Microbial Growth, Interactions and
Biogeographies from ‘Omics Data

Jed Fuhrman
University of Southern California

My lab’s contribution to CBIOMES will be three-fold: First we will use “data mining” to retrieve information about the distributions, activities, and potential activities of a broad variety of marine microorganisms, in large part from gene sequence databases. working with data experts and modelers we plan to optimize the use of these data as input towards the development of an ocean atlas of microbial identities and activities.

Second, again in collaboration with CBIOMES mathematicians and modelers, we will develop and improve models designed to use quantitative atlas data and other environmental data sources to determine associations and potential interactions among and between different kinds of microbes. Such associations could include positive ones (organisms in effect working together) or antagonistic ones (such as competition, predation, parasitism or chemical antagonism).

Thirdly we will evaluate a promising new approach to simultaneously determine the growth rates of many different kinds of microbes from the within-genome distributions of DNA extracted from mixed populations. Such growth rate information is extremely valuable when modeling an ecosystem. We expect that for some organisms at least, the information may be extracted from the billions of sequences generated by now-popular metagenomic studies, whereby the entire microbial community DNA is extracted, fragmented and sequenced as random pieces. This new approach requires determining which sequenced fragments belong in which organism and how they are ordered in the genome. We will test this method with laboratory cultures and manipulated field samples at known growth rates.

CBIOMES Collaborators in the Fuhrman Lab

News from the Fuhrman Group

CBIOMES Welcomes Yubin Raut

A warm welcome to postdoc Yubin Raut who recently joined the USC-Fuhrman CBIOMES Group. (more…)

August 2021 CBIOMES e-meeting Jake Weissman (USC)

“Predicting maximal growth rates from genomes and metagenomes for prokaryotes and eukaryotes.” Please note access to this page is restricted to CBIOMES associates. (more…)

In the Mix

The Fuhrman Group uses 'omics data to better understand microbial growth, interactions, and biogeographies. Recent research has been focused on evaluating a promising new approach to simultaneously determine the growth...

CBIOMES Welcomes New Fuhrman Lab Manager Kema Malki

A warm welcome to Kema Malki who joined the USC-Fuhrman CBIOMES Group last month. (more…)

Recordings and microtalks from the Fuhrman Lab. Please note access to this page is restricted to CBIOMES associates. (more…)


Yi-Chun Yeh, Jesse C McNichol, David M Needham, Erin B Fichot, Jed A Fuhrman, Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities and denoising algorithms, Envir. Microbiol., doi: 10.1111/1462-2920.15553 Get the...

CBIOMES Welcomes Four Graduate Students

A warm welcome to Delaney Nolin and Rae Santora from USC, and Lexi Jones and Ari Krinos from MIT as they bring their skills and energy to the CBIOMES collaboration....

February 2021 CBIOMES e-meeting Sarah Laperriere (Fuhrman Lab, USC)

"Diverse seasonal dynamics of large viruses infecting eukaryotes in a long-term metagenomic time-series" Please note access to this page is restricted to CBIOMES associates. (more…)

December 2020 CBIOMES (Poster) e-Meeting

To provide an opportunity to "pick up the conversation" and chat with colleagues about where work had gone since our Annual Meeting in June, the December gathering was an all-hands...

Using Metagenomics to Measure In-Situ Microbial Growth Rates

Growth rates are central to understanding microbial interactions and community dynamics. The Fuhrman Lab, which uses 'omics data to seek a better understanding of microbial growth, interactions, and biogeographies has...

2020 Joint Simons Marine Collaborations Meeting

Please note access to this page is restricted to CBIOMES associates only. Besides CBIOMES, the Simons Foundation supports three other marine collaborations: BIOS-SCOPE, PriME, and SCOPE. A joint meeting, October...


Long, Andrew M., Shengwei Hou, J. Cesar Ignacio-Espinoza, Jed A. Fuhrman (2020), Benchmarking microbial growth rate predictions from metagenomes, ISME Journal, doi: 10.1038/s41396-020-00773-1 Get the PDF [Requires login]

August 2020 CBIOMES e-meeting – Shengwei Hou (Fuhrman Lab,USC)

"Measuring Marine Microbial Growth Rates Through the Lens of Incubation Experiments" Please note access to this page is restricted to CBIOMES associates. (more…)

The Fuhrman Group goes to Annual Meeting

Jed Fuhrman's USC-CBIOMES group leads the Microbial Growth, Interactions and Biogeographies from ‘Omics’ Data project. In this video, Jed presents an overview of his team's progress and advertises team members'...


Weili Wang, Jie Ren, Kujin Tang, Emily Dart, Julio Cesar Ignacio-Espinoza, Jed A. Fuhrman, Jonathan Braun, Fengzhu Sun, and Nathan A. Ahlgren (2020), A network-based integrated framework for predicting virus–prokaryote...

May 2020 CBIOMES e-meeting – Jed Fuhrman (USC)

“RNA sequencing for universal taxon-resolved biomass estimation?” Please note access to this page is restricted to CBIOMES associates. (more…)

February 2020 CBCBIOMES e-meeting – Julio Cesar Ignacio Espinoza (USC-Fuhrman)

'Long term stability and red queen dynamics in marine viruses.' Please note access to this page is restricted to CBIOMES associates. (more…)


Jie Ren, Kai Song, Chao Deng, Nathan A. Ahlgren, Jed A. Fuhrman, Yi Li, Xiaohui Xie, Ryan Poplin & Fengzhu Sun (2020), Identifying viruses from metagenomic data using deep learning,...

CBIOMES Goes to Ocean Sciences 2020

Look out for members of the CBIOMES team, sharing their work at this year’s Ocean Sciences conference taking place February 16-21 in San Diego, California. (more…)

Germ Warfare Between Bacteria and Viruses at a Standoff

Members of the USC-CBIOMES Group J. Cesar Ignacio-Espinoza, and Jed A. Fuhrman, have found that the endless struggle between viruses and bacteria ends in a stalemate, scientific proof of the...

CBIOMES Welcomes Sarah Laperriere

by Helen Hill for CBIOMES A warm welcome to postdoc Sarah Laperriere who joins Jed Fuhrman's USC CBIOMES Group this month. (more…)

Working in the Dark

Most of the viruses in the ocean are unknown, but scientists are working to fix this information gap. One of the ways to discover viruses is by sampling ocean water...

Recent Research in the Fuhrman Lab

by Jed Fuhrman for CBIOMES Please note access to this page is restricted to CBIOMES associates only. (more…)

Past Annual Reporting

2020 | 2019 | 2018  [login required]