Afshinnekoo E, Scott RT, MacKay MJ, Pariset E, Cekanaviciute E, Barker R, et al. Fundamental Biological Features of Spaceflight: Advancing the Field to Enable Deep-Space Exploration. Cell. 2020;183(5):1162–84. https://doi.org/10.1016/j.cell.2020.10.050.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andrews S. 2015. FastQC: a quality tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Google Scholar
Arango-Argoty G, Garner E, Pruden A, Heath LS, Vikesland P, Zhang L. DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome. 2018;6(1):23. https://doi.org/10.1186/s40168-018-0401-z.
Article
PubMed
PubMed Central
Google Scholar
Aunins TR, Erickson KE, Prasad N, et al. Spaceflight modifies escherichia coli gene expression in response to antibiotic exposure and reveals role of oxidative stress response. Front Microbiol. 2018;9:310. Published 2018 Mar 16. https://doi.org/10.3389/fmicb.2018.00310.
Article
PubMed
PubMed Central
Google Scholar
Avila-Herrera A, Thissen J, Urbaniak C, et al. Crewmember microbiome may influence microbial composition of ISS habitable surfaces. PLoS One. 2020;15(4):e0231838.
Article
CAS
Google Scholar
Aziz RK, Bartels D, Best AA, Dejongh M, Disz T, Edwards RA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.
Article
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77. https://doi.org/10.1089/cmb.2012.0021.
Article
CAS
PubMed
PubMed Central
Google Scholar
Be NA, Avila-Herrera A, Allen JE, et al. Whole metagenome profiles of particulates collected from the International Space Station. Microbiome. 2017;5(1):81. https://doi.org/10.1186/s40168-017-0292-4 Published 2017 Jul 17.
Article
PubMed
PubMed Central
Google Scholar
Berglund F, Österlund T, Boulund F, Marathe NP, Larsson DGJ, Kristiansson E. Identification and reconstruction of novel antibiotic resistance genes from metagenomes. Microbiome. 2019;7(1):52. https://doi.org/10.1186/s40168-019-0670-1 Published 2019 Apr 1.
Article
PubMed
PubMed Central
Google Scholar
Bijlani S, Singh NK, Mason CE, Wang CCC, Venkateswaran K. Draft Genome Sequences of Sphingomonas Species Associated with the International Space Station. Microbiol Resour Announc. 2020;9(25):e00578–20. https://doi.org/10.1128/MRA.00578-20 Published 2020 Jun 18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bijlani S, Singh NK, Mason CE, Wang CCC, Venkateswaran K. Draft Genome Sequences of Tremellomycetes Strains Isolated from the International Space Station. Microbiol Resour Announc. 2020b;9(26):e00504–20. https://doi.org/10.1128/MRA.00504-20 Published 2020 Jun 25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Article
CAS
Google Scholar
Boolchandani M, D'Souza AW, Dantas G. Sequencing-based methods and resources to study antimicrobial resistance. Nat Rev Genet. 2019;20(6):356–70. https://doi.org/10.1038/s41576-019-0108-4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Checinska Sielaff A, Urbaniak C, Mohan GBM, Stepanov VG, Tran Q, Wood JM, et al. Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces. Microbiome. 2019;7(1):50. https://doi.org/10.1186/s40168-019-0666-x.
Article
PubMed
PubMed Central
Google Scholar
Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90. https://doi.org/10.1093/bioinformatics/bty560.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chowdhury AS, Call DR, Broschat SL. Antimicrobial resistance prediction for gram-negative bacteria via game theory-based feature evaluation [published correction appears in Sci Rep. 2020 Jan 30;10(1):1846]. Sci Rep. 2019;9(1):14487. https://doi.org/10.1038/s41598-019-50686-z Published 2019 Oct 9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O. PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data [published correction appears in PLoS One. 2013;8(12). doi:10.1371/annotation/b84e1af7-c127-45c3-be22-76abd977600f]. PLoS One. 2013;8(10):e77302. https://doi.org/10.1371/journal.pone.0077302.
Article
CAS
PubMed
PubMed Central
Google Scholar
Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, et al. International MetaSUB Consortium. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell. 2021;184(13):3376–93.
Article
CAS
Google Scholar
Danko DC, Singh N, Butler DJ, Mozsary C, Jiang P, Keshavarzian A, et al. Genetic and immunological evidence for microbial transfer between the international space station and an astronaut. bioRxiv. 2020. 11.10.376954. https://doi.org/10.1101/2020.11.10.376954.
Daury L, Orange F, Taveau JC, Verchere A, Monlezun L, Gounou C, et al. Tripartite assembly of RND multidrug efflux pumps. Nat Commun. 2016;7:10731.
Article
CAS
Google Scholar
Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23(6):673–9. https://doi.org/10.1093/bioinformatics/btm009.
Article
CAS
PubMed
Google Scholar
Dierick K, Van Coillie E, Swiecicka I, Meyfroidt G, et al. Fatal family outbreak of Bacillus cereus-associated food poisoning. J Clin Microbiol. 2005;43(8):4277–9.
Article
Google Scholar
Du B, Daniels VR, Vaksman Z, Boyd JL, Crady C, Putcha L. Evaluation of physical and chemical changes in pharmaceuticals flown on space missions. AAPS J. 2011;13(2):299–308. https://doi.org/10.1208/s12248-011-9270-0.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fukuda T, Fukuda K, Takahashi A, et al. Analysis of deletion mutations of the rpsL gene in the yeast Saccharomyces cerevisiae detected after long-term flight on the Russian space station Mir. Mutat Res. 2000;470(2):125–32. https://doi.org/10.1016/s1383-5742(00)00054-5.
Article
CAS
PubMed
Google Scholar
Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, et al. The NASA twins study: a multidimensional analysis of a year-long human spaceflight. Science. 2019;364(6436):eaau8650. https://doi.org/10.1126/science.aau8650.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29:1072–5. https://doi.org/10.1093/bioinformatics/btt086.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hadjadj L, Baron SA, Diene SM, Rolain JM. How to discover new antibiotic resistance genes? Expert Rev Mol Diagn. 2019;19(4):349–62. https://doi.org/10.1080/14737159.2019.1592678.
Article
CAS
PubMed
Google Scholar
Hammond TG, Stodieck L, Birdsall HH, et al. Effects of microgravity on the virulence of Listeria monocytogenes, Enterococcus faecalis, Candida albicans, and methicillin-resistant Staphylococcus aureus. Astrobiology. 2013;13(11):1081–90. https://doi.org/10.1089/ast.2013.0986.
Article
CAS
PubMed
Google Scholar
Hendriksen RS, Bortolaia V, Tate H, Tyson GH, Aarestrup FM, McDermott PF. Using Genomics to Track Global Antimicrobial Resistance. Front Public Health. 2019;7:242. https://doi.org/10.3389/fpubh.2019.00242 Published 2019 Sep 4.
Article
PubMed
PubMed Central
Google Scholar
Juergensmeyer MA, Juergensmeyer EA, Guikema JA. Long-term exposure to spaceflight conditions affects bacterial response to antibiotics. Microgravity Sci Technol. 1999;12(1):41.
CAS
PubMed
Google Scholar
Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:e1165.
Article
Google Scholar
Kim W, Tengra FK, Young Z, et al. Spaceflight promotes biofilm formation by Pseudomonas aeruginosa. PLoS One. 2013;8(4):e62437 Published 2013 Apr 29.
Article
CAS
Google Scholar
Lakin SM, Kuhnle A, Alipanahi B, et al. Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences. Commun Biol. 2019;2:294. https://doi.org/10.1038/s42003-019-0545-9 Published 2019 Aug 6.
Article
PubMed
PubMed Central
Google Scholar
Mahler H, Pasi A, Kramer JM, Schulte P, et al. Fulminant liver failure in association with the emetic toxin of Bacillus cereus. N Engl J Med. 1997;336(16):1142–8.
Article
CAS
Google Scholar
Morrison MD, Thissen JB, Karouia F, Mehta S, Urbaniak C, Venkateswaran K, et al. Investigation of Spaceflight Induced Changes to Astronaut Microbiomes. Front Microbiol. 2021;12:659179. https://doi.org/10.3389/fmicb.2021.659179.
Article
PubMed
PubMed Central
Google Scholar
Nickerson CA, Ott CM, Wilson JW, Ramamurthy R, Pierson DL. Microbial responses to microgravity and other low-shear environments. Microbiol Mol Biol Rev. 2004;68(2):345–61. https://doi.org/10.1128/MMBR.68.2.345-361.2004.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.
Article
CAS
Google Scholar
Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31(22):3691–3. https://doi.org/10.1093/bioinformatics/btv421.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Article
CAS
Google Scholar
Rekha PD, Hameed A, Manzoor MAP, Suryavanshi MV, Ghate SD, Arun AB, et al. First Report of Pathogenic Bacterium Kalamiella piersonii Isolated from Urine of a Kidney Stone Patient: Draft Genome and Evidence for Role in Struvite Crystallization. Pathogens. 2020;9(9):711. https://doi.org/10.3390/pathogens9090711 PMID: 32872396; PMCID: PMC7558591.
Article
CAS
PubMed Central
Google Scholar
Ruppé E, Ghozlane A, Tap J, et al. Prediction of the intestinal resistome by a three-dimensional structure-based method. Nat Microbiol. 2019;4(1):112–23. https://doi.org/10.1038/s41564-018-0292-6.
Article
CAS
PubMed
Google Scholar
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–9. https://doi.org/10.1093/bioinformatics/btu153.
Article
CAS
PubMed
Google Scholar
Singh NK, Wood JM, Karouia F, Venkateswaran K. Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces. Microbiome. 2018;6(1):204. https://doi.org/10.1186/s40168-018-0585-2.
Article
PubMed
PubMed Central
Google Scholar
Singh NK, Bezdan D, Checinska Sielaff A, Wheeler K, Mason CE, Venkateswaran K. Multi-drug resistant Enterobacter bugandensis species isolated from the International Space Station and comparative genomic analyses with human pathogenic strains. BMC Microbiol. 2018b;18:175.
Article
CAS
Google Scholar
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;103(11):4483–97. https://doi.org/10.1007/s00253-019-09813-z.
Article
CAS
PubMed
Google Scholar
Sonnenfeld G, Shearer WT. Immune function during space flight. Nutrition. 2002;18(10):899–903. https://doi.org/10.1016/s0899-9007(02)00903-6.
Article
CAS
PubMed
Google Scholar
Su M, Satola SW, Read TD. Genome-based prediction of bacterial antibiotic resistance. J Clin Microbiol. 2019;57(3):e01405–18. https://doi.org/10.1128/JCM.01405-18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sun J, Deng Z, Yan A. Bacterial multidrug efflux pumps: mechanisms, physiology and pharmacological exploitations. Biochem Biophys Res Commun. 2014;453(2):254–67.
Article
CAS
Google Scholar
Taylor PW. Impact of space flight on bacterial virulence and antibiotic susceptibility. Infect Drug Resist. 2015;8:249–62. https://doi.org/10.2147/IDR.S67275 Published 2015 Jul 30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tixador R, Richoilley G, Gasset G, et al. Study of minimal inhibitory concentration of antibiotics on bacteria cultivated in vitro in space (Cytos 2 experiment). Aviat Space Environ Med. 1985;56(8):748–51.
CAS
PubMed
Google Scholar
Urbaniak C, Sielaff AC, Frey KG, et al. Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces. Sci Rep. 2018;8(1):814. https://doi.org/10.1038/s41598-017-18506-4 Published 2018 Jan 16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Urbaniak C, Lorenzi H, Thissen J, et al. The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation. Microbiome. 2020;8(1):56.
Article
CAS
Google Scholar
Venkateswaran K, Vaishampayan P, Cisneros J, Pierson DL, Rogers SO, Perry J. International Space Station environmental microbiome - microbial inventories of ISS filter debris. Appl Microbiol Biotechnol. 2014;98(14):6453–66. https://doi.org/10.1007/s00253-014-5650-6.
Article
CAS
PubMed
Google Scholar
Venkateswaran K, Singh NK, Checinska Sielaff A, et al. Non-Toxin-Producing Bacillus cereus Strains Belonging to the B. anthracis Clade Isolated from the International Space Station. mSystems. 2017;2(3):e00021–17. https://doi.org/10.1128/mSystems.00021-17 Published 2017 Jun 27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Voorhies AA, Mark Ott C, Mehta S, et al. Study of the impact of long-duration space missions at the International Space Station on the astronaut microbiome. Sci Rep. 2019;9(1):9911.
Article
Google Scholar
Wilson JW, Ott CM, Höner zu Bentrup K, et al. Space flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq. Proc Natl Acad Sci U S A. 2007;104(41):16299–304. https://doi.org/10.1073/pnas.0707155104.
Article
PubMed
PubMed Central
Google Scholar
Wissel EF, Talbot BM, Johnson BA, Petit RA, Hertzberg V, Dunlop A, et al. Benchmarking software to predict antibiotic resistance phenotypes in shotgun metagenomes using simulated data. bioRxiv. 2022.01.13.476279. https://doi.org/10.1101/2022.01.13.476279.
World Health Organization. Global Action Plan on Antimicrobial Resistance (2015). Available online at: https://apps.who.int/iris/bitstream/handle/10665/193736/9789241509763_eng.pdf (Accessed 27 Aug 2021).
Google Scholar
Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek. 2017;110:1281–6. https://doi.org/10.1007/s10482-017-0844-4.
Article
CAS
PubMed
Google Scholar
Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67:2640–4.
Article
CAS
Google Scholar
Zea L, Larsen M, Estante F, et al. Phenotypic Changes Exhibited by E. coli Cultured in Space. Front Microbiol. 2017;8:1598. https://doi.org/10.3389/fmicb.2017.01598 Published 2017 Aug 28.
Article
PubMed
PubMed Central
Google Scholar
Zhang X, et al. Fecal fusobacterium nucleatum for the diagnosis of colorectal tumor: a systematic review and meta-analysis. Cancer Med. 2019;8:480–91.
Article
Google Scholar