Elsevier

Microbial Pathogenesis

Volume 106, May 2017, Pages 103-112
Microbial Pathogenesis

Repertoire of human gut microbes

https://doi.org/10.1016/j.micpath.2016.06.020Get rights and content

Highlights

  • Bacterial communities, archaea, virus (including giant virus), fungi and parasites inhabits the human gut microbiota.

  • Microbial culturomics using MALDI-TOF identification coupled with metagenomics allowed to extend the gut microbiota repertoire.

  • Regarding the number of new bacteria described bacterial taxonomy must include genome sequencing as proposed by taxonogenomics.

Abstract

In 1675, Antoni Van Leeuwenhoeck was the first to observe several forms using an optical microscope that he named “animalcules”, realizing later that these were microorganisms. The first classification of living organisms proposed by Ehrenberg in 1833 was based on what we could visualize. The failure of this kind of classification arises from viral culture, which preceded direct observations that were finally achieved during the 20th century by electron microscopy.

The number of prokaryotic species is estimated at approximately 10 million, although only 1800 were known in 1980, and 14,000 to date, thanks to the advent of 16S rRNA amplification and sequencing. This highlights our inability to access the entire diversity. Indeed, a large number of bacteria are only, known as Operational Taxonomic Units (OTUs) and detected as a result of metagenomics studies, revealing an unexplored world known as the “dark matter”. Recently, the rebirth of bacterial culture through the example of culturomics has dramatically increased the human gut repertoire as well as the 18SrRNA sequencing allowed to largely extend the repertoire of Eukaryotes. Finally, filtration and co-culture on free-living protists associated with high-throughput culture elucidated a part of the megavirome.

While the majority of studies currently performed on the human gut microbiota focus on bacterial diversity, it appears that several other prokaryotes (including archaea) and eukaryotic populations also inhabit this ecosystem; their detection depending exclusively on the tools used. Rational and comprehensive establishment of this ecosystem will allow the understanding of human health associated with gut microbiota and the potential to change this.

Introduction

The exploration of the human gut microbiota has exploded during the last decade. With the tremendous changes in molecular technologies and the new “omics” strategies developed, this ecosystem is now considered for its role in metabolism, immune system and human health [1]. Moreover, numerous metagenomic studies performed during the last years have suggested an association between the microbial composition of the human gut and various diseases including for instance obesity [2], Crohn’s disease [3], or irritable bowel syndrome [4]. The gut microbiota harbours at least 1011 to 1012 bacteria per gram of faeces [5], and its composition varies with physiological factors [6] such as geographic provenance, age, dietary habits, malnutrition, and external factors can also imbalance the microbiota as probiotics or antimicrobial agents uses [7]. The relationship between the host and this complex ecosystem composed by prokaryotes, viruses, fungi and parasites is extremely complex. Recent significant efforts have been deployed to characterize the gut repertoire; however there is still a need to provide an efficient repertoire even for all microorganisms isolated or detected in the human gut [8]. Regarding viruses, giant ones have been recently showed being genuine members of the tree of life [9], [10]. Thus, their tremendous gene repertoires contain genes with homologs in cellular organisms, among which those encoding DNA-dependent RNA polymerase. This represents a change of paradigm. Indeed, the predominant use of ribosomal genes to classify organisms that was introduced in the 1970s by C. Woese, who defined three domains of life, namely Bacteria, Archea and Eukarya, led to exclude viruses because they are devoid of such genes [11]. Apart from lacking ribosomes, giant viruses share many features with other intracellular microorganisms and can be considered as microbes. This led to propose in 2013 a new classification of microbes in four ‘TRUC’, an acronym for Things Resisting Uncompleted Classifications, that does not rely on ribosomal genes but takes into account giant viruses alongside with bacteria, archaea and eukaryotic microbes and should allow more comprehensive description of human gut microbiota [10]. In this review we are focusing on human gut components of the bacterial, fungal, parasites and archaeal diversity, as well as on the gut virome discovery.

Section snippets

Culture-based methods as the pioneer strategy for human gut microbiota research

The first discrepancy arose from initial culture studies [5]. At that time, the 1970s, gram-staining and microscopic examination performed directly on stool samples were the techniques used to study gut microbiota composition [12], [13], [14]. While such techniques revealed the predominance of gram-negative bacteria in stool samples [12], culture counts identified a majority of gram-positive bacteria [14] and anaerobes dominated the community. The second discrepancy was named few years later by

The archaeal diversity

The Archaea community constitutes the third domain of life, separate from bacteria and eukaryote kingdoms [50], although archaea share many characteristics with both bacteria and eukaryotes [51]. Extremophile species, which live in extreme environments under high salt concentrations and extreme pH and temperatures, were the first to be discovered in the late 1970s [52]. However, we now know that archaeal mesophilic species also represents a large part of the diversity and inhabit non-extreme

The existence of a human gut microbial virome

By contrast with the bacterial microbiota, only a few studies have explored the “human gut virome”, which represents a fairly new concept [66], [67]. This appears paradoxical, as the existence of pathogenic viruses was discovered in human faeces a long time ago [68]. Studying viral diversity in the gut appears more difficult than for cellular organisms because they are, for most of them, not visible under a light microscope, and they are devoid of any conserved gene that is shared by all of

Eukaryotes

Research on this subdominant gut component is fairly recent, as evidenced by the first molecular study published in 2008 [90]. Eukaryotes, defined by the presence of a nucleus and organelles, represent the third domain of life besides Bacteria and Archaea [91]. The taxonomy of human gut eukaryotes is highly complex [91], [92] and highlights five major groups (Amoebozoa, Opisthokonta, Excavata, Sar and Archaeplastida) based on recent molecular phylogenetic classification [92]. Fungal species

Perspectives

As described by Robert Koch, “a pure culture remains the foundation of all research in microbiology” [42]. The rebirth of the culture through the example of culturomics due to the efficient, cost-effective and rapid MALDI-TOF identification method opens broad perspectives for the study of complex ecosystems [42]. This revolution now largely recognized in bacterial culture is relevant for eukaryote identification [91].

However, we have a major lack of tools that can list both prokaryotes and

Acknowledgments

We thank TradOnline (http://www.tradonline.fr/en/) and Karolina Griffiths for providing English corrections.

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