In microbial communities, each species often has multiple, distinct phenotypes, but studies of ecological stability have largely ignored this subpopulation structure. Here, we show that such implicit averaging over phenotypes leads to incorrect linear stability results. We then analyze the effect of phenotypic switching in detail in an asymptotic limit and partly overturn classical stability paradigms: abundant phenotypic variation is linearly destabilizing but, surprisingly, a rare phenotype such as bacterial persisters has a stabilizing effect. Finally, we extend these results by showing how phenotypic variation modifies the stability of the system to large perturbations such as antibiotic treatments.
The metabolic activity of microbes has played an essential role in the evolution and persistence of life on Earth. Microbial metabolism plays a primary role in the flow of carbon, nitrogen and other elements through the biosphere on a global scale. Microbes perform these metabolic activities in the context of complex communities comprised of many species that interact in dynamic and spatially-structured environments. Molecular genetics has revealed many of the metabolic pathways microbes utilize to generate energy and biomass. However, most of this knowledge is derived from model organisms, so…
Microorganisms self-organize in very large communities exhibiting complex fluctuations. Despite recent advances, still the mechanism by which these systems are able to exhibit large variability at the one hand and dynamical robustness on the other, is not fully explained. With that motivation, here we analyze three aspects of the dynamics of the microbiota and plankton: the density fluctuations, the correlation structure and the avalanching dynamics. In all communities under study we find that the results exhibits scale-free density fluctuations, anomalous variance' scaling, scale-free abundan…
Recent studies have revealed effects of various tree species on soil physical and chemical properties. However, effects of various tree species on composition and activity of soil microbiota and the relevant controls remain poorly understood. We evaluated the influence of tree species associated with two different mycorrhizal types, ectomycorrhiza (EcM) and arbuscular mycorrhiza (AM), on growth, biomass and metabolic activity of soil fungal and bacterial communities using common garden tree species experiments throughout Denmark. The soil microbial communities differed between six European tre…
Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for a dozen species. A heuristic search that improves community function by adding or removing one species at a time is more practical, but it is unknown whether this strategy can discover an optimal or nearly optimal community. Using consumer-resource models with and without cross-f…
The dynamics of microbial communities is incredibly complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform substrates to products. In many anoxic environments, these reactions are close to thermodynamic equilibrium and growth is slow. To understand the community structure in these energy-limited environments, we developed a microbial community consumer-resource model incorporating energetic and thermodynamic constraints on an interconnected metabolic network. The cent…
Travelling waves of invasion in microbial communities with phenotypic switching
Max Planck Institute for the Physics of Complex Systems（马克斯·普朗克复杂系统物理研究所）；Max Planck Institute of Molecular Cell Biology and Genetics（马克斯·普朗克分子细胞生物学与遗传学研究所）；Center for Systems Biology Dresden（德累斯顿系统生物学中心）
Towards a Taxonomical Consensus: Diversity and Richness Inference from Large Scale rRNA gene Analysis
种群分析一直具有挑战性，但重要的是，导致确定微生物群落成员的多样性和功能预测。在这里，我们详细介绍了我们的生物信息学方法，用于分析大型微生物群落的种群分布和多样性。这是通过以下方式实现的：（i）基于同源性的方法，用于稳健的多态性类型确定，等同于核糖体数据库项目（RDP）分类器的分类准确度，但提供了密切相关序列的改进的关联;（ii）比较不同的聚类方法，用于实现更准确的丰富度估计。我们的方法，我们开发的RDP审查16 S rRNA基因序列集，通过测试它对一个大的16 S rRNA基因数据集的约2300个序列，我们从土壤微生物群落研究。我们的结论是，最好的方法，以获得准确的微生物群落的遗传学概况的基础上，16 S rRNA基因序列信息，是应用优化的爆破分类。这种方法得到了使用完整连锁聚类对密切相关序列进行分组的补充，以计算群落的丰富度和均匀度指数。
Università di Bologna（博洛尼亚大学）；European Centre for Living Technology（欧洲生命技术中心）；Institute for Systems Biology（系统生物学研究所）
Mixed microbial communities, usually composed of various bacterial and fungal species, are fundamental in a plethora of environments, from soil to human gut and skin. Their evolution is a paradigmatic example of intertwined dynamics, where not just the relations among species plays a role, but also the opportunities -- and possible harms -- that each species presents to the others. These opportunities are in fact \textit{affordances}, which can be seized by heritable variation and selection. In this paper, starting from a systemic viewpoint of mixed microbial communities, we focus on the pivot…
A 454 survey of the community composition and core microbiome of the common bed bug, Cimex lectularius, reveals significant microbial community structure across an urban landscape
阐明与节肢动物宿主相关的微生物群落的空间动态和核心成分对于可能传播人类或农业病原体的昆虫至关重要。嗜血的温带臭虫（Cimex lectularius）被称为常见的臭虫，最近在北美和全世界死灰复燃，这可能是由于旅行增加和对杀虫剂的抗药性。迄今为止，尚未对臭虫微生物组进行全面调查，也没有对其微生物组的空间动态进行评估。在这里，我们提出了一个调查臭虫微生物群落扩增的V4-V6高变区的16 S rDNA基因区，然后454钛测序使用31个人从8个自然种群收集的住宅在辛辛那提，OH。在所有样品中，97%的微生物群落由两种主要OTU组成，被鉴定为α-变形杆菌Wolbachia和来自肠杆菌科的未命名的γ-变形杆菌。微生物群落在宿主种群中的群落多样性的措施，并表现出显着的人口结构。我们还发现了两种主要OTU丰度的强烈负相关性，这表明它们可能扮演着与营养互惠者相似的角色。这项广泛的调查代表了迄今为止对与臭虫相关的微生物的最全面的评估，并揭示了臭虫微生物组两个主要成员之间潜在拮抗作用的证据。
Microbial communities are ubiquitous in nature and come in a multitude of forms, ranging from communities dominated by a handful of species to communities containing a wide variety of metabolically distinct organisms. This huge range in diversity is not a curiosity - microbial diversity has been linked to outcomes of substantial ecological and medical importance. However, the mechanisms underlying microbial diversity are still under debate, as simple mathematical models only permit as many species to coexist as there are resources. A plethora of mechanisms have been proposed to explain the ori…
In this research, we study biological networks at different scales: a gene autoregulatory network at the single-cell level and the gut microbiota at the population level. Proteins are the main actors in cells, they are the building blocks, act as enzymes and antibodies. The production of proteins is mediated by transcription factors. In some cases, a protein acts as its own transcription factor, this is called autoregulation. It is known that autorepression speeds up the response and that autoactivation can lead to multiple stable equilibria. In this thesis, we study the effects of the combina…
