A blueprint for contemporary studies of microbiomes

Laure B Bindels^{1

2}, Joy E M Watts³, Kevin R Theis⁴, Víctor J Carrion^{5

6

7

8}, Adam Ossowicki^{5

6}, Jana Seifert⁹, Julia Oh¹⁰, Yongqi Shao¹¹, Markus Hilty¹², Purnima Kumar¹³, Falk Hildebrand^{14

15}, Connie Lovejoy¹⁶, Paul Wigley¹⁷, Ke Yu¹⁸, Meiling Zhang¹⁹, Tong Zhang^{20

21}, Jens Walter²², Mahesh S Desai²³, Sharon Ann Huws²⁴, Lynn M Schriml²⁵, Jacques Ravel^{26

27}, W Florian Fricke^{28

29}, Emiley A Eloe-Fadrosh³⁰, Charles K Lee^{31

32}, Thomas Clavel³³

Affiliations

¹ Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium. laure.bindels@uclouvain.be.
² Welbio Department, WEL Research Institute, Wavre, Belgium. laure.bindels@uclouvain.be.
³ School of Environment and Life Sciences, University of Portsmouth, Portsmouth, UK.
⁴ Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA.
⁵ Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, Málaga, Spain.
⁶ Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain.
⁷ Institute of Biology, Leiden University, Leiden, The Netherlands.
⁸ Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.
⁹ HoLMiR - Hohenheim Center for Livestock Microbiome Research, Functional Microbiology of Livestock, University of Hohenheim, Stuttgart, Germany.
¹⁰ Department of Dermatology, Duke University, Durham, NC, USA.
¹¹ Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China.
¹² Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
¹³ Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI, USA.
¹⁴ Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
¹⁵ Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
¹⁶ Département de Biologie and Institut de Biologie Intégrative Et Des Systèmes, Université Laval, Québec, QC, Canada.
¹⁷ Bristol Veterinary School, Langford Campus, University of Bristol, Bristol, UK.
¹⁸ Shenzhen Graduate School, Peking University, Shenzhen, China.
¹⁹ School of Life Sciences, East China Normal University, Shanghai, 200241, China.
²⁰ Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong, China.
²¹ School of Public Health, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
²² APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland.
²³ Nutrition, Microbiome and Immunity Group, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette, Luxembourg.
²⁴ School of Biological Sciences, Institute for Global Food Security, Queen's University, Belfast, UK.
²⁵ Department of Epidemiology and Public Health, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
²⁶ Center for Advanced Microbiome Research and Innovation, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
²⁷ Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
²⁸ Department of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.
²⁹ Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
³⁰ DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
³¹ Environmental Research Institute, University of Waikato, Hamilton, New Zealand.
³² School of Science, University of Waikato, Hamilton, New Zealand.
³³ Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany.

PMID: 40200306
PMCID: PMC11977902
DOI: 10.1186/s40168-025-02091-0

Editorial

A blueprint for contemporary studies of microbiomes

Laure B Bindels et al. Microbiome. 2025.

. 2025 Apr 8;13(1):95.

doi: 10.1186/s40168-025-02091-0.

Authors

Affiliations

¹ Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium. laure.bindels@uclouvain.be.
² Welbio Department, WEL Research Institute, Wavre, Belgium. laure.bindels@uclouvain.be.
³ School of Environment and Life Sciences, University of Portsmouth, Portsmouth, UK.
⁴ Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA.
⁵ Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, Málaga, Spain.
⁶ Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain.
⁷ Institute of Biology, Leiden University, Leiden, The Netherlands.
⁸ Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.
⁹ HoLMiR - Hohenheim Center for Livestock Microbiome Research, Functional Microbiology of Livestock, University of Hohenheim, Stuttgart, Germany.
¹⁰ Department of Dermatology, Duke University, Durham, NC, USA.
¹¹ Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China.
¹² Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
¹³ Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI, USA.
¹⁴ Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
¹⁵ Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
¹⁶ Département de Biologie and Institut de Biologie Intégrative Et Des Systèmes, Université Laval, Québec, QC, Canada.
¹⁷ Bristol Veterinary School, Langford Campus, University of Bristol, Bristol, UK.
¹⁸ Shenzhen Graduate School, Peking University, Shenzhen, China.
¹⁹ School of Life Sciences, East China Normal University, Shanghai, 200241, China.
²⁰ Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong, China.
²¹ School of Public Health, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
²² APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland.
²³ Nutrition, Microbiome and Immunity Group, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette, Luxembourg.
²⁴ School of Biological Sciences, Institute for Global Food Security, Queen's University, Belfast, UK.
²⁵ Department of Epidemiology and Public Health, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
²⁶ Center for Advanced Microbiome Research and Innovation, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
²⁷ Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
²⁸ Department of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.
²⁹ Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
³⁰ DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
³¹ Environmental Research Institute, University of Waikato, Hamilton, New Zealand.
³² School of Science, University of Waikato, Hamilton, New Zealand.
³³ Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany.

PMID: 40200306
PMCID: PMC11977902
DOI: 10.1186/s40168-025-02091-0

Abstract

This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opportunity to clarify our expectations for the articles submitted to the journal. At Microbiome, we are seeking studies that provide either new mechanistic insights into the role of microbiomes in health and environmental systems or substantial conceptual or technical advances. Manuscripts need to meet high standards of language accuracy, quality of microbiome analyses, and data and protocol availability, including detailed reporting of wet-lab and in silico protocols, all of which can critically enhance transparency and reproducibility. We think that such efforts are essential to push the boundaries of our knowledge on microbiomes in a concerted, international effort.

PubMed Disclaimer

Conflict of interest statement

Declarations. Competing interests: Jacques Ravel is Editor-in-Chief of Microbiome, and all other authors of this Editorial are Senior Editors of Microbiome. Mahesh S. Desai works as a consultant and an advisory board member at Theralution GmbH, Germany.

References

1. Shanahan F, Hill C. Language, numeracy and logic in microbiome science. Nat Rev Gastroenterol Hepatol. 2019;16(7):387–8. - PubMed
1. Marchesi JR, Ravel J. The vocabulary of microbiome research: a proposal. Microbiome. 2015;3:31. - PMC - PubMed
1. Berg G, Rybakova D, Fischer D, Cernava T, Verges MC, Charles T, et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome. 2020;8(1):103. - PMC - PubMed
1. Vandeputte D, Kathagen G, D’Hoe K, Vieira-Silva S, Valles-Colomer M, Sabino J, et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature. 2017;551(7681):507–11. - PubMed
1. Jian C, Luukkonen P, Yki-Jarvinen H, Salonen A, Korpela K. Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling. PLoS ONE. 2020;15(1):e0227285. - PMC - PubMed

Publication types

Actions

MeSH terms

Actions
Actions

LinkOut - more resources

Full Text Sources
Miscellaneous
- NCI CPTAC Assay Portal

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

A blueprint for contemporary studies of microbiomes

Affiliations

A blueprint for contemporary studies of microbiomes

Authors

Affiliations

Abstract

Conflict of interest statement

References

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources

Miscellaneous