ArticleScientific reports2018
Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Toward reproducible pig gut microbiome profiling through standardized methodologies.ISME communications · 2026Article
- Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies.mSystems · 2025Article
- Key features and guidelines for the application of microbial alpha diversity metrics.Scientific reports · 2025Article
- Bioinformatic Methodologies in Assessing Gut Microbiota.Microbiology research · 2024Article
- Dental plaque microbiota sequence counts for microbial profiling and resistance genes detection.Applied microbiology and biotechnology · 2024Article
- Review
- Microbial community dynamics and functional potentials in the conversion of oil palm wastes into biomethane.3 Biotech · 2024Review
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- Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance.Scientific reports · 2023Article
- Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants.The ISME journal · 2023Article
- Metagenomics reveals novel microbial signatures of farm exposures in house dust.medRxiv : the preprint server for health sciences · 2023Article
- Metagenomics reveals novel microbial signatures of farm exposures in house dust.Frontiers in microbiology · 2023Article
- Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives.Animals : an open access journal from MDPI · 2022Review
- GenBank as a source to monitor and analyze Host-Microbiome data.Bioinformatics (Oxford, England) · 2022Article
- Ecosystem-specific microbiota and microbiome databases in the era of big data.Environmental microbiome · 2022Review
- Article
- Clinical Parasitology and Parasitome Maps as Old and New Tools to Improve Clinical Microbiomics.Pathogens (Basel, Switzerland) · 2021Review
- Multiplexed Workplace Measurements in Biogas Plants Reveal Compositional Changes in Aerosol Properties.Annals of work exposures and health · 2021Review
- Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes.Annual review of biomedical engineering · 2021Review
- Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota.Scientific reports · 2021Article
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5 authors.
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Abstract
In the past few years, many studies investigated the anaerobic digestion microbiome by means of 16S rRNA amplicon sequencing. Results obtained from these studies were compared to each other without taking into consideration the followed procedure for amplicons preparation and data analysis. This negligence was mainly due to the lack of knowledge regarding the biases influencing specific steps of the microbiome investigation process. In the present study, the main technical aspects of the 16S rRNA analysis were checked giving special attention to the approach used for high throughput sequencing. More specifically, the microbial compositions of three laboratory scale biogas reactors were analyzed before and after addition of sodium oleate by sequencing the microbiome with three different approaches: 16S rRNA amplicon sequencing, shotgun DNA and shotgun RNA. This comparative analysis revealed that, in amplicon sequencing, abundance of some taxa (Euryarchaeota and Spirochaetes) was biased by the inefficiency of universal primers to hybridize all the templates. Reliability of the results obtained was also influenced by the number of hypervariable regions under investigation. Finally, amplicon sequencing and shotgun DNA underestimated the Methanoculleus genus, probably due to the low 16S rRNA gene copy number encoded in this taxon.
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