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Characterization of saliva microbiota's functional feature based on metagenomic sequencing.

ABSTRACT: OBJECTIVE:Saliva, a mixture of exocrinally secretive fluids, amounts to ~1.5 L daily and harbors numerous microbial inhabitants. However, except the organismal structure of saliva microbiota, the functional profile of saliva microbiota remain elusive. METHODS:Here we used metagenomic sequencing to experimentally reconstruct the global genomic profile of saliva by sequencing total saliva DNA from two healthy and two caries-active (DMFT ? 6) adults. RESULTS:We found that saliva microbiota, representing 30-60% of total saliva DNA in our samples, might carry functional signatures that were site-specific and caries-state-specific. Among microbiota from different hosts, a prominent functional core, but not an organismal core, was identified. Each microbiota exhibited functional redundancy where dominant genomes tend to encode more functional diversity yet without necessarily contributing to dominant functions. Furthermore, genetic polymorphisms of hosts were also unraveled from salivary DNA without apparent physical or sequence bias in human chromosomes. CONCLUSIONS:The microbial functional sensitivity to disease, links to specific functions, and permission of simultaneous genotyping of hosts and microbiota suggested sequencing salivary DNA might be an advantageous venue in uncovering both human and microbial basis of oral infections.

SUBMITTER: Yang F

PROVIDER: S-EPMC5174016 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Characterization of saliva microbiota's functional feature based on metagenomic sequencing.

Yang Fang F Ning Kang K Zeng Xiaowei X Zhou Qian Q Su Xiaoquan X Yuan Xiao X

SpringerPlus 20161220 1

<h4>Objective</h4>Saliva, a mixture of exocrinally secretive fluids, amounts to ~1.5 L daily and harbors numerous microbial inhabitants. However, except the organismal structure of saliva microbiota, the functional profile of saliva microbiota remain elusive.<h4>Methods</h4>Here we used metagenomic sequencing to experimentally reconstruct the global genomic profile of saliva by sequencing total saliva DNA from two healthy and two caries-active (DMFT ≧ 6) adults.<h4>Results</h4>We found that sali ...[more]

PMID: 28053828

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Project description:BackgroundBiogas production is an economically attractive technology that has gained momentum worldwide over the past years. Biogas is produced by a biologically mediated process, widely known as "anaerobic digestion." This process is performed by a specialized and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. Deciphering the complex microbial community engaged in this process is interesting both for unraveling the network of bacterial interactions and for applicability potential to the derived knowledge.ResultsIn this study, we dissect the bioma involved in anaerobic digestion by means of high throughput Illumina sequencing (~51 gigabases of sequence data), disclosing nearly one million genes and extracting 106 microbial genomes by a novel strategy combining two binning processes. Microbial phylogeny and putative taxonomy performed using >400 proteins revealed that the biogas community is a trove of new species. A new approach based on functional properties as per network representation was developed to assign roles to the microbial species. The organization of the anaerobic digestion microbiome is resembled by a funnel concept, in which the microbial consortium presents a progressive functional specialization while reaching the final step of the process (i.e., methanogenesis). Key microbial genomes encoding enzymes involved in specific metabolic pathways, such as carbohydrates utilization, fatty acids degradation, amino acids fermentation, and syntrophic acetate oxidation, were identified. Additionally, the analysis identified a new uncultured archaeon that was putatively related to Methanomassiliicoccales but surprisingly having a methylotrophic methanogenic pathway.ConclusionThis study is a pioneer research on the phylogenetic and functional characterization of the microbial community populating biogas reactors. By applying for the first time high-throughput sequencing and a novel binning strategy, the identified genes were anchored to single genomes providing a clear understanding of their metabolic pathways and highlighting their involvement in anaerobic digestion. The overall research established a reference catalog of biogas microbial genomes that will greatly simplify future genomic studies.

Project description:BackgroundInterest in understanding the mechanisms that lead to a particular composition of the Gut Microbiota is highly increasing, due to the relationship between this ecosystem and the host health state. Particularly relevant is the study of the Relative Species Abundance (RSA) distribution, that is a component of biodiversity and measures the number of species having a given number of individuals. It is the universal behaviour of RSA that induced many ecologists to look for theoretical explanations. In particular, a simple stochastic neutral model was proposed by Volkov et al. relying on population dynamics and was proved to fit the coral-reefs and rain forests RSA. Our aim is to ascertain if this model also describes the Microbiota RSA and if it can help in explaining the Microbiota plasticity.ResultsWe analyzed 16S rRNA sequencing data sampled from the Microbiota of three different animal species by Jeraldo et al. Through a clustering procedure (UCLUST), we built the Operational Taxonomic Units. These correspond to bacterial species considered at a given phylogenetic level defined by the similarity threshold used in the clustering procedure. The RSAs, plotted in the form of Preston plot, were fitted with Volkov's model. The model fits well the Microbiota RSA, except in the tail region, that shows a deviation from the neutrality assumption. Looking at the model parameters we were able to discriminate between different animal species, giving also a biological explanation. Moreover, the biodiversity estimator obtained by Volkov's model also differentiates the animal species and is in good agreement with the first and second order Hill's numbers, that are common evenness indexes simply based on the fraction of individuals per species.ConclusionsWe conclude that the neutrality assumption is a good approximation for the Microbiota dynamics and the observation that Volkov's model works for this ecosystem is a further proof of the RSA universality. Moreover, the ability to separate different animals with the model parameters and biodiversity number are promising results if we think about future applications on human data, in which the Microbiota composition and biodiversity are in close relationships with a variety of diseases and life-styles.

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Characterization of saliva microbiota's functional feature based on metagenomic sequencing.

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Characterization of saliva microbiota's functional feature based on metagenomic sequencing.

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