Whole metagenome profiles of particulates collected from the International Space Station

Be, Nicholas A.; Avila-Herrera, Aram; Allen, Jonathan E.; Singh, Nitin; Checinska Sielaff, Aleksandra; Jaing, Crystal; Venkateswaran, Kasthuri

doi:10.1186/s40168-017-0292-4

Title: Whole metagenome profiles of particulates collected from the International Space Station

Abstract

Background The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized. Methods This study examined the whole metagenome of ISS microbes at both species- and gene-level resolution. Air filter and dust samples from the ISS were analyzed and compared to samples collected in a terrestrial cleanroom environment. Furthermore, metagenome mining was carried out to characterize dominant, virulent, and novel microorganisms. The whole genome sequences of select cultivable strains isolated from these samples were extracted from the metagenome and compared. Results Species-level composition in the ISS was found to be largely dominated by Corynebacterium ihumii GD7, with overall microbial diversity being lower in the ISS relative to the cleanroom samples. When examining detection of microbial genes relevant to human health such as antimicrobial resistance and virulence genes,more »« less

Authors:

Be, Nicholas A.; Avila-Herrera, Aram; Allen, Jonathan E.; Singh, Nitin; Checinska Sielaff, Aleksandra; Jaing, Crystal;

Publication Date:: Mon Jul 17 00:00:00 EDT 2017

Research Org.:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1618947

Alternate Identifier(s):: OSTI ID: 1395309

Grant/Contract Number:: AC52-07NA27344

Resource Type:: Published Article

Journal Name:: Microbiome

Additional Journal Information:: Journal Name: Microbiome Journal Volume: 5 Journal Issue: 1; Journal ID: ISSN 2049-2618

Publisher:: Springer Science + Business Media

Country of Publication:: United Kingdom

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; international Space Station; Microbiome; Functional metagenomics; Built environment; Cleanroom Propidium monoazide

Citation Formats


                    Be, Nicholas A., Avila-Herrera, Aram, Allen, Jonathan E., Singh, Nitin, Checinska Sielaff, Aleksandra, Jaing, Crystal, and Venkateswaran, Kasthuri. Whole metagenome profiles of particulates collected from the International Space Station.  United Kingdom: N. p., 2017. 
Web.  doi:10.1186/s40168-017-0292-4.

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                    Be, Nicholas A., Avila-Herrera, Aram, Allen, Jonathan E., Singh, Nitin, Checinska Sielaff, Aleksandra, Jaing, Crystal, & Venkateswaran, Kasthuri. Whole metagenome profiles of particulates collected from the International Space Station.  United Kingdom.  https://doi.org/10.1186/s40168-017-0292-4

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                    Be, Nicholas A., Avila-Herrera, Aram, Allen, Jonathan E., Singh, Nitin, Checinska Sielaff, Aleksandra, Jaing, Crystal, and Venkateswaran, Kasthuri. Mon .  
"Whole metagenome profiles of particulates collected from the International Space Station".  United Kingdom.  https://doi.org/10.1186/s40168-017-0292-4.

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@article{osti_1618947,

  title        = {Whole metagenome profiles of particulates collected from the International Space Station},

  author       = {Be, Nicholas A. and Avila-Herrera, Aram and Allen, Jonathan E. and Singh, Nitin and Checinska Sielaff, Aleksandra and Jaing, Crystal and Venkateswaran, Kasthuri},

  abstractNote = {Background The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized. Methods This study examined the whole metagenome of ISS microbes at both species- and gene-level resolution. Air filter and dust samples from the ISS were analyzed and compared to samples collected in a terrestrial cleanroom environment. Furthermore, metagenome mining was carried out to characterize dominant, virulent, and novel microorganisms. The whole genome sequences of select cultivable strains isolated from these samples were extracted from the metagenome and compared. Results Species-level composition in the ISS was found to be largely dominated by Corynebacterium ihumii GD7, with overall microbial diversity being lower in the ISS relative to the cleanroom samples. When examining detection of microbial genes relevant to human health such as antimicrobial resistance and virulence genes, it was found that a larger number of relevant gene categories were observed in the ISS relative to the cleanroom. Strain-level cross-sample comparisons were made for Corynebacterium, Bacillus, and Aspergillus showing possible distinctions in the dominant strain between samples. Conclusion Species-level analyses demonstrated distinct differences between the ISS and cleanroom samples, indicating that the cleanroom population is not necessarily reflective of space habitation environments. Lastly, the overall population of viable microorganisms and the functional diversity inherent to this unique closed environment are of critical interest with respect to future space habitation. Observations and studies such as these will be important to evaluating the conditions required for long-term health of human occupants in such environments.},

  doi          = {10.1186/s40168-017-0292-4},

  journal      = {Microbiome},

  number       = 1,

  volume       = 5,

  place        = {United Kingdom},

  year         = {Mon Jul 17 00:00:00 EDT 2017},

  month        = {Mon Jul 17 00:00:00 EDT 2017}

}

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Works referenced in this record:

Nonmutational compensation of the fitness cost of antibiotic resistance in mycobacteria by overexpression of tlyA rRNA methylase
journal, October 2016

Freihofer, Pietro; Akbergenov, Rashid; Teo, Youjin
RNA, Vol. 22, Issue 12
DOI: 10.1261/rna.057257.116

Comprehensive analysis of the skin fungal microbiota of astronauts during a half-year stay at the International Space Station
journal, January 2016

Sugita, Takashi; Yamazaki, Takashi; Makimura, Koichi
Medical Mycology, Vol. 54, Issue 3
DOI: 10.1093/mmy/myv121

An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii
journal, December 2007

Dijkshoorn, Lenie; Nemec, Alexandr; Seifert, Harald
Nature Reviews Microbiology, Vol. 5, Issue 12
DOI: 10.1038/nrmicro1789

A Salmonella typhimurium virulence protein is similar to a Yersinia enterocolitica invasion protein and a bacteriophage lambda outer membrane protein.
journal, January 1991

Pulkkinen, W. S.; Miller, S. I.
Journal of Bacteriology, Vol. 173, Issue 1
DOI: 10.1128/jb.173.1.86-93.1991

Staphylococcus caprae bone and joint infections: a re-emerging infection?
journal, December 2014

Seng, P.; Barbe, M.; Pinelli, P. O.
Clinical Microbiology and Infection, Vol. 20, Issue 12
DOI: 10.1111/1469-0691.12743

Genome sequence and description of Corynebacterium ihumii sp. nov.
journal, March 2014

Padmanabhan, Roshan; Dubourg, Grégory; Lagier, Jean-Christophe
Standards in Genomic Sciences, Vol. 9, Issue 3
DOI: 10.4056/sigs.5149006

Characterization of whole genome amplified (WGA) DNA for use in genotyping assay development
journal, January 2012

Han, Tao; Chang, Ching-Wei; Kwekel, Joshua C.
BMC Genomics, Vol. 13, Issue 1
DOI: 10.1186/1471-2164-13-217

Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome
journal, September 2016

Hartmann, Erica M.; Hickey, Roxana; Hsu, Tiffany
Environmental Science & Technology, Vol. 50, Issue 18
DOI: 10.1021/acs.est.6b00262

Malassezia globosa and restricta: Breakthrough Understanding of the Etiology and Treatment of Dandruff and Seborrheic Dermatitis through Whole-Genome Analysis
journal, December 2007

Dawson, Thomas L.
Journal of Investigative Dermatology Symposium Proceedings, Vol. 12, Issue 2
DOI: 10.1038/sj.jidsymp.5650049

Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities
journal, October 2015

Checinska, Aleksandra; Probst, Alexander J.; Vaishampayan, Parag
Microbiome, Vol. 3, Issue 1
DOI: 10.1186/s40168-015-0116-3

rRNA Methyltransferases and their Role in Resistance to Antibiotics
journal, July 2010

Morić, Ivana; Savić, Miloje; Ilić-Tomić, Tatjana
Journal of Medical Biochemistry, Vol. 29, Issue 3
DOI: 10.2478/v10011-010-0030-y

Microbial Monitoring of Crewed Habitats in Space—Current Status and Future Perspectives
journal, January 2014

Yamaguchi, Nobuyasu; Roberts, Michael; Castro, Sarah
Microbes and Environments, Vol. 29, Issue 3
DOI: 10.1264/jsme2.ME14031

A Novel Gene Amplification Causes Upregulation of the PatAB ABC Transporter and Fluoroquinolone Resistance in Streptococcus pneumoniae
journal, March 2015

Baylay, Alison J.; Ivens, Alasdair; Piddock, Laura J. V.
Antimicrobial Agents and Chemotherapy, Vol. 59, Issue 6
DOI: 10.1128/AAC.04858-14

Microbial contamination monitoring and control during human space missions
journal, January 2012

Van Houdt, Rob; Mijnendonckx, Kristel; Leys, Natalie
Planetary and Space Science, Vol. 60, Issue 1
DOI: 10.1016/j.pss.2011.09.001

Fast and accurate short read alignment with Burrows-Wheeler transform
journal, May 2009

Li, H.; Durbin, R.
Bioinformatics, Vol. 25, Issue 14
DOI: 10.1093/bioinformatics/btp324

Draft Genome Sequences of Two Aspergillus fumigatus Strains, Isolated from the International Space Station
journal, July 2016

Singh, Nitin Kumar; Blachowicz, Adriana; Checinska, Aleksandra
Genome Announcements, Vol. 4, Issue 4
DOI: 10.1128/genomeA.00553-16

DNA adenine methylase mutants of Salmonella typhimurium show defects in protein secretion, cell invasion, and M cell cytotoxicity
journal, September 1999

Garcia-Del Portillo, F.; Pucciarelli, M. G.; Casadesus, J.
Proceedings of the National Academy of Sciences, Vol. 96, Issue 20
DOI: 10.1073/pnas.96.20.11578

Alternaria arborescens Infection in a Healthy Individual and Literature Review of Cutaneous Alternariosis
journal, October 2014

Hu, Wenying; Ran, Yuping; Zhuang, Kaiwen
Mycopathologia, Vol. 179, Issue 1-2
DOI: 10.1007/s11046-014-9822-9

Strain-level microbial epidemiology and population genomics from shotgun metagenomics
journal, March 2016

Scholz, Matthias; Ward, Doyle V.; Pasolli, Edoardo
Nature Methods, Vol. 13, Issue 5
DOI: 10.1038/nmeth.3802

Rapid Culture-Independent Microbial Analysis Aboard the International Space Station (ISS) Stage Two: Quantifying Three Microbial Biomarkers
journal, September 2012

Morris, Heather C.; Damon, Michael; Maule, Jake
Astrobiology, Vol. 12, Issue 9
DOI: 10.1089/ast.2012.0863

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
journal, April 2014

McMurdie, Paul J.; Holmes, Susan
PLoS Computational Biology, Vol. 10, Issue 4
DOI: 10.1371/journal.pcbi.1003531

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation
journal, June 2016

Mayer, Teresa; Blachowicz, Adriana; Probst, Alexander J.
Microbiome, Vol. 4, Issue 1
DOI: 10.1186/s40168-016-0167-0

Ribosomal RNA methyltransferases contribute to Staphylococcus aureus virulence
journal, May 2015

Kyuma, Tatsuhiko; Kimura, Satoshi; Hanada, Yuichi
FEBS Journal, Vol. 282, Issue 13
DOI: 10.1111/febs.13302

Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: A review
journal, March 2013

Rizzo, L.; Manaia, C.; Merlin, C.
Science of The Total Environment, Vol. 447
DOI: 10.1016/j.scitotenv.2013.01.032

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on
journal, November 2015

Chen, Lihong; Zheng, Dandan; Liu, Bo
Nucleic Acids Research, Vol. 44, Issue D1
DOI: 10.1093/nar/gkv1239

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
journal, October 2016

Nayfach, Stephen; Rodriguez-Mueller, Beltran; Garud, Nandita
Genome Research, Vol. 26, Issue 11
DOI: 10.1101/gr.201863.115

Fast and sensitive protein alignment using DIAMOND
journal, November 2014

Buchfink, Benjamin; Xie, Chao; Huson, Daniel H.
Nature Methods, Vol. 12, Issue 1
DOI: 10.1038/nmeth.3176

Bacillus anthracis-Like Bacteria and Other B. cereus Group Members in a Microbial Community Within the International Space Station: A Challenge for Rapid and Easy Molecular Detection of Virulent B. anthracis
journal, June 2014

van Tongeren, Sandra P.; Roest, Hendrik I. J.; Degener, John E.
PLoS ONE, Vol. 9, Issue 6
DOI: 10.1371/journal.pone.0098871

International Space Station environmental microbiome — microbial inventories of ISS filter debris
journal, April 2014

Venkateswaran, Kasthuri; Vaishampayan, Parag; Cisneros, Jessica
Applied Microbiology and Biotechnology, Vol. 98, Issue 14
DOI: 10.1007/s00253-014-5650-6

Penicillium Species and Their Associated Mycotoxins
book, December 2016

Perrone, Giancarlo; Susca, Antonia
Methods in Molecular Biology
DOI: 10.1007/978-1-4939-6707-0_5

Microorganisms in Confined Habitats: Microbial Monitoring and Control of Intensive Care Units, Operating Rooms, Cleanrooms and the International Space Station
journal, October 2016

Mora, Maximilian; Mahnert, Alexander; Koskinen, Kaisa
Frontiers in Microbiology, Vol. 7
DOI: 10.3389/fmicb.2016.01573

Presence of Inducible Clindamycin Resistance Phenotype and erm Genes in Foodborne Staphylococcus aureus Isolates
journal, June 2013

Sudagidan, Mert; Aydin, Ali
Foodborne Pathogens and Disease, Vol. 10, Issue 6
DOI: 10.1089/fpd.2012.1424

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
journal, April 2013

McMurdie, Paul J.; Holmes, Susan
PLoS ONE, Vol. 8, Issue 4
DOI: 10.1371/journal.pone.0061217

Microbe-I: fungal biota analyses of the Japanese experimental module KIBO of the International Space Station before launch and after being in orbit for about 460 days: Microbe-I: fungal biota analyses of KIBO, ISS
journal, December 2011

Satoh, Kazuo; Nishiyama, Yayoi; Yamazaki, Takashi
Microbiology and Immunology, Vol. 55, Issue 12
DOI: 10.1111/j.1348-0421.2011.00386.x

Urban microbiomes and urban ecology: How do microbes in the built environment affect human sustainability in cities?
journal, September 2014

King, Gary M.
Journal of Microbiology, Vol. 52, Issue 9
DOI: 10.1007/s12275-014-4364-x

Considerations for non-invasive in-flight monitoring of astronaut immune status with potential use of MEMS and NEMS devices
journal, August 2006

Aponte, V. M.; Finch, D. S.; Klaus, D. M.
Life Sciences, Vol. 79, Issue 14
DOI: 10.1016/j.lfs.2006.04.007

Physiological impact of transposable elements encoding DDE transposases in the environmental adaptation of Streptococcus agalactiae
journal, April 2014

Flechard, M.; Gilot, P.
Microbiology, Vol. 160, Issue Pt_7
DOI: 10.1099/mic.0.077628-0

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.
journal, May 2015

Aßhauer, Kathrin P.; Wemheuer, Bernd; Daniel, Rolf
Bioinformatics, Vol. 31, Issue 17
DOI: 10.1093/bioinformatics/btv287

New perspectives on viable microbial communities in low-biomass cleanroom environments
journal, October 2012

Vaishampayan, Parag; Probst, Alexander J.; La Duc, Myron T.
The ISME Journal, Vol. 7, Issue 2
DOI: 10.1038/ismej.2012.114

Antimicrobial Resistance and Virulence: a Successful or Deleterious Association in the Bacterial World?
journal, April 2013

Beceiro, A.; Tomas, M.; Bou, G.
Clinical Microbiology Reviews, Vol. 26, Issue 2
DOI: 10.1128/CMR.00059-12

Survey of environmental biocontamination on board the International Space Station
journal, January 2006

Novikova, Natalia; De Boever, Patrick; Poddubko, Svetlana
Research in Microbiology, Vol. 157, Issue 1
DOI: 10.1016/j.resmic.2005.07.010

Regulation of Protein Function by Reversible Methionine Oxidation and the Role of Selenoprotein MsrB1
journal, October 2015

Kaya, Alaattin; Lee, Byung Cheon; Gladyshev, Vadim N.
Antioxidants & Redox Signaling, Vol. 23, Issue 10
DOI: 10.1089/ars.2015.6385

Scalable metagenomic taxonomy classification using a reference genome database
journal, July 2013

Ames, Sasha K.; Hysom, David A.; Gardner, Shea N.
Bioinformatics, Vol. 29, Issue 18
DOI: 10.1093/bioinformatics/btt389

Urinary tract infection with Corynebacterium aurimucosum after urethroplasty stricture of the urethra: a case report
journal, July 2015

Lo, Seynabou; Thiam, Issa; Fall, Bécaye
Journal of Medical Case Reports, Vol. 9, Issue 1
DOI: 10.1186/s13256-015-0638-0

Diagnosis of invasive fungal infections in haematological patients by combined use of galactomannan, 1,3-β-D-glucan, Aspergillus PCR, multifungal DNA-microarray, and Aspergillus azole resistance PCRs in blood and bronchoalveolar lavage samples: results of a prospective multicentre study
journal, October 2016

Boch, T.; Spiess, B.; Cornely, O. A.
Clinical Microbiology and Infection, Vol. 22, Issue 10
DOI: 10.1016/j.cmi.2016.06.021

Impact of three Illumina library construction methods on GC bias and HLA genotype calling
journal, March 2015

Lan, James H.; Yin, Yuxin; Reed, Elaine F.
Human Immunology, Vol. 76, Issue 2-3
DOI: 10.1016/j.humimm.2014.12.016

How to invade a susceptible host: cellular aspects of aspergillosis
journal, December 2016

Krappmann, Sven
Current Opinion in Microbiology, Vol. 34
DOI: 10.1016/j.mib.2016.10.002

Reversal of multidrug resistance by the inhibition of ATP-binding cassette pumps employing “Generally Recognized As Safe” (GRAS) nanopharmaceuticals: A review
journal, November 2013

Sosnik, Alejandro
Advanced Drug Delivery Reviews, Vol. 65, Issue 13-14
DOI: 10.1016/j.addr.2013.09.002

Evolution of the indoor biome
journal, April 2015

Martin, Laura J.; Adams, Rachel I.; Bateman, Ashley
Trends in Ecology & Evolution, Vol. 30, Issue 4
DOI: 10.1016/j.tree.2015.02.001

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003

Shannon, P.
Genome Research, Vol. 13, Issue 11
DOI: 10.1101/gr.1239303

Functional Metagenomics of Spacecraft Assembly Cleanrooms: Presence of Virulence Factors Associated with Human Pathogens
journal, September 2016

Bashir, Mina; Ahmed, Mahjabeen; Weinmaier, Thomas
Frontiers in Microbiology, Vol. 7
DOI: 10.3389/fmicb.2016.01321

Microgravity and immune responsiveness
journal, October 2002

Borchers, Andrea T.; Keen, Carl L.; Gershwin, M. Eric
Nutrition, Vol. 18, Issue 10
DOI: 10.1016/S0899-9007(02)00913-9

QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
Nature Methods, Vol. 7, Issue 5
DOI: 10.1038/nmeth.f.303

Human bloodstream infection caused by Staphylococcus pettenkoferi
journal, February 2009

Song, S. H.; Park, J. S.; Kwon, H. R.
Journal of Medical Microbiology, Vol. 58, Issue 2
DOI: 10.1099/jmm.0.004697-0

Virulence and drug resistance roles of multidrug efflux systems of Salmonella enterica serovar Typhimurium
journal, January 2006

Nishino, Kunihiko; Latifi, Tammy; Groisman, Eduardo A.
Molecular Microbiology, Vol. 59, Issue 1
DOI: 10.1111/j.1365-2958.2005.04940.x

Impaired growth under iron-limiting conditions associated with the acquisition of colistin resistance in Acinetobacter baumannii
journal, June 2016

López-Rojas, Rafael; García-Quintanilla, Meritxell; Labrador-Herrera, Gema
International Journal of Antimicrobial Agents, Vol. 47, Issue 6
DOI: 10.1016/j.ijantimicag.2016.03.010

Four-year bacterial monitoring in the International Space Station—Japanese Experiment Module “Kibo” with culture-independent approach
journal, April 2016

Ichijo, Tomoaki; Yamaguchi, Nobuyasu; Tanigaki, Fumiaki
npj Microgravity, Vol. 2, Issue 1
DOI: 10.1038/npjmgrav.2016.7

A multidrug efflux response to methyl viologen and acriflavine toxicity in the cyanobacterium Synechocystis sp. PCC6803
journal, February 2016

Ongley, Sarah E.; Pengelly, Jasper J. L.; Neilan, Brett A.
Journal of Applied Phycology, Vol. 28, Issue 5
DOI: 10.1007/s10811-016-0816-5

Hospital-associated microbiota and implications for nosocomial infections
journal, July 2015

Lax, Simon; Gilbert, Jack A.
Trends in Molecular Medicine, Vol. 21, Issue 7
DOI: 10.1016/j.molmed.2015.03.005

Corynebacterium pseudogenitalium Urinary Tract Infection
journal, February 2006

Vedel, Gérard; Toussaint, Gaëlle; Riegel, Philippe
Emerging Infectious Diseases, Vol. 12, Issue 2
DOI: 10.3201/eid1202.050950

Evidence of Pathogenic Microbes in the International Space Station Drinking Water: Reason for Concern?
journal, January 2004

La Duc, Myron T.; Sumner, Randall; Pierson, Duane
Habitation, Vol. 10, Issue 1
DOI: 10.3727/154296604774808883

Integrative analysis of environmental sequences using MEGAN4
journal, June 2011

Huson, D. H.; Mitra, S.; Ruscheweyh, H. -J.
Genome Research, Vol. 21, Issue 9
DOI: 10.1101/gr.120618.111

The microbiome of the built environment and mental health
journal, December 2015

Hoisington, Andrew J.; Brenner, Lisa A.; Kinney, Kerry A.
Microbiome, Vol. 3, Issue 1
DOI: 10.1186/s40168-015-0127-0

Mold species in dust from the International Space Station identified and quantified by mold-specific quantitative PCR
journal, July 2008

Vesper, Stephen J.; Wong, Wing; Kuo, C. Mike
Research in Microbiology, Vol. 159, Issue 6
DOI: 10.1016/j.resmic.2008.06.001

Aureobasidium pullulans infection in a patient with chronic lymphocytic leukemia
journal, September 2013

Oliveira, Leonardo Rodrigues de; Moraes-Souza, Helio; Maltos, Andre Luiz
Revista da Sociedade Brasileira de Medicina Tropical, Vol. 46, Issue 5
DOI: 10.1590/0037-8682-0117-2013

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
journal, October 2016

Jia, Baofeng; Raphenya, Amogelang R.; Alcock, Brian
Nucleic Acids Research, Vol. 45, Issue D1
DOI: 10.1093/nar/gkw1004

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014

Love, Michael I.; Huber, Wolfgang; Anders, Simon
Genome Biology, Vol. 15, Issue 12
DOI: 10.1186/s13059-014-0550-8

Works referencing / citing this record:

Fungal Biotechnology in Space: Why and How?
book, January 2020

Cortesão, Marta; Schütze, Tabea; Marx, Robert
Grand Challenges in Fungal Biotechnology, p. 501-535
DOI: 10.1007/978-3-030-29541-7_18

Chicken Gut Microbiome and Human Health: Past Scenarios, Current Perspectives, and Futuristic Applications
journal, February 2019

Sood, Utkarsh; Gupta, Vipin; Kumar, Roshan
Indian Journal of Microbiology, Vol. 60, Issue 1
DOI: 10.1007/s12088-019-00785-2

Space Station conditions are selective but do not alter microbial characteristics relevant to human health
journal, September 2019

Mora, Maximilian; Wink, Lisa; Kögler, Ines
Nature Communications, Vol. 10, Issue 1
DOI: 10.1038/s41467-019-11682-z

The influence of bioregenerative life-support system dietary structure and lifestyle on the gut microbiota: a 105-day ground-based space simulation in Lunar Palace 1: Influence of BLSS
journal, October 2018

Hao, Zikai; Li, Leyuan; Fu, Yuming
Environmental Microbiology, Vol. 20, Issue 10
DOI: 10.1111/1462-2920.14358

Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil
journal, January 2019

Blaustein, Ryan A.; McFarland, Alexander G.; Ben Maamar, Sarah
mSystems, Vol. 4, Issue 1
DOI: 10.1128/msystems.00281-18

Deciphering viral presences: two novel partial giant viruses detected in marine metagenome and in a mine drainage metagenome
journal, April 2018

Andreani, Julien; Verneau, Jonathan; Raoult, Didier
Virology Journal, Vol. 15, Issue 1
DOI: 10.1186/s12985-018-0976-9

Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces
journal, November 2018

Singh, Nitin Kumar; Wood, Jason M.; Karouia, Fathi
Microbiome, Vol. 6, Issue 1
DOI: 10.1186/s40168-018-0585-2

Metabolic phenotyping of the human microbiome
journal, January 2019

Barton, Wiley; O'Sullivan, Orla; Cotter, Paul D.
F1000Research, Vol. 8
DOI: 10.12688/f1000research.19481.1

Bioaerosols and Transmission, a Diverse and Growing Community of Practice
journal, February 2019

Mubareka, Samira; Groulx, Nicolas; Savory, Eric
Frontiers in Public Health, Vol. 7
DOI: 10.3389/fpubh.2019.00023

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Journal Article Avila-Herrera, Aram ; Thissen, James ; Urbaniak, Camilla ; ... - PLoS ONE

The International Space Station (ISS) is a complex built environment physically isolated from Earth. Assessing the interplay between the microbial community of the ISS and its crew is important for preventing biomedical and structural complications for long term human spaceflight missions. In this study, we describe one crewmember’s microbial profile from body swabs of mouth, nose, ear, skin and saliva that were collected at eight different time points pre-, during and post-flight. Additionally, environmental surface samples from eight different habitable locations in the ISS were collected from two flights. Environmental samples from one flight were collected by the crewmember andmore »« less
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https://doi.org/10.1371/journal.pone.0231838

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Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome

Journal Article Goltsman, Daniela S. Aliaga ; Sun, Christine L. ; Proctor, Diana M. ; ... - Genome Research

Recent studies suggest that the microbiome has an impact on gestational health and outcome. However, characterization of the pregnancy-associated microbiome has largely relied on 16S rRNA gene amplicon-based surveys. Here, we describe an assembly-driven, metagenomics-based, longitudinal study of the vaginal, gut, and oral microbiomes in 292 samples from 10 subjects sampled every three weeks throughout pregnancy. Nonhuman sequences in the amount of 1.53 Gb were assembled into scaffolds, and functional genes were predicted for gene- and pathway-based analyses. Vaginal assemblies were binned into 97 draft quality genomes. Redundancy analysis (RDA) of microbial community composition at all three body sites revealedmore »« less
Cited by 83
https://doi.org/10.1101/gr.236000.118

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Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

Journal Article Olm, Matthew R. ; Crits-Christoph, Alexander ; Diamond, Spencer ; ... - mSystems

Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. To avoid these biases, we compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios ofmore »« less
Cited by 69
https://doi.org/10.1128/mSystems.00731-19

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