Nitin Kumar Singh, Ph.D.

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Scientist

Nitin.k.Singh@jpl.nasa.gov
Office: 818-354-5799

Biography

Dr. Nitin Kumar Singh's 10+ years of research in Microbiology encompasses Microbial taxonomy, Microbial Genomics, Metagenomics, and Microbial ecology study, analysis, and interpretation. He is specialized in working on pathogenic microbes found in hospital environments / clean rooms (SAF) to understand how microbes adapt to become more pathogenic under anthropogenic pressures. His work on Acinetobacter sp. and Bacillus anthracis clad has helped in the taxonomic resolution of both the genus. He has played a crucial role in describing 14 novel bacterial species from various environments. He has been involved in the Genomic and Metagenomic analysis of various projects like ISS-MO, ISS-MOP, CASIS, IMPAS, SPACE-X, JPL-SAF, HEPA and MARS 2020. His work has helped narrow down ISS's dominant microbial population and establish its genomic identity through metagenome resolved genomes. He has been part of the team which described three novel species from ISS, including a novel genus. He is a member of the current JPL's; Team A, COVID-19 analysis team, murine model study, Tardigrade, and Diatom genome analysis, Human genome analysis, and MAG-based ecological descriptions. He has been instrumental in the implementation of BIG-DATA analysis, ML, AI, and visualization leading to the co-relational analysis of all the studies conducted at BPPG.

Research Interests

• Microbial detection, identification and novel species description from LEO samples.

• Pathogenicity analysis and prediction of probable human pathogens from space samples.

• Survival mechanism under extreme stress such as low nutrient and high radiation.

• Study of the space-relevant Eukaryotic genomes.

• Study of life possibilities around non-terrestrial planets and role of expansion and contraction in origin and evolution.

• Focusing on bridging PP technology/research into Astrobiology and other space biology-related programs.

• Studying the biological phenomena at atomic level through quantum descriptions.

Professional Experience

2021 – Present, Scientist

2017 – 2021, PP Engineer, Biotechnology Planetary Protection Group, JPL

2016 – 2017, Caltech Postdoc, NASA-JPL California Institute of Technology

2015, Postdoc fellow at SCELSE, NTU, Singapore

Editorial Member in

Journal of Veterinary Medicine and Animal Sciences

Laboratory Cell Biological Technic

Microbiome in Health and Disease

Biodiversity, MDPI

Reviewer in

Frontiers in Environmental Science

International Journal of Systematic and Evolutionary Microbiology

International Journal of Astrobiology

Microbiome

Indoor Air

Nature Reports

Applied Microbiology and Biotechnology

Food Chemistry Nanotechnology

Journal Life

Gene

SN Comprehensive Clinical Medicine

Education

Ph.D. Life Microbiology (2010– 2015) Institute of Microbial Technology (CSIR-IMTECH)

M.Sc. Biotechnology (2007-2009) (Gold medalist) - MNIAS, University of Bikaner

B.Sc. Biotechnology (2004 - 2007) - MNIAS, University of Bikaner,

Selected Publications

Raichand R, Kaur I, Singh NK, Mayilraj S. (2011) Pontibacterrhizosphera sp. nov., isolated from rhizosphere soil of an Indian medicinal plant Neriumindicum. Antonie van Leeuwenhoek. 100; 129-135.

Manickam N, Pareek S, Kaur I, Singh NK, and Mayilraj S. (2012) Nitratireductor lucknowense sp. nov., a novel bacterium isolated from a pesticide contaminated soil. Antonie van Leeuwenhoek. 101; 125-131.

Revti, Pareek S, Singh NK and Mayilraj S. (2012) Exiguobacterium aquaticumsp. nov., a new member of the genus Exiguobacterium. International Journal of Systematic and Evolutionary Microbiology. 62; 2150 – 2155.

Kaur C, Pinnaka AK, Singh NK, Bala M, and Mayilraj S. (2013) Agromyces arachidis sp. nov. isolated from a Peanut (Arachis hypogaea) Crop Field. International Journal of Systematic and Evolutionary Microbiology. 2013; 1-6.

Kumar S, Kaur N, Singh NK, Raghava GPS, Mayilraj S. (2013) Draft Genome Sequence of Streptomyces gancidicus Strain BKS 13-15. Genome Announcement. 1; e00150-13.

Singh NK, Kumar S, Raghava GPS, Mayilraj S. (2013) Draft Genome Sequence of Acinetobacter baumannii Strain MSP4-16. Genome Announcement. 1; e00137-13.

Singh NK, Raichand R, Kaur I, Kaur C, Pareek S, Mayilraj S. (2013) Exiguobacterium himgiriensis sp. nov. a novel member of the genus Exiguobacterium, isolated from the Indian Himalayas. Antonie van Leeuwenhoek. 103; 789–796.

Khatri I, Singh NK, Subramanian S, Mayilraj S. (2014) Genome sequencing and annotation of Acinetobacter haemolyticus Strain MTCC 9819T. Genomics Data. 2; 10-12.

Khatri I, Singh NK, Subramanian S, Mayilraj S. (2014) Genome sequencing and annotation of Acinetobacter junnii Strain MTCC 11364. Genomics Data. 2; 13-15.

Manickam N, Singh NK, Bajaj A, Kumar RM, Kaur G, Kaur N, Bala M, Kumar A, Mayilraj S. (2014) Bacillus mesophilumsp. nov., strain IITR‑54T, a novel 4‑chlorobiphenyl dechlorinating bacterium. Archives of Microbiology. 196; 517-523.

Singh NK, Kaur C, Kumar N, Velmurugan S, Citarasu T and Mayilraj S. (2014) Bacillus aequororis sp. nov., isolated from marine sediment. Current Microbiology. 69; 758-762.

Singh NK, Khatri I, Subramanian S, Mayilraj S. (2014) Genome sequencing and annotation of Acinetobacter gouillouiae Strain MSP 4-18. Genomics Data. 2; 1-3.

Singh NK, Khatri I, Subramanian S, Mayilraj S. (2014) Genome sequencing and annotation of Acinetobacter gyllenbergiistrain MTCC 11365T. Genomics Data. 2; 4-6.

Singh NK, Khatri I, Subramanian S, Mayilraj S. (2014) Genome sequencing and annotation of Acinetobacter gerneri Strain MTCC 9824T. Genomics Data. 2; 7-9.

Kumar A, Bajaj A, Kumar RM, Kaur G, Kaur N, Singh NK, Manickam N and Mayilraj S. (2015) Taxonomic description and Genome sequence of Rheinheimera mesophila sp. nov., strain IITR-13T isolated from a pesticide contaminated sandy soil. International Journal of Systematic and Evolutionary Microbiology. 65; 3666-3673.

Kumar RM, Kaur G, Kumar A, Kaur N, Bala M, Singh NK and S Mayilraj. (2015) Taxonomic description and Genome sequence of Bacillus campisalis sp. nov., a novel member of the genus Bacillus isolated from solar saltern. International Journal of Systematic and Evolutionary Microbiology. 65; 3235- 3240.

Kumar RM, Kaur G, Kumar N, Kumar A, Singh NK, Bala M, Kaur N and Mayilraj S. (2015) Taxonomic description and Genome sequence of Salinicoccus sediminis sp. nov., a novel hyper halotolerant bacterium isolated from marine sediment. International Journal of Systematic and Evolutionary Microbiology. 65; 3794-3799.

Bajaj A, Kumar A, Yadav S, Kaur G, Bala M, Singh NK, Kumar RM, Manickam N, Mayilraj S. (2016) Isolation and characterization of a novel Gram-negative bacterium Chromobacterium alkanivorans sp. nov., strain IITR-71T degrading halogenated alkanes. International Journal of Systematic and Evolutionary Microbiology. 66; 5228-5235.

Behera P, Vaishampayan P, Singh NK, Mishra SR, Raina V, Suar M, Pattnaik AK, Rastogi G. (2016) The draft genome sequence of Mangrovibacter sp. strain MP23, an endophyte isolated from the roots of Phragmites karka. Genomics Data 9; 128-129.

Mual P, Singh NK, Verma A, Schumann P, Krishnamurthi S, Dastager S, Mayilraj S. (2016) Re-classification of Bacillus isronensis Shivaji et al., 2009 as a member of the genus Solibacillus as Solibacillus isronensis comb. nov. and emended description of genus Solibacillus Krishnamurthi et al., 2009. International Journal of Systematic and Evolutionary Microbiology. 66; 2113-2120.

Nair RG, Kaur G, Khatri I, Singh NK, Maurya SK, Subramanian S, Behera A, Dahiya D, Agrewala JN and Mayilraj S. (2016) Genome Mining and Comparative Genomic Analysis of Five Coagulase-Negative Staphylococci (CNS) Isolated from Human Colon and Gall Bladder. Journal of Data Mining in Genomics and Proteomics. 7; 1-15.

Sielaff AC, Singh NK, Allen JE, Thissen J, Jaing C, Venkateswaran K. (2016) Draft Genome Sequences of BSL-2 Opportunistic Pathogens, isolated from the environmental surfaces of the International Space Station. Genome Announcement. 4; e01263-16.

Singh NK, Blachowicz A, Checinska A, Wang C, Venkateswaran K. (2016) Draft Genome Sequence of two Aspergillus fumigatus Strains Isolated from the International Space Station. Genome Announcement. 4; e00553-16.

Pal D, Kumar RM, Kaur N, Kumar N, Kaur G, Singh NK, Krishnamurthi S, Mayilraj S. (2017) Bacillus maritimus sp. nov., a novel member of the genus Bacillus isolated from marine sediment. International Journal of Systematic and Evolutionary Microbiology. 67; 60-66.

Behera P, Ramana VV, Maharana B, Joseph N, Vaishampayan P, Singh N, Shouche Y, Bhadury P, Mishra SR, Raina V, Suar M, Pattnaik AK, Rastogi G. 2017. Mangrovibacter phragmitis sp. nov., an endophyte isolated from the roots of Phragmites karka. Int J Syst Evol Microbiol doi:10.1099/ijsem.0.001789.

Venkateswaran K, Singh NK, Checinska Sielaff A, Pope RK, Bergman NH, van Tongeren SP, Patel NB, Lawson PA, Satomi M, Williamson CHD et al: Non-Toxin-Producing Bacillus cereus Strains Belonging to the B. anthracis Clade Isolated from the International Space Station. mSystems 2017, 2(3).

Singh NK, Carlson C, Sani RK, Venkateswaran K: Draft Genome Sequences of Thermophiles Isolated from Yates Shaft, a Deep-Subsurface Environment. Genome Announcements 2017, 5(22).

Be NA, Avila-Herrera A, Allen JE, Singh N, Checinska Sielaff A, Jaing C, Venkateswaran K: Whole metagenome profiles of particulates collected from the International Space Station. Microbiome 2017, 5(1):81.

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, 5(35).

Hosein et. al. (2017) MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Posttranslationally Modified Peptides. (doi: http://dx.doi.org/10.1101/227504).

Carlson, C., N. K. Singh, M. Bibra, R. K. Sani and K. Venkateswaran (2018). "Pervasiveness of UVC254-resistant Geobacillus strains in extreme environments." Appl Microbiol Biotechnol 102(4): 1869-1887.

Urbaniak, C., A. C. Sielaff, K. G. Frey, J. E. Allen, N. Singh, C. Jaing, K. Wheeler and K. Venkateswaran (2018). "Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces." Sci Rep 8(1): 814.

Jillian Romsdahl, Adriana Blachowicz, Abby Chiang, Nitin Singh, Jason Stajich, Markus Kalkum, Kasthuri Venkateswaran, and Clay Wang. (2018) "Characterization of Aspergillus niger isolated from the International Space Station". mSystems00112-18R1

Nitin K. Singh, Daniela Bezdan, Alexa B. R. McIntyre, Aleksandra Checinska Sielaff, Kevin Wheeler, Christopher E. Mason, and Kasthuri Venkateswaran. (2018) "Multi-drug resistant Enterobacter bugandensis species isolated from the International Space Station and comparative genomic analyses with human pathogenic strains". BMC microbiology (MCRO-D-18-00155R4)

Nitin Kumar Singh; Jason M Wood; Fathi Karouia; Kasthuri Venkateswaran (2018) "Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces" Microbiome MBIO-D-18-00304R2

Singh NK, Wood JM, Mhatre SS, Venkateswaran K: Metagenome to phenome approach enables isolation and genomics characterization of Kalamiella piersonii gen. nov., sp. nov. from the International Space Station. Appl Microbiol Biotechnol 2019.

Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A: MetaMiner: a scalable peptidogenomics approach for discovery of ribosomal peptide natural products with blind modifications from microbial communities. Cell systems 2019, 9(6):600-608. e604.

Afshinnekoo E, Scott RT, MacKay MJ, Pariset E, Cekanaviciute E, Barker R, Gilroy S, Hassane D, Smith SM, Zwart SR: Fundamental Biological Features of Spaceflight: Advancing the Field to Enable Deep-Space Exploration. Cell 2020, 183(5):1162-1184.

Bharadwaj A, Singh N, Wood J, Debieu M, O'Hara N, Karouia F, Mason C, Venkateswaran K: Draft genome sequences of Lactobacillales isolated from the International Space Station. Microbiol Resour Announc 9: e00942-20. In.; 2020.

Danko D, Mohan GBM, Sierra MA, Rucker M, Singh N, Regberg A, Bell MS, O'Hara N, Ounit R, Mason CE: Characterization of Spacesuit Associated Microbial Communities and Their Implications for NASA Missions. 2020.

Danko DC, Singh NK, Butler DJ, Mozsary C, Jiang P, Keshavarzian A, Maienschein-Cline M, Chlipala G, Afshinnekoo E, Bezdan D: Genetic and Immunological Evidence for Microbial Transfer Between the International Space Station and an Astronaut. bioRxiv 2020.

Mhatre S, Singh NK, Wood JM, Parker CW, Pukall R, Verbarg S, Tindall BJ, Neumann-Schaal M, Venkateswaran K: Description of chloramphenicol resistant Kineococcus rubinsiae sp. nov. isolated from a spacecraft assembly facility. Frontiers in microbiology 2020, 11:1957.

Mhatre S, Wood JM, Sielaff AC, Mora M, Duller S, Singh NK, Karouia F, Moissl-Eichinger C, Venkateswaran K: Assessing the Risk of Transfer of Microorganisms at the International Space Station Due to Cargo Delivery by Commercial Resupply Vehicles. Frontiers in microbiology 2020, 11:2729.

Mohan GBM, Parker CW, Urbaniak C, Singh NK, Hood A, Minich JJ, Knight R, Rucker M, Venkateswaran K: Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation. mSystems 2020, 5(4).

Parker CW, Singh N, Tighe S, Blachowicz A, Wood JM, Seuylemezian A, Vaishampayan P, Urbaniak C, Hendrickson R, Laaguiby P: End-to-End Protocol for the Detection of SARS-CoV-2 from Built Environments. mSystems 2020, 5(5).

Urbaniak C, Wong S, Tighe S, Arumugam A, Liu B, Parker CW, Wood JM, Singh NK, Skorupa DJ, Peyton BM: Validating an Automated Nucleic Acid Extraction Device for Omics in Space Using Whole Cell Microbial Reference Standards. Frontiers in microbiology 2020, 11:1909.

Bijlani S, Singh NK, Eedara V, Podile AR, Mason CE, Wang CC, Venkateswaran K: Methylobacterium ajmalii sp. nov., isolated from the International Space Station. Frontiers in microbiology 2021, 12:534.

Bijlani S, Stephens E, Singh NK, Venkateswaran K, Wang CC: Advances in Space Microbiology. iScience 2021:102395.

Blachowicz A, Singh NK, Wood JM, Debieu M, O'Hara NB, Mason CE, Venkateswaran K: Draft Genome Sequences of Aspergillus and Penicillium Species Isolated from the International Space Station and Crew Resupply Vehicle Capsule. Microbiology Resource Announcements 2021, 10(13).

Danko DC, Sierra MA, Benardini JN, Guan L, Wood JM, Singh N, Seuylemezian A, Butler DJ, Ryon K, Kuchin K: A comprehensive metagenomics framework to characterize organisms relevant for planetary protection. Microbiome 2021, 9(1):1-15.

Simpson AC, Urbaniak C, Singh NKw a dcccwaadw, Wood JM, Debieu M, O'Hara NB, Mason CE, Venkateswaran K: Draft Genome Sequences of Various Bacterial Phyla Isolated from the International Space Station. Microbiology Resource Announcements 2021, 10(17).