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. 2023 Jul 27:13:1195679.
doi: 10.3389/fcimb.2023.1195679. eCollection 2023.

Preliminary landscape of Candidatus Saccharibacteria in the human microbiome

Sabrina Naud  1 , Camille Valles  1 , Abdourahim Abdillah  2 , Linda Abou Chacra  2 , Fatima Zouina Mekhalif  1 , Ahmad Ibrahim  1 , Aurelia Caputo  1 , Jean-Pierre Baudoin  1 , Frédérique Gouriet  1 , Fadi Bittar  1 , Jean-Christophe Lagier  1 , Stéphane Ranque  2 , Florence Fenollar  2 , Maryam Tidjani Alou  1 , Didier Raoult  1
Affiliations

Preliminary landscape of Candidatus Saccharibacteria in the human microbiome

Sabrina Naud et al. Front Cell Infect Microbiol. .

Abstract

Introduction: Candidate Phyla Radiation (CPR) and more specifically Candidatus Saccharibacteria (TM7) have now been established as ubiquitous members of the human oral microbiota. Additionally, CPR have been reported in the gastrointestinal and urogenital tracts. However, the exploration of new human niches has been limited to date.

Methods: In this study, we performed a prospective and retrospective screening of TM7 in human samples using standard PCR, real-time PCR, scanning electron microscopy (SEM) and shotgun metagenomics.

Results: Using Real-time PCR and standard PCR, oral samples presented the highest TM7 prevalence followed by fecal samples, breast milk samples, vaginal samples and urine samples. Surprisingly, TM7 were also detected in infectious samples, namely cardiac valves and blood cultures at a low prevalence (under 3%). Moreover, we observed CPR-like structures using SEM in all sample types except cardiac valves. The reconstruction of TM7 genomes in oral and fecal samples from shotgun metagenomics reads further confirmed their high prevalence in some samples.

Conclusion: This study confirmed, through their detection in multiple human samples, that TM7 are human commensals that can also be found in clinical settings. Their detection in clinical samples warrants further studies to explore their role in a pathological setting.

Keywords: Candidate Phyla Radiation; Candidatus Saccharibacteria; electron microscopy; human microbiome; molecular detection.

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Conflict of interest statement

DR was a consultant in microbiology for the Hitachi High-Tech Corporation until March 2021. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be misconstrued as a potential conflict of interest.

Figures

Figure 1
Figure 1
Summary of the screening methodology for Candidatus Saccharibacteria in the different human sites. The human samples (A) were first analyzed by molecular biological methods (B). For this purpose, DNA was extracted (C) and analyzed using standard PCR (D) complemented by Sanger sequencing (E) and RT−PCR (F). Imaging was performed for positive samples using tabletop electron microscopy (G). Next-generation sequencing was performed for positive samples using molecular biology and electron microscopy (H) to reconstruct a new genome of Candidatus Saccharibacteria (I).
Figure 2
Figure 2
Frequency and relative abundance of samples with OTUs assigned to CPR. (A) Frequency and (B) relative abundance within the human microbiome.
Figure 3
Figure 3
Phylogenetic tree based on the amplicon sequences constructed using MEGA7. Red, amplicons from blood cultures; yellow, amplicons from urine samples; brown, amplicons from fecal samples; pink, amplicons from vaginal samples; purple, amplicons from cardiac valves; and blue, amplicons from oral samples.
Figure 4
Figure 4
Screening of Candidatus Saccharibacteria using molecular biology and electron microscopy in anatomical sites. Candidatus Saccharibacteria were detected in oral samples (A), fecal samples (B), human breast milk samples (C), urine samples (D), and vaginal swab samples (E).
Figure 5
Figure 5
Screening of Candidatus Saccharibacteria using molecular biology and electron microscopy in clinical samples. Candidatus Saccharibacteria were detected in blood cultures (A) and cardiac valve samples (B).
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Grants and funding

This work was funded by the IHU Méditerranée Infection (Marseille, France) and the French Government under the Investissements d’avenir (Investments for the future) program managed by the Agence Nationale de la Recherche (ANR, fr; National Agency for Research) (reference: Méditerranée Infection 10-IAHU-03). This work was also supported by the Region Provence Alpes Côte d’Azur and European funding FEDER PRIMI.

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