The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept

Nutrients. 2022 Jul 13;14(14):2872. doi: 10.3390/nu14142872.

Abstract

The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining the core microbiome is a complex task at several levels. In this review, we consider the current state of core human microbiome research. We consider the knowledge that has been gained, the factors limiting our ability to achieve a reliable description of the core human microbiome, and the fields most likely to improve that ability. DNA sequencing technologies and the methods for analyzing metagenomics and amplicon data will most likely facilitate higher accuracy and resolution in describing the microbiome. However, more effort should be invested in characterizing the microbiome's interactions with its human host, including the immune system and nutrition. Other components of this holobiontic system should also be emphasized, such as fungi, protists, lower eukaryotes, viruses, and phages. Most importantly, a collaborative effort of experts in microbiology, nutrition, immunology, medicine, systems biology, bioinformatics, and machine learning is probably required to identify the traits of the core human microbiome.

Keywords: NGS sequencing; core microbiome; diet; eukaryotes; gut; healthy microbiome; immune system; omics; prokaryotes; virome.

Publication types

  • Review

MeSH terms

  • Dysbiosis
  • Gastrointestinal Microbiome*
  • Humans
  • Metagenomics / methods
  • Microbiota*
  • Sequence Analysis, DNA

Grants and funding

This research was supported by the Joint Action “European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL)”and the respective national/regional funding organisations: Fund for Scientific Research (FRS—FNRS, Belgium); Research Foundation—Flanders (FWO, Belgium); INSERM Institut National de la Santé et de la Recherche Médicale (France); Federal Ministry of Food and Agriculture (BMEL, Germany) represented by Federal Office for Agriculture and Food (BLE, Germany, grant number 2819ERA10F); Federal Ministry of Education and Research Germany (BMBF, FKZ 01EA1906A, 01EA1906B) Ministry of Education, University and Research (MIUR), Ministry of agricultural, food and forestry policies (MiPAAF), Ministry of University and Research (MUR, Grant Number JTC-2017-7, Project MeaTIc) National Institute of Health (ISS) on behalf of Ministry of Health (Italy); National Institute of Health Carlos III (Spain); The Netherlands Organisation for Health Research and Development (ZonMw, The Netherlands, grant number 529051024), Austrian Research Promotion Agency (FFG) on behalf of the Austrian Federal Ministry for Education, Science and Research (BMBWF), Ministry of Science and Technology (Israel, grant number 3-16034), Formas (Sweden). BIOMIS project funded by PON RICERCA E INNOVAZIONE 2014-2020 (Cod. ARS01_01220) (Italy). Federal Ministry of Education and Research Germany (BMBF, FKZ01EA1906B). G.C: This study was funded by the Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on “Interrelation of the Intestinal Microbiome, Diet and Health” (Reference Number JTC-2017-7) and by the University of Florence (Fondo ex-60%), Italy. K.L, M.M and J.G: amedes genetics acknowledges funding by BMBF/DLR, grant number 01EA1906G. E.P: The study has been also supported by the JPI HDHL-INTIMIC - Knowledge Platform of Food, Diet, Intestinal Microbiomics and Human Health, granted by the Italian Ministry of Agricultural, Food and Forestry and Tourism Policies with ID 790.