Gut Phage Database: phage mining in the cave of wonders

Unterer, Magdalena; Mirzaei, Mohammadali Khan; Deng, Li

doi:10.1038/s41392-021-00615-2

Cited by 17 publications

(14 citation statements)

References 5 publications

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“…Details of procedures from data quality control, the quality-filtered reads co-assembly, to gene annotation and quantification were also same to our previous publication ( Lu et al, 2021 ), and here presented in Supplementary File 1 . The predicted genes were annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database ( Aoki and Kanehisa, 2005 ), the carbohydrate active enzyme (CAZyme) database ( Huang et al, 2018 ), Comprehensive Antibiotic Research Database (CARD) ( Alcock et al, 2020 ), the Virulence Factors of Pathogenic Bacteria (VFPB) database ( Liu et al, 2019 ), and the Gut Phage Database (GPD; http://ftp.ebi.ac.uk/pub/databases/metagenomics/genome_sets/gut_phage_database/ ) ( Unterer et al, 2021 ). Dysbiosis index was used to calculate the degree of microbiota dysbiosis (see Additional file 1 for calculation details; Casén et al, 2015 ).…”

Section: Methodsmentioning

confidence: 99%

Alterations in the intestinal microbiome and metabolic profile of patients with cirrhosis supplemented with lactulose, Clostridium butyricum, and Bifidobacterium longum infantis: a randomized placebo-controlled trial

Lü

Zhu²,

et al. 2023

Front. Microbiol.

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BackgroundLiver cirrhosis is commonly accompanied by intestinal dysbiosis and metabolic defects. Many clinical trials have shown microbiota-targeting strategies represent promising interventions for managing cirrhosis and its complications. However, the influences of the intestinal metagenomes and metabolic profiles of patients have not been fully elucidated.MethodsWe administered lactulose, Clostridium butyricum, and Bifidobacterium longum infantis as a synbiotic and used shotgun metagenomics and non-targeted metabolomics to characterize the results.ResultsPatients treated with the synbiotic for 12 weeks had lower dysbiosis index (DI) scores than placebo-treated patients and patients at baseline (NIP group). We identified 48 bacterial taxa enriched in the various groups, 66 differentially expressed genes, 18 differentially expressed virulence factor genes, 10 differentially expressed carbohydrate-active enzyme genes, and 173 metabolites present at differing concentrations in the Synbiotic versus Placebo group, and the Synbiotic versus NIP group. And Bifidobacteria species, especially B. longum, showed positive associations with many differentially expressed genes in synbiotic-treated patients. Metabolites pathway enrichment analysis showed that synbiotic significantly affected purine metabolism and aminoacyl-tRNA biosynthesis. And the purine metabolism and aminoacyl-tRNA biosynthesis were no longer significant differences in the Synbiotic group versus the healthy controls group. In conclusion, although littles influence on clinical parameters in the early intervention, the synbiotic showed a potential benefit to patients by ameliorating intestinal dysbiosis and metabolic defects; and the DI of intestinal microbiota is useful for the evaluation of the effect of clinical microbiota-targeting strategies on cirrhotic patients.Clinical Trial Registrationhttps://www.clinicaltrials.gov, identifiers NCT05687409.

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Section: Methodsmentioning

confidence: 99%

Alterations in the intestinal microbiome and metabolic profile of patients with cirrhosis supplemented with lactulose, Clostridium butyricum, and Bifidobacterium longum infantis: a randomized placebo-controlled trial

Lü

Zhu²,

et al. 2023

Front. Microbiol.

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“…Commonly used library preparation methods, such as randomly amplified and linker-amplified shotgun libraries, have limitations, as these methods are restricted to target only dsDNA viruses and can result in uneven coverage of viral genomes, particularly when the viruses are very different in proportional abundances 19, 21 . The transposon-based method, while fast and requiring low-input template, is still restricted to dsDNA 22 .…”

Section: Mainmentioning

confidence: 99%

A single strand-based library preparation method for unbiased virome characterization

Zhai,

Gobbi,

Kot

et al. 2024

Preprint

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The gut virome is an integral component of the gut microbiome, playing a crucial role in maintaining gut health. However, accurately depicting the entire gut virome is challenging due to the inherent limitations and biases associated with current sequencing library preparation methods. To overcome these problems, we repurposed the ligation-based single-stranded library (SSLR) preparation method for virome studies. We demonstrate that the SSLR method exhibits exceptional efficiency in quantifying viral DNA genomes (both dsDNA and ssDNA) and outperforms existing double-stranded (Nextera) and single-stranded (xGen, MDA+Nextera) library preparation approaches in terms of minimal amplification bias, evenness of coverage, and integrity of assembling viral genomes. The SSLR method can be utilized for the simultaneous library preparation of both DNA and RNA viral genomes. Furthermore, the SSLR method showed its ability to capture highly modified phage genomes, which were often lost using other library preparation approaches.

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“…Specialised databases are the logical solution to balancing efficiency with performance. Two of the largest specialised gut virome datasets are the "Human Gut Virome Database, GVD", which encompasses 13,203 viral populations (Gregory et al), and the "Gut Phage Database, GPD", which encompasses 142,809 phages (Unterer et al, 2021). Unfortunately, these are not included in the popular reference databases, such as GenBank or RefSeq, that are typically used for annotating metagenomes.…”

Section: Our Dependence On Databasesmentioning

confidence: 99%

The human gut virome: Composition, colonisation, interactions, and impacts on human health

Pargin¹,

Roach²,

Skye³

et al. 2022

Preprint

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The gut virome is an incredibly complex part of the gut ecosystem. Gut viruses play a role in many disease 9 states, but it is not yet known to what extent the gut virome impacts everyday human health. New 10 experimental and bioinformatic approaches are required to address this knowledge gap. Gut virome 11 colonisation begins at birth, becoming temporally stable over a 30-month period. The stable virome is highly 12 specific to each individual and is modulated by varying factors such as age, gender, diet, and disease state. 13 The gut virome is primarily composed of bacteriophages—predominantly crAssphage, and other 14 Caudovirales. The stability of the virome’s regular constituents is disrupted by disease. Transferring the 15 faecal microbiome and its viruses from a healthy individual can restore the functionality of the gut, and 16 alleviates the symptoms of some chronic illnesses. Investigation of the virome is a relatively novel field with 17 new genetic sequences being published at an increasing rate. Many of these present with a large percentage 18 of unknown proteins, this ‘viral dark matter’ is one of the major questions facing virologists and 19 bioinformaticians. Bioinformatics tools can be used to explore both new and existing publicly available viral 20 sequence datasets to quantify and classify viral species, but not all these tools are created equal, with some 21 being more precise, effective, and efficient than others. Here, we review the literature surrounding the gut 22 virome, how it is established, how it impacts human health, the methods used to investigate it, and the viral 23 dark matter veiling the understanding of the gut virome.

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Gut Phage Database: phage mining in the cave of wonders

Cited by 17 publications

References 5 publications

Alterations in the intestinal microbiome and metabolic profile of patients with cirrhosis supplemented with lactulose, Clostridium butyricum, and Bifidobacterium longum infantis: a randomized placebo-controlled trial

Alterations in the intestinal microbiome and metabolic profile of patients with cirrhosis supplemented with lactulose, Clostridium butyricum, and Bifidobacterium longum infantis: a randomized placebo-controlled trial

A single strand-based library preparation method for unbiased virome characterization

The human gut virome: Composition, colonisation, interactions, and impacts on human health

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