Advances in Microbiome Diagnostics

The Human Microbiome Project has spurred a large amount of research to understand the complex interactions and impact of microorganisms in health. This research is providing new insights towards the development of diagnostics, as well as prophylactics and therapeutics. The latest frontier of microbiome research is developing diagnostic methods and tests that provide accurate assessment of the taxonomic compositions of microbiomes associated with complex samples. Although this area of research is rapidly expanding, it has not yet resulted in a multitude of clinically validated tests approved by the regulatory agencies. CHI's Advances in Microbiome Diagnostics symposium will bring together researchers, thought-leaders, and laboratory professionals to present and examine the latest research on the microbiome in regards to diagnostic tests. Special attention will be paid to the antimicrobial biomarker discovery, coinfection of viral and bacterial pathogens, and cutting edge technologies used in microbiome research, their benefits, and their limitations. FDA regulation, guidelines, and policies will also be discussed. Join your colleagues to examine a variety of microbiomes found in the human body and significant contributions to the field of microbiome diagnostics.


SC5: Establishing the Value of Diagnostic Tests

*Separate registration required


8:00 am Registration & Morning Coffee


8:25 Chairperson’s Opening Remarks

Willy Valdivia, CEO, Orion Integrated Biosciences, Inc.

8:30 Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies

Rashmi_SinhaRashmi Sinha, Senior Investigator, Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute

Some of the most important attributes of any sampling method are reproducibility, stability, and accuracy. We compared seven fecal sampling methods (no additive, RNAlater, 70% ethanol, EDTA, dry swab, Fecal Immunochemical Test (FIT), and pre/post development fecal occult blood test (FOBT)) using 16S rRNA microbiome profiling in two laboratories. We evaluated nine commonly used microbiome metrics: abundance of 3 phyla, two alpha-diversities, and four beta-diversities. We determined the technical reproducibility, stability at ambient temperature, and accuracy.

9:00 Benchmarking Controls Reveal That Differences in Library Preparation Can Influence Genomic and Functional Predictions in Microbiome Research

Sarah_HighlanderSarah Highlander, Professor, Genomic Medicine, J. Craig Venter Institute

Conflicting interpretations of microbiome work has made it clear that standardized methods are needed for sample collection, storage, nucleic acid isolation, library preparation and sequencing. We used a synthetic community of bacterial DNAs, and a bacterial spike-in calibrator for stool samples, to benchmark PCR and PCR-free library preparation methods for the Illumina sequencing. Significant differences in error profiles, bias and taxonomy were observed between the methods, with PCR-free performing best.

9:30 Pacbio-Based Species-Level Microbiome Analyses

Garth_EhrlichGarth D. Ehrlich, Ph.D., FAAAS, Professor, Microbiology and Immunology, Otolaryngology Head and Neck Surgery, Drexel University College of Medicine

Microbiomics have revolutionized our understanding of microbial ecologies, but have suffered from two problems: lack of species-specificity and over-calling the number of taxa. Using the long read-lengths of the Pacbio and its ability to perform circular iterative sequencing of single DNAs, together with algorithmic improvements has overcome these limitations. As part of our validation process we analyzed a mock microbiome from which we correctly called all 19 eubacterial species present and did not call anything that was not present.

10:00 Panel Discussion: Challenges in Microbiome Sample Preparation, Storage, and Analysis

Moderator: Willy Valdivia, CEO, Orion Integrated Biosciences, Inc. 

Panelists: Rashmi Sinha, Senior Investigator, Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute 

Sarah Highlander, Professor, Genomic Medicine, J. Craig Venter Institute 

Garth D. Ehrlich, Ph.D., FAAAS, Professor, Microbiology and Immunology, Otolaryngology Head and Neck Surgery, Drexel University College of Medicine

Some of the more complicated challenges in studying the microbiome and using it in a clinical, diagnostic capacity include addressing host DNA found in microbiome samples and consistent interpretation of results. This morning’s speakers will discuss sample preparation, storage, and analysis challenges, such as:

  • • Issues regarding quality control and DNA extraction, including contamination by kits
  • • Using spike-in controls as calibrators and using mock communities to validate sequencing methods
  • • Overcoming lack of error correction for single molecule sequencing
  • • Improving specificity of microbiome methods to provide species- and strain-level data
  • • The immunocological profile of individuals and its impact on assessment of microbiomes and their relevance for clinical studies


10:30 Coffee Break


11:00 Quantitative Prediction of Microbiota Dynamics

Georg_GerberGeorg K. Gerber, M.D., Ph.D., MPH, Assistant Professor of Pathology, Harvard Medical School; Co-Director, Center for Clinical and Translation Metagenomics, Director, Computational Unit, Associate Pathologist, Department of Pathology, Brigham and Women’s Hospital

I will present our progress on discovery of networks of commensal bacteria protecting against Clostridium difficile and prediction of stability of configurations of bacteria in an immune-modulating probiotic cocktail. I will also describe the computational algorithms that we have developed that have enabled this work, the Microbial Dynamical Systems INference Engine (MDSINE), which infers dynamical systems models from noisy microbiome sequencing time-series datasets and predicts future behaviors of the microbiota.

11:30 Salivary Microbiome and Diagnostics: Emerging Biomarkers

Jennifer_KerrJennifer Kerr, Ph.D., Assistant Professor, Biology, Oral Microbiology, Notre Dame Maryland University

Our oral cavity hosts an extraordinary microbiome in both healthy and disease states. Paired with other host saliva biomarkers, the oral microbiome presents a novel noninvasive diagnostic tool for monitoring changes in human physiology and a potential shift toward disease. This talk will address novel work toward understanding the role of bacteria in diseases/conditions and carcinogenesis and how it can serve as an oral biomarker for early detection of disease.

12:00 pm Metagenomics as a Novel Strategy to Detect Colonization with Multidrug Resistant Bacteria

David_HaslamDavid Haslam, M.D., Associate Professor, Pediatrics, Cincinnati Children’s Hospital Medical Center

Prevention of multi-drug resistant (MDR) bacterial infections relies on accurate detection of these organisms. We are utilizing fecal metagenomics to identify colonization with MDR organisms. In many cases, the genome of an MDR organism could be assembled from raw metagenomic data. Phylogenetic analysis and comparison with MDR organisms from other patients has the capacity to reveal patient-to-patient transmission networks.

12:30 Sponsored Presentation (Opportunity Available)

1:00 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:30 Session Break


2:00 Chairperson’s Remarks

Keith Batchelder, M.D., CEO & Founder, Genomic Healthcare Strategies

2:05 FEATURED PRESENTATION: Metagenomics for Diagnosing Polymicrobial Infections in the Gut Microbiome

Rita_ColwellRita Colwell, Ph.D., Distinguished Professor, Department of Cell Biology & Molecular Genetics, College of Computer, Mathematical, & Natural Sciences, University of Maryland

In an era of climate change and emerging and re-emerging diseases, genomics tools are proving valuable in understanding, tracking, and diagnosing infectious disease and identifying disease agents. One finding to date is that polymicrobial infections are now frequently being detected, requiring reassessment of Koch’s postulates in this new century, with the application of metagenomics. Prime examples of waterborne infections, including cholera and related diarrhoeal diseases, will be discussed.

2:35 Predicting Chemotherapy-Induced Sepsis with the Pre-Treatment Microbiota

Dan_KnightsDan Knights, Assistant Professor, Computer Science and Engineering, Biotechnology Institute, University of Minnesota

Trillions of bacteria live in our gut, protecting us from infection and aiding our digestion. A bad mixture of bacteria, or dysbiosis, may contribute to obesity, diabetes, Crohn’s disease, infections, and other diseases, yet these microbiomes are so complex that we need advanced computational tools to study them. This talk will present new methods for building highly precise diagnostics using the microbiota, and an application to predicting life-threatening chemotherapy-induced infections.

3:05 Refreshment Break

3:35 Skin Microbiome-Based Radiation Diagnostics

Eric_HuangEric Huang, Ph.D., Professor, Dermatology, University of California, San Diego

We study the reaction of Propionibacterium acnes (P. acnes), a commensal bacterium in the human skin microbiome, to radiation to identify the early surrogate markers for radiation risk. We highlight that uncovering response of skin microbiome to radiation will facilitate the development of pre-symptomatic diagnosis of radiation risk in a battlefield exposure, nuclear accidents, terrorist attacks, or cancer imaging/therapy.

4:05 The Microbiome in Human Reproduction

Jason_FranasiakJason Franasiak, M.D., FACOG, Attending Physician, Reproductive Medicine Associates of New Jersey, Assistant Professor of Obstetrics, Gynecology, and Reproductive Sciences, Rutgers University, Reproductive Endocrinology and Infertility, Robert Wood Johnson Medical School

The human microbiome has been termed the “second human genome” and it appears every bit as complex. The microbiome in human reproduction impacts both the reproductive tract and gametogenesis. Recent data have furthered our understanding of the microbiome, the biofilms it creates, and its impact of health and disease in human reproduction.

4:35 Close of Symposium