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Microbes and Microbiomes in Health Workshop

This is an add-on workshop for an additional $50 that can be purchased alone or in combination with conference tickets.

Workshop 1: Microbes and Microbiomes in Health (Limited to 100 registrants)

Monday, September 22, 2025 | BRC Room 280

12:30pm – 6:00pm

Join us for a half-day pre-conference workshop sponsored by the Ken Kennedy Institute AI2Health cluster titled “Microbes and Microbiomes in Health”. The workshop will feature both computational and biological perspectives for studying microbes and microbiomes relevant to human health. This workshop will bring together experts in computational biology, microbiology, and microbiome science to discuss cutting-edge approaches for studying microbial communities and their impact on health.

Check-in — Located in the BRC Pre-Function Space

12:30pm – 1:00pm

Kickoff & Opening Remarks — BRC Room 280

1:00pm – 1:10pm

Opening Keynote

1:10pm – 1:50pm

Sarah Wallace, PhD (NASA Johnson Space Center)
- "Spaceflight Microbiology: Beyond the Cultures"
- Abstract: Characterization of the International Space Station (ISS) microbiome has been enabled by culture-based sampling followed by Earth-based analysis. As human exploration pushes beyond low-Earth orbit, microbial-related crew health, planetary protection, and space research requires in situ capabilities. Steps toward reducing Earth-dependence for complex sample analysis began in 2016 with the amplification of DNA within the miniPCR thermal cycler and DNA sequencing with the MinION sequencer onboard the ISS; for both, samples were prepared on Earth. In 2017, these platforms synergistically enabled the in situ identification of unknown bacteria collected and cultured from ISS surfaces, thereby shifting the paradigm that microbial cultures had to be returned to Earth. In the years that followed, a culture-independent, swab-to-sequencer method further advanced spaceflight microbiology, demonstrating that culturing could be excluded while also providing enhanced insight into the bacterial profile of ISS surfaces. This presentation will focus on these efforts toward advancing modern microbiome profiling onboard the ISS, the data collected to date, as well as future efforts in support of Artemis missions to the Moon and Mars.

Break

1:50pm – 2:00pm

Invited Talk

2:00pm – 2:45pm

Sonia Villapol, PhD (Houston Methodist Academic Institute) — 2:00pm – 2:25pm
- "What Can DNA Sequencing and the Gut Microbiome Tell Us About Concussions?"

Prashant Kalvapalle, PhD (Rice University) — 2:25pm – 2:45pm
- "Somatem: A Modular and Open Source Metagenomic Assembly and Analysis Pipeline for Long-Reads"

Break

2:45pm – 3:00pm

Invited Talks

3:00pm – 3:45pm

Michael Nute, PhD (Rice University) — 3:00pm – 3:25pm
- "Autoencoder-Based Exploration of the Human Gut Microbiome"
Santiago Segarra, PhD (Rice University) — 3:25pm – 3:45pm
- "Graph-Based Self-Supervised Learning for Repeat Detection in Metagenomic Assembly"

Break

3:45pm – 4:00pm

Closing Keynote

4:00pm – 4:40pm

Tandy Warnow, PhD (University of Illinois at Urbana-Champaign)
- "New Methods for Abundance Profiling and Species Detection in Microbiome Samples"
- Abstract: Abundance profiling and species detection are two related problems in microbiome analysis. Species detection aims to list the species found in an environmental sample, while abundance profiling aims to estimate the distribution of species (or genera, families, etc.) within the sample. Each of these problems has broad applications and together they provide insight into questions related to ecology, evolution, and human health. In this talk, I will present new methods for each of these problems: TIPP3 and TIPP3-fast (Shen et al., PloS Computational Biology 2025) for abundance profiling and TIPP-SD (ACM-BCB, to appear) for species detection. Each of these methods uses maximum likelihood phylogenetic placement of reads into labeled taxonomies, and considers statistical support in combining information from different reads. Each of these methods achieves higher accuracy for its stated problem than prior leading methods (e.g., TIPP3 achieves superior accuracy for abundance profiling compared to Kraken2, Bracken, MetaPhlAn4, and Metabuli while TIPP-SD achieves superior accuracy for species detection compared to TIPP3, Kraken2, Bracken, and Metapresence. TIPP3 and TIPP-SD are freely available at https://github.com/c5shen/TIPP3. This is joint work with Chengze Shen, Eleanor Wedell, and Mihai Pop.

Reception

4:40pm – 6:00pm

Organized By: Todd Treangen and AI2Health Research Cluster with the Ken Kennedy Institute