ArticleJournal of microbiological methods2013
Minimization of chloroplast contamination in 16S rRNA gene pyrosequencing of insect herbivore bacterial communities.
Article in Journal of microbiological methods, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers, 1 of them a synthesis that pooled it.
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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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Who cites it
115 citing papers in PubMed, 1 synthesis or guideline pooled it, 235 citations in OpenAlex.
- Pooled it
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- Characterising the gut microbiomes of two baleen whales with different feeding and migratory strategies.Animal microbiome · 2026Article
- Exploring the Algarrobo Decline in the Pómac Forest: Unraveling the Relationship between the Endomicrobiome of Neltuma pallida and Enallodiplosis discordis.Microbial ecology · 2026Article
- Argan fruit microbiomes: influence of biogeographic and soil driven environmental factors.BMC plant biology · 2026Article
- Effects of phytobiotics on intestinal barrier function and gut microbiome in weaned piglets challenged with enterotoxigenicJournal of animal science and technology · 2026Article
- Intraspecific microbiome dynamics across the life cycle of the milkweed bugMicrobial genomics · 2026Article
- Fungicides disrupt total and endophytic phyllosphere bacterial communities but a salicylic acid hyperimmune mutant shows microbiome resilience.ISME communications · 2026Article
- rCCLasso: a robust framework for microbial correlation network analysis reveals age-related microbial dynamics.Frontiers in cellular and infection microbiology · 2026Article
- Impact of peripheral circadian misalignment and alcohol on the resiliency of intestinal barrier and microbiota.Gut microbes · 2025Article
- Immune-mediated indirect interaction between gut microbiota and bacterial pathogens.BMC biology · 2025Article
- Changes in the assembly and functional adaptation of endophytic microbial communities in Amorphophallus species with different levels of resistance to necrotrophic bacterial pathogen stress.Communications biology · 2025Article
- Peptide nucleic acid (PNA) clamps reduce amplification of host chloroplast and mitochondria rRNA gene sequences and increase detected diversity in 16S rRNA gene profiling analysis of oak-associated microbiota.Environmental microbiome · 2025Article
- Tank-based bacterial profiling identifies basin-wide white band disease pathogen candidate and no bacterial associations with coral disease resistance.ISME communications · 2025Article
- Interaction with refuse piles is associated with co-occurrence of core gut microbiota in workers of the ant Aphaenogaster picea.Access microbiology · 2025Article
- Improving the profiling of wheat bacterial and fungal endophytic communities-a PCR clamping approach.Frontiers in microbiology · 2025Article
- Identification of potential insect ecological interactions using a metabarcoding approach.PeerJ · 2025Article
- Efficient recovery and DNA extraction for algae-associated microbial communities.Frontiers in plant science · 2025Article
- The Gut Microbiome of Two Wild Bumble Bee Species Native of South America: Bombus pauloensis and Bombus bellicosus.Microbial ecology · 2024Article
55 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Chloroplast sequence contamination in 16S ribosomal RNA gene (16S) analyses can be particularly problematic when sampling microbial communities in plants and folivorous arthropods. We previously encountered high levels of plastid contamination in herbivorous insect samples when we used the predominant 454 pyrosequencing 16S methodologies described in the literature. 799F, a primer previously found to exclude chloroplast sequences, was modified to enhance its efficacy, and we describe, in detail, our methodology throughout amplicon pyrosequencing. Thirteen versions of 799F were assessed for the exclusion of chloroplast sequences from our samples. We found that a shift in the mismatch between 799F and chloroplast 16S resulted in significant reduction of chloroplast reads. Our results also indicate that amplifying sequences from environmental samples in a two-step PCR process, with the addition of the multiplex identifiers and 454 adapters in a second round of PCR, further improved primer specificity. Primers that included 3' phosphorothioate bonds, which were designed to block primer degradation, did not amplify consistently across samples. The different forward primers do not appear to bias the bacterial communities detected. We provide a methodological framework for reducing chloroplast reads in high-throughput sequencing data sets that can be applied to a number of environmental samples and sequencing techniques.
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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.