Defining the healthy "core microbiome" of oral microbial communities

<p>Abstract</p> <p>Background</p> <p>Most 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).</p> <p>Results</p> <p>We 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 <it>Streptococcus</it>, family <it>Veillonellaceae</it>, genus <it>Granulicatella</it>), Proteobacteria (genus <it>Neisseria</it>, <it>Haemophilus</it>), Actinobacteria (genus <it>Corynebacterium</it>, <it>Rothia</it>, <it>Actinomyces</it>), Bacteroidetes (genus <it>Prevotella</it>, <it>Capnocytophaga, Porphyromonas</it>) and Fusobacteria (genus <it>Fusobacterium</it>).</p> <p>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).</p> <p>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.</p> <p>Conclusions</p> <p>We 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.</p

Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health

<p>Abstract</p> <p>Background</p> <p>An understanding of the relation of commensal microbiota to health is essential in preventing disease. Here we studied the oral microbial composition of children (N = 74, aged 3 - 18 years) in natural transition from their deciduous to a permanent dentition and related the microbial profiles to their oral health status. The microbial composition of saliva was assessed by barcoded pyrosequencing of the V5-V6 hypervariable regions of the 16 S rRNA, as well as by using phylogenetic microarrays.</p> <p>Results</p> <p>Pyrosequencing reads (126174 reads, 1045 unique sequences) represented 8 phyla and 113 higher taxa in saliva samples. Four phyla - Firmicutes, Bacteriodetes, Proteobacteria and Actinobacteria - predominated in all groups. The deciduous dentition harboured a higher proportion of Proteobacteria (Gammaproteobacteria, Moraxellaceae) than Bacteroidetes, while in all other groups Bacteroidetes were at least as abundant as Proteobacteria. Bacteroidetes (mainly genus <it>Prevotella</it>), Veillonellaceae family, Spirochaetes and candidate division TM7 increased with increasing age, reflecting maturation of the microbiome driven by biological changes with age.</p> <p>Microarray analysis enabled further analysis of the individual salivary microbiota. Of 350 microarray probes, 156 gave a positive signal with, on average, 77 (range 48-93) probes per individual sample.</p> <p>A caries-free oral status significantly associated with the higher signal of the probes targeting <it>Porphyromonas catoniae </it>and <it>Neisseria flavescens</it>.</p> <p>Conclusions</p> <p>The potential role of <it>P. catoniae </it>and <it>N. flavescens </it>as oral health markers should be assessed in large-scale clinical studies. The combination of both, open-ended and targeted molecular approaches provides us with information that will increase our understanding of the interplay between the human host and its microbiome.</p

Acquiring and maintaining a normal oral microbiome: current perspective

The oral microbiota survives daily physical and chemical perturbations from the intake of food and personal hygiene measures, resulting in a long-term stable microbiome. Biological properties that confer stability in the microbiome are important for the prevention of dysbiosis – a microbial shift towards a disease, e.g., periodontitis or caries. Although processes that underlie oral diseases have been studied extensively, processes involved in maintaining of a normal, healthy microbiome are poorly understood. In this review we present our hypothesis on how a healthy oral microbiome is acquired and maintained. We introduce our view on the prenatal development of tolerance for the normal oral microbiome: we propose that development of fetal tolerance towards the microbiome of the mother during pregnancy is the major factor for a successful acquisition of a normal microbiome. We describe the processes that influence the establishment of such microbiome, followed by our perspective on the process of sustaining a healthy oral microbiome. We divide microbiome-maintenance factors into host-derived and microbe-derived, while focusing on the host. Finally, we highlight the need and directions for future research

Oral health determinants of incident malnutrition in community-dwelling older adults

Objective: Poor oral health might be a modifiable determinant of malnutrition in older age. We aimed to investigate the associations of multiple oral health characteristics with incident malnutrition in community-dwelling older adults. Methods: This exploratory analysis is based on prospective data from 893 participants, aged 55–80 years without malnutrition in 2005/06 from the Longitudinal Aging Study Amsterdam. In 2007, 19 oral health characteristics from the domains teeth/dentures, oral hygiene, oral problems, and self-rated oral health were assessed by questionnaire. Incident malnutrition was defined as presence of low body mass index (<20 kg/m² in people <70 years, <22 kg/m² ≥70 years) and/or self-reported involuntary weight loss ≥5% in previous 6 months at any of the follow-ups (2008/09, 2012/13, 2015/16). Associations of oral aspects with incident malnutrition were analyzed by cox proportional hazard models and adjusted for confounders. Results: The 9-year incidence of malnutrition was 13.5%. Sixteen of 19 oral health aspects were not associated with incident malnutrition in the crude models. Adjusted hazard ratios for incident malnutrition were 2.14 (1.10–4.19, p = 0.026) for toothache while chewing, 2.10 (0.88–4.98, p = 0.094) for an unhealthy oral health status, and 1.99 (0.93–4.28, p = 0.077) for xerostomia in edentulous participants, however, the two latter ones failing to reach statistical significance. Conclusions: We identified toothache while chewing as determinant of incident malnutrition in community-dwelling older adults, and found indications that poor oral health and xerostomia in combination with having no teeth may play a role in developing malnutrition. However, these outlined tendencies need to be proven in further studies. Clinical Significance: Regarding the development of strategies to prevent malnutrition in older people toothache while chewing, xerostomia, and self-rated oral health would be of specific interest as these factors are modifiable and can be easily assessed by self-reports

On the ecosystemic network of saliva in healthy young adults

A dysbiotic state is believed to be a key factor in the onset of oral disease. Although oral diseases have been studied for decades, our understanding of oral health, the boundaries of a healthy oral ecosystem and ecological shift toward dysbiosis is still limited. Here, we present the ecobiological heterogeneity of the salivary ecosystem and relations between the salivary microbiome, salivary metabolome and host-related biochemical salivary parameters in 268 healthy adults after overnight fasting. Gender-specific differences in the microbiome and metabolome were observed and were associated with salivary pH and dietary protein intake. Our analysis grouped the individuals into five microbiome and four metabolome-based clusters that significantly related to biochemical parameters of saliva. Low salivary pH and high lysozyme activity were associated with high proportions of streptococcal phylotypes and increased membrane-lipid degradation products. Samples with high salivary pH displayed increased chitinase activity, higher abundance of Veillonella and Prevotella species and higher levels of amino acid fermentation products, suggesting proteolytic adaptation. An over-specialization toward either a proteolytic or a saccharolytic ecotype may indicate a shift toward a dysbiotic state. Their prognostic value and the degree to which these ecotypes are related to increased disease risk remains to be determined