ArticlePeerJ2016
A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms.
Article in PeerJ, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- Short- and long-term dietary supplementation as well as withdrawal of the enteric methane inhibitor 3-nitrooxypropanol reveal distinct effects on the rumen microbial community.Journal of animal science and biotechnology · 2025Article
- Ruminal Fistulation and Cannulation: A Necessary Procedure for the Advancement of Biotechnological Research in Ruminants.Animals : an open access journal from MDPI · 2021Review
- Microorganism's adaptation of Crucian carp may closely relate to its living environments.MicrobiologyOpen · 2019Article
- Analysis of Bacterial Diversity in Different Heavy Oil Wells of a Reservoir in South Oman with Alkaline pH.Scientifica · 2018Article
- A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome.BMC microbiology · 2017Article
- Analysis and comparison of the wolf microbiome under different environmental factors using three different data of Next Generation Sequencing.Scientific reports · 2017Article
- Individual Signatures Define Canine Skin Microbiota Composition and Variability.Frontiers in veterinary science · 2017Article
- Genomic analyses of multidrug resistant Pseudomonas aeruginosa PA1 resequenced by single-molecule real-time sequencing.Bioscience reports · 2016Article
- Linking Peripartal Dynamics of Ruminal Microbiota to Dietary Changes and Production Parameters.Frontiers in microbiology · 2016Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained from different platforms and analyze their effect on microbial community structure. In the present study, we compared sequencing data from both the 454 and Ion Torrent (PGM) platforms on the same DNA samples obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in the number of reads, error rate and length of reads among both platforms, we identified similar community composition between the two data sets. Procrustes analysis revealed similar correlations (M (2) = 0.319; P = 0.001) in the microbial community composition between the two platforms. Both platforms revealed the abundance of the same bacterial phyla which were Bacteroidetes and Firmicutes; however, PGM recovered an additional four phyla. Comparisons made at the genus level by each platforms revealed differences in only a few genera such as Prevotella, Ruminococcus, Succiniclasticum and Treponema (p < 0.05; chi square test). Collectively, we conclude that the output generated from PGM and 454 yielded concurrent results, provided stringent bioinformatics pipelines are employed.
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