ArticleMicrobes and environments2013
De novo semi-alignment of 16S rRNA gene sequences for deep phylogenetic characterization of next generation sequencing data.
Article in Microbes and environments, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
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- Biohacking agarwood: the impact of fire drills and brine on endophytes and metabolites of Aquilaria sinensis.BMC plant biology · 2025Article
- Intercropping of Oats with Vetch Conducts to Improve Soil Bacteriome Diversity and Structure.Microorganisms · 2025Article
- Evaluating the Effect of Dietary Protein-Energy Ratios on Yak Intestinal Microbiota Using High-Throughput 16S rRNA Gene Sequencing.Veterinary sciences · 2025Article
- Exploring vaginal microbiome: from traditional methods to metagenomic next-generation sequencing-a systematic review.Frontiers in microbiology · 2025Review
- Effects of Acute Salinity Stress on the Histological and Bacterial Community Structure and Function in Intestine ofMarine drugs · 2024Article
- Development and Evaluation of Non-Antibiotic Growth Promoters for Food Animals.Veterinary sciences · 2024Article
- Phycocyanin Additives Regulate Bacterial Community Structure and Antioxidant Activity of Alfalfa Silage.Microorganisms · 2024Article
- Gut microbiota in the association between obesity and kidney function decline: a metagenomics-based study in a rat model.Renal failure · 2024Article
- Exploring microbial diversity and function in companion planting systems of white clover and orchard grass.Scientific reports · 2024Article
- Intestinal microbiota dataset revealed by high-throughput sequencing of 16S rRNA in children with anemia in southern Peru.Data in brief · 2024Article
- Breaking the Cycle: A Yeast Mannan-Rich Fraction Beneficially Modulates Egg Quality and the Antimicrobial Resistome Associated with Layer Hen Caecal Microbiomes under Commercial Conditions.Microorganisms · 2024Article
- Article
- A New 4-Thiazolidinone Derivative (Les-6490) as a Gut Microbiota Modulator: Antimicrobial and Prebiotic Perspectives.Antibiotics (Basel, Switzerland) · 2024Article
- Influence of pancreaticoduodenectomy for periampullary carcinoma on intestinal microbiome and metabolites.Heliyon · 2024Article
- Effects of Vitamin A on Growth Performance, Antioxidants, Gut Inflammation, and Microbes in Weaned Piglets.Antioxidants (Basel, Switzerland) · 2023Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We addressed the challenges of analyzing next-generation 16S rRNA gene deep sequencing data from the uncharacterized microbial majority. This was performed using a novel de novo semi-alignment approach. The semi-alignments were based on Orthologous Tri-Nucleotides (OTNs), which are identical trinucleotides located in the same sequence region. OTNs in high error homopolymeric tracts were excluded to avoid overestimation of genetic distances. Phylogenetic information was derived assuming an exponential decay in shared OTNs between pairs of bacteria. OTN relatedness was also explored through principal component analysis (PCA). In evaluating the OTN approach we reanalyzed a dataset consisting of triplicate GS FLX titanium pyrosequencing runs for each of two experimental soil samples, in addition to analyses of the Greengenes core dataset. The conclusion from these comparisons was that the OTN approach was superior to traditional alignments both with respect to speed and accuracy. We therefore believe that our OTN-based semi-alignment approach will be a valuable contribution to future exploration of deep sequencing data.
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