1
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Li J, Yang W, Hao X, Lin Y, van Loosdrecht MCM. Little alginates synthesized in EPS: Evidences from high-throughput community and metagenes. WATER RESEARCH 2024; 265:122211. [PMID: 39137456 DOI: 10.1016/j.watres.2024.122211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/03/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024]
Abstract
As a significant structure in activated sludge, extracellular polymeric substances (EPS) hold considerable value regarding resource recovery and applications. The present study aimed to elucidate the relationship between the microbial community and the composition and properties of EPS. A biological nutrient removal (BNR) reactor was set up in the laboratory and controlled under different solid retention times (SRT), altering microbial species within the system. Then EPS was extracted from activated and analyzed by chemical and spectroscopic methods. High-throughput sequencing and metagenomic approaches were employed to investigate bacterial community and metabolic pathways. The results showed that lower SRT with a higher abundance of the family-level Proteobacteria (27.7%-53.5%) favored EPS synthesis, while another dominant group Bacteroidetes (20.0%-32.6%) may not significantly affect EPS synthesis. Furthermore, the abundance of alginates-producing bacteria including Pseudomonas spp. and Azotobacter vinelandii was only 2.53%-6.76% and 1.98%-6.34%, respectively. The alginate synthesis pathway genes Alg8 and Alg44 were also present at very low levels (0.05‱-0.11‱, 0.01‱-0.02‱, respectively). Another important gene related to alginates operons, AlgK, was absent across all the SRT-operated reactors. These findings suggest an impossible and incomplete alginate synthesis pathway within sludge. In light of these results, it can be concluded that EPS does not necessarily contain alginate components.
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Affiliation(s)
- Ji Li
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Beijing Advanced Innovation Centre of Future Urban Design, Beijing University of Civil Engineering & Architecture, Beijing 100044, PR China; Dept. of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Wanbang Yang
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Beijing Advanced Innovation Centre of Future Urban Design, Beijing University of Civil Engineering & Architecture, Beijing 100044, PR China
| | - Xiaodi Hao
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Beijing Advanced Innovation Centre of Future Urban Design, Beijing University of Civil Engineering & Architecture, Beijing 100044, PR China.
| | - Yuemei Lin
- Dept. of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Mark C M van Loosdrecht
- Dept. of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
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2
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Chen W, Zhang Y, Mi J. Assessing Antibiotic-Resistant Genes in University Dormitory Washing Machines. Microorganisms 2024; 12:1112. [PMID: 38930496 PMCID: PMC11205806 DOI: 10.3390/microorganisms12061112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
University dormitories represent densely populated environments, and washing machines are potential sites for the spread of bacteria and microbes. However, the extent of antibiotic resistance gene (ARG) variation in washing machines within university dormitories and their potential health risks are largely unknown. To disclose the occurrence of ARGs and antibiotic-resistant bacteria from university dormitories, we collected samples from washing machines in 10 dormitories and used metagenomic sequencing technology to determine microbial and ARG abundance. Our results showed abundant microbial diversity, with Proteobacteria being the dominant microorganism that harbors many ARGs. The majority of the existing ARGs were associated with antibiotic target alteration and efflux, conferring multidrug resistance. We identified tnpA and IS91 as the most abundant mobile genetic elements (MGEs) in washing machines and found that Micavibrio aeruginosavorus, Aquincola tertiaricarbonis, and Mycolicibacterium iranicum had high levels of ARGs. Our study highlights the potential transmission of pathogens from washing machines to humans and the surrounding environment. Pollution in washing machines poses a severe threat to public health and demands attention. Therefore, it is crucial to explore effective methods for reducing the reproduction of multidrug resistance.
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Affiliation(s)
- Wenbo Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China;
- Division of Bioscience, University College London, London WC1E 6BT, UK
| | - Yu Zhang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China;
| | - Jiandui Mi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China;
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
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3
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Santin YG, Sogues A, Bourigault Y, Remaut HK, Laloux G. Lifecycle of a predatory bacterium vampirizing its prey through the cell envelope and S-layer. Nat Commun 2024; 15:3590. [PMID: 38678033 PMCID: PMC11055950 DOI: 10.1038/s41467-024-48042-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/16/2024] [Indexed: 04/29/2024] Open
Abstract
Predatory bacteria feed upon other bacteria in various environments. Bdellovibrio exovorus is an obligate epibiotic predator that attaches on the prey cell surface, where it grows and proliferates. Although the mechanisms allowing feeding through the prey cell envelope are unknown, it has been proposed that the prey's proteinaceous S-layer may act as a defensive structure against predation. Here, we use time-lapse and cryo-electron microscopy to image the lifecycle of B. exovorus feeding on Caulobacter crescentus. We show that B. exovorus proliferates by non-binary division, primarily generating three daughter cells. Moreover, the predator feeds on C. crescentus regardless of the presence of an S-layer, challenging its assumed protective role against predators. Finally, we show that apparently secure junctions are established between prey and predator outer membranes.
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Affiliation(s)
- Yoann G Santin
- de Duve Institute, UCLouvain, 75 avenue Hippocrate, 1200, Brussels, Belgium
| | - Adrià Sogues
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Yvann Bourigault
- de Duve Institute, UCLouvain, 75 avenue Hippocrate, 1200, Brussels, Belgium
| | - Han K Remaut
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Géraldine Laloux
- de Duve Institute, UCLouvain, 75 avenue Hippocrate, 1200, Brussels, Belgium.
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4
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Romanowski EG, Brothers KM, Calvario RC, Stella NA, Kim T, Elsayed M, Kadouri DE, Shanks RMQ. Predatory bacteria prevent the proliferation of intraocular Serratia marcescens and fluoroquinolone-resistant Pseudomonas aeruginosa. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001433. [PMID: 38358321 PMCID: PMC10924457 DOI: 10.1099/mic.0.001433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/25/2024] [Indexed: 02/16/2024]
Abstract
Endogenous endophthalmitis caused by Gram-negative bacteria is an intra-ocular infection that can rapidly progress to irreversible loss of vision. While most endophthalmitis isolates are susceptible to antibiotic therapy, the emergence of resistant bacteria necessitates alternative approaches to combat intraocular bacterial proliferation. In this study the ability of predatory bacteria to limit intraocular growth of Pseudomonas aeruginosa, Serratia marcescens, and Staphylococcus aureus was evaluated in a New Zealand white rabbit endophthalmitis prevention model. Predatory bacteria Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus were able to reduce proliferation of keratitis isolates of P. aeruginosa and to a lesser extent S. marcescens. However, it was not able to significantly reduce the number of intraocular S. aureus, which is not a productive prey for these predatory bacteria, suggesting that the inhibitory effect on P. aeruginosa and S. marcescens requires active predation rather than an antimicrobial immune response. Similarly, UV-inactivated B. bacteriovorus were unable to prevent proliferation of P. aeruginosa. Together, these data indicate in vivo inhibition of Gram-negative bacteria proliferation within the intra-ocular environment by predatory bacteria.
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Affiliation(s)
- Eric G. Romanowski
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kimberly M. Brothers
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rachel C. Calvario
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nicholas A. Stella
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tami Kim
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - Mennat Elsayed
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - Daniel E. Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - Robert M. Q. Shanks
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
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5
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Mun W, Choi SY, Upatissa S, Mitchell RJ. Predatory bacteria as potential biofilm control and eradication agents in the food industry. Food Sci Biotechnol 2023; 32:1729-1743. [PMID: 37780591 PMCID: PMC10533476 DOI: 10.1007/s10068-023-01310-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 10/03/2023] Open
Abstract
Biofilms are a major concern within the food industry since they have the potential to reduce productivity in situ (within the field), impact food stability and storage, and cause downstream food poisoning. Within this review, predatory bacteria as potential biofilm control and eradication agents are discussed, with a particular emphasis on the intraperiplasmic Bdellovibrio-and-like organism (BALO) grouping. After providing a brief overview of predatory bacteria and their activities, focus is given to how BALOs fulfill four attributes that are essential for biocontrol agents to be successful in the food industry: (1) Broad spectrum activity against pathogens, both plant and human; (2) Activity against biofilms; (3) Safety towards humans and animals; and (4) Compatibility with food. As predatory bacteria possess all of these characteristics, they represent a novel form of biofilm biocontrol that is ripe for use within the food industry.
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Affiliation(s)
- Wonsik Mun
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 South Korea
| | - Seong Yeol Choi
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 South Korea
| | - Sumudu Upatissa
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 South Korea
| | - Robert J. Mitchell
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 South Korea
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6
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Romanowski EG, Brothers KM, Calvario RC, Stella NA, Kim T, Elsayed M, Kadouri DE, Shanks RMQ. Intra-ocular Predation of Fluoroquinolone-Resistant Pseudomonas aeruginosa and Serratia marcescens by Predatory Bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.17.558130. [PMID: 37745563 PMCID: PMC10516018 DOI: 10.1101/2023.09.17.558130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Endogenous endophthalmitis caused by Gram-negative bacteria is an intra-ocular infection that can rapidly progress to irreversible loss of vision. While most endophthalmitis isolates are susceptible to antibiotic therapy, the emergence of resistant bacteria necessitates alternative approaches to combat intraocular bacterial proliferation. In this study the ability of predatory bacteria to limit intraocular growth of Pseudomonas aeruginosa, Serratia marcescens, and Staphylococcus aureus was evaluated in a New Zealand White rabbit endophthalmitis prevention model. Predatory bacteria Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus were able to reduce proliferation of keratitis isolates of P. aeruginosa and S. marcescens. However, it was not able to significantly reduce S. aureus, which is not a productive prey for these predatory bacteria, suggesting that the inhibitory effect on P. aeruginosa requires active predation rather than an antimicrobial immune response. Similarly, UV-inactivated B. bacteriovorus were unable to prevent proliferation of P. aeruginosa. Together, these data suggest in vivo predation of Gram-negative bacteria within the intra-ocular environment.
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Affiliation(s)
- Eric G Romanowski
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA
| | - Kimberly M Brothers
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA
| | - Rachel C Calvario
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA
| | - Nicholas A Stella
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA
| | - Tami Kim
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ
| | - Mennat Elsayed
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ
| | - Robert M Q Shanks
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA
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7
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Kamada S, Wakabayashi R, Naganuma T. Phylogenetic Revisit to a Review on Predatory Bacteria. Microorganisms 2023; 11:1673. [PMID: 37512846 PMCID: PMC10385382 DOI: 10.3390/microorganisms11071673] [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: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Predatory bacteria, along with the biology of their predatory behavior, have attracted interest in terms of their ecological significance and industrial applications, a trend that has been even more pronounced since the comprehensive review in 2016. This mini-review does not cover research trends, such as the role of outer membrane vesicles in myxobacterial predation, but provides an overview of the classification and newly described taxa of predatory bacteria since 2016, particularly with regard to phylogenetic aspects. Among them, it is noteworthy that in 2020 there was a major phylogenetic reorganization that the taxa hosting Bdellovibrio and Myxococcus, formerly classified as Deltaproteobacteria, were proposed as the new phyla Bdellovibrionota and Myxococcota, respectively. Predatory bacteria have been reported from other phyla, especially from the candidate divisions. Predatory bacteria that prey on cyanobacteria and predatory cyanobacteria that prey on Chlorella have also been found. These are also covered in this mini-review, and trans-phylum phylogenetic trees are presented.
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Affiliation(s)
- Saki Kamada
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Ryoka Wakabayashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
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8
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Active predation, phylogenetic diversity, and global prevalence of myxobacteria in wastewater treatment plants. THE ISME JOURNAL 2023; 17:671-681. [PMID: 36774445 PMCID: PMC9919749 DOI: 10.1038/s41396-023-01378-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/13/2023]
Abstract
The operation of modern wastewater treatment plants (WWTPs) is driven by activated sludge microbiota, a complex assemblage of trophically interacting microorganisms. Microbial predation is crucial to fundamental understanding of how biological interactions drive microbiome structuring and functioning of WWTPs. However, predatory bacteria have received little attention regarding their diversity, activity, and ecological function in activated sludge, limiting the exploitation of food web interactions for wastewater microbiome engineering. Here, by using rRNA-stable isotope probing of activated sludge microbiota with 13C-labeled prey bacteria, we uncovered diverse as-yet-uncultivated putative predatory bacteria that actively incorporated 13C-biomass. Myxobacteria, especially Haliangium and the mle1-27 clade, were found as the dominant active predators, refreshing conventional views based on a few predatory isolates of Bdellovibrionota from WWTPs. The identified predatory bacteria showed more selective predation on prey compared with the protists dominated by ciliates, providing in situ evidence for inter-domain predation behavior divergence in activated sludge. Putative predatory bacteria were tracked over a two-year microbiome monitoring effort at a local WWTP, revealing the predominance of Myxococcota (6.5 ± 1.3%) over Bdellovibrionota (1.0 ± 0.2%) lineages. Phylogenetic analysis unveiled highly diverse myxobacteria inhabiting activated sludge and suggested a habitat filtering effect in global WWTPs. Further mining of a global activated sludge microbiome dataset revealed the prevalence of Myxococcota (5.4 ± 0.1%) species and potential impacts of myxobacterial predation on process performance. Collectively, our findings provided unique insights into the predating activity, diversity, and prevalence of Myxococcota species in activated sludge, highlighting their links with wastewater treatment processes via trophic regulation of enteric and functional bacteria.
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9
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Dueholm MKD, Besteman M, Zeuner EJ, Riisgaard-Jensen M, Nielsen ME, Vestergaard SZ, Heidelbach S, Bekker NS, Nielsen PH. Genetic potential for exopolysaccharide synthesis in activated sludge bacteria uncovered by genome-resolved metagenomics. WATER RESEARCH 2023; 229:119485. [PMID: 36538841 DOI: 10.1016/j.watres.2022.119485] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
A good floc formation of activated sludge (AS) is crucial for solid-liquid separation and production of clean effluent during wastewater treatment. Floc formation is partly controlled by self-produced extracellular polymeric substances (EPS) such as exopolysaccharides, proteins, and nucleic acids. Little is known about the composition, structure, and function of EPS in AS and which bacteria produce them. To address this knowledge gap for the exopolysaccharides, we took advantage of 1083 high-quality metagenome-assembled genomes (MAGs) obtained from 23 Danish wastewater treatment plants. We investigated the genomic potential for exopolysaccharide biosynthesis in bacterial species typical in AS systems based on genome mining and gene synteny analyses. Putative gene clusters associated with the biosynthesis of alginate, cellulose, curdlan, diutan, hyaluronic acids, Pel, poly-β-1,6-N-acetyl-d-glucosamine (PNAG), Psl, S88 capsular polysaccharide, salecan, succinoglycan, and xanthan were identified and linked to individual MAGs, providing a comprehensive overview of the genome-resolved potential for these exopolysaccharides in AS bacteria. The approach and results provide a starting point for a more comprehensive understanding of EPS composition in wastewater treatment systems, which may facilitate a more refined regulation of the activated sludge process for improved stability.
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Affiliation(s)
- Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| | - Maaike Besteman
- Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Emil Juel Zeuner
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Marie Riisgaard-Jensen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Eneberg Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Sofie Zacho Vestergaard
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Søren Heidelbach
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Nicolai Sundgaard Bekker
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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10
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Mudryi V, Peske F, Rodnina M. Translation Factor Accelerating Peptide Bond Formation on the Ribosome: EF-P and eIF5A as Entropic Catalysts and a Potential Drug Targets. BBA ADVANCES 2023; 3:100074. [PMID: 37082265 PMCID: PMC10074943 DOI: 10.1016/j.bbadva.2023.100074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
Elongation factor P (EF-P) and its eukaryotic homolog eIF5A are auxiliary translation factors that facilitate peptide bond formation when several sequential proline (Pro) residues are incorporated into the nascent chain. EF-P and eIF5A bind to the exit (E) site of the ribosome and contribute to favorable entropy of the reaction by stabilizing tRNA binding in the peptidyl transferase center of the ribosome. In most organisms, EF-P and eIF5A carry a posttranslational modification that is crucial for catalysis. The chemical nature of the modification varies between different groups of bacteria and between pro- and eukaryotes, making the EF-P-modification enzymes promising targets for antibiotic development. In this review, we summarize our knowledge of the structure and function of EF-P and eIF5A, describe their modification enzymes, and present an approach for potential drug screening aimed at EarP, an enzyme that is essential for EF-P modification in several pathogenic bacteria.
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11
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Tong L, Constancias F, Hou A, Chua SL, Drautz-Moses DI, Schuster SC, Yang L, Williams RBH, Kjelleberg S. Shotgun metagenomic sequencing analysis of ocular surface microbiome in Singapore residents with mild dry eye. Front Med (Lausanne) 2022; 9:1034131. [PMID: 36438051 PMCID: PMC9684611 DOI: 10.3389/fmed.2022.1034131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/24/2022] [Indexed: 07/30/2023] Open
Abstract
The ocular surface microbiome has implications for ocular surface inflammation and immunology. Previous shotgun metagenomics analyses were performed in China, showing results that differed according to environment and age. Patients with Sjogren's syndrome were reported to have altered conjunctival microbiome, but such studies have not been done in milder dry eye. The aim of this study is to describe the conjunctival microbiome in people with mild dry eye in Singapore. Samples were collected from 14 participants with mild dry eye and 10 age-matched comparison participants recruited from Singapore National Eye Centre (SNEC) clinics. Shotgun metagenomic sequencing analysis was employed to evaluate the conjunctival microbiome composition. Proteobacteria formed the predominant phylum in the conjunctiva. As in a study from a coastal city in China, Achromobacter spp. was numerically most abundant. Compared to age-matched controls, the conjunctival microbial composition in mild dry eye was similar. Several microorganisms, including Streptococcus spp. increased in representation with age, and the abundance of Staphylococcus correlated with Schirmer readings. In addition, when cultured corneal epithelial cells were exposed to three strains of Achromobacter xylosoxidans, cytokines such as TNF-α and IL-6 were upregulated in the cell lysates and supernatants. Ourresults suggest that age is an important factor that affects composition of the conjunctival microbiome, and relative abundance of specific microorganism may vary according to the environment of the human host.
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Affiliation(s)
- Louis Tong
- Ocular Surface Research Group, Singapore Eye Research Institute, Singapore, Singapore
- Corneal and External Eye Disease Service, Singapore National Eye Centre, Singapore, Singapore
- Eye-Academic Clinical Programme, Office of Clinical, Academic and Faculty Affairs, Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Florentin Constancias
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Aihua Hou
- Ocular Surface Research Group, Singapore Eye Research Institute, Singapore, Singapore
- Eye-Academic Clinical Programme, Office of Clinical, Academic and Faculty Affairs, Duke-NUS Medical School, Singapore, Singapore
| | - Song Lin Chua
- Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore, Singapore
| | - Daniela I. Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Stephan Christoph Schuster
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Rohan B. H. Williams
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Centre for Marine Science and Innovation, School of Biological Earth and Environmental Sciences, University of New South Wales, Kensington, NSW, Australia
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12
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Cavallaro A, Rhoads WJ, Huwiler SG, Stachler E, Hammes F. Potential probiotic approaches to control Legionella in engineered aquatic ecosystems. FEMS Microbiol Ecol 2022; 98:6604835. [PMID: 35679082 PMCID: PMC9333994 DOI: 10.1093/femsec/fiac071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/20/2022] [Accepted: 06/07/2022] [Indexed: 11/25/2022] Open
Abstract
Opportunistic pathogens belonging to the genus Legionella are among the most reported waterborne-associated pathogens in industrialized countries. Legionella colonize a variety of engineered aquatic ecosystems and persist in biofilms where they interact with a multitude of other resident microorganisms. In this review, we assess how some of these interactions could be used to develop a biological-driven “probiotic” control approach against Legionella. We focus on: (i) mechanisms limiting the ability of Legionella to establish and replicate within some of their natural protozoan hosts; (ii) exploitative and interference competitive interactions between Legionella and other microorganisms; and (iii) the potential of predatory bacteria and phages against Legionella. This field is still emergent, and we therefore specifically highlight research for future investigations, and propose perspectives on the feasibility and public acceptance of a potential probiotic approach.
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Affiliation(s)
- Alessio Cavallaro
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland.,Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - William J Rhoads
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Simona G Huwiler
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Elyse Stachler
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Frederik Hammes
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
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13
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Abstract
The phylum "Candidatus Omnitrophica" (candidate division OP3) is ubiquitous in anaerobic habitats but is currently characterized only by draft genomes from metagenomes and single cells. We had visualized cells of the phylotype OP3 LiM in methanogenic cultures on limonene as small epibiotic cells. In this study, we enriched OP3 cells by double density gradient centrifugation and obtained the first closed genome of an apparently clonal OP3 cell population by applying metagenomics and PCR for gap closure. Filaments of acetoclastic Methanosaeta, the largest morphotype in the culture community, contained empty cells, cells devoid of rRNA or of both rRNA and DNA, and dead cells according to transmission electron microscopy (TEM), thin-section TEM, scanning electron microscopy (SEM), catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH), and LIVE/DEAD imaging. OP3 LiM cells were ultramicrobacteria (200 to 300 nm in diameter) and showed two physiological stages in CARD-FISH fluorescence signals: strong signals of OP3 LiM cells attached to Bacteria and to Archaea indicated many rRNA molecules and an active metabolism, whereas free-living OP3 cells had weak signals. Metaproteomics revealed that OP3 LiM lives with highly expressed secreted proteins involved in depolymerization and uptake of macromolecules and an active glycolysis and energy conservation by the utilization of pyruvate via a pyruvate:ferredoxin oxidoreductase and an Rnf complex (ferredoxin:NAD oxidoreductase). Besides sugar fermentation, a nucleotidyl transferase may contribute to energy conservation by phosphorolysis, the phosphate-dependent depolymerization of nucleic acids. Thin-section TEM showed distinctive structures of predation. Our study demonstrated a predatory metabolism for OP3 LiM cells, and therefore, we propose the name "Candidatus Velamenicoccus archaeovorus" gen. nov., sp. nov., for OP3 LiM. IMPORTANCE Epibiotic bacteria are known to live on and off bacterial cells. Here, we describe the ultramicrobacterial anaerobic epibiont OP3 LiM living on Archaea and Bacteria. We detected sick and dead cells of the filamentous archaeon Methanosaeta in slowly growing methanogenic cultures. OP3 LiM lives as a sugar fermenter, likely on polysaccharides from outer membranes, and has the genomic potential to live as a syntroph. The predatory lifestyle of OP3 LiM was supported by its genome, the first closed genome for the phylum "Candidatus Omnitrophica," and by images of cell-to-cell contact with prey cells. We propose naming OP3 LiM "Candidatus Velamenicoccus archaeovorus." Its metabolic versatility explains the ubiquitous presence of "Candidatus Omnitrophica" 3 in anoxic habitats and gives ultramicrobacterial epibionts an important role in the recycling and remineralization of microbial biomass. The removal of polysaccharides from outer membranes by ultramicrobacteria may also influence biological interactions between pro- and eukaryotes.
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14
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Novick RP. Antibacterial particles and predatory bacteria as alternatives to antibacterial chemicals in the era of antibiotic resistance. Curr Opin Microbiol 2021; 64:109-116. [PMID: 34688038 DOI: 10.1016/j.mib.2021.09.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022]
Abstract
This review is focused on the subset of antibacterial agents whose action involves one-on-one targeting of infecting bacteria. These agents target individual bacteria and their efficacy is based on particle numbers in contrast to chemical agents such as antibiotics, whose efficacy is based on minimal inhibitory concentrations. Four extant members of this class are predatory bacteria, functional (plaque-forming) phages, and engineered particulate systems, phagemids (plasmids that contain a phage packaging signal) and antibacterial drones (ABDs) that package chromosomal island DNA carrying antibacterial genes. We differentiate the natural predators, phages and predatory bacteria, from the engineered delivery vehicles, phagemids and ABDs, because the latter are much more versatile and can largely bypass the historical warfare that informs the predator-prey interactions.
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15
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Ezzedine JA, Desdevises Y, Jacquet S. Bdellovibrio and like organisms: current understanding and knowledge gaps of the smallest cellular hunters of the microbial world. Crit Rev Microbiol 2021; 48:428-449. [PMID: 34595998 DOI: 10.1080/1040841x.2021.1979464] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Almost sixty years ago, Bdellovibrio and like organisms (BALOs) were discovered as the first obligate bacterial predators of other bacteria known to science. Since then, they were shown to be diverse and ubiquitous in the environment, and to bear astonishing ecological, physiological, and metabolic capabilities. The last decade has seen important strides made in understanding the mechanistic basis of their life cycle, the dynamics of their interactions with prey, along with significant developments towards their use in medicine, agriculture, and industry. This review details these achievements, identify current understanding and knowledge gaps to encourage and guide future BALO research.
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Affiliation(s)
- Jade A Ezzedine
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France.,Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, IRIG, Université Grenoble Alpes, Grenoble, France
| | - Yves Desdevises
- CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Stéphan Jacquet
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
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16
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Qian H, Hou C, Liao H, Wang L, Han S, Peng S, Chen W, Huang Q, Luo X. The species evenness of "prey" bacteria correlated with Bdellovibrio-and-like-organisms (BALOs) in the microbial network supports the biomass of BALOs in a paddy soil. FEMS Microbiol Ecol 2021; 96:5911575. [PMID: 32975583 DOI: 10.1093/femsec/fiaa195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/23/2020] [Indexed: 11/14/2022] Open
Abstract
To seek how soil biotic and abiotic factors which might shape the Bdellovibrio-and-like-organisms community, we sampled paddy soils under different fertilization treatments including fertilization without nitrogen (Control), the nitrogen use treatment (N) and the nitrogen overuse one (HNK) at three rice growing stages. The abundances of BALOs were impacted by the rice-growing stages but not the fertilization treatments. The abundances of Bdellovibrionaceae-like were positively associated with soil moisture, which showed a negative relationship with Bacteriovoracaceae-like bacteria. High-throughput sequencing analysis of the whole bacterial community revealed that the α-diversity of BALOs was not correlated with any soil properties data. Network analysis detected eight families directly linked to BALOs, namely, Pseudomonadaceae, Peptostreptococcaceae, Flavobacteriaceae, Sediment-4, Verrucomicrobiaceae, OM27, Solirubrobacteraceae and Roseiflexaceae. The richness and composition of OTUs in the eight families were correlated with different soil properties, while the evenness of them had a positive effect on the predicted BALO biomass. These results highlighted that the bottom-up control of BALOs in paddy soil at least partially relied on the changes of soil water content and the diversity of bacteria directly linked to BALOs in the microbial network.
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Affiliation(s)
- Hang Qian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunli Hou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Liao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Shun Han
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shaobing Peng
- Crop Physiology and Production Center (CPPC), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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17
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Waso M, Reyneke B, Havenga B, Khan S, Khan W. Insights into Bdellovibrio spp. mechanisms of action and potential applications. World J Microbiol Biotechnol 2021; 37:85. [PMID: 33860852 DOI: 10.1007/s11274-021-03054-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/09/2021] [Indexed: 11/28/2022]
Abstract
Recent studies investigating Bdellovibrio spp. have found that although this predator predominantly preys on Gram-negative organisms, under certain conditions (nutrient/prey limitation), it will adapt to survive and grow axenically (without prey) or in the presence of Gram-positive bacterial prey. These advances in the understanding of predatory bacteria have stimulated a renewed interest in these organisms and the potential applications of Bdellovibrio spp. to the benefit of society. Early studies primarily focused on the application of predatory bacteria as "live antibiotics" in the medical field, probiotics in aquaculture and veterinary medicine and their use in agriculture. Additionally, studies have investigated their prevalence in wastewater and environmental sources. However, comprehending that Bdellovibrio spp. may also prey on and target Gram-positive organisms, implies that these predators could specifically be applied for the bioremediation or removal of mixed bacterial communities. Recent studies have also indicated that Bdellovibrio spp. may be useful in controlling food spoilage organisms and subsequently decrease our reliance on food additives. This review will thus highlight recent developments in understanding Bdellovibrio spp. predation strategies and focus on potential new applications of these organisms for water treatment, food preservation, enhancement of industrial processes, and in combination therapies with bacteriophages and/or antibiotics to combat multi-drug resistant organisms.
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Affiliation(s)
- Monique Waso
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Benjamin Havenga
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Sehaam Khan
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa.
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18
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Coutinho FH, von Meijenfeldt FAB, Walter JM, Haro-Moreno JM, Lopéz-Pérez M, van Verk MC, Thompson CC, Cosenza CAN, Appolinario L, Paranhos R, Cabral A, Dutilh BE, Thompson FL. Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142758. [PMID: 33183813 DOI: 10.1016/j.scitotenv.2020.142758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 05/18/2023]
Abstract
The unique combination of depth, salinity, and water masses make the South Atlantic Ocean an ecosystem of special relevance within the global ocean. Yet, the microbiome of this ecosystem has received less attention than other regions of the global Ocean. This has hampered our understanding of the diversity and metabolic potential of the microorganisms that dwell in this habitat. To fill this knowledge gap, we analyzed a collection of 31 metagenomes from the Atlantic Ocean that spanned the epipelagic, mesopelagic and bathypelagic zones (surface to 4000 m). Read-centric and gene-centric analysis revealed the unique taxonomic and functional composition of metagenomes from each depth zone, which was driven by differences in physical and chemical parameters. In parallel, a total of 40 metagenome-assembled genomes were obtained, which recovered one third of the total community. Phylogenomic reconstruction revealed that many of these genomes are derived from poorly characterized taxa of Bacteria and Archaea. Genomes derived from heterotrophic bacteria of the aphotic zone displayed a large apparatus of genes suited for the utilization of recalcitrant organic compounds such as cellulose, chitin and alkanes. In addition, we found genomic evidence suggesting that mixotrophic bacteria from the bathypelagic zone could perform carbon fixation through the Calvin-Benson-Bassham cycle, fueled by sulfur oxidation. Finally, we found that the viral communities shifted throughout the water column regarding their targeted hosts and virus-to-microbe ratio, in response to shifts in the composition and functioning their microbial counterparts. Our findings shed light on the microbial and viral drivers of important biogeochemical processes that take place in the South Atlantic Ocean.
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Affiliation(s)
- F H Coutinho
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre/Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands; Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - F A B von Meijenfeldt
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands
| | - J M Walter
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - J M Haro-Moreno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - M Lopéz-Pérez
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - M C van Verk
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands
| | - C C Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - C A N Cosenza
- COPPE/SAGE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - L Appolinario
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - R Paranhos
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - A Cabral
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - B E Dutilh
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre/Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands
| | - F L Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; COPPE/SAGE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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19
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Thompson AW, Ward AC, Sweeney CP, Sutherland KR. Host-specific symbioses and the microbial prey of a pelagic tunicate (Pyrosoma atlanticum). ISME COMMUNICATIONS 2021; 1:11. [PMID: 36721065 PMCID: PMC9723572 DOI: 10.1038/s43705-021-00007-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/12/2021] [Accepted: 02/24/2021] [Indexed: 02/03/2023]
Abstract
Pyrosomes are widely distributed pelagic tunicates that have the potential to reshape marine food webs when they bloom. However, their grazing preferences and interactions with the background microbial community are poorly understood. This is the first study of the marine microorganisms associated with pyrosomes undertaken to improve the understanding of pyrosome biology, the impact of pyrosome blooms on marine microbial systems, and microbial symbioses with marine animals. The diversity, relative abundance, and taxonomy of pyrosome-associated microorganisms were compared to seawater during a Pyrosoma atlanticum bloom in the Northern California Current System using high-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry. We found that pyrosomes harbor a microbiome distinct from the surrounding seawater, which was dominated by a few novel taxa. In addition to the dominant taxa, numerous more rare pyrosome-specific microbial taxa were recovered. Multiple bioluminescent taxa were present in pyrosomes, which may be a source of the iconic pyrosome luminescence. We also discovered free-living marine microorganisms in association with pyrosomes, suggesting that pyrosome feeding impacts all microbial size classes but preferentially removes larger eukaryotic taxa. This study demonstrates that microbial symbionts and microbial prey are central to pyrosome biology. In addition to pyrosome impacts on higher trophic level marine food webs, the work suggests that pyrosomes also alter marine food webs at the microbial level through feeding and seeding of the marine microbial communities with their symbionts. Future efforts to predict pyrosome blooms, and account for their ecosystem impacts, should consider pyrosome interactions with marine microbial communities.
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Affiliation(s)
- Anne W Thompson
- Department of Biology, Portland State University, Portland, OR, USA.
| | - Anna C Ward
- Oregon Institute of Marine Biology, University of Oregon, Eugene, OR, USA
| | - Carey P Sweeney
- Department of Biology, Portland State University, Portland, OR, USA
| | - Kelly R Sutherland
- Oregon Institute of Marine Biology, University of Oregon, Eugene, OR, USA
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20
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Pérez J, Contreras-Moreno FJ, Marcos-Torres FJ, Moraleda-Muñoz A, Muñoz-Dorado J. The antibiotic crisis: How bacterial predators can help. Comput Struct Biotechnol J 2020; 18:2547-2555. [PMID: 33033577 PMCID: PMC7522538 DOI: 10.1016/j.csbj.2020.09.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/30/2022] Open
Abstract
Discovery of antimicrobials in the past century represented one of the most important advances in public health. Unfortunately, the massive use of these compounds in medicine and other human activities has promoted the selection of pathogens that are resistant to one or several antibiotics. The current antibiotic crisis is creating an urgent need for research into new biological weapons with the ability to kill these superbugs. Although a proper solution requires this problem to be addressed in a variety of ways, the use of bacterial predators is emerging as an excellent strategy, especially when used as whole cell therapeutic agents, as a source of new antimicrobial agents by awakening silent metabolic pathways in axenic cultures, or as biocontrol agents. Moreover, studies on their prey are uncovering mechanisms of resistance that can be shared by pathogens, representing new targets for novel antimicrobial agents. In this review we discuss potential of the studies on predator-prey interaction to provide alternative solutions to the problem of antibiotic resistance.
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Key Words
- AR, antibiotic resistance
- ARB, antibiotic-resistant bacteria
- ARG, antibiotic-resistant gene
- Antibiotic crisis
- BALOs
- BALOs, Bdellovibrio and like organisms
- BGC, biosynthetic gene cluster
- Bacterial predators
- HGT, horizontal gene transfer
- MDRB, multi-drug resistant bacteria
- Myxobacteria
- NRPS, nonribosomal peptide synthetase
- OMV, outer membrane vesicle
- OSMAC, one strain many compounds
- PKS, polyketide synthase
- SM, secondary metabolite
- WHO, World Health Organization
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Affiliation(s)
- Juana Pérez
- Departamento de Microbiología, Facultad de Ciencias, Avda. Fuentenueva s/n, Universidad de Granada, 18071 Granada, Spain
| | | | | | - Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Facultad de Ciencias, Avda. Fuentenueva s/n, Universidad de Granada, 18071 Granada, Spain
| | - José Muñoz-Dorado
- Departamento de Microbiología, Facultad de Ciencias, Avda. Fuentenueva s/n, Universidad de Granada, 18071 Granada, Spain
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21
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Wang S, Mu D, Du ZJ. Persicimonas caeni gen. nov., sp. nov., the Representative of a Novel Wide-Ranging Predatory Taxon in Bradymonadales. Front Microbiol 2020; 11:698. [PMID: 32390976 PMCID: PMC7188933 DOI: 10.3389/fmicb.2020.00698] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/25/2020] [Indexed: 11/29/2022] Open
Abstract
A novel bacterial strain, designated YN101T, was isolated from a marine solar saltern in the coast of Weihai, Shandong Province, China. Strain YN101T was Gram-stain negative, facultatively anaerobic, oxidase and catalase negative bacterium with the ability to prey on other microbes. A cross-streaking culture method was utilized to analyze the predatory activity of strain YN101T. The results showed strain YN101T could prey on various bacteria, either Gram-stain negative or Gram-stain positive. According to the predatory assays, different species in the same genus may behave differently when attacked by strain YN101T. The predatory behavior of strain YN101T to four typical species was analyzed, and furthermore, predation to Algoriphagus marinus am2T were quantitatively studied by fluorogenic quantitative PCR, and the gene copies decreased over two magnitudes. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN101T shared the greatest sequence similarity of 93.9% to Bradymonas sediminis FA350T. The complete genome sequence of strain YN101T was 8,047,306 bp in size and the genomic DNA G + C content was 63.8 mol%. The digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) values between strain YN101T and B. sediminis FA350T were 13.9 and 74.0%. The genetic features showed that the biosynthesis of many important compounds was deficient in genome of strain YN101T, which may lead to its predation. Moreover, its genome encoded many genes affiliated with type IV pili, secretion system, membrane proteins and transduction proteins. Similar with myxobacteria and Bdellovibrio and like organisms (BALOs), these genes should play important roles in motility, adhesion or virulence to attack prey cells during predation. The predominant polar lipid profile of strain YN101T consisted of phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), and one unidentified aminophospholipid (APL). The major cellular fatty acid of strain YN101T was iso-C17:0, and the sole respiratory quinone was MK-7. Based on the chemotaxonomic, physiological and biochemical characteristics, strain YN101T represents a novel species of a novel genus in the family Bradymonadaceae, for which the name Persicimonas caeni gen. nov., sp. nov. is proposed. The type strain is YN101T (=KCTC 72083T = MCCC 1H00374T).
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Affiliation(s)
- Shuo Wang
- Marine College, Shandong University, Weihai, China
| | - Dashuai Mu
- Marine College, Shandong University, Weihai, China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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22
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Thompson AF, English EL, Nock AM, Willsey GG, Eckstrom K, Cairns B, Bavelock M, Tighe SW, Foote A, Shulman H, Pericleous A, Gupta S, Kadouri DE, Wargo MJ. Characterizing species interactions that contribute to biofilm formation in a multispecies model of a potable water bacterial community. MICROBIOLOGY (READING, ENGLAND) 2020; 166:34-43. [PMID: 31585061 PMCID: PMC7137775 DOI: 10.1099/mic.0.000849] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/16/2019] [Indexed: 12/17/2022]
Abstract
Microbial biofilms are ubiquitous in drinking water systems, yet our understanding of drinking water biofilms lags behind our understanding of those in other environments. Here, a six-member model bacterial community was used to identify the interactions and individual contributions of each species to community biofilm formation. These bacteria were isolated from the International Space Station potable water system and include Cupriavidus metallidurans, Chryseobacterium gleum, Ralstonia insidiosa, Ralstonia pickettii, Methylorubrum (Methylobacterium) populi and Sphingomonas paucimobilis, but all six species are common members of terrestrial potable water systems. Using reconstituted assemblages, from pairs to all 6 members, community biofilm formation was observed to be robust to the absence of any single species and only removal of the C. gleum/S. paucimobilis pair, out of all 15 possible 2-species subtractions, led to loss of community biofilm formation. In conjunction with these findings, dual-species biofilm formation assays supported the view that the contribution of C. gleum to community biofilm formation was dependent on synergistic biofilm formation with either R. insidiosa or C. metallidurans. These data support a model of multiple, partially redundant species interactions to generate robustness in biofilm formation. A bacteriophage and multiple predatory bacteria were used to test the resilience of the community to the removal of individual members in situ, but the combination of precise and substantial depletion of a single target species was not achievable. We propose that this assemblage can be used as a tractable model to understand the molecular bases of the interactions described here and to decipher other functions of drinking water biofilms.
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Affiliation(s)
- Alex F. Thompson
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont Gradaute College, Burlington, VT 05405, USA
| | - Erika L. English
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicin, Burlington, VT 05405, USA
| | - Adam M. Nock
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicin, Burlington, VT 05405, USA
- Present address: Host Parasite Interactions Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Graham G. Willsey
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicin, Burlington, VT 05405, USA
- The Vermont Lung Center, University of Vermont Larner College of Medicine, Burlington, VT 05405, USA
| | - Korin Eckstrom
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicin, Burlington, VT 05405, USA
| | - Brynn Cairns
- Department of Natural Sciences, Northern Vermont University, Johnson, VT 05656, USA
| | | | - Scott W. Tighe
- The Vermont Integrated Genomics Resource, University of Vermont Larner College of Medicine, Burlington, VT 05405, USA
| | - Andrea Foote
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont Gradaute College, Burlington, VT 05405, USA
| | - Hannah Shulman
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicin, Burlington, VT 05405, USA
| | | | - Shilpi Gupta
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ 07103
| | - Daniel E. Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ 07103
| | - Matthew J. Wargo
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicin, Burlington, VT 05405, USA
- The Vermont Lung Center, University of Vermont Larner College of Medicine, Burlington, VT 05405, USA
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Ye XS, Chen MX, Li HY, He XY, Zhao Y. Halobacteriovorax vibrionivorans sp. nov., a novel prokaryotic predator isolated from coastal seawater of China. Int J Syst Evol Microbiol 2019; 69:3917-3923. [PMID: 31498060 DOI: 10.1099/ijsem.0.003703] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three prokaryotic predator strains, BL9T, BL10 and BL28, were isolated with Vibrio alginolyticus from coastal seawater of PR China. Cells of the strains were Gram-negative, vibrioid-shaped and motile with a single sheathed flagellum (25-28 nm wide). Cells were around 0.3×0.5-1.0 µm in size. The three strains were obligate predators that exhibited a biphasic life cycle: a free-swimming attack phase and an intraperiplasmic growth phase within the prey. Bdelloplasts were formed. NaCl was required for growth. Optimum growth occurred at ~37 °C, with 2-4 % (w/v) NaCl and at pH 7.0-8.0. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the three strains shared 99.9 % similarity to each other, were affiliated with the genus Halobacteriovorax in the class Oligoflexia, and represented the same new species. Strain BL9T (=MCCC 1K03527T=JCM 32962T) was designated as the type strain. Genome sequencing of strain BL9T revealed a genome size of 3.14 Mb and a G+C content of 35.8 mol%. The estimated digital DNA-DNA hybridization (dDDH) values and the whole genome average nucleotide identity (gANI) values between the genome of strain BL9T and those of Bdellovibrionales and Bacteriovoracales were 12.5-19 and 63.49-76.15 %, respectively. On the basis of life cycle features, results of physiological analyses, gANI data and dDDH data, strain BL9T represents a new species within the genus Halobacteriovorax, for which the name Halobacteriovoraxvibrionivorans sp. nov. is proposed.
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Affiliation(s)
- Xiao-Sheng Ye
- College of Chemical Engineering, Huaqiao University, 668 Jimei Road, Fujian Xiamen 361021, PR China
| | - Ming-Xia Chen
- College of Chemical Engineering, Huaqiao University, 668 Jimei Road, Fujian Xiamen 361021, PR China
- Key Laboratory of Chemical Biology and Molecular Engineering (Huaqiao University), Fujian Province University, 668 Jimei Road, Fujian Xiamen 361021, PR China
| | - He-Yang Li
- Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Fujian Xiamen 361005, PR China
| | - Xiao-Yu He
- College of Chemical Engineering, Huaqiao University, 668 Jimei Road, Fujian Xiamen 361021, PR China
| | - Yan Zhao
- College of Chemical Engineering, Huaqiao University, 668 Jimei Road, Fujian Xiamen 361021, PR China
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Allan ERO, Tennessen JA, Sharpton TJ, Blouin MS. Allelic Variation in a Single Genomic Region Alters the Microbiome of the Snail Biomphalaria glabrata. J Hered 2019; 109:604-609. [PMID: 29566237 DOI: 10.1093/jhered/esy014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/15/2018] [Indexed: 12/17/2022] Open
Abstract
Freshwater snails are the intermediate hosts for numerous parasitic worms which can have negative consequences for human health and agriculture. Understanding the transmission of these diseases requires a more complete characterization of the immunobiology of snail hosts. This includes the characterization of its microbiome and genetic factors which may interact with this important commensal community. Allelic variation in the Guadeloupe resistance complex (GRC) genomic region of Guadeloupean Biomphalaria glabrata influences their susceptibility to schistosome infection and may have other roles in the snail immune response. In the present study, we examined whether a snail's GRC genotype has a role in shaping the bacterial diversity and composition present on or in whole snails. We show that the GRC haplotype, including the resistant genotype, has a significant effect on the diversity of bacterial species present in or on whole snails, including the relative abundances of Gemmatimonas aurantiaca and Micavibrio aeruginosavorus. These findings support the hypothesis that the GRC region is likely involved in pathways that can modify the microbial community of these snails and may have more immune roles in B. glabrata than originally believed. This is also one of few examples in which allelic variation at a particular locus has been shown to affect the microbiome in any species.
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Affiliation(s)
- Euan R O Allan
- Department of Integrative Biology, College of Science, Oregon State University, Corvallis, OR
| | - Jacob A Tennessen
- Department of Integrative Biology, College of Science, Oregon State University, Corvallis, OR
| | - Thomas J Sharpton
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR.,Department of Statistics, College of Science, Oregon State University, Corvallis, OR
| | - Michael S Blouin
- Department of Integrative Biology, College of Science, Oregon State University, Corvallis, OR
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25
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Whitworth DE. Interspecies conflict affects RNA expression. FEMS Microbiol Lett 2019; 365:4966981. [PMID: 29648585 DOI: 10.1093/femsle/fny096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/09/2018] [Indexed: 12/13/2022] Open
Abstract
Predation is an extreme form of competition between bacteria, involving the secretion of antimicrobial substances by predators, often packaged within outer membrane vesicles (OMVs). Recent studies into the Myxococcus xanthus/Escherichia coli predator/prey relationship have illuminated transcriptional changes during predation, identifying likely targets of predatory attack in the prey and nutrient assimilation strategies of the predator. Abundant non-coding RNAs can be observed in the predator and prey transcriptomes, with evidence of predation-dependent regulation of RNA levels. Given the observed secretion of regulatory RNAs within OMVs by bacteria, it will next be exciting to test whether the intercellular trafficking of regulatory RNAs is employed by predator and/or prey in their survival struggles.
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Affiliation(s)
- David E Whitworth
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK
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26
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Garcia CJ, Pericleous A, Elsayed M, Tran M, Gupta S, Callaghan JD, Stella NA, Franks JM, Thibodeau PH, Shanks RMQ, Kadouri DE. Serralysin family metalloproteases protects Serratia marcescens from predation by the predatory bacteria Micavibrio aeruginosavorus. Sci Rep 2018; 8:14025. [PMID: 30232396 PMCID: PMC6145908 DOI: 10.1038/s41598-018-32330-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 09/03/2018] [Indexed: 12/16/2022] Open
Abstract
Micavibrio aeruginosavorus is an obligate Gram-negative predatory bacterial species that feeds on other Gram-negative bacteria by attaching to the surface of its prey and feeding on the prey's cellular contents. In this study, Serratia marcescens with defined mutations in genes for extracellular cell structural components and secreted factors were used in predation experiments to identify structures that influence predation. No change was measured in the ability of the predator to prey on S. marcescens flagella, fimbria, surface layer, prodigiosin and phospholipase-A mutants. However, higher predation was measured on S. marcescens metalloprotease mutants. Complementation of the metalloprotease gene, prtS, into the protease mutant, as well as exogenous addition of purified serralysin metalloprotease, restored predation to wild type levels. Addition of purified serralysin also reduced the ability of M. aeruginosavorus to prey on Escherichia coli. Incubating M. aeruginosavorus with purified metalloprotease was found to not impact predator viability; however, pre-incubating prey, but not the predator, with purified metalloprotease was able to block predation. Finally, using flow cytometry and fluorescent microscopy, we were able to confirm that the ability of the predator to bind to the metalloprotease mutant was higher than that of the metalloprotease producing wild-type. The work presented in this study shows that metalloproteases from S. marcescens could offer elevated protection from predation.
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Affiliation(s)
- Carlos J Garcia
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Androulla Pericleous
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Mennat Elsayed
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Michael Tran
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Shilpi Gupta
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Jake D Callaghan
- Department of Ophthalmology, Charles T. Campbell Laboratory of Ophthalmic Microbiology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Nicholas A Stella
- Department of Ophthalmology, Charles T. Campbell Laboratory of Ophthalmic Microbiology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Jonathan M Franks
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Patrick H Thibodeau
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15221, USA
| | - Robert M Q Shanks
- Department of Ophthalmology, Charles T. Campbell Laboratory of Ophthalmic Microbiology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA.
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27
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Gupta S, Lemenze A, Donnelly RJ, Connell ND, Kadouri DE. Keeping it together: absence of genetic variation and DNA incorporation by the predatory bacteria Micavibrio aeruginosavorus and Bdellovibrio bacteriovorus during predation. Res Microbiol 2018; 169:237-243. [PMID: 29751066 DOI: 10.1016/j.resmic.2018.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/13/2018] [Accepted: 03/26/2018] [Indexed: 12/20/2022]
Abstract
The use of predatory bacteria as a potential live therapeutic to control human infection is gaining increased attention. Earlier work with Micavibrio spp. and Bdellovibrio spp. has demonstrated the ability of these predators to control drug-resistant Gram-negative pathogens, Tier-1 select agents and biofilms. Additional studies also confirmed that introducing high doses of the predators into animals does not negatively impact animal well-being and might assist in reducing bacterial burden in vivo. The survival of predators requires extreme proximity to the prey cell, which might bring about horizontal transfer of genetic material, such as genes encoding for pathogenic genetic islands that would indirectly facilitate the spread of genetic material to other organisms. In this study, we examined the genetic makeup of several lab isolates of the predators Bdellovibriobacteriovorus and Micavibrioaeruginosavorus that were cultured repeatedly and stored over a course of 13 years. We also conducted controlled experiments in which the predators were sequentially co-cultured on Klebsiella pneumoniae followed by genetic analysis of the predator. In both cases, we saw little genetic variation and no evidence of horizontally transferred chromosomal DNA from the prey during predator-prey interaction. Culturing the predators repeatedly did not cause any change in predation efficacy.
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Affiliation(s)
- Shilpi Gupta
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ 07101, USA
| | - Alexander Lemenze
- Department of Medicine and the Center for Emerging Pathogens, Rutgers, New Jersey Medical School, Newark, NJ 07101, USA; Molecular Resource Facility, Rutgers, New Jersey Medical School, Newark, NJ 07101, USA
| | - Robert J Donnelly
- Molecular Resource Facility, Rutgers, New Jersey Medical School, Newark, NJ 07101, USA
| | - Nancy D Connell
- Department of Medicine and the Center for Emerging Pathogens, Rutgers, New Jersey Medical School, Newark, NJ 07101, USA
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ 07101, USA.
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28
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Livingstone PG, Millard AD, Swain MT, Whitworth DE. Transcriptional changes when Myxococcus xanthus preys on Escherichia coli suggest myxobacterial predators are constitutively toxic but regulate their feeding. Microb Genom 2018; 4:e000152. [PMID: 29345219 PMCID: PMC5857379 DOI: 10.1099/mgen.0.000152] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 12/21/2017] [Indexed: 01/01/2023] Open
Abstract
Predation is a fundamental ecological process, but within most microbial ecosystems the molecular mechanisms of predation remain poorly understood. We investigated transcriptome changes associated with the predation of Escherichia coli by the myxobacterium Myxococcus xanthus using mRNA sequencing. Exposure to pre-killed prey significantly altered expression of 1319 predator genes. However, the transcriptional response to living prey was minimal, with only 12 genes being significantly up-regulated. The genes most induced by prey presence (kdpA and kdpB, members of the kdp regulon) were confirmed by reverse transcriptase quantitative PCR to be regulated by osmotic shock in M. xanthus, suggesting indirect sensing of prey. However, the prey showed extensive transcriptome changes when co-cultured with predator, with 40 % of its genes (1534) showing significant changes in expression. Bacteriolytic M. xanthus culture supernatant and secreted outer membrane vesicles (OMVs) also induced changes in expression of large numbers of prey genes (598 and 461, respectively). Five metabolic pathways were significantly enriched in prey genes up-regulated on exposure to OMVs, supernatant and/or predatory cells, including those for ribosome and lipopolysaccharide production, suggesting that the prey cell wall and protein production are primary targets of the predator's attack. Our data suggest a model of the myxobacterial predatome (genes and proteins associated with predation) in which the predator constitutively produces secretions which disable its prey whilst simultaneously generating a signal that prey is present. That signal then triggers a regulated feeding response in the predator.
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Affiliation(s)
- Paul G. Livingstone
- IBERS, Aberystwyth University, Cledwyn Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3DD, UK
| | | | - Martin T. Swain
- IBERS, Aberystwyth University, Cledwyn Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3DD, UK
| | - David E. Whitworth
- IBERS, Aberystwyth University, Cledwyn Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3DD, UK
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29
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Feichtmayer J, Deng L, Griebler C. Antagonistic Microbial Interactions: Contributions and Potential Applications for Controlling Pathogens in the Aquatic Systems. Front Microbiol 2017; 8:2192. [PMID: 29184541 PMCID: PMC5694486 DOI: 10.3389/fmicb.2017.02192] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/25/2017] [Indexed: 12/21/2022] Open
Abstract
Despite the active and intense treatment of wastewater, pathogenic microorganisms and viruses are frequently introduced into the aquatic environment. For most human pathogens, however, this is a rather hostile place, where starvation, continuous inactivation, and decay generally occur, rather than successful reproduction. Nevertheless, a great diversity of the pathogenic microorganisms can be detected, in particular, in the surface waters receiving wastewater. Pathogen survival depends majorly on abiotic factors such as irradiation, changes in water ionic strength, temperature, and redox state. In addition, inactivation is enhanced by the biotic interactions in the environment. Although knowledge of the antagonistic biotic interactions has been available since a long time, certain underlying processes and mechanisms still remain unclear. Others are well-appreciated and increasingly are applied to the present research. Our review compiles and discusses the presently known biotic interactions between autochthonous microbes and pathogens introduced into the aquatic environment, including protozoan grazing, virus-induced bacterial cell lysis, antimicrobial substances, and predatory bacteria. An overview is provided on the present knowledge, as well as on the obvious research gaps. Individual processes that appear promising for future applications in the aquatic environment are presented and discussed.
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Affiliation(s)
- Judith Feichtmayer
- Institute of Groundwater Ecology, Helmholtz Zentrum München GmbH, Neuherberg, Germany
| | - Li Deng
- Institute of Groundwater Ecology, Helmholtz Zentrum München GmbH, Neuherberg, Germany
- Institute of Virology, Helmholtz Zentrum München GmbH, Neuherberg, Germany
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Zentrum München GmbH, Neuherberg, Germany
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30
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Shatzkes K, Singleton E, Tang C, Zuena M, Shukla S, Gupta S, Dharani S, Rinaggio J, Kadouri DE, Connell ND. Examining the efficacy of intravenous administration of predatory bacteria in rats. Sci Rep 2017; 7:1864. [PMID: 28500337 PMCID: PMC5431856 DOI: 10.1038/s41598-017-02041-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/06/2017] [Indexed: 12/20/2022] Open
Abstract
The proteobacteria Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus are obligate predators of Gram-negative bacteria, and have been proposed to be used to treat multidrug-resistant bacterial infections. The ability of predatory bacteria to reduce bacterial burden in vivo within the lungs of rats has been demonstrated, but it was unknown if predatory bacteria can attenuate systemic bacterial burden administered intravenously. In this study, we first assessed the safety of intravenous inoculation of predatory bacteria in rats. No rat morbidity or adverse histopathology of various organs due to predatory bacteria administration was observed. An increase in proinflammatory cytokines (TNFα and KC/GRO) was observed at two hours post-inoculation; however, cytokines returned to baseline levels by 18 hours. Furthermore, bacterial dissemination analysis demonstrated that predatory bacteria were efficiently cleared from the host by 20 days post-injection. To determine whether predatory bacteria could reduce bacterial burden in vivo, Klebsiella pneumoniae was injected into the tail veins of rats and followed with multiple doses of predatory bacteria over 16 or 24 hours. Predatory bacteria were unable to significantly reduce K. pneumoniae burden in the blood or prevent dissemination to other organs. The results suggest that predatory bacteria may not be effective for treatment of acute blood infections.
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Affiliation(s)
- Kenneth Shatzkes
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Eric Singleton
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Chi Tang
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Michael Zuena
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Sean Shukla
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Shilpi Gupta
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Sonal Dharani
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Joseph Rinaggio
- Department of Diagnostic Sciences, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Nancy D Connell
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
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31
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Identification and Characterization of Differentially-Regulated Type IVb Pilin Genes Necessary for Predation in Obligate Bacterial Predators. Sci Rep 2017; 7:1013. [PMID: 28432347 PMCID: PMC5430801 DOI: 10.1038/s41598-017-00951-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/17/2017] [Indexed: 11/08/2022] Open
Abstract
Bdellovibrio bacteriovorus is an obligate predator of bacteria that grows and divides within the periplasm of its prey. Functions involved in the early steps of predation have been identified and characterized, but mediators of prey invasion are still poorly detailed. By combining omics data available for Bdellovibrio and like organisms (BALO’s), we identified 43 genes expressed in B. bacteriovorus during the early interaction with prey. These included genes in a tight adherence (TAD) operon encoding for two type IVb fimbriae-like pilin proteins (flp1 and flp2), and their processing and export machinery. Two additional flp genes (flp3 and flp4) were computationally identified at other locations along the chromosome, defining the largest and most diverse type IVb complement known in bacteria to date. Only flp1, flp2 and flp4 were expressed; their respective gene knock-outs resulted in a complete loss of the predatory ability without losing the ability to adhere to prey cells. Additionally, we further demonstrate differential regulation of the flp genes as the TAD operon of BALOs with different predatory strategies is controlled by a flagellar sigma factor FliA, while flp4 is not. Finally, we show that FliA, a known flagellar transcriptional regulator in other bacteria, is an essential Bdellovibrio gene.
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32
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Effect of predatory bacteria on the gut bacterial microbiota in rats. Sci Rep 2017; 7:43483. [PMID: 28262674 PMCID: PMC5337950 DOI: 10.1038/srep43483] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/24/2017] [Indexed: 01/14/2023] Open
Abstract
Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus are Gram-negative proteobacteria that are obligate predators of other Gram-negative bacteria and are considered potential alternatives to antibiotics. Most studies focusing on predatory bacteria have been performed in vitro, thus the effect of predatory bacteria on a live host, including the impact on the ecology of the native microbiota, has yet to be fully examined. In this study, intrarectal inoculations of Sprague-Dawley rats with predatory bacteria were performed. Additionally, feces were collected for seven days post-inoculation to determine the effect on gut bacterial diversity. Rat colonic tissue exhibited no abnormal histopathological effects due to predatory bacteria. A modest increase in pro-inflammatory cytokines was measured in the colons of rats inoculated with predatory bacteria by 24 and 48 hours, with all but IL-13 returning to baseline by seven days. V4 16S rRNA gene sequencing of fecal DNA demonstrated minimal shifts in taxonomic representation over the week due to predatory bacteria. Changes in bacterial populations due to exposure to B. bacteriovorus are predicted to contribute to health, however, an overgrowth of Prevotella was observed due to exposure to M. aeruginosavorus. This study further addresses safety concerns associated with the potential use of predatory bacteria to treat infections.
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33
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Wang J, Haapalainen M, Schott T, Thompson SM, Smith GR, Nissinen AI, Pirhonen M. Genomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its comparison with haplotype A and B genomes. PLoS One 2017; 12:e0171531. [PMID: 28158295 PMCID: PMC5291501 DOI: 10.1371/journal.pone.0171531] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/23/2017] [Indexed: 01/28/2023] Open
Abstract
Haplotypes A and B of 'Candidatus Liberibacter solanacearum' (CLso) are associated with diseases of solanaceous plants, especially Zebra chip disease of potato, and haplotypes C, D and E are associated with symptoms on apiaceous plants. To date, one complete genome of haplotype B and two high quality draft genomes of haplotype A have been obtained for these unculturable bacteria using metagenomics from the psyllid vector Bactericera cockerelli. Here, we present the first genomic sequences obtained for the carrot-associated CLso. These two genomic sequences of haplotype C, FIN114 (1.24 Mbp) and FIN111 (1.20 Mbp), were obtained from carrot psyllids (Trioza apicalis) harboring CLso. Genomic comparisons between the haplotypes A, B and C revealed that the genome organization differs between these haplotypes, due to large inversions and other recombinations. Comparison of protein-coding genes indicated that the core genome of CLso consists of 885 ortholog groups, with the pan-genome consisting of 1327 ortholog groups. Twenty-seven ortholog groups are unique to CLso haplotype C, whilst 11 ortholog groups shared by the haplotypes A and B, are not found in the haplotype C. Some of these ortholog groups that are not part of the core genome may encode functions related to interactions with the different host plant and psyllid species.
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Affiliation(s)
- Jinhui Wang
- Department of Agricultural Sciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Minna Haapalainen
- Department of Agricultural Sciences, FI-00014 University of Helsinki, Helsinki, Finland
| | | | - Sarah M. Thompson
- The New Zealand Institute for Plant & Food Research Limited, Lincoln, New Zealand
- Plant Biosecurity Cooperative Research Centre, Canberra, ACT, Australia
| | - Grant R. Smith
- The New Zealand Institute for Plant & Food Research Limited, Lincoln, New Zealand
- Plant Biosecurity Cooperative Research Centre, Canberra, ACT, Australia
- Better Border Biosecurity, Lincoln, New Zealand
| | - Anne I. Nissinen
- Management and Production of Renewable Resources, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Minna Pirhonen
- Department of Agricultural Sciences, FI-00014 University of Helsinki, Helsinki, Finland
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34
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Shatzkes K, Singleton E, Tang C, Zuena M, Shukla S, Gupta S, Dharani S, Onyile O, Rinaggio J, Connell ND, Kadouri DE. Predatory Bacteria Attenuate Klebsiella pneumoniae Burden in Rat Lungs. mBio 2016; 7:e01847-16. [PMID: 27834203 PMCID: PMC5101354 DOI: 10.1128/mbio.01847-16] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 10/11/2016] [Indexed: 12/26/2022] Open
Abstract
Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus are predatory bacteria that naturally-and obligately-prey on other Gram-negative bacteria, and their use has been proposed as a potential new approach to control microbial infection. The ability of predatory bacteria to prey on Gram-negative human pathogens in vitro is well documented; however, the in vivo safety and efficacy of predatory bacteria have yet to be fully assessed. In this study, we examined whether predatory bacteria can reduce bacterial burden in the lungs in an in vivo mammalian system. Initial safety studies were performed by intranasal inoculation of rats with predatory bacteria. No adverse effects or lung pathology were observed in rats exposed to high concentrations of predatory bacteria at up to 10 days postinoculation. Enzyme-linked immunosorbent assay (ELISA) of the immune response revealed a slight increase in inflammatory cytokine levels at 1 h postinoculation that was not sustained by 48 h. Additionally, dissemination experiments showed that predators were efficiently cleared from the host by 10 days postinoculation. To measure the ability of predatory bacteria to reduce microbial burden in vivo, we introduced sublethal concentrations of Klebsiella pneumoniae into the lungs of rats via intranasal inoculation and followed with multiple doses of predatory bacteria over 24 h. Predatory bacteria were able to reduce K. pneumoniae bacterial burden, on average, by more than 3.0 log10 in the lungs of most rats as measured by CFU plating. The work presented here provides further support for the idea of developing predatory bacteria as a novel biocontrol agent. IMPORTANCE A widely held notion is that antibiotics are the greatest medical advance of the last 50 years. However, the rise of multidrug-resistant (MDR) bacterial infections has become a global health crisis over the last decade. As we enter the postantibiotic era, it is crucial that we begin to develop new strategies to combat bacterial infection. Here, we report one such new approach: the use of predatory bacteria (Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus) that naturally-and obligately-prey on other Gram-negative bacteria. To our knowledge, this is the first study that demonstrated the ability of predatory bacteria to attenuate the bacterial burden of a key human pathogen in an in vivo mammalian system. As the prevalence of MDR infections continues to rise each year, our results may represent a shift in how we approach treating microbial infections in the future.
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Affiliation(s)
- Kenneth Shatzkes
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Eric Singleton
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Chi Tang
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Michael Zuena
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Sean Shukla
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Shilpi Gupta
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, New Jersey, USA
| | - Sonal Dharani
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, New Jersey, USA
| | - Onoyom Onyile
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Joseph Rinaggio
- Department of Diagnostic Sciences, Rutgers School of Dental Medicine, Newark, New Jersey, USA
| | - Nancy D Connell
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, New Jersey, USA
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Gupta S, Tang C, Tran M, Kadouri DE. Effect of Predatory Bacteria on Human Cell Lines. PLoS One 2016; 11:e0161242. [PMID: 27579919 PMCID: PMC5006992 DOI: 10.1371/journal.pone.0161242] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/02/2016] [Indexed: 01/18/2023] Open
Abstract
Predatory bacteria are Gram-negative bacteria that prey on other Gram-negative bacteria and have been considered as potential therapeutic agents against multi-drug resistant pathogens. In vivo animal models have demonstrated that predatory bacteria are non-toxic and non-immunogenic in rodents. In order to consider the use of predatory bacteria as live antibiotics, it is important to investigate their effect on human cells. The aim of this study was to determine the effect of Bdellovibrio bacteriovorus strains 109J and HD100, and Micavibrio aeruginosavorus strain ARL-13 on cell viability and inflammatory responses of five human cell lines, representative of clinically relevant tissues. We found that the predators were not cytotoxic to any of the human cell lines tested. Microscopic imaging showed no signs of cell detachment, as compared to predator-free cells. In comparison to an E. coli control, exposure to higher concentrations of the predators did not trigger a significant elevation of pro-inflammatory cytokines in four of the five human cell lines tested. Our work underlines the non-pathogenic attributes of predatory bacteria on human cells and highlights their potential use as live antibiotics against human pathogens.
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Affiliation(s)
- Shilpi Gupta
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, United States of America
| | - Chi Tang
- Department of Medicine and the Center for Emerging Pathogens, Rutgers, New Jersey Medical School, Newark, NJ, United States of America
| | - Michael Tran
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, United States of America
| | - Daniel E. Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, United States of America
- * E-mail:
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Pérez J, Moraleda-Muñoz A, Marcos-Torres FJ, Muñoz-Dorado J. Bacterial predation: 75 years and counting! Environ Microbiol 2016; 18:766-79. [PMID: 26663201 DOI: 10.1111/1462-2920.13171] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/23/2015] [Accepted: 12/01/2015] [Indexed: 11/30/2022]
Abstract
The first documented study on bacterial predation was carried out using myxobacteria three quarters of a century ago. Since then, many predatory strains, diverse hunting strategies, environmental consequences and potential applications have been reported by groups all over the world. Now we know that predatory bacteria are distributed in a wide variety of environments and that interactions between predatory and non-predatory populations seem to be the most important factor in bacterial selection and mortality in some ecosystems. Bacterial predation has now been proposed as an evolutionary driving force. The structure and diversity of the predatory bacterial community is beginning to be recognized as an important factor in biodiversity due to its potential role in controlling and modelling bacterial populations in the environment. In this paper, we review the current understanding of bacterial predation, going over the strategies used by the main predatory bacteria to kill their prey. We have also reviewed and integrated the accumulated advances of the last 75 years with the interesting new insights that are provided by the analyses of genomes, predatomes, predatosomes and other comparative genomics studies, focusing on potential applications that derive from all of these areas of study.
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Affiliation(s)
- Juana Pérez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, E-18071, Granada, Spain
| | - Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, E-18071, Granada, Spain
| | - Francisco Javier Marcos-Torres
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, E-18071, Granada, Spain
| | - José Muñoz-Dorado
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, E-18071, Granada, Spain
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Russo R, Chae R, Mukherjee S, Singleton EJ, Occi JL, Kadouri DE, Connell ND. Susceptibility of Select Agents to Predation by Predatory Bacteria. Microorganisms 2015; 3:903-12. [PMID: 27682124 PMCID: PMC5023276 DOI: 10.3390/microorganisms3040903] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/08/2015] [Accepted: 11/13/2015] [Indexed: 01/07/2023] Open
Abstract
Select Agents are microorganisms and toxins considered to be exploitable as biological weapons. Although infections by many Select Agents can be treated by conventional antibiotics, the risk of an emerging or engineered drug resistant strain is of great concern. One group of microorganisms that is showing potential to control drug resistant Gram-negative bacteria are the predatory bacteria from the genera Bdellovibrio spp. and Micavibrio spp. In this study, we have examined the ability of Bdellovibrio bacteriovorus (B. bacteriovorus) strain 109J, HD100 and Micavibrio aeruginosavorus (M. aeruginosavorus) ARL-13 to prey on a variety of Select Agents. Our findings demonstrate that B. bacteriovorus and M. aeruginosavorus are able to prey efficiently on Yersinia pestis and Burkholderia mallei. Modest predation was also measured in co-cultures of B. bacteriovorus and Francisella tularensis. However, neither of the predators showed predation when Burkholderia pseudomallei and Brucella melitensis were used as prey.
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Affiliation(s)
- Riccardo Russo
- Department of Medicine and the Center for Emerging Pathogens, Rutgers, New Jersey Medical School, Newark, NJ 07101, USA.
| | - Richard Chae
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ 07101, USA.
| | - Somdatta Mukherjee
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ 07101, USA.
| | - Eric J Singleton
- Department of Medicine and the Center for Emerging Pathogens, Rutgers, New Jersey Medical School, Newark, NJ 07101, USA.
| | - James L Occi
- Department of Medicine and the Center for Emerging Pathogens, Rutgers, New Jersey Medical School, Newark, NJ 07101, USA.
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ 07101, USA.
| | - Nancy D Connell
- Department of Medicine and the Center for Emerging Pathogens, Rutgers, New Jersey Medical School, Newark, NJ 07101, USA.
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Rajkovic A, Witzky A, Navarre W, Darwin AJ, Ibba M. Elongation factor-P at the crossroads of the host-endosymbiont interface. MICROBIAL CELL 2015; 2:360-362. [PMID: 28357263 PMCID: PMC5354580 DOI: 10.15698/mic2015.10.232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Elongation factor P (EF-P) is an ancient bacterial translational factor that aids the ribosome in polymerizing oligo-prolines. EF-P structurally resembles tRNA and binds in-between the exit and peptidyl sites of the ribosome to accelerate the intrinsically slow reaction of peptidyl-prolyl bond formation. Recent studies have identified in separate organisms, two evolutionarily convergent EF-P post-translational modification systems (EPMS), split predominantly between gammaproteobacteria, and betaproteobacteria. In both cases EF-P receives a post-translational modification, critical for its function, on a highly conserved residue that protrudes into the peptidyl-transfer center of the ribosome. EPMSs are comprised of a gene(s) that synthesizes the precursor molecule used in modifying EF-P, and a gene(s) encoding an enzyme that reacts with the precursor molecule to catalyze covalent attachment to EF-P. However, not all organisms genetically encode a complete EPMS. For instance, some symbiotic bacteria harbor efp and the corresponding gene that enzymatically attaches the modification, but lack the ability to synthesize the substrate used in the modification reaction. Here we highlight the recent discoveries made regarding EPMSs, with a focus on how these incomplete modification pathways shape or have been shaped by the endosymbiont-host relationship.
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Affiliation(s)
- Andrei Rajkovic
- Molecular, Cellular and Developmental Biology Program, Ohio State University, Columbus, Ohio, USA
| | - Anne Witzky
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio, USA
| | - William Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Andrew J Darwin
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Michael Ibba
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, Ohio, USA
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Examining the safety of respiratory and intravenous inoculation of Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus in a mouse model. Sci Rep 2015; 5:12899. [PMID: 26250699 PMCID: PMC4528228 DOI: 10.1038/srep12899] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/30/2015] [Indexed: 02/08/2023] Open
Abstract
Bdellovibrio spp. and Micavibrio spp. are Gram-negative predators that feed on other Gram-negative bacteria, making predatory bacteria potential alternatives to antibiotics for treating multi-drug resistant infections. While the ability of predatory bacteria to control bacterial infections in vitro is well documented, the in vivo effect of predators on a living host has yet to be extensively examined. In this study, respiratory and intravenous inoculations were used to determine the effects of predatory bacteria in mice. We found no reduction in mouse viability after intranasal or intravenous inoculation of B. bacteriovorus 109J, HD100 or M. aeruginosavorus. Introducing predators into the respiratory tract of mice provoked a modest inflammatory response at 1 hour post-exposure, but was not sustained at 24 hours, as measured by RT-qPCR and ELISA. Intravenous injection caused an increase of IL-6 in the kidney and spleen, TNF in the liver and CXCL-1/KC in the blood at 3 hours post-exposure, returning to baseline levels by 18 hours. Histological analysis of tissues showed no pathological changes due to predatory bacteria. Furthermore, qPCR detected predators were cleared from the host quickly and efficiently. This work addresses some of the safety concerns regarding the potential use of predatory bacteria as a live antibiotic.
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Abstract
Elongation factor P (EF-P) is a ubiquitous bacterial protein that is required for the synthesis of poly-proline motifs during translation. In Escherichia coli and Salmonella enterica, the posttranslational β-lysylation of Lys34 by the PoxA protein is critical for EF-P activity. PoxA is absent from many bacterial species such as Pseudomonas aeruginosa, prompting a search for alternative EF-P posttranslation modification pathways. Structural analyses of P. aeruginosa EF-P revealed the attachment of a single cyclic rhamnose moiety to an Arg residue at a position equivalent to that at which β-Lys is attached to E. coli EF-P. Analysis of the genomes of organisms that both lack poxA and encode an Arg32-containing EF-P revealed a highly conserved glycosyltransferase (EarP) encoded at a position adjacent to efp. EF-P proteins isolated from P. aeruginosa ΔearP, or from a ΔrmlC::acc1 strain deficient in dTDP-l-rhamnose biosynthesis, were unmodified. In vitro assays confirmed the ability of EarP to use dTDP-l-rhamnose as a substrate for the posttranslational glycosylation of EF-P. The role of rhamnosylated EF-P in translational control was investigated in P. aeruginosa using a Pro4-green fluorescent protein (Pro4GFP) in vivo reporter assay, and the fluorescence was significantly reduced in Δefp, ΔearP, and ΔrmlC::acc1 strains. ΔrmlC::acc1, ΔearP, and Δefp strains also displayed significant increases in their sensitivities to a range of antibiotics, including ertapenem, polymyxin B, cefotaxim, and piperacillin. Taken together, our findings indicate that posttranslational rhamnosylation of EF-P plays a key role in P. aeruginosa gene expression and survival. Infections with pathogenic Salmonella, E. coli, and Pseudomonas isolates can all lead to infectious disease with potentially fatal sequelae. EF-P proteins contribute to the pathogenicity of the causative agents of these and other diseases by controlling the translation of proteins critical for modulating antibiotic resistance, motility, and other traits that play key roles in establishing virulence. In Salmonella spp. and E. coli, the attachment of β-Lys is required for EF-P activity, but the proteins required for this posttranslational modification pathway are absent from many organisms. Instead, bacteria such as P. aeruginosa activate EF-P by posttranslational modification with rhamnose, revealing a new role for protein glycosylation that may also prove useful as a target for the development of novel antibiotics.
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Soo RM, Woodcroft BJ, Parks DH, Tyson GW, Hugenholtz P. Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus. PeerJ 2015; 3:e968. [PMID: 26038723 PMCID: PMC4451040 DOI: 10.7717/peerj.968] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/30/2015] [Indexed: 01/03/2023] Open
Abstract
An uncultured non-photosynthetic basal lineage of the Cyanobacteria, the Melainabacteria, was recently characterised by metagenomic analyses of aphotic environmental samples. However, a predatory bacterium, Vampirovibrio chlorellavorus, originally described in 1972 appears to be the first cultured representative of the Melainabacteria based on a 16S rRNA sequence recovered from a lyophilised co-culture of the organism. Here, we sequenced the genome of V. chlorellavorus directly from 36 year-old lyophilised material that could not be resuscitated confirming its identity as a member of the Melainabacteria. We identified attributes in the genome that likely allow V. chlorellavorus to function as an obligate predator of the microalga Chlorella vulgaris, and predict that it is the first described predator to use an Agrobacterium tumefaciens-like conjugative type IV secretion system to invade its host. V. chlorellavorus is the first cyanobacterium recognised to have a predatory lifestyle and further supports the assertion that Melainabacteria are non-photosynthetic.
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Affiliation(s)
- Rochelle M Soo
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD , Australia
| | - Ben J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD , Australia
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD , Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD , Australia ; Advanced Water Management Centre, The University of Queensland , St Lucia, QLD , Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD , Australia ; Institute for Molecular Bioscience, The University of Queensland , St Lucia, QLD , Australia
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Li N, Chen H, Williams HN. Genome-wide comparative analysis of ABC systems in the Bdellovibrio-and-like organisms. Gene 2015; 562:132-7. [PMID: 25707746 DOI: 10.1016/j.gene.2015.02.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/14/2015] [Accepted: 02/19/2015] [Indexed: 11/28/2022]
Abstract
Bdellovibrio-and-like organisms (BALOs) are gram-negative, predatory bacteria with wide variations in genome sizes and GC content and ecological habitats. The ATP-binding cassette (ABC) systems have been identified in several prokaryotes, fungi and plants and have a role in transport of materials in and out of cells and in cellular processes. However, knowledge of the ABC systems of BALOs remains obscure. A total of 269 putative ABC proteins were identified in BALOs. The genes encoding these ABC systems occupy nearly 1.3% of the gene content in freshwater Bdellovibrio strains and about 0.7% in their saltwater counterparts. The proteins found belong to 25 ABC system families based on their structural characteristics and functions. Among these, 16 families function as importers, 6 as exporters and 3 are involved in various cellular processes. Eight of these 25 ABC system families were deduced to be the core set of ABC systems conserved in all BALOs. All Bacteriovorax strains have 28 or less ABC systems. On the contrary, the freshwater Bdellovibrio strains have more ABC systems, typically around 51. In the genome of Bdellovibrio exovorus JSS (CP003537.1), 53 putative ABC systems were detected, representing the highest number among all the BALO genomes examined in this study. Unexpected high numbers of ABC systems involved in cellular processes were found in all BALOs. Phylogenetic analysis suggests that the majority of ABC proteins can be assigned into many separate families with high bootstrap supports (>50%). In this study, a general framework of sequence-structure-function connections for the ABC systems in BALOs was revealed providing novel insights for future investigations.
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Affiliation(s)
- Nan Li
- School of the Environment, Florida A&M University, Tallahassee, FL, USA
| | - Huan Chen
- National High Magnetic Field Laboratory, Tallahassee, FL, USA
| | - Henry N Williams
- School of the Environment, Florida A&M University, Tallahassee, FL, USA.
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An integrated phylogenomic approach toward pinpointing the origin of mitochondria. Sci Rep 2015; 5:7949. [PMID: 25609566 PMCID: PMC4302308 DOI: 10.1038/srep07949] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 12/18/2014] [Indexed: 01/27/2023] Open
Abstract
Overwhelming evidence supports the endosymbiosis theory that mitochondria originated once from the Alphaproteobacteria. However, its exact position in the tree of life remains highly debated. This is because systematic errors, including biased taxonomic sampling, high evolutionary rates and sequence composition bias have long plagued the mitochondrial phylogenetics. In this study, we address this issue by 1) increasing the taxonomic representation of alphaproteobacterial genomes by sequencing 18 phylogenetically novel species. They include 5 Rickettsiales and 4 Rhodospirillales, two orders that have shown close affiliations with mitochondria previously, 2) using a set of 29 slowly evolving mitochondria-derived nuclear genes that are less biased than mitochondria-encoded genes as the alternative “well behaved” markers for phylogenetic analysis, 3) applying site heterogeneous mixture models that account for the sequence composition bias. With the integrated phylogenomic approach, we are able to for the first time place mitochondria unequivocally within the Rickettsiales order, as a sister clade to the Rickettsiaceae and Anaplasmataceae families, all subtended by the Holosporaceae family. Our results suggest that mitochondria most likely originated from a Rickettsiales endosymbiont already residing in the host, but not from the distantly related free-living Pelagibacter and Rhodospirillales.
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Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proc Natl Acad Sci U S A 2015; 112:244-9. [PMID: 25535390 PMCID: PMC4291631 DOI: 10.1073/pnas.1419038112] [Citation(s) in RCA: 304] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The candidate phylum TM7 is globally distributed and often associated with human inflammatory mucosal diseases. Despite its prevalence, the TM7 phylum remains recalcitrant to cultivation, making it one of the most enigmatic phyla known. In this study, we cultivated a TM7 phylotype (TM7x) from the human oral cavity. This extremely small coccus (200-300 nm) has a distinctive lifestyle not previously observed in human-associated microbes. It is an obligate epibiont of an Actinomyces odontolyticus strain (XH001) yet also has a parasitic phase, thereby killing its host. This first completed genome (705 kb) for a human-associated TM7 phylotype revealed a complete lack of amino acid biosynthetic capacity. Comparative genomics analyses with uncultivated environmental TM7 assemblies show remarkable conserved gene synteny and only minimal gene loss/gain that may have occurred as TM7x adapted to conditions within the human host. Transcriptomic and metabolomic profiles provided the first indications, to our knowledge, that there is signaling interaction between TM7x and XH001. Furthermore, the induction of TNF-α production in macrophages by XH001 was repressed in the presence of TM7x, suggesting its potential immune suppression ability. Overall, our data provide intriguing insights into the uncultivability, pathogenicity, and unique lifestyle of this previously uncharacterized oral TM7 phylotype.
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Blanco Y, Rivas LA, García-Moyano A, Aguirre J, Cruz-Gil P, Palacín A, van Heerden E, Parro V. Deciphering the prokaryotic community and metabolisms in South African deep-mine biofilms through antibody microarrays and graph theory. PLoS One 2014; 9:e114180. [PMID: 25531640 PMCID: PMC4273990 DOI: 10.1371/journal.pone.0114180] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/05/2014] [Indexed: 11/18/2022] Open
Abstract
In the South African deep mines, a variety of biofilms growing in mine corridor walls as water seeps from intersections or from fractures represents excellent proxies for deep-subsurface environments. However, they may be greatly affected by the oxygen inputs through the galleries of mining activities. As a consequence, the interaction between the anaerobic water coming out from the walls with the oxygen inputs creates new conditions that support rich microbial communities. The inherent difficulties for sampling these delicate habitats, together with transport and storage conditions may alter the community features and composition. Therefore, the development of in situ monitoring methods would be desirable for quick evaluation of the microbial community. In this work, we report the usefulness of an antibody-microarray (EMChip66) immunoassay for a quick check of the microbial diversity of biofilms located at 1.3 km below surface within the Beatrix deep gold mine (South Africa). In addition, a deconvolution method, previously described and used for environmental monitoring, based on graph theory and applied on antibody cross-reactivity was used to interpret the immunoassay results. The results were corroborated and further expanded by 16S rRNA gene sequencing analysis. Both culture-independent techniques coincided in detecting features related to aerobic sulfur-oxidizers, aerobic chemoorganotrophic Alphaproteobacteria and metanotrophic Gammaproteobacteria. 16S rRNA gene sequencing detected phylotypes related to nitrate-reducers and anaerobic sulfur-oxidizers, whereas the EMChip66 detected immunological features from methanogens and sulfate-reducers. The results reveal a diverse microbial community with syntrophic metabolisms both anaerobic (fermentation, methanogenesis, sulphate and nitrate reduction) and aerobic (methanotrophy, sulphur oxidation). The presence of oxygen-scavenging microbes might indicate that the system is modified by the artificial oxygen inputs from the mine galleries.
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Affiliation(s)
- Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Luis A. Rivas
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Antonio García-Moyano
- TIA/UFS Metagenomics Platform, Department of Biotechnology, University of the Free State, P. O. Box 339, Bloemfontein, 9300, South Africa
| | - Jacobo Aguirre
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Patricia Cruz-Gil
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Arantxa Palacín
- Centro de Biotecnología y Genómica de Plantas, Campus de Montegancedo, Autopista M40, km 38, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Esta van Heerden
- TIA/UFS Metagenomics Platform, Department of Biotechnology, University of the Free State, P. O. Box 339, Bloemfontein, 9300, South Africa
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain
- * E-mail:
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Pasternak Z, Njagi M, Shani Y, Chanyi R, Rotem O, Lurie-Weinberger MN, Koval S, Pietrokovski S, Gophna U, Jurkevitch E. In and out: an analysis of epibiotic vs periplasmic bacterial predators. THE ISME JOURNAL 2014; 8:625-635. [PMID: 24088628 PMCID: PMC3930308 DOI: 10.1038/ismej.2013.164] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 07/14/2013] [Accepted: 08/17/2013] [Indexed: 01/17/2023]
Abstract
Bdellovibrio and like organisms (BALO) are obligate predators of Gram-negative bacteria, belonging to the α- and δ-proteobacteria. BALO prey using either a periplasmic or an epibiotic predatory strategy, but the genetic background underlying these phenotypes is not known. Here we compare the epibiotic Bdellovibrio exovorus and Micavibrio aeruginosavorus to the periplasmic B. bacteriovorus and Bacteriovorax marinus. Electron microscopy showed that M. aeruginosavorus, but not B. exovorus, can attach to prey cells in a non-polar manner through its longitudinal side. Both these predators were resistant to a surprisingly high number of antibiotic compounds, possibly via 26 and 19 antibiotic-resistance genes, respectively, most of them encoding efflux pumps. Comparative genomic analysis of all the BALOs revealed that epibiotic predators have a much smaller genome (ca. 2.5 Mbp) than the periplasmic predators (ca. 3.5 Mbp). Additionally, periplasmic predators have, on average, 888 more proteins, at least 60% more peptidases, and one more rRNA operon. Fifteen and 219 protein families were specific to the epibiotic and the periplasmic predators, respectively, the latter clearly forming the core of the periplasmic 'predatome', which is upregulated during the growth phase. Metabolic deficiencies of epibiotic genomes include the synthesis of inosine, riboflavin, vitamin B6 and the siderophore aerobactin. The phylogeny of the epibiotic predators suggests that they evolved by convergent evolution, with M. aeruginosavorus originating from a non-predatory ancestor while B. exovorus evolved from periplasmic predators by gene loss.
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Affiliation(s)
- Z Pasternak
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel.
| | - M Njagi
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Y Shani
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - R Chanyi
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - O Rotem
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - M N Lurie-Weinberger
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - S Koval
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - S Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - U Gophna
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - E Jurkevitch
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
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Affiliation(s)
- Robert MQ Shanks
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ 07101, USA
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Di Nocera PP, De Gregorio E, Rocco F. GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes. BMC Genomics 2013; 14:522. [PMID: 23902135 PMCID: PMC3733652 DOI: 10.1186/1471-2164-14-522] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/30/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND REPs (Repetitive Extragenic Palindromes) are small (20-40 bp) palindromic repeats found in high copies in some prokaryotic genomes, hypothesized to play a role in DNA supercoiling, transcription termination, mRNA stabilization. RESULTS We have monitored a large number of REP elements in prokaryotic genomes, and found that most can be sorted into two large DNA super-families, as they feature at one end unpaired motifs fitting either the GTAG or the CGTC consensus. Tagged REPs have been identified in >80 species in 8 different phyla. GTAG and CGTC repeats reside predominantly in microorganisms of the gamma and alpha division of Proteobacteria, respectively. However, the identification of members of both super- families in deeper branching phyla such Cyanobacteria and Planctomycetes supports the notion that REPs are old components of the bacterial chromosome. On the basis of sequence content and overall structure, GTAG and CGTC repeats have been assigned to 24 and 4 families, respectively. Of these, some are species-specific, others reside in multiple species, and several organisms contain different REP types. In many families, most units are close to each other in opposite orientation, and may potentially fold into larger secondary structures. In different REP-rich genomes the repeats are predominantly located between unidirectionally and convergently transcribed ORFs. REPs are predominantly located downstream from coding regions, and many are plausibly transcribed and function as RNA elements. REPs located inside genes have been identified in several species. Many lie within replication and global genome repair genes. It has been hypothesized that GTAG REPs are miniature transposons mobilized by specific transposases known as RAYTs (REP associated tyrosine transposases). RAYT genes are flanked either by GTAG repeats or by long terminal inverted repeats (TIRs) unrelated to GTAG repeats. Moderately abundant families of TIRs have been identified in multiple species. CONCLUSIONS CGTC REPs apparently lack a dedicated transposase. Future work will clarify whether these elements may be mobilized by RAYTs or other transposases, and assess if de-novo formation of either GTAG or CGTC repeats type still occurs.
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Affiliation(s)
- Pier Paolo Di Nocera
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Via S, Pansini 5 80131, Naples, Italy.
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Measurement of predation and biofilm formation under different ambient oxygen conditions using a simple gasbag-based system. Appl Environ Microbiol 2013; 79:5264-71. [PMID: 23811501 DOI: 10.1128/aem.01193-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus are Gram-negative bacteria characterized by predatory behavior. The aim of this study was to evaluate the ability of the predators to prey in different oxygen environments. When placed on an orbital shaker, a positive association between the rate of aeration and predation was observed. To further examine the effects of elevated ambient oxygen levels on predation, a simple gasbag system was developed. Using the system, we were able to conduct experiments at ambient oxygen levels of 3% to 86%. When placed in gasbags and inflated with air, 50% O2, and 100% O2, positive predation was seen on both planktonic and biofilm-grown prey cells. However, in low-oxygen environments, predatory bacteria were able to attack only prey cells grown as biofilms. To further evaluate the gasbag system, biofilm development of Gram-positive and Gram-negative microorganisms was also measured. Although the gasbag system was found to be suitable for culturing bacteria that require a low-oxygen environment, it was not capable of supporting, with its current configuration, the growth of obligate anaerobes in liquid or agar medium.
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Shanks RMQ, Davra VR, Romanowski EG, Brothers KM, Stella NA, Godboley D, Kadouri DE. An Eye to a Kill: Using Predatory Bacteria to Control Gram-Negative Pathogens Associated with Ocular Infections. PLoS One 2013; 8:e66723. [PMID: 23824756 PMCID: PMC3688930 DOI: 10.1371/journal.pone.0066723] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 05/10/2013] [Indexed: 11/18/2022] Open
Abstract
Ocular infections are a leading cause of vision loss. It has been previously suggested that predatory prokaryotes might be used as live antibiotics to control infections. In this study, Pseudomonas aeruginosa and Serratia marcescens ocular isolates were exposed to the predatory bacteria Micavibrio aeruginosavorus and Bdellovibrio bacteriovorus. All tested S. marcescens isolates were susceptible to predation by B. bacteriovorus strains 109J and HD100. Seven of the 10 P. aeruginosa isolates were susceptible to predation by B. bacteriovorus 109J with 80% being attacked by M. aeruginosavorus. All of the 19 tested isolates were found to be sensitive to at least one predator. To further investigate the effect of the predators on eukaryotic cells, human corneal-limbal epithelial (HCLE) cells were exposed to high concentrations of the predators. Cytotoxicity assays demonstrated that predatory bacteria do not damage ocular surface cells in vitro whereas the P. aeruginosa used as a positive control was highly toxic. Furthermore, no increase in the production of the proinflammatory cytokines IL-8 and TNF-alpha was measured in HCLE cells after exposure to the predators. Finally, injection of high concentration of predatory bacteria into the hemocoel of Galleria mellonella, an established model system used to study microbial pathogenesis, did not result in any measurable negative effect to the host. Our results suggest that predatory bacteria could be considered in the near future as a safe topical bio-control agent to treat ocular infections.
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Affiliation(s)
- Robert M. Q. Shanks
- Department of Ophthalmology, Campbell Laboratory of Ophthalmic Microbiology, University of Pittsburgh, Pittsburgh, United States of America
| | - Viral R. Davra
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
| | - Eric G. Romanowski
- Department of Ophthalmology, Campbell Laboratory of Ophthalmic Microbiology, University of Pittsburgh, Pittsburgh, United States of America
| | - Kimberly M. Brothers
- Department of Ophthalmology, Campbell Laboratory of Ophthalmic Microbiology, University of Pittsburgh, Pittsburgh, United States of America
| | - Nicholas A. Stella
- Department of Ophthalmology, Campbell Laboratory of Ophthalmic Microbiology, University of Pittsburgh, Pittsburgh, United States of America
| | - Dipti Godboley
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
| | - Daniel E. Kadouri
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
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