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Le S, Wei L, Wang J, Tian F, Yang Q, Zhao J, Zhong Z, Liu J, He X, Zhong Q, Lu S, Liang H. Bacteriophage protein Dap1 regulates evasion of antiphage immunity and Pseudomonas aeruginosa virulence impacting phage therapy in mice. Nat Microbiol 2024; 9:1828-1841. [PMID: 38886583 DOI: 10.1038/s41564-024-01719-5] [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: 10/26/2023] [Accepted: 04/30/2024] [Indexed: 06/20/2024]
Abstract
Bacteriophages have evolved diverse strategies to overcome host defence mechanisms and to redirect host metabolism to ensure successful propagation. Here we identify a phage protein named Dap1 from Pseudomonas aeruginosa phage PaoP5 that both modulates bacterial host behaviour and contributes to phage fitness. We show that expression of Dap1 in P. aeruginosa reduces bacterial motility and promotes biofilm formation through interference with DipA, a c-di-GMP phosphodiesterase, which causes an increase in c-di-GMP levels that trigger phenotypic changes. Results also show that deletion of dap1 in PaoP5 significantly reduces genome packaging. In this case, Dap1 directly binds to phage HNH endonuclease, prohibiting host Lon-mediated HNH degradation and promoting phage genome packaging. Moreover, PaoP5Δdap1 fails to rescue P. aeruginosa-infected mice, implying the significance of dap1 in phage therapy. Overall, these results highlight remarkable dual functionality in a phage protein, enabling the modulation of host behaviours and ensuring phage fitness.
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Affiliation(s)
- Shuai Le
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, China
- State Key Laboratory of Trauma and Chemical Poisoning, Chongqing, China
| | - Leilei Wei
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
- College of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jing Wang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, China
- State Key Laboratory of Trauma and Chemical Poisoning, Chongqing, China
| | - Fang Tian
- College of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Qian Yang
- College of Life Sciences, Northwest University, Xi'an, China
| | - Jingru Zhao
- College of Life Sciences, Northwest University, Xi'an, China
| | - Zhuojun Zhong
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, China
- State Key Laboratory of Trauma and Chemical Poisoning, Chongqing, China
| | - Jiazhen Liu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, China
- State Key Laboratory of Trauma and Chemical Poisoning, Chongqing, China
| | - Xuesong He
- The ADA Forsyth Institute, Cambridge, MA, USA
| | - Qiu Zhong
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Shuguang Lu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University, Chongqing, China
- State Key Laboratory of Trauma and Chemical Poisoning, Chongqing, China
| | - Haihua Liang
- College of Medicine, Southern University of Science and Technology, Shenzhen, China.
- University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China.
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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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Li D, Liang W, Huang Z, Ma W, Liu Q. The spontaneously produced lysogenic prophage phi456 promotes bacterial resistance to adverse environments and enhances the colonization ability of avian pathogenic Escherichia coli strain DE456. Vet Res 2024; 55:37. [PMID: 38532498 DOI: 10.1186/s13567-024-01292-z] [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: 01/18/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
In the last decade, prophages that possess the ability of lysogenic transformation have become increasingly significant. Their transfer and subsequent activity in the host have a significant impact on the evolution of bacteria. Here, we investigate the role of prophage phi456 with high spontaneous induction in the bacterial genome of Avian pathogenic Escherichia coli (APEC) DE456. The phage particles, phi456, that were released from DE456 were isolated, purified, and sequenced. Additionally, phage particles were no longer observed either during normal growth or induced by nalidixic acid in DE456Δphi456. This indicated that the released phage particles from DE456 were only phi456. We demonstrated that phi456 contributed to biofilm formation through spontaneous induction of the accompanying increase in the eDNA content. The survival ability of DE456Δphi456 was decreased in avian macrophage HD11 under oxidative stress and acidic conditions. This is likely due to a decrease in the transcription levels of three crucial genes-rpoS, katE, and oxyR-which are needed to help the bacteria adapt to and survive in adverse environments. It has been observed through animal experiments that the presence of phi456 in the DE456 genome enhances colonization ability in vivo. Additionally, the number of type I fimbriae in DE456Δphi456 was observed to be reduced under transmission electron microscopy when compared to the wild-type strain. The qRT-PCR results indicated that the expression levels of the subunit of I fimbriae (fimA) and its apical adhesin (fimH) were significantly lower in DE456Δphi456. Therefore, it can be concluded that phi456 plays a crucial role in helping bacterial hosts survive in unfavorable conditions and enhancing the colonization ability in DE456.
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Affiliation(s)
- Dezhi Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wei Liang
- The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Zhiqiang Huang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Wenwen Ma
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Qing Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China.
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Wu M, Zhu Y, Yang Y, Gong Y, Chen Z, Liao B, Xiong Y, Zhou X, Li Y. SVep1, a temperate phage of human oral commensal Streptococcus vestibularis. Front Microbiol 2023; 14:1256669. [PMID: 37779698 PMCID: PMC10536254 DOI: 10.3389/fmicb.2023.1256669] [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: 07/11/2023] [Accepted: 08/18/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Bacteriophages play a vital role in the human oral microbiome, yet their precise impact on bacterial physiology and microbial communities remains relatively understudied due to the limited isolation and characterization of oral phages. To address this gap, the current study aimed to isolate and characterize novel oral phages. Methods To achieve this, oral bacteria were isolated using a culture-omics method from 30 samples collected from healthy individuals. These bacteria were then cultured in three different types of media under both aerobic and anaerobic conditions. The samples were subsequently subjected to full-length 16S rRNA gene sequencing for analysis. Subsequently, we performed the isolation of lytic and lysogenic phages targeting all these bacteria. Results In the initial step, a total of 75 bacterial strains were successfully isolated, representing 30 species and 9 genera. Among these strains, Streptococcus was found to have the highest number of species. Using a full-length 16S rRNA gene similarity threshold of 98.65%, 14 potential novel bacterial species were identified. In the subsequent phase, a temperate phage, which specifically targets the human oral commensal bacterium S. vestibularis strain SVE8, was isolated. The genome of S. vestibularis SVE8 consists of a 1.96-megabase chromosome, along with a 43,492-base pair prophage designated as SVep1. Annotation of SVep1 revealed the presence of 62 open reading frames (ORFs), with the majority of them associated with phage functions. However, it is worth noting that no plaque formation was observed in S. vestibularis SVE8 following lytic induction using mitomycin C. Phage particles were successfully isolated from the supernatant of mitomycin C-treated cultures of S. vestibularis SVE8, and examination using transmission electron microscopy confirmed that SVep1 is a siphovirus. Notably, phylogenetic analysis suggested a common ancestral origin between phage SVep1 and the cos-type phages found in S. thermophilus. Discussion The presence of SVep1 may confer immunity to S. vestibularis against infection by related phages and holds potential for being engineered as a genetic tool to regulate oral microbiome homeostasis and oral diseases.
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Affiliation(s)
- Miaomiao Wu
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yanpeng Zhu
- Department of Oral and Maxillofacial Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yuhui Yang
- School of Nursing, Army Medical University, Chongqing, China
| | - Yali Gong
- State Key Laboratory of Trauma, Burn and Combined Injury, Third Military Medical University, Chongqing, China
| | - Zongyue Chen
- School of Nursing, Army Medical University, Chongqing, China
| | - Binyou Liao
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yu Xiong
- Department of Oral and Maxillofacial Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Xia Zhou
- State Key Laboratory of Trauma, Burn and Combined Injury, Third Military Medical University, Chongqing, China
- Department of Stomatology, Daping Hospital, Army Medical University, Chongqing, China
| | - Yan Li
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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de Lima Júnior AA, de Sousa EC, de Oliveira THB, de Santana RCF, da Silva SKR, Coelho LCBB. Genus Streptomyces: Recent advances for biotechnological purposes. Biotechnol Appl Biochem 2023; 70:1504-1517. [PMID: 36924211 DOI: 10.1002/bab.2455] [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: 10/27/2022] [Revised: 02/06/2023] [Accepted: 02/26/2023] [Indexed: 03/18/2023]
Abstract
Actinomycetes are a distinct group of filamentous bacteria. The Streptomyces genus within this group has been extensively studied over the years, with substantial contributions to society and science. This genus is known for its antimicrobial production, as well as antitumor, biopesticide, and immunomodulatory properties. Therefore, the extraordinary plasticity of the Streptomyces genus has inspired new research techniques. The newest way of exploring Streptomyces has comprised the discovery of new natural metabolites and the application of emerging tools such as CRISPR technology in drug discovery. In this narrative review, we explore relevant published literature concerning the ongoing novelties of the Streptomyces genus.
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Affiliation(s)
- Apolonio Alves de Lima Júnior
- Departamento de Bioquímica, Centro de Biociências, CB, Universidade Federal de Pernambuco (UFPE), Avenida Professor Moraes Rego, S/N, Cidade Universitária, Recife, Pernambuco, Brazil
| | | | - Thales Henrique Barbosa de Oliveira
- Departamento de Bioquímica, Centro de Biociências, CB, Universidade Federal de Pernambuco (UFPE), Avenida Professor Moraes Rego, S/N, Cidade Universitária, Recife, Pernambuco, Brazil
| | | | | | - Luana Cassandra Breitenbach Barroso Coelho
- Departamento de Bioquímica, Centro de Biociências, CB, Universidade Federal de Pernambuco (UFPE), Avenida Professor Moraes Rego, S/N, Cidade Universitária, Recife, Pernambuco, Brazil
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Abstract
The oral cavity is an unique ecosystem formed by different structures, tissues, and a complex microbial community formed by hundreds of different species of bacteria, fungi, viruses, phages, and the candidate phyla radiation (CPR) group, all living in symbiosis with healthy individuals. In an opposite state, dental caries is a biofilm-mediated dysbiosis that involves changes in the core microbiome composition and function, which leads to the demineralization of tooth tissues due to the fermentation of dietary carbohydrates, producing acid by select oral bacteria. The cariogenic biofilm is typically characterized by bacterial species with the ability of adhering to the saliva-coated tooth surface, production of exopolysaccharides-rich matrix (which will limit the diffusion of acidic products of carbohydrate fermentation), and the ability of surviving in this acidic environment. Besides years of research and dental treatment, dental caries remains the most common chronic disease in children worldwide. This article aims to bring an insightful discussion about important questions that remain unanswered in the Cariology and Oral Microbiology fields, to move Science forward, characterize the interrelationships of these communities, and understand mechanistic functions between microorganisms and the host, therefore leading to translatable knowledge that benefits the provision of care to our pediatric patients.
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Affiliation(s)
- Apoena Aguiar Ribeiro
- Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, USA
- CONTACT Apoena Aguiar Ribeiro Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, 150 Dental Circle, Chapel Hill, CB 7450, USA
| | - Bruce J. Paster
- Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, USA
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Li D, Liang W, Hu Q, Ren J, Xue F, Liu Q, Tang F. The effect of a spontaneous induction prophage, phi458, on biofilm formation and virulence in avian pathogenic Escherichia coli. Front Microbiol 2022; 13:1049341. [PMID: 36452923 PMCID: PMC9701743 DOI: 10.3389/fmicb.2022.1049341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/24/2022] [Indexed: 12/25/2023] Open
Abstract
Prophage sequences are present in most bacterial genomes and account for up to 20% of its host genome. Integration of temperate phages may have an impact on the expression of host genes, while some prophages could turn into the lytic cycle and affect bacterial host biological characteristics. We investigated the role of spontaneous induction prophages in avian pathogenic Escherichia coli (APEC), which is the causative agent of avian colibacillosis in poultry, and considered a potential zoonotic bacterium related to the fact it serves as an armory of extraintestinal pathogenic E. coli. We found that APEC strain DE458 had a high spontaneous induction rate in vivo and in vitro. The released phage particles, phi458, were isolated, purified, and sequenced, and the deletion mutant, DE458Δphi458, was constructed and characterized. Biofilm formation of DE458Δphi458 was strongly decreased compared to that of the wild-type strain (p < 0.01). In addition, while the addition of DNase (100 μg/ml) did not affect prophage release but could digest eDNA, it significantly reduced the biofilm production of DE458 biofilm to a level close to that of DE458Δphi458. Compared to DE458, the adhesion and invasion abilities of DE458Δphi458 increased by approximately 6-20 times (p < 0.05). The virulence of DE458Δphi458 was enhanced by approximately 10-fold in chickens based on a 50% lethal dose. Furthermore, avian infection assays showed that the bacterial loads of DE458Δphi458 in the lung and liver were increased by 16.5- and 10-fold (p < 0.05), respectively, compared with those of the WT strain. The qRT-PCR revealed that deletion of phi458 led to upregulation of type I fimbriate-related gene fimH and curli-related gene csgC by 3- and 2.8-fold, respectively (p < 0.01). Our study revealed that phi458 promoted biofilm formation by spontaneously inducing and decreasing virulence by repressing virulence genes.
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Affiliation(s)
- Dezhi Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wei Liang
- The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi, China
| | - Qingyue Hu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Jianluan Ren
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Qing Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Fang Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Exploitation of a Bacterium-Encoded Lytic Transglycosylase by a Human Oral Lytic Phage To Facilitate Infection. J Virol 2022; 96:e0106322. [PMID: 36000841 PMCID: PMC9472602 DOI: 10.1128/jvi.01063-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Bacteriophages (phages) are an integral part of the human oral microbiome. Their roles in modulating bacterial physiology and shaping microbial communities have been discussed but remain understudied due to limited isolation and characterization of oral phage. Here, we report the isolation of LC001, a lytic phage targeting human oral Schaalia odontolytica (formerly known as Actinomyces odontolyticus) strain XH001. We showed that LC001 attached to and infected surface-grown, but not planktonic, XH001 cells, and it displayed remarkable host specificity at the strain level. Whole-genome sequencing of spontaneous LC001-resistant, surface-grown XH001 mutants revealed that the majority of the mutants carry nonsense or frameshift mutations in XH001 gene APY09_05145 (renamed ltg-1), which encodes a putative lytic transglycosylase (LT). The mutants are defective in LC001 binding, as revealed by direct visualization of the significantly reduced attachment of phage particles to the XH001 spontaneous mutants compared that to the wild type. Meanwhile, targeted deletion of ltg-1 produced a mutant that is defective in LC001 binding and resistant to LC001 infection even as surface-grown cells, while complementation of ltg-1 in the mutant background restored the LC001-sensitive phenotype. Intriguingly, similar expression levels of ltg-1 were observed in surface-grown and planktonic XH001, which displayed LC001-binding and nonbinding phenotypes, respectively. Furthermore, the overexpression of ltg-1 failed to confer an LC001-binding and -sensitive phenotype to planktonic XH001. Thus, our data suggested that rather than directly serving as a phage receptor, ltg-1-encoded LT may increase the accessibility of phage receptor, possibly via its enzymatic activity, by cleaving the peptidoglycan structure for better receptor exposure during peptidoglycan remodeling, a function that can be exploited by LC001 to facilitate infection. IMPORTANCE The evidence for the presence of a diverse and abundant phage population in the host-associated oral microbiome came largely from metagenomic analysis or the observation of virus-like particles within saliva/plaque samples, while the isolation of oral phage and investigation of their interaction with bacterial hosts are limited. Here, we report the isolation of LC001, the first lytic phage targeting oral Schaalia odontolytica. Our study suggested that LC001 may exploit the host bacterium-encoded lytic transglycosylase function to gain access to the receptor, thus facilitating its infection.
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Li X, Liu Y, Yang X, Li C, Song Z. The Oral Microbiota: Community Composition, Influencing Factors, Pathogenesis, and Interventions. Front Microbiol 2022; 13:895537. [PMID: 35572634 PMCID: PMC9100676 DOI: 10.3389/fmicb.2022.895537] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 12/12/2022] Open
Abstract
The human oral cavity provides a habitat for oral microbial communities. The complexity of its anatomical structure, its connectivity to the outside, and its moist environment contribute to the complexity and ecological site specificity of the microbiome colonized therein. Complex endogenous and exogenous factors affect the occurrence and development of the oral microbiota, and maintain it in a dynamic balance. The dysbiotic state, in which the microbial composition is altered and the microecological balance between host and microorganisms is disturbed, can lead to oral and even systemic diseases. In this review, we discuss the current research on the composition of the oral microbiota, the factors influencing it, and its relationships with common oral diseases. We focus on the specificity of the microbiota at different niches in the oral cavity, the communities of the oral microbiome, the mycobiome, and the virome within oral biofilms, and interventions targeting oral pathogens associated with disease. With these data, we aim to extend our understanding of oral microorganisms and provide new ideas for the clinical management of infectious oral diseases.
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Affiliation(s)
- Xinyi Li
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Yanmei Liu
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Xingyou Yang
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Chengwen Li
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
- *Correspondence: Chengwen Li,
| | - Zhangyong Song
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
- Zhangyong Song,
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Zhang J, Arif M, Shen H, Sun D, Pu X, Hu J, Lin B, Yang Q. Genomic Comparisons and Phenotypic Diversity of Dickeya zeae Strains Causing Bacterial Soft Rot of Banana in China. FRONTIERS IN PLANT SCIENCE 2022; 13:822829. [PMID: 35222482 PMCID: PMC8864124 DOI: 10.3389/fpls.2022.822829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Bacterial soft rot of banana, caused by Dickeya zeae, is spreading rapidly in important banana growing areas in China and seriously threatens banana production. In this study, we sequenced the high-quality complete genomes of three typical banana strains, MS1 (size: 4,831,702-bp; genome coverages: 538x), MS_2014 (size: 4,740,000-bp; genome coverages: 586x) and MS_2018 (size: 4,787,201-bp; genome coverages: 583x), isolated in 2009, 2014, and 2018, respectively. To determine their genomic and phenotypic diversity with respect to their hosts of origin, they were compared with other D. zeae strains, including another representative banana strain MS2 from China. The sequenced strains were similar in utilization of carbon source and chemical substrates, and general genomic features of GC content, and tRNA and rRNA regions. They were also conserved in most virulence determinants, including gene-encoding secretion systems, plant cell wall degrading enzymes, and exopolysaccharides. We further explored their genomic diversity in the predicted genomic islands (GIs). These GIs were rich in integrases and transposases, where some genomic dissimilarity was observed in the flagellar gene cluster and several secondary metabolite gene clusters. Different constituents of core biosynthetic modules were found within the bacteriocin and aryl polyene (APE) pigment gene clusters, and the strains from banana showed different phenotypes with respect to antibiosis effects and colony pigmentation. Additionally, clustered regularly interspaced short palindromic repeat (CRISPR) and prophage elements, such as type I-F and III-A CRISPR arrays and an intact prophage of MS1-P5, contributed to bacterial diversity. Phylogenetic tree analysis and genome-genome nucleotide comparison confirmed the genomic divergence among the strains isolated from banana. Considering these characteristics, MS2 and MS_2014 probably diverged later than MS1, while MS_2018 was different and more similar to foreign strains isolated from other hosts in several characteristics. Strain MS_2018 caused severe symptoms on banana varieties previously considered moderately resistant or moderately susceptible, including varieties of Cavendish (Musa AAA) and Plantain (Musa ABB). Our study of genomic and phenotypic diversity raises public attention to the risk of spreading new pathogenic variants within banana growing regions and supports development of predictive strategies for disease control.
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Affiliation(s)
- Jingxin Zhang
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Huifang Shen
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dayuan Sun
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoming Pu
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - John Hu
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Birun Lin
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qiyun Yang
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Serrage HJ, Jepson MA, Rostami N, Jakubovics NS, Nobbs AH. Understanding the Matrix: The Role of Extracellular DNA in Oral Biofilms. FRONTIERS IN ORAL HEALTH 2022; 2:640129. [PMID: 35047995 PMCID: PMC8757797 DOI: 10.3389/froh.2021.640129] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/09/2021] [Indexed: 12/13/2022] Open
Abstract
Dental plaque is the key etiological agent in caries formation and the development of the prevalent chronic oral inflammatory disease, periodontitis. The dental plaque biofilm comprises a diverse range of microbial species encased within a rich extracellular matrix, of which extracellular DNA (eDNA) has been identified as an important component. The molecular mechanisms of eDNA release and the structure of eDNA have yet to be fully characterized. Nonetheless, key functions that have been proposed for eDNA include maintaining biofilm structural integrity, initiating adhesion to dental surfaces, acting as a nutrient source, and facilitating horizontal gene transfer. Thus, eDNA is a potential therapeutic target for the management of oral disease–associated biofilm. This review aims to summarize advances in the understanding of the mechanisms of eDNA release from oral microorganisms and in the methods of eDNA detection and quantification within oral biofilms.
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Affiliation(s)
- Hannah J Serrage
- Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Mark A Jepson
- Wolfson Bioimaging Facility, University of Bristol, Bristol, United Kingdom
| | - Nadia Rostami
- School of Dental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Nicholas S Jakubovics
- School of Dental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Angela H Nobbs
- Bristol Dental School, University of Bristol, Bristol, United Kingdom
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12
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Hao Y, Wang S, Zhang M, Tang Q, Meng C, Wang L, Fan Q, Yan Y, Xiao X, Jian H. Isolation and characterization of a novel linear-plasmid phage from the sediment of the Mariana Trench. Virol Sin 2022; 37:311-313. [PMID: 35234616 PMCID: PMC9170930 DOI: 10.1016/j.virs.2022.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/20/2021] [Indexed: 11/24/2022] Open
Abstract
HMP1 is the first bacteriophage isolated from hadal sediment, with the highest water depth on record up to now. The isolation of HMP1 extends the habitat of linear plasmid phages from the surface to the deep ocean. The genomic and morphological features of HMP1 provide hints on the vertical exchange of viral communities in the ocean. HMP1 and Halomonas sp. MT08-1 contribute a useful hadal phage-host system for in-depth analysis in the future.
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13
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Abstract
Mediators of the initiation, development, and recurrence of periodontitis include the oral microbiome embedded in subgingival plaque and the host immune response to a dysbiosis within this dynamic and complex microbial community. Although mediators have been studied extensively, researchers in the field have been unable to fully ascribe certain clinical presentations of periodontitis to their nature. Emergence of high-throughput sequencing technologies has resulted in better characterization of the microbial oral dysbiosis that extends beyond the extensively studied putative bacterial periodontopathogens to a shift in the oral virome composition during disease conditions. Although the biological dark matter inserted by retroviruses was once believed to be nonfunctional, research has revealed that it encodes historical viral-eukaryotic interactions and influences host development. The objective of this review is to evaluate the proposed association of herpesviruses to the etiology and pathogenesis of periodontal disease and survey the highly abundant prokaryotic viruses to delineate their potential roles in biofilm dynamics, as well as their interactions with putative bacterial periodontopathogens and eukaryotic cells. The findings suggest that potential novel periodontal therapies targeting or utilizing the oral virome can alleviate certain clinical presentations of periodontitis. Perhaps it is time to embrace the viral dark matter within the periodontal environment to fully comprehend the pathogenesis and systemic implications of periodontitis.
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Affiliation(s)
- April Martínez
- Orofacial Sciences DepartmentSchool of DentistryUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Ryutaro Kuraji
- Orofacial Sciences DepartmentSchool of DentistryUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
- Department of Life Science DentistryThe Nippon Dental UniversityTokyoJapan
- Department of PeriodontologyThe Nippon Dental University School of Life Dentistry at TokyoTokyoJapan
| | - Yvonne L. Kapila
- Orofacial Sciences DepartmentSchool of DentistryUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
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14
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Song M, Wu D, Hu Y, Luo H, Li G. Characterization of an Enterococcus faecalis Bacteriophage vB_EfaM_LG1 and Its Synergistic Effect With Antibiotic. Front Cell Infect Microbiol 2021; 11:698807. [PMID: 34336721 PMCID: PMC8322680 DOI: 10.3389/fcimb.2021.698807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/25/2021] [Indexed: 12/14/2022] Open
Abstract
Enterococcus faecalis is a Gram-positive opportunistic pathogen that could cause pneumonia and bacteremia in stroke patients. The development of antibiotic resistance in hospital-associated E. faecalis is a formidable public health threat. Bacteriophage therapy is a renewed solution to treat antibiotic-resistant bacterial infections. However, bacteria can acquire phage resistance quite quickly, which is a significant barrier to phage therapy. Here, we characterized a lytic E. faecalis bacteriophage Vb_EfaM_LG1 with lytic activity. Its genome did not contain antibiotic resistance or virulence genes. Vb_EfaM_LG1 effectively inhibits E. faecalis growth for a short period, and phage resistance developed within hours. However, the combination of antibiotics and phage has a tremendous synergistic effect against E. faecalis, prevents the development of phage resistance, and disrupts the biofilm efficiently. Our results show that the phage-antibiotic combination has better killing efficiency against E. faecalis.
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Affiliation(s)
- Min Song
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dongmei Wu
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yang Hu
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haiyan Luo
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Gongbo Li
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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15
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Abstract
Bacteriophages and bacterial biofilms are widely present in natural environments, a fact that has accelerated the evolution of phages and their bacterial hosts in these particular niches. Phage-host interactions in biofilm communities are rather complex, where phages are not always merely predators but also can establish symbiotic relationships that induce and strengthen biofilms. In this review we provide an overview of the main features affecting phage-biofilm interactions as well as the currently available methods of studying these interactions. In addition, we address the applications of phages for biofilm control in different contexts.
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Affiliation(s)
- Diana P Pires
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
| | - Luís D R Melo
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
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16
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Townsend EM, Kelly L, Muscatt G, Box JD, Hargraves N, Lilley D, Jameson E. The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome. Front Cell Infect Microbiol 2021; 11:643214. [PMID: 34150671 PMCID: PMC8213399 DOI: 10.3389/fcimb.2021.643214] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.
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Affiliation(s)
- Eleanor M Townsend
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Lucy Kelly
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - George Muscatt
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Joshua D Box
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Nicole Hargraves
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Daniel Lilley
- Warwick Medical School, The University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
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17
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Abstract
Oral bacteriophages (or phages), especially periodontal ones, constitute a growing area of interest, but research on oral phages is still in its infancy. Phages are bacterial viruses that may persist as intracellular parasitic deoxyribonucleic acid (DNA) or use bacterial metabolism to replicate and cause bacterial lysis. The microbiomes of saliva, oral mucosa, and dental plaque contain active phage virions, bacterial lysogens (ie, carrying dormant prophages), and bacterial strains containing short fragments of phage DNA. In excess of 2000 oral phages have been confirmed or predicted to infect species of the phyla Actinobacteria (>300 phages), Bacteroidetes (>300 phages), Firmicutes (>1000 phages), Fusobacteria (>200 phages), and Proteobacteria (>700 phages) and three additional phyla (few phages only). This article assesses the current knowledge of the diversity of the oral phage population and the mechanisms by which phages may impact the ecology of oral biofilms. The potential use of phage-based therapy to control major periodontal pathogens is also discussed.
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Affiliation(s)
- Szymon P Szafrański
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
| | - Jørgen Slots
- Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, California, USA
| | - Meike Stiesch
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
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18
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Duan X, Chen X, Gupta M, Seriwatanachai D, Xue H, Xiong Q, Xu T, Li D, Mo A, Tang X, Zhou X, Li Y, Yuan Q. Salivary microbiome in patients undergoing hemodialysis and its associations with the duration of the dialysis. BMC Nephrol 2020; 21:414. [PMID: 32993533 PMCID: PMC7523083 DOI: 10.1186/s12882-020-02009-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/04/2020] [Indexed: 02/08/2023] Open
Abstract
Background Chronic kidney disease (CKD) patients, especially those with end stage renal disease (ESRD) undergoing hemodialysis (HD), exhibit high prevalence of periodontitis. This cross-sectional study aimed to investigate the periodontal status of HD patients and its relationship with salivary microbiome. Methods One hundred eight HD patients and one hundred healthy control individuals were recruited. They were subjected to periodontal examination followed by saliva samples collection for 16S rRNA gene sequencing. Results The HD patients were with worse periodontal health status, and exhibited higher salivary microbial diversity and lower richness. The periodontal pathogens were significantly enriched in the HD patients. The inferred functional analyze showed microbes enriched in the HD patients were mainly related to metabolism. Despite the periodontal status and overall structure of the microbiome were not significantly altered as the HD duration prolonged, the abundance of Lachnospiraceae [G-2] sp. |HMT_096| is positively correlated with the duration of HD and the community periodontal index (CPI). Five OTUs (operational taxonomic units) belonging to the phyla Firmicutes were enriched as the duration prolonged, and four OTUs originated from the phyla Proteobacteria were negatively related with the CPI index. ESRD patients undergoing HD exhibited microbiota structural, compositional and functional differences compared with the healthy controls. And the species changed as the duration of hemodialysis prolonged. Conclusions End stage renal disease changes salivary microbiome and is a risk factor for oral dysbiosis.
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Affiliation(s)
- Xiaobo Duan
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China
| | - Xiaolei Chen
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, China
| | - Megha Gupta
- Department of Preventive Dental Sciences, Division of Pedodontics, College of Dentistry, Al-Showajra Academic Campus, Jazan University, Jazan, Kingdom of Saudi Arabia
| | | | - Hanxiao Xue
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China
| | - Qiuchan Xiong
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China
| | - Tong Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China
| | - Dan Li
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China
| | - Anchun Mo
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xi Tang
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China.
| | - Quan Yuan
- State Key Laboratory of Oral Diseases & National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China. .,Department of Preventive Dental Sciences, Division of Pedodontics, College of Dentistry, Al-Showajra Academic Campus, Jazan University, Jazan, Kingdom of Saudi Arabia.
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19
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Gilbert RA, Townsend EM, Crew KS, Hitch TCA, Friedersdorff JCA, Creevey CJ, Pope PB, Ouwerkerk D, Jameson E. Rumen Virus Populations: Technological Advances Enhancing Current Understanding. Front Microbiol 2020; 11:450. [PMID: 32273870 PMCID: PMC7113391 DOI: 10.3389/fmicb.2020.00450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/02/2020] [Indexed: 01/07/2023] Open
Abstract
The rumen contains a multi-kingdom, commensal microbiome, including protozoa, bacteria, archaea, fungi and viruses, which enables ruminant herbivores to ferment and utilize plant feedstuffs that would be otherwise indigestible. Within the rumen, virus populations are diverse and highly abundant, often out-numbering the microbial populations that they both predate on and co-exist with. To date the research effort devoted to understanding rumen-associated viral populations has been considerably less than that given to the other microbial populations, yet their contribution to maintaining microbial population balance, intra-ruminal microbial lysis, fiber breakdown, nutrient cycling and genetic transfer may be highly significant. This review follows the technological advances which have contributed to our current understanding of rumen viruses and drawing on knowledge from other environmental and animal-associated microbiomes, describes the known and potential roles and impacts viruses have on rumen function and speculates on the future directions of rumen viral research.
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Affiliation(s)
- Rosalind A. Gilbert
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eleanor M. Townsend
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Kathleen S. Crew
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
| | - Thomas C. A. Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Jessica C. A. Friedersdorff
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Christopher J. Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Phillip B. Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Diane Ouwerkerk
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eleanor Jameson
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
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20
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Payne AT, Davidson AJ, Kan J, Peipoch M, Bier R, Williamson K. Widespread cryptic viral infections in lotic biofilms. Biofilm 2019; 2:100016. [PMID: 33447802 PMCID: PMC7798469 DOI: 10.1016/j.bioflm.2019.100016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/06/2019] [Accepted: 11/29/2019] [Indexed: 12/01/2022] Open
Abstract
Viruses have important impacts on aquatic microbial ecology and have been studied at length in the global ocean. However, the roles of bacteriophages in lotic ecosystems, particularly in benthic biofilms, have been largely under-studied. The main goals of this work were to determine whether viruses are consistent members of natural benthic biofilm communities of freshwater streams; whether temperate phages are present and active in such biofilms; and whether community profiling approaches like RAPD-PCR can be adapted to characterize biofilm virus communities. Results from both field and laboratory experiments suggest that viruses are consistent members of lotic biofilm communities. Interestingly, prophage induction was statistically significant but only a small percentage of the total bacterial population appeared to harbor prophage or engaged in induction. Finally, while the use of RAPD-PCR for the community level profiling of biofilm viral communities suggests temporal change in response to biofilm maturity, further refinements are required for broad-scale quantitative application.
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Affiliation(s)
| | | | - Jinjun Kan
- Stroud Water Research Center, 970 Spencer Rd, Avondale, PA, 19311, USA
| | - Marc Peipoch
- Stroud Water Research Center, 970 Spencer Rd, Avondale, PA, 19311, USA
| | - Raven Bier
- Stroud Water Research Center, 970 Spencer Rd, Avondale, PA, 19311, USA
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21
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Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches. ISME JOURNAL 2019; 13:2500-2522. [PMID: 31201356 PMCID: PMC6776037 DOI: 10.1038/s41396-019-0450-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/07/2019] [Accepted: 05/26/2019] [Indexed: 12/19/2022]
Abstract
Aggregatibacter and Haemophilus species are relevant human commensals and opportunistic pathogens. Consequently, their bacteriophages may have significant impact on human microbial ecology and pathologies. Our aim was to reveal the prevalence and diversity of bacteriophages infecting Aggregatibacter and Haemophilus species that colonize the human body. Genome mining with comparative genomics, screening of clinical isolates, and profiling of metagenomes allowed characterization of 346 phages grouped in 52 clusters and 18 superclusters. Less than 10% of the identified phage clusters were represented by previously characterized phages. Prophage diversity patterns varied significantly for different phage types, host clades, and environmental niches. A more diverse phage community lysogenizes Haemophilus influenzae and Haemophilus parainfluenzae strains than Aggregatibacter actinomycetemcomitans and “Haemophilus ducreyi”. Co-infections occurred more often in “H. ducreyi”. Phages from Aggregatibacter actinomycetemcomitans preferably lysogenized strains of specific serotype. Prophage patterns shared by subspecies clades of different bacterial species suggest similar ecoevolutionary drivers. Changes in frequencies of DNA uptake signal sequences and guanine–cytosine content reflect phage-host long-term coevolution. Aggregatibacter and Haemophilus phages were prevalent at multiple oral sites. Together, these findings should help exploring the ecoevolutionary forces shaping virus-host interactions in the human microbiome. Putative lytic phages, especially phiKZ-like, may provide new therapeutic options.
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22
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Big Impact of the Tiny: Bacteriophage-Bacteria Interactions in Biofilms. Trends Microbiol 2019; 27:739-752. [PMID: 31128928 DOI: 10.1016/j.tim.2019.04.006] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/10/2019] [Accepted: 04/19/2019] [Indexed: 01/17/2023]
Abstract
Bacteriophages (phages) have been shaping bacterial ecology and evolution for millions of years, for example, by selecting for defence strategies. Evidence supports that bacterial biofilm formation is one such strategy and that biofilm-mediated protection against phage infection depends on maturation and composition of the extracellular matrix. Interestingly, studies have revealed that phages can induce and strengthen biofilms. Here we review interactions between bacteria and phages in biofilms, discuss the underlying mechanisms, the potential of phage therapy for biofilm control, and emphasize the importance of considering biofilms in future phage research. This is especially relevant as biofilms are associated with increased tolerance towards antibiotics and are implicated in the majority of chronic infections.
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