High Diversity of the Saliva Microbiome in Batwa Pygmies

Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
PLoS ONE (Impact Factor: 3.23). 08/2011; 6(8):e23352. DOI: 10.1371/journal.pone.0023352
Source: PubMed


We describe the saliva microbiome diversity in Batwa Pygmies, a former hunter-gatherer group from Uganda, using next-generation sequencing of partial 16S rRNA sequences. Microbial community diversity in the Batwa is significantly higher than in agricultural groups from Sierra Leone and the Democratic Republic of Congo. We found 40 microbial genera in the Batwa, which have previously not been described in the human oral cavity. The distinctive composition of the salvia microbiome of the Batwa may have been influenced by their recent different lifestyle and diet.

Download full-text


Available from: Roland Schröder, May 26, 2015
20 Reads
  • Source
    • "The other observed genera include taxa that are not significantly represented in saliva microbiota previously reported. These studies and others indicate that the microbiota may adopt a relatively large number of configurations in both health and disease (Cephas et al., 2011; Nasidze et al., 2011; Luo et al., 2012; Ling et al., 2013). The phylogenetic representation of related species in bacterial communities confer functional redundancy since their genomes encode a relatively high frequency of homologous protein functions. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Dental caries remains a significant public health problem and is considered pandemic worldwide. The prediction of dental caries based on profiling of microbial species involved in disease and equally important, the identification of species conferring dental health has proven more difficult than anticipated due to high interpersonal and geographical variability of dental plaque microbiota. We have used RNA-Seq to perform global gene expression analysis of dental plaque microbiota derived from 19 twin pairs that were either concordant (caries-active or caries-free) or discordant for dental caries. The transcription profiling allowed us to define a functional core microbiota consisting of nearly 60 species. Similarities in gene expression patterns allowed a preliminary assessment of the relative contribution of human genetics, environmental factors and caries phenotype on the microbiota's transcriptome. Correlation analysis of transcription allowed the identification of numerous functional networks, suggesting that inter-personal environmental variables may co-select for groups of genera and species. Analysis of functional role categories allowed the identification of dominant functions expressed by dental plaque biofilm communities, that highlight the biochemical priorities of dental plaque microbes to metabolize diverse sugars and cope with the acid and oxidative stress resulting from sugar fermentation. The wealth of data generated by deep sequencing of expressed transcripts enables a greatly expanded perspective concerning the functional expression of dental plaque microbiota.
    Frontiers in Cellular and Infection Microbiology 08/2014; 4(108). DOI:10.3389/fcimb.2014.00108 · 3.72 Impact Factor
  • Source
    • "This may include pathogenic organisms, such as Aggregatibacter actinomycetemcomitans, the causative agent of adolescent periodontal disease, which is common in those of African descent [50] and a member of a relatively abundant genus in the KhoeSan. Further study of the microbiomes associated with the KhoeSan and other diverse human populations (e.g., [51]), the microbiomic differences between these populations (e.g., [52,53]), especially across a variety of host physiological conditions, and the biology of commensal microbiota that are underrepresented in Western populations is needed to comprehensively differentiate the sources of variations observed between populations and to understand the coevolution between humans and their microbiome. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Targeted capture of genomic regions reduces sequencing cost while generating higher coverage by allowing biomedical researchers to focus on specific loci of interest, such as exons. Targeted capture also has the potential to facilitate the generation of genomic data from DNA collected via saliva or buccal cells. DNA samples derived from these cell types tend to have a lower human DNA yield, may be degraded from age and/or have contamination from bacteria or other ambient oral microbiota. However, thousands of samples have been previously collected from these cell types, and saliva collection has the advantage that it is a non-invasive and appropriate for a wide variety of research. We demonstrate successful enrichment and sequencing of 15 South African KhoeSan exomes and 2 full genomes with samples initially derived from saliva. The expanded exome dataset enables us to characterize genetic diversity free from ascertainment bias for multiple KhoeSan populations, including new exome data from six HGDP Namibian San, revealing substantial population structure across the Kalahari Desert region. Additionally, we discover and independently verify thirty-one previously unknown KIR alleles using methods we developed to accurately map and call the highly polymorphic HLA and KIR loci from exome capture data. Finally, we show that exome capture of saliva-derived DNA yields sufficient non-human sequences to characterize oral microbial communities, including detection of bacteria linked to oral disease (e.g. Prevotella melaninogenica). For comparison, two samples were sequenced using standard full genome library preparation without exome capture and we found no systematic bias of metagenomic information between exome-captured and non-captured data. DNA from human saliva samples, collected and extracted using standard procedures, can be used to successfully sequence high quality human exomes, and metagenomic data can be derived from non-human reads. We find that individuals from the Kalahari carry a higher oral pathogenic microbial load than samples surveyed in the Human Microbiome Project. Additionally, rare variants present in the exomes suggest strong population structure across different KhoeSan populations.Jeffrey M Kidd and Thomas J Sharpton are contributed equally to this manuscript.
    BMC Genomics 04/2014; 15(1):262. DOI:10.1186/1471-2164-15-262 · 3.99 Impact Factor
  • Source
    • "A few studies have investigated the bacterial composition of saliva in oral health (5, 23–25) and verified that a salivary bacterial profile resembles that of the throat, tonsils, and dorsum of the tongue (26). In addition, the salivary microbiome has been shown to be highly diverse and is proposed to depend on lifestyle and diet intake (25, 27). Also, oral disease may influence the bacterial profile, and recently it has been shown that both dental caries and periodontitis are associated with characteristic bacterial profiles of saliva different from that of oral health (28, 29). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The bacterial profile of saliva is composed of bacteria from different oral surfaces. The objective of this study was to determine whether different diet intake, lifestyle, or socioeconomic status is associated with characteristic bacterial saliva profiles. Stimulated saliva samples from 292 participants with low levels of dental caries and periodontitis, enrolled in the Danish Health Examination Survey (DANHES), were analyzed for the presence of approximately 300 bacterial species by means of the Human Oral Microbe Identification Microarray (HOMIM). Using presence and levels (mean HOMIM-value) of bacterial probes as endpoints, the influence of diet intake, lifestyle, and socioeconomic status on the bacterial saliva profile was analyzed by Mann-Whitney tests with Benjamini-Hochberg's correction for multiple comparisons and principal component analysis. Targets for 131 different probes were identified in 292 samples, with Streptococcus and Veillonella being the most predominant genera identified. Two bacterial taxa (Streptococcus sobrinus and Eubacterium [11][G-3] brachy) were more associated with smokers than non-smokers (adjusted p-value<0.01). Stratification of the group based on extreme ends of the parameters age, gender, alcohol consumption, body mass index (BMI), and diet intake had no statistical influence on the composition of the bacterial profile of saliva. Conversely, differences in socioeconomic status were reflected by the bacterial profiles of saliva. The bacterial profile of saliva seems independent of diet intake, but influenced by smoking and maybe socioeconomic status.
    Journal of Oral Microbiology 04/2014; 6(1). DOI:10.3402/jom.v6.23609
Show more