Next-generation sequencing has taken a central role in studies of microbial ecology, especially with regard to culture-independent methods based on molecular phylogenies of the small-subunit ribosomal RNA gene (16S rRNA gene). The ability to relate trends at the species or genus level to host/environmental parameters using 16S profiling has proven powerful. Within the rumen and lower gastrointestinal tract (GIT), the diverse microbial ecosystems present are essential for the host to digest plant material and regulate nutrient uptake and utilization. Their examination utilizing next-generation technologies has been instrumental to aid in the understanding of the microbial-associated interactions throughout the gut with intake, growth, and feed efficiency. Using a feed efficiency design in which steers were selected from two contemporary groups and were ranked based on their standardized distance from the bivariate mean (ADG and ADFI), four steers with the greatest deviation within each Cartesian quadrant were sampled (n = 16/group; 2 groups) to examine the association of the microbiome throughout the gut with ADG, average daily DMI (ADFI), and feed efficiency. In addition, phylogenetic analyses of the ruminal bacterial community were compared based on varying sequencing technologies, 16S variable region selection, and short read 16S amplicons, near full-length 16S amplicons, and metagenomic sequence. In all studies, although no differences in bacterial diversity and richness metrics were revealed among the quadrants, finer changes in the relative abundance of microbial populations and operational taxonomic units did reveal differences between feed efficiency groups (P < 0.05), suggesting throughout the GIT, the microbial communities differ at the 16S level in cattle that vary in ADG, ADFI, and feed efficiency. However, additional phylogenetic analyses on the rumen bacterial community demonstrated that utilizing near full-length 16S reads may be useful in conducting a more thorough study, or for developing a niche-specific database to utilize in analyzing data from shorter read technologies when budgetary constraints preclude use of near-full length 16S sequencing. Partially funded by National Institute of Food and Agriculture Grant no. 2011–68004–30214, National Program for Genetic Improvement of Feed Efficiency in Beef Cattle.
Research regarding the association between the microbial community and host feed efficiency in cattle has primarily focused on the rumen. However, the various microbial populations within the gastrointestinal tract as a whole are critical to the overall well-being of the host and need to be examined when determining the interplay between host and nonhost factors affecting feed efficiency. The objective of this study was to characterize the microbial communities of the jejunum among steers differing in feed efficiency. Within 2 contemporary groups of steers, individual ADFI and ADG were determined from animals fed the same diet. At the end of each feeding period, steers were ranked based on their standardized distance from the bivariate mean (ADG and ADFI). Four steers with the greatest deviation within each Cartesian quadrant were sampled ( = 16/group; 2 groups). Bacterial 16S rRNA gene amplicons were sequenced from the jejunum content using next-generation sequencing technology. The phylum Firmicutes accounted for up to 90% of the populations within all samples and was dominated by the families Clostridiaceae and Ruminococcaceae. UniFrac principal coordinate analyses did not indicate any separation of microbial communities within the jejunum based on feed efficiency phenotype, and no significant changes were indicated by bacterial diversity or richness metrics. The relative abundances of microbial populations and operational taxonomic units did reveal significant differences between feed efficiency groups ( < 0.05), including the phylum Proteobacteria ( = 0.030); the families Lachnospiraceae ( = 0.035), Coriobacteriaceae ( = 0.012), and Sphingomonadaceae ( = 0.035); and the genera ( = 0.019), ( = 0.018), and ( = 0.022). The study identified jejunal microbial associations with feed efficiency, ADG, and ADFI. This study suggests the association of the jejunum microbial community as a factor influencing feed efficiency at the 16S level.
Ruminal microbial fermentation plays an essential role in host nutrition, and as a result, the rumen microbiota have been a major focus of research examining bovine feed efficiency. Microbial communities within other sections of the gastrointestinal tract may also be important with regard to feed efficiency, since it is critical to the health and nutrition of the host. The objective of this study was to characterize the microbial communities of the colon among steers differing in feed efficiency. Individual feed intake (FI) and body weight (BW) gain were determined from animals fed the same ration, within two contemporary groups of steers. Four steers from each contemporary group within each Cartesian quadrant were sampled (n = 16/group) from the bivariate distribution of average daily BW gain and average daily FI. Bacterial 16S rRNA gene amplicons were sequenced from the colon content using next-generation sequencing technology. Within the colon content, UniFrac principal coordinate analyses did not detect any separation of microbial communities, and bacterial diversity or richness did not differ between efficiency groups. Relative abundances of microbial populations and operational taxonomic units did reveal significant differences between efficiency groups. The phylum Firmicutes accounted for up to 70% of the populations within all samples, and families Ruminococcaceae and Clostridiaceae were highly abundant. Significant population shifts in taxa were detected, including the families Ruminococcaceae, Lachnospiraceae, and Sphingomonadaceae, and the genera Butyrivibrio, Pseudobutyrivibrio, Prevotella, Faecalibacterium and Oscillospira. This study suggests the association of the colon microbial communities as a factor influencing feed efficiency at the 16S level.
We report the complete genome sequence of <i>Ligilactobacillus animalis</i> strain NP51, a probiotic strain used extensively in the beef cattle industry.
No abstract is provided for this article.
These data were collected from Angus heifers during a feed efficiency trial. Data were collected using an iStat per manufacturer protocol.
The diverse rumen microbiome converts low-quality feedstuffs into usable energy and provides approximately 70% of the energy required by its ruminant host through fermentation byproducts. Due to microbial impacts on host health and productivity, numerous studies have associated rumen microbiome variation with important sustainability phenotypes, such as feed efficiency and methane emissions. Although diet, genetics, and environment contribute to variation in feed efficiency, selection for feed-efficient beef cattle using genetic improvement technologies has helped to understand and improve the persistence and longevity of such phenotypes within the herd. While diet has been considered to be the primary driver for the composition and structure of the rumen microbiome, recent studies have indicated the microbial communities present in the rumen are under low-to-moderate host genetic control. The mutualistic, commensal, and parasitic microorganisms that reside in the rumen and lower gastrointestinal tract of cattle and other ruminants exert enormous influence over animal physiology and performance. The ability to interrogate these systems at great depth has permitted a greater understanding of the microbiological and molecular mechanisms involved in ruminant nutrition and health. The work in our group in the field of beef cattle gut microbiology, as it relates to feed efficiency, permits the exploration of these critical microbial community networks. This knowledge will aid researchers seeking to address the grand challenge of maintaining host-efficient gut microbiomes throughout cattle production operations. This work is supported by the Agriculture and Food Research Initiative grant no. 2020-67015-30832 from the USDA National Institute of Food and Agriculture.
The cattle rumen has a diverse microbial ecosystem that is essential for the host to digest plant material. Extremes in body weight (BW) gain in mice and humans have been associated with different intestinal microbial populations. The objective of this study was to characterize the microbiome of the cattle rumen among steers differing in feed efficiency. Two contemporary groups of steers (n=148 and n=197) were fed a ration (dry matter basis) of 57.35% dry-rolled corn, 30% wet distillers grain with solubles, 8% alfalfa hay, 4.25% supplement, and 0.4% urea for 63 days. Individual feed intake (FI) and BW gain were determined. Within contemporary group, the four steers within each Cartesian quadrant were sampled (n=16/group) from the bivariate distribution of average daily BW gain and average daily FI. Bacterial 16S rRNA gene amplicons were sequenced from the harvested bovine rumen fluid samples using next-generation sequencing technology. No significant changes in diversity or richness were indicated, and UniFrac principal coordinate analysis did not show any separation of microbial communities within the rumen. However, the abundances of relative microbial populations and operational taxonomic units did reveal significant differences with reference to feed efficiency groups. Bacteroidetes and Firmicutes were the dominant phyla in all ruminal groups, with significant population shifts in relevant ruminal taxa, including phyla Firmicutes and Lentisphaerae, as well as genera Succiniclasticum, Lactobacillus, Ruminococcus, and Prevotella. This study suggests the involvement of the rumen microbiome as a component influencing the efficiency of weight gain at the 16S level, which can be utilized to better understand variations in microbial ecology as well as host factors that will improve feed efficiency.
Biochar, a byproduct from the biofuels industry, may be a potential feed additive in ruminant diets due to possible improvements in microbial fermentation. Therefore, the objective of this study was to determine the nutritive value, in vitro digestibility, volatile fatty acid (VFA) production, and gas production of biochar inclusion to an orchard grass (Dactylis glomerata) basal diet. The study was designed as a 3 × 2 factorial arrangement with 3 different biochar sources and 2 biochar processed sizes as the main effects factors. Experimental treatments were biochar from 3 different tree types: 1) Chestnut Oak (Quercus prinus L.; CO), 2) Yellow Poplar (Liriodendron tulipifera; YP), or 3) White Pine (Pinus strobus L.; WP), and processed at 2 different biochar particle sizes: a) μm (Fine) or b) >178 μm (Coarse). Biochar was added to the basal diet of orchard grass hay (872.35 g/kg of DM, 98.31 g/kg of CP, and 704.02 g/kg of aNDF, DM basis) at a rate of 81 g/kg DM. Biochar residual ash content was greater (P < 0.01) for Fine particle size and greater (P < 0.01) for CO and YP biochar sources. Biochar aNDF content exhibited a type × size interaction (P = 0.01) with lower aNDF content in both WP sizes compared with their respective biochar type and size. Gas production was not influenced (P = 0.23) by biochar tree type; however, gas production was increased (P = 0.05) by Fine particle size compared with Coarse biochar. The in vitro true digestibility (IVTD) of orchard grass hay was increased (P = 0.01) by the inclusion of Fine biochar particle size compared with Coarse particle size. Additionally, in vitro CP true digestibility (DCP) exhibited a type × size interaction (P = 0.01). Crude protein digestibility was lower for Fine particle-sized CO and WP biochar sources compared with Coarse particle-sized CO and WP (P ≤ 0.004). However, DCP was not different between Coarse and Fine particlesized YP biochar (P = 0.70). Volatile fatty acids (acetate, propionate, and butyrate) were not altered by biochar type (P ≥ 0.66) or particle size (P≥ 0.19). These results indicate that both tree type and particle size of biochar may need to be carefully considered before incorporating into a ruminant diet. Furthermore, Fine particle-sized biochar may be the most effective to incorporate as a feed additive in a ruminant diet based on digestibility parameters.
