Defining the healthy "core microbiome" of oral microbial communities

By Egija Zaura, Bart J. F. Keijser, Susan M. Huse, Wim Crielaard. BMC Microbiology, 2009

1,204 citations recorded by the source corpus.

BackgroundMost studies examining the commensal human oral microbiome are focused on disease or are limited in methodology. In order to diagnose and treat diseases at an early and reversible stage an in-depth definition of health is indispensible. The aim of this study therefore was to define the healthy oral microbiome using recent advances in sequencing technology (454 pyrosequencing).ResultsWe sampled and sequenced microbiomes from several intraoral niches (dental surfaces, cheek, hard palate, tongue and saliva) in three healthy individuals. Within an individual oral cavity, we found over 3600 unique sequences, over 500 different OTUs or "species-level" phylotypes (sequences that clustered at 3% genetic difference) and 88 - 104 higher taxa (genus or more inclusive taxon). The predominant taxa belonged to Firmicutes (genus Streptococcus, family Veillonellaceae, genus Granulicatella), Proteobacteria (genus Neisseria, Haemophilus), Actinobacteria (genus Corynebacterium, Rothia, Actinomyces), Bacteroidetes (genus Prevotella, Capnocytophaga, Porphyromonas) and Fusobacteria (genus Fusobacterium).Each individual sample harboured on average 266 "species-level" phylotypes (SD 67; range 123 - 326) with cheek samples being the least diverse and the dental samples from approximal surfaces showing the highest diversity. Principal component analysis discriminated the profiles of the samples originating from shedding surfaces (mucosa of tongue, cheek and palate) from the samples that were obtained from solid surfaces (teeth).There was a large overlap in the higher taxa, "species-level" phylotypes and unique sequences among the three microbiomes: 84% of the higher taxa, 75% of the OTUs and 65% of the unique sequences were present in at least two of the three microbiomes. The three individuals shared 1660 of 6315 unique sequences. These 1660 sequences (the "core microbiome") contributed 66% of the reads. The overlapping OTUs contributed to 94% of the reads, while nearly all reads (99.8%) belonged to the shared higher taxa.ConclusionsWe obtained the first insight into the diversity and uniqueness of individual oral microbiomes at a resolution of next-generation sequencing. We showed that a major proportion of bacterial sequences of unrelated healthy individuals is identical, supporting the concept of a core microbiome at health.

Subfields: Molecular Biology, Periodontics

View Paper: https://www.semanticscholar.org/paper/f3a75ff7709ecbe9131f70f0a84d4344e20dcf35

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Citations in the corpus

Bacterial diversity in the oral cavity of ten healthy individuals (2010, background): “Two recent 16S rRNA gene-tag pyrosequencing-based studies have suggested that there are B250–300 species-level phylotypes in the mouth of any given individual, and that they segregate based on mucosal versus dental surfaces (Keijser et al., 2008; Zaura et al., 2009).”
Beyond the Venn diagram: the hunt for a core microbiome. (2012, neutral): “Conversely, there was a large overlap among oral microbiota phylotypes across communities from three individuals (Zaura et al., 2009).”
The oral microbiome in health and disease. (2013, background): “Firmicutes (Granulicatella and streptococcus genus and family veillonellaceae) Bacteroides (genus capnocytophaga, prevotella, porphyromonas) Fusobacteria (genus fusobacterium) actinobacteria (genus corynebacterium, Rothia, Actinomyces) Proteobacteria (genus Neisseria , haemophilus) are found to be t”
Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing (2011, background): “The advent of 454 pyrosequencing of 16S rRNA genes has allowed the collection of thousands of sequences per sample (Keijser et al., 2008; Zaura et al., 2009), and provides the power to comprehensively study bacterial community composition at the level of species.”
Microbial Co-occurrence Relationships in the Human Microbiome (2012, background): “Several previous studies have identified individual microbial interactions that are essential for community stability in the healthy commensal microbiota [12,13,14,15], and many are further implicated in dysbioses and overgrowth of pathogens linked to disease [16].”
Biogeography of a human oral microbiome at the micron scale (2016, background): “With deep sequencing, it has become clear that many taxa in the oral microbiota are shared across individuals but are abundant in some samples and almost vanishingly rare in others (19, 38).”
Oral multispecies biofilm development and the key role of cell–cell distance (2010, background): “More exhaustive surveys using pyrosequencing technologies have suggested that the diversity of bacteria in an individual oral cavity may be slightly higher, around 500 specie”
Insect Gut Bacterial Diversity Determined by Environmental Habitat, Diet, Developmental Stage, and Phylogeny of Host (2014, background): “Microbiomes such as the human gut (69), the human oral cavity (70), and zebrafish guts (71) have also been investigated using a deep-sequencing approach.”