J. Friedman

Reversion to metabolic autonomy underpins evolutionary rescue of a bacterial obligate mutualism

This study shows that evolutionary rescue in a bacterial mutualism occurs when one strain reverts to metabolic autonomy, allowing the community to survive lethal stresses despite the other strain's sensitivity.

Degradation of indole-3-acetic acid by plant-associated microbes

This study identifies bacterial isolates capable of degrading indole-3-acetic acid (IAA) from Arabidopsis and rice roots, revealing their functional roles and association with IAA producers.

Evolution in microbial microcosms is highly parallel regardless of the presence of interacting species

This study shows that microbial evolution in microcosms is largely parallel across different interacting species, suggesting abiotic factors drive adaptation more than biotic interactions.

Interactions between culturable bacteria are highly non-additive

The paper examines how multiple bacterial species interact with a focal species, finding that community effects are non-additive and dominated by the strongest individual effect.

Interactions between culturable bacteria are predicted by individual species' growth

The paper predicts bacterial interspecies interactions using machine learning, achieving high accuracy in predicting interaction signs and strengths without relying on direct interaction data.

Arabidopsis thaliana induces multigenerational stress tolerance against biotic and abiotic stressors and memorization of host colonization in Bacillus subtilis

This study shows that Arabidopsis thaliana secretions induce multigenerational stress tolerance in Bacillus subtilis, enhancing its colonization and resistance to stressors.

Combination treatment can hinder the evolution of resistance to antimicrobial peptides

This study shows that combination antimicrobial peptide treatments can delay and reduce the evolution of resistance in S. aureus compared to single AMPs.

Fitness and mating consequences of variation in male allocation in a wind pollinated plant

This study manipulates male function allocation in wind pollinated plants and finds a linear relationship between male investment and fitness, with flowering time affecting mating success and diversity.

Autopolyploid establishment depends on life history strategy and the mating outcomes of clonal architecture

This study uses agent-based models to show that polyploid establishment depends on life history strategy and clonal architecture, with perennial plants and mixed reproductive strategies increasing success.

Complexity-stability relationship in empirical microbial ecosystems

The paper demonstrates a trade-off between species richness and connectance in microbial ecosystems, supporting the complexity-stability theory in natural microbiomes.

Resolving the conflict between antibiotic production and rapid growth by recognition of peptidoglycan of susceptible competitors

The paper shows that B. subtilis uses non-ribosomal peptides to outcompete rivals, but only when detecting peptidoglycan from sensitive competitors, balancing growth and antibiotic production.

Deciphering Functional Redundancy in the Human Microbiome

The paper investigates functional redundancy in the human microbiome by analyzing genomic content networks and developing a genome evolution model to explain their topological features.

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

This study tracks microbial community composition over evolutionary timescales and finds that changes are predictable and consistent across replicate communities.

Positive interactions within and between populations decrease the likelihood of evolutionary rescue

This study shows positive interactions reduce evolutionary rescue likelihood by increasing adaptation requirements and competition, increasing population collapse risk.

Population genomic and historical analysis reveals a global invasion by bridgehead processes in Mimulus guttatus

The paper traces the global invasion of Mimulus guttatus, showing it originated from North America to Europe and the Southwest Pacific via bridgehead populations and admixture.

Positive interactions are common among culturable bacteria

The paper measures over 150,000 bacterial cocultures and finds that growth-promoting interactions are common and depend on differences in nutrient consumption preferences.

A Novel Therapeutic Approach to Corneal Alkaline Burn Model by Targeting Fidgetin-like 2, a Microtubule Regulator

This paper evaluates FL2-NPsi, a nanoparticle-encapsulated siRNA targeting FL2, in a rat model of corneal alkaline burn, finding it enhances wound healing without toxicity.

Tumor control via targeting PD-L1 with chimeric antigen receptor modified NK cells

This study shows PD-L1 CAR-engineered NK cells kill cancer cells and inhibit tumor growth by targeting PD-L1, reducing myeloid cells in both preclinical models and patient blood.

Emergence of alternative stable states in microbial communities in a fluctuating environment

The paper shows that environmental fluctuations can lead to alternative stable states in microbial communities, with outcomes dependent on initial conditions and not timing, confirmed by both experiments and a Lotka-Volterra model.

Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy

Mortality causes universal changes in microbial community composition

The paper shows that increased mortality favors faster-growing microbes in multispecies communities, reversing competitive outcomes based on growth rate and competitive ability tradeoffs.

Mapping the ecological networks of microbial communities

This paper introduces a method to infer microbial ecological networks from steady-state data without assuming population dynamics models, validated on simulated and experimental datasets.

Community structure follows simple assembly rules in microbial microcosms

The paper demonstrates that a simple assembly rule can predict microbial community structure from pairwise competition outcomes with high accuracy.