MSc. Rohit Ghai, Ph.D.

Job Position: Research Scientist - Department of Aquatic Microbial Ecology (AME)

Contact details

Phone: +420 38777 5819
Room: 022


Research interests

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.


Curriculum vitae

Curriculum Vitae

2009-2015 Postdoctoral Researcher: Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain led by Prof. Francisco Rodriguez-Valera (

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.


Genomes of Abundant and Widespread Viruses from the Deep Ocean

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: 28 records
Mujakic I., Andrei A., Shabarova T., Kolesár Fecskeová L., Salcher M., Piwosz K., Ghai R., Koblížek M. (2021) Common presence of phototrophic Gemmatimonadota in temperate freshwater lakes. mSystems 6 : e01241-20.
DOI: 10.1128/mSystems.01241-20
Saha S., Bulzu P., Urajová P., Mareš J., Konert G., Manoel J.C., Macho M. , Ewe D., Hrouzek P., Masojídek J., Ghai R., Sourav K. (2021) Quorum-sensing signals from epibiont mediate the induction of novel microviridins in the mat-forming cyanobacterial genus Nostoc. mSphere 6 : e00562-21.
DOI: 10.1128/mSphere.00562-21
Cabello-Yeves P.J., Zemskaya T.I., Zakharenko A.S., Sakirko M.V., Ivanov V.G., Ghai R., Rodriguez-Valera F. (2020) Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat Limnology and Oceanography 65 : 1471–1488.
Inoue K. , Tsunoda S.P., Singh M., Tomida S., Hososhima S., Konno M., Nakamura R., Watanabe H. , Bulzu P.A., Banciu H.L., Andrei A., Uchihashi T., Ghai R., Béjà O., Kandori H. (2020) Schizorhodopsins: A family of rhodopsins from Asgard archaea that function as light-driven inward H+ pumps Science Advances 6 : eaaz2441.
DOI: 10.1126/sciadv.aaz2441
Mukherjee I., Salcher M., Andrei A., Kavagutti V., Shabarova T., Grujčić V., Haber M., Layoun P., Hodoki Y., Nakano S., Šimek K., Ghai R. (2020) A freshwater radiation of diplonemids Environmental Microbiology 22 : 4658–4668.
Park S.J., Andrei A., Bulzu P., Kavagutti V., Ghai R., Mosier A.C. (2020) Expanded diversity and metabolic versatility of marine nitrite-oxidizing bacteria revealed by cultivation-and genomics-based approaches. Applied and Environmental Microbiology 86 : e01667-20.
Salcher M., Andrei A., Bulzu P., Keresztes Z.G., Banciu H.L., Ghai R. (2020) Visualization of Lokiarchaeia and Heimdallarchaeia (Asgardarchaeota) by fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) mSphere 5 : e00686-20.
Andrei A., Salcher M., Mehrshad M., Rychtecký P., Znachor P., Ghai R. (2019) Niche-directed evolution modulates genome architecture in freshwater Planctomycetes ISME Journal 13 : 1056–1071.
DOI: 10.1038/s41396-018-0332-5
Bulzu P.A., Andrei A., Salcher M., Mehrshad M., Inoue K. , Kandori H. , Béjà O., Ghai R., Banciu H.L. (2019) Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche Nature Microbiology 4 : 1129–1137 .
DOI: 10.1038/s41564-019-0404-y
Durán-Viseras A., Andrei A., Ghai R., Sánchez-Porro C., Ventosa A. (2019) New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea Frontiers in Microbiology 10 : 1928.
DOI: 10.3389/fmicb.2019.01928
Flores-Uribe J., Hevroni G. , Ghai R., Pushkarev A. , Inoue K. , Kandori H. , Béjà O. (2019) Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity Environmental Microbiology Reports 11 : 419-424.
DOI: 10.1111/1758-2229.12730
Kavagutti V., Andrei A., Mehrshad M., Salcher M., Ghai R. (2019) Phage-centric ecological interactions in aquatic ecosystems revealed through ultradeep metagenomics Microbiome 7 : 135.
DOI: 10.1186/s40168-019-0752-0
Salcher M., Schaefle D., Kaspar M., Neuenschwander S., Ghai R. (2019) Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae ISME Journal 13 : 2764–2777.
DOI: 10.1038/s41396-019-0471-3
Vavourakis C.D. , Mehrshad M., Balkema C., van Hall R., Andrei A., Ghai R., Sorokin D., Muyzer G. (2019) Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake BMC Biology 17 : 69.
DOI: 10.1186/s12915-019-0688-7
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 12 : 655-668 .
DOI: 10.1038/s41396-017-0009-5
Mehrshad M., Salcher M.M., Okazaki Y., Nakano S., Šimek K., Andrei A., Ghai R. (2018) Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi Microbiome 6 : 176.
DOI: 10.1186/s40168-018-0563-8
Neuenschwander S., Ghai R., Pernthaler J., Salcher M. (2018) Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria ISME Journal 12 : 185-198 .
DOI: 10.1038/ismej.2017.156
Vavourakis C.D. , Andrei A., Mehrshad M., Ghai R., Sorokyn D. Y., Muyzer G. (2018) A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments Microbiome 6 : 168.
DOI: 10.1186/s40168-018-0548-7
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 8 : 105115-105125.
DOI: 10.18632/oncotarget.22428
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 8 : 2131.
DOI: 10.3389/fmicb.2017.02131

More publications


Biology Centre CAS
Institute of Hydrobiology
Na Sádkách 702/7
370 05 České Budějovice

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