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Human Microbiome project

Traditional Indian meals typically conclude with curd rice or curd and sugar. During summer, offering butter milk to guests is quite common. Many of us have been advised by our elders to have a glass of milk before going to bed. The main intention of consuming milk and  milk-products like curd and buttermilk is to increase the bacterial load in our bodies. These bacteria largely stimulate fermentation in the large intestine. Thus, Indian traditional foods are recognised as functional foods owing to the presence of functional components including body-healing chemicals, antioxidants, dietary fibres, and probiotics. Such functional molecules help in weight control, blood sugar level balance while supporting immunity and providing many health benefits. Functional properties of these foods are further enhanced through sprouting, malting, and fermentation [[1]].  In the recent past, advanced studies like sequencing and analysis of 16S rRNA genes, identifying opportunistic bacteria and immunological studies have led researchers to believe that food habits and lifestyles play  vital roles in determining  health and wellbeing [[2]].

“Human microbiome” is the aggregate collection of the microbiota (bacteria, fungi archaea, protists and viruses) that resides in the human body, including the skin, mammary glands, placenta, seminal fluid, uterus, ovarian follicles, lungs, saliva, mucosa, conjunctiva and the gastrointestinal tract [[3]]. There are complex assemblies of microorganisms colonising the human gastrointestinal tract which act as key players in determining human health and disease. The essential functions of the gut microbiome on the human host validate its importance. These include fermenting food components into absorbable metabolites, synthesising essential vitamins, expelling toxins, out-competing pathogens, strengthening the intestinal barrier, and stimulating and regulating the immune system. These functions are highly interconnected and tightly intertwined with human physiology. For example, products of microbial fermentation like short-chain fatty acids are essential substrates for intestinal cells and play a key role in immunomodulation. Researchers at Israel’s Weizmann Institute of Science and the Hospital for Sick Children in Toronto,  pegged the total number of bacteria in the human body to 40 trillion, whereas the number of human cells is 30 trillion.

Often, after heavy meals we experience changes in our moods, uneasiness or discomfort. Changes in food habits modify the microbial ratio which in turn alters various metabolic conditions in the body. The Gut-Brain Axis involves bidirectional communication between the central and the enteric nervous systems, mainly through signalling from gut-microbiota to brain and vice versa through neural, endocrine, immune and humoral links [[4]]. Thus, emotional and cognitive centres in the brain are linked to peripheral intestinal functions and indicate the importance of gut microbiota in influencing such interactions.  The American Gut project observed that certain kinds of bacteria are more common in people suffering from depression [[5]]. During the process of natural birth, babies pick microbes from the mother’s vagina and bowel which could potentially make them less vulnerable to asthma, diabetes, obesity and allergies. Breast milk also plays a crucial role in influencing the microbial composition in a child’s gut. Hence, the human microbiome is receiving a lot of attention owing to the close relationship between the microbiome and diseases or disorders.

Several factors may be attributed to determining the composition of the microbiome. Depending upon genetics, dietary habits, age, geographic location and ethnicity, different parts of the human body are occupied by characteristic microbial communities.  Dr. Yogesh Shouche, senior scientist at the National Centre for Cell Science (NCCS) in Pune vouches that such studies lay a strong foundation in deciphering the microbiome’s implications on health and a range of diseases.  With the aim of uncovering its link to diseases, India has launched a project named Human Microbiome Project (HMP). This Union government-funded, Rs150 crore project was initiated in 2019 by the Department of Biotechnology. It will enable tracing trillions of microbes found in Indians, particularly on their skin. The methodology includes collection of saliva, stool and skin swabs of around 20,000 Indians across various ethnic groups from different geographical regions. Interestingly, people of 32 tribes from different regions including Changpa in Ladakh, Warli in Maharashtra, Mankidia in Odisha, Ao in Nagaland and Koya in Telangana have been included in the study.  The HMP is a collaborative effort between eleven public and private research institutes and universities across India, including the All India Institute of Medical Sciences, New Delhi, the Institute of Advanced Study in Science and Technology in Guwahati and Symbiosis International University in Pune. This study is being led by Pune’s National Centre for Microbial Resource (NCMR), which is a part of the National Centre for Cell Science.

The ambitious HMP in India has been initiated keeping the following objectives in mind

  • Generating the baseline microbiome data of Indians.
  • Defining the core microbiome of tribal populations unaffected by modern lifestyle.
  • Understanding the links between microbial composition and disease risks.
  • Creating a repository of microbial samples from healthy individuals that can help develop probiotic-like solutions.

India has a significant portion of tribal population that is largely unaffected by “modern” diet and lifestyles. Thus lifestyle-related disorders including obesity and diabetes are significantly less prevalent among them compared to non-tribal populations globally. Studying such tribal populations would enhance the knowledge of the evolution of mutualism between the gut microbiota and the host.  The HMP thus aims to generate baseline microbiome data of Indians and define the core microbiome of tribals unaffected by modern lifestyle. It has promising benefits in that it can foster wellbeing by enhancing the understanding of important links between microbial composition and disease risks along with the creation of  a repository of microbial samples from healthy individuals for development of probiotic-like solutions. Such studies to map the microbiome composition of India’s diverse communities is essential to determine how genetics, diet and environment impact Indians differently.


[1]. PreetamS, Lohith KDH, Chanda D, Shubham SP, Ruplal C. Traditional and ayurvedic foods of Indian origin. Journal of Ethnic Foods. 2015, 2(3), 97-109.

[2]. Yanbei W, JiaweiW, Uyory C, Quynhchi P, Norberta W. S, Qiang H, Bin L, Liangli Y, Thomas T.Y.W. Interactions Between Food and Gut Microbiota: Impact on Human Health. Annual Review of Food Science and Technology. 2019, 10,389–408.

[3]. Marchesi JR, Ravel J The vocabulary of microbiome research: a proposal. Microbiome. 2015, 3, 31.

[4]. Marilia C, Annunziata S, Maria A M, Carola S. The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems. Annals of Gastroenterology. 2015, 28(2), 203–209.

[5]. Stephanie GC, Ariel RG, Anne-Catrin U, John JM, Jeffrey MM,Elizabeth MS. Systematic Review of Gut Microbiota and Major Depression. Frontiers in Psychiatry. 2019, 10(34),1-17.

About the author

Ajay S.K

Dr. Ajay S.K. is presently an Assistant Professor at SDM Research Institute for Biomedical Sciences, Shri Dharmasthala Manjunatheshwara University Dharwad. He completed his Ph.D in Biochemistry from NITTE Deemed to be University, Mangalore in 2013. He went on to work as Assistant Professor of Biochemistry, College Fisheries, Mangalore, he was actively involved in academics and research. He has also been an external examiner and BOS and BOE member for other universities and colleges during this tenure. His area of research mainly focuses on protein purification, In-vitro evaluation of pharmacological properties of natural products-Ayurveda and Marine products and has recently developed interest on the Intricate relationship between Gut microbiota and Pancreatic health & diseases. He has presented his work in a number of conferences and workshops globally and his research papers have been published in several international and national peer-reviewed journals.

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