Profiling Community-Wide Gene Expression

The microbial flora within and on the surface of the human body, especially the gut, are well-established to have an important relationship to human health status1. Dysbiosis in the gut microflora can contribute to the development of pathological conditions such as chronic inflammatory bowel disease, diet-induced obesity, Type 1 and 2 diabetes, colorectal cancer, and peptic ulcer disease2-7. Furthermore, these imbalances are implicated in liver disease progression, AIDS development in HIV-infected patients, autism spectrum disorders, depression, multiple sclerosis, and rheumatic diseases7-12.

While the transcriptome is a complete collection of RNAs encoded by an organism’s genome, the metatranscriptome includes all RNAs encoded by a group of organisms. Metatranscriptomics analyses are relevant to biomarker and drug discovery studies in numerous ways. Some major applications include:

  • Determine drug treatment responses with measurable changes in microflora composition and gene expression
  • Identify microflora RNA signatures which can be associated with specific-disease subtypes and enable patient stratification, including identification of non-responders
  • Investigations of induction or repression of specific metabolic pathways in response to diet changes or disease development
  • General mechanism of action studies
  • Improve diagnostics for infectious disease status and susceptibility
  • Study interactions between symbiotic bacteria and host

Sample Processing for Metatranscriptomic Analysis at ORB

Advances in sample preparation and rRNA depletion, sequencing, and bioinformatics have enabled effective and efficient analysis of complex microorganism communities colonizing in vivo samples13. Well-validated protocols for extraction of RNA from feces and other common biospecimens have been developed by ORB scientists. Examples of accepted types are given below.

  • Stool / Feces
  • Tissue biopsies
  • Cells
  • Saliva
  • Bronchial lavage
  • Sputum
  • Buccal swabs
  • Oral biofilms
  • Soil
  • Plants
  • Food items

The Illumina ScriptSeq Epidemiology kit is used to prepare sequencing libraries depleted of RNA arising from both prokaryotic and eukaryotic sources. This methodology allows sequencing of cDNA derived from not only microbial symbionts and parasites but also the host mammalian cells. High coverage sequencing is achieved using either the NextSeq 500, HiSeq 2500, or HiSeq 4000 instruments from Illumina.

Bioinformatic Services for Metatranscriptomic Data Sets


ORB offers comprehensive processing and analysis of metatranscriptomic sequencing data using up to three independent analytic approaches including taxonomic classification using Kraken software, de novo transcriptome assembly and counting, and alignment and counting using a customized database of expected microbial genomes. Analysis can remain focused or cover all three domains of living organisms (archea, prokaryote, and eukaryotes) as well as viruses. Analysis reports include interactive taxonomic classification tables and graphs providing the relative abundance of detectable species, as well as gene-level expression analysis and visualization. Visit the metatranscriptomics bioinformatics page for more information.

Sample Submission Instructions

The preparation of stool samples is critical to obtaining long RNA of sufficient yield and quality for metatranscriptomics analysis14. Fecal matter generally contains high level of nucleases and endogenous substances which can serve as inhibitors to downstream processing (e.g. complex polysaccharides, immunoglobulins, glycogens, lipids, and metabolites15-17). ORB recommends flash-freezing fecal samples to ensure the best results from RNA sequencing applications. A minimum submission of 0.25 milligrams of feces per sample is needed. Please complete a sample submission checklist prior to shipping samples.

When shipping, enclose a completed sample submission checklist in a separate dry compartment with the sample shipment. Also send a digital file version of the sample submission checklist to and provide notification of the sample shipment to by calling 754-600-5128 on the day samples are shipped.

Contact Us to discuss processing other sample types using ORB’s metatranscriptomic analysis services!

Related Applications and Services


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  2. Jostins, L., Ripke, S., Weersma, R. K., Duerr, R. H., McGovern, D. P., Hui, K. Y., & Essers, J. (2012). International IBD Genetics Consortium (IIBDGC)(2012). Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature491(7422), 119-124.
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  9. Cao, X., Lin, P., Jiang, P., & Li, C. (2013). Characteristics of the gastrointestinal microbiome in children with autism spectrum disorder: a systematic review. Shanghai Arch Psychiatry25(6), 342-53.
  10. Lyte, M. (2013). Microbial endocrinology in the microbiome-gut-brain axis: how bacterial production and utilization of neurochemicals influence behavior. PLoS Pathog9(11), e1003726.
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