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Lee J, Hunter B, Shim H. A pangenome analysis of ESKAPE bacteriophages: the underrepresentation may impact machine learning models. Front Mol Biosci 2024; 11:1395450. [PMID: 38974320 PMCID: PMC11224154 DOI: 10.3389/fmolb.2024.1395450] [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: 03/03/2024] [Accepted: 05/31/2024] [Indexed: 07/09/2024] Open
Abstract
Bacteriophages are the most prevalent biological entities in the biosphere. However, limitations in both medical relevance and sequencing technologies have led to a systematic underestimation of the genetic diversity within phages. This underrepresentation not only creates a significant gap in our understanding of phage roles across diverse biosystems but also introduces biases in computational models reliant on these data for training and testing. In this study, we focused on publicly available genomes of bacteriophages infecting high-priority ESKAPE pathogens to show the extent and impact of this underrepresentation. First, we demonstrate a stark underrepresentation of ESKAPE phage genomes within the public genome and protein databases. Next, a pangenome analysis of these ESKAPE phages reveals extensive sharing of core genes among phages infecting the same host. Furthermore, genome analyses and clustering highlight close nucleotide-level relationships among the ESKAPE phages, raising concerns about the limited diversity within current public databases. Lastly, we uncover a scarcity of unique lytic phages and phage proteins with antimicrobial activities against ESKAPE pathogens. This comprehensive analysis of the ESKAPE phages underscores the severity of underrepresentation and its potential implications. This lack of diversity in phage genomes may restrict the resurgence of phage therapy and cause biased outcomes in data-driven computational models due to incomplete and unbalanced biological datasets.
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Affiliation(s)
- Jeesu Lee
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, Republic of Korea
| | - Branden Hunter
- Department of Biology, California State University, Fresno, CA, United States
| | - Hyunjin Shim
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, Republic of Korea
- Department of Biology, California State University, Fresno, CA, United States
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2
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Shchyogolev SY, Burygin GL, Dykman LA, Matora LY. Phylogenetic and pangenomic analyses of members of the family Micrococcaceae related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (Solanum tuberosum L.). Vavilovskii Zhurnal Genet Selektsii 2024; 28:308-316. [PMID: 38952705 PMCID: PMC11214901 DOI: 10.18699/vjgb-24-35] [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: 09/15/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 07/03/2024] Open
Abstract
We report the results of taxonomic studies on members of the family Micrococcaceae that, according to the 16S rRNA, internal transcribed spacer 1 (ITS1), average nucleotide identity (ANI), and average amino acid identity (AAI) tests, are related to Kocuria rosea strain RCAM04488, a plant-growth-promoting rhizobacterium (PGPR) isolated from the rhizosphere of potato (Solanum tuberosum L.). In these studies, we used whole-genome phylogenetic tests and pangenomic analysis. According to the ANI > 95 % criterion, several known members of K. salina, K. polaris, and K. rosea (including K. rosea type strain ATCC 186T) that are related most closely to isolate RCAM04488 in the ITS1 test should be assigned to the same species with appropriate strain verification. However, these strains were isolated from strongly contrasting ecological and geographical habitats, which could not but affect their genotypes and phenotypes and which should be taken into account in evaluation of their systematic position. This contradiction was resolved by a pangenomic analysis, which showed that the strains differed strongly in the number of accessory and strain-specific genes determining their individuality and possibly their potential for adaptation to different ecological niches. Similar results were obtained in a full-scale AAI test against the UniProt database (about 250 million records), by using the AAI-profiler program and the proteome of K. rosea strain ATCC 186T as a query. According to the AAI > 65 % criterion, members of the genus Arthrobacter and several other genera belonging to the class Actinomycetes, with a very wide geographical and ecological range of sources of isolation, should be placed into the same genus as Kocuria. Within the paradigm with vertically inherited phylogenetic markers, this could be regarded as a signal for their following taxonomic reclassification. An important factor in this case may be the detailing of the gene composition of the strains and the taxonomic ratios resulting from analysis of the pangenomes of the corresponding clades.
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Affiliation(s)
- S Yu Shchyogolev
- Institute of Biochemistry and Physiology of Plants and Microorganisms - Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of Sciences, Saratov, Russia
| | - G L Burygin
- Institute of Biochemistry and Physiology of Plants and Microorganisms - Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of Sciences, Saratov, Russia Saratov State Vavilov Agrarian University, Saratov, Russia
| | - L A Dykman
- Institute of Biochemistry and Physiology of Plants and Microorganisms - Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of Sciences, Saratov, Russia
| | - L Yu Matora
- Institute of Biochemistry and Physiology of Plants and Microorganisms - Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of Sciences, Saratov, Russia
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Li J, Wu H, Pu Q, Zhang C, Chen Y, Lin Z, Hu X, Li O. Complete genome of Sphingomonas paucimobilis ZJSH1, an endophytic bacterium from Dendrobium officinale with stress resistance and growth promotion potential. Arch Microbiol 2023; 205:132. [PMID: 36959350 DOI: 10.1007/s00203-023-03459-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/25/2023]
Abstract
Sphingomonas paucimobilis ZJSH1 is an endophytic bacterium isolated from the roots of Dendrobium officinale with the ability to promote plant growth. It was found that the genome of strain ZJSH1 had gene fragment rearrangement compared with the genomes of the other four strains of S. paucimobilis, and the genome was integrated with phage genes. Functional analysis showed that the strain contained colonization-related genes, chemotaxis and invasion. A variety of genes encoding active materials, such as hormones (IAA, SA, ABA and zeaxanthin), phosphate cycle, antioxidant enzymes, and polysaccharides were identified which provide the strain with growth promotion and stress-resistant characteristics. Experiments proved that S. paucimobilis ZJSH1 grew well in media containing 80 g/L sodium chloride, 240 g/L polyethylene glycol and 800 μmol/L Cd2+, indicating its potential for resistance to stresses of salt, drought and cadmium, respectively. S. paucimobilis ZJSH1 is the only endophytic bacterium of this species that has been reported to promote plant growth. The analysis of its genome is conducive to understanding its growth-promoting mechanism and laying a foundation for the development and utilization of this species in the field of agriculture.
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Affiliation(s)
- Jin Li
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928th Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Hangtao Wu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928th Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Qian Pu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928th Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Chu Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928th Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Ying Chen
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928th Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Zhengxin Lin
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928th Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Xiufang Hu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928th Second Avenue, Hangzhou, 310018, People's Republic of China.
| | - Ou Li
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928th Second Avenue, Hangzhou, 310018, People's Republic of China.
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Rehman MNU, Dawar FU, Zeng J, Fan L, Feng W, Wang M, Yang N, Guo G, Zheng J. Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile. Front Vet Sci 2023; 10:1140655. [PMID: 36968469 PMCID: PMC10034365 DOI: 10.3389/fvets.2023.1140655] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/08/2023] [Indexed: 03/11/2023] Open
Abstract
Edwardsiella tarda is a Gram-negative, facultative anaerobic rod-shaped bacterium and the causative agent of the systemic disease “Edwardsiellosis”. It is commonly prevalent in aquatic organisms with subsequent economic loss and hence has attracted increasing attention from researchers. In this study, we investigated the complete genome sequence of a highly virulent isolate Edwardsiella tarda SC002 isolated from hatchlings of the Siamese crocodile. The genome of SC002 consisted of one circular chromosome of length 3,662,469 bp with a 57.29% G+C content and four novel plasmids. A total of 3,734 protein-coding genes, 12 genomic islands (GIs), 7 prophages, 48 interspersed repeat sequences, 248 tandem repeat sequences, a CRISPR component with a total length of 175 bp, and 171 ncRNAs (tRNA = 106, sRNA = 37, and rRNA = 28) were predicted. In addition, the coding genes of assembled genome were successfully annotated against eight general databases (NR = 3,618/3,734, COG = 2,947/3,734, KEGG = 3,485/3,734, SWISS-PROT = 2,787/3,734, GO = 2,648/3,734, Pfam = 2,648/3,734, CAZy = 130/3,734, and TCDB = 637/3,734) and four pathogenicity-related databases (ARDB = 11/3,734, CARD = 142/3,734, PHI = 538/3,734, and VFDB = 315/3,734). Pan-genome and comparative genome analyses of the complete sequenced genomes confirmed their evolutionary relationships. The present study confirmed that E. tarda SC002 is a potential pathogen bearing a bulk amount of antibiotic resistance, virulence, and pathogenic genes and its open pan-genome may enhance its host range in the future.
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Affiliation(s)
- Muhammad Nafees Ur Rehman
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Farman Ullah Dawar
- Department of Zoology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Jifeng Zeng
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, China
| | - Lixia Fan
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Wei Feng
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Mengqi Wang
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Nuo Yang
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Guiying Guo
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Jiping Zheng
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, China
- *Correspondence: Jiping Zheng
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Liu D, Zhang Y, Fan G, Sun D, Zhang X, Yu Z, Wang J, Wu L, Shi W, Ma J. IPGA: A handy integrated prokaryotes genome and pan-genome analysis web service. IMETA 2022; 1:e55. [PMID: 38867900 PMCID: PMC10989949 DOI: 10.1002/imt2.55] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/11/2022] [Accepted: 08/20/2022] [Indexed: 06/14/2024]
Abstract
Pan-genomics is one of the most powerful means to study genomic variation and obtain a sketch of genes within a defined clade of species. Though there are a lot of computational tools to achieve this, an integrated framework to evaluate their performance and offer the best choice to users has never been achieved. To ease the process of large-scale prokaryotic genome analysis, we introduce Integrated Prokaryotes Genome and pan-genome Analysis (IPGA), a one-stop web service to analyze, compare, and visualize pan-genome as well as individual genomes, that rids users of installing any specific tools. IPGA features a scoring system that helps users to evaluate the reliability of pan-genome profiles generated by different packages. Thus, IPGA can help users ascertain the profiling method that is most suitable for their data set for the following analysis. In addition, IPGA integrates several downstream comparative analysis and genome analysis modules to make users achieve diverse targets.
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Affiliation(s)
- Dongmei Liu
- Microbial Resource and Big Data Center, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yifei Zhang
- Central LaboratoryPeking University School and Hospital of StomatologyBeijingChina
| | - Guomei Fan
- Microbial Resource and Big Data Center, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Dingzhong Sun
- Microbial Resource and Big Data Center, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Xingjiao Zhang
- Microbial Resource and Big Data Center, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Zhengfei Yu
- Microbial Resource and Big Data Center, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Jinfeng Wang
- College of Food Science and Nutritional EngineeringChina Agricultural UniversityBeijingChina
| | - Linhuan Wu
- Microbial Resource and Big Data Center, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- National Microbiology Data CenterBeijingChina
| | - Wenyu Shi
- Microbial Resource and Big Data Center, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Juncai Ma
- Microbial Resource and Big Data Center, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- National Microbiology Data CenterBeijingChina
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Tan XJ, Zhang ZW, Xiao JJ, Wang W, He F, Gao X, Jiang B, Shen L, Wang X, Sun Y, Zhu GP. Genomic and phenotypic biology of a novel Dickeya zeae WH1 isolated from rice in China: Insights into pathogenicity and virulence factors. Front Microbiol 2022; 13:997486. [PMID: 36386707 PMCID: PMC9650423 DOI: 10.3389/fmicb.2022.997486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/03/2022] [Indexed: 10/06/2023] Open
Abstract
Soft rot caused by Dickeya zeae is an important bacterial disease affecting rice and other plants worldwide. In this study, Nanopore and Illumina sequencing platforms were used to sequence the high-quality complete genome of a novel D. zeae strain WH1 (size: 4.68 Mb; depth: 322.37x for Nanopore, 243.51x for Illumina; GC content: 53.59%), which was isolated from healthy rice root surface together with Paenibacillus polymyxa, a potential biocontrol bacterium against D. zeae strain WH1. However, the pure WH1 culture presented severe pathogenicity. Multilocus sequence analysis (MLSA) indicated that strains WH1, EC1, and EC2 isolated from rice were grouped into a clade differentiated from other D. zeae strains. The average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) analyses demonstrated that WH1 was phylogenetically closest to EC2. Furthermore, the pathogenicity determinants and virulence factors of WH1 were mainly analyzed through genomic comparison with complete genomes of other D. zeae strains with high virulence (EC1, EC2, MS1, and MS2). The results revealed that plant cell wall-degrading extracellular enzymes (PCWDEs), flagellar and chemotaxis, and quorum sensing were highly conserved in all analyzed genomes, which were confirmed through phenotypic assays. Besides, WH1 harbored type I, II, III, and VI secretion systems (T1SS, T2SS, T3SS, and T6SS), but lost T4SS and T5SS. Like strains MS1 and MS2 isolated from bananas, WH1 harbored genes encoding both capsule polysaccharide (CPS) and exopolysaccharide (EPS) biosynthesis. The results of pathogenicity assays demonstrated that WH1 produced severe soft rot symptoms on potato tubers, carrots, radishes, and Chinese cabbage. Meanwhile, WH1 also produced phytotoxin(s) to inhibit rice seed germination with an 87% inhibitory rate in laboratory conditions. More importantly, we confirmed that phytotoxin(s) produced by WH1 are different from zeamines produced by EC1. Comparative genomics analyses and phenotypic and pathogenicity assays suggested that WH1 likely evolved through a pathway different from the other D. zeae strains from rice, producing a new type of rice foot rot pathogen. These findings highlight the emergence of a new type of D. zeae strain with high virulence, causing soft rot in rice and other plants.
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Affiliation(s)
- Xiao-Juan Tan
- College of Life Sciences, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Anhui Normal University, Wuhu, Anhui, China
| | - Zhi-Wei Zhang
- College of Life Sciences, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Anhui Normal University, Wuhu, Anhui, China
| | - Jing-Jing Xiao
- College of Life Sciences, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Anhui Normal University, Wuhu, Anhui, China
| | - Wei Wang
- Wuhu Qingyijiang Seed Industry Co., Ltd., Wuhu, Anhui, China
| | - Feng He
- College of Life Sciences, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Anhui Normal University, Wuhu, Anhui, China
| | - Xuan Gao
- College of Life Sciences, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Anhui Normal University, Wuhu, Anhui, China
| | - Bin Jiang
- College of Life Sciences, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Anhui Normal University, Wuhu, Anhui, China
| | - Liang Shen
- College of Life Sciences, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Anhui Normal University, Wuhu, Anhui, China
| | - Xu Wang
- College of Life Sciences, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Anhui Normal University, Wuhu, Anhui, China
| | - Yang Sun
- College of Life Sciences, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Anhui Normal University, Wuhu, Anhui, China
| | - Guo-Ping Zhu
- College of Life Sciences, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Anhui Normal University, Wuhu, Anhui, China
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Dereeper A, Summo M, Meyer DF. PanExplorer: a web-based tool for exploratory analysis and visualization of bacterial pan-genomes. Bioinformatics 2022; 38:4412-4414. [PMID: 35916725 PMCID: PMC9477528 DOI: 10.1093/bioinformatics/btac504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 07/09/2022] [Accepted: 07/29/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION As pan-genome approaches are largely employed for bacterial comparative genomics and evolution analyses, but still difficult to be carried out by non-bioinformatician biologists, there is a need for an innovative tool facilitating the exploration of bacterial pan-genomes. RESULTS PanExplorer is a web application providing various genomic analyses and reports, giving intuitive views that enable a better understanding of bacterial pan-genomes. As an example, we produced the pan-genome for 121 Anaplasmataceae strains (including 30 Ehrlichia, 15 Anaplasma, 68 Wolbachia). AVAILABILITY AND IMPLEMENTATION PanExplorer is written in Perl CGI and relies on several JavaScript libraries for visualization (hotmap.js, MauveViewer, CircosJS). It is freely available at http://panexplorer.southgreen.fr. The source code has been released in a GitHub repository https://github.com/SouthGreenPlatform/PanExplorer. A documentation section is available on PanExplorer website.
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Affiliation(s)
| | - Marilyne Summo
- French Institute of Bioinformatics (IFB)—South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France,CIRAD, UMR AGAP, F-34398 Montpellier, France
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Kuncharoen N, Yuki M, Kudo T, Okuma M, Booncharoen A, Mhuantong W, Tanasupawat S. Comparative genomics and proposal of Streptomyces radicis sp. nov., an endophytic actinomycete from roots of plants in Thailand. Microbiol Res 2021; 254:126889. [PMID: 34689101 DOI: 10.1016/j.micres.2021.126889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 08/29/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Abstract
Strains DS1-2T and AZ1-7, which were isolated from roots of plants, were taxonomically characterized based on polyphasic taxonomic and taxogenomic approaches. Both strains were Gram-stain-positive and filamentous bacteria which contained LL-diaminopimelic acid in cell-wall peptidoglycan and glucose and ribose in whole-cell hydrolysates. MK-9(H6), MK-10(H6), MK-9(H8), MK-10(H8) and MK-10(H4) were major menaquinones; iso-C16:0 and iso-C16:1G were predominant cellular fatty acids; diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol mannoside presented as major phospholipids; and the DNA G+C contents of 73.2 mol%. Strains DS1-2T and AZ1-7 showed 97.6-98.0 % 16S rRNA gene sequence similarity, 81.0-82.0 % ANIb, 84.8-85.3 % ANIm and 22.0-23.1 % digital DDH to their related type strains: S. specialis GW41-1564T and S. hoynatensis S1412T. Comparative genomics results of these strains and their related type strains also revealed the differences and distributions of key genes associated with stress responses, environmental variables, plant interactions and bioactive metabolites. Based on the phenotypic, chemotaxonomic and genomic data, strains DS1-2T and AZ1-7 could be assigned to the novel species within the genus Streptomyces for which the name Streptomyces radicis sp. nov. is proposed. The type strain is DS1-2T (=JCM 32152T =KCTC 39738T =TISTR 2403T).
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Affiliation(s)
- Nattakorn Kuncharoen
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Okuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Auttaporn Booncharoen
- Food Biotechnology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Research Team, Biorefinery and Bioproducts Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand.
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Silva de Oliveira M, Thyeska Castro Alves J, Henrique Caracciolo Gomes de Sá P, Veras AADO. PAN2HGENE-tool for comparative analysis and identifying new gene products. PLoS One 2021; 16:e0252414. [PMID: 34048479 PMCID: PMC8162609 DOI: 10.1371/journal.pone.0252414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 05/14/2021] [Indexed: 12/02/2022] Open
Abstract
Advances in next-generation sequencing (NGS) platforms have had a positive impact on biological research, leading to the development of numerous omics approaches, including genomics, transcriptomics, metagenomics, and pangenomics. These analyses provide insights into the gene contents of various organisms. However, to understand the evolutionary processes of these genes, comparative analysis, which is an important tool for annotation, is required. Using comparative analysis, it is possible to infer the functions of gene contents and identify orthologs and paralogous genes via their homology. Although several comparative analysis tools currently exist, most of them are limited to complete genomes. PAN2HGENE, a computational tool that allows identification of gene products missing from the original genome sequence, with automated comparative analysis for both complete and draft genomes, can be used to address this limitation. In this study, PAN2HGENE was used to identify new products, resulting in altering the alpha value behavior in the pangenome without altering the original genomic sequence. Our findings indicate that this tool represents an efficient alternative for comparative analysis, with a simple and intuitive graphical interface. The PAN2HGENE have been uploaded to SourceForge and are available via: https://sourceforge.net/projects/pan2hgene-software
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Affiliation(s)
- Mônica Silva de Oliveira
- Postgraduate Program in Applied Computing, Federal University of Pará Campus Tucuruí (CAMTUC-UFPA), Pará, Brazil
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Mavrodi OV, McWilliams JR, Peter JO, Berim A, Hassan KA, Elbourne LDH, LeTourneau MK, Gang DR, Paulsen IT, Weller DM, Thomashow LS, Flynt AS, Mavrodi DV. Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas. Front Microbiol 2021; 12:651282. [PMID: 33936009 PMCID: PMC8079746 DOI: 10.3389/fmicb.2021.651282] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialog between eight well-characterized beneficial strains of the Pseudomonas fluorescens group and Brachypodium distachyon, a model for economically important food, feed, forage, and biomass crops of the grass family. We collected and analyzed root exudates of B. distachyon and demonstrated the presence of multiple carbohydrates, amino acids, organic acids, and phenolic compounds. The subsequent screening of bacteria by Biolog Phenotype MicroArrays revealed that many of these metabolites provide carbon and energy for the Pseudomonas strains. RNA-seq profiling of bacterial cultures amended with root exudates revealed changes in the expression of genes encoding numerous catabolic and anabolic enzymes, transporters, transcriptional regulators, stress response, and conserved hypothetical proteins. Almost half of the differentially expressed genes mapped to the variable part of the strains’ pangenome, reflecting the importance of the variable gene content in the adaptation of P. fluorescens to the rhizosphere lifestyle. Our results collectively reveal the diversity of cellular pathways and physiological responses underlying the establishment of mutualistic interactions between these beneficial rhizobacteria and their plant hosts.
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Affiliation(s)
- Olga V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Janiece R McWilliams
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Jacob O Peter
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Anna Berim
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Karl A Hassan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Liam D H Elbourne
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Melissa K LeTourneau
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - David R Gang
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - David M Weller
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda S Thomashow
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Alex S Flynt
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Dmitri V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
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11
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Costa SS, Guimarães LC, Silva A, Soares SC, Baraúna RA. First Steps in the Analysis of Prokaryotic Pan-Genomes. Bioinform Biol Insights 2020; 14:1177932220938064. [PMID: 32843837 PMCID: PMC7418249 DOI: 10.1177/1177932220938064] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/26/2020] [Indexed: 01/14/2023] Open
Abstract
Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues.
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Affiliation(s)
- Sávio Souza Costa
- Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, Brazil
- Laboratório de Engenharia Biológica, Espaço Inovação, Parque de Ciência e Tecnologia Guamá, Belém, Brazil
| | - Luís Carlos Guimarães
- Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, Brazil
| | - Artur Silva
- Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, Brazil
- Laboratório de Engenharia Biológica, Espaço Inovação, Parque de Ciência e Tecnologia Guamá, Belém, Brazil
| | - Siomar Castro Soares
- Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Rafael Azevedo Baraúna
- Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, Brazil
- Laboratório de Engenharia Biológica, Espaço Inovação, Parque de Ciência e Tecnologia Guamá, Belém, Brazil
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12
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Anani H, Zgheib R, Hasni I, Raoult D, Fournier PE. Interest of bacterial pangenome analyses in clinical microbiology. Microb Pathog 2020; 149:104275. [PMID: 32562810 DOI: 10.1016/j.micpath.2020.104275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022]
Abstract
Thanks to the progress and decreasing costs in genome sequencing technologies, more than 250,000 bacterial genomes are currently available in public databases, covering most, if not all, of the major human-associated phylogenetic groups of these microorganisms, pathogenic or not. In addition, for many of them, sequences from several strains of a given species are available, thus enabling to evaluate their genetic diversity and study their evolution. In addition, the significant cost reduction of bacterial whole genome sequencing as well as the rapid increase in the number of available bacterial genomes have prompted the development of pangenomic software tools. The study of bacterial pangenome has many applications in clinical microbiology. It can unveil the pathogenic potential and ability of bacteria to resist antimicrobials as well identify specific sequences and predict antigenic epitopes that allow molecular or serologic assays and vaccines to be designed. Bacterial pangenome constitutes a powerful method for understanding the history of human bacteria and relating these findings to diagnosis in clinical microbiology laboratories in order to optimize patient management.
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Affiliation(s)
- Hussein Anani
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Rita Zgheib
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Issam Hasni
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
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13
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Sun Z, Zhou D, Zhang X, Li Q, Lin H, Lu W, Liu H, Lu J, Lin X, Li K, Xu T, Bao Q, Zhang H. Determining the Genetic Characteristics of Resistance and Virulence of the "Epidermidis Cluster Group" Through Pan-Genome Analysis. Front Cell Infect Microbiol 2020; 10:274. [PMID: 32596166 PMCID: PMC7303328 DOI: 10.3389/fcimb.2020.00274] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/07/2020] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus caprae, Staphylococcus capitis, and Staphylococcus epidermidis belong to the “Epidermidis Cluster Group” (ECG) and are generally opportunistic pathogens. In this work, whole genome sequencing, molecular cloning and pan-genome analysis were performed to investigate the genetic characteristics of the resistance, virulence and genome structures of 69 ECG strains, including a clinical isolate (S. caprae SY333) obtained in this work. Two resistance genes (blaZ and aadD2) encoded on the plasmids pSY333-41 and pSY333-45 of S. caprae SY333 were confirmed to be functional. The bla region in ECG exhibited three distinct structures, and these chromosome- and plasmid-encoded bla operons seemed to follow two different evolutionary paths. Pan-genome analysis revealed their pan-genomes tend to be “open.” For the virulence-related factors, the genes involved in primary attachment were observed almost exclusively in S. epidermidis, while the genes associated with intercellular aggregation were observed more frequently in S. caprae and S. capitis. The type VII secretion system was present in all strains of S. caprae and some of S. epidermidis but not in S. capitis. Moreover, the isd locus (iron regulated surface determinant) was first found to be encoded on the genomes of S. caprae and S. capitis. These findings suggested that the plasmid and chromosome encoded bla operons of ECG species underwent different evolution paths, as well as they differed in the abundance of virulence genes associated with adherence, invasion, secretion system and immune evasion. Identification of isd loci in S. caprae and S. capitis indicated their ability to acquire heme as nutrient iron during infection.
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Affiliation(s)
- Zhewei Sun
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Danying Zhou
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Hailong Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Wei Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Hongmao Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
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14
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Rajkumari J, Chakraborty S, Pandey P. Distinctive features gleaned from the comparative genomes analysis of clinical and non-clinical isolates of Klebsiella pneumoniae. Bioinformation 2020; 16:256-268. [PMID: 32308268 PMCID: PMC7147497 DOI: 10.6026/97320630016256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/10/2020] [Accepted: 03/15/2020] [Indexed: 11/23/2022] Open
Abstract
It is of interest to describe the distinctive features gleaned from the comparative genome analysis of clinical and non-clinical isolates of Klebsiella pneumoniae. The core genome of K. pneumoinae consisted of 3568 genes. Comparative genome analysis shows that mdtABCD, toxin-antitoxin systems are unique to clinical isolates and catB, benA, and transporter genes for citrate utilization are exclusive to non-clinical isolates. We further noted aromatic compound degrading genes in non-clinical isolates unlike in the later isolates. We grouped 88 core genes into 3 groups linked to infections, drug-resistance or xenobiotic metabolism using codon usage variation analysis. It is inferred using the neutrality plot analysis of GC12 with GC3 that codon usage variation is dominant over mutation pressure. Thus, we document data to distinguish clinical and non-clinical isolates of K. pneumoniae using comparative genomes analysis for understanding of genome diversity during speciation.
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Affiliation(s)
- Jina Rajkumari
- Department of Microbiology, Assam University, Silchar 788011, Assam, India
| | | | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar 788011, Assam, India
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15
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Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. Mar Drugs 2019; 17:md17100576. [PMID: 31614509 PMCID: PMC6835618 DOI: 10.3390/md17100576] [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: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022] Open
Abstract
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.
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16
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Avram O, Rapoport D, Portugez S, Pupko T. M1CR0B1AL1Z3R-a user-friendly web server for the analysis of large-scale microbial genomics data. Nucleic Acids Res 2019; 47:W88-W92. [PMID: 31114912 PMCID: PMC6602433 DOI: 10.1093/nar/gkz423] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/29/2019] [Accepted: 05/06/2019] [Indexed: 11/21/2022] Open
Abstract
Large-scale mining and analysis of bacterial datasets contribute to the comprehensive characterization of complex microbial dynamics within a microbiome and among different bacterial strains, e.g., during disease outbreaks. The study of large-scale bacterial evolutionary dynamics poses many challenges. These include data-mining steps, such as gene annotation, ortholog detection, sequence alignment and phylogeny reconstruction. These steps require the use of multiple bioinformatics tools and ad-hoc programming scripts, making the entire process cumbersome, tedious and error-prone due to manual handling. This motivated us to develop the M1CR0B1AL1Z3R web server, a 'one-stop shop' for conducting microbial genomics data analyses via a simple graphical user interface. Some of the features implemented in M1CR0B1AL1Z3R are: (i) extracting putative open reading frames and comparative genomics analysis of gene content; (ii) extracting orthologous sets and analyzing their size distribution; (iii) analyzing gene presence-absence patterns; (iv) reconstructing a phylogenetic tree based on the extracted orthologous set; (v) inferring GC-content variation among lineages. M1CR0B1AL1Z3R facilitates the mining and analysis of dozens of bacterial genomes using advanced techniques, with the click of a button. M1CR0B1AL1Z3R is freely available at https://microbializer.tau.ac.il/.
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Affiliation(s)
- Oren Avram
- The School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dana Rapoport
- The School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shir Portugez
- The School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tal Pupko
- The School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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