MSc. Rohit Ghai, Ph.D.
Job Position: Research Scientist - Department of Aquatic Microbial Ecology (AME)
+420 38777 5819
My primary research focus is on the fundamental aspects of co-evolution of microbial and phage populations in aquatic ecosystems. The availability of next-generation sequencing technologies has tremendously improved our understanding of the uncultured diversity in the microscopic world, and as a part of our work we aim to understand the breadth and scale of this diversity, processes related to its maintenance and ultimately the consequences for interactions between the microbial and viral components.
We mainly use the freshwater ecosystems as models for our work. Freshwaters (all rivers, lakes and reservoirs together) comprise less than 1% of the total water on earth, but are nevertheless critical for our survival. Remarkably, the vast majority of microbial inhabitants have remained largely unknown and out of bounds of traditional culture-based approaches. Owing to recent developments in sequencing we are now beginning to put together a picture of the microbial communities in these habitats. This has enormous repercussions for microbiology at large, providing us with the ability to partially bypass culture based methods and directly access genomic information, thereby opening a whole new vista of the enormous genetic diversity of these microbes. We use high-resolution sequencing based analyses of freshwater ecosystems to reconstruct genomes of entire natural microbial populations and relate their genomic adapations and dynamics to their environment.
Prokaryotic populations cannot be isolated from the extensive viral world they live in, which is numerically at least ten times as large. Uncultured viruses (frequently of uncultured bacterial hosts) present their own set of challenges to our understanding of the real viral world. If we have now begun to shed light on the vast uncultured microbial majority, estimated to be 99% at the turn of the century, we have barely even begun to scratch the surface of the viral universe. We also use the metagenomic approach towards understanding viral diversity, evolutionary diversifications in natural viral populations and adaptations that affect interactions with their microbial hosts.
We collaborate with several labs, combining metagenomics, genomics, data from cultures of environmentally relevant strains and the environment gained via e.g. specific FISH probes targeting the major bacterioplankton players, interactions with microbial predators etc to refine our understanding and of the microbial communities in aquatic environments.
2009-2015 Postdoctoral Researcher: Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain led by Prof. Francisco Rodriguez-Valera (http://egg.umh.es)
2006-2008 Postdoctoral Researcher: Institute of Medical Microbiology, University of Giessen, Giessen, Germany, 2006-2008
2003-2006 PhD, Natural Sciences (Dr. rer. nat). University of Giessen, (summa cum laude) . Prof. Dr. Trinad Chakraborty. Institute of Medical Microbiology, University of Giessen, Giessen, Germany, 2003-2006
Selected Recent Publications:
Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria.
R Ghai, M Mehrshad, CM Mizuno, F Rodriguez-Valera. ISME Journal. 2016 Aug 9.
CM Mizuno, R Ghai, A Saghaï, P López-García, F Rodriguez-Valera. mBio 7 (4), e00805-16
Genomes of Planktonic Acidimicrobiales: Widening Horizons for Marine Actinobacteria by Metagenomics
CM Mizuno, F Rodriguez-Valera, R Ghai. mBio vol. 6 no. 1 e02083-14, 2015
Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing.
R Ghai, CM Mizuno ,A Picazo, A Camacho, F Rodriguez-Valera Molecular Ecology 2014 Oct 30
Expanding the marine virosphere using metagenomics.
CM Mizuno, F Rodriguez-Valera, NE Kimes, R Ghai. PLoS Genetics 9 (12), e1003987, 2013
|Total found: 12 records
Mehrshad M., Rodriguez-Valera F. , Amoozegar M. A., López-García P., Ghai R. (2018) The enigmatic SAR202 cluster up close: Shedding light on a globally distributed dark ocean lineage involved in sulfur cycling The ISME Journal
: 655-668 .
Neuenschwander S., Ghai R., Pernthaler J.,
Salcher M. (2018) Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria ISME Journal
: 185-198 .
Al-Qahtani A.A., Al-Anazi M.R., Nazir N., Ghai R., Abdo A.A. , Sanai F.M. , Al-Hamoudi W.K. , Alswat K.A. , Al-Ashgar H.I. , Khan M.Q. , Albenmousa A., Cruz D.D. , Bohol M.F.F. , Al-Ahdal M.N. (2017) Hepatitis B virus (HBV) X gene mutations and their association with liver disease progression in HBV-infected patients Oncotarget
Cabello-Yeves P.J., Ghai R.,
Mehrshad M., Picazo A., Camacho A. , Rodriguez-Valera F. (2017) Reconstruction of diverse Verrucomicrobial genomes from metagenome datasets of freshwater reservoirs Frontiers in Microbiology
Cabello-Yeves P.J., Haro-Moreno J.M., Martin-Cuadrado A.B., Ghai R., Picazo A., Camacho A. , Rodriguez-Valera F. (2017) Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs Frontiers in Microbiology
Carda-Diegez M. , Ghai R., Rodriguez-Valera F. , Amaro C. (2017) Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution. Microbiome
Ghai R., Mehrshad M., Megumi Mizuno C., Rodriguez-Valera F. (2017) Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria. ISME Journal
Koh H. W., Hur M., Kang M. S., Ku Y. B., Ghai R., Park S. J. (2017) Physiological and genomic insights into the lifestyle of arsenite-oxidizing Herminiimonas arsenitoxidans Scientific Reports
: 15007 .
Shevchenko V., Mager T., Kovalev K., Polovinkin V., Alekseev A., Juettner J., Chizhov I., Bamann C., Vavourakis C., Ghai R., Gushchin I., Borshchevskiy V., Rogachev A. , Melnikov I. , Popov A. , Balandin T. , Rodriguez-Valera F., Manstein D.J., Bueldt G., Bamberg E., Gordeliy V. (2017) Inward H+ pump xenorhodopsin: Mechanism and alternative optogenetic approach Science Advances
: e1603187 .
|Ghai R., Mehrshad M., Mizuno C., Rodriguez-Valera F. (2016) Metagenomic recovery of phage genomes of uncultured freshwater Actinobacteria The ISME Journal DOI: doi:10.1038/ismej.2016.110|
Mizuno C., Ghai R., López-García P., Rodriguez-Valera F. (2016) Genomes of Abundant and Widespread Viruses from the Deep Ocean mBio
Vavourakis C.D. , Ghai R., Rodriguez-Valera F., Sorokin D., Tringe S., Hugenholtz P., Muyzer G. (2016) Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines. Frontiers in Microbiology