Multi-omics revealed the long-term effect of ruminal keystone bacteria and the microbial metabolome on lactation performance in adult dairy goats

BACKGROUND

The increased growth rate of young animals can lead to higher lactation performance in adult goats; however, the effects of the ruminal microbiome on the growth of young goats, and the contribution of the early-life rumen microbiome to lifelong growth and lactation performance in goats has not yet been well defined. Hence, this study assessed the rumen microbiome in young goats with different average daily gains (ADG) and evaluated its contribution to growth and lactation performance during the first lactation period.

RESULTS

Based on monitoring of a cohort of 99 goats from youth to first lactation, the 15 highest ADG (HADG) goats and 15 lowest ADG (LADG) goats were subjected to rumen fluid microbiome and metabolome profiling. The comparison of the rumen metagenome of HADG and LADG goats revealed that ruminal carbohydrate metabolism and amino acid metabolism function were enhanced in HADG goats, suggesting that the rumen fluid microbiome of HADG goats has higher feed fermentation ability. Co-occurrence network and correlation analysis revealed that Streptococcus, Candidatus Saccharimonans, and Succinivibrionaceae UCG-001 were significantly positively correlated with young goats' growth rates and some HADG-enriched carbohydrate and protein metabolites, such as propionate, butyrate, maltoriose, and amino acids, while several genera and species of Prevotella and Methanogens exhibited a negative relationship with young goats' growth rates and correlated with LADG-enriched metabolites, such as rumen acetate as well as methane. Additionally, some functional keystone bacterial taxa, such as Prevotella, in the rumen of young goats were significantly correlated with the same taxa in the rumen of adult lactation goats. Prevotella also enriched the rumen of LADG lactating goats and had a negative effect on rumen fermentation efficiency in lactating goats. Additional analysis using random forest machine learning showed that rumen fluid microbiota and their metabolites of young goats, such as Prevotellaceae UCG-003, acetate to propionate ratio could be potential microbial markers that can potentially classify high or low ADG goats with an accuracy of prediction of > 81.3%. Similarly, the abundance of Streptococcus in the rumen of young goats could be predictive of milk yield in adult goats with high accuracy (area under the curve 91.7%).

CONCLUSIONS

This study identified the keystone bacterial taxa that influence carbohydrate and amino acid metabolic functions and shape the rumen fluid microbiota in the rumen of adult animals. Keystone bacteria and their effects on rumen fluid microbiota and metabolome composition during early life can lead to higher lactation performance in adult ruminants. These findings suggest that the rumen microbiome together with their metabolites in young ruminants have long-term effect on feed efficiency and animal performance. The fundamental knowledge may allow us to develop advanced methods to manipulate the rumen microbiome and improve production efficiency of ruminants. Video Abstract.

Growth rate and behaviour in separated, partially separated or non-separated kids and the corresponding milk production of their mothers

We address the hypothesis that keeping kids and mothers together would have positive effects on the milk composition of the mother and the behaviour of the kids. Kids were either permanently separated (SEP), daily separated between 7.30 and 15 h (DAY-SEP) or kept with mothers 24 h/d (NON-SEP). The NON-SEP kids were only allowed to suckle one teat. All kids had similar growth rate throughout the study (lactation days 5-70). DAY-SEP kids spent 24% of their time with their mother at both ages. NON-SEP spent only 15% of the time with their mothers at 2 weeks of age and this increased to 28% at 2 months of age. NON-SEP kids showed more hiding behaviour at 2 weeks and SEP were more active alone, at both 2 weeks and 2 months, compared to the other treatments. The mean available milk yield and fat concentration were higher in DAY-SEP goats (2420 g ± 119 g and 4.9 ± 0.1%) compared with NON-SEP goats (2149 ± 79 g and 4.4 ± 0.1%). There were no differences between DAY-SEP and NON-SEP goats in total protein, lactose, or casein concentrations. Based on these data it was estimated that 7.1 kg milk was needed to produce 1 kg semi-hard cheese in DAY-SEP goats and 7.5 kg in NON-SEP goats, respectively. When comparing milk yield and composition between udder halves, the milk yield was, as expected, higher from the machine milked teat than from the suckled one in the NON-SEP goats but there was no difference between right and left udder halves in DAY-SEP goats. Milk fat concentration varied between teats at morning and afternoon milkings in NON-SEP goats, but there was no difference in milk fat between udder-halves in DAY-SEP goats. In conclusion, the kid growth rate was similar in all treatments, however, an altered behaviour was seen in permanently separated kids (SEP). The results show that it is possible to have a high milk yield and fat concentration with one kid together with the dam.

Review: Milking routines and cluster detachment levels in small ruminants

Small ruminants not only differ on mammary gland anatomy, milk's properties and the amount of milk yielded comparable to those of dairy cattle, but also on the milking routine strategies and machine milking settings to maximize daily milk secretion. The udder compartment is proportionally larger in dairy sheep and goats, which requires modifications in the milking machine settings, milking procedures and allows the use of different milking strategies as they better tolerate extension of milking intervals. Depending on the breed, cisternal milk in goats varies from 70% to 90%, whereas in dairy sheep it varies from 50% to 78% of the total gland capacity. This explains why these species are commonly milked without pre-milking teat preparation, while in goats it is applied only in cases of high prevalence of intramammary infection in the herd. Recent French researchers observed that 40% of the goats presented an unbalanced udder as well as unbalanced morphology (21% to 30%) and functional milk flow (around 10% to 20% more) which could induce overmilking. In dairy sheep, selection for higher milk production increases teat angle insertion. Thus, to increase machine milk fraction, it is recommended to use either the 'Sagi hook' as an alternative for lifting up the 'pendulous' udder during milking or to perform machine stripping. There are three cluster removal strategies for small ruminants: manual, timed and milk flow driven automatic cluster removal (ACR). Automatic cluster removal reduces overmilking, improves teat condition, enables labour saving and provides a consistent milking routine in small ruminants. There are three to five main milk flow profiles in ewes and goats, which result in curves with one or two peaks (or plateau) and different patterns of the milk flow decreasing phase due to the degree of mammary gland imbalance and teat characteristics. When taking into account our current knowledge, ACR recommended take-off settings for goats are: 200 g/min+10 s delay time (DT) for a long decreasing phase or two plateau curves and 500 g/min+5 s DT for a short decreasing phase and one plateau curve. The ACR take-off settings for ewes are: 150 g/min +10 s DT for long decreasing phase and 200 g /min+5 s DT for a short decreasing phase. This review is intended to be useful for scientists and producers seeking basic knowledge of milking routines and cluster detachment settings for parlour performance and milk quality.

Milk processing quality of suckled/milked goats: effects of milk accumulation interval and milking regime

Milk with a high concentration of fat and casein is required for cheese production, and these components have a major impact for both quality and yield of the curd. Recent observations have shown that suckling can elevate milk fat concentration in goats and our aim was therefore to check the hypothesis that animal welfare and cheese-processing properties of goat milk could be optimised by appropriate management of suckled/milked goats. Twelve Swedish dairy goats were kept together with one kid each in 4 different mixed management-systems (milking combined with partial suckling) in a cross-over design. Two milk accumulation intervals were tested; Short = dams and kids were together for 16 h (T16) and Long = ; dams and kids were together for 8 h (T8 h). In addition, two milking regimes were used; Suckled Before Milking = S and Milked Before Suckling = M. Milk accumulation interval referred to how long dams and kids were separated. The milk yield available for processing (milk offtake), was weighed and analysed from each milking occasion and the suckled milk yield was estimated by a weigh-suckle-weigh method (WSW) in combination with observing the suckling behaviour during the free suckling periods. Milking managements, such as 'suckling before milking (S)', increased milk fat concentration compared to milking before suckling (M) and 'Short accumulation treatments (T16)' gave higher milk fat, casein concentration and individual curd yield (%) compared to the 'Long accumulation treatment (T8)'. The total individual curd yield (g) was the same despite treatment, but the animal welfare was most likely higher in T16 where dams and kids spent more time together.

Mammary epithelial cells isolated from milk are a valuable, non-invasive source of mammary transcripts

Milk is produced in the udder by mammary epithelial cells (MEC). Milk contains MEC, which are gradually exfoliated from the epithelium during lactation. Isolation of MEC from milk using immunomagnetic separation may be a useful non-invasive method to investigate transcriptional regulations in ruminants' udder. This review aims to describe the process of isolating MEC from milk, to provide an overview on the studies that use this method to analyze gene expression by qRT PCR and to evaluate the validity of this method by analyzing and comparing the results between studies. In several goat and cow studies, consistent reductions in alpha-lactalbumin mRNA levels during once-daily milking (ODM) and in SLC2A1 mRNA level during feed restriction are observed. The effect of ODM on alpha-lactalbumin mRNA level was similarly observed in milk isolated MEC and mammary biopsy. Moreover, we and others showed decreasing alpha-lactalbumin and increasing BAX mRNA levels with advanced stages of lactation in dairy cows and buffalo. The relevance of using the milk-isolated MEC method to analyze mammary gene expression is proven, as the transcript variations were also consistent with milk yield and composition variations under the effect of different factors such as prolactin inhibition or photoperiod. However, the RNA from milk-isolated MEC is particularly sensitive to degradation. This could explain the differences obtained between milk-isolated MEC and mammary biopsy in two studies where gene expression was compared using qRT-PCR or RNA Sequencing analyses. As a conclusion, when the RNA quality is conserved, MEC isolated from milk are a valuable, non-invasive source of mammary mRNA to study various factors that impact milk yield and composition (ODM, feeding level, endocrine status, photoperiod modulation, and stage of lactation).

The effects of parity, litter size, physiological state, and milking frequency on the metabolic profile of Lacaune dairy ewes

Effects of parity (primiparous, PRIM vs multiparous, MULT) and litter size (singletons, SING vs twins, TWIN) on metabolic profiles from 1 wk before lambing to the end of lactation were studied in 48 Lacaune dairy ewes reared in confinement during most of the year and grazed on improved pastures at the end of lactation (summer). Another group of 48 ewes was incorporated during the milking period (ie, from 1 wk after weaning), to measure the effects of milking frequency (1 vs 2 milkings per day) on intake, milk production and composition, and body energy usage. Thus, in a 2 × 2 × 2 factorial design, ewes (n = 96) were allocated to homogeneous groups according to body weight (BW) and body condition score (BCS) and were monitored from late pregnancy to late lactation as a function of parity (PRIM, n = 48; MULT, n = 48), litter size (LSi) (SING, n = 40; TWIN, n = 56) and daily milking frequency (FREQ; milked once, ONE; n = 48; or twice, TWO; n = 48). Individual BW, BCS, plasma metabolites, and metabolic hormones were measured regularly (ie, 9 consecutive sampling dates). The BW was higher in MULT but no differences because of LSi or FREQ were detected at the intra-parity group level. The BCS was higher in MULT and in ewes with SING throughout the experiment. The latter was related to the demands for body reserves mobilization, as expressed by higher nonesterified fatty acids and β-hydroxybutyrate concentrations in ewes with TWIN from late pregnancy to weaning (35 d postpartum) in both PRIM and MULT ewes. This was consistent with higher insulin in MULT and higher triiodothyronine, leptin and insulin-like growth factor 1 in ewes with SING during this period. Differences in energy balance because of FREQ were evident after interpretation of plasma nonesterified fatty acids, glucose, insulin, and leptin concentration during the milking period. At similar feed intakes, ewes in ONE were in positive balance with regard to TWO. Overall, clear effects of parity, LSi, physiological states, and FREQ on metabolic profiles were found because of differences in nutrient partitioning when combining these experimental factors. Without considering FREQ, changes in metabolic measures in milking period were marginal compared with the periparturient adjustments performed until weaning to compensate energy deficiencies.

Short-term effects of milking frequency on milk yield, milk composition, somatic cell count and milk protein profile in dairy goats

Goats in Canary Islands are milked once a day by tradition, but in most countries with high technology on farms, goats are milked twice a day, which is known to improve milk yield. Therefore it is important to know whether the increase of milking frequency can improve the production without impairing milk quality. The objective of this study was to investigate the short term effects of three milking frequencies on milk yield, milk composition, somatic cell count (SCC) and milk protein profile in dairy goats traditionally milked once a day. Twelve Majorera goats in early lactation (48±4 d in milk) were used. During a 5-week period, goats were milked once a day (X1) in weeks 1 and 5, twice a day (X2) in weeks 2 and 4, and three times a day (X3) in week 3. Milk recording and sampling were done on the last day of each experimental week. Milk yield increased by 26% from X1 to X2. No differences were obtained when goats were switched from X2 to X3, and from X3 to X2. The goats recovered the production level when they returned to X1. Different patterns of changes in the milk constituents due to the milking frequency effect were observed. Fat percentage increased when switched from X1 to X2, then decreased from X2 to X3, and from X3 to X2, whereas it did not show significant differences from X2 to X1. Milking frequency did not affect the protein and lactose percentages. SCC values were unaffected when goats were milked X1, X2 and X3, but then they increased slightly when milking frequency was returned to X2 and X1. Finally, quantitative analysis showed an increase in intensities of milk protein bands from X1 to X2, but the intensities of casein bands (α(S1)-CN, α(S2)-CN, β-CN, κ-CN) and major whey proteins (α-La, β-Lg) decreased from X2 to X3.

An integrated genomics approach to identify genetic regions associated with neonatal growth trait in mice

Neonatal growth during the early post-partum period is closely associated with lactation performance. Neonatal growth reflects milk output and is a complex variable trait among inbred mouse strains, but few studies have compared this trait systematically across more than a few strains. In the present study, 11 inbred strains of mice were measured for a neonatal growth phenotype during the first eight days of lactation. Significant differences in neonatal growth trait were observed with QSi5 (3.71±0.05 g) and DBA/1J (2.67±0.06 g) strains defining the two extremes of the phenotype. In silico association analysis was performed for trait variability using the high density SNP information on inbred strains of mice. We found strong evidence to refine a previously identified large neonatal growth QTL on mouse chromosome 9, Neogq1. When an integrated strategy that combined fine mapping and analysis of mammary transcriptome expression profiles of lactating mice with divergent phenotypes was applied, we identified neogenin (Neo1), a gene important for mammary gland morphogenesis, as a likely quantitative trait gene (QTG) underlying the Neogq1 QTL in mice.

Unilateral once daily milking locally induces differential gene expression in both mammary tissue and milk epithelial cells revealing mammary remodeling

Once daily milking reduces milk yield, but the underlying mechanisms are not yet fully understood. Local regulation due to milk stasis in the tissue may contribute to this effect, but such mechanisms have not yet been fully described. To challenge this hypothesis, one udder half of six Holstein dairy cows was milked once a day (ODM), and the other twice a day (TDM). On the 8th day of unilateral ODM, mammary epithelial cells (MEC) were purified from the milk using immunomagnetic separation. Mammary biopsies were harvested from both udder halves. The differences in transcript profiles between biopsies from ODM and TDM udder halves were analyzed by a 22k bovine oligonucleotide array, revealing 490 transcripts that were differentially expressed. The principal category of upregulated transcripts concerned mechanisms involved in cell proliferation and death. We further confirmed remodeling of the mammary tissue by immunohistochemistry, which showed less cell proliferation and more apoptosis in ODM udder halves. Gene expression analyzed by RT-qPCR in MEC purified from milk and mammary biopsies showed a common downregulation of six transcripts (ABCG2, FABP3, NUCB2, RNASE1 and 5, and SLC34A2) but also some discrepancies. First, none of the upregulated transcripts in biopsies varied in milk-purified MEC. Second, only milk-purified MEC showed significant LALBA downregulation, which suggests therefore that they correspond to a mammary epithelial cell subpopulation. Our results, obtained after unilateral milking, suggest that cell remodeling during ODM is due to a local effect, which may be triggered by milk accumulation.

Effect of sunflower oil supplementation and milking frequency reduction on sheep milk production and composition

The aim of this study was to investigate the effects of milking frequency reduction and dietary lipid supplementation on intake, BW, and milk yield and composition in high yielding dairy ewes. Ten lactating Assaf ewes were allocated into 2 experimental groups (n=5). Ewes were fed alfalfa hay ad libitum and 34 g·kg(-1) of BW of a concentrate feed with either 0 (Control group) or 43 g of sunflower oil·kg(-1) of DM (SO group). The experiment lasted 63 d and consisted of 3 periods. During Period 1 (from d 1 to 21), ewes were milked twice a day. During Period 2 (from d 22 to 49), ewes were unilaterally milked, so that each gland of each ewe was milked either once or twice daily. During Period 3 (from d 50 to the end of the experiment), both udder halves were again milked twice daily. Intake, BW, and milk composition were controlled weekly and milk production from each half udder was recorded twice a week. Total DM intake, BW, and milk yield in Period 1 were not significantly (P>0.10) affected by dietary treatments. Milk yield tended to be increased in the ewes fed the SO diet in periods 2 (P=0.093) and 3 (P=0.067). Oil supplementation (SO diet) significantly (P<0.05) decreased milk protein and total solids concentrations in the 3 experimental periods and fat content in Period 3, and tended (P=0.077) to decline fat content in Period 2. Lactose content and somatic cell count (SCC) were unaffected (P>0.10) by dietary lipid supplementation in any of the experimental periods. There were no significant (P>0.10) differences between half udders in milk yield and composition in Period 1, and in SCC in any of the experimental periods. Fat and total solids contents were unaffected (P>0.10) by reducing milking frequency. Nevertheless, milk protein content was increased (P<0.001) when glands were milked only once daily whereas milk yield and lactose content were decreased (P=0.001). The interaction between gland and diet was significant for lactose in Period 2, suggesting a greater effect of milking frequency reduction on tight junctions in Control ewes. In fact, the ratio between glands for milk yield was significantly (P<0.05) greater in SO (0.82) than in Control (0.72) ewes. In Period 3, this ratio increased but it was still lower in Control ewes (0.92 vs. 0.78, P<0.05). Thus, milking frequency reduction and SO supplementation seem to have counteracting effects on milk production and composition. Our results suggest that SO-supplemented ewes have a better capacity of adaptation to changes in milking frequency, probably due to processes induced in the mammary gland.

Use of milk epithelial cells to study regulation of cell activity and apoptosis during once-daily milking in goats

Generally, once-daily milking (ODM) decreases milk yield. This effect may be the consequence of a decrease in mammary epithelial cell (MEC) activity or a reduction in their number. The aim of this study was to determine the effect of ODM on the synthetic activity and rate of apoptosis of MEC using a non-invasive method. Eight Alpine goats were subjected to ODM or twice-daily milking for two 5-week periods. MECs were purified by centrifugation and immunocytochemical binding in milk after 1 and 5 weeks of each period. mRNA levels of some proteins involved in lactose and milk protein synthesis and in apoptosis were evaluated using real-time PCR. Isolation of MEC from milk was a useful method to investigate transcriptional regulation in a timeline study. ODM induced greater decreases in milk, lactose and protein yields after 1 week than after 5 weeks. This suggests an adaptation of the mammary gland to ODM, which reduces the inhibitory effect of this practice. Reductions in milk component yields were associated with lower α-lactalbumin transcripts, suggesting a transcriptional decrease of lactose synthesis during ODM. Glucose transporter GLUT1 transcripts were downregulated under ODM, suggesting that lactose precursor uptake by MEC might be involved in the regulation of lactose synthesis. κ-Casein mRNA levels tended to be lower during ODM. ODM increased levels of the pro-apoptotic transcript Bax after both 1 and 5 weeks, but no variation was observed in the Bax/Bcl-2 ratio. ODM affected cell synthetic activity through transcriptional regulation and may have induced apoptosis. The reduction of the negative effect of ODM on milk yield suggests that Alpine goats are able to adapt to ODM. Further studies are needed to investigate the effect of ODM on MEC turnover.

Effect of reduction of milking frequency and supplementation of vitamin E and selenium above requirements on milk yield and composition in Assaf ewes

The aim of this research was to study the effect of milking frequency and supplementation with a vitamin-mineral complex above requirements on intake, body weight (BW), and milk yield and composition in high-yielding Assaf ewes. Sixteen lactating Assaf ewes were used in this study, separated into 4 groups of 4 ewes each. Animals in 2 of the groups (control groups) did not receive any extra vitamin-mineral supplement, whereas animals in the other 2 groups (supplement groups) received daily an oral dose of 1g of vitamin E (1,000 IU, DL-α-tocopherol acetate) and 0.4 mg of selenium (sodium selenite anhydrous). The experiment consisted of 2 consecutive periods of 3 wk (twice-daily milking in both mammary glands) and 8 wk (once-daily milking in one mammary gland and twice-daily milking in the other gland). Intake, BW, and milk composition were controlled weekly, and milk production was recorded 3 times a week. Administration of the vitamin-mineral supplement had no effect on dry matter intake, BW, or milk production and composition. The reduction of milking from twice to once a day caused a decrease in milk production and lactose concentration and a significant increase in protein concentration, total solids, and somatic cell count, without affecting the fat content. Administration of a vitamin E and Se supplement at the doses used in the present study does not seem to exert, in the short term, a noticeable effect on the mammary gland when milking frequency is reduced.

Lactation curve and effects of milking regimen on milk yield and quality, and udder health in Martina Franca jennies (Equus asinus)

Three experiments were conducted on Martina Franca jennies. Experiment 1 tested Wood's model for evaluating the lactation curve. Data from the entire lactation period of 12 jennies were used. The results showed that Wood's model was able to recognize the shape of the lactation curve from pooled data (r(2) = 0.11; P < 0.01), with the lactation peak occurring at 48 d. Individual curves showed wide variability. Experiment 2 aimed to evaluate the effects of the daily number of milkings (1, 3, or 6) and the interval between the separation of foals from dams and milking (2 or 3 h) on milk yield and udder health. Four groups of jennies (n = 5) were considered: 1 × 3H, milked once per day (1×) with a 3-h interval from the time of foal removal (3H) from the dams to mechanical milking (3-h interval); 3 × 3H, milked 3 times per day with 3-h intervals; 3 × 2H, milked 3 times per day with 2-h intervals; and 6 × 2H, milked 6 times per day with 2-h intervals. The milk somatic cell count (SCC) was monitored. Better efficiency was observed for 3 vs. 1 milking per day and for 3-h vs. 2-h intervals. The regimen of 6 daily milkings at 2-h intervals did not increase milk yield and was related to an increase in the SCC compared with 3 daily milkings. In Exp. 3, the effects of the interval from foal removal to milking (3, 5, or 8 h) on yield, gross chemical composition, organoleptic characteristics of the milk, and udder health of the jennies were evaluated. The effects of milking time were also evaluated. Twenty jennies milked twice daily (2×) were subdivided into 4 groups (n = 5): 2 × 3H, with milkings at 1200 h and 1900 h and an interval of 3 h; 2 × 5H, milked at 1200 h and 1900 h with a 5-h interval; 2 × 8H(1), milked at 1200 h and 2200 h with an 8-h interval; and 2 × 8H(2), milked at 0700 h and 1900 h with an 8-h interval. Milk yield was greater by 28.4% when an 8-h interval was used compared with a 3-h interval and at the morning vs. the evening milking. The milk yield per milking was greatest at 0700 h, indicating the existence of a circadian rhythm in milk secretion processes. Intervals of 5 and 8 h caused significant decreases in the fat and lactose content and organoleptic characteristics of the milk, whereas an 8-h interval led to an increase in the SCC. In conclusion, a milking regimen of twice-daily milking at 0700 h and 1900 h with an 8-h interval provided the maximum yield per day. In terms of milk quality, a 3-h interval yielded the best results.