A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data

Computational and Structural Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19, P. 6301 - 6314

Published: Jan. 1, 2021

Metagenomic sequencing provides a culture-independent avenue to investigate the complex microbial communities by constructing metagenome-assembled genomes (MAGs). A MAG represents genome group of sequences from assembly with similar characteristics. It enables us identify novel species and understand their potential functions in dynamic ecosystem. Many computational tools have been developed construct annotate MAGs metagenomic sequencing, however, there is prominent gap comprehensively introduce background practical performance. In this paper, we thoroughly investigated designed for both upstream downstream analyses, including metagenome assembly, binning, gene prediction, functional annotation, taxonomic classification, profiling. We categorized commonly used into unique groups based on introduced underlying core algorithms associated information demonstrate comparative outlook. Furthermore, emphasized requisition offered guidance users select most efficient tools. Finally, indicated current limitations, solutions, future perspectives further improving construction annotation. believe that our work consolidated resource stage studies shed light development more effective analysis sequencing.

Language: Английский

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Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation

Microbiome, Journal Year: 2022, Volume and Issue: 10(1)

Published: May 11, 2022

Although there is now an extensive understanding of the diversity microbial life on earth through culture-independent metagenomic DNA sequence analyses, isolation and cultivation microbes remains critical to directly study them confirm their metabolic physiological functions, ecological roles. The majority environmental are as yet uncultured however; therefore, bringing these rare or poorly characterized groups into culture a priority further understand microbiome functions. Moreover, cultivated isolates may find utility in range applications, such new probiotics, biocontrol agents, agents for industrial processes. growing abundance meta-transcriptomic information from wide environments provides more opportunities guide interest. In this paper, we discuss successful methodologies applications that have underpinned recent metagenome-guided microbe efforts. These approaches include determining specific conditions enrich taxa interest, complex strategies specifically target capture species antibody engineering genome editing strategies. With greater degree genomic available uncultivated members, via metagenome-assembled genomes, theoretical requirements will enable possibilities ultimately gain comprehensive microbiomes. Video Abstract.

Language: Английский

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Metagenome assembly of high-fidelity long reads with hifiasm-meta

Nature Methods, Journal Year: 2022, Volume and Issue: 19(6), P. 671 - 674

Published: May 9, 2022

Language: Английский

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Current and emerging trends in techniques for plant pathogen detection

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: May 8, 2023

Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting economic and social adversity. The spread of such plant pathogens the emergence new diseases is facilitated by human practices as monoculture farming global trade. Therefore, early detection identification utmost importance to reduce associated agricultural losses. In this review, techniques that are currently available detect discussed, including culture-based, PCR-based, sequencing-based, immunology-based techniques. Their working principles explained, followed an overview main advantages disadvantages, examples their use pathogen detection. addition more conventional commonly used techniques, we also point some recent evolutions field potential point-of-care devices, biosensors, have gained popularity. These devices can provide fast analysis, easy use, most importantly be for on-site diagnosis, allowing farmers take rapid disease management decisions.

Language: Английский

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Unraveling metagenomics through long-read sequencing: a comprehensive review

Journal of Translational Medicine, Journal Year: 2024, Volume and Issue: 22(1)

Published: Jan. 28, 2024

Abstract The study of microbial communities has undergone significant advancements, starting from the initial use 16S rRNA sequencing to adoption shotgun metagenomics. However, a new era emerged with advent long-read (LRS), which offers substantial improvements over its predecessor, short-read (SRS). LRS produces reads that are several kilobases long, enabling researchers obtain more complete and contiguous genomic information, characterize structural variations, epigenetic modifications. current leaders in technologies Pacific Biotechnologies (PacBio) Oxford Nanopore Technologies (ONT), each offering distinct set advantages. This review covers workflow metagenomics sequencing, including sample preparation (sample collection, extraction, library preparation), processing (quality control, assembly, binning), analysis (taxonomic annotation functional annotation). Each section provides concise outline key concept methodology, presenting original as well how it is challenged or modified context LRS. Additionally, introduces range tools compatible can be utilized execute process. aims present metagenomics, highlight transformative impact LRS, provide selection suitable for this task.

Language: Английский

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Sequencing-based analysis of microbiomes

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(12), P. 829 - 845

Published: June 25, 2024

Language: Английский

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Plant–Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

International Journal of Molecular Sciences, Journal Year: 2021, Volume and Issue: 22(19), P. 10388 - 10388

Published: Sept. 27, 2021

Soil health and fertility issues are constantly addressed in the agricultural industry. Through continuous prolonged use of chemical heavy systems, most lands have been impacted, resulting plateaued or reduced productivity. As such, to invigorate industry, we would resort alternative practices that will restore soil fertility. Therefore, recent decades, studies directed towards taking a Magellan voyage rhizosphere region, identify diversity, density, microbial population structure soil, predict possible ways health. Microbes inhabit this region possess niche functions, such as stimulation promotion plant growth, disease suppression, management toxicity, cycling utilization nutrients. should be conducted microbes groups organisms assigned functions. Based on above, article reviews aboveground below-ground microbiomes, their roles immunity, physiological challenges tools available studying these organisms. The information collected over years may contribute toward future applications, designing sustainable agriculture.

Language: Английский

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Digital ecologies: Materialities, encounters, governance

Progress in Environmental Geography, Journal Year: 2022, Volume and Issue: 2(1-2), P. 3 - 32

Published: Dec. 26, 2022

Digital technologies increasingly mediate relations between humans and nonhumans in a range of contexts including environmental governance, surveillance, entertainment. Combining approaches from more-than-human digital geographies, we proffer ‘digital ecologies’ as an analytical framework for examining digitally-mediated human–nonhuman entanglement. We identify entanglement compelling basis which to articulate critique diverse situated contexts. Three questions guide this approach: What infrastructures give rise entanglement, with what material consequences? is at stake socially, politically, economically when encounters are digitised? And how enrolled programmes governance? develop our ecologies across three core conceptual themes wider interest geographers: (i) materialities, considering the enable connections their socioenvironmental impacts; (ii) encounters, political economic consequences convivial potentials digitising contact zones; (iii) questioning produce novel forms governance. affirm that mediations worlds can potentially cultivate environmentally progressive communities, just such note urgency these conversations.

Language: Английский

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Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture

Microbiological Research, Journal Year: 2022, Volume and Issue: 265, P. 127180 - 127180

Published: Sept. 6, 2022

Language: Английский

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PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(15), P. e83 - e83

Published: June 27, 2023

Plasmids are mobile genetic elements that carry important accessory genes. Cataloging plasmids is a fundamental step to elucidate their roles in promoting horizontal gene transfer between bacteria. Next generation sequencing (NGS) the main source for discovering new today. However, NGS assembly programs tend return contigs, making plasmid detection difficult. This problem particularly grave metagenomic assemblies, which contain short contigs of heterogeneous origins. Available tools contig still suffer from some limitations. In particular, alignment-based miss diverged while learning-based often have lower precision. this work, we develop tool PLASMe capitalizes on strength alignment and methods. Closely related can be easily identified using component predicted order-specific Transformer models. By encoding sequences as language defined protein cluster-based token set, learn importance proteins correlation through positionally embedding attention mechanism. We compared other detecting complete plasmids, assembled CAMI2 simulated data. achieved highest F1-score. After validating data with known labels, also tested it real plasmidome The examination commonly used marker genes shows exhibits more reliable performance than tools.

Language: Английский

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