Literature DB >> 33763385

Commentary: How to Count Our Microbes? The Effect of Different Quantitative Microbiome Profiling Approaches.

Ching Jian1, Anne Salonen1, Katri Korpela1.   

Abstract

Entities:  

Keywords:  absolute abundance; compositional data; flow cytometry; microbiome; next-generation sequencing; quantitative PCR

Mesh：

Substances：

Year:  2021        PMID： 33763385      PMCID： PMC7982878          DOI： 10.3389/fcimb.2021.627910

Source DB:  PubMed          Journal:  Front Cell Infect Microbiol        ISSN： 2235-2988            Impact factor:   5.293


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  9 in total

1.  Genetic diversity of viable, injured, and dead fecal bacteria assessed by fluorescence-activated cell sorting and 16S rRNA gene analysis.

Authors:  Kaouther Ben-Amor; Hans Heilig; Hauke Smidt; Elaine E Vaughan; Tjakko Abee; Willem M de Vos
Journal:  Appl Environ Microbiol       Date:  2005-08       Impact factor: 4.792

2.  Towards standards for human fecal sample processing in metagenomic studies.

Authors:  Paul I Costea; Georg Zeller; Shinichi Sunagawa; Eric Pelletier; Adriana Alberti; Florence Levenez; Melanie Tramontano; Marja Driessen; Rajna Hercog; Ferris-Elias Jung; Jens Roat Kultima; Matthew R Hayward; Luis Pedro Coelho; Emma Allen-Vercoe; Laurie Bertrand; Michael Blaut; Jillian R M Brown; Thomas Carton; Stéphanie Cools-Portier; Michelle Daigneault; Muriel Derrien; Anne Druesne; Willem M de Vos; B Brett Finlay; Harry J Flint; Francisco Guarner; Masahira Hattori; Hans Heilig; Ruth Ann Luna; Johan van Hylckama Vlieg; Jana Junick; Ingeborg Klymiuk; Philippe Langella; Emmanuelle Le Chatelier; Volker Mai; Chaysavanh Manichanh; Jennifer C Martin; Clémentine Mery; Hidetoshi Morita; Paul W O'Toole; Céline Orvain; Kiran Raosaheb Patil; John Penders; Søren Persson; Nicolas Pons; Milena Popova; Anne Salonen; Delphine Saulnier; Karen P Scott; Bhagirath Singh; Kathleen Slezak; Patrick Veiga; James Versalovic; Liping Zhao; Erwin G Zoetendal; S Dusko Ehrlich; Joel Dore; Peer Bork
Journal:  Nat Biotechnol       Date:  2017-10-02       Impact factor: 54.908

3.  Quantitative microbiome profiling links gut community variation to microbial load.

Authors:  Doris Vandeputte; Gunter Kathagen; Kevin D'hoe; Sara Vieira-Silva; Mireia Valles-Colomer; João Sabino; Jun Wang; Raul Y Tito; Lindsey De Commer; Youssef Darzi; Séverine Vermeire; Gwen Falony; Jeroen Raes
Journal:  Nature       Date:  2017-11-15       Impact factor: 49.962

Review 4.  Microbiome Datasets Are Compositional: And This Is Not Optional.

Authors:  Gregory B Gloor; Jean M Macklaim; Vera Pawlowsky-Glahn; Juan J Egozcue
Journal:  Front Microbiol       Date:  2017-11-15       Impact factor: 5.640

5.  A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities.

Authors:  Jacob T Barlow; Said R Bogatyrev; Rustem F Ismagilov
Journal:  Nat Commun       Date:  2020-05-22       Impact factor: 14.919

6.  Flow Cytometric Assessment of Bacterial Abundance in Soils, Sediments and Sludge.

Authors:  Aline Frossard; Frederik Hammes; Mark O Gessner
Journal:  Front Microbiol       Date:  2016-06-14       Impact factor: 5.640

7.  How to Count Our Microbes? The Effect of Different Quantitative Microbiome Profiling Approaches.

Authors:  Gianluca Galazzo; Niels van Best; Birke J Benedikter; Kevin Janssen; Liene Bervoets; Christel Driessen; Melissa Oomen; Mayk Lucchesi; Pascalle H van Eijck; Heike E F Becker; Mathias W Hornef; Paul H Savelkoul; Frank R M Stassen; Petra F Wolffs; John Penders
Journal:  Front Cell Infect Microbiol       Date:  2020-08-07       Impact factor: 5.293

8.  Gut microbiota density influences host physiology and is shaped by host and microbial factors.

Authors:  Eduardo J Contijoch; Graham J Britton; Chao Yang; Ilaria Mogno; Zhihua Li; Ruby Ng; Sean R Llewellyn; Sheela Hira; Crystal Johnson; Keren M Rabinowitz; Revital Barkan; Iris Dotan; Robert P Hirten; Shih-Chen Fu; Yuying Luo; Nancy Yang; Tramy Luong; Philippe R Labrias; Sergio Lira; Inga Peter; Ari Grinspan; Jose C Clemente; Roman Kosoy; Seunghee Kim-Schulze; Xiaochen Qin; Anabella Castillo; Amanda Hurley; Ashish Atreja; Jason Rogers; Farah Fasihuddin; Merjona Saliaj; Amy Nolan; Pamela Reyes-Mercedes; Carina Rodriguez; Sarah Aly; Kenneth Santa-Cruz; Lauren Peters; Mayte Suárez-Fariñas; Ruiqi Huang; Ke Hao; Jun Zhu; Bin Zhang; Bojan Losic; Haritz Irizar; Won-Min Song; Antonio Di Narzo; Wenhui Wang; Benjamin L Cohen; Christopher DiMaio; David Greenwald; Steven Itzkowitz; Aimee Lucas; James Marion; Elana Maser; Ryan Ungaro; Steven Naymagon; Joshua Novak; Brijen Shah; Thomas Ullman; Peter Rubin; James George; Peter Legnani; Shannon E Telesco; Joshua R Friedman; Carrie Brodmerkel; Scott Plevy; Judy H Cho; Jean-Frederic Colombel; Eric E Schadt; Carmen Argmann; Marla Dubinsky; Andrew Kasarskis; Bruce Sands; Jeremiah J Faith
Journal:  Elife       Date:  2019-01-22       Impact factor: 8.140

9.  Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling.

Authors:  Ching Jian; Panu Luukkonen; Hannele Yki-Järvinen; Anne Salonen; Katri Korpela
Journal:  PLoS One       Date:  2020-01-15       Impact factor: 3.240
  9 in total
  3 in total

Review 1.  Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research.

Authors:  Ethan W Morgan; Gary H Perdew; Andrew D Patterson
Journal:  Toxicol Sci       Date:  2022-05-26       Impact factor: 4.109

Review 2.  Infant gut microbiota restoration: state of the art.

Authors:  Katri Korpela; Willem M de Vos
Journal:  Gut Microbes       Date:  2022 Jan-Dec

3.  Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf.

Authors:  Liam MacNeil; Dhwani K Desai; Maycira Costa; Julie LaRoche
Journal:  Sci Rep       Date:  2022-07-29       Impact factor: 4.996
  3 in total

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