Literature DB >> 33093661

Innovations to culturing the uncultured microbial majority.

William H Lewis1, Guillaume Tahon1, Patricia Geesink1, Diana Z Sousa1, Thijs J G Ettema2.   

Abstract

Despite the surge of microbial genome data, experimental testing is important to confirm inferences about the cell biology, ecological roles and evolution of microorganisms. As the majority of archaeal and bacterial diversity remains uncultured and poorly characterized, culturing is a priority. The growing interest in and need for efficient cultivation strategies has led to many rapid methodological and technological advances. In this Review, we discuss common barriers that can hamper the isolation and culturing of novel microorganisms and review emerging, innovative methods for targeted or high-throughput cultivation. We also highlight recent examples of successful cultivation of novel archaea and bacteria, and suggest key microorganisms for future cultivation attempts.

Year:  2020        PMID: 33093661     DOI: 10.1038/s41579-020-00458-8

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


  134 in total

1.  Growing unculturable bacteria.

Authors:  Eric J Stewart
Journal:  J Bacteriol       Date:  2012-06-01       Impact factor: 3.490

Review 2.  Cultivating the uncultivated: a community genomics perspective.

Authors:  Gene W Tyson; Jillian F Banfield
Journal:  Trends Microbiol       Date:  2005-09       Impact factor: 17.079

Review 3.  Present and Future of Culturing Bacteria.

Authors:  Jörg Overmann; Birte Abt; Johannes Sikorski
Journal:  Annu Rev Microbiol       Date:  2017-07-21       Impact factor: 15.500

4.  A new view of the tree of life.

Authors:  Laura A Hug; Brett J Baker; Karthik Anantharaman; Christopher T Brown; Alexander J Probst; Cindy J Castelle; Cristina N Butterfield; Alex W Hernsdorf; Yuki Amano; Kotaro Ise; Yohey Suzuki; Natasha Dudek; David A Relman; Kari M Finstad; Ronald Amundson; Brian C Thomas; Jillian F Banfield
Journal:  Nat Microbiol       Date:  2016-04-11       Impact factor: 17.745

Review 5.  Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life.

Authors:  Cindy J Castelle; Jillian F Banfield
Journal:  Cell       Date:  2018-03-08       Impact factor: 41.582

6.  A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile.

Authors:  Takuro Nunoura; Yoshito Chikaraishi; Rikihisa Izaki; Takashi Suwa; Takaaki Sato; Takeshi Harada; Koji Mori; Yumiko Kato; Masayuki Miyazaki; Shigeru Shimamura; Katsunori Yanagawa; Aya Shuto; Naohiko Ohkouchi; Nobuyuki Fujita; Yoshihiro Takaki; Haruyuki Atomi; Ken Takai
Journal:  Science       Date:  2018-02-01       Impact factor: 47.728

7.  A "Cultural" Renaissance: Genomics Breathes New Life into an Old Craft.

Authors:  Paul Carini
Journal:  mSystems       Date:  2019-05-07       Impact factor: 6.496

8.  Culturing the Uncultured: Risk versus Reward.

Authors:  J Cameron Thrash
Journal:  mSystems       Date:  2019-05-21       Impact factor: 6.496

9.  Complete nitrification by Nitrospira bacteria.

Authors:  Holger Daims; Elena V Lebedeva; Petra Pjevac; Ping Han; Craig Herbold; Mads Albertsen; Nico Jehmlich; Marton Palatinszky; Julia Vierheilig; Alexandr Bulaev; Rasmus H Kirkegaard; Martin von Bergen; Thomas Rattei; Bernd Bendinger; Per H Nielsen; Michael Wagner
Journal:  Nature       Date:  2015-11-26       Impact factor: 49.962

10.  Isolation of an archaeon at the prokaryote-eukaryote interface.

Authors:  Hiroyuki Imachi; Masaru K Nobu; Nozomi Nakahara; Yuki Morono; Miyuki Ogawara; Yoshihiro Takaki; Yoshinori Takano; Katsuyuki Uematsu; Tetsuro Ikuta; Motoo Ito; Yohei Matsui; Masayuki Miyazaki; Kazuyoshi Murata; Yumi Saito; Sanae Sakai; Chihong Song; Eiji Tasumi; Yuko Yamanaka; Takashi Yamaguchi; Yoichi Kamagata; Hideyuki Tamaki; Ken Takai
Journal:  Nature       Date:  2020-01-15       Impact factor: 69.504

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  53 in total

1.  Isolation Chip Increases Culturable Bacterial Diversity and Reduces Cultivation Bias.

Authors:  Xinwu Liu; Miaoxiao Wang; Yong Nie; Xiao-Lei Wu
Journal:  Curr Microbiol       Date:  2021-04-05       Impact factor: 2.188

Review 2.  Insights into microbial diversity on plastisphere by multi-omics.

Authors:  Neha Tiwari; Megha Bansal; Deenan Santhiya; Jai Gopal Sharma
Journal:  Arch Microbiol       Date:  2022-03-22       Impact factor: 2.552

Review 3.  Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting.

Authors:  Manigundan Kaari; Radhakrishnan Manikkam; Abirami Baskaran
Journal:  Mar Biotechnol (NY)       Date:  2022-04-08       Impact factor: 3.619

Review 4.  Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities.

Authors:  Lindsay K Caesar; Rana Montaser; Nancy P Keller; Neil L Kelleher
Journal:  Nat Prod Rep       Date:  2021-11-17       Impact factor: 13.423

5.  Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques.

Authors:  Alyssa M Demko; Nastassia V Patin; Paul R Jensen
Journal:  Environ Microbiol       Date:  2021-10-11       Impact factor: 5.491

6.  Microscopic Control of Nonequilibrium Systems: When Electrochemistry Meets Nanotechnology.

Authors:  Chong Liu
Journal:  Nano Lett       Date:  2021-09-08       Impact factor: 12.262

Review 7.  Cultivation of previously uncultured microorganisms with a continuous-flow down-flow hanging sponge (DHS) bioreactor, using a syntrophic archaeon culture obtained from deep marine sediment as a case study.

Authors:  Hiroyuki Imachi; Masaru K Nobu; Masayuki Miyazaki; Eiji Tasumi; Yumi Saito; Sanae Sakai; Miyuki Ogawara; Akiyoshi Ohashi; Ken Takai
Journal:  Nat Protoc       Date:  2022-09-14       Impact factor: 17.021

8.  Progress and Challenges in Studying the Ecophysiology of Archaea.

Authors:  Panagiotis S Adam; Till L V Bornemann; Alexander J Probst
Journal:  Methods Mol Biol       Date:  2022

9.  Genomic Insights into the Ecological Role and Evolution of a Novel Thermoplasmata Order, "Candidatus Sysuiplasmatales".

Authors:  Yang Yuan; Jun Liu; Tao-Tao Yang; Shao-Ming Gao; Bin Liao; Li-Nan Huang
Journal:  Appl Environ Microbiol       Date:  2021-09-15       Impact factor: 4.792

10.  Insights into the Cultured Bacterial Fraction of Corals.

Authors:  Michael Sweet; Helena Villela; Tina Keller-Costa; Rodrigo Costa; Stefano Romano; David G Bourne; Anny Cárdenas; Megan J Huggett; Allison H Kerwin; Felicity Kuek; Mónica Medina; Julie L Meyer; Moritz Müller; F Joseph Pollock; Michael S Rappé; Mathieu Sere; Koty H Sharp; Christian R Voolstra; Nathan Zaccardi; Maren Ziegler; Raquel Peixoto
Journal:  mSystems       Date:  2021-06-22       Impact factor: 6.496

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