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Applied Microbiology and Biotechnology

, Volume 103, Issue 11, pp 4483–4497 | Cite as

Metagenome to phenome approach enables isolation and genomics characterization of Kalamiella piersonii gen. nov., sp. nov. from the International Space Station

  • Nitin Kumar Singh
  • Jason M. Wood
  • Snehit S. Mhatre
  • Kasthuri VenkateswaranEmail author
Genomics, transcriptomics, proteomics
  • 164 Downloads

Abstract

Several evolutionarily distinct, near full-length draft metagenome-resolved genomes (MRG), were assembled from sequences recovered from the International Space Station (ISS) environments. The retrieval of MRGs facilitated the exploration of a large collection of archived strains (~ 500 isolates) and assisted in isolating seven related strains. The whole genome sequences (WGS) of seven ISS strains exhibited 100% identity to the 4.85 × 106 bp of four MRGs. The “metagenome to phenome” approach led to the description of a novel bacterial genus from the ISS samples. The phylogenomics and traditional taxonomic approaches suggested that these seven ISS strains and four MRGs were not phylogenetically affiliated to any validly described genera of the family Erwiniaceae, but belong to a novel genus with the proposed name Kalamiella. Comparative genomic analyses of Kalamiella piersonii strains and MRGs showed genes associated with carbohydrate (348 genes), amino acid (384), RNA (59), and protein (214) metabolisms; membrane transport systems (108), pathways for biosynthesis of cofactors, vitamins, prosthetic groups, and pigments (179); as well as mechanisms for virulence, disease, and defense (50). Even though Kalamiella genome annotation and disc diffusion tests revealed multidrug resistance, the PathogenFinder algorithm predicted that K. piersonii strains are not human pathogens. This approach to isolating microbes allows for the characterization of functional pathways and their potential virulence properties that can directly affect human health. The isolation of novel strains from the ISS has broad applications in microbiology, not only because of concern for astronaut health but it might have a great potential for biotechnological relevance. The metagenome to phenome approach will help to improve our understanding of complex metabolic networks that control fundamental life processes under microgravity and in deep space.

Keywords

Kalamiella piersonii Metagenome-resolved genomes Genome-inferred phenotype Phylogenomics MLSA 

Notes

Acknowledgments

We thank Aleksandra Checinska Sielaff for isolating the ISS strains, Arman Seuylemezian for MALDI-TOF analysis. Ganesh Babu Malli Mohan, Cynthia Ly, and Tristan Grams for their technical help rendered in reviving and isolating DNA of the ISS strains when needed. © 2019 California Institute of Technology. Government sponsorship is acknowledged.

Authors’ contributions

KV and NKS conceived and designed the experiments. NKS, JMW, and SSM performed the experiments. NKS analyzed the data. JMW performed analysis of the de novo assemblies, including contig alignment, and annotation checks. SSM carried out the phenotypic assays Biolog-based biochemical characterization. NKS, JMW, SSM, and KV wrote the paper. All authors read and approved the final manuscript.

Funding

Part of the research described in this publication was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with National Aeronautics and Space Administration. This research was funded by a 2012 Space Biology NNH12ZTT001N grant no. 19-12829-26 under Task Order NNN13D111T award to KV, which also funded the post-doctoral fellowships for NKS, JMW and SSM.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Informed consent

Not applicable.

Supplementary material

253_2019_9813_MOESM1_ESM.pdf (565 kb)
ESM 1 (PDF 565 kb)

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© This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply  2019

Authors and Affiliations

  1. 1.Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, M/S 89-2California Institute of TechnologyPasadenaUSA

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