Predictive biology: modelling, understanding and harnessing microbial complexity

AJ Lopatkin, JJ Collins - Nature Reviews Microbiology, 2020 - nature.com
Predictive biology is the next great chapter in synthetic and systems biology, particularly for
microorganisms. Tasks that once seemed infeasible are increasingly being realized such as …

[HTML][HTML] Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria

IPA Lee, OT Eldakar, JP Gogarten, CP Andam - Iscience, 2023 - cell.com
Prosocial behavior is ubiquitous in nature despite the relative fitness costs carried by
cooperative individuals. However, the stability of cooperation in populations is fragile and …

The mechanisms and cell signaling pathways of programmed cell death in the bacterial world

RP Smith, I Barraza, RJ Quinn, MC Fortoul - International Review of Cell …, 2020 - Elsevier
While programmed cell death was once thought to be exclusive to eukaryotic cells, there are
now abundant examples of well regulated cell death mechanisms in bacteria. The …

Interactions between metabolism and growth can determine the co-existence of Staphylococcus aureus and Pseudomonas aeruginosa

C Pajon, MC Fortoul, G Diaz-Tang, EM Meneses… - Elife, 2023 - elifesciences.org
Most bacteria exist and interact within polymicrobial communities. These interactions
produce unique compounds, increase virulence and augment antibiotic resistance. One …

Disturbing the Spatial Organization of Biofilm Communities Affects Expression of agr-Regulated Virulence Factors in Staphylococcus aureus

I Barraza, C Pajon, G Diaz-Tang… - Applied and …, 2023 - Am Soc Microbiol
Staphylococcus aureus uses quorum sensing and nutrient availability to control the
expression of agr-regulated virulence factors. Quorum sensing is mediated by autoinducing …

Do organic substrates drive microbial community interactions in Arctic snow?

B Bergk Pinto, L Maccario, A Dommergue… - Frontiers in …, 2019 - frontiersin.org
The effect of nutrients on microbial interactions, including competition and collaboration, has
mainly been studied in laboratories, but their potential application to complex ecosystems is …

Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth

RJ van Tatenhove-Pel, DH de Groot… - The ISME …, 2021 - academic.oup.com
As natural selection acts on individual organisms the evolution of costly cooperation
between microorganisms is an intriguing phenomenon. Introduction of spatial structure to …

Periodically Disturbing the Spatial Structure of Biofilms Can Affect the Production of an Essential Virulence Factor in Pseudomonas aeruginosa

RJ Quinn, I Barraza, L García-Diéguez, C Pajon… - Msystems, 2021 - Am Soc Microbiol
Understanding the environmental factors that affect the production of virulence factors has
major implications in evolution and medicine. While spatial structure is important in virulence …

MetFish: a metabolomics pipeline for studying microbial communities in chemically extreme environments

C Xu, SP Couvillion, RL Sontag, NG Isern, Y Maezato… - Msystems, 2021 - Am Soc Microbiol
Metabolites have essential roles in microbial communities, including as mediators of nutrient
and energy exchange, cell-to-cell communication, and antibiosis. However, detecting and …

Heavy metal stress strengthens the stability and complexity of microbial molecular ecological networks in Sanyang wetland sediments

S Wu, H Zou, N Li, X Yan, W Liu - Journal of Oceanology and Limnology, 2024 - Springer
Pollution from heavy metals (HMs)(Cd, As, Cr, and Ni, etc.) has become a serious
environmental issue in urban wetland ecosystems with more and more attention. Previous …