Background:The Boran (Bos indicus), indigenous Zebu cattle breed from subSaharan Africa, is remarkably well adapted to harsh tropical environments. Due to financial constraints and low-quality forage, African livestock are rarely fed at 100% maintenance energy requirements (MER) and the effect of sub-optimal restricted feeding on the rumen microbiome of African Zebu cattle remains largely unexplored. We collected 24 rumen fluid samples from six Boran cattle fed at suboptimal and optimal MER levels and characterised their rumen microbial composition by performing shotgun metagenomics and de novo assembly of metagenome-assembled genomes (MAGs). These MAGs were used as reference database to investigate the effect of diet restriction on the composition and functional potential of the rumen microbiome of African cattle.

Results: We report 1200 newly discovered MAGs from the rumen of Boran cattle. A total of 850 were dereplicated, and their uniqueness confirmed with pairwise comparisons (based on Mash distances) between African MAGs and other publicly available genomes from the rumen. A genome-centric investigation into sub-optimal diets highlighted a statistically significant effect on rumen microbial abundance profiles and a previously unobserved relationship between whole microbiome shifts in functional potential and taxon-level associations in metabolic pathways.

Conclusions: This study is the first to identify 1200 high-quality African rumen specific MAGs and provides further insight into the rumen function in harsh environments with food scarcity. The genomic information from the rumen microbiome of an indigenous African cattle breed sheds light on the microbiome contribution to rumen functionality and constitutes a vital resource in addressing food security in developing countries.

Effects of feeding levels below maintenance requirements of metabolizable energy (MER) and of feed supplementation on fecal nutrient and microbial C concentrations were evaluated. In experiment 1, Rhodes grass hay only was offered to Boran steers at 80%, 60%, and 40% of individual MER, while steers at 100% MER additionally received a concentrated mixture. This reduction in MER decreased N, increased fungal C but did not affect bacterial C concentrations in feces. In experiment 2, Holstein × Boran heifers were offered a poor-quality roughage diet without supplement, with sweet potato vine silage or with a urea-molasses block. These two supplements did not affect the fecal chemical composition or fungal C but increased bacterial C concentrations in feces. Across all data, the fungal C/bacterial C ratio was positively related to N and negatively to neutral detergent fiber concentrations in feces, indicating diet-induced shifts in the fecal microbial community.

The relationship between feed intake at production levels and enteric CH₄ production in ruminants consuming forage-based diets is well described and considered to be strongly linear. Unlike temperate grazing systems, the intake of ruminants in rain-fed tropical systems is typically below maintenance requirements for part of the year (dry seasons). The relationship between CH₄ production and feed intake in animals fed well below maintenance is unexplored, but changes in key digestive parameters in animals fed at low levels suggest that this relationship may be altered. We conducted a study using Boran yearling steers (n 12; live weight: 162·3 kg) in a 4 × 4 Latin square design to assess the effect of moderate to severe undernutrition on apparent digestibility, rumen turnover and enteric CH₄ production of cattle consuming a tropical forage diet. We concluded that while production of CH₄ decreased (1133·3–65·0 g CH₄/d; P < 0·0001), over the range of feeding from about 1·0 to 0·4 maintenance energy requirement, both CH₄ yield (29·0−31·2 g CH₄/kg DM intake; P < 0·001) and CH₄ conversion factor (Y_m 9·1–10·1 MJ CH₄/MJ gross energy intake; P < 0·01) increased as intake fell and postulate that this may be attributable to changes in nutrient partitioning. We suggest there is a case for revising emission factors of ruminants where there are seasonal nutritional deficits and both environmental and financial benefits for improved feeding of animals under nutritional stress.

In Africa, cattle are often fed low quality tropical roughages resulting in low yielding animals with high methane (CH₄) emission intensity (EI, g CH₄/per unit of product). Supplementation with protein is known to improve the nutritive value of the otherwise low-quality diets. However, animal nutrition studies in East Africa that are accompanied by CH₄ emission measurements are lacking. Thus, an animal experiment was conducted to quantify the effect of supplementing cattle fed mainly on low-quality Urochloa brizantha hay (control diet; CON; crude protein (CP) = 7.4%) or supplemented with either a tannin-rich leguminous fodder, Desmodium intortum hay (DES) or a commercial dairy concentrate (CUBES) on voluntary dry matter intake (DMI), nutrient apparent total tract digestibility, nitrogen (N) retention, enteric CH₄ production and animal performance (milk and average daily gain). Twelve midlactating crossbred (Friesian × Boran) cows (initial liveweight = 335 kg) were used in a 3×3 (Period × Diet) Latin square design with each period running for four weeks. Compared to CON, DES decreased nutrient (DM, OM, CP) intake, apparent total tract digestibility and daily milk yield. In contrast, CUBES increased nutrient intake and animal performance compared to CON, while nutrients’ apparent total tract digestibility was not different, except for CP digestibility that increased. Compared to CON, DES and CUBES improved overall N retention by the animals as a proportion of N intake. The DES diet compared with CON and CUBES, shifted the proportion of N excretion via urine to the fecal route, likely because of its tannin content. Both DES and CUBES, compared to CON, reduced methane yield (MY, g CH₄/kg DMI) by 15% and 9%, respectively. The DES diet reduced absolute enteric CH₄ emissions by 26% while CUBES increased emissions by 11% compared to CON. Based on the present findings, high supplementation levels (>50%) of Desmodium intortum hay is not recommended especially when the basal diet is low in CP content. Supplementation with lower levels of better managed Desmodium intortum forage however, need to be investigated to establish optimal inclusion levels that will improve animal productivity and reduce environmental impact of livestock in smallholder tropical contexts.