Introduction to Human Microbiome Analysis
Human microbiome analysis is the study of microbial communities found in and on the human body. The goal of human microbiome studies is to understand the role of microbes in health and disease.
Traditionally, studying samples from human skin, stool, or blood 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 methods.
Next-Generation Sequencing for Studying the Human Microbiome
The advent of next-generation sequencing (NGS) enabled several high-profile collaborative projects including the Human Microbiome Project and MetaHIT, which have published a wide range of data on the human microbiome using NGS as a foundational tool.
The throughput and cost savings of NGS have fueled metagenomics studies capable of surveying the genomes of entire communities, including those of unculturable organisms.
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
This webinar introduces a novel gene-level bioinformatics approach for identifying microbial species and strains associated with human disease 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 new sequencing methods, including those generating synthetic long reads, 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 WebinarMicrobial 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, while comparing against previous kit versions.
Read Technical Note
Human Microbiome Research Stories
The Time is Now for Microbiome Studies
Whole-genome shotgun sequencing and transcriptomics provide researchers and pharmaceutical companies with data to refine drug discovery and development.
Read Article
Sequencing a Mouthful of Microbes
The MiSeq System is enabling the Saca la Lengua project research team to sequence 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 current and emerging applications. 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, and explore the possibilities that exome sequencing, target enrichment, single-cell profiling, and transcriptome sequencing enable.
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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.
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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's 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.