-
1
-
-
85030318437
-
Viral communities of the human gut: metagenomic analysis of composition and dynamics
-
Aggarwala, V., Liang, G., and Bushman, F.D. (2017). Viral communities of the human gut: metagenomic analysis of composition and dynamics. Mob. DNA 8, 12.
-
(2017)
Mob. DNA
, vol.8
, pp. 12
-
-
Aggarwala, V.1
Liang, G.2
Bushman, F.D.3
-
2
-
-
85067029575
-
Clades of huge phage from across Earth's ecosystems
-
Al-Shayeb, B., Sachdeva, R., Chen, L.-X., Ward, F., Munk, P., Devoto, A., Castelle, C.J., Olm, M.R., Bouma-Gregson, K., Amano, Y., et al. (2019). Clades of huge phage from across Earth's ecosystems. bioRxiv, doi: 10.1101/572362.
-
(2019)
bioRxiv
-
-
Al-Shayeb, B.1
Sachdeva, R.2
Chen, L.-X.3
Ward, F.4
Munk, P.5
Devoto, A.6
Castelle, C.J.7
Olm, M.R.8
Bouma-Gregson, K.9
Amano, Y.10
-
3
-
-
84875092761
-
Virus-host swinging party in the oceans: Incorporating biological complexity into paradigms of antagonistic coexistence
-
Avrani, S., Schwartz, D.A., and Lindell, D. (2012). Virus-host swinging party in the oceans: Incorporating biological complexity into paradigms of antagonistic coexistence. Mob. Genet. Elements 2, 88-95.
-
(2012)
Mob. Genet. Elements
, vol.2
, pp. 88-95
-
-
Avrani, S.1
Schwartz, D.A.2
Lindell, D.3
-
4
-
-
85067692775
-
What is (not) known about the dynamics of the human gut virome in health and disease
-
Beller, L., and Matthijnssens, J. (2019). What is (not) known about the dynamics of the human gut virome in health and disease. Curr. Opin. Virol. 37, 52-57.
-
(2019)
Curr. Opin. Virol.
, vol.37
, pp. 52-57
-
-
Beller, L.1
Matthijnssens, J.2
-
5
-
-
85065314281
-
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
-
Bin Jang, H., Bolduc, B., Zablocki, O., Kuhn, J.H., Roux, S., Adriaenssens, E.M., Brister, J.R., Kropinski, A.M., Krupovic, M., Lavigne, R., et al. (2019). Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat. Biotechnol. 37, 632-639.
-
(2019)
Nat. Biotechnol.
, vol.37
, pp. 632-639
-
-
Bin Jang, H.1
Bolduc, B.2
Zablocki, O.3
Kuhn, J.H.4
Roux, S.5
Adriaenssens, E.M.6
Brister, J.R.7
Kropinski, A.M.8
Krupovic, M.9
Lavigne, R.10
-
6
-
-
84905049901
-
Trimmomatic: a flexible trimmer for Illumina sequence data
-
Bolger, A.M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120.
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
7
-
-
0141891348
-
Metagenomic analyses of an uncultured viral community from human feces
-
Breitbart, M., Hewson, I., Felts, B., Mahaffy, J.M., Nulton, J., Salamon, P., and Rohwer, F. (2003). Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 185, 6220-6223.
-
(2003)
J. Bacteriol.
, vol.185
, pp. 6220-6223
-
-
Breitbart, M.1
Hewson, I.2
Felts, B.3
Mahaffy, J.M.4
Nulton, J.5
Salamon, P.6
Rohwer, F.7
-
8
-
-
49349118069
-
Viral diversity and dynamics in an infant gut
-
Breitbart, M., Haynes, M., Kelley, S., Angly, F., Edwards, R.A., Felts, B., Mahaffy, J.M., Mueller, J., Nulton, J., Rayhawk, S., et al. (2008). Viral diversity and dynamics in an infant gut. Res. Microbiol. 159, 367-373.
-
(2008)
Res. Microbiol.
, vol.159
, pp. 367-373
-
-
Breitbart, M.1
Haynes, M.2
Kelley, S.3
Angly, F.4
Edwards, R.A.5
Felts, B.6
Mahaffy, J.M.7
Mueller, J.8
Nulton, J.9
Rayhawk, S.10
-
9
-
-
85048013849
-
Phage puppet masters of the marine microbial realm
-
Breitbart, M., Bonnain, C., Malki, K., and Sawaya, N.A. (2018). Phage puppet masters of the marine microbial realm. Nat. Microbiol. 3, 754-766.
-
(2018)
Nat. Microbiol.
, vol.3
, pp. 754-766
-
-
Breitbart, M.1
Bonnain, C.2
Malki, K.3
Sawaya, N.A.4
-
10
-
-
85041821165
-
Contig annotation tool CAT robustly classifies assembled metagenomic contigs and long sequences
-
Cambuy, D.D., Coutinho, F.H., and Dutilh, B.E. (2016). Contig annotation tool CAT robustly classifies assembled metagenomic contigs and long sequences. bioRxiv, doi: 10.1101/072868.
-
(2016)
bioRxiv
-
-
Cambuy, D.D.1
Coutinho, F.H.2
Dutilh, B.E.3
-
11
-
-
85041387387
-
Assessment of the gorilla gut virome in association with natural simian immunodeficiency virus infection
-
D'arc, M., Furtado, C., Siqueira, J.D., Seuanez, H.N., Ayouba, A., Peeters, M., and Soares, M.A. (2018). Assessment of the gorilla gut virome in association with natural simian immunodeficiency virus infection. Retrovirology 15, 19.
-
(2018)
Retrovirology
, vol.15
, pp. 19
-
-
D'arc, M.1
Furtado, C.2
Siqueira, J.D.3
Seuánez, H.N.4
Ayouba, A.5
Peeters, M.6
Soares, M.A.7
-
12
-
-
84910057313
-
Host lifestyle affects human microbiota on daily timescales
-
David, L.A., Materna, A.C., Friedman, J., Campos-Baptista, M.I., Blackburn, M.C., Perrotta, A., Erdman, S.E., and Alm, E.J. (2014). Host lifestyle affects human microbiota on daily timescales. Genome Biol. 15, R89.
-
(2014)
Genome Biol.
, vol.15
, pp. R89
-
-
David, L.A.1
Materna, A.C.2
Friedman, J.3
Campos-Baptista, M.I.4
Blackburn, M.C.5
Perrotta, A.6
Erdman, S.E.7
Alm, E.J.8
-
13
-
-
85060602468
-
“I will survive”: A tale of bacteriophage-bacteria coevolution in the gut
-
De Sordi, L., Lourenco, M., and Debarbieux, L. (2019a). “I will survive”: A tale of bacteriophage-bacteria coevolution in the gut. Gut Microbes 10, 92-99.
-
(2019)
Gut Microbes
, vol.10
, pp. 92-99
-
-
De Sordi, L.1
Lourenço, M.2
Debarbieux, L.3
-
14
-
-
85060770052
-
The Battle Within: Interactions of Bacteriophages and Bacteria in the Gastrointestinal Tract
-
De Sordi, L., Lourenco, M., and Debarbieux, L. (2019b). The Battle Within: Interactions of Bacteriophages and Bacteria in the Gastrointestinal Tract. Cell Host Microbe 25, 210-218.
-
(2019)
Cell Host Microbe
, vol.25
, pp. 210-218
-
-
De Sordi, L.1
Lourenço, M.2
Debarbieux, L.3
-
15
-
-
85060806368
-
Megaphages infect Prevotella and variants are widespread in gut microbiomes
-
Devoto, A.E., Santini, J.M., Olm, M.R., Anantharaman, K., Munk, P., Tung, J., Archie, E.A., Turnbaugh, P.J., Seed, K.D., Blekhman, R., et al. (2019). Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nat. Microbiol. 4, 693-700.
-
(2019)
Nat. Microbiol.
, vol.4
, pp. 693-700
-
-
Devoto, A.E.1
Santini, J.M.2
Olm, M.R.3
Anantharaman, K.4
Munk, P.5
Tung, J.6
Archie, E.A.7
Turnbaugh, P.J.8
Seed, K.D.9
Blekhman, R.10
-
16
-
-
85058316436
-
Long-term colonisation with donor bacteriophages following successful faecal microbial transplantation
-
Draper, L.A., Ryan, F.J., Smith, M.K., Jalanka, J., Mattila, E., Arkkila, P.A., Ross, R.P., Satokari, R., and Hill, C. (2018). Long-term colonisation with donor bacteriophages following successful faecal microbial transplantation. Microbiome 6, 220.
-
(2018)
Microbiome
, vol.6
, pp. 220
-
-
Draper, L.A.1
Ryan, F.J.2
Smith, M.K.3
Jalanka, J.4
Mattila, E.5
Arkkila, P.A.6
Ross, R.P.7
Satokari, R.8
Hill, C.9
-
17
-
-
84905041075
-
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
-
Dutilh, B.E., Cassman, N., McNair, K., Sanchez, S.E., Silva, G.G.Z., Boling, L., Barr, J.J., Speth, D.R., Seguritan, V., Aziz, R.K., et al. (2014). A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun. 5, 4498.
-
(2014)
Nat. Commun.
, vol.5
, pp. 4498
-
-
Dutilh, B.E.1
Cassman, N.2
McNair, K.3
Sanchez, S.E.4
Silva, G.G.Z.5
Boling, L.6
Barr, J.J.7
Speth, D.R.8
Seguritan, V.9
Aziz, R.K.10
-
18
-
-
33846975418
-
PILER-CR: fast and accurate identification of CRISPR repeats
-
Edgar, R.C. (2007). PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics 8, 18.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 18
-
-
Edgar, R.C.1
-
19
-
-
84975275010
-
Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses
-
Enault, F., Briet, A., Bouteille, L., Roux, S., Sullivan, M.B., and Petit, M.-A. (2017). Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses. ISME J. 11, 237-247.
-
(2017)
ISME J.
, vol.11
, pp. 237-247
-
-
Enault, F.1
Briet, A.2
Bouteille, L.3
Roux, S.4
Sullivan, M.B.5
Petit, M.-A.6
-
20
-
-
84879744885
-
The long-term stability of the human gut microbiota
-
Faith, J.J., Guruge, J.L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A.L., Clemente, J.C., Knight, R., Heath, A.C., Leibel, R.L., et al. (2013). The long-term stability of the human gut microbiota. Science 341, 1237439.
-
(2013)
Science
, vol.341
, pp. 1237439
-
-
Faith, J.J.1
Guruge, J.L.2
Charbonneau, M.3
Subramanian, S.4
Seedorf, H.5
Goodman, A.L.6
Clemente, J.C.7
Knight, R.8
Heath, A.C.9
Leibel, R.L.10
-
21
-
-
85074020628
-
Akkermansia muciniphila in the Human Gastrointestinal Tract: When, Where, and How?
-
Geerlings, S.Y., Kostopoulos, I., de Vos, W.M., and Belzer, C. (2018). Akkermansia muciniphila in the Human Gastrointestinal Tract: When, Where, and How? Microorganisms 6, 75.
-
(2018)
Microorganisms
, vol.6
, pp. 75
-
-
Geerlings, S.Y.1
Kostopoulos, I.2
de Vos, W.M.3
Belzer, C.4
-
22
-
-
85016101251
-
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation
-
Grazziotin, A.L., Koonin, E.V., and Kristensen, D.M. (2017). Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res. 45 (D1), D491-D498.
-
(2017)
Nucleic Acids Res.
, vol.45
, Issue.D1
, pp. D491-D498
-
-
Grazziotin, A.L.1
Koonin, E.V.2
Kristensen, D.M.3
-
23
-
-
85056591119
-
Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut
-
Guerin, E., Shkoporov, A., Stockdale, S.R., Clooney, A.G., Ryan, F.J., Sutton, T.D.S., Draper, L.A., Gonzalez-Tortuero, E., Ross, R.P., and Hill, C. (2018). Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut. Cell Host Microbe 24, 653-664.e6.
-
(2018)
Cell Host Microbe
, vol.24
, pp. 653-664.e6
-
-
Guerin, E.1
Shkoporov, A.2
Stockdale, S.R.3
Clooney, A.G.4
Ryan, F.J.5
Sutton, T.D.S.6
Draper, L.A.7
Gonzalez-Tortuero, E.8
Ross, R.P.9
Hill, C.10
-
24
-
-
84875876463
-
β-Lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity
-
Gutierrez, A., Laureti, L., Crussard, S., Abida, H., Rodriguez-Rojas, A., Blazquez, J., Baharoglu, Z., Mazel, D., Darfeuille, F., Vogel, J., and Matic, I. (2013). β-Lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity. Nat. Commun. 4, 1610.
-
(2013)
Nat. Commun.
, vol.4
, pp. 1610
-
-
Gutierrez, A.1
Laureti, L.2
Crussard, S.3
Abida, H.4
Rodríguez-Rojas, A.5
Blázquez, J.6
Baharoglu, Z.7
Mazel, D.8
Darfeuille, F.9
Vogel, J.10
Matic, I.11
-
25
-
-
84956696379
-
Viral metagenomics: are we missing the giants?
-
Halary, S., Temmam, S., Raoult, D., and Desnues, C. (2016). Viral metagenomics: are we missing the giants? Curr. Opin. Microbiol. 31, 34-43.
-
(2016)
Curr. Opin. Microbiol.
, vol.31
, pp. 34-43
-
-
Halary, S.1
Temmam, S.2
Raoult, D.3
Desnues, C.4
-
26
-
-
85066807634
-
Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model
-
Hsu, B.B., Gibson, T.E., Yeliseyev, V., Liu, Q., Lyon, L., Bry, L., Silver, P.A., and Gerber, G.K. (2019). Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model. Cell Host Microbe 25, 803-814.e5.
-
(2019)
Cell Host Microbe
, vol.25
, pp. 803-814.e5
-
-
Hsu, B.B.1
Gibson, T.E.2
Yeliseyev, V.3
Liu, Q.4
Lyon, L.5
Bry, L.6
Silver, P.A.7
Gerber, G.K.8
-
27
-
-
79960854386
-
Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms
-
Jalanka-Tuovinen, J., Salonen, A., Nikkila, J., Immonen, O., Kekkonen, R., Lahti, L., Palva, A., and de Vos, W.M. (2011). Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms. PLoS One 6, e23035.
-
(2011)
PLoS One
, vol.6
, pp. e23035
-
-
Jalanka-Tuovinen, J.1
Salonen, A.2
Nikkilä, J.3
Immonen, O.4
Kekkonen, R.5
Lahti, L.6
Palva, A.7
de Vos, W.M.8
-
28
-
-
83155190998
-
Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses
-
Kim, K.-H., and Bae, J.-W. (2011). Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl. Environ. Microbiol. 77, 7663-7668.
-
(2011)
Appl. Environ. Microbiol.
, vol.77
, pp. 7663-7668
-
-
Kim, K.-H.1
Bae, J.-W.2
-
29
-
-
84873510063
-
A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets
-
Koren, O., Knights, D., Gonzalez, A., Waldron, L., Segata, N., Knight, R., Huttenhower, C., and Ley, R.E. (2013). A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput. Biol. 9, e1002863.
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1002863
-
-
Koren, O.1
Knights, D.2
Gonzalez, A.3
Waldron, L.4
Segata, N.5
Knight, R.6
Huttenhower, C.7
Ley, R.E.8
-
30
-
-
79955894106
-
Microviridae goes temperate: microvirus-related proviruses reside in the genomes of Bacteroidetes
-
Krupovic, M., and Forterre, P. (2011). Microviridae goes temperate: microvirus-related proviruses reside in the genomes of Bacteroidetes. PLoS One 6, e19893.
-
(2011)
PLoS One
, vol.6
, pp. e19893
-
-
Krupovic, M.1
Forterre, P.2
-
31
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359.
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
32
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R.; 1000 Genome Project Data Processing Subgroup (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
33
-
-
80053386018
-
A modular view of the bacteriophage genomic space: identification of host and lifestyle marker modules
-
Lima-Mendez, G., Toussaint, A., and Leplae, R. (2011). A modular view of the bacteriophage genomic space: identification of host and lifestyle marker modules. Res. Microbiol. 162, 737-746.
-
(2011)
Res. Microbiol.
, vol.162
, pp. 737-746
-
-
Lima-Mendez, G.1
Toussaint, A.2
Leplae, R.3
-
34
-
-
85030771846
-
Strains, functions and dynamics in the expanded Human Microbiome Project
-
Lloyd-Price, J., Mahurkar, A., Rahnavard, G., Crabtree, J., Orvis, J., Hall, A.B., Brady, A., Creasy, H.H., McCracken, C., Giglio, M.G., et al. (2017). Strains, functions and dynamics in the expanded Human Microbiome Project. Nature 550, 61-66.
-
(2017)
Nature
, vol.550
, pp. 61-66
-
-
Lloyd-Price, J.1
Mahurkar, A.2
Rahnavard, G.3
Crabtree, J.4
Orvis, J.5
Hall, A.B.6
Brady, A.7
Creasy, H.H.8
McCracken, C.9
Giglio, M.G.10
-
35
-
-
85008423062
-
Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics
-
Lopez-Siles, M., Duncan, S.H., Garcia-Gil, L.J., and Martinez-Medina, M. (2017). Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. ISME J. 11, 841-852.
-
(2017)
ISME J.
, vol.11
, pp. 841-852
-
-
Lopez-Siles, M.1
Duncan, S.H.2
Garcia-Gil, L.J.3
Martinez-Medina, M.4
-
36
-
-
85042880915
-
A human gut phage catalog correlates the gut phageome with type 2 diabetes
-
Ma, Y., You, X., Mai, G., Tokuyasu, T., and Liu, C. (2018). A human gut phage catalog correlates the gut phageome with type 2 diabetes. Microbiome 6, 24.
-
(2018)
Microbiome
, vol.6
, pp. 24
-
-
Ma, Y.1
You, X.2
Mai, G.3
Tokuyasu, T.4
Liu, C.5
-
37
-
-
84879801014
-
Identification of a new P335 subgroup through molecular analysis of lactococcal phages Q33 and BM13
-
Mahony, J., Martel, B., Tremblay, D.M., Neve, H., Heller, K.J., Moineau, S., and van Sinderen, D. (2013). Identification of a new P335 subgroup through molecular analysis of lactococcal phages Q33 and BM13. Appl. Environ. Microbiol. 79, 4401-4409.
-
(2013)
Appl. Environ. Microbiol.
, vol.79
, pp. 4401-4409
-
-
Mahony, J.1
Martel, B.2
Tremblay, D.M.3
Neve, H.4
Heller, K.J.5
Moineau, S.6
van Sinderen, D.7
-
38
-
-
84987654794
-
Healthy human gut phageome
-
Manrique, P., Bolduc, B., Walk, S.T., van der Oost, J., de Vos, W.M., and Young, M.J. (2016). Healthy human gut phageome. Proc. Natl. Acad. Sci. USA 113, 10400-10405.
-
(2016)
Proc. Natl. Acad. Sci. USA
, vol.113
, pp. 10400-10405
-
-
Manrique, P.1
Bolduc, B.2
Walk, S.T.3
van der Oost, J.4
de Vos, W.M.5
Young, M.J.6
-
39
-
-
80053528043
-
The human gut virome: inter-individual variation and dynamic response to diet
-
Minot, S., Sinha, R., Chen, J., Li, H., Keilbaugh, S.A., Wu, G.D., Lewis, J.D., and Bushman, F.D. (2011). The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 21, 1616-1625.
-
(2011)
Genome Res.
, vol.21
, pp. 1616-1625
-
-
Minot, S.1
Sinha, R.2
Chen, J.3
Li, H.4
Keilbaugh, S.A.5
Wu, G.D.6
Lewis, J.D.7
Bushman, F.D.8
-
40
-
-
84880652104
-
Rapid evolution of the human gut virome
-
Minot, S., Bryson, A., Chehoud, C., Wu, G.D., Lewis, J.D., and Bushman, F.D. (2013). Rapid evolution of the human gut virome. Proc. Natl. Acad. Sci. USA 110, 12450-12455.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 12450-12455
-
-
Minot, S.1
Bryson, A.2
Chehoud, C.3
Wu, G.D.4
Lewis, J.D.5
Bushman, F.D.6
-
41
-
-
84961777823
-
Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome
-
Monaco, C.L., Gootenberg, D.B., Zhao, G., Handley, S.A., Ghebremichael, M.S., Lim, E.S., Lankowski, A., Baldridge, M.T., Wilen, C.B., Flagg, M., et al. (2016). Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome. Cell Host Microbe 19, 311-322.
-
(2016)
Cell Host Microbe
, vol.19
, pp. 311-322
-
-
Monaco, C.L.1
Gootenberg, D.B.2
Zhao, G.3
Handley, S.A.4
Ghebremichael, M.S.5
Lim, E.S.6
Lankowski, A.7
Baldridge, M.T.8
Wilen, C.B.9
Flagg, M.10
-
42
-
-
85061025040
-
Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins
-
Moreno-Gallego, J.L., Chou, S.-P., Di Rienzi, S.C., Goodrich, J.K., Spector, T.D., Bell, J.T., Youngblut, N.D., Hewson, I., Reyes, A., and Ley, R.E. (2019). Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins. Cell Host Microbe 25, 261-272.e5.
-
(2019)
Cell Host Microbe
, vol.25
, pp. 261-272.e5
-
-
Moreno-Gallego, J.L.1
Chou, S.-P.2
Di Rienzi, S.C.3
Goodrich, J.K.4
Spector, T.D.5
Bell, J.T.6
Youngblut, N.D.7
Hewson, I.8
Reyes, A.9
Ley, R.E.10
-
43
-
-
77953050946
-
A catalog of reference genomes from the human microbiome
-
Human Microbiome Jumpstart Reference Strains Consortium, Nelson, K.E., Weinstock, G.M., Highlander, S.K., Worley, K.C., Creasy, H.H., Wortman, J.R., Rusch, D.B., Mitreva, M., Sodergren, E., et al.; (2010). A catalog of reference genomes from the human microbiome. Science 328, 994-999.
-
(2010)
Science
, vol.328
, pp. 994-999
-
-
Nelson, K.E.1
Weinstock, G.M.2
Highlander, S.K.3
Worley, K.C.4
Creasy, H.H.5
Wortman, J.R.6
Rusch, D.B.7
Mitreva, M.8
Sodergren, E.9
-
44
-
-
84922245262
-
Disease-specific alterations in the enteric virome in inflammatory bowel disease
-
Norman, J.M., Handley, S.A., Baldridge, M.T., Droit, L., Liu, C.Y., Keller, B.C., Kambal, A., Monaco, C.L., Zhao, G., Fleshner, P., et al. (2015). Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 160, 447-460.
-
(2015)
Cell
, vol.160
, pp. 447-460
-
-
Norman, J.M.1
Handley, S.A.2
Baldridge, M.T.3
Droit, L.4
Liu, C.Y.5
Keller, B.C.6
Kambal, A.7
Monaco, C.L.8
Zhao, G.9
Fleshner, P.10
-
45
-
-
85019133486
-
metaSPAdes: a new versatile metagenomic assembler
-
Nurk, S., Meleshko, D., Korobeynikov, A., and Pevzner, P.A. (2017). metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824-834.
-
(2017)
Genome Res.
, vol.27
, pp. 824-834
-
-
Nurk, S.1
Meleshko, D.2
Korobeynikov, A.3
Pevzner, P.A.4
-
46
-
-
84976871272
-
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
-
O'Leary, N.A., Wright, M.W., Brister, J.R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016). Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44 (D1), D733-D745.
-
(2016)
Nucleic Acids Res.
, vol.44
, Issue.D1
, pp. D733-D745
-
-
O'Leary, N.A.1
Wright, M.W.2
Brister, J.R.3
Ciufo, S.4
Haddad, D.5
McVeigh, R.6
Rajput, B.7
Robbertse, B.8
Smith-White, B.9
Ako-Adjei, D.10
-
47
-
-
85072691300
-
Multiple phase-variable mechanisms, including capsular polysaccharides, modify bacteriophage susceptibility in Bacteroides thetaiotaomicron
-
Porter, N.T., Hryckowian, A.J., Merrill, B.D., Gardner, J.O., Singh, S., Sonnenburg, J.L., and Martens, E.C. (2019). Multiple phase-variable mechanisms, including capsular polysaccharides, modify bacteriophage susceptibility in Bacteroides thetaiotaomicron. bioRxiv, doi: 10.1101/521070.
-
(2019)
bioRxiv
-
-
Porter, N.T.1
Hryckowian, A.J.2
Merrill, B.D.3
Gardner, J.O.4
Singh, S.5
Sonnenburg, J.L.6
Martens, E.C.7
-
48
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., et al.; MetaHIT Consortium (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65.
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
Li, R.2
Raes, J.3
Arumugam, M.4
Burgdorf, K.S.5
Manichanh, C.6
Nielsen, T.7
Pons, N.8
Levenez, F.9
Yamada, T.10
-
49
-
-
77954627922
-
Viruses in the faecal microbiota of monozygotic twins and their mothers
-
Reyes, A., Haynes, M., Hanson, N., Angly, F.E., Heath, A.C., Rohwer, F., and Gordon, J.I. (2010). Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334-338.
-
(2010)
Nature
, vol.466
, pp. 334-338
-
-
Reyes, A.1
Haynes, M.2
Hanson, N.3
Angly, F.E.4
Heath, A.C.5
Rohwer, F.6
Gordon, J.I.7
-
50
-
-
84890281518
-
Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut
-
Reyes, A., Wu, M., McNulty, N.P., Rohwer, F.L., and Gordon, J.I. (2013). Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut. Proc. Natl. Acad. Sci. USA 110, 20236-20241.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 20236-20241
-
-
Reyes, A.1
Wu, M.2
McNulty, N.P.3
Rohwer, F.L.4
Gordon, J.I.5
-
51
-
-
84942883364
-
Gut DNA viromes of Malawian twins discordant for severe acute malnutrition
-
Reyes, A., Blanton, L.V., Cao, S., Zhao, G., Manary, M., Trehan, I., Smith, M.I., Wang, D., Virgin, H.W., Rohwer, F., and Gordon, J.I. (2015). Gut DNA viromes of Malawian twins discordant for severe acute malnutrition. Proc. Natl. Acad. Sci. USA 112, 11941-11946.
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 11941-11946
-
-
Reyes, A.1
Blanton, L.V.2
Cao, S.3
Zhao, G.4
Manary, M.5
Trehan, I.6
Smith, M.I.7
Wang, D.8
Virgin, H.W.9
Rohwer, F.10
Gordon, J.I.11
-
52
-
-
84863838397
-
Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads
-
Roux, S., Krupovic, M., Poulet, A., Debroas, D., and Enault, F. (2012). Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads. PLoS One 7, e40418.
-
(2012)
PLoS One
, vol.7
, pp. e40418
-
-
Roux, S.1
Krupovic, M.2
Poulet, A.3
Debroas, D.4
Enault, F.5
-
53
-
-
84939526110
-
Viral dark matter and virus-host interactions resolved from publicly available microbial genomes
-
Roux, S., Hallam, S.J., Woyke, T., and Sullivan, M.B. (2015a). Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife 4, e08490.
-
(2015)
Elife
, vol.4
, pp. e08490
-
-
Roux, S.1
Hallam, S.J.2
Woyke, T.3
Sullivan, M.B.4
-
54
-
-
84930658013
-
VirSorter: mining viral signal from microbial genomic data
-
Roux, S., Enault, F., Hurwitz, B.L., and Sullivan, M.B. (2015b). VirSorter: mining viral signal from microbial genomic data. PeerJ 3, e985.
-
(2015)
PeerJ
, vol.3
, pp. e985
-
-
Roux, S.1
Enault, F.2
Hurwitz, B.L.3
Sullivan, M.B.4
-
55
-
-
85006073389
-
Towards quantitative viromics for both double-stranded and single-stranded DNA viruses
-
Roux, S., Solonenko, N.E., Dang, V.T., Poulos, B.T., Schwenck, S.M., Goldsmith, D.B., Coleman, M.L., Breitbart, M., and Sullivan, M.B. (2016). Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ 4, e2777.
-
(2016)
PeerJ
, vol.4
, pp. e2777
-
-
Roux, S.1
Solonenko, N.E.2
Dang, V.T.3
Poulos, B.T.4
Schwenck, S.M.5
Goldsmith, D.B.6
Coleman, M.L.7
Breitbart, M.8
Sullivan, M.B.9
-
56
-
-
85060885011
-
Benchmarking viromics: An in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
-
PeerJ Inc.
-
Roux, S., Emerson, J.B., Eloe-Fadrosh, E.A., and Sullivan, M.B. (2017). Benchmarking viromics: An in silico evaluation of metagenome-enabled estimates of viral community composition and diversity (PeerJ Inc.).
-
(2017)
-
-
Roux, S.1
Emerson, J.B.2
Eloe-Fadrosh, E.A.3
Sullivan, M.B.4
-
57
-
-
85068207292
-
Microbial genes and pathways in inflammatory bowel disease
-
Schirmer, M., Garner, A., Vlamakis, H., and Xavier, R.J. (2019). Microbial genes and pathways in inflammatory bowel disease. Nat. Rev. Microbiol. 17, 497-511.
-
(2019)
Nat. Rev. Microbiol.
, vol.17
, pp. 497-511
-
-
Schirmer, M.1
Garner, A.2
Vlamakis, H.3
Xavier, R.J.4
-
58
-
-
85060870452
-
Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome
-
Shkoporov, A.N., and Hill, C. (2019). Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome. Cell Host Microbe 25, 195-209.
-
(2019)
Cell Host Microbe
, vol.25
, pp. 195-209
-
-
Shkoporov, A.N.1
Hill, C.2
-
59
-
-
85052907786
-
Reproducible protocols for metagenomic analysis of human faecal phageomes
-
Shkoporov, A.N., Ryan, F.J., Draper, L.A., Forde, A., Stockdale, S.R., Daly, K.M., McDonnell, S.A., Nolan, J.A., Sutton, T.D.S., Dalmasso, M., et al. (2018a). Reproducible protocols for metagenomic analysis of human faecal phageomes. Microbiome 6, 68.
-
(2018)
Microbiome
, vol.6
, pp. 68
-
-
Shkoporov, A.N.1
Ryan, F.J.2
Draper, L.A.3
Forde, A.4
Stockdale, S.R.5
Daly, K.M.6
McDonnell, S.A.7
Nolan, J.A.8
Sutton, T.D.S.9
Dalmasso, M.10
-
60
-
-
85056598186
-
ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis
-
Shkoporov, A.N., Khokhlova, E.V., Fitzgerald, C.B., Stockdale, S.R., Draper, L.A., Ross, R.P., and Hill, C. (2018b). ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis. Nat. Commun. 9, 4781.
-
(2018)
Nat. Commun.
, vol.9
, pp. 4781
-
-
Shkoporov, A.N.1
Khokhlova, E.V.2
Fitzgerald, C.B.3
Stockdale, S.R.4
Draper, L.A.5
Ross, R.P.6
Hill, C.7
-
61
-
-
85021813111
-
Piggyback-the-Winner in host-associated microbial communities
-
Silveira, C.B., and Rohwer, F.L. (2016). Piggyback-the-Winner in host-associated microbial communities. NPJ Biofilms Microbiomes 2, 16010.
-
(2016)
NPJ Biofilms Microbiomes
, vol.2
, pp. 16010
-
-
Silveira, C.B.1
Rohwer, F.L.2
-
62
-
-
85061415696
-
-
Hill, C. Viral Dark Matter in the Gut Virome of Elderly Humans. Preprints, 2018070101,.
-
Stockdale, S., Ryan, F., McCann, A., Dalmasso, M., Ross, P., and Hill, C. (2018). Viral Dark Matter in the Gut Virome of Elderly Humans. Preprints, 2018070101, https://doi.org/10.20944/preprints201807.0101.v1.
-
(2018)
-
-
Stockdale, S.1
Ryan, F.2
McCann, A.3
Dalmasso, M.4
Ross, P.5
-
63
-
-
85067123220
-
-
Hill, C. Giant oversights in the human gut virome. Gut. Published online June 11, 2019.
-
Sutton, T.D.S., Clooney, A.G., and Hill, C. (2019). Giant oversights in the human gut virome. Gut. Published online June 11, 2019. https://doi.org/10.1136/gutjnl-2019-319067.
-
(2019)
-
-
Sutton, T.D.S.1
Clooney, A.G.2
-
64
-
-
85063317689
-
Transmission and persistence of crAssphage, a ubiquitous human-associated bacteriophage
-
Tamburini, F.B., Sherlock, G.J., and Bhatt, A.S. (2018). Transmission and persistence of crAssphage, a ubiquitous human-associated bacteriophage. bioRxiv, doi: 10.1101/460113.
-
(2018)
bioRxiv
-
-
Tamburini, F.B.1
Sherlock, G.J.2
Bhatt, A.S.3
-
65
-
-
60549094505
-
Aquatic Phage Ecology
-
S.T. Abedon Cambridge University Press Cambridge
-
Thingstad, T.F., Bratbak, G., and Heldal, M. (2008). Aquatic Phage Ecology. In Bacteriophage Ecology, Population Growth, Evolution, and Impact of Bacterial Viruses, S.T. Abedon, ed. (Cambridge: Cambridge University Press), pp. 251-280.
-
(2008)
Bacteriophage Ecology, Population Growth, Evolution, and Impact of Bacterial Viruses
, pp. 251-280
-
-
Thingstad, T.F.1
Bratbak, G.2
Heldal, M.3
-
66
-
-
84964994621
-
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
-
Truong, D.T., Franzosa, E.A., Tickle, T.L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C., and Segata, N. (2015). MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat. Methods 12, 902-903.
-
(2015)
Nat. Methods
, vol.12
, pp. 902-903
-
-
Truong, D.T.1
Franzosa, E.A.2
Tickle, T.L.3
Scholz, M.4
Weingart, G.5
Pasolli, E.6
Tett, A.7
Huttenhower, C.8
Segata, N.9
-
67
-
-
85069527298
-
Phage-Resistant Phase-Variant Sub-populations Mediate Herd Immunity Against Bacteriophage Invasion of Bacterial Meta-Populations
-
Turkington, C.J.R., Morozov, A., Clokie, M.R.J., and Bayliss, C.D. (2019). Phage-Resistant Phase-Variant Sub-populations Mediate Herd Immunity Against Bacteriophage Invasion of Bacterial Meta-Populations. Front. Microbiol. 10, 1473.
-
(2019)
Front. Microbiol.
, vol.10
, pp. 1473
-
-
Turkington, C.J.R.1
Morozov, A.2
Clokie, M.R.J.3
Bayliss, C.D.4
-
68
-
-
84952942226
-
Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates
-
Vandeputte, D., Falony, G., Vieira-Silva, S., Tito, R.Y., Joossens, M., and Raes, J. (2016). Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut 65, 57-62.
-
(2016)
Gut
, vol.65
, pp. 57-62
-
-
Vandeputte, D.1
Falony, G.2
Vieira-Silva, S.3
Tito, R.Y.4
Joossens, M.5
Raes, J.6
-
69
-
-
85034861639
-
Quantitative microbiome profiling links gut community variation to microbial load
-
Vandeputte, D., Kathagen, G., D'hoe, K., Vieira-Silva, S., Valles-Colomer, M., Sabino, J., Wang, J., Tito, R.Y., De Commer, L., Darzi, Y., et al. (2017). Quantitative microbiome profiling links gut community variation to microbial load. Nature 551, 507-511.
-
(2017)
Nature
, vol.551
, pp. 507-511
-
-
Vandeputte, D.1
Kathagen, G.2
D'hoe, K.3
Vieira-Silva, S.4
Valles-Colomer, M.5
Sabino, J.6
Wang, J.7
Tito, R.Y.8
De Commer, L.9
Darzi, Y.10
-
70
-
-
70349397986
-
In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli
-
Weiss, M., Denou, E., Bruttin, A., Serra-Moreno, R., Dillmann, M.-L., and Brussow, H. (2009). In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli. Virology 393, 16-23.
-
(2009)
Virology
, vol.393
, pp. 16-23
-
-
Weiss, M.1
Denou, E.2
Bruttin, A.3
Serra-Moreno, R.4
Dillmann, M.-L.5
Brüssow, H.6
-
71
-
-
84899090573
-
Kraken: ultrafast metagenomic sequence classification using exact alignments
-
Wood, D.E., and Salzberg, S.L. (2014). Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46.
-
(2014)
Genome Biol.
, vol.15
, pp. R46
-
-
Wood, D.E.1
Salzberg, S.L.2
-
72
-
-
31144459030
-
RNA viral community in human feces: prevalence of plant pathogenic viruses
-
Zhang, T., Breitbart, M., Lee, W.H., Run, J.-Q., Wei, C.L., Soh, S.W.L., Hibberd, M.L., Liu, E.T., Rohwer, F., and Ruan, Y. (2006). RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 4, e3.
-
(2006)
PLoS Biol.
, vol.4
, pp. e3
-
-
Zhang, T.1
Breitbart, M.2
Lee, W.H.3
Run, J.-Q.4
Wei, C.L.5
Soh, S.W.L.6
Hibberd, M.L.7
Liu, E.T.8
Rohwer, F.9
Ruan, Y.10
-
73
-
-
85062658723
-
Gut mucosal virome alterations in ulcerative colitis
-
Zuo, T., Lu, X.-J., Zhang, Y., Cheung, C.P., Lam, S., Zhang, F., Tang, W., Ching, J.Y.L., Zhao, R., Chan, P.K.S., et al. (2019). Gut mucosal virome alterations in ulcerative colitis. Gut 68, 1169-1179.
-
(2019)
Gut
, vol.68
, pp. 1169-1179
-
-
Zuo, T.1
Lu, X.-J.2
Zhang, Y.3
Cheung, C.P.4
Lam, S.5
Zhang, F.6
Tang, W.7
Ching, J.Y.L.8
Zhao, R.9
Chan, P.K.S.10
|