The biggest project of life sciences – the human microbiome project – an overview
This is one of the biggest projects of mankind which is the human microbiome project. It involves the extensive characterisation of the microbial flora in the human system.
The human microflora are very important in maintaining the body balance. We host a wide variety of microflora and it is believed that the number of that micro-flora exceeds even the number of cells within the body. It is reported that there are millions of microbes per square inch of the body. The microflora are distributed across the human body with there being different concentrations of such microbial colonies at different places. The microbiota would include bacteria, fungi, viruses, archaebacteria, protozoa etc. Hence attempts have been made to study and to characterise this microbiota.
The characteristics of the major classes of microorganisms are as follows:
1. Bacteria- unicellular microorganisms with cellwall and cell membrane, having nucleic acids as genetic material which are not organised into chromosomes. Also, there are no cellular organelles. They can be of different shapes and exist singly or as colonies. They can be beneficial such as fermentative bacteria or may cause diseases such as tuberculosis, cholera etc.
2.Archaebacteria – are similar to bacteria but are quite ancient and include bacteria which can survive in extremes of environments such as extreme salt, temperatures etc
3. There are also the protozoans which may be present as parasites.
What roles does the microbiota play in the body? The microbiota within the body perform many important functions. These include:
1. Vitamin synthesis as well as other help to capture and store other nutrients which are required by the body.
2. Metabolism of xenobiotics
3. Help in the maintenance of the epithelial cells (which line the intestinal passage or gut)
4. Help in the strengthening and activity of the immune system
5. movement and cardiac issues.
Potential Distribution of the Human Microbiota That Has Helped the Human Microbiome Project
In this direction, the Human Microbiome Project was established to systematically research and account the microbial communities. And to correlate the changes in the quantity and quality of these communities with changes in metabolism/disease in human beings. The possible questions which the Human Microbiome Project (HMP) propose to answer are as follows:
1. Stability of an individual’s microbiota population and what are the changes in it over time, during a day, year and the entire duration of life. This will help correlate it to other significant changes occurring in the body
2. Comparisons of the microbiomes of individuals, within families, their immediate communities and between communities, going up to cities and country level and to determine the similarities and differences.
3. To identify the microbiome component unique to each human, besides the shared components.
4. Research will also look into the aspects of how changes in microbiome occur. How a microbiome is established within a human, and how it can be shared or transmitted with other humans or animals?
5. What factors causes changes in the genetic diversity of the microbiome? How does the diversity of the microbiome affect the lifestyle of the host and the microorganisms as in adaptation to different conditions and physiological states?
Exciting Work Done on the Human Microbiome Project
What is exciting about this Human Microbiome Project is the likelihood to bring down the barriers between microbial and environmental ecology and to create a vaster, more integrated field. This project is supported by the National Institutes of Health supported Common Fund. The work carried out as a result of this project represents the largest and most extensive detailed analysis of the human microbiome.
Microbiomes will need to be characterized by comparing limited data types collected from a limited set of individuals. The research is carried out at a population level and is aimed at generating and collating protocols for metagenomics analysis of the data sets obtained. It also aims to develop standardised methods for creating, processing and interpreting these data. The project has so far generated resources from a sample size of 242 adults. The sampling has been carried out at two levels: time based and on the basis of the biological territoria analysus. The scales used for the biogeographical sampling are micrometres, centimetres and meters.
Sampling for microbial communities was carried out at around 15 -18 sites on the body and the whole process was repeated around three times. The result of this has been stupendous. Around 5177 microbial profiles have been captured using data based on the analysis of the 16 rRNA genes and 3.5 Tb metagenomic sequence. The data generated from these limited data sets and the technologies involved include bionformatic analysis tools, high throughput DNA and RNA sequencing technologies, computational and metagenomic tools for assembling and annotating the sequence data.
Data includes the data from the analysis of microbial communities of humans as well as microbial reference data sets. Various kinds of annotation protocols have been provided which would be of immense help to scientists who are working on this area or related areas and they can use this to verify their results. The classification can be carried without using phylogenetic marker genes and the matching of genes to the respective organism can be carried out using Markov based models or homology based sequencing. The latter enables sequencing and placement of gene sequences obtained as a result of metagenomic sequencing efforts, on the basis of similarity to known genes from organisms sharing homology, using a multiple alignment and phylogenetics. Scientists prefer to use a mix of both in order to cover as much of the genome as is possible.
The Human Microbiome Project also involves studying the effect on the normal micro-flora of human beings under different medical conditions and building up an information bank on that. The research project also encompasses other aspects such as social, ethical and legal issues with related to this area.
Potential Difficulties in the Human Microbiome Project
Some issues which are coming up during the progress of the Human Microbiome Project are:
1. The difficulties of the occurrence of horizontal gene transfer between microbes may create challenges for the Microbiome project as more and more gene jumping would lead to more variations and differences and hence the picture of the microbiome you get may differ. This is a serious issue in terms of the amount of expenditure incurred.
2. The methods should be faster and tailored to handle large amounts of data in a lesser amount of time to make it more efficient.
Ultimately, this major effort should help in development of new biomarkers as well as achieve improvements in medical diagnosis and generation of diet and drug regimen besides the overall program objectives.
Christine Rodriguez, Ph.D. Harvard Outreach 2012 Summer 2012 Workshop in Biology and Multimedia for High School Teachers