Human Microbiome Analysis with NGS
Introduction to Human Microbiome and Metratranscriptome Analysis
Human microbiome analysis is the study of microbial communities found in and on the human body. The goal of human microbiome profiling studies is to understand the role of microbes in health and disease. Next-generation sequencing (NGS) has fueled studies capable of surveying the genomes of entire microbial communities, including those of unculturable organisms.
Previously, studying human microbiome samples relied on time- and labor-intensive microbiology techniques of growing and isolating individual organisms followed by phenotypic or genotypic analysis. Microbial community profiling within a single sample was not possible with these older methods.
Microbial transcriptomics, or metatranscriptomics, provides key insights into the expressed RNAs encoded by a group of organisms in a complex sample. High-quality metatranscriptomics data enables researchers to quantify gene expression changes, predict resistance or susceptibility to specific treatments, understand host-pathogen immune interactions, and track disease progression.
NGS for Studying the Human Microbiome
The advent of next-generation sequencing enabled several high-profile collaborative projects such as the Human Microbiome Project, which has published a wide range of data on the human microbiome using NGS as a foundational tool.
NGS methods allow scientists to perform culture-free identification and classification of complex microbial communities. These methods can also accelerate discovery of novel species in microbiome samples and facilitate detection of virulence and antimicrobial resistance genes.
Experimental NGS methods for analyzing the human microbiome include:
Shotgun metagenomic sequencing
- A DNA sequencing method that enables comprehensive sampling of all genes in all organisms in a given complex microbial sample.
16S rRNA sequencing
- A 16S ribosomal RNA gene sequencing method used to identify and compare bacteria present within a given sample.
Microbial metatranscriptomics
- Analysis of all RNAs encoded by a group of microorganisms within a complex sample.
Topics in Microbiome Analysis
Gene-Level Metagenomics for Microbiome Research
Learn about a gene-level bioinformatics approach for identifying disease-associated microbial species and strains from metagenomic sequencing data sets. Samuel Minot, PhD also demonstrates an interactive microbiome discovery portal.
Access WebinarMicrobiome Sequencing in High-host and
Low-biomass Samples
This webinar discusses emerging NGS methods, with a focus on their relevance for microbial community analysis. Dr. Stefan J. Green addresses practical approaches to high host and low microbial biomass issues.
Access WebinarMetatranscriptomics: Challenges and Opportunities
In this webinar, you'll hear from three leading experts in the field as they share their insights and key considerations on sample collection and processing, rRNA depletion, and bioinformatic analysis.
Watch Webinar
Scientists Discuss NGS-Based Microbiome Studies
The Time is Now for Microbiome Studies
NGS-based whole-genome shotgun sequencing and transcriptomics methods provide researchers and pharmaceutical companies with data to refine drug discovery and development.
Read Article
Sequencing a Mouthful of Microbes
The Saca la Lengua project research team uses Illumina NGS to analyze thousands of samples to identify the variety of bacteria and fungi that live in the human mouth.
Read Article
NGS is Revealing the Mysterious World of Microbes
Researchers at Microba are investigating the genomes of microbes to improve our understanding of human health, disease, and microbial evolution.
Read ArticleUnderstanding your Microbiome with Dr. Rob Knight
Learn how human microbes, the community of tiny single-cell organisms living inside our bodies, have a huge—and largely unexplored—impact on our health.
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Explore the NextSeq 1000 and 2000 Systems
The NextSeq 1000 and 2000 Systems empower sequencing for a broad range of applications, from target enrichment to single-cell profiling, metagenomics, transcriptome sequencing, and more. With over 75 updates, the systems offer dry instrumentation, easier run setup, and fast secondary analysis with DRAGEN software onboard. Experience our simplest workflows yet.
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A Guide to Diet-Microbiome Study Design
Learn how to design microbiome studies that maximize power and chances of success within a given research budget, and better understand how personalized diet-microbiome interactions could be affecting outcomes of your studies.
View Webinar
Microbial Transcriptomics with rRNA Depletion
The Ribo-Zero Plus rRNA Depletion Kit removes rRNA before RNA-Seq, enabling you to focus on high-value portions of the transcriptome. This technical note demonstrates rRNA depletion performance on microbial isolate and community samples.
Read Technical Note
Related Human Microbiome Research
Cancer Microbiome Research
Microbial communities can influence host immune response, affecting cancer progression and treatment efficacy. As NGS-based research continues to explore host–microbiome interactions, there is hope that information about the human microbiome might inform immunotherapeutic strategies.
Learn About Cancer Microbiome Studies
How Microbiome Multi-Omics Can Bolster Human Health
Sequencing technologies are enabling a deeper analysis of the gut microbiome. Researchers can now explore what our microbial inhabitants are doing and how they contribute to, or protect from, disease.
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Additional Resources
Microbial Sequencing for Microbiome Studies
See how Illumina NGS is being used to sequence complex microbial populations.
Metagenomics for Virus Discovery on Skin
Illumina sequencers offer deep coverage to identify novel HPV types correlated with non-melanoma skin cancers.
References
- The Human Microbiome Consortium (2012) A framework for human microbiome research Nature 48: 215–221.
- Qin J, Li Y, Cai Z, Li S, Zhu J et al. (2012) A metagenome-wide association of gut microbiota in type 2 diabetes. Nature 490:55–60.
- Maurice CF, Haiser HJ, Turnbaugh PJ. (2013) Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152:39–50.
- Karlsson FH, Tremaroli V, Nookaew I, Bergstrӧm G, Behre CJ, et al. (2013) Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 498:99–103.
- Penders J, Stobberingh EE, Savelkoul PH, Wolffs PE. (2013) The human microbiome as a reservoir of antimicrobial resistance. Front Microbiol 4:87.