ArticlePeerJ2021
Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets.
Article in PeerJ, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 61 citations in OpenAlex.
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- Comparing the Performance of Double-Stranded and Single-Stranded DNA Libraries for Ancient Oral Microbiome Reconstruction.Molecular ecology resources · 2026Article
- The Oral Microbiome of King Richard III of England.American journal of biological anthropology · 2026Article
- A Subphenotype of Obesity With Reduced Enteroendocrine Glucagon-Like Peptide 1 Synthesis and Enhanced Tirzepatide Response.Gastroenterology · 2026Article
- Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper.Nature biotechnology · 2026Article
- Genome-resolved multi-omics provide new insights into microbial nitrogen utilization by the rumen microbiota.Microbiome · 2026Article
- Antibiotic growth promoter and phytogenic feed additive consistently alter microbial community structure in chicken cecum.Frontiers in microbiology · 2026Article
- Integrated meta-omics reveals AFBMicrobiome · 2025Article
- Ecogenomics and functional biogeography of the Roseobacter group in the global oceans based on 653 MAGs and SAGs.Microbiome · 2025Article
- Alteration of gut microbial ecology by the direct activation of the brain: Inverse gut-microbiome-brain dynamics.iScience · 2025Article
- UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog.NPJ biofilms and microbiomes · 2025Article
- Article
- Microbial metagenomes from Lake Soyang, the largest freshwater reservoir in South Korea.Scientific data · 2025Article
- Metagenomic insights of microbial functions under conventional and conservation agriculture.World journal of microbiology & biotechnology · 2025Article
- Streptococcus abundance and oral site tropism in humans and non-human primates reflects host and lifestyle differences.NPJ biofilms and microbiomes · 2025Article
- Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines.Microbial genomics · 2025Article
- PartialFrontiers in veterinary science · 2025Article
- Personalized modeling of gut microbiome metabolism throughout the first year of life.Communications medicine · 2024Article
- MBCN: A novel reference database for Effcient Metagenomic analysis of human gut microbiome.Heliyon · 2024Article
- Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes.Nature communications · 2024Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mapping metagenome reads to reference databases is the standard approach for assessing microbial taxonomic and functional diversity from metagenomic data. However, public reference databases often lack recently generated genomic data such as metagenome-assembled genomes (MAGs), which can limit the sensitivity of read-mapping approaches. We previously developed the Struo pipeline in order to provide a straight-forward method for constructing custom databases; however, the pipeline does not scale well enough to cope with the ever-increasing number of publicly available microbial genomes. Moreover, the pipeline does not allow for efficient database updating as new data are generated. To address these issues, we developed Struo2, which is >3.5 fold faster than Struo at database generation and can also efficiently update existing databases. We also provide custom Kraken2, Bracken, and HUMAnN3 databases that can be easily updated with new genomes and/or individual gene sequences. Efficient database updating, coupled with our pre-generated databases, enables "assembly-enhanced" profiling, which increases database comprehensiveness via inclusion of native genomic content. Inclusion of newly generated genomic content can greatly increase database comprehensiveness, especially for understudied biomes, which will enable more accurate assessments of microbiome diversity.
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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.