Deep discovery informs difficult deployment in plant microbiome science

D Russ, CR Fitzpatrick, PJPL Teixeira, JL Dangl - Cell, 2023 - cell.com
Plant-associated microbiota can extend plant immune system function, improve nutrient
acquisition and availability, and alleviate abiotic stresses. Thus, naturally beneficial …

Community standards and future opportunities for synthetic communities in plant–microbiota research

TR Northen, M Kleiner, M Torres, ÁT Kovács… - Nature …, 2024 - nature.com
Harnessing beneficial microorganisms is seen as a promising approach to enhance
sustainable agriculture production. Synthetic communities (SynComs) are increasingly …

Identifying microbiota community patterns important for plant protection using synthetic communities and machine learning

B Emmenegger, J Massoni, CM Pestalozzi… - Nature …, 2023 - nature.com
Plant-associated microbiomes contribute to important ecosystem functions such as host
resistance to biotic and abiotic stresses. The factors that determine such community …

From microbiome composition to functional engineering, one step at a time

SD Burz, S Causevic, A Dal Co… - Microbiology and …, 2023 - Am Soc Microbiol
Communities of microorganisms (microbiota) are present in all habitats on Earth and are
relevant for agriculture, health, and climate. Deciphering the mechanisms that determine …

Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens

S Pfeilmeier, A Werz, M Ote, M Bortfeld-Miller… - Nature …, 2024 - nature.com
In healthy plants, the innate immune system contributes to maintenance of microbiota
homoeostasis, while disease can be associated with microbiome perturbation or dysbiosis …

Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis

EPI Loo, P Durán, TY Pang, P Westhoff, C Deng… - Cell Host & Microbe, 2024 - cell.com
Plant roots are functionally heterogeneous in cellular architecture, transcriptome profile,
metabolic state, and microbial immunity. We hypothesized that axial differentiation may also …

Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium

Q Peng, C Zhao, X Wang, K Cheng, C Wang… - Nature …, 2025 - nature.com
Lignin, as the abundant carbon polymer, is essential for carbon cycle and biorefinery.
Microorganisms interact to form communities for lignin biodegradation, yet it is a challenge …

Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling

Z Ruan, K Chen, W Cao, L Meng, B Yang, M Xu… - Nature …, 2024 - nature.com
Engineering natural microbiomes for biotechnological applications remains challenging, as
metabolic interactions within microbiomes are largely unknown, and practical principles and …

Metabolomics and Microbial Metabolism: Toward a Systematic Understanding

D Holbrook-Smith, J Trouillon… - Annual Review of …, 2023 - annualreviews.org
Over the past decades, our understanding of microbial metabolism has increased
dramatically. Metabolomics, a family of techniques that are used to measure the quantities of …

Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags

BBJ Daniel, Y Steiger, A Sintsova, CM Field… - Nature …, 2024 - nature.com
Microbiomes feature recurrent compositional structures under given environmental
conditions. However, these patterns may conceal diverse underlying population dynamics …