People


Exometabolomics Lab

Environmental Genomics and Systems Biology

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

Principal Investigators

TrentNorthen

Trent Northen
Email
Publications
Eco-FAB
Understanding the dynamic processes by which microbial community metabolism transform biopolymers and metabolites within their environment.
We are interested how microbial communities are structured by the biopolymers and metabolites in their environment and the dynamic and reciprocal processes by which they transform these pools. Central to these efforts are the development of mass spectrometry approaches to study these processes including exoenzyme activity profiling, exometabolomics and mass spectrometry imaging. Together these allow us to comprehensively characterize metabolic activities, dynamics and localization within complex cellular systems to predict responses and design interventions.

BenBowen

Ben Bowen
Email
Publications
OpenMSI
Metabolite Atlas
Understanding biological mechanisms associated with change
Understanding complex, dynamic metabolic networks in an environmental context will require utilization of emerging technologies. These datasets generated are often large-scale both in terms of complexity and raw-size making them difficult to mine for biological insight. Ben is leading several computational efforts including Metabolite Atlas and OpenMSI to make the most high-performance, advanced data management, model building, analysis and visualization resources for mass spectrometry accessible to all scientists via the web.
Staff

SuzieKosina

Suzie Kosina
Email
Publications
Using exometabolomics to predict microbial interactions
In many ecological systems, microorganisms exist in communities. What drives the interactions between these organisms and with their environments is of great interest for predicting the effects that changes to environmental conditions (rainfall, temperature and flora/fauna) will have on soil fertility, green house gas sequestration/release, community structure, etc. I use mass spectrometry based exometabolomics data and total organic carbon analysis to understand how individual microorganisms transform their environments and use this information to predict and test interactions between microorganisms.

AndreaKuftin

Andrea Kuftin
Email
JGI Metabolomics User Program

As part of the Metabolomics group at JGI, we characterize the metabolite profile of organisms to gain insight and create linkages between sequence and function.

BeccaLau

Rebecca Lau
Email
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

Katherine Louie
Email
Publications
JGI Metabolomics User Program

As part of the Metabolomics group at JGI, we characterize the metabolite profile of organisms to gain insight and create linkages between sequence and function.

NorthenLab

Tami Swenson
Email
Publications
Microbial nutrient cycling in soil
How 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.
Post-doctoral researchers

NorthenLab

Peter Andeer
Email
Nutrient turnover in grassland soils
Grassland soils contain a significant portion of the Earth’s carbon, yet the mechanisms that influence nutrient cycling in these ecosystems are not well understood. In collaboration with the laboratories of Prof. Jill Banfield (UC Berkeley) and Dr. Chongle Pan (Oak Ridge National Laboratory) we are performing multi-omics analyses of soils at Angelo Coastal Reserve to examine the interrelationships between microbial communities and metabolites surrounding Fall rainfalls. I am then using stable isotope probing to determine direct linkages between the sequenced microbial communities and the compounds identified using untargeted exometabolomics.

NorthenLab

Estelle Couradeau
Email
ResearchGate
Personal Website
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

Markus de Raad
Email
Publications
LinkedIn
Increasing throughput: developing high throughput mass spectrometry-based assays
Traditional LC/GC-MS methods are often low-throughput. Nanostructure-initiator mass spectrometry (NIMS) presents a powerful alternative to standard LC/GC-MS methods. NIMS has extremely high sensitivity and lateral resolution, which allows the disposition and analysis of ~10,000 samples. I am developing novel high-throughput mass spectrometry assays by integrating nanoscale sample deposition methods into NIMS. I apply these assays, for example, on activity screening of peptoid/peptide libraries and small molecule uptake/synthesis in microbial/cellular systems.

NorthenLab

Todd Duncombe
Email
Publications
JBEI
LinkedIn
Assay development at the interface of droplet microfluidics and mass spectrometry to streamline the discovery and optimization of biomanufacturing pathways.

NorthenLab

Onur Erbilgin
Email
Publications
LinkedIn
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

Jian Gao
Email
Publications
ResearchGate
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

Joshua Heinemann
Email
JBEI
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.

NorthenLab

Andrea Lubbe
Email
LinkedIn
Publications
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.

NorthenLab

Joelle Schlapfer
Email
LinkedIn
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.

KaterynaZhalnina

Katerina Zhalnina
Email
The role of microorganisms in the rhizosphere priming of soil organic matter decomposition.
I am interested in physiological, biochemical and evolutionary aspects of plant-microbial interactions and how these interactions mediate biogeochemical cycles.
Plant-soil-microbial crosstalk is operated through complex nutrient exchanges, where plant-released exudates can be consumed by rhizosphere communities. This can mediate microbial metabolism triggering microbial response that may be involved in nutrient stabilization/destabilization in soils – rhizosphere priming. I am using genomic analysis of a rhizosphere community to define metabolic traits that outline mutualistic relationships between microorganisms and plants in soil (e.g. extracellular enzymes, nutrient transporters). I am also using exometabolomic analysis and profiling of exoenzymes activities to evaluate what microbes uptake from the plant-exuded compounds, and how they respond to the plant exudation through release of metabolites and changing exoenzymatic activities.

ZheyunZhang

Zheyun Zhang
Email
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.
Research affiliates

NorthenLab

Kai Deng
Email
JBEI
Development of high throughput enzyme assays to study glycoside hydrolases and lignases
Enzymes play the central role in converting celluloses (hemicelluoses) into simple fermentable sugars and in the deconstruction of lignin. I am developing new assays and high-throughput assay platforms to provide functional annotations for various enzymes and enzyme-variants. This involves the utilization of surface-based nanostructure-initiator mass spectrometry (NIMS), Labman, Biomek automation workstation and microscale liquid handling by acoustic printer. The goal is to provide rapid feedback of the activities of enzymes of interest and help the development of high performance strains.

NorthenLab

Tristan de Rond
Keasling Lab
Tristan is a graduate student in Jay Keasling’s lab and collaborates with the Northen lab on expanding the scope of enzymatic reactions that can be monitored using NIMS

NorthenLab

Spencer Diamond
Publications
LinkedIn
ResearchGate
Metagenomics and Metabolomics of Grassland Soils.
I am using a combinatoral approach of genomics and untargeted metabolomics to asses how metabolites are cycled in the terrestrial subsurface of grassland soils. This research means to asses how bacteria on a species level respond to rainfall events, as well as increased rainfall in our study area (the Angelo Coast Reserve). This study is a collaboration between the Northern laboratory and the laboratory of Prof. Jill Banfield at UC Berkeley.

NorthenLab

Ulas Karaoz
Email
Publications
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

Manuel Porcar
Publications
Porcar Lab at University of Valencia
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

Jinshao Ye
Visiting Professor from Jinan University
Publications
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.
Student/Intern Researchers

JasonCole

Jason Cole
Email
Student Assistant

KyleLewald

Kyle Lewald
Email
Student Assistant
Administrative support

Jane Tanamachi

jane_tanamachi

Margaret Lozano

Alumni

NorthenLab

Richard Baran
postdoctoral researcher
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

 

NorthenLab

Xiaoliang Cheng
postdoctoral researcher
 

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.

NorthenLab

Megan Danielewicz
postdoctoral researcher
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

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

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.

ConnieLy

Connie Ly
Administrative Support

NorthenLab

Oséias Rodrigues Feitosa Junior

affiliate, visiting graduate student

Graduate Student at Universidade de São Paulo (USP). Instituto de Química (IQ)

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

Margarita Ros Munoz
Affiliate, visiting researcherPublications
AgroWaste
Visiting Research Scientist from CEBAS-CSIC in Spain

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.

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

LinLin Wang
Affiliate,
Visiting graduate student from Jinan University
Visiting graduate student from Jinan University

Molecular recognition and interaction between triphenyltin and amino acids, inactive proteins, and active proteins of Bacillus thuringiensis.

NorthenLab

Jordan Wilson
Undergraduate Student Assistant
UC Berkeley Internship Program
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)