Site Specialization of Human Oral
            <i>Veillonella</i>
            Species

Giacomini, Jonathan J.; Torres-Morales, Julian; Dewhirst, Floyd E.; Borisy, Gary G.; Welch, Jessica L. Mark

doi:10.1128/spectrum.04042-22

Cited by 11 publications

(12 citation statements)

References 70 publications

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“…However, throughout this diversity, oral bacteria, particularly Veillonella and Streptococcus, continued to be the dominant bacteria in most tissue samples. While Veillonella is a common oral bacterium, it is present in lower abundance within a healthy population compared to our findings, suggesting that oral dysbiosis may be occurring in patients with PDAC [30].…”

Section: Discussioncontrasting

confidence: 72%

Translocation of Oral Microbiota into the Pancreatic Ductal Adenocarcinoma Tumor Microenvironment

et al. 2023

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Oral dysbiosis has long been associated with pancreatic ductal adenocarcinoma (PDAC). In this work, we explore the relationship between the oral and tumor microbiomes of patients diagnosed with PDAC. Salivary and tumor microbiomes were analyzed using a variety of sequencing methods, resulting in a high prevalence and relative abundance of oral bacteria, particularly Veillonella and Streptococcus, within tumor tissue. The most prevalent and abundant taxon found within both saliva and tumor tissue samples, Veillonella atypica, was cultured from patient saliva, sequenced and annotated, identifying genes that potentially contribute to tumorigenesis. High sequence similarity was observed between sequences recovered from patient matched saliva and tumor tissue, indicating that the taxa found in PDAC tumors may derive from the mouth. These findings may have clinical implications in the care and treatment of patients diagnosed with PDAC.

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Section: Discussioncontrasting

confidence: 72%

Translocation of Oral Microbiota into the Pancreatic Ductal Adenocarcinoma Tumor Microenvironment

et al. 2023

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“…The sequencing of full length 16S rRNA gene is a promising tool for analyzing microbial composition because it improves the taxonomic annotation resolution power allowing to discern between closely related organisms at species or even clone level. This has become a necessity since microbiome studies have proven that species from the same genus can have considerably different functional roles or be associated with either health or disease [11,35].…”

Section: Discussionmentioning

confidence: 99%

“…Secondly, the length of Illumina reads (approximately 300 bp) limits the taxonomic annotation power of the obtained sequences and only a genus taxonomic rank can be achieved with reliable accuracy [9]. This is particularly important for bacterial genera that contain multiple species with highly similar 16S rRNA gene sequence, for example streptococci or the Escherichia/Shigella group, or with different ecologies [10,11]. Considering that species from the same genus can be associated with disease or health it is important to assure the annotation at the lowest possible taxonomic rank, and computer simulations shown that this is improved by the extension of the read's length analyzed [9,12].…”

Section: Introductionmentioning

confidence: 99%

Full-length 16S rRNA gene sequencing by PacBio improves taxonomic resolution in microbiome samples

Buetas

Lopez

Roldán

et al. 2023

Preprint

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Background. Sequencing variable regions of the 16S rRNA gene (≃300bp) with Illumina technology is commonly used to study the composition of human microbiota. Unfortunately, short reads are unable to differentiate between highly similar species. Considering that species from the same genus can be associated with health or disease it is important to identify them at the lowest possible taxonomic rank. Third-generation sequencing platforms such as PacBio SMRT, increase read lengths allowing to sequence the whole gene with the maximum taxonomic resolution. Despite its potential, full length 16S rRNA gene sequencing is not widely used yet. The aim of the current study was to compare the sequencing output and taxonomic annotation performance of the two approaches (Illumina short read sequencing and PacBio long read sequencing of 16S rRNA gene) in different human microbiome samples. Results. DNA from saliva, oral biofilms and faeces of 9 volunteers was isolated. Regions V3-V4 and V1-V9 were amplified and sequenced by Illumina Miseq and by PacBio Sequel II sequencers, respectively. With both platforms, a similar percentage of reads was assigned to the genus level (94.79% and 95.06% respectively) but with PacBio a higher proportion of reads were further assigned to the species level (55.23% vs 74.14%). Regarding overall bacterial composition, samples clustered by niche and not by sequencing platform. In addition, all genera with > 0.1% abundance were detected in both platforms for all types of samples. Although some genera such as Streptococcus tended to be observed at higher frequency in PacBio than in Illumina (20.14% vs 14.12% in saliva, 10.63% vs 6.59% in biofilm samples) none of the differences were statistically significant when correcting for multiple testing. Conclusions. The results presented in the current manuscript suggest that samples sequenced using Illumina and PacBio are mostly comparable. Considering that PacBio reads were assigned at the species level with higher accuracy than Illumina, our data support the use of PacBio technology for future microbiome studies, although a higher cost is currently required to obtain an equivalent number of reads per sample.

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“…Veillonella strains are versatile commensals inhabiting various regions of the human body, including the oral cavity, lungs (Dickson et al 2017 ), and vagina (Piot et al 1982 ). Veillonella parvula is a primary inhabitant and early colonizer of the oral cavity (Giacomini et al 2023 ). Regarding potential ectopic colonization from the oral cavity to distant sites, this bacterium has been shown to colonize the intestinal tract in a mouse model of colitis.…”

Section: Pathophysiological and Molecular Mechanisms Associated With ...mentioning

confidence: 99%

Ectopic colonization by oral bacteria as an emerging theme in health and disease

Hernández-Cabanyero,

Vonaesch

2024

FEMS Microbiology Reviews

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The number of research papers published on the involvement of the oral microbiota in systemic diseases has grown exponentially over the last four years clearly demonstrating the growing interest in this field. Indeed, accumulating evidence highlights the central role of ectopic colonization by oral bacteria in numerous non-communicable diseases including inflammatory bowel diseases (IBDs), undernutrition, pre-term birth, neurological diseases, liver diseases, lung diseases, heart diseases or colonic cancer. There is thus much interest in understanding the molecular mechanisms that lead to the colonization and maintenance of ectopic oral bacteria. The aim of this review is to summarize and conceptualize the current knowledge about ectopic colonization by oral bacteria, highlight wherever possible the underlying molecular mechanisms and describe its implication in health and disease. The focus lies on the newly discovered molecular mechanisms, showcasing shared pathophysiological mechanisms across different body sites and syndromes and highlighting open questions in the field regarding the pathway from oral microbiota dysbiosis to non-communicable diseases.

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Site Specialization of Human Oral Veillonella Species

Cited by 11 publications

References 70 publications

Translocation of Oral Microbiota into the Pancreatic Ductal Adenocarcinoma Tumor Microenvironment

Translocation of Oral Microbiota into the Pancreatic Ductal Adenocarcinoma Tumor Microenvironment

Full-length 16S rRNA gene sequencing by PacBio improves taxonomic resolution in microbiome samples

Ectopic colonization by oral bacteria as an emerging theme in health and disease

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