metagenomics approaches in systems microbiology

José M. Vieites, María-Eugenia Guazzaroni, Ana Beloqui, Peter N. Golyshin, Manuel Ferrer
2009 FEMS Microbiology Reviews  
In this review, we conducted a survey of important methodologies in metagenomics and describe systems microbiology-like approaches for gaining a mechanistic understanding of complex microbial systems to  ...  The review also discusses how metagenomics can be used as a holistic indicator for ecosystem response in terms of matter, nutrient and energy sources and functional networking.  ...  new computational tools now provide a new toolbox for systems microbiology to get an integrated insight into the functioning of the microbial community as a whole and to study cellular and physiological  ... 
doi:10.1111/j.1574-6976.2008.00152.x pmid:19054115 fatcat:65yehsiwlze3nl6nscofedgt5y

Toward Accurate and Quantitative Comparative Metagenomics

Stephen Nayfach, Katherine S. Pollard
2016 Cell  
Bioinformatics and statistics research has produced a first generation of tools for estimating the taxonomic and functional composition of a microbial community from shotgun metagenomics data (Box 1).  ...  This tool offers a powerful means for characterizing the immense microbial diversity on earth.  ... 
doi:10.1016/j.cell.2016.08.007 pmid:27565341 pmcid:PMC5080976 fatcat:o6dv5cegbvalzapujrygwqpwcu

New insight into the gut microbiome through metagenomics

Jens Nielsen, Boyang Ji
2015 Advances in Genomics and Genetics  
The human host provides a nutrient-rich environment, and the microbiota provides some necessary functions that humans cannot perform.  ...  A comprehensive analysis of the human gut microbiome is thus important for revealing the mechanisms of these host-microbe interactions.  ...  Disclosure Jens Nielsen is a shareholder in MetaboGen AB. The authors report no other conflicts of interest in this work.  ... 
doi:10.2147/agg.s57215 fatcat:mbpttyjl55boblocef4os5hhp4

New insight into the gut microbiome through metagenomics

Ji B, Nielsen J
2015 Advances in Genomics and Genetics  
The human host provides a nutrient-rich environment, and the microbiota provides some necessary functions that humans cannot perform.  ...  A comprehensive analysis of the human gut microbiome is thus important for revealing the mechanisms of these host–microbe interactions.  ...  After assembly, the functional diversity of the microbial communities can be quantified by inferring the functional annotations of these metagenomic sequences.  ... 
doaj:becf1dc1b606466d80e46ea29725f989 fatcat:y4uqfliamzd6lbigojimkyksua

MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome

Preecha Patumcharoenpol, Massalin Nakphaichit, Gianni Panagiotou, Anchalee Senavonge, Narissara Suratannon, Wanwipa Vongsangnak, Sergei L. Kosakovsky Pond
2021 PLoS Computational Biology  
One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences.  ...  Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.  ...  In addition, we also would like to thank Chakkapan Sapkaew, Amorntep Kingkaw, and Nachon Raethong for their assistance on fruitful discussion.  ... 
doi:10.1371/journal.pcbi.1008487 pmid:33406089 fatcat:deqh6ohj6vdidabkmbc2jgbxuq

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

Luis M. Rodriguez-R, Santosh Gunturu, James M. Tiedje, James R. Cole, Konstantinos T. Konstantinidis, Anthony Fodor
2018 mSystems  
genomic study that aims to robustly assess the sequence diversity present in a sample.  ...  Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable  ...  ACKNOWLEDGMENTS We thank Chengwei Luo and Mark Borodovsky for helpful discussions. We also thank Jiarong Guo for initial test implementations and other testing.  ... 
doi:10.1128/msystems.00039-18 pmid:29657970 pmcid:PMC5893860 fatcat:p3bjvl63izeutmtcg44fld24mq

Bioinformatic approaches for functional annotation and pathway inference in metagenomics data

C. De Filippo, M. Ramazzotti, P. Fontana, D. Cavalieri
2012 Briefings in Bioinformatics  
Metagenomic approaches are increasingly recognized as a baseline for understanding the ecology and evolution of microbial ecosystems.  ...  The development of methods for pathway inference from metagenomics data is of paramount importance to link a phenotype to a cascade of events stemming from a series of connected sets of genes or proteins  ...  flux of interactions between them and identify the metabolic functions that make a complex microbial community.  ... 
doi:10.1093/bib/bbs070 pmid:23175748 pmcid:PMC3505041 fatcat:rm3rv7rp3nht7jyqxkurirfcl4

Comparative fecal metagenomics unveils unique functional capacity of the swine gut

Regina Lamendella, Jorge W Santo Domingo, Shreya Ghosh, John Martinson, Daniel B Oerther
2011 BMC Microbiology  
Results: Analysis of 637, 722 pyrosequencing reads (130 megabases) generated from Yorkshire pig fecal DNA extracts was performed to help better understand the microbial diversity and largely unknown functional  ...  Nonetheless, limited information on the functional diversity of the swine gut microbiome is available.  ...  It has been subjected to the Agency's administrative review and has been approved for external publication.  ... 
doi:10.1186/1471-2180-11-103 pmid:21575148 pmcid:PMC3123192 fatcat:k2tsqc3zwffcvlvnekl6eohauq

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies

Jiwoong Kim, Min Soo Kim, Andrew Y. Koh, Yang Xie, Xiaowei Zhan
2016 BMC Bioinformatics  
Given the lack of a complete and comprehensive library of microbial reference genomes, determining the functional profile of diverse microbial communities is challenging.  ...  Conclusion: FMAP is a comprehensive tool for providing functional analysis of metagenomic/metatranscriptomic sequencing data.  ...  Acknowledgements The authors thank Brandi Cantarel and Jessie Norris for the manuscript preparation.  ... 
doi:10.1186/s12859-016-1278-0 pmid:27724866 pmcid:PMC5057277 fatcat:zzf6trtbhzbhxihitwb7n7bcjq

Mixture models for analysis of the taxonomic composition of metagenomes

Peter Meinicke, Kathrin Petra Aßhauer, Thomas Lingner
2011 Computer applications in the biosciences : CABIOS  
Motivation: Inferring the taxonomic profile of a microbial community from a large collection of anonymous DNA sequencing reads is a challenging task in metagenomics.  ...  Availability: A platform-independent implementation of the mixture modeling approach is available in terms of a MATLAB/Octave toolbox at  ...  ACKNOWLEDGEMENT We would like to thank Peter Gumrich for programming the Taxy tool for Windows and Christian Opitz, Stefanie Mühlhausen and Alexander Kaever for additional technical support.  ... 
doi:10.1093/bioinformatics/btr266 pmid:21546400 pmcid:PMC3106201 fatcat:is652mryjvc53fn4i4patopt7q

Class Prediction and Feature Selection with Linear Optimization for Metagenomic Count Data

Zhenqiu Liu, Dechang Chen, Li Sheng, Amy Y. Liu, Mikael Boden
2013 PLoS ONE  
In this study, we presented a novel statistical learning method for simultaneous association prediction and feature selection with metagenomic samples from two or multiple treatment populations on the  ...  The amount of metagenomic data is growing rapidly while the computational methods for metagenome analysis are still in their infancy.  ...  Matlab also has a linprog function in its optimization toolbox. Efficient large-scale interior point algorithm is implemented in both functions.  ... 
doi:10.1371/journal.pone.0053253 pmid:23555553 pmcid:PMC3608598 fatcat:ustthvgj3neutkwhnhoskrtpcm

Reads Binning Improves Alignment-Free Metagenome Comparison

Kai Song, Jie Ren, Fengzhu Sun
2019 Frontiers in Genetics  
Comparing metagenomic samples is a critical step in understanding the relationships among microbial communities.  ...  Recently, next-generation sequencing (NGS) technologies have produced a massive amount of short reads data for microbial communities from different environments.  ...  Beta-Diversity Analysis and evaluation Methods Detection of group relationships among metagenomic samples and the identification of external gradients driving shifts in microbial community structure are  ... 
doi:10.3389/fgene.2019.01156 pmid:31824565 pmcid:PMC6881972 fatcat:d25fktgvdvg4lbmz7xya6ir72i

Ab initio gene identification in metagenomic sequences

Wenhan Zhu, Alexandre Lomsadze, Mark Borodovsky
2010 Nucleic Acids Research  
We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities.  ...  Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters.  ...  ACKNOWLEDGEMENT We wish to thank Konstantinos Mavromatis, Natalia Ivanova and Nikos Kyrpides for interest to the project and useful discussions.  ... 
doi:10.1093/nar/gkq275 pmid:20403810 pmcid:PMC2896542 fatcat:w4xe2if7fzhktpoadiqd2y2fei

Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in Escherichia coli

Cauã A. Westmann, Luana de Fátima Alves, Rafael Silva-Rocha, María-Eugenia Guazzaroni
2018 Frontiers in Microbiology  
The results presented here demonstrates the potential of functional metagenomics for exploring environmental bacterial communities as a source of novel regulatory genetic parts to expand the toolbox for  ...  Although functional metagenomics has been widely employed for the discovery of genes relevant to biotechnology and biomedicine, its potential for assessing the diversity of transcriptional regulatory elements  ...  ACKNOWLEDGMENTS The authors are thanks to lab colleagues for insightful discussion about this manuscript.  ... 
doi:10.3389/fmicb.2018.01344 pmid:29973927 pmcid:PMC6019500 fatcat:2dokxqpixfguzhhg3pgj5rsq7e
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