Repertoire of human gut microbes.
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.
Institut Pasteur, Unité de Biologie des Spirochètes, Paris, France.
Perrine
P
Hugon
Aix-Marseille Université URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France.
Jean-Christophe
JC
Lagier
Aix-Marseille Université URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France.
Philippe
P
Colson
Aix-Marseille Université URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France.
Fadi
F
Bittar
Aix-Marseille Université URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia. Electronic address: didier.raoult@gmail.com.
Didier
D
Raoult
D000818:Animals; D001105:Archaea / Q000145:classification; D001419:Bacteria / Q000145:classification / Q000235:genetics; D044822:Biodiversity; D018920:Coculture Techniques; D005658:Fungi / Q000145:classification; D000069196:Gastrointestinal Microbiome / Q000235:genetics; D041981:Gastrointestinal Tract / Q000382:microbiology*; D000072139:Giant Viruses; D057166:High-Throughput Screening Assays / Q000379:methods; D006801:Humans; D056186:Metagenomics; D016533:Mycological Typing Techniques / Q000379:methods; D010271:Parasites / Q000145:classification; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017421:Sequence Analysis / Q000379:methods; D014780:Viruses / Q000145:classification
D012336:RNA, Ribosomal, 16S
16SrRNA; Culturomics; Eukaryotes; Giant viruses; Gut microbiota; Megavirales; Prokaryotes; Taxonogenomics