1
|
Xu C, Han D, Song X, Zhang X, Liu C, Zhang J, Shen B, Li Z, Ma R, Li Y, Xin Y, Ji W, Zhang L, Wang X, Hu C, Li X. The possibly role of GnIH in stress and gut dysfunction in chicken. Poult Sci 2024; 103:103757. [PMID: 38697006 PMCID: PMC11070904 DOI: 10.1016/j.psj.2024.103757] [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: 01/06/2024] [Revised: 03/21/2024] [Accepted: 04/06/2024] [Indexed: 05/04/2024] Open
Abstract
Stress is known to disrupt the intestinal barrier and induce intestinal dysfunction. A critical role for gonadotropin inhibitory hormone (GnIH) in stress has emerged. However, whether GnIH mediates stress-induced intestinal dysfunction remains unknown. The present study explored this question through in vivo and in vitro experiments in hens. Our in vivo experiments showed that continuous intraperitoneal injection of GnIH not only significantly increased the concentration of stress hormones in serum, but also significantly elevated the mRNA expression of glucocorticoid receptor (GR) in the duodenum and jejunum. Moreover, morphological and molecular analyses revealed that GnIH disrupted the physical and chemical barriers of the intestine and dramatically increased inflammatory factor levels in the intestine and serum of hens. Interestingly, the microbiomics results showed that GnIH altered the structure and composition of the gut flora in the cecum, revealing an increased abundance of harmful intestinal bacteria such as Desulfovibrionaceae. Similar results were found in in vitro studies in which the GnIH-induced intestinal mucosal barrier was disrupted, and inflammation increased in jejunal explants, although no significant difference was found in the expression of GR between the control and GnIH groups. Our results demonstrated that GnIH not only directly damaged intestinal barriers and elevated intestinal inflammation but also mediated stress and microflora imbalance-induced intestinal function disorder, suggesting that GnIH is a potential therapeutic target for gut dysfunction, stress-induced intestinal function disorder, and inflammatory bowel disease in animals and humans.
Collapse
Affiliation(s)
- Changlin Xu
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Dongyang Han
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Xingxing Song
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Xin Zhang
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Chengcheng Liu
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Jiani Zhang
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Bingqian Shen
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Zixin Li
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Runwen Ma
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Yinan Li
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Yuanyuan Xin
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Wantong Ji
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Lingyuan Zhang
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Xiaoye Wang
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Chuanhuo Hu
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China
| | - Xun Li
- College of Animal Science and Technology, Guangxi University; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, RP 530004, China.
| |
Collapse
|
2
|
Zhang M, Xiong J, Zhou L, Li J, Fan J, Li X, Zhang T, Yin Z, Yin H, Liu X, Meng D. Community ecological study on the reduction of soil antimony bioavailability by SRB-based remediation technologies. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132256. [PMID: 37567138 DOI: 10.1016/j.jhazmat.2023.132256] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Sulfate-reducing bacteria (SRB) were effective in stabilizing Sb. However, the influence of electron donors and acceptors during SRB remediation, as well as the ecological principles involved, remained unclear. In this study, Desulfovibrio desulfuricans ATCC 7757 was utilized to stabilize soil Sb within microcosm. Humic acid (HA) or sodium sulfate (Na2SO4) were employed to enhance SRB capacity. The SRB+HA treatment exhibited the highest Sb stabilization rate, achieving 58.40%. Bacterial community analysis revealed that SRB altered soil bacterial diversity, community composition, and assembly processes, with homogeneous selection as the predominant assembly processes. When HA and Na2SO4 significantly modified the stimulated microbial community succession trajectories, shaped the taxonomic composition and interactions of the bacterial community, they showed converse effect in shaping bacterial community which were both helpful for promoting dissimilatory sulfate reduction. Na2SO4 facilitated SRB-mediated anaerobic reduction and promoted interactions between SRB and bacteria involved in nitrogen and sulfur cycling. The HA stimulated electron generation and storage, and enhanced the interactions between SRB and bacteria possessing heavy metal tolerance or carbohydrate degradation capabilities.
Collapse
Affiliation(s)
- Min Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Jing Xiong
- Hunan urban and Rural Environmental Construction Co., Ltd, Changsha 410118, China
| | - Lei Zhou
- Beijing Research Institute of Chemical Engineering and Metallurgy, Beijing 101148, China
| | - Jingjing Li
- Technology Center, China Tobacco Fujian Industrial Co., Ltd., Xiamen, Fujian 361000, China
| | - Jianqiang Fan
- Technology Center, China Tobacco Fujian Industrial Co., Ltd., Xiamen, Fujian 361000, China
| | - Xing Li
- Hunan HIKEE Environmental Technology CO., LTD, Changsha 410221, China
| | - Teng Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Hunan urban and Rural Environmental Construction Co., Ltd, Changsha 410118, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Zhuzhong Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China.
| |
Collapse
|
3
|
McKerral JC, Papudeshi B, Inglis LK, Roach MJ, Decewicz P, McNair K, Luque A, Dinsdale EA, Edwards RA. The Promise and Pitfalls of Prophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.537752. [PMID: 37131798 PMCID: PMC10153245 DOI: 10.1101/2023.04.20.537752] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Phages dominate every ecosystem on the planet. While virulent phages sculpt the microbiome by killing their bacterial hosts, temperate phages provide unique growth advantages to their hosts through lysogenic conversion. Many prophages benefit their host, and prophages are responsible for genotypic and phenotypic differences that separate individual microbial strains. However, the microbes also endure a cost to maintain those phages: additional DNA to replicate and proteins to transcribe and translate. We have never quantified those benefits and costs. Here, we analysed over two and a half million prophages from over half a million bacterial genome assemblies. Analysis of the whole dataset and a representative subset of taxonomically diverse bacterial genomes demonstrated that the normalised prophage density was uniform across all bacterial genomes above 2 Mbp. We identified a constant carrying capacity of phage DNA per bacterial DNA. We estimated that each prophage provides cellular services equivalent to approximately 2.4 % of the cell's energy or 0.9 ATP per bp per hour. We demonstrate analytical, taxonomic, geographic, and temporal disparities in identifying prophages in bacterial genomes that provide novel targets for identifying new phages. We anticipate that the benefits bacteria accrue from the presence of prophages balance the energetics involved in supporting prophages. Furthermore, our data will provide a new framework for identifying phages in environmental datasets, diverse bacterial phyla, and from different locations.
Collapse
Affiliation(s)
- Jody C. McKerral
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Laura K. Inglis
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw, 02-096, Poland
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- The Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
| | - Antoni Luque
- The Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
| | - Elizabeth A. Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| |
Collapse
|
4
|
Aman Mohammadi M, Maximiano MR, Hosseini SM, Franco OL. CRISPR-Cas engineering in food science and sustainable agriculture: recent advancements and applications. Bioprocess Biosyst Eng 2023; 46:483-497. [PMID: 36707422 DOI: 10.1007/s00449-022-02842-5] [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: 08/20/2022] [Accepted: 12/14/2022] [Indexed: 01/29/2023]
Abstract
The developments in the food supply chain to support the growing population of the world is one of today's most pressing issues, and to achieve this goal improvements should be performed in both crops and microbes. For this purpose, novel approaches such as genome editing (GE) methods have upgraded the biological sciences for genome manipulation and, among such methods, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are the main exciting innovations since the Green Revolution. CRISPR/Cas systems can be a potent tool for the food industry, improvement of agricultural crops and even for protecting food-grade bacteria from foreign genetic invasive elements. This review introduces the history and mechanism of the CRISPR-Cas system as a genome editing tool and its applications in the vaccination of starter cultures, production of antimicrobials and bioactive compounds, and genome editing of microorganisms.
Collapse
Affiliation(s)
- Masoud Aman Mohammadi
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences, Food Science and Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mariana Rocha Maximiano
- S-Inova Biotech, Graduate Program in Biotechnology, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Graduate Program in Genomic Science and Biotechnology, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Seyede Marzieh Hosseini
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences, Food Science and Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Octavio Luiz Franco
- S-Inova Biotech, Graduate Program in Biotechnology, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Graduate Program in Genomic Science and Biotechnology, Universidade Católica de Brasília, Brasília, DF, Brazil
| |
Collapse
|
5
|
Dutra J, García G, Gomes R, Cardoso M, Côrtes Á, Silva T, de Jesus L, Rodrigues L, Freitas A, Waldow V, Laguna J, Campos G, Américo M, Akamine R, de Sousa M, Groposo C, Figueiredo H, Azevedo V, Góes-Neto A. Effective Biocorrosive Control in Oil Industry Facilities: 16S rRNA Gene Metabarcoding for Monitoring Microbial Communities in Produced Water. Microorganisms 2023; 11:846. [PMID: 37110269 PMCID: PMC10141917 DOI: 10.3390/microorganisms11040846] [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: 01/28/2023] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
Microbiologically influenced corrosion (MIC) or biocorrosion is a complex biological and physicochemical process, Strategies for monitoring MIC are frequently based on microbial cultivation methods, while microbiological molecular methods (MMM) are not well-established in the oil industry in Brazil. Thus, there is a high demand for the development of effective protocols for monitoring biocorrosion with MMM. The main aim of our study was to analyze the physico-chemi- cal features of microbial communities occurring in produced water (PW) and in enrichment cultures in oil pipelines of the petroleum industry. In order to obtain strictly comparable results, the same samples were used for both culturing and metabarcoding. PW samples displayed higher phylogenetic diversity of bacteria and archaea whereas PW enrichments cultures showed higher dominance of bacterial MIC-associated genera. All samples had a core community composed of 19 distinct genera, with MIC-associated Desulfovibrio as the dominant genus. We observed significant associations between the PW and cultured PW samples, with a greater number of associations found between the cultured sulfate-reducing bacteria (SRB) samples and the uncultured PW samples. When evaluating the correlation between the physicochemical characteristics of the environment and the microbiota of the uncultivated samples, we suggest that the occurrence of anaerobic digestion metabolism can be characterized by well-defined phases. Therefore, the detection of microorganisms in uncultured PW by metabarcoding, along with physi-cochemical characterization, can be a more efficient method compared to the culturing method, as it is a less laborious and cost-effective method for monitoring MIC microbial agents in oil industry facilities.
Collapse
Affiliation(s)
- Joyce Dutra
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (J.D.); (R.G.); (V.A.)
- Department of Genetics Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (Á.C.); (T.S.); (L.d.J.); (A.F.); (J.L.); (G.C.); (M.A.)
| | - Glen García
- Departments of Bioinformatic, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (G.G.); (M.C.)
| | - Rosimeire Gomes
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (J.D.); (R.G.); (V.A.)
| | - Mariana Cardoso
- Departments of Bioinformatic, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (G.G.); (M.C.)
| | - Árley Côrtes
- Department of Genetics Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (Á.C.); (T.S.); (L.d.J.); (A.F.); (J.L.); (G.C.); (M.A.)
| | - Tales Silva
- Department of Genetics Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (Á.C.); (T.S.); (L.d.J.); (A.F.); (J.L.); (G.C.); (M.A.)
| | - Luís de Jesus
- Department of Genetics Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (Á.C.); (T.S.); (L.d.J.); (A.F.); (J.L.); (G.C.); (M.A.)
| | - Luciano Rodrigues
- Department of Veterinary Medicine, Faculty of Veterinary, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.R.); (H.F.)
| | - Andria Freitas
- Department of Genetics Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (Á.C.); (T.S.); (L.d.J.); (A.F.); (J.L.); (G.C.); (M.A.)
| | - Vinicius Waldow
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro 21941-915, RJ, Brazil; (V.W.); (R.A.); (M.d.S.); (C.G.)
| | - Juliana Laguna
- Department of Genetics Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (Á.C.); (T.S.); (L.d.J.); (A.F.); (J.L.); (G.C.); (M.A.)
| | - Gabriela Campos
- Department of Genetics Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (Á.C.); (T.S.); (L.d.J.); (A.F.); (J.L.); (G.C.); (M.A.)
| | - Monique Américo
- Department of Genetics Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (Á.C.); (T.S.); (L.d.J.); (A.F.); (J.L.); (G.C.); (M.A.)
| | - Rubens Akamine
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro 21941-915, RJ, Brazil; (V.W.); (R.A.); (M.d.S.); (C.G.)
| | - Maíra de Sousa
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro 21941-915, RJ, Brazil; (V.W.); (R.A.); (M.d.S.); (C.G.)
| | - Claudia Groposo
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro 21941-915, RJ, Brazil; (V.W.); (R.A.); (M.d.S.); (C.G.)
| | - Henrique Figueiredo
- Department of Veterinary Medicine, Faculty of Veterinary, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.R.); (H.F.)
| | - Vasco Azevedo
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (J.D.); (R.G.); (V.A.)
- Department of Genetics Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (Á.C.); (T.S.); (L.d.J.); (A.F.); (J.L.); (G.C.); (M.A.)
- Departments of Bioinformatic, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (G.G.); (M.C.)
| | - Aristóteles Góes-Neto
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (J.D.); (R.G.); (V.A.)
- Departments of Bioinformatic, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (G.G.); (M.C.)
| |
Collapse
|
6
|
Dutra J, Gomes R, Yupanqui García GJ, Romero-Cale DX, Santos Cardoso M, Waldow V, Groposo C, Akamine RN, Sousa M, Figueiredo H, Azevedo V, Góes-Neto A. Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies. PeerJ 2023; 11:e14642. [PMID: 36655046 PMCID: PMC9841911 DOI: 10.7717/peerj.14642] [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: 08/03/2022] [Accepted: 12/05/2022] [Indexed: 01/15/2023] Open
Abstract
The objective of the current systematic review was to evaluate the taxonomic composition and relative abundance of bacteria and archaea associated with the microbiologically influenced corrosion (MIC), and the prediction of their metabolic functions in different sample types from oil production and transport structures worldwide. To accomplish this goal, a total of 552 published studies on the diversity of microbial communities using 16S amplicon metagenomics in oil and gas industry facilities indexed in Scopus, Web of Science, PubMed and OnePetro databases were analyzed on 10th May 2021. The selection of articles was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Only studies that performed amplicon metagenomics to obtain the microbial composition of samples from oil fields were included. Studies that evaluated oil refineries, carried out amplicon metagenomics directly from cultures, and those that used DGGE analysis were removed. Data were thoroughly investigated using multivariate statistics by ordination analysis, bivariate statistics by correlation, and microorganisms' shareability and uniqueness analysis. Additionally, the full deposited databases of 16S rDNA sequences were obtained to perform functional prediction. A total of 69 eligible articles was included for data analysis. The results showed that the sulfidogenic, methanogenic, acid-producing, and nitrate-reducing functional groups were the most expressive, all of which can be directly involved in MIC processes. There were significant positive correlations between microorganisms in the injection water (IW), produced water (PW), and solid deposits (SD) samples, and negative correlations in the PW and SD samples. Only the PW and SD samples displayed genera common to all petroliferous regions, Desulfotomaculum and Thermovirga (PW), and Marinobacter (SD). There was an inferred high microbial activity in the oil fields, with the highest abundances of (i) cofactor, (ii) carrier, and (iii) vitamin biosynthesis, associated with survival metabolism. Additionally, there was the presence of secondary metabolic pathways and defense mechanisms in extreme conditions. Competitive or inhibitory relationships and metabolic patterns were influenced by the physicochemical characteristics of the environments (mainly sulfate concentration) and by human interference (application of biocides and nutrients). Our worldwide baseline study of microbial communities associated with environments of the oil and gas industry will greatly facilitate the establishment of standardized approaches to control MIC.
Collapse
Affiliation(s)
- Joyce Dutra
- Graduate Program in Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rosimeire Gomes
- Graduate Program in Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Glen Jasper Yupanqui García
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Mariana Santos Cardoso
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vinicius Waldow
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Rubens N. Akamine
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maira Sousa
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Henrique Figueiredo
- Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|
7
|
Li JT, Jia P, Wang XJ, Ou SN, Yang TT, Feng SW, Lu JL, Fang Z, Liu J, Liao B, Shu WS, Liang JL. Metagenomic and metatranscriptomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland. NPJ Biofilms Microbiomes 2022; 8:71. [PMID: 36068230 PMCID: PMC9448743 DOI: 10.1038/s41522-022-00333-9] [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: 02/21/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
The widespread occurrence of sulfate-reducing microorganisms (SRMs) in temporarily oxic/hypoxic aquatic environments indicates an intriguing possibility that SRMs can prevail in constantly oxic/hypoxic terrestrial sulfate-rich environments. However, little attention has been given to this possibility, leading to an incomplete understanding of microorganisms driving the terrestrial part of the global sulfur (S) cycle. In this study, genome-centric metagenomics and metatranscriptomics were employed to explore the diversity, metabolic potential, and gene expression profile of SRMs in a revegetated acidic mine wasteland under constantly oxic/hypoxic conditions. We recovered 16 medium- to high-quality metagenome-assembled genomes (MAGs) containing reductive dsrAB. Among them, 12 and four MAGs belonged to Acidobacteria and Deltaproteobacteria, respectively, harboring three new SRM genera. Comparative genomic analysis based on seven high-quality MAGs (completeness >90% and contamination <10%; including six acidobacterial and one deltaproteobacterial) and genomes of three additional cultured model species showed that Acidobacteria-related SRMs had more genes encoding glycoside hydrolases, oxygen-tolerant hydrogenases, and cytochrome c oxidases than Deltaproteobacteria-related SRMs. The opposite pattern was observed for genes encoding superoxide reductases and thioredoxin peroxidases. Using VirSorter, viral genome sequences were found in five of the 16 MAGs and in all three cultured model species. These prophages encoded enzymes involved in glycoside hydrolysis and antioxidation in their hosts. Moreover, metatranscriptomic analysis revealed that 15 of the 16 SRMs reported here were active in situ. An acidobacterial MAG containing a prophage dominated the SRM transcripts, expressing a large number of genes involved in its response to oxidative stress and competition for organic matter.
Collapse
Affiliation(s)
- Jin-Tian Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China.,School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Pu Jia
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Xiao-Juan Wang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Shu-Ning Ou
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Tao-Tao Yang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Shi-Wei Feng
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Jing-Li Lu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Zhou Fang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Jun Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China.
| |
Collapse
|
8
|
Fong K, Lu YT, Brenner T, Falardeau J, Wang S. Prophage Diversity Across Salmonella and Verotoxin-Producing Escherichia coli in Agricultural Niches of British Columbia, Canada. Front Microbiol 2022; 13:853703. [PMID: 35935192 PMCID: PMC9355379 DOI: 10.3389/fmicb.2022.853703] [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: 01/12/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
Prophages have long been regarded as an important contributor to the evolution of Salmonella and Verotoxin-producing E. coli (VTEC), members of the Enterobacteriaceae that cause millions of cases of foodborne illness in North America. In S. Typhimurium, prophages provide many of the genes required for invasion; similarly, in VTEC, the Verotoxin-encoding genes are located in cryptic prophages. The ability of prophages to quickly acquire and lose genes have driven their rapid evolution, leading to highly diversified populations of phages that can infect distantly-related bacterial hosts. To defend against foreign genetic materials (i.e., phages), bacteria have evolved Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immunity, consisting of variable spacer regions that match short nucleic acid sequences of invaders previously encountered. The number of spacer regions varies widely amongst Enterobacteriaceae, and there is currently no clear consensus if the accumulation of spacers is linked to genomic prophage abundance. Given the immense prophage diversity and contribution to bacterial host phenotypes, we analyzed the prophage sequences within 118 strains of Salmonella and VTEC, 117 of which are of agricultural origin. Overall, 130 unique prophage sequences were identified and they were found to be remarkably diverse with <50% nucleotide similarity, particularly with the Gifsy-1 group which was identified in several Salmonella serovars and interestingly, a strain of VTEC. Additionally, we identified a novel plasmid-like phage that carried antibiotic resistance and bacteriocin resistance genes. The strains analyzed carried at least six distinct spacers which did not possess homology to prophages identified in the same genome. In fact, only a fraction of all identified spacers (14%) possessed significant homology to known prophages. Regression models did not discern a correlation between spacer and prophage abundance in our strains, although the relatively high number of spacers in our strains (an average of 27 in Salmonella and 19 in VTEC) suggest that high rates of infection may occur in agricultural niches and be a contributing driver in bacterial evolution. Cumulatively, these results shed insight into prophage diversity of Salmonella and VTEC, which will have further implications when informing development of phage therapies against these foodborne pathogens.
Collapse
|
9
|
Maltseva AL, Lobov AA, Pavlova PA, Panova M, Gafarova ER, Marques JP, Danilov LG, Granovitch AI. Orphan gene in Littorina: An unexpected role of symbionts in the host evolution. Gene 2022; 824:146389. [PMID: 35257790 DOI: 10.1016/j.gene.2022.146389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/29/2022] [Accepted: 02/28/2022] [Indexed: 11/16/2022]
Abstract
Mechanisms of reproductive isolation between closely related sympatric species are of high evolutionary significance as they may function as initial drivers of speciation and protect species integrity afterwards. Proteins involved in the establishment of reproductive barriers often evolve fast and may be key players in cessation of gene flow between the incipient species. The five Atlantic Littorina (Neritrema) species represent a notable example of recent radiation. The geographic ranges of these young species largely overlap and the mechanisms of reproductive isolation are poorly understood. In this study, we performed a detailed analysis of the reproductive protein LOSP, previously identified in Littorina. We showed that this protein is evolutionary young and taxonomically restricted to the genus Littorina. It has high sequence variation both within and between Littorina species, which is compatible with its presumable role in the reproductive isolation. The strongest differences in the LOSP structure were detected between Littorina subgenera with distinctive repetitive motifs present exclusively in the Neritrema species, but not in L. littorea. Moreover, the sequence of these repetitive structural elements demonstrates a high homology with genetic elements of bacteria, identified as components of Littorina associated microbiomes. We suggest that these elements were acquired from a symbiotic bacterial donor via horizontal genetic transfer (HGT), which is indirectly confirmed by the presence of multiple transposable elements in the LOSP flanking and intronic regions. Furthermore, we hypothesize that this HGT-driven evolutionary innovation promoted LOSP function in reproductive isolation, which might be one of the factors determining the intensive cladogenesis in the Littorina (Neritrema) lineage in contrast to the anagenesis in the L. littorea clade.
Collapse
Affiliation(s)
- A L Maltseva
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.
| | - A A Lobov
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia; Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Sciences, St Petersburg, Russia
| | - P A Pavlova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - M Panova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia; Department of Marine Sciences - Tjärnö, University of Gothenburg, Sweden
| | - E R Gafarova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - J P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências do Porto, 4169-007 Porto, Portugal; ISEM, Univ Montpellier, CNRS, EPHE, IRD, 34095 Montpellier, France
| | - L G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - A I Granovitch
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| |
Collapse
|
10
|
Hungaro HM, Vidigal PMP, do Nascimento EC, Gomes da Costa Oliveira F, Gontijo MTP, Lopez MES. Genomic Characterisation of UFJF_PfDIW6: A Novel Lytic Pseudomonas fluorescens-Phage with Potential for Biocontrol in the Dairy Industry. Viruses 2022; 14:v14030629. [PMID: 35337036 PMCID: PMC8951688 DOI: 10.3390/v14030629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/12/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
In this study, we have presented the genomic characterisation of UFJF_PfDIW6, a novel lytic Pseudomonas fluorescens-phage with potential for biocontrol in the dairy industry. This phage showed a short linear double-stranded DNA genome (~42 kb) with a GC content of 58.3% and more than 50% of the genes encoding proteins with unknown functions. Nevertheless, UFJF_PfDIW6’s genome was organised into five functional modules: DNA packaging, structural proteins, DNA metabolism, lysogenic, and host lysis. Comparative genome analysis revealed that the UFJF_PfDIW6’s genome is distinct from other viral genomes available at NCBI databases, displaying maximum coverages of 5% among all alignments. Curiously, this phage showed higher sequence coverages (38–49%) when aligned with uncharacterised prophages integrated into Pseudomonas genomes. Phages compared in this study share conserved locally collinear blocks comprising genes of the modules’ DNA packing and structural proteins but were primarily differentiated by the composition of the DNA metabolism and lysogeny modules. Strategies for taxonomy assignment showed that UFJF_PfDIW6 was clustered into an unclassified genus in the Podoviridae clade. Therefore, our findings indicate that this phage could represent a novel genus belonging to the Podoviridae family.
Collapse
Affiliation(s)
- Humberto Moreira Hungaro
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora 36036-900, MG, Brazil; (E.C.d.N.); (F.G.d.C.O.)
- Correspondence: (H.M.H.); (M.E.S.L.); Tel.: +55-32-2102-3804 (H.M.H.); +57-310-469-02-04 (M.E.S.L.)
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Campus da UFV, Universidade Federal de Viçosa (UFV), Viçosa 36570-900, MG, Brazil;
| | - Edilane Cristina do Nascimento
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora 36036-900, MG, Brazil; (E.C.d.N.); (F.G.d.C.O.)
| | - Felipe Gomes da Costa Oliveira
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora 36036-900, MG, Brazil; (E.C.d.N.); (F.G.d.C.O.)
| | - Marco Túlio Pardini Gontijo
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-872, SP, Brazil;
| | - Maryoris Elisa Soto Lopez
- Departamento de Engenharia de Alimentos, Universidade de Córdoba (UNICORDOBA), Córdoba 230002, Colombia
- Correspondence: (H.M.H.); (M.E.S.L.); Tel.: +55-32-2102-3804 (H.M.H.); +57-310-469-02-04 (M.E.S.L.)
| |
Collapse
|
11
|
Pattenden T, Eagles C, Wahl LM. Host life-history traits influence the distribution of prophages and the genes they carry. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200465. [PMID: 34839698 PMCID: PMC8628077 DOI: 10.1098/rstb.2020.0465] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/06/2021] [Indexed: 01/19/2023] Open
Abstract
Bacterial strains with a short minimal doubling time-'fast-growing' hosts-are more likely to contain prophages than their slow-growing counterparts. Pathogenic bacterial species are likewise more likely to carry prophages. We develop a bioinformatics pipeline to examine the distribution of prophages in fast- and slow-growing lysogens, and pathogenic and non-pathogenic lysogens, analysing both prophage length and gene content for each class. By fitting these results to a mathematical model of the evolutionary forces acting on prophages, we predict whether the observed differences can be attributed to different rates of lysogeny among the host classes, or other evolutionary pressures. We also test for significant differences in gene content among prophages, identifying genes that are preferentially lost or maintained in each class. We find that fast-growing hosts and pathogens have a greater fraction of full-length prophages, and our analysis predicts that induction rates are significantly reduced in slow-growing hosts and non-pathogenic hosts. Consistent with previous results, we find that several proteins involved in the packaging of new phage particles and lysis are preferentially lost in cryptic prophages. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
Collapse
Affiliation(s)
- Tyler Pattenden
- School of Management, Economics and Mathematics, King’s University College, Western University, London, Ontario, Canada N6A 2M3
| | - Christine Eagles
- Faculty of Mathematics, University of Waterloo, Waterloo, Ontario, Canada N6A 3K7
| | - Lindi M. Wahl
- School of Mathematical and Statistical Sciences, Western University, London, Ontario, Canada N2L 3G1
| |
Collapse
|
12
|
KALBASSI S, YARAHMADI M, MOHAMMADIFARD H, AHMADI F. The antibiofilm and antibacterial effects of medicinal plant extracts on isolated sulfate-reducing bacteria from orthodontic appliances. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.38322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
Dien LT, Ky LB, Huy BT, Mursalim MF, Kayansamruaj P, Senapin S, Rodkhum C, Dong HT. Characterization and protective effects of lytic bacteriophage pAh6.2TG against a pathogenic multidrug-resistant Aeromonas hydrophila in Nile tilapia (Oreochromis niloticus). Transbound Emerg Dis 2021; 69:e435-e450. [PMID: 34514728 DOI: 10.1111/tbed.14321] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/25/2021] [Accepted: 09/08/2021] [Indexed: 12/21/2022]
Abstract
Bacteriophage (phage) is considered as one of the alternatives to antibiotics and an environmentally friendly approach to tackle antimicrobial resistance (AMR) in aquaculture. Here, we reported isolation, morphology and genomic characterizations of a newly isolated lytic phage, designated pAh6.2TG. Host range and stability of pAh6.2TG in different environmental conditions, and protective efficacy against a pathogenic multidrug-resistant (MDR) Aeromonas hydrophila in Nile tilapia were subsequently evaluated. The results showed that pAh6.2TG is a member of the new family Chaseviridae which has genome size of 51,780 bp, encoding 65 putative open reading frames (ORFs) and is most closely related to Aeromonas phage PVN02 (99.33% nucleotide identity). The pAh6.2TG was highly specific to A. hydrophila and infected 83.3% tested strains of MDR A. hydrophila (10 out of 12) with relative stability at pH 7-9, temperature 0-40°C and salinity 0-40 ppt. In experimental challenge, pAh6.2TG treatments significantly improved survivability of Nile tilapia exposed to a lethal dose of the pathogenic MDR A. hydrophila, with relative per cent survival (RPS) of 73.3% and 50% for phage multiplicity of infection (MOI) 1.0 and 0.1, respectively. Phage treatment significantly reduced the concentration of A. hydrophila in both water and fish body. Interestingly, the surviving fish from A. hydrophila challenged groups provoked specific antibody (IgM) against this bacterium. In summary, the findings suggested that the lytic phage pAh6.2TG is an effective alternative to antibiotics to control MDR A. hydrophila in tilapia and possibly other freshwater fish.
Collapse
Affiliation(s)
- Le Thanh Dien
- Faculty of Veterinary Science, Center of Excellent in Fish Infectious Diseases (CEFID), Department of Veterinary Microbiology, Chulalongkorn University, Bangkok, Thailand.,Faculty of Veterinary Science, The International Graduate Program of Veterinary Science and Technology (VST), Chulalongkorn University, Bangkok, Thailand.,Faculty of Technology, Van Lang University, Ho Chi Minh City, Vietnam.,Faculty of Agriculture and Food Technology, Department of Biotechnology and Plant Protection, Tien Giang University, Tien Giang, Vietnam
| | - Le Buu Ky
- Faculty of Agriculture and Food Technology, Department of Biotechnology and Plant Protection, Tien Giang University, Tien Giang, Vietnam
| | - Bui The Huy
- Faculty of Agriculture and Food Technology, Department of Biotechnology and Plant Protection, Tien Giang University, Tien Giang, Vietnam
| | - Muhammad Fadhlullah Mursalim
- Faculty of Veterinary Science, Center of Excellent in Fish Infectious Diseases (CEFID), Department of Veterinary Microbiology, Chulalongkorn University, Bangkok, Thailand.,Faculty of Veterinary Science, The International Graduate Program of Veterinary Science and Technology (VST), Chulalongkorn University, Bangkok, Thailand.,Faculty of Medicine, Veterinary Study Program, Hasanuddin University, Makassar, Indonesia
| | - Pattanapon Kayansamruaj
- Faculty of Fisheries, Center of Excellence in Aquatic Animal Health Management, Kasetsart University, Bangkok, Thailand.,Faculty of Fisheries, Department of Aquaculture, Kasetsart University, Bangkok, Thailand
| | - Saengchan Senapin
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.,Faculty of Science, Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Bangkok, Thailand
| | - Channarong Rodkhum
- Faculty of Veterinary Science, Center of Excellent in Fish Infectious Diseases (CEFID), Department of Veterinary Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Ha Thanh Dong
- School of Environment, Resources and Development, Department of Food, Agriculture and Bioresources, Asian Institute of Technology, Pathum Thani, Thailand
| |
Collapse
|
14
|
Lou Y, Chang W, Cui T, Wang J, Qian H, Ma L, Hao X, Zhang D. Microbiologically influenced corrosion inhibition mechanisms in corrosion protection: A review. Bioelectrochemistry 2021; 141:107883. [PMID: 34246844 DOI: 10.1016/j.bioelechem.2021.107883] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/24/2021] [Accepted: 06/29/2021] [Indexed: 01/08/2023]
Abstract
Microbial activities can change the properties of biofilm/metal interfaces to accelerate or decelerate the corrosion of metals in a given environment. Microbiologically influenced corrosion inhibition (MICI) is the inhibition of corrosion that is directly or indirectly induced by microbial action. Compared with conventional methods for protection from corrosion, MICI is environmentally friendly and an emerging approach for the prevention and treatment of (bio)corrosion. However, due to the diversity of microorganisms and the fact that their metabolic processes are greatly complicated by environmental factors, MICI is still facing challenges for practical application. This review provides a comprehensive overview of the mechanisms of MICI under different conditions and their advantages and disadvantages for potential applications in corrosion protection.
Collapse
Affiliation(s)
- Yuntian Lou
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Weiwei Chang
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Tianyu Cui
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jinke Wang
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Hongchang Qian
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; BRI Southeast Asia Network for Corrosion and Protection (MOE), Shunde Graduate School of University of Science and Technology Beijing, Foshan 528399, China
| | - Lingwei Ma
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; BRI Southeast Asia Network for Corrosion and Protection (MOE), Shunde Graduate School of University of Science and Technology Beijing, Foshan 528399, China
| | - Xiangping Hao
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; BRI Southeast Asia Network for Corrosion and Protection (MOE), Shunde Graduate School of University of Science and Technology Beijing, Foshan 528399, China.
| | - Dawei Zhang
- National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China; Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China; BRI Southeast Asia Network for Corrosion and Protection (MOE), Shunde Graduate School of University of Science and Technology Beijing, Foshan 528399, China.
| |
Collapse
|
15
|
Forcone K, Coutinho FH, Cavalcanti GS, Silveira CB. Prophage Genomics and Ecology in the Family Rhodobacteraceae. Microorganisms 2021; 9:microorganisms9061115. [PMID: 34064105 PMCID: PMC8224337 DOI: 10.3390/microorganisms9061115] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of Rhodobacteraceae. These prophages represented 1.3 ± 0.15% of the bacterial genomes and had no to low homology with reference and metagenome-assembled viral genomes from aquatic and terrestrial ecosystems. Among the newly identified putative prophages, 35% encoded auxiliary metabolic genes (AMGs), mostly involved in secondary metabolism, amino acid metabolism, and cofactor and vitamin production. The analysis of integration sites and gene homology showed that 22 of the putative prophages were actually gene transfer agents (GTAs) similar to a GTA of Rhodobacter capsulatus. Twenty-three percent of the predicted prophages were observed in the TARA Oceans viromes generated from free viral particles, suggesting that they represent active prophages capable of induction. The distribution of these prophages was significantly associated with latitude and temperature. The prophages most abundant at high latitudes encoded acpP, an auxiliary metabolic gene involved in lipid synthesis and membrane fluidity at low temperatures. Our results show that prophages and gene transfer agents are significant sources of genomic diversity in roseobacter, with potential roles in the ecology of this globally distributed bacterial group.
Collapse
Affiliation(s)
- Kathryn Forcone
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Felipe H. Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, Aptdo. 18, Ctra. Alicante-Valencia, s/n, 03550 San Juan de Alicante, Spain;
| | - Giselle S. Cavalcanti
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Cynthia B. Silveira
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
- Correspondence:
| |
Collapse
|
16
|
Orellana R, Arancibia A, Badilla L, Acosta J, Arancibia G, Escar R, Ferrada G, Seeger M. Ecophysiological Features Shape the Distribution of Prophages and CRISPR in Sulfate Reducing Prokaryotes. Microorganisms 2021; 9:microorganisms9050931. [PMID: 33925267 PMCID: PMC8146710 DOI: 10.3390/microorganisms9050931] [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: 03/13/2021] [Revised: 04/18/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
Sulfate reducing prokaryotes (SRP) are a phylogenetically and physiologically diverse group of microorganisms that use sulfate as an electron acceptor. SRP have long been recognized as key players of the carbon and sulfur cycles, and more recently, they have been identified to play a relevant role as part of syntrophic and symbiotic relations and the human microbiome. Despite their environmental relevance, there is a poor understanding about the prevalence of prophages and CRISPR arrays and how their distribution and dynamic affect the ecological role of SRP. We addressed this question by analyzing the results of a comprehensive survey of prophages and CRISPR in a total of 91 genomes of SRP with several genotypic, phenotypic, and physiological traits, including genome size, cell volume, minimum doubling time, cell wall, and habitat, among others. Our analysis discovered 81 prophages in 51 strains, representing the 56% of the total evaluated strains. Prophages are non-uniformly distributed across the SRP phylogeny, where prophage-rich lineages belonged to Desulfovibrionaceae and Peptococcaceae. Furthermore, our study found 160 CRISPR arrays in 71 SRP, which is more abundant and widely spread than previously expected. Although there is no correlation between presence and abundance of prophages and CRISPR arrays at the strain level, our analysis showed that there is a directly proportional relation between cellular volumes and number of prophages per cell. This result suggests that there is an additional selective pressure for strains with smaller cells to get rid of foreign DNA, such as prophages, but not CRISPR, due to less availability of cellular resources. Analysis of the prophage genes encoding viral structural proteins reported that 44% of SRP prophages are classified as Myoviridae, and comparative analysis showed high level of homology, but not synteny, among prophages belonging to the Family Desulfovibrionaceae. We further recovered viral-like particles and structures that resemble outer membrane vesicles from D. vulgaris str. Hildenborough. The results of this study improved the current understanding of dynamic interactions between prophages and CRISPR with their hosts in both cultured and hitherto-uncultured SRP strains, and how their distribution affects the microbial community dynamics in several sulfidogenic natural and engineered environments.
Collapse
Affiliation(s)
- Roberto Orellana
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
- Correspondence:
| | - Alejandra Arancibia
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
| | - Leonardo Badilla
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
| | - Jonathan Acosta
- Departamento de Estadística, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860, Santiago 7820436, Chile;
| | - Gabriela Arancibia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Rodrigo Escar
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Gustavo Ferrada
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| |
Collapse
|
17
|
Genome-Wide Identification and Analysis of Chromosomally Integrated Putative Prophages Associated with Clinical Klebsiella pneumoniae Strains. Curr Microbiol 2021; 78:2015-2024. [PMID: 33813641 DOI: 10.1007/s00284-021-02472-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 03/18/2021] [Indexed: 10/21/2022]
Abstract
Klebsiella pneumoniae, an opportunistic pathogen found in the environment and human mucosal surfaces, is a leading cause of nosocomial infections. K. pneumoniae is now considered a global threat owing to the emergence of multidrug-resistant strains making its infections untreatable. In this study, 254 strains of K. pneumoniae were screened for the presence of prophages using the PHASTER tool. Very few strains lacked prophages (3.1%), while the remaining harboured both intact (811) and defective prophages (709). A subset of 42 unique strains of K. pneumoniae was chosen for further analysis. Our analysis revealed the presence of 110 complete prophages which were further classified as belonging to Myoviridae (67.3%), Siphoviridae (28.2%) and Podoviridae family (4.5%). An alignment of the 110 complete, prophage genome sequences clustered the prophages into 16 groups and 3 singletons. While none of the prophages encoded for virulence factors, 2 (1.8%) prophages were seen to encode for the antibiotic resistance-related genes. The CRISPR-Cas system was prevalent in 10 (23.8%) out of the 42 strains. Further analysis of the CRISPR spacers revealed 11.42% of the total spacers integrated in K. pneumoniae chromosome to match prophage protein sequences.
Collapse
|
18
|
Balarjishvili N, Kvachadze L, Tevdoradze E, Skhirtladze N, Leshkasheli L, Bolkvadze D, Pataridze T, Meskhi T, Chakraborty R, Kutateladze M, Torok T. Significance of lysogeny for the metabolism of Desulfovibrio spp. strains isolated from aquatic environments of Georgia. J Appl Microbiol 2021; 131:1344-1359. [PMID: 33555060 DOI: 10.1111/jam.15030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 01/21/2023]
Abstract
AIMS Sulphate-reducing bacteria (SRB) are ecologically important group of anaerobic micro-organisms that can reduce sulphate to form hydrogen sulphide-a toxic gas causing iron corrosion on metal surfaces. In this work, SRB strains were isolated from aquatic environments in the country of Georgia to determine their lysogenicity and the role of temperate phages in host metabolism. METHODS AND RESULTS SRB strains were isolated in samples from the Black Sea coast of Georgia. Based on their genetic, cytological and physiological properties of bacteria, 10 Georgian isolates were assigned to the genus Desulfovibrio. Temperate bacteriophages were induced from three out of ten strains by UV-exposure. Comparison of metal (Fe and Cr) reduction and utilization of various carbon sources by the wild-type (lysogenic) bacterial strains and their UV-irradiated counterparts was done. CONCLUSIONS Temperate phage in the cells of SRB could alter significant functions of bacteria and may have a contribution in the acquisition of different traits by SRB. SIGNIFICANCE AND IMPACT OF THE STUDY This article pointed to a significant role for temperate bacteriophages in the metabolism and metabolic potential of host strains of SRB, which were first isolated from the aquatic environment of Georgia.
Collapse
Affiliation(s)
- N Balarjishvili
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - L Kvachadze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - E Tevdoradze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - N Skhirtladze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - L Leshkasheli
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - D Bolkvadze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA.,Ilia State University, Tbilisi, GA, USA
| | - T Pataridze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - T Meskhi
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - R Chakraborty
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - M Kutateladze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - T Torok
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| |
Collapse
|
19
|
Environmental Impact of Sulfate-Reducing Bacteria, Their Role in Intestinal Bowel Diseases, and Possible Control by Bacteriophages. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11020735] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sulfate-reducing bacteria (SRB) represent a group of prokaryotic microorganisms that are widely spread in the anoxic environment (seabed, riverbed and lakebed sediments, mud, intestinal tract of humans and animals, metal surfaces). SRB species also have an impact on processes occurring in the intestinal tract of humans and animals, including the connections between their presence and inflammatory bowel disease (IBD). Since these SRB can develop antimicrobial resistance toward the drugs, including antibiotics and antimicrobial agents, bacteriophages could represent an additional potential effective treatment. The main objectives of the review were as follows: (a) to review SRB (both from intestinal and environmental sources) regarding their role in intestinal diseases as well as their influence in environmental processes; and (b) to review, according to literature data, the influence of bacteriophages on SRB and their possible applications. Since SRB can have a significant adverse influence on industry as well as on humans and animals health, phage treatment of SRB can be seen as a possible effective method of SRB inhibition. However, there are relatively few studies concerning the influence of phages on SRB strains. Siphoviridae and Myoviridae families represent the main sulfide-producing bacteria phages. The most recent studies induced, by UV light, bacteriophages from Desulfovibrio vulgaris NCIMB 8303 and Desulfovibrio desulfuricans ATCC 13541. Notwithstanding costly and medically significant negative impacts of phages on SRB, they have been the subject of relatively few studies. The current search for alternatives to chemical biocides and antibiotics has led to the renewed interest in phages as antibacterial biocontrol and therapeutic agents, including their use against SRB. Hence, phages might represent a promising treatment against SRB in the future.
Collapse
|
20
|
Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages. PLoS Comput Biol 2020; 16:e1008482. [PMID: 33275597 PMCID: PMC7744054 DOI: 10.1371/journal.pcbi.1008482] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 12/16/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022] Open
Abstract
Integrated into their bacterial hosts' genomes, prophage sequences exhibit a wide diversity of length and gene content, from highly degraded cryptic sequences to intact, functional prophages that retain a full complement of lytic-function genes. We apply three approaches-bioinformatics, analytical modelling and computational simulation-to understand the diverse gene content of prophages. In the bioinformatics work, we examine the distributions of over 50,000 annotated prophage genes identified in 1384 prophage sequences, comparing the gene repertoires of intact and incomplete prophages. These data indicate that genes involved in the replication, packaging, and release of phage particles have been preferentially lost in incomplete prophages, while tail fiber, transposase and integrase genes are significantly enriched. Consistent with these results, our mathematical and computational approaches predict that genes involved in phage lytic function are preferentially lost, resulting in shorter prophages that often retain genes that benefit the host. Informed by these models, we offer novel hypotheses for the enrichment of integrase and transposase genes in cryptic prophages. Overall, we demonstrate that functional and cryptic prophages represent a diversity of genetic sequences that evolve along a parasitism-mutualism continuum.
Collapse
|
21
|
A Novel Inducible Prophage from Burkholderia Vietnamiensis G4 is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia. Viruses 2020; 12:v12060601. [PMID: 32486377 PMCID: PMC7354579 DOI: 10.3390/v12060601] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/30/2022] Open
Abstract
Burkholderia species have environmental, industrial and medical significance, and are important opportunistic pathogens in individuals with cystic fibrosis (CF). Using a combination of existing and newly determined genome sequences, this study investigated prophage carriage across the species B. vietnamiensis, and also isolated spontaneously inducible prophages from a reference strain, G4. Eighty-one B. vietnamiensis genomes were bioinformatically screened for prophages using PHASTER (Phage Search Tool Enhanced Release) and prophage regions were found to comprise up to 3.4% of total genetic material. Overall, 115 intact prophages were identified and there was evidence of polylysogeny in 32 strains. A novel, inducible Mu-like phage (vB_BvM-G4P1) was isolated from B. vietnamiensis G4 that had lytic activity against strains of five Burkholderia species prevalent in CF infections, including the Boston epidemic B. dolosa strain SLC6. The cognate prophage to vB_BvM-G4P1 was identified in the lysogen genome and was almost identical (>93.5% tblastx identity) to prophages found in 13 other B. vietnamiensis strains (17% of the strain collection). Phylogenomic analysis determined that the G4P1-like prophages were widely distributed across the population structure of B. vietnamiensis. This study highlights how genomic characterization of Burkholderia prophages can lead to the discovery of novel bacteriophages with potential therapeutic or biotechnological applications.
Collapse
|
22
|
Khan A, Wahl LM. Quantifying the forces that maintain prophages in bacterial genomes. Theor Popul Biol 2019; 133:168-179. [PMID: 31758948 DOI: 10.1016/j.tpb.2019.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 10/25/2022]
Abstract
Genome sequencing has revealed that prophages, viral sequences integrated in a bacterial chromosome, are abundant, accounting for as much as 20% of the bacterial genome. These sequences can confer fitness benefits to the bacterial host, but may also instigate cell death through induction. Several recent investigations have revealed that the distribution of prophage lengths is bimodal, with a clear distinction between small and large prophages. Here we develop a mathematical model of the evolutionary forces affecting the prophage size distribution, and fit this model to three recent data sets. This approach offers quantitative estimates for the relative rates of lysogeny, induction, mutational degradation and selection acting on a wide class of prophage sequences. The model predicts that large prophages are predominantly maintained by the introduction of new prophage sequences through lysogeny, whereas shorter prophages can be enriched when they no longer encode the genes necessary for induction, but still offer selective benefits to their hosts.
Collapse
Affiliation(s)
- Amjad Khan
- Department of Applied Mathematics, Western University, London, ON, Canada
| | - Lindi M Wahl
- Department of Applied Mathematics, Western University, London, ON, Canada.
| |
Collapse
|
23
|
Rezaei Javan R, Ramos-Sevillano E, Akter A, Brown J, Brueggemann AB. Prophages and satellite prophages are widespread in Streptococcus and may play a role in pneumococcal pathogenesis. Nat Commun 2019; 10:4852. [PMID: 31649284 PMCID: PMC6813308 DOI: 10.1038/s41467-019-12825-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/27/2019] [Indexed: 02/06/2023] Open
Abstract
Prophages (viral genomes integrated within a host bacterial genome) can confer various phenotypic traits to their hosts, such as enhanced pathogenicity. Here we analyse >1300 genomes of 70 different Streptococcus species and identify nearly 800 prophages and satellite prophages (prophages that do not encode their own structural components but rely on the bacterial host and another helper prophage for survival). We show that prophages and satellite prophages are widely distributed among streptococci in a structured manner, and constitute two distinct entities with little effective genetic exchange between them. Cross-species transmission of prophages is not uncommon. Furthermore, a satellite prophage is associated with virulence in a mouse model of Streptococcus pneumoniae infection. Our findings highlight the potential importance of prophages in streptococcal biology and pathogenesis. Prophages are viral genomes integrated within bacterial genomes. Here, Rezaei Javan et al. identify nearly 800 prophages and satellite prophages in > 1300 Streptococcus genomes, and show that a satellite prophage is associated with virulence in a mouse model of pneumococcal infection.
Collapse
Affiliation(s)
| | | | - Asma Akter
- Department of Medicine, Imperial College London, London, UK
| | - Jeremy Brown
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Angela B Brueggemann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK. .,Department of Medicine, Imperial College London, London, UK. .,Nuffield Department of Population Health, University of Oxford, Oxford, UK.
| |
Collapse
|
24
|
Batinovic S, Wassef F, Knowler SA, Rice DTF, Stanton CR, Rose J, Tucci J, Nittami T, Vinh A, Drummond GR, Sobey CG, Chan HT, Seviour RJ, Petrovski S, Franks AE. Bacteriophages in Natural and Artificial Environments. Pathogens 2019; 8:pathogens8030100. [PMID: 31336985 PMCID: PMC6789717 DOI: 10.3390/pathogens8030100] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages (phages) are biological entities that have attracted a great deal of attention in recent years. They have been reported as the most abundant biological entities on the planet and their ability to impact the composition of bacterial communities is of great interest. In this review, we aim to explore where phages exist in natural and artificial environments and how they impact communities. The natural environment in this review will focus on the human body, soils, and the marine environment. In these naturally occurring environments there is an abundance of phages suggesting a role in the maintenance of bacterial community homeostasis. The artificial environment focuses on wastewater treatment plants, industrial processes, followed by pharmaceutical formulations. As in natural environments, the existence of bacteria in manmade wastewater treatment plants and industrial processes inevitably attracts phages. The presence of phages in these environments can inhibit the bacteria required for efficient water treatment or food production. Alternatively, they can have a positive impact by eliminating recalcitrant organisms. Finally, we conclude by describing how phages can be manipulated or formulated into pharmaceutical products in the laboratory for use in natural or artificial environments.
Collapse
Affiliation(s)
- Steven Batinovic
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Flavia Wassef
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Sarah A Knowler
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Daniel T F Rice
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Cassandra R Stanton
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Jayson Rose
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Joseph Tucci
- Department of Pharmacy & Biomedical Sciences, La Trobe University, Bendigo, VIC 3550, Australia
| | - Tadashi Nittami
- Division of Materials Science and Chemical Engineering, Yokohama National University, Yokohama 240-8501, Japan
| | - Antony Vinh
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Grant R Drummond
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Christopher G Sobey
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Hiu Tat Chan
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Robert J Seviour
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Ashley E Franks
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| |
Collapse
|
25
|
Crispim JS, Dias RS, Laguardia CN, Araújo LC, da Silva JD, Vidigal PMP, de Sousa MP, da Silva CC, Santana MF, de Paula SO. Desulfovibrio alaskensis prophages and their possible involvement in the horizontal transfer of genes by outer membrane vesicles. Gene 2019; 703:50-57. [DOI: 10.1016/j.gene.2019.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/22/2019] [Accepted: 04/05/2019] [Indexed: 12/15/2022]
|
26
|
Fu Y, Wu Y, Yuan Y, Gao M. Prevalence and Diversity Analysis of Candidate Prophages to Provide An Understanding on Their Roles in Bacillus Thuringiensis. Viruses 2019; 11:v11040388. [PMID: 31027262 PMCID: PMC6521274 DOI: 10.3390/v11040388] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/04/2019] [Accepted: 04/24/2019] [Indexed: 01/03/2023] Open
Abstract
Bacillus thuringiensis (Bt) is widely used in producing biological insecticides. Phage contaminations during Bt fermentation can cause severe losses of yields. Lots of strategies have been engaged to control extrinsic phage contamination during Bt fermentation, but their effectiveness is low. In this study, the candidate endogenous prophages (prophages) in 61 Bt chromosomes that had been deposited in GenBank database were analyzed. The results revealed that all chromosomes contained prophage regions, and 398 candidate prophage regions were predicted, including 135 putative complete prophages and 263 incomplete prophage regions. These putative complete prophages showed highly diverse genetic backgrounds. The inducibility of the prophages of ten Bt strains (4AJ1, 4BD1, HD-1, HD-29, HD-73, HD-521, BMB171, 4CC1, CT-43, and HD-1011) was tested, and the results showed that seven of the ten strains’ prophages were inducible. These induced phages belonged to the Siphoviridae family and exhibited a broad host spectrum against the non-original strains. The culture supernatants of the two strains (BMB171, 4CC1) could lyse Bt cells, but no virions were observed, which was speculated to be caused by lysin. The functional analysis of the putative complete prophage proteins indicated that some proteins, such as antibiotic resistance-associated proteins and restriction endonucleases, might increase the fitness of the Bt strains to different environments. The findings of this study provided understanding on the high prevalence and diversity of Bt prophages, as well as pointed out the role of prophages in the life cycle of Bt.
Collapse
Affiliation(s)
- Yajuan Fu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Yan Wu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Yihui Yuan
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
- Present address: State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 571158, China.
| | - Meiying Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| |
Collapse
|
27
|
Liu J, Chang R, Zhang X, Wang Z, Wen J, Zhou T. Non-isoflavones Diet Incurred Metabolic Modifications Induced by Constipation in Rats via Targeting Gut Microbiota. Front Microbiol 2018; 9:3002. [PMID: 30564225 PMCID: PMC6288237 DOI: 10.3389/fmicb.2018.03002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/20/2018] [Indexed: 01/03/2023] Open
Abstract
Isoflavones, presenting in leguminous plants and the normal chow diet, are known to alter intestinal microbiota, yet their deficiency has not been widely studied for its effect on constipation in biochemical state of rats. Our previous study discovered the differences in pharmacokinetic traits of isoflavones from Semen sojae praeparatum fed with normal chow diet (ISO) and non-isoflavones diet (NISO). To gain insight into the key role of intestinal microbiota in constipation and metabolic differences caused by isoflavones deficiency, we observed a significant decrease in fecal pellet numbers, fecal water content, intestinal transit rate together with the serum concentrations of substance P (SP) and vasoactive intestinal peptide (VIP) in NISO group, compared with those in the ISO group. Following 16S rRNA compositional sequencing, results excluded the changes in intestinal microbiota over time and highlighted that a total of 5 phyla and 21 genera changed significantly, among which Firmicutes, Bacteroidetes, Blautia, Prevotella, Lactobacillus and Bifidobacterium were closely related to constipation. In addition, Lactobacillus, produceing β-glucosidase which contribute to biotransform glycosides into aglycons and exert the bioactivities consequently, was decreased after non-isoflavones diet intake. Meanwhile, predicted metagenomics indicated that the pathway of glycan biosynthesis and metabolism was markedly down-regulated after non-isoflavones diet intake. Taken together, the findings suggested that the changes in the dietary components could alter the biochemical state of rats, which may be triggered by the abnormal modifications facilitated by β-glucosidase-producing bacteria. Our study shed a new strategy to explore the relationship among disease phenotypes (D), intestinal microbiota (I), enzymes (E) and traits of metabolism (T) named as "DIET," which can provide a reference for further study of the mechanism in regulation of intestinal bacteria-mediated diet on diseases.
Collapse
Affiliation(s)
| | | | | | | | | | - Tingting Zhou
- School of Pharmacy, Second Military Medical University, Shanghai, China
| |
Collapse
|