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Meyer F, Robertson G, Deng ZL, Koslicki D, Gurevich A, McHardy AC. CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software. Nucleic Acids Res 2025:gkaf369. [PMID: 40331433 DOI: 10.1093/nar/gkaf369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2025] [Revised: 04/17/2025] [Accepted: 04/23/2025] [Indexed: 05/08/2025] Open
Abstract
Finding appropriate software and parameter settings to process shotgun metagenome data is essential for meaningful metagenomic analyses. To enable objective and comprehensive benchmarking of metagenomic software, the community-led initiative for the Critical Assessment of Metagenome Interpretation (CAMI) promotes standards and best practices. Since 2015, CAMI has provided comprehensive datasets, benchmarking guidelines, and challenges. However, benchmarking had to be conducted offline, requiring substantial time and technical expertise and leading to gaps in results between challenges. We introduce the CAMI Benchmarking Portal-a central repository of CAMI resources and web server for the evaluation and ranking of metagenome assembly, binning, and taxonomic profiling software. The portal simplifies evaluation, enabling users to easily compare their results with previous and other users' submissions through a variety of metrics and visualizations. As a demonstration, we benchmark software performance on the marine dataset of the CAMI II challenge. The portal currently hosts 28 675 results and is freely available at https://cami-challenge.org/.
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Affiliation(s)
- Fernando Meyer
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
- Initiative for the Critical Assessment of Metagenome Interpretation (CAMI )
| | - Gary Robertson
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
- Initiative for the Critical Assessment of Metagenome Interpretation (CAMI )
| | - Zhi-Luo Deng
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
- Initiative for the Critical Assessment of Metagenome Interpretation (CAMI )
| | - David Koslicki
- Initiative for the Critical Assessment of Metagenome Interpretation (CAMI )
- Computer Science and Engineering, Penn State University, University Park, PA 16802, United States
- Biology, Penn State University , University Park, PA 16802, United States
| | - Alexey Gurevich
- Initiative for the Critical Assessment of Metagenome Interpretation (CAMI )
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany
- Center for Bioinformatics Saar and Saarland University, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
- Initiative for the Critical Assessment of Metagenome Interpretation (CAMI )
- German Center for Infection Research (DZIF), partner site Hannover Braunschweig, 38124 Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
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Williams NR, Sisk MR, Lampton TP, Justiniano YAV, Harris SW, Higgins CM, Hooda ZA, Parello GZ, DeSilva AE, Cassilly CD, Bray MH, Liles MR. Solid rocket motor insulation adhesives with sporicidal activity promote planetary protection for deep space missions. LIFE SCIENCES IN SPACE RESEARCH 2025; 45:81-90. [PMID: 40280646 DOI: 10.1016/j.lssr.2025.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 02/10/2025] [Accepted: 02/11/2025] [Indexed: 04/29/2025]
Abstract
To prevent microbial contamination of extraterrestrial biospheres, NASA has established planetary protection requirements for spacecraft bioburden reduction. For missions to land on the icy moons of the outer planets, solid rocket motors (SRM) commonly used as de-orbit and braking stages are of particular concern for planetary protection since microbial contamination may occur during spacecraft manufacturing and assembly and debris from the SRM can spread over large portions of the planetary surface after impact. In concept spacecraft designs for deep space missions, certain SRM regions are not expected to reach temperatures sufficient for sterilization prior to landing on Europa's icy and potentially viable surface. This study evaluated the antimicrobial properties of candidate primers, adhesives, and insulations commonly used in SRM designs. We observed significant reductions in the number of viable spores of Bacillus atrophaeus (75.0%), Bacillus pumilus (88.9%) or Bacillus subtilis (87.6%) by application of the Chemlok® 205 + 6450 adhesive, compared to no-adhesive controls, when applied onto a polybenzimidazole (PBI) insulation substrate. More consistent reductions in viable spores were observed after adhesives were applied to PBI insulation compared to other insulation types tested. An aqueous extract of Chemlok® 205 primer was observed to have sporicidal activity, and LC-MS analysis indicated the presence of multiple water-soluble compounds predicted to have antibacterial activity. The reduction in recovery of viable spores observed in this study was due to sporicidal compounds present in adhesives, the spore-binding capacity of insulation types, and physical damage to spores due to cryogrinding. Compounds within rocket motor primers, adhesives, and insulations can contribute to planetary protection efforts, particularly in missions to land on the icy moons of the outer planets. The combination of insulation and adhesive may be optimized for the purpose of bioburden reduction, and ultimately planetary protection risk mitigation.
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Affiliation(s)
- Natalie R Williams
- Department of Biological Sciences, Auburn University, Auburn AL 36849, USA
| | - Morgan R Sisk
- Department of Biological Sciences, Auburn University, Auburn AL 36849, USA
| | | | | | - Samuel W Harris
- Department of Biological Sciences, Auburn University, Auburn AL 36849, USA
| | - Courtney M Higgins
- Department of Biological Sciences, Auburn University, Auburn AL 36849, USA
| | - Zahra A Hooda
- Department of Biological Sciences, Auburn University, Auburn AL 36849, USA
| | - Gianni Z Parello
- Department of Biological Sciences, Auburn University, Auburn AL 36849, USA
| | - Ashley E DeSilva
- Department of Biological Sciences, Auburn University, Auburn AL 36849, USA
| | | | | | - Mark R Liles
- Department of Biological Sciences, Auburn University, Auburn AL 36849, USA
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Brown SM, Mayer-Bacon C, Freeland S. Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It. Life (Basel) 2023; 13:2281. [PMID: 38137883 PMCID: PMC10744825 DOI: 10.3390/life13122281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.
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Simpson AC, Tighe S, Wong S, Leo P, Parker C, Chander AM, Williams M, Wu HW, Venkateswaran K, Singh NK. Analysis of Microbiomes from Ultra-Low Biomass Surfaces Using Novel Surface Sampling and Nanopore Sequencing. J Biomol Tech 2023; 34:3fc1f5fe.bac4a5b3. [PMID: 37969875 PMCID: PMC10644977 DOI: 10.7171/3fc1f5fe.bac4a5b3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The rapid assessment of microbiomes from ultra-low biomass environments such as cleanrooms or hospital operating rooms has a number of applications for human health and spacecraft manufacturing. Current techniques often employ lengthy protocols using short-read DNA sequencing technology to analyze amplified DNA and have the disadvantage of a longer analysis time and lack of portability. Here, we demonstrate a rapid (~24 hours) on-site nanopore-based sequencing approach to characterize the microbiome of a NASA Class 100K cleanroom where spacecraft components are assembled. This approach employs a modified protocol of Oxford Nanopore's Rapid PCR Barcoding Kit in combination with the recently developed Squeegee-Aspirator for Large Sampling Area (SALSA) surface sampling device. Results for these ultra-low biomass samples revealed DNA amplification ~1 to 2 orders of magnitude above process control samples and were dominated primarily by Paracoccus and Acinetobacter species. Negative control samples were collected to provide critical data on background contamination, including Cutibacerium acnes, which most likely originated from the sampling reagents-associated microbiome (kitome). Overall, these results provide data on a novel approach for rapid low-biomass DNA profiling using the SALSA sampler combined with modified nanopore sequencing. These data highlight the critical need for employing multiple negative controls, along with using DNA-free reagents and techniques, to enable a proper assessment of ultra-low biomass samples.
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Affiliation(s)
- Anna C. Simpson
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
| | - Scott Tighe
- Vermont Integrative GenomicsUniversity of VermontBurlingtonVermont
| | | | - Patrick Leo
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
| | - Ceth Parker
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
| | - Atul M. Chander
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
| | - Michael Williams
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
| | - Hao-Wei Wu
- AI Biosciences, Inc.College StationTexas
| | - Kasthuri Venkateswaran
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
| | - Nitin K. Singh
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
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Green SJ, Torok T, Allen JE, Eloe-Fadrosh E, Jackson SA, Jiang SC, Levine SS, Levy S, Schriml LM, Thomas WK, Wood JM, Tighe SW. Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report. ASTROBIOLOGY 2023; 23:897-907. [PMID: 37102710 PMCID: PMC10457625 DOI: 10.1089/ast.2022.0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 01/23/2023] [Indexed: 06/19/2023]
Abstract
Molecular biology methods and technologies have advanced substantially over the past decade. These new molecular methods should be incorporated among the standard tools of planetary protection (PP) and could be validated for incorporation by 2026. To address the feasibility of applying modern molecular techniques to such an application, NASA conducted a technology workshop with private industry partners, academics, and government agency stakeholders, along with NASA staff and contractors. The technical discussions and presentations of the Multi-Mission Metagenomics Technology Development Workshop focused on modernizing and supplementing the current PP assays. The goals of the workshop were to assess the state of metagenomics and other advanced molecular techniques in the context of providing a validated framework to supplement the bacterial endospore-based NASA Standard Assay and to identify knowledge and technology gaps. In particular, workshop participants were tasked with discussing metagenomics as a stand-alone technology to provide rapid and comprehensive analysis of total nucleic acids and viable microorganisms on spacecraft surfaces, thereby allowing for the development of tailored and cost-effective microbial reduction plans for each hardware item on a spacecraft. Workshop participants recommended metagenomics approaches as the only data source that can adequately feed into quantitative microbial risk assessment models for evaluating the risk of forward (exploring extraterrestrial planet) and back (Earth harmful biological) contamination. Participants were unanimous that a metagenomics workflow, in tandem with rapid targeted quantitative (digital) PCR, represents a revolutionary advance over existing methods for the assessment of microbial bioburden on spacecraft surfaces. The workshop highlighted low biomass sampling, reagent contamination, and inconsistent bioinformatics data analysis as key areas for technology development. Finally, it was concluded that implementing metagenomics as an additional workflow for addressing concerns of NASA's robotic mission will represent a dramatic improvement in technology advancement for PP and will benefit future missions where mission success is affected by backward and forward contamination.
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Affiliation(s)
- Stefan J. Green
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, Illinois, USA
| | - Tamas Torok
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Emiley Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Scott A. Jackson
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Sunny C. Jiang
- Department of Civil and Environmental Engineering, University of California, Irvine, California, USA
| | - Stuart S. Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Lynn M. Schriml
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - W. Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Jason M. Wood
- Research Informatics Core, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Scott W. Tighe
- Vermont Integrative Genomics, University of Vermont, Burlington, Vermont, USA
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Lu Y, Yang J, Zhang L, Chen F, Han P, Fu Y. Characteristics of bacterial community and ARG profiles in the surface and air environments in a spacecraft assembly cleanroom. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121613. [PMID: 37087089 DOI: 10.1016/j.envpol.2023.121613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/13/2023] [Accepted: 04/09/2023] [Indexed: 05/03/2023]
Abstract
Understanding the microbial communities and antibiotic resistance genes (ARGs) in spacecraft assembly cleanrooms is crucial for spacecraft microbial control and astronaut safety. However, there have been few reports of ARG profiles and their relationship with microbiomes in such environments. In the present study, we assessed the bacterial community and ARGs in the air dust and surface environments of a typical spacecraft assembly cleanroom. Our results show a significant difference in bacterial composition between surfaces and air dust, as they belong to two distinct ecostates. Bacillus and Acinetobacter were significantly enriched in the air samples. Bacterial community network analysis revealed lower topological parameters and robustness of bacterial networks in the air samples. We also observed different distribution patterns of some typical ARGs between surface and air dust samples. Notably, the ermB gene exhibited a relatively high copy number and was enriched in the surface environment, compared to that in the air. Overall, our study provides insight into the complex microbial community and the distribution and transfer of ARGs in spacecraft assembly cleanrooms, and offers important input for developing control strategies against ARGs.
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Affiliation(s)
- Yueying Lu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Jianlou Yang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Lantao Zhang
- Institute of Manned Space System and Engineering, China Academy of Space Technology, Beijing, 100094, China.
| | - Fangqi Chen
- Shen Yuan Honors College, Beihang University, Beijing, 100191, China.
| | - Pei Han
- Laboratory of Space Utilization, Technology and Engineering Center for Space Utilization, Chinese Academy of Sciences, Beijing, 100094, China.
| | - Yuming Fu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China.
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Mogul R, Miller DR, Ramos B, Lalla SJ. Metabolomic and cultivation insights into the tolerance of the spacecraft-associated Acinetobacter toward Kleenol 30, a cleanroom floor detergent. Front Microbiol 2023; 14:1090740. [PMID: 36950167 PMCID: PMC10025500 DOI: 10.3389/fmicb.2023.1090740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/20/2023] [Indexed: 03/08/2023] Open
Abstract
Introduction Stringent cleaning procedures during spacecraft assembly are critical to maintaining the integrity of life-detection missions. To ensure cleanliness, NASA spacecraft are assembled in cleanroom facilities, where floors are routinely cleansed with Kleenol 30 (K30), an alkaline detergent. Methods Through metabolomic and cultivation approaches, we show that cultures of spacecraft-associated Acinetobacter tolerate up to 1% v/v K30 and are fully inhibited at ≥2%; in comparison, NASA cleanrooms are cleansed with ~0.8-1.6% K30. Results For A. johnsonii 2P08AA (isolated from a cleanroom floor), cultivations with 0.1% v/v K30 yield (1) no changes in cell density at late-log phase, (2) modest decreases in growth rate (~17%), (3) negligible lag phase times, (4) limited changes in the intracellular metabolome, and (5) increases in extracellular sugar acids, monosaccharides, organic acids, and fatty acids. For A. radioresistens 50v1 (isolated from a spacecraft surface), cultivations yield (1) ~50% survivals, (2) no changes in growth rate, (3) ~70% decreases in the lag phase time, (4) differential changes in intracellular amino acids, compatible solutes, nucleotide-related metabolites, dicarboxylic acids, and saturated fatty acids, and (5) substantial yet differential impacts to extracellular sugar acids, monosaccharides, and organic acids. Discussion These combined results suggest that (1) K30 manifests strain-dependent impacts on the intracellular metabolomes, cultivation kinetics, and survivals, (2) K30 influences extracellular trace element acquisition in both strains, and (3) K30 is better tolerated by the floor-associated strain. Hence, this work lends support towards the hypothesis that repeated cleansing during spacecraft assembly serve as selective pressures that promote tolerances towards the cleaning conditions.
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Affiliation(s)
- Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
- Blue Marble Institute of Science, Seattle, WA, United States
| | - Daniel R. Miller
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
| | - Brian Ramos
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
| | - Sidharth J. Lalla
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
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Ryon KA, Tierney BT, Frolova A, Kahles A, Desnues C, Ouzounis C, Gibas C, Bezdan D, Deng Y, He D, Dias-Neto E, Elhaik E, Afshin E, Grills G, Iraola G, Suzuki H, Werner J, Udekwu K, Schriml L, Bhattacharyya M, Oliveira M, Zambrano MM, Hazrin-Chong NH, Osuolale O, Łabaj PP, Tiasse P, Rapuri S, Borras S, Pozdniakova S, Shi T, Sezerman U, Rodo X, Sezer ZH, Mason CE. A history of the MetaSUB consortium: Tracking urban microbes around the globe. iScience 2022; 25:104993. [PMID: 36299999 PMCID: PMC9589169 DOI: 10.1016/j.isci.2022.104993] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic. The consortium has optimized their workflow for the collection, isolation, and sequencing of DNA and RNA collected from these various sites and processing them for metagenomics analysis, including the identification of SARS-CoV-2 and its variants. Here, the Consortium describes its foundations, and its ongoing work to expand on this network and to focus its scope on the mapping, annotation, and prediction of emerging pathogens, mapping microbial evolution and antibiotic resistance, and the discovery of novel organisms and biosynthetic gene clusters.
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Affiliation(s)
- Krista A. Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA
- Weill Cornell Medicine, New York, NY, USA
| | - Braden T. Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA
- Weill Cornell Medicine, New York, NY, USA
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
- Kyiv Academic University, Kyiv, Ukraine
| | - Andre Kahles
- ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christelle Desnues
- Mediterranean Institute of Oceanography, 163 Avenue de Luminy Bâtiment Méditerranée, 13288, Marseille Cedex 9, France
| | | | | | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- GermanyNGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
- yuri GmbH, Meckenbeuren, Germany
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Ding He
- University of Copenhagen, Copenhagen, Denmark
| | | | | | - Evan Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Gregorio Iraola
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | | | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Klas Udekwu
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Lynn Schriml
- University of Maryland School of Medicine, University of Maryland, Baltimore, MD, USA
| | | | | | | | | | | | | | | | - Sampath Rapuri
- The Community Lab; Los Alamos Makers, Los Alamos, NM 87544, USA
| | - Silvia Borras
- Barcelona Institute for Global Health, Rosselló, 132, 708036 Barcelona, Spain
| | - Sofya Pozdniakova
- Barcelona Institute for Global Health, Rosselló, 132, 708036 Barcelona, Spain
| | - Tieliu Shi
- East China Normal University, Zhongshan Rd (N), 3663, 200050 Shanghai, Putuo, China
| | - Ugur Sezerman
- Department of Biostatistics, Acibadem University, Istanbul, Turkey
| | - Xavier Rodo
- Barcelona Institute for Global Health, Rosselló, 132, 708036 Barcelona, Spain
| | | | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
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Bhattacharya C, Tierney BT, Ryon KA, Bhattacharyya M, Hastings JJA, Basu S, Bhattacharya B, Bagchi D, Mukherjee S, Wang L, Henaff EM, Mason CE. Supervised Machine Learning Enables Geospatial Microbial Provenance. Genes (Basel) 2022; 13:1914. [PMID: 36292799 PMCID: PMC9601318 DOI: 10.3390/genes13101914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/04/2022] Open
Abstract
The recent increase in publicly available metagenomic datasets with geospatial metadata has made it possible to determine location-specific, microbial fingerprints from around the world. Such fingerprints can be useful for comparing microbial niches for environmental research, as well as for applications within forensic science and public health. To determine the regional specificity for environmental metagenomes, we examined 4305 shotgun-sequenced samples from the MetaSUB Consortium dataset-the most extensive public collection of urban microbiomes, spanning 60 different cities, 30 countries, and 6 continents. We were able to identify city-specific microbial fingerprints using supervised machine learning (SML) on the taxonomic classifications, and we also compared the performance of ten SML classifiers. We then further evaluated the five algorithms with the highest accuracy, with the city and continental accuracy ranging from 85-89% to 90-94%, respectively. Thereafter, we used these results to develop Cassandra, a random-forest-based classifier that identifies bioindicator species to aid in fingerprinting and can infer higher-order microbial interactions at each site. We further tested the Cassandra algorithm on the Tara Oceans dataset, the largest collection of marine-based microbial genomes, where it classified the oceanic sample locations with 83% accuracy. These results and code show the utility of SML methods and Cassandra to identify bioindicator species across both oceanic and urban environments, which can help guide ongoing efforts in biotracing, environmental monitoring, and microbial forensics (MF).
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Affiliation(s)
- Chandrima Bhattacharya
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- Integrated Design and Media, Center for Urban Science and Progress, NYU Tandon School of Engineering, Brooklyn, New York, NY 11201, USA
| | - Braden T. Tierney
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Krista A. Ryon
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Malay Bhattacharyya
- Center for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata 700108, India
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Jaden J. A. Hastings
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Srijani Basu
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Bodhisatwa Bhattacharya
- Department of Electrical and Electronics Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Debneel Bagchi
- Department of Metallurgy & Materials Engineering, Indian Institute of Engineering Science & Technology, Shibpur, Howrah 711103, India
| | - Somsubhro Mukherjee
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Lu Wang
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Elizabeth M. Henaff
- Integrated Design and Media, Center for Urban Science and Progress, NYU Tandon School of Engineering, Brooklyn, New York, NY 11201, USA
| | - Christopher E. Mason
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- Integrated Design and Media, Center for Urban Science and Progress, NYU Tandon School of Engineering, Brooklyn, New York, NY 11201, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
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10
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Microbial Burden Estimation of Food Items, Built Environments, and the International Space Station Using Film Media. Microorganisms 2022; 10:microorganisms10091714. [PMID: 36144316 PMCID: PMC9503880 DOI: 10.3390/microorganisms10091714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022] Open
Abstract
The use of film media involves considerably less preparation, waste, and incubator space than conventional agar-media-based assays and has proven in past studies to provide counts of cultivable microbes similar to those of traditional agar media. Film media also have the advantage of allowing sample volumes similar to those used in pour plates and, therefore, are well-suited for cultivable microbial counts in extremely low-biomass environments such as clean rooms or space habitats, particularly where the subsequent isolation of colonies is necessary. As the preparation of film media plates relies on water cohesion/adhesion rather than manual spreading, they may have future applications in low- or microgravity settings. In this study, cultivable microbial count performance was compared between agar media and film media in three kinds of samples: food items, surfaces in built environments on Earth (homes), and on the environmental surfaces of the International Space Station (ISS). Easy Plates (Kikkoman Corporation) and Petrifilm (3M) were compared with traditional agar plating for food and home surfaces, while only Easy Plates were compared with agar for ISS samples. For both food items and built environments on Earth, both types of film media performed comparably to agar media for bacterial counts, with R2 values of 0.94–0.96. Fungal counts for built-environment samples had a lower correlation between film and agar counts, with R2 values of 0.72–0.73. Samples from the ISS, which ranged from below detection to 103 CFU per 100 cm2, had R2 values of 0.80 for bacterial counts and 0.73 for fungal counts, partially due to multiple samples recording below the detection limit for agar or too numerous to count, and the growth of fungal species on R2A medium. The species compositions of isolates picked from agar vs. film media plates were similar; however, further phylogenetic analysis is needed to confirm the differential microbial diversity composition. Overall, film media such as Easy Plates and Petrifilm are viable alternatives to agar plates for low-biomass built environments as well as for food samples, and the two brands tested in this study performed equally well.
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11
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Contamination analysis of Arctic ice samples as planetary field analogs and implications for future life-detection missions to Europa and Enceladus. Sci Rep 2022; 12:12379. [PMID: 35896693 PMCID: PMC9329357 DOI: 10.1038/s41598-022-16370-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/08/2022] [Indexed: 11/09/2022] Open
Abstract
Missions to detect extraterrestrial life are being designed to visit Europa and Enceladus in the next decades. The contact between the mission payload and the habitable subsurface of these satellites involves significant risk of forward contamination. The standardization of protocols to decontaminate ice cores from planetary field analogs of icy moons, and monitor the contamination in downstream analysis, has a direct application for developing clean approaches crucial to life detection missions in these satellites. Here we developed a comprehensive protocol that can be used to monitor and minimize the contamination of Arctic ice cores in processing and downstream analysis. We physically removed the exterior layers of ice cores to minimize bioburden from sampling. To monitor contamination, we constructed artificial controls and applied culture-dependent and culture-independent techniques such as 16S rRNA amplicon sequencing. We identified 13 bacterial contaminants, including a radioresistant species. This protocol decreases the contamination risk, provides quantitative and qualitative information about contamination agents, and allows validation of the results obtained. This study highlights the importance of decreasing and evaluating prokaryotic contamination in the processing of polar ice cores, including in their use as analogs of Europa and Enceladus.
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12
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Ricciardi A, Cassey P, Leuko S, Woolnough AP. Planetary Biosecurity: Applying Invasion Science to Prevent Biological Contamination from Space Travel. Bioscience 2021. [DOI: 10.1093/biosci/biab115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
As plans for space exploration and commercial use expand rapidly, biosecurity measures and risk assessments that inform them must adapt. Sophisticated protocols are required to prevent biological contamination of extraterrestrial environments from Earth and vice versa. Such protocols should be informed by research on biological invasions—human-assisted spread of organisms into novel environments—which has revealed, inter alia, that (1) invasion risk is driven by the timing and frequency of introduction events, whose control requires addressing the least secure human activities associated with organismal transport; (2) invasions and their impacts are difficult to predict, because these phenomena are governed by context dependencies involving traits of the organism and the receiving environment; and (3) early detection and rapid response are crucial for prevention but undermined by taxonomic methods that fail to recognize what is “alien” versus what is native. Collaboration among astrobiologists, invasion biologists, and policymakers could greatly enhance planetary biosecurity protocols.
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Affiliation(s)
| | | | | | - Andrew P Woolnough
- University of Melbourne, Melbourne, and the University of Adelaide, Adelaide, both in Australia
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13
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Danko D, Malli Mohan GB, Sierra MA, Rucker M, Singh NK, Regberg AB, Bell MS, O’Hara NB, Ounit R, Mason CE, Venkateswaran K. Characterization of Spacesuit Associated Microbial Communities and Their Implications for NASA Missions. Front Microbiol 2021; 12:608478. [PMID: 34394013 PMCID: PMC8358432 DOI: 10.3389/fmicb.2021.608478] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 06/16/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Crewed National Aeronautics and Space Administration (NASA) missions to other solar system bodies are currently being planned. One high-profile scientific focus during such expeditions would be life detection, specifically the discovery of past or present microbial life, if they exist. However, both humans and associated objects typically carry a high microbial burden. Thus, it is essential to distinguish between microbes brought with the expedition and those present on the exploring planets. Modern spacesuits are unique, customized spacecraft which provide protection, mobility and life support to crew during spacewalks, yet they vent, and the mobility of microbes through spacesuits has not been studied. RESULTS To evaluate the microbial colonization of spacesuits, NASA used an Extravehicular Activity swab kit to examine viable microbial populations of 48 samples from spacesuits using both traditional microbiological methods and molecular sequencing methods. The cultivable microbial population ranged from below the detection limit to 9 × 102 colony forming units per 25 cm2 of sample and also significantly varied by the location. The cultivable microbial diversity was dominated by members of Bacillus, Arthrobacter, and Ascomycota. However, 16S rRNA-based viable bacterial burden ranged from 105 to 106 copies per 25 cm2 of sample. Shotgun metagenome sequencing revealed the presence of a diverse microbial population on the spacesuit surfaces, including Curtobacterium and Methylobacterium from across all sets of spacesuits in high abundance. Among bacterial species identified, higher abundance of Cutibacterium acnes, Methylobacterium oryzae, and M. phyllosphaerae reads were documented. CONCLUSION The results of this study provide evidence that identical microbial strains may live on the wrist joint, inner gauntlet, and outer gauntlet of spacesuits. This raises the possibility, but does not confirm that microbial contaminants on the outside of the suits could contaminate planetary science operations unless additional measures are taken. Overall, these data provide the first estimate of microbial distribution associated with spacesuit surfaces, which will help future mission planners develop effective planetary protection strategies.
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Affiliation(s)
- David Danko
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, Manhattan, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Ganesh Babu Malli Mohan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Maria A. Sierra
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, Manhattan, NY, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Michelle Rucker
- Exploration Mission Planning Office, Johnson Space Center, Houston, TX, United States
| | - Nitin K. Singh
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, Manhattan, NY, United States
| | - Aaron B. Regberg
- Astromaterials Research and Exploration Science Division, Johnson Space Center, Houston, TX, United States
| | - Mary S. Bell
- Jacobs@NASA/Johnson Space Center, Houston, TX, United States
| | - Niamh B. O’Hara
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Rachid Ounit
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA, United States
| | - Christopher E. Mason
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, United States
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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