Plants are in constant interactions with a large diversity of microorganisms, that belong to various biological kingdoms including archaea, bacteria, fungi and protista. In nature, these inter-kingdom interactions can be both cooperative and detrimental to the host-plants. My major research focus is to understand the dynamics of inter-kingdom microbiome-interactions and how it affects the crop production. We use cutting-edge culture-independent (metagenomics, metatranscriptomics and metabolomics) and culture-dependent (culturomics) methods combined with computational biology. We especially employ a systematics-based approach, so that we can identify individual organisms involved in these interactions, their biological functions, impacts on neighboring niches, and metabolic activity.

The research has several direct biotechnological applications, and the research in our lab focuses on the following:

• Develop bioferlitizers/biopesticides: By disentangling the microbial functions that are essential for different growth stages of crop plants, we intend to develop “soil probiotics” to improve crop health. In order to achieve this, we study natural ecosystems and wild plants related to crops. The technology developed will be sustainable and environmentally friendly. Our current research focuses on developing microbial inoculum assemblages from teosinte (ancestor of modern maize) and transferring the microbiota to maize to improve pest and pathogen resistance.

• Pathobiomes of plants: The concept of pathobiome is an emerging field in pathogen biology. In recent times, it has been noted that pathogens do not act alone in natural ecosystems, but along with a mob of other microorganisms. Deciphering the interaction between a plant pathogen and its associated microbiomes is necessary to understand pathogensis and also to design control measures. Research in my lab specifically focusses on mycosphere bacterial microbiota of pathogenic fungi. Our recent research focusses on pathobiomes associated with Fusarium wilt of cotton.

• Indicators of microbial dysbiosis: Dysbiosis is a microbial imbalance caused by perturbation in an ecosystem or a niche. Plant microbiomes experience dysbiosis during biotic (disease) and abiotic (drought, flooding, heat etc) stress. We study dysbiosis to understand shift in microbial processes, detect stress indicators and design stress alleviation measures including developing microbial inoculum (biofertilizers).

BESC 203 Social Life in Microbiomes and their Environment

PLPA 604 Plant Bacterial Diseases

Associate editor – BMC Microbiome (2019 – present)

Associate editor – BMC Environmental Microbiome (2019 – present)

1. Thomas, VE., Isakeit, T., and Antony-Babu, S (2023 – online) Draft genomes of five Fusarium oxysporum f. sp. niveum strains isolated from infected watermelon from Texas with temporal and spatial differences. Phytofrontiers DOI: 10.1094/PHYTOFR-11-22-0134-A
2. Khanal, S., Antony-Babu, S., Gaire, SP. & Zhou, XG (2022) Multi-locus sequence analysis reveals diversity of the rice kernel smut population in the United States. Frontiers in Microbiology, May 4;13:874120. DOI: 10.3389/fmicb.2022.874120
3. Imran, M., Khanal, S., Zhou, XG., Antony-Babu, S. & Atiq, M (2022) First report of Fusarium Sheath Rot of rice caused by Fusarium incarnatum-equiseti species complex in the United States. Plant Disease, Apr 29. DOI: 10.1094/PDIS-12-21-2693-PDN
4. Imran, M., Khanal, S., Zhou, XG., Antony-Babu, S. & Atiq, M (2022) First report of leaf spot of rice caused by Epicoccum sorghinum in the United States. Plant Disease, Mar 10. DOI: 10.1094/PDIS-10-21-2177-PDN
5. Imran, M., Khanal, S., Zhou, XG., Antony-Babu, S. & Atiq, M (2022) First report of brown leaf spot of rice caused by Curvularia hawaiiensis in the United States. Plant Disease, Feb 14. DOI: 10.1094/PDIS-10-21-2253-PDN
6. Yadav, P., Antony-Babu, S., Hayes, E., Healy, OM., Pan, D., Yang, WH., Silver, WL., Anderson, CL., Voshall, A., Fernando, SC., Moriyama, E., & Weber, KA., (2021) Complete genome sequence of Geobacter sp. strain FeAm09 a moderately acidophilic soil bacterium. Microbiology Resource Announcements, 8, 12 DOI 10.1128/MRA.00979-20
7. Fiore, N., Dunigan, D., Shaffer, J., Roberts, R., Antony-Babu, S., Plantz, B., Nickerson, K., Benson, A. & Weber, KA., (2019) Microbial community of saline, alkaline lakes in the Nebraska Sandhills based on 16S rRNA gene amplicon sequence data. Microbiology Resource Announcements, 8, 12 DOI 10.1128/MRA.00063-19
8. Antony-Babu, S., Stein, D., Eparvier, V., Parrot, D., Tomasi, S. & Suzuki, MT (2017) Multiple Streptomyces species with distinct secondary metabolomes have identical 16S rRNA gene sequences. Nature Scientific Reports,7, 11089 DOI: 10.1038/s41598-017-11363-1 (https://www.nature.com/articles/s41598-017-11363-1)
9. Deveau, A., Antony-Babu, S., Le Tacon, F., Robin, C., Frey-Klett, P. & Uroz, S (2016) Temporal changes of bacterial communities in Tuber melanosporum ectomycorrizhisozphere during ascocarp development. Mycorrhizae. DOI: 10.​1007/​s00572-015-0679-7
10. Picanço, LCS., Bittencourt, JAHM., Henriques, SVC., da Silva, JS., Oliveira, JMS., Ribeiro, JR., Antony-Babu, S., Carvalho, JCT., Stien, D. & da Silva, JO (2016) Pharmacological activity of Costus spicatus (Jacq.) Sw in experimental Bothrops atrox Pharmaceutical Biology. DOI: 10.3109/13880209.2016.1145703
11. Deveau, A., Antony-Babu, S., Robin, C., Uroz, S. & Frey-Klett, P (2016) Les bactéries, des partenaires méconnus de la truffe. Le Trufficulteur Français 2 (87), 16. DOI: 10.​1007/​s00572-015-0679-7
12. Parrot, D., Antony-Babu, S., Intertaglia, L., Bourrain, M., Grube, M., Tomasi, S. & Suzuki, M (2015) Littoral lichens as a source of potentially bioactive actinobacteria. Nature Scientific Reports, 5, 15839 DOI: 10.1038/srep15839 (http://www.nature.com/articles/srep15839)
13. Antony-Babu, S., Deveau, A., van Nostrand, J., Zhou, J., Le Tacon, F., Robin, C., Frey-Klett, P. & Uroz, S (2013) Black truffle associated bacterial communities during the development and maturation of Tuber melanosporum ascocarps and putative functional roles. Environmental Microbiology DOI: 10.1111/1462-2920.12294
14. Antony-Babu, S., Deveau, A., Murat, C., Le Tacon, F., Frey-Klett, P. & Uroz, S (2013) A method to extract community genomic DNA from soils under the influence of Tuber melanosporum for metagenomic methods. Journal of Applied Microbiology.  DOI: 10.1111/jam.12205
15. Oktarina, H., Antony-Babu, S. & Singleton, I (2012) The effect of low level ozone on growth and development of Rhizopus In vitro. Jurnal Biologi Edukasi. 4 (1): 11- 17
16. Dheeman, DS., Antony-Babu, S., Henehan, GTM. & Frias, GM (2011) Production of a 1, 3 specific lipase from a novel strain of Penicillium olsonii in submerged fermentation: activity and stability in aqueous media and organic solvents. Journal of Molecular Catalysis B: Enzymatic. DOI: j.molcatb.2011.06.013
17. Antony-Babu, S., & Singleton, I (2011) Effects of ozone exposure on the xerophilic fungus, Eurotium amstelodami IS-SAB-01, isolated from naan bread. International Journal of Food Microbiology. 144 (3): 331 – 336. DOI: 10.1016/j.ijfoodmicro.2010.09.019
18. Dass, SC., Abu-Ghannam, N., Cummins, EJ. & Antony-Babu, S (2010) Ecology and molecular typing of Listeria monocytogenes in a processing plant for cold-smoked salmon in the Republic of Ireland. Food Research International. 43 (5): 1529-1536. DOI: 10.1016/j.foodres.2010.04.030
19. Antony-Babu, S., Stach, JEM. & Goodfellow, M. (2010) Computer-assisted numerical analysis of colour-group data for dereplication of streptomycetes for bioprospecting and ecological purposes. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology. 97(3): 231-239. DOI: 10.1007/s10482-009-9404-x
20. Antony-Babu, S., & Singleton, I (2009). Effect of ozone on spore germination, spore production and biomass production in two Aspergillus Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology 96 (4): 413 – 422. DOI: 10.1007/s10482-008-9246-y
21. Savelev, SU., Antony-Babu, S., Roberts, SC., Wang, H., Clare, AS., Gosling, LM., Petrie, M., Goodfellow, M., O’Donnell, AG. & Ward, AC. (2008) Individual variation in 3-methylbutanol- a putative link between HLA and skin microflora. Journal of Chemical Ecology 34 (9): 1253- 1257. DOI: 10.1007/s10482-008-9246-y
22. Antony-Babu, S., Stach, JEM. & Goodfellow, M. (2008) Genetic and phenotypic evidence for Streptomyces griseus ecovars isolated from a beach and sand dune system. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology  94 (1): 63 -74. DOI: 10.1007/s10886-008-9524-1
23. Antony-Babu, S. & Goodfellow, M. (2008) Biosystematics of alkaliphilic streptomycetes from seven locations across a beach and dune sand system. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology 94 (4): 581-591. DOI: 10.1007/s10482-008-9277-4