ArticleMicrobiome2017
A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis.
Article in Microbiome, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
49 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Fecal Microbiome Alterations in Colorectal Cancer: A Systematic Review of Compositional Changes and Microbial Biomarkers.MicrobiologyOpen · 2026Pooled it
- Gut Microbiota Profile in Patients with Type 1 Diabetes Based on 16S rRNA Gene Sequencing: A Systematic Review.Disease markers · 2020Pooled it
- Impact of CFTR modulation with Ivacaftor on Gut Microbiota and Intestinal Inflammation.Scientific reports · 2018Trial
- The role of gut microbiota in chronic intestinal pseudo-obstruction: exploring fecal microbiota transplantation as a treatment option.Gut microbes · 2026Article
- Investigation of the Gut Microbiome in Treatment-Resistant Schizophrenia Compared to Healthy Controls: A Cross-Sectional Pilot Study: Étude du microbiome intestinal chez les patients atteints de schizophrénie résistante au traitement par rapport aux témoins sains : étude pilote transversale.Canadian journal of psychiatry. Revue canadienne de psychiatrie · 2026Article
- PixelCut: A Unified Solution for Zero-Configuration 16S rRNA Trimming via Computer Vision.Current issues in molecular biology · 2025Article
- Probiotic Strain Limosilactobacillus reuteri 29B is Proven Safe and Exhibits Potential Probiotic Traits in a Murine Vaginal Model.Probiotics and antimicrobial proteins · 2024Article
- Vasoactive Intestinal Polypeptide Plays a Key Role in the Microbial-Neuroimmune Control of Intestinal Motility.Cellular and molecular gastroenterology and hepatology · 2024Article
- Leveraging the microbiome to understand clinical heterogeneity in depression: findings from the T-RAD study.Translational psychiatry · 2023Article
- Industrial and Ruminant Trans-Fatty Acids-Enriched Diets Differentially Modulate the Microbiome and Fecal Metabolites in C57BL/6 Mice.Nutrients · 2023Article
- Cultivation modes impacting root microbiomes and metabolites in medicinal orchidFrontiers in microbiomes · 2023Article
- Fecal microbiota transplantation ameliorates bone loss in mice with ovariectomy-induced osteoporosis via modulating gut microbiota and metabolic function.Journal of orthopaedic translation · 2022Article
- Metformin-induced reductions in tumor growth involves modulation of the gut microbiome.Molecular metabolism · 2022Article
- The Airway Microbiota Signatures of Infection and Rejection in Lung Transplant Recipients.Microbiology spectrum · 2022Article
- Microbe-Immune Crosstalk: Evidence That T Cells Influence the Development of the Brain Metabolome.International journal of molecular sciences · 2022Article
- Effects of Plantation Type and Soil Depth on Microbial Community Structure and Nutrient Cycling Function.Frontiers in microbiology · 2022Article
- Fecal microbiome differs between patients with systemic sclerosis with and without small intestinal bacterial overgrowth.Journal of scleroderma and related disorders · 2021Article
- Endometrial microbiota is more diverse in people with endometriosis than symptomatic controls.Scientific reports · 2021Observational
- Ingestion of Lactobacillus rhamnosus modulates chronic stress-induced feather pecking in chickens.Scientific reports · 2021Article
- Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences.Frontiers in microbiology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
backgroundAdvances in next-generation sequencing technologies have allowed for detailed, molecular-based studies of microbial communities such as the human gut, soil, and ocean waters. Sequencing of the 16S rRNA gene, specific to prokaryotes, using universal PCR primers has become a common approach to studying the composition of these microbiota. However, the bioinformatic processing of the resulting millions of DNA sequences can be challenging, and a standardized protocol would aid in reproducible analyses.
methodsThe short-read library 16S rRNA gene sequencing pipeline (sl1p, pronounced "slip") was designed with the purpose of mitigating this lack of reproducibility by combining pre-existing tools into a computational pipeline. This pipeline automates the processing of raw 16S rRNA gene sequencing data to create human-readable tables, graphs, and figures to make the collected data more readily accessible.
resultsData generated from mock communities were compared using eight OTU clustering algorithms, two taxon assignment approaches, and three 16S rRNA gene reference databases. While all of these algorithms and options are available to sl1p users, through testing with human-associated mock communities, AbundantOTU+, the RDP Classifier, and the Greengenes 2011 reference database were chosen as sl1p's defaults based on their ability to best represent the known input communities.
conclusionssl1p promotes reproducible research by providing a comprehensive log file, and reduces the computational knowledge needed by the user to process next-generation sequencing data. sl1p is freely available at https://bitbucket.org/fwhelan/sl1p .
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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.