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Nature Biotechnology Jun 2020
Topics: Computational Biology; Genes, Bacterial; Metagenome; Metagenomics; RNA, Ribosomal, 16S; Software
PubMed: 32483366
DOI: 10.1038/s41587-020-0548-6 -
Nature Communications Feb 2021Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes...
Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.
Topics: Animals; Bacteria; Female; Gastrointestinal Microbiome; Genes, Microbial; High-Throughput Nucleotide Sequencing; Metagenome; Metagenomics; Phylogeny; Species Specificity; Swine
PubMed: 33597514
DOI: 10.1038/s41467-021-21295-0 -
Applied Biochemistry and Biotechnology Oct 2017Microorganisms are found throughout every corner of nature, and vast number of microorganisms is difficult to cultivate by classical microbiological techniques. The... (Review)
Review
Microorganisms are found throughout every corner of nature, and vast number of microorganisms is difficult to cultivate by classical microbiological techniques. The advent of metagenomics has revolutionized the field of microbial biotechnology. Metagenomics allow the recovery of genetic material directly from environmental niches without any cultivation techniques. Currently, metagenomic tools are widely employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the uncultivable component of microbial communities. The employment of next-generation sequencing techniques for metagenomics resulted in the generation of large sequence data sets derived from various environments, such as soil, the human body and ocean water. This review article describes the state-of-the-art techniques and tools in metagenomics and discusses the potential of metagenomic approaches for the bioprospecting of industrial enzymes from various environmental samples. We also describe the unusual novel enzymes discovered via metagenomic approaches and discuss the future prospects for metagenome technologies.
Topics: Enzymes; Metagenome; Metagenomics
PubMed: 28815469
DOI: 10.1007/s12010-017-2568-3 -
Microbiological Research Jul 2022Reference genomes are essential for analyzing the metabolic and functional potentials of microbiomes. However, microbial genome resources are limited because most of... (Review)
Review
Reference genomes are essential for analyzing the metabolic and functional potentials of microbiomes. However, microbial genome resources are limited because most of microorganisms are difficult to culture. Genome binning is a culture-independent approach that can recover a vast number of microbial genomes from short-read high throughput shotgun metagenomic sequencing data. In this review, we summarize methods commonly used for reconstructing metagenome-assembled genomes (MAGs) to provide a reference for researchers to choose propriate software programs among the numerous and complicated tools and pipelines that are available for these analyses. In addition, we discuss application prospects, challenges, and opportunities for recovering MAGs from metagenomic sequencing data.
Topics: High-Throughput Nucleotide Sequencing; Metagenome; Metagenomics; Microbiota
PubMed: 35430490
DOI: 10.1016/j.micres.2022.127023 -
Methods in Molecular Biology (Clifton,... 2022Microbial communities' taxonomic and functional diversity has been broadly studied since sequencing technologies enabled faster and cheaper data obtainment....
Microbial communities' taxonomic and functional diversity has been broadly studied since sequencing technologies enabled faster and cheaper data obtainment. Nevertheless, the programming skills needed and the amount of software available may be overwhelming to someone trying to analyze these data. Here, we present a comprehensive and straightforward pipeline that takes shotgun metagenomics data through the needed steps to obtain valuable results. The raw data goes through a quality control process, metagenomic assembly, binning (the obtention of single genomes from a metagenome), taxonomic assignment, and taxonomic diversity analysis and visualization.
Topics: Computational Biology; Metagenome; Metagenomics; Microbiota; Sequence Analysis, DNA; Software
PubMed: 35818005
DOI: 10.1007/978-1-0716-2429-6_10 -
Cell Aug 2019Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform... (Review)
Review
Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the complexity of metagenomic data make it important that researchers are able to benchmark their performance. Here, we review current approaches for metagenomic analysis and evaluate the performance of 20 metagenomic classifiers using simulated and experimental datasets. We describe the key metrics used to assess performance, offer a framework for the comparison of additional classifiers, and discuss the future of metagenomic data analysis.
Topics: Bacteria; Benchmarking; Databases, Genetic; Fungi; Metagenome; Metagenomics; Phylogeny; Polymerase Chain Reaction; Sequence Analysis, DNA; Software; Viruses
PubMed: 31398336
DOI: 10.1016/j.cell.2019.07.010 -
MSphere Nov 2020Continued influx of metagenome-derived proteins with misannotated taxonomy into conventional databases, including RefSeq, threatens to eliminate the value of taxonomy...
Continued influx of metagenome-derived proteins with misannotated taxonomy into conventional databases, including RefSeq, threatens to eliminate the value of taxonomy identifiers. To prevent this, urgent efforts should be undertaken by submitters of metagenomic data sets as well as by database managers.
Topics: Algorithms; Databases, Genetic; Metagenome; Metagenomics; Proteins
PubMed: 33148820
DOI: 10.1128/mSphere.00854-20 -
Current Opinion in Biotechnology Feb 2021Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the... (Review)
Review
Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities. While metagenomics is shaping our understanding of microbial functions in ecosystems via gene-centric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous samples remains challenging. Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to increase our understanding of microbial taxonomy, function, ecology, and evolution in the environment.
Topics: Ecology; High-Throughput Nucleotide Sequencing; Metagenome; Metagenomics; Microbiota; Sequence Analysis, DNA
PubMed: 33592536
DOI: 10.1016/j.copbio.2021.01.019 -
The Yale Journal of Biology and Medicine Sep 2016Advances in sequencing technologies have led to the increased use of high throughput sequencing in characterizing the microbial communities associated with our bodies... (Review)
Review
Advances in sequencing technologies have led to the increased use of high throughput sequencing in characterizing the microbial communities associated with our bodies and our environment. Critical to the analysis of the resulting data are sequence assembly algorithms able to reconstruct genes and organisms from complex mixtures. Metagenomic assembly involves new computational challenges due to the specific characteristics of the metagenomic data. In this survey, we focus on major algorithmic approaches for genome and metagenome assembly, and discuss the new challenges and opportunities afforded by this new field. We also review several applications of metagenome assembly in addressing interesting biological problems.
Topics: Algorithms; Animals; Humans; Metagenome; Metagenomics; Sequence Analysis, DNA
PubMed: 27698619
DOI: No ID Found -
Briefings in Bioinformatics Sep 2023Microbial genome recovery from metagenomes can further explain microbial ecosystem structures, functions and dynamics. Thus, this study developed the Additional...
Microbial genome recovery from metagenomes can further explain microbial ecosystem structures, functions and dynamics. Thus, this study developed the Additional Clustering Refiner (ACR) to enhance high-purity prokaryotic and eukaryotic metagenome-assembled genome (MAGs) recovery. ACR refines low-quality MAGs by subjecting them to iterative k-means clustering predicated on contig abundance and increasing bin purity through validated universal marker genes. Synthetic and real-world metagenomic datasets, including short- and long-read sequences, evaluated ACR's effectiveness. The results demonstrated improved MAG purity and a significant increase in high- and medium-quality MAG recovery rates. In addition, ACR seamlessly integrates with various binning algorithms, augmenting their strengths without modifying core features. Furthermore, its multiple sequencing technology compatibilities expand its applicability. By efficiently recovering high-quality prokaryotic and eukaryotic genomes, ACR is a promising tool for deepening our understanding of microbial communities through genome-centric metagenomics.
Topics: Metagenome; Eukaryota; Microbiota; Algorithms; Metagenomics; Cluster Analysis
PubMed: 37889119
DOI: 10.1093/bib/bbad381