ArticleScientific reports2015
MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 147 papers, 1 of them a synthesis that pooled it.
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Who cites it
147 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Early melanoma invasivity correlates with gut fungal and bacterial profiles.The British journal of dermatology · 2022Pooled it
- VSL#3British journal of biomedical science · 2026Trial
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- Comparative Analysis of Tumor Microbiota Identifies a Metastatic-Specific Bacterial Signature, HighlightingOncology research · 2026Article
- Preoperative malnutrition is associated with suppressed intratumoral T cell function and distinct tumor-associated microbiota in colorectal cancer: a prospective pilot study.Frontiers in nutrition · 2026Article
- Marmot gut microbiomes are stable against dietary variation.Oecologia · 2025Article
- Combined tumor-associated microbiome and immune gene expression profiling predict response to neoadjuvant chemo-radiotherapy in locally advanced rectal cancer.Oncoimmunology · 2025Article
- Assessment of bacterial diversity in bovine bulk tank milk samples from Brazil.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Girgentana's Goat Milk Microbiota Investigated in an Organic Farm During Dry Season.Animals : an open access journal from MDPI · 2025Article
- Nasopharyngeal and oral microbiota profiling in SARS-CoV-2 infected pregnant women.Scientific reports · 2025Article
- DNA metabarcoding analysis of stomach flushing contents reveals the exceptionally diverse diet of the golden alpine salamander.Scientific reports · 2025Article
- The blueberry phyllosphere microbiota: tissue-specific core communities and their stability across cultivars and years.BMC plant biology · 2025Article
- More Than Meets the Eye: Unraveling the Interactions Between Skin Microbiota and Habitat in an Opportunistic Amphibian.Microbial ecology · 2025Article
- Use of approved cefazolin based intramammary dry goat treatment and its effects on the milk microbiota.Scientific reports · 2025Article
- Bacterial dynamics and exchange in plant-insect interactions.Current research in insect science · 2025Article
87 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project.
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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.