Parag Vaishampayan

Parag Vaishampayan joined JPL in 2008 as a Caltech postdoctoral fellow and then got hired as a staff scientist (2011) at Biotechnology and Planetary Protection Group (BPPG). His current research focus is on development and implementation of advanced molecular techniques to detect and characterize the microbial diversity of extreme environmental niches on earth and in space, encompassing Icelandic hot springs, stratospheric air samples, high altitude caves, Deep mine, hydrothermal vents and International Space Station (ISS) to name few. He is instrumental in developing several novel molecular approaches and bioinformatics analysis tools, which are widely used by microbial ecologists. He is a leading microbial ecologist and bioinformatician working in the field of Astrobiology and planetary protection. He is also interested in applying the unique technologies developed at JPL Planetary Protection group for solving challenging problems in medical research (breast cancer, Antibiotic resistance) through JPL’s Medical Engineering Forum initiative. He was instrumental in teaming up with engineers at JPL, industry partners and vendors for testing, validation, and implementation of a real-time simultaneous bioaerosol and inert particle air monitoring system, rapid microbial identification technology (MALDI-TOF) and metagenome analysis of samples from the low-biomass environments (spacecraft and associated surfaces). His research findings will allow NASA to implement efficient microbial decontamination and sterilization techniques during the future spacecraft assembly process. At present, he is supporting planetary protection implementation activities of InSight, M2020, and Psyche missions. Results of his research work have appeared in more than 50 peer-reviewed publications, book chapters, and several (more than 50) presentations.


Education: 
  • 2000-2005 - Ph. D, University of Pune, India
  • 1997-1999 - MS (Microbiology) Haffkine Research Institute, Mumbai University, India.
  • 1994-1997 - BS (Microbiology) Mumbai University, India.

Research Interests: 

Microbial ecology, Exobiology, bioinformatics, planetary protection, astrobiology and life in extreme environments.


Professional Experience: 

Current Position:

  • 2011-present:  Scientist, Jet Propulsion Laboratory (JPL), NASA, California Institute of Technology, CA.
  • 2015-present:  Scientist at Blue Marble Space Institute of Science.  

 

Previous Positions:

  • 2014 Adjunct Faculty, Department of Biological Sciences, California State Polytechnic University, Pomona.   
  • 2013 Adjunct Faculty, Department of Biological Sciences, California State University, Los Angeles.
  • 2012 Consultant, Second Genome, Inc. the microbiome company.
  • 2008-2010 Postdoctoral fellow, California Institute of Technology, JPL, CA.  
  • 2006-2007 Postdoctoral fellow, Lawrence Berkeley National Laboratory, CA.

 


Selected Awards: 
  • NASA Exceptional Public Service Medal (2017): Exceptional service in research, new technology, and implementation for planetary protection and bioinformatics.
  • Voyager award (2016): Leadership in bioinformatics and collaboration with Dr. Susan Love Foundation on characterization of microbiome of nipple aspirate fluid of breast cancer survivors.
  • Voyager award (2016): Innovation and application of new technology in support of the Mars PP archive; and mentoring of the next generation of astrobiologists.
  • Explorer award (2016): For scientific and technical excellence in Planetary Protection, developing innovative molecular approaches and bioinformatics analysis tools.
  • Voyager award (2015): For outstanding achievements as an international planetary protection ambassador.
  • Mariner award (2012): In recognition of outstanding contributions in Planetary Protection by generating/writing reports, publications, NTRs and a provisional patent.
  • Recognition for the creative development of a technical innovation published as a NASA Tech Brief (total 6).

Selected Publications: 

Microbial Ecology Publications

  1. Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Paulino-Lima IG, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, Balk M, Huttenhower C, Nocker A, Vaishampayan P, Rothschild LJ. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. Microbiome. 2017 Aug16;5(1):86.
  2. Mogul R, Vaishampayan P, Bashir M, et al., Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the Central Mojave Desert. Front Microbiol. 2017 Oct 23;8:1974.
  3. Lee KH, Ab Samad LS, Lwin PM, Riedel SF, Magin A, Bashir M, Vaishampayan PA, Lin WJ. On the Rocks: Microbiological Quality and Microbial Diversity of Packaged Ice in Southern California. J Food Prot. 2017 Jun;80(6):1041-1049.
  4. Bashir M, Ahmed M, Weinmaier T, Ciobanu D, Ivanova N, Pieber TR, Vaishampayan PA. Functional Metagenomics of Spacecraft Assembly Cleanrooms: Presence of Virulence Factors Associated with Human Pathogens. Front Microbiol. 2016 Sep 9;7:1321.
  5. Chan AA, Bashir M, Rivas MN, Duvall K, Sieling PA, Pieber TR, Vaishampayan PA, Love SM, Lee DJ. Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors. Sci Rep. 2016 Jun 21;6:28061.
  6. Mayer T, Blachowicz A, Probst AJ, Vaishampayan P, Checinska A, Swarmer T, de Leon P, Venkateswaran K. Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation. Microbiome. 2016 Jun 2;4(1):22.
  7. Weinmaier T, Probst AJ, La Duc MT, Ciobanu D, Cheng JF, Ivanova N, Rattei T, Vaishampayan P. A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses. Microbiome. 2015 Dec 8;3:62.
  8. Mahnert, A., Vaishampayan, P., Probst, A. J., Auerbach, A., Moissl-Eichinger, C., Venkateswaran, K., Berg., G. (2015) Cleanroom Maintenance Significantly Reduces Abundance but Not Diversity of Indoor Microbiomes. PLOSone 10 (8).
  9. Checinska A, Probst AJ, Vaishampayan P, White JR, Kumar D, Stepanov VG, Fox GE, Nilsson HR, Pierson DL, Perry J, Venkateswaran K. Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities. Microbiome. 2015 Oct 27;3:50.
  10. Barton HA, Giarrizzo JG, Suarez P, Robertson CE, Broering MJ, Banks ED, Vaishampayan PA, Venkateswaran K. Microbial diversity in a Venezuelan orthoquartzite cave is dominated by the Chloroflexi (Class Ktedonobacterales) and Thaumarchaeota Group I.1c. Front Microbiol. 2014 Nov 26;5:615.
  11. Venkateswaran K, Vaishampayan P, Cisneros J, Pierson DL, Rogers SO, Perry J. International Space Station environmental microbiome - microbial inventories of ISS filter debris. Appl Microbiol Biotechnol. 2014;98(14):6453-66.
  12. Krebs JE, Vaishampayan P, Probst AJ, Tom LM, Marteinsson VT, Andersen GL, Venkateswaran K. Microbial community structures of novel Icelandic hot spring systems revealed by PhyloChip G3 analysis. Astrobiology. 2014 Mar;14(3):229-40.
  13. Venkateswaran K, Vaishampayan P, Benardini JN 3rd, Rooney AP, Spry JA. Deposition of extreme-tolerant bacterial strains isolated during different phases of Phoenix spacecraft assembly in a public culture collection. Astrobiology. 2014 Jan;14(1):24-6.
  14. Marteinsson V, Vaishampayan P, Kviderova J, Mapelli F, Medori M, Calfapietra  C, Aguilera A, Hamisch D, Reynisson E, Magnússon S, Marasco R, Borin S, Calzada A, Souza-Egipsy V, González-Toril E, Amils R, Elster J, Hänsch R. A Laboratory of Extremophiles: Iceland Coordination Action for Research Activities on Life in Extreme Environments (CAREX) Field Campaign. Life (Basel). 2013 Feb 25;3(1):211-33.
  15. Bargoma, E., La Duc, M.T., Kwan, K., Vaishampayan, P. and Venkateswaran, K. (2013) Differential Recovery of Phylogenetically Disparate Microbes from Spacecraft-Qualified Metal Surfaces. Astrobiology 13, 189-202. 
  16. La Duc MT, Vaishampayan P, Nilsson HR, Torok T, Venkateswaran K. Pyrosequencing-derived bacterial, archaeal, and fungal diversity of spacecraft hardware destined for Mars. Appl Environ Microbiol. 2012 Aug;78(16):5912-22.
  17. de Vries LE, Vallès Y, Agersø Y, Vaishampayan PA, García-Montaner A, Kuehl JV, Christensen H, Barlow M, Francino MP. The gut as reservoir of antibiotic resistance: microbial diversity of tetracycline resistance in mother and infant.  PLoS One. 2011;6(6):e21644.
  18. Cooper M, La Duc MT, Probst A, Vaishampayan P, Stam C, Benardini JN, Piceno YM, Andersen GL, Venkateswaran K. Comparison of innovative molecular approaches and standard spore assays for assessment of surface cleanliness. Appl Environ Microbiol. 2011 Aug;77(15):5438-44.
  19. Kwan, K., Cooper, M., La Duc, M. T., Vaishampayan, P., Stam, C., Benardini, J. N., Scalzi, G., Moissl-Eichinger, C. & Venkateswaran, K. (2011). Evaluation of procedures for the collection, processing, and analysis of biomolecules from low-biomass surfaces. Applied and environmental microbiology 77, 2943-2953.
  20. Vaishampayan PA, Kuehl JV, Froula JL, Morgan JL, Ochman H, Francino MP. Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol Evol. 2010 Jan 6;2:53-66.
  21. Ghosh S, Osman S, Vaishampayan P, Venkateswaran K. Recurrent isolation of extremotolerant bacteria from the clean room where Phoenix spacecraft components were assembled. Astrobiology. 2010 Apr;10(3):325-35.
  22. Probst A, Vaishampayan P, Osman S, Moissl-Eichinger C, Andersen GL, Venkateswaran K. Diversity of anaerobic microbes in spacecraft assembly clean rooms. Appl Environ Microbiol. 2010 May;76(9):2837-45. doi: 10.1128/AEM.02167-09. Epub 2010 Mar 12.
  23. Rastogi G, Osman S, Vaishampayan PA, Andersen GL, Stetler LD, Sani RK. Microbial diversity in uranium mining-impacted soils as revealed by high-density  16S microarray and clone library. Microb Ecol. 2010 Jan;59(1):94-108.
  24. Vaishampayan P, Osman S, Andersen G, Venkateswaran K. High-density 16S microarray and clone library-based microbial community composition of the Phoenix spacecraft assembly clean room. Astrobiology. 2010 Jun;10(5):499-508.
  25. La Duc MT, Osman S, Vaishampayan P, Piceno Y, Andersen G, Spry JA, Venkateswaran K. Comprehensive census of bacteria in clean rooms by using DNA microarray and cloning methods. Appl Environ Microbiol. 2009 Oct;75(20):6559-67.
  26. Newcombe, D. A., LaDuc, M. T., Vaishampayan, P. & Venkateswaran, K. (2008). Impact of assembly, testing, and launch operations on the airborne bacterial diversity within a spacecraft assembly facility clean-room. Intern J Astrobiol 7, 223-236.
  27. Vaishampayan PA, Dhotre DP, Gupta RP, Lalwani P, Ghate H, Patole MS, Shouche YS. Molecular evidence and phylogenetic affiliations of Wolbachia in cockroaches. Mol Phylogenet Evol. 2007 Sep;44(3):1346-51.
  28. Vaishampayan, P., Kanekar, P., & Dhakephalkar, P. (2007) Isolation and characterization of Arthrobacter sp. strain MCM B-436, an Atrazine degrading bacterium, from rhizospheric soil. International Biodeterioration and Biodegradation, 60, 273-278.
  29. Raut AD, Kapadnis BP, Shashidhar R, Bandekar JR, Vaishampayan P, Shouche YS. Nonspecific PCR amplification of the 16S rRNA gene segment in different bacteria by use of primers specific for Campylobacter, Arcobacter, and Helicobacter spp. J Clin Microbiol. 2007 Apr;45(4):1376-7.

 

Microbial Taxonomy Publications

  1. Seuylemezian A, Cooper K, Schubert W, Vaishampayan P. Draft Genome Sequences of 12 Dry-Heat-Resistant Bacillus Strains Isolated from the Cleanrooms Where the Viking Spacecraft Were Assembled. Genome Announc. 2018 Mar 22;6(12).
  2. Seuylemezian A, Vaishampayan P, Cooper K, Venkateswaran K. Draft Genome Sequences of Acinetobacter and Bacillus Strains Isolated from Spacecraft-Associated Surfaces. Genome Announc. 2018 Feb 8;6(6).
  3. Seuylemezian A, Singh NK, Vaishampayan P, Venkateswaran K. Draft Genome Sequence of Solibacillus kalamii, Isolated from an Air Filter Aboard the International Space Station. Genome Announc. 2017 Aug 31;5(35).
  4. Behera P, Venkata Ramana V, Maharana B, Joseph N, Vaishampayan P, Singh NK, Shouche Y, Bhadury P, Mishra SR, Raina V, Suar M, Pattnaik AK, Rastogi G. Mangrovibacter phragmitis sp. nov., an endophyte isolated from the roots of Phragmites karka. Int J Syst Evol Microbiol. 2017 May;67(5):1228-1234.
  5. Behera P, Vaishampayan P, Singh NK, Mishra SR, Raina V, Suar M, Pattnaik AK, Rastogi G. The draft genome sequence of Mangrovibacter sp. strain MP23, an endophyte isolated from the roots of Phragmites karka. Genom Data. 2016 Jul 19;9:128-9.
  6. Vaishampayan P, Roberts AH, Augustus A, Pukall R, Schumann P, Schwendner P, Mayilraj S, Salmassi T, Venkateswaran K. Deinococcus phoenicis sp. nov., an extreme ionizing-radiation-resistant bacterium isolated from the Phoenix Lander assembly facility. Int J Syst Evol Microbiol. 2014 Oct;64(Pt 10):3441-6.
  7. Stepanov VG, Vaishampayan P, Venkateswaran K, Fox GE. Draft Genome Sequence of Deinococcus phoenicis, a Novel Strain Isolated during the Phoenix Lander Spacecraft Assembly. Genome Announc. 2014 Apr 24;2(2).
  8. Vaishampayan P, Moissl-Eichinger C, Pukall R, Schumann P, Spröer C, Augustus A, Roberts AH, Namba G, Cisneros J, Salmassi T, Venkateswaran K. Description of Tersicoccus phoenicis gen. nov., sp. nov. isolated from spacecraft assembly clean room environments. Int J Syst Evol Microbiol. 2013 Jul;63(Pt 7):2463-71.
  9. Benardini JN, Vaishampayan PA, Schwendner P, Swanner E, Fukui Y, Osman S, Satomi M, Venkateswaran K. Paenibacillus phoenicis sp. nov., isolated from the Phoenix Lander assembly facility and a subsurface molybdenum mine. Int J Syst Evol Microbiol. 2011 Jun;61(Pt 6):1338-43.
  10. Vaishampayan P, Probst A, Krishnamurthi S, Ghosh S, Osman S, McDowall A, Ruckmani A, Mayilraj S, Venkateswaran K. Bacillus horneckiae sp. nov., isolated from a spacecraft-assembly clean room. Int J Syst Evol Microbiol. 2010 May;60(Pt 5):1031-7.
  11. Shivaji S, Chaturvedi P, Begum Z, Pindi PK, Manorama R, Padmanaban DA, Shouche YS, Pawar S, Vaishampayan P, Dutt CB, Datta GN, Manchanda RK, Rao UR, Bhargava PM, Narlikar JV. Janibacter hoylei sp. nov., Bacillus isronensis sp. nov. and Bacillus aryabhattai sp. nov., isolated from cryotubes used for collecting air from the upper atmosphere. Int J Syst Evol Microbiol. 2009 Dec;59(Pt 12):2977-86.
  12. Vaishampayan P, Miyashita M, Ohnishi A, Satomi M, Rooney A, La Duc MT, Venkateswaran K. Description of Rummeliibacillus stabekisii gen. nov., sp. nov. and reclassification of Bacillus pycnus Nakamura et al. 2002 as Rummeliibacillus  pycnus comb. nov. Int J Syst Evol Microbiol. 2009 May;59(Pt 5):1094-9.
  13. Limaye SS, Mogul R, Smith DJ, Ansari AH, Słowik GP, Vaishampayan P. Venus' Spectral Signatures and the Potential for Life in the Clouds. Astrobiology. 2018. 18 (10).
  14. Venkateswaran, K., Vaishampayan, P., Benardini, J. N., Rooney, A.P.  and Spry, A. (2014) Deposition of Extreme-Tolerant Bacterial Strains Isolated during Different Phases of Phoenix Spacecraft Assembly in a Public Culture Collection. 14 (1) 1-3.
  15. Vaishampayan PA, Rabbow E, Horneck G, Venkateswaran KJ. Survival of Bacillus pumilus spores for a prolonged period of time in real space conditions. Astrobiology. 2012 May;12(5):487-97.
  16. Horneck G, Moeller R, Cadet J, Douki T, Mancinelli RL, Nicholson WL, Panitz C, Rabbow E, Rettberg P, Spry A, Stackebrandt E, Vaishampayan P, Venkateswaran KJ. Resistance of bacterial endospores to outer space for planetary protection purposes--experiment PROTECT of the EXPOSE-E mission. Astrobiology. 2012 May;12(5):445-56.
  17. Nicholson WL, Moeller R; PROTECT Team, Horneck G. Transcriptomic responses of germinating Bacillus subtilis spores exposed to 1.5 years of space and simulated martian conditions on the EXPOSE-E experiment PROTECT. Astrobiology. 2012 May;12(5):469-86.
  18. Vaishampayan, P., Fox, G., and Venkateswaran, K. (2010) Survival of Bacillus pumilus SAFR-032 in simulated Mars atmosphere in real space conditions. Proc. of SPIE, Vol. 7819 78190Q-1

 

Bioinformatics Publications

  1. Nilsson. H., Tedersoo, L., Abarenkov, K., Ryberg, M., Kristiansson, E., Hartmann, M., Schoch, C.L., Nylander, J., Bergsten, J., Porter, T.M.,  Jumpponen, A., Vaishampayan, P., Ovaskainen, O., Hallenberg, N., Bengtsson-Palme, J., Martin Eriksson, K.,   Larsson, K., Larsson, E., and Kõljalg, U. (2012) Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys 4, 37–63.
  2. Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH. Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets. Res Microbiol. 2012 Jul;163(6-7):407-12.
  3. Zhu D, Vaishampayan PA, Venkateswaran K, Fox GE. STITCH: algorithm to splice, trim, identify, track, and capture the uniqueness of 16S rRNAs sequence pairs using public or in-house database. Microb Ecol. 2011 Apr;61(3):669-75.
  4. Hartmann M, Howes CG, Veldre V, Schneider S, Vaishampayan PA, Yannarell AC, Quince C, Johansson P, Björkroth KJ, Abarenkov K, Hallam SJ, Mohn WW, Nilsson RH. V-REVCOMP: automated high-throughput detection of reverse complementary 16S rRNA gene sequences in large environmental and taxonomic datasets. FEMS Microbiol Lett. 2011 Jun;319(2):140-5.

 

Technology Development Publications

  1. Friedline AW, Zachariah MM, Middaugh AN, Garimella R, Vaishampayan PA, Rice CV. Sterilization Resistance of Bacterial Spores Explained with Water Chemistry. J Phys Chem B. 2015 Nov 5;119(44):14033-44. 
  2. Friedline AW, Zachariah MM, Johnson K, Thomas KJ 3rd, Middaugh AN, Garimella R, Powell DR, Vaishampayan PA, Rice CV. Water behavior in bacterial spores by deuterium NMR spectroscopy. J Phys Chem B. 2014 Jul 31;118(30):8945-55.
  3. Vaishampayan P, Probst AJ, La Duc MT, Bargoma E, Benardini JN, Andersen GL, Venkateswaran K. New perspectives on viable microbial communities in low-biomass cleanroom environments. ISME J. 2013 Feb;7(2):312-24.

 

Book Chapters

  1. Pradnya Pralhad Kanekar, Seema Shreepad Sarnaik, Parag Avinash Vaishampayan, Prafulla Namdeo Shede (2016) Phytoremediation of organic chemopollutants. Environmental Biotechnology. Apple Academic Press and CRC Press. 
  2. Parag Vaishampayan, James N. Benardini, Myron T. La Duc, and Kasthuri Venkateswaran (2010) Microbial persistence in low-biomass, extreme environments: the great unknown. Handbook of Molecular Microbial Ecology I:  Metagenomics and Complementary Approaches. Wiley publisher. Editor Frans de Bruijn

 

Patent

  1. Provisional patent: Deinococcus Phoenicis sp. nov. A Extreme Ionizing Radiation Resistant Bacterium Isolated from the Phoenix Lander Assembly Facility (CIT-5945-P)

 

Lectures / Presentations (out of >50)

  1. Invited talk at California State Polytechnic University, Pomona, RISE program, January 19, 2018.
  2. Invited talk at California State University, Northridge, biophysics seminar series November 1, 2017
  3. Invited talk at University of Edinburgh, UK, Astrobiology seminar series, Oct. 5, 2017 
  4. Invited talk at University of California Santa Barbara, February 19, 2016.
  5. Invited talk at the 2nd Theodor Escherich symposium on medical micro biome research at Medical University of Graz, Austria on Oct. 19, 2015.
  6. Invited talk at Montana State University, Center for Biofilm Engineering, October 17, 2013.
  7. The CSULA chapter of Tri Beta Biological Honors Society and ASI, May 21, 2013. 
  8. 112th General Meeting for the American Society for Microbiology, San Francisco on June 18, 2012.
  9. Astrobiology Science Conference 2012, Atlanta April 19, 2012. 
  10. Invited talk at Cal State LA, supported by US Department of Homeland Security, March 23, 2012.
  11. Invited talk at SCAS Microbiology Symposium 2010 at Cal State LA, on May 7, 2010.
  12. Invited talk at Cal Poly Pomona for RISE program, funded by NIH on July 16, 2010.
  13. Invited lecture at Northern Kentucky University. 2010.
Parag Vaishampayan
Address: 
4800 Oak Grove Dr.
Pasadena, CA 91109
Phone: 818.393.7025
Fax Number: 818.393.4176