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 (M2 = 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.
Highlights
Microbes are integral components of a diverse group of ecosystems and have co-evolved with their host/habitat in a mutually symbiotic relationship (Hobson & Stewart, 1997)
The transition period in dairy cows refers to a critical phase in the lactation cycle, lasting from three weeks before calving to three weeks post-calving, where the dairy cow experiences stress due to changes in diet, metabolism and physiological status
At the genus level, Prevotella was abundant in both platforms, the lower abundance of Prevotella observed in Ion Torrent compared to Roche 454 may be due to an increase in number (14) of several genera that were not detected in the Roche 454 data. Despite these differences at the genus level, the effect of age and diet on different bacterial genera in the rumen of dairy cows was consistent between the two platforms. It has become evident in the recent past that the rumen microbiome plays a significant role in improving the production efficiencies of dairy cows
Summary
Microbes are integral components of a diverse group of ecosystems and have co-evolved with their host/habitat in a mutually symbiotic relationship (Hobson & Stewart, 1997). The foregut (rumen) of ruminants is comprised of a complex microbial genetic web (rumen microbiome) that plays a pivotal role in the host nutrition and ultimate wellbeing of the animals (Hobson & Stewart, 1997). Elucidation of the interactions among microbial domains in dairy cows has the potential to improve production such as feed efficiency and milk fat synthesis (Weimer, 2015). The dynamics of rumen bacteria during the transition period has received attention in the recent past (Lima et al, 2015; Pitta et al, 2014; Wang et al, 2012), further studies are required to understand the rumen microbial dynamics during the different phases of lactation across a large group of dairy cows
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