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

NEW CBIOMES PUBLICATION

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 go 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'...

NEW CBIOMES PUBLICATION

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 CBIOMES 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…)

NEW CBIOMES PUBLICATION

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…)

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

2019 | 2018  [login required]