NorthenLab: Exometabolomics linking genomes with environments to understand how webs of microbes sustain biomes

People

Exometabolomics Lab

Environmental Genomics and Systems Biology

The Northen Lab is a multidisciplinary team of researchers based at the Lawrence Berkeley National Laboratory, a U.S. Department of Energy Office of Science supported lab, managed by the University of California, Berkeley. Our team supports various divisions of LBNL, including Environmental Genomics and Systems Biology (focused on understanding ecosystem dynamics), the Joint Genome Institute (a DOE Office of Science User Facility), and the Joint BioEnergy Institute (a research partnership dedicated to developing advanced biofuels).

Northen Lab Group
Joint Genome Institute (JGI) – Trent Northen’s group.


Current lab membersAlumni

Trent Northen

Principal Investigator

Ben Bowen

Principal Investigator

Amber Golini

Research Assistant

La Zhen Han

Research Assistant

Andrea Kuftin

Research Assistant

Noel Ha

Post-Doctoral Researcher

Yuntao Hu

Post-Doctoral Researcher

Rachel Neurath

Post-Doctoral Researcher

Lauren Jabusch

Post-Doctoral Researcher

Vlastimil Novak

Post-Doctoral Researcher

Andrew Osborn

Post-Doctoral Researcher

Marc Van Goethem

Post-Doctoral Researcher

Ying Wang

Post-Doctoral Researcher

Qing Zheng

Post-Doctoral Researcher

Margaret Lozano

Administrative Support

Vanessa Brisson

Research Affiliate

Kai Deng

Research Affiliate

Spencer Diamond

Research Affiliate

Johan Leveau

Research Affiliate

NorthenLab

Zoila Aponte
Email
Investigating microbial interactions and communities through grasses
I’m a first-year microbiology Ph.D. student at UC Berkeley. My main research interest is in microbial metabolic interactions and their impact on community establishment and dynamics. During my rotation in the Northen lab, I’m working to further understand interactions between Brachypodium distachyon and single bacteria and bacterial communities. We can do this by studying plant metabolic exudation and phenotypes in the presence or absence of bacteria, as well as by measuring the impact of plant exudates on bacterial growth.

NorthenLab

Richard Baran
Postdoc
Publications
Linkedin
Post-Northen Lab: Thermo Fisher Scientific, then Baran Biosciences
Research in Northen Lab: Mapping microbial metabolism and metabolic interactions
Essentially every untargeted metabolite profiling experiment we perform on bacteria reveals some portion of poorly or uncharacterized metabolites. This raises the intriguing question: are these metabolites the result of metabolic side reactions or are they physiologically important? Using metabolic footprinting and stable isotope tracing experiments we have shown that many of these compounds are taken up from the environment and catabolized or used biosynthetically. Using high-throughput screening of mutant libraries we have been able to identify transporters and enzymes required for the utilization of specific metabolites. We are currently using metabolite profiling to characterize metabolic interactions among soil bacteria (ENIGMA) and among members of biological soil crusts.

NorthenLab

Bailey Bonet
Affiliate
Graduate student at UC Berkeley

Sarah Brecht

Sarah Brecht
Student Assistant
Toxicology master student at North Carolina State University

NorthenLab

Xiaoliang Cheng
Postdoc
Research in Northen Lab: High throughput metabolic and activity screening
A major challenge in Synthetic Genomics is the disconnect between the rate of gene discovery and functional analysis. Determining the function of a gene now requires a disproportionate amount of effort relative to that required for gene identification. Similarly, construction of multigene pathways for biofuel production at Joint Bioenergy Institute (JBEI) is relatively straightforward and results in enormous clone libraries, however, only a small fraction of clones can be tested due to analysis constraints inherent with traditional LC/GC-MS analysis. We are addressing this analytical bottleneck using acoustic printing to transfer nanoliter volumes onto nanostructure-initiator mass spectrometry surfaces, enabling us to perform 10,000’s of assays/day, an increase in throughput of 1000-fold.

matthew_chu

Matthew Chu
Student Assistant
 

JasonCole

Jason Cole
Student Assistant
 Student at California State University, East Bay

NorthenLab

Estelle Couradeau
Email
ResearchGate
Personal Website
Research in Northen Lab: Soil physical structure matters!
Recent advances in microbial ecology have demonstrated that microbial communities are ubiquitous, diverse and provide critical ecological services. I aim to take these surveys of microbial diversity one step further by implementing labeling techniques to determine which fraction of the community is metabolically active and which microbes physically interact. This particular project will use BONCAT labeling coupled to single particle sorting in order to answer these fundamental questions in the framework of soil science.

NorthenLab

Megan Danielewicz
Postdoc
Post-Northen Lab: Gilead Sciences, Inc.
Research in Northen Lab: Metabolomics of Microbial Interactions
Environmental microbes exist as part of complex, structured and interdependent communities that are central to earth’s biogeochemical processes and as we are learning human health. Indeed the multicellularity of these communities improves metabolic efficiency and robustness over isolated cells. However, the rules governing the assembly and interactions that define the structure and stability of these communities are essentially unknown. Both known and unknown interactions are examined using GCMS and LCMS to observe the uptake and release of small molecules to elucidate the basis of their interactions.

NorthenLab

David Deng
Student Assistant
Research in Northen Lab: Learning to use python for metabolite analysis

NorthenLab

Tristan de Rond
Affiliate graduate student from Keasling Lab
Research in Northen Lab: Expanding the scope of enzymatic reactions monitored using NIMS

NorthenLab

Todd Duncombe
Postdoc
Publications
JBEI
LinkedIn
Post-Northen Lab: ETH Zurich
Research in Northen Lab: Assay development at the interface of droplet microfluidics and mass spectrometry to streamline the discovery and optimization of biomanufacturing pathways.

NorthenLab

Onur Erbilgin
Postdoc
Publications
LinkedIn
Post-Northen Lab: Amyris, Inc.
Microbial Community Dynamics
Bacteria are often faced with several choices of what they’ll eat for lunch, and their options – as well as choices – can change gradually with the seasons or instantaneously once the cheeseburger you ate reaches your gut. Microbes generally live in very diverse consortia, where every species is trying to survive; this competition may affect the decisions that bacteria make when deciding what to eat. I am using exometabolomics to understand the resource preferences of microbes and using that information to try to understand how mixed-species communities might react to perturbations in the environment. My goal is to be able to harness this knowledge and change, or design, microbial communities to have a beneficial output.

NorthenLab

Oséias Rodrigues Feitosa Junior
Affiliate, visiting graduate student
Graduate Student at Universidade de São Paulo (USP). Instituto de Química (IQ)
Research in Northen Lab: Unveiling a plant-pathogen’s metabolome
The phytopathogen Xylella fastidiosa colonize and cause disease on susceptible plant hosts such as orange trees and grapevines. Specifically, we use LCMS/GCMS/MSI metabolomics approaches to investigate the virulence and pathogenicity mechanisms evolved by X. fastidiosa strains, including the role of XFDSF (diffusible signal factor, molecule relevant for quorum sensing system) on metabolites profile, as well as whether it can influence the metabolic profile produced in co-culture. Finally, these studies aim to a better understanding of X. fastidiosa to establish mechanisms in the plant considering the competition and/or cooperation with endophytic.

NorthenLab

Curt Fischer
Affiliate
Publications
 Post-Northen Lab: Head of the Metabolic Chemistry Analysis Center at Stanford University

NorthenLab

Jian Gao
Postdoc
Publications
ResearchGate
Research in Northen Lab: High Sensitivity Nanostructure-Initiator Mass Spectrometry (NIMS)
NIMS is a matrix free laser desorption/ionization mass spectrometry technique, and has high sensitivity and low background of direct analyzing a wide range of samples, such as small molecules, biofluids, tissues, peptides and single cells. NIMS sensitivity highly replies on its nanostructured surface, which is traditionally generated by electrochemical etching of highly doped crystalline silicon in a hydrofluoric acid bath. My research interests are focused on understanding the morphology-selectivity relationships of this nanostructured NIMS surface, and also developing alternative approaches of fabricating NIMS surface with high reproducibility and sensitivity.

NorthenLab

Kristen Geibel
Email
Research in Northen Lab: Development of fabricated ecosystems I make custom fabricated ecosystems (EcoFABS) and set up and maintain live plants for experiments.

NorthenLab

Joshua Heinemann
Postdoc
JBEI
Post-Northen Lab: Cascade Fluidics
Research in Northen Lab: Development of microfluidics based NIMS techniques to improve engineered organisms for biofuel and natural product synthesis
One goal of the Joint BioEnergy Institute at LBNL is to engineer organisms for synthesis of biofuel and other natural products. However, the amount of biological diversity in nature makes it difficult for scientists to test all enzymatic systems and conditions for optimal natural product synthesis. To overcome this, I develop technology which integrates droplet based microfluidics with nanostructure-initiator mass spectrometry (NIMS) to simultaneously screen thousands of different biological conditions. This technology aims to support the informed design of engineered organisms in biofuel and natural product synthesis.

Nicole Ing
Email
Development of high-throughput enzyme assays to study enzymes involved in lignocellulosic breakdown
Identifying enzymes responsible for the deconstruction of lignin and cellulose (hemicellulose) is critical for the development of biofuels and bioproducts. I am utilizing nanostructure-initiator mass spectrometry (NIMS) to identify and characterize the activities of enzymes acting on lignin and cellulose substrates. Our high-throughput platform enables rapid characterization of enzymatic activity and can be used to screen large libraries of strains. The goal of this research is to better understand and optimize specific enzyme activities to ultimately enhance the production of lignocellulose-derived biofuels and bioproducts.

StefanJenkins

Stefan Jenkins
Staff
Post-Northen Lab: Intrexon Corp.
Research in Northen Lab: Developing large-scale profiling applications to understand complex metabolic processes in cellular systems
Despite significant interest and efforts in mass spectrometry-based metabolic profiling, there remain many technical and experimental challenges compared to other genomics and proteomics approaches. I am developing and applying robust and standardized experimental and computational workflows to increase metabolite coverage and enable the large-scale experiments necessary to understand complex metabolic processes and interactions in cellular systems and microbial communities.

NorthenLab

Mia Jones
Student Assistant
Post-Northen Lab: Imperial College London, Bachelor’s degree program in biochemistry

NorthenLab

Jacob Jordan
Email
Metabolomics Sample Processing

NorthenLab

Ashley Kang
Email
 

NorthenLab

Ulas Karaoz
Email
Publications
Research in Northen Lab: Understanding how microbiomes are structured and controlled using high-throughput sequencing and computational tools
As a computational biologist and bioinformatician, I have extensive experience handling large amounts of sequence (Gbs) and microarray data as well as using/developing statistical methods for their biological interpretation. My current research involves microbial communities from a wide range of environments some of which include foregut microbiomes from patients with esophageal adenocarcinoma, insect gut microbiomes, and soil and subsurface sediment microbiomes.

NorthenLab

Albina Khasanova
Email
Researching the impact of genetics and environment on plant roots and shoots
My current research interests center around the impact of genetics and environment on variation in root and shoot traits that effect plant establishment, growth, and resource use efficiency. I am currently utilizing the developing C4 perennial grass model system, Panicum hallii and its close relative switchgrass (P. virgatum, a leading biofuel candidate) to understand the genetic architecture of root traits and their relationship with shoot traits in order to develop a more complete picture of the adaptive differences that arise between ecotypes in response to abiotic and biotic changes in the environment. At the Northen lab, I will be working on profiling the root exudate composition of P. hallii ecotypes in the presence of synthetic microbial communities in order to investigate plant exudate/microbiome relationships and examine the impact of select microbiomes on plant productivity.

BeccaLau

Rebecca Lau Post-Northen Lab: UC San Diego
Research in Northen Lab: Exchange and cycling of nutrients – the stability and health of soils
We are trying to understand the role that soil microbes play in this process in two different environments – biological soil crusts that are made up of mostly sand, and a grassland field site in Oak Ridge, Tennessee – and how the composition and diversity of these microbial communities changes with metabolite availability. By profiling the metabolite uptake from individual microbes from these environments, we can try to infer their role in their ecosystem and how they may interact with other microbes.

NorthenLab

Hanneke Leegwater
Email
The Northen lab has developed MAGI (Metabolite Annotation and Gene Integration) to combine genomic information with metabolomics data. I will work on further development of MAGI and I will be using MAGI for untargeted metabolomics.

Carolina Leguina
Email
Determining relationships between copper, quorum sensing, and the rhizosphere microbes
In agriculture, copper has largely been utilized as sulphate or oxychloride salts for the control of phytopathogenic fungi. My project originates from the hypothesis that the presence of elevated concentrations of copper produces an alteration of the Quorum Sensing (QS) activity in rhizosphere microorganisms, which could have detrimental effects on plant growth-promoting microorganisms. QS systems are cell-to-cell signaling mechanisms that control the microbial physiology in response to signal molecules. The aim of this project is to increase the understanding of the interactions mediated by QS between rhizosphere microorganisms and the influence of copper on them by doing a study at a molecular level using metabolomics.

KyleLewald

Kyle Lewald
Student Assistant
 Student at University of California, Berkeley

NorthenLab

Andrea Lubbe
LinkedIn
Publications
Research in Northen Lab: Designing synthetic microbial consortia
Harnessing the bioprocessing capabilities of microbial consortia holds great potential for sustainable biofuel production from plant material. I am employing a Mass Spectrometry-based exometabolomics approach to track metabolite uptake, release and exchange between lignocellulose-degrading consortium members. By understanding these metabolic interactions, I aim to predictively construct a stable synthetic microbial consortium optimized for high energy biofuel production.

ConnieLy

Connie Ly
Administrative Support
 

NorthenLab

Maximino Manzanera
Affiliate
Visiting professor from the University of Granada in Spain studying plant growth promotion and microbial interactions.

Ritesh Mewalal
Email
Investigating plant-microbe interactions to increase agricultural production
I am interested in sustainable agriculture and how beneficial plant-microbe cohorts can be used to enhance the productivity of a wide range of crops including leafy greens, fruits, and vegetables. My research uses the EcoFABs with exometabolomics to validate and gain a mechanistic understanding of a microbial formulation specifically designed for increasing productivity of agricultural crops.

NorthenLab

Margarita Ros Munoz
Affiliate, visiting researcher
Publications
AgroWaste
Visiting Research Scientist from CEBAS-CSIC in Spain
Research in Northen Lab: The role of microbes in suppressive soils for the management of plant pathogens
I study the role that soil microbial communities play in suppressing plant pathogens using a combination of genetic, microbiology and metabolomics studies.

NorthenLab

Manuel Porcar
Publications
Porcar Lab at University of Valencia
Research in Northen Lab: Describing the microbial communities of extreme environments
I am an applied microbiologist leading the Biotechnology and Synthetic Biology Lab at the Cavanilles Institute of Biodiversity and Evolutionary Biology and the Integrative Systems Biology Institute of the University of Valencia (Spain). My research interests deal with bioprospecting (the search of microorganisms with biotechnological potential), particularly from extreme, undescribed and/or artificial environments such as insect guts feeding on toxic plants, coffee capsules machines or solar panels. I also work on the social perception of new technologies such as biotech and SynBio. In the Northen Lab, I will be performing metabolomics and metagenomics analyses of microbial communities collected from Berkeley area solar panels and comparing the results to existing data from Spain (see: dx.doi.org/doi:10.1038/srep29235).

NorthenLab

Nicholas Saicheck
Email
LinkedIn
High-throughput approaches for investigation of microbial interactions within synthetic microbial communities
There is an urgent need to improve our understanding of the connections between microbial community composition and interactions to their in situ activities. As a means of accomplishing this, my research focuses on the development of new tools and techniques that allow us to link biomarker-based proteomics with metabolomics in order to get a complete understanding of microbial dynamics in simple synthetic communities (SynComs).

Yasmeen Sawyer
Administrative Support
Email
 

NorthenLab

Joelle Schlapfer
Postdoc
Email
LinkedIn
Post-Northen Lab: Postdoc at the University of Zurich, Department of Plant and Microbial Biology
Research in Northen Lab: Plants interactions with beneficial and pathogenic microbes
Plants produce a vast variety of primary and secondary metabolites that are exported and sensed by microorganisms, Such processes are poorly understood to date. In the current project, I focus on understanding metabolite exchange between host plants and the pathogen powdery mildew.

LeslieSilva

Leslie Silva
Staff
Publications
Joint Genome Institute
Post-Northen Lab: Director of Analytical Chemistry at Ava Winery
Research in Northen Lab: Understanding microbial metabolism can help us understand soil metabolites and how microbes live in communities (JGI Metabolomics User Program)
My research focuses on a large scale exometabolomic study of soil microbes (actinobacteria and proteobacteria) from multiple field sites; we aim to understand substrate preferences, secondary metabolite production, and how these microbes coexist in diverse communities and extreme environments. Additionally, I run exometabolomic samples for the JGI user community which are typically related to understanding complex metabolic processes and interactions in microbial/plant communities (boiling springs, ocean, soil microbes, plant-microbe interactions). We also verify secondary metabolite production for the synthetic biology program within the JGI.

NorthenLab

Anita Silver
Email
Quantifying interactions between microbes using exometabolomic data
I am using concepts from community ecology, mechanistic modelling and statistics to develop quantitative metrics for predicting interactions between microbe strains from the exometabolomic data of individual strains. The data I am working with comes from the Web of Microbes, a database created by the Northen Lab, which contains changes in metabolite concentrations associated with individual microbes in different environments.

NorthenLab

Tami Swenson
Email
Publications
Post-Northen Lab: Toxicology Study Director at Covance
Research in Northen Lab: Microbial nutrient cycling in soilHow are nutrient levels affecting microbial communities and metabolites in soils- the largest pool of terrestrial organic carbon? I am using mass spectrometry based metabolite analysis and stable isotope probing to understand metabolite cycling in soils. Specifically, I am investigating the metabolite profiles of a variety of soils and exploring the accessibility and turnover of microbial-produced metabolites in soils and minerals. I am also interested in understanding how nutrients are stored in arid biological soil crust systems and how metabolite availability impacts microbial community structure.

NorthenLab

Jane Tanamachi
Administrative Assistant

NorthenLab

Tim Veth
Student Assistant
 

NorthenLab

Hayden Veytia
Student Assistant
 

Forrest Vogel
Email
Post-Northen Lab: Loyola Marymount University
Building fabricated ecosystemsI make custom fabricated ecosystems (EcoFABs) for use in plant microbiome studies.

NorthenLab

Michael Vu Research in Northen Lab: Sample Processing

NorthenLab

LinLin Wang
Affiliate
Visiting graduate student from Jinan UniversityMolecular recognition and interaction between triphenyltin and amino acids, inactive proteins, and active proteins of Bacillus thuringiensis.

NorthenLab

Katherine Whiting
Student Assistant
Post-Northen Lab: University of Edinburgh, Master’s degree program in neuroscience

NorthenLab

Jordan Wilson
Undergraduate Student Assistant
UC Berkeley Internship Program

NorthenLab

Jinshao Ye
Visiting Professor from Jinan University
Publications
Research in Northen Lab: The role of microbes in bioremediation processes
My research interests mainly focus on revealing the role of microbes in bioremediation processes, including extracellular degradation, microbial surface binding, active transport and intracellular transformation of pollutants by using proteomics and metabolomics approaches.

ZheyunZhang

Zheyun Zhang
Postdoc
Research in Northen Lab: EcoFAB – discovering the genetic basis of beneficial microbiomes to improve crop productivity
The plant microbiome plays a crucial role in plant health and productivity. Harnessing beneficial plant microbiomes has the potential to sustainably increase agricultural productivity, improve soil fertility and decrease the environmental impact of agriculture. Using EcoFAB (Ecosystem Fabricator) integrated with exometabolomics and isotope labeling, we aim to discover mechanisms and principles for plant – soil microbiome interactions in the rhizosphere. Using synthetic biology tools, we can unravel the spatial-temporal distribution of metabolite production and control beneficial plant-microbiomes for enhancing both low-input crop productivity and metabolite storage.
Additional alumni: Wolfgang Reindl (Evotec), Nicholas Justice (UC Berkeley), Karen Andrade, David Soendjojo, Bin Yoo, Do Yup Lee (Kookmin University), Nicholas Jose, Kriti Sondhi (Amazon), Annika Mosier (University of Colorado, Denver), Manpreet Kaur (Teach for America), Daniel Hartono (Capricor Therapeutics), Alexandra Walling, Jasmine Sanghera (UC Berkeley), Erika Cagampan (UC Berkeley), Gabriella Boulton (UC Berkeley)