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My Passion

Exploration of Earth's microbial and viral diversity is a major scientific frontier. Sequencing DNA - the blueprint of life - collected directly from the environment provides a powerful way to access the uncatalogued microbial diversity on our planet. These uncharacterized lifeforms are ripe with novel functions, metabolisms, the potential for biotechnological and medical applications, and will inform us on the evolution of all life.

My previous work has explored the nature and extent of microbial life underground and below the seafloor using tools rooted in molecular biology, biogeochemistry, and microbiology. Now I am working to explore novel microbial diversity in additional environments through the leveraging of ultra-powerful computational resources and true access to massive genome databases (i.e. big data).

Check out my work featured in popular media outlets!

                                            

Curriculum Vitae

Programming (4 pages)     Academic, Short (4 pages)     Academic, Long (20 pages)

Professional Appointments

2019-present, Data Scientist, Lawrence Berkeley National Laboratory, Department of Environmental Genomics & Systems Biology, Berkeley, CA

2019-present, Affiliate Scientist, University of California, Department of Bioengineering, Berkeley, CA

2017-2019, Computational Biologist Fellow, Lawrence Berkeley National Laboratory, Joint Genome Institute, Walnut Creek, CA

2016-2017, Independent Scientist, Honolulu, HI

2015-2016, Research Associate, University of Southern California, Department of Earth Sciences, Honolulu, HI

2014-2015, Research Scholar, University of Hawaii, Department of Oceanography, Honolulu, HI

Education

2014  PhD  Oceanography, University of Hawaii

2007  BS   Biology and Bacteriology, University of Wisconsin

Selected Awards and Honors

U.S. Department of Energy Joint Genome Institute Computational Biology Postdoctoral Fellowship, Recipient

University-National Oceanographic Laboratory System Deep-Submergence Science Leadership Cruise, Invited Participant

Deep Carbon Observatory Origins and Movements of Subsurface Microorganisms Workshop, Invited Participant

Consortium for Ocean Leadership U.S. Science Support Program Marine Geoscience Leadership Symposium, Invited Participant

National Science Foundation Ecological Dissertations in the Aquatic Sciences Symposium, Invited Participant

Center for Dark Energy Biosphere Investigations Graduate Student Fellowship, Recipient

Consortium for Ocean Leadership U.S. Science Support Program Schlanger Ocean Drilling Fellowship, Recipient

Teaching

Fundamentals of Oceanography
Fundamentals of Microbiology

Selected Presentations

Jungbluth SP, Kirton E, Roux S, Wu D, Nielsen T, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA (2017, July) Illuminating the phylogenetic breadth and metabolic potential of microbial life with thousands of archaeal metagenome-assembled genomes. Archaea: Ecology, Metabolism & Molecular Biology – Gordon Research Conference, Waterville Valley, NH.

Rappe MS, Jungbluth SP, Lin H-T, Nigro OD, Steward GF (2016, March) The distribution, diversity, and function of microbial and viral communities inhabiting anoxic crustal fluids within deep subseafloor basalt. Presented at the Joint Genome Institute Users Meeting, Walnut Creek, CA.

Jungbluth SP, Glavina del Rio T, Tringe S, Stepanauskas R, Rappe MS (2015, December) Ecogenomic characterization of a marine microorganism belonging to a Firmicutes lineage that is widespread in both terrestrial and oceanic subsurface environments. Presented at the fall meeting of the American Geophysical Union, San Francisco, CA.

Nigro O, Jungbluth SP, Lin H-T, Rappe MS, Steward G (2015, December) Archaeal viruses contribute to the novel viral assemblage inhabiting oceanic, basalt-hosted deep subsurface crustal fluids. Presented at the fall meeting of the American Geophysical Union, San Francisco, CA.

Nigro O, Jungbluth SP, Lin H-T, Hsieh C-C, Mueller J, Schvarcz C, Rappe MS, Steward G (2015, February) A first look at a deep subsurface viral community from the basement fluids of the Juan de Fuca Ridge flank. Presented at the American Society for Limnology and Oceanography Aquatic Sciences Meeting, Grenada, Spain.

Lloyd KG, Bird J, Steen AD, Buongiorno J, Jungbluth SP (2015, January) Insights from the first deep subsurface single cell genomes and development of digestR, a new tool for metagenomic analysis. Presented at the Center for Dark Energy Biosphere Investigations NSF Site Visit, Los Angeles, CA.

Jungbluth SP, Lin H-T, Hsieh C-C, Rappe MS (2014, December) High-resolution temporal analysis of deep subseafloor microbial communities inhabiting basement fluids. Presented at the fall meeting of the American Geophysical Union, San Francisco, CA.

Carr S, Jungbluth SP, Lin H-T, Rappe MS (2014, December) Investigating chemotactic potential within crustal fluid communities. Presented at the fall meeting of the American Geophysical Union, San Francisco, CA.

Orcutt BN, Sylvan J, Rogers D, Lee R, Girguis P, Carr S, Jungbluth SP, Rappe MS (2014, December) Carbon fixation in oceanic crust: does it happen, and is it important?. Presented at the fall meeting of the American Geophysical Union, San Francisco, CA. (Invited Presentation)

Jungbluth SP, Bowers R, Lin, H-T, Hsieh C-C, Cowen JP, Rappe MS (2012, December) Microbial diversity within Juan de Fuca ridge basement fluids sampled from oceanic borehole observatories. Presented at the fall meeting of the American Geophysical Union, San Francisco, CA. (Invited Presentation)

Invited Seminars

Jungbluth SP (2019, January) Microbial genomics of marine and terrestrial biomes and opportunities for collaborative science. Seminar presented to the Systems Biology Knowledge Base (KBase). Lawrence Berkeley National Laboratory, Berkeley, California

Jungbluth SP (2016, January) Investigating novel microbial life in the deep igneous oceanic crust. Seminar presented at the Department of Earth Sciences Paleoenvironmental Seminar Series. University of Southern California, Los Angeles, California

Jungbluth SP (2015, November) Microbial life in the deep subseafloor igneous basement: a frontier of exploration. Seminar presented at the Marine Environmental Biology Department Retreat. USC Wrigley Institute for Environmental Studies, Catalina Island, California

Jungbluth SP (2014, October) Juan de Fuca Ridge flank basement fluid microbiology. Seminar presented as part of the Center for Dark Energy Biosphere Investigations Networked Speaker Seminar Series. [Broadcast Online]

Jungbluth SP (2014, October) Microbial diversity in anoxic, subseafloor basaltic fluids. Seminar presented at the Astrobiology Seminar Series. University of Hawaii, Honolulu, Hawaii

Professional Activities

Member of: American Society for Microbiology, Association for the Sciences of Limnology and Oceanography, American Association for the Advancement of Science, American Geophysical Union, Astrobiology Society, International Society for Microbial Ecology, International Society for Subsurface Microbiology, The Oceanography Society

Reviewer for: Environmental Microbiology, Frontiers in Microbiology, The ISME Journal, National Science Foundation (Biological Oceanography), PLoS ONE

My research

Exploration of the Deep Biosphere

Summary: For over seven years I worked on a team that was tasked with exploration of the deep subseafloor biosphere using manned and unmanned deep submersibles and ocean drilling program boreholes. In the deep-sea, we sampled fluids filling the spaces and microfractures in the basaltic rock using hundred meter long pipes installed into the seafloor. This technology provided an access point to the remote deep ocean volcanic rock and the extreme microbial lifeforms that live there.

CORK-infographic

Above: Infographic describing how we access microorganisms in the deep subseafloor. Full-size Version (6.7 MB)

Genomics of Subsurface Bacteria and Archaea

Summary: The genomic repertoire of bacteria and archaea inhabiting the subsurface are revealing clues to the adaptations required for life to survive in an environment devoid of sunlight. Cutting-edge DNA sequencing techniques and bioinformatics tools allow for recovery of near-complete genomes from environmental samples and are allowing for unprecedented investigations into the genomic potential of microbial communities.

genomics

Above: Genomic comparisons reveal clues to the metabolic features and adaptations of deep subsurface life.

Diversity of Microorganisms Inhabiting Igneous Rock

Summary: The diversity of microbial life inhabiting the rocky parts of Earth are poorly described. Microbes living on and inside rocks slowly eat the minerals and participate in the weathering of the Earth on global scales. Understanding the diversity of Bacteria and Archaea in the subsurface of the global ocean and basins and the role of this diversity in establishing community functioning is of high interest to me.

microbial-div

Above: Understanding the abundance and diversity of microbes in the environment helps to understand the hidden functions that occur there.

Viruses in the Deep Subsurface

Summary: The diversity of viruses on the planet is among the least catalogued of all life. I have been working to describe the diversity of novel viruses in the deep marine subseafloor and explore their genomic composition and potential for interaction with the other domains of life.

viruses

Above: Viral diversity investigations enabled by viral metagenomics are revealing novel thermophilic viruses. Analysis of microbial CRISPR sequences and spacers allows for understanding of virus-host dynamics in the environment.

Professional Development for Scientists

Summary: In addition to research, I believe it is important to promote diverse professional development opportuntities for young scientists. There are more professionally-trained scientists than academic positions allow, so additional useful modes of employment must be made available to trainees.

prof-dev

Above: Trainees are facing a harsh employment situation upon graduation and networking is key to success.

Image Portfolio

Science communication relies on the art of figure design. Here are some example figures I've designed for research publications - please enjoy!

Publications

Google Scholar     PubMed     ORCID     Mendeley     ResearcherID    

Publication Graphical Summary

For a full list of publications, see Google Scholar.

Consulting

Computational biology is a rapidly developing field, and so knowledge of the best workflow or required suite of packages necessitates an understanding of biology and scripting. That's where my knowledge of microbiology, molecular biology, genomics and informatics can help! Bioinformatic consultation services I can provide will allow you to construct fully-customized informatic pipelines.

Academic and commercial clients are provided consultation for an hourly or fixed price fee. Rates are negotiable and are on a case-by-case basis. Please contact me if interested.

Published Software

Links correspond to various software and tools I've written and published online.

Applications

kb_iMAG-viz

kb_iMAG-viz is a KBase implementation of the iMAG-viz pipeline. iMAG-viz is a tool designed for quality-checking microbial genome data. Stay tuned for a more complete description and working demo.

under-construction

Tools/Utilities

git-commit-timeline

Git Commit Timeline is a Shell utility to show your Github commit history as a series of histogram plots separated by repository. I wrote this one weekend while taking a deep dive into the nuances of Shell scripting.

git-commit-timeline

kb_sdk_icon_generator

kb_sdk_icon_generator is a tool for auto-generation of icons for KBase SDK Apps. I wrote this to speed up the process of generating files/content for these applications.

kb_sdk_icon_generator

scholar-annotator (unpublished; under development)

scholar-annotator is an Rscript to, through the use of visualization, produce a narrative to accompany one's Google Scholar publication record. I wrote this because I was tired of updating my personal website to reflect newest publications, etc., and further, I thought that the information and convenient data structures provided by Google Scholar were a relatively untapped opportunity to explore further.

scholar-annotator

KBase-app-navigator (unpublished; under development)

KBase-app-navigator presents a way to visualize the relatedness of KBase Apps based on the required input and output data types. I wrote this application because I found it challenging to sense the available KBase Apps for distinct analysis workflows. My current plan is to develop this further before releasing.

kbase-app-navigator
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Data

Subseafloor Biosphere

BCO-DMO

Link to BCO-DMO Data Entree

Download BCO-DMO Data (.xlsx)

The BCO-DMO link will help you access data related to my publications. Please let me know if you can't find some data or information that you need.

Jungbluth et al. 2013 The ISME Journal

NCBI Genbank Sequences (n=501)

This link takes you to the SSU rRNA sequence data from borehole crustal fluid and seawater microbial communities. These sequences were published with the paper.

NCBI Genbank Sequences (n=27) from unpublished data.

This link takes you to the SSU rRNA sequence data from borehole crustal fluid microbial communities. These data are unpublished but generated with different gene primers from an identical sample used in the publication.

Jungbluth et al. 2013 Proceedings of the Integrated Ocean Drilling Program

NCBI Genbank Sequences (n=80)

This link takes you to the SSU rRNA sequence data from sediment microbial communities.

Jungbluth et al. 2014 Frontiers in Microbiology

NCBI Genbank Sequences (n=99)

This link takes you to the SSU rRNA sequence data from borehole crustal fluid microbial communities.

Robador et al. 2015 Frontiers in Microbiology

NCBI Genbank Sequences (n=31)

This link takes you to the dsrAB sequence data from borehole crustal fluid microbial communities.

NCBI BioProject entree

This link takes you to the SSU rRNA amplicon sequence data from borehole crustal fluid microbial communities.

Jungbluth et al. 2016 The ISME Journal

NCBI Genbank Sequences (n=192)

This link takes you to the SSU rRNA sequence data from borehole crustal fluid, sediment, and seawater microbial communities.

NCBI BioProject entree

This link takes you to the SSU rRNA amplicon sequence data from borehole crustal fluid, sediment, and seawater microbial communities.

Jungbluth et al. 2017 Scientific Data

NCBI BioProject entree for samples used for metagenomics.

IMG/MER sample entree for U1362A metagenome data.

IMG/MER sample entree for U1362B metagenome data.

Files needed to isolate scaffold sets for all 98 metagenome-assembled genomes (MAGs) in IMG/M.

FASTA files containing the contigs of all 98 metagenome-assembled genomes (MAGs).

FASTA file containing 54 SSU rRNA genes with length >300 base pairs extracted from the 98 metagenome-assembled genomes (MAGs).

IMG/M annotations associated with the scaffolds of all 98 metagenome-assembled genomes (MAGs).

Jungbluth et al. 2017 PeerJ

EMIRGE reconstructed SSU rRNA genes from U1362A and U1362B metagenome data.

Basaltic Ice Cave

Unpublished data

NCBI BioProject entree unpublished samples used for SSU rRNA amplicon sequencing.

This link takes you to the SSU rRNA amplicon sequence data from Hawaii ice cave microbial communities.

News

2017, Mar 7: A new publication lead by Olivia Nigro is now published! Check out the first description of the virosphere in Earth's deep subseafloor aquifers!

2017, Feb 1: I'm excited to be starting as a Computational Biology Postdoctoral Fellowship at the DOE Joint Genome Institute! Here I'll be working with Dr. Emiley Eloe-Fadrosh and others to explore new lineages of life!

Contact

jungbluth dot sean at gmail dot com

Fun Science Stuff

Oceanographic Expeditions and Field Work

Above: Map of locations where I've embarked on oceanographic expeditions and other field work.

Atlantic Continental Shelf, URI Inner Space Center shore-based participant, AT36 (Aug 3 – Aug 8, 2016)

Atlantic Continental Shelf, R/V Atlantis – HOV ALVIN-II and AUV Sentry cruise participant, AT36 (July 28 – Aug 2, 2016)

Juan de Fuca Ridge flank, R/V Atlantis – HOV ALVIN-II cruise participant, AT26-18 (August 10 – August 24, 2014)

Juan de Fuca Ridge flank, R/V Atlantis – ROV JASON-II cruise participant, AT26-03 (July 13 – July 26, 2013)

North Pacific Subtropical Gyre, R/V Kilo Moana cruise participant, KM12-23 & HOT 247 (October 6-10, 2012)

North Pacific Subtropical Gyre, R/V Kilo Moana cruise participant, KM12-18 & HOT 245 (August 16-20, 2012)

North Pacific Subtropical Gyre, R/V Kilo Moana cruise participant, KM12-16 & HOT 244 (July 30 – August 3, 2012)

North Pacific Subtropical Gyre, R/V Kilo Moana cruise participant, KM12-13 & HOT 243 (June 25-29, 2012)

North Pacific Subtropical Gyre, R/V Ka’Imikai-O-Kanaloa cruise participant, KOK12-05 & HOT 242 (May 29 – June 2, 2012)

North Pacific Subtropical Gyre, R/V Ka’Imikai-O-Kanaloa cruise participant, KOK12-02 & HOT 241 (April 30 – May 4, 2012)

North Pacific Subtropical Gyre, R/V Kilo Moana cruise participant, KM12-05 & HOT 240 (March 23-27, 2012)

North Pacific Subtropical Gyre, R/V Ka’Imikai-O-Kanaloa cruise participant, KOK12-01 & HOT 239 (January 17-21, 2012)

Juan de Fuca Ridge flank, R/V Atlantis – ROV JASON-II cruise participant, AT18-07 (June 28 – July 14, 2011)

Juan de Fuca Ridge flank, D/V JOIDES Resolution shore-based participant, IODP Expedition 327

Juan de Fuca Ridge flank, R/V Atlantis – ROV JASON-II cruise participant, AT15-66 (June 13 – July 1, 2010)

Juan de Fuca Ridge and ridge flank, R/V Atlantis – DSV Alvin cruise participant, AT15-51 (August 20 – September 6, 2009)

West Coast of Oahu, Hawaii, R/V Kilo Moana cruise participant, KM09-06 (February 12 – February 15, 2009)

Juan de Fuca Ridge flank, R/V Atlantis – DSV Alvin cruise participant, AT15-35 (July 24 – August 14, 2008)

Photos

jQuery Slider

Videos

Under Construction

Rank Country Population % of world population Date
1 中华人民共和国 (People's Republic of China) 1,370,570,000 18.9% June 24, 2015
2 India 1,273,140,000 17.6% June 24, 2015
3 United States "USA" 321,268,000 4.43% June 24, 2015
4 Indonesia 255,461,700 3.52% July 1, 2015
5 Brazil 204,503,000 2.82% June 24, 2015
6 Pakistan 190,156,000 2.62% June 24, 2015
7 Nigeria 183,523,000 2.53% July 1, 2015
8 Bangladesh 126,880,000 2.19% June 24, 2015