ArticleApplied and environmental microbiology2006
Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification.
Article in Applied and environmental microbiology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
86 citing papers in PubMed.
- Stratification-driven divergence between taxonomic and functional diversity in a deep lake microbiome.FEMS microbiology ecology · 2025Article
- Improved Sensitivity of Quantitative Polymerase Chain Reaction and Next Generation Sequencing for Detection of Salmonella spp. in Mixed Environmental Communities Using Whole Genome Amplification.MicrobiologyOpen · 2025Article
- TEAL-Seq: targeted expression analysis sequencing.mSphere · 2025Article
- Upper circumpolar deep water influences microbial functional gene composition and diversity along the southern Central Indian Ridge and eastern Southwest Indian Ridge.Microbiology spectrum · 2025Article
- Article
- Back to Basics: A Simplified Improvement to Multiple Displacement Amplification for Microbial Single-Cell Genomics.International journal of molecular sciences · 2023Article
- Improved single-cell genome amplification by a high-efficiency phi29 DNA polymerase.Frontiers in bioengineering and biotechnology · 2023Article
- Diversity of CRESS DNA Viruses in Squamates Recapitulates Hosts Dietary and Environmental Sources of Exposure.Microbiology spectrum · 2022Article
- Macroecological distributions of gene variants highlight the functional organization of soil microbial systems.The ISME journal · 2022Article
- Macroecological distributions of gene variants highlight the functional organization of soil microbial systems.The ISME journal · 2022Article
- Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon.The ISME journal · 2019Article
- Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities.mSystems · 2019Article
- Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers.Frontiers in microbiology · 2019Article
- Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses.Microbiome · 2018Article
- Nitrogen Cycle Evaluation (NiCE) Chip for Simultaneous Analysis of Multiple N Cycle-Associated Genes.Applied and environmental microbiology · 2018Article
- Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.mBio · 2018Article
- Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession.Frontiers in microbiology · 2018Article
- Divergent Responses of Forest Soil Microbial Communities under Elevated COApplied and environmental microbiology · 2018Article
- Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence.Scientific reports · 2017Article
- Template-dependent multiple displacement amplification for profiling human circulating RNA.BioTechniques · 2017Article
26 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously, but low microbial biomass often prevents application of this technology to many natural microbial communities. We developed a whole-community genome amplification-assisted microarray detection approach based on multiple displacement amplification. The representativeness of amplification was evaluated using several types of microarrays and quantitative indexes. Representative detection of individual genes or genomes was obtained with 1 to 100 ng DNA from individual or mixed genomes, in equal or unequal abundance, and with 1 to 500 ng community DNAs from groundwater. Lower concentrations of DNA (as low as 10 fg) could be detected, but the lower template concentrations affected the representativeness of amplification. Robust quantitative detection was also observed by significant linear relationships between signal intensities and initial DNA concentrations ranging from (i) 0.04 to 125 ng (r2 = 0.65 to 0.99) for DNA from pure cultures as detected by whole-genome open reading frame arrays, (ii) 0.1 to 1,000 ng (r2 = 0.91) for genomic DNA using community genome arrays, and (iii) 0.01 to 250 ng (r2 = 0.96 to 0.98) for community DNAs from ethanol-amended groundwater using 50-mer functional gene arrays. This method allowed us to investigate the oligotrophic microbial communities in groundwater contaminated with uranium and other metals. The results indicated that microorganisms containing genes involved in contaminant degradation and immobilization are present in these communities, that their spatial distribution is heterogeneous, and that microbial diversity is greatly reduced in the highly contaminated environment.
Indexed as
Identifiers
What OpenQuestion holds
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.