ArticleISME communications2021
Identification of core and rare species in metagenome samples based on shotgun metagenomic sequencing, Fourier transforms and spectral comparisons.
Article in ISME communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Effects of elexacaftor/tezacaftor/ivacaftor on the nasal microbial metagenome in cystic fibrosis.Microbiology spectrum · 2026Article
- The evaluation of shotgun sequencing and rpoB metabarcoding for taxonomic profiling of bacterial communities.BMC microbiology · 2025Article
- Exploring alterations of gut/blood microbes in addressing iron overload-induced gut dysbiosis and cognitive impairment in thalassemia patients.Scientific reports · 2024Article
- Sputum metagenomics of people with bronchiectasis.ERJ open research · 2024Article
- A self-supervised deep learning method for data-efficient training in genomics.Communications biology · 2023Article
- Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome.NPJ science of food · 2023Article
- Longitudinal development of the airway metagenome of preterm very low birth weight infants during the first two years of life.ISME communications · 2023Article
- Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome.Nature communications · 2023Article
- Article
- Impact of Elexacaftor/Tezacaftor/Ivacaftor Therapy on the Cystic Fibrosis Airway Microbial Metagenome.Microbiology spectrum · 2022Article
- Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation.Microbiome · 2022Article
- Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life.Computational and structural biotechnology journal · 2022Article
- Article
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Authors and funding
2 authors.
Funding
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Abstract
In shotgun metagenomic sequencing applications, low signal-to-noise ratios may complicate species-level differentiation of genetically similar core species and impede high-confidence detection of rare species. However, core and rare species can take pivotal roles in their habitats and should hence be studied as one entity to gain insights into the total potential of microbial communities in terms of taxonomy and functionality. Here, we offer a solution towards increased species-level specificity, decreased false discovery and omission rates of core and rare species in complex metagenomic samples by introducing the rare species identifier (raspir) tool. The python software is based on discrete Fourier transforms and spectral comparisons of biological and reference frequency signals obtained from real and ideal distributions of short DNA reads mapping towards circular reference genomes. Simulation-based testing of raspir enabled the detection of rare species with genome coverages of less than 0.2%. Species-level differentiation of rare Escherichia coli and Shigella spp., as well as the clear delineation between human Streptococcus spp. was feasible with low false discovery (1.3%) and omission rates (13%). Publicly available human placenta sequencing data were reanalysed with raspir. Raspir was unable to identify placental microbial communities, reinforcing the sterile womb paradigm.
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