Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray.
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ABSTRACT:
SUBMITTER: Schatz MC
PROVIDER: S-EPMC2918976 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Environmental microbial community analysis typically involves amplification by PCR, despite well-documented biases. We have developed two methods of PCR-independent microbial community analysis using the high-density microarray PhyloChip: direct hybridization of 16S rRNA (dirRNA) or rRNA converted to double-stranded cDNA (dscDNA). We compared dirRNA and dscDNA communities to PCR-amplified DNA communities using a mock community of eight taxa, as well as experiments derived from three environmental sample types: chromium-contaminated aquifer groundwater, tropical forest soil, and secondary sewage in seawater. Community profiles by both direct hybridization methods showed differences that were expected based on accompanying data but that were missing in PCR-amplified communities. Taxon richness decreased in RNA compared to that in DNA communities, suggesting a subset of 20% in soil and 60% in groundwater that is active; secondary sewage showed no difference between active and inactive populations. Direct hybridization of dscDNA and RNA is thus a viable alternative to PCR-amplified microbial community analysis, providing identification of the active populations within microbial communities that attenuate pollutants, drive global biogeochemical cycles, or proliferate disease states.
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Project description:Next-generation sequencing techniques, and PhyloChip, have made simultaneous phylogenetic analyses of hundreds of microbial communities possible. Insight into community structure has been limited by the inability to integrate and visualize such vast datasets. Fast UniFrac overcomes these issues, allowing integration of larger numbers of sequences and samples into a single analysis. Its new array-based implementation offers orders of magnitude improvements over the original version. New 3D visualization of principal coordinates analysis results, with the option to view multiple coordinate axes simultaneously, provides a powerful way to quickly identify patterns that relate vast numbers of microbial communities. We show the potential of Fast UniFrac using examples from three data types: Sanger-sequencing studies of diverse free-living and animal-associated bacterial assemblages and from the gut of obese humans as they diet, pyrosequencing data integrated from studies of the human hand and gut, and PhyloChip data from a study of citrus pathogens. We show that a Fast UniFrac analysis using a reference tree recaptures patterns that could not be detected without considering phylogenetic relationships and that Fast UniFrac, coupled with BLAST-based sequence assignment, can be used to quickly analyze pyrosequencing runs containing hundreds of thousands of sequences, showing patterns relating human and gut samples. Finally, we show that the application of Fast UniFrac to PhyloChip data could identify well-defined subcategories associated with infection. Together, these case studies point the way toward a broad range of applications and show some of the new features of Fast UniFrac.
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Project description:Membrane biofilm reactors (MBfRs) have attracted more and more attention in the field of wastewater treatment due to their advantages of high mass transfer efficiency and low-carbon emissions. There are many factors affecting their nitrogen removal abilities, such as operation time, electron donor types, and operation modes. The operation time is directly related to the growth status of microorganisms, so it is very important to understand the effect of different operation times on microbial composition and community succession. In this study, two parallel H2-based MBfRs were operated, and differences in microbial composition, community succession, and NO3--N removal efficiency were investigated on the 30th day and the 60th day of operation. The nitrogen removal efficiency of MBfRs with an operation time of 60 days was higher than that of MBfRs with an operation time of 30 days. Proteobacteria was the dominant phylum in both MBfRs; however, the composition of the microbial community was quite different. At the class level, the community composition of Proteobacteria was similar between the two MBfRs. Alphaproteobacteria was the dominant class in MBfR, and Betaproteobacteria and Gammaproteobacteria were also in high proportion. Combined with the analysis of microbial relative abundance and concentration, the similarity of microbial distribution in the MBfRs was very low on day 30 and day 60, and the phylogenetic relationships of the top 50 dominant universal bacteria and Proteobacteria were different. Although the microbial concentration decreased with the extension of the operation time, the microbial abundance and diversity of specific functional microorganisms increased further. Therefore, the operation time had a significant effect on microbial composition and community succession.
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Project description:UNLABELLED:Air travel can rapidly transport infectious diseases globally. To facilitate the design of biosensors for infectious organisms in commercial aircraft, we characterized bacterial diversity in aircraft air. Samples from 61 aircraft high-efficiency particulate air (HEPA) filters were analyzed with a custom microarray of 16S rRNA gene sequences (PhyloChip), representing bacterial lineages. A total of 606 subfamilies from 41 phyla were detected. The most abundant bacterial subfamilies included bacteria associated with humans, especially skin, gastrointestinal and respiratory tracts, and with water and soil habitats. Operational taxonomic units that contain important human pathogens as well as their close, more benign relatives were detected. When compared to 43 samples of urban outdoor air, aircraft samples differed in composition, with higher relative abundance of Firmicutes and Gammaproteobacteria lineages in aircraft samples, and higher relative abundance of Actinobacteria and Betaproteobacteria lineages in outdoor air samples. In addition, aircraft and outdoor air samples differed in the incidence of taxa containing human pathogens. Overall, these results demonstrate that HEPA filter samples can be used to deeply characterize bacterial diversity in aircraft air and suggest that the presence of close relatives of certain pathogens must be taken into account in probe design for aircraft biosensors. PRACTICAL IMPLICATIONS:A biosensor that could be deployed in commercial aircraft would be required to function at an extremely low false alarm rate, making an understanding of microbial background important. This study reveals a diverse bacterial background present on aircraft, including bacteria closely related to pathogens of public health concern. Furthermore, this aircraft background is different from outdoor air, suggesting different probes may be needed to detect airborne contaminants to achieve minimal false alarm rates. This study also indicates that aircraft HEPA filters could be used with other molecular techniques to further characterize background bacteria and in investigations in the wake of a disease outbreak.
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