151
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Antimicrobial resistance mechanisms and potential synthetic treatments. Future Sci OA 2018; 4:FSO290. [PMID: 29682325 PMCID: PMC5905577 DOI: 10.4155/fsoa-2017-0109] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/15/2018] [Indexed: 12/26/2022] Open
Abstract
Since the discovery of antibiotics by Sir Alexander Fleming they have been used throughout medicine and play a vital role in combating microorganisms. However, with their vast use, development of resistance has become more prevalent and their use is currently under threat. Antibiotic resistance poses a global threat to human and animal health, with many bacterial species having developed some form of resistance and in some cases within a year of first exposure to antimicrobial agents. This review aims to examine some of the mechanisms behind resistance. Additionally, re-engineering organisms, re-sensitizing bacteria to antibiotics and gene-editing techniques such as the clustered regularly interspaced short palindromic repeats-Cas9 system are providing novel approaches to combat bacterial resistance. To that extent, we have reviewed some of these novel and innovative technologies. In 1928, penicillin was discovered, changing the field of modern medicine as it provided an opportunity to treat microbial infections. Since then, microorganisms such as bacteria have evolved and now have the ability to resist a wide variety of agents that might otherwise prevent their growth. By 2050, it is estimated that around 10 million lives each year will be lost due to these bacteria. This article provides an insight into how bacteria resist antibiotics and potential new methods of treating these organisms.
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152
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Forde A, Hill C. Phages of life - the path to pharma. Br J Pharmacol 2018; 175:412-418. [PMID: 29266197 PMCID: PMC5773946 DOI: 10.1111/bph.14106] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/15/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022] Open
Abstract
Bacteriophage (phage) therapy has encountered both enthusiasm and scepticism in the past century. New antimicrobial strategies against lethal pathogens are now a top priority for the World Health Organization, and although compassionate use of phages recently met with significant success, regulated clinical interventions seem unlikely in the near future. The hundredth anniversary of their discovery seems an appropriate time for a revival of phage therapy, particularly as the dilemma of antibiotic resistance grows. Phages are ubiquitous in the environment, on our food and in and on our bodies. Their influence on human health is currently being evaluated, and in this mini-review, we examine data from recent metagenomic studies that propose a role for phages in the structure of the microbiome and in health and disease. We assess evidence for phages as vehicles for gene transfer in the context of antibiotic resistance and discuss challenges and opportunities along the critical path from phage discovery to a patient-focused pharmaceutical intervention.
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Affiliation(s)
- Amanda Forde
- APC Microbiome InstituteUniversity College CorkCorkIreland
| | - Colin Hill
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome InstituteUniversity College CorkCorkIreland
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153
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Braga LPP, Soucy SM, Amgarten DE, da Silva AM, Setubal JC. Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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154
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Tikhe CV, Husseneder C. Metavirome Sequencing of the Termite Gut Reveals the Presence of an Unexplored Bacteriophage Community. Front Microbiol 2018; 8:2548. [PMID: 29354098 PMCID: PMC5759034 DOI: 10.3389/fmicb.2017.02548] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/08/2017] [Indexed: 12/25/2022] Open
Abstract
The Formosan subterranean termite; Coptotermes formosanus is nutritionally dependent on the complex and diverse community of bacteria and protozoa in their gut. Although, there have been many studies to decipher the taxonomic and functional diversity of bacterial communities in the guts of termites, their bacteriophages remain unstudied. We sequenced the metavirome of the guts of Formosan subterranean termite workers to study the diversity of bacteriophages and other associated viruses. Results showed that the termites harbor a virome in their gut comprised of varied and previously unknown bacteriophages. Between 87-90% of the predicted dsDNA virus genes by Metavir showed similarity to the tailed bacteriophages (Caudovirales). Many predicted genes from the virome matched to bacterial prophage regions. These data are suggestive of a virome dominated by temperate bacteriophages. We predicted the genomes of seven novel Caudovirales bacteriophages from the termite gut. Three of these predicted bacteriophage genomes were found in high proportions in all the three termite colonies tested. Two bacteriophages are predicted to infect endosymbiotic bacteria of the gut protozoa. The presence of these putative bacteriophages infecting endosymbionts of the gut protozoa, suggests a quadripartite relationship between the termites their symbiotic protozoa, endosymbiotic bacteria of the protozoa and their bacteriophages. Other than Caudovirales, ss-DNA virus related genes were also present in the termite gut. We predicted the genomes of 12 novel Microviridae phages from the termite gut and seven of those possibly represent a new proposed subfamily. Circovirus like genomes were also assembled from the termite gut at lower relative abundance. We predicted 10 novel circovirus genomes in this study. Whether these circoviruses infect the termites remains elusive at the moment. The functional and taxonomical annotations suggest that the termites may harbor a core virome comprised of the bacteriophages infecting endosymbionts of the gut protozoa.
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Affiliation(s)
- Chinmay V Tikhe
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Claudia Husseneder
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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155
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Pratama AA, van Elsas JD. The 'Neglected' Soil Virome - Potential Role and Impact. Trends Microbiol 2018; 26:649-662. [PMID: 29306554 DOI: 10.1016/j.tim.2017.12.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/10/2017] [Accepted: 12/11/2017] [Indexed: 12/29/2022]
Abstract
Bacteriophages are among the most abundant and diverse biological units in the biosphere. They have contributed to our understanding of the central dogma of biology and have been instrumental in the evolutionary success of bacterial pathogens. In contrast to our current understanding of marine viral communities, the soil virome and its function in terrestrial ecosystems has remained relatively understudied. Here, we examine, in a comparative fashion, the knowledge gathered from studies performed in soil versus marine settings. We address the information with respect to the abundance, diversity, ecological significance, and effects of, in particular, bacteriophages on their host's evolutionary trajectories. We also identify the main challenges that soil virology faces and the studies that are required to accompany the current developments in marine settings.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
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156
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Letarov AV, Kulikov EE. Adsorption of bacteriophages on bacterial cells. BIOCHEMISTRY (MOSCOW) 2018. [DOI: 10.1134/s0006297917130053] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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157
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Shakya M, Soucy SM, Zhaxybayeva O. Insights into origin and evolution of α-proteobacterial gene transfer agents. Virus Evol 2017; 3:vex036. [PMID: 29250433 PMCID: PMC5721377 DOI: 10.1093/ve/vex036] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Several bacterial and archaeal lineages produce nanostructures that morphologically resemble small tailed viruses, but, unlike most viruses, contain apparently random pieces of the host genome. Since these elements can deliver the packaged DNA to other cells, they were dubbed gene transfer agents (GTAs). Because many genes involved in GTA production have viral homologs, it has been hypothesized that the GTA ancestor was a virus. Whether GTAs represent an atypical virus, a defective virus, or a virus co-opted by the prokaryotes for some function, remains to be elucidated. To evaluate these possibilities, we examined the distribution and evolutionary histories of genes that encode a GTA in the α-proteobacterium Rhodobacter capsulatus (RcGTA). We report that although homologs of many individual RcGTA genes are abundant across bacteria and their viruses, RcGTA-like genomes are mainly found in one subclade of α-proteobacteria. When compared with the viral homologs, genes of the RcGTA-like genomes evolve significantly slower, and do not have higher %A+T nucleotides than their host chromosomes. Moreover, they appear to reside in stable regions of the bacterial chromosomes that are generally conserved across taxonomic orders. These findings argue against RcGTA being an atypical or a defective virus. Our phylogenetic analyses suggest that RcGTA ancestor likely originated in the lineage that gave rise to contemporary α-proteobacterial orders Rhizobiales, Rhodobacterales, Caulobacterales, Parvularculales, and Sphingomonadales, and since that time the RcGTA-like element has co-evolved with its host chromosomes. Such evolutionary history is compatible with maintenance of these elements by bacteria due to some selective advantage. As for many other prokaryotic traits, horizontal gene transfer played a substantial role in the evolution of RcGTA-like elements, not only in shaping its genome components within the orders, but also in occasional dissemination of RcGTA-like regions across the orders and even to different bacterial phyla.
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Affiliation(s)
- Migun Shakya
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
| | - Shannon M Soucy
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA.,Department of Computer Science, Dartmouth College, 6211 Sudikoff Lab, Hanover, NH 03755, USA
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158
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Modulation of Global Transcriptional Regulatory Networks as a Strategy for Increasing Kanamycin Resistance of the Translational Elongation Factor-G Mutants in Escherichia coli. G3-GENES GENOMES GENETICS 2017; 7:3955-3966. [PMID: 29046437 PMCID: PMC5714492 DOI: 10.1534/g3.117.300284] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Evolve and resequence experiments have provided us a tool to understand bacterial adaptation to antibiotics. In our previous work, we used short-term evolution to isolate mutants resistant to the ribosome targeting antibiotic kanamycin, and reported that Escherichia coli develops low cost resistance to kanamycin via different point mutations in the translation Elongation Factor-G (EF-G). Furthermore, we had shown that the resistance of EF-G mutants could be increased by second site mutations in the genes rpoD/cpxA/topA/cyaA Mutations in three of these genes had been discovered in earlier screens for aminoglycoside resistance. In this work, we expand our understanding of these second site mutations, the goal being to understand how these mutations affect the activities of the mutated gene products to confer resistance. We show that the mutation in cpxA most likely results in an active Cpx stress response. Further evolution of an EF-G mutant in a higher concentration of kanamycin than what was used in our previous experiments identified the cpxA locus as a primary target for a significant increase in resistance. The mutation in cyaA results in a loss of catalytic activity and probably results in resistance via altered CRP function. Despite a reduction in cAMP levels, the CyaAN600Y mutant has a transcriptome indicative of increased CRP activity, pointing to an unknown role for CyaA and / or cAMP in gene expression. From the transcriptomes of double and single mutants, we describe the epistasis between the mutation in EF-G and these second site mutations. We show that the large scale transcriptomic changes in the topoisomerase I (FusAA608E-TopAS180L) mutant likely result from increased negative supercoiling in the cell. Finally, genes with known roles in aminoglycoside resistance were present among the misregulated genes in the mutants.
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159
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Phage-mediated dissemination of virulence factors in pathogenic bacteria facilitated by antibiotic growth promoters in animals: a perspective. Anim Health Res Rev 2017; 18:160-166. [DOI: 10.1017/s1466252317000147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AbstractAddition of sub-therapeutic antibiotics to the feed of food-producing animals for growth promotion and disease prevention has become a common agricultural practice in many countries. The emergence of antibiotic-resistant pathogens is a looming concern associated with the use of antibiotic growth promoters (AGPs) around the world. In addition, some studies have shown that AGPs may not only affect antibiotic resistance but may also stimulate the dissemination of virulence factors via bacteriophages. Although only a few studies are currently available in the literature regarding this topic, in this article we endeavor to provide a perspective about how AGPs would impact the transmission of virulence factors by horizontal gene transfer via phages in a few pathogenic bacterial species significant to livestock production.
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160
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Harrison E, Brockhurst MA. Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn't Kill You Makes You Stronger. Bioessays 2017; 39. [PMID: 28983932 DOI: 10.1002/bies.201700112] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/30/2017] [Indexed: 01/04/2023]
Abstract
Infection by a temperate phage can lead to death of the bacterial cell, but sometimes these phages integrate into the bacterial chromosome, offering the potential for a more long-lasting relationship to be established. Here we define three major ecological and evolutionary benefits of temperate phage for bacteria: as agents of horizontal gene transfer (HGT), as sources of genetic variation for evolutionary innovation, and as weapons of bacterial competition. We suggest that a coevolutionary perspective is required to understand the roles of temperate phages in bacterial populations.
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Affiliation(s)
- Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Arthur Willis Environment Centre, Sheffield, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Sheffield, UK
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161
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Valero-Rello A, López-Sanz M, Quevedo-Olmos A, Sorokin A, Ayora S. Molecular Mechanisms That Contribute to Horizontal Transfer of Plasmids by the Bacteriophage SPP1. Front Microbiol 2017; 8:1816. [PMID: 29018417 PMCID: PMC5615212 DOI: 10.3389/fmicb.2017.01816] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/06/2017] [Indexed: 01/02/2023] Open
Abstract
Natural transformation and viral-mediated transduction are the main avenues of horizontal gene transfer in Firmicutes. Bacillus subtilis SPP1 is a generalized transducing bacteriophage. Using this lytic phage as a model, we have analyzed how viral replication and recombination systems contribute to the transfer of plasmid-borne antibiotic resistances. Phage SPP1 DNA replication relies on essential phage-encoded replisome organizer (G38P), helicase loader (G39P), hexameric replicative helicase (G40P), recombinase (G35P) and in less extent on the partially dispensable 5′→3′ exonuclease (G34.1P), the single-stranded DNA binding protein (G36P) and the Holliday junction resolvase (G44P). Correspondingly, the accumulation of linear concatemeric plasmid DNA, and the formation of transducing particles were blocked in the absence of G35P, G38P, G39P, and G40P, greatly reduced in the G34.1P, G36P mutants, and slightly reduced in G44P mutants. In contrast, establishment of injected linear plasmid DNA in the recipient host was independent of viral-encoded functions. DNA homology between SPP1 and the plasmid, rather than a viral packaging signal, enhanced the accumulation of packagable plasmid DNA. The transfer efficiency was also dependent on plasmid copy number, and rolling-circle plasmids were encapsidated at higher frequencies than theta-type replicating plasmids.
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Affiliation(s)
- Ana Valero-Rello
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain.,Micalis Institute, INRA, AgroParisTech, Universite Paris-SaclayJouy-en-Josas, France
| | - María López-Sanz
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Alvaro Quevedo-Olmos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Alexei Sorokin
- Micalis Institute, INRA, AgroParisTech, Universite Paris-SaclayJouy-en-Josas, France
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain
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162
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Geng P, Tian S, Yuan Z, Hu X. Identification and genomic comparison of temperate bacteriophages derived from emetic Bacillus cereus. PLoS One 2017; 12:e0184572. [PMID: 28886124 PMCID: PMC5590980 DOI: 10.1371/journal.pone.0184572] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/25/2017] [Indexed: 01/21/2023] Open
Abstract
Cereulide-producing Bacillus cereus isolates can cause serious emetic (vomiting) syndrome and even acute lethality. As mobile genetic elements, the exploration of prophages derived from emetic B. cereus isolates will help in our understanding of the genetic diversity and evolution of these pathogens. In this study, five temperate phages derived from cereulide-producing B. cereus strains were induced, with four of them undergoing genomic sequencing. Sequencing revealed that they all belong to the Siphoviridae family, but presented in different forms in their hosts. PfNC7401 and PfIS075 have typical icosahedral heads, probably existing alone as phagemids in the host with self-replicating capability in the lysogenic state. PfEFR-4, PfEFR-5, and PfATCC7953 have elongated heads, with the genomes of the former two identified as linear dsDNA, which could be integrated into the host genome during the lysogenic state. Genomic comparison of the four phages with others also derived from emetic B. cereus isolates showed similar genome structures and core genes, thus displaying host spectrum specificity. In addition, phylogenic analysis based on the complete genome and conserved tail fiber proteins of 36 Bacillus species-derived phages confirmed that the phages derived from emetic B. cereus strains were highly similar. Furthermore, one endolysin LysPfEFR-4 was cloned and showed lytic activity against all tested emetic B. cereus strains and cross-lytic activity against some other pathogenic bacteria, implying a potential to control bacterial contamination in the food supply.
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Affiliation(s)
- Peiling Geng
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Shen Tian
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zhiming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (XH); (ZY)
| | - Xiaomin Hu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (XH); (ZY)
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163
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Tripathi C, Mishra H, Khurana H, Dwivedi V, Kamra K, Negi RK, Lal R. Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes. Front Microbiol 2017; 8:1410. [PMID: 28798737 PMCID: PMC5529391 DOI: 10.3389/fmicb.2017.01410] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/11/2017] [Indexed: 01/27/2023] Open
Abstract
Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C) using PacBio RSII SMRT technique. The small genome (2.01 Mbp) comprises a chromosome (1.87 Mbp) and a plasmid (143 Kbp), designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%). We performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenetic relatedness as well as niche specific attributes prevalent among the group. We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI), conserved marker genes (31 and 400), pan genome and tetranucleotide frequency. The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. We demonstrated the presence of metagenomic islands (chromosome:5, plasmid:5) by recruiting raw metagenomic data (from the same niche) against the genomic replicons of T. parvatiensis. We also dissected the CRISPR loci wide all genomes and found widespread presence of this system across Thermus genomes. Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness.
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Affiliation(s)
- Charu Tripathi
- Department of Zoology, University of DelhiNew Delhi, India
| | | | - Himani Khurana
- Department of Zoology, University of DelhiNew Delhi, India
| | | | - Komal Kamra
- Ciliate Biology Laboratory, Sri Guru Tegh Bahadar Khalsa College, University of DelhiNew Delhi, India
| | - Ram K Negi
- Department of Zoology, University of DelhiNew Delhi, India
| | - Rup Lal
- Department of Zoology, University of DelhiNew Delhi, India
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