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Antonelli F, Iafrate S, Tescari M, Giandomenico M, Kumbaric A, Bartolini M. The Hypogeous Roman Archeological Museum of Positano: Study of the Evolution of Biological Threaten and Development of Adequate Control Protocols. Microorganisms 2024; 12:1520. [PMID: 39203363 PMCID: PMC11356633 DOI: 10.3390/microorganisms12081520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/13/2024] [Accepted: 07/19/2024] [Indexed: 09/03/2024] Open
Abstract
Hypogea are natural or artificial spaces located underground often of great interest from an anthropological, archeological, religious, artistic, or historic point of view. Due to their features, these environments usually present conservative problems and biological colonization could be considered as one of the main threats. The present three-year study was carried out by specialists of the Central Institute for Restoration of Rome (ICR) in the hypogeous site preserved in the Roman Archeological Museum of Positano (Positano MAR) and focused on characterizing biological alterations present on the mural paintings; setting up efficient strategies and protocols for biodeterioration control; and monitoring the efficacy of direct and indirect interventions. Patinas with different morphologies were analyzed through microscopic observations, cultural analyses and next-generation sequencing. The results proved that the alterations comprised a great variety of microorganisms forming very distinct communities, differently distributed over space and time. The main taxa represented were bacteria of phyla Pseudomonadota and Actinomycetota, fungi belonging to the genus Fusarium and Gliocladium, and algae of the genus Chlorococcum. Preservation protocols were set up considering the alterations' composition and included the application of biocides, limiting daily temperature changes, decreasing illuminance values on painted surfaces, and the screening of natural light sources.
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Affiliation(s)
- Federica Antonelli
- Biology Laboratory, Central Institute for Restoration, Via di San Michele 25, 00153 Rome, Italy; (A.K.); (M.B.)
- Bio.Co.Ré. Lab, Via Reatina, 10, 67068 Scurcola Marsicana, Italy
| | - Sara Iafrate
- Mural Paintings Laboratory, Central Institute for Restoration, Via di San Michele 25, 00153 Rome, Italy; (S.I.); (M.G.)
| | - Marco Tescari
- Biology Laboratory, Central Institute for Restoration, Support Staff Ales S.p.A., Via di San Michele 25, 00153 Rome, Italy;
| | - Manuel Giandomenico
- Mural Paintings Laboratory, Central Institute for Restoration, Via di San Michele 25, 00153 Rome, Italy; (S.I.); (M.G.)
- Department of Science of Antiquities, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Alma Kumbaric
- Biology Laboratory, Central Institute for Restoration, Via di San Michele 25, 00153 Rome, Italy; (A.K.); (M.B.)
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Marco Bartolini
- Biology Laboratory, Central Institute for Restoration, Via di San Michele 25, 00153 Rome, Italy; (A.K.); (M.B.)
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Mettler MK, Goemann HM, Mueller RC, Vanegas OA, Lopez G, Singh N, Venkateswaran K, Peyton BM. Development of Martian saline seep models and their implications for planetary protection. Biofilm 2023; 5:100127. [PMID: 37252227 PMCID: PMC10209689 DOI: 10.1016/j.bioflm.2023.100127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/04/2023] [Accepted: 04/21/2023] [Indexed: 05/31/2023] Open
Abstract
While life on Mars has not been found, Earth-based microorganisms may contaminate the Red Planet during rover expeditions and human exploration. Due to the survival advantages conferred by the biofilm morphology to microorganisms, such as resistance to UV and osmotic stress, biofilms are particularly concerning from a planetary protection perspective. Modeling and data from the NASA Phoenix mission indicate that temporary liquid water might exist on Mars in the form of high salinity brines. These brines could provide colonization opportunities for terrestrial microorganisms brought by spacecraft or humans. To begin testing for potential establishment of microbes, results are presented from a simplified laboratory model of a Martian saline seep inoculated with sediment from Hailstone Basin, a terrestrial saline seep in Montana (USA). The seep was modeled as a sand-packed drip flow reactor at room temperature fed media with either 1 M MgSO4 or 1 M NaCl. Biofilms were established within the first sampling point of each experiment. Endpoint 16S rRNA gene community analysis showed significant selection of halophilic microorganisms by the media. Additionally, we detected 16S rRNA gene sequences highly similar to microorganisms previously detected in two spacecraft assembly cleanrooms. These experimental models provide an important foundation for identifying microbes that could hitch-hike on spacecraft and may be able to colonize Martian saline seeps. Future model optimization will be vital to informing cleanroom sterilization procedures.
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Affiliation(s)
- Madelyn K. Mettler
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Hannah M. Goemann
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Rebecca C. Mueller
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- USDA Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | | | | | - Nitin Singh
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | - Brent M. Peyton
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA
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3
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Xie J, Acosta EM, Gitai Z. Bacterial viability in the built environment of the home. PLoS One 2023; 18:e0288092. [PMID: 37939059 PMCID: PMC10631670 DOI: 10.1371/journal.pone.0288092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/15/2023] [Indexed: 11/10/2023] Open
Abstract
The built environment (BE) consists of human-made structures and, much like living organisms, is colonized by bacteria that make up the BE microbiome. The BE microbiome can potentially affect human health because of the constant proximity of these bacteria to humans. This has led to increasing public concern of whether the bacteria in the BE are harmful. Previous studies have used approaches based on DNA sequencing to assess the composition of the BE microbiome. However, the extent to which the bacterial DNA in the BE represents viable bacterial cells that could infect human hosts remains unknown. To address this open question we used both culture-based and culture-independent molecular methods to profile bacterial viability of the microbiomes from several BE sites. As part of an undergraduate-led project, we found that the vast majority of the bacterial DNA from the BE is not associated with viable bacteria, suggesting that most bacteria in the BE are dead. To begin to understand the determinants of bacterial viability in the BE we used mock bacterial communities to investigate the effects of temperature, relative humidity, and human interaction on bacterial viability. We found that relative humidity, temperature, and surface material did not have statistically significant effects on BE microbiome viability, but environmental exposure decreased bacterial viability. These results update our conception of the BE microbiome and begin to define the factors that affect BE microbiome viability.
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Affiliation(s)
- Joy Xie
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Ellen M. Acosta
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
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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: 1.0] [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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Sengupta P, Sivabalan SKM, Mahesh A, Palanikumar I, Kuppa Baskaran DK, Raman K. Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes. J Indian Inst Sci 2023; 103:1-17. [PMID: 37362854 PMCID: PMC10073628 DOI: 10.1007/s41745-023-00370-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/05/2023] [Indexed: 06/28/2023]
Abstract
Microorganisms are ubiquitous in nature and form complex community networks to survive in various environments. This community structure depends on numerous factors like nutrient availability, abiotic factors like temperature and pH as well as microbial composition. Categorising accessible biomes according to their habitats would help in understanding the complexity of the environment-specific communities. Owing to the recent improvements in sequencing facilities, researchers have started to explore diverse microbiomes rapidly and attempts have been made to study microbial crosstalk. However, different metagenomics sampling, preprocessing, and annotation methods make it difficult to compare multiple studies and hinder the recycling of data. Huge datasets originating from these experiments demand systematic computational methods to extract biological information beyond microbial compositions. Further exploration of microbial co-occurring patterns across the biomes could help us in designing cross-biome experiments. In this review, we catalogue databases with system-specific microbiomes, discussing publicly available common databases as well as specialised databases for a range of microbiomes. If the new datasets generated in the future could maintain at least biome-specific annotation, then researchers could use those contemporary tools for relevant and bias-free analysis of complex metagenomics data.
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Affiliation(s)
- Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | | | - Amrita Mahesh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | - Indumathi Palanikumar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | - Dinesh Kumar Kuppa Baskaran
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
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Krüger GI, Pardo-Esté C, Zepeda P, Olivares-Pacheco J, Galleguillos N, Suarez M, Castro-Severyn J, Alvarez-Thon L, Tello M, Valdes JH, Saavedra CP. Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line. Front Microbiol 2023; 14:1072793. [PMID: 37007466 PMCID: PMC10061128 DOI: 10.3389/fmicb.2023.1072793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
The presence of mobile genetic elements in Salmonella isolated from a chicken farm constitutes a potential risk for the appearance of emerging bacteria present in the food industry. These elements contribute to increased pathogenicity and antimicrobial resistance through genes that are related to the formation of biofilms and resistance genes contained in plasmids, integrons, and transposons. One hundred and thirty-three Salmonella isolates from different stages of the production line, such as feed manufacturing, hatchery, broiler farm, poultry farm, and slaughterhouse, were identified, serotyped and sequenced. The most predominant serotype was Salmonella Infantis. Phylogenetic analyses demonstrated that the diversity and spread of strains in the pipeline are serotype-independent, and that isolates belonging to the same serotype are very closely related genetically. On the other hand, Salmonella Infantis isolates carried the pESI IncFIB plasmid harboring a wide variety of resistance genes, all linked to mobile genetic elements, and among carriers of these plasmids, the antibiograms showed differences in resistance profiles and this linked to a variety in plasmid structure, similarly observed in the diversity of Salmonella Heidelberg isolates carrying the IncI1-Iα plasmid. Mobile genetic elements encoding resistance and virulence genes also contributed to the differences in gene content. Antibiotic resistance genotypes were matched closely by the resistance phenotypes, with high frequency of tetracycline, aminoglycosides, and cephalosporins resistance. In conclusion, the contamination in the poultry industry is described throughout the entire production line, with mobile genetic elements leading to multi-drug resistant bacteria, thus promoting survival when challenged with various antimicrobial compounds.
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Affiliation(s)
- Gabriel I. Krüger
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Phillippi Zepeda
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Jorge Olivares-Pacheco
- Grupo de Resistencia Antibacteriana en Bacterias Patógenas Ambientales GRABPA, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Nicolas Galleguillos
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Marcia Suarez
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
| | - Luis Alvarez-Thon
- Facultad de Ingeniería y Arquitectura, Universidad Central de Chile, Santiago, Chile
| | - Mario Tello
- Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Jorge H. Valdes
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- *Correspondence: Claudia P. Saavedra,
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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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Pausan MR, Blohs M, Mahnert A, Moissl-Eichinger C. The sanitary indoor environment-a potential source for intact human-associated anaerobes. NPJ Biofilms Microbiomes 2022; 8:44. [PMID: 35650275 PMCID: PMC9160270 DOI: 10.1038/s41522-022-00305-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 05/04/2022] [Indexed: 02/06/2023] Open
Abstract
A healthy human microbiome relies on the interaction with and exchange of microbes that takes place between the human body and its environment. People in high-income countries spend most of their time indoors and for this reason, the built environment (BE) might represent a potent source of commensal microbes. Anaerobic microbes are of particular interest, as researchers have not yet sufficiently clarified how the human microbiome acquires oxygen-sensitive microbes. We sampled the bathrooms in ten households and used propidium monoazide (PMA) to assess the viability of the collected prokaryotes. We compared the microbiome profiles based on 16S rRNA gene sequencing and confirmed our results by genetic and cultivation-based analyses. Quantitative and qualitative analysis revealed that most of the microbial taxa in the BE samples are human-associated. Less than 25% of the prokaryotic signatures originate from intact cells, indicating that aerobic and stress resistant taxa display an apparent survival advantage. However, we also confirmed the presence of intact, strictly anaerobic taxa on bathroom floors, including methanogenic archaea. As methanogens are regarded as highly sensitive to aerobic conditions, oxygen-tolerance experiments were performed with human-associated isolates to validate their survival. These results show that human-associated methanogens can survive oxic conditions for at least 6 h. We collected strong evidence that supports the hypothesis that obligate anaerobic taxa can survive in the BE for a limited amount of time. This suggests that the BE serves as a potential source of anaerobic human commensals.
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Affiliation(s)
- Manuela-Raluca Pausan
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Steigerwald Arzneimittelwerk GmbH, Bayer Consumer Health, Darmstadt, Germany
| | - Marcus Blohs
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.
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Fedor L, Nakládalová M, Štěpánek L, Holý O, Matoušková I. Effectiveness of anti-epidemic measures on ensuring indoor air quality of cleanrooms in a tertiary care hospital. Cent Eur J Public Health 2022; 30:74-78. [PMID: 35876594 DOI: 10.21101/cejph.a7060] [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: 08/17/2021] [Accepted: 04/12/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Maintaining cleanrooms in a hospital is a key part of preventing healthcare-associated infections (HAIs). The aim of this work was to verify the effectiveness of anti-epidemic measures to ensure air quality in cleanrooms in a tertiary care hospital. METHODS The study was based on the application of anti-epidemic measures and verification of their effectiveness by regular indoor air monitoring between the years 2014-2019. Monitoring was performed according to a recommended procedure based on European standards for cleanrooms. RESULTS The results demonstrate a reduction in the number of airborne particles and the number of colonies, as well as the elimination of fungi and conditioned pathogens in air samples. CONCLUSIONS The authors emphasize the importance of established anti-epidemic measures and regular monitoring for the prevention of HAIs.
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Affiliation(s)
- Lukáš Fedor
- Department of Occupational Medicine, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic.,Department of Hospital Hygiene, University Hospital Olomouc, Olomouc, Czech Republic
| | - Marie Nakládalová
- Department of Occupational Medicine, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Ladislav Štěpánek
- Department of Occupational Medicine, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Ondřej Holý
- Department of Public Health, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Ivanka Matoušková
- Department of Public Health, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
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10
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Are There Bad ICU Rooms? Temporal Relationship between Patient and ICU Room Microbiome, and Influence on Vancomycin-Resistant Enterococcus Colonization. mSphere 2022; 7:e0100721. [PMID: 35107335 PMCID: PMC8809377 DOI: 10.1128/msphere.01007-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The gut microbiome of an individual can shape the local environmental surface microbiome. We sought to determine how the intensive care unit (ICU) patient gut microbiome shapes the ICU room surface microbiome, focusing on vancomycin-resistant Enterococcus (VRE), a common ICU pathogen. This was an ICU-based prospective cohort study. Rectal swabs were performed in adult ICU patients immediately at the time of ICU admission and environmental surface swabs were performed at five predetermined time points. All swabs underwent 16S rRNA gene sequencing and culture for VRE. 304 ICU patients and 24 ICU rooms were sampled (5 longitudinal samples per ICU room). Spatially adjacent ICU rooms were no more microbially similar than nonadjacent rooms. Microbial signatures within rooms diverged rapidly over time: in 14 days, ICU rooms were as similar to other ICU rooms as they were to their prior selves. This divergence over time was more pronounced in rooms with higher patient turnover. Examining VRE status by culture, patient VRE gut colonization had modest agreement with room surface VRE (kappa statistic 0.36). There were no ICU rooms that consistently cultured positive for VRE, including those that housed VRE positive patients. Individual ICU patients had a limited impact on ICU room surface microbiome, and rooms diverged similarly over time regardless of patients. Patient VRE gut colonization may have a modest influence on room surface VRE but there were no “bad rooms” that consistently cultured positive for VRE. These results may be useful in planning infection control measures. IMPORTANCE This study found that intensive care unit (ICU) room microbial signatures diverged from their baseline quickly: within 2 weeks, individual ICU rooms had lost distinguishing characteristics and were as similar to other ICU rooms as they were to their former selves. Patient turnover within rooms accelerated this drift. Patient gut colonization with vancomycin-resistant Enterococcus (VRE) was associated with ICU room surface contamination with VRE; again, within 2 weeks, this association was substantially diminished. These results provide dynamic information regarding how patients control the microbiota on local hospital room surfaces and may facilitate decision making for infection prevention and control measures targeting VRE or other organisms.
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11
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Kawai M. [Environmental Monitoring in a Pharmaceutical Manufacturing Facility Using a Culture Independent Approach]. YAKUGAKU ZASSHI 2022; 142:33-37. [PMID: 34980749 DOI: 10.1248/yakushi.21-00161-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Strict microbial control is required in manufacturing facilities to ensure the quality of pharmaceuticals and foods. Environmental microbial monitoring plays a fundamental role in reducing the risk of microbial contamination. Appropriate microbial control requires an understanding of abundance and community structures of microbes in the target environment. However, most of these microbes are not culturable using conventional methods. In this study, we determined the number of microbial particles and assessed the environmental microbiome in a pharmaceutical manufacturing facility, using high-throughput sequencing of rRNA gene fragments. Our results provide fundamental data for the evaluation and control of microbes in the pharmaceutical and food industries.
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Affiliation(s)
- Mako Kawai
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University
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Hendrickson R, Urbaniak C, Minich JJ, Aronson HS, Martino C, Stepanauskas R, Knight R, Venkateswaran K. Clean room microbiome complexity impacts planetary protection bioburden. MICROBIOME 2021; 9:238. [PMID: 34861887 PMCID: PMC8643001 DOI: 10.1186/s40168-021-01159-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/13/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND The Spacecraft Assembly Facility (SAF) at the NASA's Jet Propulsion Laboratory is the primary cleanroom facility used in the construction of some of the planetary protection (PP)-sensitive missions developed by NASA, including the Mars 2020 Perseverance Rover that launched in July 2020. SAF floor samples (n=98) were collected, over a 6-month period in 2016 prior to the construction of the Mars rover subsystems, to better understand the temporal and spatial distribution of bacterial populations (total, viable, cultivable, and spore) in this unique cleanroom. RESULTS Cleanroom samples were examined for total (living and dead) and viable (living only) microbial populations using molecular approaches and cultured isolates employing the traditional NASA standard spore assay (NSA), which predominantly isolated spores. The 130 NSA isolates were represented by 16 bacterial genera, of which 97% were identified as spore-formers via Sanger sequencing. The most spatially abundant isolate was Bacillus subtilis, and the most temporally abundant spore-former was Virgibacillus panthothenticus. The 16S rRNA gene-targeted amplicon sequencing detected 51 additional genera not found in the NSA method. The amplicon sequencing of the samples treated with propidium monoazide (PMA), which would differentiate between viable and dead organisms, revealed a total of 54 genera: 46 viable non-spore forming genera and 8 viable spore forming genera in these samples. The microbial diversity generated by the amplicon sequencing corresponded to ~86% non-spore-formers and ~14% spore-formers. The most common spatially distributed genera were Sphinigobium, Geobacillus, and Bacillus whereas temporally distributed common genera were Acinetobacter, Geobacilllus, and Bacillus. Single-cell genomics detected 6 genera in the sample analyzed, with the most prominent being Acinetobacter. CONCLUSION This study clearly established that detecting spores via NSA does not provide a complete assessment for the cleanliness of spacecraft-associated environments since it failed to detect several PP-relevant genera that were only recovered via molecular methods. This highlights the importance of a methodological paradigm shift to appropriately monitor bioburden in cleanrooms for not only the aeronautical industry but also for pharmaceutical, medical industries, etc., and the need to employ molecular sequencing to complement traditional culture-based assays. Video abstract.
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Affiliation(s)
- Ryan Hendrickson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Camilla Urbaniak
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Jeremiah J Minich
- Marine Biology Research Division, Scripps Institute of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Heidi S Aronson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Cameron Martino
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | | | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA.
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Pardo-Esté C, Lorca D, Castro-Severyn J, Krüger G, Alvarez-Thon L, Zepeda P, Sulbaran-Bracho Y, Hidalgo A, Tello M, Molina F, Molina L, Remonsellez F, Castro-Nallar E, Saavedra C. Genetic Characterization of Salmonella Infantis with Multiple Drug Resistance Profiles Isolated from a Poultry-Farm in Chile. Microorganisms 2021; 9:2370. [PMID: 34835497 PMCID: PMC8621671 DOI: 10.3390/microorganisms9112370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 11/30/2022] Open
Abstract
Salmonella comprises over 2500 serotypes and foodborne contamination associated with this pathogen remains an important health concern worldwide. During the last decade, a shift in serotype prevalence has occurred as traditionally less prevalent serotypes are increasing in frequency of infections, especially those related to poultry meat contamination. S. Infantis is one of the major emerging serotypes, and these strains commonly display antimicrobial resistance and can persist despite cleaning protocols. Thus, this work aimed to isolate S. Infantis strains from a poultry meat farm in Santiago, Chile and to characterize genetic variations present in them. We determined their genomic and phenotypic profiles at different points along the production line. The results indicate that the strains encompass 853 polymorphic sites (core-SNPs) with isolates differing from one another by 0-347 core SNPs, suggesting variation among them; however, we found discrete correlations with the source of the sample in the production line. Furthermore, the pan-genome was composed of 4854 total gene clusters of which 2618 (53.9%) corresponds to the core-genome and only 181 (3.7%) are unique genes (those present in one particular strain). This preliminary analysis will enrich the surveillance of Salmonella, yet further studies are required to assess their evolution and phylogeny.
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Affiliation(s)
- Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (C.P.-E.); (D.L.); (G.K.); (P.Z.); (Y.S.-B.)
| | - Diego Lorca
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (C.P.-E.); (D.L.); (G.K.); (P.Z.); (Y.S.-B.)
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta 1240000, Chile; (J.C.-S.); (F.R.)
| | - Gabriel Krüger
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (C.P.-E.); (D.L.); (G.K.); (P.Z.); (Y.S.-B.)
| | - Luis Alvarez-Thon
- Facultad de Ingeniería y Arquitectura, Universidad Central de Chile, Santa Isabel 1186, Santiago 8330601, Chile;
| | - Phillippi Zepeda
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (C.P.-E.); (D.L.); (G.K.); (P.Z.); (Y.S.-B.)
| | - Yoelvis Sulbaran-Bracho
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (C.P.-E.); (D.L.); (G.K.); (P.Z.); (Y.S.-B.)
| | - Alejandro Hidalgo
- Escuela de Química y Farmacia, Facultad de Medicina, Universidad Andres Bello, Santiago 8370071, Chile;
| | - Mario Tello
- Laboratorio de Metagenomica Bacteriana, Centro de Biotecnología Acuicola, Universidad de Santiago, Alameda, Estación Central, Santiago 9170002, Chile;
| | - Franck Molina
- Sys2Diag, UMR9005 CNRS ALCEDIAG, 34184 Montpellier, France; (F.M.); (L.M.)
| | - Laurence Molina
- Sys2Diag, UMR9005 CNRS ALCEDIAG, 34184 Montpellier, France; (F.M.); (L.M.)
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta 1240000, Chile; (J.C.-S.); (F.R.)
- Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta 1240000, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile;
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Claudia Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (C.P.-E.); (D.L.); (G.K.); (P.Z.); (Y.S.-B.)
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Wang X, Howe S, Deng F, Zhao J. Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions. Microorganisms 2021; 9:1797. [PMID: 34576694 PMCID: PMC8467167 DOI: 10.3390/microorganisms9091797] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/16/2021] [Accepted: 08/21/2021] [Indexed: 11/17/2022] Open
Abstract
High throughput sequencing has emerged as one of the most important techniques for characterizing microbial dynamics and revealing bacteria and host interactions. However, data interpretation using this technique is mainly based on relative abundance and ignores total bacteria load. In certain cases, absolute abundance is more important than compositional relative data, and interpretation of microbiota data based solely on relative abundance can be misleading. The available approaches for absolute quantification are highly diverse and challenging, especially for quantification in differing biological situations, such as distinguishing between live and dead cells, quantification of specific taxa, enumeration of low biomass samples, large sample size feasibility, and the detection of various other cellular features. In this review, we first illustrate the importance of integrating absolute abundance into microbiome data interpretation. Second, we briefly discuss the most widely used cell-based and molecular-based bacterial load quantification methods, including fluorescence spectroscopy, flow cytometry, 16S qPCR, 16S qRT-PCR, ddPCR, and reference spike-in. Last, we present a specific decision-making scheme for absolute quantification methods based on different biological questions and some of the latest quantitative methods and procedure modifications.
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Affiliation(s)
- Xiaofan Wang
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Samantha Howe
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Feilong Deng
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
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Assembly of Bacterial Genome Sequences from Metagenomes of Spacecraft Assembly Cleanrooms. Microbiol Resour Announc 2021; 10:10/7/e01439-20. [PMID: 33602737 PMCID: PMC7892670 DOI: 10.1128/mra.01439-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Characterizing the microbiome of spacecraft assembly cleanrooms is important for planetary protection. We report two bacterial metagenome-assembled genome sequences (MAGs) reconstructed from metagenomes produced from cleanroom samples from the Kennedy Space Center’s Payload Hazardous Servicing Facility (KSC-PHSF) during the handling of the Phoenix spacecraft. Characterization of these MAGs will enable identification of the strategies underpinning their survival. Characterizing the microbiome of spacecraft assembly cleanrooms is important for planetary protection. We report two bacterial metagenome-assembled genomes (MAGs) reconstructed from metagenomes produced from cleanroom samples from the Kennedy Space Center’s Payload Hazardous Servicing Facility (KSC-PHSF) during the handling of the Phoenix spacecraft. Characterization of these MAGs will enable identification of the strategies underpinning their survival.
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Regberg AB, Castro CL, Connolly HC, Davis RE, Dworkin JP, Lauretta DS, Messenger SR, Mclain HL, McCubbin FM, Moore JL, Righter K, Stahl-Rommel S, Castro-Wallace SL. Prokaryotic and Fungal Characterization of the Facilities Used to Assemble, Test, and Launch the OSIRIS-REx Spacecraft. Front Microbiol 2020; 11:530661. [PMID: 33250861 PMCID: PMC7676328 DOI: 10.3389/fmicb.2020.530661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 09/30/2020] [Indexed: 01/04/2023] Open
Abstract
To characterize the ATLO (Assembly, Test, and Launch Operations) environment of the OSIRIS-REx spacecraft, we analyzed 17 aluminum witness foils and two blanks for bacterial, archaeal, fungal, and arthropod DNA. Under NASA’s Planetary Protection guidelines, OSIRIS-REx is a Category II outbound, Category V unrestricted sample return mission. As a result, it has no bioburden restrictions. However, the mission does have strict organic contamination requirements to achieve its primary objective of returning pristine carbonaceous asteroid regolith to Earth. Its target, near-Earth asteroid (101955) Bennu, is likely to contain organic compounds that are biologically available. Therefore, it is useful to understand what organisms were present during ATLO as part of the larger contamination knowledge effort—even though it is unlikely that any of the organisms will survive the multi-year deep space journey. Even though these samples of opportunity were not collected or preserved for DNA analysis, we successfully amplified bacterial and archaeal DNA (16S rRNA gene) from 16 of the 17 witness foils containing as few as 7 ± 3 cells per sample. Fungal DNA (ITS1) was detected in 12 of the 17 witness foils. Despite observing arthropods in some of the ATLO facilities, arthropod DNA (COI gene) was not detected. We observed 1,009 bacterial and archaeal sOTUs (sub-operational taxonomic units, 100% unique) and 167 fungal sOTUs across all of our samples (25–84 sOTUs per sample). The most abundant bacterial sOTU belonged to the genus Bacillus. This sOTU was present in blanks and may represent contamination during sample handling or storage. The sample collected from inside the fairing just prior to launch contained several unique bacterial and fungal sOTUs that describe previously uncharacterized potential for contamination during the final phase of ATLO. Additionally, fungal richness (number of sOTUs) negatively correlates with the number of carbon-bearing particles detected on samples. The total number of fungal sequences positively correlates with total amino acid concentration. These results demonstrate that it is possible to use samples of opportunity to characterize the microbiology of low-biomass environments while also revealing the limitations imposed by sample collection and preservation methods not specifically designed with biology in mind.
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Affiliation(s)
- Aaron B Regberg
- Astromaterials Research and Exploration Science Division, National Aeronautics and Space Administration (NASA) Johnson Space Center, Houston TX, United States
| | | | - Harold C Connolly
- Department of Geology, Rowan University, Glassboro, NJ, United States.,Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ, United States
| | - Richard E Davis
- Jacobs@NASA/Johnson Space Center, Houston, TX, United States
| | - Jason P Dworkin
- Astrochemistry Laboratory, Goddard Space Flight Center, Greenbelt, MD, United States
| | - Dante S Lauretta
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ, United States
| | - Scott R Messenger
- Astromaterials Research and Exploration Science Division, National Aeronautics and Space Administration (NASA) Johnson Space Center, Houston TX, United States
| | - Hannah L Mclain
- Astrochemistry Laboratory, Goddard Space Flight Center, Greenbelt, MD, United States
| | - Francis M McCubbin
- Astromaterials Research and Exploration Science Division, National Aeronautics and Space Administration (NASA) Johnson Space Center, Houston TX, United States
| | - Jamie L Moore
- Lockheed Martin Space Systems, Littleton, CO, United States
| | - Kevin Righter
- Astromaterials Research and Exploration Science Division, National Aeronautics and Space Administration (NASA) Johnson Space Center, Houston TX, United States
| | | | - Sarah L Castro-Wallace
- Biomedical Research and Environmental Sciences Division, Johnson Space Center, Houston, TX, United States
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17
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Mhatre S, Wood JM, Sielaff AC, Mora M, Duller S, Singh NK, Karouia F, Moissl-Eichinger C, Venkateswaran K. Assessing the Risk of Transfer of Microorganisms at the International Space Station Due to Cargo Delivery by Commercial Resupply Vehicles. Front Microbiol 2020; 11:566412. [PMID: 33240227 PMCID: PMC7677455 DOI: 10.3389/fmicb.2020.566412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/08/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND With increasing numbers of interplanetary missions, there is a need to establish robust protocols to ensure the protection of extraterrestrial planets being visited from contamination by terrestrial life forms. The current study is the first report comparing the commercial resupply vehicle (CRV) microbiome with the International Space Station (ISS) microbiome to understand the risks of contamination, thus serving as a model system for future planetary missions. RESULTS Samples obtained from the internal surfaces and ground support equipment of three CRV missions were subjected to various molecular techniques for microbial diversity analysis. In total, 25 samples were collected with eight defined locations from each CRV mission prior to launch. In general, the internal surfaces of vehicles were clean, with an order of magnitude fewer microbes compared to ground support equipment. The first CRV mission had a larger microbial population than subsequent CRV missions, which were clean as compared to the initial CRV locations sampled. Cultivation assays showed the presence of Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes and members of Ascomycota and Basidiomycota. As expected, shotgun metagenome analyses revealed the presence of more microbial taxa compared to cultivation-based assays. The internal locations of the CRV microbiome reportedly showed the presence of microorganisms capable of tolerating ultraviolet radiation (e.g., Bacillus firmus) and clustered separately from the ISS microbiome. CONCLUSIONS The metagenome sequence comparison of the CRV microbiome with the ISS microbiome revealed significant differences showing that CRV microbiomes were a negligible part of the ISS environmental microbiome. These findings suggest that the maintenance protocols in cleaning CRV surfaces are highly effective in controlling the contaminating microbial population during cargo transfer to the ISS via the CRV route.
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Affiliation(s)
- Snehit Mhatre
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Jason M. Wood
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Aleksandra Checinska Sielaff
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Maximilian Mora
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Stefanie Duller
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Nitin Kumar Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Fathi Karouia
- Space Bioscience Division, NASA Ames Research Center, Moffett Field, CA, United States
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Schwendner P, Jobson ME, Schuerger AC. Addition of anaerobic electron acceptors to solid media did not enhance growth of 125 spacecraft bacteria under simulated low-pressure Martian conditions. Sci Rep 2020; 10:18290. [PMID: 33106561 PMCID: PMC7588431 DOI: 10.1038/s41598-020-75222-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/06/2020] [Indexed: 11/25/2022] Open
Abstract
To protect Mars from microbial contamination, research on growth of microorganisms found in spacecraft assembly clean rooms under simulated Martian conditions is required. This study investigated the effects of low atmospheric pressure on the growth of chemoorganotrophic spacecraft bacteria and whether the addition of Mars relevant anaerobic electron acceptors might enhance growth. The 125 bacteria screened here were recovered from actual Mars spacecraft. Growth at 7 hPa, 0 °C, and a CO2-enriched anoxic atmosphere (called low-PTA conditions) was tested on five TSA-based media supplemented with anaerobic electron acceptors. None of the 125 spacecraft bacteria showed active growth under the tested low-PTA conditions and amended media. In contrast, a decrease in viability was observed in most cases. Growth curves of two hypopiezotolerant strains, Serratia liquefaciens and Trichococcus pasteurii, were performed to quantify the effects of the added anaerobic electron acceptors. Slight variations in growth rates were determined for both bacteria. However, the final cell densities were similar for all media tested, indicating no general preference for any specific anaerobic electron acceptor. By demonstrating that a broad diversity of chemoorganotrophic and culturable spacecraft bacteria do not grow under the tested conditions, we conclude that there may be low risk of growth of chemoorganotrophic bacteria typically recovered from Mars spacecraft during planetary protection bioburden screenings.
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Affiliation(s)
- Petra Schwendner
- Space Life Sciences Lab, University of Florida, 505 Odyssey Way, Exploration Park, Merritt Island, FL, 32953, USA.
| | - Mary-Elizabeth Jobson
- Space Life Sciences Lab, University of Florida, 505 Odyssey Way, Exploration Park, Merritt Island, FL, 32953, USA
| | - Andrew C Schuerger
- Space Life Sciences Lab, University of Florida, 505 Odyssey Way, Exploration Park, Merritt Island, FL, 32953, USA
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Ribič U, Jakše J, Toplak N, Koren S, Kovač M, Klančnik A, Jeršek B. Transporters and Efflux Pumps Are the Main Mechanisms Involved in Staphylococcus epidermidis Adaptation and Tolerance to Didecyldimethylammonium Chloride. Microorganisms 2020; 8:E344. [PMID: 32121333 PMCID: PMC7143832 DOI: 10.3390/microorganisms8030344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 01/28/2023] Open
Abstract
Staphylococcus epidermidis cleanroom strains are often exposed to sub-inhibitory concentrations of disinfectants, including didecyldimethylammonium chloride (DDAC). Consequently, they can adapt or even become tolerant to them. RNA-sequencing was used to investigate adaptation and tolerance mechanisms of S. epidermidis cleanroom strains (SE11, SE18), with S. epidermidis SE11Ad adapted and S. epidermidis SE18To tolerant to DDAC. Adaptation to DDAC was identified with up-regulation of genes mainly involved in transport (thioredoxin reductase [pstS], the arsenic efflux pump [gene ID, SE0334], sugar phosphate antiporter [uhpT]), while down-regulation was seen for the Agr system (agrA, arC, agrD, psm, SE1543), for enhanced biofilm formation. Tolerance to DDAC revealed the up-regulation of genes associated with transporters (L-cysteine transport [tcyB]; uracil permease [SE0875]; multidrug transporter [lmrP]; arsenic efflux pump [arsB]); the down-regulation of genes involved in amino-acid biosynthesis (lysine [dapE]; histidine [hisA]; methionine [metC]), and an enzyme involved in peptidoglycan, and therefore cell wall modifications (alanine racemase [SE1079]). We show for the first time the differentially expressed genes in DDAC-adapted and DDAC-tolerant S. epidermidis strains, which highlight the complexity of the responses through the involvement of different mechanisms.
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Affiliation(s)
- Urška Ribič
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (U.R.); (A.K.)
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia;
| | - Nataša Toplak
- Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia; (N.T.); (S.K.); (M.K.)
| | - Simon Koren
- Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia; (N.T.); (S.K.); (M.K.)
| | - Minka Kovač
- Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia; (N.T.); (S.K.); (M.K.)
| | - Anja Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (U.R.); (A.K.)
| | - Barbara Jeršek
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (U.R.); (A.K.)
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Ribič U, Polak T, Lušnic Polak M, Klančnik A, Jeršek B. Adaptation Response Mechanisms of Staphylococcus epidermidis Strains Exposed to Increasing Concentrations of Didecyldimethylammonium Chloride. Microb Drug Resist 2020; 26:583-593. [PMID: 31910354 DOI: 10.1089/mdr.2019.0064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Staphylococcus epidermidis is a commensal inhabitant of human skin and mucosa, and a common nosocomial pathogen in immunocompromised patients. S. epidermidis strains were isolated from places with precisely defined and controlled air quality and regular cleaning and disinfection regimes-cleanrooms. These strains were adapted to increasing concentrations of the quaternary ammonium disinfectant didecyldimethylammonium chloride (DDAC). Compared to nonadapted strains, these strains became adapted to up to 180-fold higher concentrations of DDAC, as seen by their increased minimal inhibitory concentrations. Examination of the stability of adaptation showed that three strains became permanently adapted to DDAC and named as resistant strains, and four strains were temporarily adapted to DDAC and named as strains with higher tolerance to DDAC. Some adapted strains showed cross-resistance to benzalkonium chloride and/or antibiotics. The adaptation response mechanisms of these DDAC-adapted strains were also investigated. The majority of adapted strains showed modifications to cell size and fatty acid composition. Some of the adapted strains showed changes in biofilm formation and overexpression of efflux pumps. Three adapted strains also showed altered growth rates. In this first report of adaptation of S. epidermidis strains to DDAC, the fatty acid profiling showed that the majority of strains had reduced ratio of saturated to unsaturated fatty acids and decreased content of straight-chain fatty acids, at the expense of the anteiso-branched fatty acids. We can conclude that S. epidermidis strains can adapt or become resistant to DDAC. We have revealed several adaptive response mechanisms that can be targeted for control and inhibition of S. epidermidis in cleanrooms and other clean processing environments.
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Affiliation(s)
- Urška Ribič
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaž Polak
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Mateja Lušnic Polak
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Anja Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Barbara Jeršek
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Kawai M, Ichijo T, Takahashi Y, Noguchi M, Katayama H, Cho O, Sugita T, Nasu M. Culture independent approach reveals domination of human-oriented microbes in a pharmaceutical manufacturing facility. Eur J Pharm Sci 2019; 137:104973. [PMID: 31254644 DOI: 10.1016/j.ejps.2019.104973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/13/2019] [Accepted: 06/24/2019] [Indexed: 01/13/2023]
Abstract
Strict microbial control is required in pharmaceutical manufacturing facilities, for which environmental microbial monitoring is fundamental. Appropriate microbial control is based on understanding the abundance and community structure of the microbes in the target environment, but most microbes are not culturable by conventional methods. Here, we determined the bacterial abundance and assessed the environmental microbiome in a pharmaceutical manufacturing facility using rRNA gene-targeted quantitative PCR (qPCR) and high-throughput sequencing of rRNA gene fragments. A commercially available microbial particle counter was also used for real-time measurements. In the air of the first gowning room and the passageway of the facility, the microbial particle number determined by both the particle counter and qPCR was ca. 104/m3; the number of microbial particles was about 100 times the number of culturable bacteria. Thus, the measurement of microbes using the particle counter was accurate. In the second gowning room of the facility, managed by a HEPA filter, the number of particles in the air was dependent on human movement, and was below the detection limit around 10 min after movement. Bacteria of the phyla Proteobacteria, Firmicutes, and Actinobacteria were frequently detected in samples from the facility; these bacteria are constituents of the human microbiota. Among fungi, Aspergillus and Cladosporium were detected in the air, and Malassezia was dominant on the walls. Our results provide fundamental data for the evaluation and control of microbes in pharmaceutical and food industry facilities.
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Affiliation(s)
- Mako Kawai
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji, Hyogo 670-8524, Japan.
| | - Tomoaki Ichijo
- Faculty of Health & Nutrition, Osaka Shoin Women's University, 4-2-26 Hishiya-nishi, Higashi-Osaka, Osaka 577-8550, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yuji Takahashi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Miyako Noguchi
- Bayer Yakuhin Ltd., 121-1 Toriino, Koka-cho, Koka, Shiga 520-3493, Japan
| | - Hirohito Katayama
- Bayer Yakuhin Ltd., 121-1 Toriino, Koka-cho, Koka, Shiga 520-3493, Japan
| | - Otomi Cho
- Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Takashi Sugita
- Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan.
| | - Masao Nasu
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka 584-8540, Japan.
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22
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Thombre RS, Shivakarthik E, Sivaraman B, Vaishampayan PA, Seuylemezian A, Meka JK, Vijayan S, Kulkarni PP, Pataskar T, Patil BS. Survival of Extremotolerant Bacteria from the Mukundpura Meteorite Impact Crater. ASTROBIOLOGY 2019; 19:785-796. [PMID: 31081685 DOI: 10.1089/ast.2018.1928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Carbonaceous meteorites provide clues with regard to prebiotic chemistry and the origin of life. Geological Survey of India recorded a carbonaceous chondrite meteorite fall in Mukundpura, India, on June 6, 2017. We conducted a study to investigate the microbial community that survived the meteorite impact. 16S rRNA metagenomic sequencing indicates the presence of Actinobacteria, Proteobacteria, and Acidobacteria in meteorite impact soil. Comparative phylogenetic analysis revealed an intriguing abundance of class Bacilli in the impact soil. Bacillus thermocopriae IR-1, a moderately thermotolerant organism, was isolated from a rock, impacted by the Mukundpura meteorite. We investigated the resilience of B. thermocopriae IR-1 to environmental stresses and impact shock in a Reddy shock tube. Bacillus thermocopriae IR-1 survived (28.82% survival) the effect of shock waves at a peak shock pressure of 300 kPa, temperature 400 K, and Mach number of 1.47. This investigation presents the first report on the effect of impact shock on B. thermocopriae IR-1. The study is also the first report on studying the microbial diversity and isolation of bacteria from impact crater soil immediately after meteorite impact event.
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Affiliation(s)
- Rebecca S Thombre
- 1 Department of Biotechnology, Modern College of Arts, Science and Commerce, Pune, India
| | - E Shivakarthik
- 2 Atomic, Molecular and Optical Physics Division, Physical Research Laboratory, Ahmedabad, India
| | - Bhalamurugan Sivaraman
- 2 Atomic, Molecular and Optical Physics Division, Physical Research Laboratory, Ahmedabad, India
| | - Parag A Vaishampayan
- 3 Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Arman Seuylemezian
- 3 Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - J K Meka
- 2 Atomic, Molecular and Optical Physics Division, Physical Research Laboratory, Ahmedabad, India
| | - S Vijayan
- 2 Atomic, Molecular and Optical Physics Division, Physical Research Laboratory, Ahmedabad, India
| | - P P Kulkarni
- 1 Department of Biotechnology, Modern College of Arts, Science and Commerce, Pune, India
| | - T Pataskar
- 1 Department of Biotechnology, Modern College of Arts, Science and Commerce, Pune, India
| | - B S Patil
- 1 Department of Biotechnology, Modern College of Arts, Science and Commerce, Pune, India
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23
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Ramírez GA, Jørgensen SL, Zhao R, D'Hondt S. Minimal Influence of Extracellular DNA on Molecular Surveys of Marine Sedimentary Communities. Front Microbiol 2018; 9:2969. [PMID: 30564217 PMCID: PMC6288230 DOI: 10.3389/fmicb.2018.02969] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/18/2018] [Indexed: 11/18/2022] Open
Abstract
Extracellular DNA has been reported to comprise a large fraction of total DNA in near-seafloor sediment. However, the potential effect of extracellular DNA, arising from dead or moribund cells, on sequencing surveys is a critical concern that has largely not been addressed for marine sedimentary habitats. To address this concern, we interrogated freshly collected Arctic and Pacific sediment for extracellular 16S rRNA genes using the photoactive DNA-binding dye Propidium Monoazide. Significant differences between relative abundances of total (intracellular + extracellular) Bacterial 16S rRNA genes and relative abundances of intracellular Bacterial 16S rRNA genes are only detected in three of twelve shallow [10 cm below seafloor (cmbsf)] samples. Relative abundances of total Bacterial 16S rRNA genes are statistically indistinguishable from relative abundances of intracellular Bacterial 16S rRNA genes in all interrogated samples from depths greater than 10 cmbsf. 16S rRNA gene sequencing shows that even where significantly higher abundances of extracellular genes are detected, they have little or no influence on prokaryote community composition. Taxon-level analyses suggest that extracellular DNA, arising from in situ death, may be sourced from different organisms in sediment of different ages. However, the overall effect of extracellular genes on sequencing surveys of marine sedimentary prokaryotes is minimal.
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Affiliation(s)
- Gustavo A Ramírez
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, United States
| | - Steffen L Jørgensen
- K.G. Jebsen Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Rui Zhao
- K.G. Jebsen Centre for Deep Sea Research, Department of Biology, University of Bergen, Bergen, Norway
| | - Steven D'Hondt
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, United States
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24
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Mogul R, Barding GA, Lalla S, Lee S, Madrid S, Baki R, Ahmed M, Brasali H, Cepeda I, Gornick T, Gunadi S, Hearn N, Jain C, Kim EJ, Nguyen T, Nguyen VB, Oei A, Perkins N, Rodriguez J, Rodriguez V, Savla G, Schmitz M, Tedjakesuma N, Walker J. Metabolism and Biodegradation of Spacecraft Cleaning Reagents by Strains of Spacecraft-Associated Acinetobacter. ASTROBIOLOGY 2018; 18:1517-1527. [PMID: 29672134 PMCID: PMC6276816 DOI: 10.1089/ast.2017.1814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/23/2018] [Indexed: 05/17/2023]
Abstract
Spacecraft assembly facilities are oligotrophic and low-humidity environments, which are routinely cleaned using alcohol wipes for benchtops and spacecraft materials, and alkaline detergents for floors. Despite these cleaning protocols, spacecraft assembly facilities possess a persistent, diverse, dynamic, and low abundant core microbiome, where the Acinetobacter are among the dominant members of the community. In this report, we show that several spacecraft-associated Acinetobacter metabolize or biodegrade the spacecraft cleaning reagents of ethanol (ethyl alcohol), 2-propanol (isopropyl alcohol), and Kleenol 30 (floor detergent) under ultraminimal conditions. Using cultivation and stable isotope labeling studies, we show that ethanol is a sole carbon source when cultivating in 0.2 × M9 minimal medium containing 26 μM Fe(NH4)2(SO4)2. Although cultures expectedly did not grow solely on 2-propanol, cultivations on mixtures of ethanol and 2-propanol exhibited enhanced plate counts at mole ratios of ≤0.50. In support, enzymology experiments on cellular extracts were consistent with oxidation of ethanol and 2-propanol by a membrane-bound alcohol dehydrogenase. In the presence of Kleenol 30, untargeted metabolite profiling on ultraminimal cultures of Acinetobacter radioresistens 50v1 indicated (1) biodegradation of Kleenol 30 into products including ethylene glycols, (2) the potential metabolism of decanoate (formed during incubation of Kleenol 30 in 0.2 × M9), and (3) decreases in the abundances of several hydroxy- and ketoacids in the extracellular metabolome. In ultraminimal medium (when using ethanol as a sole carbon source), A. radioresistens 50v1 also exhibits a remarkable survival against hydrogen peroxide (∼1.5-log loss, ∼108 colony forming units (cfu)/mL, 10 mM H2O2), indicating a considerable tolerance toward oxidative stress under nutrient-restricted conditions. Together, these results suggest that the spacecraft cleaning reagents may (1) serve as nutrient sources under oligotrophic conditions and (2) sustain extremotolerances against the oxidative stresses associated with low-humidity environments. In perspective, this study provides a plausible biochemical rationale to the observed microbial ecology dynamics of spacecraft-associated environments.
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Affiliation(s)
- Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Gregory A. Barding
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Sidharth Lalla
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Sooji Lee
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Steve Madrid
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Ryan Baki
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Mahjabeen Ahmed
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Hania Brasali
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Ivonne Cepeda
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Trevor Gornick
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Shawn Gunadi
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Nicole Hearn
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Chirag Jain
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Eun Jin Kim
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Thi Nguyen
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Vinh Bao Nguyen
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Alex Oei
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Nicole Perkins
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Joseph Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Veronica Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Gautam Savla
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Megan Schmitz
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Nicholas Tedjakesuma
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Jillian Walker
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
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25
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Tirumalai MR, Stepanov VG, Wünsche A, Montazari S, Gonzalez RO, Venkateswaran K, Fox GE. Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates. BMC Microbiol 2018; 18:57. [PMID: 29884123 PMCID: PMC5994023 DOI: 10.1186/s12866-018-1191-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022] Open
Abstract
Background Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis. Results The FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results. Conclusions It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. pumilus likely belong to the B. safensis group. Electronic supplementary material The online version of this article (10.1186/s12866-018-1191-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Madhan R Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Andrea Wünsche
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Saied Montazari
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Racquel O Gonzalez
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Kasturi Venkateswaran
- Biotechnology & Planetary Protection Group, NASA Jet Propulsion Laboratories, California Institute of Technology, Pasadena, CA, 91109, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA.
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26
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Gomez-Silvan C, Leung MHY, Grue KA, Kaur R, Tong X, Lee PKH, Andersen GL. A comparison of methods used to unveil the genetic and metabolic pool in the built environment. MICROBIOME 2018; 6:71. [PMID: 29661230 PMCID: PMC5902888 DOI: 10.1186/s40168-018-0453-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/28/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs. biological-based differences in both ribosomal transcript (rRNA) and gene (DNA) sequence community analysis. Based on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting. RESULTS We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at - 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community. CONCLUSIONS Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics.
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Affiliation(s)
- Cinta Gomez-Silvan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Katherine A. Grue
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Current affiliation: Department of Physical Therapy and Rehabilitation Science, University of California, San Francisco, CA USA
| | - Randeep Kaur
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Gary L. Andersen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. mSystems 2018; 3:mSystems00218-17. [PMID: 29577086 PMCID: PMC5864415 DOI: 10.1128/msystems.00218-17] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/06/2018] [Indexed: 01/15/2023] Open
Abstract
Various indoor, outdoor, and host-associated environments contain small quantities of microbial biomass and represent a niche that is often understudied because of technical constraints. Many studies that attempt to evaluate these low-biomass microbiome samples are riddled with erroneous results that are typically false positive signals obtained during the sampling process. We have investigated various low-biomass kits and methods to determine the limit of detection of these pipelines. Here we present KatharoSeq, a high-throughput protocol combining laboratory and bioinformatic methods that can differentiate a true positive signal in samples with as few as 50 to 500 cells. We demonstrate the application of this method in three unique low-biomass environments, including a SAF, a hospital NICU, and an abalone-rearing facility. Microbiome analyses of low-biomass samples are challenging because of contamination and inefficiencies, leading many investigators to employ low-throughput methods with minimal controls. We developed a new automated protocol, KatharoSeq (from the Greek katharos [clean]), that outperforms single-tube extractions while processing at least five times as fast. KatharoSeq incorporates positive and negative controls to reveal the whole bacterial community from inputs of as few as 50 cells and correctly identifies 90.6% (standard error, 0.013%) of the reads from 500 cells. To demonstrate the broad utility of KatharoSeq, we performed 16S rRNA amplicon and shotgun metagenome analyses of the Jet Propulsion Laboratory spacecraft assembly facility (SAF; n = 192, 96), 52 rooms of a neonatal intensive care unit (NICU; n = 388, 337), and an endangered-abalone-rearing facility (n = 192, 123), obtaining spatially resolved, unique microbiomes reproducible across hundreds of samples. The SAF, our primary focus, contains 32 sOTUs (sub-OTUs, defined as exact sequence matches) and their inferred variants identified by the deblur algorithm, with four (Acinetobacter lwoffii, Paracoccus marcusii, Mycobacterium sp., and Novosphingobium) being present in >75% of the samples. According to microbial spatial topography, the most abundant cleanroom contaminant, A. lwoffii, is related to human foot traffic exposure. In the NICU, we have been able to discriminate environmental exposure related to patient infectious disease, and in the abalone facility, we show that microbial communities reflect the marine environment rather than human input. Consequently, we demonstrate the feasibility and utility of large-scale, low-biomass metagenomic analyses using the KatharoSeq protocol. IMPORTANCE Various indoor, outdoor, and host-associated environments contain small quantities of microbial biomass and represent a niche that is often understudied because of technical constraints. Many studies that attempt to evaluate these low-biomass microbiome samples are riddled with erroneous results that are typically false positive signals obtained during the sampling process. We have investigated various low-biomass kits and methods to determine the limit of detection of these pipelines. Here we present KatharoSeq, a high-throughput protocol combining laboratory and bioinformatic methods that can differentiate a true positive signal in samples with as few as 50 to 500 cells. We demonstrate the application of this method in three unique low-biomass environments, including a SAF, a hospital NICU, and an abalone-rearing facility.
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28
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Marotz CA, Sanders JG, Zuniga C, Zaramela LS, Knight R, Zengler K. Improving saliva shotgun metagenomics by chemical host DNA depletion. MICROBIOME 2018; 6:42. [PMID: 29482639 PMCID: PMC5827986 DOI: 10.1186/s40168-018-0426-3] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/19/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Shotgun sequencing of microbial communities provides in-depth knowledge of the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon sequencing approaches that assess taxonomy but not function and are taxonomically limited. However, mammalian DNA can dominate host-derived samples, obscuring changes in microbial populations because few DNA sequence reads are from the microbial component. We developed and optimized a novel method for enriching microbial DNA from human oral samples and compared its efficiency and potential taxonomic bias with commercially available kits. RESULTS Three commercially available host depletion kits were directly compared with size filtration and a novel method involving osmotic lysis and treatment with propidium monoazide (lyPMA) in human saliva samples. We evaluated the percentage of shotgun metagenomic sequencing reads aligning to the human genome, and taxonomic biases of those not aligning, compared to untreated samples. lyPMA was the most efficient method of removing host-derived sequencing reads compared to untreated sample (8.53 ± 0.10% versus 89.29 ± 0.03%). Furthermore, lyPMA-treated samples exhibit the lowest taxonomic bias compared to untreated samples. CONCLUSION Osmotic lysis followed by PMA treatment is a cost-effective, rapid, and robust method for enriching microbial sequence data in shotgun metagenomics from fresh and frozen saliva samples and may be extensible to other host-derived sample types.
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Affiliation(s)
- Clarisse A Marotz
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Cristal Zuniga
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Livia S Zaramela
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
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29
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Dworkin JP, Adelman LA, Ajluni T, Andronikov AV, Aponte JC, Bartels AE, Beshore E, Bierhaus EB, Brucato JR, Bryan BH, Burton AS, Callahan MP, Castro-Wallace SL, Clark BC, Clemett SJ, Connolly HC, Cutlip WE, Daly SM, Elliott VE, Elsila JE, Enos HL, Everett DF, Franchi IA, Glavin DP, Graham HV, Hendershot JE, Harris JW, Hill SL, Hildebrand AR, Jayne GO, Jenkens RW, Johnson KS, Kirsch JS, Lauretta DS, Lewis AS, Loiacono JJ, Lorentson CC, Marshall JR, Martin MG, Matthias LL, McLain HL, Messenger SR, Mink RG, Moore JL, Nakamura-Messenger K, Nuth JA, Owens CV, Parish CL, Perkins BD, Pryzby MS, Reigle CA, Righter K, Rizk B, Russell JF, Sandford SA, Schepis JP, Songer J, Sovinski MF, Stahl SE, Thomas-Keprta K, Vellinga JM, Walker MS. OSIRIS-REx Contamination Control Strategy and Implementation. SPACE SCIENCE REVIEWS 2018; 214:19. [PMID: 30713357 PMCID: PMC6350808 DOI: 10.1007/s11214-017-0439-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 10/27/2017] [Indexed: 05/10/2023]
Abstract
OSIRIS-REx will return pristine samples of carbonaceous asteroid Bennu. This article describes how pristine was defined based on expectations of Bennu and on a realistic understanding of what is achievable with a constrained schedule and budget, and how that definition flowed to requirements and implementation. To return a pristine sample, the OSIRIS-REx spacecraft sampling hardware was maintained at level 100 A/2 and <180 ng/cm2 of amino acids and hydrazine on the sampler head through precision cleaning, control of materials, and vigilance. Contamination is further characterized via witness material exposed to the spacecraft assembly and testing environment as well as in space. This characterization provided knowledge of the expected background and will be used in conjunction with archived spacecraft components for comparison with the samples when they are delivered to Earth for analysis. Most of all, the cleanliness of the OSIRIS-REx spacecraft was achieved through communication among scientists, engineers, managers, and technicians.
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Affiliation(s)
- J P Dworkin
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - L A Adelman
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Arctic Slope Research Corporation, Beltsville, MD USA
| | - T Ajluni
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Arctic Slope Research Corporation, Beltsville, MD USA
| | | | - J C Aponte
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Catholic University of America, Washington, DC, USA
| | - A E Bartels
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - E Beshore
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ, USA
| | - E B Bierhaus
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - J R Brucato
- INAF Astrophysical Observatory of Arcetri, Florence, Italy
| | - B H Bryan
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - A S Burton
- NASA Johnson Space Center, Houston, TX, USA
| | | | | | - B C Clark
- Space Science Institute, Boulder, CO, USA
| | - S J Clemett
- NASA Johnson Space Center, Houston, TX, USA
- Jacobs Technology, Tullahoma, TN, USA
| | | | - W E Cutlip
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - S M Daly
- NASA Kennedy Space Center, Titusville, FL, USA
| | - V E Elliott
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - J E Elsila
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - H L Enos
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ, USA
| | - D F Everett
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | | | - D P Glavin
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - H V Graham
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- University of Maryland, College Park, MD, USA
| | - J E Hendershot
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Ball Aerospace, Boulder, CO, USA
| | - J W Harris
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - S L Hill
- Jacobs Technology, Tullahoma, TN, USA
- NASA Kennedy Space Center, Titusville, FL, USA
| | | | - G O Jayne
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Arctic Slope Research Corporation, Beltsville, MD USA
| | - R W Jenkens
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - K S Johnson
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - J S Kirsch
- Jacobs Technology, Tullahoma, TN, USA
- NASA Kennedy Space Center, Titusville, FL, USA
| | - D S Lauretta
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ, USA
| | - A S Lewis
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - J J Loiacono
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - C C Lorentson
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | | | - M G Martin
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Catholic University of America, Washington, DC, USA
| | - L L Matthias
- NASA Kennedy Space Center, Titusville, FL, USA
- Analex, Titusville, FL, USA
| | - H L McLain
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Catholic University of America, Washington, DC, USA
| | | | - R G Mink
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - J L Moore
- Lockheed Martin Space Systems, Littleton, CO, USA
| | | | - J A Nuth
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - C V Owens
- NASA Kennedy Space Center, Titusville, FL, USA
| | - C L Parish
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - B D Perkins
- NASA Kennedy Space Center, Titusville, FL, USA
| | - M S Pryzby
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- ATA Aerospace, Albuquerque, NM, USA
| | - C A Reigle
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - K Righter
- NASA Johnson Space Center, Houston, TX, USA
| | - B Rizk
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ, USA
| | - J F Russell
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - S A Sandford
- NASA Ames Research Center, Moffett Field, CA, USA
| | - J P Schepis
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - J Songer
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - M F Sovinski
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - S E Stahl
- NASA Johnson Space Center, Houston, TX, USA
- JES Tech., Houston, TX, USA
| | - K Thomas-Keprta
- NASA Johnson Space Center, Houston, TX, USA
- Jacobs Technology, Tullahoma, TN, USA
| | - J M Vellinga
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - M S Walker
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
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Pervasiveness of UVC254-resistant Geobacillus strains in extreme environments. Appl Microbiol Biotechnol 2018; 102:1869-1887. [DOI: 10.1007/s00253-017-8712-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/09/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022]
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Koskinen K, Rettberg P, Pukall R, Auerbach A, Wink L, Barczyk S, Perras A, Mahnert A, Margheritis D, Kminek G, Moissl-Eichinger C. Microbial biodiversity assessment of the European Space Agency's ExoMars 2016 mission. MICROBIOME 2017; 5:143. [PMID: 29070062 PMCID: PMC5657055 DOI: 10.1186/s40168-017-0358-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/27/2017] [Indexed: 06/01/2023]
Abstract
BACKGROUND The ExoMars 2016 mission, consisting of the Trace Gas Orbiter and the Schiaparelli lander, was launched on March 14 2016 from Baikonur, Kazakhstan and reached its destination in October 2016. The Schiaparelli lander was subject to strict requirements for microbial cleanliness according to the obligatory planetary protection policy. To reach the required cleanliness, the ExoMars 2016 flight hardware was assembled in a newly built, biocontrolled cleanroom complex at Thales Alenia Space in Turin, Italy. In this study, we performed microbiological surveys of the cleanroom facilities and the spacecraft hardware before and during the assembly, integration and testing (AIT) activities. METHODS Besides the European Space Agency (ESA) standard bioburden assay, that served as a proxy for the microbiological contamination in general, we performed various alternative cultivation assays and utilised molecular techniques, including quantitative PCR and next generation sequencing, to assess the absolute and relative abundance and broadest diversity of microorganisms and their signatures in the cleanroom and on the spacecraft hardware. RESULTS Our results show that the bioburden, detected microbial contamination and microbial diversity decreased continuously after the cleanroom was decontaminated with more effective cleaning agents and during the ongoing AIT. The studied cleanrooms and change room were occupied by very distinct microbial communities: Overall, the change room harboured a higher number and diversity of microorganisms, including Propionibacterium, which was found to be significantly increased in the change room. In particular, the so called alternative cultivation assays proved important in detecting a broader cultivable diversity than covered by the standard bioburden assay and thus completed the picture on the cleanroom microbiota. CONCLUSION During the whole project, the bioburden stayed at acceptable level and did not raise any concern for the ExoMars 2016 mission. The cleanroom complex at Thales Alenia Space in Turin is an excellent example of how efficient microbiological control is performed.
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Affiliation(s)
- Kaisa Koskinen
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Petra Rettberg
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Rüdiger Pukall
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anna Auerbach
- Department for Microbiology, University of Regensburg, Regensburg, Germany
| | - Lisa Wink
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
| | - Simon Barczyk
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Alexandra Perras
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
- Department for Microbiology, University of Regensburg, Regensburg, Germany
| | - Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | | | - Christine Moissl-Eichinger
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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Impact of the Mk VI SkinSuit on skin microbiota of terrestrial volunteers and an International Space Station-bound astronaut. NPJ Microgravity 2017; 3:23. [PMID: 28894789 PMCID: PMC5589758 DOI: 10.1038/s41526-017-0029-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 08/15/2017] [Accepted: 08/15/2017] [Indexed: 12/11/2022] Open
Abstract
Microgravity induces physiological deconditioning due to the absence of gravity loading, resulting in bone mineral density loss, atrophy of lower limb skeletal and postural muscles, and lengthening of the spine. SkinSuit is a lightweight compression suit designed to provide head-to-foot (axial) loading to counteract spinal elongation during spaceflight. As synthetic garments may impact negatively on the skin microbiome, we used 16S ribosomal RNA (rRNA) gene amplicon procedures to define bacterial skin communities at sebaceous and moist body sites of five healthy male volunteers undergoing SkinSuit evaluation. Each volunteer displayed a diverse, distinct bacterial population at each skin site. Short (8 h) periods of dry hyper-buoyancy flotation wearing either gym kit or SkinSuit elicited changes in the composition of the skin microbiota at the genus level but had little or no impact on community structure at the phylum level or the richness and diversity of the bacterial population. We also determined the composition of the skin microbiota of an astronaut during pre-flight training, during an 8-day visit to the International Space Station involving two 6–7 h periods of SkinSuit wear, and for 1 month after return. Changes in composition of bacterial skin communities at five body sites were strongly linked to changes in geographical location. A distinct ISS bacterial microbiota signature was found which reversed to a pre-flight profile on return. No changes in microbiome complexity or diversity were noted, with little evidence for colonisation by potentially pathogenic bacteria; we conclude that short periods of SkinSuit wear induce changes to the composition of the skin microbiota but these are unlikely to compromise the healthy skin microbiome. A compression garment that applies gravity-like pressure to the skin alters the composition of skin microbes, but not in a dangerous manner. A team led by Peter Taylor from University College London, UK, characterised the bacterial skin communities at dry and moist body sites of five Earth-bound volunteers before and after wearing the Mk VI SkinSuit, which creates a pressure loading system that simulates gravity’s effects. 8 h in the SkinSuit changed the skin microbiota at the genus level but had little to no impact in community structure. The researchers observed more dramatic changes in one astronaut who wore the garment on the International Space Station. However, the microbial makeup reverted back to pre-flight profiles upon the astronaut’s return to Earth. The findings suggest that short-term SkinSuit wear is unlikely to compromise bacterial skin health.
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Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Paulino-Lima IG, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, Balk M, Huttenhower C, Nocker A, Vaishampayan P, Rothschild LJ. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. MICROBIOME 2017; 5:86. [PMID: 28810907 PMCID: PMC5558654 DOI: 10.1186/s40168-017-0285-3] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/05/2017] [Indexed: 05/16/2023]
Abstract
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.
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Affiliation(s)
- Joanne B. Emerson
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 USA
- Current Address: Department of Plant Pathology, University of California, Davis, CA USA
| | - Rachel I. Adams
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Clarisse M. Betancourt Román
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Brandon Brooks
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA 94720 USA
| | - David A. Coil
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Katherine Dahlhausen
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Holly H. Ganz
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Erica M. Hartmann
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Tiffany Hsu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Nicholas B. Justice
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
| | - Ivan G. Paulino-Lima
- Universities Space Research Association, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 377, Moffett Field, CA 94035-1000 USA
| | - Julia C. Luongo
- Department of Mechanical Engineering, University of Colorado at Boulder, 1111 Engineering Drive, 427 UCB, Boulder, CO 80309 USA
| | - Despoina S. Lymperopoulou
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Cinta Gomez-Silvan
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94702 USA
| | | | - Melike Balk
- Department of Earth Sciences – Petrology, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Andreas Nocker
- IWW Water Centre, Moritzstrasse 26, 45476 Mülheim an der Ruhr, Germany
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Lynn J. Rothschild
- Planetary Sciences and Astrobiology, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 361, Moffett Field, CA 94035-1000 USA
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Karouia F, Peyvan K, Pohorille A. Toward biotechnology in space: High-throughput instruments for in situ biological research beyond Earth. Biotechnol Adv 2017; 35:905-932. [PMID: 28433608 DOI: 10.1016/j.biotechadv.2017.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/27/2017] [Accepted: 04/12/2017] [Indexed: 12/18/2022]
Abstract
Space biotechnology is a nascent field aimed at applying tools of modern biology to advance our goals in space exploration. These advances rely on our ability to exploit in situ high throughput techniques for amplification and sequencing DNA, and measuring levels of RNA transcripts, proteins and metabolites in a cell. These techniques, collectively known as "omics" techniques have already revolutionized terrestrial biology. A number of on-going efforts are aimed at developing instruments to carry out "omics" research in space, in particular on board the International Space Station and small satellites. For space applications these instruments require substantial and creative reengineering that includes automation, miniaturization and ensuring that the device is resistant to conditions in space and works independently of the direction of the gravity vector. Different paths taken to meet these requirements for different "omics" instruments are the subjects of this review. The advantages and disadvantages of these instruments and technological solutions and their level of readiness for deployment in space are discussed. Considering that effects of space environments on terrestrial organisms appear to be global, it is argued that high throughput instruments are essential to advance (1) biomedical and physiological studies to control and reduce space-related stressors on living systems, (2) application of biology to life support and in situ resource utilization, (3) planetary protection, and (4) basic research about the limits on life in space. It is also argued that carrying out measurements in situ provides considerable advantages over the traditional space biology paradigm that relies on post-flight data analysis.
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Affiliation(s)
- Fathi Karouia
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA; NASA Ames Research Center, Flight Systems Implementation Branch, Moffett Field, CA 94035, USA.
| | | | - Andrew Pohorille
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA.
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Ribič U, Klančnik A, Jeršek B. Characterization of Staphylococcus epidermidis strains isolated from industrial cleanrooms under regular routine disinfection. J Appl Microbiol 2017; 122:1186-1196. [PMID: 28231617 DOI: 10.1111/jam.13424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/30/2017] [Accepted: 02/16/2017] [Indexed: 11/29/2022]
Abstract
AIMS The purpose of this study was the genotypic and phenotypic characterization of 57 strains of Staphylococcus epidermidis isolated from cleanroom environments, based on their biofilm formation and antimicrobial resistance profiles. METHODS AND RESULTS Biofilm formation was investigated using real-time PCR (icaA, aap, bhp genes), the Congo red agar method and the crystal violet assay. The majority of the strains (59·7%; 34/57) did not form biofilms according to the crystal violet assay, although the biofilm-associated genes were present in 94·7% (54/57) of the strains. Of the biofilm formers (40·4%; 23/57), 39·1% (9/23) have been identified as strong biofilm formers (>4× crystal violet absorbance cut-off). Resistance to a commercial disinfectant and its quaternary ammonium active component, didecyl-dimethyl-ammonium chloride (DDAC), was determined according to minimum inhibitory concentrations (MICs) and the presence of the qac (quaternary ammonium compound) genes. More than 95% (55/57) of the Staph. epidermidis strains had the qacA/B and qacC genes, but not the other qac genes. The MICs for the disinfectant and DDAC varied among the Staph. epidermidis strains, although none were resistant. CONCLUSIONS Although 59·6% of the Staph. epidermidis strains did not form biofilms and none were resistant to DDAC, more than 94% had the genetic basis for development of resistance to quaternary ammonium compounds, and among them at least 14·0% (8/57) might represent a high risk to cleanroom hygiene as strong biofim formers with qacA/B and qacC genes. SIGNIFICANCE AND IMPACT OF THE STUDY To assure controlled cleanroom environments, bacterial strains isolated from cleanroom environments need to be characterized regularly using several investigative methods.
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Affiliation(s)
- U Ribič
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - A Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - B Jeršek
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Mora M, Mahnert A, Koskinen K, Pausan MR, Oberauner-Wappis L, Krause R, Perras AK, Gorkiewicz G, Berg G, Moissl-Eichinger C. Microorganisms in Confined Habitats: Microbial Monitoring and Control of Intensive Care Units, Operating Rooms, Cleanrooms and the International Space Station. Front Microbiol 2016; 7:1573. [PMID: 27790191 PMCID: PMC5061736 DOI: 10.3389/fmicb.2016.01573] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/20/2016] [Indexed: 01/15/2023] Open
Abstract
Indoor environments, where people spend most of their time, are characterized by a specific microbial community, the indoor microbiome. Most indoor environments are connected to the natural environment by high ventilation, but some habitats are more confined: intensive care units, operating rooms, cleanrooms and the international space station (ISS) are extraordinary living and working areas for humans, with a limited exchange with the environment. The purposes for confinement are different: a patient has to be protected from infections (intensive care unit, operating room), product quality has to be assured (cleanrooms), or confinement is necessary due to extreme, health-threatening outer conditions, as on the ISS. The ISS represents the most secluded man-made habitat, constantly inhabited by humans since November 2000 – and, inevitably, also by microorganisms. All of these man-made confined habitats need to be microbiologically monitored and controlled, by e.g., microbial cleaning and disinfection. However, these measures apply constant selective pressures, which support microbes with resistance capacities against antibiotics or chemical and physical stresses and thus facilitate the rise of survival specialists and multi-resistant strains. In this article, we summarize the available data on the microbiome of aforementioned confined habitats. By comparing the different operating, maintenance and monitoring procedures as well as microbial communities therein, we emphasize the importance to properly understand the effects of confinement on the microbial diversity, the possible risks represented by some of these microorganisms and by the evolution of (antibiotic) resistances in such environments – and the need to reassess the current hygiene standards.
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Affiliation(s)
- Maximilian Mora
- Department for Internal Medicine, Medical University of Graz, Graz Austria
| | - Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, Graz Austria
| | - Kaisa Koskinen
- Department for Internal Medicine, Medical University of Graz, GrazAustria; BioTechMed-Graz, GrazAustria
| | - Manuela R Pausan
- Department for Internal Medicine, Medical University of Graz, Graz Austria
| | | | - Robert Krause
- Department for Internal Medicine, Medical University of Graz, Graz Austria
| | - Alexandra K Perras
- Department for Internal Medicine, Medical University of Graz, GrazAustria; Department for Microbiology, University of Regensburg, RegensburgGermany
| | - Gregor Gorkiewicz
- BioTechMed-Graz, GrazAustria; Department of Pathology, Medical University of Graz, GrazAustria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz Austria
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Bashir M, Ahmed M, Weinmaier T, Ciobanu D, Ivanova N, Pieber TR, Vaishampayan PA. Functional Metagenomics of Spacecraft Assembly Cleanrooms: Presence of Virulence Factors Associated with Human Pathogens. Front Microbiol 2016; 7:1321. [PMID: 27667984 PMCID: PMC5017214 DOI: 10.3389/fmicb.2016.01321] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 08/10/2016] [Indexed: 01/09/2023] Open
Abstract
Strict planetary protection practices are implemented during spacecraft assembly to prevent inadvertent transfer of earth microorganisms to other planetary bodies. Therefore, spacecraft are assembled in cleanrooms, which undergo strict cleaning and decontamination procedures to reduce total microbial bioburden. We wanted to evaluate if these practices selectively favor survival and growth of hardy microorganisms, such as pathogens. Three geographically distinct cleanrooms were sampled during the assembly of three NASA spacecraft: The Lockheed Martin Aeronautics' Multiple Testing Facility during DAWN, the Kennedy Space Center's Payload Hazardous Servicing Facility (KSC-PHSF) during Phoenix, and the Jet Propulsion Laboratory's Spacecraft Assembly Facility during Mars Science Laboratory. Sample sets were collected from the KSC-PHSF cleanroom at three time points: before arrival of the Phoenix spacecraft, during the assembly and testing of the Phoenix spacecraft, and after removal of the spacecraft from the KSC-PHSF facility. All samples were subjected to metagenomic shotgun sequencing on an Illumina HiSeq 2500 platform. Strict decontamination procedures had a greater impact on microbial communities than sampling location Samples collected during spacecraft assembly were dominated by Acinetobacter spp. We found pathogens and potential virulence factors, which determine pathogenicity in all the samples tested during this study. Though the relative abundance of pathogens was lowest during the Phoenix assembly, potential virulence factors were higher during assembly compared to before and after assembly, indicating a survival advantage. Decreased phylogenetic and pathogenic diversity indicates that decontamination and preventative measures were effective against the majority of microorganisms and well implemented, however, pathogen abundance still increased over time. Four potential pathogens, Acinetobacter baumannii, Acinetobacter lwoffii, Escherichia coli and Legionella pneumophila, and their corresponding virulence factors were present in all cleanroom samples. This is the first functional metagenomics study describing presence of pathogens and their corresponding virulence factors in cleanroom environments. The results of this study should be considered for microbial monitoring of enclosed environments such as schools, homes, hospitals and more isolated habitation such the International Space Station and future manned missions to Mars.
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Affiliation(s)
- Mina Bashir
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of TechnologyPasadena, CA, USA; Division of Endocrinology and Diabetology, Medical University of GrazGraz, Austria
| | - Mahjabeen Ahmed
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of TechnologyPasadena, CA, USA; Department of Biological Sciences, California State Polytechnic UniversityPomona, CA, USA
| | - Thomas Weinmaier
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| | - Doina Ciobanu
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Natalia Ivanova
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Thomas R Pieber
- Division of Endocrinology and Diabetology, Medical University of Graz Graz, Austria
| | - Parag A Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology Pasadena, CA, USA
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Mayer T, Blachowicz A, Probst AJ, Vaishampayan P, Checinska A, Swarmer T, de Leon P, Venkateswaran K. Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation. MICROBIOME 2016; 4:22. [PMID: 27250991 PMCID: PMC4890489 DOI: 10.1186/s40168-016-0167-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/18/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND For potential future human missions to the Moon or Mars and sustained presence in the International Space Station, a safe enclosed habitat environment for astronauts is required. Potential microbial contamination of closed habitats presents a risk for crewmembers due to reduced human immune response during long-term confinement. To make future habitat designs safer for crewmembers, lessons learned from characterizing analogous habitats is very critical. One of the key issues is that how human presence influences the accumulation of microorganisms in the closed habitat. RESULTS Molecular technologies, along with traditional microbiological methods, were utilized to catalog microbial succession during a 30-day human occupation of a simulated inflatable lunar/Mars habitat. Surface samples were collected at different time points to capture the complete spectrum of viable and potential opportunistic pathogenic bacterial population. Traditional cultivation, propidium monoazide (PMA)-quantitative polymerase chain reaction (qPCR), and adenosine triphosphate (ATP) assays were employed to estimate the cultivable, viable, and metabolically active microbial population, respectively. Next-generation sequencing was used to elucidate the microbial dynamics and community profiles at different locations of the habitat during varying time points. Statistical analyses confirm that occupation time has a strong influence on bacterial community profiles. The Day 0 samples (before human occupation) have a very different microbial diversity compared to the later three time points. Members of Proteobacteria (esp. Oxalobacteraceae and Caulobacteraceae) and Firmicutes (esp. Bacillaceae) were most abundant before human occupation (Day 0), while other members of Firmicutes (Clostridiales) and Actinobacteria (esp. Corynebacteriaceae) were abundant during the 30-day occupation. Treatment of samples with PMA (a DNA-intercalating dye for selective detection of viable microbial population) had a significant effect on the microbial diversity compared to non-PMA-treated samples. CONCLUSIONS Statistical analyses revealed a significant difference in community structure of samples over time, particularly of the bacteriomes existing before human occupation of the habitat (Day 0 sampling) and after occupation (Day 13, Day 20, and Day 30 samplings). Actinobacteria (mainly Corynebacteriaceae) and Firmicutes (mainly Clostridiales Incertae Sedis XI and Staphylococcaceae) were shown to increase over the occupation time period. The results of this study revealed a strong relationship between human presence and succession of microbial diversity in a closed habitat. Consequently, it is necessary to develop methods and tools for effective maintenance of a closed system to enable safe human habitation in enclosed environments on Earth and beyond.
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Affiliation(s)
- Teresa Mayer
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Adriana Blachowicz
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Alexander J Probst
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Aleksandra Checinska
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Tiffany Swarmer
- Department of Space Studies, University of North Dakota, Grand Forks, ND, 58202, USA
| | - Pablo de Leon
- Department of Space Studies, University of North Dakota, Grand Forks, ND, 58202, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
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Weinmaier T, Probst AJ, La Duc MT, Ciobanu D, Cheng JF, Ivanova N, Rattei T, Vaishampayan P. A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses. MICROBIOME 2015; 3:62. [PMID: 26642878 PMCID: PMC4672508 DOI: 10.1186/s40168-015-0129-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/29/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Recent studies posit a reciprocal dependency between the microbiomes associated with humans and indoor environments. However, none of these metagenome surveys has considered the viability of constituent microorganisms when inferring impact on human health. RESULTS Reported here are the results of a viability-linked metagenomics assay, which (1) unveil a remarkably complex community profile for bacteria, fungi, and viruses and (2) bolster the detection of underrepresented taxa by eliminating biases resulting from extraneous DNA. This approach enabled, for the first time ever, the elucidation of viral genomes from a cleanroom environment. Upon comparing the viable biomes and distribution of phylotypes within a cleanroom and adjoining (uncontrolled) gowning enclosure, the rigorous cleaning and stringent control countermeasures of the former were observed to select for a greater presence of anaerobes and spore-forming microflora. Sequence abundance and correlation analyses suggest that the viable indoor microbiome is influenced by both the human microbiome and the surrounding ecosystem(s). CONCLUSIONS The findings of this investigation constitute the literature's first ever account of the indoor metagenome derived from DNA originating solely from the potential viable microbial population. Results presented in this study should prove valuable to the conceptualization and experimental design of future studies on indoor microbiomes aimed at inferring impact on human health.
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Affiliation(s)
- Thomas Weinmaier
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
| | - Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.
| | - Myron T La Duc
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA.
- Precis Scientific, Scottsdale, AZ, USA.
| | | | | | | | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA.
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Checinska A, Probst AJ, Vaishampayan P, White JR, Kumar D, Stepanov VG, Fox GE, Nilsson HR, Pierson DL, Perry J, Venkateswaran K. Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities. MICROBIOME 2015; 3:50. [PMID: 26502721 PMCID: PMC4624184 DOI: 10.1186/s40168-015-0116-3] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/28/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND The International Space Station (ISS) is a unique built environment due to the effects of microgravity, space radiation, elevated carbon dioxide levels, and especially continuous human habitation. Understanding the composition of the ISS microbial community will facilitate further development of safety and maintenance practices. The primary goal of this study was to characterize the viable microbiome of the ISS-built environment. A second objective was to determine if the built environments of Earth-based cleanrooms associated with space exploration are an appropriate model of the ISS environment. RESULTS Samples collected from the ISS and two cleanrooms at the Jet Propulsion Laboratory (JPL, Pasadena, CA) were analyzed by traditional cultivation, adenosine triphosphate (ATP), and propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) assays to estimate viable microbial populations. The 16S rRNA gene Illumina iTag sequencing was used to elucidate microbial diversity and explore differences between ISS and cleanroom microbiomes. Statistical analyses showed that members of the phyla Actinobacteria, Firmicutes, and Proteobacteria were dominant in the samples examined but varied in abundance. Actinobacteria were predominant in the ISS samples whereas Proteobacteria, least abundant in the ISS, dominated in the cleanroom samples. The viable bacterial populations seen by PMA treatment were greatly decreased. However, the treatment did not appear to have an effect on the bacterial composition (diversity) associated with each sampling site. CONCLUSIONS The results of this study provide strong evidence that specific human skin-associated microorganisms make a substantial contribution to the ISS microbiome, which is not the case in Earth-based cleanrooms. For example, Corynebacterium and Propionibacterium (Actinobacteria) but not Staphylococcus (Firmicutes) species are dominant on the ISS in terms of viable and total bacterial community composition. The results obtained will facilitate future studies to determine how stable the ISS environment is over time. The present results also demonstrate the value of measuring viable cell diversity and population size at any sampling site. This information can be used to identify sites that can be targeted for more stringent cleaning. Finally, the results will allow comparisons with other built sites and facilitate future improvements on the ISS that will ensure astronaut health.
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Affiliation(s)
- Aleksandra Checinska
- Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 89-2 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Alexander J Probst
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Parag Vaishampayan
- Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 89-2 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | | | - Deepika Kumar
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Henrik R Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | | | - Jay Perry
- Marshall Space Flight Center, Huntsville, AL, USA
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 89-2 4800 Oak Grove Dr., Pasadena, CA, 91109, USA.
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