Literature DB >> 24148301

Bringing the gut microbiota into focus through microbial culture: recent progress and future perspective.

Emma Allen-Vercoe1.   

Abstract

Ever-more-powerful 'omics'-based technologies are allowing us to pry deeper and more clearly into the workings of the human gut microbiota. Culture of the component microbes has fallen somewhat behind these efforts for a number of reasons, not least of which being the perceived difficulty in growing microbial species that have previously eluded all efforts to tame them. However, recent advances in the field are beginning to bring success in this area, allowing holistic study of microbes and microbial communities in defined systems. Innovative approaches to the culture and study of the human microbiota will ultimately guide medical practice, as the importance of a robust gut microbial ecosystem in the maintenance of health is increasingly realized.
Copyright © 2013 Elsevier Ltd. All rights reserved.

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Year:  2013        PMID: 24148301      PMCID: PMC3859468          DOI: 10.1016/j.mib.2013.09.008

Source DB:  PubMed          Journal:  Curr Opin Microbiol        ISSN: 1369-5274            Impact factor:   7.934


  34 in total

1.  Genome-based design of a cell-free culture medium for Tropheryma whipplei.

Authors:  Patricia Renesto; Nicolas Crapoulet; Hiroyuki Ogata; Bernard La Scola; Guy Vestris; Jean-Michel Claverie; Didier Raoult
Journal:  Lancet       Date:  2003-08-09       Impact factor: 79.321

2.  Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model.

Authors:  Julie A K McDonald; Kathleen Schroeter; Susana Fuentes; Ineke Heikamp-Dejong; Cezar M Khursigara; Willem M de Vos; Emma Allen-Vercoe
Journal:  J Microbiol Methods       Date:  2013-08-27       Impact factor: 2.363

Review 3.  Microbial cultivation and the role of microbial resource centers in the omics era.

Authors:  Om Prakash; Yogesh Shouche; Kamlesh Jangid; Joel E Kostka
Journal:  Appl Microbiol Biotechnol       Date:  2012-11-09       Impact factor: 4.813

4.  Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon.

Authors:  Xiaolei Ze; Sylvia H Duncan; Petra Louis; Harry J Flint
Journal:  ISME J       Date:  2012-02-16       Impact factor: 10.302

5.  Enterotypes of the human gut microbiome.

Authors:  Manimozhiyan Arumugam; Jeroen Raes; Eric Pelletier; Denis Le Paslier; Takuji Yamada; Daniel R Mende; Gabriel R Fernandes; Julien Tap; Thomas Bruls; Jean-Michel Batto; Marcelo Bertalan; Natalia Borruel; Francesc Casellas; Leyden Fernandez; Laurent Gautier; Torben Hansen; Masahira Hattori; Tetsuya Hayashi; Michiel Kleerebezem; Ken Kurokawa; Marion Leclerc; Florence Levenez; Chaysavanh Manichanh; H Bjørn Nielsen; Trine Nielsen; Nicolas Pons; Julie Poulain; Junjie Qin; Thomas Sicheritz-Ponten; Sebastian Tims; David Torrents; Edgardo Ugarte; Erwin G Zoetendal; Jun Wang; Francisco Guarner; Oluf Pedersen; Willem M de Vos; Søren Brunak; Joel Doré; María Antolín; François Artiguenave; Hervé M Blottiere; Mathieu Almeida; Christian Brechot; Carlos Cara; Christian Chervaux; Antonella Cultrone; Christine Delorme; Gérard Denariaz; Rozenn Dervyn; Konrad U Foerstner; Carsten Friss; Maarten van de Guchte; Eric Guedon; Florence Haimet; Wolfgang Huber; Johan van Hylckama-Vlieg; Alexandre Jamet; Catherine Juste; Ghalia Kaci; Jan Knol; Omar Lakhdari; Severine Layec; Karine Le Roux; Emmanuelle Maguin; Alexandre Mérieux; Raquel Melo Minardi; Christine M'rini; Jean Muller; Raish Oozeer; Julian Parkhill; Pierre Renault; Maria Rescigno; Nicolas Sanchez; Shinichi Sunagawa; Antonio Torrejon; Keith Turner; Gaetana Vandemeulebrouck; Encarna Varela; Yohanan Winogradsky; Georg Zeller; Jean Weissenbach; S Dusko Ehrlich; Peer Bork
Journal:  Nature       Date:  2011-04-20       Impact factor: 49.962

6.  Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium.

Authors:  Muriel Derrien; Elaine E Vaughan; Caroline M Plugge; Willem M de Vos
Journal:  Int J Syst Evol Microbiol       Date:  2004-09       Impact factor: 2.747

7.  Influence of mucin on glycosidase, protease and arylamidase activities of human gut bacteria grown in a 3-stage continuous culture system.

Authors:  G T Macfarlane; S Hay; G R Gibson
Journal:  J Appl Bacteriol       Date:  1989-05

8.  Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.

Authors:  Jeffrey S McLean; Mary-Jane Lombardo; Jonathan H Badger; Anna Edlund; Mark Novotny; Joyclyn Yee-Greenbaum; Nikolay Vyahhi; Adam P Hall; Youngik Yang; Christopher L Dupont; Michael G Ziegler; Hamidreza Chitsaz; Andrew E Allen; Shibu Yooseph; Glenn Tesler; Pavel A Pevzner; Robert M Friedman; Kenneth H Nealson; J Craig Venter; Roger S Lasken
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-10       Impact factor: 11.205

9.  A framework for human microbiome research.

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

Review 10.  Some are more equal than others: the role of "keystone" species in the degradation of recalcitrant substrates.

Authors:  Xiaolei Ze; Fanny Le Mougen; Sylvia H Duncan; Petra Louis; Harry J Flint
Journal:  Gut Microbes       Date:  2013-04-02
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  20 in total

Review 1.  The dormant blood microbiome in chronic, inflammatory diseases.

Authors:  Marnie Potgieter; Janette Bester; Douglas B Kell; Etheresia Pretorius
Journal:  FEMS Microbiol Rev       Date:  2015-05-03       Impact factor: 16.408

Review 2.  The microbiome of the urinary tract--a role beyond infection.

Authors:  Samantha A Whiteside; Hassan Razvi; Sumit Dave; Gregor Reid; Jeremy P Burton
Journal:  Nat Rev Urol       Date:  2015-01-20       Impact factor: 14.432

Review 3.  Investigating a holobiont: Microbiota perturbations and transkingdom networks.

Authors:  Renee Greer; Xiaoxi Dong; Andrey Morgun; Natalia Shulzhenko
Journal:  Gut Microbes       Date:  2016-03-16

4.  Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel.

Authors:  Jonas Cremer; Igor Segota; Chih-Yu Yang; Markus Arnoldini; John T Sauls; Zhongge Zhang; Edgar Gutierrez; Alex Groisman; Terence Hwa
Journal:  Proc Natl Acad Sci U S A       Date:  2016-09-28       Impact factor: 11.205

5.  An in vitro intestinal platform with a self-sustaining oxygen gradient to study the human gut/microbiome interface.

Authors:  Raehyun Kim; Peter J Attayek; Yuli Wang; Kathleen L Furtado; Rita Tamayo; Christopher E Sims; Nancy L Allbritton
Journal:  Biofabrication       Date:  2019-11-06       Impact factor: 9.954

Review 6.  Organoid-based Models to Study the Role of Host-microbiota Interactions in IBD.

Authors:  Martina Poletti; Kaline Arnauts; Marc Ferrante; Tamas Korcsmaros
Journal:  J Crohns Colitis       Date:  2021-07-05       Impact factor: 10.020

7.  Enteric short-chain fatty acids: microbial messengers of metabolism, mitochondria, and mind: implications in autism spectrum disorders.

Authors:  Derrick F MacFabe
Journal:  Microb Ecol Health Dis       Date:  2015-05-29

8.  GUT in FOCUS Symposium NOBEL FORUM, Karolinska Institutet, February 2nd 2015.

Authors: 
Journal:  Microb Ecol Health Dis       Date:  2015-05-29

9.  Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes.

Authors:  Seth R Bordenstein; Kevin R Theis
Journal:  PLoS Biol       Date:  2015-08-18       Impact factor: 8.029

10.  A simple coculture system shows mutualism between anaerobic faecalibacteria and epithelial Caco-2 cells.

Authors:  Mehdi Sadaghian Sadabad; Julius Z H von Martels; Muhammed Tanweer Khan; Tjasso Blokzijl; Giuseppe Paglia; Gerard Dijkstra; Hermie J M Harmsen; Klaas Nico Faber
Journal:  Sci Rep       Date:  2015-12-15       Impact factor: 4.379

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