ArticleJournal of microbiology (Seoul, Korea)2020
Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists.
Article in Journal of microbiology (Seoul, Korea), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 77 citations in OpenAlex.
- Fecal Microbiome Composition Does Not Predict Diet-Induced TMAO Production in Healthy Adults.Journal of the American Heart Association · 2021Trial
- Temporal and Functional Profiling of the Microbiome of High and Low Nitrogen Content Barley Seed in Silo Storage.Food science & nutrition · 2026Article
- Microbial landscape: composition and health associations of environmental microbiome in key functional spaces of premium elderly care facilities.Microbiology spectrum · 2026Article
- Integrative Bioinformatics Approaches in Environmental Biotechnology: A Review.TheScientificWorldJournal · 2026Review
- Dynamic multi-omics analysis reveals the correlation between aroma compounds and symbiotic microbial community during tobacco leaf aging process.BMC plant biology · 2025Article
- Gut-Microbiota-Derived Metabolites and Probiotic Strategies in Colorectal Cancer: Implications for Disease Modulation and Precision Therapy.Nutrients · 2025Review
- Effects ofFrontiers in veterinary science · 2025Article
- Comparison of Culture-Dependent and Culture-Independent Methods for Routine Identification of Airborne Microorganisms in Speleotherapeutic Caves.Microorganisms · 2024Article
- A metagenomic assessment of bacterial community in spices sold open-air markets in Saint-Louis, Senegal.Scientific reports · 2024Article
- Community Diversity of Fungi Carried by Four Common Woodpeckers in Heilongjiang Province, China.Journal of fungi (Basel, Switzerland) · 2024Article
- The diversity of endophytic fungi in Tartary buckwheat (Frontiers in microbiology · 2024Article
- The infants' gut microbiome: setting the stage for the early onset of obesity.Frontiers in microbiology · 2024Article
- Genome mining ofFrontiers in microbiology · 2024Article
- Article
- The Future Is Now: Unraveling the Expanding Potential of Human (Necro)Microbiome in Forensic Investigations.Microorganisms · 2023Review
- Structure and ecological function of the soil microbiome associated with 'Sanghuang' mushrooms suffering from fungal diseases.BMC microbiology · 2023Article
- Analysis of differences in tobacco leaf microbial communities after redrying in Chinese provinces and from abroad.AMB Express · 2023Article
- Impact of coprophagy prevention on the growth performance, serum biochemistry, and intestinal microbiome of rabbits.BMC microbiology · 2023Article
- ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning.PLoS computational biology · 2023Article
- The roles of gut microbiota and its metabolites in diabetic nephropathy.Frontiers in microbiology · 2023Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted ("shotgun") sequencing of all ("meta") microbial genomes ("genomic") present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.