Role of biofilm architecture in gene transfer dynamics

从基因组比较中可以推断出细菌间广泛的水平基因转移。目前尚不清楚生物膜中的共存是增强还是限制了基因转移。在这里，我们的目的是描述不同淋病奈瑟菌临床分离株之间和奈瑟氏奈瑟菌属不同物种之间转化的全基因组影响。在第一步中，我们将开发一种实验性的进化试验，将来自不同临床分离株和共生奈瑟氏菌的基因组DNA重复转化受体淋球菌。通过全基因组测序，我们将检测同源替换、插入、缺失和从头突变。这项测试将使我们能够评估基因转移对浮游性淋球菌基因组动力学的影响。在第二步中，我们将讨论生物膜形成对基因转移的影响。为此，我们将研究淋球菌菌落内DNA的迁移率、菌落内同源替换和从头获得基因的比率，以及不同淋球菌分离株之间的生态相互作用。最后，将上述所有方面整合在一起，并将研究共培养淋球菌菌株的基因组动力学。从长远来看，我们设想利用实验室进化和共培养实验，通过水平基因转移的方式解决多药耐药的进化问题。

Extensive horizontal gene transfer across bacteria has been inferred from genomic comparisons. It is currently unclear whether co-existence in biofilms enhances or restricts gene transfer. Here, we aim at characterizing genome-wide effects of transformation between different clinical isolates of Neisseria gonorrhoeae and between different species of the genus Neisseria. In the first step, we will develop an experimental evolution assay where recipient gonococci are repeatedly transformed with genomic DNA from different clinical isolates and commensal Neisseria. By means of whole genome sequencing, we will detect orthologous replacement, insertions, deletions, and de novo mutations. This assay will allow us to assess the effect of gene transfer on genome dynamics of planktonic gonococci. In the second step, we will address the effect of biofilm formation on gene transfer. To this end, we will characterize DNA mobility within gonococcal colonies, the rates of orthologous replacement and de novo gene acquisition in colonies, and ecological interactions between different gonococcal isolates. Finally, all aspects addressed above will be integrated and genome dynamics of co-cultivated gonococcal strains will be studied. In the long term, we envision using the laboratory evolution and co-cultivation experiments for addressing the evolution of multi-drug resistance by means of horizontal gene transfer.