About

Mark Mandel, Ph.D., is a Professor of Medical Microbiology & Immunology at the University of Wisconsin-Madison. His laboratory is located in the Microbial Sciences Building at 1550 Linden Drive. Dr. Mandel's research focuses on microbial sciences and immunology, contributing to the understanding of microbial and immune system interactions. He is actively involved in mentoring students and postdoctoral researchers, fostering advancements in microbiology and immunology through his leadership and scientific expertise.

Research topics

• Biology
• Genetics
• Ecology
• Microbiology
• Evolutionary biology
• Bioinformatics
• Computational biology

Selected publications

• <i>Euprymna berryi</i> as a comparative model host for <i>Vibrio fischeri</i> light organ symbiosis

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-13

  preprintOpen accessSenior authorCorresponding

  ABSTRACT Functional studies of host-microbe interactions benefit from natural model systems that enable exploration of molecular mechanisms at the host-microbe interface. Bioluminescent Vibrio fischeri colonize the light organ of the Hawaiian bobtail squid, Euprymna scolopes , and this binary model has enabled advances in understanding host-microbe communication, colonization specificity, in vivo biofilms, intraspecific competition, and quorum sensing. The hummingbird bobtail squid, Euprymna berryi, can be generationally bred and maintained in lab settings and has had multiple genes deleted by CRISPR approaches. The prospect of expanding the utility of the light organ model system by producing multigenerational host lines led us to determine the extent to which the E. berryi light organ symbiosis parallels known processes in E. scolopes . However, the nature of the E. berryi light organ, including its microbial constituency and specificity for microbial partners, have not been examined. In this report, we isolate bacteria from E. berryi animals and tank water. Assays of bacterial behaviors required in the host, as well as host responses to bacterial colonization, illustrate largely parallel phenotypes in E. berryi and E. scolopes hatchlings. This study reveals E. berryi to be a valuable comparative model to complement studies in E. scolopes . IMPORTANCE Microbiome studies have been substantially advanced by model systems that enable functional interrogation of the roles of the partners and the molecular communication between those partners. The Euprymna scolopes-Vibrio fischeri system has contributed foundational knowledge, revealing key roles for bacterial quorum sensing broadly and in animal hosts, for bacteria in stimulating animal development, for bacterial motility in accessing host sites, and for in vivo biofilm formation in development and specificity of an animal’s microbiome. Euprymna berryi is a second bobtail squid host, and one that has recently been shown to be robust to laboratory husbandry and amenable to gene knockout. This study identifies E. berryi as a strong symbiosis model host due to features that are conserved with those of E. scolopes , which will enable extension of functional studies in bobtail squid symbioses.

  PublisherOA PDFDOI

• Sedative choice alters <i>Klebsiella pneumoniae</i> lung pathogenesis and dissemination

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-27

  preprintOpen access

  ABSTRACT Klebsiella pneumoniae make up 85% of carbapenem-resistant Enterobacteriaceae (CRE), bacteria that have become an urgent threat to public health. K. pneumoniae is largely transmitted in healthcare settings, where inpatients and outpatients are often anesthetized with the widely-used anesthetic induction agent propofol. Recent evidence obtained from rodent infection models indicates that propofol exposure can dramatically increase host susceptibility to microbial infections. Given that intensive care patients who are at a greater risk for K. pneumoniae lung infections are often given propofol during their hospitalization, we investigated the outcome of K. pneumoniae infections in mice briefly sedated with either propofol or ketamine/xylazine as control. Propofol-sedated mice experienced more rapid dissemination from the lungs to secondary sites of infection and their lungs exhibited more severe pathology. Based on these observations, we investigated bacterial factors involved in infection and dissemination in mice with propofol or ketamine/xylazine sedation using a high throughput insertion sequencing (INSeq) approach. We identified numerous novel potential virulence factors together with previously identified gene products, confirming the validity of our screen. We further characterized a mutant lacking the phospholipid retrograde trafficking chaperone MlaC and found that the degree of mutant attenuation was dependent upon sedation method. These results highlight the importance of sedative choice when studying hospital-acquired microbial infections and suggest that sedation can influence outcome of K. pneumoniae infection and dissemination in animal models. IMPORTANCE Host sedation by either propofol or ketamine exposure differentially impacted the severity of K. pneumoniae lung infection following intranasal inoculation of mice. While propofol-sedated mice exhibited increased lung pathology, some bacterial mutants, such as those lacking the MlaC gene product associated with the maintenance of inner and outer membrane lipid asymmetry, exhibited more severe attenuation following propofol sedation versus ketamine/xylazine. Given the dominating use of propofol in health care settings for the induction and maintenance of anesthesia, procedural sedation, and sedation for intensive care patients, this work provides important perspective as to how the choice of an anesthetic agent may impact the outcome of healthcare-associated infections.

  PublisherOA PDFDOI

• <i>Euprymna berryi</i> as a comparative model host for <i>Vibrio fischeri</i> light organ symbiosis

  Applied and Environmental Microbiology · 2025-07-10 · 4 citations

  articleOpen accessSenior author

  ABSTRACT Functional studies of host-microbe interactions benefit from natural model systems that enable the exploration of molecular mechanisms at the host-microbe interface. Bioluminescent Vibrio fischeri colonize the light organ of the Hawaiian bobtail squid, Euprymna scolopes , and this binary model has enabled advances in understanding host-microbe communication, colonization specificity, in vivo biofilms, intraspecific competition, and quorum sensing. The hummingbird bobtail squid, Euprymna berryi, can be generationally bred and maintained in lab settings and has had multiple genes deleted by CRISPR approaches. The prospect of expanding the utility of the light organ model system by producing multigenerational host lines led us to determine the extent to which the E. berryi light organ symbiosis parallels known processes in E. scolopes . However, the nature of the E. berryi light organ, including its microbial constituency and specificity for microbial partners, has not been examined. In this report, we isolated bacteria from E. berryi animals and tank water. Assays of bacterial behaviors required in the host, as well as host responses to bacterial colonization, illustrate largely parallel phenotypes in E. berryi and E. scolopes hatchlings. This study reveals E. berryi to be a valuable comparative model to complement studies in E. scolopes . IMPORTANCE Microbiome studies have been substantially advanced by model systems that enable functional interrogation of the roles of the partners and the molecular communication between those partners. The Euprymna scolopes-Vibrio fischeri system has contributed foundational knowledge, revealing key roles for bacterial quorum sensing broadly and in animal hosts, for bacteria in stimulating animal development, for bacterial motility in accessing host sites, and for in vivo biofilm formation in development and specificity of an animal’s microbiome. Euprymna berryi is a second bobtail squid host, and one that has recently been shown to be robust to laboratory husbandry and amenable to gene knockout. This study identifies E. berryi as a strong symbiosis model host due to features that are conserved with those of E. scolopes , which will enable the extension of functional studies in bobtail squid symbioses.

  PublisherDOI

• Embracing the systems complexity of microbial ecology and evolution: call for papers

  mSystems · 2025-02-20 · 1 citations

  paratextOpen access

  International audience

  PublisherDOI

• RtmR is a membrane-embedded RRM-family RNA-binding protein that regulates biofilm formation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-11

  preprintOpen accessSenior authorCorresponding

  ABSTRACT The animal symbiont Vibrio fischeri has served as a model organism for molecular processes underlying bacterial group behaviors, including quorum sensing and biofilm development. Here, using a genetic approach to identify negative regulators of biofilm formation in V. fischeri , we identified a membrane-bound RNA-binding protein, RtmR (VF_2432), that acts as an inhibitor of the symbiosis polysaccharide (SYP) biofilm. Membrane localization of the protein seems to be required for protein stability, as truncation of the transmembrane helices led to an inability to detect the protein. The conserved RNP1 and RNP2 motifs in RtmR’s cytoplasmic RNA recognition motif (RRM) domain are required for function, and we demonstrate binding to RNA substrates. Identification of RtmR RNA ligands was conducted with a CLIP-seq approach that revealed a large interactome. One transcript identified was that of the biofilm regulatory histidine kinase RscS. We found that RtmR biofilm inhibition depends on RscS activity and that RtmR negatively regulates levels of RscS. Overall, this work characterizes a novel type of bacterial RNA-binding protein. IMPORTANCE Bacterial RNA-binding proteins (RBPs) perform key functions to regulate stress responses and development. Bacterial RBPs including the RNA chaperones Hfq and ProQ, the global regulator CsrA, and the cold shock proteins (Csps) have been extensively studied, although additional classes of RBPs have been predicted by bioinformatic methods including those carrying an RRM domain. This work expands on recent studies of RRM domain proteins in bacteria to characterize a membrane-bound RRM protein that regulates bacterial biofilm development. Given our rapidly-expanding knowledge regarding the role for RNA-binding proteins in bacterial molecular biology, this work contributes a new class of membrane-bound regulators with homologs in human pathogens and marine symbionts.

  PublisherOA PDFDOI

• Special Collection on the 28th Annual Midwest Microbial Pathogenesis Conference

  Infection and Immunity · 2024-03-17

  editorialOpen accessSenior author

  The Midwest Microbial Pathogenesis Conference (MMPC) is a longstanding annual meeting that brings together scientists from across the Midwest and across career stages to discuss the latest advances in infectious diseases and host-microbe interactions.

  PublisherOA PDFDOI

• Mobile-CRISPRi as a powerful tool for modulating <i>Vibrio</i> gene expression

  Applied and Environmental Microbiology · 2024-05-22 · 10 citations

  articleOpen access

  ABSTRACT CRISPRi (Clustered Regularly Interspaced Palindromic Repeats interference) is a gene knockdown method that uses a deactivated Cas9 protein (dCas9) that binds a specific gene target locus dictated by an encoded guide RNA (sgRNA) to block transcription. Mobile-CRISPRi is a suite of modular vectors that enable CRISPRi knockdowns in diverse bacteria by integrating IPTG-inducible dcas9 and sgRNA genes into the genome using Tn 7 transposition. Here, we show that the Mobile-CRISPRi system functions robustly and specifically in multiple Vibrio species: Vibrio cholerae , Vibrio fischeri , Vibrio vulnificus , Vibrio parahaemolyticus , and Vibrio campbellii . We demonstrate efficacy by targeting both essential and non-essential genes that function to produce defined, measurable phenotypes: bioluminescence, quorum sensing, cell division, and growth arrest. We anticipate that Mobile-CRISPRi will be used in Vibrio species to systematically probe gene function and essentiality in various behaviors and native environments. IMPORTANCE The genetic manipulation of bacterial genomes is an invaluable tool in experimental microbiology. The development of CRISPRi (Clustered Regularly Interspaced Palindromic Repeats interference) tools has revolutionized genetics in many organisms, including bacteria. Here, we optimized the use of Mobile-CRISPRi in five Vibrio species, each of which has significant impacts on marine environments and organisms that include squid, shrimp, shellfish, finfish, corals, and multiple of which pose direct threats to human health. The Mobile-CRISPRi technology is easily adaptable, moveable from strain to strain, and enables researchers to selectively turn off gene expression. Our experiments demonstrate Mobile-CRISPRi is effective and robust at repressing gene expression of both essential and non-essential genes in Vibrio species.

  PublisherOA PDFDOI

• Generation of Barcode‐Tagged <i>Vibrio fischeri</i> Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions

  Current Protocols · 2024-10-01 · 3 citations

  articleOpen accessSenior authorCorresponding

  Vibrio fischeri is a model mutualist for studying molecular processes affecting microbial colonization of animal hosts. We present a detailed protocol for a barcode sequencing (BarSeq) approach that combines targeted gene deletion with short-read sequencing technology to enable studies of mixed bacterial populations. This protocol includes wet lab steps to plan and produce the deletions, approaches to scale up mutant generation, protocols to prepare and conduct the strain competition, library preparation for sequencing on an Illumina iSeq 100 instrument, and data analysis with the barseq python package. Aspects of this protocol could be readily adapted for tagging wild-type V. fischeri strains with a neutral barcode for examination of population dynamics or BarSeq analyses in other species. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Production of the erm-bar DNA Basic Protocol 2: Generation of a targeted and barcoded deletion strain of V. fischeri Alternate Protocol: Parallel generation of multiple barcode-tagged V. fischeri deletion strains Basic Protocol 3: Setting up mixed populations of barcode-tagged strains Basic Protocol 4: Performing a competitive growth assay Basic Protocol 5: Amplicon library preparation and equimolar pooling Basic Protocol 6: Sequencing on Illumina iSeq 100 Basic Protocol 7: BarSeq data analysis.

  PublisherOA PDFDOI

• Microbial Metabolomics’ Latest SICRIT: Soft Ionization by Chemical Reaction In-Transfer Mass Spectrometry

  Journal of the American Society for Mass Spectrometry · 2024-09-30 · 4 citations

  articleOpen access

  Microbial metabolomics studies are a common approach for identifying microbial strains that have a capacity to produce new chemistries both in vitro and in situ. A limitation to applying microbial metabolomics to the discovery of new chemical entities is the rediscovery of known compounds, or “known unknowns.” One factor contributing to this rediscovery is that the majority of laboratories use one ionization source─electrospray ionization (ESI)─to conduct metabolomics studies. Although ESI is an efficient, widely adopted ionization method, its widespread use may contribute to the reidentification of known metabolites. Here, we present the use of a dielectric barrier discharge ionization (DBDI) for microbial metabolomics applications through the use of soft ionization chemical reaction in-transfer (SICRIT). Additionally, we compared SICRIT to ESI using two different Vibrio species: Vibrio fischeri, a symbiotic marine bacterium, and Vibrio cholerae, a pathogenic bacterium. Overall, we found that the SICRIT source ionizes a different set of metabolites than ESI, and it has the ability to ionize lipids more efficiently than ESI in the positive mode. This work highlights the value of using more than one ionization source for the detection of metabolites.

  PublisherDOI

• Bacterial growth dynamics in a rhythmic symbiosis

  Molecular Biology of the Cell · 2024-04-10 · 6 citations

  articleOpen access

  The symbiotic relationship between the bioluminescent bacterium Vibrio fischeri and the bobtail squid Euprymna scolopes serves as a valuable system to investigate bacterial growth and peptidoglycan (PG) synthesis within animal tissues. To better understand the growth dynamics of V. fischeri in the crypts of the light-emitting organ of its juvenile host, we showed that, after the daily dawn-triggered expulsion of most of the population, the remaining symbionts rapidly proliferate for ∼6 h. At that point the population enters a period of extremely slow growth that continues throughout the night until the next dawn. Further, we found that PG synthesis by the symbionts decreases as they enter the slow-growing stage. Surprisingly, in contrast to the most mature crypts (i.e., Crypt 1) of juvenile animals, most of the symbiont cells in the least mature crypts (i.e., Crypt 3) were not expelled and, instead, remained in the slow-growing state throughout the day, with almost no cell division. Consistent with this observation, the expression of the gene encoding the PG-remodeling enzyme, L,D-transpeptidase (LdtA), was greatest during the slowly growing stage of Crypt 1 but, in contrast, remained continuously high in Crypt 3. Finally, deletion of the ldtA gene resulted in a symbiont that grew and survived normally in culture, but was increasingly defective in competing against its parent strain in the crypts. This result suggests that remodeling of the PG to generate additional 3–3 linkages contributes to the bacterium’s fitness in the symbiosis, possibly in response to stresses encountered during the very slow-growing stage.

  PublisherOA PDFDOI

Recent grants

• Regulation of Host Colonization Specificity

  NSF · $343k · 2017–2019

• NIH Grant F32GM078760

  NIH · $145k · 2009

• Genetic Analysis of Beneficial Bacterial Colonization

  NIH · $2.2M · 2016–2022

• Regulation of Host Colonization Specificity

  NSF · $636k · 2015–2017

• NIH Grant R21AI117262

  NIH · $408k · 2019

Frequent coauthors

• Val Woodward

  University of Plymouth

  16 shared

• Nathan Richman

  16 shared

• S. K. Dutta

  Institute of Medical Sciences

  16 shared

• Edward G. Ruby

  California Institute of Technology

  14 shared

• Ruth Y. Isenberg

  University of Wisconsin–Madison

  12 shared

• Denise A. Ludvik

  University of Wisconsin–Madison

  9 shared

• Margaret McFall‐Ngai

  University of Hawaiʻi at Mānoa

  9 shared

• Katherine M. Bultman

  University of Wisconsin–Madison

  8 shared

Labs

• Mandel LaboratoryPI

  Not provided

Education

• B.S.

  Cornell University

  1999

• Ph.D.

  Princeton University

  2005

• Other

  University of Wisconsin

  2009