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Nami Y, Imeni N, Panahi B. Application of machine learning in bacteriophage research. BMC Microbiol 2021; 21:193. [PMID: 34174831 PMCID: PMC8235560 DOI: 10.1186/s12866-021-02256-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022] Open
Abstract
Phages are one of the key components in the structure, dynamics, and interactions of microbial communities in different bins. It has a clear impact on human health and the food industry. Bacteriophage characterization using in vitro approaches are time/cost consuming and laborious tasks. On the other hand, with the advent of new high-throughput sequencing technology, the development of a powerful computational framework to characterize the newly identified bacteriophages is inevitable for future research. Machine learning includes powerful techniques that enable the analysis of complex datasets for knowledge discovery and pattern recognition. In this study, we have conducted a comprehensive review of machine learning methods application using different types of features were applied in various aspects of bacteriophage research including, automated curation, identification, classification, host species recognition, virion protein identification, and life cycle prediction. Moreover, potential limitations and advantages of the developed frameworks were discussed.
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Affiliation(s)
- Yousef Nami
- Department of Food Biotechnology, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
| | - Nazila Imeni
- Young Researchers and Elite Clube, Marand Branch, Islamic Azad University, Marand, Iran
| | - Bahman Panahi
- Department of Genomics, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran.
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Plant virus evolution under strong drought conditions results in a transition from parasitism to mutualism. Proc Natl Acad Sci U S A 2021; 118:2020990118. [PMID: 33526695 DOI: 10.1073/pnas.2020990118] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Environmental conditions are an important factor driving pathogens' evolution. Here, we explore the effects of drought stress in plant virus evolution. We evolved turnip mosaic potyvirus in well-watered and drought conditions in Arabidopsis thaliana accessions that differ in their response to virus infection. Virus adaptation occurred in all accessions independently of watering status. Drought-evolved viruses conferred a significantly higher drought tolerance to infected plants. By contrast, nonsignificant increases in tolerance were observed in plants infected with viruses evolved under standard watering. The magnitude of this effect was dependent on the plant accessions. Differences in tolerance were correlated to alterations in the expression of host genes, some involved in regulation of the circadian clock, as well as in deep changes in the balance of phytohormones regulating defense and growth signaling pathways. Our results show that viruses can promote host survival in situations of abiotic stress, with the magnitude of such benefit being a selectable trait.
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53
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Lee S, Park JH. Characteristics on host specificity, infection, and temperature stability of Weissella phages from watery kimchi. Food Sci Biotechnol 2021; 30:843-851. [PMID: 34249390 DOI: 10.1007/s10068-021-00920-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/30/2021] [Accepted: 05/14/2021] [Indexed: 10/21/2022] Open
Abstract
Three bacteriophages (phage), ΦWC53, ΦWC54, and ΦWC56, of Weissella were isolated from watery kimchi and characterized. ΦWC53 belonged to Siphoviridae and ΦWC54 and ΦWC56 belonged to Myoviridae family. By one-step growth, the burst sizes were 5-260 particles/infected cells and the latent periods were 20-45 min. The phages infected Weissella spp., Leuconostoc mesenteroides, and Lactobacillus spp., differently by showing clear or turbid plaques. The phage adsorption rates on lactic acid bacteria were high on Weissella and low on Leuconostoc and Lactobacillus. However, the adsorption of ΦWC53 occurred variously among Weissella spp. and Weissella host grew well in the liquid culture without lysis after challenging by ΦWC53. Tolerances of these phages to temperature showed more various than those to pH. ΦWC53 was stable at 7 °C and 30 °C, but ΦWC54 and ΦWC56 were stable only at 7 °C. Therefore, three Weissella phages belonged to the different families and indicated diverse infection patterns on Weissella, Leuconostoc, and Lactobacillus with various stabilities for pH and temperature.
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Affiliation(s)
- Soomin Lee
- Department of Food Science and Biotechnology, Gachon University, Seongnamdae-ro, 13120 Republic of Korea
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, Gachon University, Seongnamdae-ro, 13120 Republic of Korea
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Sørensen MCH, Vitt A, Neve H, Soverini M, Ahern SJ, Klumpp J, Brøndsted L. Campylobacter phages use hypermutable polyG tracts to create phenotypic diversity and evade bacterial resistance. Cell Rep 2021; 35:109214. [PMID: 34107245 DOI: 10.1016/j.celrep.2021.109214] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/15/2020] [Accepted: 05/12/2021] [Indexed: 12/16/2022] Open
Abstract
Phase variation is a common mechanism for creating phenotypic heterogeneity of surface structures in bacteria important for niche adaptation. In Campylobacter, phase variation occurs by random variation in hypermutable homonucleotide 7-11 G (polyG) tracts. To elucidate how phages adapt to phase-variable hosts, we study Fletchervirus phages infecting Campylobacter dependent on a phase-variable receptor. Our data demonstrate that Fletcherviruses mimic their host and encode hypermutable polyG tracts, leading to phase-variable expression of two of four receptor-binding proteins. This creates phenotypically diverse phage populations, including a sub-population that infects the bacterial host when the phase-variable receptor is not expressed. Such population dynamics of both phage and host promote co-existence in a shared niche. Strikingly, we identify polyG tracts in more than 100 phage genera, infecting more than 70 bacterial species. Future experimental work may confirm phase variation as a widespread strategy for creating phenotypically diverse phage populations.
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Affiliation(s)
- Martine C Holst Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark.
| | - Amira Vitt
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max-Rubner Institut, 24103 Kiel, Germany
| | - Matteo Soverini
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Gentofte, Denmark
| | - Stephen James Ahern
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Jochen Klumpp
- Institute for Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
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55
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Deng S, Xu Q, Fu Y, Liang L, Wu Y, Peng F, Gao M. Genomic Analysis of a Novel Phage Infecting the Turkey Pathogen Escherichia coli APEC O78 and Its Endolysin Activity. Viruses 2021; 13:v13061034. [PMID: 34072620 PMCID: PMC8229158 DOI: 10.3390/v13061034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 01/13/2023] Open
Abstract
Due to the increasing spread of multidrug-resistant (MDR) bacteria, phage therapy is considered one of the most promising methods for addressing MDR bacteria. Escherichia coli lives symbiotically in the intestines of humans and some animals, and most strains are beneficial in terms of maintaining a healthy digestive tract. However, some E. coli strains can cause serious zoonotic diseases, including diarrhea, pneumonia, urinary tract infections, and hemolytic uremic syndrome. In this study, we characterized a newly isolated Myoviridae phage, vB_EcoM_APEC. The phage vB_EcoM_APEC was able to infect E. coli APEC O78, which is the most common MDR E. coli serotype in turkeys. Additionally, the phage's host range included Klebsiella pneumoniae and other E. coli strains. The genome of phage vB_EcoM_APEC (GenBank accession number MT664721) was 35,832 bp in length, with 52 putative open reading frames (ORFs) and a GC content of 41.3%. The genome of vB_EcoM_APEC exhibited low similarity (79.1% identity and 4.0% coverage) to the genome of Acinetobacter phage vB_AbaM_IME284 (GenBank no. MH853787.1) according to the nucleotide Basic Local Alignment Search Tool (BLASTn). Phylogenetic analysis revealed that vB_EcoM_APEC was a novel phage, and its genome sequence showed low similarity to other available phage genomes. Gene annotation indicated that the protein encoded by orf11 was an endolysin designated as LysO78, which exhibited 64.7% identity (91.0% coverage) with the putative endolysin of Acinetobacter baumannii phage vB_AbaM_B9. The LysO78 protein belongs to glycoside hydrolase family 19, and was described as being a chitinase class I protein. LysO78 is a helical protein with 12 α-helices containing a large domain and a small domain in terms of the predicted three-dimensional structure. The results of site-directed mutagenesis indicated that LysO78 contained the catalytic residues E54 and E64. The purified endolysin exhibited broad-spectrum bacteriolytic activity against Gram-negative strains, including the genera Klebsiella, Salmonella, Shigella, Burkholderia, Yersinia, and Pseudomonas, as well as the species Chitinimonas arctica, E. coli, Ralstonia solanacearum, and A. baumannii. An enzymatic assay showed that LysO78 had highly lytic peptidoglycan hydrolases activity (64,620,000 units/mg) against E. coli APEC O78, and that LysO78 had lytic activity in the temperature range of 4-85 °C, with an optimal temperature of 28 °C and optimal pH of 8.0, and was active at pH 3.0-12.0. Overall, the results suggested that LysO78 might be a promising therapeutic agent for controlling MDR E. coli APEC O78 and nosocomial infections caused by multidrug-resistant bacteria.
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Affiliation(s)
- Sangsang Deng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (S.D.); (Y.F.); (L.L.); (Y.W.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Qiang Xu
- China Center for Type Culture Collection(CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, China;
| | - Yajuan Fu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (S.D.); (Y.F.); (L.L.); (Y.W.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Leiqin Liang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (S.D.); (Y.F.); (L.L.); (Y.W.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Wu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (S.D.); (Y.F.); (L.L.); (Y.W.)
| | - Fang Peng
- China Center for Type Culture Collection(CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, China;
- Correspondence: (F.P.); (M.G.)
| | - Meiying Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (S.D.); (Y.F.); (L.L.); (Y.W.)
- Correspondence: (F.P.); (M.G.)
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56
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Park DS, Park JH. Characteristics of Bacteriophage Isolates and Expression of Shiga Toxin Genes Transferred to Non Shiga Toxin-Producing E. coli by Transduction. J Microbiol Biotechnol 2021; 31:710-716. [PMID: 33782222 PMCID: PMC9705938 DOI: 10.4014/jmb.2102.02040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022]
Abstract
A risk analysis of Shiga toxin (Stx)-encoding bacteriophage was carried out by confirming the transduction phage to non-Stx-producing Escherichia coli (STEC) and subsequent expression of the Shiga toxin genes. The virulence factor stx1 was identified in five phages, and both stx1 and stx2 were found in four phages from a total of 19 phage isolates with seven non-O157 STEC strains. The four phages, designated as φNOEC41, φNOEC46, φNOEC47, and φNOEC49, belonged morphologically to the Myoviridae family. The stabilities of these phages to temperature, pH, ethanol, and NaClO were high with some variabilities among the phages. The infection of five non-STEC strains by nine Stx-encoding phages occurred at a rate of approximately 40%. Non-STEC strains were transduced by Stx-encoding phage to become lysogenic strains, and seven convertant strains had stx1 and/or stx2 genes. Only the stx1 gene was transferred to the receptor strains without any deletion. Gene expression of a convertant having both stx1 and stx2 genes was confirmed to be up to 32 times higher for Stx1 in 6% NaCl osmotic media and twice for Stx2 in 4% NaCl media, compared with expression in low-salt environments. Therefore, a new risk might arise from the transfer of pathogenic genes from Stx-encoding phages to otherwise harmless hosts. Without adequate sterilization of food exposed to various environments, there is a possibility that the toxicity of the phages might increase.
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Affiliation(s)
- Da-Som Park
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam 13120, Republic of Korea
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam 13120, Republic of Korea,Corresponding author Phone: +82-31-750-5523 Fax: +82-31-750-5283 E-mail:
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57
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Aghaee BL, Mirzaei MK, Alikhani MY, Mojtahedi A. Sewage and sewage-contaminated environments are the most prominent sources to isolate phages against Pseudomonas aeruginosa. BMC Microbiol 2021; 21:132. [PMID: 33931013 PMCID: PMC8088035 DOI: 10.1186/s12866-021-02197-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 04/15/2021] [Indexed: 01/21/2023] Open
Abstract
Background P. aeruginosa is the primary source of hospital-acquired infections. Unfortunately, antibiotic resistance is growing to precariously high levels, making the infections by this pathogen life-threatening and hard to cure. One possible alternative to antibiotics is to use phages. However, the isolation of phages suitable for phage therapy— be lytic, be efficient, and have a broad host range —against some target bacteria has proven difficult. To identify the best places to look for these phages against P. aeruginosa we screened hospital sewages, soils, and rivers in two cities. Results We isolated eighteen different phages, determined their host range, infection property, and plaque morphology. We found that the sewage and sewage-contaminated environments are the most reliable sources for the isolation of Pseudomonas phages. In addition, phages isolated from hospital sewage showed the highest efficiency in lysing the bacteria used for host range determination. In contrast, phages from the river had larger plaque size and lysed bacteria with higher levels of antibiotic resistance. Conclusions Our findings provided additional support for the importance of sewage as the source of phage isolation. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02197-z.
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Affiliation(s)
- Bahareh Lashtoo Aghaee
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Center Munich and Technical University of Munich, 85764, Neuherberg, Bavaria, Germany
| | - Mohammad Yousef Alikhani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran. .,Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran. .,Brucellosis research center, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Ali Mojtahedi
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran.
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Molina F, Simancas A, Ramírez M, Tabla R, Roa I, Rebollo JE. A New Pipeline for Designing Phage Cocktails Based on Phage-Bacteria Infection Networks. Front Microbiol 2021; 12:564532. [PMID: 33664712 PMCID: PMC7920989 DOI: 10.3389/fmicb.2021.564532] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 01/18/2021] [Indexed: 12/17/2022] Open
Abstract
In recent years, the spread of antibiotic-resistant bacteria and efforts to preserve food microbiota have induced renewed interest in phage therapy. Phage cocktails, instead of a single phage, are commonly used as antibacterial agents since the hosts are unlikely to become resistant to several phages simultaneously. While the spectrum of activity might increase with cocktail complexity, excessive phages could produce side effects, such as the horizontal transfer of genes that augment the fitness of host strains, dysbiosis or high manufacturing costs. Therefore, cocktail formulation represents a compromise between achieving substantial reduction in the bacterial loads and restricting its complexity. Despite the abovementioned points, the observed bacterial load reduction does not increase significantly with the size of phage cocktails, indicating the requirement for a systematic approach to their design. In this work, the information provided by host range matrices was analyzed after building phage-bacteria infection networks (PBINs). To this end, we conducted a meta-analysis of 35 host range matrices, including recently published studies and new datasets comprising Escherichia coli strains isolated during ripening of artisanal raw milk cheese and virulent coliphages from ewes' feces. The nestedness temperature, which reflects the host range hierarchy of the phages, was determined from bipartite host range matrices using heuristic (Nestedness Temperature Calculator) and genetic (BinMatNest) algorithms. The latter optimizes matrix packing, leading to lower temperatures, i.e., it simplifies the identification of the phages with the broadest host range. The structure of infection networks suggests that generalist phages (and not specialist phages) tend to succeed in infecting less susceptible bacteria. A new metric (Φ), which considers some properties of the host range matrices (fill, temperature, and number of bacteria), is proposed as an estimator of phage cocktail size. To identify the best candidates, agglomerative hierarchical clustering using Ward's method was implemented. Finally, a cocktail was formulated for the biocontrol of cheese-isolated E. coli, reducing bacterial counts by five orders of magnitude.
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Affiliation(s)
- Felipe Molina
- Genetics, Department of Biochemistry Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Alfredo Simancas
- Genetics, Department of Biochemistry Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Manuel Ramírez
- Microbiology, Department of Biomedical Sciences, University of Extremadura, Badajoz, Spain
| | - Rafael Tabla
- Dairy Department, Scientific and Technological Research Centre of Extremadura, Technological Institute of Food and Agriculture, Junta de Extremadura, Badajoz, Spain
| | - Isidro Roa
- Dairy Department, Scientific and Technological Research Centre of Extremadura, Technological Institute of Food and Agriculture, Junta de Extremadura, Badajoz, Spain
| | - José Emilio Rebollo
- Genetics, Department of Biochemistry Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
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A Spontaneous rapZ Mutant Impairs Infectivity of Lytic Bacteriophage vB_EcoM_JS09 against Enterotoxigenic Escherichia coli. mSphere 2021; 6:6/2/e01286-20. [PMID: 33658278 PMCID: PMC8546717 DOI: 10.1128/msphere.01286-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Our understanding of the mechanisms underlying phage-bacterium interactions remains limited. In Escherichia coli, RapZ regulates glucosamine-6-phosphate (GlcN6P) metabolism, the formation of which initiates synthesis of the bacterial cell envelope, including lipopolysaccharides (LPS). However, the role of RapZ, if any, on phage infectivity remains to be investigated. Here, we isolated strains of enterotoxigenic E. coli (ETEC) resistant to its specific lytic bacteriophage vB_EcoM_JS09 (JS09) in a phage aerosol spray experiment. Whole-genome analysis of phage-resistant bacteria revealed the rapZ gene acquired a premature stop mutation at amino acid 227. Here, we report that the mutation in the rapZ gene confers resistance by inhibiting 93.5% phage adsorption. Furthermore, this mutation changes the morphology of phage plaques, reduces efficiency of plating and phage propagation efficiency, and impairs the infectivity of phage JS09 against ETEC. Using scanning electron microscopy assays, we attribute the inability of the phage to adsorb to the loss of receptors in strains with defective RapZ. Analysis of the LPS profile shows that strains with defective RapZ inhibit phage infection by changing the LPS profile in E. coli. Preincubation of phage JS09 with LPS extracted from a wild-type (WT) strain blocked infection, suggesting LPS is the host receptor for phage JS09 adsorption. Our data uncover the mechanism by which ETEC resists infection of phage JS09 by mutating the rapZ gene and then increasing the expression of glmS and changing the phage receptor-LPS profile. These findings provide insight into the function of the rapZ gene for efficient infection of phage JS09. IMPORTANCE The development of phage-resistant bacteria is a challenging problem for phage therapy. However, our knowledge of phage resistance mechanisms is still limited. RapZ is an RNase adaptor protein encoded by the rapZ gene and plays an important function in Gram-positive and Gram-negative bacteria. Here, we report the whole-genome analysis of a phage-resistant enterotoxigenic Escherichia coli (ETEC) strain, which revealed that the rapZ gene acquired a premature stop mutation (E227Stop). We show that the premature stop mutation of rapZ impairs the infectivity of phage JS09 in ETEC. Furthermore, our findings indicate that ETEC becomes resistant against the adsorption and infection of phage JS09 by mutating the rapZ gene, increasing the expression of glmS, and changing the phage receptor-LPS profile. It is also first reported here that RapZ is essential for efficient infection of phage JS09.
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Whon TW, Shin NR, Kim JY, Roh SW. Omics in gut microbiome analysis. J Microbiol 2021; 59:292-297. [DOI: 10.1007/s12275-021-1004-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022]
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Balance between promiscuity and specificity in phage λ host range. ISME JOURNAL 2021; 15:2195-2205. [PMID: 33589767 DOI: 10.1038/s41396-021-00912-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 01/18/2021] [Accepted: 01/25/2021] [Indexed: 01/21/2023]
Abstract
As hosts acquire resistance to viruses, viruses must overcome that resistance to re-establish infectivity, or go extinct. Despite the significant hurdles associated with adapting to a resistant host, viruses are evolutionarily successful and maintain stable coevolutionary relationships with their hosts. To investigate the factors underlying how pathogens adapt to their hosts, we performed a deep mutational scan of the region of the λ tail fiber tip protein that mediates contact with the receptor on λ's host, Escherichia coli. Phages harboring amino acid substitutions were subjected to selection for infectivity on wild type E. coli, revealing a highly restrictive fitness landscape, in which most substitutions completely abrogate function. A subset of positions that are tolerant of mutation in this assay, but diverse over evolutionary time, are associated with host range expansion. Imposing selection for phage infectivity on three λ-resistant hosts, each harboring a different missense mutation in the λ receptor, reveals hundreds of adaptive variants in λ. We distinguish λ variants that confer promiscuity, a general ability to overcome host resistance, from those that drive host-specific infectivity. Both processes may be important in driving adaptation to a novel host.
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Boeckaerts D, Stock M, Criel B, Gerstmans H, De Baets B, Briers Y. Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins. Sci Rep 2021; 11:1467. [PMID: 33446856 PMCID: PMC7809048 DOI: 10.1038/s41598-021-81063-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/30/2020] [Indexed: 12/04/2022] Open
Abstract
Nowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.
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Affiliation(s)
- Dimitri Boeckaerts
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Michiel Stock
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Bjorn Criel
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Hans Gerstmans
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
- MeBioS-Biosensors group, Department of BioSystems, KU Leuven, Leuven, Belgium
| | - Bernard De Baets
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium.
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Khan Mirzaei M, Deng L. Sustainable Microbiome: a symphony orchestrated by synthetic phages. Microb Biotechnol 2021; 14:45-50. [PMID: 33171009 PMCID: PMC7888444 DOI: 10.1111/1751-7915.13697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 12/21/2022] Open
Abstract
We are surrounded by microbes, mostly bacteria and their viruses or phages, on the inside and outside of our bodies. These bacteria in constant interactions with phages are regulating multiple functions critical to our health. Luckily, they are amenable, but we need precise tools for their safe manipulation and improving human health. Here, we argue that recent advances in single-cell technologies, culturomics and synthetic biology offer exciting opportunities to create these tools as well as revealing specific phages-bacteria interactions in the body.
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Affiliation(s)
- Mohammadali Khan Mirzaei
- Institute of VirologyHelmholtz Centre Munich and Technical University of MunichNeuherbergBavaria85764Germany
| | - Li Deng
- Institute of VirologyHelmholtz Centre Munich and Technical University of MunichNeuherbergBavaria85764Germany
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64
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The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification. Nat Ecol Evol 2020; 4:1650-1660. [PMID: 33077929 DOI: 10.1038/s41559-020-01312-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 08/14/2020] [Indexed: 01/21/2023]
Abstract
As a heritable sequence-specific adaptive immune system, CRISPR-Cas is a powerful force shaping strain diversity in host-virus systems. While the diversity of CRISPR alleles has been explored, the associated structure and dynamics of host-virus interactions have not. We explore the role of CRISPR in mediating the interplay between host-virus interaction structure and eco-evolutionary dynamics in a computational model and compare the results with three empirical datasets from natural systems. We show that the structure of the networks describing who infects whom and the degree to which strains are immune, are respectively modular (containing groups of hosts and viruses that interact strongly) and weighted-nested (specialist hosts are more susceptible to subsets of viruses that in turn also infect the more generalist hosts with many spacers matching many viruses). The dynamic interplay between these networks influences transitions between dynamical regimes of virus diversification and host control. The three empirical systems exhibit weighted-nested immunity networks, a pattern our theory shows is indicative of hosts able to suppress virus diversification. Previously missing from studies of microbial host-pathogen systems, the immunity network plays a key role in the coevolutionary dynamics.
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Molina F, Simancas A, Tabla R, Gómez A, Roa I, Rebollo JE. Diversity and Local Coadaptation of Escherichia coli and Coliphages From Small Ruminants. Front Microbiol 2020; 11:564522. [PMID: 33178150 PMCID: PMC7596221 DOI: 10.3389/fmicb.2020.564522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/17/2020] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages are highly specific predators that drive bacterial diversity through coevolution while striking tradeoffs among preserving host populations for long-term exploitation and increasing their virulence, structural stability, or host range. Escherichia coli and other coliform bacteria present in the microbiota of milk and during early ripening of raw milk cheeses have been linked to the production of gas, manifested by the appearance of eyes, and the development of off-flavors; thus, they might cause early blowing and cheese spoilage. Here, we report the characterization of coliphages isolated from manure from small ruminant farms and E. coli strains isolated from goat and sheep raw milk cheese. Additionally, the virulence and host range of locally isolated and laboratory collection phages were determined by comparing the susceptibility of E. coli strains from different sources. In agreement with the high genetic diversity found within the species E. coli, clustering analysis of whole-cell protein revealed a total of 13 distinct profiles but none of the raw milk cheese isolates showed inhibition of growth by reference or water-isolated coliphages. Conversely, 10 newly isolated phages had a broad host range (i.e., able to lyse ≥50% of bacterial hosts tested), thus exhibiting utility for biocontrol and only one cheese-isolated E. coli strain was resistant to all the phages. Whereas there was a high positive correlation between bacterial susceptibility range and lysis intensity, the phages virulence decreased as range increased until reaching a plateau. These results suggest local gene-for-gene coevolution between hosts and phages with selective tradeoffs for both resistance and competitive ability of the bacteria and host-range extension and virulence of the phage populations. Hence, different phage cocktail formulations might be required when devising long-term and short-term biocontrol strategies.
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Affiliation(s)
- Felipe Molina
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Alfredo Simancas
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Rafael Tabla
- Dairy Department, Technological Institute of Food and Agriculture - Scientific and Technological Research Centre of Extremadura, Junta de Extremadura, Badajoz, Spain
| | - Antonia Gómez
- Dairy Department, Technological Institute of Food and Agriculture - Scientific and Technological Research Centre of Extremadura, Junta de Extremadura, Badajoz, Spain
| | - Isidro Roa
- Dairy Department, Technological Institute of Food and Agriculture - Scientific and Technological Research Centre of Extremadura, Junta de Extremadura, Badajoz, Spain
| | - José Emilio Rebollo
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
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66
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Mutalik VK, Adler BA, Rishi HS, Piya D, Zhong C, Koskella B, Kutter EM, Calendar R, Novichkov PS, Price MN, Deutschbauer AM, Arkin AP. High-throughput mapping of the phage resistance landscape in E. coli. PLoS Biol 2020; 18:e3000877. [PMID: 33048924 PMCID: PMC7553319 DOI: 10.1371/journal.pbio.3000877] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage-specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.
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Affiliation(s)
- Vivek K. Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
| | - Benjamin A. Adler
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
| | - Harneet S. Rishi
- Biophysics Graduate Group, University of California – Berkeley, Berkeley, California, United States of America
- Designated Emphasis Program in Computational and Genomic Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Denish Piya
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
| | - Crystal Zhong
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Britt Koskella
- Department of Integrative Biology, University of California – Berkeley, Berkeley, California, United States of America
| | | | - Richard Calendar
- Department of Molecular and Cell Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Pavel S. Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Morgan N. Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
- Biophysics Graduate Group, University of California – Berkeley, Berkeley, California, United States of America
- Designated Emphasis Program in Computational and Genomic Biology, University of California – Berkeley, Berkeley, California, United States of America
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Lourenço M, Chaffringeon L, Lamy-Besnier Q, Pédron T, Campagne P, Eberl C, Bérard M, Stecher B, Debarbieux L, De Sordi L. The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages. Cell Host Microbe 2020; 28:390-401.e5. [DOI: 10.1016/j.chom.2020.06.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/30/2020] [Accepted: 06/02/2020] [Indexed: 02/08/2023]
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68
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Massol F, Macke E, Callens M, Decaestecker E. A methodological framework to analyse determinants of host-microbiota networks, with an application to the relationships between Daphnia magna's gut microbiota and bacterioplankton. J Anim Ecol 2020; 90:102-119. [PMID: 32654135 DOI: 10.1111/1365-2656.13297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 06/25/2020] [Indexed: 01/04/2023]
Abstract
The past 30 years have seen both a surge of interest in assessing ecological interactions using tools borrowed from network theory and an explosion of data on the occurrence of microbial symbionts thanks to next-generation sequencing. Given that classic network methods cannot currently measure the respective effects of different environmental and biological drivers on network structure, we here present two methods to elucidate the determinants of bipartite interaction networks. The first method is based on classifications and compares communities within networks to the grouping of nodes by treatment or similar controlling groups. The second method assesses the link between multivariate explanatory variables and network structure using redundancy analyses after singular value decomposition. In both methods, the significance of effects can be gauged through two randomizations. Our methods were applied to experimental data on Daphnia magna and its interactions with gut microbiota and bacterioplankton. The whole network was affected by Daphnia's diet (algae and/or cyanobacteria) and sample type, but not by Daphnia genotype. At coarse grains, bacterioplankton and gut microbiota communities were different. At this scale, the structure of the gut microbiota-based network was not linked to any explanatory factors, while the bacterioplankton-based network was related to both Daphnia's diet and genotype. At finer grains, Daphnia's diet and genotype affected both microbial networks, but the effect of diet on gut microbiota network structure was mediated solely by differences in microbial richness. While no reciprocal effect between the microbial communities could be found, fine-grained analyses presented a more nuanced picture, with bacterioplankton likely affecting the composition of the gut microbiota. Our methods are widely applicable to bipartite networks, can elucidate both controlled and environmental effects in experimental setting using a large amount of sequencing data and can tease apart reciprocal effects of networks on one another. The twofold approach we propose has the advantage of being able to tease apart effects at different scales of network structure, thus allowing for detailed assessment of reciprocal effects of linked networks on one another. As such, our network methods can help ecologists understand huge datasets reporting microbial co-occurrences within different hosts.
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Affiliation(s)
- François Massol
- UMR 8198 Evo-Eco-Paleo, SPICI Group, University of Lille, Lille, France.,CNRS, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, University of Lille, Lille, France
| | - Emilie Macke
- Laboratory of Aquatic Biology, Department of Biology, KU Leuven (Kulak), Kortrijk, Belgium
| | - Martijn Callens
- Laboratory of Aquatic Biology, Department of Biology, KU Leuven (Kulak), Kortrijk, Belgium.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, Department of Biology, KU Leuven (Kulak), Kortrijk, Belgium
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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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70
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Chaos may lurk under a cloak of neutrality. Proc Natl Acad Sci U S A 2020; 117:16104-16106. [PMID: 32601229 DOI: 10.1073/pnas.2010120117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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71
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Simmons EL, Bond MC, Koskella B, Drescher K, Bucci V, Nadell CD. Biofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible Bacteria. mSystems 2020; 5:e00877-19. [PMID: 32576653 PMCID: PMC7311319 DOI: 10.1128/msystems.00877-19] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/29/2020] [Indexed: 01/21/2023] Open
Abstract
Encounters among bacteria and their viral predators (bacteriophages) are among the most common ecological interactions on Earth. These encounters are likely to occur with regularity inside surface-bound communities that microbes most often occupy in natural environments. Such communities, termed biofilms, are spatially constrained: interactions become limited to near neighbors, diffusion of solutes and particulates can be reduced, and there is pronounced heterogeneity in nutrient access and physiological state. It is appreciated from prior theoretical work that phage-bacteria interactions are fundamentally different in spatially structured contexts, as opposed to well-mixed liquid culture. Spatially structured communities are predicted to promote the protection of susceptible host cells from phage exposure, and thus weaken selection for phage resistance. The details and generality of this prediction in realistic biofilm environments, however, are not known. Here, we explore phage-host interactions using experiments and simulations that are tuned to represent the essential elements of biofilm communities. Our simulations show that in biofilms, phage-resistant cells-as their relative abundance increases-can protect clusters of susceptible cells from phage exposure, promoting the coexistence of susceptible and phage-resistant bacteria under a large array of conditions. We characterize the population dynamics underlying this coexistence, and we show that coexistence is recapitulated in an experimental model of biofilm growth measured with confocal microscopy. Our results provide a clear view into the dynamics of phage resistance in biofilms with single-cell resolution of the underlying cell-virion interactions, linking the predictions of canonical theory to realistic models and in vitro experiments of biofilm growth.IMPORTANCE In the natural environment, bacteria most often live in communities bound to one another by secreted adhesives. These communities, or biofilms, play a central role in biogeochemical cycling, microbiome functioning, wastewater treatment, and disease. Wherever there are bacteria, there are also viruses that attack them, called phages. Interactions between bacteria and phages are likely to occur ubiquitously in biofilms. We show here, using simulations and experiments, that biofilms will in most conditions allow phage-susceptible bacteria to be protected from phage exposure, if they are growing alongside other cells that are phage resistant. This result has implications for the fundamental ecology of phage-bacteria interactions, as well as the development of phage-based antimicrobial therapeutics.
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Affiliation(s)
- Emilia L Simmons
- Department of Biological Sciences, Dartmouth, Hanover, New Hampshire, USA
| | - Matthew C Bond
- Department of Biological Sciences, Dartmouth, Hanover, New Hampshire, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Carey D Nadell
- Department of Biological Sciences, Dartmouth, Hanover, New Hampshire, USA
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Abstract
Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment. Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments. IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.
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73
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Stabilization of extensive fine-scale diversity by ecologically driven spatiotemporal chaos. Proc Natl Acad Sci U S A 2020; 117:14572-14583. [PMID: 32518107 DOI: 10.1073/pnas.1915313117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
It has recently become apparent that the diversity of microbial life extends far below the species level to the finest scales of genetic differences. Remarkably, extensive fine-scale diversity can coexist spatially. How is this diversity stable on long timescales, despite selective or ecological differences and other evolutionary processes? Most work has focused on stable coexistence or assumed ecological neutrality. We present an alternative: extensive diversity maintained by ecologically driven spatiotemporal chaos, with no assumptions about niches or other specialist differences between strains. We study generalized Lotka-Volterra models with antisymmetric correlations in the interactions inspired by multiple pathogen strains infecting multiple host strains. Generally, these exhibit chaos with increasingly wild population fluctuations driving extinctions. But the simplest spatial structure, many identical islands with migration between them, stabilizes a diverse chaotic state. Some strains (subspecies) go globally extinct, but many persist for times exponentially long in the number of islands. All persistent strains have episodic local blooms to high abundance, crucial for their persistence as, for many, their average population growth rate is negative. Snapshots of the abundance distribution show a power law at intermediate abundances that is essentially indistinguishable from the neutral theory of ecology. But the dynamics of the large populations are much faster than birth-death fluctuations. We argue that this spatiotemporally chaotic "phase" should exist in a wide range of models, and that even in rapidly mixed systems, longer-lived spores could similarly stabilize a diverse chaotic phase.
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74
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Measuring Coevolutionary Dynamics in Species-Rich Communities. Trends Ecol Evol 2020; 35:539-550. [DOI: 10.1016/j.tree.2020.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/24/2020] [Accepted: 02/03/2020] [Indexed: 12/18/2022]
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Mapping co-ancestry connections between the genome of a Medieval individual and modern Europeans. Sci Rep 2020; 10:6843. [PMID: 32321996 PMCID: PMC7176696 DOI: 10.1038/s41598-020-64007-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 04/06/2020] [Indexed: 11/08/2022] Open
Abstract
Historical genetic links among similar populations can be difficult to establish. Identity by descent (IBD) analyses find genomic blocks that represent direct genealogical relationships among individuals. However, this method has rarely been applied to ancient genomes because IBD stretches are progressively fragmented by recombination and thus not recognizable after few tens of generations. To explore such genealogical relationships, we estimated long IBD blocks among modern Europeans, generating networks to uncover the genetic structures. We found that Basques, Sardinians, Icelanders and Orcadians form, each of them, highly intraconnected sub-clusters in a European network, indicating dense genealogical links within small, isolated populations. We also exposed individual genealogical links -such as the connection between one Basque and one Icelandic individual- that cannot be uncovered with other, widely used population genetics methods such as PCA or ADMIXTURE. Moreover, using ancient DNA technology we sequenced a Late Medieval individual (Barcelona, Spain) to high genomic coverage and identified IBD blocks shared between her and modern Europeans. The Medieval IBD blocks are statistically overrepresented only in modern Spaniards, which is the geographically closest population. This approach can be used to produce a fine-scale reflection of shared ancestry across different populations of the world, offering a direct genetic link from the past to the present.
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76
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Braga LPP, Spor A, Kot W, Breuil MC, Hansen LH, Setubal JC, Philippot L. Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios. MICROBIOME 2020; 8:52. [PMID: 32252805 PMCID: PMC7137350 DOI: 10.1186/s40168-020-00822-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/03/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Bacteriophages, the viruses infecting bacteria, are biological entities that can control their host populations. The ecological relevance of phages for microbial systems has been widely explored in aquatic environments, but the current understanding of the role of phages in terrestrial ecosystems remains limited. Here, our objective was to quantify the extent to which phages drive the assembly and functioning of soil bacterial communities. We performed a reciprocal transplant experiment using natural and sterilized soil incubated with different combinations of two soil microbial communities, challenged against native and non-native phage suspensions as well as against a cocktail of phage isolates. We tested three different community assembly scenarios by adding phages: (a) during soil colonization, (b) after colonization, and (c) in natural soil communities. One month after inoculation with phage suspensions, bacterial communities were assessed by 16S rRNA amplicon gene sequencing. RESULTS By comparing the treatments inoculated with active versus autoclaved phages, our results show that changes in phage pressure have the potential to impact soil bacterial community composition and diversity. We also found a positive effect of active phages on the soil ammonium concentration in a few treatments, which indicates that increased phage pressure may also be important for soil functions. CONCLUSIONS Overall, the present work contributes to expand the current knowledge about soil phages and provide some empirical evidence supporting their relevance for soil bacterial community assembly and functioning. Video Abstract.
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Affiliation(s)
- Lucas P P Braga
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, 21000, Dijon, France.
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
| | - Aymé Spor
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, 21000, Dijon, France
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Marie-Christine Breuil
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, 21000, Dijon, France
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, 21000, Dijon, France.
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Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems. mSystems 2020; 5:5/2/e00098-20. [PMID: 32184367 PMCID: PMC7380583 DOI: 10.1128/msystems.00098-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Interactions between viral communities and their microbial hosts have been the subject of many recent studies in a wide range of ecosystems. The degree of coordination between ecological assembly processes influencing viral and microbial communities, however, has been explored to a much lesser degree. By using a combined null modeling approach, this study investigated the ecological assembly processes influencing both viral and microbial community structure within hydraulically fractured shale environments. Among other results, significant relationships between the structuring processes affecting both the viral and microbial community were observed, indicating that ecological assembly might be coordinated between these communities despite differing selective pressures. Within this deep subsurface ecosystem, these results reveal a potentially important balance of ecological dynamics that must be maintained to enable long-term microbial community persistence. More broadly, this relationship begins to provide insight into the development of communities across trophic levels. The ecological drivers that concurrently act upon both a virus and its host and that drive community assembly are poorly understood despite known interactions between viral populations and their microbial hosts. Hydraulically fractured shale environments provide access to a closed ecosystem in the deep subsurface where constrained microbial and viral community assembly processes can be examined. Here, we used metagenomic analyses of time-resolved-produced fluid samples from two wells in the Appalachian Basin to track viral and host dynamics and to investigate community assembly processes. Hypersaline conditions within these ecosystems should drive microbial community structure to a similar configuration through time in response to common osmotic stress. However, viral predation appears to counterbalance this potentially strong homogeneous selection and pushes the microbial community toward undominated assembly. In comparison, while the viral community was also influenced by substantial undominated processes, it assembled, in part, due to homogeneous selection. When the overall assembly processes acting upon both these communities were directly compared with each other, a significant relationship was revealed, suggesting an association between microbial and viral community development despite differing selective pressures. These results reveal a potentially important balance of ecological dynamics that must be in maintained within this deep subsurface ecosystem in order for the microbial community to persist over extended time periods. More broadly, this relationship begins to provide knowledge underlying metacommunity development across trophic levels. IMPORTANCE Interactions between viral communities and their microbial hosts have been the subject of many recent studies in a wide range of ecosystems. The degree of coordination between ecological assembly processes influencing viral and microbial communities, however, has been explored to a much lesser degree. By using a combined null modeling approach, this study investigated the ecological assembly processes influencing both viral and microbial community structure within hydraulically fractured shale environments. Among other results, significant relationships between the structuring processes affecting both the viral and microbial community were observed, indicating that ecological assembly might be coordinated between these communities despite differing selective pressures. Within this deep subsurface ecosystem, these results reveal a potentially important balance of ecological dynamics that must be maintained to enable long-term microbial community persistence. More broadly, this relationship begins to provide insight into the development of communities across trophic levels.
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78
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Coexistence of nestedness and modularity in host-pathogen infection networks. Nat Ecol Evol 2020; 4:568-577. [PMID: 32152533 DOI: 10.1038/s41559-020-1130-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/28/2020] [Indexed: 01/08/2023]
Abstract
The long-term coevolution of hosts and pathogens in their environment forms a complex web of multi-scale interactions. Understanding how environmental heterogeneity affects the structure of host-pathogen networks is a prerequisite for predicting disease dynamics and emergence. Although nestedness is common in ecological networks, and theory suggests that nested ecosystems are less prone to dynamic instability, why nestedness varies in time and space is not fully understood. Many studies have been limited by a focus on single habitats and the absence of a link between spatial variation and structural heterogeneity such as nestedness and modularity. Here we propose a neutral model for the evolution of host-pathogen networks in multiple habitats. In contrast to previous studies, our study proposes that local modularity can coexist with global nestedness, and shows that real ecosystems are found in a continuum between nested-modular and nested networks driven by intraspecific competition. Nestedness depends on neutral mechanisms of community assembly, whereas modularity is contingent on local adaptation and competition. The structural pattern may change spatially and temporally but remains stable over evolutionary timescales. We validate our theoretical predictions with a longitudinal study of plant-virus interactions in a heterogeneous agricultural landscape.
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79
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Segar ST, Fayle TM, Srivastava DS, Lewinsohn TM, Lewis OT, Novotny V, Kitching RL, Maunsell SC. The Role of Evolution in Shaping Ecological Networks. Trends Ecol Evol 2020; 35:454-466. [PMID: 32294426 DOI: 10.1016/j.tree.2020.01.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 01/12/2020] [Accepted: 01/20/2020] [Indexed: 11/17/2022]
Abstract
The structure of ecological networks reflects the evolutionary history of their biotic components, and their dynamics are strongly driven by ecoevolutionary processes. Here, we present an appraisal of recent relevant research, in which the pervasive role of evolution within ecological networks is manifest. Although evolutionary processes are most evident at macroevolutionary scales, they are also important drivers of local network structure and dynamics. We propose components of a blueprint for further research, emphasising process-based models, experimental evolution, and phenotypic variation, across a range of distinct spatial and temporal scales. Evolutionary dimensions are required to advance our understanding of foundational properties of community assembly and to enhance our capability of predicting how networks will respond to impending changes.
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Affiliation(s)
- Simon T Segar
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; University of South Bohemia in Ceske Budejovice, Faculty of Science, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; Department of Crop and Environment Sciences, Harper Adams University, Newport, Shropshire, TF10 8NB, UK.
| | - Tom M Fayle
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; University of South Bohemia in Ceske Budejovice, Faculty of Science, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; Institute for Tropical Biology and Conservation,Universiti Malaysia Sabah,Kota Kinabalu, Sabah, Malaysia
| | - Diane S Srivastava
- Department of Zoology & Biodiversity Research Centre, University of British Columbia6270 University Blvd Vancouver BC, Canada V6T 1Z4
| | - Thomas M Lewinsohn
- Departamento Biologia Animal, Instituto de Biologia, University of Campinas, Campinas 13083-870, São Paulo, Brazil; Wissenschaftskolleg zu Berlin, Berlin 14193, Germany
| | - Owen T Lewis
- Department of Zoology, South Parks Road, Oxford, OX1 3PS, UK
| | - Vojtech Novotny
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; University of South Bohemia in Ceske Budejovice, Faculty of Science, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Roger L Kitching
- Environmental Futures Research Institute,Griffith University, Brisbane, Queensland 4111, Australia
| | - Sarah C Maunsell
- Department of Organismic and EvolutionaryBiology, Harvard University, Cambridge, MA, 02138, USA
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80
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Diversity and Host Interactions Among Virulent and Temperate Baltic Sea Flavobacterium Phages. Viruses 2020; 12:v12020158. [PMID: 32019073 PMCID: PMC7077304 DOI: 10.3390/v12020158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 02/06/2023] Open
Abstract
Viruses in aquatic environments play a key role in microbial population dynamics and nutrient cycling. In particular, bacteria of the phylum Bacteriodetes are known to participate in recycling algal blooms. Studies of phage–host interactions involving this phylum are hence important to understand the processes shaping bacterial and viral communities in the ocean as well as nutrient cycling. In this study, we isolated and sequenced three strains of flavobacteria—LMO6, LMO9, LMO8—and 38 virulent phages infecting them. These phages represent 15 species, occupying three novel genera. Additionally, one temperate phage was induced from LMO6 and was found to be competent at infecting LMO9. Functions could be predicted for a limited number of phage genes, mainly representing roles in DNA replication and virus particle formation. No metabolic genes were detected. While the phages isolated on LMO8 could infect all three bacterial strains, the LMO6 and LMO9 phages could not infect LMO8. Of the phages isolated on LMO9, several showed a host-derived reduced efficiency of plating on LMO6, potentially due to differences in DNA methyltransferase genes. Overall, these phage–host systems contribute novel genetic information to our sequence databases and present valuable tools for the study of both virulent and temperate phages.
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81
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Goehlich H, Roth O, Wendling CC. Filamentous phages reduce bacterial growth in low salinities. ROYAL SOCIETY OPEN SCIENCE 2019; 6:191669. [PMID: 31903215 PMCID: PMC6936277 DOI: 10.1098/rsos.191669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Being non-lytic, filamentous phages can replicate at high frequencies and often carry virulence factors, which are important in the evolution and emergence of novel pathogens. However, their net effect on bacterial fitness remains unknown. To understand the ecology and evolution between filamentous phages and their hosts, it is important to assess (i) fitness effects of filamentous phages on their hosts and (ii) how these effects depend on the environment. To determine how the net effect on bacterial fitness by filamentous phages changes across environments, we constructed phage-bacteria infection networks at ambient 15 practical salinity units (PSU) and stressful salinities (11 and 7 PSU) using the marine bacterium, Vibrio alginolyticus and its derived filamentous phages as model system. We observed no significant difference in network structure at 15 and 11 PSU. However, at 7 PSU phages significantly reduced bacterial growth changing network structure. This pattern was mainly driven by a significant increase in bacterial susceptibility. Our findings suggest that filamentous phages decrease bacterial growth, an indirect measure of fitness in stressful environmental conditions, which might impact bacterial communities, alter horizontal gene transfer events and possibly favour the emergence of novel pathogens in environmental Vibrios.
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Affiliation(s)
- Henry Goehlich
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Olivia Roth
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Carolin C. Wendling
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
- ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, CHN D 33, 8092 Zürich, Switzerland
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82
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83
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Smith MW, Herfort L, Rivers AR, Simon HM. Genomic Signatures for Sedimentary Microbial Utilization of Phytoplankton Detritus in a Fast-Flowing Estuary. Front Microbiol 2019; 10:2475. [PMID: 31749780 PMCID: PMC6848030 DOI: 10.3389/fmicb.2019.02475] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/15/2019] [Indexed: 01/21/2023] Open
Abstract
In fast-flowing, river-dominated estuaries, “hotspots” of microbial biogeochemical cycling can be found within areas of extended water retention. Lateral bays located off of the North and South channels of the Columbia River estuary are proposed to be such hotspots. Previous metagenomic studies on water samples indicated that these regions function both as sources and sinks of biogenic particles, with potential to impact organic matter fluxes in the estuary. To extend this work, we analyzed 11 sediment metagenomes from three disparate bays: the freshwater Cathlamet Bay, and the brackish Youngs Bay and more saline Baker Bay located nearer the mouth to the south and north of the main channel, respectively. Samples were collected from upper layers of sediments in August of 2011 and 2013 for DNA extraction and metagenome sequencing. All metagenomes were dominated by bacterial sequences, although diatom sequences as high as 26% of the total annotated sequences were observed in the higher salinity samples. Unsupervised 2D hierarchical clustering analysis resulted in the eleven metagenome samples clustered into four groups by microbial taxonomic composition, with Bacteroides, diatom, and phage levels driving most of the grouping. Results of functional gene clustering further indicated that diatom bloom degradation stage (early vs. late) was an important factor. While the Flavobacteriia and Cytophagia classes were well represented in metagenomes containing abundant diatoms, taxa from the Bacteroidia class, along with certain members of the Sphingobacteriia class, were particularly abundant in metagenomes representing later stages of diatom decomposition. In contrast, the sediment metagenomes with low relative abundance of diatom and Bacteroidetes sequences appeared to have a metabolic potential biased toward microbial growth under nutrient limitation. While differences in water salinity clearly also influenced the microbial community composition and metabolic potential, our results highlight a central role for allochthonous labile organic matter (i.e., diatom detritus), in shaping bacterial taxonomic and functional properties in the Columbia River estuary lateral bay sediments. These results suggest that in fast-flowing, river-dominated estuaries, sediment microbial communities in areas of extended water retention, such as the lateral bays, may contribute disproportionately to estuarine organic matter degradation and recycling.
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Affiliation(s)
- Maria W Smith
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, United States
| | - Lydie Herfort
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, United States.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, United States
| | - Adam R Rivers
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Holly M Simon
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, United States.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, United States
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84
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Zhao F, Ding T, Li M, Wang Y, Zhang X, Ren H, Tong Y. Complete genome analysis of a novel temperate bacteriophage induced from Corynebacterium striatum. Arch Virol 2019; 164:2877-2880. [PMID: 31451964 DOI: 10.1007/s00705-019-04370-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
A temperate bacteriophage, IME1320_01, was induced by mitomycin C treatment from Corynebacterium striatum. This phage possesses a double-stranded DNA genome of 40,086 bp with a G+C content of 58%. A total of 53 putative open reading frames (ORFs) were identified in its genome. BLASTn analysis revealed that IME1320_01 had the highest sequence similarity to Corynebacterium striatum strain 216, with a genome homology coverage of 44% and highest sequence identity of 95%. The termini of the phage genome was non-redundant, with a 13-nt 3'-protruding cohesive end. To the best of our knowledge, phage IME1320_01 is the first inducible phage to be identified in Corynebacterium striatum.
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Affiliation(s)
- Feiyang Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Tongyan Ding
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Manli Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yuanyuan Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China. .,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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85
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Abstract
Strategies to manage plant disease-from use of resistant varieties to crop rotation, elimination of reservoirs, landscape planning, surveillance, quarantine, risk modeling, and anticipation of disease emergences-all rely on knowledge of pathogen host range. However, awareness of the multitude of factors that influence the outcome of plant-microorganism interactions, the spatial and temporal dynamics of these factors, and the diversity of any given pathogen makes it increasingly challenging to define simple, all-purpose rules to circumscribe the host range of a pathogen. For bacteria, fungi, oomycetes, and viruses, we illustrate that host range is often an overlapping continuum-more so than the separation of discrete pathotypes-and that host jumps are common. By setting the mechanisms of plant-pathogen interactions into the scales of contemporary land use and Earth history, we propose a framework to assess the frontiers of host range for practical applications and research on pathogen evolution.
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Affiliation(s)
| | - Benoît Moury
- Pathologie Végétale, INRA, 84140, Montfavet, France;
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86
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González R, Butković A, Elena SF. Role of host genetic diversity for susceptibility-to-infection in the evolution of virulence of a plant virus. Virus Evol 2019; 5:vez024. [PMID: 31768264 PMCID: PMC6863064 DOI: 10.1093/ve/vez024] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Predicting viral emergence is difficult due to the stochastic nature of the underlying processes and the many factors that govern pathogen evolution. Environmental factors affecting the host, the pathogen and the interaction between both are key in emergence. In particular, infectious disease dynamics are affected by spatiotemporal heterogeneity in their environments. A broad knowledge of these factors will allow better estimating where and when viral emergence is more likely to occur. Here, we investigate how the population structure for susceptibility-to-infection genes of the plant Arabidopsis thaliana shapes the evolution of Turnip mosaic virus (TuMV). For doing so we have evolved TuMV lineages in two radically different host population structures: (1) a metapopulation subdivided into six demes (subpopulations); each one being composed of individuals from only one of six possible A. thaliana ecotypes and (2) a well-mixed population constituted by equal number of plants from the same six A. thaliana ecotypes. These two populations were evolved for twelve serial passages. At the end of the experimental evolution, we found faster adaptation of TuMV to each ecotype in the metapopulation than in the well-mixed heterogeneous host populations. However, viruses evolved in well-mixed populations were more pathogenic and infectious than viruses evolved in the metapopulation. Furthermore, the viruses evolved in the demes showed stronger signatures of local specialization than viruses evolved in the well-mixed populations. These results illustrate how the genetic diversity of hosts in an experimental ecosystem favors the evolution of virulence of a pathogen.
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Affiliation(s)
- Rubén González
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, València 46980, Spain
| | - Anamarija Butković
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, València 46980, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, València 46980, Spain.,The Santa Fe Institute, Santa Fe, 1399 Hyde Park Road, NM 87501, USA
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87
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Understanding and Exploiting Phage-Host Interactions. Viruses 2019; 11:v11060567. [PMID: 31216787 PMCID: PMC6630733 DOI: 10.3390/v11060567] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 01/05/2023] Open
Abstract
Initially described a century ago by William Twort and Felix d’Herelle, bacteriophages are bacterial viruses found ubiquitously in nature, located wherever their host cells are present. Translated literally, bacteriophage (phage) means ‘bacteria eater’. Phages interact and infect specific bacteria while not affecting other bacteria or cell lines of other organisms. Due to the specificity of these phage–host interactions, the relationship between phages and their host cells has been the topic of much research. The advances in phage biology research have led to the exploitation of these phage–host interactions and the application of phages in the agricultural and food industry. Phages may provide an alternative to the use of antibiotics, as it is well known that the emergence of antibiotic-resistant bacterial infections has become an epidemic in clinical settings. In agriculture, pre-harvest and/or post-harvest application of phages to crops may prevent the colonisation of bacteria that are detrimental to plant or human health. In addition, the abundance of data generated from genome sequencing has allowed the development of phage-derived bacterial detection systems of foodborne pathogens. This review aims to outline the specific interactions between phages and their host and how these interactions may be exploited and applied in the food industry.
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88
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Fortuna MA, Barbour MA, Zaman L, Hall AR, Buckling A, Bascompte J. Coevolutionary dynamics shape the structure of bacteria-phage infection networks. Evolution 2019; 73:1001-1011. [PMID: 30953575 DOI: 10.1111/evo.13731] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/18/2019] [Indexed: 01/21/2023]
Abstract
Coevolution-reciprocal evolutionary change among interacting species driven by natural selection-is thought to be an important force in shaping biodiversity. This ongoing process takes place within tangled networks of species interactions. In microbial communities, evolutionary change between hosts and parasites occurs at the same time scale as ecological change. Yet, we still lack experimental evidence of the role of coevolution in driving changes in the structure of such species interaction networks. Filling this gap is important because network structure influences community persistence through indirect effects. Here, we quantified experimentally to what extent coevolutionary dynamics lead to contrasting patterns in the architecture of bacteria-phage infection networks. Specifically, we look at the tendency of these networks to be organized in a nested pattern by which the more specialist phages tend to infect only a proper subset of those bacteria infected by the most generalist phages. We found that interactions between coevolving bacteria and phages become less nested over time under fluctuating dynamics, and more nested under arms race dynamics. Moreover, when coevolution results in high average infectivity, phages and bacteria differ more from each other over time under arms race dynamics than under fluctuating dynamics. The tradeoff between the fitness benefits of evolving resistance/infectivity traits and the costs of maintaining them might explain these differences in network structure. Our study shows that the interaction pattern between bacteria and phages at the community level depends on the way coevolution unfolds.
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Affiliation(s)
- Miguel A Fortuna
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Matthew A Barbour
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Luis Zaman
- Center for the Study of Complex Systems, Ecology, and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Alex R Hall
- Institute of Integrative Biology, ETH-Zurich, Zurich, Switzerland
| | - Angus Buckling
- ESI & CEC, Biosciences, University of Exeter, Penryn, Cornwall, UK
| | - Jordi Bascompte
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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89
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Mizuno CM, Prajapati B, Lucas‐Staat S, Sime‐Ngando T, Forterre P, Bamford DH, Prangishvili D, Krupovic M, Oksanen HM. Novel haloarchaeal viruses from Lake Retba infecting
Haloferax
and
Halorubrum
species. Environ Microbiol 2019; 21:2129-2147. [DOI: 10.1111/1462-2920.14604] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/15/2019] [Accepted: 03/21/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Carolina M. Mizuno
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Bina Prajapati
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
| | - Soizick Lucas‐Staat
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Telesphore Sime‐Ngando
- CNRS UMR 6023, Université Clermont‐AuvergneLaboratoire "Microorganismes: Génome et Environnement" (LMGE) F‐63000, Clermont‐Ferrand France
| | - Patrick Forterre
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Dennis H. Bamford
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
| | - David Prangishvili
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
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90
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Gencay YE, Gambino M, Prüssing TF, Brøndsted L. The genera of bacteriophages and their receptors are the major determinants of host range. Environ Microbiol 2019; 21:2095-2111. [PMID: 30888719 DOI: 10.1111/1462-2920.14597] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 01/21/2023]
Abstract
The host range of phages is a key to understand their impact on bacterial ecology and evolution. Because of the complexity of phage-host interactions, the variables that determine the breadth of a phage host range remain poorly understood. Here, we propose a novel holistic approach to identify the host range determinants of a new collection of phages infecting Salmonella, isolated from animal, environmental and wastewater samples that were able to infect 58 of the 71 Salmonella strains in our collection. By using a set of statistic approaches (non-metric dimensional scaling, Bray-Curtis distance, PERMANOVA), we analysed phenotypic (host range on wild-type and receptor mutants) and genetic data (taxonomic assignment and receptor binding proteins) to evaluate the impact of isolation strain and niche, phage receptor and genus on the host range. Statistical analysis revealed that two phage characteristics influence the host range by explaining the most variance: the receptor by 45% and the genus by 51%. Interestingly, phage genus and receptor in combination explained 79% of the variance, establishing these characteristics as the major determinants of the host range. This study demonstrates the power and the novelty of applying statistical approaches to phenotypic and genetic data to investigate the ecology of phage-host interactions.
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Affiliation(s)
- Yilmaz Emre Gencay
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Michela Gambino
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Tessa From Prüssing
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
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91
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Larsen ML, Wilhelm SW, Lennon JT. Nutrient stoichiometry shapes microbial coevolution. Ecol Lett 2019; 22:1009-1018. [DOI: 10.1111/ele.13252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/10/2018] [Accepted: 02/18/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Megan L. Larsen
- Department of Biology Indiana University Bloomington IN47405USA
| | - Steven W. Wilhelm
- Department of Microbiology University of Tennessee Knoxville TN37996 USA
| | - Jay T. Lennon
- Department of Biology Indiana University Bloomington IN47405USA
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92
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Luhtanen AM, Eronen-Rasimus E, Oksanen HM, Tison JL, Delille B, Dieckmann GS, Rintala JM, Bamford DH. The first known virus isolates from Antarctic sea ice have complex infection patterns. FEMS Microbiol Ecol 2019; 94:4898008. [PMID: 29481638 DOI: 10.1093/femsec/fiy028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/21/2018] [Indexed: 01/21/2023] Open
Abstract
Viruses are recognized as important actors in ocean ecology and biogeochemical cycles, but many details are not yet understood. We participated in a winter expedition to the Weddell Sea, Antarctica, to isolate viruses and to measure virus-like particle abundance (flow cytometry) in sea ice. We isolated 59 bacterial strains and the first four Antarctic sea-ice viruses known (PANV1, PANV2, OANV1 and OANV2), which grow in bacterial hosts belonging to the typical sea-ice genera Paraglaciecola and Octadecabacter. The viruses were specific for bacteria at the strain level, although OANV1 was able to infect strains from two different classes. Both PANV1 and PANV2 infected 11/15 isolated Paraglaciecola strains that had almost identical 16S rRNA gene sequences, but the plating efficiencies differed among the strains, whereas OANV1 infected 3/7 Octadecabacter and 1/15 Paraglaciecola strains and OANV2 1/7 Octadecabacter strains. All the phages were cold-active and able to infect their original host at 0°C and 4°C, but not at higher temperatures. The results showed that virus-host interactions can be very complex and that the viral community can also be dynamic in the winter-sea ice.
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Affiliation(s)
- Anne-Mari Luhtanen
- Marine Research Centre, Finnish Environment Institute, Helsinki, Finland.,Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | | | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jean-Louis Tison
- Laboratoire de Glaciologie, DGES, Université Libre de Bruxelles, Belgium
| | - Bruno Delille
- Unité d'Océanographie Chimique, Université de Liège, Belgium
| | - Gerhard S Dieckmann
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Janne-Markus Rintala
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland.,Department of Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Dennis H Bamford
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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93
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Delmas E, Besson M, Brice MH, Burkle LA, Dalla Riva GV, Fortin MJ, Gravel D, Guimarães PR, Hembry DH, Newman EA, Olesen JM, Pires MM, Yeakel JD, Poisot T. Analysing ecological networks of species interactions. Biol Rev Camb Philos Soc 2019; 94:16-36. [PMID: 29923657 DOI: 10.1111/brv.12433] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 05/08/2018] [Accepted: 05/14/2018] [Indexed: 01/24/2023]
Abstract
Network approaches to ecological questions have been increasingly used, particularly in recent decades. The abstraction of ecological systems - such as communities - through networks of interactions between their components indeed provides a way to summarize this information with single objects. The methodological framework derived from graph theory also provides numerous approaches and measures to analyze these objects and can offer new perspectives on established ecological theories as well as tools to address new challenges. However, prior to using these methods to test ecological hypotheses, it is necessary that we understand, adapt, and use them in ways that both allow us to deliver their full potential and account for their limitations. Here, we attempt to increase the accessibility of network approaches by providing a review of the tools that have been developed so far, with - what we believe to be - their appropriate uses and potential limitations. This is not an exhaustive review of all methods and metrics, but rather, an overview of tools that are robust, informative, and ecologically sound. After providing a brief presentation of species interaction networks and how to build them in order to summarize ecological information of different types, we then classify methods and metrics by the types of ecological questions that they can be used to answer from global to local scales, including methods for hypothesis testing and future perspectives. Specifically, we show how the organization of species interactions in a community yields different network structures (e.g., more or less dense, modular or nested), how different measures can be used to describe and quantify these emerging structures, and how to compare communities based on these differences in structures. Within networks, we illustrate metrics that can be used to describe and compare the functional and dynamic roles of species based on their position in the network and the organization of their interactions as well as associated new methods to test the significance of these results. Lastly, we describe potential fruitful avenues for new methodological developments to address novel ecological questions.
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Affiliation(s)
- Eva Delmas
- Département de Sciences Biologiques, Université de Montréal, Montréal, H2V 2J7, Canada.,Québec Centre for Biodiversity Sciences, McGill University, Montréal, H3A 1B1, Canada
| | - Mathilde Besson
- Département de Sciences Biologiques, Université de Montréal, Montréal, H2V 2J7, Canada.,Québec Centre for Biodiversity Sciences, McGill University, Montréal, H3A 1B1, Canada
| | - Marie-Hélène Brice
- Département de Sciences Biologiques, Université de Montréal, Montréal, H2V 2J7, Canada.,Québec Centre for Biodiversity Sciences, McGill University, Montréal, H3A 1B1, Canada
| | - Laura A Burkle
- Department of Ecology, Montana State University, Bozeman, MT 59715, U.S.A
| | - Giulio V Dalla Riva
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada
| | - Dominique Gravel
- Québec Centre for Biodiversity Sciences, McGill University, Montréal, H3A 1B1, Canada.,Département de Biologie, Université de Sherbrooke, Sherbrooke, J1K 2R1, Canada
| | - Paulo R Guimarães
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brazil
| | - David H Hembry
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, U.S.A
| | - Erica A Newman
- School of Natural Resources and Environment, University of Arizona, Tucson, AZ 85721, U.S.A.,Pacific Wildland Fire Sciences Laboratory, USDA Forest Service, Seattle, WA 98103, U.S.A
| | - Jens M Olesen
- Department of Bioscience, Aarhus University, Aarhus, 8000, Denmark
| | - Mathias M Pires
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, 13083-862, Brazil
| | - Justin D Yeakel
- Life & Environmental Sciences, University of California Merced, Merced, CA 95343, U.S.A.,Santa Fe Institute, Santa Fe, NM 87501, U.S.A
| | - Timothée Poisot
- Département de Sciences Biologiques, Université de Montréal, Montréal, H2V 2J7, Canada.,Québec Centre for Biodiversity Sciences, McGill University, Montréal, H3A 1B1, Canada
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94
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De Sordi L, Lourenço M, Debarbieux L. The Battle Within: Interactions of Bacteriophages and Bacteria in the Gastrointestinal Tract. Cell Host Microbe 2019; 25:210-218. [DOI: 10.1016/j.chom.2019.01.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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95
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Topka G, Bloch S, Nejman-Faleńczyk B, Gąsior T, Jurczak-Kurek A, Necel A, Dydecka A, Richert M, Węgrzyn G, Węgrzyn A. Characterization of Bacteriophage vB-EcoS-95, Isolated From Urban Sewage and Revealing Extremely Rapid Lytic Development. Front Microbiol 2019; 9:3326. [PMID: 30697202 PMCID: PMC6340994 DOI: 10.3389/fmicb.2018.03326] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/21/2018] [Indexed: 01/05/2023] Open
Abstract
Morphological, biological, and genetic characteristics of a virulent Siphoviridae phage, named vB-EcoS-95, is reported. This phage was isolated from urban sewage. It was found to infect some Escherichia coli strains giving clear plaques. The genome of this phage is composed of 50,910 bp and contains 89 ORFs. Importantly, none of the predicted ORFs shows any similarity with known pathogenic factors that would prevent its use in medicine. Genome sequence analysis of vB-EcoS-95 revealed 74% similarity to genomic sequence of Shigella phage pSf-1. Compared to pSf-1, phage vb-EcoS-95 does not infect Shigella strains and has an efficient bacteriolytic activity against some E. coli strains. One-step growth analysis revealed that this phage has a very short latent period (4 min), and average burst size of 115 plaque forming units per cell, which points to its high infectivity of host cells and strong lytic activity. The bacteriolytic effect of vB-EcoS-95 was tested also on biofilm-producing strains. These results indicate that vB-EcoS-95 is a newly discovered E. coli phage that may be potentially used to control the formation of biofilms.
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Affiliation(s)
- Gracja Topka
- Department of Molecular BiologyUniversity of Gdańsk, Gdańsk, Poland
| | - Sylwia Bloch
- Department of Molecular BiologyUniversity of Gdańsk, Gdańsk, Poland
| | | | - Tomasz Gąsior
- Laboratory of Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of Sciences, Gdańsk, Poland
| | | | - Agnieszka Necel
- Department of Molecular BiologyUniversity of Gdańsk, Gdańsk, Poland
| | | | - Malwina Richert
- Laboratory of Electron MicroscopyUniversity of Gdańsk, Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular BiologyUniversity of Gdańsk, Gdańsk, Poland
| | - Alicja Węgrzyn
- Laboratory of Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of Sciences, Gdańsk, Poland
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96
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Evolution of plant-virus interactions: host range and virus emergence. Curr Opin Virol 2019; 34:50-55. [PMID: 30654270 DOI: 10.1016/j.coviro.2018.12.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/11/2018] [Indexed: 12/11/2022]
Abstract
Changes in host range are central to virus emergence. Host range, together with its evolution, is determined by virus intrinsic factors, such as genetic traits determining its fitness in different hosts. Experimental analyses have shown the relevance in host range evolution of across-host fitness trade-offs. Host range is also determined by ecological factors extrinsic to the virus such as the distribution, abundance, and interaction of species, and understanding their role in host range evolution is a current challenge. Indeed, intrinsic and extrinsic factors, and the complexity of biotic and abiotic interactions, must be considered in order to provide generalisations on patterns of transmission, host range evolution, and disease emergence. This exciting new field of research is still in its infancy.
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97
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Nazarian P, Tran F, Boedicker JQ. Modeling Multispecies Gene Flow Dynamics Reveals the Unique Roles of Different Horizontal Gene Transfer Mechanisms. Front Microbiol 2018; 9:2978. [PMID: 30564220 PMCID: PMC6288448 DOI: 10.3389/fmicb.2018.02978] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/19/2018] [Indexed: 12/23/2022] Open
Abstract
Horizontal gene transfer within diverse bacterial populations occurs through multiple mechanisms of exchange. The most established routes of gene transfer, transduction, transformation, and conjugation, have been characterized in detail, revealing the advantages and limitations of each mechanism. More recently, interspecies gene exchange via extracellular vesicles has been reported and characterized, making vesicle-mediated exchange a fourth, general mechanism of gene transfer. Despite an understanding of each individual pathway, how all of these mechanisms act in concert has not been explored. Here we develop a model of gene exchange in a multispecies bacterial community that takes into account the rates and limitations of all four gene transfer mechanisms. Our results reveal unique roles for each gene exchange mechanism, and highlight how multiple pathways working together are required for widespread gene exchange within diverse bacterial populations.
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Affiliation(s)
- Phillip Nazarian
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, United States
| | - Frances Tran
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - James Q Boedicker
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, United States.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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98
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Pannekens M, Kroll L, Müller H, Mbow FT, Meckenstock RU. Oil reservoirs, an exceptional habitat for microorganisms. N Biotechnol 2018; 49:1-9. [PMID: 30502541 PMCID: PMC6323355 DOI: 10.1016/j.nbt.2018.11.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 01/21/2023]
Abstract
Water-containing parts within oil reservoirs extend the zone of biodegradation. Biodegradation is controlled by environmental factors. Proteobacteria and Euryarchaeota are ubiquitous in oil reservoirs over all temperature ranges. Biofilms as microbial adaption in oil reservoirs. Viruses as potential control for microbial activity and function.
Microorganisms are present in oil reservoirs around the world where they degrade oil and lead to changes in oil quality. Unfortunately, our knowledge about processes in deep oil reservoirs is limited due to the lack of undisturbed samples. In this review, we discuss the distribution of microorganisms at the oil-water transition zone as well as in water saturated parts of the oil leg and their possible physiological adaptations to abiotic and biotic ecological factors such as temperature, salinity and viruses. We show the importance of studying the water phase within the oil, because small water inclusions and pockets within the oil leg provide an exceptional habitat for microorganisms within a natural oil reservoir and concurrently enlarge the zone of oil biodegradation. Environmental factors such as temperature and salinity control oil biodegradation. Temperature determines the type of microorganisms which are able to inhabit the reservoir. Proteobacteria and Euryarchaeota, are ubiquitous in oil reservoirs over all temperature ranges, whereas some others are tied to specific temperatures. It is proposed that biofilm formation is the dominant way of life within oil reservoirs, enhancing nutrient uptake, syntrophic interactions and protection against environmental stress. Literature shows that viruses are abundant in oil reservoirs and the possible impact on microbial community composition due to control of microbial activity and function is discussed.
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Affiliation(s)
- Mark Pannekens
- University of Duisburg-Essen, Biofilm Centre, Universitätsstr. 5, 41451, Essen, Germany
| | - Lisa Kroll
- University of Duisburg-Essen, Biofilm Centre, Universitätsstr. 5, 41451, Essen, Germany
| | - Hubert Müller
- University of Duisburg-Essen, Biofilm Centre, Universitätsstr. 5, 41451, Essen, Germany
| | - Fatou Tall Mbow
- University of Duisburg-Essen, Biofilm Centre, Universitätsstr. 5, 41451, Essen, Germany
| | - Rainer U Meckenstock
- University of Duisburg-Essen, Biofilm Centre, Universitätsstr. 5, 41451, Essen, Germany.
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99
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Leite DMC, Brochet X, Resch G, Que YA, Neves A, Peña-Reyes C. Computational prediction of inter-species relationships through omics data analysis and machine learning. BMC Bioinformatics 2018; 19:420. [PMID: 30453987 PMCID: PMC6245486 DOI: 10.1186/s12859-018-2388-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Antibiotic resistance and its rapid dissemination around the world threaten the efficacy of currently-used medical treatments and call for novel, innovative approaches to manage multi-drug resistant infections. Phage therapy, i.e., the use of viruses (phages) to specifically infect and kill bacteria during their life cycle, is one of the most promising alternatives to antibiotics. It is based on the correct matching between a target pathogenic bacteria and the therapeutic phage. Nevertheless, correctly matching them is a major challenge. Currently, there is no systematic method to efficiently predict whether phage-bacterium interactions exist and these pairs must be empirically tested in laboratory. Herein, we present our approach for developing a computational model able to predict whether a given phage-bacterium pair can interact based on their genome. RESULTS Based on public data from GenBank and phagesDB.org, we collected more than a thousand positive phage-bacterium interactions with their complete genomes. In addition, we generated putative negative (i.e., non-interacting) pairs. We extracted, from the collected genomes, a set of informative features based on the distribution of predictive protein-protein interactions and on their primary structure (e.g. amino-acid frequency, molecular weight and chemical composition of each protein). With these features, we generated multiple candidate datasets to train our algorithms. On this base, we built predictive models exhibiting predictive performance of around 90% in terms of F1-score, sensitivity, specificity, and accuracy, obtained on the test set with 10-fold cross-validation. CONCLUSION These promising results reinforce the hypothesis that machine learning techniques may produce highly-predictive models accelerating the search of interacting phage-bacteria pairs.
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Affiliation(s)
- Diogo Manuel Carvalho Leite
- School of Business and Engineering Vaud (HEIG-VD), University of Applied Sciences Western Switzerland (HES-SO), Route. de Cheseaux 1, Yverdon-Les-Bains, 1400 Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Xavier Brochet
- School of Business and Engineering Vaud (HEIG-VD), University of Applied Sciences Western Switzerland (HES-SO), Route. de Cheseaux 1, Yverdon-Les-Bains, 1400 Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Grégory Resch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, 1015 Switzerland
| | - Yok-Ai Que
- Department of Intensive Care Medicine, Bern University Hospital (Inselspital), Freiburgstrasse, Bern, 3010 Switzerland
| | - Aitana Neves
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Carlos Peña-Reyes
- School of Business and Engineering Vaud (HEIG-VD), University of Applied Sciences Western Switzerland (HES-SO), Route. de Cheseaux 1, Yverdon-Les-Bains, 1400 Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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100
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Wright RCT, Friman VP, Smith MCM, Brockhurst MA. Cross-resistance is modular in bacteria-phage interactions. PLoS Biol 2018; 16:e2006057. [PMID: 30281587 PMCID: PMC6188897 DOI: 10.1371/journal.pbio.2006057] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 10/15/2018] [Accepted: 09/24/2018] [Indexed: 01/21/2023] Open
Abstract
Phages shape the structure of natural bacterial communities and can be effective therapeutic agents. Bacterial resistance to phage infection, however, limits the usefulness of phage therapies and could destabilise community structures, especially if individual resistance mutations provide cross-resistance against multiple phages. We currently understand very little about the evolution of cross-resistance in bacteria–phage interactions. Here we show that the network structure of cross-resistance among spontaneous resistance mutants of Pseudomonas aeruginosa evolved against each of 27 phages is highly modular. The cross-resistance network contained both symmetric (reciprocal) and asymmetric (nonreciprocal) cross-resistance, forming two cross-resistance modules defined by high within- but low between-module cross-resistance. Mutations conferring cross-resistance within modules targeted either lipopolysaccharide or type IV pilus biosynthesis, suggesting that the modularity of cross-resistance was structured by distinct phage receptors. In contrast, between-module cross-resistance was provided by mutations affecting the alternative sigma factor, RpoN, which controls many lifestyle-associated functions, including motility, biofilm formation, and quorum sensing. Broader cross-resistance range was not associated with higher fitness costs or weaker resistance against the focal phage used to select resistance. However, mutations in rpoN, providing between-module cross-resistance, were associated with higher fitness costs than mutations associated with within-module cross-resistance, i.e., in genes encoding either lipopolysaccharide or type IV pilus biosynthesis. The observed structure of cross-resistance predicted both the frequency of resistance mutations and the ability of phage combinations to suppress bacterial growth. These findings suggest that the evolution of cross-resistance is common, is likely to play an important role in the dynamic structure of bacteria–phage communities, and could inform the design principles for phage therapy treatments. Phage therapy is a promising alternative to antibiotics for treating bacterial infections. Yet as with antibiotics, bacteria readily evolve resistance to phage attack, including cross-resistance that protects against multiple phages at once and so limits the usefulness of phage cocktails. Here we show, using laboratory experimental evolution of resistance against 27 phages in P. aeruginosa, that cross-resistance is common and determines the ability of phage combinations to suppress bacterial growth. Using whole-genome sequencing, we show that cross-resistance is most common against multiple phages that use the same receptor but that global regulator mutations provide generalist resistance, probably by simultaneously affecting the expression of multiple different phage receptors. Future trials should test if these features of cross-resistance evolution translate to more complex in vivo environments and can therefore be exploited to design more effective phage therapies for the clinic.
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Affiliation(s)
- Rosanna C. T. Wright
- Department of Biology, University of York, York, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | | | | - Michael A. Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
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