The comprehension of the underlying mechanisms of the interactions within microbial communities represents a major challenge to be faced to control their outcome. Joint efforts of in vitro, in vivo and ecological models are crucial to controlling human health, including chronic infections. In a broader perspective, considering that polymicrobial communities are ubiquitous in nature, the understanding of these mechanisms is the groundwork to control and modulate bacterial response to any environmental condition. The reduction of the complex nature of communities of microorganisms to a single bacterial strain could not suffice to recapitulate the in vivo situation observed in mammals. Furthermore, some bacteria can adapt to various physiological or arduous environments embedding themselves in three-dimensional matrices, secluding from the external environment. Considering the increasing awareness that dynamic complex and dynamic population of microorganisms (microbiota), inhabiting different apparatuses, regulate different health states and protect against pathogen infections in a fragile and dynamic equilibrium, we underline the need to produce models to mimic the three-dimensional niches in which bacteria, and microorganisms in general, self-organize within a microbial consortium, strive and compete. This review mainly focuses, as a case study, to lung pathology-related dysbiosis and life-threatening diseases such as cystic fibrosis and bronchiectasis, where the co-presence of different bacteria and the altered 3D-environment, can be considered as worst-cases for chronic polymicrobial infections. We illustrate the state-of-art strategies used to study biofilms and bacterial niches in chronic infections, and multispecies ecological competition. Although far from the rendering of the 3D-environments and the polymicrobial nature of the infections, they represent the starting point to face their complexity. The increase of knowledge respect to the above aspects could positively affect the actual healthcare scenario. Indeed, infections are becoming a serious threat, due to the increasing bacterial resistance and the slow release of novel antibiotics on the market.

中文翻译：

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三维生态位中复杂和多微生物群落体外建模的开放挑战

对微生物群落内相互作用的潜在机制的理解代表了控制其结果所面临的主要挑战。体外、体内和生态模型的共同努力对于控制包括慢性感染在内的人类健康至关重要。从更广泛的角度来看，考虑到多种微生物群落在自然界中无处不在，对这些机制的理解是控制和调节细菌对任何环境条件的反应的基础。将微生物群落的复杂性质减少为单个细菌菌株并不足以概括在哺乳动物中观察到的体内情况。此外，一些细菌可以适应各种生理或艰苦的环境，将自己嵌入三维矩阵中，与外部环境隔绝。考虑到人们越来越意识到动态复杂和动态的微生物群（微生物群）栖息在不同的装置中，调节不同的健康状态并在脆弱和动态平衡中防止病原体感染，我们强调需要制作模型来模拟三维生态位其中细菌和一般的微生物在微生物群落内自我组织，相互竞争。作为案例研究，本综述主要关注与肺病理相关的生态失调和危及生命的疾病，如囊性纤维化和支气管扩张，其中不同细菌的共同存在和改变的 3D 环境可被视为最坏的情况用于慢性多种微生物感染。我们说明了用于研究慢性感染和多物种生态竞争中的生物膜和细菌生态位的最新策略。尽管与 3D 环境的渲染和感染的多种微生物性质相去甚远，但它们代表了面对其复杂性的起点。有关上述方面的知识的增加可能会对实际的医疗保健场景产生积极的影响。事实上，由于细菌耐药性的增加和市场上新型抗生素的缓慢释放，感染正成为一种严重的威胁。有关上述方面的知识的增加可能会对实际的医疗保健场景产生积极的影响。事实上，由于细菌耐药性的增加和市场上新型抗生素的缓慢释放，感染正成为一种严重的威胁。有关上述方面的知识的增加可能会对实际的医疗保健场景产生积极的影响。事实上，由于细菌耐药性的增加和市场上新型抗生素的缓慢释放，感染正成为一种严重的威胁。