Investigating microbiome-host interactions in the preterm gut using metagenomics and stem-cell derived enteroid "mini guts"

早产儿出生小于32周的妊娠代表了一个独特的群体，并且非常容易发生败血症和/或坏死性小肠结肠炎（NEC;肠道炎症），其中30%的早产儿发生这些疾病之一。肠上皮屏障的渗漏和肠上皮免疫应答的不成熟被认为是关键的促成因素。此外，基于关联的研究已经证明，肠道微生物组（即，微生物的收集及其功能）与早产儿健康和疾病有重要联系。具体来说，我们小组最近的证据表明，某些细菌，如双歧杆菌，可能会增加粘膜免疫的成熟，并提供保护，从这些疾病的发作。 该项目旨在广泛研究早产儿肠道微生物组，并随后研究细菌和早产儿肠道上皮细胞如何相互作用。这为更好地预测、诊断和治疗有疾病风险的婴儿提供了令人兴奋的可能性。这将通过以下目标来实现：1）进行来自早产儿和母乳的粪便的宏基因组测序和细菌分离。 2)利用来源于患者干细胞的人类肠（“迷你肠”），进行与肠上皮细胞相互作用的优势早产细菌的离体共培养。 3)系统地探索不同的细菌分离株和更全面的样本（例如，母乳）影响上皮完整性和功能。这将使用广泛的尖端方法来确定，包括跨上皮电阻、RNA测序、定量PCR、代谢组学、质谱细胞计数和显微镜检查。 这个多学科项目结合了湿实验室和基于最先进技术的计算元素。临床重点工作包括发现和转化两个方面。 学生将接受宏基因组和转录组测序，微生物学，代谢组学，组织培养，干细胞，体外建模，细胞成像，生物信息学，统计学和分析技术的广泛培训。

Preterm infants born <32 weeks gestation represent a unique population and are extremely vulnerable to sepsis and/or necrotising enterocolitis (NEC; inflammatory condition of the gut), with 30% of preterm infants developing one of these diseases. Leakiness of the intestinal epithelial barrier and immaturity of the intestinal epithelial immune response are implicated as key contributory factors. Furthermore, association-based studies have demonstrated that the gut microbiome (i.e., collection of microorganisms and their function) has important links to preterm health and disease. Specifically, recent evidence from our group suggests certain bacteria, such as Bifidobacterium, may increase maturation of mucosal immunity and provide protection from the onset of these diseases. This project seeks to extensively characterise the preterm gut microbiome and to subsequently investigate how bacteria and preterm gut epithelial cells interact. This holds exciting possibilities to better predict, diagnose, and treat infants at risk of disease. This will be achieved through the following objectives: 1) Carry out metagenomic sequencing and bacterial isolation of stool from preterm infants and maternal breast milk. 2) Perform ex vivo co-culture of dominant preterm bacteria interact with intestinal epithelial cells, utilizing human enteroids ("mini guts") derived from patient stem cells. 3) Systematically explore how the different bacterial isolates and more holistic samples (e.g., breast milk) influence epithelial integrity and functioning. This will be determined using a wide range of cutting edge approaches including trans-epithelial electrical resistance, RNA-sequencing, quantitative PCR, metabolomics, mass cytometry, and microscopy. This multi-disciplinary project combines wet-lab and computational elements based on state-of-the-art technologies. The clinically focused work incorporates both discovery and translational aspects. The student will receive extensive training in metagenomic and transcriptomic sequencing, microbiology, metabolomics, tissue culture, stem cells, ex vivo modeling, cellular imaging, bioinformatics, statistics, and analytical techniques.