Metatax: Metataxonomics with a Compi-Based Pipeline for Precision Medicine

Graña‐Castro, Osvaldo; López-Fernández, Hugo; Nogueira-Rodríguez, Alba; Fdez-Riverola, Florentino; Al‐Shahrour, Fátima; Glez-Peña, Daniel

doi:10.1007/s12539-020-00368-6

Cited by 2 publications

(2 citation statements)

References 35 publications

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“…Bioinformatics analysis of bacteria 16S rRNA sequencing data was conducted by using QIIME 2 software [21,22] (version 2018.11, https ://qiime 2.org). Raw sequence data were developed into clean data by cut off the barcode and primer sequences (Cutadapt plugin), de-multiplexed (demux plugin), and denoised with DADA2 (Dada2 plugin) [23].…”

Section: Bioinformatics Analysismentioning

confidence: 99%

Bioconversion variation of ginsenoside CK mediated by human gut microbiota from healthy volunteers and colorectal cancer patients

et al. 2021

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Background Ginsenoside CK (GCK) serves as the potential anti-colorectal cancer (CRC) protopanaxadiol (PPD)-type saponin, which could be mainly bio-converted to yield PPD by gut microbiota. Meanwhile, the anti-CRC effects of GCK could be altered by gut microbiota due to their different diversity in CRC patients. We aimed to investigate the bioconversion variation of GCK mediated by gut microbiota from CRC patients by comparing with healthy subjects. Methods Gut microbiota profiled by 16S rRNA gene sequencing were collected from healthy volunteers and CRC patients. GCK was incubated with gut microbiota in vitro. A LC-MS/MS method was validated to quantify GCK and PPD after incubation at different time points. Results The bioconversion of GCK in healthy subjects group was much faster than CRC group, as well as the yield of PPD. Moreover, significant differences of PPD concentration between healthy subjects group and CRC group could be observed at 12 h, 48 h and 72 h check points. According to 16S rRNA sequencing, the profiles of gut microbiota derived from healthy volunteers and CRC patients significantly varied, in which 12 differentially abundant taxon were found, such as Bifidobacterium, Roseburia, Bacteroides and Collinsella. Spearman’s correlation analysis showed bacteria enriched in healthy subjects group were positively associated with the biotransformation of GCK, while bacteria enriched in CRC group displayed non correlation character. Among them, Roseburia which could secrete β-glycosidase showed the strongest positive association with the bioconversion of GCK. Conclusions The bioconversion of GCK in healthy subjects was much faster than CRC patients mediated by gut microbiota, which might alter the anti-CRC effects of GCK.

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Section: Bioinformatics Analysismentioning

confidence: 99%

Bioconversion variation of ginsenoside CK mediated by human gut microbiota from healthy volunteers and colorectal cancer patients

et al. 2021

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“…Likewise, pipelines developed with Compi in collaboration with other research groups have already been published. These are: Metatax, a pipeline to analyze biological samples based on 16S rRNA gene sequencing ( Graña Castro et al, 2020a ; Graña Castro et al, 2020b ), FastScreen, a pipeline for inferring positive selection in large viral datasets ( López-Fernández et al, 2020 ), and GenomeFastScreen, an extension of the FastScreen pipeline ( López-Fernández et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Compi: a framework for portable and reproducible pipelines

López-Fernández

Graña‐Castro

Nogueira-Rodríguez

et al. 2021

PeerJ Computer Science

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Compi is an application framework to develop end-user, pipeline-based applications with a primary emphasis on: (i) user interface generation, by automatically generating a command-line interface based on the pipeline specific parameter definitions; (ii) application packaging, with compi-dk, which is a version-control-friendly tool to package the pipeline application and its dependencies into a Docker image; and (iii) application distribution provided through a public repository of Compi pipelines, named Compi Hub, which allows users to discover, browse and reuse them easily. By addressing these three aspects, Compi goes beyond traditional workflow engines, having been specially designed for researchers who want to take advantage of common workflow engine features (such as automatic job scheduling or logging, among others) while keeping the simplicity and readability of shell scripts without the need to learn a new programming language. Here we discuss the design of various pipelines developed with Compi to describe its main functionalities, as well as to highlight the similarities and differences with similar tools that are available. An open-source distribution under the Apache 2.0 License is available from GitHub (available at https://github.com/sing-group/compi). Documentation and installers are available from https://www.sing-group.org/compi. A specific repository for Compi pipelines is available from Compi Hub (available at https://www.sing-group.org/compihub.

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Metatax: Metataxonomics with a Compi-Based Pipeline for Precision Medicine

Cited by 2 publications

References 35 publications

Bioconversion variation of ginsenoside CK mediated by human gut microbiota from healthy volunteers and colorectal cancer patients

Bioconversion variation of ginsenoside CK mediated by human gut microbiota from healthy volunteers and colorectal cancer patients

Compi: a framework for portable and reproducible pipelines

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