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McDonnell B, Parlindungan E, Vasiliauskaite E, Bottacini F, Coughlan K, Krishnaswami LP, Sassen T, Lugli GA, Ventura M, Mastroleo F, Mahony J, van Sinderen D. Viromic and Metagenomic Analyses of Commercial Spirulina Fermentations Reveal Remarkable Microbial Diversity. Viruses 2024; 16:1039. [PMID: 39066202 PMCID: PMC11281685 DOI: 10.3390/v16071039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Commercially produced cyanobacteria preparations sold under the name spirulina are widely consumed, due to their traditional use as a nutrient-rich foodstuff and subsequent marketing as a superfood. Despite their popularity, the microbial composition of ponds used to cultivate these bacteria is understudied. A total of 19 pond samples were obtained from small-scale spirulina farms and subjected to metagenome and/or virome sequencing, and the results were analysed. A remarkable level of prokaryotic and viral diversity was found to be present in the ponds, with Limnospira sp. and Arthrospira sp. sometimes being notably scarce. A detailed breakdown of prokaryotic and viral components of 15 samples is presented. Twenty putative Limnospira sp.-infecting bacteriophage contigs were identified, though no correlation between the performance of these cultures and the presence of phages was found. The high diversity of these samples prevented the identification of clear trends in sample performance over time, between ponds or when comparing successful and failed fermentations.
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Affiliation(s)
- Brian McDonnell
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Elvina Parlindungan
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Erika Vasiliauskaite
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
- Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland
| | - Keith Coughlan
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Lakshmi Priyadarshini Krishnaswami
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Tom Sassen
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
- Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium;
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (G.A.L.); (M.V.)
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, 43124 Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (G.A.L.); (M.V.)
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, 43124 Parma, Italy
| | - Felice Mastroleo
- Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium;
| | - Jennifer Mahony
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, T12 Y337 Cork, Ireland; (B.M.); (E.V.); (K.C.); (L.P.K.); (J.M.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland;
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Shang J, Peng C, Liao H, Tang X, Sun Y. PhaBOX: a web server for identifying and characterizing phage contigs in metagenomic data. BIOINFORMATICS ADVANCES 2023; 3:vbad101. [PMID: 37641717 PMCID: PMC10460485 DOI: 10.1093/bioadv/vbad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/05/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
Motivation There is accumulating evidence showing the important roles of bacteriophages (phages) in regulating the structure and functions of the microbiome. However, lacking an easy-to-use and integrated phage analysis software hampers microbiome-related research from incorporating phages in the analysis. Results In this work, we developed a web server, PhaBOX, which can comprehensively identify and analyze phage contigs in metagenomic data. It supports integrated phage analysis, including phage contig identification from the metagenomic assembly, lifestyle prediction, taxonomic classification, and host prediction. Instead of treating the algorithms as a black box, PhaBOX also supports visualization of the essential features for making predictions. The web server is designed with a user-friendly graphical interface that enables both informatics-trained and nonspecialist users to analyze phages in microbiome data with ease. Availability and implementation The web server of PhaBOX is available via: https://phage.ee.cityu.edu.hk. The source code of PhaBOX is available at: https://github.com/KennthShang/PhaBOX.
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Affiliation(s)
- Jiayu Shang
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong (SAR), China
| | - Cheng Peng
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong (SAR), China
| | - Herui Liao
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong (SAR), China
| | - Xubo Tang
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong (SAR), China
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong (SAR), China
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Huang D, Yuan MM, Chen J, Zheng X, Wong D, Alvarez PJJ, Yu P. The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes. ISME COMMUNICATIONS 2023; 3:46. [PMID: 37142716 PMCID: PMC10160068 DOI: 10.1038/s43705-023-00249-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
Prokaryotic antiviral systems are important mediators for prokaryote-phage interactions, which have significant implications for the survival of prokaryotic community. However, the prokaryotic antiviral systems under environmental stress are poorly understood, limiting the understanding of microbial adaptability. Here, we systematically investigated the profile of the prokaryotic antiviral systems at the community level and prokaryote-phage interactions in the drinking water microbiome. Chlorine disinfectant was revealed as the main ecological driver for the difference in prokaryotic antiviral systems and prokaryote-phage interactions. Specifically, the prokaryotic antiviral systems in the microbiome exhibited a higher abundance, broader antiviral spectrum, and lower metabolic burden under disinfectant stress. Moreover, significant positive correlations were observed between phage lysogenicity and enrichment of antiviral systems (e.g., Type IIG and IV restriction-modification (RM) systems, and Type II CRISPR-Cas system) in the presence of disinfection, indicating these antiviral systems might be more compatible with lysogenic phages and prophages. Accordingly, there was a stronger prokaryote-phage symbiosis in disinfected microbiome, and the symbiotic phages carried more auxiliary metabolic genes (AMGs) related to prokaryotic adaptability as well as antiviral systems, which might further enhance prokaryote survival in drinking water distribution systems. Overall, this study demonstrates that the prokaryotic antiviral systems had a close association with their symbiotic phages, which provides novel insights into prokaryote-phage interactions and microbial environmental adaptation.
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Affiliation(s)
- Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Mengting Maggie Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Xiaoxuan Zheng
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Dongsheng Wong
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
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