Draft Genome Sequences of
            <i>Enterobacteriales</i>
            Strains Isolated from the International Space Station

Bharadwaj, Achintya R.; Daudu, Robert; Singh, Nitin Kumar; Wood, Jason M.; Debieu, Marilyne; O’Hara, Niamh B.; Karouia, Fathi; Mason, Christopher E.; Venkateswaran, Kasthuri

doi:10.1128/mra.00817-20

Cited by 8 publications

(4 citation statements)

References 12 publications

(17 reference statements)

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“…Candidate flight species to use in our analysis were determined from literature 42 – 44 . Isolates from the ISS were identified in the NCBI databases 18 by searching the BioSample database for “geo_loc_name=USA: International Space Station”[attr] AND “SPECIES NAME”.…”

Section: Methodsmentioning

confidence: 99%

Microbial adaptation to spaceflight is correlated with bacteriophage-encoded functions

Irby,

Broddrick

2024

Nat Commun

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Evidence from the International Space Station suggests microbial populations are rapidly adapting to the spacecraft environment; however, the mechanism of this adaptation is not understood. Bacteriophages are prolific mediators of bacterial adaptation on Earth. Here we survey 245 genomes sequenced from bacterial strains isolated on the International Space Station for dormant (lysogenic) bacteriophages. Our analysis indicates phage-associated genes are significantly different between spaceflight strains and their terrestrial counterparts. In addition, we identify 283 complete prophages, those that could initiate bacterial lysis and infect additional hosts, of which 21% are novel. These prophage regions encode functions that correlate with increased persistence in extreme environments, such as spaceflight, to include antimicrobial resistance and virulence, DNA damage repair, and dormancy. Our results correlate microbial adaptation in spaceflight to bacteriophage-encoded functions that may impact human health in spaceflight.

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Section: Methodsmentioning

confidence: 99%

Microbial adaptation to spaceflight is correlated with bacteriophage-encoded functions

Irby,

Broddrick

2024

Nat Commun

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“…Candidate ight species to use in our analysis were determined from literature (43)(44)(45). Isolates from the ISS were identi ed in the NCBI databases (18) by searching the BioSample database for "geo_loc_name = USA: International Space Station"[attr] AND "SPECIES NAME".…”

Section: Flight and Terrestrial Genomesmentioning

confidence: 99%

Microbial adaptation to spaceflight is correlated with bacteriophage-encoded functions

Irby

Broddrick

2023

Preprint

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Evidence from the International Space Station suggests microbial populations are rapidly adapting to the spacecraft environment; however, the mechanism of this adaptation is not understood. Bacteriophages are prolific mediators of bacterial adaptation on Earth. We surveyed 245 genomes sequenced from bacterial strains isolated on the International Space Station for dormant (lysogenic) bacteriophages. Our analysis indicated phage-associated genes are significantly different between spaceflight strains and their terrestrial counterparts. Additionally, we identified 283 complete prophages, those that could initiate bacterial lysis and infect additional hosts, of which 46% are novel. These prophage regions encode functions that are correlated with increased persistence in extreme environments, such as spaceflight, to include antimicrobial resistance and virulence, DNA damage repair, and dormancy. Our results correlate microbial adaptation in spaceflight to bacteriophage-encoded functions that may impact human health in spaceflight.

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“…Previous attempts to isolate microorganisms from ISS environmental surfaces revealed that they generally consist of predominantly benign and commensal microorganisms ( Mhatre et al, 2020 ; Bijlani et al, 2021 ), but potentially pathogenic microorganisms were also sporadically isolated ( Knox et al, 2016 ; Singh et al, 2018a ). In 2015, several bacterial strains were collected from the observation deck (Cupola) of the ISS, and whole-genome sequences (WGS) were generated for these isolates ( Bharadwaj et al, 2020a , b ; Bijlani et al, 2020a , b ; Daudu et al, 2020a , b ; Solomon et al, 2020 ; Simpson et al, 2021 ). Based on preliminary genomic analyses, three ISS strains were identified as belonging to the Agrobacterium genomospecies 3 (also known as A. tumefaciens genomovar G3 or Agrobacterium G3).…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.

et al. 2021

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Strains of Agrobacterium genomospecies 3 (i.e., genomovar G3 of the Agrobacterium tumefaciens species complex) have been previously isolated from diverse environments, including in association with plant roots, with algae, as part of a lignocellulose degrading community, from a hospital environment, as a human opportunistic pathogen, or as reported in this study, from a surface within the International Space Station. Polyphasic taxonomic methods revealed the relationship of Agrobacterium G3 strains to other Agrobacterium spp., which supports the description of a novel species. The G3 strains tested (n = 9) were phenotypically distinguishable among the strains from other genomospecies of the genus Agrobacterium. Phylogenetic analyses of the 16S rRNA gene, gyrB gene, multi-locus sequence analysis, and 1,089-gene core-genome gene concatenate concur that tested G3 strains belong to the Agrobacterium genus and they form a clade distinct from other validly described Agrobacterium species. The distinctiveness of this clade was confirmed by average nucleotide identity (ANI) and in silico digital DNA–DNA hybridization (dDDH) comparisons between the G3 tested strains and all known Agrobacterium species type strains, since obtained values were considerably below the 95% (ANI) and 70% (dDDH) thresholds used for the species delineation. According to the core-genome phylogeny and ANI comparisons, the closest relatives of G3 strains were Agrobacterium sp. strains UGM030330-04 and K599, members of a novel genomospecies we propose to call genomovar G21. Using this polyphasic approach, we characterized the phenotypic and genotypic synapomorphies of Agrobacterium G3, showing it is a bona fide bacterial species, well separated from previously named Agrobacterium species or other recognized genomic species. We thus propose the name Agrobacterium tomkonis for this species previously referred to as Agrobacterium genomospecies 3. The type strain of A. tomkonis is IIF1SW-B1T (= LMG 32164 = NRRL B-65602). Comparative genomic analysis show A. tomkonis strains have species-specific genes associated with secretion of secondary metabolites, including an exopolysaccharide and putative adhesins and resistance to copper. A. tomkonis specific gene functions notably relate to surface adhesion and could be involved to colonize nutrient-poor and harsh habitats. The A. tomkonis strains from the ISS showed presence of a 40-kbp plasmid and several other potential mobile genetic elements detected that could also be part of conjugative elements or integrated prophages.

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Draft Genome Sequences of Enterobacteriales Strains Isolated from the International Space Station

Cited by 8 publications

References 12 publications

Microbial adaptation to spaceflight is correlated with bacteriophage-encoded functions

Microbial adaptation to spaceflight is correlated with bacteriophage-encoded functions

Microbial adaptation to spaceflight is correlated with bacteriophage-encoded functions

Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.

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