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Cameron SJS, Edwards A, Lambert RJ, Stroud M, Mur LAJ. Participants in the Trans-Antarctic Winter Traverse Expedition Showed Increased Bacterial Load and Diversity in Saliva but Maintained Individual Differences within Stool Microbiota and Across Metabolite Fingerprints. Int J Mol Sci 2023; 24:ijms24054850. [PMID: 36902282 PMCID: PMC10002533 DOI: 10.3390/ijms24054850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Understanding the impact of long-term physiological and environmental stress on the human microbiota and metabolome may be important for the success of space flight. This work is logistically difficult and has a limited number of available participants. Terrestrial analogies present important opportunities to understand changes in the microbiota and metabolome and how this may impact participant health and fitness. Here, we present work from one such analogy: the Transarctic Winter Traverse expedition, which we believe is the first assessment of the microbiota and metabolome from different bodily locations during prolonged environmental and physiological stress. Bacterial load and diversity were significantly higher during the expedition when compared with baseline levels (p < 0.001) in saliva but not stool, and only a single operational taxonomic unit assigned to the Ruminococcaceae family shows significantly altered levels in stool (p < 0.001). Metabolite fingerprints show the maintenance of individual differences across saliva, stool, and plasma samples when analysed using flow infusion electrospray mass spectrometry and Fourier transform infrared spectroscopy. Significant activity-associated changes in terms of both bacterial diversity and load are seen in saliva but not in stool, and participant differences in metabolite fingerprints persist across all three sample types.
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Affiliation(s)
- Simon J. S. Cameron
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Chlorine Gardens, Belfast BT9 5DL, UK
- Correspondence: (S.J.S.C.); (L.A.J.M.)
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth SY23 3FG, UK
| | - Robert J. Lambert
- Department of Orthopaedics, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Mike Stroud
- NIHR BRC Nutrition, University of Southampton Medical School, Southampton SO16 6YD, UK
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth SY23 3FG, UK
- Correspondence: (S.J.S.C.); (L.A.J.M.)
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2
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Shenker NS, Perdones-Montero A, Burke A, Stickland S, McDonald JAK, Cameron SJS. Human Milk from Tandem Feeding Dyads Does Not Differ in Metabolite and Metataxonomic Features When Compared to Single Nursling Dyads under Six Months of Age. Metabolites 2022; 12:metabo12111069. [PMID: 36355152 PMCID: PMC9696481 DOI: 10.3390/metabo12111069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Given the long-term advantages of exclusive breastfeeding to infants and their mothers, there is both an individual and public health benefit to its promotion and support. Data on the composition of human milk over the course of a full period of lactation for a single nursling is sparse, but data on human milk composition during tandem feeding (feeding children of different ages from different pregnancies) is almost entirely absent. This leaves an important knowledge gap that potentially endangers the ability of parents to make a fully informed choice on infant feeding. We compared the metataxonomic and metabolite fingerprints of human milk samples from 15 tandem feeding dyads to that collected from ten exclusively breastfeeding single nursling dyads where the nursling is under six months of age. Uniquely, our cohort also included three tandem feeding nursling dyads where each child showed a preferential side for feeding-allowing a direct comparison between human milk compositions for different aged nurslings. Across our analysis of volume, total fat, estimation of total microbial load, metabolite fingerprinting, and metataxonomics, we showed no statistically significant differences between tandem feeding and single nursling dyads. This included comparisons of preferential side nurslings of different ages. Together, our findings support the practice of tandem feeding of nurslings, even when feeding an infant under six months.
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Affiliation(s)
- Natalie S. Shenker
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Alvaro Perdones-Montero
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Adam Burke
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Sarah Stickland
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Julie A. K. McDonald
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Simon J. S. Cameron
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK
- Correspondence: ; Tel.: +44-(0)28-9097-6421
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Plekhova V, Van Meulebroek L, De Graeve M, Perdones-Montero A, De Spiegeleer M, De Paepe E, Van de Walle E, Takats Z, Cameron SJS, Vanhaecke L. Rapid ex vivo molecular fingerprinting of biofluids using laser-assisted rapid evaporative ionization mass spectrometry. Nat Protoc 2021; 16:4327-4354. [PMID: 34341579 DOI: 10.1038/s41596-021-00580-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 05/31/2021] [Indexed: 01/29/2023]
Abstract
Of the many metabolites involved in any clinical condition, only a narrow range of biomarkers is currently being used in the clinical setting. A key to personalized medicine would be to extend this range. Metabolic fingerprinting provides a more comprehensive insight, but many methods used for metabolomics analysis are too complex and time-consuming to be diagnostically useful. Here, a rapid evaporative ionization mass spectrometry (REIMS) system for direct ex vivo real-time analysis of biofluids with minor sample pretreatment is detailed. The REIMS can be linked to various laser wavelength systems (such as optical parametric oscillator or CO2 laser) and with automation for high-throughput analysis. Laser-induced sample evaporation occurs within seconds through radiative heating with the plume guided to the MS instrument. The presented procedure includes (i) laser setup with automation, (ii) analysis of biofluids (blood/urine/stool/saliva/sputum/breast milk) and (iii) data analysis. We provide the optimal settings for biofluid analysis and quality control, enabling sensitive, precise and robust analysis. Using the automated setup, 96 samples can be analyzed in ~35-40 min per ionization mode, with no intervention required. Metabolic fingerprints are made up of 2,000-4,000 features, for which relative quantification can be achieved at high repeatability when total ion current normalization is applied. With saliva and feces as example matrices, >70% of features had a coefficient of variance ≤30%. However, to achieve acceptable long-term reproducibility, additional normalizations by, e.g., LOESS are recommended, especially for positive ionization.
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Affiliation(s)
- Vera Plekhova
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | - Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium.,ProDigest BV, Zwijnaarde, Belgium
| | - Marilyn De Graeve
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | | | | | - Ellen De Paepe
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | - Emma Van de Walle
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | - Zoltan Takats
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Simon J S Cameron
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Lynn Vanhaecke
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium. .,School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, Northern Ireland, UK.
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Cameron SJS, Perdones-Montero A, Van Meulebroek L, Burke A, Alexander-Hardiman K, Simon D, Schaffer R, Balog J, Karancsi T, Rickards T, Rebec M, Stead S, Vanhaecke L, Takáts Z. Sample Preparation Free Mass Spectrometry Using Laser-Assisted Rapid Evaporative Ionization Mass Spectrometry: Applications to Microbiology, Metabolic Biofluid Phenotyping, and Food Authenticity. J Am Soc Mass Spectrom 2021; 32:1393-1401. [PMID: 33980015 DOI: 10.1021/jasms.0c00452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Mass spectrometry has established itself as a powerful tool in the chemical, biological, medical, environmental, and agricultural fields. However, experimental approaches and potential application areas have been limited by a traditional reliance on sample preparation, extraction, and chromatographic separation. Ambient ionization mass spectrometry methods have addressed this challenge but are still somewhat restricted in requirements for sample manipulation to make it suitable for analysis. These limitations are particularly restrictive in view of the move toward high-throughput and automated analytical workflows. To address this, we present what we consider to be the first automated sample-preparation-free mass spectrometry platform utilizing a carbon dioxide (CO2) laser for sample thermal desorption linked to the rapid evaporative ionization mass spectrometry (LA-REIMS) methodology. We show that the pulsatile operation of the CO2 laser is the primary factor in achieving high signal-to-noise ratios. We further show that the LA-REIMS automated platform is suited to the analysis of three diverse biological materials within different application areas. First, clinical microbiology isolates were classified to species level with an accuracy of 97.2%, the highest accuracy reported in current literature. Second, fecal samples from a type 2 diabetes mellitus cohort were analyzed with LA-REIMS, which allowed tentative identification of biomarkers which are potentially associated with disease pathogenesis and a disease classification accuracy of 94%. Finally, we showed the ability of the LA-REIMS system to detect instances of adulteration of cooking oil and determine the geographical area of production of three protected olive oil products with 100% classification accuracy.
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Affiliation(s)
- Simon J S Cameron
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, U.K
| | - Alvaro Perdones-Montero
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Ghent University, Ghent B-9820, Belgium
| | - Adam Burke
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Kate Alexander-Hardiman
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Daniel Simon
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
- Waters Research Center, Budapest 1031, Hungary
| | | | - Julia Balog
- Waters Research Center, Budapest 1031, Hungary
| | | | - Tony Rickards
- Department of Microbiology, Imperial College Healthcare NHS Trust, London W6 8RD, U.K
| | - Monica Rebec
- Department of Microbiology, Imperial College Healthcare NHS Trust, London W6 8RD, U.K
| | - Sara Stead
- Waters Corporation, Wilmslow SK9 4AX, U.K
| | - Lynn Vanhaecke
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, U.K
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Ghent University, Ghent B-9820, Belgium
| | - Zoltán Takáts
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, U.K
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5
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Gowers GOF, Cameron SJS, Perdones-Montero A, Bell D, Chee SM, Kern M, Tew D, Ellis T, Takáts Z. Off-Colony Screening of Biosynthetic Libraries by Rapid Laser-Enabled Mass Spectrometry. ACS Synth Biol 2019; 8:2566-2575. [PMID: 31622554 DOI: 10.1021/acssynbio.9b00243] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
By leveraging advances in DNA synthesis and molecular cloning techniques, synthetic biology increasingly makes use of large construct libraries to explore large design spaces. For biosynthetic pathway engineering, the ability to screen these libraries for a variety of metabolites of interest is essential. If the metabolite of interest or the metabolic phenotype is not easily measurable, screening soon becomes a major bottleneck involving time-consuming culturing, sample preparation, and extraction. To address this, we demonstrate the use of automated laser-assisted rapid evaporative ionization mass spectrometry (LA-REIMS)-a form of ambient laser desorption ionization mass spectrometry-to perform rapid mass spectrometry analysis direct from agar plate yeast colonies without sample preparation or extraction. We use LA-REIMS to assess production levels of violacein and betulinic acid directly from yeast colonies at a rate of 6 colonies per minute. We then demonstrate the throughput enabled by LA-REIMS by screening over 450 yeast colonies within <4 h, while simultaneously generating recoverable glycerol stocks of each colony in real time. This showcases LA-REIMS as a prescreening tool to complement downstream quantification methods such as liquid chromatography-mass spectroscopy (LCMS). By prescreening several hundred colonies with LA-REIMS, we successfully isolate and verify a strain with a 2.5-fold improvement in betulinic acid production. Finally, we show that LA-REIMS can detect 20 out of a panel of 27 diverse biological molecules, demonstrating the broad applicability of LA-REIMS to metabolite detection. The rapid and automated nature of LA-REIMS makes this a valuable new technology to complement existing screening technologies currently employed in academic and industrial workflows.
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Affiliation(s)
- Glen-Oliver F. Gowers
- Imperial College Centre for Synthetic Biology (IC−CSynB), Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Simon J. S. Cameron
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
- Ambimass, London W12 0BZ, United Kingdom
| | - Alvaro Perdones-Montero
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
- Ambimass, London W12 0BZ, United Kingdom
| | - David Bell
- SynbiCITE, Imperial College London, London SW7 2AZ, United Kingdom
| | - Soo Mei Chee
- SynbiCITE, Imperial College London, London SW7 2AZ, United Kingdom
| | - Marcelo Kern
- GlaxoSmithKline, Stevenage SG1 2NY, United Kingdom
| | - David Tew
- GlaxoSmithKline, Stevenage SG1 2NY, United Kingdom
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology (IC−CSynB), Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Zoltan Takáts
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
- Ambimass, London W12 0BZ, United Kingdom
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6
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Cameron SJS, Alexander JL, Bolt F, Burke A, Ashrafian H, Teare J, Marchesi JR, Kinross J, Li JV, Takáts Z. Evaluation of Direct from Sample Metabolomics of Human Feces Using Rapid Evaporative Ionization Mass Spectrometry. Anal Chem 2019; 91:13448-13457. [DOI: 10.1021/acs.analchem.9b02358] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Simon J. S. Cameron
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - James L. Alexander
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Frances Bolt
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Adam Burke
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Hutan Ashrafian
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Julian Teare
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Julian R. Marchesi
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, U.K
| | - James Kinross
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Jia V. Li
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Zoltán Takáts
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
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7
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Bardin EE, Cameron SJS, Perdones-Montero A, Hardiman K, Bolt F, Alton EWFW, Bush A, Davies JC, Takáts Z. Metabolic Phenotyping and Strain Characterisation of Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients Using Rapid Evaporative Ionisation Mass Spectrometry. Sci Rep 2018; 8:10952. [PMID: 30026575 PMCID: PMC6053451 DOI: 10.1038/s41598-018-28665-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 06/22/2018] [Indexed: 01/16/2023] Open
Abstract
Rapid evaporative ionisation mass spectrometry (REIMS) is a novel technique for the real-time analysis of biological material. It works by conducting an electrical current through a sample, causing it to rapidly heat and evaporate, with the analyte containing vapour channelled to a mass spectrometer. It was used to characterise the metabolome of 45 Pseudomonas aeruginosa (P. aeruginosa) isolates from cystic fibrosis (CF) patients and compared to 80 non-CF P. aeruginosa. Phospholipids gave the highest signal intensity; 17 rhamnolipids and 18 quorum sensing molecules were detected, demonstrating that REIMS has potential for the study of virulence-related metabolites. P. aeruginosa isolates obtained from respiratory samples showed a higher diversity, which was attributed to the chronic nature of most respiratory infections. The analytical sensitivity of REIMS allowed the detection of a metabolome that could be used to classify individual P. aeruginosa isolates after repeated culturing with 81% accuracy, and an average 83% concordance with multilocus sequence typing. This study underpins the capacities of REIMS as a tool with clinical applications, such as metabolic phenotyping of the important CF pathogen P. aeruginosa, and highlights the potential of metabolic fingerprinting for fine scale characterisation at a sub-species level.
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Affiliation(s)
- Emmanuelle E Bardin
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Simon J S Cameron
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | | | - Kate Hardiman
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Frances Bolt
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Eric W F W Alton
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Andrew Bush
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom
| | - Jane C Davies
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom
| | - Zoltan Takáts
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
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8
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Cameron SJS, Lewis KE, Huws SA, Hegarty MJ, Lewis PD, Pachebat JA, Mur LAJ. A pilot study using metagenomic sequencing of the sputum microbiome suggests potential bacterial biomarkers for lung cancer. PLoS One 2017; 12:e0177062. [PMID: 28542458 PMCID: PMC5444587 DOI: 10.1371/journal.pone.0177062] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 04/23/2017] [Indexed: 01/20/2023] Open
Abstract
Lung cancer (LC) is the most prevalent cancer worldwide, and responsible for over 1.3 million deaths each year. Currently, LC has a low five year survival rates relative to other cancers, and thus, novel methods to screen for and diagnose malignancies are necessary to improve patient outcomes. Here, we report on a pilot-sized study to evaluate the potential of the sputum microbiome as a source of non-invasive bacterial biomarkers for lung cancer status and stage. Spontaneous sputum samples were collected from ten patients referred with possible LC, of which four were eventually diagnosed with LC (LC+), and six had no LC after one year (LC-). Of the seven bacterial species found in all samples, Streptococcus viridans was significantly higher in LC+ samples. Seven further bacterial species were found only in LC-, and 16 were found only in samples from LC+. Additional taxonomic differences were identified in regards to significant fold changes between LC+ and LC-cases, with five species having significantly higher abundances in LC+, with Granulicatella adiacens showing the highest level of abundance change. Functional differences, evident through significant fold changes, included polyamine metabolism and iron siderophore receptors. G. adiacens abundance was correlated with six other bacterial species, namely Enterococcus sp. 130, Streptococcus intermedius, Escherichia coli, S. viridans, Acinetobacter junii, and Streptococcus sp. 6, in LC+ samples only, which could also be related to LC stage. Spontaneous sputum appears to be a viable source of bacterial biomarkers which may have utility as biomarkers for LC status and stage.
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Affiliation(s)
- Simon J. S. Cameron
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, United Kingdom
| | - Keir E. Lewis
- Department of Respiratory Medicine, Prince Phillip Hospital, Hywel Dda University Health Board, Llanelli, United Kingdom
- College of Medicine, Swansea University, Swansea, United Kingdom
| | - Sharon A. Huws
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, United Kingdom
| | - Matthew J. Hegarty
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, United Kingdom
| | - Paul D. Lewis
- College of Medicine, Swansea University, Swansea, United Kingdom
| | - Justin A. Pachebat
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, United Kingdom
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, United Kingdom
- * E-mail:
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9
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O'Shea K, Cameron SJS, Lewis KE, Lu C, Mur LAJ. Corrigendum to Metabolomic-based biomarker discovery for non-invasive lung cancer screening: A case study [Biochimica et Biophysica Acta (BBA) - General subjects, vol. 1860 (2016), pp. 2682-2687]. Biochim Biophys Acta Gen Subj 2017; 1861:1895. [PMID: 28216027 DOI: 10.1016/j.bbagen.2017.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Keiron O'Shea
- Institute of Biological, Environmental and Rural Studies, Aberystwyth University, Aberystwyth, Wales SY23 3DA, UK
| | - Simon J S Cameron
- Institute of Biological, Environmental and Rural Studies, Aberystwyth University, Aberystwyth, Wales SY23 3DA, UK; Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London W6 8RP, UK
| | - Keir E Lewis
- Department of Respiratory Medicine, Prince Philip Hospital, Llanelli, Wales SA14 8LY, UK
| | - Chuan Lu
- Department of Computer Science, Aberystwyth University, Aberystwyth, Wales SY23 3DA, UK
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Studies, Aberystwyth University, Aberystwyth, Wales SY23 3DA, UK.
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10
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Bolt F, Cameron SJS, Karancsi T, Simon D, Schaffer R, Rickards T, Hardiman K, Burke A, Bodai Z, Perdones-Montero A, Rebec M, Balog J, Takats Z. Automated High-Throughput Identification and Characterization of Clinically Important Bacteria and Fungi using Rapid Evaporative Ionization Mass Spectrometry. Anal Chem 2016; 88:9419-9426. [DOI: 10.1021/acs.analchem.6b01016] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Frances Bolt
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Simon J. S. Cameron
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Tamas Karancsi
- Waters Research
Centre, 7 Zahony Street, Budapest, 1031, Hungary
| | - Daniel Simon
- Waters Research
Centre, 7 Zahony Street, Budapest, 1031, Hungary
| | - Richard Schaffer
- Waters Research
Centre, 7 Zahony Street, Budapest, 1031, Hungary
| | - Tony Rickards
- Department
of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross
Hospital, London W6 8RF, United Kingdom
| | - Kate Hardiman
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Adam Burke
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Zsolt Bodai
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Alvaro Perdones-Montero
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Monica Rebec
- Department
of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross
Hospital, London W6 8RF, United Kingdom
| | - Julia Balog
- Waters Research
Centre, 7 Zahony Street, Budapest, 1031, Hungary
| | - Zoltan Takats
- Section
of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, United Kingdom
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11
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O'Shea K, Cameron SJS, Lewis KE, Lu C, Mur LAJ. Metabolomic-based biomarker discovery for non-invasive lung cancer screening: A case study. Biochim Biophys Acta Gen Subj 2016; 1860:2682-7. [PMID: 27423423 DOI: 10.1016/j.bbagen.2016.07.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/09/2016] [Accepted: 07/11/2016] [Indexed: 12/23/2022]
Abstract
BACKGROUND Lung cancer (LC) is one of the leading lethal cancers worldwide, with an estimated 18.4% of all cancer deaths being attributed to the disease. Despite developments in cancer diagnosis and treatment over the previous thirty years, LC has seen little to no improvement in the overall five year survival rate after initial diagnosis. METHODS In this paper, we extended a recent study which profiled the metabolites in sputum from patients with lung cancer and age-matched volunteers smoking controls using flow infusion electrospray ion mass spectrometry. We selected key metabolites for distinguishing between different classes of lung cancer, and employed artificial neural networks and leave-one-out cross-validation to evaluate the predictive power of the identified biomarkers. RESULTS The neural network model showed excellent performance in classification between lung cancer and control groups with the area under the receiver operating characteristic curve of 0.99. The sensitivity and specificity of for detecting cancer from controls were 96% and 94% respectively. Furthermore, we have identified six putative metabolites that were able to discriminate between sputum samples derived from patients suffering small cell lung cancer (SCLC) and non-small cell lung cancer. These metabolites achieved excellent cross validation performance with a sensitivity of 80% and specificity of 100% for predicting SCLC. CONCLUSIONS These results indicate that sputum metabolic profiling may have potential for screening of lung cancer and lung cancer recurrence, and may greatly improve effectiveness of clinical intervention. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
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Affiliation(s)
- Keiron O'Shea
- Institute of Biological, Environmental and Rural Studies, Aberystwyth University, Aberystwyth, Wales SY23 3DA, UK
| | - Simon J S Cameron
- Institute of Biological, Environmental and Rural Studies, Aberystwyth University, Aberystwyth, Wales SY23 3DA, UK; Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, W6 8RP, UK
| | - Keir E Lewis
- Department of Respiratory Medicine, Prince Philip Hospital, Llanelli, Wales SA14 8LY, UK
| | - Chuan Lu
- Department of Computer Science, Aberystwyth University, Aberystwyth, Wales SY23 3DA, UK
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Studies, Aberystwyth University, Aberystwyth, Wales SY23 3DA, UK.
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Cameron SJS, Lewis KE, Huws SA, Lin W, Hegarty MJ, Lewis PD, Mur LAJ, Pachebat JA. Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease Severity. PLoS One 2016; 11:e0149095. [PMID: 26872143 PMCID: PMC4752236 DOI: 10.1371/journal.pone.0149095] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 01/27/2016] [Indexed: 01/01/2023] Open
Abstract
Chronic Obstructive Pulmonary Disease (COPD) is a major source of mortality and morbidity worldwide. The microbiome associated with this disease may be an important component of the disease, though studies to date have been based on sequencing of the 16S rRNA gene, and have revealed unequivocal results. Here, we employed metagenomic sequencing of the upper bronchial tract (UBT) microbiome to allow for greater elucidation of its taxonomic composition, and revealing functional changes associated with the disease. The bacterial metagenomes within sputum samples from eight COPD patients and ten 'healthy' smokers (Controls) were sequenced, and suggested significant changes in the abundance of bacterial species, particularly within the Streptococcus genus. The functional capacity of the COPD UBT microbiome indicated an increased capacity for bacterial growth, which could be an important feature in bacterial-associated acute exacerbations. Regression analyses correlated COPD severity (FEV1% of predicted) with differences in the abundance of Streptococcus pneumoniae and functional classifications related to a reduced capacity for bacterial sialic acid metabolism. This study suggests that the COPD UBT microbiome could be used in patient risk stratification and in identifying novel monitoring and treatment methods, but study of a longitudinal cohort will be required to unequivocally relate these features of the microbiome with COPD severity.
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Affiliation(s)
- Simon J S Cameron
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3FG, United Kingdom
| | - Keir E Lewis
- Department of Respiratory Medicine, Prince Phillip Hospital, Hywel Dda University Health Board, Llanelli, SA14 8QF, United Kingdom.,College of Medicine, Swansea University, Swansea, SA2 8PP, United Kingdom
| | - Sharon A Huws
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3FG, United Kingdom
| | - Wanchang Lin
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3FG, United Kingdom
| | - Matthew J Hegarty
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3FG, United Kingdom
| | - Paul D Lewis
- College of Medicine, Swansea University, Swansea, SA2 8PP, United Kingdom
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3FG, United Kingdom
| | - Justin A Pachebat
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3FG, United Kingdom
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Cameron SJS, Lewis KE, Beckmann M, Allison GG, Ghosal R, Lewis PD, Mur LAJ. The metabolomic detection of lung cancer biomarkers in sputum. Lung Cancer 2016; 94:88-95. [PMID: 26973212 DOI: 10.1016/j.lungcan.2016.02.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 02/04/2016] [Accepted: 02/06/2016] [Indexed: 12/23/2022]
Abstract
OBJECTIVES Developing screening and diagnosis methodologies based on novel biomarkers should allow for the detection of the lung cancer (LC) and possibly at an earlier stage and thereby increase the effectiveness of clinical interventions. Here, our primary objective was to evaluate the potential of spontaneous sputum as a source of non-invasive metabolomic biomarkers for LC status. MATERIALS AND METHODS Spontaneous sputum was collected and processed from 34 patients with suspected LC, alongside 33 healthy controls. Of the 34 patients, 23 were subsequently diagnosed with LC (LC(+), 16 NSCLC, six SCLC, and one radiological diagnosis), at various stages of disease progression. The 67 samples were analysed using flow infusion electrospray ion mass spectrometry (FIE-MS) and gas-chromatography mass spectrometry (GC-MS). RESULTS Principal component analysis identified negative mode FIE-MS as having the main separating power between samples from healthy and LC. Discriminatory metabolites were identified using ANOVA and Random Forest. Indications of potential diagnostic accuracy involved the use of receiver operating characteristic/area under the curve (ROC/AUC) analyses. This approach identified metabolites changes that were only observed with LC. Metabolites with AUC values of greater than 0.8 which distinguished between LC(+)/LC(-) binary classifications where identified and included Ganglioside GM1 which has previously been linked to LC. CONCLUSION This study indicates that metabolomics based on sputum can yield metabolites that can be used as a diagnostic and/or discriminator tool. These could aid clinical intervention and targeted diagnosis of LC within an 'at risk' LC(-) population group. The use of sputum as a non-invasive source of metabolite biomarkers may aid in the development of an at-risk population screening programme for lung cancer or enhanced clinical diagnostic pathways.
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Affiliation(s)
- Simon J S Cameron
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion SY23 3FG, UK
| | - Keir E Lewis
- Department of Respiratory Medicine, Prince Phillip Hospital, Llanelli SA14 8LY, UK; College of Medicine, Swansea University, Swansea SA2 8PP, UK
| | - Manfred Beckmann
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion SY23 3FG, UK
| | - Gordon G Allison
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion SY23 3FG, UK
| | - Robin Ghosal
- Department of Respiratory Medicine, Prince Phillip Hospital, Llanelli SA14 8LY, UK
| | - Paul D Lewis
- College of Medicine, Swansea University, Swansea SA2 8PP, UK
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion SY23 3FG, UK.
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Cameron SJS, Huws SA, Hegarty MJ, Smith DPM, Mur LAJ. The human salivary microbiome exhibits temporal stability in bacterial diversity. FEMS Microbiol Ecol 2015. [DOI: 10.1093/femsec/fiv091] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Huws SA, Kim EJ, Cameron SJS, Girdwood SE, Davies L, Tweed J, Vallin H, Scollan ND. Characterization of the rumen lipidome and microbiome of steers fed a diet supplemented with flax and echium oil. Microb Biotechnol 2014; 8:331-41. [PMID: 25223749 PMCID: PMC4353346 DOI: 10.1111/1751-7915.12164] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 08/05/2014] [Accepted: 08/06/2014] [Indexed: 12/03/2022] Open
Abstract
Developing novel strategies for improving the fatty acid composition of ruminant products relies upon increasing our understanding of rumen bacterial lipid metabolism. This study investigated whether flax or echium oil supplementation of steer diets could alter the rumen fatty acids and change the microbiome. Six Hereford × Friesian steers were offered grass silage/sugar beet pulp only (GS), or GS supplemented either with flax oil (GSF) or echium oil (GSE) at 3% kg−1 silage dry matter in a 3 × 3 replicated Latin square design with 21-day periods with rumen samples taken on day 21 for the analyses of the fatty acids and microbiome. Flax oil supplementation of steer diets increased the intake of polyunsaturated fatty acids, but a substantial degree of rumen biohydrogenation was seen. Likewise, echium oil supplementation of steer diets resulted in increased intake of 18:4n-3, but this was substantially biohydrogenated within the rumen. Microbiome pyrosequences showed that 50% of the bacterial genera were core to all diets (found at least once under each dietary intervention), with 19.10%, 5.460% and 12.02% being unique to the rumen microbiota of steers fed GS, GSF and GSE respectively. Higher 16S rDNA sequence abundance of the genera Butyrivibrio, Howardella, Oribacterium, Pseudobutyrivibrio and Roseburia was seen post flax feeding. Higher 16S rDNA abundance of the genus Succinovibrio and Roseburia was seen post echium feeding. The role of these bacteria in biohydrogenation now requires further study.
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Affiliation(s)
- Sharon Ann Huws
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais Campus, Aberystwyth, SY23 3DA, UK
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Jones AW, Cameron SJS, Thatcher R, Beecroft MS, Mur LAJ, Davison G. Effects of bovine colostrum supplementation on upper respiratory illness in active males. Brain Behav Immun 2014; 39:194-203. [PMID: 24200515 DOI: 10.1016/j.bbi.2013.10.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/08/2013] [Accepted: 10/27/2013] [Indexed: 11/28/2022] Open
Abstract
Bovine colostrum (COL) has been advocated as a nutritional countermeasure to exercise-induced immune dysfunction and increased risk of upper respiratory illness (URI) in athletic populations, however, the mechanisms remain unclear. During winter months, under double-blind procedures, 53 males (mean training load±SD, 50.5±28.9 MET-hweek(-1)) were randomized to daily supplementation of 20g of COL (N=25) or an isoenergetic/isomacronutrient placebo (PLA) (N=28) for 12weeks. Venous blood was collected at baseline and at 12weeks and unstimulated saliva samples at 4 weeks intervals. There was a significantly lower proportion of URI days and number of URI episodes with COL compared to PLA over the 12weeks (p<0.05). There was no effect of COL on in vitro neutrophil oxidative burst, salivary secretory IgA or salivary antimicrobial peptides (p>0.05), which does not support previously suggested mechanisms. In a subset of participants (COL=14, PLA=17), real-time quantitative PCR, targeting the 16S rRNA gene showed there was an increase in salivary bacterial load over the 12 weeks period with PLA (p<0.05) which was not as evident with COL. Discriminant function analysis of outputs received from serum metabolomics showed changes across time but not between groups. This is the first study to demonstrate that COL limits the increased salivary bacterial load in physically active males during the winter months which may provide a novel mechanism of immune-modulation with COL and a relevant marker of in vivo (innate) immunity and risk of URI.
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Affiliation(s)
- Arwel W Jones
- Department of Sport and Exercise Science, Aberystwyth University, Aberystwyth, UK; Clinical Research Centre, Prince Phillip Hospital, Llanelli, UK.
| | - Simon J S Cameron
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Rhys Thatcher
- Department of Sport and Exercise Science, Aberystwyth University, Aberystwyth, UK
| | - Marikka S Beecroft
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Glen Davison
- Endurance Research Group, School of Sport and Exercise Sciences, University of Kent at Medway, Chatham, UK
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