Literature DB >> 22864264

Going viral: next-generation sequencing applied to phage populations in the human gut.

Alejandro Reyes1, Nicholas P Semenkovich, Katrine Whiteson, Forest Rohwer, Jeffrey I Gordon.   

Abstract

Over the past decade, researchers have begun to characterize viral diversity using metagenomic methods. These studies have shown that viruses, the majority of which infect bacteria, are probably the most genetically diverse components of the biosphere. Here, we briefly review the incipient rise of a phage biology renaissance, which has been catalysed by advances in next-generation sequencing. We explore how work characterizing phage diversity and lifestyles in the human gut is changing our view of ourselves as supra-organisms. Finally, we discuss how a renewed appreciation of phage dynamics may yield new applications for phage therapies designed to manipulate the structure and functions of our gut microbiomes.

Entities:  

Mesh:

Substances:

Year:  2012        PMID: 22864264      PMCID: PMC3596094          DOI: 10.1038/nrmicro2853

Source DB:  PubMed          Journal:  Nat Rev Microbiol        ISSN: 1740-1526            Impact factor:   60.633


  133 in total

1.  Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins.

Authors:  Peter J Turnbaugh; Christopher Quince; Jeremiah J Faith; Alice C McHardy; Tanya Yatsunenko; Faheem Niazi; Jason Affourtit; Michael Egholm; Bernard Henrissat; Rob Knight; Jeffrey I Gordon
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-02       Impact factor: 11.205

2.  Functional metagenomic profiling of nine biomes.

Authors:  Elizabeth A Dinsdale; Robert A Edwards; Dana Hall; Florent Angly; Mya Breitbart; Jennifer M Brulc; Mike Furlan; Christelle Desnues; Matthew Haynes; Linlin Li; Lauren McDaniel; Mary Ann Moran; Karen E Nelson; Christina Nilsson; Robert Olson; John Paul; Beltran Rodriguez Brito; Yijun Ruan; Brandon K Swan; Rick Stevens; David L Valentine; Rebecca Vega Thurber; Linda Wegley; Bryan A White; Forest Rohwer
Journal:  Nature       Date:  2008-03-12       Impact factor: 49.962

3.  Phages in nature.

Authors:  Martha Rj Clokie; Andrew D Millard; Andrey V Letarov; Shaun Heaphy
Journal:  Bacteriophage       Date:  2011-01

4.  Comparative metagenomics of microbial traits within oceanic viral communities.

Authors:  Itai Sharon; Natalia Battchikova; Eva-Mari Aro; Carmela Giglione; Thierry Meinnel; Fabian Glaser; Ron Y Pinter; Mya Breitbart; Forest Rohwer; Oded Béjà
Journal:  ISME J       Date:  2011-02-10       Impact factor: 10.302

5.  A third gyrovirus species in human faeces.

Authors:  Tung G Phan; Linlin Li; Miguel G O'Ryan; Hector Cortes; Nora Mamani; Isidore J O Bonkoungou; Chunling Wang; Christian M Leutenegger; Eric Delwart
Journal:  J Gen Virol       Date:  2012-03-14       Impact factor: 3.891

6.  High abundance of viruses found in aquatic environments.

Authors:  O Bergh; K Y Børsheim; G Bratbak; M Heldal
Journal:  Nature       Date:  1989-08-10       Impact factor: 49.962

7.  The phylogeny of prokaryotes.

Authors:  G E Fox; E Stackebrandt; R B Hespell; J Gibson; J Maniloff; T A Dyer; R S Wolfe; W E Balch; R S Tanner; L J Magrum; L B Zablen; R Blakemore; R Gupta; L Bonen; B J Lewis; D A Stahl; K R Luehrsen; K N Chen; C R Woese
Journal:  Science       Date:  1980-07-25       Impact factor: 47.728

8.  Foreign (M13) DNA ingested by mice reaches peripheral leukocytes, spleen, and liver via the intestinal wall mucosa and can be covalently linked to mouse DNA.

Authors:  R Schubbert; D Renz; B Schmitz; W Doerfler
Journal:  Proc Natl Acad Sci U S A       Date:  1997-02-04       Impact factor: 11.205

9.  In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli.

Authors:  Marietta Weiss; Emmanuel Denou; Anne Bruttin; Ruth Serra-Moreno; Marie-Lise Dillmann; Harald Brüssow
Journal:  Virology       Date:  2009-08-21       Impact factor: 3.616

10.  Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins.

Authors:  Elizabeth E Hansen; Catherine A Lozupone; Federico E Rey; Meng Wu; Janaki L Guruge; Aneesha Narra; Jonathan Goodfellow; Jesse R Zaneveld; Daniel T McDonald; Julia A Goodrich; Andrew C Heath; Rob Knight; Jeffrey I Gordon
Journal:  Proc Natl Acad Sci U S A       Date:  2011-02-11       Impact factor: 11.205

View more
  174 in total

Review 1.  Resident commensals shaping immunity.

Authors:  Deniz Erturk-Hasdemir; Dennis L Kasper
Journal:  Curr Opin Immunol       Date:  2013-07-02       Impact factor: 7.486

Review 2.  Emerging tools for synthetic genome design.

Authors:  Bo-Rahm Lee; Suhyung Cho; Yoseb Song; Sun Chang Kim; Byung-Kwan Cho
Journal:  Mol Cells       Date:  2013-05-02       Impact factor: 5.034

Review 3.  The role of diet on intestinal microbiota metabolism: downstream impacts on host immune function and health, and therapeutic implications.

Authors:  Jason R Goldsmith; R Balfour Sartor
Journal:  J Gastroenterol       Date:  2014-03-21       Impact factor: 7.527

4.  PCR-activated cell sorting as a general, cultivation-free method for high-throughput identification and enrichment of virus hosts.

Authors:  Shaun W Lim; Shea T Lance; Kenneth M Stedman; Adam R Abate
Journal:  J Virol Methods       Date:  2016-12-29       Impact factor: 2.014

5.  Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement.

Authors:  Elyse Stachler; Catherine Kelty; Mano Sivaganesan; Xiang Li; Kyle Bibby; Orin C Shanks
Journal:  Environ Sci Technol       Date:  2017-07-25       Impact factor: 9.028

Review 6.  Microbial ecology in Hydra: why viruses matter.

Authors:  Thomas C G Bosch; Juris A Grasis; Tim Lachnit
Journal:  J Microbiol       Date:  2015-03-03       Impact factor: 3.422

7.  Breastfeeding influences the neonatal virome.

Authors:  Frederic D Bushman; Guanxiang Liang
Journal:  Nature       Date:  2021-05-14       Impact factor: 49.962

8.  Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens.

Authors:  Ben Busby; David M Kristensen; Eugene V Koonin
Journal:  Environ Microbiol       Date:  2012-10-04       Impact factor: 5.491

Review 9.  Enteric Virome and Carcinogenesis in the Gut.

Authors:  Cade Emlet; Mack Ruffin; Regina Lamendella
Journal:  Dig Dis Sci       Date:  2020-03       Impact factor: 3.199

Review 10.  The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.

Authors:  Christian Milani; Sabrina Duranti; Francesca Bottacini; Eoghan Casey; Francesca Turroni; Jennifer Mahony; Clara Belzer; Susana Delgado Palacio; Silvia Arboleya Montes; Leonardo Mancabelli; Gabriele Andrea Lugli; Juan Miguel Rodriguez; Lars Bode; Willem de Vos; Miguel Gueimonde; Abelardo Margolles; Douwe van Sinderen; Marco Ventura
Journal:  Microbiol Mol Biol Rev       Date:  2017-11-08       Impact factor: 11.056

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.