1
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Lu YT, Wu YY, Li YN, Zheng WY, Liu WZ. Saccharopolyspora mangrovi sp. nov., a novel mangrove soil actinobacterium with distinct metabolic potential revealed by comparative genomic analysis. Arch Microbiol 2024; 206:342. [PMID: 38967823 DOI: 10.1007/s00203-024-04069-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 06/17/2024] [Accepted: 06/22/2024] [Indexed: 07/06/2024]
Abstract
A novel mangrove soil-derived actinomycete, strain S2-29T, was found to be most closely related to Saccharopolyspora karakumensis 5K548T based on 16 S rRNA sequence (99.24% similarity) and genomic phylogenetic analyses. However, significant divergence in digital DNA-DNA hybridization, average nucleotide identity, and unique biosynthetic gene cluster possession distinguished S2-29T as a distinct Saccharopolyspora species. Pan genome evaluation revealed exceptional genomic flexibility in genus Saccharopolyspora, with > 95% accessory genome content. Strain S2-29T harbored 718 unique genes, largely implicated in energetic metabolisms, indicating different metabolic capacities from its close relatives. Several uncharacterized biosynthetic gene clusters in strain S2-29T highlighted the strain's untapped capacity to produce novel functional compounds with potential biotechnological applications. Designation as novel species Saccharopolyspora mangrovi sp. nov. (type strain S2-29T = JCM 34,548T = CGMCC 4.7716T) was warranted, expanding the known Saccharopolyspora diversity and ecology. The discovery of this mangrove-adapted strain advances understanding of the genus while highlighting an untapped source of chemical diversity.
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Affiliation(s)
- Yi-Ting Lu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
| | - Yi-Yi Wu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
| | - Ya-Nan Li
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
- Department of Pharmaceutical Laboratory, Anhui Sunhere Pharmaceutical Excipients Co., Ltd, Huainan, Anhui Province, 232000, China
| | - Wei-Yi Zheng
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China.
| | - Wen-Zheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China.
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2
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Sandalova E, Goh J, Lim ZX, Lim ZM, Barardo D, Dorajoo R, Kennedy BK, Maier AB. Alpha-ketoglutarate supplementation and BiologicaL agE in middle-aged adults (ABLE)-intervention study protocol. GeroScience 2023; 45:2897-2907. [PMID: 37217632 PMCID: PMC10643463 DOI: 10.1007/s11357-023-00813-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Targeting molecular processes of aging will enable people to live healthier and longer lives by preventing age-related diseases. Geroprotectors are compounds with the potential to increase healthspan and lifespan. Even though many of them have been tested in animal models, the translation to humans is limited. Alpha-Ketoglutarate (AKG) has been studied widely in model animals, but there are few studies testing its geroprotective properties in humans. ABLE is a double blinded placebo-controlled randomized trial (RCT) of 1 g sustained release Ca-AKG versus placebo for 6 months of intervention and 3 months follow up including 120 40-60-year-old healthy individuals with a higher DNA methylation age compared to their chronological age. The primary outcome is the decrease in DNA methylation age from baseline to the end of the intervention. A total of 120 participants will be randomized to receive either sustained release Ca-AKG or placebo. Secondary outcomes include changes in the inflammatory and metabolic parameters in blood, handgrip strength and leg extension strength, arterial stiffness, skin autofluorescence, and aerobic capacity from baseline to 3 months, 6 months, and 9 months. This study will recruit middle-aged participants with an older DNA methylation age compared to their chronological age, and test whether supplementation with Ca-AKG can reduce DNA methylation age. This study is unique in its inclusion of biologically older participants.
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Affiliation(s)
- Elena Sandalova
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore.
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore.
| | - Jorming Goh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Zi Xiang Lim
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore
| | - Zhi Meng Lim
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore
| | - Diogo Barardo
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Brian K Kennedy
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore
| | - Andrea B Maier
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore.
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore.
- Department of Human Movement Sciences, @AgeAmsterdam, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam, Netherlands.
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3
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Ge X, Yang S, Zhen C, Liu W. Actinophytocola gossypii sp. nov. and Streptomyces gossypii sp. nov., two novel actinomycetes isolated from rhizosphere soil of cotton. Int J Syst Evol Microbiol 2023; 73. [PMID: 37068120 DOI: 10.1099/ijsem.0.005832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Two Gram-positive, aerobic and non-motile actinomycetes, designated S1-96T and N2-109T, were isolated from soils collected from a cotton field. They are described as representing two novel species of genera Actinophytocola and Streptomyces through a polyphasic approach. Analysis of 16S rRNA gene sequences revealed that strains S1-96T and N2-109T showed highest similarity to Actinophytocola xinjiangensis CGMCC 4.4663T (99.10 %) and Streptomyces iconiensis BNT558T (98.21 %), respectively. Phylogenetic analyses based on 16S rRNA and core genes confirmed the close relationships of these strains. Genomic analyses further supported the novel taxonomic delimitation of these two species based on digital DNA-DNA hybridization and average nucleotide identity. Strains S1-96T and N2-109T contained MK-9(H4) and MK-9(H6) as the most abundant menaquinone, respectively. High abundances of iso-fatty acids were detected in both strains, which was similar to their close relatives. Physiological and polar lipid analyses also revealed differences between these strains and their phylogenetic neighbours, supporting their taxonomic delimitation as novel species. The names Actinophytocola gossypii sp. nov. (type strain S1-96T=JCM 34412T=CGMCC 4.7707T) and Streptomyces gossypii sp. nov. (type strain N2-109T=JCM 34628T=CGMCC 4.7717T) are proposed.
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Affiliation(s)
- Xianfeng Ge
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Shenrong Yang
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Cheng Zhen
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Wenzheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
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4
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Zhen C, Chen XK, Ge XF, Liu WZ. Streptomonospora mangrovi sp. nov., isolated from mangrove soil showing similar metabolic capabilities, but distinct secondary metabolites profiles. Arch Microbiol 2023; 205:148. [PMID: 36991151 DOI: 10.1007/s00203-023-03501-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023]
Abstract
A novel actinomycete, designated strain S1-112 T, was isolated from a mangrove soil sample from Hainan, China, and characterized using a polyphasic approach. Strain S1-112 T showed the highest similarity of the 16S rRNA gene to Streptomonospora nanhaiensis 12A09T (99.24%). Their close relationship was further supported by phylogenetic analyses, which placed these two strains within a stable clade. The highest values of digital DNA-DNA hybridization (dDDH, 41.4%) and average nucleotide identity (ANI, 90.55%) were detected between strain S1-112 T and Streptomonospora halotolerans NEAU-Jh2-17 T. Genotypic and phenotypic characteristics demonstrated that strain S1-112 T could be distinguished from its closely related relatives. We also profiled the pan-genome and metabolic features of genomic assemblies of strains belonging to the genus Streptomonospora, indicating similar functional capacities and metabolic activities. However, all of these strains showed promising potential for producing diverse types of secondary metabolites. In conclusion, strain S1-112 T represents a novel species of the genus Streptomonospora, for which the name Streptomonospora mangrovi sp. nov. was proposed. The type strain is S1-112 T (= JCM 34292 T).
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Affiliation(s)
- Cheng Zhen
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Xin-Kai Chen
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Xian-Feng Ge
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Wen-Zheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China.
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5
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Reynolds NK, Stajich JE, Benny GL, Barry K, Mondo S, LaButti K, Lipzen A, Daum C, Grigoriev IV, Ho HM, Crous PW, Spatafora JW, Smith ME. Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi. Genome Biol Evol 2023; 15:evac185. [PMID: 36617272 PMCID: PMC9866270 DOI: 10.1093/gbe/evac185] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023] Open
Abstract
Improved sequencing technologies have profoundly altered global views of fungal diversity and evolution. High-throughput sequencing methods are critical for studying fungi due to the cryptic, symbiotic nature of many species, particularly those that are difficult to culture. However, the low coverage genome sequencing (LCGS) approach to phylogenomic inference has not been widely applied to fungi. Here we analyzed 171 Kickxellomycotina fungi using LCGS methods to obtain hundreds of marker genes for robust phylogenomic reconstruction. Additionally, we mined our LCGS data for a set of nine rDNA and protein coding genes to enable analyses across species for which no LCGS data were obtained. The main goals of this study were to: 1) evaluate the quality and utility of LCGS data for both phylogenetic reconstruction and functional annotation, 2) test relationships among clades of Kickxellomycotina, and 3) perform comparative functional analyses between clades to gain insight into putative trophic modes. In opposition to previous studies, our nine-gene analyses support two clades of arthropod gut dwelling species and suggest a possible single evolutionary event leading to this symbiotic lifestyle. Furthermore, we resolve the mycoparasitic Dimargaritales as the earliest diverging clade in the subphylum and find four major clades of Coemansia species. Finally, functional analyses illustrate clear variation in predicted carbohydrate active enzymes and secondary metabolites (SM) based on ecology, that is biotroph versus saprotroph. Saprotrophic Kickxellales broadly lack many known pectinase families compared with saprotrophic Mucoromycota and are depauperate for SM but have similar numbers of predicted chitinases as mycoparasitic.
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Affiliation(s)
| | - Jason E Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California–Riverside
| | | | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Stephen Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
- Department of Plant and Microbial Biology, University of California Berkeley
| | - Hsiao-Man Ho
- Department of Science Education, University of Education, 134, Section 2, Heping E. Road, National Taipei, Taipei 106, Taiwan
| | - Pedro W Crous
- Department of Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
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6
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Hoy MJ, Heitman J. Drug Target Elucidation Through Isolation and Analysis of Drug-Resistant Mutants in Cryptococcus neoformans. Methods Mol Biol 2023; 2658:127-143. [PMID: 37024699 PMCID: PMC10602406 DOI: 10.1007/978-1-0716-3155-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Drug target identification is an essential component to antifungal drug development. Many methods, including large chemical library screening, natural product screening, and drug repurposing efforts, can identify compounds with favorable in vitro antifungal activity. However, these approaches will often identify compounds with no known mechanism of action. Herein, we describe a method utilizing the human fungal pathogen Cryptococcus neoformans to identify antifungal drug targets through the isolation of spontaneous resistant mutants, antifungal testing, whole-genome sequencing, and variant analysis.
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Affiliation(s)
- Michael J Hoy
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.
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7
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Rai A, Saha SP, Manvar T, Bhattacharjee A. A shotgun approach to explore the bacterial diversity and a brief insight into the glycoside hydrolases of Samiti lake located in the Eastern Himalayas. J Genet Eng Biotechnol 2022; 20:162. [PMID: 36469176 PMCID: PMC9723087 DOI: 10.1186/s43141-022-00444-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 11/12/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND The Himalayas have always been an enigma and, being biodiversity hotspots, are considered extremely important from an ecological point of view. Recent advances in studies regarding high-altitude lakes have garnered relevant importance as these habitats could harbor potential psychrophilic and psychrotrophic microbes with bio-prospective applications. Contemplating the above scenario, the present study has been undertaken to understand the diversity and the functional capacities of the microbes thriving in this lake. RESULTS In our present study on Samiti Lake, the abundance of Proteobacteria as the major phylum was seen in both the soil and water samples. Incase of the ABSLW (water) and ABS1 (soil) sample, 148,066 and 239,754 predicted genes, were taken for functional analysis. The KEGG analysis showed that ABSLW and ABS1 had 122,911 and 160,268, genes assigned to KO terms respectively. Whereas in case of COG functional analysis, 104,334 and 130,191 genes were assigned to different COG classes for ABSLW and ABS1 respectively. Further, on studying the glycoside hydrolases, an abundance of GH13, GH2, GH3, GH43, and GH23 in both the soil and water samples were seen. CONCLUSION Our study has provided a comprehensive report about the bacterial diversity and functional capacities of microbes thriving in Samiti Lake. It has also thrown some light on the occurrence of glycoside hydrolases in this region, as they have numerous biotechnological applications in different sectors.
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Affiliation(s)
- Aditi Rai
- grid.412222.50000 0001 1188 5260Department of Microbiology, University of North Bengal, P.O. NBU, District Darjeeling, West Bengal, Pin-734013 India
| | - Shyama Prasad Saha
- grid.412222.50000 0001 1188 5260Department of Microbiology, University of North Bengal, P.O. NBU, District Darjeeling, West Bengal, Pin-734013 India
| | - Toral Manvar
- Xcelris Labs Ltd, Ahmedabad, Gujarat 380006 India
| | - Arindam Bhattacharjee
- grid.412222.50000 0001 1188 5260Department of Microbiology, University of North Bengal, P.O. NBU, District Darjeeling, West Bengal, Pin-734013 India
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8
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Balimponya EG, Dwiyanti MS, Ito T, Sakaguchi S, Yamamori K, Kanaoka Y, Koide Y, Nagayoshi Y, Kishima Y. Seed management using NGS technology to rapidly eliminate a deleterious allele from rice breeder seeds. BREEDING SCIENCE 2022; 72:362-371. [PMID: 36776441 PMCID: PMC9895803 DOI: 10.1270/jsbbs.22058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/26/2022] [Indexed: 06/18/2023]
Abstract
Spontaneous mutations are stochastic phenomena that occur in every population. However, deleterious mutated allele present in seeds distributed to farmers must be detected and removed. Here, we eliminated undesirable mutations from the parent population in one generation through a strategy based on next-generation sequencing (NGS). This study dealt with a spontaneous albino mutant in the 'Hinohikari' rice variety grown at the Miyazaki Comprehensive Agricultural Experiment Station, Japan. The incidence of albinism in the population was 1.36%. NGS analysis revealed the genomic basis for differences between green and albino phenotypes. Every albino plant had a C insertion in the Snow-White Leaf1 (SWL1) gene on chromosome 4 causing a frameshift mutation. Selfing plants heterozygous for the mutant allele, swl1-R332P, resulted in a 3:1 green/albino ratio, confirming that a single recessive gene controls albinism. Ultrastructural leaf features in the swl1-R332P mutants displayed deformed chlorophyll-associated organelles in albino plants that were similar to those of previously described swl1 mutants. Detection of the causative gene and its confirmation using heterozygous progenies were completed within a year. The NGS technique outlined here facilitates rapid identification of spontaneous mutations that can occur in breeder seeds.
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Affiliation(s)
- Elias G. Balimponya
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Maria S. Dwiyanti
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Toshiaki Ito
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Shuntaro Sakaguchi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Koichi Yamamori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Yoshitaka Kanaoka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
| | - Yoshifumi Nagayoshi
- Miyazaki Comprehensive Agricultural Experiment Station, Miyazaki 880-0212, Japan
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060‑8589, Japan
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9
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Ge X, Huang R, Liu W. Occultella gossypii sp. nov., an alkali-resistant isolate from soil sampled in a cotton field. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A non-spore-forming, motile and alkali-resistant actinobacterium, designated N2-46T, was isolated from an alkaline soil sample collected from a cotton field in the Xinjiang region of PR China. Strain N2-46T formed creamy colonies on tryptone soy agar and managed to survive in extreme alkaline conditions at a pH value of 11. Strain N2-46T displayed the highest 16S rRNA gene similarity of 99.65 % to
Haloactinobacterium kanbiaonis
HY164T, followed by
Occultella aeris
F300T (99.61%) and
Occultella glacieicola
T3246-1T (98.54 %). 16S rRNA-directed phylogenetic analysis showed that strain N2-46T was embedded in a subclade with
O. aeris
F300T with a bootstrap value of 71.8 %. The phylogenetic tree based on core genes of genome sequences showed that strain N2-46T formed a unique subclade next to
H. kanbiaonis
HY164T and
O. aeris
F300T with a bootstrap value of 100 %. Digital DNA–DNA hybridization and the average nucleotide identity analyses showed that strain N2-46T displayed the highest values of 67.1 % (63.2–70.7 %) and 91.82 % with
H. kanbiaonis
HY164T, respectively. Comparative genomic analysis indicated that strain N2-46T and its three closest neighbours exhibited comparable distribution patterns in heavy metal resistance genes and biosynthetic gene clusters, while displaying distinctions probably related to ecological adaptation. MK-8(H4) was identified as the predominant isoprenoid quinone. The main fatty acids were identified as iso-C14 : 0 and anteiso-C15 : 0. Polar lipids are composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, mono and diacylated phosphatidylinositol dimannosides, as well as several uncharacterized polar lipid, glycolipid, and phospholipids. Genotypic and physiological analyses support the view that strain N2-46T (=JCM 34413T=CGMCC 1.18819T) should be classified as a novel species of the genus
Occultella
, for which the name Occultella gossypii sp. nov. is proposed.
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Affiliation(s)
- Xianfeng Ge
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Ruirui Huang
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Wenzheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
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10
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Yin X, Wang W, Wang A, He M, Lin C, Ouyang W, Liu X. Microbial community structure and metabolic potential in the coastal sediments around the Yellow River Estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151582. [PMID: 34785215 DOI: 10.1016/j.scitotenv.2021.151582] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
The Yellow River Estuary and Laizhou Bay are located on the northern Shandong Peninsula in the Bohai Sea in China and have been polluted by intensive anthropogenic activity. However, few studies have focused on the effect of these activities on the microbial communities and their ecological functions in this area. In this study, the combination of 16S rDNA gene sequencing and GeoChip technology was used to analyzed the microbial community component and their functional genes. Thaumarchaeot and Bacteroidetes are the most abundant phyla. The results of correlation analysis and redundancy analysis (RDA) showed water depth (r2 = 0.76, P = 0.005), total Na content (r2 = 0.63, P = 0.021) and total Ca content (r2 = 0.53, P = 0.05) in the sediments were the most significant environmental factors affecting the microbial community. The diversity of the microbial community and signal intensity of functional genes at nearshore sites (N sites) were higher than that at the offshore sites (O sites), but the component of microbial community and functional genes was similar in general. Functional genes for C, N, P and S cycle were detected at both nearshore and offshore sites, which illustrated that microbial communities were active in nutrient cycle. Proteobacteria contributes significantly to material cycle in microbial community. In addition, functional genes related to organic remediation and metal detoxification are also abundant. It indicated that the environmental pollution caused by anthropogenic activities has greatly affected the microbial community components and their biochemical functions in the Yellow River Estuary and surrounding areas. This study reveals the effect of anthropogenic activities on microbial communities and provides the basis for environmental management.
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Affiliation(s)
- Xiaobo Yin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wenting Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Aihua Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Mengchang He
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Chunye Lin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Ouyang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xitao Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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Li Y, Chen K, Liu S, Liang X, Wang Y, Zhou X, Yin Y, Cao Y, An W, Qin K, Sun Y. Diversity and spatiotemporal dynamics of fungal communities in the rhizosphere soil of Lycium barbarum L.: a new insight into the mechanism of geoherb formation. Arch Microbiol 2022; 204:197. [PMID: 35217917 PMCID: PMC8881256 DOI: 10.1007/s00203-022-02781-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 01/14/2022] [Accepted: 01/28/2022] [Indexed: 12/24/2022]
Abstract
Lycium barbarum L. is a well-known traditional geoherb in Ningxia, China. The fruits of L. barbarum contain several dietary constituents, and thus, they exert many beneficial effects on human health. However, a few studies have been conducted on the geoherb L. barbarum and its rhizosphere soil fungal community. In this study, we determined the physicochemical properties and fungal community structure of rhizosphere soil of L. barbarum from three regions of China, namely Ningxia (NX), Qinghai (QH), and Xinjiang (XJ), during three development stages of L. barbarum. Soil pH varied between 7.56 and 8.60 across the three regions, indicating that alkaline soil is conducive to the growth of L. barbarum. The majority of soil properties in NX, an authentic geoherb-producing area, were substantially inferior to those in XJ and QH during all three developmental stages. Total sugar, polysaccharide (LBP), and flavonoid contents were the highest in wolfberry fruits from NX. High-throughput sequencing showed that the abundance of the soil fungal population in NX was higher than that in QH and XJ during the flowering and fruiting stage and summer dormant stage. Moreover, the soil fungal diversity increased with the development of wolfberry. Ascomycota and Mortierellomycota were the predominant phyla in the rhizosphere fungal communities in all samples. Redundancy analysis showed a significant correlation of the soil-available phosphorus and LBP of wolfberry fruits with the fungal community composition. The characteristics of rhizosphere fungal communities determined in the present study provide insights into the mechanism of geoherb formation in NX wolfberry.
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Affiliation(s)
- Yuekun Li
- National Wolfberry Engineering Research Center, Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Kaili Chen
- The College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Siyang Liu
- The College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Xiaojie Liang
- National Wolfberry Engineering Research Center, Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Yajun Wang
- National Wolfberry Engineering Research Center, Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Xuan Zhou
- National Wolfberry Engineering Research Center, Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Yue Yin
- National Wolfberry Engineering Research Center, Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Youlong Cao
- National Wolfberry Engineering Research Center, Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Wei An
- National Wolfberry Engineering Research Center, Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Ken Qin
- National Wolfberry Engineering Research Center, Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Yanfei Sun
- The College of Life Sciences, Shihezi University, Shihezi, 832003, China.
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12
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Louha S, Herman C, Gupta M, Patel D, Kelley J, OH JHM, Guru J, Lemoine JF, Chang MA, Venkatachalam U, Rogier E, Talundzic E. Evaluation of a parasite-density based pooled targeted amplicon deep sequencing (TADS) method for molecular surveillance of Plasmodium falciparum drug resistance genes in Haiti. PLoS One 2022; 17:e0262616. [PMID: 35030215 PMCID: PMC8759662 DOI: 10.1371/journal.pone.0262616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/30/2021] [Indexed: 12/04/2022] Open
Abstract
Sequencing large numbers of individual samples is often needed for countrywide antimalarial drug resistance surveillance. Pooling DNA from several individual samples is an alternative cost and time saving approach for providing allele frequency (AF) estimates at a population level. Using 100 individual patient DNA samples of dried blood spots from a 2017 nationwide drug resistance surveillance study in Haiti, we compared codon coverage of drug resistance-conferring mutations in four Plasmodium falciparum genes (crt, dhps, dhfr, and mdr1), for the same deep sequenced samples run individually and pooled. Samples with similar real-time PCR cycle threshold (Ct) values (+/- 1.0 Ct value) were combined with ten samples per pool. The sequencing success for samples in pools were higher at a lower parasite density than the individual samples sequence method. The median codon coverage for drug resistance-associated mutations in all four genes were greater than 3-fold higher in the pooled samples than in individual samples. The overall codon coverage distribution for pooled samples was wider than the individual samples. The sample pools with < 40 parasites/μL blood showed more discordance in AF calls for dhfr and mdr1 between the individual and pooled samples. This discordance in AF estimation may be due to low amounts of parasite DNA, which could lead to variable PCR amplification efficiencies. Grouping samples with an estimated ≥ 40 parasites/μL blood prior to pooling and deep sequencing yielded the expected population level AF. Pooling DNA samples based on estimates of > 40 parasites/μL prior to deep sequencing can be used for rapid genotyping of a large number of samples for these four genes and possibly other drug resistant markers in population-based studies. As Haiti is a low malaria transmission country with very few mixed infections and continued chloroquine sensitivity, the pooled sequencing approach can be used for routine national molecular surveillance of resistant parasites.
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Affiliation(s)
- Swarnali Louha
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
- * E-mail:
| | - Camelia Herman
- Centers for Disease Control and Prevention Foundation, Atlanta, GA, United States America
| | - Mansi Gupta
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
| | - Dhruviben Patel
- Williams Consulting LLC, Atlanta, GA, United States America
- Division of Parasitic Diseases and Malaria, Malaria Branch, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States America
| | - Julia Kelley
- Centers for Disease Control and Prevention Foundation, Atlanta, GA, United States America
- Division of Parasitic Diseases and Malaria, Malaria Branch, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States America
| | - Je-Hoon M. OH
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
| | - Janani Guru
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, United States America
| | - Jean F. Lemoine
- Programme National de Contrôle de la Malaria, MSPP, Port-au-Prince, Haiti
| | - Michelle A. Chang
- Division of Parasitic Diseases and Malaria, Malaria Branch, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States America
| | - Udhayakumar Venkatachalam
- Division of Parasitic Diseases and Malaria, Malaria Branch, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States America
| | - Eric Rogier
- Division of Parasitic Diseases and Malaria, Malaria Branch, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States America
| | - Eldin Talundzic
- Division of Parasitic Diseases and Malaria, Malaria Branch, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States America
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13
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Huang RR, Ge XF, Chen XK, Yang SR, Zhen C, Wen ZQ, Li YN, Liu WZ. Steroidobacter gossypii sp. nov., isolated from cotton field soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 34343063 DOI: 10.1099/ijsem.0.004935] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative bacterium, designated S1-65T, was isolated from soil samples collected from a cotton field located in the Xinjiang region of PR China. Results of 16S rRNA gene sequence analysis revealed that strain S1-65T was affiliated to the genus Steroidobacter with its closest phylogenetic relatives being 'Steroidobacter cummioxidans' 35Y (98.4 %), 'Steroidobacter agaridevorans' SA29-B (98.3 %) and Steroidobacter agariperforans KA5-BT (98.3 %). 16S rRNA-directed phylogenetic analysis showed that strain S1-65T formed a unique phylogenetic subclade next to 'S. agaridevorans' SA29-B and S. agariperforans KA5-BT, suggesting that strain S1-65T should be identified as a member of the genus Steroidobacter. Further, substantial differences between the genotypic properties of strain S1-65T and the members of the genus Steroidobacter, including average nucleotide identity and digital DNA-DNA hybridization, resolved the taxonomic position of strain S1-65T and suggested its positioning as representing a novel species of the genus Steroidobacter. The DNA G+C content of strain S1-65T was 62.5 mol%, based on its draft genome sequence. The predominant respiratory quinone was ubiquinone-8. The main fatty acids were identified as summed feature 3 (C16:1ω6c/C16:1ω7c), C16 : 0 and iso-C15 : 0. In addition, its polar lipid profile was composed of aminophospholipid, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Here, we propose a novel species of the genus Steroidobacter: Steroidobacter gossypii sp. nov. with the type strain S1-65T (=JCM 34287T=CGMCC 1.18736T).
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Affiliation(s)
- Rui-Rui Huang
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Xian-Feng Ge
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Xin-Kai Chen
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Shen-Rong Yang
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Cheng Zhen
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Zhi-Qiang Wen
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Ya-Nan Li
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Wen-Zheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
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14
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Evaluating coverage bias in next-generation sequencing of Escherichia coli. PLoS One 2021; 16:e0253440. [PMID: 34166413 PMCID: PMC8224930 DOI: 10.1371/journal.pone.0253440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 06/05/2021] [Indexed: 01/18/2023] Open
Abstract
Whole-genome sequencing is essential to many facets of infectious disease research. However, technical limitations such as bias in coverage and tagmentation, and difficulties characterising genomic regions with extreme GC content have created significant obstacles in its use. Illumina has claimed that the recently released DNA Prep library preparation kit, formerly known as Nextera Flex, overcomes some of these limitations. This study aimed to assess bias in coverage, tagmentation, GC content, average fragment size distribution, and de novo assembly quality using both the Nextera XT and DNA Prep kits from Illumina. When performing whole-genome sequencing on Escherichia coli and where coverage bias is the main concern, the DNA Prep kit may provide higher quality results; though de novo assembly quality, tagmentation bias and GC content related bias are unlikely to improve. Based on these results, laboratories with existing workflows based on Nextera XT would see minor benefits in transitioning to the DNA Prep kit if they were primarily studying organisms with neutral GC content.
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15
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Hong N, Chen M, Xu J. Molecular Markers Reveal Epidemiological Patterns and Evolutionary Histories of the Human Pathogenic Cryptococcus. Front Cell Infect Microbiol 2021; 11:683670. [PMID: 34026667 PMCID: PMC8134695 DOI: 10.3389/fcimb.2021.683670] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 04/22/2021] [Indexed: 01/02/2023] Open
Abstract
The human pathogenic Cryptococcus species are the main agents of fungal meningitis in humans and the causes of other diseases collectively called cryptococcosis. There are at least eight evolutionary divergent lineages among these agents, with different lineages showing different geographic and/or ecological distributions. In this review, we describe the main strain typing methods that have been used to analyze the human pathogenic Cryptococcus and discuss how molecular markers derived from the various strain typing methods have impacted our understanding of not only cryptococcal epidemiology but also its evolutionary histories. These methods include serotyping, multilocus enzyme electrophoresis, electrophoretic karyotyping, random amplified polymorphic DNA, restriction fragment length polymorphism, PCR-fingerprinting, amplified fragment length polymorphism, multilocus microsatellite typing, single locus and multilocus sequence typing, matrix-assisted laser desorption/ionization time of flight mass spectrometry, and whole genome sequencing. The major findings and the advantages and disadvantages of each method are discussed. Together, while controversies remain, these strain typing methods have helped reveal (i) the broad phylogenetic pattern among these agents, (ii) the centers of origins for several lineages and their dispersal patterns, (iii) the distributions of genetic variation among geographic regions and ecological niches, (iv) recent hybridization among several lineages, and (v) specific mutations during infections within individual patients. However, significant challenges remain. Multilocus sequence typing and whole genome sequencing are emerging as the gold standards for continued strain typing and epidemiological investigations of cryptococcosis.
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Affiliation(s)
- Nan Hong
- Department of Dermatology, Shanghai Key Laboratory of Medical Mycology, Changzheng Hospital, Naval Medical University, Shanghai, China.,Department of Burn and Plastic Surgery, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Min Chen
- Department of Dermatology, Shanghai Key Laboratory of Medical Mycology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
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16
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Kim HM, Jeon S, Chung O, Jun JH, Kim HS, Blazyte A, Lee HY, Yu Y, Cho YS, Bolser DM, Bhak J. Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing. Gigascience 2021; 10:giab014. [PMID: 33710328 PMCID: PMC7953489 DOI: 10.1093/gigascience/giab014] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 09/03/2020] [Accepted: 02/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND DNBSEQ-T7 is a new whole-genome sequencer developed by Complete Genomics and MGI using DNA nanoball and combinatorial probe anchor synthesis technologies to generate short reads at a very large scale-up to 60 human genomes per day. However, it has not been objectively and systematically compared against Illumina short-read sequencers. FINDINGS By using the same KOREF sample, the Korean Reference Genome, we have compared 7 sequencing platforms including BGISEQ-500, DNBSEQ-T7, HiSeq2000, HiSeq2500, HiSeq4000, HiSeqX10, and NovaSeq6000. We measured sequencing quality by comparing sequencing statistics (base quality, duplication rate, and random error rate), mapping statistics (mapping rate, depth distribution, and percent GC coverage), and variant statistics (transition/transversion ratio, dbSNP annotation rate, and concordance rate with single-nucleotide polymorphism [SNP] genotyping chip) across the 7 sequencing platforms. We found that MGI platforms showed a higher concordance rate for SNP genotyping than HiSeq2000 and HiSeq4000. The similarity matrix of variant calls confirmed that the 2 MGI platforms have the most similar characteristics to the HiSeq2500 platform. CONCLUSIONS Overall, MGI and Illumina sequencing platforms showed comparable levels of sequencing quality, uniformity of coverage, percent GC coverage, and variant accuracy; thus we conclude that the MGI platforms can be used for a wide range of genomics research fields at a lower cost than the Illumina platforms.
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Affiliation(s)
- Hak-Min Kim
- Clinomics Inc., Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Oksung Chung
- Clinomics Inc., Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Je Hoon Jun
- Clinomics Inc., Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Hui-Su Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Hwang-Yeol Lee
- Clinomics Inc., Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Youngseok Yu
- Clinomics Inc., Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Yun Sung Cho
- Clinomics Inc., Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Dan M Bolser
- Geromics Ltd., 222 Mill Road, Cambridge, CB1 3NF, United Kingdom
| | - Jong Bhak
- Clinomics Inc., Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
- Geromics Ltd., 222 Mill Road, Cambridge, CB1 3NF, United Kingdom
- Personal Genomics Institute (PGI), Genome Research Foundation, Osong saengmyong1ro, Cheongju, 28160, Republic of Korea
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17
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Yu LS, Rodriguez-Manzano J, Moser N, Moniri A, Malpartida-Cardenas K, Miscourides N, Sewell T, Kochina T, Brackin A, Rhodes J, Holmes AH, Fisher MC, Georgiou P. Rapid Detection of Azole-Resistant Aspergillus fumigatus in Clinical and Environmental Isolates by Use of a Lab-on-a-Chip Diagnostic System. J Clin Microbiol 2020; 58:e00843-20. [PMID: 32907990 PMCID: PMC7587087 DOI: 10.1128/jcm.00843-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/27/2020] [Indexed: 12/16/2022] Open
Abstract
Aspergillus fumigatus has widely evolved resistance to the most commonly used class of antifungal chemicals, the azoles. Current methods for identifying azole resistance are time-consuming and depend on specialized laboratories. There is an urgent need for rapid detection of these emerging pathogens at point-of-care to provide the appropriate treatment in the clinic and to improve management of environmental reservoirs to mitigate the spread of antifungal resistance. Our study demonstrates the rapid and portable detection of the two most relevant genetic markers linked to azole resistance, the mutations TR34 and TR46, found in the promoter region of the gene encoding the azole target cyp51A. We developed a lab-on-a-chip platform consisting of: (i) tandem-repeat loop-mediated isothermal amplification; (ii) state-of-the-art complementary metal-oxide-semiconductor microchip technology for nucleic acid amplification detection; and (iii) a smartphone application for data acquisition, visualization, and cloud connectivity. Specific and sensitive detection was validated with isolates from clinical and environmental samples from 6 countries across 5 continents, showing a lower limit of detection of 10 genomic copies per reaction in less than 30 min. When fully integrated with a sample preparation module, this diagnostic system will enable the detection of this ubiquitous fungus at the point-of-care, and could help to improve clinical decision making, infection control, and epidemiological surveillance.
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Affiliation(s)
- Ling-Shan Yu
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Jesus Rodriguez-Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Nicolas Moser
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Ahmad Moniri
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Kenny Malpartida-Cardenas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Nicholas Miscourides
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Thomas Sewell
- MRC Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Tatiana Kochina
- MRC Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Amelie Brackin
- MRC Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Johanna Rhodes
- MRC Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Alison H Holmes
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
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18
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Vanhove M, Sicard A, Ezennia J, Leviten N, Almeida RPP. Population structure and adaptation of a bacterial pathogen in California grapevines. Environ Microbiol 2020; 22:2625-2638. [PMID: 32114707 DOI: 10.1111/1462-2920.14965] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/03/2020] [Accepted: 02/26/2020] [Indexed: 12/30/2022]
Abstract
Xylella fastidiosa subsp. fastidiosa causes Pierce's disease of grapevine (PD) and has been present in California for over a century. A singly introduced genotype spread across the state causing large outbreaks and damaging the grapevine industry. This study presents 122 X. fastidiosa subsp. fastidiosa genomes from symptomatic grapevines, and explores pathogen genetic diversity associated with PD in California. A total of 5218 single-nucleotide polymorphisms (SNPs) were found in the dataset. Strong population genetic structure was found; isolates split into five genetic clusters divided into two lineages. The core/soft-core genome constituted 41.2% of the total genome, emphasizing the high genetic variability of X. fastidiosa genomes. An ecological niche model was performed to estimate the environmental niche of the pathogen within California and to identify key climatic factors involved in dispersal. A landscape genomic approach was undertaken aiming to link local adaptation to climatic factors. A total of 18 non-synonymous polymorphisms found to be under selective pressures were correlated with at least one environmental variable highlighting the role of temperature, precipitation and elevation on X. fastidiosa adaptation to grapevines in California. Finally, the contribution to virulence of three of the genes under positive selective pressure and of one recombinant gene was studied by reverse genetics.
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Affiliation(s)
- Mathieu Vanhove
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
| | - Anne Sicard
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
| | - Jeffery Ezennia
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
| | - Nina Leviten
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
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19
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Plasmid Reconstruction from Next-Gen Data: A Detailed Protocol for the Use of PLACNETw for the Reconstruction of Plasmids from WGS Datasets. Methods Mol Biol 2020; 2075:323-339. [PMID: 31584173 DOI: 10.1007/978-1-4939-9877-7_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mobile Genetic Elements (MGE) play essential roles in adaptive bacterial evolution, facilitating genetic exchange for extrachromosomal DNA, especially antibiotic resistance genes and virulence factors. For this reason, high-throughput next-generation sequencing of bacteria is of great relevance, especially for clinical pathogenic bacteria. Accurate identification of MGE from whole-genome sequencing (WGS) datasets is one of the major challenges, still hindered by methodological limitations and high sequencing costs.This chapter encompasses the protocol used for plasmid reconstruction by applying the PLACNETw methodology, from raw reads to assembled plasmids and chromosome. PLACNETw is a graphical user-friendly interface to visualize and reconstruct MGE from short-read WGS datasets. No bioinformatic background or sophisticated computational resources are required and high precision and sensitivity are achieved.
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20
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Vanhove M, Retchless AC, Sicard A, Rieux A, Coletta-Filho HD, De La Fuente L, Stenger DC, Almeida RPP. Genomic Diversity and Recombination among Xylella fastidiosa Subspecies. Appl Environ Microbiol 2019; 85:e02972-18. [PMID: 31028021 PMCID: PMC6581164 DOI: 10.1128/aem.02972-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/19/2019] [Indexed: 12/21/2022] Open
Abstract
Xylella fastidiosa is an economically important bacterial plant pathogen. With insights gained from 72 genomes, this study investigated differences among the three main subspecies, which have allopatric origins: X. fastidiosa subsp. fastidiosa, multiplex, and pauca The origin of recombinogenic X. fastidiosa subsp. morus and sandyi was also assessed. The evolutionary rate of the 622 genes of the species core genome was estimated at the scale of an X. fastidiosa subsp. pauca subclade (7.62 × 10-7 substitutions per site per year), which was subsequently used to estimate divergence time for the subspecies and introduction events. The study characterized genes present in the accessory genome of each of the three subspecies and investigated the core genome to detect genes potentially under positive selection. Recombination is recognized to be the major driver of diversity in X. fastidiosa, potentially facilitating shifts to novel plant hosts. The relative effect of recombination in comparison to point mutation was calculated (r/m = 2.259). Evidence of recombination was uncovered in the core genome alignment; X. fastidiosa subsp. fastidiosa in the United States was less prone to recombination, with an average of 3.22 of the 622 core genes identified as recombining regions, whereas a specific clade of X. fastidiosa subsp. multiplex was found to have on average 9.60 recombining genes, 93.2% of which originated from X. fastidiosa subsp. fastidiosa Interestingly, for X. fastidiosa subsp. morus, which was initially thought to be the outcome of genome-wide recombination between X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex, intersubspecies homologous recombination levels reached 15.30% in the core genome. Finally, there is evidence of X. fastidiosa subsp. pauca strains from citrus containing genetic elements acquired from strains infecting coffee plants as well as genetic elements from both X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex In summary, our data provide new insights into the evolution and epidemiology of this plant pathogen.IMPORTANCEXylella fastidiosa is an important vector-borne plant pathogen. We used a set of 72 genomes that constitutes the largest assembled data set for this bacterial species so far to investigate genetic relationships and the impact of recombination on phylogenetic clades and to compare genome content at the subspecies level, and we used a molecular dating approach to infer the evolutionary rate of X. fastidiosa The results demonstrate that recombination is important in shaping the genomes of X. fastidiosa and that each of the main subspecies is under different selective pressures. We hope insights from this study will improve our understanding of X. fastidiosa evolution and biology.
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Affiliation(s)
- Mathieu Vanhove
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Adam C Retchless
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Anne Sicard
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | | | | | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Drake C Stenger
- San Joaquin Valley Agricultural Sciences Center, Agricultural Research Service, U.S. Department of Agriculture, Parlier, California, USA
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
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21
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Pochon X, Wecker P, Stat M, Berteaux-Lecellier V, Lecellier G. Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons. PeerJ 2019; 7:e6898. [PMID: 31139503 PMCID: PMC6521813 DOI: 10.7717/peerj.6898] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/02/2019] [Indexed: 11/20/2022] Open
Abstract
High-throughput sequencing is revolutionizing our ability to comprehensively characterize free-living and symbiotic Symbiodiniaceae, a diverse dinoflagellate group that plays a critical role in coral reef ecosystems. Most studies however, focus on a single marker for metabarcoding Symbiodiniaceae, potentially missing important ecological traits that a combination of markers may capture. In this proof-of-concept study, we used a small set of symbiotic giant clam (Tridacna maxima) samples obtained from nine French Polynesian locations and tested a dual-index sequence library preparation method that pools and simultaneously sequences multiple Symbiodiniaceae gene amplicons per sample for in-depth biodiversity assessments. The rationale for this approach was to allow the metabarcoding of multiple genes without extra costs associated with additional single amplicon dual indexing and library preparations. Our results showed that the technique effectively recovered very similar proportions of sequence reads and dominant Symbiodiniaceae clades among the three pooled gene amplicons investigated per sample, and captured varying levels of phylogenetic resolution enabling a more comprehensive assessment of the diversity present. The pooled Symbiodiniaceae multi-gene metabarcoding approach described here is readily scalable, offering considerable analytical cost savings while providing sufficient phylogenetic information and sequence coverage.
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Affiliation(s)
- Xavier Pochon
- Coastal & Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | | | - Michael Stat
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | | | - Gaël Lecellier
- UMR250/9220 ENTROPIE, IRD-CNRS-UR, LabEx CORAIL, Nouméa, New-Caledonia
- Université Paris-Saclay, UVSQ, Versailles Cedex, France
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22
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Draft Genome Sequence of Halotolerant Bacterium Chromohalobacter salexigens ANJ207, Isolated from Salt Crystal Deposits in Pipelines. Microbiol Resour Announc 2019; 8:8/15/e00049-19. [PMID: 30975796 PMCID: PMC6460019 DOI: 10.1128/mra.00049-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chromohalobacter salexigens ANJ207 was isolated from a salt crystal and is known to tolerate up to 30% NaCl concentration. Here, we report the de novo draft assembly of C. salexigens ANJ207. Chromohalobacter salexigens ANJ207 was isolated from a salt crystal and is known to tolerate up to 30% NaCl concentration. Here, we report the de novo draft assembly of C. salexigens ANJ207. The genome was determined to have 3.66 Mb represented in 13 scaffolds, with a total of 3,406 genes predicted.
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23
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Almeida OGG, De Martinis ECP. Bioinformatics tools to assess metagenomic data for applied microbiology. Appl Microbiol Biotechnol 2018; 103:69-82. [DOI: 10.1007/s00253-018-9464-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 12/14/2022]
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24
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Song X, Pan Y, Li L, Wu X, Wang Y. Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields. PLoS One 2018. [PMID: 29538438 PMCID: PMC5851603 DOI: 10.1371/journal.pone.0193811] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis.
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Affiliation(s)
- Xuhong Song
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource, Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Yuan Pan
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource, Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Longyun Li
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource, Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
- * E-mail:
| | - Xiaoli Wu
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource, Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Yu Wang
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource, Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
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25
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Cuomo CA, Rhodes J, Desjardins CA. Advances in Cryptococcus genomics: insights into the evolution of pathogenesis. Mem Inst Oswaldo Cruz 2018. [PMID: 29513784 PMCID: PMC5851040 DOI: 10.1590/0074-02760170473] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Cryptococcus species are the causative agents of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals. Initial work on the molecular epidemiology of this fungal pathogen utilized genotyping approaches to describe the genetic diversity and biogeography of two species, Cryptococcus neoformans and Cryptococcus gattii. Whole genome sequencing of representatives of both species resulted in reference assemblies enabling a wide array of downstream studies and genomic resources. With the increasing availability of whole genome sequencing, both species have now had hundreds of individual isolates sequenced, providing fine-scale insight into the evolution and diversification of Cryptococcus and allowing for the first genome-wide association studies to identify genetic variants associated with human virulence. Sequencing has also begun to examine the microevolution of isolates during prolonged infection and to identify variants specific to outbreak lineages, highlighting the potential role of hyper-mutation in evolving within short time scales. We can anticipate that further advances in sequencing technology and sequencing microbial genomes at scale, including metagenomics approaches, will continue to refine our view of how the evolution of Cryptococcus drives its success as a pathogen.
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Affiliation(s)
| | - Johanna Rhodes
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
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26
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Abstract
Long-term studies enable the identification of eco-evolutionary processes that occur over extended time periods. In addition, they provide key empirical data that may be used in predictive modelling to forecast evolutionary responses of natural ecosystems to future environmental changes. However, excluding a few exceptional cases, long-term studies are scarce because of logistic difficulties associated with accessing temporal samples. Temporal dynamics are frequently studied in the laboratory or in controlled mesocosm experiments with exceptional studies that reconstruct the evolution of natural populations in the wild. Here, a standard operating procedure (SOP) is provided to revive or resurrect dormant Daphnia magna, a widespread zooplankton keystone species in aquatic ecosystems, to dramatically advance the state-of-the-art longitudinal data collection in natural systems. The field of Resurrection Ecology was defined in 1999 by Kerfoot and co-workers, even though the first attempts at hatching diapausing zooplankton eggs date back to the late 1980s. Since Kerfoot's seminal paper, the methodology of resurrecting zooplankton species has been increasingly frequently applied, though propagated among laboratories only via direct knowledge transfer. Here, an SOP is described that provides a step-by-step protocol on the practice of resurrecting dormant Daphnia magna eggs. Two key studies are provided in which the fitness response of resurrected Daphnia magna populations to warming is measured, capitalizing on the ability to study historical and modern populations in the same settings. Finally, the application of next generation sequencing technologies to revived or still dormant stages is discussed. These technologies provide unprecedented power in dissecting the processes and mechanisms of evolution if applied to populations that have experienced changes in selection pressure over time.
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Affiliation(s)
| | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, University of Birmingham;
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27
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Eoche-Bosy D, Gautier M, Esquibet M, Legeai F, Bretaudeau A, Bouchez O, Fournet S, Grenier E, Montarry J. Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida. Mol Ecol 2017; 26:4700-4711. [PMID: 28734070 DOI: 10.1111/mec.14240] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 12/30/2022]
Abstract
Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaVvrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole-genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a)virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability.
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Affiliation(s)
- D Eoche-Bosy
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - M Gautier
- CBGP, INRA, IRD, CIRAD, Montpellier SupAgro, Montferrier-sur-Lez, France.,IBC, Montpellier, France
| | - M Esquibet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - F Legeai
- IGEPP, BIPAA, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France.,IRISA, GenScale, INRIA, Rennes, France
| | - A Bretaudeau
- IGEPP, BIPAA, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France.,IRISA, GenOuest COre Facility, INRIA, Rennes, France
| | - O Bouchez
- GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France.,GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - S Fournet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - E Grenier
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - J Montarry
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
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28
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Chen H, Wang L, Liu X, Hu L, Wang S, Cheng X. De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development. BMC Genet 2017; 18:65. [PMID: 28693419 PMCID: PMC5504845 DOI: 10.1186/s12863-017-0531-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 06/28/2017] [Indexed: 01/14/2023] Open
Abstract
Background Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding of cowpea. The objectives of this study were to analyse the cowpea transcriptome and develop genic molecular markers for future genetic studies of this genus. Results Approximately 54 million high-quality cDNA sequence reads were obtained from cowpea based on Illumina paired-end sequencing technology and were de novo assembled to generate 47,899 unigenes with an N50 length of 1534 bp. Sequence similarity analysis revealed 36,289 unigenes (75.8%) with significant similarity to known proteins in the non-redundant (Nr) protein database, 23,471 unigenes (49.0%) with BLAST hits in the Swiss-Prot database, and 20,654 unigenes (43.1%) with high similarity in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Further analysis identified 5560 simple sequence repeats (SSRs) as potential genic molecular markers. Validating a random set of 500 SSR markers yielded 54 polymorphic markers among 32 cowpea accessions. Conclusions This transcriptomic analysis of cowpea provided a valuable set of genomic data for characterizing genes with important agronomic traits in Vigna unguiculata and a new set of genic SSR markers for further genetic studies and breeding in cowpea and related Vigna species. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0531-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Honglin Chen
- The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lixia Wang
- The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoyan Liu
- The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liangliang Hu
- The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Suhua Wang
- The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xuzhen Cheng
- The National Key Facility for Crop Gene, Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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29
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A Population Genomics Approach to Assessing the Genetic Basis of Within-Host Microevolution Underlying Recurrent Cryptococcal Meningitis Infection. G3-GENES GENOMES GENETICS 2017; 7:1165-1176. [PMID: 28188180 PMCID: PMC5386865 DOI: 10.1534/g3.116.037499] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Recurrence of meningitis due to Cryptococcus neoformans after treatment causes substantial mortality in HIV/AIDS patients across sub-Saharan Africa. In order to determine whether recurrence occurred due to relapse of the original infecting isolate or reinfection with a different isolate weeks or months after initial treatment, we used whole-genome sequencing (WGS) to assess the genetic basis of infection in 17 HIV-infected individuals with recurrent cryptococcal meningitis (CM). Comparisons revealed a clonal relationship for 15 pairs of isolates recovered before and after recurrence showing relapse of the original infection. The two remaining pairs showed high levels of genetic heterogeneity; in one pair we found this to be a result of infection by mixed genotypes, while the second was a result of nonsense mutations in the gene encoding the DNA mismatch repair proteins MSH2, MSH5, and RAD5. These nonsense mutations led to a hypermutator state, leading to dramatically elevated rates of synonymous and nonsynonymous substitutions. Hypermutator phenotypes owing to nonsense mutations in these genes have not previously been reported in C. neoformans, and represent a novel pathway for rapid within-host adaptation and evolution of resistance to first-line antifungal drugs.
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30
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Vanhove M, Beale MA, Rhodes J, Chanda D, Lakhi S, Kwenda G, Molloy S, Karunaharan N, Stone N, Harrison TS, Bicanic T, Fisher MC. Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort. Mol Ecol 2017; 26:1991-2005. [PMID: 27862555 PMCID: PMC5412878 DOI: 10.1111/mec.13891] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 10/15/2016] [Accepted: 10/17/2016] [Indexed: 12/21/2022]
Abstract
Emerging infections caused by fungi have become a widely recognized global phenomenon and are causing an increasing burden of disease. Genomic techniques are providing new insights into the structure of fungal populations, revealing hitherto undescribed fine-scale adaptations to environments and hosts that govern their emergence as infections. Cryptococcal meningitis is a neglected tropical disease that is responsible for a large proportion of AIDS-related deaths across Africa; however, the ecological determinants that underlie a patient's risk of infection remain largely unexplored. Here, we use genome sequencing and ecological genomics to decipher the evolutionary ecology of the aetiological agents of cryptococcal meningitis, Cryptococcus neoformans and Cryptococcus gattii, across the central African country of Zambia. We show that the occurrence of these two pathogens is differentially associated with biotic (macroecological) and abiotic (physical) factors across two key African ecoregions, Central Miombo woodlands and Zambezi Mopane woodlands. We show that speciation of Cryptococcus has resulted in adaptation to occupy different ecological niches, with C. neoformans found to occupy Zambezi Mopane woodlands and C. gattii primarily recovered from Central Miombo woodlands. Genome sequencing shows that C. neoformans causes 95% of human infections in this region, of which over three-quarters belonged to the globalized lineage VNI. We show that VNI infections are largely associated with urbanized populations in Zambia. Conversely, the majority of C. neoformans isolates recovered in the environment belong to the genetically diverse African-endemic lineage VNB, and we show hitherto unmapped levels of genomic diversity within this lineage. Our results reveal the complex evolutionary ecology that underpins the reservoirs of infection for this, and likely other, deadly pathogenic fungi.
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MESH Headings
- Adaptation, Physiological/genetics
- Cryptococcus gattii/genetics
- Cryptococcus neoformans/genetics
- DNA Barcoding, Taxonomic
- DNA, Fungal/genetics
- DNA, Ribosomal Spacer/genetics
- Forests
- Genetics, Population
- Genome, Fungal
- Genomics
- Humans
- Meningitis, Cryptococcal/epidemiology
- Meningitis, Cryptococcal/microbiology
- Models, Biological
- Phylogeny
- Plant Bark/microbiology
- Polymorphism, Single Nucleotide
- Soil Microbiology
- Trees/microbiology
- Zambia
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Affiliation(s)
- Mathieu Vanhove
- Department of Infectious Disease Epidemiology, St Mary's Hospital, Imperial College London, London, W2 1PG, UK
| | - Mathew A Beale
- Department of Infectious Disease Epidemiology, St Mary's Hospital, Imperial College London, London, W2 1PG, UK
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
- Division of Infection & Immunity, University College London, Gower St, London WC1E 6BT, UK
| | - Johanna Rhodes
- Department of Infectious Disease Epidemiology, St Mary's Hospital, Imperial College London, London, W2 1PG, UK
| | - Duncan Chanda
- School of Medicine, University of Zambia, Nationalist Road, PO Box 50110, Lusaka, Zambia
| | - Shabir Lakhi
- School of Medicine, University of Zambia, Nationalist Road, PO Box 50110, Lusaka, Zambia
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Sile Molloy
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Natasha Karunaharan
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Neil Stone
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Thomas S Harrison
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Tihana Bicanic
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology, St Mary's Hospital, Imperial College London, London, W2 1PG, UK
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31
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Nascimento FS, Wei-Pridgeon Y, Arrowood MJ, Moss D, da Silva AJ, Talundzic E, Qvarnstrom Y. Evaluation of library preparation methods for Illumina next generation sequencing of small amounts of DNA from foodborne parasites. J Microbiol Methods 2016; 130:23-26. [PMID: 27553132 PMCID: PMC10750217 DOI: 10.1016/j.mimet.2016.08.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/19/2016] [Accepted: 08/19/2016] [Indexed: 10/21/2022]
Abstract
Illumina library preparation methods for ultra-low input amounts were compared using genomic DNA from two foodborne parasites (Angiostrongylus cantonensis and Cyclospora cayetanensis) as examples. The Ovation Ultralow method resulted in libraries with the highest concentration and produced quality sequencing data, even when the input DNA was in the picogram range.
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Affiliation(s)
- Fernanda S Nascimento
- Parasitic Disease Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, United States.
| | - Yuping Wei-Pridgeon
- Parasitic Disease Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, United States; IHRC Inc, 2 Ravinia Drive, Suite 1750, Atlanta, GA 30346, United States.
| | - Michael J Arrowood
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Enteric and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA, 30329, United States.
| | - Delynn Moss
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Enteric and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA, 30329, United States.
| | - Alexandre J da Silva
- Parasitic Disease Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, United States.
| | - Eldin Talundzic
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, United States; Atlanta Research and Education Foundation, 1670 Clairmont Road, Suite 5A104, Decatur, GA 30033, United States..
| | - Yvonne Qvarnstrom
- Parasitic Disease Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, United States.
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32
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Stålsby Lundborg C, Diwan V, Pathak A, Purohit MR, Shah H, Sharma M, Mahadik VK, Tamhankar AJ. Protocol: a 'One health' two year follow-up, mixed methods study on antibiotic resistance, focusing children under 5 and their environment in rural India. BMC Public Health 2015; 15:1321. [PMID: 26714632 PMCID: PMC4696104 DOI: 10.1186/s12889-015-2632-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/16/2015] [Indexed: 11/27/2022] Open
Abstract
Background Antibiotic resistance has been referred to as ‘the greatest malice of the 21st century’ and a global action plan was adopted by the World Health Assembly in 2015. There is a wealth of independent studies regarding antibiotics and resistant bacteria in humans, animals and their environment, however, integrated studies are lacking, particularly ones that simultaneously also take into consideration the health related behaviour of participants and healthcare providers. Such, ‘One health’ studies are difficult to implement, because of the complex teamwork that they entail. This paper describes the protocol of a study that investigates ‘One health’ issues regarding antibiotic use and antibiotic resistance in children and their environment in Indian villages. Methods/Design Both quantitative and qualitative studies are planned for a cohort of children, from 6 villages, and their surrounding environment. Repeated or continues data collection is planned over 2 years for quantitative studies. Qualitative studies will be conducted once. Studies include parents’ health seeking behavior for their children (1–3 years of age at the onset), prescribing pattern of formal and informal healthcare providers, analysis of phenotypic antibiotic resistance of Escherichia coli from samples of stool from children and village animals, household drinking water, village source water and waste water, and investigation on molecular mechanisms governing resistance. Analysis of interrelationship of these with each other will also be done as basis for future interventions. Ethics approval has been obtained from the Institutional Ethics Committee R.D. Gardi Medical College, Ujjain, India (No: 2013/07/17-311). Discussion The findings of the study presented in this protocol will add to our knowledge about the multi-factorial nature of causes governing antibiotic use and antibiotic resistance from a ‘One health’ perspective. Our study will be the first of its kind addressing antibiotic use and resistance issues related to children in a One-health approach, particularly for rural India.
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Affiliation(s)
- Cecilia Stålsby Lundborg
- Department of Public Health Sciences, Global Health - Health Systems and Policy (HSP): Medicines, focusing antibiotics, Karolinska Institutet, 171 77, Stockholm, Sweden.
| | - Vishal Diwan
- Department of Public Health Sciences, Global Health - Health Systems and Policy (HSP): Medicines, focusing antibiotics, Karolinska Institutet, 171 77, Stockholm, Sweden. .,Department of Public Health and Environment, R.D. Gardi Medical College, Ujjain, India. .,International Center for Health Research, R.D. Gardi Medical College, Ujjain, India.
| | - Ashish Pathak
- Department of Public Health Sciences, Global Health - Health Systems and Policy (HSP): Medicines, focusing antibiotics, Karolinska Institutet, 171 77, Stockholm, Sweden. .,Department of Pediatrics, R.D. Gardi Medical College, Ujjain, India. .,Department of Women and Children's Health, International Maternal and Child Health Unit, Uppsala University, Uppsala, Sweden.
| | - Manju R Purohit
- Department of Public Health Sciences, Global Health - Health Systems and Policy (HSP): Medicines, focusing antibiotics, Karolinska Institutet, 171 77, Stockholm, Sweden. .,Department of Pathology, R.D. Gardi Medical College, Ujjain, India. .,Central Clinical Laboratory, Ujjain Charitable Trust Hospital and Research Centre, Ujjain, India.
| | - Harshada Shah
- Department of Microbiology, R.D. Gardi Medical College, Ujjain, India.
| | - Megha Sharma
- Department of Public Health Sciences, Global Health - Health Systems and Policy (HSP): Medicines, focusing antibiotics, Karolinska Institutet, 171 77, Stockholm, Sweden. .,Department of Pharmacology, R.D. Gardi Medical College, Ujjain, India.
| | - Vijay K Mahadik
- Ujjain Charitable Trust Hospital and Research Centre, Ujjain, India.
| | - Ashok J Tamhankar
- Department of Public Health Sciences, Global Health - Health Systems and Policy (HSP): Medicines, focusing antibiotics, Karolinska Institutet, 171 77, Stockholm, Sweden. .,Indian Initiative for Management of Antibiotic Resistance, Department of Environmental Medicine, R.D. Gardi Medical College, Ujjain, India.
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Beale MA, Sabiiti W, Robertson EJ, Fuentes-Cabrejo KM, O’Hanlon SJ, Jarvis JN, Loyse A, Meintjes G, Harrison TS, May RC, Fisher MC, Bicanic T. Genotypic Diversity Is Associated with Clinical Outcome and Phenotype in Cryptococcal Meningitis across Southern Africa. PLoS Negl Trop Dis 2015; 9:e0003847. [PMID: 26110902 PMCID: PMC4482434 DOI: 10.1371/journal.pntd.0003847] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/24/2015] [Indexed: 12/21/2022] Open
Abstract
Cryptococcal meningitis is a major cause of mortality throughout the developing world, yet little is known about the genetic markers underlying Cryptococcal virulence and patient outcome. We studied a cohort of 230 Cryptococcus neoformans (Cn) isolates from HIV-positive South African clinical trial patients with detailed clinical follow-up using multi-locus sequence typing and in vitro phenotypic virulence assays, correlating these data with clinical and fungal markers of disease in the patient. South African Cn displayed high levels of genetic diversity and locus variability compared to globally distributed types, and we identified 50 sequence types grouped within the main molecular types VNI, VNII and VNB, with 72% of isolates typed into one of seven 'high frequency' sequence types. Spatial analysis of patients’ cryptococcal genotype was not shown to be clustered geographically, which might argue against recent local acquisition and in favour of reactivation of latent infection. Through comparison of MLST genotyping data with clinical parameters, we found a relationship between genetic lineage and clinical outcome, with patients infected with the VNB lineage having significantly worse survival (n=8, HR 3.35, CI 1.51-7.20, p=0.003), and this was maintained even after adjustment for known prognostic indicators and treatment regimen. Comparison of fungal genotype with in vitro phenotype (phagocytosis, laccase activity and CSF survival) performed on a subset of 89 isolates revealed evidence of lineage-associated virulence phenotype, with the VNII lineage displaying increased laccase activity (p=0.001) and ex vivo CSF survival (p=0.0001). These findings show that Cryptococcus neoformans is a phenotypically heterogeneous pathogen, and that lineage plays an important role in cryptococcal virulence during human infection. Furthermore, a detailed understanding of the genetic diversity in Southern Africa will support further investigation into how genetic diversity is structured across African environments, allowing assessment of the risks different ecotypes pose to infection. Cryptococcus neoformans (Cn) is a yeast that commonly causes meningitis in HIV infected individuals in Africa, where it may account for up to 500,000 deaths every year. In this highly translational and multidisciplinary study, we used genetic analysis techniques to show that Cryptococcus found in Southern Africa represents a hotspot of genetic diversity. We combined this data with the results of microbiological techniques that assess the natural virulence traits that the yeast uses to survive and infect humans to further show that genetic diversity is associated with differences in cryptococcal phenotype. Finally, we analysed detailed clinical data on patients to investigate the clinical effects of infection with different lineages, and showed that one genetic lineage (VNB) is significantly associated with worse survival. Whilst much of our prior knowledge regarding the genetic basis of virulence is derived from studies on laboratory-adapted cryptococcal strains, our findings from this large and comprehensive MLST genotyping study of clinical isolates—linking genotype, phenotype, clinical presentation and outcome—provide direct insights into the contribution of pathogen lineage to virulence in human cryptococcal meningitis.
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Affiliation(s)
- Mathew A. Beale
- Institute of Infection and Immunity, St. George’s University London, London, United Kingdom
- Department of Infectious Disease Epidemiology, Imperial College School of Public Health, London, United Kingdom
| | - Wilber Sabiiti
- Institute of Infection and Immunity, St. George’s University London, London, United Kingdom
- School of Medicine University of St. Andrews, St. Andrews, United Kingdom
| | - Emma J. Robertson
- Institute of Infection and Immunity, St. George’s University London, London, United Kingdom
| | | | - Simon J. O’Hanlon
- Department of Infectious Disease Epidemiology, Imperial College School of Public Health, London, United Kingdom
| | - Joseph N. Jarvis
- Botswana-UPenn Partnership, Gaborone, Botswana
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Angela Loyse
- Institute of Infection and Immunity, St. George’s University London, London, United Kingdom
| | - Graeme Meintjes
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Thomas S. Harrison
- Institute of Infection and Immunity, St. George’s University London, London, United Kingdom
| | - Robin C. May
- Institute of Microbiology and Infection and the School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- National Institute for Health Research (NIHR) Surgical Reconstruction and Microbiology Research Centre, University Hospitals of Birmingham National Health Service (NHS) Foundation Trust, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Matthew C. Fisher
- Department of Infectious Disease Epidemiology, Imperial College School of Public Health, London, United Kingdom
- * E-mail: (MCF); (TB)
| | - Tihana Bicanic
- Institute of Infection and Immunity, St. George’s University London, London, United Kingdom
- * E-mail: (MCF); (TB)
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Kofler R, Nolte V, Schlötterer C. The impact of library preparation protocols on the consistency of allele frequency estimates in Pool-Seq data. Mol Ecol Resour 2015; 16:118-22. [PMID: 26014582 PMCID: PMC4744716 DOI: 10.1111/1755-0998.12432] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/17/2015] [Accepted: 05/22/2015] [Indexed: 11/29/2022]
Abstract
Sequencing pools of individuals (Pool‐Seq) is a cost‐effective method to determine genome‐wide allele frequency estimates. Given the importance of meta‐analyses combining data sets, we determined the influence of different genomic library preparation protocols on the consistency of allele frequency estimates. We found that typically no more than 1% of the variation in allele frequency estimates could be attributed to differences in library preparation. Also read length had only a minor effect on the consistency of allele frequency estimates. By far, the most pronounced influence could be attributed to sequence coverage. Increasing the coverage from 30‐ to 50‐fold improved the consistency of allele frequency estimates by at least 27%. We conclude that Pool‐Seq data can be easily combined across different library preparation methods, but sufficient sequence coverage is key to reliable results.
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Affiliation(s)
- Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
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35
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Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing. mBio 2015; 6:e00536. [PMID: 26037120 PMCID: PMC4453006 DOI: 10.1128/mbio.00536-15] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A rapid and global emergence of azole resistance has been observed in the pathogenic fungus Aspergillus fumigatus over the past decade. The dominant resistance mechanism appears to be of environmental origin and involves mutations in the cyp51A gene, which encodes a protein targeted by triazole antifungal drugs. Whole-genome sequencing (WGS) was performed for high-resolution single-nucleotide polymorphism (SNP) analysis of 24 A. fumigatus isolates, including azole-resistant and susceptible clinical and environmental strains obtained from India, the Netherlands, and the United Kingdom, in order to assess the utility of WGS for characterizing the alleles causing resistance. WGS analysis confirmed that TR34/L98H (a mutation comprising a tandem repeat [TR] of 34 bases in the promoter of the cyp51A gene and a leucine-to-histidine change at codon 98) is the sole mechanism of azole resistance among the isolates tested in this panel of isolates. We used population genomic analysis and showed that A. fumigatus was panmictic, with as much genetic diversity found within a country as is found between continents. A striking exception to this was shown in India, where isolates are highly related despite being isolated from both clinical and environmental sources across >1,000 km; this broad occurrence suggests a recent selective sweep of a highly fit genotype that is associated with the TR34/L98H allele. We found that these sequenced isolates are all recombining, showing that azole-resistant alleles are segregating into diverse genetic backgrounds. Our analysis delineates the fundamental population genetic parameters that are needed to enable the use of genome-wide association studies to identify the contribution of SNP diversity to the generation and spread of azole resistance in this medically important fungus. Resistance to azoles in the ubiquitous ascomycete fungus A. fumigatus was first reported from clinical isolates collected in the United States during the late 1980s. Over the last decade, an increasing number of A. fumigatus isolates from the clinic and from nature have been found to show resistance to azoles, suggesting that resistance is emerging through selection by the widespread usage of agricultural azole antifungal compounds. Aspergillosis is an emerging clinical problem, with high rates of treatment failures necessitating the development of new techniques for surveillance and for determining the genome-wide basis of azole resistance in A. fumigatus.
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36
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Uyaguari-Diaz MI, Slobodan JR, Nesbitt MJ, Croxen MA, Isaac-Renton J, Prystajecky NA, Tang P. Automated Gel Size Selection to Improve the Quality of Next-generation Sequencing Libraries Prepared from Environmental Water Samples. J Vis Exp 2015. [PMID: 25938488 DOI: 10.3791/52685] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Next-generation sequencing of environmental samples can be challenging because of the variable DNA quantity and quality in these samples. High quality DNA libraries are needed for optimal results from next-generation sequencing. Environmental samples such as water may have low quality and quantities of DNA as well as contaminants that co-precipitate with DNA. The mechanical and enzymatic processes involved in extraction and library preparation may further damage the DNA. Gel size selection enables purification and recovery of DNA fragments of a defined size for sequencing applications. Nevertheless, this task is one of the most time-consuming steps in the DNA library preparation workflow. The protocol described here enables complete automation of agarose gel loading, electrophoretic analysis, and recovery of targeted DNA fragments. In this study, we describe a high-throughput approach to prepare high quality DNA libraries from freshwater samples that can be applied also to other environmental samples. We used an indirect approach to concentrate bacterial cells from environmental freshwater samples; DNA was extracted using a commercially available DNA extraction kit, and DNA libraries were prepared using a commercial transposon-based protocol. DNA fragments of 500 to 800 bp were gel size selected using Ranger Technology, an automated electrophoresis workstation. Sequencing of the size-selected DNA libraries demonstrated significant improvements to read length and quality of the sequencing reads.
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Affiliation(s)
- Miguel I Uyaguari-Diaz
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, The University of British Columbia;
| | | | | | - Matthew A Croxen
- British Columbia Public Health Microbiology and Reference Laboratory
| | - Judith Isaac-Renton
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, The University of British Columbia; British Columbia Public Health Microbiology and Reference Laboratory
| | - Natalie A Prystajecky
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, The University of British Columbia; British Columbia Public Health Microbiology and Reference Laboratory
| | - Patrick Tang
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, The University of British Columbia; British Columbia Public Health Microbiology and Reference Laboratory
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