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A statistical toolbox for metagenomics: assessing functional diversity in microbial communities
2008
BMC Bioinformatics
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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
2009
FEMS Microbiology Reviews
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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
2016
Cell
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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
2015
Advances in Genomics and Genetics
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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
2015
Advances in Genomics and Genetics
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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
2021
PLoS Computational Biology
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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
2018
mSystems
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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
2012
Briefings in Bioinformatics
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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
2011
BMC Microbiology
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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
2016
BMC Bioinformatics
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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
2011
Computer applications in the biosciences : CABIOS
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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 http://gobics.de/peter/taxy. ...
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
2013
PLoS ONE
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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
2019
Frontiers in Genetics
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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
2010
Nucleic Acids Research
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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
2018
Frontiers in Microbiology
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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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