Skip to main content
NCBI home page
Microbiology Resource Announcements logoLink to Microbiology Resource Announcements
. 2021 Apr 29;10(17):e00214-21. doi: 10.1128/MRA.00214-21

Draft Genome Sequences of Various Bacterial Phyla Isolated from the International Space Station

Anna C Simpson a, Camilla Urbaniak a, Nitin K Singh a, Jason M Wood a, Marilyne Debieu b, Niamh B O’Hara b,c, Christopher E Mason d,e, Kasthuri Venkateswaran a,✉
Editor: David Raskof
PMCID: PMC8086211  PMID: 33927037

Whole-genome sequences were generated from 96 bacterial strains of 14 species that were isolated from International Space Station surfaces during the Microbial Tracking 2 study. Continued characterization of this closed habitat's microbiome enables tracking of the spread and evolution of secondary pathogens, which is vital for astronaut health.

ABSTRACT

Whole-genome sequences were generated from 96 bacterial strains of 14 species that were isolated from International Space Station surfaces during the Microbial Tracking 2 study. Continued characterization of this closed habitat's microbiome enables tracking of the spread and evolution of secondary pathogens, which is vital for astronaut health.

ANNOUNCEMENT

The International Space Station (ISS) is currently the only long-term human habitat in space. Microgravity disrupts human immune function (1), and close monitoring of the ISS microbiome for increased pathogenicity is thus an ongoing critical task. Here, we report the draft genomes of 96 bacterial strains that were isolated from the ISS (Table 1). Eleven of the 14 species found are common members of the human microbiome, and most can act as opportunistic human pathogens.

TABLE 1.

Accession numbers, sampling locations, and assembly details for bacterial strains isolated from the ISS

Sample name Bacterial species WGS accession no. SRA accession no. Flight no. Locationa Medium, temp (°C)b No. of contigs Genome size (bp) N50 (bp) Depth of coverage (×) G+C content (%) No. of filtered reads
F8_7S_12B Acinetobacter pittii JAFDRK000000000 SRR13530731 F8 Lab 3 overhead R2A, 25 66 3,996,855 150,281 922.13 38.75 23,547,006
F8_7S_13B Acinetobacter pittii JAFDRL000000000 SRR13530730 F8 Lab 3 overhead R2A, 25 71 3,995,968 150,376 735.67 38.75 18,785,602
F8_7S_14B Acinetobacter pittii JAFDRM000000000 SRR13530729 F8 Lab 3 overhead R2A, 25 68 3,996,346 150,379 908.88 38.75 23,208,680
F8_7S_15B Acinetobacter pittii JAFDRN000000000 SRR13530728 F8 Lab 3 overhead R2A, 25 70 3,995,502 132,238 679.63 38.74 17,354,664
F8_7S_16B Acinetobacter pittii JAFDRO000000000 SRR13530727 F8 Lab 3 overhead R2A, 25 67 3,996,494 150,378 768.58 38.75 19,625,886
F8_7S_17B Acinetobacter pittii JAFDRP000000000 SRR13530725 F8 Lab 3 overhead R2A, 25 69 3,996,521 150,203 717.48 38.75 18,321,172
F8_7S_18B Acinetobacter pittii JAFDRQ000000000 SRR13530724 F8 Lab 3 overhead R2A, 25 69 3,995,985 150,209 813.82 38.75 20,781,150
F8_7S_4B Acinetobacter pittii JAFDRX000000000 SRR13530717 F8 Lab 3 overhead R2A, 25 69 3,995,609 150,378 704.76 38.74 17,996,396
F8_7S_5B Acinetobacter pittii JAFDRY000000000 SRR13530716 F8 Lab 3 overhead R2A, 25 66 3,995,688 150,370 583.20 38.74 14,892,212
F8_7S_6P Acinetobacter pittii JAFDSA000000000 SRR13530713 F8 Lab 3 overhead BA, 37 67 3,996,523 150,212 1,115.49 38.75 28,484,452
F8_7S_7B Acinetobacter pittii JAFDSB000000000 SRR13530712 F8 Lab 3 overhead R2A, 25 70 3,996,147 132,238 828.46 38.75 21,155,182
F8_8S_11B Acinetobacter pittii JAFDSE000000000 SRR13530709 F8 Crew quarters R2A, 25 70 3,997,471 150,204 735.21 38.75 18,773,974
F8_8S_12B Acinetobacter pittii JAFDSF000000000 SRR13530708 F8 Crew quarters R2A, 25 71 3,996,218 150,204 903.60 38.75 23,073,890
F8_8S_2P Acinetobacter pittii JAFDSJ000000000 SRR13530703 F8 Crew quarters BA, 37 70 3,994,221 150,204 1,039.96 38.74 26,555,916
F8_8S_6P Acinetobacter pittii JAFDSL000000000 SRR13530701 F8 Crew quarters BA, 37 71 3,997,028 150,211 939.87 38.75 24,000,022
F8_2S_1P Cytobacillus horneckiae JAFDQP000000000 SRR13530754 F8 WHC BA, 37 44 5,324,298 329,620 397.27 37.7 14,551,974
F5_7S_P6 Kocuria indica JAFDPQ000000000 SRR13530782 F5 Lab 3 overhead BA, 37 28 2,803,228 245,667 825.53 68.78 15,829,868
F6_3S_P_1B Kocuria indica JAFDPV000000000 SRR13530776 F6 ARED BA, 37 27 2,803,211 245,667 1,412.10 68.78 27,077,776
F5_7S_P11C Kocuria palustris JAFDPC000000000 SRR13530748 F5 Lab 3 overhead BA, 37 36 2,843,288 191,163 862.77 70.54 16,418,232
F5_7S_P2A Kocuria palustris JAFDPI000000000 SRR13530790 F5 Lab 3 overhead BA, 37 33 2,844,036 191,163 873.89 70.54 16,629,878
F5_7S_P2B Kocuria palustris JAFDPJ000000000 SRR13530789 F5 Lab 3 overhead BA, 37 32 2,843,686 262,144 1,100.95 70.54 20,950,750
F5_7S_P7 Kocuria palustris JAFDPR000000000 SRR13530780 F5 Lab 3 overhead BA, 37 32 2,844,494 271,586 897.37 70.54 17,076,656
F5_7S_P8 Kocuria palustris JAFDPS000000000 SRR13530779 F5 Lab 3 overhead BA, 37 49 2,843,644 130,397 648.47 70.54 12,340,212
F6_1S_P_2 Kocuria palustris JAFDPT000000000 SRR13530778 F6 Cupola BA, 37 31 2,844,162 271,218 1,262.76 70.54 24,029,822
F6_7S_B_1 Kocuria palustris JAFDQD000000000 SRR13530767 F6 Lab 3 overhead R2A, 25 34 2,843,704 191,187 595.66 70.54 11,335,110
F4_5S_F1_F Methylobacterium organophilum JAFDOX000000000 SRR13530793 F4 Overhead 4 PDA, 25 219 7,153,721 73,806 525.12 71 23,633,880
F5_7S_P10B Micrococcus luteus JAFDOZ000000000 SRR13530781 F5 Lab 3 overhead BA, 37 309 2,634,797 18,596 695.07 72.51 11,589,510
F5_7S_P11A Micrococcus luteus JAFDPA000000000 SRR13530770 F5 Lab 3 overhead BA, 37 249 2,437,588 21,893 526.53 72.95 8,779,392
F5_7S_P1A Micrococcus luteus JAFDPG000000000 SRR13530704 F5 Lab 3 overhead BA, 37 289 2,643,054 17,191 831.59 72.54 13,865,910
F5_7S_P1B Micrococcus luteus JAFDPH000000000 SRR13530791 F5 Lab 3 overhead BA, 37 163 2,662,630 32,991 717.06 72.61 11,956,220
F5_7S_P2C Micrococcus luteus JAFDPK000000000 SRR13530788 F5 Lab 3 overhead BA, 37 274 2,435,899 17,792 894.45 72.84 14,913,960
F5_7S_P3 Micrococcus luteus JAFDPL000000000 SRR13530787 F5 Lab 3 overhead BA, 37 534 2,325,956 7,231 679.00 72.6 11,321,680
F6_3S_P_1A Micrococcus luteus JAFDPU000000000 SRR13530777 F6 ARED BA, 37 68 2,461,417 58,867 1,075.33 73.05 17,930,076
F6_7S_P_2 Micrococcus luteus JAFDQF000000000 SRR13530765 F6 Lab 3 overhead BA, 37 103 2,458,603 49,739 1,387.39 73.03 23,133,344
F6_3S_P_6 Pseudoclavibacter alba JAFDPW000000000 SRR13530775 F6 ARED BA, 37 8 2,211,951 1,246,034 2,314.39 64.46 33,024,422
F8_1S_1P Pseudomonas fulva JAFDQI000000000 SRR13530762 F8 Cupola BA, 37 52 5,220,099 212,004 747.60 61.24 23,764,838
F8_1S_2P Pseudomonas fulva JAFDQJ000000000 SRR13530761 F8 Cupola BA, 37 49 5,219,879 271,973 527.41 61.24 16,765,304
F8_1S_3P Pseudomonas fulva JAFDQK000000000 SRR13530760 F8 Cupola BA, 37 45 5,222,637 279,059 640.19 61.24 20,350,344
F8_1S_4B Pseudomonas fulva JAFDQL000000000 SRR13530758 F8 Cupola R2A, 25 50 5,219,467 212,004 595.41 61.24 18,927,008
F8_1S_5B Pseudomonas fulva JAFDQM000000000 SRR13530757 F8 Cupola R2A, 25 50 5,220,771 212,004 522.35 61.24 16,604,570
F8_1S_6B Pseudomonas fulva JAFDQN000000000 SRR13530756 F8 Cupola R2A, 25 51 5,220,269 228,990 581.78 61.24 18,493,586
F8_2S_1B Pseudomonas fulva JAFDQO000000000 SRR13530755 F8 WHC R2A, 25 51 5,220,561 212,004 672.65 61.24 21,382,176
F8_2S_2P Pseudomonas fulva JAFDQQ000000000 SRR13530753 F8 WHC BA, 37 51 5,220,953 212,004 504.33 61.24 16,031,608
F8_2S_3P Pseudomonas fulva JAFDQR000000000 SRR13530752 F8 WHC BA, 37 51 5,219,857 266,892 746.18 61.24 23,719,826
F8_4S_1B Pseudomonas fulva JAFDQS000000000 SRR13530751 F8 Dining table R2A, 25 47 5,221,731 212,004 679.90 61.24 21,612,934
F8_5S_16B Pseudomonas fulva JAFDQT000000000 SRR13530750 F8 Overhead 4 R2A, 25 46 5,221,547 266,892 690.69 61.24 21,955,880
F8_6S_10B Pseudomonas fulva JAFDQU000000000 SRR13530749 F8 PMM port 1 R2A, 25 43 5,222,049 276,378 692.43 61.24 22,011,252
F8_6S_11B Pseudomonas fulva JAFDQV000000000 SRR13530747 F8 PMM port 1 R2A, 25 45 5,221,141 272,009 763.66 61.24 24,275,474
F8_6S_12B Pseudomonas fulva JAFDQW000000000 SRR13530746 F8 PMM port 1 R2A, 25 47 5,220,530 212,004 553.11 61.24 17,582,460
F8_6S_13B Pseudomonas fulva JAFDQX000000000 SRR13530745 F8 PMM port 1 R2A, 25 46 5,222,282 228,990 767.70 61.24 24,403,836
F8_6S_14B Pseudomonas fulva JAFDQY000000000 SRR13530744 F8 PMM port 1 R2A, 25 165 5,214,942 53,221 58.63 61.25 1,863,658
F8_6S_15B Pseudomonas fulva JAFDQZ000000000 SRR13530743 F8 PMM port 1 R2A, 25 45 5,221,469 212,004 644.90 61.24 20,500,186
F8_6S_1P Pseudomonas fulva JAFDRA000000000 SRR13530742 F8 PMM port 1 BA, 37 47 5,219,969 212,004 1,065.14 61.24 33,859,008
F8_6S_3B Pseudomonas fulva JAFDRB000000000 SRR13530741 F8 PMM port 1 R2A, 25 45 5,222,269 271,999 911.16 61.24 28,964,010
F8_6S_3P Pseudomonas fulva JAFDRC000000000 SRR13530740 F8 PMM port 1 BA, 37 45 5,221,425 212,004 1,002.77 61.24 31,876,344
F8_6S_4B Pseudomonas fulva JAFDRD000000000 SRR13530739 F8 PMM port 1 R2A, 25 47 5,220,883 212,004 587.52 61.24 18,676,250
F8_6S_5B Pseudomonas fulva JAFDRE000000000 SRR13530738 F8 PMM port 1 R2A, 25 44 5,222,120 276,382 507.87 61.24 16,144,410
F8_6S_7B Pseudomonas fulva JAFDRF000000000 SRR13530736 F8 PMM port 1 R2A, 25 48 5,221,613 266,937 817.23 61.24 25,978,110
F8_6S_8B Pseudomonas fulva JAFDRG000000000 SRR13530735 F8 PMM port 1 R2A, 25 48 5,220,807 266,892 666.04 61.24 21,172,172
F8_6S_9B Pseudomonas fulva JAFDRH000000000 SRR13530734 F8 PMM port 1 R2A, 25 47 5,221,098 266,892 857.16 61.24 27,247,530
F8_7S_10B Pseudomonas fulva JAFDRI000000000 SRR13530733 F8 Lab 3 overhead R2A, 25 45 5,221,475 248,885 615.92 61.24 19,579,074
F8_7S_11B Pseudomonas fulva JAFDRJ000000000 SRR13530732 F8 Lab 3 overhead R2A, 25 44 5,223,496 276,366 714.44 61.24 22,710,854
F8_7S_1B Pseudomonas fulva JAFDRR000000000 SRR13530723 F8 Lab 3 overhead R2A, 25 46 5,221,397 248,885 734.17 61.24 23,338,010
F8_7S_1P Pseudomonas fulva JAFDRS000000000 SRR13530722 F8 Lab 3 overhead BA, 37 43 5,221,447 266,892 995.57 61.24 31,647,224
F8_7S_2B Pseudomonas fulva JAFDRT000000000 SRR13530721 F8 Lab 3 overhead R2A, 25 46 5,221,320 248,885 792.01 61.24 25,176,512
F8_7S_2P Pseudomonas fulva JAFDRU000000000 SRR13530720 F8 Lab 3 overhead BA, 37 48 5,221,068 211,998 726.98 61.24 23,109,428
F8_7S_3B Pseudomonas fulva JAFDRV000000000 SRR13530719 F8 Lab 3 overhead R2A, 25 43 5,222,387 279,059 657.54 61.24 20,901,852
F8_7S_3P Pseudomonas fulva JAFDRW000000000 SRR13530718 F8 Lab 3 overhead BA, 37 47 5,220,873 211,998 916.50 61.24 29,133,940
F8_7S_6B Pseudomonas fulva JAFDRZ000000000 SRR13530714 F8 Lab 3 overhead R2A, 25 48 5,222,006 211,998 610.88 61.24 19,418,924
F8_7S_8B Pseudomonas fulva JAFDSC000000000 SRR13530711 F8 Lab 3 overhead R2A, 25 45 5,221,151 211,998 675.48 61.24 21,472,302
F8_7S_9B Pseudomonas fulva JAFDSD000000000 SRR13530710 F8 Lab 3 overhead R2A, 25 43 5,221,838 248,885 817.24 61.24 25,978,556
F8_8S_13B Pseudomonas fulva JAFDSG000000000 SRR13530707 F8 Crew quarters R2A, 25 48 5,220,177 276,366 396.21 61.24 12,594,644
F8_8S_1B Pseudomonas fulva JAFDSH000000000 SRR13530706 F8 Crew quarters R2A, 25 45 5,222,394 326,740 612.35 61.24 19,465,438
F8_8S_2B Pseudomonas fulva JAFDSI000000000 SRR13530705 F8 Crew quarters R2A, 25 47 5,220,003 211,998 950.52 61.24 30,215,290
F8_8S_3B Pseudomonas fulva JAFDSK000000000 SRR13530702 F8 Crew quarters R2A, 25 49 5,220,696 228,990 740.00 61.24 23,523,202
F8_8S_7P Pseudomonas fulva JAFDSM000000000 SRR13530700 F8 Crew quarters BA, 37 48 5,221,111 212,004 877.89 61.24 27,906,690
F8_8S_8P Pseudomonas fulva JAFDSN000000000 SRR13530699 F8 Crew quarters BA, 37 50 5,221,099 212,004 1,153.25 61.24 36,659,886
F8_8S_9P Pseudomonas fulva JAFDSO000000000 SRR13530698 F8 Crew quarters BA, 37 44 5,216,552 212,004 725.04 61.25 23,047,660
F6_4S_P_1A Pseudomonas granadensis JAFDPY000000000 SRR13530773 F6 Dining table BA, 37 32 6,075,880 499,949 543.50 60.13 21,534,088
F6_4S_P_1B Pseudomonas granadensis JAFDPZ000000000 SRR13530772 F6 Dining table BA, 37 40 6,075,550 404,503 681.05 60.13 26,983,966
F6_4S_P_1C Pseudomonas granadensis JAFDQA000000000 SRR13530771 F6 Dining table BA, 37 36 6,074,831 411,755 526.75 60.13 20,870,328
F6_4S_P_2 Pseudomonas granadensis JAFDQB000000000 SRR13530769 F6 Dining table BA, 37 36 6,075,345 409,624 849.89 60.13 33,673,758
F6_4S_P_5C Pseudomonas granadensis JAFDQC000000000 SRR13530768 F6 Dining table BA, 37 35 6,076,644 529,557 356.66 60.13 14,131,340
F6_7S_P_1 Staphylococcus capitis JAFDQE000000000 SRR13530766 F6 Lab 3 overhead BA, 37 23 2,502,093 1,289,580 716.11 32.83 11,624,446
F6_7S_P_4 Staphylococcus capitis JAFDQG000000000 SRR13530764 F6 Lab 3 overhead BA, 37 16 2,451,586 1,282,189 1,422.62 32.78 23,092,982
F5_7S_P12B Staphylococcus caprae JAFDPE000000000 SRR13530726 F5 Lab 3 overhead BA, 37 12 2,636,914 684,748 848.08 33.49 14,738,340
F6_3S_P_7 Staphylococcus epidermidis JAFDPX000000000 SRR13530774 F6 ARED BA, 37 32 2,474,746 167,947 1,420.95 32.03 22,991,394
F5_7S_P10A Staphylococcus saprophyticus JAFDOY000000000 SRR13530792 F5 Lab 3 overhead BA, 37 27 2,660,926 711,481 814.84 32.99 14,003,764
F5_7S_P11B Staphylococcus saprophyticus JAFDPB000000000 SRR13530759 F5 Lab 3 overhead BA, 37 26 2,617,222 1,361,305 964.97 32.98 16,583,928
F5_7S_P12A Staphylococcus saprophyticus JAFDPD000000000 SRR13530737 F5 Lab 3 overhead BA, 37 27 2,663,655 707,529 1,202.62 32.99 20,668,282
F5_7S_P13 Staphylococcus saprophyticus JAFDPF000000000 SRR13530715 F5 Lab 3 overhead BA, 37 24 2,662,145 711,479 1,165.31 32.99 20,027,056
F5_7S_P5A Staphylococcus saprophyticus JAFDPN000000000 SRR13530785 F5 Lab 3 overhead BA, 37 27 2,661,845 711,479 1,391.99 32.99 23,922,656
F5_7S_P5B Staphylococcus saprophyticus JAFDPO000000000 SRR13530784 F5 Lab 3 overhead BA, 37 27 2,661,424 711,481 989.97 32.99 17,013,600
F5_7S_P5C Staphylococcus saprophyticus JAFDPP000000000 SRR13530783 F5 Lab 3 overhead BA, 37 25 2,663,767 711,481 1,176.36 32.99 20,216,888
F6_7S_P_5 Staphylococcus saprophyticus JAFDQH000000000 SRR13530763 F6 Lab 3 overhead BA, 37 23 2,664,922 711,479 1,502.54 32.99 25,822,574
F5_7S_P4 Staphylococcus warneri JAFDPM000000000 SRR13530786 F5 Lab 3 overhead BA, 37 26 2,558,875 420,301 813.75 32.46 13,169,560
Open in a new tab
a

WHC, waste and hygiene compartment; ARED, advanced resistive exercise device; PMM, permanent multipurpose module.

b

BA, blood agar.

Four species from the phylum Actinobacteria were isolated, from the genera Pseudoclavibacter, Kocuria, and Micrococcus, all of which are common in both environmental and human microbiomes (2–5). Kocuria palustris and Micrococcus luteus are opportunistic pathogens (5, 6). M. luteus can survive in a dormant state under extreme oligotrophic conditions (7) and has increased growth and increased biomass yield in microgravity (8).

Multiple coagulase-negative staphylococci (CoNS) were also isolated. CoNS are normal components of human skin flora (9) and are often resistant to antibiotics because of their ability to form biofilms (10); all CoNS in this report are documented opportunistic pathogens (11–15).

Three species from the phylum Proteobacteria were identified. Acinetobacter pittii is a less common nosocomial pathogen that causes pneumonia and meningitis in intensive care patients (16), Pseudomonas fulva is a commensal plant endophyte (17) that can also infect immunocompromised patients (18, 19), and Pseudomonas granadensis is a recently discovered soil bacterium (20).

Two other species in this report that are not associated with the human microbiome are Cytobacillus horneckiae, a Gram-positive UV-resistant endospore-former that was isolated from a clean room at the Kennedy Space Center (21), and Methylobacterium organophilum, a facultative methylotroph (22).

All strains reported here were collected aboard the ISS over the course of five flight missions between June 2017 and December 2018 (Table 1). Premoistened polyester wipes were used to collect samples from eight predetermined surfaces during each flight (see Table 1 for locations). After transport to Earth, the wipes were agitated in sterile phosphate-buffered saline, and the buffer was concentrated with an InnovaPrep CP-150 concentrator. Concentrates were plated onto Reasoner’s 2A (R2A) agar (25°C for 7 days), potato dextrose agar (PDA) (25°C for 7 days), and blood agar (37°C for 2 days) using appropriate concentrations for microbial isolation. Isolated colonies were restreaked on tryptic soy agar (TSA) (25°C), and genomic DNA was extracted using the ZymoBIOMICS DNA MagBead kit according to the manufacturer’s instructions. Libraries for whole-genome shotgun sequencing (WGS) were prepared using the Illumina Nextera DNA Flex library preparation kit as in previous studies (23) and were sequenced using the NovaSeq 6000 S4 flow cell paired-end 2 × 150-bp platform.

Sequencing reads were quality filtered and trimmed, and adapter sequences were removed, using FastQC v0.11.7 (24) and fastp v0.20.0 (25). Scaffolds were assembled with SPAdes v3.11.1 (26). QUAST v5.0.2 (27) was used to determine assembly quality, including the number of contigs, genome size, and N50 value. Default settings were used for all steps except for fastp, which included 512 adapters screening. OrthoANIu (28) was used to confirm the species identity for each strain against the species type strain sequence, with a minimum average nucleotide identity of 95% for identification. Genomes were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (29).

Data availability.

The WGS data and raw data have been deposited in GenBank under the BioProject accession number PRJNA690512. This project has also been deposited in the NASA GeneLab system (30) under the project number GLDS-361. The versions described in this paper are the first versions.

ACKNOWLEDGMENTS

Part of the research described was carried out at the Jet Propulsion Laboratory of the California Institute of Technology under a contract with NASA. This research was funded by a 2014 Space Biology NNH14ZTT002N award (grant 80NSSC18K0113) to Crystal Jaing and K.V., which also partially funded postdoctoral fellowships for C.U. and J.M.W. Additionally, A.C.S. was supported by grant 80NM0018D0004, funded to K.V.

We thank astronauts Colonel Jack Fischer, Colonel Mark Vande Hei, Norishige Kanai, and Alexander Gerst for collecting samples aboard the ISS, the implementation team (Fathi Karouia) at NASA Ames Research Center for coordinating this effort, and Crystal Jaing (Lawrence Livermore National Laboratory), principal investigator of the team. We thank Ryan Kemp (Zymo Corp.) for extracting the DNA and Dan Butler (Weill Cornell Medicine) for generating the shotgun sequencing. The Jet Propulsion Laboratory supercomputing facility staff is acknowledged, notably, Narendra J. Patel (Jimmy) and Edward Villanueva, for continuous support in providing the best possible infrastructure for BIG-DATA analysis.

REFERENCES

  • 1.Taylor PW. 2015. Impact of space flight on bacterial virulence and antibiotic susceptibility. Infect Drug Resist 8:249–262. doi: 10.2147/IDR.S67275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Lin Y-C, Uemori K, de Briel DA, Arunpairojana V, Yokota A. 2004. Zimmermannella helvola gen. nov., sp. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae. Int J Syst Evol Microbiol 54:1669–1676. doi: 10.1099/ijs.0.02741-0. [DOI] [PubMed] [Google Scholar]
  • 3.Dastager SG, Tang S-K, Srinivasan K, Lee J-C, Li W-J. 2014. Kocuria indica sp. nov., isolated from a sediment sample. Int J Syst Evol Microbiol 64:869–874. doi: 10.1099/ijs.0.052548-0. [DOI] [PubMed] [Google Scholar]
  • 4.Lee K, Ganzorig M, Jung JY, Badaya SK, Lim JY. 2019. Complete genome sequence of Kocuria indica CE7, isolated from human skin. Microbiol Resour Announc 8:e00607-19. doi: 10.1128/MRA.00607-19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Kooken JM, Fox KF, Fox A. 2012. Characterization of Micrococcus strains isolated from indoor air. Mol Cell Probes 26:1–5. doi: 10.1016/j.mcp.2011.09.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Mattern R, Ding J. 2014. Keratitis with Kocuria palustris and Rothia mucilaginosa in vitamin A deficiency. Case Rep Ophthalmol 5:72–77. doi: 10.1159/000360391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Greenblatt CL, Baum J, Klein BY, Nachshon S, Koltunov V, Cano RJ. 2004. Micrococcus luteus-survival in amber. Microb Ecol 48:120–127. doi: 10.1007/s00248-003-2016-5. [DOI] [PubMed] [Google Scholar]
  • 8.Mauclaire L, Egli M. 2010. Effect of simulated microgravity on growth and production of exopolymeric substances of Micrococcus luteus space and earth isolates. FEMS Immunol Med Microbiol 59:350–356. doi: 10.1111/j.1574-695X.2010.00683.x. [DOI] [PubMed] [Google Scholar]
  • 9.Gowda A, Pensiero AL, Packer CD. 2018. Staphylococcus caprae: a skin commensal with pathogenic potential. Cureus 10:e3485. doi: 10.7759/cureus.3485. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Becker K, Heilmann C, Peters G. 2014. Coagulase-negative staphylococci. Clin Microbiol Rev 27:870–926. doi: 10.1128/CMR.00109-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Cameron D, Jiang J-H, Hassan K, Elbourne L, Tuck K, Paulsen I, Peleg A. 2015. Insights on virulence from the complete genome of Staphylococcus capitis. Front Microbiol 6:980. doi: 10.3389/fmicb.2015.00980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Laurent F, Butin M. 2019. Staphylococcus capitis and NRCS-A clone: the story of an unrecognized pathogen in neonatal intensive care units. Clin Microbiol Infect 25:1081–1085. doi: 10.1016/j.cmi.2019.03.009. [DOI] [PubMed] [Google Scholar]
  • 13.Xu Z, Misra R, Jamrozy D, Paterson GK, Cutler RR, Holmes MA, Gharbia S, Mkrtchyan HV. 2018. Whole genome sequence and comparative genomics analysis of multi-drug resistant environmental Staphylococcus epidermidis ST59. G3 (Bethesda) 8:2225–2230. doi: 10.1534/g3.118.200314. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Raz R, Colodner R, Kunin CM. 2005. Who are you: Staphylococcus saprophyticus? Clin Infect Dis 40:896–898. doi: 10.1086/428353. [DOI] [PubMed] [Google Scholar]
  • 15.Campoccia D, Montanaro L, Visai L, Corazzari T, Poggio C, Pegreffi F, Maso A, Pirini V, Ravaioli S, Cangini I, Speziale P, Arciola CR. 2010. Characterization of 26 Staphylococcus warneri isolates from orthopedic infections. Int J Artif Organs 33:575–581. doi: 10.1177/039139881003300903. [DOI] [PubMed] [Google Scholar]
  • 16.Wisplinghoff H, Paulus T, Lugenheim M, Stefanik D, Higgins PG, Edmond MB, Wenzel RP, Seifert H. 2012. Nosocomial bloodstream infections due to Acinetobacter baumannii, Acinetobacter pittii and Acinetobacter nosocomialis in the United States. J Infect 64:282–290. doi: 10.1016/j.jinf.2011.12.008. [DOI] [PubMed] [Google Scholar]
  • 17.Adeniji AA, Aremu OS, Loots DT, Babalola OO. 2020. Pseudomonas fulva HARBPS9.1: candidate anti-Fusarium agent in South Africa. Eur J Plant Pathol 157:767–781. doi: 10.1007/s10658-020-02035-4. [DOI] [Google Scholar]
  • 18.Almuzara MN, Vazquez M, Tanaka N, Turco M, Ramirez MS, Lopez EL, Pasteran F, Rapoport M, Procopio A, Vay CA. 2010. First case of human infection due to Pseudomonas fulva, an environmental bacterium isolated from cerebrospinal fluid. J Clin Microbiol 48:660–664. doi: 10.1128/JCM.01849-09. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.Seok Y, Shin H, Lee Y, Cho I, Na S, Yong D, Jeong SH, Lee K. 2010. First report of bloodstream infection caused by Pseudomonas fulva. J Clin Microbiol 48:2656–2657. doi: 10.1128/JCM.01609-09. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Pascual J, García-López M, Bills GF, Genilloud O. 2015. Pseudomonas granadensis sp. nov., a new bacterial species isolated from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain. Int J Syst Evol Microbiol 65:625–632. doi: 10.1099/ijs.0.069260-0. [DOI] [PubMed] [Google Scholar]
  • 21.Vaishampayan P, Probst A, Krishnamurthi S, Ghosh S, Osman S, McDowall A, Ruckmani A, Mayilraj S, Venkateswaran K. 2010. Bacillus horneckiae sp. nov., isolated from a spacecraft-assembly clean room. Int J Syst Evol Microbiol 60:1031–1037. doi: 10.1099/ijs.0.008979-0. [DOI] [PubMed] [Google Scholar]
  • 22.Green PN. 2015. Methylobacterium. In DeVos P, Dedysh S, Hedlund B, Kämpfer P, Rainey F, Trujillo ME, Bowman JP, Brown DR, Glöckner FO, Oren A, Paster BJ, Wade W, Ward N, Busse H-J, Reysenbach AL (ed), Bergey's manual of systematics of archaea and bacteria. John Wiley & Sons, Hoboken, NJ. doi: 10.1002/9781118960608.gbm00830. [DOI] [Google Scholar]
  • 23.Be NA, Avila-Herrera A, Allen JE, Singh N, Checinska Sielaff A, Jaing C, Venkateswaran K. 2017. Whole metagenome profiles of particulates collected from the International Space Station. Microbiome 5:81. doi: 10.1186/s40168-017-0292-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Andrews S. 2011. FastQC: a quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc.
  • 25.Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890. doi: 10.1093/bioinformatics/bty560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 26.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. doi: 10.1093/bioinformatics/btt086. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. doi: 10.1007/s10482-017-0844-4. [DOI] [PubMed] [Google Scholar]
  • 29.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. doi: 10.1093/nar/gkw569. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 30.Ray S, Gebre S, Fogle H, Berrios DC, Tran PB, Galazka JM, Costes SV. 2019. GeneLab: Omics database for spaceflight experiments. Bioinformatics 35:1753–1759. doi: 10.1093/bioinformatics/bty884. [DOI] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The WGS data and raw data have been deposited in GenBank under the BioProject accession number PRJNA690512. This project has also been deposited in the NASA GeneLab system (30) under the project number GLDS-361. The versions described in this paper are the first versions.

Articles from Microbiology Resource Announcements are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES