Accessing Dietary Effects on the Rumen Microbiome: Different Sequencing Methods Tell Different Stories

Abstract

The current study employed both amplicon and shotgun sequencing to examine and compare the rumen microbiome in Angus bulls fed with either a backgrounding diet (BCK) or finishing diet (HG), to assess if both methods produce comparable results. Rumen digesta samples from 16 bulls were subjected for microbial profiling. Distinctive microbial profiles were revealed by the two methods, indicating that choice of sequencing approach may be a critical facet in studies of the rumen microbiome. Shotgun-sequencing identified the presence of 303 bacterial genera and 171 archaeal species, several of which exhibited differential abundance. Amplicon-sequencing identified 48 bacterial genera, 4 archaeal species, and 9 protozoal species. Among them, 20 bacterial genera and 5 protozoal species were differentially abundant between the two diets. Overall, amplicon-sequencing showed a more drastic diet-derived effect on the ruminal microbial profile compared to shotgun-sequencing. While both methods detected dietary differences at various taxonomic levels, few consistent patterns were evident. Opposite results were seen for the phyla Firmicutes and Bacteroidetes, and the genus Selenomonas. This study showcases the importance of sequencing platform choice and suggests a need for integrative methods that allow robust comparisons of microbial data drawn from various omic approaches, allowing for comprehensive comparisons across studies.

Using a multi-omics approach to explore potential associations with rumen content and serum of cows with different milk production levels based on genomic predicted transmitting ability for milk and phenotypic milk production

“…There was a total of 2,376,039,364 unmapped reads across all samples, with 327,090,238 mapped reads. Thus, 12.1% of reads were successfully aligned which is similar to that observed in other studies for rumen content [ 24 ]. From a total of 1,368,211,945 input reads across all samples, 14,768,103 or 1.1% of the reads were classified to a specific taxonomic group, which is comparable to the percentage classified in other studies [ 11 ].…”

Rumen microbiome response to sustained release mineral bolus supplement with low- and high-quality forages

“…Rumen bacterial communities were predominated by members of the phyla Bacteriodota and Fermicutes which is consistent with other studies (Myer et al, 2015;Liu et al, 2016;Gharechahi et al, 2021;Zhou et al, 2021). The genus Prevotella, a member of the phylum Bacteriodota, was strongly associated with the high-quality forage diet 8 hours post feeding (Figure 3).…”

Distinctive roles between rumen epimural and content bacterial communities on beef cattle feed efficiency: A combined analysis

“…As such we were not able to provide direct evidence of the functional differences between RC and RT communities. While the identified predominant microbiota was different between using 16S rRNA gene amplicon-based method (current study) and using functional gene-based method ( Li and Guan, 2017 ; Zhou et al., 2021 ), and different phylotypes of the same genus may have diverse functions (e.g. a broad range of fermentation potentials reported from different Prevotella species) ( Zhao et al., 2014 ; Hernandez-Sanabria et al., 2012 ), better sequence resolution may also help to classify the microbial phylotypes at more detailed phylogenic levels (e.g.…”