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Kang Y, Wang J, Wang Y, Li Z. Profiles of phage in global hospital wastewater: Association with microbial hosts, antibiotic resistance genes, metal resistance genes, and mobile genetic elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171766. [PMID: 38513871 DOI: 10.1016/j.scitotenv.2024.171766] [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: 12/24/2023] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
Abstract
Hospital wastewater (HWW) is known to host taxonomically diverse microbial communities, yet limited information is available on the phages infecting these microorganisms. To fill this knowledge gap, we conducted an in-depth analysis using 377 publicly available HWW metagenomic datasets from 16 countries across 4 continents in the NCBI SRA database to elucidate phage-host dynamics and phage contributions to resistance gene transmission. We first assembled a metagenomic HWW phage catalog comprising 13,812 phage operational taxonomic units (pOTUs). The majority of these pOTUs belonged to the Caudoviricetes order, representing 75.29 % of this catalog. Based on the lifestyle of phages, we found that potentially virulent phages predominated in HWW. Specifically, 583 pOTUs have been predicted to have the capability to lyse 81 potentially pathogenic bacteria, suggesting the promising role of HWW phages as a viable alternative to antibiotics. Among all pOTUs, 1.56 % of pOTUs carry 108 subtypes of antibiotic resistance genes (ARGs), 0.96 % of pOTUs carry 76 subtypes of metal resistance genes (MRGs), and 0.96 % of pOTUs carry 22 subtypes of non-phage mobile genetic elements (MGEs). Predictions indicate that certain phages carrying ARGs, MRGs, and non-phage MGEs could infect bacteria hosts, even potential pathogens. This suggests that phages in HWW may contribute to the dissemination of resistance-associated genes in the environment. This meta-analysis provides the first global catalog of HWW phages, revealing their correlations with microbial hosts and pahge-associated ARGs, MRG, and non-phage MGEs. The insights gained from this research hold promise for advancing the applications of phages in medical and industrial contexts.
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Affiliation(s)
- Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- North China University of Science and Technology, Basic Medical College, Tangshan, Hebei 063210, P.R. China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China.
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Torres-Quintero MC, Santamaría RI, Martínez-Flores I, Bustos P, Girard L, Cevallos MÁ, Rodríguez-Sánchez C, González V. Role of core lipopolysaccharide biosynthetic genes in the infection and adsorption of broad-host-range bacteriophages of Rhizobium etli. Microbiol Res 2024; 285:127766. [PMID: 38788349 DOI: 10.1016/j.micres.2024.127766] [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: 03/13/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
In this study, we examined the role of the lipopolysaccharide (LPS) core of Rhizobium etli in facilitating the adsorption and infection of phages with broad host range. When the plasmid-encoded LPS biosynthesis genes, wreU and wreV, were disrupted, distinct and contrasting effects on phage infection were observed. The wreU mutant strains exhibited wild-type adsorption and infection properties, whereas the wreV mutant demonstrated resistance to phage infection, but retained the capacity to adsorb phages. Complementation of the wreV mutant strains with a recombinant plasmid containing the wreU and wreV, restored the susceptibility to the phages. However, the presence of this recombinant plasmid in a strain devoid of the native lps-encoding plasmid was insufficient to restore phage susceptibility. These results suggest that the absence of wreV impedes the proper assembly of the complete LPS core, potentially affecting the formation of UDP-KdgNAg or KDO precursors for the O-antigen. In addition, a protein not yet identified, but residing in the native lps-encoding plasmid, may be necessary for complete phage infection.
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Affiliation(s)
- Mary Carmen Torres-Quintero
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - Rosa Isela Santamaría
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - Irma Martínez-Flores
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - Patricia Bustos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - Lourdes Girard
- Programa de Microbiología Genómica, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - Miguel Ángel Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - César Rodríguez-Sánchez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - Víctor González
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico.
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Guo X, Wang X, Shi J, Ren J, Zeng J, Li J, Li Y. A review and new perspective on oral bacteriophages: manifestations in the ecology of oral diseases. J Oral Microbiol 2024; 16:2344272. [PMID: 38698893 PMCID: PMC11064738 DOI: 10.1080/20002297.2024.2344272] [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: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 05/05/2024] Open
Abstract
Objective To explore the manifestations of bacteriophages in different oral disease ecologies, including periodontal diseases, dental caries, endodontic infections, and oral cancer, as well as to propel phage therapy for safer and more effective clinical application in the field of dentistry. Methods In this literature review, we outlined interactions between bacteriophages, bacteria and even oral cells in the oral ecosystem, especially in disease states. We also analyzed the current status and future prospects of phage therapy in the perspective of different oral diseases. Results Various oral bacteriophages targeting at periodontal pathogens as Porphyromonas gingivalis, Fusobacterium nucleatum, Treponema denticola and Aggregatibacter actinomycetemcomitans, cariogenic pathogen Streptococcus mutans, endodontic pathogen Enterococcus faecalis were predicted or isolated, providing promising options for phage therapy. In the realm of oral cancer, aside from displaying tumor antigens or participating in tumor-targeted therapies, phage-like particle vaccines demonstrated the potential to prevent oral infections caused by human papillomaviruses (HPVs) associated with head-and-neck cancers. Conclusion Due to their intricate interactions with bacteria and oral cells, bacteriophages are closely linked to the progression and regression of diverse oral diseases. And there is an urgent need for research to explore additional possibilities of bacteriophages in the management of oral diseases.
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Affiliation(s)
- Xinyu Guo
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaowan Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jia Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiayi Ren
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jinquan Li
- State Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Center for Archaeological Science, Sichuan University, Chengdu, China
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Tadeu AD, Duarte J, Trindade D, Costa P, Venâncio C, Lopes I, Oliveira V, Gomes NCM, Almeida A, Pereira C. Bacteriophages to control Vibrio alginolyticus in live feeds prior to their administration in larviculture. J Appl Microbiol 2024; 135:lxae115. [PMID: 38710582 DOI: 10.1093/jambio/lxae115] [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: 02/20/2024] [Revised: 04/16/2024] [Accepted: 05/04/2024] [Indexed: 05/08/2024]
Abstract
AIMS This study aimed to evaluate the efficiency of two phages [VB_VaC_TDDLMA (phage TDD) and VB_VaC_SRILMA (phage SRI)] alone and in a cocktail to control Vibrio alginolyticus in brine shrimp before their administration in larviculture. METHODS AND RESULTS Phages were isolated from seawater samples and characterized by host spectrum, growth parameters, adsorption rate, genomic analysis, and inactivation efficiency. Both phages belong to the Caudoviricetes class and lack known virulence or antibiotic-resistance genes. They exhibit specificity, infecting only their host, V. alginolyticus CECT 521. Preliminary experiments in a culture medium showed that phage TDD (reduction of 5.8 log CFU ml-1 after 10 h) outperformed phage SRI (reduction of 4.6 log CFU ml-1 after 6 h) and the cocktail TDD/SRI (reduction of 5.2 log CFU ml-1 after 8 h). In artificial marine water experiments with Artemia franciscana, both single phage suspensions and the phage cocktail, effectively inactivated V. alginolyticus in culture water (reduction of 4.3, 2.1, and 1.9 log CFU ml-1 for phages TDD, SRI, and the phage cocktail, respectively, after 12 h) and in A. franciscana (reduction of 51.6%, 87.3%, and 85.3% for phages TDD, SRI, and the phage cocktail, respectively, after 24 h). The two phages and the phage cocktail did not affect A. franciscana natural microbiota or other Vibrio species in the brine shrimp. CONCLUSIONS The results suggest that phages can safely and effectively control V. alginolyticus in A. franciscana prior to its administration in larviculture.
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Affiliation(s)
- Amanda Dias Tadeu
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - João Duarte
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - David Trindade
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Pedro Costa
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Cátia Venâncio
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Isabel Lopes
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Vanessa Oliveira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Newton C M Gomes
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Carla Pereira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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Chen T, Mo C, Yuan Y, Li S, Wu Y, Liao X, Yang Y. Short-, long-read metagenome and virome reveal the profile of phage-mediated ARGs in anoxic-oxic processes for swine wastewater treatment. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133789. [PMID: 38394893 DOI: 10.1016/j.jhazmat.2024.133789] [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: 09/02/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024]
Abstract
Phages are among the most widely spread viruses, but their profiles and the antibiotic resistance genes (ARGs) they carry in swine wastewater remain underexplored. The present study investigated the distribution characteristics of phages and their ARG risk in anoxic/oxic (A/O) wastewater treatment processes of swine farms using short- and long-read metagenome and virome. The results demonstrated that the virome could extract more phage sequences than the total metagenome; thus, it was more suited for studying phages in wastewater settings. Intriguingly, phages had significantly lower abundance of ARG than ARGs harbored by total microorganisms (P < 0.01). Eleven ARGs co-occurred with phages and bacteria (R > 0.6 and P < 0.05), with Siphoviridae being the phage co-occurring with the most ARGs (5). Horizontal gene transfer (HGT) events were observed between Proteobacteria and the major phyla except for Bacteroidota. Furthermore, there were prophage sequences and ARGs on the same contig in bacterial MAGs. These data strongly demonstrate that phages promote horizontal transfer of ARG between bacterial hosts in A/O processes for swine wastewater treatment. Therefore, the risk of phage-mediated horizontal transfer of ARGs cannot be overlooked despite the low abundance of phage ARGs (pARG).
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Affiliation(s)
- Tao Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Chunhao Mo
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yilin Yuan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Shengjie Li
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Yinbao Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Xindi Liao
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yiwen Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China.
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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.
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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.
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Upadhyay M, Nair D, Moseley GW, Srivastava S, Kondabagil K. Giant Virus Global Proteomics Innovation: Comparative Evaluation of In-Gel and In-Solution Digestion Methods. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:170-181. [PMID: 38621149 DOI: 10.1089/omi.2024.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
With their unusually large genome and particle sizes, giant viruses (GVs) defy the conventional definition of viruses. Although most GVs isolated infect unicellular protozoans, such as amoeba, studies in the last decade have established their much wider prevalence infecting most eukaryotic supergroups and some giant viral families with the potential to be human pathogens. Their complexity, almost autonomous life cycle, and enigmatic evolution necessitate the study of GVs. The accurate assessment of GV proteome is a veritable challenge. We have compared the coverage of global protein identification using different methods for GVs isolated in Mumbai, Mimivirus Bombay (MVB), Powai Lake Megavirus (PLMV), and Kurlavirus (KV), along with two previously studied GVs, Acanthamoeba polyphaga Mimivirus (APMV) and Marseillevirus (MV). Our study shows that the simultaneous use of in-gel and in-solution digestion methods can significantly increase the coverage of protein identification in the global proteome analysis of purified GV particles. Combining the two methods of analyses, we identified an additional 72 proteins in APMV and 114 in MV compared with what have been previously reported. Similarly, proteomes of MVB, PLMV, and KV were analyzed, and a total of 242 proteins in MVB, 287 proteins in PLMV, and 174 proteins in KV were identified. Our results suggest that a combined methodology of in-gel and in-solution methods is more efficient and opens up new avenues for innovation in global proteome analysis of GVs. Future planetary health research on GVs can benefit from consideration of a broader range of proteomics methodologies as illustrated by the present study.
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Affiliation(s)
- Monica Upadhyay
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Divya Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Gregory W Moseley
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Xiong X, Gong J, Lu T, Yuan L, Lan Y, Tu X. Characteristics of intestinal bacteriophages and their relationship with Bacteria and serum metabolites during quail sexual maturity transition. BMC Vet Res 2024; 20:93. [PMID: 38459523 PMCID: PMC10921806 DOI: 10.1186/s12917-024-03945-9] [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: 10/16/2023] [Accepted: 02/20/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Bacteriophages are prokaryotic viruses that rank among the most abundant microbes in the gut but remain among the least understood, especially in quails. In this study, we surveyed the gut bacteriophage communities in 22 quails at different ages (days 20 and 70) using shotgun metagenomic sequencing. We then systematically evaluated the relationships with gut bacteria and host serum metabolites. RESULTS We discovered that Myoviridae and Siphoviridae were the dominant bacteriophage families in quails. Through a random forest and LEfSe analysis, we identified 23 differential bacteriophages with overlapping presence. Of these, 21 bacteriophages (e.g., Enterococcus phage IME-EFm5 and Enterococcus phage IME-EFm1) showed higher abundances in the day 20 group, while two bacteriophages (Bacillus phage Silence and Bacillus virus WPh) were enriched in the day 70 group. These key bacteriophages can serve as biomarkers for quail sexual maturity. Additionally, the differential bacteriophages significantly correlated with specific bacterial species and shifts in the functional capacities of the gut microbiome. For example, Enterococcus phages (e.g., Enterococcus phage EFP01, Enterococcus phage IME-EFm5, and Enterococcus phage IME-EFm1) were significantly (P < 0.001, FDR) and positively correlated with Enterococcus faecalis. However, the relationships between the host serum metabolites and either bacteriophages or bacterial species varied. None of the bacteriophages significantly (P > 0.05, FDR) correlated with nicotinamide riboside and triacetate lactone. In contrast, some differential bacterial species (e.g., Christensenella massiliensis and Bacteroides neonati) significantly (P < 0.05, FDR) correlated with nicotinamide riboside and triacetate lactone. Furthermore, characteristic successional alterations in gut bacteriophages, bacteria, and host serum metabolites across different ages highlighted a sexual maturity transition coexpression network. CONCLUSION This study improves our understanding of the gut bacteriophage characteristics in quails and offers profound insights into the interactions among gut bacteriophages, bacteria, and host serum metabolites during the quail's sexual maturity transition.
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Affiliation(s)
- Xinwei Xiong
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China.
| | - Jishang Gong
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Tian Lu
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Liuying Yuan
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Yuehang Lan
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Xutang Tu
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China.
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Beckett SJ, Demory D, Coenen AR, Casey JR, Dugenne M, Follett CL, Connell P, Carlson MCG, Hu SK, Wilson ST, Muratore D, Rodriguez-Gonzalez RA, Peng S, Becker KW, Mende DR, Armbrust EV, Caron DA, Lindell D, White AE, Ribalet F, Weitz JS. Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre. Nat Commun 2024; 15:2105. [PMID: 38453897 PMCID: PMC10920773 DOI: 10.1038/s41467-024-46165-3] [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: 05/15/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024] Open
Abstract
Photosynthesis fuels primary production at the base of marine food webs. Yet, in many surface ocean ecosystems, diel-driven primary production is tightly coupled to daily loss. This tight coupling raises the question: which top-down drivers predominate in maintaining persistently stable picocyanobacterial populations over longer time scales? Motivated by high-frequency surface water measurements taken in the North Pacific Subtropical Gyre (NPSG), we developed multitrophic models to investigate bottom-up and top-down mechanisms underlying the balanced control of Prochlorococcus populations. We find that incorporating photosynthetic growth with viral- and predator-induced mortality is sufficient to recapitulate daily oscillations of Prochlorococcus abundances with baseline community abundances. In doing so, we infer that grazers in this environment function as the predominant top-down factor despite high standing viral particle densities. The model-data fits also reveal the ecological relevance of light-dependent viral traits and non-canonical factors to cellular loss. Finally, we leverage sensitivity analyses to demonstrate how variation in life history traits across distinct oceanic contexts, including variation in viral adsorption and grazer clearance rates, can transform the quantitative and even qualitative importance of top-down controls in shaping Prochlorococcus population dynamics.
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Affiliation(s)
- Stephen J Beckett
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Department of Biology, University of Maryland, College Park, MD, USA.
| | - David Demory
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Sorbonne Université, CNRS, USR 3579, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls-sur-Mer, France.
| | - Ashley R Coenen
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - John R Casey
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Mathilde Dugenne
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Sorbonne Université, CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer (LOV), Villefranche-sur-Mer, France
| | - Christopher L Follett
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Paige Connell
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Biology Department, San Diego Mesa College, San Diego, CA, USA
| | - Michael C G Carlson
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Biological Sciences, California State University, Long Beach, CA, USA
| | - Sarah K Hu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Oceanography, Texas A&M University, College Station, TX, USA
| | - Samuel T Wilson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Muratore
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Santa Fe Institute, Santa Fe, NM, USA
| | | | - Shengyun Peng
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Adobe, San Jose, CA, USA
| | - Kevin W Becker
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | | | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Debbie Lindell
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Angelicque E White
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - François Ribalet
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Department of Biology, University of Maryland, College Park, MD, USA.
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA.
- Institut de Biologie, École Normale Supérieure, Paris, France.
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10
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Jo H, Han G, Kim EB, Kong C, Kim BG. Effects of supplemental bacteriophage on the gut microbiota and nutrient digestibility of ileal-cannulated pigs. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2024; 66:340-352. [PMID: 38628684 PMCID: PMC11016748 DOI: 10.5187/jast.2023.e96] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/02/2023] [Accepted: 09/10/2023] [Indexed: 04/19/2024]
Abstract
This study measured the potential changes of the microbiota in the gastrointestinal tract and energy and nutrient digestibility by supplemental bacteriophages in pigs. Twelve castrated male pigs (initial mean body weight = 29.5 ± 2.3 kg) were surgically cannulated using T-cannula. The animals were housed individually in pens equipped with a feeder and a nipple waterer. The pigs were allotted to 1 of 3 experimental diets in a quadruplicated 3 × 2 Latin square design with 3 experimental diets, 2 periods, and 12 pigs resulting in 8 replicates per diet. The 3 diets were a control mainly based on corn and soybean meal with no antibiotics or bacteriophages, a diet containing 0.1% antibiotics, and a diet containing 0.2% bacteriophages. On day 5 of the experimental period, feces were collected and on days 6 and 7, ileal digesta were collected. Genomic DNA for bacteria were extracted from the ileal digesta and feces and the V4 region of the 16S rRNA gene was amplified. The ileal and fecal digestibility of energy, dry matter, organic matter, crude protein, and fiber was unaffected by dietary antibiotics or bacteriophages. At the phylum level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Firmicutes (p = 0.059) and a lower proportion of Bacteroidetes (p = 0.099) in the ileal digesta samples compared with the control group with no difference between the antibiotic and bacteriophage groups. At the genus level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Lactobacillus (p = 0.062) and a lower proportion of Bacteroides (p = 0.074) and Streptococcus (p = 0.088) in the ileal digesta compared with the control group with no difference between the antibiotic and bacteriophage groups. In the feces, supplemental antibiotics or bacteriophages reduced the proportion of Bifidobacterium compared with the control group (p = 0.029) with no difference between the antibiotic and bacteriophage groups. Overall, supplemental antibiotics and bacteriophages showed positive effect on the microbiota of in the ileal digesta without largely affecting energy or nutrient digestibility, with no differences between the antibiotic and bacteriophage groups in growing pigs.
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Affiliation(s)
- Hyunwoong Jo
- Monogastric Animal Feed Research
Institute, Konkuk University, Seoul 05029, Korea
| | - Geongoo Han
- Molecular Microbiology and Immunology,
Brown University, Providence 02912, Rhode Island, USA
| | - Eun Bae Kim
- Department of Applied Animal Science,
Kangwon National University, Chuncheon 24341, Korea
| | - Changsu Kong
- Department of Animal Science, Kyungpook
National University, Sangju 37224, Korea
| | - Beob Gyun Kim
- Monogastric Animal Feed Research
Institute, Konkuk University, Seoul 05029, Korea
- Department of Animal Science and
Technology, Konkuk University, Seoul 05029, Korea
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11
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Wang M, Zhang J, Wei J, Jiang L, Jiang L, Sun Y, Zeng Z, Wang Z. Phage-inspired strategies to combat antibacterial resistance. Crit Rev Microbiol 2024; 50:196-211. [PMID: 38400715 DOI: 10.1080/1040841x.2023.2181056] [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: 12/09/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023]
Abstract
Antimicrobial resistance (AMR) in clinically priority pathogensis now a major threat to public health worldwide. Phages are bacterial parasites that efficiently infect or kill specific strains and represent the most abundant biological entities on earth, showing great attraction as potential antibacterial therapeutics in combating AMR. This review provides a summary of phage-inspired strategies to combat AMR. We firstly cover the phage diversity, and then explain the biological principles of phage therapy that support the use of phages in the post-antimicrobial era. Furthermore, we state the versatility methods of phage therapy both from direct access as well as collateral access. Among the direct access approaches, we discuss the use of phage cocktail therapy, phage-encoded endolysins and the bioengineering for function improvement of used phages or endolysins. On the other hand, we introduce the collateral access, including the phages antimicrobial immunity combined therapy and phage-based novel antibacterial mimic molecules. Nowadays, more and more talented and enthusiastic scientist, doctors, pharmacists, media, authorities, and industry are promoting the progress of phage therapy, and proposed more phages-inspired strategy to make them more tractable to combat AMR and benefit more people, more animal and diverse environment in "one health" framework.
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Affiliation(s)
- Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Junxuan Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jingyi Wei
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Lei Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Li Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yongxue Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhenling Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou, China
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12
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Han P, Lin W, Fan H, Tong Y. Characterization of phage evolution and phage resistance in drug-resistant Stenotrophomonas maltophilia. J Virol 2024; 98:e0124923. [PMID: 38189285 PMCID: PMC10878236 DOI: 10.1128/jvi.01249-23] [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: 10/23/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Phage therapy has become a viable antimicrobial treatment as an alternative to antibiotic treatment, with an increase in antibiotic resistance. Phage resistance is a major limitation in the therapeutic application of phages, and the lack of understanding of the dynamic changes between bacteria and phages constrains our response strategies to phage resistance. In this study, we investigated the changing trends of mutual resistance between Stenotrophomonas maltophilia (S. maltophilia) and its lytic phage, BUCT603. Our results revealed that S. maltophilia resisted phage infection through mutations in the cell membrane proteins, while the evolved phage re-infected the resistant strain primarily through mutations in structure-related proteins. Compared with the wild-type strain (SMA118), the evolved phage-resistant strain (R118-2) showed reduced virulence, weakened biofilm formation ability, and reduced resistance to aminoglycosides. In addition, the evolved phage BUCT603B1 in combination with kanamycin could inhibit the development of phage-resistant S. maltophilia in vitro and significantly improve the survival rate of S. maltophilia-infected mice. Altogether, these results suggest that in vitro characterization of bacteria-phage co-evolutionary relationships is a useful research tool to optimize phages for the treatment of drug-resistant bacterial infections.IMPORTANCEPhage therapy is a promising approach to treat infections caused by drug-resistant Stenotrophomonas maltophilia (S. maltophilia). However, the rapid development of phage resistance has hindered the therapeutic application of phages. In vitro evolutionary studies of bacteria-phage co-cultures can elucidate the mechanism of resistance development between phage and its host. In this study, we investigated the resistance trends between S. maltophilia and its phage and found that inhibition of phage adsorption is the primary strategy by which bacteria resist phage infection in vitro, while phages can re-infect bacterial cells by identifying other adsorption receptors. Although the final bacterial mutants were no longer infected by phages, they incurred a fitness cost that resulted in a significant reduction in virulence. In addition, the combination treatment with phage and aminoglycoside antibiotics could prevent the development of phage resistance in S. maltophilia in vitro. These findings contribute to increasing the understanding of the co-evolutionary relationships between phages and S. maltophilia.
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Affiliation(s)
- Pengjun Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Wei Lin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
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13
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Ho SX, Law JH, Png CW, Alberts R, Zhang Y, Chu JJH, Tan KK. Alterations in colorectal cancer virome and its persistence after surgery. Sci Rep 2024; 14:2819. [PMID: 38307921 PMCID: PMC10837111 DOI: 10.1038/s41598-024-53041-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/27/2024] [Indexed: 02/04/2024] Open
Abstract
Viruses are a key component of the colon microbiome, but the relationship between virome and colorectal cancer (CRC) remains poorly understood. We seek to identify alterations in the viral community that is characteristic of CRC and examine if they persist after surgery. Forty-nine fecal samples from 25 non-cancer (NC) individuals and 12 CRC patients, before and 6-months after surgery, were collected for metagenomic analysis. The fecal virome of CRC patients demonstrated an increased network connectivity as compared to NC individuals. Co-exclusion of influential viruses to bacterial species associated with healthy gut status was observed in CRC, suggesting an altered virome induced a change in the healthy gut bacteriome. Network analysis revealed lower connectivity within the virome and trans-kingdom interactions in NC. After surgery, the number of strong correlations decreased for trans-kingdom and within the bacteria and virome networks, indicating lower connectivity within the microbiome. Some co-occurrence patterns between dominant viruses and bacteria were also lost after surgery, suggesting a possible return to the healthy state of gut microbiome. Microbial signatures characteristic of CRC include an altered virome besides an altered bacterial composition. Elevated viral correlations and network connectivity were observed in CRC patients relative to healthy individuals, alongside distinct changes in the cross-kingdom correlation network unique to CRC patients. Some patterns of dysbiosis persist after surgery. Future studies should seek to verify if dysbiosis truly persists after surgery in a larger sample size with microbiome data collected at various time points after surgery to explore if there is field-change in the remaining colon, as well as to examine if persistent dysbiosis correlates with patient outcomes.
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Affiliation(s)
- Si Xian Ho
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Jia-Hao Law
- Division of Colorectal Surgery, Department of Surgery, National University Hospital, 1E, Kent Ridge Road, NUHS Tower Block, Level 8, Singapore, 119228, Singapore
| | - Chin-Wen Png
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rudi Alberts
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yongliang Zhang
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Ker-Kan Tan
- Division of Colorectal Surgery, Department of Surgery, National University Hospital, 1E, Kent Ridge Road, NUHS Tower Block, Level 8, Singapore, 119228, Singapore.
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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14
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Kim KE, Joo HM, Kim YJ, Kang D, Lee TK, Jung SW, Ha SY. Ecological Interaction between Bacteriophages and Bacteria in Sub-Arctic Kongsfjorden Bay, Svalbard, Norway. Microorganisms 2024; 12:276. [PMID: 38399681 PMCID: PMC10893223 DOI: 10.3390/microorganisms12020276] [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: 12/30/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Marine virus diversity and their relationships with their hosts in the marine environment remain unclear. This study investigated the co-occurrence of marine DNA bacteriophages (phages) and bacteria in the sub-Arctic area of Kongsfjorden Bay in Svalbard (Norway) in April and June 2018 using metagenomics tools. Of the marine viruses identified, 48-81% were bacteriophages of the families Myoviridae, Siphoviridae, and Podoviridae. Puniceispirillum phage HMO-2011 was dominant (7.61%) in April, and Puniceispirillum phage HMO-2011 (3.32%) and Pelagibacter phage HTVC008M (3.28%) were dominant in June. Gammaproteobacteria (58%), including Eionea flava (14.3%) and Pseudomonas sabulinigri (12.2%), were dominant in April, whereas Alphaproteobacteria (87%), including Sulfitobacter profundi (51.5%) and Loktanella acticola (32.4%), were dominant in June. The alpha diversity of the bacteriophages and bacterial communities exhibited opposite patterns. The diversity of the bacterial community was higher in April and lower in June. Changes in water temperature and light can influence the relationship between bacteria and bacteriophages.
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Affiliation(s)
- Kang Eun Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (K.E.K.); (Y.J.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea;
| | - Hyoung Min Joo
- Unit of Next Generation IBRV Building Program, Korea Polar Research Institute, Incheon 21990, Republic of Korea;
| | - Yu Jin Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (K.E.K.); (Y.J.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea;
| | - Donhyug Kang
- Marine Domain & Security Research Department, Korea Institute of Ocean Science & Technology, Busan 49111, Republic of Korea;
| | - Taek-Kyun Lee
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea;
- Risk Assessment Research Center, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
| | - Seung Won Jung
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (K.E.K.); (Y.J.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea;
| | - Sun-Yong Ha
- Division of Polar Ocean Science Research, Korea Polar Research Institute, Incheon 21990, Republic of Korea
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15
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Samson R, Dharne M, Khairnar K. Bacteriophages: Status quo and emerging trends toward one health approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168461. [PMID: 37967634 DOI: 10.1016/j.scitotenv.2023.168461] [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: 08/21/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
The alarming rise in antimicrobial resistance (AMR) among the drug-resistant pathogens has been attributed to the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sp., and Escherichia coli). Recently, these AMR microbes have become difficult to treat, as they have rendered the existing therapeutics ineffective. Thus, there is an urgent need for effective alternatives to lessen or eliminate the current infections and limit the spread of emerging diseases under the "One Health" framework. Bacteriophages (phages) are naturally occurring biological resources with extraordinary potential for biomedical, agriculture/food safety, environmental protection, and energy production. Specific unique properties of phages, such as their bactericidal activity, host specificity, potency, and biocompatibility, make them desirable candidates in therapeutics. The recent biotechnological advancement has broadened the repertoire of phage applications in nanoscience, material science, physical chemistry, and soft-matter research. Herein, we present a comprehensive review, coupling the substantial aspects of phages with their applicability status and emerging opportunities in several interdependent areas under one health concept. Consolidating the recent state-of-the-art studies that integrate human, animal, plant, and environment health, the following points have been highlighted: (i) The biomedical and pharmacological advantages of phages and their antimicrobial derivatives with particular emphasis on in-vivo and clinical studies. (ii) The remarkable potential of phages to be altered, improved, and applied for drug delivery, biosensors, biomedical imaging, tissue engineering, energy, and catalysis. (iii) Resurgence of phages in biocontrol of plant, food, and animal-borne pathogens. (iv) Commercialization of phage-based products, current challenges, and perspectives.
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Affiliation(s)
- Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Krishna Khairnar
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Environmental Virology Cell (EVC), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India.
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16
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Stelmakh LV, Sagadatova RR, Alatartseva OS. The effect of viral infection on the Black Sea microalgae Tetraselmis viridis: the role of nutrients and copper ions. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23114. [PMID: 38194582 DOI: 10.1071/fp23114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024]
Abstract
The TvV-SM2 virus, isolated from the coastal waters of the Black Sea, causes lysis of its host, the algae Tetraselmis viridis (Chlorophyta). Under optimal conditions for nutrients, an increase in the initial abundance of algae cells by four times caused a 3-fold reduction in the latent period of viral infection. During the period of the most rapid cell lysis of T. viridis , nitrogen deficiency leads to a decrease in the average daily rate of death of cells affected by the virus by 3.2times relative to the replete conditions, while in the case of phosphorus deficiency, this process slows down by up to 2.4times. Under deplete conditions, the rate of cell death was only 34% lower than under replete conditions. The effect of copper ions (100μgL-1 ) on the viral suspension for 6h led to the complete suppression of its activity. In the presence of the host of this virus, its activity is only partially suppressed. As a result, cell lysis under the influence of a viral infection occurred in two stages. The first stage was noted only during the first 6h of the experiment. The second main stage took place within 78-170h. This study showed that in conditions of nutrient deficiency and in the presence of copper ions in seawater, the impact of viruses on microalgae will be weaker.
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Affiliation(s)
- Liudmila V Stelmakh
- A.O. Kovalevsky Institute of Biology of the Southern Seas, Russian Academy of Sciences, Sevastopol, Russia
| | - Raisa R Sagadatova
- A.O. Kovalevsky Institute of Biology of the Southern Seas, Russian Academy of Sciences, Sevastopol, Russia
| | - Olga S Alatartseva
- A.O. Kovalevsky Institute of Biology of the Southern Seas, Russian Academy of Sciences, Sevastopol, Russia
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17
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Bellanger M, Visscher P, White RA. Viral enumeration using cost-effective wet-mount epifluorescence microscopy for aquatic ecosystems and modern microbialites. Appl Environ Microbiol 2023; 89:e0174423. [PMID: 38014959 PMCID: PMC10734538 DOI: 10.1128/aem.01744-23] [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: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Low-cost and robust viral enumeration is a critical first step toward understanding the global virome. Our method is a deep drive integration providing a window into viral dark matter within aquatic ecosystems. We enumerated the viruses within Green Lake and Great Salt Lake microbialites, EPS, and water column. The entire weight of all the viruses in Green Lake and Great Salt Lake are ~598 g and ~2.2 kg, respectively.
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Affiliation(s)
- Madeline Bellanger
- Department of Bioinformatics and Genomics, North Carolina Research Campus, The University of North Carolina at Charlotte, Kannapolis, North Carolina, USA
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), The University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Pieter Visscher
- Department of Marine Sciences and Geoscience, University of Connecticut, Storrs, Connecticut, USA
| | - Richard Allen White
- Department of Bioinformatics and Genomics, North Carolina Research Campus, The University of North Carolina at Charlotte, Kannapolis, North Carolina, USA
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), The University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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18
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Jordá J, Lorenzo-Rebenaque L, Montoro-Dasi L, Marco-Fuertes A, Vega S, Marin C. Phage-Based Biosanitation Strategies for Minimizing Persistent Salmonella and Campylobacter Bacteria in Poultry. Animals (Basel) 2023; 13:3826. [PMID: 38136863 PMCID: PMC10740442 DOI: 10.3390/ani13243826] [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: 11/21/2023] [Revised: 12/05/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
Control strategies to minimize pathogenic bacteria in food animal production are one of the key components in ensuring safer food for consumers. The most significant challenges confronting the food industry, particularly in the major poultry and swine sectors, are antibiotic resistance and resistance to cleaning and disinfection in zoonotic bacteria. In this context, bacteriophages have emerged as a promising tool for zoonotic bacteria control in the food industry, from animals and farm facilities to the final product. Phages are viruses that infect bacteria, with several advantages as a biocontrol agent such as high specificity, self-replication, self-limitation, continuous adaptation, low inherent toxicity and easy isolation. Their development as a biocontrol agent is of particular interest, as it would allow the application of a promising and even necessary "green" technology to combat pathogenic bacteria in the environment. However, bacteriophage applications have limitations, including selecting appropriate phages, legal restrictions, purification, dosage determination and bacterial resistance. Overcoming these limitations is crucial to enhance phage therapy's effectiveness against zoonotic bacteria in poultry. Thus, this review aims to provide a comprehensive view of the phage-biosanitation strategies for minimizing persistent Salmonella and Campylobacter bacteria in poultry.
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Affiliation(s)
- Jaume Jordá
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, 46115 Alfara del Patriarca, Spain; (J.J.); (L.M.-D.); (A.M.-F.); (S.V.)
| | - Laura Lorenzo-Rebenaque
- Institute of Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
| | - Laura Montoro-Dasi
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, 46115 Alfara del Patriarca, Spain; (J.J.); (L.M.-D.); (A.M.-F.); (S.V.)
| | - Ana Marco-Fuertes
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, 46115 Alfara del Patriarca, Spain; (J.J.); (L.M.-D.); (A.M.-F.); (S.V.)
| | - Santiago Vega
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, 46115 Alfara del Patriarca, Spain; (J.J.); (L.M.-D.); (A.M.-F.); (S.V.)
| | - Clara Marin
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, 46115 Alfara del Patriarca, Spain; (J.J.); (L.M.-D.); (A.M.-F.); (S.V.)
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Vitale M. Antibiotic Resistance: Do We Need Only Cutting-Edge Methods, or Can New Visions Such as One Health Be More Useful for Learning from Nature? Antibiotics (Basel) 2023; 12:1694. [PMID: 38136728 PMCID: PMC10740918 DOI: 10.3390/antibiotics12121694] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Antibiotic resistance is an increasing global problem for public health, and focusing on biofilms has provided further insights into resistance evolution in bacteria. Resistance is innate in many bacterial species, and many antibiotics are derived from natural molecules of soil microorganisms. Is it possible that nature can help control AMR diffusion? In this review, an analysis of resistance mechanisms is summarized, and an excursus of the different approaches to challenging resistance spread based on natural processes is presented as "lessons from Nature". On the "host side", immunotherapy strategies for bacterial infections have a long history before antibiotics, but continuous new inputs through biotechnology advances are enlarging their applications, efficacy, and safety. Antimicrobial peptides and monoclonal antibodies are considered for controlling antibiotic resistance. Understanding the biology of natural predators is providing new, effective, and safe ways to combat resistant bacteria. As natural enemies, bacteriophages were used to treat severe infections before the discovery of antibiotics, marginalized during the antibiotic era, and revitalized upon the diffusion of multi-resistance. Finally, sociopolitical aspects such as education, global action, and climate change are also considered as important tools for tackling antibiotic resistance from the One Health perspective.
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Affiliation(s)
- Maria Vitale
- Genetics of Microorganisms Laboratory, Molecular Biology Department, Istituto Zooprofilattico Sperimentale della Sicilia "A. Mirri", 90129 Palermo, Italy
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20
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Van de Waal DB, White LA, Everett R, Asik L, Borer ET, Frenken T, González AL, Paseka R, Seabloom EW, Strauss AT, Peace A. Reconciling contrasting effects of nitrogen on host immunity and pathogen transmission using stoichiometric models. Ecology 2023; 104:e4170. [PMID: 37755721 DOI: 10.1002/ecy.4170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/10/2023] [Accepted: 07/29/2023] [Indexed: 09/28/2023]
Abstract
Hosts rely on the availability of nutrients for growth, and for defense against pathogens. At the same time, changes in host nutrition can alter the dynamics of pathogens that rely on their host for reproduction. For primary producer hosts, enhanced nutrient loads may increase host biomass or pathogen reproduction, promoting faster density-dependent pathogen transmission. However, the effect of elevated nutrients may be reduced if hosts allocate a growth-limiting nutrient to pathogen defense. In canonical disease models, transmission is not a function of nutrient availability. Yet, including nutrient availability is necessary to mechanistically understand the response of infection to changes in the environment. Here, we explore the implications of nutrient-mediated pathogen infectivity and host immunity on infection outcomes. We developed a stoichiometric disease model that explicitly integrates the contrasting dependencies of pathogen infectivity and host immunity on nitrogen (N) and parameterized it for an algal-host system. Our findings reveal dynamic shifts in host biomass build-up, pathogen prevalence, and the force of infection along N supply gradients with N-mediated host infectivity and immunity, compared with a model in which the transmission rate was fixed. We show contrasting responses in pathogen performance with increasing N supply between N-mediated infectivity and N-mediated immunity, revealing an optimum for pathogen transmission at intermediate N supply. This was caused by N limitation of the pathogen at a low N supply and by pathogen suppression via enhanced host immunity at a high N supply. By integrating both nutrient-mediated pathogen infectivity and host immunity into a stoichiometric model, we provide a theoretical framework that is a first step in reconciling the contrasting role nutrients can have on host-pathogen dynamics.
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Affiliation(s)
- Dedmer B Van de Waal
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Lauren A White
- National Socio-Environmental Synthesis Center (SESYNC), University of Maryland, Annapolis, Maryland, USA
| | - Rebecca Everett
- Department of Mathematics and Statistics, Haverford College, Haverford, Pennsylvania, USA
| | - Lale Asik
- Department of Mathematics and Statistics, University of the Incarnate Word, San Antonio, Texas, USA
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, Texas, USA
| | - Elizabeth T Borer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Thijs Frenken
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Great Lakes Institute for Environmental Research (GLIER), University of Windsor, Windsor, Ontario, Canada
| | - Angélica L González
- Department of Biology and Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
| | - Rachel Paseka
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Eric W Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Alexander T Strauss
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
- Odum School of Ecology, University of Georgia, Athens, Georgia, USA
- River Basin Center, University of Georgia, Athens, Georgia, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, USA
| | - Angela Peace
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, Texas, USA
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21
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Merges D, Schmidt A, Schmitt I, Neuschulz EL, Dal Grande F, Bálint M. Metatranscriptomics reveals contrasting effects of elevation on the activity of bacteria and bacterial viruses in soil. Mol Ecol 2023; 32:6552-6563. [PMID: 36321191 DOI: 10.1111/mec.16756] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 08/24/2022] [Accepted: 10/13/2022] [Indexed: 11/21/2022]
Abstract
Soil microbial diversity affects ecosystem functioning and global biogeochemical cycles. Soil bacterial communities catalyse a diversity of biogeochemical reactions and have thus sparked considerable scientific interest. One driver of bacterial community dynamics in natural ecosystems has so far been largely neglected: the predator-prey interactions between bacterial viruses (bacteriophages) and bacteria. To generate ground level knowledge on environmental drivers of these particular predator-prey dynamics, we propose an activity-based ecological framework to simultaneous capture community dynamics of bacteria and bacteriophages in soils. An ecological framework and specifically the analyses of community dynamics across latitudinal and elevational gradients have been widely used in ecology to understand community-wide responses of innumerable taxa to environmental change, in particular to climate. Here, we tested the hypothesis that the activity of bacteria and bacteriophages codeclines across an elevational gradient. We used metatranscriptomics to investigate bacterial and bacteriophage activity patterns at five sites across 400 elevational metres in the Swiss Alps in 2015 and 2017. We found that metabolic activity (transcription levels) of bacteria declined significantly with increasing elevation, but activity of bacteriophages did not. We showed that bacteriophages are consistently active in soil along the entire gradient, making bacteriophage activity patterns divergent from that of their putative bacterial prey. Future efforts will be necessary to link the environment-activity relationship to predator-prey dynamics, and to understand the magnitude of viral contributions to carbon, nitrogen and phosphorus cycling when infection causes bacterial cell death, a process that may represent an overlooked component of soil biogeochemical cycles.
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Affiliation(s)
- Dominik Merges
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Alexandra Schmidt
- Department of Biology, Limnological Institute, University Konstanz, Konstanz, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Eike Lena Neuschulz
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Department of Biology, University of Padova, Padua, Italy
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Institute of Insect Biotechnology, Justus Liebig University Gießen, Gießen, Germany
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22
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Valadez-Cano C, Reyes-Prieto A, Lawrence J. Novel virulent and temperate cyanophages predicted to infect Microcoleus associated with anatoxin-producing benthic mats. Environ Microbiol 2023; 25:3319-3332. [PMID: 37849433 DOI: 10.1111/1462-2920.16527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023]
Abstract
Cyanophages are crucial for regulating cyanobacterial populations, but their influence on anatoxin-producing Microcoleus mat dynamics remains unexplored. Here, we use metagenomics to explore phage presence in benthic mats from the Wolastoq|Saint John River (New Brunswick, Canada) and the Eel River (California, USA). We recovered multiple viral-like sequences associated with different putative bacterial hosts, including two cyanophage genomes with apparently different replication strategies. A temperate cyanophage was found integrated in the genomes of Microcoleus sp. 3 recovered from the Eel River and is phylogenetically related to Phormidium phages. We also recovered novel virulent cyanophage genomes from Wolastoq and Eel River mats that were dominated by anatoxin-producing Microcoleus species predicted to be the host. Despite the geographical distance, these genomes have similar sizes (circa 239 kbp) and share numerous orthologous genes with high sequence identity. A considerable reduction of the anatoxin-producing Microcoleus species in Wolastoq mats following the emergence of the virulent phage suggests that phage infections have an important role in limiting the abundance of this toxigenic cyanobacterium and releasing anatoxins into the surrounding water. Our results constitute the first report of cyanophages predicted to infect mat-forming Microcoleus species associated with anatoxin production.
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Affiliation(s)
- Cecilio Valadez-Cano
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Janice Lawrence
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
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23
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Zhou K, Wong TY, Long L, Anantharaman K, Zhang W, Wong WC, Zhang R, Qian PY. Genomic and transcriptomic insights into complex virus-prokaryote interactions in marine biofilms. THE ISME JOURNAL 2023; 17:2303-2312. [PMID: 37875603 PMCID: PMC10689801 DOI: 10.1038/s41396-023-01546-2] [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: 06/15/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023]
Abstract
Marine biofilms are complex communities of microorganisms that play a crucial ecological role in oceans. Although prokaryotes are the dominant members of these biofilms, little is known about their interactions with viruses. By analysing publicly available and newly sequenced metagenomic data, we identified 2446 virus-prokaryote connections in 84 marine biofilms. Most of these connections were between the bacteriophages in the Uroviricota phylum and the bacteria of Proteobacteria, Cyanobacteria and Bacteroidota. The network of virus-host pairs is complex; a single virus can infect multiple prokaryotic populations or a single prokaryote is susceptible to several viral populations. Analysis of genomes of paired prokaryotes and viruses revealed the presence of 425 putative auxiliary metabolic genes (AMGs), 239 viral genes related to restriction-modification (RM) systems and 38,538 prokaryotic anti-viral defence-related genes involved in 15 defence systems. Transcriptomic evidence from newly established biofilms revealed the expression of viral genes, including AMGs and RM, and prokaryotic defence systems, indicating the active interplay between viruses and prokaryotes. A comparison between biofilms and seawater showed that biofilm prokaryotes have more abundant defence genes than seawater prokaryotes, and the defence gene composition differs between biofilms and the surrounding seawater. Overall, our study unveiled active viruses in natural biofilms and their complex interplay with prokaryotes, which may result in the blooming of defence strategists in biofilms. The detachment of bloomed defence strategists may reduce the infectivity of viruses in seawater and result in the emergence of a novel role of marine biofilms.
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Affiliation(s)
- Kun Zhou
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Tin Yan Wong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Lexin Long
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Weipeng Zhang
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Wai Chuen Wong
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
| | - Pei-Yuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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24
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Oh H, Koo J, An SY, Hong SH, Suh JY, Bae E. Structural and functional investigation of GajB protein in Gabija anti-phage defense. Nucleic Acids Res 2023; 51:11941-11951. [PMID: 37897358 PMCID: PMC10681800 DOI: 10.1093/nar/gkad951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/13/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Bacteriophages (phages) are viruses that infect bacteria and archaea. To fend off invading phages, the hosts have evolved a variety of anti-phage defense mechanisms. Gabija is one of the most abundant prokaryotic antiviral systems and consists of two proteins, GajA and GajB. GajA has been characterized experimentally as a sequence-specific DNA endonuclease. Although GajB was previously predicted to be a UvrD-like helicase, its function is unclear. Here, we report the results of structural and functional analyses of GajB. The crystal structure of GajB revealed a UvrD-like domain architecture, including two RecA-like core and two accessory subdomains. However, local structural elements that are important for the helicase function of UvrD are not conserved in GajB. In functional assays, GajB did not unwind or bind various types of DNA substrates. We demonstrated that GajB interacts with GajA to form a heterooctameric Gabija complex, but GajB did not exhibit helicase activity when bound to GajA. These results advance our understanding of the molecular mechanism underlying Gabija anti-phage defense and highlight the role of GajB as a component of a multi-subunit antiviral complex in bacteria.
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Affiliation(s)
- Hyejin Oh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jasung Koo
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - So Young An
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Sung-Hyun Hong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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25
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Sudhakari PA, Ramisetty BCM. An Eco-evolutionary Model on Surviving Lysogeny Through Grounding and Accumulation of Prophages. MICROBIAL ECOLOGY 2023; 86:3068-3081. [PMID: 37843655 DOI: 10.1007/s00248-023-02301-y] [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: 06/20/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023]
Abstract
Temperate phages integrate into the bacterial genomes propagating along with the bacterial genomes. Multiple phage elements, representing diverse prophages, are present in most bacterial genomes. The evolutionary events and the ecological dynamics underlying the accumulation of prophage elements in bacterial genomes have yet to be understood. Here, we show that the local wastewater had 7% of lysogens (hosting mitomycin C-inducible prophages), and they showed resistance to superinfection by their corresponding lysates. Genomic analysis of four lysogens and four non-lysogens revealed the presence of multiple prophages (belonging to Myoviridae and Siphoviridae) in both lysogens and non-lysogens. For large-scale comparison, 2180 Escherichia coli genomes isolated from various sources across the globe and 523 genomes specifically isolated from diverse wastewaters were analyzed. A total of 15,279 prophages were predicted among 2180 E. coli genomes and 2802 prophages among 523 global wastewater isolates, with a mean of ~ 5 prophages per genome. These observations indicate that most putative prophages are relics of past bacteria-phage conflicts; they are "grounded" prophages that cannot excise from the bacterial genome. Prophage distribution analysis based on the sequence homology suggested the random distribution of E. coli prophages within and between E. coli clades. The independent occurrence pattern of these prophages indicates extensive horizontal transfers across the genomes. We modeled the eco-evolutionary dynamics to reconstruct the events that could have resulted in the prophage accumulation accounting for infection, superinfection immunity, and grounding. In bacteria-phage conflicts, the bacteria win by grounding the prophage, which could confer superinfection immunity.
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Affiliation(s)
- Pavithra Anantharaman Sudhakari
- Laboratory of Molecular Biology and Evolution, School of Chemical and Biotechnology, SASTRA Deemed University, 312@ASK1, Thanjavur, India
| | - Bhaskar Chandra Mohan Ramisetty
- Laboratory of Molecular Biology and Evolution, School of Chemical and Biotechnology, SASTRA Deemed University, 312@ASK1, Thanjavur, India.
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26
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Han M, Niu X, Xiong G, Ruan C, Chen G, Wu H, Liu Y, Zhu K, Wang G. Isolation, characterization and genomic analysis of the novel Arthrobacter sp. phage SWEP2. Arch Virol 2023; 168:276. [PMID: 37864004 DOI: 10.1007/s00705-023-05898-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 09/01/2023] [Indexed: 10/22/2023]
Abstract
A new virulent phage, SWEP2, infecting the Arthrobacter sp. 5B strain, was isolated from black soil samples in northeastern China. SWEP2 has a latent period of 80 min and a burst size of 45 PFU (evaluated at an MOI of 0.1). Genomic analysis revealed that the 43,398-bp dsDNA genome of phage SWEP2 contains 64 open reading frames (ORFs) and one tRNA gene. Phylogenetic analysis indicated a close relationship between SWEP2 and Arthrobacter phage Liebe, with 82.98% identity and a query coverage of 48%. Based on its distinct phenotypic and genetic characteristics, SWEP2 is identified as a novel Arthrobacter phage.
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Affiliation(s)
- Miao Han
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xinyao Niu
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Guangzhou Xiong
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Chujin Ruan
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
- Department of Environmental Microbiology, Eawag, 8600, Dübendorf, Switzerland
| | - Guowei Chen
- School of Civil and Hydraulic Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Hanqing Wu
- The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Ying Liu
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Kun Zhu
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Gang Wang
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China.
- National Black Soil and Agriculture Research, China Agricultural University, Beijing, 100193, China.
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27
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Sabbagh EI, Calleja ML, Daffonchio D, Morán XAG. Seasonality of top-down control of bacterioplankton at two central Red Sea sites with different trophic status. Environ Microbiol 2023; 25:2002-2019. [PMID: 37286523 DOI: 10.1111/1462-2920.16439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 05/22/2023] [Indexed: 06/09/2023]
Abstract
The role of bottom-up (nutrient availability) and top-down (grazers and viruses mortality) controls on tropical bacterioplankton have been rarely investigated simultaneously from a seasonal perspective. We have assessed them through monthly samplings over 2 years in inshore and offshore waters of the central Red Sea differing in trophic status. Flow cytometric analysis allowed us to distinguish five groups of heterotrophic bacteria based on physiological properties (nucleic acid content, membrane integrity and active respiration), three groups of cyanobacteria (two populations of Synechococcus and Prochlorococcus), heterotrophic nanoflagellates (HNFs) and three groups of viruses based on nucleic acid content. The dynamics of bacterioplankton and their top-down controls varied with season and location, being more pronounced in inshore waters. HNFs abundances showed a strong preference for larger prey inshore (r = -0.62 to -0.59, p = 0.001-0.002). Positive relationships between viruses and heterotrophic bacterioplankton abundances were more marked inshore (r = 0.67, p < 0.001) than offshore (r = 0.44, p = 0.03). The negative correlation between HNFs and viruses abundances (r = -0.47, p = 0.02) in shallow waters indicates a persistent seasonal switch between protistan grazing and viral lysis that maintains the low bacterioplankton stocks in the central Red Sea area.
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Affiliation(s)
- Eman I Sabbagh
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maria Ll Calleja
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Climate Geochemistry, Max Plank Institute for Chemistry (MPIC), Mainz, Germany
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xosé Anxelu G Morán
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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28
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Mao X, Wu Y, Ma R, Li L, Wang L, Tan Y, Li Z, Liu H, Han K, Cao Y, Li Y, Peng H, Li X, Hu C, Wang X. Oral phage therapy with microencapsulated phage A221 against Escherichia coli infections in weaned piglets. BMC Vet Res 2023; 19:165. [PMID: 37730566 PMCID: PMC10510151 DOI: 10.1186/s12917-023-03724-y] [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: 03/01/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Escherichia coli (E. coli) is a common pathogen that often causes diarrhea in piglets. Since bacteria are becoming more and more resistant to antibiotics, phages have become a promising alternative therapy. However, the therapy of oral phage often fails to achieve the desired effect. A novel phage named A221 was isolated by using E. coli GXXW-1103 as host strain, characterized by electron microscopy, genomic sequencing and analyzed by measuring lysis ability in vitro. RESULTS Phage A221 was identified as a member of Ackermannviridae, Aglimvirinae, Agtrevirus with 153297 bp genome and effectively inhibited bacterial growth in vitro for 16 h. This study was conducted to evaluate the therapeutic effect of oral microencapsulated phage A221 on E. coli GXXW-1103 infections in weaned piglets. The protective effect of phage was evaluated by body weight analysis, bacterial load and histopathological changes. The results showed that with the treatment of phage A221, the body weight of piglets increased, the percentage of Enterobacteriaceae in duodenum decreased to 0.64%, the lesions in cecum and duodenum were alleviated, and the bacterial load in the jejunal lymph nodes, cecum and spleen were also significantly different with infected group (P < 0.001). CONCLUSIONS The results showed that phage A221 significantly increased the daily weight gain of piglets, reduced the bacterial load of tissues and the intestinal lesions, achieved the same therapeutic effect as antibiotic Florfenicol. Taken together, oral microencapsulated phage A221 has a good therapeutic effect on bacterial diarrhea of weaned piglets, which provides guidance for the clinical application of phage therapy in the future.
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Affiliation(s)
- Xinyu Mao
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Yuxing Wu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Runwen Ma
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Lei Li
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Leping Wang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Yizhou Tan
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Ziyong Li
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Hui Liu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Kaiou Han
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Yajie Cao
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Yinan Li
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Hao Peng
- Guangxi Veterinary Research Institute, Nanning, 530004, Guangxi, China
| | - Xun Li
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Chuanhuo Hu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China
| | - Xiaoye Wang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, P. R. China.
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, Guangxi, China.
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29
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Attrill EL, Łapińska U, Westra ER, Harding SV, Pagliara S. Slow growing bacteria survive bacteriophage in isolation. ISME COMMUNICATIONS 2023; 3:95. [PMID: 37684358 PMCID: PMC10491631 DOI: 10.1038/s43705-023-00299-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023]
Abstract
The interactions between bacteria and bacteriophage have important roles in the global ecosystem; in turn changes in environmental parameters affect the interactions between bacteria and phage. However, there is a lack of knowledge on whether clonal bacterial populations harbour different phenotypes that respond to phage in distinct ways and whether the abundance of such phenotypes within bacterial populations is affected by variations in environmental parameters. Here we study the impact of variations in nutrient availability, bacterial growth rate and phage abundance on the interactions between the phage T4 and individual Escherichia coli cells confined in spatial refuges. Surprisingly, we found that fast growing bacteria survive together with all of their clonal kin cells, whereas slow growing bacteria survive in isolation. We also discovered that the number of bacteria that survive in isolation decreases at increasing phage doses possibly due to lysis inhibition in the presence of secondary adsorptions. We further show that these changes in the phenotypic composition of the E. coli population have important consequences on the bacterial and phage population dynamics and should therefore be considered when investigating bacteria-phage interactions in ecological, health or food production settings in structured environments.
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Affiliation(s)
- Erin L Attrill
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK
| | - Edze R Westra
- Environment and Sustainability Institute and Biosciences, University of Exeter, Penryn, UK
| | - Sarah V Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK.
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30
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Ortmann AC, Cobanli SE, Wohlgeschaffen G, Poon HY, Ryther C, Greer CW, Wasserscheid J, Elias M, Robinson B, King TL. Factors that affect water column hydrocarbon concentrations have minor impacts on microbial responses following simulated diesel fuel spills. MARINE POLLUTION BULLETIN 2023; 194:115358. [PMID: 37567129 DOI: 10.1016/j.marpolbul.2023.115358] [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: 02/01/2023] [Revised: 07/24/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023]
Abstract
Effects of season and mixing on hydrocarbon concentrations and the microbial community response was explored in a series of mesocosm experiments simulating surface spills of diesel into coastal waters. Mixing of any amount contributed to hydrocarbons entering the water column, but diesel fuel composition had a significant effect on hydrocarbon concentrations. Higher initial concentrations of aromatic hydrocarbons resulted in higher water column concentrations, with minimal differences among seasons due to high variability. Regardless of the concentrations of hydrocarbons, prokaryotes increased and there were higher relative abundances of hydrocarbon affiliated bacteria with indications of biodegradation within 4 d of exposure. As concentrations decreased over time, the eukaryote community shifted from the initial community to one which appeared to be composed of organisms with some resilience to hydrocarbons. This series of experiments demonstrates the wide range of conditions under which natural attenuation of diesel fuel is an effective response.
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Affiliation(s)
- Alice C Ortmann
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada.
| | - Susan E Cobanli
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Gary Wohlgeschaffen
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Ho Yin Poon
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Camilla Ryther
- Dalhousie University, 6299 South Street, Halifax, NS B3H 4R2, Canada
| | - Charles W Greer
- National Research Council of Canada, Energy, Mining and Environment Research Centre, 6100 Royalmount Ave, Montreal, PQ H4P 2R2, Canada
| | - Jessica Wasserscheid
- National Research Council of Canada, Energy, Mining and Environment Research Centre, 6100 Royalmount Ave, Montreal, PQ H4P 2R2, Canada
| | - Miria Elias
- National Research Council of Canada, Energy, Mining and Environment Research Centre, 6100 Royalmount Ave, Montreal, PQ H4P 2R2, Canada
| | - Brian Robinson
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Thomas L King
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
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31
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Chen X, Hu C, Wei W, Yang Y, Weinbauer MG, Li H, Ren S, Ma R, Huang Y, Luo T, Jiao N, Zhang R. Virus-Host Interactions Drive Contrasting Bacterial Diel Dynamics in the Ocean. RESEARCH (WASHINGTON, D.C.) 2023; 6:0213. [PMID: 37614364 PMCID: PMC10443526 DOI: 10.34133/research.0213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/05/2023] [Indexed: 08/25/2023]
Abstract
Marine organisms perform a sea of diel rhythmicity. Planktonic diel dynamics have been shown to be driven by light, energy resources, circadian rhythms, and the coordinated coupling of photoautotrophs and heterotrophic bacterioplankton. Here, we explore the diel fluctuation of viral production and decay and their impact on the total and active bacterial community in the coastal and open seawaters of the South China Sea. The results showed that the night-production diel pattern of lytic viral production was concurrent with the lower viral decay at night, contributing to the accumulation of the viral population size during the night for surface waters. The diel variations in bacterial activity, community composition, and diversity were found highly affected by viral dynamics. This was revealed by the finding that bacterial community diversity was positively correlated to lytic viral production in the euphotic zone of the open ocean but was negatively related to lysogenic viral production in the coastal ocean. Such distinct but contrasting correlations suggest that viral life strategies can not only contribute to diversifying bacterial community but also potentially piggyback their host to dominate bacterial community, suggesting the tightly synchronized depth-dependent and habitat-specific diel patterns of virus-host interactions. It further implies that viruses serve as an ecologically important driver of bacterial diel dynamics across the ocean, highlighting the viral roles in bacterial ecological and biogeochemical processes in the ocean.
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Affiliation(s)
- Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Chen Hu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, PR China
| | - Wei Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, PR China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, PR China
| | - Markus G Weinbauer
- Sorbonne Universités, UPMC, Université Paris 06, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), Villefranche-sur-Mer 06230, France
| | - Hongbo Li
- National Marine Environmental Monitoring Center, Ministry of Ecological Environment, Dalian 116023, PR China
| | - Shiying Ren
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Ruijie Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Yibin Huang
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
- NOAA/OAR Pacific Marine Environmental Laboratory, Seattle, WA, USA
| | - Tingwei Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
- Institute for Advanced Study, Shenzhen University, Shenzhen 518055, PR China
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32
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Dot EW, Thomason LC, Chappie JS. Everything OLD is new again: How structural, functional, and bioinformatic advances have redefined a neglected nuclease family. Mol Microbiol 2023; 120:122-140. [PMID: 37254295 DOI: 10.1111/mmi.15074] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 06/01/2023]
Abstract
Overcoming lysogenization defect (OLD) proteins are a conserved family of ATP-powered nucleases that function in anti-phage defense. Recent bioinformatic, genetic, and crystallographic studies have yielded new insights into the structure, function, and evolution of these enzymes. Here we review these developments and propose a new classification scheme to categorize OLD homologs that relies on gene neighborhoods, biochemical properties, domain organization, and catalytic machinery. This taxonomy reveals important similarities and differences between family members and provides a blueprint to contextualize future in vivo and in vitro findings. We also detail how OLD nucleases are related to PARIS and Septu anti-phage defense systems and discuss important mechanistic questions that remain unanswered.
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Affiliation(s)
- Elena Wanvig Dot
- Department of Molecular Medicine, Cornell University, Ithaca, New York, USA
| | - Lynn C Thomason
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, New York, USA
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33
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Du X, Li X, Cheng K, Zhao W, Cai Z, Chen G, Zhou J. Virome reveals effect of Ulva prolifera green tide on the structural and functional profiles of virus communities in coastal environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163609. [PMID: 37100126 DOI: 10.1016/j.scitotenv.2023.163609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/15/2023] [Accepted: 04/16/2023] [Indexed: 06/03/2023]
Abstract
Viruses are widely distributed in marine environments, where they influence the transformation of matter and energy by modulating host metabolism. Driven by eutrophication, green tides are a rising concern in Chinese coastal areas, and are a serious ecological disaster that negatively affects coastal ecosystems and disrupts biogeochemical cycles. Although the composition of bacterial communities in green algae has been investigated, the diversity and roles of viruses in green algal blooms are largely unexplored. Therefore, the diversity, abundance, lifestyle, and metabolic potential of viruses in a natural bloom in Qingdao coastal area were investigated at three different stages (pre-bloom, during-bloom, and post-bloom) by metagenomics analysis. The dsDNA viruses, Siphoviridae, Myoviridae, Podoviridae, and Phycodnaviridae, were found to dominate the viral community. The viral dynamics exhibited distinct temporal patterns across different stages. The composition of the viral community varied during the bloom, especially in populations with low abundance. The lytic cycle was most predominant, and the abundance of lytic viruses increased slightly in the post-bloom stage. The diversity and richness of the viral communities varied distinctly during the green tide, and the post-bloom stage favored viral diversity and richness. The total organic carbon, dissolved oxygen, NO3-, NO2-, PO43-, chlorophyll-a contents, and temperature variably co-influenced the viral communities. The primary hosts included bacteria, algae, and other microplankton. Network analysis revealed the closer links between the viral communities as the bloom progressed. Functional prediction revealed that the viruses possibly influenced the biodegradation of microbial hydrocarbons and carbon by metabolic augmentation via auxiliary metabolic genes. The composition, structure, metabolic potential, and interaction taxonomy of the viromes differed significantly across the different stages of the green tide. The study demonstrated that the ecological event shaped the viral communities during algal bloom, and the viral communities played a significant role in phycospheric microecology.
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Affiliation(s)
- Xiaopeng Du
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Xinyang Li
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Keke Cheng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Wei Zhao
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, Shandong Province, PR China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China.
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34
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Riber L, Carstens AB, Dougherty PE, Roy C, Willenbücher K, Hille F, Franz CMAP, Hansen LH. Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus. Microorganisms 2023; 11:1831. [PMID: 37513003 PMCID: PMC10385605 DOI: 10.3390/microorganisms11071831] [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: 06/24/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
Bacteriophages are viral agents that infect and replicate within bacterial cells. Despite the increasing importance of phage ecology, environmental phages-particularly those targeting phyllosphere-associated bacteria-remain underexplored, and current genomic databases lack high-quality phage genome sequences linked to specific environmentally important bacteria, such as the ubiquitous sphingomonads. Here, we isolated three novel phages from a Danish wastewater treatment facility. Notably, these phages are among the first discovered to target and regulate a Sphingomonas genus within the wheat phyllosphere microbiome. Two of the phages displayed a non-prolate Siphovirus morphotype and demonstrated a narrow host range when tested against additional Sphingomonas strains. Intergenomic studies revealed limited nucleotide sequence similarity within the isolated phage genomes and to publicly available metagenome data of their closest relatives. Particularly intriguing was the limited homology observed between the DNA polymerase encoding genes of the isolated phages and their closest relatives. Based on these findings, we propose three newly identified genera of viruses: Longusvirus carli, Vexovirus birtae, and Molestusvirus kimi, following the latest ICTV binomial nomenclature for virus species. These results contribute to our current understanding of phage genetic diversity in natural environments and hold promising implications for phage applications in phyllosphere microbiome manipulation strategies.
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Affiliation(s)
- Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Alexander Byth Carstens
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Peter Erdmann Dougherty
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Chayan Roy
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Katharina Willenbücher
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Strasse 1, 24103 Kiel, Germany
| | - Frank Hille
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Strasse 1, 24103 Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Strasse 1, 24103 Kiel, Germany
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
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35
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Zou G, He L, Rao J, Song Z, Du H, Li R, Wang W, Zhou Y, Liang L, Chen H, Li J. Improving the safety and efficacy of phage therapy from the perspective of phage-mammal interactions. FEMS Microbiol Rev 2023; 47:fuad042. [PMID: 37442611 DOI: 10.1093/femsre/fuad042] [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: 12/14/2022] [Revised: 06/30/2023] [Accepted: 07/12/2023] [Indexed: 07/15/2023] Open
Abstract
Phage therapy has re-emerged as a promising solution for combating antimicrobial-resistant bacterial infections. Increasingly, studies have revealed that phages possess therapeutic potential beyond their antimicrobial properties, including regulating the gut microbiome and maintain intestinal homeostasis, as a novel nanocarrier for targeted drug delivery. However, the complexity and unpredictability of phage behavior during treatment pose a significant challenge in clinical practice. The intricate interactions established between phages, humans, and bacteria throughout their long coexistence in the natural ecosystem contribute to the complexity of phage behavior in therapy, raising concerns about their efficacy and safety as therapeutic agents. Revealing the mechanisms by which phages interact with the human body will provide a theoretical basis for increased application of promising phage therapy. In this review, we provide a comprehensive summary of phage-mammal interactions, including signaling pathways, adaptive immunity responses, and phage-mediated anti-inflammatory responses. Then, from the perspective of phage-mammalian immune system interactions, we present the first systematic overview of the factors affecting phage therapy, such as the mode of administration, the physiological status of the patient, and the biological properties of the phage, to offer new insights into phage therapy for various human diseases.
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Affiliation(s)
- Geng Zou
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijun He
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Rao
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiyong Song
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Hu Du
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Runze Li
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenjing Wang
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhou
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Liang
- School of Bioscience, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinquan Li
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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36
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Borer ET, Kendig AE, Holt RD. Feeding the fever: Complex host-pathogen dynamics along continuous resource gradients. Ecol Evol 2023; 13:e10315. [PMID: 37502304 PMCID: PMC10368943 DOI: 10.1002/ece3.10315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023] Open
Abstract
Food has long been known to perform dual functions of nutrition and medicine, but mounting evidence suggests that complex host-pathogen dynamics can emerge along continuous resource gradients. Empirical examples of nonmonotonic responses of infection with increasing host resources (e.g., low prevalence at low and high resource supply but high prevalence at intermediate resources) have been documented across the tree of life, but these dynamics, when observed, often are interpreted as nonintuitive, idiosyncratic features of pathogen and host biology. Here, by developing generalized versions of existing models of resource dependence for within- and among-host infection dynamics, we provide a synthetic view of nonmonotonic infection dynamics. We demonstrate that where resources jointly impact two (or more) processes (e.g., growth, defense, transmission, mortality, predation), nonmonotonic infection dynamics, including alternative states, can emerge across a continuous resource supply gradient. We review the few empirical examples that concurrently measured resource effects on multiple rates and pair this with a wide range of examples in which resource dependence of multiple rates could generate nonmonotonic infection outcomes under realistic conditions. This review and generalized framework highlight the likely generality of such resource effects in natural systems and point to opportunities ripe for future empirical and theoretical work.
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Affiliation(s)
- Elizabeth T. Borer
- Department of Ecology, Evolution, and BehaviorUniversity of MinnesotaSaint PaulMinnesotaUSA
| | - Amy E. Kendig
- Agronomy DepartmentUniversity of FloridaGainesvilleFloridaUSA
- Minnesota Department of Natural ResourcesMinnesota Biological SurveySaint PaulMinnesotaUSA
| | - Robert D. Holt
- Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
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37
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Kaur R, Mandal D, Kumar A. Phage therapy for Acinetobacter baumannii infection. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:303-324. [PMID: 37739559 DOI: 10.1016/bs.pmbts.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Acinetobacter is a gram-negative nosocomial pathogenic bacteria. The contributing factor for the pathogenicity of Acinetobacter is severe due to its property of antibacterial drug resistance. Often antibiotic treatment is used to treat bacterial infection, however due to the resistance of a broad range of antibiotics by Acinetobacter the treatment viability of this bacterial species seems to be reduced. To combat this diverse treatment options are being incorporated with phage therapy being an effective choice due to its intrinsic property to infect bacteria. In this chapter the various phage therapy used in recent times has been elaborated on. The phage therapy is considered to be in response to Carbapenem resistance. The various mode of phage propagation has been mentioned in this chapter along with the type of resistance conferred to the administered therapy. The chapter deals with the advances observed due to therapy of Acibel004, Acibel007, vB-GEC_Ab-M-G7, ZZ1 and Bacteriophage p54 containing Endolysin LysAB54 bacteriophages have been elucidated.
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Affiliation(s)
- Ramneet Kaur
- Department of Basic and Applied Sciences, RIMT University, Punjab, India
| | - Dibita Mandal
- Department of Biosciences, SBST, Vellore Institute of Technology, Vellore, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India.
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38
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Santamaría-Corral G, Senhaji-Kacha A, Broncano-Lavado A, Esteban J, García-Quintanilla M. Bacteriophage-Antibiotic Combination Therapy against Pseudomonas aeruginosa. Antibiotics (Basel) 2023; 12:1089. [PMID: 37508185 PMCID: PMC10376841 DOI: 10.3390/antibiotics12071089] [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: 04/04/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Phage therapy is an alternative therapy that is being used as the last resource against infections caused by multidrug-resistant bacteria after the failure of standard treatments. Pseudomonas aeruginosa can cause pneumonia, septicemia, urinary tract, and surgery site infections mainly in immunocompromised people, although it can cause infections in many different patient profiles. Cystic fibrosis patients are particularly vulnerable. In vitro and in vivo studies of phage therapy against P. aeruginosa include both bacteriophages alone and combined with antibiotics. However, the former is the most promising strategy utilized in clinical infections. This review summarizes the recent studies of phage-antibiotic combinations, highlighting the synergistic effects of in vitro and in vivo experiments and successful treatments in patients.
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Affiliation(s)
| | - Abrar Senhaji-Kacha
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Av. Reyes Católicos 2, 28040 Madrid, Spain
- CIBERINFEC-Infectious Diseases CIBER, 28029 Madrid, Spain
| | - Antonio Broncano-Lavado
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Av. Reyes Católicos 2, 28040 Madrid, Spain
| | - Jaime Esteban
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Av. Reyes Católicos 2, 28040 Madrid, Spain
- CIBERINFEC-Infectious Diseases CIBER, 28029 Madrid, Spain
| | - Meritxell García-Quintanilla
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Av. Reyes Católicos 2, 28040 Madrid, Spain
- CIBERINFEC-Infectious Diseases CIBER, 28029 Madrid, Spain
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Arora P, Jain A, Kumar A. Phage design and directed evolution to evolve phage for therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:103-126. [PMID: 37739551 DOI: 10.1016/bs.pmbts.2023.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Phage therapy or Phage treatment is the use of bacteriolysing phage in treating bacterial infections by using the viruses that infects and kills bacteria. This technique has been studied and practiced very long ago, but with the advent of antibiotics, it has been neglected. This foregone technique is now witnessing a revival due to development of bacterial resistance. Nowadays, with the awareness of genetic sequence of organisms, it is required that informed choices of phages have to be made for the most efficacious results. Furthermore, phages with the evolving genes are taken into consideration for the subsequent improvement in treating the patients for bacterial diseases. In addition, direct evolution methods are increasingly developing, since these are capable of creating new biological molecules having changed or unique activities, such as, improved target specificity, evolution of novel proteins with new catalytic properties or creation of nucleic acids that are capable of recognizing required pathogenic bacteria. This system is incorporates continuous evolution such as protein or genes are put under continuous evolution by providing continuous mutagenesis with least human intervention. Although, this system providing continuous directed evolution is very effective, it imposes some challenges due to requirement of heavy investment of time and resources. This chapter focuses on development of phage as a therapeutic agent against various bacteria causing diseases and it improvement using direct evolution of proteins and nucleic acids such that they target specific organisms.
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Affiliation(s)
- Priyancka Arora
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India
| | - Avni Jain
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India.
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Tong D, Wang Y, Yu H, Shen H, Dahlgren RA, Xu J. Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil. THE ISME JOURNAL 2023:10.1038/s41396-023-01438-5. [PMID: 37248401 DOI: 10.1038/s41396-023-01438-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 05/13/2023] [Accepted: 05/22/2023] [Indexed: 05/31/2023]
Abstract
Viruses are critical for regulating microbial communities and biogeochemical processes affecting carbon/nutrient cycling. However, the role of soil phages in controlling microbial physiological traits and intrinsic dissolved organic matter (DOM) properties remains largely unknown. Herein, microcosm experiments with different soil phage concentrates (including no-added phages, inactive phages, and three dilutions of active phages) at two temperatures (15 °C and 25 °C) were conducted to disclose the nutrient and DOM dynamics associated with viral lysing. Results demonstrated three different phases of viral impacts on CO2 emission at both temperatures, and phages played a role in maintaining Q10 within bounds. At both temperatures, microbial nutrient limitations (especially P limitation) were alleviated by viral lysing as determined by extracellular enzyme activity (decreased Vangle with active phages). Additionally, the re-utilization of lysate-derived DOM by surviving microbes stimulated an increase of microbial metabolic efficiency and recalcitrant DOM components (e.g., SUV254, SUV260 and HIX). This research provides direct experimental evidence that the "viral shuttle" exists in soils, whereby soil phages increase recalcitrant DOM components. Our findings advance the understanding of viral controls on soil biogeochemical processes, and provide a new perspective for assessing whether soil phages provide a net "carbon sink" vs. "carbon source" in soils.
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Affiliation(s)
- Di Tong
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Youjing Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Haodan Yu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Haojie Shen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China.
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Zia S, Alkheraije KA. Recent trends in the use of bacteriophages as replacement of antimicrobials against food-animal pathogens. Front Vet Sci 2023; 10:1162465. [PMID: 37303721 PMCID: PMC10247982 DOI: 10.3389/fvets.2023.1162465] [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: 02/09/2023] [Accepted: 04/06/2023] [Indexed: 06/13/2023] Open
Abstract
A major public health impact is associated with foodborne illnesses around the globe. Additionally, bacteria are becoming more resistant to antibiotics, which pose a global threat. Currently, many scientific efforts have been made to develop and implement new technologies to combat bacteria considering the increasing emergence of multidrug-resistant bacteria. In recent years, there has been considerable interest in using phages as biocontrol agents for foodborne pathogens in animals used for food production and in food products themselves. Foodborne outbreaks persist, globally, in many foods, some of which lack adequate methods to control any pathogenic contamination (like fresh produce). This interest may be attributed both to consumers' desire for more natural food and to the fact that foodborne outbreaks continue to occur in many foods. Poultry is the most common animal to be treated with phage therapy to control foodborne pathogens. A large number of foodborne illnesses worldwide are caused by Salmonella spp. and Campylobacter, which are found in poultry and egg products. Conventional bacteriophage-based therapy can prevent and control humans and animals from various infectious diseases. In this context, describing bacteriophage therapy based on bacterial cells may offer a breakthrough for treating bacterial infections. Large-scale production of pheasants may be economically challenging to meet the needs of the poultry market. It is also possible to produce bacteriophage therapy on a large scale at a reduced cost. Recently, they have provided an ideal platform for designing and producing immune-inducing phages. Emerging foodborne pathogens will likely be targeted by new phage products in the future. In this review article, we will mainly focus on the Bacteriophages (phages) that have been proposed as an alternative strategy to antibiotics for food animal pathogens and their use for public health and food safety.
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Affiliation(s)
- Sana Zia
- Department of Zoology, Government Sadiq College Women University Bahawalpur, Bahawalpur, Pakistan
| | - Khalid A. Alkheraije
- Department of Veterinary Medicine College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia
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Kopylov AI, Zabotkina EA, Sazhin AF, Romanova N, Belyaev N, Drozdova A. Virioplankton and virus-induced mortality of prokaryotes in the Kara Sea (Arctic) in summer. PeerJ 2023; 11:e15457. [PMID: 37250716 PMCID: PMC10215763 DOI: 10.7717/peerj.15457] [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: 11/04/2022] [Accepted: 05/03/2023] [Indexed: 05/31/2023] Open
Abstract
Among the Arctic seas, the largest volume of river runoff (~45% of the total river-water inflow into the Arctic Ocean) enters the Siberian Kara Sea. The viral communities of the Kara Sea are important for the functioning of the marine ecosystem. Studies of virus-prokaryote interactions on the Kara Sea shelf have been conducted only in spring and autumn. Here, we investigated the abundance of free viruses, viruses attached to prokaryotes, and pico-sized detrital particles; the morphology (shape and size) of the viruses, viral infection and virus-mediated mortality of prokaryotes in early summer, i.e., during a seasonal ice melting period and maximum inflow of river-water volumes with high concentrations of dissolved and suspended organic carbon. Seawater samples for microbial analyses were collected across the Kara Sea shelf zone on board the Norilskiy Nickel as a research platform from June 29 to July 15, 2018. Abundances of prokaryotes (range (0.6-25.3) × 105 cells mL-1) and free viruses (range (10-117) × 105 viruses mL-1) were correlated (r = 0.63, p = 0.005) with an average virus: prokaryote ratio of 23.9 ± 5.3. The abundance of free viruses and viral-mediated mortality of prokaryotes were significantly higher in early summer than in early spring and autumn. Free viruses with a capsid diameter of 16-304 nm were recorded in the examined water samples. Waters in the Kara Sea shelf contained high concentrations of suspended organic particles 0.25-4.0 µm in size (range (0.6-25.3) × 105 particles mL-1). The proportions of free viruses, viruses attached to prokaryotes, and viruses attached to pico-sized detrital particles were 89.8 ± 6.0%, 2.2 ± 0.6% and 8.0 ± 1.3%, respectively, of the total virioplankton abundance (on average (61.5 ± 6.2) × 105 viruses mL-1). Viruses smaller than 60 nm clearly dominated at all studied sites. The majority of free viruses were not tailed. We estimated that an average of 1.4% (range 0.4-3.5%) of the prokaryote community was visibly infected by viruses, suggesting that a significant proportion of prokaryotic secondary production, 11.4% on average (range 4.0-34.0%), was lost due to viral lysis. There was a negative correlation between the abundance of pico-sized detrital particles and the frequency of visibly infected prokaryotic cells: r = -0.67, p = 0.0008.
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Affiliation(s)
| | | | | | - Nadezda Romanova
- Shirshov Institute of Oceanology of Russian Academy of Sciences, Moscow, Russia
| | - Nikolay Belyaev
- Shirshov Institute of Oceanology of Russian Academy of Sciences, Moscow, Russia
| | - Anastasia Drozdova
- Shirshov Institute of Oceanology of Russian Academy of Sciences, Moscow, Russia
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Tang X, Zhong L, Tang L, Fan C, Zhang B, Wang M, Dong H, Zhou C, Rensing C, Zhou S, Zeng G. Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity. THE ISME JOURNAL 2023:10.1038/s41396-023-01425-w. [PMID: 37161002 DOI: 10.1038/s41396-023-01425-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]
Abstract
Emerging evidence from genomics gives us a glimpse into the potential contribution of lysogenic bacteriophages (phages) to the environmental adaptability of their hosts. However, it is challenging to quantify this kind of contribution due to the lack of appropriate genetic markers and the associated controllable environmental factors. Here, based on the unique transformable nature of arsenic (the controllable environmental factor), a series of flooding microcosms was established to investigate the contribution of arsM-bearing lysogenic phages to their hosts' adaptation to trivalent arsenic [As(III)] toxicity, where arsM is the marker gene associated with microbial As(III) detoxification. In the 15-day flooding period, the concentration of As(III) was significantly increased, and this elevated As(III) toxicity visibly inhibited the bacterial population, but the latter quickly adapted to As(III) toxicity. During the flooding period, some lysogenic phages re-infected new hosts after an early burst, while others persistently followed the productive cycle (i.e., lytic cycle). The unique phage-host interplay contributed to the rapid spread of arsM among soil microbiota, enabling the quick recovery of the bacterial community. Moreover, the higher abundance of arsM imparted a greater arsenic methylation capability to soil microbiota. Collectively, this study provides experimental evidence for lysogenic phages assisting their hosts in adapting to an extreme environment, which highlights the ecological perspectives on lysogenic phage-host mutualism.
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Affiliation(s)
- Xiang Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
| | - Lin Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
| | - Changzheng Fan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China.
| | - Baowei Zhang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
| | - Mier Wang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
| | - Haoran Dong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
| | - Chengyun Zhou
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, P. R. China.
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Chen Y, Li W, Shi K, Fang Z, Yang Y, Zhang R. Isolation and characterization of a novel phage belonging to a new genus against Vibrio parahaemolyticus. Virol J 2023; 20:81. [PMID: 37127579 PMCID: PMC10152775 DOI: 10.1186/s12985-023-02036-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Vibrio parahaemolyticus is a major foodborne pathogen that contaminates aquatic products and causes great economic losses to aquaculture. Because of the emergence of multidrug-resistant V. parahaemolyticus strains, bacteriophages are considered promising agents for their biocontrol as an alternative or supplement to antibiotics. In this study, a lytic vibriophage, vB_VpaM_R16F (R16F), infecting V. parahaemolyticus 1.1997T was isolated, characterized and evaluated for its biocontrol potential. METHODS A vibriophage R16F was isolated from sewage from a seafood market with the double-layer agar method. R16F was studied by transmission electron microscopy, host range, sensitivity of phage particles to chloroform, one-step growth curve and lytic activity. The phage genome was sequenced and in-depth characterized, including phylogenetic and taxonomic analysis. RESULTS R16F belongs to the myovirus morphotype and infects V. parahaemolyticus, but not nine other Vibrio spp. As characterized by determining its host range, one-step growth curve, and lytic activity, phage R16F was found to highly effective in lysing host cells with a short latent period (< 10 min) and a small burst size (13 plaque-forming units). R16F has a linear double-stranded DNA with genome size 139,011 bp and a G + C content of 35.21%. Phylogenetic and intergenomic nucleotide sequence similarity analysis revealed that R16F is distinct from currently known vibriophages and belongs to a novel genus. Several genes (e.g., encoding ultraviolet damage endonuclease and endolysin) that may enhance environmental competitiveness were found in the genome of R16F, while no antibiotic resistance- or virulence factor-related gene was detected. CONCLUSIONS In consideration of its biological and genetic properties, this newly discovered phage R16F belongs to a novel genus and may be a potential alternate biocontrol agent.
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Affiliation(s)
- Yubing Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, 43900, Selangor, Malaysia
| | - Wenqing Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China
| | - Keming Shi
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China
| | - Zheng Fang
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, 43900, Selangor, Malaysia
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China.
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518061, Guangdong, China.
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Zaki BM, Mohamed AA, Dawoud A, Essam K, Hammouda ZK, Abdelsattar AS, El-Shibiny A. Isolation, screening and characterization of phage. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:13-60. [PMID: 37739553 DOI: 10.1016/bs.pmbts.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Bacterial resistance threatens public health due to a lack of novel antibacterial classes since the 21st century. Bacteriophages, the most ubiquitous microorganism on Earth and natural predators of bacteria, have the potential to save the world from the post-antibiotic era. Therefore, phage isolation and characterization are in high demand to find suitable phages for therapeutic and bacterial control applications. The chapter presents brief guidance supported by recommendations on the isolation of phages, and initial screening of phage antimicrobial efficacy, in addition to, conducting comprehensive characterization addressing morphological, biological, genomic, and taxonomic features.
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Affiliation(s)
- Bishoy Maher Zaki
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Amira A Mohamed
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Kareem Essam
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Zainab K Hammouda
- Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Abdallah S Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Faculty of Environmental Agricultural Sciences, Arish University, Arish, Egypt
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Rodríguez-Ramos J, Oliverio A, Borton MA, Danczak R, Mueller BM, Schulz H, Ellenbogen J, Flynn RM, Daly RA, Schopflin L, Shaffer M, Goldman A, Lewandowski J, Stegen JC, Wrighton KC. Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535500. [PMID: 37066413 PMCID: PMC10104031 DOI: 10.1101/2023.04.04.535500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Although river ecosystems comprise less than 1% of Earth's total non-glaciated area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. As a result, the relevance of microbiome interactions and the impacts they have over time on biogeochemical cycles are poorly understood. To assess how viral and microbial communities change over time, we sampled surface water and pore water compartments of the wastewater-impacted River Erpe in Germany every 3 hours over a 48-hour period resulting in 32 metagenomes paired to geochemical and metabolite measurements. We reconstructed 6,500 viral and 1,033 microbial genomes and found distinct communities associated with each river compartment. We show that 17% of our vMAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to carbon and nitrogen cycling. Together, these findings demonstrate that microbial and viral communities in surface waters of this urban river can exist as stable communities along a flowing river; and raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.
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Liu R, Li Z, Han G, Cun S, Hou D, Yu Z, Xue K, Liu X. Microbial density-dependent viral dynamics and low activity of temperate phages in the activated sludge process. WATER RESEARCH 2023; 232:119709. [PMID: 36764107 DOI: 10.1016/j.watres.2023.119709] [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: 10/16/2022] [Revised: 01/31/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
The ecological behavior of bacteriophages (phages), the most abundant biological entity in wastewater treatment systems, is poorly understood, especially that of temperate phages. Here, the temporal dynamics of lytic and temperate phages in a laboratory-scale activated sludge reactor with a sludge bulking issue was investigated using coupled sludge metagenomic and viromic analyses. The lysogenic fragments (prophages) identified were widely distributed in the reconstructed metagenome-assembled genomes (61.7%, n = 227). However, only 12.3% of the identified prophages experienced lysogenic-lytic switching, and the abundance contribution of prophages to free virus communities was only 0.02-0.3%, indicating low activity of temperate phages. Although the sludge community changed dramatically during reactor operation, no massive prophage induction events were detected. Statistical analyses showed strong correlations between sludge concentration and free virus and temperate phage communities, suggesting microbial density-dependent virus dynamics in the sludge microbiota.
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Affiliation(s)
- Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China; Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou City, Shandong Province, China.
| | - Zong Li
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Ganghua Han
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Shujuan Cun
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Deyin Hou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China.
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Turzynski V, Griesdorn L, Moraru C, Soares AR, Simon SA, Stach TL, Rahlff J, Esser SP, Probst AJ. Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition. Viruses 2023; 15:v15040910. [PMID: 37112890 PMCID: PMC10143303 DOI: 10.3390/v15040910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap of knowledge by studying viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a period of four years. Using virus-targeted direct-geneFISH (virusFISH) whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections from 2019 to 2022. Based on fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by sulfate-reducing members affiliated with Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the uncultivated virus-host system described herein represents a suitable model system for studying deep biosphere virus-host interactions in future research endeavors.
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Affiliation(s)
- Victoria Turzynski
- Environmental Microbiology and Biotechnology (EMB), Department of Chemistry, Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Universitätsstraße 150, 44780 Bochum, Germany
- Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Lea Griesdorn
- Environmental Microbiology and Biotechnology (EMB), Department of Chemistry, Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Universitätsstraße 150, 44780 Bochum, Germany
- Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - André R. Soares
- Environmental Microbiology and Biotechnology (EMB), Department of Chemistry, Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Universitätsstraße 150, 44780 Bochum, Germany
- Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Sophie A. Simon
- Environmental Microbiology and Biotechnology (EMB), Department of Chemistry, Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Universitätsstraße 150, 44780 Bochum, Germany
- Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Tom L. Stach
- Environmental Microbiology and Biotechnology (EMB), Department of Chemistry, Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Universitätsstraße 150, 44780 Bochum, Germany
- Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Janina Rahlff
- Environmental Microbiology and Biotechnology (EMB), Department of Chemistry, Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Sarah P. Esser
- Environmental Microbiology and Biotechnology (EMB), Department of Chemistry, Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Universitätsstraße 150, 44780 Bochum, Germany
- Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Alexander J. Probst
- Environmental Microbiology and Biotechnology (EMB), Department of Chemistry, Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Universitätsstraße 150, 44780 Bochum, Germany
- Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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49
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Detection and Level Evaluation of Antibodies Specific to Environmental Bacteriophage I11mO19 and Related Coliphages in Non-Immunized Human Sera. Antibiotics (Basel) 2023; 12:antibiotics12030586. [PMID: 36978455 PMCID: PMC10044619 DOI: 10.3390/antibiotics12030586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Bacteriophages (phages) are viruses infecting bacteria. They are widely present in the environment, food, and normal microflora. The human microbiome is a mutually interdependent network of bacteria, bacteriophages, and human cells. The stability of these tri-kingdom interactions may be essential for maintaining immunologic and metabolic health. Phages, as with each other’s antigens, may evoke an immune response during a human’s lifetime and induce specific antibody generation. In this manuscript, we labeled these antibodies as naturally generated. Naturally generated antibodies may be one of the most important factors limiting the efficacy of phage therapy. Herein, we attempted to determine the physiological level of these antibodies specific to a population bacteriophage named I11mO19 in human sera, using an ELISA-based assay. First, we purified the phage particles and assessed the immunoreactivity of phage proteins. Then, affinity chromatography was performed on columns with immobilized phage proteins to obtain a fraction of human polyclonal anti-phage antibodies. These antibodies were used as a reference to elaborate an immunoenzymatic test that was used to determine the level of natural anti-phage antibodies. We estimated the average level of anti-I11mO19 phage antibodies at 190 µg per one milliliter of human serum. However, immunoblotting revealed that cross-reactivity occurs between some proteins of I11mO19 and two other coliphages: T4 and ΦK1E. The antigens probably share common epitopes, suggesting that the determined level of anti-I11mO19 phage might be overestimated and reflects a group of antibodies reactive to a broad range of other E. coli phages. Anti-I11mO19 antibodies did not react with Pseudomonas bacteriophage F8, confirming specificity to the coliphage group. In this work, we wanted to show whether it is possible to determine the presence and level of anti-phage antibodies in nontargeted-immunized sera, using an immunoenzymatic assay. The conclusion is that it is possible, and specific antibodies can be determined. However, the specificity refers to a broader coliphage group of phages, not only the single phage strain.
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50
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Tu Q, Pu M, Li Y, Wang Y, Li M, Song L, Li M, An X, Fan H, Tong Y. Acinetobacter Baumannii Phages: Past, Present and Future. Viruses 2023; 15:v15030673. [PMID: 36992382 PMCID: PMC10057898 DOI: 10.3390/v15030673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Acinetobacter baumannii (A. baumannii) is one of the most common clinical pathogens and a typical multi-drug resistant (MDR) bacterium. With the increase of drug-resistant A. baumannii infections, it is urgent to find some new treatment strategies, such as phage therapy. In this paper, we described the different drug resistances of A. baumannii and some basic properties of A. baumannii phages, analyzed the interaction between phages and their hosts, and focused on A. baumannii phage therapies. Finally, we discussed the chance and challenge of phage therapy. This paper aims to provide a more comprehensive understanding of A. baumannii phages and theoretical support for the clinical application of A. baumannii phages.
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Affiliation(s)
- Qihang Tu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mingfang Pu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yahao Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuer Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Maochen Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Correspondence: (H.F.); (Y.T.)
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), Beijing University of Chemical Technology, Beijing 100029, China
- Correspondence: (H.F.); (Y.T.)
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