QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

Current Protocols in Bioinformatics, Journal Year: 2020, Volume and Issue: 70(1)

Published: April 28, 2020

QIIME 2 is a completely re-engineered microbiome bioinformatics platform based on the popular platform, which it has replaced. facilitates comprehensive and fully reproducible data science, improving accessibility to diverse users by adding multiple user interfaces. can be combined with Qiita, an open-source web-based re-use available for meta-analysis. The following basic protocol describes how install single computer analyze sequence data, from processing of raw DNA reads through generating publishable interactive figures. These figures allow readers study interact same ease as its authors, advancing science transparency reproducibility. We also show plug-ins developed community add analysis capabilities installed used 2, enhancing various aspects analyses-e.g., taxonomic classification accuracy. Finally, we illustrate perform meta-analyses combining different datasets using readily public Qiita. In this tutorial, subset Early Childhood Antibiotics Microbiome (ECAM) study, tracked composition development 43 infants in United States birth years age, identifying associations antibiotic exposure, delivery mode, diet. For more information about see https://qiime2.org. To troubleshoot or ask questions analysis, join active at https://forum.qiime2.org. © 2020 Authors. Basic Protocol: Using Support Further analyses.

Language: Английский

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Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

mSystems, Journal Year: 2022, Volume and Issue: 7(2)

Published: April 4, 2022

We introduce the operational genomic unit (OGU) method, a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as minimum for assessing diversity of microbial communities and their relevance environmental factors. This approach is independent taxonomic classification, granting possibility maximal resolution community composition, organizes features into an accurate hierarchy using phylogenomic tree. The outputs are suitable contemporary analytical protocols ecology, differential abundance, supervised learning while supporting phylogenetic methods, such UniFrac phylofactorization, seldom applied shotgun metagenomics despite being prevalent in 16S rRNA gene amplicon studies. As demonstrated two real-world case studies, OGU method produces biologically meaningful patterns from microbiome data sets. Such further remain detectable at very low metagenomic sequencing depths. Compared with unit-based analyses implemented currently adopted tools, variants, this shows superiority informing relevant insights, including stronger correlation body environment host sex on Human Microbiome Project set more prediction human age by gut microbiomes Finnish individuals included FINRISK 2002 cohort. provide Woltka, bioinformatics tool implement full integration QIIME 2 package Qiita web platform, facilitate adoption future

Language: Английский

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Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Foods, Journal Year: 2023, Volume and Issue: 12(11), P. 2140 - 2140

Published: May 25, 2023

Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase discoveries related to microbial world. Newly discovered microbiomes different ecologies provide meaningful information on diversity functions of microorganisms Earth. Therefore, results metagenomic studies new microbe-based applications human health, agriculture, food industry, among others. This review summarizes fundamental procedures recent advances bioinformatic tools. It also explores up-to-date study, plant research, environmental sciences, other fields. Finally, is powerful tool for studying world, it still numerous that are currently hidden awaiting discovery. this discusses future perspectives

Language: Английский

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An open label, non-randomized study assessing a prebiotic fiber intervention in a small cohort of Parkinson’s disease participants

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Feb. 18, 2023

Abstract A pro-inflammatory intestinal microbiome is characteristic of Parkinson’s disease (PD). Prebiotic fibers change the and this study sought to understand utility prebiotic for use in PD patients. The first experiments demonstrate that fermentation patient stool with increased production beneficial metabolites (short chain fatty acids, SCFA) changed microbiota demonstrating capacity respond favorably prebiotics. Subsequently, an open-label, non-randomized was conducted newly diagnosed, non-medicated ( n = 10) treated participants wherein impact 10 days intervention evaluated. Outcomes well tolerated (primary outcome) safe (secondary associated biological changes microbiota, SCFA, inflammation, neurofilament light chain. Exploratory analyses indicate effects on clinically relevant outcomes. This proof-of-concept offers scientific rationale placebo-controlled trials using ClinicalTrials.gov Identifier: NCT04512599.

Language: Английский

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The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: July 8, 2021

Autism spectrum disorders (ASD) are associated with dysregulation of the microbiota-gut-brain axis, changes in microbiota composition as well fecal, serum, and urine levels microbial metabolites. Yet a causal relationship between axis ASD remains to be demonstrated. Here, we hypothesized that metabolite p-Cresol, which is more abundant patients compared neurotypical individuals, could induce ASD-like behavior mice.Mice exposed p-Cresol for 4 weeks drinking water presented social deficits, stereotypies, perseverative behaviors, but no anxiety, locomotion, or cognition. Abnormal induced by was decreased activity central dopamine neurons involved reward circuit. Further, deficits transferred from p-Cresol-treated mice control fecal transplantation (FMT). We also showed transplanted exhibited increased excretion, mice. In addition, identified possible bacterial producers. Lastly, rescued interactions, excitability, when mice.The induces selectively core behavioral symptoms Social dependant on composition. Our study paves way therapeutic interventions targeting production treat ASD. Video abstract.

Language: Английский

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COVID-19 pandemic reveals the peril of ignoring metadata standards

Scientific Data, Journal Year: 2020, Volume and Issue: 7(1)

Published: June 19, 2020

Efficient response to the pandemic through mobilization of larger scientific community is challenged by limited reusability available primary genomic data. Here, Genomic Standards Consortium board highlights essential need for contextual data FAIRness, empowering key data-driven biological questions.

Language: Английский

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Depth-resolved microbial diversity and functional profiles of trichloroethylene-contaminated soils for Biolog EcoPlate-based biostimulation strategy

Journal of Hazardous Materials, Journal Year: 2021, Volume and Issue: 424, P. 127266 - 127266

Published: Sept. 24, 2021

Language: Английский

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DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

Microorganisms, Journal Year: 2021, Volume and Issue: 9(2), P. 361 - 361

Published: Feb. 12, 2021

Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth health. Therefore, the identification, taxonomic characterization determination of role members soil microbial communities have become topics interest. The development continuous improvement high-throughput sequencing platforms further stimulated study complex microbiota soils plants. most frequently used approach to composition, diversity dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with subsequent amplicons. This methodological called DNA metabarcoding. Over last decade, metabarcoding has rapidly emerged as a powerful cost-effective method for description environmental samples. However, this involves several processing steps, each which might introduce significant biases that can considerably compromise reliability output. aim review provide state-of-the-art background knowledge needed make appropriate decisions at step workflow, highlighting crucial steps that, if considered, ensures an accurate standardized studies.

Language: Английский

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Ecological Role of Bacteria Involved in the Biogeochemical Cycles of Mangroves Based on Functional Genes Detected through GeoChip 5.0

mSphere, Journal Year: 2022, Volume and Issue: 7(1)

Published: Jan. 12, 2022

Bacteria have important functions in biogeochemical cycles, but studies on their function an ecosystem, mangroves, are still limited. Here, we investigated the ecological role of bacteria involved cycles seven representative mangroves southern China.

Language: Английский

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metabaR: An r package for the evaluation and improvement of DNA metabarcoding data quality

Methods in Ecology and Evolution, Journal Year: 2021, Volume and Issue: 12(4), P. 586 - 592

Published: Jan. 18, 2021

Abstract DNA metabarcoding is becoming the tool of choice for biodiversity assessment across taxa and environments. Yet, artefacts present in datasets often preclude a proper interpretation ecological patterns. Bioinformatic pipelines to remove experimental noise exist. However, these only partially target produced artefacts, or are marker specific. In addition, assessments data curation quality chosen filtering thresholds seldom available existing pipelines, partly due lack appropriate visualisation tools. Here, we metabaR , an r package that provides comprehensive suite tools effectively curate after basic bioinformatic analyses. particular, uses negative positive controls identify different types artefactual sequences, is, contaminants tag‐jumps. It also flags potentially dysfunctional PCRs based on PCR replicate similarities when those available. Finally, visualise characteristics their context as well distribution, facilitates appropriateness thresholds. applicable any design but most powerful includes replicates. More generally, simplicity flexibility makes it marker, generated with sequencing platform, pre‐analysed pipeline. Its outputs easily usable downstream analyses package. complements bioinformatics by providing scientists variety functions clean avoid serious misinterpretations. thus offers promising platform automatised environmental research biomonitoring.

Language: Английский

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