Research

CEMI’s mission is to enable Caltech researchers to tackle important problems involving microbes in bold and innovative ways. Toward that end, we offer competitive pilot grants once a year (announced at the beginning of the summer and due in the early fall) to allow students or postdocs to explore high-risk interdisciplinary projects for a one-year period.

Labs

CEMI Pilot Projects

Number of projects: 125

Year Title Lead PI Grant Recipient
2024 Mining microbial genomes to unlock new routes to biodegradation of persistent organic pollutants Frances Arnold Ariane Mora 
2024 Examining plant root – microbial biofilm interactions at high magnification Gozde Demirer Catherine Griffin 
2024 Recreating synthetic microbial phase variation to engineer and probe microbial communities Michael Elowitz Matt Kratz 
2024 Exploring the twilight zone of prokaryotic protein homology using protein language models Woody Fischer Calvin Rusley 
2024 Exploring environmental virulence gene removal using a 'non-transgenic' plasmid curing strategy Bruce Hay Thomas Adamo-Schmidt 
2024 Synthetic cell-based biosensors for monitoring plant-microbiome communication in soil Smruthi Karthikeyan Sal Ibarra 
2024 Deepening understanding of nitrogenase diversity to enable cell-free nitrogen fixation Smruthi Karthikeyan Zahra Shivji 
2024 A high-throughput workout: directing evolution to train cytochromes for enhanced electron transfer Karthish Manthiram Clara Seo 
2024 Deciphering neuroactive microbial metabolites via chemical metabolomics Sarkis Mazmanian Danny Dumitrescu 
2024 Cell-free synthesis of phage particles for large DNA delivery Richard Murray Han Zhang 
2024 Light sheet fluorescence microscope for rhizosphere imaging Dianne Newman Reinaldo Alcalde 
2024 Protein turnover of anaerobic methane-oxidizing communities in carbonate rocks using SIP-metaproteomics Victoria Orphan Magdalena Mayr 
2024 A submersible holographic microscope for deep sea, in-situ, environmental microbiology Victoria Orphan Alex Ramirez 
2024 Conditional guide RNAs for cell-selective readout and regulation within bacteria and microbiomes Niles Pierce Eric Lei 
2024 Symbionts under epigenetic control: impact on the early development of host-microbe association Ned Ruby Viridiana Avila-Magana 
2024 Evaluation of pyrroloiminoquinone alkaloid cytotoxicity in opportunistic pathogens Brian Stoltz Jonathan Farhi and Korbi Thalhammer
2024 Basewise correction of synthetic DNA Kaihang Wang Daniel Graves 
2024 A new paradigm for streamlined gut microbiome engineering Kaihang Wang and Sarkis Mazmanian Charles Sanfiorenzo, Jeongsoo Hur, and Nastya Oguienko
2024 Development of a micro-Raman platform for live-cell sorting for integrated multi-omics of gut microbiota Lu Wei Rahuljeet Chadha 
2023 Elucidating the biodegradation of dimethylsilanediol by soil microbes Frances Arnold Ryen O'Meara
2023 Structural studies on Runella zeae prokaryotic Argonaute protein Tsui-Fen Chou Kate Radford
2023 Reoptimizing plant microbiomes through exudate engineering Gözde Demirer Chiara Berruto
2023 Exploration of the aging Parkinson’s microbiome Rustem Ismagilov Natalie Wu-Woods
2023 An integrated-omics approach to assess carbon fluxes in soil microbiomes under drought stress Smruthi Karthikeyan Grace Solini
2023 Cell-free systems as a universal platform for phage production Richard Murray Yan Zhang
2023 Quantifying the basal power requirement during microbial energy-limitation in the lab Dianne Newman John Ciemniecki
2023 Aerobic short-chain alkane oxidation with novel particulate Cu-monooxygenases on carbonates at methane seeps Victoria Orphan Magdalena Mayr
2023 Understanding the responses of bacteria growth dynamics to the host environment Ned Ruby Liu Yang
2023 Toward injectable sub-mm wireless living electronic sensors Mikhail Shapiro Josh Chen
2023 Multiplex generation of chimeric bacterial strains via conjugation and CRISPR-associated transposons Kaihang Wang Tomasz Gawda
2022 Feasibility of mapping all DNA within each bacterial cell from a microbial community Rustem Ismagilov Matt Ratanapanichkich
2022 Identification of determinants of lithotrophic manganese oxidation via heterologous expression of a random Manganitrophus-genome library Jared Leadbetter and Dianne Newman Lydia Varesio
2022 A living voltmeter: Protein chimeras quantifying transmembrane electron transfer Karthish Manthiram James Wang
2022 ‘Re-wilding’ the microbiome of laboratory mice promotes sociability Sarkis Mazmanian and Mikhail Shapiro Jessica Griffiths and Claire Rabut
2022 Snapshot of host-microbe interactions in the squid-vibrio system Margaret McFall-Ngai and Lior Pachter Vera Beilinson
2022 Model-based design of microbial self-assembly response to environmental conditions Richard Murray and Victoria Orphan Alex Johnson and Ayush Pandey
2022 Formulating a defined medium to study chronic wound infections Dianne Newman Chelsey VanDrisse
2022 Targeted sequencing of ANME-3 genomes from enrichment cultures and FACS Victoria Orphan Philip Woods
2022 Quantifying stochastic geometry and physiology in polymicrobial communities Rob Phillips and Dianne Newman Gabe Salmon
2022 Studying the spatiotemporal dynamics of native gut microbes with acoustic reporter genes Mikhail Shapiro and Sarkis Mazmanian Whee-Soo Kim
2022 Constructing synthetic large DNA molecules with toehold assisted DNA assembly Kaihang Wang Noah Robinson and Jeongsoo Hur
2022 Megabase DNA insertion in Agrobacterium tumefaciens for plant genome engineering Kaihang Wang Raymond Zhang and Charles Sanfiorenzo
2022 Recoded bacteria strain as predator release factory Kaihang Wang Jolena Zhou
2021 Searching for traces of microbial life in exceptionally well-preserved Paleoarchean black cherts from South Africa Joe Kirschvink, George Rossman, and John Eiler Noah Tashbook
2021 Interaction between programmable nuclease defense systems: Argonaute proteins and CRISPR-Cas Alexei Aravin Anton Kuzmenko
2021 Interaction between programmable nuclease defense systems: Argonaute proteins and CRISPR-Cas Alexei Aravin Anton Kuzmenko
2021 Mechanistic studies of a bacterial arsenic efflux system with implications for bioremediation Bil Clemons, Dianne Newman and Doug Rees Shivansh Mahajan
2021 A minimal gene cassette for probing magnetosome biomineralization Ryan Hadt and Doug Rees Christian Totoiu
2021 Mathematically rigorous quantitative microbiome analysis tools Rustem Ismagilov and Matt Thomson Matt Cooper and Jialong Jiang
2021 Identification and characterization of proteins involved in symbiosis in the entomopathogenic nematode Steinernema hermaphroditum Paul Sternberg Chieh-Hsiang Tan and Mengyi Cao
2020 Teasing out the structural and evolutionary origins of the Get3 family William Clemons Shyam Saladi
2020 Microbes underlie regenerative capacity in a poorly regenerative jellyfish model Lea Goentoro Aki Ohdera and Zevin Condiotte
2020 Culture-free detection of functional bacteriophage-host interactions in the mouse cecum by single-cell isolation and genome sequencing Rustem Ismagilov Eric Liaw
2020 The mechanics of microbial rainbows: optomechanical properties of iridescent biofilms Julia Kornfield Priya Chittur
2020 Engineering probiotics that sense and regulate inflammation Richard Murray and Sarkis Mazmanian Richard Murray and Sarkis Mazmanian
2020 Experimental and theoretical approaches to studying the physiology of single cells in structured environments Dianne Newman and Rob Phillips Avi Flamholz
2020 High-throughput enrichment and physiological study of microbial metabolic symbioses of the Asgard Archaea Victoria Orphan Yanzhe Zhu
2020 Horizontal transmission of an insect primary endosymbiont Joe Parker Sheila Kitchen
2020 Isotopic fingerprinting of serine to probe carbon flows in phytoplankton Alex Sessions and John Eiler Elise Wilkes
2020 Time-resolved, state-selective proteomic interrogation of P. aeruginosa & S. aureus co-culture dynamics Dave Tirrell Grace Wang
2020 Designing orthogonal transcription and translation memory circuits Kaihang Wang and Richard Murray Bryan Gerber and Matthieu Kratz
2019 Machine learning for directed evolution Frances Arnold and Yisong Yue Bruce Wittmann
2019 High-resolution structure determination of bacterial gas vesicle protein shells Grant Jensen and Mikhail Shapiro Lauren Metskas
2019 Multiplex recombineering for genome scale mutant libraries in diverse bacteria Dianne Newman and Kaihang Wang Scott Saunders
2019 Towards scalable closed-loop control using conditional guide RNAs Niles Pierce and Richard Murray Jining Huang
2019 In situ distribution of ANME-SRB aggregates in seep sea methane seep sediments David Van Valen and Victoria Orphan Haley Sapers
2018 Structural characterization of UvrC, the essential endonuclease in nucleotide excision repair Jacqueline Barton Rebekah Silva
2018 Photomethanotrophy as a methane sink in the warming Arctic Woodward Fischer and Christian Frankenburg Woodward Fischer and Christian Frankenberg
2018 Metabolic coupling in mixed microbial communities of aerobes and anaerobes Rustem Ismagilov Tahmineh Khazaei
2018 Understanding carbon flow in the first obligate manganese-oxidizing consortium Jared Leadbetter Hank Yu
2018 Electron cryotomography of crystalline cellulose synthesis by Gluconacetobacter hansenii Elliot Meyerowitz William Nicolas
2018 Genetic novelty through ancient horizontal gene transfer: would the real arthropod polyketide-synthase please stand up? Joe Parker Adrian Brueckner
2018 Deciphering the mechanism that triggers 2 H-enrichment in lipids under oxidative and salt stress Alex Sessions Reto Wijker
2018 Directed evolution of bacteria-derived gas nanostructures as acoustic reporter genes Mikhail Shapiro  Robert Hurt
2018 Concurrent transcriptomic characterization of host-pathogen populations in chronic skin wounds Matt Thomson Sisi Chen
2018 The time-resolved proteomic analysis of mazEF-mediated cell stasis and revival in Escherichia coli David Tirrell Elliot Mackrell
2017 The role of microbes in the development and aging of primitive animals Lea Goentoro David Gold
2017 Structural studies of bacterial and archaeal extracellular electron transport components under near-native conditions Grant Jensen Poorna Subramanian
2017 Cultivation and analysis of the first chemolithoautotrophic bacteria to utilize Mn(II) as electron donor for growth Jared Leadbetter Jared Leadbetter
2017 Novel microbe-mediated neuro-immune interactions in the gastrointestinal tract Sarkis Mazmanian Bryan Yoo
2017 Dynamics and control of metabolically cross-linked microbial consortia Richard Murray Rory Williams
2017 Investigation of a novel proteolytic pathway in bacteria and its role in stress survival of the opportunistic pathogen Pseudomonas aeruginosa Dianne Newman David Basta
2017 Microbial involvement in a beetle-ant symbiosis Joe Parker Joe Parker
2017 Understanding nitrogen fixation via electrochemistry Jonas Peters Matthew Chalkley
2017 Conditional guide RNAs for scalable biological control Niles Pierce Mikhail Hanewich-Hollatz
2016 Selective killing of latently infected CD4+ T-cells by conditionally replicating viruses that detect HIV transcripts Pamela Bjorkman Magnus Hoffmann
2016 Transmission of viruses through fine particles (PM2.5) Michael Hoffmann Lijie (Sara) Li
2016 Structural studies of bacterial and archaeal extracellular electron transport components under near-native conditions Grant Jensen Poorna Subramanian
2016 The cell biology of starvation: Polyphosphate granule dynamics in Pseudomonas aeruginosa Suliana Manley Lisa Racki
2016 Life on lava flows: Which microbes grow on volcanic deposits and why? Victoria Orphan Ranjani Murali
2016 Genomic rearrangements and the origins of immunity Rob Phillips Soichi Hirokawa
2015 Sequence-level prediction and control of integral membrane protein expression William Clemons Stephen Marshall
2015 A rapid approach to characterize spatial patterns of microbial colonization of host tissue Rustem Ismagilov Antti Lignell and Octavio Mondragon-Palomino
2015 How widespread among bacteria is the ability to sporulate Grant Jensen Davi Ortega and Will DePas
2015 Symbiosis within a symbiosis: Cultivation and characterization of a novel, protozoan-associated deltaproteobacterial acetogen from termite guts Jared Leadbetter Ella Yanay
2015 Microbiome-based autism treatment through gut barrier repair Sarkis Mazmanian Brittany Needham
2015 Do different hopanoid types facilitate active transport of organic solutes? Dianne Newman Gargi Kulkarni
2015 Characterization of protein responsible for extracellular electron transport in Euryarchaeota Victoria Orphan Grayson Chadwick
2015 Unveiling the nutritional capabilities of heterotrophic deep-sea bacterial symbionts using NanoSIMS Victoria Orphan Shana Goffredi
2015 The proteomic response of Staphylococcus aureus to the innate immune system in vivo David Tirrell Shannon Stone
2014 Evolution and structural analysis of microbial rhodopsin based sensors Frances Arnold Austin Rice
2014 In situ "sequencing" by FISH (seqFISH) for cell ID and transcription profiling Long Cai Timur Zhiyentayev
2014 Using optogenetic tools to manipulate the membrane potential of pathogens Viviana Gradinaru Sripriya Ravindra Kumar and Ruth Lee
2014 Uncovering serotonergic members of the human microbiota Rustem Ismagilov Elaine Hsiao
2014 Microfluidic isolation of microbes that inactivate nematode signaling molecules Rustem Ismagilov Liang Ma 
2014 Substrate coordination to the active site cofactor of nitrogenase Jonas Peters Jon Rittle
2014 Mapping biological magnetism at the nanoscale: Bringing a key technology to Caltech CEMI Mikhail Shapiro Pradeep Ramesh
2014 Detection of nematode-induced transcripts in the nematophagous fungus A. oligospora using Fluorescence in situ hybridization Paul Sternberg Yen-Ping Hsueh and Ting-Fan He
2014 Site-specific labeling of bacterial proteins in-situ using N-Myristoyltransferase for correlated, cryogenic Stochastic Optical Reconstruction Microscopy (cryo-STORM) David Tirrell Samuel Ho
2013 DNA signaling among proteins with 4Fe-4S clusters Jacqueline Barton Michael Grodick
2013 Mechanosensitive channels: Their role in photosynthetic cell biology Ian Booth Vojtech Prazak
2013 Imaging chromosome conformation in single bacteria cells Long Cai Timur Zhiyentayev
2013 Constructing mutants of Saccharomyces cerevisiae with CRISPR/CAS9 and characterization of genes involved in mutagenesis Judith Campbell Martin Budd
2013 Evolution of photosynthesis in cyanobacteria Woodward Fischer James Hemp and Jena Johnson
2013 An integrated MEMS device for use as a microbial monitoring system in wastewater treatment Michael Hoffmann Penvipha Satsanarukkit
2013 Structure and organization of the bacterial chromosome Grant Jensen Yi-Wei Chang
2013 A novel probiotic therapy for Parkinson's disease in animal models Sarkis Mazmanian Catherine (Katie) Schretter
2013 X-ray absorption spectroscopic studies of nitrogen fixation Douglas Rees Limei Zhang
2012 Argonaute proteins in bacteria: A glimpse into the ancient non-coding RNA world Alexei Aravin Ivan Olovnikov
2012 Characterization of a novel membrane protein-targeting pathway in photosynthetic bacteria William Clemons Vijay Somalinga
2012 Understanding the physiological roles of subpopulations in clonal bacterial communities Michael Elowitz Adam Rosenthal
2012 Evolution and mechanism of type VI secretion-related nanomachines Grant Jensen Martin Pilhofer
2012 Diverse studies in microbial diversity Jared Leadbetter N/A - Supplies
2012 Probing microbial energetics with microcalorimetry: The environmental and energetic meaning of heat production Victoria Orphan Jeff Marlow 
2012 Quantitative dissection of iron-mediated gene regulation in Pseudomonas aeruginosa Rob Phillips James Boedicker

How to Apply for a Pilot Grant

We have a limited pool of resources to advance novel, collaborative pilot projects conducted by students or postdocs. Research awards support stipend and tuition (students) or salary and benefits (post-doctoral fellows) for 1 year (starting in fall to be spent within the academic year). Candidates from any Division at Caltech may apply. Contact the CEMI administrator with questions.

Download How to Apply for a Pilot Grant