The bacterial microbiota in the oral mucosa of rural Amerindians

Abstract

The oral microbiota plays an important role in buccal health and in diseases such as periodontitis and meningitis. The study of the human oral bacteria has so far focused on subjects from Western societies, while little is known about subjects from isolated communities. This work determined the composition of the oral mucosa microbiota from six Amazon Amerindians, and tested a sample preservation alternative to freezing. Paired oral swabs were taken from six adults of Guahibo ethnicity living in the community of Platanillal, Amazonas State, Venezuela. Replicate swabs were preserved in liquid nitrogen and in Aware Messenger fluid (Calypte). Buccal DNA was extracted, and the V2 region of the 16S rRNA gene was amplified and pyrosequenced. A total of 17 214 oral bacterial sequences were obtained from the six subjects; these were binned into 1034 OTUs from 10 phyla, 30 families and 51 genera. The oral mucosa was highly dominated by four phyla: Firmicutes (mostly the genera Streptococcus and Veillonella), Proteobacteria (mostly Neisseria), Bacterioidetes (Prevotella) and Actinobacteria (Micrococcineae). Although the microbiota were similar at the phylum level, the Amerindians shared only 62 % of the families and 23 % of the genera with non-Amerindians from previous studies, and had a lower richness of genera (51 vs 177 reported in non-Amerindians). The Amerindians carried unidentified members of the phyla Bacteroidetes, Firmicutes and Proteobacteria and their microbiota included soil bacteria Gp1 (Acidobacteriaceae) and Xylanibacter (Prevotellaceae), and the rare genus Phocoenobacter (Pasteurellaceae). Preserving buccal swabs in the Aware Messenger oral fluid collection device substantially altered the bacterial composition in comparison to freezing, and therefore this method cannot be used to preserve samples for the study of microbial communities.

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood

“…Detailed information about the subjects and sequencing barcodes can be found in Supplemental Table S1. It has been previously described (Bik et al 2010;Contreras et al 2010;Lazarevic et al 2010) that the main bacterial phyla in saliva were Firmicutes (with predominant genera Streptococcus, Veillonella, Gemella, and Granulicatella), Proteobacteria (Neisseria), Bacteroidetes (Prevotella), and Actinobacteria (Rothia). We additionally found Fusobacteria, TM7, Cyanobacteria, SR1, Spirochaetes, and Tenericutes.…”

Ancient human microbiomes

“…Studies of remote and indigenous communities (Contreras et al, 2010; Yatsunenko et al, 2012; Schnorr et al, 2014) and crowdsourcing projects such as the American Gut (www.americangut.org), the Earth Microbiome Project (www.earthmicrobiome.org), and uBiome (www.uBiome.com) are attempting to characterize modern microbiomes across a range of contemporary environments. Nevertheless, even the most extensive sampling of modern microbiota will provide limited insight into Pre-Industrial microbiomes.…”

Non-pathogenic Neisseria: members of an abundant, multi-habitat, diverse genus

“…10 individuals from each of 12 geographical locations across four continents), in which Neisseria was present in the saliva of participants from all locations at high frequency (107 out of 120) (Nasidze et al, 2009). While most oral microbiome studies have been conducted on Caucasians or Asians (Keijser et al, 2008;Ling et al, 2013;Said et al, 2014;Zaura et al, 2009), an interesting investigation focused on isolated communities, with oral swabs taken from six adult Amerindian participants of Guahibo ethnicity living in an isolated rural community of Platanillal, Amazonas State, Venezuela (Contreras et al, 2010). Although the genera detected in the Amerindians were substantially less diverse than in non-Amerindians, Neisseria was still the predominant genus among the Proteobacteria, which itself was one of the four most abundant phyla along with Firmicutes, Bacteroidetes and Actinobacteria (Contreras et al, 2010).…”