The human body is host to a diverse collection of microbial cells; predominantly Bacteria and to a lesser extent Archaea. These micro-organisms, numbering between ~1012 - 1013 cells, and their genomic content, is collectively referred to as the human microbiome. The distribution of microbial species across body sites is non-uniform, with microbial assemblages showing differences in composition, structure, and function, depending on the particular body-site they are associated with.

The human microbiome performs a crucial role in the maintenance of normal physiological process in the human body including nutrient processing, energy acquisition, educating the immune system, and protecting from infectious agents. Alterations in this interaction has the potential to result in chronic inflammatory and metabolic diseases.

The structure and function of the human microbiome is impacted by several host associated and environmental factors including Age, Sex, Diet, Geographic location, etc. It is thus essential to distinguish normal variation observed in the microbiome from those associated with dysbiosis.

Recent Changes in the Human Microbiome

Changes in dietary lifestyle, specifically the increased consumption of processed foods, coupled with industrial food production practices and sanitized living environments, have resulted in a drastic shift in the composition of the human microbiome. These typically manifest as reduced microbial richness, specifically the reduced prevalence or even near-absence of certain microbial taxa among industrial populations. Isolating and characterizing these "extirpated" microbes is a major topic of interest in our group.

Characterizing the role of uncultured Microbes

A key challenge in microbial ecology is the inability of a vast majority of microbes to be isolated in pure culture.


Hypersaline environments are characterized by salt concentrations greater than 3.5% NaCl (Sea Water). Evaporative processes cause a progressive increase in salinity, resulting in the precipitation of minerals such as Dolomite [CaMg(CO3)2], Calcite [CaCO3], Gypsum [CaSO4.2H2O], Halite [NaCl], etc. The type of evaporite mineral formed is determined by the ionic composition of the parent salt solution (Brine), while the order of precipitation is determined by solubility.

Despite the environmental challenges (high uv exposure, high salinity, low water activity), these ecosystems are host to a diverse collection of Halotolerant and Halophilic organisms including Bacteria, Archaea, Algae, and Fungi. These organisms typically have a suite of adaptative mechanisms including production of compatible solutes (Glycine, Glycerol, Ectoines, etc.), preferential accumulation of K+, Low prevalence of hydrophobic amino acids, and DNA-bound carotenoid pigments, allowing for their survival in these harsh conditions.

Figure: created by Krithi Sankaranarayanan. Data obtained from KEGG, SwissProt, and NCBI

Long Term Survival in Hypsaline Environments

Halophilic Archaea entombed in fluid inclusions have been succesfully revived from halite crystals that are tens of thousands of years old. However, the mechanisms underlying this long-term survival are yet to be accurately characterized. Prevailing hypotheses include the activation of a reduced metabolic state allowing for the maintenance of key DNA-repair mechanisms (Starvation-Survival), use of glycerol produced by co-entombed algae as a carbon source to maintain cellular activity, and high genome copy numbers protecting against prolonged DNA damage and potential deleterius mutations.

Algal-Archaeal Interactions in Hypersaline Environments

Algae belonging to the genus Dunaliella are well known for their high salinity tolerance. Molecular surveys of hypersaline environments show


Recent advances in high throughput sequencing has allowed for the rapid accumulation of genomic information, far outpacing data obtained from classic microbiology and biochemical methods.

Figure: created by Krithi Sankaranarayanan. Data obtained from KEGG, SwissProt, and NCBI

InSilico Approaches to PolyPhasic Taxonomy

Improved Predictive Models for Carbohydrate Metabolism