About

Michael Louis Patnode grew up in the Seattle area and completed his undergraduate degree at the University of Washington, majoring in Biochemistry. He pursued graduate training at the University of California, San Francisco in the lab of Dr. Steven Rosen, focusing on immunology and glycobiology. Following his Ph.D., he conducted postdoctoral research with Dr. Jeffrey Gordon at Washington University in St. Louis, where he explored how host diet shapes gut microbial communities. In November 2020, Michael Patnode joined the faculty in the METX Department. His research centers on understanding the interactions between diet, the gut immune system, and the microbiome, aiming to elucidate how the food we eat influences gut immune function and microbial ecology.

Research topics

• Microbiology
• Biology
• Biochemistry
• Immunology
• Cell biology
• Ecology
• Genetics

Selected publications

• Bayesian Covariate-Varying Interaction Analysis for Multivariate Count Data: Application to Microbiome Studies

  arXiv (Cornell University) · 2026-03-12

  articleOpen access

  Understanding covariate-varying interdependencies among features is of great interest in various applications. Motivated by microbiome studies where microbial abundances and interactions vary with environmental factors, we develop a Bayesian covariate-varying factor model. This model flexibly estimates heteroscedasticity in the covariance matrix as a function of covariates. Specifically, our approach employs covariance regression through linear regression on a lower-dimensional factor loading matrix. This formulation, combined with joint sparsity induced by the Dirichlet--Horseshoe prior for the factor loadings, provides robust estimation of covariate-varying covariance in high-dimensional settings. The model simultaneously incorporates a regression structure for the mean abundance and jointly addresses the covariate-varying mean and covariance structure. Furthermore, the model tackles key statistical challenges such as discreteness, over-dispersion, compositionality, and high dimensionality, common in microbiome data analysis, using a flexible nonparametric Bayesian framework. We thoroughly investigate the properties of the model and conduct extensive simulation studies to examine its performance. Real microbiome data examples are provided for illustration.

  PublisherOA PDF

• The Yeh pilus adhesin is equipped with an α-helical flap motif, which contributes to pectin adherence

  Science Advances · 2026-01-07

  articleOpen access

  The Yeh chaperone-usher pathway (CUP) pilus adhesin is encoded in one-half of all Escherichia coli . Yet little is known about its structure and function in E. coli persistence and pathogenesis. Structural investigations reveal that the adhesin receptor binding domains (RBDs) of YehD and its relative YhlD both share a canonical β-rich core and an α-helical flap motif that is hinged at the distal end of the core. This flap was observed in both open and closed conformations using molecular dynamics simulations. The closed conformation is dependent on a hydrophobic patch of amino acids on the distal end of the flap. Functionally, YehD RBD is able to bind pectin, a polysaccharide ubiquitous in plant material. Mutations that interrupt the closed conformation increase the affinity of the protein to pectin, suggesting that the flap contributes mechanistically to pectin binding. Furthermore, in vivo, the pilus contributes to gastrointestinal (GI) tract colonization in the absence of the type 1 pilus. Hence, we report the ability of YehD to bind pectin representing a possible colonization mechanism of the GI tract via a structurally distinct CUP adhesin.

  PublisherDOI

• Bayesian Covariate-Varying Interaction Analysis for Multivariate Count Data: Application to Microbiome Studies

  arXiv (Cornell University) · 2026-03-12

  preprintOpen access

  Understanding covariate-varying interdependencies among features is of great interest in various applications. Motivated by microbiome studies where microbial abundances and interactions vary with environmental factors, we develop a Bayesian covariate-varying factor model. This model flexibly estimates heteroscedasticity in the covariance matrix as a function of covariates. Specifically, our approach employs covariance regression through linear regression on a lower-dimensional factor loading matrix. This formulation, combined with joint sparsity induced by the Dirichlet--Horseshoe prior for the factor loadings, provides robust estimation of covariate-varying covariance in high-dimensional settings. The model simultaneously incorporates a regression structure for the mean abundance and jointly addresses the covariate-varying mean and covariance structure. Furthermore, the model tackles key statistical challenges such as discreteness, over-dispersion, compositionality, and high dimensionality, common in microbiome data analysis, using a flexible nonparametric Bayesian framework. We thoroughly investigate the properties of the model and conduct extensive simulation studies to examine its performance. Real microbiome data examples are provided for illustration.

  PublisherDOI

• Tracking intestinal translocation and tissue deposition of orally ingested polymeric compounds 4809

  The Journal of Immunology · 2025-11-01

  article1st authorCorresponding

  Abstract Description The gut epithelial barrier is exposed to a diverse collection of macromolecular structures derived from commensal gut bacteria and dietary inputs. Movement of material from the gut lumen into the tissues can occur via M-cell mediated transcytosis and dendritic cell uptake, but whether these pathways contribute to translocation of dietary glycan substrates remains unclear. We sought to test whether dietary plant polysaccharides can cross the epithelium under homeostatic conditions, and determine the immunological consequences of their accumulation in the lamina propria. We began by generating 40 distinct dietary polysaccharide-biotin conjugates which we orally administered to mice to assess translocation and tissue deposition. Surprisingly, we found that control preparations consisting entirely of polymeric biotin were detected in liver lysates 17 hours after gavage. Liver tissue sections revealed that polymeric biotin was not localized within Kupffer cells, and instead appeared in discrete collections of hepatocytes surrounding endothelial cells. Polymeric biotin did not induce IL1b or IL10 production in macrophages in vitro, and thus may be a viable vehicle for shuttling orally ingested polysaccharide substrates across the gut epithelium to study their immunostimulatory properties. Funding Sources NIH GM150732 Topic Categories Mucosal and Regional Immunology (MUC)

  PublisherDOI

• Microbe-induced antibody responses against dietary plant glycans 3886

  The Journal of Immunology · 2025-11-01

  articleOpen access1st authorCorresponding

  Abstract Description Protein and glycan antigens on gut microbial surfaces stimulate the production of circulating and secreted antibodies in mammals. Despite the high abundance of plant glycans (derived from dietary fiber) in the intestine, it remains unclear whether these foreign structures also serve as B-cell antigens. We screened for antibodies that bind diverse dietary fibers using a panel of artificial food particles consisting of microscopic magnetic beads, each simultaneously tagged with a fluorescent barcode and coated with a different dietary glycan preparation. We observed circulating fiber-specific antibodies that were significantly reduced when mice were deprived of fiber for multiple generations. Furthermore, fiber supplementation added to a normal chow diet induced glycan specific antibodies that were independent of T-cells. Germ-free and monocolonized mice failed to exhibit fiber-induced antibody responses, demonstrating that microbial stimulation is required. However, transient antibiotic treatment had no effect on antibody induction during fiber supplementation, implicating microbial sensitization prior to fiber feeding. We stained mouse gut microbes with a library of glycan-specific monoclonal antibodies and identified bacteria whose surfaces mimic commonly consumed dietary plant glycans. Our results raise the possibility that contact with gut microbes whose surfaces resemble dietary plants sensitizes the host to subsequent dietary exposures. Funding Sources NIH GM150732 Topic Categories Mucosal and Regional Immunology (MUC)

  PublisherOA PDFDOI

• Bacterial interactions on nutrient-rich surfaces in the gut lumen

  Infection and Immunity · 2024 · 3 citations

  Senior authorCorresponding
  • Biology
  • Microbiology
  • Cell biology

  The intestinal lumen is a turbulent, semi-fluid landscape where microbial cells and nutrient-rich particles are distributed with high heterogeneity. Major questions regarding the basic physical structure of this dynamic microbial ecosystem remain unanswered. Most gut microbes are non-motile, and it is unclear how they achieve optimum localization relative to concentrated aggregations of dietary glycans that serve as their primary source of energy. In addition, a random spatial arrangement of cells in this environment is predicted to limit sustained interactions that drive co-evolution of microbial genomes. The ecological consequences of random versus organized microbial localization have the potential to control both the metabolic outputs of the microbiota and the propensity for enteric pathogens to participate in proximity-dependent microbial interactions. Here, we review evidence suggesting that several bacterial species adopt organized spatial arrangements in the gut via adhesion. We highlight examples where localization could contribute to antagonism or metabolic interdependency in nutrient degradation, and we discuss imaging- and sequencing-based technologies that have been used to assess the spatial positions of cells within complex microbial communities.

  PublisherOA PDFDOI

• Circulating Antibodies Specific for Dietary Fiber Glycans

  The Journal of Immunology · 2023

  1st authorCorresponding
  • Biology
  • Microbiology
  • Biochemistry

  Abstract The mammalian gut lumen contains an extremely diverse collection of microbial species and dietary constituents. Protein and carbohydrate antigens on commensal bacterial surfaces stimulate the production of specific antibodies, which can be secreted and bind their epitopes in the lumen. Despite the high abundance of plant polysaccharides (dietary fiber) in the intestine, it remains unclear whether these foreign carbohydrates stimulate the production of secreted anti-fiber antibodies. Here, we characterize antibody specificity in mice using a panel of artificial food particles composed of microscopic magnetic beads, each simultaneously tagged with a fluorescent barcode and coated with one of 64 different dietary or host glycan preparations. Using this approach, we detected secreted antibodies in the cecum and circulating antibodies in serum that selectively bind subsets of dietary glycans. Alteration of the host diet to include supplemental dietary fiber led to a significant increase in anti-fiber antibodies in serum. In contrast, cecal fiber-specific antibody reactivity was not increased after fiber feeding. Analysis of the gut microbiota revealed that relative abundances of Akkermansia muciniphila were significantly higher in mice fed supplemental fiber relative to mice fed a control diet. This work raises the possibility that taxa such as A. muciniphila are involved in the production of antibodies specific for dietary components. Supported by a grant from NIH (K01 DK124445)

  PublisherOA PDFDOI

• Strain-level functional variation in the human gut microbiota based on bacterial binding to artificial food particles

  Cell Host & Microbe · 2021 · 53 citations

  1st authorCorresponding
  • Biology
  • Microbiology
  • Biochemistry
  PublisherOA PDFDOI

• Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans

  Cell · 2019-09-01 · 335 citations

  articleOpen access1st author
  PublisherOA PDFDOI

• Physiological mechanisms of sustained fumagillin-induced weight loss

  JCI Insight · 2018-03-07 · 14 citations

  articleOpen access

  Current obesity interventions suffer from lack of durable effects and undesirable complications. Fumagillin, an inhibitor of methionine aminopeptidase-2, causes weight loss by reducing food intake, but with effects on weight that are superior to pair-feeding. Here, we show that feeding of rats on a high-fat diet supplemented with fumagillin (HF/FG) suppresses the aggressive feeding observed in pair-fed controls (HF/PF) and alters expression of circadian genes relative to the HF/PF group. Multiple indices of reduced energy expenditure are observed in HF/FG but not HF/PF rats. HF/FG rats also exhibit changes in gut hormones linked to food intake, increased energy harvest by gut microbiota, and caloric spilling in the urine. Studies in gnotobiotic mice reveal that effects of fumagillin on energy expenditure but not feeding behavior may be mediated by the gut microbiota. In sum, fumagillin engages weight loss-inducing behavioral and physiologic circuits distinct from those activated by simple caloric restriction.

  PublisherOA PDFDOI

Recent grants

• Mechanisms for Selective Modulation of Beneficial Human Gut Microbes by Specific Dietary Plant Polysaccharides

  NIH · $124k · 2016–2018

Frequent coauthors

• Steven D. Rosen

  University of California, San Francisco

  12 shared

• Matthew F. Krummel

  University of California, San Francisco

  9 shared

• Richard M. Locksley

  University of California, San Francisco

  9 shared

• Jennifer K. Bando

  Washington University in St. Louis

  9 shared

• Bernard Henrissat

  Centre National de la Recherche Scientifique

  6 shared

• Nicolas Terrapon

  Architecture et Fonction des Macromolécules Biologiques

  4 shared

• Steven Thomas

  University of Pennsylvania

  3 shared

• Liping Wang

  University of Utah

  3 shared

Labs

• Patnode LabPI

Education

• Ph.D., Biomedical Sciences

  University of California, San Francisco

  2014

• BS, Biochemistry

  University of Washington

  2006