MetaPhinder—Identifying Bacteriophage Sequences in Metagenomic Data Sets

Jurtz, Vanessa Isabell; Villarroel, Julia; Lund, Ole; Larsen, Mette Voldby; Nielsen, Morten

doi:10.1371/journal.pone.0163111

“…Phage genes were identified from the human, mouse, pig, and cynomolgus macaque gut gene catalogs using Metafinder [ 41 ] (ANI >1.7%). Phage genes that differed in abundance between samples from cynomolgus macaques fed the low-fat/high-fiber diet and the high-fat/low-fiber diet were selected by Wilcoxon rank sum test (P < 0.05).…”

Section: Methodsmentioning

confidence: 99%

“…In total 311,017 (15.62%) of the genes in the cynomolgus macaque gut gene catalog were predicted as bacterial phage sequences by Metafinder [ 41 ] (ANI >1.7%). Similar ratios of phage genes in the human, mouse, and pig gut gene catalogs were also predicted using the same pipeline (Additional File 15).…”

Section: Analysesmentioning

confidence: 99%

Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig, and mouse gut microbiomes

Li

¹

,

Liang

²

,

Xia

³

et al. 2018

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Macaca fascicularis, the cynomolgus macaque, is a widely used model in biomedical research and drug development as its genetics and physiology are close to those of humans. Detailed information on the cynomolgus macaque gut microbiota, the functional interplay between the gut microbiota and host physiology, and possible similarities to humans and other mammalians is very limited. The aim of this study was to construct the first cynomolgus macaque gut microbial gene catalog and compare this catalog to the human, pig, and mouse gut microbial gene catalogs. We performed metagenomic sequencing on fecal samples from 20 cynomolgus macaques and identified 1.9 million non-redundant bacterial genes of which 39.49% and 25.45% are present in the human and pig gut bacterial gene catalogs, respectively, whereas only 0.6% of the genes are present in the mouse gut bacterial gene catalog. By contrast, at the functional levels, more than 76% Kyoto Encyclopedia of Genes and Genomes orthologies are shared between the gut microbiota of all four mammalians. Thirty-two highly abundant bacterial genera could be defined as core genera of these mammalians. We demonstrated significant differences in the composition and functional potential of the gut microbiota as well as in the distribution of predicted bacterial phage sequences in cynomolgus macaques fed either a low-fat/high-fiber diet or a high-fat/low-fiber diet. Interestingly, the gut microbiota of cynomolgus macaques fed the high-fat/low-fiber diet became more similar to the gut microbiota of humans.

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“…Taxonomer is an ultrafast taxonomy assigner, which assigns and classifies reads to human, bacterial, viral, phage, fungal, phix, ambiguous (i.e., reads fit to more than one bin) and "unknown" bins. For identification and classification of viral contigs, we used MetaPhinder (v2.1, Jurtz et al, 2016) through the web interface hosted at the Center for Genomic Epidemiology at the Danish Technical University (DTU). Additionally, we queried the Viral_rep and Phage_F domains of the PFAM database using hmmsearch (HMMER v3, Eddy, 2011) to identify ssDNA contigs (Trubl et al, 2019).…”

Section: Bioinformatic Analysesmentioning

confidence: 99%

Benchmarking protocols for the metagenomic analysis of stream biofilm viromes

Bekliz

¹

,

Brandani

²

,

Bourquin

³

et al. 2019

Preprint

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Viruses drive microbial diversity, function and evolution and influence important biogeochemical cycles in aquatic ecosystems. Despite their relevance, we currently lack an understanding of their potential impacts on stream biofilm structure and function. This is surprising given the critical role of biofilms for stream ecosystem processes. Currently, the study of viruses in stream biofilms is hindered by the lack of an optimized protocol for their extraction, concentration and purification. Here, we evaluate a range of methods to separate viral particles from stream biofilms, and to concentrate and purify them prior to DNA extraction and metagenome sequencing. Based on epifluorescence microscopy counts of viral-like particles (VLP) and DNA yields, we optimize a protocol including treatment with tetrasodium pyrophosphate and ultra-sonication to disintegrate biofilms, tangential-flow filtration to extract and concentrate VLP, followed by ultracentrifugation in a sucrose density gradient to isolate VLP from the biofilm slurry. Viromes derived from biofilms sampled from three different streams were dominated by Siphoviridae, Myoviridae and Podoviridae and provide first insights into the viral diversity of stream biofilms. Our protocol optimization provides an important step towards a better understanding of the ecological role of viruses in stream biofilms.

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“…Taxonomer is an ultrafast taxonomy assigner, which assigns and classifies reads to human, bacterial, viral, phage, fungal, phix, ambiguous (i.e., reads fit to more than one bin) and "unknown" bins. For identification and classification of viral contigs, we used MetaPhinder (v2.1, Jurtz et al, 2016) through the web interface hosted at the Center for Genomic Epidemiology at the Danish Technical University (DTU). We mapped the reads to the contigs using BWA-MEM (http://bio-bwa.sourceforge.net/) using default setting (e.g.…”

Section: Bioinformatic Analysesmentioning

confidence: 99%

Peer Review #2 of "Benchmarking protocols for the metagenomic analysis of stream biofilm viromes (v0.2)"

Breitbart¹

2019

0

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Viruses drive microbial diversity, function and evolution and influence important biogeochemical cycles in aquatic ecosystems. Despite their relevance, we currently lack an understanding of their potential impacts on stream biofilm structure and function. This is surprising given the critical role of biofilms for stream ecosystem processes. Currently, the study of viruses in stream biofilms is hindered by the lack of an optimized protocol for their extraction, concentration and purification. Here, we evaluate a range of methods to separate viral particles from stream biofilms, and to concentrate and purify them prior to DNA extraction and metagenome sequencing. Based on epifluorescence microscopy counts of viral-like particles (VLP) and DNA yields, we optimize a protocol including treatment with tetrasodium pyrophosphate and ultra-sonication to disintegrate biofilms, tangential-flow filtration to extract and concentrate VLP, followed by ultracentrifugation in a sucrose density gradient to isolate VLP from the biofilm slurry. Viromes derived from biofilms sampled from three different streams were dominated by Siphoviridae, Myoviridae and Podoviridae and provide first insights into the viral diversity of stream biofilms. Our protocol optimization provides an important step towards a better understanding of the ecological role of viruses in stream biofilms.

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MetaPhinder—Identifying Bacteriophage Sequences in Metagenomic Data Sets

Cited by 67 publications

References 42 publications

Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig, and mouse gut microbiomes

Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig, and mouse gut microbiomes

Benchmarking protocols for the metagenomic analysis of stream biofilm viromes

Peer Review #2 of "Benchmarking protocols for the metagenomic analysis of stream biofilm viromes (v0.2)"

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