Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation
ABSTRACT The growing application of metagenomics to different ecological and microbiome niches in recent years has enhanced our knowledge of global microbial biodiversity. Among these abundant and widespread microbes, the candidate phyla radiation (CPR) group has been recognized as representing a la...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2021-12-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01069-21 |
| _version_ | 1830201103772286976 |
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| author | Ahmad Ibrahim Mohamad Maatouk Andriamiharimamy Rajaonison Rita Zgheib Gabriel Haddad Jacques Bou Khalil Didier Raoult Fadi Bittar |
| author_facet | Ahmad Ibrahim Mohamad Maatouk Andriamiharimamy Rajaonison Rita Zgheib Gabriel Haddad Jacques Bou Khalil Didier Raoult Fadi Bittar |
| author_sort | Ahmad Ibrahim |
| collection | DOAJ |
| description | ABSTRACT The growing application of metagenomics to different ecological and microbiome niches in recent years has enhanced our knowledge of global microbial biodiversity. Among these abundant and widespread microbes, the candidate phyla radiation (CPR) group has been recognized as representing a large proportion of the microbial kingdom (>26%). CPR are characterized by their obligate symbiotic or exoparasitic activity with other microbial hosts, mainly bacteria. Currently, isolating CPR is still considered challenging for microbiologists. The idea of this study was to develop an adapted protocol for the coculture of CPR with a suitable bacterial host. Based on various sputum samples, we tried to enrich CPR (Saccharibacteria members) and to cocultivate them with pure hosts (Schaalia odontolytica). This protocol was monitored by TaqMan real-time quantitative PCR (qPCR) using a system specific for Saccharibacteria designed in this study, as well as by electron microscopy and sequencing. We succeeded in coculturing and sequencing the complete genomes of two new Saccharibacteria species, “Candidatus Minimicrobia naudis” and “Candidatus Minimicrobia vallesae.” In addition, we noticed a decrease in the CT values of Saccharibacteria and a significant multiplication through their physical association with Schaalia odontolytica strains in the enriched medium that we developed. This work may help bridge gaps in the genomic database by providing new CPR members, and in the future, their currently unknown characteristics may be revealed. IMPORTANCE In this study, the first TaqMan real-time quantitative PCR (qPCR) system, targeting Saccharibacteria phylum, has been developed. This technique can specifically quantify Saccharibacteria members in any sample of interest in order to investigate their prevalence. In addition, another easy, specific, and sensitive protocol has been developed to maintain the viability of Saccharibacteria cells in an enriched medium with their bacterial host. The use of this protocol facilitates subsequent studies of the phenotypic characteristics of CPR and their physical interactions with bacterial species, as well as the sequencing of new genomes to improve the current database. |
| first_indexed | 2024-12-18T02:46:31Z |
| format | Article |
| id | doaj.art-98bfde0ac434471bb27be834ae4e42e7 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-12-18T02:46:31Z |
| publishDate | 2021-12-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-98bfde0ac434471bb27be834ae4e42e72022-12-21T21:23:33ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972021-12-019310.1128/spectrum.01069-21Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla RadiationAhmad Ibrahim0Mohamad Maatouk1Andriamiharimamy Rajaonison2Rita Zgheib3Gabriel Haddad4Jacques Bou Khalil5Didier Raoult6Fadi Bittar7IHU Méditerranée Infection, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceABSTRACT The growing application of metagenomics to different ecological and microbiome niches in recent years has enhanced our knowledge of global microbial biodiversity. Among these abundant and widespread microbes, the candidate phyla radiation (CPR) group has been recognized as representing a large proportion of the microbial kingdom (>26%). CPR are characterized by their obligate symbiotic or exoparasitic activity with other microbial hosts, mainly bacteria. Currently, isolating CPR is still considered challenging for microbiologists. The idea of this study was to develop an adapted protocol for the coculture of CPR with a suitable bacterial host. Based on various sputum samples, we tried to enrich CPR (Saccharibacteria members) and to cocultivate them with pure hosts (Schaalia odontolytica). This protocol was monitored by TaqMan real-time quantitative PCR (qPCR) using a system specific for Saccharibacteria designed in this study, as well as by electron microscopy and sequencing. We succeeded in coculturing and sequencing the complete genomes of two new Saccharibacteria species, “Candidatus Minimicrobia naudis” and “Candidatus Minimicrobia vallesae.” In addition, we noticed a decrease in the CT values of Saccharibacteria and a significant multiplication through their physical association with Schaalia odontolytica strains in the enriched medium that we developed. This work may help bridge gaps in the genomic database by providing new CPR members, and in the future, their currently unknown characteristics may be revealed. IMPORTANCE In this study, the first TaqMan real-time quantitative PCR (qPCR) system, targeting Saccharibacteria phylum, has been developed. This technique can specifically quantify Saccharibacteria members in any sample of interest in order to investigate their prevalence. In addition, another easy, specific, and sensitive protocol has been developed to maintain the viability of Saccharibacteria cells in an enriched medium with their bacterial host. The use of this protocol facilitates subsequent studies of the phenotypic characteristics of CPR and their physical interactions with bacterial species, as well as the sequencing of new genomes to improve the current database.https://journals.asm.org/doi/10.1128/spectrum.01069-21candidate phyla radiationSaccharibacteriaSchaalia odontolyticacocultureMinimicrobiaprotocol |
| spellingShingle | Ahmad Ibrahim Mohamad Maatouk Andriamiharimamy Rajaonison Rita Zgheib Gabriel Haddad Jacques Bou Khalil Didier Raoult Fadi Bittar Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation Microbiology Spectrum candidate phyla radiation Saccharibacteria Schaalia odontolytica coculture Minimicrobia protocol |
| title | Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation |
| title_full | Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation |
| title_fullStr | Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation |
| title_full_unstemmed | Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation |
| title_short | Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation |
| title_sort | adapted protocol for saccharibacteria cocultivation two new members join the club of candidate phyla radiation |
| topic | candidate phyla radiation Saccharibacteria Schaalia odontolytica coculture Minimicrobia protocol |
| url | https://journals.asm.org/doi/10.1128/spectrum.01069-21 |
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