ArticleFEMS microbiology ecology2011
Optimizing the analysis of human intestinal microbiota with phylogenetic microarray.
Article in FEMS microbiology ecology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- Nanobiosensors: A Potential Tool to Decipher the Nexus Between SARS-CoV-2 Infection and Gut Dysbiosis.Sensors (Basel, Switzerland) · 2026Review
- Diet Supplementation with Pomegranate Fruit Alters Distal Gut Microbiota of Healthy Female College Students.Microorganisms · 2025Article
- Characterization of endophytic bacteriome diversity and associated beneficial bacteria inhabiting a macrophyteFrontiers in plant science · 2023Article
- Biosensors for point-of-care testing and personalized monitoring of gastrointestinal microbiota.Frontiers in microbiology · 2023Review
- Diversity and Structure of the Endophytic Bacterial Communities Associated With Three Terrestrial Orchid Species as Revealed by 16S rRNA Gene Metabarcoding.Frontiers in microbiology · 2020Article
- Dietary Fatty Acids Sustain the Growth of the Human Gut Microbiota.Applied and environmental microbiology · 2018Article
- Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome.Microbiome · 2015Article
- Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing.Journal of clinical bioinformatics · 2014Article
- CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.Microbiome · 2014Article
- Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation.Microbiome · 2014Article
- A DNA microarray for the versatile diagnosis of infectious diarrhea.APMIS : acta pathologica, microbiologica, et immunologica Scandinavica · 2013Article
- Transcriptional responses of uropathogenic Escherichia coli to increased environmental osmolality caused by salt or urea.Infection and immunity · 2013Article
- Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes.PloS one · 2013Article
- Alterations in the gut microbiome of children with severe ulcerative colitis.Inflammatory bowel diseases · 2012Article
- Application of phylogenetic microarrays to interrogation of human microbiota.FEMS microbiology ecology · 2012Review
- Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays.Bioinformatics (Oxford, England) · 2011Article
- Distal gut microbiota of adolescent children is different from that of adults.FEMS microbiology ecology · 2011Article
- Functional metagenomic investigations of the human intestinal microbiota.Frontiers in microbiology · 2011Article
- Article
- Article
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
Abstract
Phylogenetic microarrays present an attractive strategy to high-throughput interrogation of complex microbial communities. In this work, we present several approaches to optimize the analysis of intestinal microbiota with the recently developed Microbiota Array. First, we determined how 16S rDNA-specific PCR amplification influenced bacterial detection and the consistency of measured abundance values. Bacterial detection improved with an increase in the number of PCR amplification cycles, but 25 cycles were sufficient to achieve the maximum possible detection. A PCR-caused deviation in the measured abundance values was also observed. We also developed two mathematical algorithms that aimed to account for a predicted cross-hybridization of 16S rDNA fragments among different species, and to adjust the measured hybridization signal based on the number of 16S rRNA gene copies per species genome. The 16S rRNA gene copy adjustment indicated that the presence of members of the class Clostridia might be overestimated in some 16S rDNA-based studies. Finally, we show that the examination of total community RNA with phylogenetic microarray can provide estimates of the relative metabolic activity of individual community members. Complementary profiling of genomic DNA and total RNA isolated from the same sample presents an opportunity to assess population structure and activity in the same microbial community.
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.