What will we do with the samples we collect?
Longer answer: The core of our analysis will be the following four methods, applied to all the stool samples from every participant:
1) 16S rRNA gene sequence analysis, which is a census of the types of microbe that are present, and tells us their approximate relative abundance.
2) Metagenomic sequencing, used to assess which genes are carried by all the microbes in the gut. This gives us clues about the functional potential of the microbiota - what activities it can do.
3) Metatranscriptomics, used to determine which microbial genes are being expressed at what levels. This lets us infer what microbial activities are actually being done.
4) Metabolomics, which is a method to identify and measure the concentrations of hundreds of chemical compounds simultaneously. This tells us about the effects microbes are having on their environment (i.e., the human colon, and the entire body).
In addition, urine samples will be used for metabolomics analysis to obtain integrated whole-body measures of human-microbial co-metabolism. We will develop some new statistical tools for the joint analysis of these different types of data over time, so that we can recognize, for example, what genes are being expressed in which microbial strains that could account for particular changes in the chemical environment. These statistical tools will also be used to relate microbial data to the information we have about participants, derived from questionnaires about diet, health etc., as well as from blood measurements, genetic testing, and/or physiological testing for participants who agree to those procedures.
Click here for the very long answer.
1) 16S rRNA gene sequence analysis, which is a census of the types of microbe that are present, and tells us their approximate relative abundance.
2) Metagenomic sequencing, used to assess which genes are carried by all the microbes in the gut. This gives us clues about the functional potential of the microbiota - what activities it can do.
3) Metatranscriptomics, used to determine which microbial genes are being expressed at what levels. This lets us infer what microbial activities are actually being done.
4) Metabolomics, which is a method to identify and measure the concentrations of hundreds of chemical compounds simultaneously. This tells us about the effects microbes are having on their environment (i.e., the human colon, and the entire body).
In addition, urine samples will be used for metabolomics analysis to obtain integrated whole-body measures of human-microbial co-metabolism. We will develop some new statistical tools for the joint analysis of these different types of data over time, so that we can recognize, for example, what genes are being expressed in which microbial strains that could account for particular changes in the chemical environment. These statistical tools will also be used to relate microbial data to the information we have about participants, derived from questionnaires about diet, health etc., as well as from blood measurements, genetic testing, and/or physiological testing for participants who agree to those procedures.
Click here for the very long answer.