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.

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Available from: Roland Schröder, May 26, 2015
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    • "However, before considering such a strategy further, it is pivotal to address possible influence of internal and external factors on the salivary bacterial composition. Previous studies have suggested that smoking[24]and other lifestyleassociated factors may have a general impact on the salivary microbiota242526. Unfortunately , little is known about if the salivary microbiome varies in composition over a 24 hour period, e.g., diurnal variation, and previous studies have reported conflicting results in relation to long stability of the salivary microbiota2728. "
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    ABSTRACT: Objectives: Saliva is a biological fluid suitable for biomarker analysis, and differences in the salivary microbiota in oral health and disease have been reported. For such comparative analyses, time of sampling is critical since the bacterial composition may vary throughout the day, i.e., diurnal variation. The purpose of this study is to compare the salivary microbiome over time to determine the optimal time for sampling. Design: Stimulated saliva samples were collected from 5 orally healthy individuals in 4 h intervals for 24 h, and collection was repeated 7 days later (number of samples per person, n = 12, total number of samples, n = 60). Salivary microbiota was analyzed using the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS), and statistical analysis was performed using the Kruskal-Wallis test with Benjamini-Hochberg's correction for multiple comparisons, cluster analysis, principal component analysis and correspondence analysis. Results: From a total of 60 saliva samples, 477 probe targets were collectively identified with a mean number of probes per sample of 207 (range: 153-307). Little or no variation in microbial profiles within subjects was observed over time. Conclusions: Although there was considerable variation between subjects, microbial profiles within subjects were stable throughout a 24 hour period and after 1 week. Since there is little or no evidence of diurnal variation of the salivary microbiome, time of sampling of saliva is not critical for perturbation or other microbial studies.
    Full-text · Article · Jan 2016 · PLoS ONE
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    • "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. "
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    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.
    Full-text · Article · Aug 2014 · Frontiers in Cellular and Infection Microbiology
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    • "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. "
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    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.
    Full-text · Article · Apr 2014 · BMC Genomics
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