Microbiome Datasets Are Compositional: And This Is Not Optional

Frontiers in Microbiology, Journal Year: 2017, Volume and Issue: 8

Published: Nov. 15, 2017

Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers, metagenomes or metatranscriptomes are commonplace and being used to study human disease states, ecological differences between sites, the built environment. There is increasing awareness that microbiome datasets generated HTS compositional because they have an arbitrary total imposed instrument. However, many investigators either unaware this assume specific properties data. The purpose review alert dangers inherent in ignoring nature data, point out derived from studies can should be treated as compositions at all stages analysis. We briefly introduce illustrate pathologies occur when data analyzed inappropriately, finally give guidance resources examples for analysis using

Language: Английский

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MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

Nucleic Acids Research, Journal Year: 2017, Volume and Issue: 45(W1), P. W180 - W188

Published: April 12, 2017

The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling the genetic contents microbial communities. How to analyze resulting large complex datasets remains a key challenge in current studies. Over past decade, powerful computational pipelines and robust protocols have been established enable efficient raw data processing annotation. focus shifted toward downstream statistical analysis functional interpretation. Here, we introduce MicrobiomeAnalyst, user-friendly tool that integrates recent progress statistics visualization techniques, coupled with novel knowledge bases, comprehensive common outputs produced from MicrobiomeAnalyst contains four modules - Marker Data Profiling module offers various options for community profiling, comparative prediction based on 16S rRNA marker gene data; Shotgun supports exploratory analysis, metabolic network shotgun metagenomics or metatranscriptomics Taxon Set Enrichment Analysis helps interpret taxonomic signatures via enrichment against >300 taxon sets manually curated literature public databases; finally, Projection Public allows users visually explore their reference pattern discovery biological insights. is freely available at http://www.microbiomeanalyst.ca.

Language: Английский

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Best practices for analysing microbiomes

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 16(7), P. 410 - 422

Published: May 23, 2018

Language: Английский

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Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data

Nature Protocols, Journal Year: 2020, Volume and Issue: 15(3), P. 799 - 821

Published: Jan. 15, 2020

Language: Английский

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Multivariable association discovery in population-scale meta-omics studies

PLoS Computational Biology, Journal Year: 2021, Volume and Issue: 17(11), P. e1009442 - e1009442

Published: Nov. 16, 2021

It is challenging to associate features such as human health outcomes, diet, environmental conditions, or other metadata microbial community measurements, due in part their quantitative properties. Microbiome multi-omics are typically noisy, sparse (zero-inflated), high-dimensional, extremely non-normal, and often the form of count compositional measurements. Here we introduce an optimized combination novel established methodology assess multivariable association with complex population-scale observational studies. Our approach, MaAsLin 2 (Microbiome Multivariable Associations Linear Models), uses generalized linear mixed models accommodate a wide variety modern epidemiological studies, including cross-sectional longitudinal designs, well data types (e.g., counts relative abundances) without covariates repeated To construct this method, conducted large-scale evaluation broad range scenarios under which straightforward identification meta-omics associations can be challenging. These simulation studies reveal that 2’s model preserves statistical power presence measures multiple covariates, while accounting for nuances controlling false discovery. We also applied dataset from Integrative Human (HMP2) project which, addition reproducing results, revealed unique, integrated landscape inflammatory bowel diseases (IBD) across time points omics profiles.

Language: Английский

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Analysis of compositions of microbiomes with bias correction

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: July 14, 2020

Abstract Differential abundance (DA) analysis of microbiome data continues to be a challenging problem due the complexity data. In this article we define notion “sampling fraction” and demonstrate major hurdle in performing DA is bias introduced by differences sampling fractions across samples. We introduce methodology called Analysis Compositions Microbiomes with Bias Correction ( ANCOM-BC ), which estimates unknown corrects induced their among The absolute are modeled using linear regression framework. This formulation makes fundamental advancement field because, unlike existing methods, it (a) provides statistically valid test appropriate p-values, (b) confidence intervals for differential each taxon, (c) controls False Discovery Rate (FDR), (d) maintains adequate power, (e) computationally simple implement.

Language: Английский

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Stress and stability: applying the Anna Karenina principle to animal microbiomes

Nature Microbiology, Journal Year: 2017, Volume and Issue: 2(9)

Published: Aug. 23, 2017

Language: Английский

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American Gut: an Open Platform for Citizen Science Microbiome Research

mSystems, Journal Year: 2018, Volume and Issue: 3(3)

Published: May 14, 2018

Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging integrate extent of microbial molecular diversity in stool remains unknown. Using standardized protocols Earth Microbiome Project sample contributions over 10,000 citizen-scientists, together with an open research network, we compare specimens primarily United States, Kingdom, Australia one another environmental samples. Our results show unexpected range beta-diversity microbiomes compared samples; demonstrate utility procedures for removing effects overgrowth during room-temperature shipping revealing phenotype correlations; uncover new molecules kinds communities metabolome; examine emergent associations among microbiome, metabolome, plants that are consumed (rather than relying on reductive categorical variables such as veganism, which little or no explanatory power). We also living resource cross-cohort comparison confirm existing between psychiatric illness reveal change within individual surgery, providing a paradigm education. IMPORTANCE citizen science, self-selected cohort samples through mail at room temperature recaptures many known clinically collected cohorts reveals ones. Of particular interest is integrating n = 1 study population data, showing after events surgery can exceed differences distinct biomes, effect diverse diet, untargeted metabolomics hundreds

Language: Английский

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The Human Gut Microbiome: From Association to Modulation

Cell, Journal Year: 2018, Volume and Issue: 172(6), P. 1198 - 1215

Published: March 1, 2018

Language: Английский

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Recovery of gut microbiota of healthy adults following antibiotic exposure

Nature Microbiology, Journal Year: 2018, Volume and Issue: 3(11), P. 1255 - 1265

Published: Oct. 17, 2018

Language: Английский

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