Rob Knight

Rob Knight

Principal Investigator

Rob Knight, Principal Investigator
Rob Knight is a Professor in the Department of Pediatrics, with an additional appointment in the Department of Computer Science, at the University of California San Diego. He was chosen as one of 50 HHMI Early Career Scientists in 2009, is a Senior Editor at the ISME Journal, a member of the Steering Committee of the Earth Microbiome Project, and a co-founder of the American Gut Project.
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Administration

Michiko Souza
Michiko Souza
Executive Assistant

I have been working with the Knight Lab since February 2015. In my free time, I enjoy traveling, yoga and walking on the beach.

Brent Erickson
Brent Erickson
Administrative Assistant

I joined the Knight Lab in March 2016 and am looking forward to supporting research projects investigating the links between human and environmental health.

Post-Doctoral Research Associates

Se Jin Song
Se Jin Song
Post-doctoral Research Fellow

Much of my research interests are centered around understanding the factors that influence the evolution of host-microbe interactions and determine the composition of microbial communities associated with vertebrate hosts (including humans). My main focus is on investigating the potential role of the microbiome in the convergent evolution of phenotypic traits in animals. However, I am currently involved in a variety of projects ranging from understanding the shifts in human-to-home microbial relationships with Westernization to characterizing the composition and function of the microbes found in the myriad ecosystems around the world (i.e. Earth Microbiome Project).

Justine Debelius
Justine Debelius
Post-doctoral Research Associate

I study the role of the gut microbiome in human health and inflammation.
I am interested in the way the microbiome and immune system interact to predict tolerance or autoimmunity. To this end, I work on both characterizing microbial communities in the context of disease as well as establishing relationships between our lifestyle choices and our bacterial communities.

Stefan Janssen
Stefan Janssen
Post-Doctoral Research Associate

I have been trained as a bioinformatitian in Bielefeld Germany where I acquired a strong background in dynamic programming algorithms and RNA secondary structure prediction. My previous post doc position in Brunswick (DE) introduced me to the field of metagenomics and especially community profiling on whole metagenome shotgun sequencing data. I am eager to upscale current RNA algorithms to match needs of high throughput analyses as in metagenomics and wheel functional RNA into the focus of state of the art research.

Chris Callewaert
Chris Callewaert
Post-Doctoral Research Associate

My research focuses on the microbiome of the armpit, skin, clothes and washing machines, in relation to (mal)odor formation. We try to improve one’s body odor by performing an armpit bacterial transplantation, where bacteria from a non-odorous armpit are brought onto the washed armpit of a smelly armpit. I have a background in applied biosciences and bioengineering and obtained my PhD at Ghent University in Belgium. More details can be found in the website below.

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Amnon Amir
Amnon Amir
Post-doctoral Research Associate

Main research interests:
- Oral microbiome
- Development of analysis methods and algorithms for 16S data (see heatsequer on github)
- High resolution 16S analysis (sub OTU)
- Artifacts in 16S analysis (storage,contamination, etc.)
- Analysis of 16S experiments

Zhenjiang (Zech) Xu
Zhenjiang (Zech) Xu
Post-doctoral Research Associate

Microbiota has tremendous impacts on environment and host health and can be engineered for the better. My interests are mainly centered around linking microbiota composition and function to host phenotypes or environmental factors. I have been working on miscellaneous projects using microbiome as biomarkers for forensics, disease diagnostics and prognostics with statistical and machine learning techniques. Towards that goal, I am also developing new computational tools (e.g. micronota) to improve our understanding of microbial composition and their functions.

Tomasz Kościółek
Tomasz Kościółek
Post-doctoral Research Associate

I have a background in chemistry and structural bioinformatics, with experience in computational chemistry, computer-aided drug design and protein structure predictions. My efforts in the lab concentrate on expanding our knowledge of the microbiome by annotating metagenomic information and microbiome-wide protein structure and function predictions.

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Jerry Kennedy
Jerry Kennedy
Post-doctoral Research Associate

I am currently a Post-doctoral Research Associate in the Knight Lab.

Jon Sanders
Jon Sanders
Post-doctoral Research Associate

The relationships we have with our microbial denizens have important consequences. But how have those relationships evolved? My research starts with exploring the diversity of animal-associated microbes in the present day, and then seeks to use those associations to make inferences about their histories. Ultimately, these stories should teach us something about the rules governing these complex communities, allowing us to make more informed decisions about their preservation and management.

Qiyun Zhu
Qiyun Zhu
Post-Doctoral Research Associate

I have a mixed background in experimental biology and bioinformatics. My main interest is shotgun metagenomics, including taxonomic and functional profiling, de novo assembly, binning, and draft genome finishing. I am also interested in evolutionary biology, especially in host-parasite co-evolution and horizontal gene transfer.

Contact Qiyun

Professional Research Assistants

Gail Ackermann
Gail Ackermann
Professional Research Assistant

I moved to Rob's lab in 2011, where I have accepted responsibility for many things. This includes IRB, IBC and IACUC protocols. I assist with metadata curation and upload of projects to the database.

Greg Humphrey
Greg Humphrey
Professional Research Assistant

I have been working with the Knight Lab since 2009 and I am currently in charge of wet lab processing and the sequencing queue. I am interested in temporal variability of the microbiome and micro culturing.

Jeremiah 'Jake' Minich
Jeremiah 'Jake' Minich
Professional Research Assistant

I am interested in understanding how the host microbiome is related to organismal health, with applications to improved diagnostics along with intervention. In Malawi, I am studying how fertilization regimes of different animal manures influence the water microbial composition which in turn influences the fish gut microbes (for better or for worse) to ultimately improve aquaculture performance (tilapia and catfish) by discovery of probiotics or prebiotics. I hope to continue searching for ‘golden microbes’ across the tremendously diverse fish of the world ultimately to find novel methods for probiotic/prebiotic therapies and disease prevention. I am also very interested in integrating new technologies in genomics with high throughput systems.

Daniel McDonald
Daniel McDonald
Programmer Analyst

My research emphasis is on the development of computational methods that enable analysis of microbiome data at scale irrespective of the environment (although poop is fun). I am a core developer on many of the software projects the lab is involved in, and have a strong interest in open source and open access processes. I am a former American Gut project manager overseeing the effort from June 2013 to August 2015 including its expansion into the British Gut and an Australian aggregation site.

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Antonio González Peña
Antonio González Peña
Programmer Analyst

My main interest is developing new computational methods to compare large numbers of microbial communities and to put these comparisons in a temporal and spatial context, with the ultimate goal of understanding and controlling microbial communities to improve health in different environments. I have worked on many projects in environments from soils to the human body, leading to the development of novel analysis methods and software packages including QIIME, Qiita, SitePainter, Emperor, and Evident.

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Karenina Sanders
Karenina Sanders
Professional Research Assistant

I joined the Knight lab because of my interest in the current and future projects, and also to gain experience in preparation for grad school. My background is in Decision Science and Physiology, but I am excited to learn more about the connection between microbiota and the mind/mental health. I currently work in the wet lab, assisting with sample processing. ​

Caitriona Brennan
Caitriona Brennan

I contribute to the work involved with processing samples in the wet lab. I obtained my bachelors degree in University College Cork, where I specialized in microbiology. I have keen interest in the relations between the microbiome and various diseases such as parkinson’s, multiple sclerosis and cancer, and also in the development of personalized medication. In the future, I would like to perform field research in various parts of the globe and I plan on attending grad school.

Contact Caitriona

Elaine Wolfe
Elaine Wolfe
Professional Research Assistant

My primary focus is the American Gut project, including facilitating participation and helping to guide participants through the process of understanding their microbiomes.

Lindsay DeRight Goldasich
Lindsay DeRight Goldasich
Professional Research Associate

I have been a part of the wet lab since March, 2015 and help process samples for all types of projects. I earned my BS from UC San Diego in Physiology and Neuroscience and am currently working on my Masters in Biology with Dr. James Nieh. My research is on the effects of neonicotinoid pesticides on honey bee foraging behavior and the impacts on food web interactions. When I am not in the lab, I love to surf, travel, and backpack.

Embriette Hyde
Embriette Hyde
Assistant Project Scientist, Project Manager - American Gut Project

I have been interested in the microbiome and it's impact on human health since early 2011, when I decided to pursue a PhD with my thesis topic being the human microbiome. I am particularly interested in studying environmental microbes and how our interactions with those microbiomes affect our health. Using tools developed by the Knight lab and Knight lab collaborators, I've explored differences in host-environment microbial sharing in humans and animals living in closed environments and in open environments. Additionally, I have always been interested in involving the public in science as a means to raise public awareness about the importance of our work-and to get the public excited and involved! As project manager for the American Gut project, I am able to achieve this goal. American Gut is a crowd sourced citizen science project aimed at characterizing the human microbiome and identifying important associations with health and lifestyle behaviors. I enjoy reaching out to various groups-from athletes to nurses to university students-getting them involved in American Gut and increasing their knowledge about the importance of the microbiome. For more information about my research, past and present, please visit my personal web page below.

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Graduate Students

Bryn C. Taylor
Bryn C. Taylor
Graduate Student

I’m a PhD student in Biomedical Sciences, co-advised by Dr. Rommie E. Amaro in Chemistry. I use tools from the fields of computational chemistry and biophysics (protein folding, molecular dynamics, Markov state models, and more) to investigate microbial proteomes and elucidate the function of the microbiome.

José Antonio Navas Molina
José Antonio Navas Molina
Graduate student

I'm currently a PhD student in Computer Science. I've been always interested in High Performance Computing and Data visualization, and searching ways to apply this to improve people's life. When I joined the Knight Lab in Spring 2012, I found Computational Biology the perfect mix of my two passions. My research is mainly focused on the development of the software package Qiita, sequence clustering, new high-performance visualization tools and analysis of datasets that push the limit of current analysis techniques.

Alison Vrbanac
Alison Vrbanac
Graduate Student

I’m a Biomedical Sciences PhD student, co-advised by Dr. Victor Nizet. My primary research focus concerns the interplay between host microbiota and the development of antibiotic resistant pathogens. Additionally, I’m interested in investigating the role of commensal microbiota in the development of systemic immunity.

Yoshiki Vazquez Baeza
Yoshiki Vazquez Baeza
Graduate Student

I'm a graduate student in the Computer Science and Engineering department. I am interested in analyzing high dimensional and large datasets, most of my experience has been with data that links the human microbiome to health. For more information about me, see my personal website below.

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Lisa Marotz
Lisa Marotz
Graduate Student

I am a graduate student in the Biomedical Sciences program co-advised by Dr. Karsten Zengler. My current project focuses on isolating anaerobes for functional experiments on the skin microbiome.

Anupriya Tripathi (Priya)
Anupriya Tripathi (Priya)
Graduate Student

I'm a PhD student in the Department of Biology. I am interested in ecological and evolutionary interactions within the microbiome, especially phageome-microbiome dynamics and mobilization of multi-drug resistance in poly-microbial communities. Other interests include niche modelling, synthetic microbiota design and mind & microbiome.

Contact Priya

James Morton
James Morton
Graduate student

I'm currently a PhD student in the Computer Science and Engineering program.
I'm interested in developing algorithms and statistical theory to better understand microbial ecosystems.
Currently, I am involved with the American Gut project and Emperor.

Robert Mills
Robert Mills
Graduate Student

I'm pursuing a PhD in the Biomedical Sciences Program. Co-advised by Dr. David Gonzalez in the department of pharmacology, I aim to utilize proteomics to study the microbiome. I'm interested in how a change in the microbiome mediates disease states and to what extent the host is altered by these fluctuations.

Serene Lingjing Jiang
Serene Lingjing Jiang

I am a PhD student in Biostatistics in the Department of Family Medicine and Public Health. My interest is in performing high-level analysis of microbiome data to better understand the relationship between microbial world and human health, and in developing new statistical and mathematical methods to bring more insights into the analysis of high dimensional data.

Former Lab Members

Postdocs:
Jenya Kopylov (2014-2016), Clarity Genomics
Luke Thompson (2013-2016), NOAA
Jessica Metcalf (2011-2016), Colorado State University
Georg Loss (2014-2016), University of Munich
Katherine Amato (2014-2015), Northwestern University
Dorota Porazinska (2013-2015), University of Colorado Boulder
Douglas Woodhams (2012-2015), University of Massachussetts Boston
Christian Lauber (2008-2014), Nestle
Laura Parfrey (2011-2013), University of British Columbia
Jose Carlos Clemente Litran (2010-2013), Icahn School of Medicine at Mount Sinai
Catherine Lozupone (2007-2013), University of Colorado Denver
Jesse Stombaugh (2009-2012), Thermo Fisher Scientific
Bharath Prithiviraj (2011), CGCS
Dana Willer (2010), University of Illinois at Urbana-Champaign
J Gregory Caporaso (2009-2011), Northern Arizona University
Jens Reeder (2008-2010), Genentech
Sara Nakielny (2009-2010), University of California San Fransisco
Elizabeth Costello (2008-2009), Stanford University
Zongzhi Liu (2006-2008), Yale
Jana Chocholousova (2006), Institute of Organic and Biochemistry, Czech Republic
 
Research Associates:
James Gaffney (2013-2016), ASCUS
Joshua Shorenstein (2015-2016), Muse Biotechnology
Grant Gogul (2013-2015), ASCUS
Emily TerAvest (2013-2015)
Will van Treuren (2012-2014), Stanford University
Michael Oberg (2013-2014), University of Colorado Boulder
Elijah Lovelace (2014)
Matthew Gebert (2011-2013), University of Colorado Denver
Donna Berg-Lyons (2008-2014)
Juanma Peralta (2013-2013), UGR
Doug Wendel (2009-2013), Archer
Daniel McDonald (2008-2011)
Bill Shaffer (2009-2010)
Bob Larsen (2009-2010)
John Hayes (2009)
 
Visitors:
Sonia Rodriguez Ruano (2014)
Merete Eggesbo (2013)
Fred Delsuc (2012)
Juanma Peralta (2012)
Hongwei Zhou (2012)
 
Grad Students:
Jad Kanbar (2016)
Joshua Shorenstein (2012-2014)
Samuel Way (2013-2014)
Adam Robbins-Pianka (2013-2015), Elyxor
Sophie Weiss (2013-2015), SomaLogic
Daniel McDonald (2011-2015), Institute of Systems Biology
Luke Ursell (2011-2015), Biota
Nigel Cook (2010-2011)
Meg Pirrung (2009-2013)
Tony Walters (2009-2014), Max Planck Institute
Antonio Gonzalez-Peña (2010-2012)
Jeremy Widmann (2005-2007), Archer
Dan Knights (2009-2012), University of Minnesota
Justin Kuczynski (2008-2011), Second Genome
Jessica Metcalf (2006-2011), Colorado State University
Jesse Zaneveld (2006-2011), Oregon State University
Micah Hamady (2004-2009), TwistBio
Sandra Smit (2004-2008), Wageningen
Shandy Wikmann (2004-2006)
 

Undergraduates:
Kayla Orlinsky (2015-present)
Lindsay Deright Goldasich (2015-present)
Megan Lau (2015)
Cole Heale (2015-present)
Zach Owyang (2015-present)
Michael Leung (2015-present)
Alec Bibat (2013-2014)
Matthew Malone (2014)
Genevieve Bennett (2014)
Tim Vigers (2013)
Kathy Holt (2013)
Elijah Lovelace (2013)
Catherine Nichols (2012-2013)
Kyle Keeper (2012-2013)
Kumar Thurimella (2012-2013)
Will van Treuren (2009-2012), Stanford University
Becky Paulson (2009-2010)
Greg Humphrey (2009-2010)
Reece Gesumaria (2009-2010)
Ryan Kennedy (2007-2009)
Julia Goodrich (2008-2010)
Daniel McDonald (2004-2008)
Anh Vu (2007-2009)
Jonathan Griego (2008)
Jason Forbes (2006-2007)
Hazel Ozuna (summer 2007)
Nick Zhou (summer 2007)
Vikas Malaiya (2005-2007)
Stephanie Wilson (2005-2007)
Matthew Iyer (2006-2007)
John Quinn (2005-2006)
Preston Galais (2006)
Ian Sharp (2006)
Johnross Ford (2005)
Ravi Kumar (2005)
Michael Eaton (2004)
Roberto Marquez (summer 2004)