ArticleFrontiers in microbiology2020
Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis.
Article in Frontiers in microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Integrative analysis of the meibum microbiome in dry eye disease: from dysbiosis and diagnostic biomarkers to immunomodulation by Bradyrhizobium-derived outer membrane vesicles.Journal of translational medicine · 2026Article
- Microbial colonisation of the neonatal beef calf gastrointestinal tract: limited influence of birth delivery method across five anatomical regions.Frontiers in microbiology · 2026Article
- System design and habitat type drive microbial communities in recirculating aquaculture systems: comparison of conventional fish-only and sustainable aquaponic systems.Frontiers in microbiology · 2026Article
- Associations between subclinical bovine respiratory disease, growth patterns, and the nasal and fecal microbiota in dairy replacement heifers: a retrospective study.Frontiers in veterinary science · 2026Article
- Characterisation of the bacterial and archaeal microbiota in processed colostrum collected from a spring-calving dairy herd.PloS one · 2026Article
- Mushroom stem-based diets elicit region-specific shifts in rainbow trout gut microbiota.Scientific reports · 2025Article
- Article
- Anatomical site and environmental exposure differentially shape the microbiota across mucosal tissues in rainbow trout (Oncorhynchus mykiss).Scientific reports · 2025Article
- Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?Poultry science · 2025Review
- 16S rRNA metabarcoding applied to the microbiome of insect products (novel food): a comparative analysis of three reference databases.Italian journal of food safety · 2025Article
- The inclusion of a companion legume or herb, in combination with perennial ryegrass increased growth performance and reduced enteric methane emissions in lambs postweaning.Journal of animal science · 2025Article
- Temporal establishment of the colon microbiota in Angus calves from birth to post-weaning.PloS one · 2025Article
- Characterisation of the bacterial and archaeal microbiota in fresh colostrum collected from a single, spring-calving dairy herd.PloS one · 2025Article
- Impact of the diet in the gut microbiota after an inter-species microbial transplantation in fish.Scientific reports · 2024Article
- Sward type alters enteric methane emissions, nitrogen output and the relative abundance of the rumen microbial ecosystem in sheep.Journal of animal science · 2024Article
- Methane emissions and rumen microbiome response during compensatory growth on either a forage or grain-based finishing diet in beef cattle.Translational animal science · 2024Article
- Health-associated changes of the fecal microbiota in dairy heifer calves during the pre-weaning period.Frontiers in microbiology · 2024Article
- Comparative study of the gut microbial communities collected by scraping and swabbing in a fish model: a comprehensive guide to promote non-lethal procedures for gut microbial studies.Frontiers in veterinary science · 2024Article
- The potential of a combination of pungent spices as a novel supplement in gilthead seabream (Frontiers in immunology · 2023Article
- Modulation of gut microbiota and intestinal immune response in gilthead seabream (Frontiers in microbiology · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Our understanding of complex microbial communities, such as those residing in the rumen, has drastically advanced through the use of high throughput sequencing (HTS) technologies. Indeed, with the use of barcoded amplicon sequencing, it is now cost effective and computationally feasible to identify individual rumen microbial genera associated with ruminant livestock nutrition, genetics, performance and greenhouse gas production. However, across all disciplines of microbial ecology, there is currently little reporting of the use of internal controls for validating HTS results. Furthermore, there is little consensus of the most appropriate reference database for analyzing rumen microbiota amplicon sequencing data. Therefore, in this study, a synthetic rumen-specific sequencing standard was used to assess the effects of database choice on results obtained from rumen microbial amplicon sequencing. Four DADA2 reference training sets (RDP, SILVA, GTDB, and RefSeq + RDP) were compared to assess their ability to correctly classify sequences included in the rumen-specific sequencing standard. In addition, two thresholds of phylogenetic bootstrapping, 50 and 80, were applied to investigate the effect of increasing stringency. Sequence classification differences were apparent amongst the databases. For example the classification of
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