Application of computational approaches to analyze metagenomic data

Gwak, Ho Jin; Lee, Seung-Jae; Rho, Mina

doi:10.1007/s12275-021-0632-8

Cited by 12 publications

(7 citation statements)

References 76 publications

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“…40 However, the main disadvantages of this method are computational requirements, higher susceptibility to contamination in low biomass samples, effects of host DNA contamination, data complexity, and analysis issues. 33…”

Section: Metagenomicsmentioning

confidence: 99%

“…32 Recently, in addition to the decreasing sequencing costs, the introduction of new data analysis approaches such as metagenomic classification and profiling, microbial genome reconstructions from metagenomes and integration of metagenomic and metabolomic data to predict functional profile contributed to broadening use of this method. 33 At present, shotgun metagenomics has an increasing use in the microbiome field for microbial community profiling, identification of microbial biomarkers, assessment of the functional potential of microbial community members and microbiome-based classifications of sample groups.…”

Section: Omics Analysis Typesmentioning

confidence: 99%

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Integrated multi-omics analyses of microbial communities: a review of the current state and future directions

Arıkan

Muth

2023

Mol. Omics

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Section: Metagenomicsmentioning

confidence: 99%

Section: Omics Analysis Typesmentioning

confidence: 99%

Integrated multi-omics analyses of microbial communities: a review of the current state and future directions

Arıkan

Muth

2023

Mol. Omics

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“…Metagenomic analysis has become a very popular tool for understanding the microbial diversity and their metabolic potentials in different environments. In the past decade, the rapidly expanding field of metagenomics has produced a vast amount of environmental genomic data, from the world’s oceans to human gut microbiota [ 80 , 81 , 82 ]. Previous analyses of the relationship between living conditions and Se utilization in sequenced prokaryotes have revealed that certain environmental factors can affect not only the distribution of different selenoprotein families but also the selenoproteomes [ 46 , 65 ]; however, so far, very limited studies have been performed to explore the utilization and function of Se in microbial communities, almost all of which have focused on marine environments.…”

Section: Comparative Metagenomics Of Selenium Utilizationmentioning

confidence: 99%

Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective

et al. 2022

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Selenium (Se) is an important trace element that mainly occurs in the form of selenocysteine in selected proteins. In prokaryotes, Se is also required for the synthesis of selenouridine and Se-containing cofactor. A large number of selenoprotein families have been identified in diverse prokaryotic organisms, most of which are thought to be involved in various redox reactions. In the last decade or two, computational prediction of selenoprotein genes and comparative genomics of Se metabolic pathways and selenoproteomes have arisen, providing new insights into the metabolism and function of Se and their evolutionary trends in bacteria and archaea. This review aims to offer an overview of recent advances in bioinformatics analysis of Se utilization in prokaryotes. We describe current computational strategies for the identification of selenoprotein genes and generate the most comprehensive list of prokaryotic selenoproteins reported to date. Furthermore, we highlight the latest research progress in comparative genomics and metagenomics of Se utilization in prokaryotes, which demonstrates the divergent and dynamic evolutionary patterns of different Se metabolic pathways, selenoprotein families, and selenoproteomes in sequenced organisms and environmental samples. Overall, bioinformatics analyses of Se utilization, function, and evolution may contribute to a systematic understanding of how this micronutrient is used in nature.

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“…Similarly, longer reads can be used to complement short reads for finishing genome assembly and gap solving, as illustrated in seven bacterial genomes in Utturkar et al (2017) . An extensive review of all computational tools for generating metagenome-assembled genomes can be found in Gwak et al (2021) and Yang et al (2021) .…”

Section: Generation and Analysis Of Genomics Data For The Study Of Mi...mentioning

confidence: 99%

Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels

et al. 2022

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The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented.

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Application of computational approaches to analyze metagenomic data

Cited by 12 publications

References 76 publications

Integrated multi-omics analyses of microbial communities: a review of the current state and future directions

Integrated multi-omics analyses of microbial communities: a review of the current state and future directions

Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective

Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels

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