Complex microbial systems across different levels of description

Bronk, Benedikt von; Götz, Alexandra; Opitz, Madeleine

doi:10.1088/1478-3975/aac473

Cited by 6 publications

(6 citation statements)

References 179 publications

(225 reference statements)

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“…Recent studies have utilized high-throughput RNA sequencing (RNA-seq) to examine gene expression in F. prausnitzii strain A2-165, mostly with the goal of identifying differential gene expression under different conditions [21][22][23]. However, certain underlying properties can only be explained by studying organisms as complex systems [24][25][26]. To this end, expression data can be used to accurately group genes into functional modules based on co-expression patterns.…”

Section: Introductionmentioning

confidence: 99%

Gene co-expression network analysis of the human gut commensal bacterium Faecalibacterium prausnitzii in R-Shiny

et al. 2022

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Faecalibacterium prausnitzii is abundant in the healthy human intestinal microbiota, and the absence or scarcity of this bacterium has been linked with inflammatory diseases and metabolic disorders. F. prausnitzii thus shows promise as a next-generation probiotic for use in restoring the balance of the gut microbial flora and, due to its strong anti-inflammatory properties, for the treatment of certain pathological conditions. However, very little information is available about gene function and regulation in this species. Here, we utilized a systems biology approach—weighted gene co-expression network analysis (WGCNA)–to analyze gene expression in three publicly available RNAseq datasets from F. prausnitzii strain A2-165, all obtained in different laboratory conditions. The co-expression network was then subdivided into 24 co-expression gene modules. A subsequent enrichment analysis revealed that these modules are associated with different kinds of biological processes, such as arginine, histidine, cobalamin, or fatty acid metabolism as well as bacteriophage function, molecular chaperones, stress response, or SOS response. Some genes appeared to be associated with mechanisms of protection against oxidative stress and could be essential for F. prausnitzii’s adaptation and survival under anaerobic laboratory conditions. Hub and bottleneck genes were identified by analyses of intramodular connectivity and betweenness, respectively; this highlighted the high connectivity of genes located on mobile genetic elements, which could promote the genetic evolution of F. prausnitzii within its ecological niche. This study provides the first exploration of the complex regulatory networks in F. prausnitzii, and all of the “omics” data are available online for exploration through a graphical interface at https://shiny.migale.inrae.fr/app/faeprau.

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Section: Introductionmentioning

confidence: 99%

Gene co-expression network analysis of the human gut commensal bacterium Faecalibacterium prausnitzii in R-Shiny

et al. 2022

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“…For the latter question, we particularly highlight the capacity of spatial structure to provide a means for emergent dynamics . We note that, while the term ‘self-organization’ has been used before to describe swarming, emerging from motility and chemical or hydrodynamic interactions [ 28 ], the use of emergent dynamics should capture a broader range of possible behaviours arising from feedbacks between cell movement and physiology, evolution and environmental gradients (similar to the discussion in [ 31 ]). In the microbial world, these feedbacks can be intertwined due to short doubling times.…”

Section: Introductionmentioning

confidence: 99%

Formation and emergent dynamics of spatially organized microbial systems

et al. 2023

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Spatial organization is the norm rather than the exception in the microbial world. While the study of microbial physiology has been dominated by studies in well-mixed cultures, there is now increasing interest in understanding the role of spatial organization in microbial physiology, coexistence and evolution. Where studied, spatial organization has been shown to influence all three of these aspects. In this mini review and perspective article, we emphasize that the dynamics within spatially organized microbial systems (SOMS) are governed by feedbacks between local physico-chemical conditions, cell physiology and movement, and evolution. These feedbacks can give rise to emergent dynamics, which need to be studied through a combination of spatio-temporal measurements and mathematical models. We highlight the initial formation of SOMS and their emergent dynamics as two open areas of investigation for future studies. These studies will benefit from the development of model systems that can mimic natural ones in terms of species composition and spatial structure.

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“…In the past, studies into bacterial communities have mainly focused on the characterisation of biochemical and molecular mechanisms [24]. However, the last decade has seen a rapid advancement in the biophysical characterisation of microbial emergent dynamics [25][26][27]. It is now evident that not only the biochemical and genetic pathways, but also the physical interactionse.g.…”

Section: Introductionmentioning

confidence: 99%

Biofilm and swarming emergent behaviours controlled through the aid of biophysical understanding and tools

Grobas

Bazzoli

Asally

2020

Biochemical Society Transactions

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Bacteria can organise themselves into communities in the forms of biofilms and swarms. Through chemical and physical interactions between cells, these communities exhibit emergent properties that individual cells alone do not have. While bacterial communities have been mainly studied in the context of biochemistry and molecular biology, recent years have seen rapid advancements in the biophysical understanding of emergent phenomena through physical interactions in biofilms and swarms. Moreover, new technologies to control bacterial emergent behaviours by physical means are emerging in synthetic biology. Such technologies are particularly promising for developing engineered living materials (ELM) and devices and controlling contamination and biofouling. In this minireview, we overview recent studies unveiling physical and mechanical cues that trigger and affect swarming and biofilm development. In particular, we focus on cell shape, motion and density as the key parameters for mechanical cell–cell interactions within a community. We then showcase recent studies that use physical stimuli for patterning bacterial communities, altering collective behaviours and preventing biofilm formation. Finally, we discuss the future potential extension of biophysical and bioengineering research on microbial communities through computational modelling and deeper investigation of mechano-electrophysiological coupling.

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Complex microbial systems across different levels of description

Cited by 6 publications

References 179 publications

Gene co-expression network analysis of the human gut commensal bacterium Faecalibacterium prausnitzii in R-Shiny

Gene co-expression network analysis of the human gut commensal bacterium Faecalibacterium prausnitzii in R-Shiny

Formation and emergent dynamics of spatially organized microbial systems

Biofilm and swarming emergent behaviours controlled through the aid of biophysical understanding and tools

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