General Unified Microbiome Profiling Pipeline (GUMPP) was developed for large scale, streamlined and reproducible analysis of bacterial 16S rRNA data and prediction of microbial metagenomes, enzymatic reactions and metabolic pathways from amplicon data. GUMPP workflow introduces reproducible data analyses at each of the three levels of resolution (genus; operational taxonomic units (OTUs); amplicon sequence variants (ASVs)). The ability to support reproducible analyses enables production of datasets that ultimately identify the biochemical pathways characteristic of disease pathology. These datasets coupled to biostatistics and mathematical approaches of machine learning can play a significant role in extraction of truly significant and meaningful information from a wide set of 16S rRNA datasets. The adoption of GUMPP in the gut-microbiota related research enables focusing on the generation of novel biomarkers that can lead to the development of mechanistic hypotheses applicable to the development of novel therapies in personalized medicine.
| Language: | English |
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| Keywords: | 16S rRNA, amplicon, Mothur, PICRUSt 2, Piphillin, genus, OTU, ASV, predicted metagenomes, predicted enzymatic reactions, predicted metabolic pathways, reproducible analyses, human microbiome, gut, intestine, mice |
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| Work type: | Article |
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| Typology: | 1.01 - Original Scientific Article |
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| Organization: | FE - Faculty of Electrical Engineering
BF - Biotechnical Faculty
FGG - Faculty of Civil and Geodetic Engineering
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| Publication status: | Published |
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| Publication version: | Version of Record |
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| Year: | 2021 |
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| Number of pages: | 14 str. |
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| Numbering: | Vol. 11, iss. 6, art. 336 |
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| PID: | 20.500.12556/RUL-135449  |
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| UDC: | 579 |
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| ISSN on article: | 2218-1989 |
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| DOI: | 10.3390/metabo11060336 |
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| COBISS.SI-ID: | 64527363 |
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| Publication date in RUL: | 15.03.2022 |
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| Views: | 693 |
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| Downloads: | 136 |
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