My part in this network is “to expand the bioinformatics toolkit for studying the Fungus-Host-Microbiota interplay” by integrating sequence and clinical data obtained from fecal and vaginal samples collected from volunteers. This work is based in the microbiome lab of Vall d’Hebron Research Institute (VHIR), a multidisciplinary biomedical research public center that promotes and develops innovative biomedical research in Barcelona.
Background
As has been described in the whole project, the aim of FunHoMic is to study the interaction between three key players that influence the severity of the fungal infection: the fungus itself, the host and the microbiota. While analysis of the bacterial microbiota has become routine, that of the fungal microbiota – mycobiota -- is still hampered by the lack of robust fungal databases and efficient analytical pipelines.
Objectives
My thesis will dedicate to the development of databases and pipelines for the simultaneous analysis of bacterial and fungal components of the microbiota, including several main objectives:
• To standardize the routine of analyzing human fungi, from genetic samples extraction to bioinformatic and statistical processing of generated sequencing datasets
• To build a gene catalogue that will serve as a reference database for human fungi in mycobiota analysis
• To explore the Fungus-Host-Microbiota interplay by integrating both bacterial and fungal components of the microbiota at DNA and RNA levels
• To evaluate whether specific myco- and microbial signatures in the GI or vaginal tract correlate with variable levels of colonization by Candida, host antifungal response and recurrence of vaginal infection
At the end, we hope that this my project could help to improve the normalization of human fungal analysis and to assess the impact of the microbiota-host interplay on the severity of fungal infection.
我在这个联合研究会中的工作主要是通过收集志愿者的粪便和阴道微生物样本，并整合从中获得的序列和临床数据，从而来扩展用于研究真菌-宿主-微生物群落相互作用的生物信息学工具。这部分工作主要在西班牙巴塞罗那Vall d’Hebron研究所（VHIR）的微生物组实验室进行，该实验室是一个跨学科的生物医学研究公共中心，致力于在巴塞罗那促进生物医学的创新研究。
背景
如前文所述，FunHoMic的目的是研究影响真菌感染严重性的三个关键因素之间的相互作用：真菌本身，宿主和微生物群。虽然已经有很多规范化的流程来分析细菌微生物群，但对于真菌微生物群来说，由于缺乏稳健的真菌数据库和有效的分析手段，真菌菌群的研究仍受到阻碍。
目标
我的课题将致力于数据库和分析流程的搭建，以服务于同步分析微生物群的细菌和真菌成分，主要包括一下几个目标：
•从遗传样品的提取到生成序列数据集的生物信息学和统计学处理，规范化分析人类真菌的流程
•构建一个基因目录，作为真菌菌群分析中人类真菌的参考数据库
•通过在DNA和RNA水平上整合菌群的细菌和真菌成分，探索真菌-宿主-菌群的相互作用
•评估胃肠道或阴道中的真菌和微生物的某些特征是否与念珠菌定植的变化水平，宿主抗真菌反应以及阴道感染的复发有关
最后，我们希望这个项目可以帮助改善人类真菌分析的标准化，并评估微生物群与宿主之间的相互作用对真菌感染严重性的影响。