Effect of feeding dried distillers grains with solubles on ruminal biohydrogenation, intestinal fatty acid profile, and gut microbial diversity evaluated through DNA pyro-sequencing

Abstract

The objectives of this study were to evaluate the effect of dried distillers grains with solubles (DDGS) on ruminal biohydrogenation and duodenal flow of fatty acids, and to evaluate effects on the ruminal and duodenal microbial community using Roche 454 pyro-sequencing. Three crossbred steers (average BW 780 ± 137 kg) fitted with ruminal and duodenal cannulae were used in a 3-diet, 6-period crossover design. Animals were housed in individual free stalls and fed twice daily at 0700 and 1900 h. Diets (DM basis) were 1) CONTROL, 19.5% corn bran, 20% sorghum silage, 60% brome hay, 0.5% trace minerals, and 0.25% urea, but no DDGS; 2) LOW DDGS, inclusion of 9.75% DDGS replacing equal percentage of corn bran; 3) HIGH DDGS, inclusion of 19.5% DDGS completely replacing corn bran. Feed ingredients and duodenal digesta samples were analyzed for fatty acid composition. The DNA was extracted from isolated mixed ruminal bacterial samples and from intestinal digesta samples. The V1-V3 region of the 16S rRNA gene was sequenced, and bacterial phylogenetic analysis was conducted. Data were analyzed using the MIXED procedure of SAS. Biohydrogenation of C18:1 increased (P < 0.01) with DDGS inclusion; means were 68.3, 75.6, and 79.3 ± 4.3% for CONTROL, LOW DDGS, and HIGH DDGS, respectively. In the same order, means of biohydrogenation of C18:2 (P < 0.05) were 84.1, 91.5, and 93.3 ± 3.4%. Duodenal flow of total fatty acids increased (P < 0.01) with DDGS inclusion; means were 134, 168, and 223 ± 33 g/d for CONTROL, LOW DDGS, and HIGH DDGS, respectively. In the same order, means of C18:0 flow (P < 0.01) were 51, 86, and 121 ± 18 g/d. DDGS did not affect the predominant bacterial phyla in the gut, which were Bacteroidetes (P = 0.62) and Firmicutes (P = 0.71). However, the phylum Fibrobacteres decreased (P < 0.01) when DDGS was fed with means of 5.5, 6.0 and 3.7 ± 0.6% for CONTROL, LOW DDGS, and HIGH DDGS, respectively. Fibrobacteres were lower (P < 0.01) in isolated ruminal bacterial samples compared to duodenal digesta samples with means of 0.1 and 10.1 ± 0.6%, respectively. Overall, the inclusion of DDGS in diets increased ruminal biohydrogenation of C18:1 and C18:2, which increased duodenal flow of C18:0. In addition, the bacterial community of the rumen clustered separately from that of the duodenum suggesting different bacterial diversity between isolated ruminal bacteria and duodenal digesta.

Effect of partially replacing a barley-based concentrate with flaxseed-based products on the rumen bacterial population of lactating Holstein dairy cows

“…Taxonomic analyses at the family and genus levels agree with previous findings using DNA pyrosequencing indicating that the ruminal microbiome is largely composed of the bacterial families Prevotellaceae, Lachnospiraceae and Ruminococcaceae and the genera Prevotella , Succiniclasticum and Ruminococcus (Castillo‐Lopez et al . ). Prevotella , the largest bacterial genus detected, is composed of versatile organisms that can utilize a variety of nutrients including protein, starch, pectins and hemicellulose (Russell ), and has also been reported to predominate in the rumen of cattle being fed forage‐based diets supplemented with corn distillers grains (Ramirez Ramirez et al .…”

“…Compared to other sequencing platforms such as 454 Roche pyrosequencing (Castillo‐Lopez et al . ) or Illumina (Castillo‐Lopez et al . ), the use of ion torrent may have some limitations due to sequencing errors (Frey et al .…”

“…The hypothesis is that, if the treatment affects the microbial community, this effect should be present across multiple animals on the same treatment. Therefore, the analysis of the core microbiome allows identification of the effects that might otherwise be hidden in the data (Benson et al 2010;Castillo-Lopez et al 2014.…”

“…Compared to other sequencing platforms such as 454 Roche pyrosequencing (Castillo-Lopez et al 2014) or Illumina (Castillo-Lopez et al 2017), the use of ion torrent may have some limitations due to sequencing errors (Frey et al 2014;Salipante et al 2014). However, the quality control steps outlined by previous researchers such as initial quality control using the ion Torrent Suite Software, screening for chimeric sequences and preclustering using the pseudo-single linkage-clustering algorithm were specifically aimed at removing erroneous reads.…”

“…This research gap can now be addressed using molecular techniques in combination with bioinformatics, which have enabled researchers to evaluate the impact of diets on bacterial community structure (Krause et al 2013;Chaucheyras-Durand and Ossa 2014;Castillo-Lopez et al 2017). For example, high-throughput DNA sequencing provides new insights into the broad bacterial population of the rumen (Callaway et al 2010;Aldai et al 2012;Castillo-Lopez et al 2014).…”