Rumen Microbial Population Dynamics Driven By the Interactions Between the Host and Diet in Cattle with Different Feed Efficiencies

Current understanding regarding the impact of interactions between diet and host on the rumen microbiome is limited. The objectives of this study were to: (i) investigate rumen microbial population dynamics in beef cattle fed grain-based (high starch content) and/or forage-based diets (rich in neutral detergent fiber, NDF) over two 80-day feeding periods (with a 20-day adaptation in between) and (ii) evaluate the rumen microbiota of cattle exhibiting different feed efficiencies. Sixty purebred Angus bulls (mean age: 249 ± 22 days; average body weight: 313.9 ± 32 kg; mean ± SD) were raised in confinement at the Glenlea Research Station (University of Manitoba, CA) and randomly assigned into four pens fed the following diets in periods one and two, respectively: pen 1, forage/forage; pen 2, forage/grain; pen 3, grain/forage; and pen 4, grain/grain. Microbial populations were estimated using quantitative PCR (qPCR) for bacteria, archaea, fungi and protozoa from two rumen fluid samples collected per period using a Geishauser oral probe. Thereafter, individual hosts were classified into three groups based on the magnitude of the microbial population shift between each feeding period using log₂-fold change (log₂fc < -1, low; -1 < log₂fc < 1, stable; and log₂fc > 1, high) in 16S rRNA gene copy number for bacteria/archaea and 18S rRNA/ITS (internal transcribed spacer) for protozoa/fungi. The effects of starch/NDF intakes, feed conversion rate (FCR), and CH₄ on the rumen microbes and their interactions with the three groups of host-microbial abundance variation were analyzed through log-normal generalized linear mixed models. Starch intake was associated with a marked decline in bacteria and fungi in the low group (P < 0.001 and P = 0.012, respectively) and NDF consumption increased bacteria and fungi only in the high group (P < 0.011), while no relationship was observed for archaea and protozoa across groups. Cattle in the low group produced more CH₄ as bacteria density increased (P = 0.028), whereas bacterial abundance and CH₄ remained constant in the stable and high groups. Bulls in the stable group were more efficient when linked to a higher bacterial abundance while bulls categorized in the low and high groups utilized the diet more efficiently when associated with the lowest bacteria densities. These findings suggest the potential use of the individualized rumen microbiota in host-tailored precision feeding systems, specially designed to improve feed efficiency in cattle.