ArticlePLoS computational biology2015
Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Regulatory T cells as a potential treatment for autoimmune inflammatory rheumatic and musculoskeletal diseases.Clinical rheumatology · 2026Review
- Whole metagenome sequencing: not deep enough for complete microbial function recovery.Microbiome · 2026Article
- Annotation of glycoside hydrolases in unassembled metagenomes using CAZyOBioinformatics advances · 2026Article
- RFW captures species-level metagenomic functions by integrating genome annotation information.Cell reports methods · 2024Article
- Current Trends and Challenges of Microbiome Research in Prostate Cancer.Current oncology reports · 2024Review
- MetaFunc: taxonomic and functional analyses of high throughput sequencing for microbiomes.Gut microbiome (Cambridge, England) · 2023Article
- Decoding microbial genomes to understand their functional roles in human complex diseases.iMeta · 2022Review
- Metagenomics Versus Metatranscriptomics of the Murine Gut Microbiome for Assessing Microbial Metabolism During Inflammation.Frontiers in microbiology · 2022Article
- Gulf of Mexico blue hole harbors high levels of novel microbial lineages.The ISME journal · 2021Article
- Article
- RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing.Microorganisms · 2020Article
- Article
- An Improved Approach to Identify Bacterial Pathogens to Human in Environmental Metagenome.Journal of microbiology and biotechnology · 2020Article
- Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.Microbial genomics · 2020Review
- Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes.BMC bioinformatics · 2020Article
- Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads.Genome biology · 2020Article
- Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods.Computational and structural biotechnology journal · 2020Review
- Article
- Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes.Genome biology and evolution · 2019Review
- Deep-Sourced Fluids From a Convergent Margin Host Distinct Subseafloor Microbial Communities That Change Upon Mud Flow Expulsion.Frontiers in microbiology · 2019Article
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Authors and funding
8 authors.
Funding
Abstract
Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP). ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn's disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease.
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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.