1
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Tan CAZ, Chong KKL, Yeong DYX, Ng CHM, Ismail MH, Yap ZH, Khetrapal V, Tay VSY, Drautz-Moses DI, Ali Y, Chen SL, Kline KA. Purine and carbohydrate availability drive Enterococcus faecalis fitness during wound and urinary tract infections. mBio 2024; 15:e0238423. [PMID: 38078746 PMCID: PMC10790769 DOI: 10.1128/mbio.02384-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/24/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Although E. faecalis is a common wound pathogen, its pathogenic mechanisms during wound infection are unexplored. Here, combining a mouse wound infection model with in vivo transposon and RNA sequencing approaches, we identified the E. faecalis purine biosynthetic pathway and galactose/mannose MptABCD phosphotransferase system as essential for E. faecalis acute replication and persistence during wound infection, respectively. The essentiality of purine biosynthesis and the MptABCD PTS is driven by the consumption of purine metabolites by E. faecalis during acute replication and changing carbohydrate availability during the course of wound infection. Overall, our findings reveal the importance of the wound microenvironment in E. faecalis wound pathogenesis and how these metabolic pathways can be targeted to better control wound infections.
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Affiliation(s)
- Casandra Ai Zhu Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Kelvin Kian Long Chong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Daryl Yu Xuan Yeong
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Celine Hui Min Ng
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Muhammad Hafiz Ismail
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Zhei Hwee Yap
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Varnica Khetrapal
- Infectious Diseases Translational Research Programme, Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Vanessa Shi Yun Tay
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Daniela I. Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Yusuf Ali
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
- Singapore Eye Research Institute (SERI), Singapore General Hospital, Singapore, Singapore
| | - Swaine L. Chen
- Infectious Diseases Translational Research Programme, Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Laboratory of Bacterial Genomics, Genome Institute of Singapore, Singapore, Singapore
| | - Kimberly A. Kline
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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2
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Lau KJX, Gusareva ES, Luhung I, Premkrishnan BNV, Wong A, Poh TY, Uchida A, Oliveira EL, Drautz-Moses DI, Junqueira ACM, Schuster SC. Structure vs. chemistry: Alternate mechanisms for controlling leaf microbiomes. PLoS One 2023; 18:e0275734. [PMID: 36943839 PMCID: PMC10030040 DOI: 10.1371/journal.pone.0275734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 09/22/2022] [Indexed: 03/23/2023] Open
Abstract
The analysis of phyllosphere microbiomes traditionally relied on DNA extracted from whole leaves. To investigate the microbial communities on the adaxial (upper) and abaxial (lower) leaf surfaces, swabs were collected from both surfaces of two garden plants, Rhapis excelsa and Cordyline fruticosa. Samples were collected at noon and midnight and at five different locations to investigate if the phyllosphere microbial communities change with time and location. The abaxial surface of Rhapis excelsa and Cordyline fruticosa had fewer bacteria in contrast to its adaxial counterpart. This observation was consistent between noon and midnight and across five different locations. Our co-occurrence network analysis further showed that bacteria were found almost exclusively on the adaxial surface while only a small group of leaf blotch fungi thrived on the abaxial surface. There are higher densities of stomata on the abaxial surface and these openings are vulnerable ports of entry into the plant host. While one might argue about the settling of dust particles and microorganisms on the adaxial surface, we detected differences in reactive chemical activities and microstructures between the adaxial and abaxial surfaces. Our results further suggest that both plant species deploy different defence strategies to deter invading pathogens on the abaxial surface. We hypothesize that chemical and mechanical defence strategies evolved independently for harnessing and controlling phyllosphere microbiomes. Our findings have also advanced our understanding that the abaxial leaf surface is distinct from the adaxial surface and that the reduced microbial diversity is likely a consequence of plant-microbe interactions.
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Affiliation(s)
- Kenny J X Lau
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Elena S Gusareva
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Irvan Luhung
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Balakrishnan N V Premkrishnan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Anthony Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Tuang Yeow Poh
- Translational Respiratory Research Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Akira Uchida
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Elaine L Oliveira
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ana Carolina M Junqueira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
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3
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Tong L, Constancias F, Hou A, Chua SL, Drautz-Moses DI, Schuster SC, Yang L, Williams RBH, Kjelleberg S. Shotgun metagenomic sequencing analysis of ocular surface microbiome in Singapore residents with mild dry eye. Front Med (Lausanne) 2022; 9:1034131. [PMID: 36438051 PMCID: PMC9684611 DOI: 10.3389/fmed.2022.1034131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 09/06/2022] [Accepted: 10/24/2022] [Indexed: 07/30/2023] Open
Abstract
The ocular surface microbiome has implications for ocular surface inflammation and immunology. Previous shotgun metagenomics analyses were performed in China, showing results that differed according to environment and age. Patients with Sjogren's syndrome were reported to have altered conjunctival microbiome, but such studies have not been done in milder dry eye. The aim of this study is to describe the conjunctival microbiome in people with mild dry eye in Singapore. Samples were collected from 14 participants with mild dry eye and 10 age-matched comparison participants recruited from Singapore National Eye Centre (SNEC) clinics. Shotgun metagenomic sequencing analysis was employed to evaluate the conjunctival microbiome composition. Proteobacteria formed the predominant phylum in the conjunctiva. As in a study from a coastal city in China, Achromobacter spp. was numerically most abundant. Compared to age-matched controls, the conjunctival microbial composition in mild dry eye was similar. Several microorganisms, including Streptococcus spp. increased in representation with age, and the abundance of Staphylococcus correlated with Schirmer readings. In addition, when cultured corneal epithelial cells were exposed to three strains of Achromobacter xylosoxidans, cytokines such as TNF-α and IL-6 were upregulated in the cell lysates and supernatants. Ourresults suggest that age is an important factor that affects composition of the conjunctival microbiome, and relative abundance of specific microorganism may vary according to the environment of the human host.
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Affiliation(s)
- Louis Tong
- Ocular Surface Research Group, Singapore Eye Research Institute, Singapore, Singapore
- Corneal and External Eye Disease Service, Singapore National Eye Centre, Singapore, Singapore
- Eye-Academic Clinical Programme, Office of Clinical, Academic and Faculty Affairs, Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Florentin Constancias
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Aihua Hou
- Ocular Surface Research Group, Singapore Eye Research Institute, Singapore, Singapore
- Eye-Academic Clinical Programme, Office of Clinical, Academic and Faculty Affairs, Duke-NUS Medical School, Singapore, Singapore
| | - Song Lin Chua
- Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore, Singapore
| | - Daniela I. Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Stephan Christoph Schuster
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Rohan B. H. Williams
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Centre for Marine Science and Innovation, School of Biological Earth and Environmental Sciences, University of New South Wales, Kensington, NSW, Australia
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4
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Li L, Mac Aogáin M, Xu T, Jaggi TK, Chan LLY, Qu J, Wei L, Liao S, Cheng HS, Keir HR, Dicker AJ, Tan KS, De Yun W, Koh MS, Ong TH, Lim AYH, Abisheganaden JA, Low TB, Hassan TM, Long X, Wark PAB, Oliver B, Drautz-Moses DI, Schuster SC, Tan NS, Fang M, Chalmers JD, Chotirmall SH. Neisseria species as pathobionts in bronchiectasis. Cell Host Microbe 2022; 30:1311-1327.e8. [PMID: 36108613 DOI: 10.1016/j.chom.2022.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 12/02/2021] [Revised: 05/30/2022] [Accepted: 07/18/2022] [Indexed: 02/07/2023]
Abstract
Neisseria species are frequently identified in the bronchiectasis microbiome, but they are regarded as respiratory commensals. Using a combination of human cohorts, next-generation sequencing, systems biology, and animal models, we show that bronchiectasis bacteriomes defined by the presence of Neisseria spp. associate with poor clinical outcomes, including exacerbations. Neisseria subflava cultivated from bronchiectasis patients promotes the loss of epithelial integrity and inflammation in primary epithelial cells. In vivo animal models of Neisseria subflava infection and metabolipidome analysis highlight immunoinflammatory functional gene clusters and provide evidence for pulmonary inflammation. The murine metabolipidomic data were validated with human Neisseria-dominant bronchiectasis samples and compared with disease in which Pseudomonas-, an established bronchiectasis pathogen, is dominant. Metagenomic surveillance of Neisseria across various respiratory disorders reveals broader importance, and the assessment of the home environment in bronchiectasis implies potential environmental sources of exposure. Thus, we identify Neisseria species as pathobionts in bronchiectasis, allowing for improved risk stratification in this high-risk group.
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Affiliation(s)
- Liang Li
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China; Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Micheál Mac Aogáin
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital, Dublin, Ireland; Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Tengfei Xu
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, PRC
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Louisa L Y Chan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jing Qu
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lan Wei
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shumin Liao
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hong Sheng Cheng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Holly R Keir
- University of Dundee, Ninewells Hospital, Medical School, Dundee, Scotland
| | - Alison J Dicker
- University of Dundee, Ninewells Hospital, Medical School, Dundee, Scotland
| | - Kai Sen Tan
- Department of Otolaryngology, Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wang De Yun
- Department of Otolaryngology, Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mariko Siyue Koh
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Thun How Ong
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Albert Yick Hou Lim
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - John A Abisheganaden
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Teck Boon Low
- Department of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore, Singapore
| | | | - Xiang Long
- Department of Respiratory Medicine and Critical Care, Peking University Shenzhen Hospital, Shenzhen, China
| | - Peter A B Wark
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, Australia; Department of Respiratory and Sleep Medicine, John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - Brian Oliver
- Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, Australia; School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Nguan Soon Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore; Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - James D Chalmers
- University of Dundee, Ninewells Hospital, Medical School, Dundee, Scotland
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore.
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5
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Haryono MAS, Law YY, Arumugam K, Liew LCW, Nguyen TQN, Drautz-Moses DI, Schuster SC, Wuertz S, Williams RBH. Recovery of High Quality Metagenome-Assembled Genomes From Full-Scale Activated Sludge Microbial Communities in a Tropical Climate Using Longitudinal Metagenome Sampling. Front Microbiol 2022; 13:869135. [PMID: 35756038 PMCID: PMC9230771 DOI: 10.3389/fmicb.2022.869135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/05/2022] [Indexed: 01/23/2023] Open
Abstract
The analysis of metagenome data based on the recovery of draft genomes (so called metagenome-assembled genomes, or MAG) has assumed an increasingly central role in microbiome research in recent years. Microbial communities underpinning the operation of wastewater treatment plants are particularly challenging targets for MAG analysis due to their high ecological complexity, and remain important, albeit understudied, microbial communities that play ssa key role in mediating interactions between human and natural ecosystems. Here we consider strategies for recovery of MAG sequence from time series metagenome surveys of full-scale activated sludge microbial communities. We generate MAG catalogs from this set of data using several different strategies, including the use of multiple individual sample assemblies, two variations on multi-sample co-assembly and a recently published MAG recovery workflow using deep learning. We obtain a total of just under 9,100 draft genomes, which collapse to around 3,100 non-redundant genomic clusters. We examine the strengths and weaknesses of these approaches in relation to MAG yield and quality, showing that co-assembly may offer advantages over single-sample assembly in the case of metagenome data obtained from closely sampled longitudinal study designs. Around 1,000 MAGs were candidates for being considered high quality, based on single-copy marker gene occurrence statistics, however only 58 MAG formally meet the MIMAG criteria for being high quality draft genomes. These findings carry broader broader implications for performing genome-resolved metagenomics on highly complex communities, the design and implementation of genome recoverability strategies, MAG decontamination and the search for better binning methodology.
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Affiliation(s)
- Mindia A S Haryono
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Ying Yu Law
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Krithika Arumugam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Larry C-W Liew
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Thi Quynh Ngoc Nguyen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
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6
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Gusareva ES, Gaultier NE, Uchida A, Premkrishnan BNV, Heinle CE, Phung WJ, Wong A, Lau KJX, Yap ZH, Koh Y, Ang PN, Putra A, Panicker D, Lee JGH, Neves LC, Drautz-Moses DI, Schuster SC. Short-range contributions of local sources to ambient air. PNAS Nexus 2022; 1:pgac043. [PMID: 36713329 PMCID: PMC9802476 DOI: 10.1093/pnasnexus/pgac043] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/07/2022] [Indexed: 06/18/2023]
Abstract
Recent developments in aerobiology have enabled the investigation of airborne biomass with high temporal and taxonomic resolution. In this study, we assess the contributions of local sources to ambient air within a 160,000 m2 tropical avian park (AP). We sequenced and analyzed 120 air samples from seven locations situated 160 to 400 m apart, representing distinct microhabitats. Each microhabitat contained a characteristic air microbiome, defined by the abundance and richness of its airborne microbial community members, supported by both, PCoA and Random Forest analysis. Each outdoor microhabitat contained 1% to 18.6% location-specific taxa, while a core microbiome of 27.1% of the total taxa was shared. To identify and assess local sources, we compared the AP dataset with a DVE reference dataset from a location 2 km away, collected during a year-round sampling campaign. Intersection of data from the two sites demonstrated 61.6% of airborne species originated from local sources of the AP, 34.5% from ambient air background, and only 3.9% of species were specific to the DVE reference site. In-depth taxonomic analysis demonstrated association of bacteria-dominated air microbiomes with indoor spaces, while fungi-dominated airborne microbial biomass was predominant in outdoor settings with ample vegetation. The approach presented here demonstrates an ability to identify local source contributions against an ambient air background, despite the prevailing mixing of air masses caused by atmospheric turbulences.
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Affiliation(s)
| | | | - Akira Uchida
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Balakrishnan N V Premkrishnan
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Cassie E Heinle
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Wen J Phung
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Anthony Wong
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Kenny J X Lau
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Zhei H Yap
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yanqing Koh
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Poh N Ang
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Alexander Putra
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Deepa Panicker
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jessica G H Lee
- Mandai Nature, 80 Mandai Lake Rd, Singapore 729826, Singapore
| | - Luis C Neves
- Animal Care Department, Mandai Wildlife Group, 80 Mandai Lake Rd, Singapore 729826, Singapore
| | - Daniela I Drautz-Moses
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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7
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Drautz-Moses DI, Luhung I, Gusareva ES, Kee C, Gaultier NE, Premkrishnan BNV, Lee CF, Leong ST, Park C, Yap ZH, Heinle CE, Lau KJX, Purbojati RW, Lim SBY, Lim YH, Kutmutia SK, Aung NW, Oliveira EL, Ng SG, Dacanay J, Ang PN, Spence S, Phung WJ, Wong A, Kennedy RJ, Kalsi N, Sasi SP, Chandrasekaran L, Uchida A, Junqueira ACM, Kim HL, Hankers R, Feuerle T, Corsmeier U, Schuster SC. Vertical stratification of the air microbiome in the lower troposphere. Proc Natl Acad Sci U S A 2022; 119:e2117293119. [PMID: 35131944 PMCID: PMC8851546 DOI: 10.1073/pnas.2117293119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/11/2021] [Indexed: 12/11/2022] Open
Abstract
The troposphere constitutes the final frontier of global ecosystem research due to technical challenges arising from its size, low biomass, and gaseous state. Using a vertical testing array comprising a meteorological tower and a research aircraft, we conducted synchronized measurements of meteorological parameters and airborne biomass (n = 480) in the vertical air column up to 3,500 m. The taxonomic analysis of metagenomic data revealed differing patterns of airborne microbial community composition with respect to time of day and height above ground. The temporal and spatial resolution of our study demonstrated that the diel cycle of airborne microorganisms is a ground-based phenomenon that is entirely absent at heights >1,000 m. In an integrated analysis combining meteorological and biological data, we demonstrate that atmospheric turbulence, identified by potential temperature and high-frequency three-component wind measurements, is the key driver of bioaerosol dynamics in the lower troposphere. Multivariate regression analysis shows that at least 50% of identified airborne microbial taxa (n = ∼10,000) are associated with either ground or height, allowing for an understanding of dispersal patterns of microbial taxa in the vertical air column. Due to the interconnectedness of atmospheric turbulence and temperature, the dynamics of microbial dispersal are likely to be impacted by rising global temperatures, thereby also affecting ecosystems on the planetary surface.
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Affiliation(s)
- Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Irvan Luhung
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Elena S Gusareva
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
- The Asian School of the Environment, Nanyang Technological University, Singapore 637459
| | - Carmon Kee
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Nicolas E Gaultier
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | | | - Choou Fook Lee
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - See Ting Leong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Changsook Park
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Zhei Hwee Yap
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Cassie E Heinle
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Kenny J X Lau
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Rikky W Purbojati
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Serene B Y Lim
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Yee Hui Lim
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Shruti Ketan Kutmutia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Ngu War Aung
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Elaine L Oliveira
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Soo Guek Ng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Justine Dacanay
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Poh Nee Ang
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Sam Spence
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Wen Jia Phung
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Anthony Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Ryan J Kennedy
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Namrata Kalsi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Santhi Puramadathil Sasi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Lakshmi Chandrasekaran
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Akira Uchida
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Ana Carolina M Junqueira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil
| | - Hie Lim Kim
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
- The Asian School of the Environment, Nanyang Technological University, Singapore 637459
| | - Rudolf Hankers
- Institute of Flight Guidance, Technische Universität, 38108 Braunschweig, Germany
| | - Thomas Feuerle
- Institute of Flight Guidance, Technische Universität, 38108 Braunschweig, Germany
| | - Ulrich Corsmeier
- Institute of Meteorology and Climate Research, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551;
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8
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Ang AX, Luhung I, Ahidjo BA, Drautz-Moses DI, Tambyah PA, Mok CK, Lau KJ, Tham SM, Chu JJH, Allen DM, Schuster SC. Airborne SARS-CoV-2 surveillance in hospital environment using high-flowrate air samplers and its comparison to surface sampling. Indoor Air 2022; 32:e12930. [PMID: 34519380 DOI: 10.1111/ina.v32.110.1111/ina.12930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/15/2021] [Accepted: 09/02/2021] [Indexed: 05/18/2023]
Abstract
Reliable methods to detect the presence of SARS-CoV-2 at venues where people gather are essential for epidemiological surveillance to guide public policy. Communal screening of air in a highly crowded space has the potential to provide early warning on the presence and potential transmission of SARS-CoV-2 as suggested by studies early in the epidemic. As hospitals and public facilities apply varying degrees of restrictions and regulations, it is important to provide multiple methodological options to enable environmental SARS-CoV-2 surveillance under different conditions. This study assessed the feasibility of using high-flowrate air samplers combined with RNA extraction kit designed for environmental sample to perform airborne SARS-CoV-2 surveillance in hospital setting, tested by RT-qPCR. The success rate of the air samples in detecting SARS-CoV-2 was then compared with surface swab samples collected in the same proximity. Additionally, positive RT-qPCR samples underwent viral culture to assess the viability of the sampled SARS-CoV-2. The study was performed in inpatient ward environments of a quaternary care university teaching hospital in Singapore housing active COVID-19 patients within the period of February to May 2020. Two types of wards were tested, naturally ventilated open-cohort ward and mechanically ventilated isolation ward. Distances between the site of air sampling and the patient cluster in the investigated wards were also recorded. No successful detection of airborne SARS-CoV-2 was recorded when 50 L/min air samplers were used. Upon increasing the sampling flowrate to 150 L/min, our results showed a high success rate in detecting the presence of SARS-CoV-2 from the air samples (72%) compared to the surface swab samples (9.6%). The positive detection rate of the air samples along with the corresponding viral load could be associated with the distance between sampling site and patient. The furthest distance from patient with PCR-positive air samples was 5.5 m. The airborne SARS-CoV-2 detection was comparable between the two types of wards with 60%-87.5% success rate. High prevalence of the virus was found in toilet areas, both on surfaces and in air. Finally, no successful culture attempt was recorded from the environmental air or surface samples.
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Affiliation(s)
- Alicia Xy Ang
- Department of Medicine, Division of Infectious Diseases, National University Hospital, Singapore, Singapore
| | - Irvan Luhung
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Bintou A Ahidjo
- Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore
- BSL3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Paul A Tambyah
- Department of Medicine, Division of Infectious Diseases, National University Hospital, Singapore, Singapore
- Department of Medicine, Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chee Keng Mok
- Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore
- BSL3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kenny Jx Lau
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sai Meng Tham
- Department of Medicine, Division of Infectious Diseases, National University Hospital, Singapore, Singapore
| | - Justin Jang Hann Chu
- Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore
- BSL3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - David M Allen
- Department of Medicine, Division of Infectious Diseases, National University Hospital, Singapore, Singapore
- Department of Medicine, Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
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9
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Lay C, Chu CW, Purbojati RW, Acerbi E, Drautz-Moses DI, de Sessions PF, Jie S, Ho E, Kok YJ, Bi X, Chen S, Mak SY, Chua MC, Goh AEN, Chiang WC, Rao R, Chaithongwongwatthana S, Khemapech N, Chongsrisawat V, Martin R, Roeselers G, Ho YS, Hibberd ML, Schuster SC, Knol J. A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants. BMC Microbiol 2021; 21:191. [PMID: 34172012 PMCID: PMC8229302 DOI: 10.1186/s12866-021-02230-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/17/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The compromised gut microbiome that results from C-section birth has been hypothesized as a risk factor for the development of non-communicable diseases (NCD). In a double-blind randomized controlled study, 153 infants born by elective C-section received an infant formula supplemented with either synbiotic, prebiotics, or unsupplemented from birth until 4 months old. Vaginally born infants were included as a reference group. Stool samples were collected from day 3 till week 22. Multi-omics were deployed to investigate the impact of mode of delivery and nutrition on the development of the infant gut microbiome, and uncover putative biological mechanisms underlying the role of a compromised microbiome as a risk factor for NCD. RESULTS As early as day 3, infants born vaginally presented a hypoxic and acidic gut environment characterized by an enrichment of strict anaerobes (Bifidobacteriaceae). Infants born by C-section presented the hallmark of a compromised microbiome driven by an enrichment of Enterobacteriaceae. This was associated with meta-omics signatures characteristic of a microbiome adapted to a more oxygen-rich gut environment, enriched with genes associated with reactive oxygen species metabolism and lipopolysaccharide biosynthesis, and depleted in genes involved in the metabolism of milk carbohydrates. The synbiotic formula modulated expression of microbial genes involved in (oligo)saccharide metabolism, which emulates the eco-physiological gut environment observed in vaginally born infants. The resulting hypoxic and acidic milieu prevented the establishment of a compromised microbiome. CONCLUSIONS This study deciphers the putative functional hallmarks of a compromised microbiome acquired during C-section birth, and the impact of nutrition that may counteract disturbed microbiome development. TRIAL REGISTRATION The study was registered in the Dutch Trial Register (Number: 2838 ) on 4th April 2011.
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Affiliation(s)
| | | | - Rikky Wenang Purbojati
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Enzo Acerbi
- Danone Nutricia Research, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | | | - Song Jie
- Genome Institute of Singapore, Singapore, Singapore
| | - Eliza Ho
- Genome Institute of Singapore, Singapore, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Xuezhi Bi
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Shi Ya Mak
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Mei Chien Chua
- KK Women's and Children's Hospital, Singapore, Singapore
| | - Anne E N Goh
- KK Women's and Children's Hospital, Singapore, Singapore
| | | | - Rajeshwar Rao
- KK Women's and Children's Hospital, Singapore, Singapore
| | | | - Nipon Khemapech
- King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Voranush Chongsrisawat
- King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rocio Martin
- Danone Nutricia Research, Utrecht, The Netherlands
| | | | - Ying Swan Ho
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Martin L Hibberd
- Genome Institute of Singapore, Singapore, Singapore
- London School of Hygiene and Tropical Medicine, London, UK
| | - Stephan C Schuster
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands.
- Wageningen University, Wageningen, The Netherlands.
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10
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Saini MK, Sebastian A, Shirotori Y, Soulier NT, Garcia Costas AM, Drautz-Moses DI, Schuster SC, Albert I, Haruta S, Hanada S, Thiel V, Tank M, Bryant DA. Genomic and Phenotypic Characterization of Chloracidobacterium Isolates Provides Evidence for Multiple Species. Front Microbiol 2021; 12:704168. [PMID: 34220789 PMCID: PMC8245765 DOI: 10.3389/fmicb.2021.704168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Chloracidobacterium is the first and until now the sole genus in the phylum Acidobacteriota (formerly Acidobacteria) whose members perform chlorophyll-dependent phototrophy (i.e., chlorophototrophy). An axenic isolate of Chloracidobacterium thermophilum (strain B T ) was previously obtained by using the inferred genome sequence from an enrichment culture and diel metatranscriptomic profiling analyses in situ to direct adjustments to the growth medium and incubation conditions, and thereby a defined growth medium for Chloracidobacterium thermophilum was developed. These advances allowed eight additional strains of Chloracidobacterium spp. to be isolated from microbial mat samples collected from Mushroom Spring, Yellowstone National Park, United States, at temperatures of 41, 52, and 60°C; an axenic strain was also isolated from Rupite hot spring in Bulgaria. All isolates are obligately photoheterotrophic, microaerophilic, non-motile, thermophilic, rod-shaped bacteria. Chloracidobacterium spp. synthesize multiple types of (bacterio-)chlorophylls and have type-1 reaction centers like those of green sulfur bacteria. Light harvesting is accomplished by the bacteriochlorophyll a-binding, Fenna-Matthews-Olson protein and chlorosomes containing bacteriochlorophyll c. Their genomes are approximately 3.7 Mbp in size and comprise two circular chromosomes with sizes of approximately 2.7 Mbp and 1.0 Mbp. Comparative genomic studies and phenotypic properties indicate that the nine isolates represent three species within the genus Chloracidobacterium. In addition to C. thermophilum, the microbial mats at Mushroom Spring contain a second species, tentatively named Chloracidobacterium aggregatum, which grows as aggregates in liquid cultures. The Bulgarian isolate, tentatively named Chloracidobacterium validum, will be proposed as the type species of the genus, Chloracidobacterium. Additionally, Chloracidobacterium will be proposed as the type genus of a new family, Chloracidobacteriaceae, within the order Blastocatellales, the class Blastocatellia, and the phylum Acidobacteriota.
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Affiliation(s)
- Mohit Kumar Saini
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Aswathy Sebastian
- The Huck Institutes for the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Yoshiki Shirotori
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Nathan T. Soulier
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Amaya M. Garcia Costas
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- Department of Biology, Colorado State University-Pueblo, Pueblo, CO, United States
| | - Daniela I. Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stephan C. Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Istvan Albert
- The Huck Institutes for the Life Sciences, The Pennsylvania State University, University Park, PA, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- DSMZ – German Culture Collection of Microorganisms and Cell Cultures, GmbH, Braunschweig, Germany
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- DSMZ – German Culture Collection of Microorganisms and Cell Cultures, GmbH, Braunschweig, Germany
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
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11
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Arumugam K, Bessarab I, Haryono MAS, Liu X, Zuniga-Montanez RE, Roy S, Qiu G, Drautz-Moses DI, Law YY, Wuertz S, Lauro FM, Huson DH, Williams RBH. Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing. NPJ Biofilms Microbiomes 2021; 7:23. [PMID: 33727564 PMCID: PMC7966762 DOI: 10.1038/s41522-021-00196-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/12/2021] [Indexed: 01/31/2023] Open
Abstract
New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an ensemble of activated sludge enrichment bioreactors we recover 22 closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses, specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Candidatus Accumulibacter and Dechloromonas, and Micropruina, Defluviicoccus and Candidatus Contendobacter, respectively), and filamentous bacteria (Thiothrix) associated with the formation and stability of activated sludge flocs. Additionally we demonstrate the recovery of close to 100 circularised plasmids, phages and small microbial genomes from these microbial communities using long read assembled sequence. We describe methods for validating long read assembled genomes using their counterpart short read metagenome-assembled genomes, and assess the influence of different correction procedures on genome quality and predicted gene quality. Our findings establish the feasibility of performing long read metagenome-assembled genome recovery for both chromosomal and non-chromosomal replicons, and demonstrate the value of parallel sampling of moderately complex enrichment communities to obtaining high quality reference genomes of key functional species relevant for wastewater bioprocesses.
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Affiliation(s)
- Krithika Arumugam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Mindia A S Haryono
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rogelio E Zuniga-Montanez
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Civil and Environmental Engineering, One Shields Avenue, University of California, Davis, CA, USA
| | - Samarpita Roy
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Guanglei Qiu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Environment and Energy, South China University of Technology, Guangzhou, China
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ying Yu Law
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| | - Federico M Lauro
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Daniel H Huson
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.
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12
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Premkrishnan BNV, Heinle CE, Uchida A, Purbojati RW, Kushwaha KK, Putra A, Santhi PS, Khoo BWY, Wong A, Vettath VK, Drautz-Moses DI, Junqueira ACM, Schuster SC. The genomic characterisation and comparison of Bacillus cereus strains isolated from indoor air. Gut Pathog 2021; 13:6. [PMID: 33516253 PMCID: PMC7847026 DOI: 10.1186/s13099-021-00399-4] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/15/2021] [Indexed: 12/22/2022] Open
Abstract
Background Bacillus cereus is ubiquitous in nature, found in environments such as soil, plants, air, and part of the insect and human gut microbiome. The ability to produce endospores and biofilms contribute to their pathogenicity, classified in two types of food poisoning: diarrheal and emetic syndromes. Here we report gap-free, whole-genome sequences of two B. cereus strains isolated from air samples and analyse their emetic and diarrheal potential. Results Genome assemblies of the B. cereus strains consist of one chromosome and seven plasmids each. The genome size of strain SGAir0260 is 6.30-Mb with 6590 predicted coding sequences (CDS) and strain SGAir0263 is 6.47-Mb with 6811 predicted CDS. Macrosynteny analysis showed 99% collinearity between the strains isolated from air and 90.2% with the reference genome. Comparative genomics with 57 complete B. cereus genomes suggests these strains from air are closely associated with strains isolated from foodborne illnesses outbreaks. Due to virulence potential of B. cereus and its reported involvement in nosocomial infections, antibiotic resistance analyses were performed and confirmed resistance to ampicillin and fosfomycin, with susceptibility to ciprofloxacin, tetracycline and vancomycin in both strains. Conclusion Phylogenetic analysis combined with detection of haemolytic (hblA, hblC, and hblD) and non-haemolytic (nheA, nheB, and nheC) enterotoxin genes in both air-isolated strains point to the diarrheic potential of the air isolates, though not emetic. Characterization of these airborne strains and investigation of their potential disease-causing genes could facilitate identification of environmental sources of contamination leading to foodborne illnesses and nosocomial infections transported by air.
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Affiliation(s)
- Balakrishnan N V Premkrishnan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Cassie E Heinle
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Akira Uchida
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rikky W Purbojati
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Kavita K Kushwaha
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Alexander Putra
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Puramadathil Sasi Santhi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Benjamin W Y Khoo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Anthony Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Vineeth Kodengil Vettath
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ana Carolina M Junqueira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
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13
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Gusareva ES, Gaultier NPE, Premkrishnan BNV, Kee C, Lim SBY, Heinle CE, Purbojati RW, Nee AP, Lohar SR, Yanqing K, Kharkov VN, Drautz-Moses DI, Stepanov VA, Schuster SC. Taxonomic composition and seasonal dynamics of the air microbiome in West Siberia. Sci Rep 2020; 10:21515. [PMID: 33299064 PMCID: PMC7726148 DOI: 10.1038/s41598-020-78604-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 07/16/2020] [Accepted: 11/24/2020] [Indexed: 12/18/2022] Open
Abstract
Here, we describe taxonomical composition, as well as seasonal and diel dynamics of airborne microbial communities in West Siberia. A total of 78 airborne biomass samples from 39 time intervals were analysed, within a temperature range of 48 °C (26 °C to - 22 °C). We observed a 5-170-fold decrease in DNA yield extracted from the airborne biomass in winter compared to summer, nevertheless, yielding sufficient material for metagenomic analysis. The airborne microbial communities included Actinobacteria and Proteobacteria, Ascomycota and Basidiomycota fungi as major components, as well as some Streptophyta plants. In summer, bacterial and fungal plant pathogens, and wood-rotting saprophytes were predominant. In winter, Ascomycota moulds and cold-related or stress environment bacterial species were enriched, while the fraction of wood-rotting and mushroom-forming Basidiomycota fungi was largely reduced. As recently reported for the tropical climate, the airborne microbial communities performed a diel cycle in summer, however, in winter diel dynamics were not observed.
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Affiliation(s)
- Elena S Gusareva
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Nicolas P E Gaultier
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Balakrishnan N V Premkrishnan
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Carmon Kee
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Serene Boon Yuean Lim
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Cassie E Heinle
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Rikky W Purbojati
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Ang Poh Nee
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Sachin R Lohar
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Koh Yanqing
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Vladimir N Kharkov
- Research Institute of Medical Genetics, Tomsk National Research Medical Centre, Russian Academy of Sciences, Tomsk, Russian Federation, 634050
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Vadim A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Centre, Russian Academy of Sciences, Tomsk, Russian Federation, 634050
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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14
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Mac Aogáin M, Lau KJX, Cai Z, Kumar Narayana J, Purbojati RW, Drautz-Moses DI, Gaultier NE, Jaggi TK, Tiew PY, Ong TH, Siyue Koh M, Lim Yick Hou A, Abisheganaden JA, Tsaneva-Atanasova K, Schuster SC, Chotirmall SH. Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease. Am J Respir Crit Care Med 2020; 202:433-447. [PMID: 32320621 PMCID: PMC7397787 DOI: 10.1164/rccm.201911-2202oc] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Rationale: Long-term antibiotic use for managing chronic respiratory disease is increasing; however, the role of the airway resistome and its relationship to host microbiomes remains unknown.Objectives: To evaluate airway resistomes and relate them to host and environmental microbiomes using ultradeep metagenomic shotgun sequencing.Methods: Airway specimens from 85 individuals with and without chronic respiratory disease (severe asthma, chronic obstructive pulmonary disease, and bronchiectasis) were subjected to metagenomic sequencing to an average depth exceeding 20 million reads. Respiratory and device-associated microbiomes were evaluated on the basis of taxonomical classification and functional annotation including the Comprehensive Antibiotic Resistance Database to determine airway resistomes. Co-occurrence networks of gene-microbe association were constructed to determine potential microbial sources of the airway resistome. Paired patient-inhaler metagenomes were compared (n = 31) to assess for the presence of airway-environment overlap in microbiomes and/or resistomes.Measurements and Main Results: Airway metagenomes exhibit taxonomic and metabolic diversity and distinct antimicrobial resistance patterns. A "core" airway resistome dominated by macrolide but with high prevalence of β-lactam, fluoroquinolone, and tetracycline resistance genes exists and is independent of disease status or antibiotic exposure. Streptococcus and Actinomyces are key potential microbial reservoirs of macrolide resistance including the ermX, ermF, and msrD genes. Significant patient-inhaler overlap in airway microbiomes and their resistomes is identified where the latter may be a proxy for airway microbiome assessment in chronic respiratory disease.Conclusions: Metagenomic analysis of the airway reveals a core macrolide resistome harbored by the host microbiome.
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Affiliation(s)
| | - Kenny J X Lau
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Zhao Cai
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | | | - Rikky W Purbojati
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Nicolas E Gaultier
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | | | - Pei Yee Tiew
- Lee Kong Chian School of Medicine and.,Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Thun How Ong
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Mariko Siyue Koh
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Albert Lim Yick Hou
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore; and
| | - John A Abisheganaden
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore; and
| | - Krasimira Tsaneva-Atanasova
- Department of Mathematics, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
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15
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Ta LDH, Chan JCY, Yap GC, Purbojati RW, Drautz-Moses DI, Koh YM, Tay CJX, Huang CH, Kioh DYQ, Woon JY, Tham EH, Loo EXL, Shek LP, Karnani N, Goh A, Van Bever HP, Teoh OH, Chan YH, Lay C, Knol J, Yap F, Tan KH, Chong YS, Godfrey KM, Kjelleberg S, Schuster SC, Chan ECY, Lee BW. A compromised developmental trajectory of the infant gut microbiome and metabolome in atopic eczema. Gut Microbes 2020; 12:1-22. [PMID: 33023370 PMCID: PMC7553750 DOI: 10.1080/19490976.2020.1801964] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Evidence is accumulating that the establishment of the gut microbiome in early life influences the development of atopic eczema. In this longitudinal study, we used integrated multi-omics analyses to infer functional mechanisms by which the microbiome modulates atopic eczema risk. We measured the functionality of the gut microbiome and metabolome of 63 infants between ages 3 weeks and 12 months with well-defined eczema cases and controls in a sub-cohort from the Growing Up in Singapore Toward healthy Outcomes (GUSTO) mother-offspring cohort. At 3 weeks, the microbiome and metabolome of allergen-sensitized atopic eczema infants were characterized by an enrichment of Escherichia coli and Klebsiella pneumoniae, associated with increased stool D-glucose concentration and increased gene expression of associated virulence factors. A delayed colonization by beneficial Bacteroides fragilis and subsequent delayed accumulation of butyrate and propionate producers after 3 months was also observed. Here, we describe an aberrant developmental trajectory of the gut microbiome and stool metabolome in allergen sensitized atopic eczema infants. The infographic describes an impaired developmental trajectory of the gut microbiome and metabolome in allergen-sensitized atopic eczema (AE) infants and infer its contribution in modulating allergy risk in the Singaporean mother-offspring GUSTO cohort. The key microbial signature of AE is characterized by (1) an enrichment of Escherichia coli and Klebsiella pneumoniae which are associated with accumulation of pre-glycolysis intermediates (D-glucose) via the trehalose metabolic pathway, increased gene expression of associated virulence factors (invasin, adhesin, flagellin and lipopolysaccharides) by utilizing ATP from oxidative phosphorylation and delayed production of butyrate and propionate, (2) depletion of Bacteroides fragilis which resulted in lower expression of immunostimulatory bacterial cell envelope structure and folate (vitamin B9) biosynthesis pathway, and (3) accompanied depletion of bacterial groups with the ability to derive butyrate and propionate through direct or indirect pathways which collectively resulted in reduced glycolysis, butyrate and propionate biosynthesis.
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Affiliation(s)
- Le Duc Huy Ta
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - James Chun Yip Chan
- Skin Research Institute of Singapore, A*STAR, Singapore,Innovations in Food & Chemical Safety Programme, A*STAR
| | - Gaik Chin Yap
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rikky W. Purbojati
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Daniela I. Drautz-Moses
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Yanqing Michelle Koh
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Carina Jing Xuan Tay
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chiung-Hui Huang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Dorinda Yan Qin Kioh
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore
| | - Jia Yun Woon
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore
| | - Elizabeth Huiwen Tham
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Khoo Teck Puat-National University Children’s Medical Institute, National University Health System, Singapore
| | - Evelyn Xiu Ling Loo
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lynette P.C. Shek
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Khoo Teck Puat-National University Children’s Medical Institute, National University Health System, Singapore
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Anne Goh
- Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore
| | - Hugo P.S. Van Bever
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Khoo Teck Puat-National University Children’s Medical Institute, National University Health System, Singapore
| | - Oon Hoe Teoh
- Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore
| | - Yiong Huak Chan
- Biostatistics Unit, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christophe Lay
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,Danone Nutricia Research, Singapore
| | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands,Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Fabian Yap
- Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore
| | - Kok Hian Tan
- Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore
| | - Yap-Seng Chong
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore,Department of Obstetrics & Gynaecology, National University of Singapore, Singapore
| | - Keith M. Godfrey
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Staffan Kjelleberg
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Stephan C. Schuster
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Eric Chun Yong Chan
- Innovations in Food & Chemical Safety Programme, A*STAR,Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore,Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore,Eric Chun Yong Chan Department of Paediatrics, National University of Singapore (NUS) Tahir Foundation Building (MD1), Level 15, 12 Science Drive 2, Singapore, Singapore 117549
| | - Bee Wah Lee
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,CONTACT Bee Wah Lee
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16
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Tiew PY, Ko FWS, Pang SL, Matta SA, Sio YY, Poh ME, Lau KJX, Mac Aogáin M, Jaggi TK, Ivan FX, Gaultier NE, Uchida A, Drautz-Moses DI, Xu H, Koh MS, Hui DSC, Tee A, Abisheganaden JA, Schuster SC, Chew FT, Chotirmall SH. Environmental fungal sensitisation associates with poorer clinical outcomes in COPD. Eur Respir J 2020; 56:13993003.00418-2020. [PMID: 32341102 PMCID: PMC7453645 DOI: 10.1183/13993003.00418-2020] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/15/2020] [Indexed: 01/26/2023]
Abstract
Introduction Allergic sensitisation to fungi such as Aspergillus are associated to poor clinical outcomes in asthma, bronchiectasis and cystic fibrosis; however, clinical relevance in COPD remains unclear. Methods Patients with stable COPD (n=446) and nondiseased controls (n=51) were prospectively recruited across three countries (Singapore, Malaysia and Hong Kong) and screened against a comprehensive allergen panel including house dust mites, pollens, cockroach and fungi. For the first time, using a metagenomics approach, we assessed outdoor and indoor environmental allergen exposure in COPD. We identified key fungi in outdoor air and developed specific-IgE assays against the top culturable fungi, linking sensitisation responses to COPD outcomes. Indoor air and surface allergens were prospectively evaluated by metagenomics in the homes of 11 COPD patients and linked to clinical outcome. Results High frequencies of sensitisation to a broad range of allergens occur in COPD. Fungal sensitisation associates with frequent exacerbations, and unsupervised clustering reveals a “highly sensitised fungal predominant” subgroup demonstrating significant symptomatology, frequent exacerbations and poor lung function. Outdoor and indoor environments serve as important reservoirs of fungal allergen exposure in COPD and promote a sensitisation response to outdoor air fungi. Indoor (home) environments with high fungal allergens associate with greater COPD symptoms and poorer lung function, illustrating the importance of environmental exposures on clinical outcomes in COPD. Conclusion Fungal sensitisation is prevalent in COPD and associates with frequent exacerbations representing a potential treatable trait. Outdoor and indoor (home) environments represent a key source of fungal allergen exposure, amenable to intervention, in “sensitised” COPD. Fungal sensitisation associates with frequent exacerbations in COPD, and represents a treatable trait. Outdoor and indoor environments represent a key source of fungal allergen exposure, amenable to intervention, in “sensitised” COPD patients.https://bit.ly/2Vw3kHi
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Affiliation(s)
- Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Dept of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Fanny Wai San Ko
- Dept of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Sze Lei Pang
- Dept of Biological Sciences, National University of Singapore, Singapore
| | - Sri Anusha Matta
- Dept of Biological Sciences, National University of Singapore, Singapore
| | - Yang Yie Sio
- Dept of Biological Sciences, National University of Singapore, Singapore
| | - Mau Ern Poh
- Dept of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kenny J X Lau
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Micheál Mac Aogáin
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Nicolas E Gaultier
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Akira Uchida
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Huiying Xu
- Dept of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Mariko Siyue Koh
- Dept of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - David Shu Cheong Hui
- Dept of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Augustine Tee
- Dept of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore
| | | | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Fook Tim Chew
- Dept of Biological Sciences, National University of Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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17
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Loo EXL, Zain A, Yap GC, Purbojati RW, Drautz-Moses DI, Koh YQ, Chong YS, Tan KH, Gluckman PD, Yap F, Eriksson JG, Tham E, Shek LPC, Kjelleberg S, Schuster SC, Banerjee R, Lee BW. Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema. BMC Infect Dis 2020; 20:312. [PMID: 32345218 PMCID: PMC7189448 DOI: 10.1186/s12879-020-05000-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/29/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND While there is increasing knowledge about the gut microbiome, the factors influencing and the significance of the gut resistome are still not well understood. Infant gut commensals risk transferring multidrug-resistant antibiotic resistance genes (ARGs) to pathogenic bacteria. The rapid spread of multidrug-resistant pathogenic bacteria is a worldwide public health concern. Better understanding of the naïve infant gut resistome may build the evidence base for antimicrobial stewardship in both humans and in the food industry. Given the high carriage rate of extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in Asia, we aimed to evaluate community prevalence, dynamics, and longitudinal changes in antibiotic resistance gene (ARG) profiles and prevalence of ESBL-producing E. coli and K. pneumoniae in the intestinal microbiome of infants participating in the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) study, a longitudinal cohort study of pregnant women and their infants. METHODS We analysed ARGs in the first year of life among 75 infants at risk of eczema who had stool samples collected at multiple timepoints using metagenomics. RESULTS The mean number of ARGs per infant increased with age. The most common ARGs identified confer resistance to aminoglycoside, beta-lactam, macrolide and tetracycline antibiotics; all infants harboured these antibiotic resistance genes at some point in the first year of life. Few ARGs persisted throughout the first year of life. Beta-lactam resistant Escherichia coli and Klebsiella pneumoniae were detected in 4 (5.3%) and 32 (42.7%) of subjects respectively. CONCLUSION In this longitudinal cohort study of infants living in a region with high endemic antibacterial resistance, we demonstrate that majority of the infants harboured several antibiotic resistance genes in their gut and showed that the infant gut resistome is diverse and dynamic over the first year of life.
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Affiliation(s)
- Evelyn Xiu Ling Loo
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Amanda Zain
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
| | - Gaik Chin Yap
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rikky W Purbojati
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Yan Qing Koh
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Kok Hian Tan
- Department of Maternal Fetal Medicine, KK Women's and Children's Hospital (KKH), Singapore, Singapore
| | - Peter D Gluckman
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Fabian Yap
- Department of Endocrinology KK Women's and Children's Hospital (KKH), Singapore, Singapore
| | - Johan Gunnar Eriksson
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Elizabeth Tham
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
| | - Lynette Pei-Chi Shek
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Stephan C Schuster
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Ritu Banerjee
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bee Wah Lee
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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18
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Gupta AB, Gaultier NE, Aung NW, Purbojati RW, Oliveira EL, Wong A, Panicker D, Putra A, Uchida A, Drautz-Moses DI, Schuster SC. Complete Genome Sequence of Penicillium oxalicum Strain SGAir0226 Isolated from Outdoor Tropical Air in Singapore. Mycopathologia 2020; 185:591-594. [PMID: 32270395 DOI: 10.1007/s11046-019-00422-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 10/22/2019] [Accepted: 12/20/2019] [Indexed: 11/28/2022]
Abstract
Penicillium oxalicum strain SGAir0226 was isolated from a tropical air sample collected in Singapore. The complete genome was assembled from long reads obtained from single-molecule real-time sequencing and was further polished and error corrected using short read sequencing data. The assembly comprises 20 contigs with a total length of 30.7 Mb. The genome was predicted to contain 8310 protein-coding genes, 237 tRNAs and 83 rRNAs.
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Affiliation(s)
- Anjali Bansal Gupta
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Nicolas E Gaultier
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Ngu War Aung
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Rikky W Purbojati
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Elaine L Oliveira
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Anthony Wong
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Deepa Panicker
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Alexander Putra
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Akira Uchida
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Stephan C Schuster
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore.
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19
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Palanivel M, Mac Aogáin M, Purbojati RW, Uchida A, Aung NW, Lim SBY, Putra A, Drautz-Moses DI, Seaton S, Rogers TR, Schuster SC, Chotirmall SH. Whole-Genome Sequencing of Aspergillus terreus Species Complex. Mycopathologia 2020; 185:405-408. [PMID: 32108289 DOI: 10.1007/s11046-020-00433-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 09/23/2019] [Accepted: 02/07/2020] [Indexed: 02/07/2023]
Abstract
Aspergillus terreus species complex is an opportunistic fungal pathogen increasingly implicated in invasive infection, as well as chronic respiratory disease. Currently, an understanding of A. terreus pathogenicity is impeded by a limited number of whole-genome sequences of this fungal pathogen. We here describe a high-quality whole-genome assembly of European A. terreus clinical isolate M6925, derived by single-molecule real-time sequencing with short-read polishing.
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Affiliation(s)
- Mathangi Palanivel
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Micheál Mac Aogáin
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Rikky W Purbojati
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Akira Uchida
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ngu War Aung
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Serene B Y Lim
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Alexander Putra
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Shila Seaton
- UK NEQAS for Microbiology, Products and Services, National Infection Service, Public Health England, London, UK
| | - Thomas R Rogers
- Department of Clinical Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore.
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20
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Uchida A, Kim HL, Purbojati RW, Vettath VK, Gupta AB, Houghton JNI, Chénard C, Wong A, Clare ME, Kushwaha KK, Panicker D, Putra A, Heinle CE, Premkrishnan BNV, Junqueira ACM, Drautz-Moses DI, Schuster SC. Complete genome of Enterobacter sichuanensis strain SGAir0282 isolated from air in Singapore. Gut Pathog 2020; 12:12. [PMID: 32127921 PMCID: PMC7045367 DOI: 10.1186/s13099-020-00350-z] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/15/2020] [Indexed: 03/12/2023] Open
Abstract
Background Enterobacter cloacae complex (ECC) bacteria, such as E. cloacae, E. sichuanensis, E. kobei, and E. roggenkampii, have been emerging as nosocomial pathogens. Many strains isolated from medical clinics were found to be resistant to antibiotics, and in the worst cases, acquired multidrug resistance. We present the whole genome sequence of SGAir0282, isolated from the outdoor air in Singapore, and its relevance to other ECC bacteria by in silico genomic analysis. Results Complete genome assembly of E. sichuanensis strain SGAir0282 was generated using PacBio RSII and Illumina MiSeq platforms, and the datasets were used for de novo assembly using Hierarchical Genome Assembly Process (HGAP) and error corrected with Pilon. The genome assembly consisted of a single contig of 4.71 Mb and with a G+C content of 55.5%. No plasmid was detected in the assembly. The genome contained 4371 coding genes, 83 tRNA and 25 rRNA genes, as predicted by NCBI's Prokaryotic Genome Annotation Pipeline (PGAP). Among the genes, the antibiotic resistance related genes were included: Streptothricin acetdyltransferase (SatA), fosfomycin resistance protein (FosA) and metal-dependent hydrolases of the beta-lactamase superfamily I (BLI). Conclusion Based on whole genome alignment and phylogenetic analysis, the strain SGAir0282 was identified to be Enterobacter sichuanensis. The strain possesses gene clusters for virulence, disease and defence, that can also be found in other multidrug resistant ECC type strains.
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Affiliation(s)
- Akira Uchida
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Hie Lim Kim
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,2Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Rikky W Purbojati
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Vineeth Kodengil Vettath
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Anjali B Gupta
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - James N I Houghton
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Caroline Chénard
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Anthony Wong
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Megan E Clare
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Kavita K Kushwaha
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Deepa Panicker
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Alexander Putra
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Cassie E Heinle
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Balakrishnan N V Premkrishnan
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ana Carolina M Junqueira
- 3Departamento de Genética, Instituto de Biologia, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daniela I Drautz-Moses
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stephan C Schuster
- 1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,4School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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21
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Kundu P, Lee HU, Garcia-Perez I, Tay EXY, Kim H, Faylon LE, Martin KA, Purbojati R, Drautz-Moses DI, Ghosh S, Nicholson JK, Schuster S, Holmes E, Pettersson S. Neurogenesis and prolongevity signaling in young germ-free mice transplanted with the gut microbiota of old mice. Sci Transl Med 2019; 11:11/518/eaau4760. [DOI: 10.1126/scitranslmed.aau4760] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 02/11/2019] [Accepted: 05/20/2019] [Indexed: 12/12/2022]
Abstract
The gut microbiota evolves as the host ages, yet the effects of these microbial changes on host physiology and energy homeostasis are poorly understood. To investigate these potential effects, we transplanted the gut microbiota of old or young mice into young germ-free recipient mice. Both groups showed similar weight gain and skeletal muscle mass, but germ-free mice receiving a gut microbiota transplant from old donor mice unexpectedly showed increased neurogenesis in the hippocampus of the brain and increased intestinal growth. Metagenomic analysis revealed age-sensitive enrichment in butyrate-producing microbes in young germ-free mice transplanted with the gut microbiota of old donor mice. The higher concentration of gut microbiota–derived butyrate in these young transplanted mice was associated with an increase in the pleiotropic and prolongevity hormone fibroblast growth factor 21 (FGF21). An increase in FGF21 correlated with increased AMPK and SIRT-1 activation and reduced mTOR signaling. Young germ-free mice treated with exogenous sodium butyrate recapitulated the prolongevity phenotype observed in young germ-free mice receiving a gut microbiota transplant from old donor mice. These results suggest that gut microbiota transplants from aged hosts conferred beneficial effects in responsive young recipients.
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Affiliation(s)
- Parag Kundu
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore
- The Center for Microbes, Development and Health, Key Laboratory for Microbiota-Host Interactions, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hae Ung Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Isabel Garcia-Perez
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Sir Alexander Fleming Building, Imperial College London, SW72AZ London, UK
| | - Emmy Xue Yun Tay
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117557, Singapore
| | - Hyejin Kim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Llanto Elma Faylon
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore
| | - Katherine A. Martin
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Rikky Purbojati
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore
| | | | - Sujoy Ghosh
- Duke-NUS Medical School, Singapore 169857, Singapore
- National Heart Research Institute, Singapore 169609, Singapore
- Penningtion Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Jeremy K. Nicholson
- Australian National Phenome Center, Murdoch University Perth, Perth, Western Australia, WA6150 Australia
| | - Stephan Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore
| | - Elaine Holmes
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Sir Alexander Fleming Building, Imperial College London, SW72AZ London, UK
- UK Dementia Research Institute at Imperial College London, Burlington Danes Building, Hammersmith Hospital, London, W12 0NN, UK
| | - Sven Pettersson
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore
- Department of Neurobiology, Care Sciences and Society, Karolinska Institute, SE 17 177 Stockholm, Sweden
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22
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Zhou L, Ng HK, Drautz-Moses DI, Schuster SC, Beck S, Kim C, Chambers JC, Loh M. Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing. Sci Rep 2019; 9:10383. [PMID: 31316107 PMCID: PMC6637168 DOI: 10.1038/s41598-019-46875-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [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: 07/05/2019] [Accepted: 07/05/2019] [Indexed: 01/30/2023] Open
Abstract
Whole genome bisulfite sequencing (WGBS), with its ability to interrogate methylation status at single CpG site resolution epigenome-wide, is a powerful technique for use in molecular experiments. Here, we aim to advance strategies for accurate and efficient WGBS for application in future large-scale epidemiological studies. We systematically compared the performance of three WGBS library preparation methods with low DNA input requirement (Swift Biosciences Accel-NGS, Illumina TruSeq and QIAGEN QIAseq) on two state-of-the-art sequencing platforms (Illumina NovaSeq and HiSeq X), and also assessed concordance between data generated by WGBS and methylation arrays. Swift achieved the highest proportion of CpG sites assayed and effective coverage at 26x (P < 0.001). TruSeq suffered from the highest proportion of PCR duplicates, while QIAseq failed to deliver across all quality metrics. There was little difference in performance between NovaSeq and HiSeq X, with the exception of higher read duplication rate on the NovaSeq (P < 0.05), likely attributable to the higher cluster densities on its flow cells. Systematic biases exist between WGBS and methylation arrays, with lower precision observed for WGBS across the range of depths investigated. To achieve a level of precision broadly comparable to the methylation array, a minimum coverage of 100x is recommended.
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Affiliation(s)
- Li Zhou
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Hong Kiat Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Stephan Beck
- University College London Cancer Institute, London, WC1E 6BT, United Kingdom
| | | | - John Campbell Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.,Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, United Kingdom.,Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Southall, UB1 3HW, United Kingdom.,Imperial College Healthcare NHS Trust, London, W12 0HS, United Kingdom
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore. .,Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, United Kingdom. .,Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore.
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23
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Guo S, Tay MY, Aung KT, Seow KL, Ng LC, Purbojati RW, Drautz-Moses DI, Schuster SC, Schlundt J. Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.12.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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24
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Yuan M, Chua SL, Liu Y, Drautz-Moses DI, Yam JKH, Aung TT, Beuerman RW, Salido MMS, Schuster SC, Tan CH, Givskov M, Yang L, Nielsen TE. Repurposing the anticancer drug cisplatin with the aim of developing novel Pseudomonas aeruginosa infection control agents. Beilstein J Org Chem 2018; 14:3059-3069. [PMID: 30591828 PMCID: PMC6296412 DOI: 10.3762/bjoc.14.284] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/02/2018] [Indexed: 12/29/2022] Open
Abstract
Antibiotic resistance threatens effective treatment of microbial infections globally. This situation has spurred the hunt for new antimicrobial compounds in both academia and the pharmaceutical industry. Here, we report how the widely used antitumor drug cisplatin may be repurposed as an effective antimicrobial against the nosocomial pathogen Pseudomonas aeruginosa. Cisplatin was found to effectively kill strains of P. aeruginosa. In such experiments, transcriptomic profiling showed upregulation of the recA gene, which is known to be important for DNA repair, implicating that cisplatin could interfere with DNA replication in P. aeruginosa. Cisplatin treatment significantly repressed the type III secretion system (T3SS), which is important for the secretion of exotoxins. Furthermore, cisplatin was also demonstrated to eradicate in vitro biofilms and in vivo biofilms in a murine keratitis model. This showed that cisplatin could be effectively used to eradicate biofilm infections which were otherwise difficult to be treated by conventional antibiotics. Although cisplatin is highly toxic for humans upon systemic exposure, a low toxicity was demonstrated with topical treatment. This indicated that higher-than-minimal inhibitory concentration (MIC) doses of cisplatin could be topically applied to treat persistent and recalcitrant P. aeruginosa infections.
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Affiliation(s)
- Mingjun Yuan
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Song Lin Chua
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 639798
| | - Yang Liu
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Thet Tun Aung
- School of Biological Sciences, Nanyang Technological University, Singapore 639798.,Singapore Eye Research Institute, Singapore 169879
| | - Roger W Beuerman
- Singapore Eye Research Institute, Singapore 169879.,SRP Neuroscience and Behavioural Disorders and Emerging Infectious Diseases, Duke-NUS, Singapore 169857.,Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 168751
| | | | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.,School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Choon-Hong Tan
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Michael Givskov
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.,Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, 2200 København N, Denmark
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.,School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Thomas E Nielsen
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.,Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, 2200 København N, Denmark
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25
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Wang K, Chen YQ, Salido MM, Kohli GS, Kong JL, Liang HJ, Yao ZT, Xie YT, Wu HY, Cai SQ, Drautz-Moses DI, Darling AE, Schuster SC, Yang L, Ding Y. The rapid in vivo evolution of Pseudomonas aeruginosa in ventilator-associated pneumonia patients leads to attenuated virulence. Open Biol 2018; 7:rsob.170029. [PMID: 28878043 PMCID: PMC5627047 DOI: 10.1098/rsob.170029] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 07/26/2017] [Indexed: 01/15/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes severe airway infections in humans. These infections are usually difficult to treat and associated with high mortality rates. While colonizing the human airways, P. aeruginosa could accumulate genetic mutations that often lead to its better adaptability to the host environment. Understanding these evolutionary traits may provide important clues for the development of effective therapies to treat P. aeruginosa infections. In this study, 25 P. aeruginosa isolates were longitudinally sampled from the airways of four ventilator-associated pneumonia (VAP) patients. Pacbio and Illumina sequencing were used to analyse the in vivo evolutionary trajectories of these isolates. Our analysis showed that positive selection dominantly shaped P. aeruginosa genomes during VAP infections and led to three convergent evolution events, including loss-of-function mutations of lasR and mpl, and a pyoverdine-deficient phenotype. Specifically, lasR encodes one of the major transcriptional regulators in quorum sensing, whereas mpl encodes an enzyme responsible for recycling cell wall peptidoglycan. We also found that P. aeruginosa isolated at late stages of VAP infections produce less elastase and are less virulent in vivo than their earlier isolated counterparts, suggesting the short-term in vivo evolution of P. aeruginosa leads to attenuated virulence.
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Affiliation(s)
- Ke Wang
- Department of Respiratory Disease, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China.,Centre for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Yi-Qiang Chen
- Department of Respiratory Disease, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - May M Salido
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore
| | - Gurjeet S Kohli
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore
| | - Jin-Liang Kong
- Department of Respiratory Disease, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Hong-Jie Liang
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Zi-Ting Yao
- Centre for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Yan-Tong Xie
- The First Clinical School of Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Hua-Yu Wu
- Department of Cell Biology and Genetics, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Shuang-Qi Cai
- Department of Respiratory Disease, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore
| | - Aaron E Darling
- The ithree Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yichen Ding
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore .,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.,Interdisciplinary Graduate School, SCELSE, Nanyang Technological University, Singapore 639798, Singapore
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26
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Junqueira ACM, Ratan A, Acerbi E, Drautz-Moses DI, Premkrishnan BNV, Costea PI, Linz B, Purbojati RW, Paulo DF, Gaultier NE, Subramanian P, Hasan NA, Colwell RR, Bork P, Azeredo-Espin AML, Bryant DA, Schuster SC. The microbiomes of blowflies and houseflies as bacterial transmission reservoirs. Sci Rep 2017; 7:16324. [PMID: 29176730 PMCID: PMC5701178 DOI: 10.1038/s41598-017-16353-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/10/2017] [Indexed: 12/25/2022] Open
Abstract
Blowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed and breed in fecal and decaying organic matter, but the microbiome they harbour and transport is largely uncharacterized. We sampled 116 individual houseflies and blowflies from varying habitats on three continents and subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic and metagenomic analyses of the host-associated microbiome at the species level. Both fly host species segregate based on principal coordinate analysis of their microbial communities, but they also show an overlapping core microbiome. Legs and wings displayed the largest microbial diversity and were shown to be an important route for microbial dispersion. The environmental sequencing approach presented here detected a stochastic distribution of human pathogens, such as Helicobacter pylori, thereby demonstrating the potential of flies as proxies for environmental and public health surveillance.
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Affiliation(s)
- Ana Carolina M Junqueira
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil.
| | - Aakrosh Ratan
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Enzo Acerbi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Balakrishnan N V Premkrishnan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Paul I Costea
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, 69117, Germany
| | - Bodo Linz
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, 30602, GA, USA
| | - Rikky W Purbojati
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Daniel F Paulo
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil
| | - Nicolas E Gaultier
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | | | - Nur A Hasan
- CosmosID Inc, Rockville, MD, 20850, USA
- Center for Bioinformatics and Computational Biology, University of Maryland. Institute for Computational Biology, University of Maryland College Park, College Park, MD, 20742, USA
| | - Rita R Colwell
- CosmosID Inc, Rockville, MD, 20850, USA
- Center for Bioinformatics and Computational Biology, University of Maryland. Institute for Computational Biology, University of Maryland College Park, College Park, MD, 20742, USA
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, 69117, Germany
| | - Ana Maria L Azeredo-Espin
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil
| | - Donald A Bryant
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
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27
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Chua SL, Ding Y, Liu Y, Cai Z, Zhou J, Swarup S, Drautz-Moses DI, Schuster SC, Kjelleberg S, Givskov M, Yang L. Reactive oxygen species drive evolution of pro-biofilm variants in pathogens by modulating cyclic-di-GMP levels. Open Biol 2017; 6:rsob.160162. [PMID: 27881736 PMCID: PMC5133437 DOI: 10.1098/rsob.160162] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 10/23/2016] [Indexed: 12/14/2022] Open
Abstract
The host immune system offers a hostile environment with antimicrobials and reactive oxygen species (ROS) that are detrimental to bacterial pathogens, forcing them to adapt and evolve for survival. However, the contribution of oxidative stress to pathogen evolution remains elusive. Using an experimental evolution strategy, we show that exposure of the opportunistic pathogen Pseudomonas aeruginosa to sub-lethal hydrogen peroxide (H2O2) levels over 120 generations led to the emergence of pro-biofilm rough small colony variants (RSCVs), which could be abrogated by l-glutathione antioxidants. Comparative genomic analysis of the RSCVs revealed that mutations in the wspF gene, which encodes for a repressor of WspR diguanylate cyclase (DGC), were responsible for increased intracellular cyclic-di-GMP content and production of Psl exopolysaccharide. Psl provides the first line of defence against ROS and macrophages, ensuring the survival fitness of RSCVs over wild-type P. aeruginosa Our study demonstrated that ROS is an essential driving force for the selection of pro-biofilm forming pathogenic variants. Understanding the fundamental mechanism of these genotypic and phenotypic adaptations will improve treatment strategies for combating chronic infections.
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Affiliation(s)
- Song Lin Chua
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 639798 .,Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Yichen Ding
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.,Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551
| | - Yang Liu
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Zhao Cai
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.,Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551
| | - Jianuan Zhou
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Sanjay Swarup
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.,Department of Biological Sciences, National University of Singapore, Singapore 117543.,NUS Environmental Research Institute, National University of Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Stephan Christoph Schuster
- School of Biological Sciences, Nanyang Technological University, Singapore 639798.,Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.,Center for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia
| | - Michael Givskov
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.,Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, 2200 København N, Denmark
| | - Liang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore 639798 .,Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
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28
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Chua SL, Ding Y, Liu Y, Cai Z, Zhou J, Swarup S, Drautz-Moses DI, Schuster SC, Kjelleberg S, Givskov M, Yang L. Correction to 'Reactive oxygen species drive evolution of pro-biofilm variants in pathogens by modulating cyclic-di-GMP levels'. Open Biol 2017; 7:rsob.170197. [PMID: 28954819 PMCID: PMC5627059 DOI: 10.1098/rsob.170197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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29
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Harmon M, Lane T, Staton M, Coggeshall MV, Best T, Chen CC, Liang H, Zembower N, Drautz-Moses DI, Hwee YZ, Schuster SC, Schlarbaum SE, Carlson JE, Gailing O. Development of novel genic microsatellite markers from transcriptome sequencing in sugar maple (Acer saccharum Marsh.). BMC Res Notes 2017; 10:369. [PMID: 28789702 PMCID: PMC5549316 DOI: 10.1186/s13104-017-2653-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 07/21/2017] [Indexed: 11/20/2022] Open
Abstract
Background
Sugar maple (Acer saccharum Marsh.) is a hardwood tree species native to northeastern North America and economically valued for its wood and sap. Yet, few molecular genetic resources have been developed for this species to date. Microsatellite markers have been a useful tool in population genetics, e.g., to monitor genetic variation and to analyze gene flow patterns. The objective of this study is to develop a reference transcriptome and microsatellite markers in sugar maple. Findings A set of 117,861 putative unique transcripts were assembled using 29.2 Gb of RNA sequencing data derived from different tissues and stress treatments. From this set of sequences a total of 1068 microsatellite motifs were identified. Out of 58 genic microsatellite markers tested on a population of 47 sugar maple trees in upper Michigan, 22 amplified well, of which 16 were polymorphic and 6 were monomorphic. Values for expected heterozygosity varied from 0.224 to 0.726 for individual loci. Of the 16 polymorphic markers, 15 exhibited transferability to other Acer L. species. Conclusions Genic microsatellite markers can be applied to analyze genetic variation in potentially adaptive genes relative to genomic reference markers as a basis for the management of sugar maple genetic resources in the face of climate change. Electronic supplementary material The online version of this article (doi:10.1186/s13104-017-2653-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Monica Harmon
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Thomas Lane
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Margaret Staton
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Mark V Coggeshall
- Department of Forestry, University of Missouri, Columbia, MO, 65274, USA
| | - Teodora Best
- Department of Ecosystem Science and Management and Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Chien-Chih Chen
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29630, USA.,College of Agriculture, Fisheries and Forestry, Fiji National University, Nausori, Fiji
| | - Haiying Liang
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29630, USA
| | - Nicole Zembower
- Department of Ecosystem Science and Management and Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Yap Zhei Hwee
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Scott E Schlarbaum
- Department of Forestry, Wildlife & Fisheries, The University of Tennessee, Knoxville, TN, 37996-4563, USA
| | - John E Carlson
- Department of Ecosystem Science and Management and Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Oliver Gailing
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA. .,Forest Genetics and Forest Tree Breeding, Faculty of Forest Sciences, University of Goettingen, Buesgenweg 2, 37077, Goettingen, Germany.
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30
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Acerbi E, Chénard C, Miller D, Gaultier NE, Heinle CE, Chang VWC, Uchida A, Drautz-Moses DI, Schuster SC, Lauro FM. Ecological succession of the microbial communities of an air-conditioning cooling coil in the tropics. Indoor Air 2017; 27:345-353. [PMID: 27120709 DOI: 10.1111/ina.12306] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/22/2016] [Indexed: 06/05/2023]
Abstract
Air-conditioning systems harbor microorganisms, potentially spreading them to indoor environments. While air and surfaces in air-conditioning systems are periodically sampled as potential sources of indoor microbes, little is known about the dynamics of cooling coil-associated communities and their effect on the downstream airflow. Here, we conducted a 4-week time series sampling to characterize the succession of an air-conditioning duct and cooling coil after cleaning. Using an universal primer pair targeting hypervariable regions of the 16S/18S ribosomal RNA, we observed a community succession for the condensed water, with the most abundant airborne taxon Agaricomycetes fungi dominating the initial phase and Sphingomonas bacteria becoming the most prevalent taxa toward the end of the experiment. Duplicate air samples collected upstream and downstream of the coil suggest that the system does not act as ecological filter or source/sink for specific microbial taxa during the duration of the experiment.
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Affiliation(s)
- E Acerbi
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - C Chénard
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - D Miller
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - N E Gaultier
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - C E Heinle
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - V W-C Chang
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| | - A Uchida
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - D I Drautz-Moses
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - S C Schuster
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - F M Lauro
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
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Carpi G, Kitchen A, Kim HL, Ratan A, Drautz-Moses DI, McGraw JJ, Kazimirova M, Rizzoli A, Schuster SC. Mitogenomes reveal diversity of the European Lyme borreliosis vector Ixodes ricinus in Italy. Mol Phylogenet Evol 2016; 101:194-202. [DOI: 10.1016/j.ympev.2016.05.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 05/02/2016] [Accepted: 05/04/2016] [Indexed: 01/04/2023]
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Welch AJ, Collins K, Ratan A, Drautz-Moses DI, Schuster SC, Lindqvist C. Data characterizing the chloroplast genomes of extinct and endangered Hawaiian endemic mints (Lamiaceae) and their close relatives. Data Brief 2016; 7:900-22. [PMID: 27077093 PMCID: PMC4816906 DOI: 10.1016/j.dib.2016.03.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/05/2016] [Accepted: 03/07/2016] [Indexed: 11/22/2022] Open
Abstract
These data are presented in support of a plastid phylogenomic analysis of the recent radiation of the Hawaiian endemic mints (Lamiaceae), and their close relatives in the genus Stachys, "The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)" [1]. Here we describe the chloroplast genome sequences for 12 mint taxa. Data presented include summaries of gene content and length for these taxa, structural comparison of the mint chloroplast genomes with published sequences from other species in the order Lamiales, and comparisons of variability among three Hawaiian taxa vs. three outgroup taxa. Finally, we provide a list of 108 primer pairs targeting the most variable regions within this group and designed specifically for amplification of DNA extracted from degraded herbarium material.
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Affiliation(s)
- Andreanna J. Welch
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA
- Corresponding author at: School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK.School of Biological and Biomedical Sciences, Durham University, South RoadDurhamDH1 3LEUK
| | - Katherine Collins
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA
| | - Aakrosh Ratan
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville 22908, VA, USA
| | - Daniela I. Drautz-Moses
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Stephan C. Schuster
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA
- Corresponding author at: Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY, 14260, USA.Department of Biological Sciences, University at Buffalo (SUNY)BuffaloNY14260USA
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Junqueira ACM, Azeredo-Espin AML, Paulo DF, Marinho MAT, Tomsho LP, Drautz-Moses DI, Purbojati RW, Ratan A, Schuster SC. Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity. Sci Rep 2016; 6:21762. [PMID: 26912394 PMCID: PMC4766414 DOI: 10.1038/srep21762] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/28/2016] [Indexed: 11/21/2022] Open
Abstract
True flies are insects of the order Diptera and encompass one of the most diverse groups of animals on Earth. Within dipterans, Schizophora represents a recent radiation of insects that was used as a model to develop a pipeline for generating complete mitogenomes using various sequencing platforms and strategies. 91 mitogenomes from 32 different species were sequenced and assembled with high fidelity, using amplicon, whole genome shotgun or single molecule sequencing approaches. Based on the novel mitogenomes, we estimate the origin of Schizophora within the Cretaceous-Paleogene (K-Pg) boundary, about 68.3 Ma. Detailed analyses of the blowfly family (Calliphoridae) place its origin at 22 Ma, concomitant with the radiation of grazing mammals. The emergence of ectoparasitism within calliphorids was dated 6.95 Ma for the screwworm fly and 2.3 Ma for the Australian sheep blowfly. Varying population histories were observed for the blowfly Chrysomya megacephala and the housefly Musca domestica samples in our dataset. Whereas blowflies (n = 50) appear to have undergone selective sweeps and/or severe bottlenecks in the New World, houseflies (n = 14) display variation among populations from different zoogeographical zones and low levels of gene flow. The reported high-throughput mitogenomics approach for insects enables new insights into schizophoran diversity and population history of flies.
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Affiliation(s)
- Ana Carolina M. Junqueira
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551
| | - Ana Maria L. Azeredo-Espin
- Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil
| | - Daniel F. Paulo
- Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil
| | - Marco Antonio T. Marinho
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Biologia, Universidade de São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
| | - Lynn P. Tomsho
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Daniela I. Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551
| | - Rikky W. Purbojati
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551
| | - Aakrosh Ratan
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Stephan C. Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551
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Mitra S, Drautz-Moses DI, Alhede M, Maw MT, Liu Y, Purbojati RW, Yap ZH, Kushwaha KK, Gheorghe AG, Bjarnsholt T, Hansen GM, Sillesen HH, Hougen HP, Hansen PR, Yang L, Tolker-Nielsen T, Schuster SC, Givskov M. In silico analyses of metagenomes from human atherosclerotic plaque samples. Microbiome 2015; 3:38. [PMID: 26334731 PMCID: PMC4559171 DOI: 10.1186/s40168-015-0100-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/12/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND Through several observational and mechanistic studies, microbial infection is known to promote cardiovascular disease. Direct infection of the vessel wall, along with the cardiovascular risk factors, is hypothesized to play a key role in the atherogenesis by promoting an inflammatory response leading to endothelial dysfunction and generating a proatherogenic and prothrombotic environment ultimately leading to clinical manifestations of cardiovascular disease, e.g., acute myocardial infarction or stroke. There are many reports of microbial DNA isolation and even a few studies of viable microbes isolated from human atherosclerotic vessels. However, high-resolution investigation of microbial infectious agents from human vessels that may contribute to atherosclerosis is very limited. In spite of the progress in recent sequencing technologies, analyzing host-associated metagenomes remain a challenge. RESULTS To investigate microbiome diversity within human atherosclerotic tissue samples, we employed high-throughput metagenomic analysis on: (1) atherosclerotic plaques obtained from a group of patients who underwent endarterectomy due to recent transient cerebral ischemia or stroke. (2) Presumed stabile atherosclerotic plaques obtained from autopsy from a control group of patients who all died from causes not related to cardiovascular disease. Our data provides evidence that suggest a wide range of microbial agents in atherosclerotic plaques, and an intriguing new observation that shows these microbiota displayed differences between symptomatic and asymptomatic plaques as judged from the taxonomic profiles in these two groups of patients. Additionally, functional annotations reveal significant differences in basic metabolic and disease pathway signatures between these groups. CONCLUSIONS We demonstrate the feasibility of novel high-resolution techniques aimed at identification and characterization of microbial genomes in human atherosclerotic tissue samples. Our analysis suggests that distinct groups of microbial agents might play different roles during the development of atherosclerotic plaques. These findings may serve as a reference point for future studies in this area of research.
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Affiliation(s)
- Suparna Mitra
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore.
- Norwich Medical School, University of East Anglia, Norwich, UK.
- Institute of Food Research, Norwich Research Park, Norwich, UK.
| | - Daniela I Drautz-Moses
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore.
| | - Morten Alhede
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
| | - Myat T Maw
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore.
| | - Yang Liu
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore.
| | - Rikky W Purbojati
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore.
| | - Zhei H Yap
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore.
| | - Kavita K Kushwaha
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore.
| | - Alexandra G Gheorghe
- The Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.
| | - Gorm M Hansen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
- Department of Cardiology, Gentofte University Hospital, Copenhagen, Denmark.
| | - Henrik H Sillesen
- The Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Hans P Hougen
- The Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Peter R Hansen
- Department of Cardiology, Gentofte University Hospital, Copenhagen, Denmark.
| | - Liang Yang
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore.
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
| | - Stephan C Schuster
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore.
| | - Michael Givskov
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore.
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
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