101
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Horiuk Y, Horiuk V, Kukhtyn M, Tsvihun A, Kernychnyi S. Characterization of lytic activity of Phage SAvB14 on Staphylococcus aureus variant bovis. J Adv Vet Anim Res 2020; 7:509-513. [PMID: 33005677 PMCID: PMC7521818 DOI: 10.5455/javar.2020.g447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/02/2020] [Accepted: 04/08/2020] [Indexed: 12/18/2022] Open
Abstract
Objective The objective of this study was to investigate the intensity of phage infection caused by Phage SAvB14, which was isolated from dairy farms, depending on the initial number of Staphylococcus aureus cells in the medium. Material and methods To evaluate the impact of the viable bacteria S. aureus var. bovis on the intensity of phage infection caused by Phage SAvB14, 1 mg of phagolysate (phage titer 105 CFU/ ml) was introduced in 9 ml of nutrient broth with an appropriate amount of daily culture of S. aureus var. bovis under study. The number of viable staphylococci was determined by total viable count/ml. Results In this experiment, we found that the intensity of phages lytic activity was dependent on the number of sensitive bacterial cells in the volume of the culture medium. Effective phage therapy requires a high concentration of phages in the medium (inflammation foci) for rapid contact of the virus with bacteria. Conclusion When developing a phage drug to treat subclinical mastitis, it is necessary to increase the phage titer in the drug or its dosage compared to the clinical form, as there is a lower probability of phage contact with a susceptible microbial cell. Besides, at a high concentration of bacteria, there is a gradual decrease in nutrients in the medium, resulting in phages going back to the condition of lysogeny.
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Affiliation(s)
- Yulia Horiuk
- Faculty of Veterinary Medicine and Technologies in Livestock, Department of Infectious and Parasitic Diseases, State Agrarian and Engineering University in Podilya, Kamianets-Podilskyi, Ukraine
| | - Victor Horiuk
- Faculty of Veterinary Medicine and Technologies in Livestock, Department of Veterinary Obstetrics, Pathology and Surgery, State Agrarian and Engineering University in Podilya, Kamianets-Podilskyi, Ukraine
| | - Mykola Kukhtyn
- Faculty of Engineering of Machines, Structures and Technologies, Department of Food Biotechnology and Chemistry, Ternopil Ivan Pului National Technical University, Ternopil, Ukraine
| | - Anatoliy Tsvihun
- Faculty of Veterinary Medicine and Technologies in Livestock, Department of Animal Feeding, Breeding and Feed Technology, State Agrarian and Engineering University in Podilya, Kamianets-Podilskyi, Ukraine
| | - Sergiy Kernychnyi
- Faculty of Veterinary Medicine and Technologies in Livestock, Department of Veterinary Obstetrics, Pathology and Surgery, State Agrarian and Engineering University in Podilya, Kamianets-Podilskyi, Ukraine
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102
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Tang X, Yu L, Yi Y, Wang J, Wang S, Meng C, Liu S, Hao Y, Zhang Y, Cao X, Jian H, Xiao X. Phylogenomic analysis reveals a two-stage process of the evolutionary transition of Shewanella from the upper ocean to the hadal zone. Environ Microbiol 2020; 23:744-756. [PMID: 32657519 DOI: 10.1111/1462-2920.15162] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/21/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022]
Abstract
Shewanella strains are characterized by versatile metabolic capabilities, resulting in their wide distribution in the ocean at different depths. Considering that particle sedimentation is an important dynamic process in the ocean, we hypothesized that hadal Shewanella species evolved from the upper ocean. In this study, we isolated three novel Shewanella strains from deep-sea sediments in the Southwest Indian Ocean. Genome sequencing indicated that strains YLB-06 and YLB-08 represent two novel species in the genus Shewanella. Through phylogenomic analysis, we showed that speciation and genomic changes in marine Shewanella strains are related to water depth. We further confirmed the aforementioned hypothesis and revealed a two-stage process of the evolutionary transition of Shewanella from the upper ocean to the hadal zone by comparative genomics and gene gain/loss analysis. Finally, the transcriptomic analysis demonstrated that recently obtained genes are strictly repressed and may thus play a minor role in the response to environmental changes.
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Affiliation(s)
- Xixiang Tang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.,China Ocean Sample Repository (Biology), Xiamen, 361005, China
| | - Libo Yu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.,China Ocean Sample Repository (Biology), Xiamen, 361005, China
| | - Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiahua Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Siyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Canxing Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yue Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaorong Cao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.,China Ocean Sample Repository (Biology), Xiamen, 361005, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
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103
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Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation. ISME JOURNAL 2020; 14:2980-2996. [PMID: 32732904 PMCID: PMC7784688 DOI: 10.1038/s41396-020-0726-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 01/21/2023]
Abstract
Klebsiella species are able to colonize a wide range of environments and include worrisome nosocomial pathogens. Here, we sought to determine the abundance and infectivity of prophages of Klebsiella to understand how the interactions between induced prophages and bacteria affect population dynamics and evolution. We identified many prophages in the species, placing these taxa among the top 5% of the most polylysogenic bacteria. We selected 35 representative strains of the Klebsiella pneumoniae species complex to establish a network of induced phage-bacteria interactions. This revealed that many prophages are able to enter the lytic cycle, and subsequently kill or lysogenize closely related Klebsiella strains. Although 60% of the tested strains could produce phages that infect at least one other strain, the interaction network of all pairwise cross-infections is very sparse and mostly organized in modules corresponding to the strains' capsule serotypes. Accordingly, capsule mutants remain uninfected showing that the capsule is a key factor for successful infections. Surprisingly, experiments in which bacteria are predated by their own prophages result in accelerated loss of the capsule. Our results show that phage infectiousness defines interaction modules between small subsets of phages and bacteria in function of capsule serotype. This limits the role of prophages as competitive weapons because they can infect very few strains of the species complex. This should also restrict phage-driven gene flow across the species. Finally, the accelerated loss of the capsule in bacteria being predated by their own phages, suggests that phages drive serotype switch in nature.
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104
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Yu X, Xu J, Gu Y, Zhang R, Zhu Y, Liu X. Molecular Characterization and Comparative Genomic Analysis of vB_PaeP_YA3, a Novel Temperate Bacteriophage of Pseudomonas aeruginosa. Front Microbiol 2020; 11:947. [PMID: 32655502 PMCID: PMC7326022 DOI: 10.3389/fmicb.2020.00947] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/20/2020] [Indexed: 01/21/2023] Open
Abstract
It is well known that bacteriophages play crucial roles in many aspects, such as controlling the number and the diversity of bacteria and participating in horizontal gene transfer, which is a key process in the evolution of bacteria. However, so far, the number of temperate bacteriophages is still limited, and their life processes are severely unknown, except for members of the lambdoid family of coliphages. In this study, a novel temperate phage of Pseudomonas aeruginosa, YA3 (vB_PaeP_YA3), was isolated from waste water. The morphology of YA3 suggested that it is a Podoviridae. The YA3 genome is a circular double-stranded DNA of 45,253 bp, with an average G + C content of 57.2%. A total of 65 open reading frames (ORFs) were predicted according to the sequence of YA3’s genome, of which only 32 (49.2%) ORFs were assigned with putative functions and 13 ORFs were confirmed by the structural proteome. Genome and proteome analyses confirmed the lysogenic nature of this phage, which encodes the typical lysogen-related proteins integrase, CI, Cro, and Q protein. The genome of YA3 is most closely related with that of temperate phage vB_PaeP_Tr60_Ab31, whereas the homology coverage is just 48%. There are many critical differences between their genomes, involving promoters, lysis pathways, and regulation patterns. YA3 is capable of stably lysogenizing its host P. aeruginosa PA14, targeting the integration site within the serine tRNA gene (PA14_RS20820), which is similar with phage vB_PaeP_Tr60_Ab31. The phylogenetic analysis is more complicated than we thought. Based on phage terminase large subunit (TerL) and CI proteins, phage YA3 is related with phage lambda, while their genome coverage is extremely low (<1%). Therefore, phage YA3 is a considerably novel lambda-like temperate phage, and a further study of its genome may deepen our understanding of the interaction between lysogenic phages and their bacterial hosts.
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Affiliation(s)
- Xinyan Yu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Jing Xu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Yu Gu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Ruiyang Zhang
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Yefei Zhu
- Laboratory Medicine Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoqiu Liu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
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105
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Rouïl J, Jousselin E, Coeur d’acier A, Cruaud C, Manzano-Marín A. The Protector within: Comparative Genomics of APSE Phages across Aphids Reveals Rampant Recombination and Diverse Toxin Arsenals. Genome Biol Evol 2020; 12:878-889. [PMID: 32386316 PMCID: PMC7313666 DOI: 10.1093/gbe/evaa089] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2020] [Indexed: 12/13/2022] Open
Abstract
Phages can fundamentally alter the physiology and metabolism of their hosts. Although these phages are ubiquitous in the bacterial world, they have seldom been described among endosymbiotic bacteria. One notable exception is the APSE phage that is found associated with the gammaproteobacterial Hamiltonella defensa, hosted by several insect species. This secondary facultative endosymbiont is not necessary for the survival of its hosts but can infect certain individuals or even whole populations. Its infection in aphids is often associated with protection against parasitoid wasps. This protective phenotype has actually been linked to the infection of the symbiont strain with an APSE, which carries a toxin cassette that varies among so-called "types." In the present work, we seek to expand our understanding of the diversity of APSE phages as well as the relations of their Hamiltonella hosts. For this, we assembled and annotated the full genomes of 16 APSE phages infecting Hamiltonella symbionts across ten insect species. Molecular and phylogenetic analyses suggest that recombination has occurred repeatedly among lineages. Comparative genomics of the phage genomes revealed two variable regions that are useful for phage typing. Additionally, we find that mobile elements could play a role in the acquisition of new genes in the toxin cassette. Altogether, we provide an unprecedented view of APSE diversity and their genome evolution across aphids. This genomic investigation will provide a valuable resource for the design and interpretation of experiments aiming at understanding the protective phenotype these phages confer to their insect hosts.
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Affiliation(s)
- Jeff Rouïl
- UMR 1062 Centre de Biologie pour la Gestion des Populations, INRAE, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, France
| | - Emmanuelle Jousselin
- UMR 1062 Centre de Biologie pour la Gestion des Populations, INRAE, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, France
| | - Armelle Coeur d’acier
- UMR 1062 Centre de Biologie pour la Gestion des Populations, INRAE, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, France
| | - Corinne Cruaud
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Évry, France
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106
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Is Shiga Toxin-Producing Escherichia coli O45 No Longer a Food Safety Threat? The Danger is Still Out There. Microorganisms 2020; 8:microorganisms8050782. [PMID: 32455956 PMCID: PMC7285328 DOI: 10.3390/microorganisms8050782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 01/03/2023] Open
Abstract
Many Shiga toxin-producing Escherichia coli (STEC) strains, including the serogroups of O157 and most of the top six non-O157 serotypes, are frequently associated with foodborne outbreaks. Therefore, they have been extensively studied using next-generation sequencing technology. However, related information regarding STEC O45 strains is scarce. In this study, three environmental E. coli O45:H16 strains (RM11911, RM13745, and RM13752) and one clinical E. coli O45:H2 strain (SJ7) were sequenced and used to characterize virulence factors using two reference E. coli O45:H2 strains of clinical origin. Subsequently, whole-genome-based phylogenetic analysis was conducted for the six STEC O45 strains and nine other reference STEC genomes, in order to evaluate their evolutionary relationship. The results show that one locus of enterocyte effacement pathogenicity island was found in all three STEC O45:H2 strains, but not in the STEC O45:H16 strains. Additionally, E. coli O45:H2 strains were evolutionarily close to E. coli O103:H2 strains, sharing high homology in terms of virulence factors, such as Stx prophages, but were distinct from E. coli O45:H16 strains. The findings show that E. coli O45:H2 may be as virulent as E. coli O103:H2, which is frequently associated with severe illness and can provide genomic evidence to facilitate STEC surveillance.
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107
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Castillo D, Rørbo N, Jørgensen J, Lange J, Tan D, Kalatzis PG, Svenningsen SL, Middelboe M. Phage defense mechanisms and their genomic and phenotypic implications in the fish pathogen Vibrio anguillarum. FEMS Microbiol Ecol 2020; 95:5281231. [PMID: 30624625 DOI: 10.1093/femsec/fiz004] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/08/2019] [Indexed: 01/21/2023] Open
Abstract
Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species. Although phage therapy has been proposed as an alternative treatment, the defense mechanisms against phage infection in V. anguillarum and their impact on host function are not fully understood. Here, we examined phage defense strategies in four V. anguillarum strains during exposure to the broad-host-range bacteriophage KVP40. Whole-genome sequences of phage-resistant V. anguillarum isolates showed mutations causing premature stop codons, frameshifts and amino acid changes in the OmpK phage receptor. Moreover, certain phage-resistant variants recovered susceptibility to phage infection following re-culturing, suggesting alternative protection mechanisms, such as formation of biofilm, receptor downregulation and phage inactivation by proteases. Also, the lack of phage production by some strains despite strong phage control suggested an abortive infection mechanism was in play. In addition, examination of the virulence properties and extracellular enzyme secretion of the phage-resistant variants suggested that phage resistance was associated with reduced virulence in V. anguillarum. Altogether, the results identified a variety of phage resistance mechanisms in V. anguillarum including both mutational and non-mutational defenses and demonstrated a significant fitness loss associated with mutational changes, which may explain the selection for alternative defense mechanisms.
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Affiliation(s)
- Daniel Castillo
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark
| | - Nanna Rørbo
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark
| | - Jóhanna Jørgensen
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark
| | - Janina Lange
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark.,Zoological Institute, Christian-Albrechts-University, Am botanischen Garten 1-9, G-24116 Kiel, Germany
| | - Demeng Tan
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark.,Section for Biomolecular Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark
| | - Panos G Kalatzis
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark
| | - Sine Lo Svenningsen
- Section for Biomolecular Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark
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108
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Molnár J, Magyar B, Schneider G, Laczi K, Valappil SK, Kovács ÁL, Nagy IK, Rákhely G, Kovács T. Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples. PLoS One 2020; 15:e0231864. [PMID: 32302368 PMCID: PMC7164591 DOI: 10.1371/journal.pone.0231864] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/02/2020] [Indexed: 12/21/2022] Open
Abstract
Metagenomics is a helpful tool for the analysis of unculturable organisms and viruses. Viruses that target bacteria and archaea play important roles in the microbial diversity of various ecosystems. Here we show that Methanosarcina virus MV (MetMV), the second Methanosarcina sp. virus with a completely determined genome, is characteristic of hydrocarbon pollution in environmental (soil and water) samples. It was highly abundant in Hungarian hydrocarbon polluted samples and its genome was also present in the NCBI SRA database containing reads from hydrocarbon polluted samples collected in Canada, indicating the stability of its niche and the marker feature of this virus. MetMV, as the only currently identified marker virus for pollution in environmental samples, could contribute to the understanding of the complicated network of prokaryotes and their viruses driving the decomposition of environmental pollutants.
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Affiliation(s)
- János Molnár
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | | | - György Schneider
- Institute of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | | | - Árpád L. Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Ildikó K. Nagy
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Institute of Biophysics, Biological Research Center, Szeged, Hungary
| | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
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109
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Cheng X, Delanka-Pedige HMK, Munasinghe-Arachchige SP, Abeysiriwardana-Arachchige ISA, Smith GB, Nirmalakhandan N, Zhang Y. Removal of antibiotic resistance genes in an algal-based wastewater treatment system employing Galdieria sulphuraria: A comparative study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:134435. [PMID: 31810689 PMCID: PMC6992497 DOI: 10.1016/j.scitotenv.2019.134435] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 05/04/2023]
Abstract
In this study, we compared removal of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in two wastewater treatment systems fed with the same primary effluent: a conventional wastewater treatment system (consisting of a trickling filter followed by an activated sludge process) versus an algal-based system, employing an extremophilic alga, Galdieria sulphuraria. Our results demonstrated that the algal system can reduce concentrations of erythromycin- and sulfamethoxazole-resistant bacteria in the effluent more effectively than the conventional treatment system. A decreasing trend of total bacteria and ARGs was observed in both the treatment systems. However, the relative ratio of most ARGs (qnrA, qnrB, qnrS, sul1) and intI1 in the surviving bacteria increased in the conventional system; whereas, the algal system reduced more of the relative abundance of qnrA, qnrS, tetW and intⅠ1 in the surviving bacteria. The role of bacteriophages in horizontal gene transfer (HGT) of ARGs in the two systems was indicated by a positive correlation between ARG absolute abundance in bacteriophage and ARG relative abundance in the bacteria. Four of the five detectable genes (qnrS, tetW, sul1 and intI1) were significantly reduced in the algal system in bacteriophage phase which signified a decrease in phage-mediated ARG transfer in the algal system. Results of this study demonstrate the feasibility of the algal-based wastewater treatment system in decreasing ARGs and ARB and in minimizing the spread of antibiotic resistance to the environment.
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Affiliation(s)
- Xiaoxiao Cheng
- Civil Engineering Department, New Mexico State University, Las Cruces, NM 88003, USA
| | | | | | | | - Geoffrey B Smith
- Biology Department, New Mexico State University, Las Cruces, NM 88003, USA
| | | | - Yanyan Zhang
- Civil Engineering Department, New Mexico State University, Las Cruces, NM 88003, USA.
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110
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Gilbert RA, Townsend EM, Crew KS, Hitch TCA, Friedersdorff JCA, Creevey CJ, Pope PB, Ouwerkerk D, Jameson E. Rumen Virus Populations: Technological Advances Enhancing Current Understanding. Front Microbiol 2020; 11:450. [PMID: 32273870 PMCID: PMC7113391 DOI: 10.3389/fmicb.2020.00450] [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: 11/26/2019] [Accepted: 03/02/2020] [Indexed: 01/07/2023] Open
Abstract
The rumen contains a multi-kingdom, commensal microbiome, including protozoa, bacteria, archaea, fungi and viruses, which enables ruminant herbivores to ferment and utilize plant feedstuffs that would be otherwise indigestible. Within the rumen, virus populations are diverse and highly abundant, often out-numbering the microbial populations that they both predate on and co-exist with. To date the research effort devoted to understanding rumen-associated viral populations has been considerably less than that given to the other microbial populations, yet their contribution to maintaining microbial population balance, intra-ruminal microbial lysis, fiber breakdown, nutrient cycling and genetic transfer may be highly significant. This review follows the technological advances which have contributed to our current understanding of rumen viruses and drawing on knowledge from other environmental and animal-associated microbiomes, describes the known and potential roles and impacts viruses have on rumen function and speculates on the future directions of rumen viral research.
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Affiliation(s)
- Rosalind A. Gilbert
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eleanor M. Townsend
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Kathleen S. Crew
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
| | - Thomas C. A. Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Jessica C. A. Friedersdorff
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Christopher J. Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Phillip B. Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Diane Ouwerkerk
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eleanor Jameson
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
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111
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Cury J, Oliveira PH, de la Cruz F, Rocha EPC. Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements. Mol Biol Evol 2020; 35:2230-2239. [PMID: 29905872 PMCID: PMC6107060 DOI: 10.1093/molbev/msy123] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Self-transmissible mobile genetic elements drive horizontal gene transfer between prokaryotes. Some of these elements integrate in the chromosome, whereas others replicate autonomously as plasmids. Recent works showed the existence of few differences, and occasional interconversion, between the two types of elements. Here, we enquired on why evolutionary processes have maintained the two types of mobile genetic elements by comparing integrative and conjugative elements (ICE) with extrachromosomal ones (conjugative plasmids) of the highly abundant MPFT conjugative type. We observed that plasmids encode more replicases, partition systems, and antibiotic resistance genes, whereas ICEs encode more integrases and metabolism-associated genes. ICEs and plasmids have similar average sizes, but plasmids are much more variable, have more DNA repeats, and exchange genes more frequently. On the other hand, we found that ICEs are more frequently transferred between distant taxa. We propose a model where the different genetic plasticity and amplitude of host range between elements explain the co-occurrence of integrative and extrachromosomal elements in microbial populations. In particular, the conversion from ICE to plasmid allows ICE to be more plastic, while the conversion from plasmid to ICE allows the expansion of the element's host range.
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Affiliation(s)
- Jean Cury
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.,CNRS, UMR3525, Paris, France
| | - Pedro H Oliveira
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.,CNRS, UMR3525, Paris, France
| | - Fernando de la Cruz
- Departamento de Biologia Molecular e Instituto de Biomedicina y Biotecnologia de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.,CNRS, UMR3525, Paris, France
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112
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Abstract
The discovery of bacteria in the female urinary bladder has fundamentally changed current dogma regarding the urinary tract and related urinary disorders. Previous research characterized many of the bacterial components of the female urinary tract, but the viral fraction of this community is largely unknown. Viruses within the human microbiota far outnumber bacterial cells, with the most abundant viruses being those that infect bacteria (bacteriophages). Similar to observations within the microbiota of the gut and oral cavity, preliminary surveys of the urinary tract and bladder microbiota indicate a rich diversity of uncharacterized bacteriophage (phage) species. Phages are vital members of the microbiota, having critical roles in shaping bacterial metabolism and community structure. Although phages have been discovered in the urinary tract, such as phages that infect Escherichia coli, sampling them is challenging owing to low biomass, possible contamination when using non-invasive methods and the invasiveness of methods that reduce the potential for contamination. Phages could influence bladder health, but an understanding of the association between phage communities, bacterial populations and bladder health is in its infancy. However, evidence suggests that phages can defend the host against pathogenic bacteria and, therefore, modulation of the microbiome using phages has therapeutic potential for lower urinary tract symptoms. Furthermore, as natural predators of bacteria, phages have garnered renewed interest for their use as antimicrobial agents, for instance, in the treatment of urinary tract infections.
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113
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Yang Y, Xie X, Tang M, Liu J, Tuo H, Gu J, Tang Y, Lei C, Wang H, Zhang A. Exploring the profile of antimicrobial resistance genes harboring by bacteriophage in chicken feces. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 700:134446. [PMID: 31648121 DOI: 10.1016/j.scitotenv.2019.134446] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/08/2019] [Accepted: 09/12/2019] [Indexed: 05/04/2023]
Abstract
Bacteriophage may play an important role in antimicrobial resistance genes (ARGs) transmission. However, the contribution of bacteriophage to the spread of ARGs in environment, especially in poultry farm environment, is rarely known. In this study, the prevalence of ARGs in bacteriophage DNA was investigated in chicken feces from 30 different poultry farms in China. Then the abundance of the aac(6')-Ib-cr, blaCTX-M, ermB, floR, mcr-1, sul1, tetM and intI1 genes was determined by qPCR in bacteriophage and compared with certain representative plasmid DNA samples. The results showed that 12 ARGs (aac(6')-Ib-cr, aph(3')-IIIa, blaCTX-M, ermB, ermF, floR, mcr-1, qnrS, sul1, sul2, vanA, tetM genes) and class 1 integron gene intI1 were detected in bacteriophage DNA fraction. The sul1, tetM and aac(6')-Ib-cr genes were most prevalent with high detection rates of 77%, 61% and 55%, respectively. To our best knowledge, this study firstly reported the presence of the mcr-1 gene in bacteriophage DNA derived from farms environments. We found that the gene copy (GC) numbers of the aac(6')-Ib-cr, ermB and sul1 genes were as high as 5.47, 5.22 and 5.54 log10 GC/g, respectively. Both the prevalence and abundance of ARGs in broiler fecal wastes were also generally higher than in laying hens. In addition, although the GC numbers of the aac(6')-Ib-cr, floR and tetM genes in plasmid DNA was higher than that in phage DNA fraction by 4.68, 3.59 and 3.9 orders of magnitude, respectively, the absolute abundances of the blaCTX-M and mcr-1 genes in phage DNA were close to or even higher than that in plasmid DNA at farm SIL2, SIL4 and SIB1. As potential vessels for ARGs, bacteriophage could not be ignored due to their unique extracellular persistence in environments. Overall, this is the first comprehensive survey about bacteriophage carried ARGs from farms in different regions in China.
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Affiliation(s)
- Yanxian Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xianjun Xie
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China
| | - Mengjun Tang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Jiangsu 225009, China
| | - Jinxin Liu
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, CA 95616, USA
| | - Hongmei Tuo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China
| | - Ju Gu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China
| | - Yizhi Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China
| | - Changwei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China
| | - Hongning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China
| | - Anyun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China.
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114
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Siranosian BA, Tamburini FB, Sherlock G, Bhatt AS. Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages. Nat Commun 2020; 11:280. [PMID: 31941900 PMCID: PMC6962324 DOI: 10.1038/s41467-019-14103-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/04/2019] [Indexed: 12/28/2022] Open
Abstract
CrAss-like phages are double-stranded DNA viruses that are prevalent in human gut microbiomes. Here, we analyze gut metagenomic data from mother-infant pairs and patients undergoing fecal microbiota transplantation to evaluate the patterns of acquisition, transmission and strain diversity of crAss-like phages. We find that crAss-like phages are rarely detected at birth but are increasingly prevalent in the infant microbiome after one month of life. We observe nearly identical genomes in 50% of cases where the same crAss-like clade is detected in both the mother and the infant, suggesting vertical transmission. In cases of putative transmission of prototypical crAssphage (p-crAssphage), we find that a subset of strains present in the mother are detected in the infant, and that strain diversity in infants increases with time. Putative tail fiber proteins are enriched for nonsynonymous strain variation compared to other genes, suggesting a potential evolutionary benefit to maintaining strain diversity in specific genes. Finally, we show that p-crAssphage can be acquired through fecal microbiota transplantation.
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Affiliation(s)
| | | | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA.
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115
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Prophages contribute to genome plasticity of Klebsiella pneumoniae and may involve the chromosomal integration of ARGs in CG258. Genomics 2020; 112:998-1010. [DOI: 10.1016/j.ygeno.2019.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 04/21/2019] [Accepted: 06/15/2019] [Indexed: 12/31/2022]
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116
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Abstract
Transformation is a widespread mechanism of horizontal gene transfer in bacteria. DNA uptake to the periplasmic compartment requires a DNA-uptake pilus and the DNA-binding protein ComEA. In the gram-negative bacteria, DNA is first pulled toward the outer membrane by retraction of the pilus and then taken up by binding to periplasmic ComEA, acting as a Brownian ratchet to prevent backward diffusion. A similar mechanism probably operates in the gram-positive bacteria as well, but these systems have been less well characterized. Transport, defined as movement of a single strand of transforming DNA to the cytosol, requires the channel protein ComEC. Although less is understood about this process, it may be driven by proton symport. In this review we also describe various phenomena that are coordinated with the expression of competence for transformation, such as fratricide, the kin-discriminatory killing of neighboring cells, and competence-mediated growth arrest.
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Affiliation(s)
- David Dubnau
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA;
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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117
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Affiliation(s)
- Juliet Roshini Mohan Raj
- Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, India
| | - Indrani Karunasagar
- Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, India
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118
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Khan A, Wahl LM. Quantifying the forces that maintain prophages in bacterial genomes. Theor Popul Biol 2019; 133:168-179. [PMID: 31758948 DOI: 10.1016/j.tpb.2019.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 10/25/2022]
Abstract
Genome sequencing has revealed that prophages, viral sequences integrated in a bacterial chromosome, are abundant, accounting for as much as 20% of the bacterial genome. These sequences can confer fitness benefits to the bacterial host, but may also instigate cell death through induction. Several recent investigations have revealed that the distribution of prophage lengths is bimodal, with a clear distinction between small and large prophages. Here we develop a mathematical model of the evolutionary forces affecting the prophage size distribution, and fit this model to three recent data sets. This approach offers quantitative estimates for the relative rates of lysogeny, induction, mutational degradation and selection acting on a wide class of prophage sequences. The model predicts that large prophages are predominantly maintained by the introduction of new prophage sequences through lysogeny, whereas shorter prophages can be enriched when they no longer encode the genes necessary for induction, but still offer selective benefits to their hosts.
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Affiliation(s)
- Amjad Khan
- Department of Applied Mathematics, Western University, London, ON, Canada
| | - Lindi M Wahl
- Department of Applied Mathematics, Western University, London, ON, Canada.
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119
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Felis E, Kalka J, Sochacki A, Kowalska K, Bajkacz S, Harnisz M, Korzeniewska E. Antimicrobial pharmaceuticals in the aquatic environment - occurrence and environmental implications. Eur J Pharmacol 2019; 866:172813. [PMID: 31751574 DOI: 10.1016/j.ejphar.2019.172813] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/07/2019] [Accepted: 11/15/2019] [Indexed: 11/16/2022]
Abstract
The environmental occurrence of antimicrobial pharmaceuticals and antibiotic resistant bacteria and antibiotic resistant genes has become a global phenomenon and a multifaceted threat. Integrated actions of many parties are needed to prevent further aggravation of the problem. Well-directed actions require clear understanding of the problem, which can be ensured by frequent revaluation of the existing knowledge and disseminating it among relevant audiences. The goal of this review paper is to discuss the occurrence and abundance of antimicrobial pharmaceuticals in the aquatic environment in context of adverse effects caused directly by these substances and the threat associated with the antibiotics resistance phenomenon. Several classes of antimicrobial pharmaceuticals (aminoglycosides, β-lactams, glycopeptides, macrolides, fluoroquinolones, sulfonamides and trimethoprim, tetracyclines) have been selected to illustrate their sources, environmental abundance, degradation routes (transformation products) and environmental implications including their ecotoxic effect and the spread of antibiotic resistance within the compartments of the aquatic environment and wastewater treatment plants. Wastewater treatment plants are indeed the main source responsible for the prevalence of these factors in the aquatic environment, since predominantly the plants have not been designed to retain antimicrobial pharmaceuticals. In order to limit the prevalence of these impurities into the environment, better source control is recommended as well as the establishment of stricter environmental quality standards. Counteracting all the above-mentioned threats requires to undertake integrated activities based on cooperation of professionals and scientists from various fields of science or industry, such as environmental sciences, medicine, veterinary, pharmacology, chemical engineering and others.
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Affiliation(s)
- Ewa Felis
- Silesian University of Technology, Faculty of Energy and Environmental Engineering, Environmental Biotechnology Department, Ul. Akademicka 2, 44-100, Gliwice, Poland; Silesian University of Technology, The Biotechnology Centre, Ul. B. Krzywoustego 8, 44-100, Gliwice, Poland.
| | - Joanna Kalka
- Silesian University of Technology, Faculty of Energy and Environmental Engineering, Environmental Biotechnology Department, Ul. Akademicka 2, 44-100, Gliwice, Poland
| | - Adam Sochacki
- Silesian University of Technology, Faculty of Energy and Environmental Engineering, Environmental Biotechnology Department, Ul. Akademicka 2, 44-100, Gliwice, Poland; Silesian University of Technology, The Biotechnology Centre, Ul. B. Krzywoustego 8, 44-100, Gliwice, Poland; Czech University of Life Sciences Prague, Faculty of Environmental Sciences, Kamýcká 129, 165 21, Praha 6, Czech Republic
| | - Katarzyna Kowalska
- Silesian University of Technology, Faculty of Energy and Environmental Engineering, Environmental Biotechnology Department, Ul. Akademicka 2, 44-100, Gliwice, Poland; Silesian University of Technology, The Biotechnology Centre, Ul. B. Krzywoustego 8, 44-100, Gliwice, Poland
| | - Sylwia Bajkacz
- Silesian University of Technology, Faculty of Chemistry, Department of Inorganic, Analytical Chemistry and Electrochemistry, Ul. B Krzywoustego 6, 44-100, Gliwice, Poland; Silesian University of Technology, The Biotechnology Centre, Ul. B. Krzywoustego 8, 44-100, Gliwice, Poland
| | - Monika Harnisz
- University of Warmia and Mazury in Olsztyn, Faculty of Environmental Sciences, Department of Environmental Microbiology, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Ewa Korzeniewska
- University of Warmia and Mazury in Olsztyn, Faculty of Environmental Sciences, Department of Environmental Microbiology, Prawocheńskiego 1, 10-720, Olsztyn, Poland
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120
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Okazaki Y, Nishimura Y, Yoshida T, Ogata H, Nakano SI. Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake. Environ Microbiol 2019; 21:4740-4754. [PMID: 31608575 DOI: 10.1111/1462-2920.14816] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/01/2019] [Accepted: 10/01/2019] [Indexed: 01/21/2023]
Abstract
Metagenomics has dramatically expanded the known virosphere, but freshwater viral diversity and their ecological interaction with hosts remain poorly understood. Here, we conducted a metagenomic exploration of planktonic dsDNA prokaryotic viruses by sequencing both virion (<0.22 μm) and cellular (0.22-5.0 μm) fractions collected spatiotemporally from a deep freshwater lake (Lake Biwa, Japan). This simultaneously reconstructed 183 complete (i.e., circular) viral genomes and 57 bacterioplankton metagenome-assembled genomes. Analysis of metagenomic read coverage revealed vertical partitioning of the viral community analogous to the vertically stratified bacterioplankton community. The hypolimnetic community was generally stable during stratification, but occasionally shifted abruptly, presumably due to lysogenic induction. Genes involved in assimilatory sulfate reduction were encoded in 20 (10.9%) viral genomes, including those of dominant viruses, and may aid viral propagation in sulfur-limited freshwater systems. Hosts were predicted for 40 (21.9%) viral genomes, encompassing 10 phyla (or classes of Proteobacteria) including ubiquitous freshwater bacterioplankton lineages (e.g., Ca. Fonsibacter and Ca. Nitrosoarchaeum). Comparison with viral genomes derived from published metagenomes revealed viral phylogeographic connectivity in geographically isolated habitats. Notably, analogous to their hosts, actinobacterial viruses were among the most diverse, ubiquitous and abundant viral groups in freshwater systems, with potential high lytic activity in surface waters.
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Affiliation(s)
- Yusuke Okazaki
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Yosuke Nishimura
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shin-Ichi Nakano
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan
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121
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Garmaeva S, Sinha T, Kurilshikov A, Fu J, Wijmenga C, Zhernakova A. Studying the gut virome in the metagenomic era: challenges and perspectives. BMC Biol 2019; 17:84. [PMID: 31660953 PMCID: PMC6819614 DOI: 10.1186/s12915-019-0704-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 12/12/2022] Open
Abstract
The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inhabiting bacteria, yet the viruses that infect these bacteria, known as bacteriophages, remain underexplored. In this review, we focus on what is known about the role of bacteriophages in human health and the technical challenges involved in studying the gut virome, of which they are a major component. Lastly, we discuss what can be learned from studies of bacteriophages in other ecosystems.
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Affiliation(s)
- Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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122
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Carey JN, Mettert EL, Fishman-Engel DR, Roggiani M, Kiley PJ, Goulian M. Phage integration alters the respiratory strategy of its host. eLife 2019; 8:49081. [PMID: 31650957 PMCID: PMC6814406 DOI: 10.7554/elife.49081] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022] Open
Abstract
Temperate bacteriophages are viruses that can incorporate their genomes into their bacterial hosts, existing there as prophages that refrain from killing the host cell until induced. Prophages are largely quiescent, but they can alter host phenotype through factors encoded in their genomes (often virulence factors) or by disrupting host genes as a result of integration. Here we describe another mechanism by which a prophage can modulate host phenotype. We show that a temperate phage that integrates in Escherichia coli reprograms host regulation of an anaerobic respiratory system, thereby inhibiting a bet hedging strategy. The phage exerts this effect by upregulating a host-encoded signal transduction protein through transcription initiated from a phage-encoded promoter. We further show that this phenomenon occurs not only in a laboratory strain of E. coli, but also in a natural isolate that contains a prophage at this site. Animals and plants can all fall prey to viruses – and so can bacteria. The viruses that infect bacteria are called bacteriophages (or phages for short), and they are found everywhere bacteria live and probably outnumber bacteria by at least ten to one. While some phages quickly kill every bacterial cell they infect, others enter a dormant state by inserting their DNA into the DNA of their host cell. Here they lie in wait for a signal that reactivates them, triggering the production of more phages and the death of the host cell. While the phage lies dormant its DNA may harm the host by interfering with nearby bacterial genes, or it may actually provide new genes that benefit the host. In most cases the effects of dormant phages are unknown. A bacterium known as Escherichia coli is commonly found in the intestines of humans and other mammals. It can use a nutrient called trimethylamine oxide (TMAO) to help it survive rapid decreases in oxygen levels that can occur in its environment. When a phage called HK022 infects E. coli, the phage enters a dormant state by inserting its DNA between two genes that are critical for E. coli to use TMAO. However, it is not clear what effect, if any, HK022 has on E. coli’s behavior. To address this question, Carey et al. used genetic approaches to study E. coli cells carrying dormant HK022 phages. The experiments showed that the bacteria lost the ability to use TMAO to survive rapid decreases in oxygen because the dormant phages switched on one of the neighboring E. coli genes. Unexpectedly, the phage achieved this by neatly replacing the gene’s own promoter – the stretch of DNA that contains information about when the gene should be switched on, and how strongly – with a substitute promoter carried in the phage’s DNA. This substitute promoter is stronger than the normal version – meaning that the gene is more active than it should be. Phages are key players in every natural population of microbes and are therefore entwined in the health of humans and the environment. The findings of Carey et al. show a new mechanism through which phages modify their hosts. In the future it may be possible to develop this mechanism into a tool to manipulate bacteria in complex environments like infection sites, for example by introducing phages that block the mechanisms that allow bacteria to tolerate antibiotics.
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Affiliation(s)
- Jeffrey N Carey
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| | - Erin L Mettert
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, United States
| | | | - Manuela Roggiani
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Patricia J Kiley
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, United States
| | - Mark Goulian
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Biology, University of Pennsylvania, Philadelphia, United States.,Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, United States
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123
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Nagata Y, Kato H, Ohtsubo Y, Tsuda M. Lessons from the genomes of lindane-degrading sphingomonads. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:630-644. [PMID: 31063253 DOI: 10.1111/1758-2229.12762] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/29/2019] [Accepted: 05/02/2019] [Indexed: 05/27/2023]
Abstract
Bacterial strains capable of degrading man-made xenobiotic compounds are good materials to study bacterial evolution towards new metabolic functions. Lindane (γ-hexachlorocyclohexane, γ-HCH, or γ-BHC) is an especially good target compound for the purpose, because it is relatively recalcitrant but can be degraded by a limited range of bacterial strains. A comparison of the complete genome sequences of lindane-degrading sphingomonad strains clearly demonstrated that (i) lindane-degrading strains emerged from a number of different ancestral hosts that have recruited lin genes encoding enzymes that are able to channel lindane to central metabolites, (ii) in sphingomonads lin genes have been acquired by horizontal gene transfer mediated by different plasmids and in which IS6100 plays a role in recruitment and distribution of genes, and (iii) IS6100 plays a role in dynamic genome rearrangements providing genetic diversity to different strains and ability to evolve to other states. Lindane-degrading bacteria whose genomes change so easily and quickly are also fascinating starting materials for tracing the bacterial evolution process experimentally in a relatively short time period. As the origin of the specific lin genes remains a mystery, such genes will be useful probes for exploring the cryptic 'gene pool' available to bacteria.
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Affiliation(s)
- Yuji Nagata
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
| | - Hiromi Kato
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
| | - Yoshiyuki Ohtsubo
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
| | - Masataka Tsuda
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
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124
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Abstract
Antibiotic resistance is a growing concern for management of common bacterial infections. Here, we show that antibiotics can be effective at subinhibitory levels when bacteria carry latent phage. Our findings suggest that specific treatment strategies based on the identification of latent viruses in individual bacterial strains may be an effective personalized medicine approach to antibiotic stewardship. Most bacteria and archaea are infected by latent viruses that change their physiology and responses to environmental stress. We use a population model of the bacterium-phage relationship to examine the role that latent phage play in the bacterial population over time in response to antibiotic treatment. We demonstrate that the stress induced by antibiotic administration, even if bacteria are resistant to killing by antibiotics, is sufficient to control the infection under certain conditions. This work expands the breadth of understanding of phage-antibiotic synergy to include both temperate and chronic viruses persisting in their latent form in bacterial populations. IMPORTANCE Antibiotic resistance is a growing concern for management of common bacterial infections. Here, we show that antibiotics can be effective at subinhibitory levels when bacteria carry latent phage. Our findings suggest that specific treatment strategies based on the identification of latent viruses in individual bacterial strains may be an effective personalized medicine approach to antibiotic stewardship.
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125
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Frazão N, Sousa A, Lässig M, Gordo I. Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut. Proc Natl Acad Sci U S A 2019; 116:17906-17915. [PMID: 31431529 PMCID: PMC6731689 DOI: 10.1073/pnas.1906958116] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacteria evolve by mutation accumulation in laboratory experiments, but tempo and mode of evolution in natural environments are largely unknown. Here, we study the ubiquitous natural process of host colonization by commensal bacteria. We show, by experimental evolution of Escherichia coli in the mouse intestine, that the ecology of the gut controls the pace and mode of evolution of a new invading bacterial strain. If a resident E. coli strain is present in the gut, the invading strain evolves by rapid horizontal gene transfer (HGT), which precedes and outweighs evolution by accumulation of mutations. HGT is driven by 2 bacteriophages carried by the resident strain, which cause an epidemic phage infection of the invader. These dynamics are followed by subsequent evolution by clonal interference of genetically diverse lineages of phage-carrying (lysogenic) bacteria. We show that the genes uptaken by HGT enhance the metabolism of specific gut carbon sources and provide a fitness advantage to lysogenic invader lineages. A minimal dynamical model explains the temporal pattern of phage epidemics and the complex evolutionary outcome of phage-mediated selection. We conclude that phage-driven HGT is a key eco-evolutionary driving force of gut colonization-it accelerates evolution and promotes genetic diversity of commensal bacteria.
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Affiliation(s)
- Nelson Frazão
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Ana Sousa
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, 50923 Cologne, Germany
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal;
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126
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Lynn-Bell NL, Strand MR, Oliver KM. Bacteriophage acquisition restores protective mutualism. Microbiology (Reading) 2019; 165:985-989. [DOI: 10.1099/mic.0.000816] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
| | - Michael R. Strand
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Kerry M. Oliver
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
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127
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Viruses as key reservoirs of antibiotic resistance genes in the environment. ISME JOURNAL 2019; 13:2856-2867. [PMID: 31358910 DOI: 10.1038/s41396-019-0478-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/03/2019] [Accepted: 06/21/2019] [Indexed: 11/08/2022]
Abstract
Antibiotic resistance is a rapidly growing health care problem globally and causes many illnesses and deaths. Bacteria can acquire antibiotic resistance genes (ARGs) by horizontal transfer mediated by mobile genetic elements, where the role of phages in their dissemination in natural environments has not yet been clearly resolved. From metagenomic studies, we showed that the mean proportion of predicted ARGs found in prophages (0-0.0028%) was lower than those present in the free viruses (0.001-0.1%). Beta-lactamase, from viruses in the swine gut, represented 0.10 % of the predicted genes. Overall, in the environment, the ARG distribution associated with viruses was strongly linked to human activity, and the low dN/dS ratio observed advocated for a negative selection of the ARGs harbored by the viruses. Our network approach showed that viruses were linked to putative pathogens (Enterobacterales and vibrionaceae) and were considered key vehicles in ARG transfer, similar to plasmids. Therefore, these ARGs could then be disseminated at larger temporal and spatial scales than those included in the bacterial genomes, allowing for time-delayed genetic exchanges.
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128
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Bai M, Cheng YH, Sun XQ, Wang ZY, Wang YX, Cui XL, Xiao W. Nine Novel Phages from a Plateau Lake in Southwest China: Insights into Aeromonas Phage Diversity. Viruses 2019; 11:v11070615. [PMID: 31284428 PMCID: PMC6669705 DOI: 10.3390/v11070615] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/18/2019] [Accepted: 07/02/2019] [Indexed: 11/16/2022] Open
Abstract
Aeromonas species are common pathogens of fish and some of them can opportunistically cause infectious diseases in humans. The overuse of antibiotics has led to the emergence of bacterial drug-resistance. To date, only 51 complete genome sequences of Aeromonas phages are available in GenBank. Here, we report the isolation of nine Aeromonas phages from a plateau lake in China. The protein cluster, dot plot and ANI analyses were performed on all 60 currently sequenced Aeromonas phage genomes and classified into nine clusters and thirteen singletons. Among the nine isolated phages, the DNA-packaging strategy of cluster 2L372D (including 2L372D, 2L372X, 4L372D, 4L372XY) is unknown, while the other five phages use the headful (P22/Sf6) DNA-packaging strategy. Notably, the isolated phages with larger genomes conservatively encode auxiliary metabolism genes, DNA replication and metabolism genes, while in smaller phage genomes, recombination-related genes were conserved. Finally, we propose a new classification scheme for Aeromonas phages.
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Affiliation(s)
- Meng Bai
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China
| | - Ya-Hui Cheng
- Yunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming 650201, China
| | - Xue-Qin Sun
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China
| | - Zi-Yi Wang
- Yunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming 650201, China
| | - Yong-Xia Wang
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China
| | - Xiao-Long Cui
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China.
| | - Wei Xiao
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China.
- Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming 650500, China.
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129
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Fillol-Salom A, Alsaadi A, de Sousa JAM, Zhong L, Foster KR, Rocha EPC, Penadés JR, Ingmer H, Haaber J. Bacteriophages benefit from generalized transduction. PLoS Pathog 2019; 15:e1007888. [PMID: 31276485 PMCID: PMC6636781 DOI: 10.1371/journal.ppat.1007888] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/17/2019] [Accepted: 06/03/2019] [Indexed: 01/26/2023] Open
Abstract
Temperate phages are bacterial viruses that as part of their life cycle reside in the bacterial genome as prophages. They are found in many species including most clinical strains of the human pathogens, Staphylococcus aureus and Salmonella enterica serovar Typhimurium. Previously, temperate phages were considered as only bacterial predators, but mounting evidence point to both antagonistic and mutualistic interactions with for example some temperate phages contributing to virulence by encoding virulence factors. Here we show that generalized transduction, one type of bacterial DNA transfer by phages, can create conditions where not only the recipient host but also the transducing phage benefit. With antibiotic resistance as a model trait we used individual-based models and experimental approaches to show that antibiotic susceptible cells become resistant to both antibiotics and phage by i) integrating the generalized transducing temperate phages and ii) acquiring transducing phage particles carrying antibiotic resistance genes obtained from resistant cells in the environment. This is not observed for non-generalized transducing temperate phages, which are unable to package bacterial DNA, nor for generalized transducing virulent phages that do not form lysogens. Once established, the lysogenic host and the prophage benefit from the existence of transducing particles that can shuffle bacterial genes between lysogens and for example disseminate resistance to antibiotics, a trait not encoded by the phage. This facilitates bacterial survival and leads to phage population growth. We propose that generalized transduction can function as a mutualistic trait where temperate phages cooperate with their hosts to survive in rapidly-changing environments. This implies that generalized transduction is not just an error in DNA packaging but is selected for by phages to ensure their survival. Viruses (phages) that only attack bacteria are highly common. Some of these phages naturally reside within the bacterial chromosome for extended periods of time. Upon release and propagation on phage susceptible cells, new phage particles are made but occasionally bacterial rather than phage DNA is packaged into phage heads. Transfer of random pieces of bacterial DNA between cells by such transducing particles has been termed generalized transduction and has long been used as a tool for genetic engineering. We show here that bacteria and generalized transducing phages cooperate to survive adverse conditions such as the presence of antibiotics by phage integration and transduction of antibiotic resistance genes from neighboring cells. The resulting cells are resistant to phage attack due to immunity provided by the integrated prophage and they are able to exchange bacterial DNA with other cells containing a similar prophage via the transducing particles. Previously, transduction has been considered an accident in phage biology. Here we propose that rather than being an accident, generalized transduction is an evolved trait selected by some temperate phages to persist in rapidly-changing environments.
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Affiliation(s)
- Alfred Fillol-Salom
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Ahlam Alsaadi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Li Zhong
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Kevin R. Foster
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Eduardo P. C. Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail: (HI); (JH)
| | - Jakob Haaber
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail: (HI); (JH)
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130
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Abstract
Bacteriophages are the most prominent members of the gut microbiome, outnumbering their bacterial hosts by a factor of 10. Phages are bacteria-specific viruses that are gaining attention as highly influential regulators of the gut bacterial community. Dysregulation of the gut bacterial community contributes to dysbiosis, a microbiome disorder characterized by compositional and functional changes that contribute to disease. A role for phages in gut microbiome dysbiosis is emerging with evidence that the gut phage community is altered in dysbiosis-associated disorders such as colorectal cancer and inflammatory bowel disease. Several recent studies have linked successful fecal microbiota transplantation to uptake of the donor’s gut phage community, offering some insight into why some recipients respond to treatment whereas others do not. Here, we review the literature supporting a role for phages in mediating the gut bacterial community, giving special attention to Western diet dysbiosis as a case study to demonstrate a theoretical phage-based mechanism for the establishment and maintenance of dysbiosis.
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Affiliation(s)
- Derek M Lin
- Medicine Service, New Mexico VA Health Care System, Albuquerque, New Mexico, USA
| | - Henry C Lin
- Medicine Service, New Mexico VA Health Care System, Albuquerque, New Mexico, USA.,Department of Gastroenterology and Hepatology, University of New Mexico, Albuquerque, New Mexico, USA
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131
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Lerner A, Ramesh A, Matthias T. The Revival of the Battle between David and Goliath in the Enteric Viruses and Microbiota Struggle: Potential Implication for Celiac Disease. Microorganisms 2019; 7:microorganisms7060173. [PMID: 31207872 PMCID: PMC6616392 DOI: 10.3390/microorganisms7060173] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/04/2019] [Accepted: 06/11/2019] [Indexed: 02/08/2023] Open
Abstract
The human gut is inhabited by overcrowded prokaryotic communities, a major component of which is the virome, comprised of viruses, bacteriophages, archaea, eukaryotes and bacteria. The virome is required for luminal homeostasis and, by their lytic or synergic capacities, they can regulate the microbial community structure and activity. Dysbiosis is associated with numerous chronic human diseases. Since the virome can impact microbial genetics and behavior, understanding its biology, composition, cellular cycle, regulation, mode of action and potential beneficial or hostile activities can change the present paradigm of the cross-talks in the luminal gut compartment. Celiac disease is a frequent autoimmune disease in which viruses can play a role in disease development. Based on the current knowledge on the enteric virome, in relation to celiac disease pathophysiological evolvement, the current review summarizes the potential interphases between the two. Exploring and understanding the role of the enteric virome in gluten-dependent enteropathy might bring new therapeutic strategies to change the luminal eco-event for the patient’s benefit.
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Affiliation(s)
- Aaron Lerner
- AESKU.KIPP Institute, Mikroforum Ring 2, 55234 Wendelsheim, Germany.
| | - Ajay Ramesh
- AESKU.KIPP Institute, Mikroforum Ring 2, 55234 Wendelsheim, Germany.
| | - Torsten Matthias
- AESKU.KIPP Institute, Mikroforum Ring 2, 55234 Wendelsheim, Germany.
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132
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Lerner A, Ramesh A, Matthias T. The Revival of the Battle between David and Goliath in the Enteric Viruses and Microbiota Struggle: Potential Implication for Celiac Disease. Microorganisms 2019. [PMID: 31207872 DOI: 10.3390/microorganisms7060173.pmid:31207872;pmcid:pmc6616392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The human gut is inhabited by overcrowded prokaryotic communities, a major component of which is the virome, comprised of viruses, bacteriophages, archaea, eukaryotes and bacteria. The virome is required for luminal homeostasis and, by their lytic or synergic capacities, they can regulate the microbial community structure and activity. Dysbiosis is associated with numerous chronic human diseases. Since the virome can impact microbial genetics and behavior, understanding its biology, composition, cellular cycle, regulation, mode of action and potential beneficial or hostile activities can change the present paradigm of the cross-talks in the luminal gut compartment. Celiac disease is a frequent autoimmune disease in which viruses can play a role in disease development. Based on the current knowledge on the enteric virome, in relation to celiac disease pathophysiological evolvement, the current review summarizes the potential interphases between the two. Exploring and understanding the role of the enteric virome in gluten-dependent enteropathy might bring new therapeutic strategies to change the luminal eco-event for the patient's benefit.
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Affiliation(s)
- Aaron Lerner
- AESKU.KIPP Institute, Mikroforum Ring 2, 55234 Wendelsheim, Germany.
| | - Ajay Ramesh
- AESKU.KIPP Institute, Mikroforum Ring 2, 55234 Wendelsheim, Germany.
| | - Torsten Matthias
- AESKU.KIPP Institute, Mikroforum Ring 2, 55234 Wendelsheim, Germany.
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133
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Origin of a Core Bacterial Gene via Co-option and Detoxification of a Phage Lysin. Curr Biol 2019; 29:1634-1646.e6. [PMID: 31080080 DOI: 10.1016/j.cub.2019.04.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/12/2019] [Accepted: 04/10/2019] [Indexed: 11/23/2022]
Abstract
Temperate phages constitute a potentially beneficial genetic reservoir for bacterial innovation despite being selfish entities encoding an infection cycle inherently at odds with bacterial fitness. These phages integrate their genomes into the bacterial host during infection, donating new but deleterious genetic material: the phage genome encodes toxic genes, such as lysins, that kill the bacterium during the phage infection cycle. Remarkably, some bacteria have exploited the destructive properties of phage genes for their own benefit by co-opting them as toxins for functions related to bacterial warfare, virulence, and secretion. However, do toxic phage genes ever become raw material for functional innovation? Here, we report on a toxic phage gene whose product has lost its toxicity and has become a domain of a core cellular factor, SpmX, throughout the bacterial order Caulobacterales. Using a combination of phylogenetics, bioinformatics, structural biology, cell biology, and biochemistry, we have investigated the origin and function of SpmX and determined that its occurrence is the result of the detoxification of a phage peptidoglycan hydrolase gene. We show that the retained, attenuated activity of the phage-derived domain plays an important role in proper cell morphology and developmental regulation in representatives of this large bacterial clade. To our knowledge, this is the first observation of a phage gene domestication event in which a toxic phage gene has been co-opted for core cellular function at the root of a large bacterial clade.
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134
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Varble A, Meaden S, Barrangou R, Westra ER, Marraffini LA. Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci. Nat Microbiol 2019; 4:956-963. [PMID: 30886355 PMCID: PMC6533911 DOI: 10.1038/s41564-019-0400-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/31/2019] [Indexed: 11/09/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) loci and their associated (cas) genes encode an adaptive immune system that protects prokaryotes from viral1 and plasmid2 invaders. Following viral (phage) infection, a small fraction of the prokaryotic cells are able to integrate a small sequence of the invader's genome into the CRISPR array1. These sequences, known as spacers, are transcribed and processed into small CRISPR RNA guides3-5 that associate with Cas nucleases to specify a viral target for destruction6-9. Although CRISPR-cas loci are widely distributed throughout microbial genomes and often display hallmarks of horizontal gene transfer10-12, the drivers of CRISPR dissemination remain unclear. Here, we show that spacers can recombine with phage target sequences to mediate a form of specialized transduction of CRISPR elements. Phage targets in phage 85, ΦNM1, ΦNM4 and Φ12 can recombine with spacers in either chromosomal or plasmid-borne CRISPR loci in Staphylococcus, leading to either the transfer of CRISPR-adjacent genes or the propagation of acquired immunity to other bacteria in the population, respectively. Our data demonstrate that spacer sequences not only specify the targets of Cas nucleases but also can promote horizontal gene transfer.
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Affiliation(s)
- Andrew Varble
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Sean Meaden
- Environment and Sustainability Institute, Centre for Ecology and Conservation, University of Exeter, Biosciences, Penryn, Cornwall, UK
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Edze R Westra
- Environment and Sustainability Institute, Centre for Ecology and Conservation, University of Exeter, Biosciences, Penryn, Cornwall, UK
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA. .,Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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135
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Rowan-Nash AD, Korry BJ, Mylonakis E, Belenky P. Cross-Domain and Viral Interactions in the Microbiome. Microbiol Mol Biol Rev 2019; 83:e00044-18. [PMID: 30626617 PMCID: PMC6383444 DOI: 10.1128/mmbr.00044-18] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The importance of the microbiome to human health is increasingly recognized and has become a major focus of recent research. However, much of the work has focused on a few aspects, particularly the bacterial component of the microbiome, most frequently in the gastrointestinal tract. Yet humans and other animals can be colonized by a wide array of organisms spanning all domains of life, including bacteria and archaea, unicellular eukaryotes such as fungi, multicellular eukaryotes such as helminths, and viruses. As they share the same host niches, they can compete with, synergize with, and antagonize each other, with potential impacts on their host. Here, we discuss these major groups making up the human microbiome, with a focus on how they interact with each other and their multicellular host.
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Affiliation(s)
- Aislinn D Rowan-Nash
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Eleftherios Mylonakis
- Infectious Diseases Division, Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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136
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Abstract
Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes brings about numerous evolutionary innovations and shapes genome structure and function in a multitude of ways. In traditional classification systems, TEs are often being depicted in simplistic ways, based primarily on the key enzymes required for transposition, such as transposases/recombinases and reverse transcriptases. Recent progress in whole-genome sequencing and long-read assembly, combined with expansion of the familiar range of model organisms, resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. Here, we focus on such oversized eukaryotic TEs, including retrotransposons and DNA transposons, outline their complex and often combinatorial nature and closely intertwined relationship with viruses, and discuss their potential for participating in transfer of long stretches of DNA in eukaryotes.
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Affiliation(s)
- Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
- Corresponding author: E-mail:
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
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137
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Comparative analysis and characterization of Enterobacteria phage SSL-2009a and 'HK578likevirus' bacteriophages. Virus Res 2019; 259:77-84. [PMID: 30395896 DOI: 10.1016/j.virusres.2018.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/03/2018] [Accepted: 10/23/2018] [Indexed: 12/15/2022]
Abstract
Enterobacteria phage SSL-2009a is a virulent bacteriophage with strong and abroad lytic ability against lots of engineering E. coli strains. In this study, we re-sequenced its whole genome and made a detail analysis on its genomic and proteomic characteristics according to the updated genomic sequence. The genome of SSL-2009a is a circular double-stranded DNA of 44,899 base pairs in length, with a 54.67% G + C content. A total of 67 open reading frames were predicted as protein coding sequences, 24 of which encode products highly homologous to known phage proteins. There are 10 promoters and 22 terminators identified in the genome of SSL-2009a, but no tRNA is found. SSL-2009a belongs to the 'HK578likevirus' genus of Siphoviridae. Comparative analyses indicated that other twelve phages share high homology with SSL-2009a at nucleotide and amino acid levels and also should be clustered into the same genus. In-depth analysis was performed to reveal the genomic, proteomic, and morphological features of these 'HK578likevirus' phages, which may promote our understanding of Enterobacteria phage SSL-2009a and the 'HK578likevirus' genus, even the biodiversity and evolution of bacteriophages.
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138
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Exaptation at the molecular genetic level. SCIENCE CHINA-LIFE SCIENCES 2018; 62:437-452. [PMID: 30798493 DOI: 10.1007/s11427-018-9447-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 12/01/2018] [Indexed: 12/22/2022]
Abstract
The realization that body parts of animals and plants can be recruited or coopted for novel functions dates back to, or even predates the observations of Darwin. S.J. Gould and E.S. Vrba recognized a mode of evolution of characters that differs from adaptation. The umbrella term aptation was supplemented with the concept of exaptation. Unlike adaptations, which are restricted to features built by selection for their current role, exaptations are features that currently enhance fitness, even though their present role was not a result of natural selection. Exaptations can also arise from nonaptations; these are characters which had previously been evolving neutrally. All nonaptations are potential exaptations. The concept of exaptation was expanded to the molecular genetic level which aided greatly in understanding the enormous potential of neutrally evolving repetitive DNA-including transposed elements, formerly considered junk DNA-for the evolution of genes and genomes. The distinction between adaptations and exaptations is outlined in this review and examples are given. Also elaborated on is the fact that such distinctions are sometimes more difficult to determine; this is a widespread phenomenon in biology, where continua abound and clear borders between states and definitions are rare.
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139
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Wahl LM, Betti MI, Dick DW, Pattenden T, Puccini AJ. Evolutionary stability of the lysis-lysogeny decision: Why be virulent? Evolution 2018; 73:92-98. [PMID: 30430551 DOI: 10.1111/evo.13648] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 10/09/2018] [Indexed: 01/03/2023]
Abstract
Lytic viruses infect and kill host cells, producing a large number of viral copies. Temperate viruses, in contrast, are able to integrate viral genetic material into the host cell DNA, leaving a viable host cell. The evolutionary advantage of this strategy, lysogeny, has been demonstrated in complex environments that include spatial structure, oscillating population dynamics, or periodic environmental collapse. Here, we examine the evolutionary stability of the lysis-lysogeny decision, that is, we predict the long-term outcome of the evolution of lysogeny rates. We demonstrate that viruses with high rates of lysogeny are stable against invasion by more virulent viral strains even in simple environments, as long as the pool of susceptible hosts is not unlimited. This mirrors well-known results in both r-K selection theory and virulence evolution: although virulent viruses have a faster potential growth rate, temperate strains are able to maintain positive growth on a lower density of the limiting resource, susceptible hosts. We then outline scenarios in which the rate of lysogeny is predicted to evolve either toward full lysogeny or full lysis. Finally, we demonstrate conditions under which intermediate rates of lysogeny, as observed in temperate viruses in nature, can be sustained long-term. In general, intermediate lysogeny rates persist when the coupling between susceptible host density and virus density is relaxed.
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Affiliation(s)
- Lindi M Wahl
- Applied Mathematics, Western University, London, Ontario, Canada
| | - Matthew I Betti
- Mathematics and Computer Science, Mount Allison University, Sackville, New Brunswick, Canada
| | - David W Dick
- Applied Mathematics, Western University, London, Ontario, Canada
| | - Tyler Pattenden
- Applied Mathematics, Western University, London, Ontario, Canada
| | - Aaryn J Puccini
- Applied Mathematics, Western University, London, Ontario, Canada
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140
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Gehring T, Heydeck D, Niewienda A, Janek K, Kuhn H. Do lipoxygenases occur in viruses?: Expression and characterization of a viral lipoxygenase-like protein did not provide evidence for the existence of functional viral lipoxygenases. Prostaglandins Leukot Essent Fatty Acids 2018; 138:14-23. [PMID: 30392576 DOI: 10.1016/j.plefa.2018.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/24/2018] [Accepted: 10/03/2018] [Indexed: 01/13/2023]
Abstract
Lipoxygenases are lipid peroxidizing enzymes, which frequently occur in higher plants and animals. In bacteria, these enzymes are rare and have been introduced via horizontal gene transfer. Since viruses function as horizontal gene transfer vectors and since lipoxygenases may be helpful for releasing assembled virus particles from host cells we explored whether these enzymes may actually occur in viruses. For this purpose we developed a four-step in silico screening strategy and searching the publically available viral genomes for lipoxygenase-like sequences we detected a single functional gene in the genome of a mimivirus infecting Acantamoeba polyphaga. The primary structure of this protein involved two putative metal ligand clusters but the recombinant enzyme did neither contain iron nor manganese. Most importantly, it did not exhibit lipoxygenase activity. These data suggests that this viral lipoxygenase-like sequence does not encode a functional lipoxygenase and that these enzymes do not occur in viruses.
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Affiliation(s)
- Tatjana Gehring
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Dagmar Heydeck
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Agathe Niewienda
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Core facility for Mass Spectrometry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Katharina Janek
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Core facility for Mass Spectrometry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Hartmut Kuhn
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, D-10117 Berlin, Germany.
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141
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Nogueira T, David PHC, Pothier J. Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach. Drug Dev Res 2018; 80:86-97. [PMID: 30370682 DOI: 10.1002/ddr.21466] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/14/2018] [Accepted: 08/15/2018] [Indexed: 12/28/2022]
Abstract
The exposure of the human gut to antibiotics can have a great impact on human health. Antibiotics pertain to the preservation of human health and are useful tools for fighting bacterial infections. They can be used for curing infections and can play a critical role in immunocompromised or chronic patients, or in fighting childhood severe malnutrition. Yet, the genomic and phylogenetic diversity of the human gut changes under antibiotic exposure. Antibiotics can also have severe side effects on human gut health, due to the spreading of potential antibiotic resistance genetic traits and to their correlation with virulence of some bacterial pathogens. They can shape, and even disrupt, the composition and functioning diversity of the human gut microbiome. Traditionally bacterial antibiotic resistances have been evaluated at clone or population level. However, the understanding of these two apparently disparate perspectives as both friends and foes may come from the study of microbiomes as a whole and from the evaluation of both positive and negative effects of antibiotics on microbial community dynamics and diversity. In this review we present some metagenomic tools and databases that enable the studying of antibiotic resistance in human gut metagenomes, promoting the development of personalized medicine strategies, new antimicrobial therapy protocols and patient follow-up.
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Affiliation(s)
- Teresa Nogueira
- cE3c - Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro H C David
- cE3c - Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Joël Pothier
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, Muséum National d'Histoire naturelle, CNRS, EPHE, CP, Paris, France
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142
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Affiliation(s)
- Alan R Davidson
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, Canada.
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143
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Kuhn H, Humeniuk L, Kozlov N, Roigas S, Adel S, Heydeck D. The evolutionary hypothesis of reaction specificity of mammalian ALOX15 orthologs. Prog Lipid Res 2018; 72:55-74. [PMID: 30237084 DOI: 10.1016/j.plipres.2018.09.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/04/2018] [Accepted: 09/13/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Hartmut Kuhn
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Charitéplatz 1, CCO- Building, Virchowweg 6, D-10117 Berlin, Germany.
| | - Lia Humeniuk
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Charitéplatz 1, CCO- Building, Virchowweg 6, D-10117 Berlin, Germany
| | - Nikita Kozlov
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Charitéplatz 1, CCO- Building, Virchowweg 6, D-10117 Berlin, Germany
| | - Sophie Roigas
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Charitéplatz 1, CCO- Building, Virchowweg 6, D-10117 Berlin, Germany
| | - Susan Adel
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Internal Medicine, Division of Hepathology and Gastroenterology, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Dagmar Heydeck
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Charitéplatz 1, CCO- Building, Virchowweg 6, D-10117 Berlin, Germany
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144
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de Jonge PA, Nobrega FL, Brouns SJJ, Dutilh BE. Molecular and Evolutionary Determinants of Bacteriophage Host Range. Trends Microbiol 2018; 27:51-63. [PMID: 30181062 DOI: 10.1016/j.tim.2018.08.006] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/07/2018] [Accepted: 08/13/2018] [Indexed: 01/12/2023]
Abstract
The host range of a bacteriophage is the taxonomic diversity of hosts it can successfully infect. Host range, one of the central traits to understand in phages, is determined by a range of molecular interactions between phage and host throughout the infection cycle. While many well studied model phages seem to exhibit a narrow host range, recent ecological and metagenomics studies indicate that phages may have specificities that range from narrow to broad. There is a growing body of studies on the molecular mechanisms that enable phages to infect multiple hosts. These mechanisms, and their evolution, are of considerable importance to understanding phage ecology and the various clinical, industrial, and biotechnological applications of phage. Here we review knowledge of the molecular mechanisms that determine host range, provide a framework defining broad host range in an evolutionary context, and highlight areas for additional research.
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Affiliation(s)
- Patrick A de Jonge
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584 CH Utrecht, The Netherlands; Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands; Laboratory for Microbiology, Wageningen University, Stippeneng 4 6708 WE, Wageningen, The Netherlands; These authors made equal contributions
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584 CH Utrecht, The Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525GA Nijmegen, The Netherlands; These authors made equal contributions.
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145
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Durão P, Balbontín R, Gordo I. Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance. Trends Microbiol 2018; 26:677-691. [DOI: 10.1016/j.tim.2018.01.005] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/05/2018] [Accepted: 01/24/2018] [Indexed: 01/10/2023]
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146
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Chatterjee A, Duerkop BA. Beyond Bacteria: Bacteriophage-Eukaryotic Host Interactions Reveal Emerging Paradigms of Health and Disease. Front Microbiol 2018; 9:1394. [PMID: 29997604 PMCID: PMC6030379 DOI: 10.3389/fmicb.2018.01394] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 06/07/2018] [Indexed: 12/28/2022] Open
Abstract
For decades, a wealth of information has been acquired to define how host associated microbial communities contribute to health and disease. Within the human microbiota this has largely focused on bacteria, yet there is a myriad of viruses that occupy various tissue sites, the most abundant being bacteriophages that infect bacteria. Animal hosts are colonized with niche specific microbial communities where bacteria are continuously co-evolving with phages. Bacterial growth, metabolic activity, pathogenicity, antibiotic resistance, interspecies competition and evolution can all be influenced by phage infection and the beneficial nature of such interactions suggests that to an extent phages are tolerated by their hosts. With the understanding that phage-specific host–microbe interactions likely contribute to bacterial interactions with their mammalian hosts, phages and their communities may also impact aspects of mammalian health and disease that have gone unrecognized. Here, we review recent progress in understanding how bacteria acquire and tolerate phage in both pure culture and within complex communities. We apply these findings to discuss how intra-body phages interact with bacteria to influence their eukaryotic hosts through potential contributions to microbial homeostasis, mucosal immunity, immune tolerance and autoimmunity.
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Affiliation(s)
- Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
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147
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Tirumalai MR, Stepanov VG, Wünsche A, Montazari S, Gonzalez RO, Venkateswaran K, Fox GE. Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates. BMC Microbiol 2018; 18:57. [PMID: 29884123 PMCID: PMC5994023 DOI: 10.1186/s12866-018-1191-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022] Open
Abstract
Background Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis. Results The FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results. Conclusions It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. pumilus likely belong to the B. safensis group. Electronic supplementary material The online version of this article (10.1186/s12866-018-1191-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Madhan R Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Andrea Wünsche
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Saied Montazari
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Racquel O Gonzalez
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Kasturi Venkateswaran
- Biotechnology & Planetary Protection Group, NASA Jet Propulsion Laboratories, California Institute of Technology, Pasadena, CA, 91109, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA.
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148
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Peng Q, Yuan Y. Characterization of a newly isolated phage infecting pathogenic Escherichia coli and analysis of its mosaic structural genes. Sci Rep 2018; 8:8086. [PMID: 29795390 PMCID: PMC5967307 DOI: 10.1038/s41598-018-26004-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 05/01/2018] [Indexed: 01/21/2023] Open
Abstract
The outbreak of multidrug-resistant pathogenic bacteria made the discovery of novel control strategies necessary. Phages have regained attention for their specific lytic activity against pathogenic bacterium. A newly isolated phage infecting the clinical Escherichia coli isolates, including several multidrug-resistant strains, was isolated, and this phage showed high control effects against the tested pathogenic E. coli strains. Host range analysis revealed that although the phage exhibited broad lytic spectrum against the tested E. coli strains, it could not lyse strains from the other species. Comparative genomic analysis showed that phages had undergone at least three genome recombination events during the evolutionary process at the position of the three phage tail genes, which was reported to be associated with the host range determination of the phage. The recombinant tail proteins contained functional domains that were highly similar with genes of the Salmonella phage and genes of Pseudomonas and Neisseria. The findings of this study not only provide resources for developing phage therapy against E. coli, but also showed the highly variable genome structure of the phage.
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Affiliation(s)
- Qin Peng
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, P. R. China
| | - Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China.
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149
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Li X, Tong W, Wang L, Rahman SU, Wei G, Tao S. A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains. Front Microbiol 2018; 9:973. [PMID: 29867876 PMCID: PMC5968381 DOI: 10.3389/fmicb.2018.00973] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/25/2018] [Indexed: 11/13/2022] Open
Abstract
Recent horizontal gene transfer (HGT) is crucial for enabling microbes to rapidly adapt to their novel environments without relying upon rare beneficial mutations that arise spontaneously. For several years now, computational approaches have been developed to detect HGT, but they typically lack the sensitivity and ability to detect recent HGT events. Here we introduce a novel strategy, named RecentHGT. The number of genes undergoing recent HGT between two bacterial genomes was estimated by a new algorithm derived from the expectation-maximization algorithm and is based on the theoretical sequence-similarity distribution of orthologous genes. We tested the proposed strategy by applying it to a set of 10 Rhizobium genomes, and detected several large-scale recent HGT events. We also found that our strategy was more sensitive than other available HGT detection methods. These HGT events were mainly mediated by symbiotic plasmids. Our new strategy can provide clear evidence of recent HGT events and thus it brings us closer to the goal of detecting these potentially adaptive evolution processes in rhizobia as well as pathogens.
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Affiliation(s)
- Xiangchen Li
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,Bioinformatics Center, Northwest A&F University, Yangling, China
| | - Wenjun Tong
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China
| | - Lina Wang
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,Bioinformatics Center, Northwest A&F University, Yangling, China
| | - Siddiq Ur Rahman
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,Bioinformatics Center, Northwest A&F University, Yangling, China
| | - Gehong Wei
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China
| | - Shiheng Tao
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,Bioinformatics Center, Northwest A&F University, Yangling, China
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150
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Bacteriophage Interactions with Marine Pathogenic Vibrios: Implications for Phage Therapy. Antibiotics (Basel) 2018; 7:antibiotics7010015. [PMID: 29495270 PMCID: PMC5872126 DOI: 10.3390/antibiotics7010015] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 02/19/2018] [Accepted: 02/21/2018] [Indexed: 12/27/2022] Open
Abstract
A global distribution in marine, brackish, and freshwater ecosystems, in combination with high abundances and biomass, make vibrios key players in aquatic environments, as well as important pathogens for humans and marine animals. Incidents of Vibrio-associated diseases (vibriosis) in marine aquaculture are being increasingly reported on a global scale, due to the fast growth of the industry over the past few decades years. The administration of antibiotics has been the most commonly applied therapy used to control vibriosis outbreaks, giving rise to concerns about development and spreading of antibiotic-resistant bacteria in the environment. Hence, the idea of using lytic bacteriophages as therapeutic agents against bacterial diseases has been revived during the last years. Bacteriophage therapy constitutes a promising alternative not only for treatment, but also for prevention of vibriosis in aquaculture. However, several scientific and technological challenges still need further investigation before reliable, reproducible treatments with commercial potential are available for the aquaculture industry. The potential and the challenges of phage-based alternatives to antibiotic treatment of vibriosis are addressed in this review.
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