Publications | friedmanlab

Selected publications

Full publication list at Google Scholar

Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium [pdf]

Ignacio J. Melero-Jiménez, Yael Sorkin, Ami Merlin, Jiawei Li, Alejandro Couce* and Jonathan Friedman*

Nature Communications 2025.

By evolving an obligate cross-feeding pair exposed to abrupt lethal stress, we find that evolutionary rescue occurs through breakdown of the mutualism, with one strain regaining metabolic independence while the other is lost.

Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species [pdf]

Nittay Meroz, Tal Livny, Gal Toledano, Yael Sorkin, Nesli Tovi, and Jonathan Friedman

Cell Systems 2024.

By evolving multiple bacterial species alone and in pairwise communities for hundreds of generations, we find that most evolutionary changes are shared across conditions, suggesting that evolutionary outcomes can often be predicted without detailed knowledge of interaction partners.

Interactions between culturable bacteria are highly non-additive [pdf]

Amichai Baichman-Kass, Tingting Song, and Jonathan Friedman

eLife 2023.

By systematically measuring thousands of pairwise and trio interactions affecting the growth of a focal strain, we show that combined inhibitory effects are typically dominated by the single strongest interaction.

Positive interactions are common among culturable bacteria [pdf]

Jared Kehe, Anthony Ortiz, Anthony Kulesa, Jeff Gore, Paul C. Blainey*, and Jonathan Friedman*

Science Advances 2021.

Using a high-throughput nanodroplet (kChip) platform to measure tens of thousands of pairwise interactions among culturable bacteria, we show that facilitative interactions are common, challenging the view that microbial communities are dominated primarily by competition.

Community composition of microbial microcosms follows simple assembly rules at evolutionary timescales [pdf]

Nittay Meroz, Nesli Tovi, Yael Sorkin, and Jonathan Friedman

Nature Communications 2021.

By tracking dozens of replicated two- and three-species bacterial communities for ~400 generations, we show that community composition typically changes during coevolution yet remains sufficiently repeatable that simple bottom-up assembly rules can predict evolutionary shifts in multispecies communities from pairwise outcomes.