ReviewFrontiers in nutrition2016
Considerations For Optimizing Microbiome Analysis Using a Marker Gene.
Review in Frontiers in nutrition, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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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
26 citing papers in PubMed.
- Neglected kingdoms: the gut virome, mycobiome and their role in inflammatory bowel disease.Gut microbes · 2026Review
- Analytic attributes of the 16S rRNA gene sequencing methodology for human gut microbiota characterization.Applied microbiology and biotechnology · 2026Article
- Characterising the gut microbiomes of two baleen whales with different feeding and migratory strategies.Animal microbiome · 2026Article
- A mathematical framework to correct for compositionality in microbiome data sets.Applied and environmental microbiology · 2026Article
- Characteristics of Intestinal Barrier State and Immunoglobulin-Bound Fraction of Stool Microbiota in Advanced Melanoma Patients Undergoing Anti-PD-1 Therapy.International journal of molecular sciences · 2025Article
- Role of Gut Microbial Metabolites in Cardiovascular Diseases-Current Insights and the Road Ahead.International journal of molecular sciences · 2024Review
- Characterising the Tasmanian devil (Sarcophilus harrisii) pouch microbiome in lactating and non-lactating females.Scientific reports · 2024Article
- Current Trends and Challenges of Microbiome Research in Prostate Cancer.Current oncology reports · 2024Review
- Insights into Wheat Genotype‒Pathogens (Basel, Switzerland) · 2024Article
- The salivary microbiome as a diagnostic biomarker of periodontitis: a 16S multi-batch study before and after the removal of batch effects.Frontiers in cellular and infection microbiology · 2024Article
- In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea.Microbiome · 2023Article
- Protocooperative Effect ofMicroorganisms · 2023Article
- A pilot study characterizing longitudinal changes in fecal microbiota of patients with Hirschsprung-associated enterocolitis.Pediatric surgery international · 2022Article
- Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies.Microbiome · 2022Article
- Human milk microbiota: what did we learn in the last 20 years?Microbiome research reports · 2022Review
- Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales.Animal microbiome · 2021Article
- Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models.Scientific reports · 2021Article
- Early life disruption of the microbiota affects organ development and cytokine gene expression in threespine stickleback.Integrative and comparative biology · 2020Article
- Unraveling the effects of the gut microbiota composition and function on horse endurance physiology.Scientific reports · 2019Article
- Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body.Frontiers in microbiology · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing technologies have found a widespread use in the study of host-microbe interactions due to the increase in their throughput and their ever-decreasing costs. The analysis of human-associated microbial communities using a marker gene, particularly the 16S rRNA, has been greatly benefited from these technologies - the human gut microbiome research being a remarkable example of such analysis that has greatly expanded our understanding of microbe-mediated human health and disease, metabolism, and food absorption. 16S studies go through a series of in vitro and in silico steps that can greatly influence their outcomes. However, the lack of a standardized workflow has led to uncertainties regarding the transparency and reproducibility of gut microbiome studies. We, here, discuss the most common challenges in the archetypical 16S rRNA workflow, including the extraction of total DNA, its use as template in PCR with primers that amplify specific hypervariable regions of the gene, amplicon sequencing, the denoising and removal of low-quality reads, the detection and removal of chimeric sequences, the clustering of high-quality sequences into operational taxonomic units, and their taxonomic classification. We recommend the essential technical information that should be conveyed in publications for reproducibility of results and encourage non-experts to include procedures and available tools that mitigate most of the problems encountered in microbiome analysis.
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