Current Opinion in Systems Biology最新文献

Microbial communities perform metabolic processes that sustain life on Earth and promote human health. Microbial consortia sustain these functions in the face of constant structural and environmental perturbations. How do complex communities robustly sustain their functional properties despite perturbations? Most studies of functional robustness in the microbiome have been limited to biodiversity and functional redundancy, the idea that there are multiple members of the community that can sustain a specific function. Here, we propose that ideas from other complex biological systems may be applied to deepen our understanding of microbiome robustness. By surveying the causes of functional robustness in a variety of biological systems, including proteins and cells, and discussing how they can be applied to the microbiome, we build conceptual and experimental frameworks for understanding the functional robustness of microbial communities. We hope that these insights might help better predict and engineer microbiome function.

The development of bacterial chassis to increase productivity and reduce industrial costs in value-added biochemical production has gained significant attention. Current efforts have focused on model bacteria, thus limiting their suitability to produce specialized products. Therefore, there is a growing emphasis on developing specialized non-model bacterial chassis to expand the repertoire of bioproducts. However, the lack of genetic information and tools for non-model bacteria remains challenging. In this review, we categorize and introduce non-model chassis based on their characteristics in relation to the target products. We also provide an overview of the trends in the development of genome-reduced chassis to enhance productivity. Furthermore, we propose synthetic biology technologies that can be applied to a broad range of non-model bacteria.

The evolution of metabolic pathways in microbes is traditionally envisioned to take place within a single organism. The diverse repertoire of enzymes in the microbial community points to another exciting possibility: namely, that new metabolic pathways may evolve in a community setting, where pathway steps are distributed across several strains. The readiness with which microbes form stable relationships to collectively degrade manmade ‘xenobiotic’ pollutants, as evidenced from natural and laboratory-enriched consortia, provides valuable insights into the evolution of enzymes and pathways. Nonetheless, many open questions remain to be addressed. In this review, we consider the key determinants of pathway evolution in microbial communities, drawing from principles of social evolutionary theory in microbes, and also exploring the role of diffusion and horizontal gene transfer.

Microbial phototrophic communities dominated early Earth and thrive to this day, particularly in extreme environments. We focus on the impact of diel oscillations on phototrophic biofilms, especially in hot springs, where oxygenic phototrophs are keystone species that use light energy to fix carbon and often nitrogen. They exhibit photo-motility and stratification, and alter the physicochemical environment by driving O₂, CO_2, and pH oscillations. Omics analyses reveal extensive genomic and functional diversity in biofilms, but linking this to a predictive understanding of their structure and dynamics remains challenging. This can be addressed by better spatiotemporal resolution of microbial interactions, improved tools for building and manipulating synthetic communities, and integration of empirical and theoretical approaches.

A germline-soma distinction — irreversible differentiation from reproductive germline cells to sterile somatic cells — is a landmark of cellular cooperation in metazoans. Traditionally, this distinction was considered a property of only some metazoan taxa, such as vertebrates and insects. However, recent studies on a number of other metazoan taxa are challenging this traditional perspective, suggesting that a germline-soma distinction is widespread among metazoans. Here, we review recent molecular and cellular evidence supporting this suggestion and emphasise the difference between germline-soma distinction and germline segregation. We also outline the considerable diversity among metazoans in germline specification, segregation and regeneration. We finish by discussing how evolutionary explanations for this diversity can be investigated by harnessing theoretical modelling approaches.

Prophages, latent viral elements residing in bacterial genomes affect bacterial ecology and evolution in diverse ways. Do these prophage-mediated effects extend beyond the prophage-bacterial relationship? Here, I summarize the latest advances exploring how the impacts of prophages are transmitted through multiple levels of biological systems with potential impacts on ecosystem stability and functioning. The diverse effects of prophages on higher-order interactions are context-specific, ranging from contributions to global biogeochemical processes and mutualistic interactions to increased disease severity with negative impacts on ecosystem engineers and potential cascading effects for multiple species. While we have a solid understanding of the mechanisms by which prophages modulate their bacterial hosts at the cellular and population levels, future research may take an integrative approach to quantify their effects in complex ecosystems.

Bacteriophages are central to microbial ecosystems for balancing bacterial populations and promoting evolution by applying strong selection pressure. Here, we review some of the known aspects that modulate phage–bacteria interaction in a way that naturally promotes their coexistence. We focus on the modulations that arise from structural, physical, or physiological constraints. We argue they should play roles in many phage–bacteria systems providing sustainable diversity.

Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question.