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Guo X, Wang X, Shi J, Ren J, Zeng J, Li J, Li Y. A review and new perspective on oral bacteriophages: manifestations in the ecology of oral diseases. J Oral Microbiol 2024; 16:2344272. [PMID: 38698893 PMCID: PMC11064738 DOI: 10.1080/20002297.2024.2344272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 05/05/2024] Open
Abstract
Objective To explore the manifestations of bacteriophages in different oral disease ecologies, including periodontal diseases, dental caries, endodontic infections, and oral cancer, as well as to propel phage therapy for safer and more effective clinical application in the field of dentistry. Methods In this literature review, we outlined interactions between bacteriophages, bacteria and even oral cells in the oral ecosystem, especially in disease states. We also analyzed the current status and future prospects of phage therapy in the perspective of different oral diseases. Results Various oral bacteriophages targeting at periodontal pathogens as Porphyromonas gingivalis, Fusobacterium nucleatum, Treponema denticola and Aggregatibacter actinomycetemcomitans, cariogenic pathogen Streptococcus mutans, endodontic pathogen Enterococcus faecalis were predicted or isolated, providing promising options for phage therapy. In the realm of oral cancer, aside from displaying tumor antigens or participating in tumor-targeted therapies, phage-like particle vaccines demonstrated the potential to prevent oral infections caused by human papillomaviruses (HPVs) associated with head-and-neck cancers. Conclusion Due to their intricate interactions with bacteria and oral cells, bacteriophages are closely linked to the progression and regression of diverse oral diseases. And there is an urgent need for research to explore additional possibilities of bacteriophages in the management of oral diseases.
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Affiliation(s)
- Xinyu Guo
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaowan Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jia Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiayi Ren
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jinquan Li
- State Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Center for Archaeological Science, Sichuan University, Chengdu, China
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2
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Xiong X, Gong J, Lu T, Yuan L, Lan Y, Tu X. Characteristics of intestinal bacteriophages and their relationship with Bacteria and serum metabolites during quail sexual maturity transition. BMC Vet Res 2024; 20:93. [PMID: 38459523 PMCID: PMC10921806 DOI: 10.1186/s12917-024-03945-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/20/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Bacteriophages are prokaryotic viruses that rank among the most abundant microbes in the gut but remain among the least understood, especially in quails. In this study, we surveyed the gut bacteriophage communities in 22 quails at different ages (days 20 and 70) using shotgun metagenomic sequencing. We then systematically evaluated the relationships with gut bacteria and host serum metabolites. RESULTS We discovered that Myoviridae and Siphoviridae were the dominant bacteriophage families in quails. Through a random forest and LEfSe analysis, we identified 23 differential bacteriophages with overlapping presence. Of these, 21 bacteriophages (e.g., Enterococcus phage IME-EFm5 and Enterococcus phage IME-EFm1) showed higher abundances in the day 20 group, while two bacteriophages (Bacillus phage Silence and Bacillus virus WPh) were enriched in the day 70 group. These key bacteriophages can serve as biomarkers for quail sexual maturity. Additionally, the differential bacteriophages significantly correlated with specific bacterial species and shifts in the functional capacities of the gut microbiome. For example, Enterococcus phages (e.g., Enterococcus phage EFP01, Enterococcus phage IME-EFm5, and Enterococcus phage IME-EFm1) were significantly (P < 0.001, FDR) and positively correlated with Enterococcus faecalis. However, the relationships between the host serum metabolites and either bacteriophages or bacterial species varied. None of the bacteriophages significantly (P > 0.05, FDR) correlated with nicotinamide riboside and triacetate lactone. In contrast, some differential bacterial species (e.g., Christensenella massiliensis and Bacteroides neonati) significantly (P < 0.05, FDR) correlated with nicotinamide riboside and triacetate lactone. Furthermore, characteristic successional alterations in gut bacteriophages, bacteria, and host serum metabolites across different ages highlighted a sexual maturity transition coexpression network. CONCLUSION This study improves our understanding of the gut bacteriophage characteristics in quails and offers profound insights into the interactions among gut bacteriophages, bacteria, and host serum metabolites during the quail's sexual maturity transition.
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Affiliation(s)
- Xinwei Xiong
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China.
| | - Jishang Gong
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Tian Lu
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Liuying Yuan
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Yuehang Lan
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Xutang Tu
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China.
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Zolfo M, Silverj A, Blanco-Míguez A, Manghi P, Rota-Stabelli O, Heidrich V, Jensen J, Maharjan S, Franzosa E, Menni C, Visconti A, Pinto F, Ciciani M, Huttenhower C, Cereseto A, Asnicar F, Kitano H, Yamada T, Segata N. Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.19.580813. [PMID: 38464031 PMCID: PMC10925137 DOI: 10.1101/2024.02.19.580813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Viruses are an abundant and crucial component of the human microbiome, but accurately discovering them via metagenomics is still challenging. Currently, the available viral reference genomes poorly represent the diversity in microbiome samples, and expanding such a set of viral references is difficult. As a result, many viruses are still undetectable through metagenomics even when considering the power of de novo metagenomic assembly and binning, as viruses lack universal markers. Here, we describe a novel approach to catalog new viral members of the human gut microbiome and show how the resulting resource improves metagenomic analyses. We retrieved >3,000 viral-like particles (VLP) enriched metagenomic samples (viromes), evaluated the efficiency of the enrichment in each sample to leverage the viromes of highest purity, and applied multiple analysis steps involving assembly and comparison with hundreds of thousands of metagenome-assembled genomes to discover new viral genomes. We reported over 162,000 viral sequences passing quality control from thousands of gut metagenomes and viromes. The great majority of the retrieved viral sequences (~94.4%) were of unknown origin, most had a CRISPR spacer matching host bacteria, and four of them could be detected in >50% of a set of 18,756 gut metagenomes we surveyed. We included the obtained collection of sequences in a new MetaPhlAn 4.1 release, which can quantify reads within a metagenome matching the known and newly uncovered viral diversity. Additionally, we released the viral database for further virome and metagenomic studies of the human microbiome.
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Affiliation(s)
- Moreno Zolfo
- Department CIBIO, University of Trento, Italy
- Integrated Open Systems Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Andrea Silverj
- Department CIBIO, University of Trento, Italy
- Center Agriculture Food Environment (C3A), University of Trento, Italy
- Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | | | | | - Omar Rota-Stabelli
- Department CIBIO, University of Trento, Italy
- Center Agriculture Food Environment (C3A), University of Trento, Italy
- Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | | | - Jordan Jensen
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sagun Maharjan
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eric Franzosa
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, UK
| | - Alessia Visconti
- Center for Biostatistics, Epidemiology and Public Health, Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | | | | | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Hiroaki Kitano
- Integrated Open Systems Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
- The Systems Biology Institute (SBI), Tokyo, Japan
- IOM Bioworks Pvt. Ltd., Centre for Cellular and Molecular Platforms (C-CAMP), GKVK Post, Bellary Rd, Bengaluru, Karnataka-560065, India
| | - Takuji Yamada
- Integrated Open Systems Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Metagen, Inc., Yamagata, Japan
- Metagen Therapeutics, Inc., Yamagata, Japan
- digzyme, Inc., Tokyo, Japan
| | - Nicola Segata
- Department CIBIO, University of Trento, Italy
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
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4
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Bhagchandani T, Nikita, Verma A, Tandon R. Exploring the Human Virome: Composition, Dynamics, and Implications for Health and Disease. Curr Microbiol 2023; 81:16. [PMID: 38006423 DOI: 10.1007/s00284-023-03537-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/24/2023] [Indexed: 11/27/2023]
Abstract
Humans are colonized by large number of microorganisms-bacteria, fungi, and viruses. The overall genome of entire viruses that either lives on or inside the human body makes up the human virome and is indeed an essential fraction of the human metagenome. Humans are constantly exposed to viruses as they are ubiquitously present on earth. The human virobiota encompasses eukaryotic viruses, bacteriophages, retroviruses, and even giant viruses. With the advent of Next-generation sequencing (NGS) and ongoing development of numerous bioinformatic softwares, identification and taxonomic characterization of viruses have become easier. The viruses are abundantly present in humans; these can be pathogenic or commensal. The viral communities occupy various niches in the human body. The viruses start colonizing the infant gut soon after birth in a stepwise fashion and the viral composition diversify according to their feeding habits. Various factors such as diet, age, medications, etc. influence and shape the human virome. The viruses interact with the host immune system and these interactions have beneficial or detrimental effects on their host. The virome composition and abundance change during the course of disease and these alterations impact the immune system. Hence, the virome population in healthy and disease conditions influences the human host in numerous ways. This review presents an overview of assembly and composition of the human virome in healthy asymptomatic individuals, changes in the virome profiles, and host-virome interactions in various disease states.
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Affiliation(s)
- Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Nikita
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Anjali Verma
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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5
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Chopyk J, Cobián Güemes AG, Ramirez-Sanchez C, Attai H, Ly M, Jones MB, Liu R, Liu C, Yang K, Tu XM, Abeles SR, Nelson K, Pride DT. Common antibiotics, azithromycin and amoxicillin, affect gut metagenomics within a household. BMC Microbiol 2023; 23:206. [PMID: 37528343 PMCID: PMC10394940 DOI: 10.1186/s12866-023-02949-z] [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: 12/12/2022] [Accepted: 07/19/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND The microbiome of the human gut serves a role in a number of physiological processes, but can be altered through effects of age, diet, and disturbances such as antibiotics. Several studies have demonstrated that commonly used antibiotics can have sustained impacts on the diversity and the composition of the gut microbiome. The impact of the two most overused antibiotics, azithromycin, and amoxicillin, in the human microbiome has not been thoroughly described. In this study, we recruited a group of individuals and unrelated controls to decipher the effects of the commonly used antibiotics amoxicillin and azithromycin on their gut microbiomes. RESULTS We characterized the gut microbiomes by metagenomic sequencing followed by characterization of the resulting microbial communities. We found that there were clear and sustained effects of the antibiotics on the gut microbial community with significant alterations in the representations of Bifidobacterium species in response to azithromycin (macrolide antibiotic). These results were supported by significant increases identified in putative antibiotic resistance genes associated with macrolide resistance. Importantly, we did not identify these trends in the unrelated control individuals. There were no significant changes observed in other members of the microbial community. CONCLUSIONS As we continue to focus on the role that the gut microbiome plays and how disturbances induced by antibiotics might affect our overall health, elucidating members of the community most affected by their use is of critical importance to understanding the impacts of common antibiotics on those who take them. Clinical Trial Registration Number NCT05169255. This trial was retrospectively registered on 23-12-2021.
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Affiliation(s)
- Jessica Chopyk
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, MC 0612, La Jolla, San Diego, CA, 92093-0612, USA
| | - Ana Georgina Cobián Güemes
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, MC 0612, La Jolla, San Diego, CA, 92093-0612, USA
| | | | - Hedieh Attai
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, MC 0612, La Jolla, San Diego, CA, 92093-0612, USA
| | - Melissa Ly
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, MC 0612, La Jolla, San Diego, CA, 92093-0612, USA
| | - Marcus B Jones
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Roland Liu
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, MC 0612, La Jolla, San Diego, CA, 92093-0612, USA
| | - Chenyu Liu
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, San Diego, CA, 92093, USA
| | - Kun Yang
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, San Diego, CA, 92093, USA
| | - Xin M Tu
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, San Diego, CA, 92093, USA
| | - Shira R Abeles
- Department of Medicine, University of California San Diego, San Diego, CA, 92093, USA
| | - Karen Nelson
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - David T Pride
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, MC 0612, La Jolla, San Diego, CA, 92093-0612, USA.
- Department of Medicine, University of California San Diego, San Diego, CA, 92093, USA.
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6
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Qu A, Duan B, Wang Y, Cui Z, Zhang N, Wu D. Children with autism show differences in the gut DNA virome compared to non-autistic children: a case control study. BMC Pediatr 2023; 23:174. [PMID: 37060094 PMCID: PMC10105470 DOI: 10.1186/s12887-023-03981-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/30/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Several previous studies have identified a potential role that the gut microbiome can play in autism spectrum disorder (ASD) in children, but little is known about how variations in the virome may be involved in ASD. We aimed to understand the changes in the gut DNA virome of children with ASD. METHODS A case-control study was presented, in which 13 two-children families were observed while considering the age, mode of birth, history of antibiotic use, and vaccination history to minimize the influence of confounding factors. DNA viral metagenomic sequencing was successfully performed on stool samples from 11 children with ASD and 12 healthy non-ASD children. The basic composition and gene function of the participants' fecal DNA virome were detected and analyzed. Finally, the abundance and diversity of the DNA virome of children with ASD and their healthy siblings were compared. RESULTS The gut DNA virome in children aged 3-11 years was found to be dominated by the Siphoviridae family of Caudovirales. The proteins encoded by the DNA genes mainly carry out the functions of genetic information transmission and metabolism. Compared the gut DNA virome of ASD and healthy non-ASD children, their abundance of Caudovirales and Petitvirales both showed a significant negative correlation (r = -0.902, P < 0.01), there was no statistically significant difference in the relative abundance of viruses at the order and family levels, and a difference in the relative abundance at the genus level for Skunavirus (Ζ = -2.157, P = 0.031). Viral α diversity was reduced in children with ASD, but α diversity and β diversity did not differ statistically between groups. CONCLUSIONS This study indicates that elevated Skunavirus abundance and decreased α diversity in the gut DNA virulence group of children with ASD, but no statistically significant difference in the change in alpha and beta diversity. This provides preliminary cumulative information on virological aspects of the relationship between the microbiome and ASD, and should benefit future multi-omics and large sample studies on the gut microbes in children with ASD.
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Affiliation(s)
- Aina Qu
- Pediatric Neurological Rehabilitation Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Boyang Duan
- Pediatric Neurological Rehabilitation Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yue Wang
- Pediatric Neurological Rehabilitation Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhenzhen Cui
- Pediatric Neurological Rehabilitation Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Nuochen Zhang
- Pediatric Neurological Rehabilitation Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - De Wu
- Pediatric Neurological Rehabilitation Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.
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7
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Diversity and Ecology of Caudoviricetes Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts. Viruses 2022; 14:v14102305. [PMID: 36298860 PMCID: PMC9610469 DOI: 10.3390/v14102305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022] Open
Abstract
The human gut harbors numerous viruses infecting the human host, microbes, and other inhabitants of the gastrointestinal tract. Most of these viruses remain undiscovered, and their influence on human health is unknown. Here, we characterize viral genomes in gut metagenomic data from 1950 individuals from four population and patient cohorts. We focus on a subset of viruses that is highly abundant in the gut, remains largely uncharacterized, and allows confident complete genome identification—phages that belong to the class Caudoviricetes and possess genome terminal repeats. We detect 1899 species-level units belonging to this subset, 19% of which do not have complete representative genomes in major public gut virome databases. These units display diverse genomic features, are predicted to infect a wide range of microbial hosts, and on average account for <1% of metagenomic reads. Analysis of longitudinal data from 338 individuals shows that the composition of this fraction of the virome remained relatively stable over a period of 4 years. We also demonstrate that 54 species-level units are highly prevalent (detected in >5% of individuals in a cohort). Finally, we find 34 associations between highly prevalent phages and human phenotypes, 24 of which can be explained by the relative abundance of potential hosts.
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8
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin-Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio-Functionalization of PET. Angew Chem Int Ed Engl 2022; 61:e202203061. [PMID: 35656865 PMCID: PMC7613822 DOI: 10.1002/anie.202203061] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Indexed: 11/24/2022]
Abstract
We report a bioinformatic workflow and subsequent discovery of a new polyethylene terephthalate (PET) hydrolase, which we named MG8, from the human saliva metagenome. MG8 has robust PET plastic degradation activities under different temperature and salinity conditions, outperforming several naturally occurring and engineered hydrolases in degrading PET. Moreover, we genetically encoded 2,3-diaminopropionic acid (DAP) in place of the catalytic serine residue of MG8, thereby converting a PET hydrolase into a covalent binder for bio-functionalization of PET. We show that MG8(DAP), in conjunction with a split green fluorescent protein system, can be used to attach protein cargos to PET as well as other polyester plastics. The discovery of a highly active PET hydrolase from the human metagenome-currently an underexplored resource for industrial enzyme discovery-as well as the repurposing of such an enzyme into a plastic functionalization tool, should facilitate ongoing efforts to degrade and maximize reusability of PET.
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Affiliation(s)
- Bhumrapee Eiamthong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Jariya Jitdee
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Raweewan Sangsri
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Maturada Patchsung
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | | | - Shan Tang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Wipa Suginta
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | | | - M Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Worawan Bhanthumnavin
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
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9
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Chitcharoen S, Sivapornnukul P, Payungporn S. Revolutionized virome research using systems microbiology approaches. Exp Biol Med (Maywood) 2022; 247:1135-1147. [PMID: 35723062 PMCID: PMC9335507 DOI: 10.1177/15353702221102895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Currently, both pathogenic and commensal viruses are continuously being discovered and acknowledged as ubiquitous components of microbial communities. The advancements of systems microbiological approaches have changed the face of virome research. Here, we focus on viral metagenomic approach to study virus community and their interactions with other microbial members as well as their hosts. This review also summarizes challenges, limitations, and benefits of the current virome approaches. Potentially, the studies of virome can be further applied in various biological and clinical fields.
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Affiliation(s)
- Suwalak Chitcharoen
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand,Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavaret Sivapornnukul
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Sunchai Payungporn.
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10
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Bacteriophage-Mediated Perturbation of Defined Bacterial Communities in an In Vitro Model of the Human Gut. Microbiol Spectr 2022; 10:e0113522. [PMID: 35638779 PMCID: PMC9241613 DOI: 10.1128/spectrum.01135-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The study of bacteriophage communities reproducing in the gastrointestinal tract is limited by the quality of model systems supporting experimental manipulation in vitro. Traditionally, studies aiming to experimentally address phage-bacteria dynamics have utilized gnotobiotic mice inoculated with defined bacterial communities. While mouse models simulate complex interactions between microbes and their host, they also forestall the study of phage-bacteria dynamics in isolation of host factors. Here, we established a method for manipulating phage-bacteria dynamics using an in vitro chemostat bioreactor model of the distal human gut. We create defined communities representing a subset of bacteria in the feces of two human individuals, cultivated these communities in chemostat bioreactors, developed methods to purify the autochthonous viromes associated with each cultured community, and trialed a system for transmitting live or heat-killed viruses between chemostat bioreactors to decipher outcomes of virus-mediated perturbation. We found that allochthonous viromes were detectable via metagenomic sequencing against the autochthonous virome background and that shifts in bacterial community diversity and composition were detectable in relation to time posttreatment. These microbiome composition changes spanned multiple phyla, including Bacteroidetes, Firmicutes, and Actinobacteria. We also found that compositional changes occurred when using live viruses regardless of whether intrasubject or intersubject viruses were used as the perturbation agents. Our results supported the use of chemostat bioreactors as a platform for studying complex bacteria-phage dynamics in vitro. IMPORTANCE Bacteriophages are relatively ubiquitous in the environment and are highly abundant in the human microbiome. Phages can be commonly transmitted between close contacts, but the impact that such transmissions may have on their bacteria counterparts in our microbiomes is unknown. We developed a chemostat cultivation system to simulate individual-specific features of human distal gut microbiota that can be used to transmit phages between ecosystems and measure their impacts on the microbiota. We used this system to transfer phage communities between chemostats that represented different human subjects. We found that there were significant effects on overall microbiota diversity and changes in the relative abundances of Bacteroidetes, Firmicutes, and Actinobacteria, when intersubject perturbations were performed, compared to intrasubject perturbations. These changes were observed when perturbations were performed using live phages, but not when heat-killed phages were used, and they support the use of chemostat systems for studying complex human bacteria-phage dynamics.
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin-Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Bhumrapee Eiamthong
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Piyachat Meesawat
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Thanakrit Wongsatit
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Jariya Jitdee
- Chulalongkorn University Faculty of Science Chemistry THAILAND
| | | | - Maturada Patchsung
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | - Kanokpol Aphicho
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | - Surased Suraritdechachai
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | | | - Shan Tang
- MRC Laboratory of Molecular Biology Protein and nucleic acid chemistry UNITED KINGDOM
| | - Wipa Suginta
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | | | - M. Madan Babu
- St Jude Children's Research Hospital Department of Structural Biology Structural Biology UNITED STATES
| | - Jason W Chin
- MRC Laboratory of Molecular Biology Protein and nucleic acid chemistry UNITED KINGDOM
| | | | | | - Chayasith Uttamapinant
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering 555 Moo 1 PayupnaiWangchan Valley 21210 Rayong THAILAND
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Abstract
Gut viruses are important, yet often neglected, players in the complex human gut microbial ecosystem. Recently, the number of human gut virome studies has been increasing; however, we are still only scratching the surface of the immense viral diversity. In this study, 254 virus-enriched fecal metagenomes from 204 Danish subjects were used to generate the Danish Enteric Virome Catalog (DEVoC) containing 12,986 nonredundant viral scaffolds, of which the majority was previously undescribed, encoding 190,029 viral genes. The DEVoC was used to compare 91 healthy DEVoC gut viromes from children, adolescents, and adults that were used to create the DEVoC. Gut viromes of healthy Danish subjects were dominated by phages. While most phage genomes (PGs) only occurred in a single subject, indicating large virome individuality, 39 PGs were present in more than 10 healthy subjects. Among these 39 PGs, the prevalences of three PGs were associated with age. To further study the prevalence of these 39 prevalent PGs, 1,880 gut virome data sets of 27 studies from across the world were screened, revealing several age-, geography-, and disease-related prevalence patterns. Two PGs also showed a remarkably high prevalence worldwide-a crAss-like phage (20.6% prevalence), belonging to the tentative AlphacrAssvirinae subfamily, and a previously undescribed circular temperate phage infecting Bacteroides dorei (14.4% prevalence), called LoVEphage because it encodes lots of viral elements. Due to the LoVEphage's high prevalence and novelty, public data sets in which the LoVEphage was detected were de novo assembled, resulting in an additional 18 circular LoVEphage-like genomes (67.9 to 72.4 kb). IMPORTANCE Through generation of the DEVoC, we added numerous previously uncharacterized viral genomes and genes to the ever-increasing worldwide pool of human gut viromes. The DEVoC, the largest human gut virome catalog generated from consistently processed fecal samples, facilitated the analysis of the 91 healthy Danish gut viromes. Characterizing the biggest cohort of healthy gut viromes from children, adolescents, and adults to date confirmed the previously established high interindividual variation in human gut viromes and demonstrated that the effect of age on the gut virome composition was limited to the prevalence of specific phage (groups). The identification of a previously undescribed prevalent phage illustrates the usefulness of developing virome catalogs, and we foresee that the DEVoC will benefit future analysis of the roles of gut viruses in human health and disease.
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Karcher N, Nigro E, Punčochář M, Blanco-Míguez A, Ciciani M, Manghi P, Zolfo M, Cumbo F, Manara S, Golzato D, Cereseto A, Arumugam M, Bui TPN, Tytgat HLP, Valles-Colomer M, de Vos WM, Segata N. Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. Genome Biol 2021; 22:209. [PMID: 34261503 PMCID: PMC8278651 DOI: 10.1186/s13059-021-02427-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Despite its biomedical relevance, the genomic diversity of A. muciniphila remains understudied and that of closely related species, except for A. glycaniphila, unexplored. RESULTS We present a large-scale population genomics analysis of the Akkermansia genus using 188 isolate genomes and 2226 genomes assembled from 18,600 metagenomes from humans and other animals. While we do not detect A. glycaniphila, the Akkermansia strains in the human gut can be grouped into five distinct candidate species, including A. muciniphila, that show remarkable whole-genome divergence despite surprisingly similar 16S rRNA gene sequences. These candidate species are likely human-specific, as they are detected in mice and non-human primates almost exclusively when kept in captivity. In humans, Akkermansia candidate species display ecological co-exclusion, diversified functional capabilities, and distinct patterns of associations with host body mass. Analysis of CRISPR-Cas loci reveals new variants and spacers targeting newly discovered putative bacteriophages. Remarkably, we observe an increased relative abundance of Akkermansia when cognate predicted bacteriophages are present, suggesting ecological interactions. A. muciniphila further exhibits subspecies-level genetic stratification with associated functional differences such as a putative exo/lipopolysaccharide operon. CONCLUSIONS We uncover a large phylogenetic and functional diversity of the Akkermansia genus in humans. This variability should be considered in the ongoing experimental and metagenomic efforts to characterize the health-associated properties of A. muciniphila and related bacteria.
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Affiliation(s)
| | - Eleonora Nigro
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Anna Cereseto
- Department CIBIO, University of Trento, Trento, Italy
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thi Phuong Nam Bui
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Current address: Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | | | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- IEO, European Institute of Oncology IRCCS, Milan, Italy.
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El-Sayed A, Aleya L, Kamel M. Microbiota's role in health and diseases. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:36967-36983. [PMID: 34043164 PMCID: PMC8155182 DOI: 10.1007/s11356-021-14593-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/24/2021] [Indexed: 05/06/2023]
Abstract
The microbiome is a term that usually refers to the community of various microorganisms that inhabit/live inside human/animal bodies or on their skin. It forms a complex ecosystem that includes trillions of commensals, symbiotics, and even pathogenic microorganisms. The external environment, diet, and lifestyle are the major determinants influencing the microbiome's composition and vitality. Recent studies have indicated the tremendous influence of the microbiome on health and disease. Their number, constitution, variation, and viability are dynamic. All these elements are responsible for the induction, development, and treatment of many health disorders. Serious diseases such as cancer, metabolic disorders, cardiovascular diseases, and even psychological disorders such as schizophrenia are influenced directly or indirectly by microbiota. In addition, in the last few weeks, accumulating data about the link between COVID-19 and the microbiota were published. In the present work, the role of the microbiome in health and disease is discussed. A deep understanding of the exact role of microbiota in disease induction enables the prevention of diseases and the development of new therapeutic concepts for most diseases through the correction of diet and lifestyle. The present review brings together evidence from the most recent works and discusses suggested nutraceutical approaches for the management of COVID-19 pandemic.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Lotfi Aleya
- Chrono-Environnement Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, F-25030, Besançon Cedex, France
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
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15
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Aswani VH, Shukla SK. An Early History of Phage Therapy in the United States: Is it Time to Reconsider? Clin Med Res 2021; 19:82-89. [PMID: 34172535 PMCID: PMC8231696 DOI: 10.3121/cmr.2021.1605] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/30/2020] [Accepted: 04/22/2021] [Indexed: 12/16/2022]
Abstract
Frederick William Twort and Felix d'Hérelle independently discovered bacteriophages in 1915 and 1917, respectively. This led to the early trials of using bacteriophages to treat infectious diseases worldwide. The earliest reported use of bacteriophages therapeutically in the United States was in 1922. With the subsequent discovery of antibiotics in the 1940s, and because of disappointing results of phage therapy in the next decade, use of bacteriophages as therapeutic agents declined in western countries. This paper addresses two questions in the field: what is the historical record of the successes and failures of phage therapy in the United States and, what led to abandoning phage therapy in the United States? We examined the literature from 1915 to 1965, and we present a numerical analysis of the papers published during that period. We report key historical factors leading to a decline in the use of phage therapy in the United States by the 1950s. Since bacteriophages were first used therapeutically, several changes have occurred: increased antimicrobial drug resistance and a better knowledge of the biology of bacteriophages are important examples. Early assessments leading to the rejection of phage therapy in the United States were perhaps appropriate. However, it is time to reconsider the role of bacteriophages in treatment of bacterial infections.
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Affiliation(s)
- Vijay H Aswani
- Department of Internal Medicine & Pediatrics, University at Buffalo, Buffalo, New York, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
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16
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Abstract
Oral bacteriophages (or phages), especially periodontal ones, constitute a growing area of interest, but research on oral phages is still in its infancy. Phages are bacterial viruses that may persist as intracellular parasitic deoxyribonucleic acid (DNA) or use bacterial metabolism to replicate and cause bacterial lysis. The microbiomes of saliva, oral mucosa, and dental plaque contain active phage virions, bacterial lysogens (ie, carrying dormant prophages), and bacterial strains containing short fragments of phage DNA. In excess of 2000 oral phages have been confirmed or predicted to infect species of the phyla Actinobacteria (>300 phages), Bacteroidetes (>300 phages), Firmicutes (>1000 phages), Fusobacteria (>200 phages), and Proteobacteria (>700 phages) and three additional phyla (few phages only). This article assesses the current knowledge of the diversity of the oral phage population and the mechanisms by which phages may impact the ecology of oral biofilms. The potential use of phage-based therapy to control major periodontal pathogens is also discussed.
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Affiliation(s)
- Szymon P Szafrański
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
| | - Jørgen Slots
- Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, California, USA
| | - Meike Stiesch
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
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17
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Callanan J, Stockdale SR, Shkoporov A, Draper LA, Ross RP, Hill C. Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review. Microorganisms 2021; 9:524. [PMID: 33806607 PMCID: PMC8000950 DOI: 10.3390/microorganisms9030524] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/17/2021] [Accepted: 03/02/2021] [Indexed: 12/21/2022] Open
Abstract
The human gut is colonised by a vast array of microbes that include bacteria, viruses, fungi, and archaea. While interest in these microbial entities has largely focused on the bacterial constituents, recently the viral component has attracted more attention. Metagenomic advances, compared to classical isolation procedures, have greatly enhanced our understanding of the composition, diversity, and function of viruses in the human microbiome (virome). We highlight that viral extraction methodologies are crucial in terms of identifying and characterising communities of viruses infecting eukaryotes and bacteria. Different viral extraction protocols, including those used in some of the most significant human virome publications to date, have introduced biases affecting their a overall conclusions. It is important that protocol variations should be clearly highlighted across studies, with the ultimate goal of identifying and acknowledging biases associated with different protocols and, perhaps, the generation of an unbiased and standardised method for examining this portion of the human microbiome.
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Affiliation(s)
| | | | | | | | | | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, T12 YT20 Cork, Ireland; (J.C.); (S.R.S.); (A.S.); (L.A.D.); (R.P.R.)
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18
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Gregory AC, Zablocki O, Zayed AA, Howell A, Bolduc B, Sullivan MB. The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut. Cell Host Microbe 2020; 28:724-740.e8. [PMID: 32841606 PMCID: PMC7443397 DOI: 10.1016/j.chom.2020.08.003] [Citation(s) in RCA: 276] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/14/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022]
Abstract
The gut microbiome profoundly affects human health and disease, and their infecting viruses are likely as important, but often missed because of reference database limitations. Here, we (1) built a human Gut Virome Database (GVD) from 2,697 viral particle or microbial metagenomes from 1,986 individuals representing 16 countries, (2) assess its effectiveness, and (3) report a meta-analysis that reveals age-dependent patterns across healthy Westerners. The GVD contains 33,242 unique viral populations (approximately species-level taxa) and improves average viral detection rates over viral RefSeq and IMG/VR nearly 182-fold and 2.6-fold, respectively. GVD meta-analyses show highly personalized viromes, reveal that inter-study variability from technical artifacts is larger than any "disease" effect at the population level, and document how viral diversity changes from human infancy into senescence. Together, this compact foundational resource, these standardization guidelines, and these meta-analysis findings provide a systematic toolkit to help maximize our understanding of viral roles in health and disease.
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Affiliation(s)
- Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Allison Howell
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA.
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19
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Santiago-Rodriguez TM, Hollister EB. Potential Applications of Human Viral Metagenomics and Reference Materials: Considerations for Current and Future Viruses. Appl Environ Microbiol 2020; 86:e01794-20. [PMID: 32917759 PMCID: PMC7642086 DOI: 10.1128/aem.01794-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Viruses are ubiquitous particles comprising genetic material that can infect bacteria, archaea, and fungi, as well as human and other animal cells. Given that determining virus composition and function in association with states of human health and disease is of increasing interest, we anticipate that the field of viral metagenomics will continue to expand and be applied in a variety of areas ranging from surveillance to discovery and will rely heavily upon the continued development of reference materials and databases. Information regarding viral composition and function readily translates into biological and clinical applications, including the rapid sequence identification of pathogenic viruses in various sample types. However, viral metagenomic approaches often lack appropriate standards and reference materials to enable cross-study comparisons and assess potential biases which can be introduced at the various stages of collection, storage, processing, and sequence analysis. In addition, implementation of appropriate viral reference materials can aid in the benchmarking of current and development of novel assays for virus identification, discovery, and surveillance. As the field of viral metagenomics expands and standardizes, results will continue to translate into diverse applications.
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20
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Kerry RG, Das G, Golla U, Del Pilar Rodriguez-Torres M, Shin H, Patra JK. Engineered probiotic and prebiotic nutraceutical supplementations in combating non-communicable disorders: A review. Curr Pharm Biotechnol 2020; 23:72-97. [PMID: 33050862 DOI: 10.2174/1389201021666201013153142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 11/22/2022]
Abstract
Nutritional supplementations are a form of nutrition sources that may help in improving health complexities throughout the life span of a person. Under the umbrella of food supplementations, nutraceuticals are products extracted from edible sources that provide medical benefits along with primary nutritional value, these can be considered as functional foods. These nutraceutical supplementations are also evidenced in altering the commensal gut microbiota and help to prevent or fight against chronic non-communicable degenerative diseases in adults including neurological disorders (Autism Spectrum Disorder [ASD], Parkinson's disease [PD] and Multiple sclerosis [MS]) and metabolic disorder (Type-II Diabetes, Obesity and non-alcoholic fatty liver disease). Even the complexities of preterm babies like extra-uterine growth restriction, necrotizing enterocolitis, infant eczema and allergy (during pregnancy) and bronchopulmonary dysplasia, etc. could also be lessened up by providing proper nutrition. Molecular perceptive of inflammatory and apoptotic modulators regulating the pathogenesis of these health risks, their control and management by probiotics and prebiotics could further emphasize the scientific overview of their utility. The pivotal role of nutraceutical supplementations in regulating or modulating molecular pathways coupled with the above mentioned non-communicable diseases are briefly described. Lastly, an overall introduction to the sophisticated genome-editing techniques and advanced delivery systems in therapeutic activities applicable under these health risks are also emphasized in this paper.
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Affiliation(s)
| | - Gitishree Das
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Goyangsi 10326. Korea
| | - Upendarrao Golla
- Division of Hematology and Oncology, Penn State College of Medicine, Hershey, PA 17033. United States
| | - Maria Del Pilar Rodriguez-Torres
- Laboratorio de Ondas de Choque (LOCH), Centro de Física Aplicada y Tecnología Avanzada (CFATA), Universidad Nacional Autónoma de México, Campus UNAM Juriquilla Boulevard Juriquilla no. 3001, Santiago de Querétaro, Qro., C.P. 76230. Mexico
| | - HanSeung Shin
- Department of Food Science and Biotechnology, Dongguk University-Seoul, Goyangsi 10326. Korea
| | - Jayanta Kumar Patra
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Goyangsi 10326. Korea
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21
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Zolfo M, Pinto F, Asnicar F, Manghi P, Tett A, Bushman FD, Segata N. Detecting contamination in viromes using ViromeQC. Nat Biotechnol 2020; 37:1408-1412. [PMID: 31748692 DOI: 10.1038/s41587-019-0334-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
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22
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Kigerl KA, Zane K, Adams K, Sullivan MB, Popovich PG. The spinal cord-gut-immune axis as a master regulator of health and neurological function after spinal cord injury. Exp Neurol 2020; 323:113085. [PMID: 31654639 PMCID: PMC6918675 DOI: 10.1016/j.expneurol.2019.113085] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/24/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022]
Abstract
Most spinal cord injury (SCI) research programs focus only on the injured spinal cord with the goal of restoring locomotor function by overcoming mechanisms of cell death or axon regeneration failure. Given the importance of the spinal cord as a locomotor control center and the public perception that paralysis is the defining feature of SCI, this "spinal-centric" focus is logical. Unfortunately, such a focus likely will not yield new discoveries that reverse other devastating consequences of SCI including cardiovascular and metabolic disease, bladder/bowel dysfunction and infection. The current review considers how SCI changes the physiological interplay between the spinal cord, the gut and the immune system. A suspected culprit in causing many of the pathological manifestations of impaired spinal cord-gut-immune axis homeostasis is the gut microbiota. After SCI, the composition of the gut microbiota changes, creating a chronic state of gut "dysbiosis". To date, much of what we know about gut dysbiosis was learned from 16S-based taxonomic profiling studies that reveal changes in the composition and abundance of various bacteria. However, this approach has limitations and creates taxonomic "blindspots". Notably, only bacteria can be analyzed. Thus, in this review we also discuss how the application of emerging sequencing technologies can improve our understanding of how the broader ecosystem in the gut is affected by SCI. Specifically, metagenomics will provide researchers with a more comprehensive look at post-injury changes in the gut virome (and mycome). Metagenomics also allows changes in microbe population dynamics to be linked to specific microbial functions that can affect the development and progression of metabolic disease, immune dysfunction and affective disorders after SCI. As these new tools become more readily available and used across the research community, the development of an "ecogenomic" toolbox will facilitate an Eco-Systems Biology approach to study the complex interplay along the spinal cord-gut-immune axis after SCI.
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Affiliation(s)
- Kristina A Kigerl
- The Belford Center for Spinal Cord Injury, the Center for Brain and Spinal Cord Repair, Department of Neuroscience, Wexner Medical Center at The Ohio State University, USA
| | - Kylie Zane
- The Ohio State University College of Medicine, USA
| | - Kia Adams
- The Belford Center for Spinal Cord Injury, the Center for Brain and Spinal Cord Repair, Department of Neuroscience, Wexner Medical Center at The Ohio State University, USA
| | - Matthew B Sullivan
- Departments of Microbiology, Civil, Environmental and Geodetic Engineering at The Ohio State University, USA
| | - Phillip G Popovich
- The Belford Center for Spinal Cord Injury, the Center for Brain and Spinal Cord Repair, Department of Neuroscience, Wexner Medical Center at The Ohio State University, USA.
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Armitage GC. A brief history of periodontics in the United States of America: Pioneers and thought-leaders of the past, and current challenges. Periodontol 2000 2019; 82:12-25. [PMID: 31850629 DOI: 10.1111/prd.12303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This paper summarizes historical events in periodontology in the United States over the past 200 years. The contributions of some of the key thought-leaders of the past are highlighted. Throughout the 20th century, the evolution of thought, leading to the views currently held regarding the pathogenesis and treatment of periodontal diseases, was significantly influenced by: (1) major changes in health-care education; (2) the emergence of periodontics as a specialty of dentistry; (3) the publication of peer-reviewed journals with an emphasis on periodontology; (4) formation of the National Institute of Dental and Craniofacial Research (NIDCR); and (5) expansion of periodontal research programs by the NIDCR. The two major future challenges facing periodontal research are development of a better understanding of the ecological complexities of host-microbial interactions in periodontal health and disease, and identification of the relevant mechanisms involved in the predictable regeneration of damaged periodontal tissues.
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Affiliation(s)
- Gary C Armitage
- Division of Periodontology, Department of Orofacial Sciences, University of California San Francisco, San Francisco, California, USA
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Ghose C, Ly M, Schwanemann LK, Shin JH, Atab K, Barr JJ, Little M, Schooley RT, Chopyk J, Pride DT. The Virome of Cerebrospinal Fluid: Viruses Where We Once Thought There Were None. Front Microbiol 2019; 10:2061. [PMID: 31555247 PMCID: PMC6742758 DOI: 10.3389/fmicb.2019.02061] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/21/2019] [Indexed: 01/21/2023] Open
Abstract
Traditionally, medicine has held that some human body sites are sterile and that the introduction of microbes to these sites results in infections. This paradigm shifted significantly with the discovery of the human microbiome and acceptance of these commensal microbes living across the body. However, the central nervous system (CNS) is still believed by many to be sterile in healthy people. Using culture-independent methods, we examined the virome of cerebrospinal fluid (CSF) from a cohort of mostly healthy human subjects. We identified a community of DNA viruses, most of which were identified as bacteriophages. Compared to other human specimen types, CSF viromes were not ecologically distinct. There was a high alpha diversity cluster that included feces, saliva, and urine, and a low alpha diversity cluster that included CSF, body fluids, plasma, and breast milk. The high diversity cluster included specimens known to have many bacteria, while other specimens traditionally assumed to be sterile formed the low diversity cluster. There was an abundance of viruses shared among CSF, breast milk, plasma, and body fluids, while each generally shared less with urine, feces, and saliva. These shared viruses ranged across different virus families, indicating that similarities between these viromes represent more than just a single shared virus family. By identifying a virome in the CSF of mostly healthy individuals, it is now less likely that any human body site is devoid of microbes, which further highlights the need to decipher the role that viral communities may play in human health.
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Affiliation(s)
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Leila K Schwanemann
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Ji Hyun Shin
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Katayoon Atab
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Mark Little
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Robert T Schooley
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Jessica Chopyk
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - David T Pride
- Department of Pathology, University of California, San Diego, San Diego, CA, United States.,Department of Medicine, University of California, San Diego, San Diego, CA, United States
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25
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Gregory AC, Sullivan MB, Segal LN, Keller BC. Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome. Respir Res 2018; 19:174. [PMID: 30208886 PMCID: PMC6136173 DOI: 10.1186/s12931-018-0878-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/03/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The role of commensal viruses in humans is poorly understood, and the impact of the virome on lung health and smoking-related disease is particularly understudied. METHODS Genetic material from acellular bronchoalveolar lavage fluid was sequenced to identify and quantify viral members of the lower respiratory tract which were compared against concurrent bronchoalveolar lavage bacterial, metabolite, cytokine and cellular profiles, and clinical data. Twenty smoker and 10 nonsmoker participants with no significant comorbidities were studied. RESULTS Viruses that infect bacteria (phages) represented the vast majority of viruses in the lung. Though bacterial communities were statistically indistinguishable across smokers and nonsmokers as observed in previous studies, lung viromes and metabolic profiles were significantly different between groups. Statistical analyses revealed that changes in viral communities correlate most with changes in levels of arachidonic acid and IL-8, both potentially relevant for chronic obstructive pulmonary disease (COPD) pathogenesis based on prior studies. CONCLUSIONS Our assessment of human lung DNA viral communities reveals that commensal viruses are present in the lower respiratory tract and differ between smokers and nonsmokers. The associations between viral populations and local immune and metabolic tone suggest a significant role for virome-host interaction in smoking related lung disease.
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Affiliation(s)
- Ann C. Gregory
- Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210 USA
| | - Leopoldo N. Segal
- Division of Pulmonary, Critical Care & Sleep Medicine, New York University School of Medicine, New York, NY 10016 USA
| | - Brian C. Keller
- Division of Pulmonary, Critical Care & Sleep Medicine, The Ohio State University College of Medicine, 201 Davis Heart & Lung Research Institute, 473 West 12th Avenue, Columbus, OH 43210 USA
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Parras-Moltó M, Rodríguez-Galet A, Suárez-Rodríguez P, López-Bueno A. Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses. MICROBIOME 2018; 6:119. [PMID: 29954453 PMCID: PMC6022446 DOI: 10.1186/s40168-018-0507-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/19/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Viruses are key players regulating microbial ecosystems. Exploration of viral assemblages is now possible thanks to the development of metagenomics, the most powerful tool available for studying viral ecology and discovering new viruses. Unfortunately, several sources of bias lead to the misrepresentation of certain viruses within metagenomics workflows, hindering the shift from merely descriptive studies towards quantitative comparisons of communities. Therefore, benchmark studies on virus enrichment and random amplification protocols are required to better understand the sources of bias. RESULTS We assessed the bias introduced by viral enrichment on mock assemblages composed of seven DNA viruses, and the bias from random amplification methods on human saliva DNA viromes, using qPCR and deep sequencing, respectively. While iodixanol cushions and 0.45 μm filtration preserved the original composition of nuclease-protected viral genomes, low-force centrifugation and 0.22 μm filtration removed large viruses. Comparison of unamplified and randomly amplified saliva viromes revealed that multiple displacement amplification (MDA) induced stochastic bias from picograms of DNA template. However, the type of bias shifted to systematic using 1 ng, with only a marginal influence by amplification time. Systematic bias consisted of over-amplification of small circular genomes, and under-amplification of those with extreme GC content, a negative bias that was shared with the PCR-based sequence-independent, single-primer amplification (SISPA) method. MDA based on random priming provided by a DNA primase activity slightly outperformed those based on random hexamers and SISPA, which may reflect differences in ability to handle sequences with extreme GC content. SISPA viromes showed uneven coverage profiles, with high coverage peaks in regions with low linguistic sequence complexity. Despite misrepresentation of certain viruses after random amplification, ordination plots based on dissimilarities among contig profiles showed perfect overlapping of related amplified and unamplified saliva viromes and strong separation from unrelated saliva viromes. This result suggests that random amplification bias has a minor impact on beta diversity studies. CONCLUSIONS Benchmark analyses of mock and natural communities of viruses improve understanding and mitigate bias in metagenomics surveys. Bias induced by random amplification methods has only a minor impact on beta diversity studies of human saliva viromes.
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Affiliation(s)
- Marcos Parras-Moltó
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Ana Rodríguez-Galet
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Patricia Suárez-Rodríguez
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Alberto López-Bueno
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain.
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Pannaraj PS, Ly M, Cerini C, Saavedra M, Aldrovandi GM, Saboory AA, Johnson KM, Pride DT. Shared and Distinct Features of Human Milk and Infant Stool Viromes. Front Microbiol 2018; 9:1162. [PMID: 29910789 PMCID: PMC5992295 DOI: 10.3389/fmicb.2018.01162] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/14/2018] [Indexed: 01/01/2023] Open
Abstract
Infants acquire many of their microbes from their mothers during the birth process. The acquisition of these microbes is believed to be critical in the development of the infant immune system. Bacteria also are transmitted to the infant through breastfeeding, and help to form the microbiome of the infant gastrointestinal (GI) tract; it is unknown whether viruses in human milk serve to establish an infant GI virome. We examined the virome contents of milk and infant stool in a cohort of mother-infant pairs to discern whether milk viruses colonize the infant GI tract. We observed greater viral alpha diversity in milk than in infant stool, similar to the trend we found for bacterial communities from both sites. When comparing beta diversity, viral communities were mostly distinguishable between milk and infant stool, but each was quite distinct from adult stool, urine, and salivary viromes. There were significant differences in viral families in the infant stool (abundant bacteriophages from the family Siphoviridae) compared to milk (abundant bacteriophages from the family Myoviridae), which may reflect significant differences in the bacterial families identified from both sites. Despite the differences in viral taxonomy, we identified a significant number of shared viruses in the milk and stool from all mother-infant pairs. Because of the significant proportion of bacteriophages transmitted in these mother-infant pairs, we believe the transmission of milk phages to the infant GI tract may help to shape the infant GI microbiome.
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Affiliation(s)
- Pia S Pannaraj
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States.,Department of Pediatrics, Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Chiara Cerini
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Monica Saavedra
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Grace M Aldrovandi
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Abdul A Saboory
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Kevin M Johnson
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - David T Pride
- Department of Pathology, University of California, San Diego, San Diego, CA, United States.,Department of Medicine, University of California, San Diego, San Diego, CA, United States
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Gomez-Silvan C, Leung MHY, Grue KA, Kaur R, Tong X, Lee PKH, Andersen GL. A comparison of methods used to unveil the genetic and metabolic pool in the built environment. MICROBIOME 2018; 6:71. [PMID: 29661230 PMCID: PMC5902888 DOI: 10.1186/s40168-018-0453-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/28/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs. biological-based differences in both ribosomal transcript (rRNA) and gene (DNA) sequence community analysis. Based on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting. RESULTS We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at - 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community. CONCLUSIONS Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics.
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Affiliation(s)
- Cinta Gomez-Silvan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Katherine A. Grue
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Current affiliation: Department of Physical Therapy and Rehabilitation Science, University of California, San Francisco, CA USA
| | - Randeep Kaur
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Gary L. Andersen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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Shkoporov AN, Ryan FJ, Draper LA, Forde A, Stockdale SR, Daly KM, McDonnell SA, Nolan JA, Sutton TD, Dalmasso M, McCann A, Ross RP, Hill C. Reproducible protocols for metagenomic analysis of human faecal phageomes. MICROBIOME 2018; 6:68. [PMID: 29631623 PMCID: PMC5892011 DOI: 10.1186/s40168-018-0446-z] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/13/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. One important obstacle in metagenomic studies of the human gut phageome is a high level of discrepancy between results obtained by different research groups. This is often due to the use of different protocols for enriching virus-like particles, nucleic acid purification and sequencing. The goal of the present study is to develop a relatively simple, reproducible and cost-efficient protocol for the extraction of viral nucleic acids from human faecal samples, suitable for high-throughput studies. We also analyse the effect of certain potential confounding factors, such as storage conditions, repeated freeze-thaw cycles, and operator bias on the resultant phageome profile. Additionally, spiking of faecal samples with an exogenous phage standard was employed to quantitatively analyse phageomes following metagenomic sequencing. Comparative analysis of phageome profiles to bacteriome profiles was also performed following 16S rRNA amplicon sequencing. RESULTS Faecal phageome profiles exhibit an overall greater individual specificity when compared to bacteriome profiles. The phageome and bacteriome both exhibited moderate change when stored at + 4 °C or room temperature. Phageome profiles were less impacted by multiple freeze-thaw cycles than bacteriome profiles, but there was a greater chance for operator effect in phageome processing. The successful spiking of faecal samples with exogenous bacteriophage demonstrated large variations in the total viral load between individual samples. CONCLUSIONS The faecal phageome sequencing protocol developed in this study provides a valuable additional view of the human gut microbiota that is complementary to 16S amplicon sequencing and/or metagenomic sequencing of total faecal DNA. The protocol was optimised for several confounding factors that are encountered while processing faecal samples, to reduce discrepancies observed within and between research groups studying the human gut phageome. Rapid storage, limited freeze-thaw cycling and spiking of faecal samples with an exogenous phage standard are recommended for optimum results.
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Affiliation(s)
| | - Feargal J. Ryan
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - Amanda Forde
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Stephen R. Stockdale
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork Ireland
| | - Karen M. Daly
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - James A. Nolan
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - Marion Dalmasso
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Normandie Univ, UNICAEN, EA4651 ABTE, F-14032 Caen, France
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Institute, University College Cork, Cork, Ireland
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30
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Anonye BO. Commentary: Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome. Front Cell Infect Microbiol 2018; 8:104. [PMID: 29670863 PMCID: PMC5893759 DOI: 10.3389/fcimb.2018.00104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/19/2018] [Indexed: 01/21/2023] Open
Affiliation(s)
- Blessing O Anonye
- Microbiology and Infection Unit, Division of Biomedical Sciences, Warwick Medical School, Coventry, United Kingdom.,Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
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31
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Leung MHY, Tong X, Wilkins D, Cheung HHL, Lee PKH. Individual and household attributes influence the dynamics of the personal skin microbiota and its association network. MICROBIOME 2018; 6:26. [PMID: 29394957 PMCID: PMC5797343 DOI: 10.1186/s40168-018-0412-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 01/19/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Numerous studies have thus far characterized the temporal dynamics of the skin microbiota of healthy individuals. However, there is no information regarding the dynamics of different microbial association network properties. Also, there is little understanding of how living conditions, specifically cohabitation and household occupancy, may be associated with the nature and extent (or degree) of cutaneous microbiota change within individuals over time. In this study, the dynamics of the skin microbiota, and its association networks, on the skin of urban residents over four seasons were characterized. RESULTS Similar to western cohorts, the individuals of this cohort show different extents of variations in relative abundance of common skin colonizers, concomitant with individual- and household-associated changes in differential abundances of bacterial taxa. Interestingly, the individualized nature of the skin microbiota extends to various aspects of microbial association networks, including co-occurring and excluding taxa, as well as overall network structural properties. Household occupancy is correlated with the extent of variations in relative abundance of Propionibacterium, Acinetobacter, and Bacillus over multiple skin sites. In addition, household occupancy is also associated with the extent of temporal changes in microbial diversity and composition within a resident's skin. CONCLUSIONS This is the first study investigating the potential roles household occupancy has on the extent of change in one's cutaneous microbiota and its association network structures. In particular, we show that relationships between the skin microbiota of a resident, his/her cohabitants, and those of non-cohabitants over time are highly personal and are possibly governed by living conditions and nature of interactions between cohabitants within households over 1 year. This study calls for increased awareness to personal and lifestyle factors that may govern relationships between the skin microbiota of one individual and those of cohabitants, and changes in the microbial association network structures within a person over time. The current study will act as a baseline for future assessments in comparing against temporal dynamics of microbiota from individuals with different skin conditions and for identifying residential factors that are beneficial in promoting the dynamics of the skin microbiota associated with health.
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Affiliation(s)
- Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong
| | - David Wilkins
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong
| | - Hedwig H. L. Cheung
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong
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32
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Forde A, Hill C. Phages of life - the path to pharma. Br J Pharmacol 2018; 175:412-418. [PMID: 29266197 PMCID: PMC5773946 DOI: 10.1111/bph.14106] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/15/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022] Open
Abstract
Bacteriophage (phage) therapy has encountered both enthusiasm and scepticism in the past century. New antimicrobial strategies against lethal pathogens are now a top priority for the World Health Organization, and although compassionate use of phages recently met with significant success, regulated clinical interventions seem unlikely in the near future. The hundredth anniversary of their discovery seems an appropriate time for a revival of phage therapy, particularly as the dilemma of antibiotic resistance grows. Phages are ubiquitous in the environment, on our food and in and on our bodies. Their influence on human health is currently being evaluated, and in this mini-review, we examine data from recent metagenomic studies that propose a role for phages in the structure of the microbiome and in health and disease. We assess evidence for phages as vehicles for gene transfer in the context of antibiotic resistance and discuss challenges and opportunities along the critical path from phage discovery to a patient-focused pharmaceutical intervention.
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Affiliation(s)
- Amanda Forde
- APC Microbiome InstituteUniversity College CorkCorkIreland
| | - Colin Hill
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome InstituteUniversity College CorkCorkIreland
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33
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Methods for Enrichment and Sequencing of Oral Viral Assemblages: Saliva, Oral Mucosa, and Dental Plaque Viromes. Methods Mol Biol 2018; 1838:143-161. [PMID: 30128995 DOI: 10.1007/978-1-4939-8682-8_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The oral cavity is a major portal of entry for human pathogens including viruses. However, metagenomics has revealed that highly personalized and time-persistent bacteriophage assemblages dominate this habitat. Most oral bacteriophages follow lysogenic life cycles, deploying complex strategies to manage bacterial homeostasis. Although bacterial dysbiosis underlies common oral pathologies such as caries and periodontitis, the cause of these bacteria replacements remains obscure, and it is theorized that bacteriophages play an important role. The enormous sensitivity of metagenomics coupled with next-generation sequencing has made technically feasible to address the putative role of bacteriophages in oral dysbiosis and represents a valuable tool to discover new human viruses.This chapter proposes a workflow that consists of a simple viral enrichment protocol, two alternative random amplification methods, and next-generation sequencing to access virome composition in three oral environments: supragingival plaque, saliva, and mucosa. These protocols circumvent some well-known sources of bias, providing genomic information about DNA and RNA viral communities with minimal contamination from human and bacterial sources.
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The human gut virome: form and function. Emerg Top Life Sci 2017; 1:351-362. [PMID: 33525769 DOI: 10.1042/etls20170039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/18/2017] [Accepted: 10/20/2017] [Indexed: 01/15/2023]
Abstract
Advances in next-generation sequencing technologies and the application of metagenomic approaches have fuelled an exponential increase in our understanding of the human gut microbiome. These approaches are now also illuminating features of the diverse and abundant collection of viruses (termed the virome) subsisting with the microbial ecosystems residing within the human holobiont. Here, we focus on the current and emerging knowledge of the human gut virome, in particular on viruses infecting bacteria (bacteriophage or phage), which are a dominant component of this viral community. We summarise current insights regarding the form and function of this 'human gut phageome' and highlight promising avenues for future research. In doing so, we discuss the potential for phage to drive ecological functioning and evolutionary change within this important microbial ecosystem, their contribution to modulation of host-microbiome interactions and stability of the community as a whole, as well as the potential role of the phageome in human health and disease. We also consider the emerging concepts of a 'core healthy gut phageome' and the putative existence of 'viral enterotypes' and 'viral dysbiosis'.
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35
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Carding SR, Davis N, Hoyles L. Review article: the human intestinal virome in health and disease. Aliment Pharmacol Ther 2017; 46:800-815. [PMID: 28869283 PMCID: PMC5656937 DOI: 10.1111/apt.14280] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 04/07/2017] [Accepted: 08/07/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The human virome consists of animal-cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High-throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus-like particles make to the human virome, and in particular the intestinal virome. AIM To review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases. METHODS Relevant virome-related articles were selected for review following extensive language- and date-unrestricted, electronic searches of the literature. RESULTS The human intestinal virome is personalised and stable, and dominated by phages. It develops soon after birth in parallel with prokaryotic communities of the microbiota, becoming established during the first few years of life. By infecting specific populations of bacteria, phages can alter microbiota structure by killing host cells or altering their phenotype, enabling phages to contribute to maintaining intestinal homeostasis or microbial imbalance (dysbiosis), and the development of chronic infectious and autoimmune diseases including HIV infection and Crohn's disease, respectively. CONCLUSIONS Our understanding of the intestinal virome is fragmented and requires standardised methods for virus isolation and sequencing to provide a more complete picture of the virome, which is key to explaining the basis of virome-disease associations, and how enteric viruses can contribute to disease aetiologies and be rationalised as targets for interventions.
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Affiliation(s)
- S. R. Carding
- Norwich Medical SchoolUniversity of East AngliaNorwichUK,The Gut Health and Food Safety Research ProgrammeThe Quadram InstituteNorwich Research ParkNorwichUK
| | - N. Davis
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - L. Hoyles
- Department of Surgery and CancerImperial College LondonLondonUK
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Integrating the microbiome as a resource in the forensics toolkit. Forensic Sci Int Genet 2017; 30:141-147. [DOI: 10.1016/j.fsigen.2017.06.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/26/2017] [Accepted: 06/24/2017] [Indexed: 11/19/2022]
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Łusiak-Szelachowska M, Weber-Dąbrowska B, Jończyk-Matysiak E, Wojciechowska R, Górski A. Bacteriophages in the gastrointestinal tract and their implications. Gut Pathog 2017; 9:44. [PMID: 28811841 PMCID: PMC5553654 DOI: 10.1186/s13099-017-0196-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/06/2017] [Indexed: 12/22/2022] Open
Abstract
The gut microbiota plays an essential role in health and disease of humans. Bacteriophages are the most abundant members of the gut virobiota and display great diversity. Phages can translocate through the mucosa to lymph and internal organs and play a role as regulators of the bacterial population in the gut. Increasing abundance of phages in the gut mucosa may reduce colonization by bacteria. Moreover, phages may have an immunomodulatory role in the immune response in the human gut. The role of phages in inflammatory bowel disease (IBD) remains unknown. Phages may take part in the development of IBD, but there are also data suggesting the protective role of phages in the gut of patients with IBD. Furthermore, recent data suggest that phages may mediate the beneficial effects of fecal microbiota transplantation (FMT). Therefore, evidence is accumulating to highlight the protective immunomodulating activity of the gut phages.
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Affiliation(s)
- Marzanna Łusiak-Szelachowska
- Laboratory of Bacteriophages, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences (HIIET PAS), 53-114 Wrocław, Poland
| | - Beata Weber-Dąbrowska
- Laboratory of Bacteriophages, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences (HIIET PAS), 53-114 Wrocław, Poland
| | - Ewa Jończyk-Matysiak
- Laboratory of Bacteriophages, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences (HIIET PAS), 53-114 Wrocław, Poland
| | - Renata Wojciechowska
- Laboratory of Bacteriophages, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences (HIIET PAS), 53-114 Wrocław, Poland
| | - Andrzej Górski
- Laboratory of Bacteriophages, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences (HIIET PAS), 53-114 Wrocław, Poland.,Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, 02-006 Warsaw, Poland
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Nikolich-Zugich J, Goodrum F, Knox K, Smithey MJ. Known unknowns: how might the persistent herpesvirome shape immunity and aging? Curr Opin Immunol 2017; 48:23-30. [PMID: 28780492 DOI: 10.1016/j.coi.2017.07.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/08/2017] [Accepted: 07/12/2017] [Indexed: 12/11/2022]
Abstract
The microbial community that colonizes all living organisms is gaining appreciation for its contributions to both physiologic and pathogenic processes. The virome, a subset of the overall microbiome, large and diverse, including viruses that persistently inhabit host cells, endogenous viral elements genomically or epigenomically integrated into cells, and viruses that infect the other (bacterial, protozoan, fungal, and archaeal) microbiome phylla. These viruses live in the organism for its life, and therefore are to be considered part of the aging process experienced by the organism. This review considers the impact of the persistent latent virome on immune aging. Specific attention will be devoted to the role of herpesviruses, and within them, the cytomegalovirus, as the key modulators of immune aging.
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Affiliation(s)
- Janko Nikolich-Zugich
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724, United States.
| | - Felicia Goodrum
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724, United States
| | - Kenneth Knox
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724, United States; University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, United States
| | - Megan J Smithey
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724, United States.
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The Human Gut Phage Community and Its Implications for Health and Disease. Viruses 2017; 9:v9060141. [PMID: 28594392 PMCID: PMC5490818 DOI: 10.3390/v9060141] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/23/2017] [Accepted: 06/02/2017] [Indexed: 12/23/2022] Open
Abstract
In this review, we assess our current understanding of the role of bacteriophages infecting the human gut bacterial community in health and disease. In general, bacteriophages contribute to the structure of their microbial communities by driving host and viral diversification, bacterial evolution, and by expanding the functional diversity of ecosystems. Gut bacteriophages are an ensemble of unique and shared phages in individuals, which encompass temperate phages found predominately as prophage in gut bacteria (prophage reservoir) and lytic phages. In healthy individuals, only a small fraction of the prophage reservoir is activated and found as extracellular phages. Phage community dysbiosis is characterized by a shift in the activated prophage community or an increase of lytic phages, and has been correlated with disease, suggesting that a proper balance between lysis and lysogeny is needed to maintain health. Consequently, the concept of microbial dysbiosis might be extended to the phage component of the microbiome as well. Understanding the dynamics and mechanisms to restore balance after dysbiosis is an active area of research. The use of phage transplants to re-establish health suggests that phages can be used as disease treatment. Such advances represent milestones in our understanding of gut phages in human health and should fuel research on their role in health and disease.
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