Author Correction: Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle.

The current research was carried out to determine the associations between the rumen microbiota and traits related with feed efficiency in a Holstein cattle population (n = 30) using whole metagenome sequencing. Improving feed efficiency (FE) is important for a more sustainable livestock production. The variability for the efficiency of feed utilization in ruminants is partially controlled by the gastrointestinal microbiota. Modulating the microbiota composition can promote a more sustainable and efficient livestock. This study revealed that most efficient cows had larger relative abundance of Bacteroidetes (P = 0.041) and Prevotella (P = 0.003), while lower, but non-significant (P = 0.119), relative abundance of Firmicutes. Methanobacteria (P = 0.004) and Methanobrevibacter (P = 0.003) were also less abundant in the high-efficiency cows. A de novo metagenome assembly was carried out using de Bruijn graphs in MEGAHIT resulting in 496,375 contigs. An agnostic pre-selection of microbial contigs allowed high classification accuracy for FE and intake levels using hierarchical classification. These microbial contigs were also able to predict FE and intake levels with accuracy of 0.19 and 0.39, respectively, in an independent population (n = 31). Nonetheless, a larger potential accuracy up to 0.69 was foreseen in this study for datasets that allowed a larger statistical power. Enrichment analyses showed that genes within these contigs were mainly involved in fatty acids and cellulose degradation pathways. The findings indicated that there are differences between the microbiota compositions of high and low-efficiency animals both at the taxonomical and gene levels. These differences are even more evident in terms of intake levels. Some of these differences remain even between populations under different diets and environments, and can provide information on the feed utilization performance without information on the individual intake level.

Modulation of rumen pH by sodium bicarbonate and a blend of different sources of magnesium oxide in lactating dairy cows submitted to a concentrate challenge.

With the objective of evaluating the potential effects of sodium bicarbonate or a magnesium-based product on rumen pH and milk performance of dairy cattle exposed to a dietary challenge, 30 lactating Holstein cows (648 ± 67 kg of body weight; 44.4 ± 9.9 kg/d of milk yield; 155 ± 75 d in milk) were blocked by parity (9 primiparous and 21 multiparous) and randomly distributed to 3 treatment groups. One group received a total mixed ration (TMR) that acted as a control (CTR), a second group (SB) received the same TMR but with an additional supplementation of 0.8% of sodium bicarbonate, and a third group (MG) received the same TMR as CTR but an additional supplementation of 0.4% of a magnesium-based product (pHix-Up, Timab, Dinard, France). After 1 wk of exposure to this TMR, all 3 rations were supplemented with 1 kg/d of barley, which was then increased 1 kg/wk until reaching 3 kg/d of barley during wk 4 of the study. Every kilogram of barley replaced 1 kg of forage in the diet. Individual feed intake and behavior were monitored using electronic feed bins. Seven cows per treatment were equipped with an intraruminal bolus that recorded pH every 15 min. As the severity of the barley challenge increased, dry matter intake decreased, but this decrease was more pronounced in SB cows than in MG cows, with an intermediate response for CTR cows. The MG cows produced more milk when challenged with 2 or 3 kg/d of additional barley than when challenged with 1 kg/d, whereas CTR cows produced less milk with the 3 kg/d challenge compared with 1 or 2 kg/d, and the SB cows maintained milk production. Milk fat content decreased with barley challenges, with CTR cows experiencing a more severe decrease than SB cows, which maintained stable butterfat values throughout the study, and MG cows showed a decline in milk fat content only with the 3 kg/d of additional barley. Meal size was also reduced as the severity of barley challenge increased, and this reduction was more modest in MG cows than in SB cows. The number of daily meals consumed by SB and MG cows was more constant than that recorded in CTR cows. Cows on the CTR and SB treatments showed a marked decrease in rumen pH with the 3 kg/d of additional barley, whereas MG cows maintained stable rumen pH during the barley challenges and had greater average rumen pH (5.93 ± 0.04) than CTR cows (5.83 ± 0.04) with the 3 kg/d of additional barley; SB cows showed intermediate values (5.85 ± 0.04). Last, MG cows spent less time (32.3 ± 6.1%) with rumen pH ≤5.8 when exposed to the 3 kg/d of barley challenge than CTR and SB cows (50.7 ± 5.02%). In conclusion, supplementation with MG prevents the decline in dry matter intake and milk production induced by a rumen challenge, whereas supplementation with SB prevents the decay in milk production but does not prevent the decrease in feed intake. These changes were probably due to the ability of the MG treatment to prevent a reduction in rumen pH when challenging cows with 3 kg/d of additional barley in the ration.

Consequences of supplying methyl donors during pregnancy on the methylome of the offspring from lactating and non-lactating dairy cattle.

The aim of this study was to evaluate the potential effects of methyl donor supplementation of pregnant animals in the presence or absence of a concomitant lactation on the methylome of the offspring. Twenty Holstein cows, 10 nulliparous (non-lactating while pregnant) and 10 multiparous (lactating while pregnant) were blocked by parity and randomly assigned to an i.m. weekly injections of a placebo (CTRL) or a solution containing methyl donors (MET). After calving, 5 calves randomly selected from each treatment (two born to non-lactating and three to lactating dams) were blood-sampled to determine their full methylome. There were more than 2,000 CpG differentially methylated between calves born to CTRL and those born to MET, and also between calves born to lactating and non-lactating dams. Most of the differences affected genes involved in immune function, cell growth regulation and differentiation, kinase activity, and ion channeling. We conclude that the coexistence of pregnancy and lactation affects the methylome of the offspring, and that supplementation of methyl donors early in gestation has also consequences on the methylome.