1
|
Flores VS, Amgarten DE, Iha BKV, Ryon KA, Danko D, Tierney BT, Mason C, da Silva AM, Setubal JC. Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium. Sci Rep 2024; 14:7913. [PMID: 38575625 PMCID: PMC10994904 DOI: 10.1038/s41598-024-58226-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Bacteriophages are recognized as the most abundant members of microbiomes and have therefore a profound impact on microbial communities through the interactions with their bacterial hosts. The International Metagenomics and Metadesign of Subways and Urban Biomes Consortium (MetaSUB) has sampled mass-transit systems in 60 cities over 3 years using metagenomics, throwing light into these hitherto largely unexplored urban environments. MetaSUB focused primarily on the bacterial community. In this work, we explored MetaSUB metagenomic data in order to recover and analyze bacteriophage genomes. We recovered and analyzed 1714 phage genomes with size at least 40 kbp, from the class Caudoviricetes, the vast majority of which (80%) are novel. The recovered genomes were predicted to belong to temperate (69%) and lytic (31%) phages. Thirty-three of these genomes have more than 200 kbp, and one of them reaches 572 kbp, placing it among the largest phage genomes ever found. In general, the phages tended to be site-specific or nearly so, but 194 genomes could be identified in every city from which phage genomes were retrieved. We predicted hosts for 48% of the phages and observed general agreement between phage abundance and the respective bacterial host abundance, which include the most common nosocomial multidrug-resistant pathogens. A small fraction of the phage genomes are carriers of antibiotic resistance genes, and such genomes tended to be particularly abundant in the sites where they were found. We also detected CRISPR-Cas systems in five phage genomes. This study expands the previously reported MetaSUB results and is a contribution to the knowledge about phage diversity, global distribution, and phage genome content.
Collapse
Affiliation(s)
- Vinicius S Flores
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Deyvid E Amgarten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Bruno Koshin Vázquez Iha
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | | | | | - Braden T Tierney
- Weill Cornell Medicine, New York, NY, USA
- Harvard Medical School, Cambridge, MA, USA
| | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil.
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil.
| |
Collapse
|
2
|
Bagra K, Bellanger X, Merlin C, Singh G, Berendonk TU, Klümper U. Environmental stress increases the invasion success of antimicrobial resistant bacteria in river microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166661. [PMID: 37652387 DOI: 10.1016/j.scitotenv.2023.166661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023]
Abstract
Environmental microbiomes are constantly exposed to invasion events through foreign, antibiotic resistant bacteria that were enriched in the anthropic sphere. However, the biotic and abiotic factors, as well as the natural barriers that determine the invasion success of these invader bacteria into the environmental microbiomes are poorly understood. A great example of such invasion events are river microbial communities constantly exposed to resistant bacteria originating from wastewater effluents. Here, we aim at gaining comprehensive insights into the key factors that determine their invasion success with a particular focus on the effects of environmental stressors, regularly co-released in wastewater effluents. Understanding invasion dynamics of resistant bacteria is crucial for limiting the environmental spread of antibiotic resistance. To achieve this, we grew natural microbial biofilms on glass slides in rivers for one month. The biofilms were then transferred to laboratory, recirculating flume systems and exposed to a single pulse of a model resistant invader bacterium (Escherichia coli) either in presence or absence of stress induced by Cu2+. The invasion dynamics of E. coli into the biofilms were then monitored for 14 days. Despite an initially successful introduction of E. coli into the biofilms, independent of the imposed stress, over time the invader perished in absence of stress. However, under stress the invading strain successfully established and proliferated in the biofilms. Noteworthy, the increased establishment success of the invader coincided with a loss in microbial community diversity under stress conditions, likely due to additional niche space becoming available for the invader.
Collapse
Affiliation(s)
- Kenyum Bagra
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany; Department of Civil Engineering, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Xavier Bellanger
- Université de Lorraine, CNRS, LCPME, UMR 7564, Villers-lès-Nancy, France
| | - Christophe Merlin
- Université de Lorraine, CNRS, LCPME, UMR 7564, Villers-lès-Nancy, France
| | - Gargi Singh
- Department of Civil Engineering, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Thomas U Berendonk
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany
| | - Uli Klümper
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany.
| |
Collapse
|
3
|
Gionchetta G, Snead D, Semerad S, Beck K, Pruden A, Bürgmann H. Dynamics of antibiotic resistance markers and Escherichia coli invasion in riverine heterotrophic biofilms facing increasing heat and flow stagnation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 893:164658. [PMID: 37321511 DOI: 10.1016/j.scitotenv.2023.164658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
As motivation to address environmental dissemination of antimicrobial resistance (AMR) is mounting, there is a need to characterize mechanisms by which AMR can propagate under environmental conditions. Here we investigated the effect of temperature and stagnation on the persistence of wastewater-associated antibiotic resistance markers in riverine biofilms and the invasion success of genetically-tagged Escherichia coli. Biofilms grown on glass slides incubated in-situ downstream of a wastewater treatment plant effluent discharge point were transferred to laboratory-scale flumes fed with filtered river water under potentially stressful temperature and flow conditions: recirculation flow at 20 °C, stagnation at 20 °C, and stagnation at 30 °C. After 14 days, quantitative PCR and amplicon sequencing were used to quantify bacteria, biofilms diversity, resistance markers (sul1, sul2, ermB, tetW, tetM, tetB, blaCTX-M-1, intI1) and E. coli. Resistance markers significantly decreased over time regardless of the treatment applied. Although invading E. coli were initially able to colonize the biofilms, its abundance subsequently declined. Stagnation was associated with a shift in biofilm taxonomic composition, but there was no apparent effect of flow conditions or the simulated river-pool warming (30 °C) on AMR persistence or invasion success of E. coli. Results however indicated that antibiotic resistance markers in the riverine biofilms decreased under the experimental conditions in the absence of exposure to external inputs of antibiotics and AMR.
Collapse
Affiliation(s)
- G Gionchetta
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland
| | - D Snead
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, MI, USA; Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - S Semerad
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland
| | - K Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland
| | - A Pruden
- Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - H Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland.
| |
Collapse
|
4
|
Yang M, Liu S, Zhang C. Antimicrobial peptides with antiviral and anticancer properties and their modification and nanodelivery systems. CURRENT RESEARCH IN BIOTECHNOLOGY 2023. [DOI: 10.1016/j.crbiot.2023.100121] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
|
5
|
"French Phage Network" Annual Conference-Seventh Meeting Report. Viruses 2023; 15:v15020495. [PMID: 36851708 PMCID: PMC9966839 DOI: 10.3390/v15020495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
The French Phage Network (Phages.fr) has continuously grown since its foundation, eight years ago. The annual conference, held at the Institut Pasteur in Paris, attracted 164 participants from the 11th to the 13th of October 2022. Researchers from academic laboratories, hospitals and private companies shared their ongoing projects and breakthroughs in the very institute where Felix d'Hérelle developed phage therapy over a century ago. The conference was divided into four thematic sessions, each opened by a keynote lecture: "Interaction between phages, mobile genetic elements and bacterial immune system," "Ecology and evolution of phage-bacteria interactions," "Molecular interplay between phages and their hosts" and "Therapeutic and biotechnological applications of phages." A total of 32 talks and 33 posters were presented during the conference.
Collapse
|
6
|
Yu Z, Ma Y, Guan Y, Zhu Y, Wang K, Wang Y, Liu P, Chen J, Yu Y. Metagenomics of Virus Diversities in Solid-State Brewing Process of Traditional Chinese Vinegar. Foods 2022; 11:3296. [PMCID: PMC9602057 DOI: 10.3390/foods11203296] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Traditional Chinese vinegar offers an exceptional flavor and rich nutrients due to its unique solid-state fermentation process, which is a multiple microbial fermentation system including various bacteria, fungi and viruses. However, few studies on the virus diversities in traditional Chinese vinegar have been reported. In this paper, using Zhenjiang aromatic vinegar as a model system, we systemically explored the viral communities in the solid-state brewing process of traditional Chinese vinegar using bacterial and viral metagenomes. Results showed that the viral diversity in vinegar Pei was extensive and the virus communities varied along with the fermentation process. In addition, there existed some interactions between viral and bacterial communities. Moreover, abundant antibiotic resistance genes were found in viromes, indicating that viruses might protect fermentation bacteria strains from the stress of antibiotics in the fermentation environment. Remarkably, we identified abundant auxiliary carbohydrate metabolic genes (including alcohol oxidases, the key enzymes for acetic acid synthesis) from viromes, implying that viruses might participate in the acetic acid synthesis progress of the host through auxiliary metabolic genes. Taken together, our results indicated the potential roles of viruses in the vinegar brewing process and provided a new perspective for studying the fermentation mechanisms of traditional Chinese vinegar.
Collapse
Affiliation(s)
- Zhen Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Yan Ma
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Yingfen Guan
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Yuanyuan Zhu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Ke Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Yuqin Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Peng Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Juan Chen
- College of Food Science and Engineering, Moutai Institute, Renhuai 564501, China
| | - Yongjian Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
- Correspondence: ; Tel.: +86-0511-84400686
| |
Collapse
|