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Topolski C, Divo E, Li X, Hicks J, Chavez A, Castillo H. Phenotypic and transcriptional changes in Escherichia coli K12 in response to simulated microgravity on the EagleStat, a new 2D microgravity analog for bacterial studies. LIFE SCIENCES IN SPACE RESEARCH 2022; 34:1-8. [PMID: 35940684 DOI: 10.1016/j.lssr.2022.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 06/15/2023]
Abstract
Understanding the impacts of microgravity on bacteria is vital for successful long duration space missions. In this environment, bacteria have been shown to become more virulent, more resistant to antibiotics and to regulate biofilm formation. Since the study of these phenomena under true microgravity is cost- and time challenging, the use of ground-based analogs might allow researchers to test hypotheses before planning and executing experiments in the space environment. We designed and developed a 2D clinostat with capabilities robust enough for bacterial studies to allow for multiple simultaneous replicates of treatment and control conditions, thus permitting the generation of growth curves, in a single run. We used computational fluid dynamics (CFD), biofilm growth measurement and differential gene expression analysis on Escherichia coli cultures grown to late exponential phase (24 h) to validate the system's ability to simulate microgravity conditions. The CFD model with a rotational speed of 8 rpm projected cells growing homogeneously distributed along the tube, while the static condition showed the accumulation of the cells at the bottom of the container. These results were empirically validated with cultures on nutrient broth. Additionally, crystal violet assays showed that higher biofilm biomass grew on the internal walls of the gravity control tubes, compared to the simulated microgravity treatment. In contrast, when cells from both treatments were grown under standard conditions, those exposed to simulated microgravity formed significantly more biofilms than their gravity counterparts. Consistent with this result, transcriptome analysis showed the upregulation of several gene families related to biofilm formation and development such as cells adhesion, aggregation and regulation of cell motility, which provides a potential transcriptional explanation for the differential phenotype observed. Our results show that when operated under parameters for simulated microgravity, our 2D clinostat creates conditions that maintain a proportion of the cells in a constant free-falling state, consistent with the effect of microgravity. Also, the high-throughput nature of our instrument facilitates, significantly, bacterial experiments that require multiple sampling timepoints and small working volumes, making this new instrument extremely efficient.
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Affiliation(s)
- Collin Topolski
- Mechanical Engineering Department, Embry-Riddle Aeronautical University, Daytona Beach, FL, USA
| | - Eduardo Divo
- Mechanical Engineering Department, Embry-Riddle Aeronautical University, Daytona Beach, FL, USA
| | - Xiaoping Li
- Virginia Tech Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Blacksburg, VA, USA
| | - Janelle Hicks
- Human Factors and Behavioral Neurobiology Department, Embry-Riddle Aeronautical University, 1 Aerospace Blvd, COAS 401.03, Deland, Florida, 32724 USA
| | - Alba Chavez
- Human Factors and Behavioral Neurobiology Department, Embry-Riddle Aeronautical University, 1 Aerospace Blvd, COAS 401.03, Deland, Florida, 32724 USA
| | - Hugo Castillo
- Human Factors and Behavioral Neurobiology Department, Embry-Riddle Aeronautical University, 1 Aerospace Blvd, COAS 401.03, Deland, Florida, 32724 USA.
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Wang Y, Shen W, Yin M, Huang W, Ye B, Li P, Shi S, Bai G, Guo X, Jin Y, Lin K, Zhang Y, Jiang Y, Wang J, Han Y, Zhao Z. Changes in Higher-Order Chromosomal Structure of Klebsiella pneumoniae Under Simulated Microgravity. Front Microbiol 2022; 13:879321. [PMID: 35711756 PMCID: PMC9197264 DOI: 10.3389/fmicb.2022.879321] [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] [Received: 02/19/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022] Open
Abstract
Our previous work have shown that certain subpopulations of Klebsiella pneumoniae exhibit significant phenotypic changes under simulated microgravity (SMG), including enhanced biofilm formation and cellulose synthesis, which may be evoked by changes in gene expression patterns. It is well known that prokaryotic cells genomic DNA can be hierarchically organized into different higher-order three-dimensional structures, which can highly influence gene expression. It is remain elusive whether phenotypic changes induced by SMG in the subpopulations of K. pneumoniae are driven by genome higher-order structural changes. Here, we investigated the above-mentioned issue using the wild-type (WT) K. pneumoniae (WT was used as a control strain and continuously cultivated for 2 weeks under standard culture conditions of normal gravity) and two previous identified subpopulations (M1 and M2) obtained after 2 weeks of continuous incubation in a SMG device. By the combination of genome-wide chromosome conformation capture (Hi-C), RNA-seq and whole-genome methylation (WGS) analyses, we found that the along with the global chromosome interactions change, the compacting extent of M1, M2 subpopulations were much looser under SMG and even with an increase in active, open chromosome regions. In addition, transcriptome data showed that most differentially expressed genes (DEGs) were upregulated, whereas a few DEGs were downregulated in M1 and M2. The functions of both types DEGs were mainly associated with membrane fractions. Additionally, WGS analysis revealed that methylation levels were lower in M1 and M2. Using combined analysis of multi-omics data, we discovered that most upregulated DEGs were significantly enriched in the boundary regions of the variable chromosomal interaction domains (CIDs), in which genes regulating biofilm formation were mainly located. These results suggest that K. pneumoniae may regulate gene expression patterns through DNA methylation and changes in genome structure, thus resulting in new phenotypes in response to altered gravity.
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Affiliation(s)
- Yahao Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Wenlong Shen
- Beijing Institute of Biotechnology, Beijing, China
| | - Man Yin
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bingyu Ye
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Ping Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Shu Shi
- Beijing Institute of Biotechnology, Beijing, China
| | - Ge Bai
- Beijing Institute of Biotechnology, Beijing, China
| | - Xinjie Guo
- Beijing Institute of Biotechnology, Beijing, China
| | - Yifei Jin
- Beijing Institute of Biotechnology, Beijing, China
| | - Kailin Lin
- Beijing Institute of Biotechnology, Beijing, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Junfeng Wang
- Second Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Yanping Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Beijing, China
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Su X, Guo Y, Fang T, Jiang X, Wang D, Li D, Bai P, Zhang B, Wang J, Liu C. Effects of Simulated Microgravity on the Physiology of Stenotrophomonas maltophilia and Multiomic Analysis. Front Microbiol 2021; 12:701265. [PMID: 34512577 PMCID: PMC8429793 DOI: 10.3389/fmicb.2021.701265] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Abstract
Many studies have shown that the space environment plays a pivotal role in changing the characteristics of conditional pathogens, especially their pathogenicity and virulence. However, Stenotrophomonas maltophilia, a type of conditional pathogen that has shown to a gradual increase in clinical morbidity in recent years, has rarely been reported for its impact in space. In this study, S. maltophilia was exposed to a simulated microgravity (SMG) environment in high-aspect ratio rotating-wall vessel bioreactors for 14days, while the control group was exposed to the same bioreactors in a normal gravity (NG) environment. Then, combined phenotypic, genomic, transcriptomic, and proteomic analyses were conducted to compare the influence of the SMG and NG on S. maltophilia. The results showed that S. maltophilia in simulated microgravity displayed an increased growth rate, enhanced biofilm formation ability, increased swimming motility, and metabolic alterations compared with those of S. maltophilia in normal gravity and the original strain of S. maltophilia. Clusters of Orthologous Groups (COG) annotation analysis indicated that the increased growth rate might be related to the upregulation of differentially expressed genes (DEGs) involved in energy metabolism and conversion, secondary metabolite biosynthesis, transport and catabolism, intracellular trafficking, secretion, and vesicular transport. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the increased motility might be associated the upregulation of differentially expressed proteins (DEPs) involved in locomotion, localization, biological adhesion, and binding, in accordance with the upregulated DEGs in cell motility according to COG classification, including pilP, pilM, flgE, flgG, and ronN. Additionally, the increased biofilm formation ability might be associated with the upregulation of DEPs involved in biofilm formation, the bacterial secretion system, biological adhesion, and cell adhesion, which were shown to be regulated by the differentially expressed genes (chpB, chpC, rpoN, pilA, pilG, pilH, and pilJ) through the integration of transcriptomic and proteomic analyses. These results suggested that simulated microgravity might increase the level of corresponding functional proteins by upregulating related genes to alter physiological characteristics and modulate growth rate, motility, biofilm formation, and metabolism. In conclusion, this study is the first general analysis of the phenotypic, genomic, transcriptomic, and proteomic changes in S. maltophilia under simulated microgravity and provides some suggestions for future studies of space microbiology.
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Affiliation(s)
- Xiaolei Su
- Medical School of Chinese PLA, Beijing, China.,Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Yinghua Guo
- Medical School of Chinese PLA, Beijing, China.,College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Tingzheng Fang
- Medical School of Chinese PLA, Beijing, China.,Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Xuege Jiang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Dapeng Wang
- Medical School of Chinese PLA, Beijing, China.,Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Diangeng Li
- Department of Academic Research, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, China
| | - Po Bai
- Respiratory Diseases Department, PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Bin Zhang
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou, China
| | - Junfeng Wang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Changting Liu
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
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Abstract
Microbial research in space is being conducted for almost 50 years now. The closed system of the International Space Station (ISS) has acted as a microbial observatory for the past 10 years, conducting research on adaptation and survivability of microorganisms exposed to space conditions. This adaptation can be either beneficial or detrimental to crew members and spacecraft. Therefore, it becomes crucial to identify the impact of two primary stress conditions, namely, radiation and microgravity, on microbial life aboard the ISS. Elucidating the mechanistic basis of microbial adaptation to space conditions aids in the development of countermeasures against their potentially detrimental effects and allows us to harness their biotechnologically important properties. Several microbial processes have been studied, either in spaceflight or using devices that can simulate space conditions. However, at present, research is limited to only a few microorganisms, and extensive research on biotechnologically important microorganisms is required to make long-term space missions self-sustainable.
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Affiliation(s)
- Swati Bijlani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA 90089, USA
| | - Elisa Stephens
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA 90089, USA
| | - Nitin Kumar Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | | | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA 90089, USA
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Silva NBS, Alves PGV, de Andrade Marques L, Silva SF, de Oliveira Faria G, de Araújo LB, Pedroso RDS, Penatti MPA, de Paula Menezes R, von Dolinger de Brito Röder D. Quantification of biofilm produced by clinical, environment and hands' isolates Klebsiella species using colorimetric and classical methods. J Microbiol Methods 2021; 185:106231. [PMID: 33930475 DOI: 10.1016/j.mimet.2021.106231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/25/2021] [Accepted: 04/25/2021] [Indexed: 12/26/2022]
Abstract
Some species of Klebsiella, such as Klebsiella pneumoniae and Klebsiella oxytoca, are important nosocomial pathogens frequently involved in outbreaks in Neonatal Intensive Care Units (NICU) and have the ability to form a biofilm. This study aims to evaluate the biofilm production of K. pneumoniae and K. oxytoca isolates collected from the hands of health professionals, neonates' blood and the environment of a Brazilian NICU, using three colorimetric methods and a classical method of counting the colony-forming units and compare the analysis among these techniques. The biofilm formation was carried out by the microplate technique, using three colorimetric assays: crystal violet, safranin and 2,3-bis (2-methoxy-4-nitro-5-sulfophenyl) -5 [(phenylamino) arbonyl] - 2H-tetrazolium hydroxide (XTT). Also, colony-forming units were determined. Twenty-eight isolates of K. pneumoniae were collected from the blood, hands and environment and five of K. oxytoca from the hands and environment. All of them were strong biofilm producers, but K. pneumoniae isolates produced more biofilm than K. oxytoca when compared to the American Type Culture Collection (ATCC) strains used as positive controls. The number of viable cells in the biofilm produced by K. pneumoniae isolated from blood was significantly higher than in the control sample. Regarding the three colorimetric tests used in the study, the violet crystal obtained a higher absorbance average. The use of crystal-violet and XTT in the evaluation of biofilm in vitro make possible a complete analysis, since that it can quantify the total biomass (including the extracellular matrix) and evaluate the metabolic activity. In conclusion, this study identified isolates of K. pneumoniae and K. oxytoca that produce biofilms in the NICU and the bloodstream of neonates. This fact deserves attention since these patients are immunocompromised. The best methods will be chosen to answer research questions by always adopting more than one method so that more than one parameter or component of the biofilm is analyzed.
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Affiliation(s)
| | | | - Lara de Andrade Marques
- Postgraduate Program in Health Sciences, Medicine, Federal University of Uberlândia (UFU), Brazil
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Senatore G, Mastroleo F, Leys N, Mauriello G. Effect of microgravity & space radiation on microbes. Future Microbiol 2018; 13:831-847. [PMID: 29745771 DOI: 10.2217/fmb-2017-0251] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
One of the new challenges facing humanity is to reach increasingly further distant space targets. It is therefore of upmost importance to understand the behavior of microorganisms that will unavoidably reach the space environment together with the human body and equipment. Indeed, microorganisms could activate their stress defense mechanisms, modifying properties related to human pathogenesis. The host-microbe interactions, in fact, could be substantially affected under spaceflight conditions and the study of microorganisms' growth and activity is necessary for predicting these behaviors and assessing precautionary measures during spaceflight. This review gives an overview of the effects of microgravity and space radiation on microorganisms both in real and simulated conditions.
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Affiliation(s)
- Giuliana Senatore
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Naples, Italy
| | - Felice Mastroleo
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium
| | - Gianluigi Mauriello
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Naples, Italy
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