ArticlePloS one2013
Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed, 201 citations in OpenAlex.
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- Prevalence of Bacillus species in the lytic cultural heritage of Santa Lucia alle Malve Rupestrian Church.Scientific reports · 2026Article
- Molecular characterization ofOpen veterinary journal · 2026Article
- Identification and characterization of R75estA, a halophilic polyester-degrading enzyme from a marine bacterium.Frontiers in microbiology · 2026Article
- Phenotypic diversity, symbiotic effectiveness and plant growth promoting characteristics of rhizobia nodulating chickpea (Cicer arietinum L.) from central and south gondar zones, Ethiopia.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Unravelling the Probiotic Potential of Raw Goat Milk Lactic Acid Bacteria and their Antagonistic Properties Against Aquatic Pathogens Belonging to Vibrio Species.Current microbiology · 2025Article
- Microbial Dream Team: Cotton Performs Better in Salty Soil with Pseudomonas hunanensis RT-12 and Staphylococcus caprae DS-2.Current microbiology · 2025Article
- Impact of altitudinal variations on plant growth dynamics, nutritional composition, and free living rhizospheric NScientific reports · 2025Article
- Mission Tara Microplastics: a holistic set of protocols and data resources for the field investigation of plastic pollution along the land-sea continuum in Europe.Environmental science and pollution research international · 2025Article
- Human Milk Microbiota Across Lactation Stages and Free Glutamate Concentrations in Healthy Ecuadorian Women.Nutrients · 2025Article
- Assessment of the Bacterial communities associated with Anopheles gambiae larval habitats in Southern Ghana.PloS one · 2025Article
- Genomic analysis ofFrontiers in veterinary science · 2025Article
- Towards a comprehensive view of wetland benthic communities.Current research in microbial sciences · 2025Article
- Two new strains of Streptomyces with metabolic potential for biological control of pear black spot disease.BMC microbiology · 2024Article
- Bacteria from the Amycolatopsis genus associated with a toxic bird secrete protective secondary metabolites.Nature communications · 2024Article
- Short-read full-length 16S rRNA amplicon sequencing for characterisation of the respiratory bacteriome of captive and free-ranging African elephants (Loxodonta africana).Scientific reports · 2024Article
- New investigation of encoding secondary metabolites gene by genome mining of a marine bacterium, Pseudoalteromonas viridis BBR56.BMC genomics · 2024Article
28 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In microbial ecology, a fundamental question relates to how community diversity and composition change in response to perturbation. Most studies have had limited ability to deeply sample community structure (e.g. Sanger-sequenced 16S rRNA libraries), or have had limited taxonomic resolution (e.g. studies based on 16S rRNA hypervariable region sequencing). Here, we combine the higher taxonomic resolution of near-full-length 16S rRNA gene amplicons with the economics and sensitivity of short-read sequencing to assay the abundance and identity of organisms that represent as little as 0.01% of sediment bacterial communities. We used a new version of EMIRGE optimized for large data size to reconstruct near-full-length 16S rRNA genes from amplicons sheared and sequenced with Illumina technology. The approach allowed us to differentiate the community composition among samples acquired before perturbation, after acetate amendment shifted the predominant metabolism to iron reduction, and once sulfate reduction began. Results were highly reproducible across technical replicates, and identified specific taxa that responded to the perturbation. All samples contain very high alpha diversity and abundant organisms from phyla without cultivated representatives. Surprisingly, at the time points measured, there was no strong loss of evenness, despite the selective pressure of acetate amendment and change in the terminal electron accepting process. However, community membership was altered significantly. The method allows for sensitive, accurate profiling of the "long tail" of low abundance organisms that exist in many microbial communities, and can resolve population dynamics in response to environmental change.
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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.