Adapted Protocol for
            <i>Saccharibacteria</i>
            Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation

Ibrahim, Ahmad; Maatouk, Mohamad; Rajaonison, Andriamiharimamy; Zgheib, Rita; Haddad, Gabriel; Khalil, Jacques Bou; Raoult, Didier; Bittar, Fadi

doi:10.1128/spectrum.01069-21

Cited by 13 publications

(14 citation statements)

References 49 publications

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“…Our findings reveal the need to be vigilant in monitoring the pathogenicity of this commensal bacterium in patients with active UC and its potential to cause clinically significant infection. TM7x is the first obligate epibiont parasite discovered within the domain of Bacteria that requires other bacteria ( Actinomyces odontolyticus strain XH001) as a host ( Ibrahim et al., 2021 ). Actinomyces species are opportunistic pathogens mostly inhabiting the oral cavity and upper respiratory tract, and overgrowth of this genus could cause inflammation.…”

Section: Discussionmentioning

confidence: 99%

Composition and diverse differences of intestinal microbiota in ulcerative colitis patients

Zhu

Han

Liu

et al. 2022

Front. Cell. Infect. Microbiol.

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ObjectiveTo explore the composition of the intestinal microbiota in ulcerative colitis (UC) patients and to identify differences in the microbiota between patients with active disease and those in remission.MethodsBetween September 2020 and June 2021, we enrolled into our study, and collected stool samples from, patients with active UC or in remission and healthy control subjects. The diagnosis of UC was based on clinical, endoscopic, radiological, and histological findings. The composition of the intestinal microbiota was determined by sequencing of the 16S rRNA V3–V4 region and by bioinformatic methods. The functional composition of the intestinal microbiota was predicted using PICRUSt 2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) software.ResultsWe found that the intestinal flora was significantly less rich and diverse in UC patients than in healthy control subjects. Beta diversity analysis revealed notable differences in the intestinal flora compositions among the three groups, but there was no statistical difference in alpha diversity between UC patients with active disease and those in remission. At the phylum level, the relative abundances of Proteobacteria and Patescibacteria were significantly higher, and the relative abundances of Desulfobacterota and Verrucomicrobiota were lower, in UC patients with active disease than in the healthy control group. Higher levels of potential pathogens and lower levels of butyrate-producing bacteria were also detected in UC patients with active disease. Linear discriminant analysis Effect Size (LefSe) revealed that 71 bacterial taxa could serve as biomarkers, with 26 biomarkers at the genus level. In addition, network analysis showed that there was a positive correlation between Roseburia and Lachnospira. Functional predictions indicated that gene functions involving the metabolism of some substances, such as methane, lipopolysaccharide, geraniol, and ansamycins, were significantly different among the three groups.ConclusionThe richness and diversity of the intestinal microbiota differed significantly among the three groups. Richness describes the state of being rich in number of intestinal bacteria, whereas diversity is the number of different species of intestinal bacteria. Different bacterial taxa could be used as biomarkers, expanding our understanding of the relationship between the intestinal microbiota microenvironment and UC in the future.

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Section: Discussionmentioning

confidence: 99%

Composition and diverse differences of intestinal microbiota in ulcerative colitis patients

Zhu

Han

Liu

et al. 2022

Front. Cell. Infect. Microbiol.

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“…Furthermore, as of today, this methodology is considered the more suitable one to co-cultivate these microbes with the bacterial host they naturally associate with. Most studies on the CPR members co-culture is based on the filtration of the detached Saccharibacteria members from their natural host to co-cultivate them with hosts of choice for testing, such as Schaalia odontolyticus and Arachnia propionica [ 7 , 15 , 16 , 17 , 18 ]. However, thanks to reverse genomics, Cross et al have described for the first time the interaction of a Saccharibacteria member with Cellulosimicrobium cellulans [ 19 ].…”

Section: Resultsmentioning

confidence: 99%

“…To date, most CPR characteristics are only predicted from genomic analyses. Therefore, CPR member culturing is a critical and indispensable step to better understand their physiology and physiopathology [ 15 ]. This process remains a major challenge for microbiologists, who are developing different protocols and techniques to cultivate fastidious and not-yet-cultured bacteria and, more precisely, CPR cells [ 7 , 15 , 16 , 17 , 18 ].…”

Section: Introductionmentioning

confidence: 99%

Reverse Genomics: Design of Universal Epitope Sets to Isolate All Saccharibacteria Members from the Human Oral Cavity

et al. 2022

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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.

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“…Moreover, they are characterized by their unique lifestyle of obligatory exo-symbiotic/parasitic relationships with bacteria [ 6 , 7 , 8 ]. To date, few studies have succeeded in co-culturing some CPR species with their bacterial hosts [ 9 , 10 , 11 , 12 , 13 ]. One co-culture was obtained by adding kanamycin to the enrichment broth for a TM7 strain [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

New Beta-lactamases in Candidate Phyla Radiation: Owning Pleiotropic Enzymes Is a Smart Paradigm for Microorganisms with a Reduced Genome

Maatouk

Ibrahim

Pinault

et al. 2022

IJMS

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The increased exploitation of microbial sequencing methods has shed light on the high diversity of new microorganisms named Candidate Phyla Radiation (CPR). CPR are mainly detected via 16S rRNA/metabarcoding analyses or metagenomics and are found to be abundant in all environments and present in different human microbiomes. These microbes, characterized by their symbiotic/epiparasitic lifestyle with bacteria, are directly exposed to competition with other microorganisms sharing the same ecological niche. Recently, a rich repertoire of enzymes with antibiotic resistance activity has been found in CPR genomes by using an in silico adapted screening strategy. This reservoir has shown a high prevalence of putative beta-lactamase-encoding genes. We expressed and purified five putative beta-lactamase sequences having the essential domains and functional motifs from class A and class B beta-lactamase. Their enzymatic activities were tested against various beta-lactam substrates using liquid chromatography-mass spectrometry (LC-MS) and showed some beta-lactamase activity even in the presence of a beta-lactamase inhibitor. In addition, ribonuclease activity was demonstrated against RNA that was not inhibited by sulbactam and EDTA. None of these proteins could degrade single- and double-stranded-DNA. This study is the first to express and test putative CPR beta-lactamase protein sequences in vitro. Our findings highlight that the reduced genomes of CPR members harbor sequences encoding for beta-lactamases known to be multifunction hydrolase enzymes.

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Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation

Abstract: In this study, the first TaqMan real-time quantitative PCR (qPCR) system has been developed. This technique can specifically quantify Saccharibacteria members in any sample of interest in order to investigate their prevalence.

Cited by 13 publications

References 49 publications

Composition and diverse differences of intestinal microbiota in ulcerative colitis patients

Composition and diverse differences of intestinal microbiota in ulcerative colitis patients

Reverse Genomics: Design of Universal Epitope Sets to Isolate All Saccharibacteria Members from the Human Oral Cavity

New Beta-lactamases in Candidate Phyla Radiation: Owning Pleiotropic Enzymes Is a Smart Paradigm for Microorganisms with a Reduced Genome

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