ArticleScientific reports2017
Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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.
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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.
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Who cites it
11 citing papers in PubMed.
- Article
- Cellular function of the GndA microprotein during heat shock.bioRxiv : the preprint server for biology · 2025Article
- Benchmarking 16S rRNA Gene-Based Approaches to Bacterial Taxonomy Assignment Based on Amplicon Sequencing With Illumina and Oxford Nanopore.International journal of microbiology · 2025Article
- Impact of land-use and fecal contamination on Escherichia populations in environmental samples.Scientific reports · 2024Article
- Article
- Exploring Long-Read Metagenomics for Full Characterization of Shiga Toxin-ProducingMicroorganisms · 2023Article
- Review
- A step forward for Shiga toxin-producingMicrobial genomics · 2022Article
- Whole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use.Applied and environmental microbiology · 2022Article
- gndDb, a Database of PartialMicrobiology resource announcements · 2019Article
- Multi-Locus Next-Generation Sequence Typing of DNA Extracted From Pooled Colonies Detects Multiple UnrelatedFrontiers in microbiology · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current culture methods to investigate changes in Escherichia coli community structure are often slow and laborious. Genes such as gnd (6-phosphogluconate dehydrogenase) have a highly variable nucleotide sequence and may provide a target for E. coli microbiome analysis using culture-independent methods. Metabarcoded PCR primers were used to generate separate libraries from calf faecal samples for high throughput sequencing. Although a total of 348 separate gnd sequence types (gSTs) were identified, 188 were likely to be due to sequencing errors. Of the remaining 160 gSTs, 92 did not match those in a database of 319 separate gnd sequences. 'Animal' was the main determinant of E. coli diversity with limited impact of sample type or DNA extraction method on intra-host E. coli community variation from faeces and recto-anal mucosal swab samples. This culture-independent study has addressed the difficulties of quantifying bacterial intra-species diversity and revealed that, whilst individual animals may harbour >50 separate E. coli strains, communities are dominated by <10 strains alongside a large pool of subdominant strains present at low abundances. This method will be useful for characterising the diversity and population structure of E. coli in experimental studies designed to assess the impact of interventions on the gut microbiome.
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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.