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Department of Physiology and Pharmacology

Illumina MiSeq benchtop DNA sequencer with monitor and keyboard, used for high-throughput microbial sequencing.Heat map with hierarchical clustering showing differentially abundant microbial species between control and knockout samples; red indicates higher abundance and green lower abundance.Oxford Nanopore GridION sequencing device connected to a computer displaying active sequencing runs for real-time genomic analysis.Horizontal bar chart of LEfSe results highlighting microbial taxa enriched in control versus knockout groups, with LDA scores indicating effect size.Scatter plot of beta diversity showing separation between sample groups, with clustered points and ellipses indicating distinct microbial community composition.

Microbiota/Microbial Community Profiling Services

We are accepting samples for 16S rRNA gene metagenomics services for internal and external users.

Microbiome & Microbial Genomics Core (MMGC)

The Microbiome & Microbial Genomics Core provides integrated end-to-end services for high-resolution characterization of host-associated microbial communities and their functional outputs. The core supports investigators across basic, translational, and clinical domains with state-of-the-art sequencing technologies, rigorous analytics, and scalable workflows.

Core Service Areas

  1. Microbiota Profiling (16S rRNA Gene Sequencing)
    The core offers high-throughput microbiota profiling using Illumina MiSeq next-generation sequencing platforms. This approach enables cost-effective taxonomic characterization across large cohorts, with the capacity to multiplex up to 96 samples per run (~15 Gb output).

Services include:

  • DNA extraction from diverse sample types (feces, saliva, oral swabs, tissues)
  • Library preparation and sequencing
  • Bioinformatics processing and statistical analysis

Deliverables include processed FASTQ files and comprehensive analytical outputs such as:

  • Amplicon Sequence Variant (ASV) tables
  • Alpha and beta diversity metrics
  • Taxonomic summaries
  • Differential abundance and enriched taxa analyses
  1. Microbiome Metagenomic Sequencing (Long-Read Nanopore Technology)
    To enable species/strain- level resolution and functional insight, the core provides whole genomic metagenomic sequencing using Oxford Nanopore long-read platforms. This technology allows:
  • Improved genome assembly and resolution of complex microbial communities
  • Detection of structural variants, mobile genetic elements, and antimicrobial resistance genes
  • Direct sequencing of native DNA without amplification bias

Services include:

  • High-molecular-weight DNA extraction
  • Library preparation for long-read sequencing
  • Real-time sequencing and scalable throughput options
  • Advanced bioinformatics for taxonomic classification.
  • This platform is particularly suited for mechanistic studies of host鈥搈icrobiome interactions and translational applications.
  1. RNA Modification & Epitranscriptomic Profiling (Coming soon)
    The core provides emerging capabilities in RNA modification detection to support studies of microbial and host epitranscriptomics. Using nanopore-based direct RNA sequencing and complementary analytical pipelines, the core enables:
  • Detection and mapping of RNA modifications (e.g., m6A and related marks)
  • Characterization of transcriptional dynamics in microbial communities
  • Integration of RNA modification data with metagenomic and host datasets

These services support cutting-edge investigations into gene regulation, host鈥搈icrobiome signaling, and environmental responsiveness.

Additional Capabilities

  • Whole genome sequencing of cultured bacteria using Illumina Nextera XT library preparation (low input 鈮�10 ng DNA)
  • Cross-species sample processing (rodent, fish, human)
  • End-to-end project support from experimental design through statistical analysis
  • Custom pipelines tailored to hypothesis-driven research

Data Delivery

All projects include secure delivery of raw and processed data in compressed formats, accompanied by detailed reports and visualization outputs suitable for publication and grant reporting.

Access & Pricing

The core serves both internal and external investigators. For pricing, project consultation, and submission guidelines, please contact the Metagenomics Core Manager, Dr. Ramakumar Tummala (Ramakumar.tummala@utoledo.edu).

Learn more

Genetic/Genomic Core, NGS Illumina MiSeq Services

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