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An Integrative Approach for the Functional Analysis of Metagenomic Studies [chapter]

Jyotsna Talreja Wassan, Haiying Wang, Fiona Browne, Paul Wash, Brain Kelly, Cintia Palu, Nina Konstantinidou, Rainer Roehe, Richard Dewhurst, Huiru Zheng
2017 Lecture Notes in Computer Science  
In this research, we propose a framework which integrates omics-knowledge to identify suitable-reduced set of microbiomes features, for gaining insights into functional classification of the metagenomic  ...  The proposed approach has been applied to two Use Case studies, on: 1) cattle rumen microbiota samples, for differentiating nitrate and vegetable oil treated feed, for improving cattle performance, under  ...  Acknowledgement This work was supported in part by the MetaPlat project, (www.metaplat.eu) funded by H2020-MSCA-RISE-2015 and Research Strategy Fund of Ulster University.  ... 
doi:10.1007/978-3-319-63312-1_37 fatcat:jcgndid52bc5honfhmrvqp7tje

Integrating pan-genome with metagenome for microbial community profiling

Chaofang Zhong, Chaoyun Chen, Lusheng Wang, Kang Ning
2021 Computational and Structural Biotechnology Journal  
We emphasized studies in which the integrating pan-genome with metagenome approach improved the understanding of models of microbial community profiles, both structural and functional.  ...  We discussed emerging strategies for the study of microbial communities that integrate information in both pan-genome and metagenome.  ...  In this review, we discussed the existing and new integration directions of pan-genomics and metagenomics, and highlighted the strategies and applications of such an integrative approach in the study of  ... 
doi:10.1016/j.csbj.2021.02.021 pmid:33841754 pmcid:PMC8010324 fatcat:cy6ub5uvwrcx3j3bor7uy4wovu

mmnet: An R Package for Metagenomics Systems Biology Analysis

Yang Cao, Xiaofei Zheng, Fei Li, Xiaochen Bo
2015 BioMed Research International  
The package also implements a set of functions for automatic analysis pipeline construction including functional annotation of metagenomic reads, abundance estimation of enzymatic genes, community-level  ...  A metagenomic approach introduced recently integrates metagenomic data with community-level metabolic network modeling, but no comprehensive tool was available for such kind of approaches.  ...  Moreover, mmnet implements a set of functions to construct an automatic pipeline from functional annotation of metagenomic reads to integrated network analysis.  ... 
doi:10.1155/2015/167249 pmid:26421278 pmcid:PMC4573221 fatcat:im5ilijtifcifab3h53gqbgru4

Functional Metagenomics using Stable Isotope Probing: a Review

Nguyen Xuan Que Vo, Ho-Jeong Kang, Joon-Hong Park
2007 Environmental Engineering Research  
Herein, integration of metagenomics with SIP was suggested as a novel functional genomics approach to study microbial eco-physiology in environment.  ...  If functional genomes isolated by SIP can be transferred into metagenomic library, sequence analysis for such selected functional genomes would be feasible because the reduced size of clone library may  ...  Acknowledgement The subject is supported by Korea Ministry of Environmental as "The Eco-technopia 21 project" (051-071-031).  ... 
doi:10.4491/eer.2007.12.5.231 fatcat:xrrtxqnklvg2boyy6muq23njqi

Integration of Ecology and Environmental Metagenomics Conceptual and Methodological Frameworks

Diana Marco
2017 Current Issues in Molecular Biology  
Recently, calls for the need of integrating the theoretical basis and methodologies coming from metagenomics (and other meta-omics) and ecology have been made.  ...  In particular, I will emphasize the contribution of some well established concepts and methods of field ecology to a an appropriate field sampling and experimental design of environmental metagenomic studies  ...  Acknowledgements DEM is a research member of the Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Argentina.  ... 
doi:10.21775/cimb.024.001 pmid:28686565 fatcat:iryyacaz7ffejcch5gdhub4nay

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

H. Teeling, F. O. Glockner
2012 Briefings in Bioinformatics  
Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable.  ...  Continual progress in next-generation sequencing allows for generating increasingly large metagenomes and studying multiple metagenomes over time or space.  ...  FUNCTIONAL ANALYSIS Analysis of metagenomes involves functional annotation of the predicted genes by database comparison searches.  ... 
doi:10.1093/bib/bbs039 pmid:22966151 pmcid:PMC3504927 fatcat:xdfujqlljfhzjdr4ljddlznzdm

Functional metagenomics for the investigation of antibiotic resistance

Peter Mullany
2014 Virulence  
However, if functional metagenomic studies are used in conjunction with sequenced based metagenomics, this disadvantage can Has a high copy number which can be an advantage when screening for the expression  ...  However, it can only identify genes that have been shown by functional studies (either functional metagenomics or functional studies on antibiotic resistant cultivable bacteria) to encode for resistance  ... 
doi:10.4161/viru.28196 pmid:24556726 pmcid:PMC3979872 fatcat:dcqjyffh3vddzkwz5dzek5xwqi

New insight into the gut microbiome through metagenomics

Jens Nielsen, Boyang Ji
2015 Advances in Genomics and Genetics  
Herein, we describe the metagenomic methods used in human gut microbiome studies and review the roles of gut microbiota as well as the integrative analyses of metagenomic data with other omics data.  ...  A comprehensive analysis of the human gut microbiome is thus important for revealing the mechanisms of these host-microbe interactions.  ...  Acknowledgments We gratefully thank Leif Väremo, Manuel Garcia-Albornoz, and Saeed Shoaie for critical review of the manuscript.  ... 
doi:10.2147/agg.s57215 fatcat:mbpttyjl55boblocef4os5hhp4

The potential for mitigation of methane emissions in ruminants through the application of metagenomics, metabolomics, and other -OMICS technologies

Victoria Asselstine, Stephanie Lam, Filippo Miglior, Luiz F Brito, Hannah Sweett, Leluo Guan, Sinead M Waters, Graham Plastow, Angela Cánovas
2021 Journal of Animal Science  
The integration and evaluation of different levels of biological information using a systems biology approach is also discussed, which can assist in understanding the underlying genetic mechanisms and  ...  One of the largest sources of emission in the ruminant sector is methane (CH4), accounting for approximately 40% of the sectors total emissions.  ...  Acknowledgments This research was supported by the Ontario Ministry of Agriculture, Food, and Rural Affairs (OMAFRA)  ... 
doi:10.1093/jas/skab193 pmid:34586400 fatcat:xik6bk3airawfklj5wi554ucp4

Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis

Vanessa Aguiar-Pulido, Wenrui Huang, Victoria Suarez-Ulloa, Trevor Cickovski, Kalai Mathee, Giri Narasimhan
2016 Evolutionary Bioinformatics  
We conclude with a review of network-based approaches as applied to integrative studies, which we believe holds the key to in-depth understanding of microbiomes.  ...  SUPPLEMENT: Bioinformatics methods and applications for Big metagenomics Data CITATIoN: aguiar-Pulido et al. metagenomics, metatranscriptomics, and metabolomics approaches for microbiome analysis.  ...  We also discussed how the value of an integrative approach is greater than the sum of its parts.  ... 
doi:10.4137/ebo.s36436 pmid:27199545 pmcid:PMC4869604 fatcat:hdpbova2gvctvhe6hp7z5pku7q

gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms

Maria Muñoz-Benavent, Felix Hartkopf, Tim V D Bossche, Vitor C Piro, Carlos García-Ferris, Amparo Latorre, Bernhard Y Renard, Thilo Muth
2020 NAR Genomics and Bioinformatics  
The study of bacterial symbioses has grown exponentially in the recent past.  ...  metaproteomics in an integrative manner.  ...  ACKNOWLEDGEMENTS We thank Dr Nuria Jiménez and FISABIO for the help in the processing and sequencing of the metagenomics and metatranscriptomics samples and the Proteomics Service of the SCSIE for the  ... 
doi:10.1093/nargab/lqaa058 pmid:33575609 pmcid:PMC7671378 fatcat:rsea5a5bsjdhrmqgul3rlikbo4

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.  ...  This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing the role of symbiotic microbial populations in fundamental biochemical functions.  ...  The co-occurrence of microbial species in similar abundance could be seen as an indication of their being part of an integrated network, providing a set of mutually complementary functions integrated in  ... 
doi:10.1093/bib/bbs070 pmid:23175748 pmcid:PMC3505041 fatcat:rm3rv7rp3nht7jyqxkurirfcl4

Metagenomics — A Technological Drift in Bioremediation [chapter]

Pratap Devarapalli, Ranjith N. Kumavath
2015 Advances in Bioremediation of Wastewater and Polluted Soil  
The process of eliminating pollutants using microbes is termed Bioremediation. Metagenomics is a strategic approach for analysing microbial communities at a genomic level.  ...  This chapter emphasizes recent multiple case studies explaining the approaches of metagenomics in bioremediation in different contaminated environments such as soil, water etc.  ...  A comparative overview of functions and suitability of mostly used tools for metagenomic analysis IMG/M Integrated Microbial Genomes and Metagenomes (IMG/M) system supports annotation, analysis, and  ... 
doi:10.5772/60749 fatcat:eg3ym6qvergjnbmstnizkn72ui

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Muneer A. Malla, Anamika Dubey, Shweta Yadav, Ashwani Kumar, Abeer Hashem, Elsayed Fathi Abd Allah
2018 Frontiers in Microbiology  
Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches  ...  Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants  ...  Functional metagenomics is a potent and powerful method for studying the functional aspects of genes.  ... 
doi:10.3389/fmicb.2018.01132 pmid:29915565 pmcid:PMC5994547 fatcat:aswof3hdi5agzepcbud45l3b6u

Determining Microbial Products and Identifying Molecular Targets in the Human Microbiome

Regina Joice, Koji Yasuda, Afrah Shafquat, Xochitl C. Morgan, Curtis Huttenhower
2014 Cell Metabolism  
Culture-independent studies now provide an accelerated means of exploring novel bioactives in the human microbiome; however, intriguingly, a substantial fraction of the microbial metagenome cannot be mapped  ...  Meta'omic approaches, including metagenomic sequencing, metatranscriptomics, metabolomics, and integration of multiple assay types, represent an opportunity to efficiently explore this large pool of potential  ...  Regression analysis can be used as an integrative approach for combining gene and transcript data (as depicted in Figure 3A , iii) in microbiome studies, demonstrating the upregulation of a subset of  ... 
doi:10.1016/j.cmet.2014.10.003 pmid:25440055 pmcid:PMC4254638 fatcat:ig3b6us54ba43nllwhxhnqkud4
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