Metabolomics analysis of bacterial interactions with the environment : perspective from human gut and heavy metal stress

• Main Author: Jain, Abhishek
• Other Authors: Chen Wei Ning, William
• Format: Theses and Dissertations
• Language: English
• Published: 2018
• Subjects: DRNTU::Engineering::Bioengineering; DRNTU::Science::Biological sciences
• Online Access: https://hdl.handle.net/10356/88007; http://hdl.handle.net/10220/46936
• Institution: Nanyang Technological University

The number of research questions in microbiology is as many as the habitats the organisms come from. Microbes play a vital role in the number of areas from food, agricultural, environmental to medical and health technology. Therefore, it becomes important to understand how microorganisms interact with, survive in and influence their environment. Particularly, there are approximately 100 trillion microbes residing in the human gut and they are linked with health and disease. Thus, an understanding of what constitutes a health-promoting or disease-promoting microbial group becomes important. In addition to their role in human health, over the years, due to rising levels of environmental pollution, microbes capable of degrading organic xenobiotics and additionally those able to survive and biotransform toxic heavy metals, have gained economic value. Humans also take up metals through food, drinking water and inhalation, in turn, the microbiota residing in the human gut are often exposed to heavy metals. Microbes are mostly studied in ideal laboratory conditions, but it becomes important to understand how microbes detect and cope with the environmental stress (e.g. heavy metals) in their surroundings. In this thesis,we established an untargeted metabolomics platforms to study the bacterial interactions with the environment such as human gut and heavy metal stress. In our first project, we compared the fecal bacterial diversity and composition of healthy Indian and Chinese adults using next-generation sequencing. Our analysis revealed a unique community structure, dominant Firmicutes, Actinobacteria and underrepresented Bacteroides, of Indian and Chinese gut bacteria. Partial least squares discriminant analysis and non-metric multidimensional scaling plots showed dietary habit wise clustering of subjects. Thus, our finding confirmed an important role of diet in determining gut bacterial composition. Next, we established an untargeted GC-MS and LC-MS metabolomics methods to study the association of urine and fecal metabolites with diet and gut microbiome composition. Our GC-MS method enabled the detection of 122 and 86 metabolites including amino acids, phenolics, indoles, carbohydrates, sugars and metabolites of microbial origin from fecal and urine samples respectively. 41 compounds were confirmed using external standards. Partial least squares discriminant analysis and hierarchical cluster heat map vii showed dietary habit or ethnicity wise grouping of urine and fecal metabolite profiles of subjects. We have also showed a strong association of metabolites with gut bacterial profiles in the genus and species level. In our second project, we applied GC-MS metabolomics to elucidate the mechanism that allows alpha proteobacterium Caulobacter crescentus to survive in Ni (II) stress condition. We identified an increased level of nine important metabolites including TCA cycle intermediates and amino acids in Ni (II) stressed C. crescentus. This indicates that changes in central metabolism are linked with the disruption of cell division process. We further characterized the 5 metabolites including malic acid, citric acid, alanine, proline, and glutamine to 0.015 mM that showed a protective effect on Ni(II) toxicity. In summary, our results highlight the potential of using metabolomics to study the gut microbiome interaction with diet and human metabolome. Comparison between the metabolites profiles of Indian and Chinese adults demonstrates characteristic metabolites signature and their association with diet or ethnicity and gut microbiome. Metabolomics was further applied to investigate the NI(II) stress condition in C. crescentus, which revealed the metabolites that show a protective effect on Ni (II) toxicity. Metabolomics based platforms developed in this study can be applied to future research on how bacteria interact with, survive in and influence different types of environment such as human gut and heavy metal contaminated soil, water or air