https://gutworks.stanford.edu/blog daily 0.75 2020-08-15 https://gutworks.stanford.edu/blog/blog-post-four-pkzrz monthly 0.5 2019-08-22 https://images.squarespace-cdn.com/content/v1/5cdb0b54755be25d5d92bfb3/1565794519920-7ZV3FNWJON04K3BSJK6A/download.jpeg Blog - Blog Post Four https://gutworks.stanford.edu/blog/blog-post-three-7zj79 monthly 0.5 2019-08-14 https://images.squarespace-cdn.com/content/v1/5cdb0b54755be25d5d92bfb3/1565794488032-9XBL84FW5EFN7IJBCXN9/download+%281%29.jpeg Blog - Blog Post Three https://gutworks.stanford.edu/blog/blog-post-two-zm964 monthly 0.5 2019-08-14 https://images.squarespace-cdn.com/content/v1/5cdb0b54755be25d5d92bfb3/1565794203166-HK9O5SMXBCPW1RHBM3V5/image-asset.jpeg Blog - Blog Post Two https://gutworks.stanford.edu/blog/blog-post-one-e9r6k monthly 0.5 2019-08-14 https://images.squarespace-cdn.com/content/v1/5cdb0b54755be25d5d92bfb3/1565794043606-FK1PV2DOU30VI46WWL09/justice-rising-ECHO-AND-EARL-3.jpg Blog - Blog Post One https://gutworks.stanford.edu/home daily 1.0 2020-08-15 https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1597448233134-0PG272JTYJXVJJ2I7QP6/NHGRI_microbiome_outline_30395469313_c02d5ddf6b_h.jpg Home - The Challenge Although we critically need to enhance our fundamental understanding of the physiology of these bacteria, most human gut bacteria have never been studied with molecular genetic tools. Further, we can’t accurately assign gene annotations based on homology because our body’s bacteria are too distantly related to well-studied model bacteria. Systematic and multidisciplinary collaboration is urgently needed in order to unravel the functions of genes in human gut bacteria. https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1597448520261-J8AW2RHIZVO05SWQ35DK/lucas-vasques-9vnACvX2748-unsplash-researcher.jpg Home - The GutWorks Approach High-throughput genetics is an attractive approach for characterizing the biological functions of genes within the human microbiota. By applying many perturbations to large populations of genetically modified bacteria, we can carry out parallel assessment of nearly all the genes in a bacterial community. To apply this strategy, GutWorks is tackling the following challenges: · Simplify the transformation of non-model bacteria in order to exploit genetic tools · Develop a new genetic system for a non-model bacterium without extensively consuming time and resources · Make it easy to adopt multiple technologies and laboratory workflows in order to compare data across teams · Colonize ex-germ-free mice with mutants of interest for in vivo mouse experiments. https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1597449098093-4YHBKFLHVUK7B3NNUNZP/thisisengineering-raeng-CnDBjaddRWs-unsplash.jpg Home - Who We Are The GutWorks team includes leaders who are pioneering novel cultivation methods, electroporation for genetic transformation, and tools for assessing gene function in vitro and in vivo. Through our combined expertise in bacteriology, microfluidics, high-throughput screening, host-microbe interactions, and imaging, we will produce genetic tools and fitness data for the vast community of microbiota researchers at unprecedented scale. With support from our Scientific Advisory Board, GutWorks will deliver deep and transformative insights into the physiology of the human gut microbiota. https://gutworks.stanford.edu/deep-dive daily 0.75 2020-08-17 https://gutworks.stanford.edu/open-positions daily 0.75 2025-02-09 https://gutworks.stanford.edu/ourgoals daily 0.75 2020-08-17 https://gutworks.stanford.edu/ourtech daily 0.75 2020-08-15 https://gutworks.stanford.edu/donate daily 0.75 2025-05-09 https://gutworks.stanford.edu/the-team daily 0.75 2025-02-17 https://gutworks.stanford.edu/the-team/pm monthly 0.5 2020-08-25 https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/231f2cc8-f115-48b7-9e07-9d923ca2539e/anthony.jpg The Team - Project Manager - Dr. Anthony L. Shiver (Stanford) Anthony is an expert in systems biology and specializes in developing innovative large-scale genomic approaches. Before working in KC Huang’s lab as a Basic Life Science Researcher, Anthony trained in applied mathematics, biochemistry, and biophysics (University of Oregon, B.S.; University of California–San Francisco, Ph.D.). Anthony led the development of a FACS-based approach for assembling ordered mutant collections in anaerobic gut microbes, as well as multi-omic data integration for mechanistic insights into host colonization by the gut microbiome. Anthony created the first genome-scale genetic resources in a model organism for the bifidobacteria and is facilitating numerous collaborative projects in GutWorks. https://gutworks.stanford.edu/the-team/pis2 monthly 0.5 2020-08-27 https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1597512032829-3DDAFZK0C1EVA006DJ4R/Cullen+R.+Buie.jpg The Team - Principal Investigators - Dr. Cullen Buie (MIT) Cullen is an expert in the areas of electrokinetic phenomena, genetic transformation of microbes, electrochemistry, and heat and mass transfer. Over the past seven years, his lab has focused on the impacts of microscale transport phenomena on prokaryotic and micro-eukaryotic organisms. His lab has developed microfluidic electroporation platforms that facilitate high-throughput, automated genetic transformation of bacteria. He has also pioneered microfluidic assays for rapid discovery of genetic transformation conditions for previously intractable microbes. Together, these systems will serve as an enabling platform for GutWork’s efforts to illuminate the physiology of the diverse organisms that compose the human gut microbiome. https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1598546673909-6QVAXJDNO9A83Y91W5R4/NEW_ADAM.JPG The Team - Principal Investigators - Dr. Adam Deutschbauer (LBL) Adam is an expert in bacterial functional genomics and systems biology. For the past 10 years, his lab has focused on the development and application of genetic tools to rapidly characterize uncharacterized genes from diverse bacteria. His lab makes extensive use of laboratory automation, chemical libraries, and multiplexed assays to generate extensive genetic datasets in bacteria. More recently, he has been interested in understanding the roles of microorganisms in their natural environment, with a focus on rhizosphere bacteria. The Deutschbauer group is part of a large DOE-funded project and as such, is highly collaborative. In the past 5 years, his laboratory has provided guidance and resources to dozens of labs interested in high-throughput genetics. Since 2018, he has also been an adjunct assistant professor in the Plant and Microbial Biology Department at UC Berkeley. https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1597512337498-E1ER8XNYCMAWXCVUYBWD/KC.jpg The Team - Principal Investigators - Dr. KC Huang (Stanford) KC is a bacterial cell biologist and biophysicist, with a strong focus on the organizational principles of microbial communities and the physiology of gut commensal bacteria. Huang has broad expertise in computational physics and biology, with specific training in the physical modeling of bacterial physiology. His group has developed experimental synthetic biology tools that enable novel interdisciplinary studies of the role of physical forces in cellular organization. In recent years, his lab has applied these tools to complex microbial communities such as the intestinal microbiome. His group has developed a powerful experimental and computational framework for quantifying the spatial organization of the gut, which has revealed strong effects of diet on the structure of the community surrounding the mucus. His group has also developed high-throughput approaches for imaging single bacterial cells that GutWorks will use for forward genetic screens of genomic-scale libraries. https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1597512557624-XPC2MZTHA2IUTA4JAGMT/justin.jpg https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/5155bd2e-3344-4818-962a-f30e243f709e/Carlotta-Ronda-Headshot-02-sq.jpg The Team - Principal Investigators - Dr. Carlotta Ronda (Innovative Genomics Institute, UC Berkeley) Carlotta is an expert in CRISPR editing of microbiome communities. She is a Principal Investigator and WIES Fellow at the Innovative Genomics Institute at UC Berkeley. Her research has focused on genetic modification of non-model organisms and microbial communities. As a Simons Junior Fellow at Columbia University, she pioneered a landmark platform to edit microbial communities in vivo using CRISPR technology, paving the way for future microbiome-based therapies. Her recent work opens new avenues for targeted functional metagenomics in situ, enhancing our understanding of microbial communities in their native milieu. Her lab applies systems biology principles to modulate the gut microbiome and develops innovative platforms to decipher bi-directional host-microbiome signaling. Leveraging cutting-edge gut organoid co-culturing systems, CRISPR technologies, and microbiome engineering platforms, her team combines in vitro and in vivo studies with mouse models to map the host-microbiome interactome. These efforts include creating genetic and molecular systems in diverse bacterial chassis and mammalian cells, using -omic technologies to characterize fundamental genetic mechanisms. https://gutworks.stanford.edu/the-team/postdocs monthly 0.5 2020-08-25 https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1597513517768-K40PHBNT3DTMBYYVLEBX/Po-Hsun_Huang.jpg The Team - Postdoctoral and Staff Researchers - Dr. Po-Hsun Huang (Buie lab, MIT) Po-Hsun, a Postdoctoral Associate, is developing a high-throughput, automated electroporation system for bacteria transformation. He was previously a Postdoctoral Associate at Duke University with a particular interest in developing various microfluidic devices/platforms based on acoustics for chemical and biological applications, such as nanomaterials synthesis and fluids and cells manipulation. https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1598291769965-BWAHY2R4CE5N2LFYCWA0/V_Trotter.jpg The Team - Postdoctoral and Staff Researchers - Dr. Valentine Trotter (Deutschbauer lab, LBNL) Valentine, a Project Scientist, is using a combination of functional genomics and biochemistry to investigate the physiology of human gut bacteria. She will leverage expertise gained from previous projects on sulfate-reducers and Clostridia. https://gutworks.stanford.edu/the-team/grad-students monthly 0.5 2020-08-25 https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/6a770831-ae0a-4a88-966c-38c2b3a667b7/professional_picture.jpg https://gutworks.stanford.edu/the-team/advisors monthly 0.5 2020-08-27 https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1597518165293-8CSMMC4L3U5ON4KFEHX3/Alan_Grossman.jpg The Team - Scientific Advisors - Dr. Alan D. Grossman (MIT) Alan is the Praecis Professor of Biology and Department Head for Biology at MIT. Using the model organism Bacillus subtilis, the Grossman lab aims to understand fundamental and conserved physiological mechanisms for bacterial propagation and growth, horizontal gene transfer, and DNA replication initiation and its relation to gene expression. https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1597518432384-PA1108X87HYYZQG7AX6L/carol_gross.jpg The Team - Scientific Advisors - Dr. Carol Gross (UCSF) Carol is a Professor in the Departments of Microbiology and Immunology and Cell & Tissue Biology at University of California, San Francisco. The Gross lab takes genetic, biochemical, and systems approaches to study the regulatory mechanisms of bacterial stress responses, protein interactions in the bacterial transcription apparatus, and genome-wide control of gene expression. https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1597518605946-MKPEWTJWU2W7W76YRFYR/denise_monack.jpg The Team - Scientific Advisors - Dr. Denise Monack (Stanford) Denise is a Professor of Microbiology & Immunology at Stanford. The Monack lab exploits biochemical and genetic approaches to understand the genetic and molecular mechanisms of bacterial pathogenesis, with a focus on the pathogen Salmonella and crosstalk between the gut microbiome and host immune response. https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1597518874854-5EXOFVFDL3FPFY9ZR18O/Wes-Whitaker.jpg The Team - Scientific Advisors - Dr. Weston Whitaker (Novome) Weston is the co-founder and VP of Research at Novome. Novome develops unique synthetic microbiome tools to deliver precise activities to treat chronic diseases. Founded on pioneering technology from Stanford University, Novome engineers and engrafts synthetic gut microbes to treat a variety of microbiota-associated diseases. https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1598474215589-CENFM2W8158GG4YCRHHR/new_brodie_portrait.jpg The Team - Scientific Advisors - Dr. Eoin Brodie (LBNL) Eoin is a Senior Scientist at Lawrence Berkeley National Laboratory, Deputy Director of the Climate and Ecosystems Sciences Division, and holds an Adjunct Associate Professor appointment at UC Berkeley. The Brodie lab reverse engineers natural microbial communities to enable a predictive understanding of microbial diversity and function. They focus on communities that play important roles in environmental and human health and sustainable energy. https://images.squarespace-cdn.com/content/v1/5f37174ddd57b673135f66bf/1597519317961-JAPQM70P6SLY1ZL1RYO6/michiTaga.jpg The Team - Scientific Advisors - Dr. Michi Taga (UCB) Michi is an Associate Professor of Plant & Microbial Biology at University of California, Berkeley. The Taga lab combines biochemistry, genetics, molecular biology, analytical chemistry, and bioinformatics to study nutrient-sharing relationships among bacteria and their implications for microbial communities. Focusing on corrinoids, the Taga Lab dissects the molecular interactions and interdependencies that are critical to microbial communities. https://gutworks.stanford.edu/resources daily 0.75 2025-02-09 https://gutworks.stanford.edu/resources/publications monthly 0.5 2020-08-27 https://gutworks.stanford.edu/resources/protocols monthly 0.5 2025-02-07 https://gutworks.stanford.edu/resources/tools-data monthly 0.5 2020-08-24 https://gutworks.stanford.edu/resources/media monthly 0.5 2020-08-25 https://gutworks.stanford.edu/resources/ordered-mutant-collections monthly 0.5 2025-02-07