ArticleApplied and environmental microbiology2011
PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip.
Article in Applied and environmental microbiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 78 citations in OpenAlex.
- CyanoStrainChip: A Novel DNA Microarray Tool for High-Throughput Detection of Environmental Cyanobacteria at the Strain Level.Environmental science & technology · 2024Article
- Tool and techniques study to plant microbiome current understanding and future needs: an overview.Communicative & integrative biology · 2022Review
- Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil.The ISME journal · 2020Article
- Improvement of Surface-Enhanced Raman Scattering Method for Single Bacterial Cell Analysis.Frontiers in bioengineering and biotechnology · 2020Article
- In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations.PloS one · 2020Article
- Methods for quantification of growth and productivity in anaerobic microbiology and biotechnology.Folia microbiologica · 2019Review
- High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations.Molecular ecology resources · 2019Review
- Airborne bioaerosols and their impact on human health.Journal of environmental sciences (China) · 2018Review
- A comparison of methods used to unveil the genetic and metabolic pool in the built environment.Microbiome · 2018Article
- Analysis of airborne microbial communities using 16S ribosomal RNA: Potential bias due to air sampling stress.The Science of the total environment · 2018Article
- Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems.Microbiome · 2017Review
- Modification of extraction method for community DNA isolation from salt affected compact wasteland soil samples.MethodsX · 2017Article
- probeBase--an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016.Nucleic acids research · 2016Article
- The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils.Frontiers in microbiology · 2016Article
- Increasing the Size of the Microbial Biomass Altered Bacterial Community Structure which Enhances Plant Phosphorus Uptake.PloS one · 2016Article
- Library preparation methodology can influence genomic and functional predictions in human microbiome research.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Review
- High-throughput DNA microarray detection of pathogenic bacteria in shallow well groundwater in the Kathmandu Valley, Nepal.Current microbiology · 2015Article
- Effect of photosynthetic bacteria on water quality and microbiota in grass carp culture.World journal of microbiology & biotechnology · 2014Article
- The role of the human microbiome in otolaryngology-head and neck surgery: a contemporary review.The Laryngoscope · 2014Review
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.