Shed Light on the Microbiome

The composition of microbial communities can provide critical information about their local environment, whether that environment is the human gut1, an airplane cabin2, or a freshwater lake.3 As abundance of specific species rise and fall, they can signal disease and/or promote pathogenesis.

HudsonAlpha Discovery enables a broad range of microbiome studies with our metagenomic sequencing services, including whole genome shotgun metagenomic sequencing4 and metatranscriptomics.3


Explore the microbiome with our metagenomic sequencing services

  • Flexible and customizable end-to-end services
  • Extraction of nucleic acid from environmental and clinical samples
  • 16S rRNA sequencing
  • Metatranscriptomic sequencing
  • Whole genome shotgun metagenomics


  • Microbiome studies
  • Disease research
  • Environmental metagenomics
  • All research phases and activities
    •  Basic discovery
    •  Translational and pre-clinical
    •  Clinical

Whether you need end-to-end support or a subset of what we can provide, we’ll help you customize a service project to best meet your study objectives.

Highlights of Our Metagenomic Sequencing Services

Here are a few examples of what we offer:

Nucleic Acid Extraction and Library Preparation

  • Optimized extraction protocols for nearly any sample type
  • Optimized protocols for working with ultra-low amounts of nucleic acid

Bioinformatics Analysis and Data Storage

  • Tier 1: Raw BCL and FASTQ file output
  • Tier 2: Standard application-specific and quality report outputs (BCL, FASTQ, aligned BAM files and sequencing QC reports
  • Tier 3: Standard output plus variant calling (VCF, g-VCF) and genomic interpretation reports
  • Additional custom reporting options including Ingenuity Variant Analysis (Qiagen) consolidated variant reports as well as options for genomic variant annotation
  • Flexible data delivery and storage options
  • 90 days storage included with service pricing
  • Long term storage available

Microbiome sequencing

The HudsonAlpha Discovery Difference

Flexible and creative problem solving with expert scientific guidance


Optimized protocols and automated workflows that reduce technical bias


Stringent quality control parameters—we consistently exceed manufacturer specifications—for reproducible, accurate results


Massive scale with 10 Illumina NovaSeq 6000 sequencers as well as NextSeqs, MiSeqs, and iSeqs


A decade of proven experience spanning thousands of projects and hundreds of publications


Leverage the power of the HudsonAlpha Discovery division:


Featured Paper

The Microbiome of Built Environments

The Airplane Cabin Microbiome

Microb Ecol. 2019; 77(1): 87–95. PMCID: PMC6318343.

In this study, completed when the HudsonAlpha Discovery lab was still the HudsonAlpha Institute Genomic Services Lab, our metagenomic sequencing services supported a study of microbial communities in different areas of an airplane cabin, including the air and touch surfaces, and a comparison of these same sampling areas on several flights.

Their findings: The authors found significant airplane-to-airplane variability and different signatures for air versus touch surfaces with the majority of microbes being human commensals or non-pathogenic.

The significance of this work: “Despite the uniqueness of the airplane cabin as a built environment, our findings are surprisingly consistent with other recent studies of the microbiome of built environments. This consistency is reassuring in light of frequent sensationalistic media stories about dangerous germs found on airplanes. For this reason, there is no more risk from 4 to 5 hours spent in an airplane cabin than 4–5 hours spent in an office, all other exposures being the same. Our microbiome characterization also provides a baseline for non-crisis level airplane microbiome conditions.”2

Recent Publications

  1. Wallen ZD, et al. Characterizing dysbiosis of gut microbiome in PD: Evidence for overabundance of opportunistic pathogens. bioRxiv 2020.01.13.905166; doi:
  2. Weiss H, et al. The Airplane Cabin Microbiome. Microb Ecol. 2019; 77(1): 87–95. PMCID: PMC6318343.
  3. Steffen MM, et al. Ecophysiological Examination of the Lake Erie Microcystis Bloom in 2014: Linkages between Biology and the Water Supply Shutdown of Toledo, OH. Environ Sci Technol. 2017 Jun 20;51(12):6745-6755. PMID: 28535339.
  4. Zeng Q, et al. Impacts of florfenicol on the microbiota landscape and resistome as revealed by metagenomic analysis. Microbiome. 2019; 7: 155. PMCID: PMC6902485.
  5. Nowinski B, et al. Microdiversity and temporal dynamics of marine bacterial dimethylsulfoniopropionate genes. Environ Microbiol. 2019 May;21(5):1687-1701. PMID: 30761723.

To propel your projects with The Power of Discovery.™

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