1
|
Chawla H, Anand P, Garg K, Bhagat N, Varmani SG, Bansal T, McBain AJ, Marwah RG. A comprehensive review of microbial contamination in the indoor environment: sources, sampling, health risks, and mitigation strategies. Front Public Health 2023; 11:1285393. [PMID: 38074709 PMCID: PMC10701447 DOI: 10.3389/fpubh.2023.1285393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023] Open
Abstract
The quality of the indoor environment significantly impacts human health and productivity, especially given the amount of time individuals spend indoors globally. While chemical pollutants have been a focus of indoor air quality research, microbial contaminants also have a significant bearing on indoor air quality. This review provides a comprehensive overview of microbial contamination in built environments, covering sources, sampling strategies, and analysis methods. Microbial contamination has various origins, including human occupants, pets, and the outdoor environment. Sampling strategies for indoor microbial contamination include air, surface, and dust sampling, and various analysis methods are used to assess microbial diversity and complexity in indoor environments. The review also discusses the health risks associated with microbial contaminants, including bacteria, fungi, and viruses, and their products in indoor air, highlighting the need for evidence-based studies that can relate to specific health conditions. The importance of indoor air quality is emphasized from the perspective of the COVID-19 pandemic. A section of the review highlights the knowledge gap related to microbiological burden in indoor environments in developing countries, using India as a representative example. Finally, potential mitigation strategies to improve microbiological indoor air quality are briefly reviewed.
Collapse
Affiliation(s)
- Hitikk Chawla
- Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Purnima Anand
- Department of Microbiology, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, India
| | - Kritika Garg
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Neeru Bhagat
- Department of Microbiology, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, India
| | - Shivani G. Varmani
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, India
| | - Tanu Bansal
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Andrew J. McBain
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Ruchi Gulati Marwah
- Department of Microbiology, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, India
| |
Collapse
|
2
|
Chai Z, Soko WC, Xie J, Bi H. Microchip coupled with MALDI-TOF MS for the investigation of bacterial contamination of fish muscle products. Food Chem 2022; 396:133658. [PMID: 35841680 DOI: 10.1016/j.foodchem.2022.133658] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/24/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Bacterial contamination is a significant concern in food safety. Traditional methods, though being a gold standard for bacterial detection, are time-consuming. In this work, we managed to establish a simple and versatile magnetic-assisted microfluidic method for rapid bacterial detection of fish muscle products, by manipulating anti-human IgG functionalized magnetic beads in a zig-zag shaped microfluidic channel, increasing the probability for bacteria capture. The captured bacteria were characterized by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method is capable of isolating Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae from 5 μL of sablefish sarcoplasmic protein sample, and detecting Escherichia coli in the range of 6.0 to 6.0×104 CFU/mL with a detection limit of 6 CFU/mL. Bacterial growth on salmon sashimi during its period of storage was successfully monitored. The current protocol holds great potential for pathogen detection and microbial control in the food industry.
Collapse
Affiliation(s)
- Zhaoliang Chai
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, Shanghai 201306, China
| | - Winnie C Soko
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, Shanghai 201306, China
| | - Jing Xie
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, Shanghai 201306, China.
| | - Hongyan Bi
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, Shanghai 201306, China.
| |
Collapse
|
3
|
Ashfaq MY, Da'na DA, Al-Ghouti MA. Application of MALDI-TOF MS for identification of environmental bacteria: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114359. [PMID: 34959061 DOI: 10.1016/j.jenvman.2021.114359] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/07/2021] [Accepted: 12/18/2021] [Indexed: 05/22/2023]
Abstract
Bacteria play a variety of roles in the environment. They maintain the balance in the ecosystem and provide different ecosystem services such as in biogeochemical cycling of nutrients, biodegradation of toxic pollutants, and others. Therefore, isolation and identification of different environmental bacteria are important to most environmental research. Due to the high cost and time associated with the conventional molecular techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained considerable attention for routine identification of bacteria. This review aims to provide an overview of the application of MALDI-TOF MS in various environmental studies through bibliometric analysis and literature review. The bibliometric analysis helped to understand the time-variable application of MALDI-TOF MS in various environmental studies. The categorical literature review covers various environmental studies comprising areas like ecology, food microbiology, environmental biotechnology, agriculture, and plant sciences, which show the application of the technique for identification and characterization of pollutant-degrading, plant-associated, disease-causing, soil-beneficial, and other environmental bacteria. Further research should focus on bridging the gap between the phylogenetic identity of bacteria and their specific environmental functions or metabolic traits that can help in rapid advancements in environmental research, thereby, improving time and cost savings.
Collapse
Affiliation(s)
- Mohammad Y Ashfaq
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Dana A Da'na
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mohammad A Al-Ghouti
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar.
| |
Collapse
|
4
|
Roy D, Tomo S, Purohit P, Setia P. Microbiome in Death and Beyond: Current Vistas and Future Trends. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.630397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Forensic medicine has, for a long time, been relying on biochemical, anthropologic, and histopathologic evidences in solving various investigations. However, depending on the method used, lengthy sample processing time, scanty sample, and less sensitivity and accuracy pervade these procedures. Accordingly, newer arenas such as the thanatomicrobiome have come forward to aid in its quandaries; furthermore, the parallel advances in genomic and proteomic techniques have complemented and are still emerging to be used in forensic experiments and investigations. Postmortem interval (PMI) is one of the most important aspects of medico-legal investigations. The current trend in PMI estimation is toward genomic analyses of autopsy samples. Similarly, determination of cause of death, although a domain of medical sciences, is being targeted as the next level of forensic casework. With the current trend in laboratory sciences moving to the discovery of newer disease-specific markers for diagnostic and prognostic purposes, the same is being explored for the determination of the cause of death by using techniques such as Real-Time PCR, DNA micro-array, to Next-Gen Sequencing. Establishing an individual’s biological profile has been done using medicolegal methods and anthropology as well as bar-bodies/Davidson bodies (gender determination); and in cases where the determination of age/gender is a challenge using morphological characteristics; the recent advances in the field of genomics and proteomics have played a significant role, e.g., use of mitochondrial DNA in age estimation and in maternity disputes. The major hurdle forensic medical research faces is the fact that most of the studies are conducted in animal models, which are often difficult to mimic in human and real-time scenarios. Additionally, the high accuracy required in criminal investigations to be used in a court of law as evidence has prevented these results to come out of the labs and be used to the optimum. The current review aims at giving a comprehensive and critical account of the various molecular biology techniques including “thanatogenomics,” currently being utilized in the veritable fields of forensic medicine.
Collapse
|
5
|
Maghembe R, Damian D, Makaranga A, Nyandoro SS, Lyantagaye SL, Kusari S, Hatti-Kaul R. Omics for Bioprospecting and Drug Discovery from Bacteria and Microalgae. Antibiotics (Basel) 2020; 9:antibiotics9050229. [PMID: 32375367 PMCID: PMC7277505 DOI: 10.3390/antibiotics9050229] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/10/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
"Omics" represent a combinatorial approach to high-throughput analysis of biological entities for various purposes. It broadly encompasses genomics, transcriptomics, proteomics, lipidomics, and metabolomics. Bacteria and microalgae exhibit a wide range of genetic, biochemical and concomitantly, physiological variations owing to their exposure to biotic and abiotic dynamics in their ecosystem conditions. Consequently, optimal conditions for adequate growth and production of useful bacterial or microalgal metabolites are critically unpredictable. Traditional methods employ microbe isolation and 'blind'-culture optimization with numerous chemical analyses making the bioprospecting process laborious, strenuous, and costly. Advances in the next generation sequencing (NGS) technologies have offered a platform for the pan-genomic analysis of microbes from community and strain downstream to the gene level. Changing conditions in nature or laboratory accompany epigenetic modulation, variation in gene expression, and subsequent biochemical profiles defining an organism's inherent metabolic repertoire. Proteome and metabolome analysis could further our understanding of the molecular and biochemical attributes of the microbes under research. This review provides an overview of recent studies that have employed omics as a robust, broad-spectrum approach for screening bacteria and microalgae to exploit their potential as sources of drug leads by focusing on their genomes, secondary metabolite biosynthetic pathway genes, transcriptomes, and metabolomes. We also highlight how recent studies have combined molecular biology with analytical chemistry methods, which further underscore the need for advances in bioinformatics and chemoinformatics as vital instruments in the discovery of novel bacterial and microalgal strains as well as new drug leads.
Collapse
Affiliation(s)
- Reuben Maghembe
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
- Department of Biological and Marine Sciences, Marian University College, P.O. Box 47, Bagamoyo, Tanzania;
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, 22100 Lund, Sweden
| | - Donath Damian
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
| | - Abdalah Makaranga
- Department of Biological and Marine Sciences, Marian University College, P.O. Box 47, Bagamoyo, Tanzania;
- International Center for Genetic Engineering and Biotechnology (ICGEB), Omics of Algae Group, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Stephen Samwel Nyandoro
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania;
| | - Sylvester Leonard Lyantagaye
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
- Department of Biochemistry, Mbeya College of Health and Allied Sciences, University of Dar es Salaam, P.O. Box 608, Mbeya, Tanzania
| | - Souvik Kusari
- Institute of Environmental Research (INFU), Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
- Correspondence: (S.K.); (R.H.-K.); Tel.: +49-2317554086 (S.K.); +46-462224840 (R.H.-K.)
| | - Rajni Hatti-Kaul
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, 22100 Lund, Sweden
- Correspondence: (S.K.); (R.H.-K.); Tel.: +49-2317554086 (S.K.); +46-462224840 (R.H.-K.)
| |
Collapse
|
6
|
Sun X, Wu P, Zhao C, Zheng F, Hu C, Lu X, Xu G. Protein profiling analysis based on matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry and its application in typing Streptomyces isolates. Talanta 2020; 208:120439. [PMID: 31816710 DOI: 10.1016/j.talanta.2019.120439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/22/2019] [Accepted: 10/03/2019] [Indexed: 10/25/2022]
Abstract
Marine Streptomyces is a potential source of novel bioactive natural products in medicine and agriculture. The current discrimination and screening method of Streptomyces isolates is not accurate and time-consuming, and a novel method is necessary. In this study, a protein profiling method based on an ultrahigh resolution 15 T Matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICR MS) was established and applied for differentiation and bioactivity screening of marine Streptomyces isolates. To obtain robust protein profiling, the effects of the protein extraction method, the matrix-solvent, the sample deposition mode, and the culture time of isolates on protein profiling were thoroughly studied, the optimal conditions were obtained. To evaluate the performance of the developed MALDI-FTICR MS method, MALDI-time of flight (TOF) MS and 16S rRNA were applied in parallel to analyze 25 marine Streptomyces isolates. We found that the clustering result of MALDI-FTICR MS was more similar to that of 16S rRNA than MALDI-TOF MS. And MALDI-FTICR MS could effectively indicate the antibacterial activity of Streptomyces isolates against three plant pathogenic bacteria including Xanthomonas campestris, Xanthomonas oryzae and Erwinia carotovora. Furthermore, a differential protein/peptide was defined and successfully applied to predict antibacterial activity of blind samples. This study demonstrated that MALDI-FTICR MS has great potential to discriminate and screen complex microorganisms, especially those closely related strains.
Collapse
Affiliation(s)
- Xiaoshan Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peichun Wu
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Chunxia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Fujian Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| |
Collapse
|
7
|
Song M, Tang M, Ding Y, Wu Z, Xiang C, Yang K, Zhang Z, Li B, Deng Z, Liu J. Application of protein typing in molecular epidemiological investigation of nosocomial infection outbreak of aminoglycoside-resistant Pseudomonas aeruginosa. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:22437-22445. [PMID: 29249031 DOI: 10.1007/s11356-017-0960-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 12/06/2017] [Indexed: 06/07/2023]
Abstract
Pseudomonas aeruginosan has emerged as an important pathogen elated to serious infections and nosocomial outbreaks worldwide. This study was conducted to understand the prevalence of aminoglycoside (AMG)-resistant P. aeruginosa in our hospital and to provide a scientific basis for control measures against nosocomial infections. Eighty-two strains of P. aeruginosa were isolated from clinical departments and divided into AMG-resistant strains and AMG-sensitive strains based on susceptibility test results. AMG-resistant strains were typed by drug resistance gene typing (DRGT) and protein typing. Five kinds of aminoglycoside-modifying enzyme (AME) genes were detected in the AMG-resistant group. AMG-resistant P. aeruginosa strains were classified into three types and six subtypes by DRGT. Four protein peaks, namely, 9900.02, 7600.04, 9101.25 and 10,372.87 Da, were significantly and differentially expressed between the two groups. AMG-resistant P. aeruginosa strains were also categorised into three types and six subtypes at the distance level of 10 by protein typing. AMG-resistant P. aeruginosa was cloned spread in our hospital; the timely implementation of nosocomial infection prevention and control strategies were needed in preventing outbreaks and epidemic of AMG-resistant P. aeruginosa. SELDI-TOF MS technology can be used for bacterial typing, which provides a new method of clinical epidemiological survey and nosocomial infection control.
Collapse
Affiliation(s)
- Min Song
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Min Tang
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yinghuan Ding
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zecai Wu
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Chengyu Xiang
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Kui Yang
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhang Zhang
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Baolin Li
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhenghua Deng
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinbo Liu
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China.
| |
Collapse
|
8
|
Sandrin TR, Demirev PA. Characterization of microbial mixtures by mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:321-349. [PMID: 28509357 DOI: 10.1002/mas.21534] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/09/2017] [Accepted: 03/09/2017] [Indexed: 05/27/2023]
Abstract
MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.
Collapse
Affiliation(s)
- Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona
| | - Plamen A Demirev
- Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland
| |
Collapse
|
9
|
Handke J, Procopio N, Buckley M, van der Meer D, Williams G, Carr M, Williams A. Successive bacterial colonisation of pork and its implications for forensic investigations. Forensic Sci Int 2017; 281:1-8. [PMID: 29080415 DOI: 10.1016/j.forsciint.2017.10.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/01/2017] [Accepted: 10/11/2017] [Indexed: 11/26/2022]
Abstract
AIMS Bacteria are considered one of the major driving forces of the mammalian decomposition process and have only recently been recognised as forensic tools. At this point, little is known about their potential use as 'post-mortem clocks'. This study aimed to establish the proof of concept for using bacterial identification as post-mortem interval (PMI) indicators, using a multi-omics approach. METHODS AND RESULTS Pieces of pork were placed in the University's outdoor facility and surface swabs were taken at regular intervals up to 60 days. Terminal restriction fragment length polymorphism (T-RFLP) of the 16S rDNA was used to identify bacterial taxa. It succeeded in detecting two out of three key contributors involved in decomposition and represents the first study to reveal Vibrionaceae as abundant on decomposing pork. However, a high fraction of present bacterial taxa could not be identified by T-RFLP. Proteomic analyses were also performed at selected time points, and they partially succeeded in the identification of precise strains, subspecies and species of bacteria that colonized the body after different PMIs. CONCLUSION T-RFLP is incapable of reliably and fully identifying bacterial taxa, whereas proteomics could help in the identification of specific strains of bacteria. Nevertheless, microbial identification by next generation sequencing might be used as PMI clock in future investigations and in conjunction with information provided by forensic entomologists. SIGNIFICANCE AND IMPACT OF THE STUDY To the best of our knowledge, this work represents the first attempt to find a cheaper and easily accessible, culture-independent alternative to high-throughput techniques to establish a 'microbial clock', in combination with proteomic strategies to address this issue.
Collapse
Affiliation(s)
- Jessica Handke
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK; Institute for Interdisciplinary Studies, University of Amsterdam, P.O. Box 19268, 1000 GG Amsterdam, Netherlands.
| | - Noemi Procopio
- Manchester Institute of Biotechnology, 131 Princess Street, University of Manchester, Manchester M1 7DN, UK.
| | - Michael Buckley
- Manchester Institute of Biotechnology, 131 Princess Street, University of Manchester, Manchester M1 7DN, UK.
| | - Dieudonne van der Meer
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
| | - Graham Williams
- School of Law, Forensics and Policing, Staffordshire University, Stoke-on-Trent, Staffordshire ST4 2DE, UK.
| | - Martin Carr
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
| | - Anna Williams
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
| |
Collapse
|
10
|
MALDI-TOF MS for the Identification of Cultivable Organic-Degrading Bacteria in Contaminated Groundwater near Unconventional Natural Gas Extraction Sites. Microorganisms 2017; 5:microorganisms5030047. [PMID: 28796186 PMCID: PMC5620638 DOI: 10.3390/microorganisms5030047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/21/2017] [Accepted: 08/07/2017] [Indexed: 11/17/2022] Open
Abstract
Groundwater quality and quantity is of extreme importance as it is a source of drinking water in the United States. One major concern has emerged due to the possible contamination of groundwater from unconventional oil and natural gas extraction activities. Recent studies have been performed to understand if these activities are causing groundwater contamination, particularly with respect to exogenous hydrocarbons and volatile organic compounds. The impact of contaminants on microbial ecology is an area to be explored as alternatives for water treatment are necessary. In this work, we identified cultivable organic-degrading bacteria in groundwater in close proximity to unconventional natural gas extraction. Pseudomonas stutzeri and Acinetobacter haemolyticus were identified using matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF MS), which proved to be a simple, fast, and reliable method. Additionally, the potential use of the identified bacteria in water and/or wastewater bioremediation was studied by determining the ability of these microorganisms to degrade toluene and chloroform. In fact, these bacteria can be potentially applied for in situ bioremediation of contaminated water and wastewater treatment, as they were able to degrade both compounds.
Collapse
|
11
|
Pulliam CJ, Wei P, Snyder DT, Wang X, Ouyang Z, Pielak RM, Graham Cooks R. Rapid discrimination of bacteria using a miniature mass spectrometer. Analyst 2017; 141:1633-6. [PMID: 26844973 DOI: 10.1039/c5an02575c] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Bacteria colonies were analyzed using paper spray ionization coupled with a portable mass spectrometer. The spectra were averaged and processed using multivariate analysis to discriminate between different species of bacteria based on their unique phospholipid profiles. Full scan mass spectra and product ion MS/MS data were compared to those recorded using a benchtop linear ion trap mass spectrometer.
Collapse
Affiliation(s)
| | - Pu Wei
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - Dalton T Snyder
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - Xiao Wang
- Department of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Zheng Ouyang
- Department of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Rafal M Pielak
- L'Oreal California Research Center, San Francisco, CA, USA
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| |
Collapse
|
12
|
Armengaud J. Defining Diagnostic Biomarkers Using Shotgun Proteomics and MALDI-TOF Mass Spectrometry. Methods Mol Biol 2017; 1616:107-120. [PMID: 28600764 DOI: 10.1007/978-1-4939-7037-7_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Whole-cell MALDI-TOF has become a robust and widely used tool to quickly identify any pathogen. In addition to being routinely used in hospitals, it is also useful for low cost dereplication in large scale screening procedures of new environmental isolates for environmental biotechnology or taxonomical applications. Here, I describe how specific biomarkers can be defined using shotgun proteomics and whole-cell MALDI-TOF mass spectrometry. Based on MALDI-TOF spectra recorded on a given set of pathogens with internal calibrants, m/z values of interest are extracted. The proteins which contribute to these peaks are deduced from label-free shotgun proteomics measurements carried out on the same sample. Quantitative information based on the spectral count approach allows ranking the most probable candidates. Proteogenomic approaches help to define whether these proteins give the same m/z values along the whole taxon under consideration or result in heterogeneous lists. These specific biomarkers nicely complement conventional profiling approaches and may help to better define groups of organisms, for example at the subspecies level.
Collapse
Affiliation(s)
- Jean Armengaud
- CEA-Marcoule, DRF/JOLIOT/DMTS/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostics", BP 17171, 30200, Bagnols-sur-Cèze, France.
| |
Collapse
|
13
|
Chiu NHL, Jia Z, Diaz R, Wright P. Rapid differentiation of in vitro cellular responses to toxic chemicals by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2015; 34:161-166. [PMID: 25319019 DOI: 10.1002/etc.2774] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 07/24/2014] [Accepted: 10/06/2014] [Indexed: 06/04/2023]
Abstract
Changes in protein expression as a cellular response to chemical exposure have been well established. Current methods for monitoring cellular responses usually require the use of specific reagents and/or labor-intensive procedures. The present study demonstrates the concept of using mass spectral pattern to distinguish different cellular responses. The concept is based on the ability to acquire a unique mass spectral pattern directly from a specific cell culture by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The results demonstrate that distinguishable and reproducible spectral patterns can be obtained from different cellular responses.
Collapse
Affiliation(s)
- Norman H L Chiu
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA; Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, Greensboro, North Carolina, USA
| | | | | | | |
Collapse
|
14
|
Durighello E, Bellanger L, Ezan E, Armengaud J. Proteogenomic Biomarkers for Identification of Francisella Species and Subspecies by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry. Anal Chem 2014; 86:9394-8. [DOI: 10.1021/ac501840g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emie Durighello
- CEA Marcoule, DSV, IBEB, Laboratoire de Biochimie
des Systèmes Perturbés, Bagnols-sur-Cèze, F-30207, France
| | - Laurent Bellanger
- CEA Marcoule, DSV, IBEB, Laboratoire d'Ingénierie
Cellulaire et Biotechnologie, Bagnols-sur-Cèze, F-30207, France
| | - Eric Ezan
- CEA Marcoule, DSV, IBEB, Laboratoire de Biochimie
des Systèmes Perturbés, Bagnols-sur-Cèze, F-30207, France
- CEA Marcoule, DSV, IBEB, Laboratoire d'Ingénierie
Cellulaire et Biotechnologie, Bagnols-sur-Cèze, F-30207, France
| | - Jean Armengaud
- CEA Marcoule, DSV, IBEB, Laboratoire de Biochimie
des Systèmes Perturbés, Bagnols-sur-Cèze, F-30207, France
| |
Collapse
|