Abstract
Microorganisms not yet cultured represent a large proportion of the microbes described to date. Progress in sequencing and metagenomic tools continues to increase microbial diversity without providing information on their physiological and pathophysiological characteristics, such as the recent discovery of enigmatic microbes belonging to Candidate Phyla Radiation (CPR). Reverse genomics is a recent technique allowing co-cultivation of a few CPR members, affiliated to the Saccharibacteria phylum, based on the analysis of their already-available genomes. Here, our aim is to designate a common system capable of cultivating any given taxon of this phylum from human samples. We managed to design, in silico, 11 common epitopes for all Saccharibacteria species recovered from the human oral cavity and which can serve as antigens via bioinformatics analyses. These sequences allow the synthesis of target antibodies, sorting Saccharibacteria spp. by flow cytometry and co-culturing them afterwards with adapted hosts. This epitope set can facilitate the cultivation of CPR in general, which in recent years has been considered a challenge for microbiologists, and subsequently contributes to better studying this new branch on the tree of life.
Highlights
The development of high-throughput sequencing methods and continual metagenomic explorations have paved the way to many findings and discoveries in the 21st century [1]
We focused our analysis only on good quality genomes sequenced from the human oral cavity (n = 20)
[22], [22], we noticed the presence of 389 of sequences of 10–20 that are that are common among all tested genomes, distributed over different proteins
Summary
The development of high-throughput sequencing methods and continual metagenomic explorations have paved the way to many findings and discoveries in the 21st century [1] These intensive efforts have allowed microbiologists to improve the characterisation of the human microbiome, investigate microbial diversity in different ecosystems, and discover new microbial species and divisions [2,3]. This nomenclature has been attributed to these microbes, given that all their members are uncultivated axenically at this time [3,5]. Their genome is reduced compared to standard bacteria (mainly less than 1 Mgb) [7] These microorganisms present a particular lifestyle, represented by an obligatory physical attachment between them and a host cell (most often bacterial hosts), which could be either an exo-symbiotic or exo-parasitic relationship [3,6]
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