Literature DB >> 23604403

Microbiomes.

Karen E Nelson1.   

Abstract

During the past decade, there has been an explosion in the quantity of sequencing data that has come out of the studies of microbiomes. This has resulted primarily from new technological developments to interrogating any environment of choice. Additional downstream applications to interrogating these datasets include "omics" studies such as transcriptomics and proteomics, all leading to a deeper understanding of microbial diversity and the multitude of species that remain uncultured. Metagenomic studies are now being performed routinely on a wide range of environments including soils, oceans, air, plants, and various animal species. They are being used to identify novel microbial species, new pathways, and to elucidate the roles of viruses and phage in the environment. In this review, we get a perspective on where the science is headed and what we expect to learn as additional studies unfold.

Mesh:

Year:  2013        PMID: 23604403     DOI: 10.1007/s00248-013-0227-y

Source DB:  PubMed          Journal:  Microb Ecol        ISSN: 0095-3628            Impact factor:   4.552


  32 in total

1.  Viral photosynthetic reaction center genes and transcripts in the marine environment.

Authors:  Itai Sharon; Shani Tzahor; Shannon Williamson; Michael Shmoish; Dikla Man-Aharonovich; Douglas B Rusch; Shibu Yooseph; Gil Zeidner; Susan S Golden; Shannon R Mackey; Noam Adir; Uri Weingart; David Horn; J Craig Venter; Yael Mandel-Gutfreund; Oded Béjà
Journal:  ISME J       Date:  2007-08-09       Impact factor: 10.302

2.  Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases.

Authors:  Jennifer M Brulc; Dionysios A Antonopoulos; Margret E Berg Miller; Melissa K Wilson; Anthony C Yannarell; Elizabeth A Dinsdale; Robert E Edwards; Edward D Frank; Joanne B Emerson; Pirjo Wacklin; Pedro M Coutinho; Bernard Henrissat; Karen E Nelson; Bryan A White
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-30       Impact factor: 11.205

3.  Ribosomal RNA phylogeny and the primary lines of evolutionary descent.

Authors:  N R Pace; G J Olsen; C R Woese
Journal:  Cell       Date:  1986-05-09       Impact factor: 41.582

4.  Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores.

Authors:  P B Pope; S E Denman; M Jones; S G Tringe; K Barry; S A Malfatti; A C McHardy; J-F Cheng; P Hugenholtz; C S McSweeney; M Morrison
Journal:  Proc Natl Acad Sci U S A       Date:  2010-07-28       Impact factor: 11.205

5.  Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen.

Authors:  Derrick E Fouts; Sebastian Szpakowski; Janaki Purushe; Manolito Torralba; Richard C Waterman; Michael D MacNeil; Leeson J Alexander; Karen E Nelson
Journal:  PLoS One       Date:  2012-11-07       Impact factor: 3.240

6.  Structure, function and diversity of the healthy human microbiome.

Authors: 
Journal:  Nature       Date:  2012-06-13       Impact factor: 49.962

7.  Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill.

Authors:  Olivia U Mason; Terry C Hazen; Sharon Borglin; Patrick S G Chain; Eric A Dubinsky; Julian L Fortney; James Han; Hoi-Ying N Holman; Jenni Hultman; Regina Lamendella; Rachel Mackelprang; Stephanie Malfatti; Lauren M Tom; Susannah G Tringe; Tanja Woyke; Jizhong Zhou; Edward M Rubin; Janet K Jansson
Journal:  ISME J       Date:  2012-06-21       Impact factor: 10.302

8.  Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice.

Authors:  Kelly S Swanson; Scot E Dowd; Jan S Suchodolski; Ingmar S Middelbos; Brittany M Vester; Kathleen A Barry; Karen E Nelson; Manolito Torralba; Bernard Henrissat; Pedro M Coutinho; Isaac K O Cann; Bryan A White; George C Fahey
Journal:  ISME J       Date:  2010-10-21       Impact factor: 10.302

9.  The Human Microbiome Project: a community resource for the healthy human microbiome.

Authors:  Dirk Gevers; Rob Knight; Joseph F Petrosino; Katherine Huang; Amy L McGuire; Bruce W Birren; Karen E Nelson; Owen White; Barbara A Methé; Curtis Huttenhower
Journal:  PLoS Biol       Date:  2012-08-14       Impact factor: 8.029

10.  Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury.

Authors:  Derrick E Fouts; Rembert Pieper; Sebastian Szpakowski; Hans Pohl; Susan Knoblach; Moo-Jin Suh; Shih-Ting Huang; Inger Ljungberg; Bruce M Sprague; Sarah K Lucas; Manolito Torralba; Karen E Nelson; Suzanne L Groah
Journal:  J Transl Med       Date:  2012-08-28       Impact factor: 5.531

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  3 in total

1.  The fecal virome of domesticated animals.

Authors:  Eszter Mihalov-Kovács; Enikő Fehér; Vito Martella; Krisztián Bányai; Szilvia L Farkas
Journal:  Virusdisease       Date:  2014-02-01

Review 2.  Microbiota in viral infection and disease in humans and farm animals.

Authors:  Lijuan Yuan; Casey Hensley; Hassan M Mahsoub; Ashwin K Ramesh; Peng Zhou
Journal:  Prog Mol Biol Transl Sci       Date:  2020-04-24       Impact factor: 3.622

3.  A novel group of diverse Polinton-like viruses discovered by metagenome analysis.

Authors:  Natalya Yutin; Sofiya Shevchenko; Vladimir Kapitonov; Mart Krupovic; Eugene V Koonin
Journal:  BMC Biol       Date:  2015-11-11       Impact factor: 7.431

  3 in total

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