Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples

Baker, Jonathon L.

doi:10.1128/msystems.00491-22

Cited by 9 publications

(5 citation statements)

References 62 publications

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“…Ca. Saccharibacteria are detected in samples using molecular methods, namely standard PCR ( Sizova et al., 2015 ; Naud et al., 2022 ), real-time PCR (RT-PCR ( Ibrahim et al., 2021 ; Naud et al., 2022 )) as well as shotgun sequencing ( Baker, 2022 ; Naud et al., 2022 ). Moreover, as Ca.…”

Section: Methodsmentioning

confidence: 99%

Preliminary landscape of Candidatus Saccharibacteria in the human microbiome

Valles

Abdillah

Chacra

et al. 2023

Front. Cell. Infect. Microbiol.

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IntroductionCandidate 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.MethodsIn 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.ResultsUsing 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.ConclusionThis 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.

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Section: Methodsmentioning

confidence: 99%

Preliminary landscape of Candidatus Saccharibacteria in the human microbiome

Valles

Abdillah

Chacra

et al. 2023

Front. Cell. Infect. Microbiol.

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“…Samples from children with or without caries suggested significant differences in the metagenomic analysis of the microbiota. 17 Rothia , Neisseria , and Haemophilus spp. were associated with good dental health, while Prevotella spp, Streptococcus mutans , and Epstein-Barr virus were more prevalent in children with caries.…”

Section: Sequencing-based Techniquesmentioning

confidence: 99%

Omics for deciphering oral microecology

Lin,

Liang,

et al. 2024

Int J Oral Sci

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The human oral microbiome harbors one of the most diverse microbial communities in the human body, playing critical roles in oral and systemic health. Recent technological innovations are propelling the characterization and manipulation of oral microbiota. High-throughput sequencing enables comprehensive taxonomic and functional profiling of oral microbiomes. New long-read platforms improve genome assembly from complex samples. Single-cell genomics provides insights into uncultured taxa. Advanced imaging modalities including fluorescence, mass spectrometry, and Raman spectroscopy have enabled the visualization of the spatial organization and interactions of oral microbes with increasing resolution. Fluorescence techniques link phylogenetic identity with localization. Mass spectrometry imaging reveals metabolic niches and activities while Raman spectroscopy generates rapid biomolecular fingerprints for classification. Culturomics facilitates the isolation and cultivation of novel fastidious oral taxa using high-throughput approaches. Ongoing integration of these technologies holds the promise of transforming our understanding of oral microbiome assembly, gene expression, metabolites, microenvironments, virulence mechanisms, and microbe-host interfaces in the context of health and disease. However, significant knowledge gaps persist regarding community origins, developmental trajectories, homeostasis versus dysbiosis triggers, functional biomarkers, and strategies to deliberately reshape the oral microbiome for therapeutic benefit. The convergence of sequencing, imaging, cultureomics, synthetic systems, and biomimetic models will provide unprecedented insights into the oral microbiome and offer opportunities to predict, prevent, diagnose, and treat associated oral diseases.

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“…MiSeq quality filters were used for QC, and adapter sequences were removed from the Illumina data using fastp v0.23.2 ( 4 ). All data were assembled using Unicycler v0.5.0 and Canu v2.2 and polished using Polypolish v0.5.0 and RagTag v2.1.0 ( 4 , 5 ). The hybrid genome was annotated using Prokka v1.14.5, and reference mapping was performed using Minimap2-2.224 r1122 for the Nanopore data and BWA-0.7.17 r1188 for the Illumina data ( 5 ).…”

Section: Announcementmentioning

confidence: 99%

“…All data were assembled using Unicycler v0.5.0 and Canu v2.2 and polished using Polypolish v0.5.0 and RagTag v2.1.0 ( 4 , 5 ). The hybrid genome was annotated using Prokka v1.14.5, and reference mapping was performed using Minimap2-2.224 r1122 for the Nanopore data and BWA-0.7.17 r1188 for the Illumina data ( 5 ). Default parameters were used for all software except Minimap2 (-ax for long-read data).…”

Section: Announcementmentioning

confidence: 99%