The Ruminal Microbiome Alterations Associated with Diet-Induced Milk Fat Depression and Milk Fat Globule Size Reduction in Dairy Goats

The aim of this study was to evaluate the effect of conjugated linoleic acid (CLA) on milk fat globule (MFG) size and the ruminal microbiome of goats. Twenty-four mid-lactation Saanen dairy goats weighing 49 ± 4.5 kg (168 ± 27 d in milk, 1.2 ± 0.1 kg milk/d, 2-3 years old) were randomly divided into four groups-a control (CON) group, which was fed a basal diet, and three CLA supplementation groups, in which 30 g CLA (low-dose group, L-CLA), 60 g CLA (medium-dose group, M-CLA), or 90 g CLA (high-dose group, H-CLA) was added to the basal diet daily. The experiment lasted for 21 days, during which time goat milk was collected for composition and MFG size analysis. On day 21 of feeding, ruminal fluid was collected from the CON and H-CLA groups for analysis of the changes in microorganismal abundance. The results showed that CLA supplementation did not affect milk production, milk protein, or lactose content in the dairy goats (p > 0.05), but significantly reduced the milk fat content (p < 0.01) compared with the CON group. The CLA supplementation significantly decreased the D[3,2] and D[4,3] of the MFGs in a dose-dependent manner (p < 0.01). Moreover, dietary CLA inclusion increased the proportion of small-sized MFGs and decreased that of large-sized ones. The results of 16S rRNA gene sequencing showed that CLA-induced milk fat depression in dairy goats was accompanied by significant changes in the relative abundance of ruminal bacterial populations, most of which belonged to the Firmicutes and Bacteroidetes phyla. The relative abundance of Rikenellaceae_RC9_gut_group and Prevolellaceae_UCG-003 in Bacteroidetes and UCG-002, Succiniclasticum, and norank_f__norank_o__Clostridia_vadinBB60_group in Firmicutes was significantly higher in the CON group than in the H-CLA group. In contrast, the relative abundance of norank_f__UCG-011, norank_f_Eubacterium_coprostanoligenes_group, unclassified_f__Lachnospiraceae, and UCG-001 in Firmicutes and norank_f__Muribaculaceae in Bacteroidetes was significantly higher in the H-CLA group than in the CON group. Correlation analysis showed that the milk fat content was negatively correlated with the relative abundance of some bacteria, including members of Firmicutes and Bacteroidetes. Similarly, MFG size (D[3,2] and D[4,3]) was negatively correlated with several members of Firmicutes and Bacteroidetes, including Lachnospiraceae, norank_f__UCG-011, UCG-001, norank_f__Eubacterium_coprostanoligenes_group (Firmicutes), and norank_f__Muribaculaceae (Bacteroidetes), while positively correlated with the relative abundance of some members of Firmicutes and Bacteroidetes, including Mycoplasma, Succiniclasticum, norank_f__norank_o__Clostridia_vadinBB60_group, UCG-002 (Firmicutes), and Rikenellaceae_RC9_gut_group (Bacteroidetes). Overall, our data indicated that CLA treatment affected milk fat content and MFG size in dairy goats, and these effects were correlated with the relative abundance of ruminal bacterial populations. These results provide the first evidence to explain the mechanism underlying diet-induced MFG from the perspective of the ruminal microbiome in dairy goats.

Assessment of fecal bacterial viability and diversity in fresh and frozen fecal microbiota transplant (FMT) product in horses

BACKGROUND

Currently, lack of standardization for fecal microbiota transplantation (FMT) in equine practice has resulted in highly variable techniques, and there is no data on the bacterial metabolic activity or viability of the administered product. The objectives of this study were to compare the total and potentially metabolically active bacterial populations in equine FMT, and assess the effect of different frozen storage times, buffers, and temperatures on an equine FMT product. Fresh feces collected from three healthy adult horses was subjected to different storage methods. This included different preservation solutions (saline plus glycerol or saline only), temperature (-20 °C or -80 °C), and time (fresh, 30, 60, or 90 days). Samples underwent DNA extraction to assess total bacterial populations (both live and dead combined) and RNA extraction followed by reverse transcription to cDNA as a proxy to assess viable bacteria, then 16s rRNA gene amplicon sequencing using the V1-V2 region.

RESULTS

The largest difference in population indices and taxonomic composition at the genus level was seen when evaluating the results of DNA-based (total) and cDNA-based (potentially metabolically active) extraction method. At the community level, alpha diversity (observed species, Shannon diversity) was significantly decreased in frozen samples for DNA-based analysis (P < 0.05), with less difference seen for cDNA-based sequencing. Using DNA-based analysis, length of storage had a significant impact (P < 0.05) on the bacterial community profiles. For potentially metabolically active populations, storage overall had less of an effect on the bacterial community composition, with a significant effect of buffer (P < 0.05). Individual horse had the most significant effect within both DNA and cDNA bacterial communities.

CONCLUSIONS

Frozen storage of equine FMT material can preserve potentially metabolically active bacteria of the equine fecal microbiome, with saline plus glycerol preservation more effective than saline alone. Larger studies are needed to determine if these findings apply to other individual horses. The ability to freeze FMT material for use in equine patients could allow for easier clinical use of fecal transplant in horses with disturbances in their intestinal microbiome.

Potential Role of Lauric Acid in Milk Fat Synthesis in Chinese Holstein Cows Based on Integrated Analysis of Ruminal Microbiome and Metabolome

The composition and metabolic profile of the ruminal microbiome have an impact on milk composition. To unravel the ruminal microbiome and metabolome affecting milk fat synthesis in dairy cows, 16S rRNA and internal transcribed spacer (ITS) gene sequencing, as well as ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) methods were used to investigate the significant differences in ruminal bacterial and fungal communities as well as metabolome among Chinese Holstein cows with contrasting milk fat contents under the same diet (H-MF 5.82 ± 0.41% vs. L-MF 3.60 ± 0.12%). Another objective was to culture bovine mammary epithelial cells (BMECs) to assess the effect of metabolites on lipid metabolism. Results showed that the acetate-to-propionate ratio and xylanase activity in ruminal fluid were both higher in H-MF. Microbiome sequencing identified 10 types of bacteria and four types of fungi differently abundant at the genus level. Metabolomics analysis indicated 11 different ruminal metabolites between the two groups, the majority of which were lipids and organic acids. Among these, lauric acid (LA) was enriched in fatty acid biosynthesis with its concentration in milk fat of H-MF cows being greater (217 vs. 156 mg per 100 g milk), thus, it was selected for an in vitro study with BMECs. Exogenous LA led to a marked increase in intracellular triglyceride (TG) content and lipid droplet formation, and it upregulated the mRNA abundance of fatty acid uptake and activation (CD36 and ACSL1), TG synthesis (DGAT1, DGAT2 and GPAM), and transcriptional regulation (SREBP1) genes. Taken together, the greater relative abundance of xylan-fermenting bacteria and fungi, and lower abundance of bacteria suppressing short-chain fatty acid-producing bacteria or participating in fatty acid hydrogenation altered lipids and organic acids in the rumen of dairy cows. In BMECs, LA altered the expression of genes involved in lipid metabolism in mammary cells, ultimately promoting milk fat synthesis. Thus, it appears that this fatty acid plays a key role in milk fat synthesis.

Comparison of the gastrointestinal bacterial microbiota between dairy cows with and without mastitis

Mastitis causes significant losses in the global dairy industry, and the health of animals has been linked to their intestinal microbiota. To better understand the relationship between gastrointestinal microbiota and mastitis in dairy cows, we collected blood, rumen fluid, and fecal samples from 23 dairy cows, including 13 cows with mastitis and 10 healthy cows. Using ELISA kit and high-throughput sequencing, we found that cows with mastitis had higher concentrations of TNF-α, IL-1, and LPS than healthy cows (p < 0.05), but no significant differences in microbiota abundance or diversity (p > 0.05). Principal coordinate analysis (PCOA) revealed significant differences in rumen microbial structure between the two groups (p < 0.05), with Moryella as the signature for rumen in cows with mastitis. In contrast, fecal microbial structure showed no significant differences (p > 0.05), with Aeriscardovia, Lactococcus, and Bacillus as the signature for feces in healthy cows. Furthermore, the results showed distinct microbial interaction patterns in the rumen and feces of cows with mastitis compared to healthy cows. Additionally, we observed correlations between the microbiota in both the rumen and feces of cows and blood inflammatory indicators. Our study sheds new light on the prevention of mastitis in dairy cows by highlighting the relationship between gastrointestinal microbiota and mastitis.

Use of milk proteins as biomarkers of changes in the rumen metaproteome of Holstein cows fed low-fiber, high-starch diets

Dietary levels of undegraded neutral detergent fiber (uNDF240) and rumen-fermentable starch (RFS) can affect the rumen microbiome and milk composition. The objective of the study is to investigate the use of milk proteins as biomarkers of rumen microbial activity through a comparative evaluation of the rumen microbial and milk protein profiles produced by Holstein cows fed diets with varying contents of physically effective uNDF240 (peuNDF240) and RFS. Eight ruminally cannulated lactating Holstein cows were included in a larger study as part of a 4 × 4 Latin square design with 4 28-d periods to assess 4 diets varying in peuNDF240 and RFS content. For this experiment, cows received one of 2 dietary treatments: (1) low-peuNDF240, high-RFS (LNHR) diet or (2) high-peuNDF240, low-RFS (HNLR) diet. Within each period, rumen fluid samples were collected from each cow on d 26 (1400 h) and d 27 (0600 h and 1000 h), and milk samples were collected from each cow on d 25 (2030 h), d 26 (0430 h, 1230 h, and 2030 h), and d 27 (0430 h and 1230 h). Microbial proteins were isolated from each rumen fluid sample. For milk samples, milk proteins were fractionated, and the whey fraction was subsequently isolated. Isolated proteins within each rumen fluid or milk sample were isobarically labeled and analyzed by liquid chromatography-tandem mass spectrometry. Product ion spectra acquired from rumen fluid samples were searched using SEQUEST against 71 composite databases. In contrast, product ion spectra acquired from milk samples were searched against the Bos taurus database. Data were analyzed using the PROC MIXED procedure in SAS 9.4 to assess the effect of diet and time of sampling. To increase stringency, the false discovery rate-adjusted P-value (PFDR) was also calculated to account for multiple comparisons. Using the mixed procedure, a total of 129 rumen microbial proteins were quantified across 24 searched microbial species. Of these, the abundance of 14 proteins across 9 microbial species was affected due to diet and diet × time interaction, including 7 proteins associated with energetics pathways. Among the 159 quantified milk proteins, the abundance of 21 proteins was affected due to the diet and diet × time interaction. The abundance of 19 of these milk proteins was affected due to diet × time interactions. Of these, 16 proteins had the disparity across diets at the 0430 h sampling time, including proteins involved in host defense, nutrient synthesis, and transportation, suggesting that biological shifts resulting from diet-induced rumen changes are not diurnally uniform across milkings. The concentration of lipoprotein lipase (LPL) was statistically higher in the milk from the cows fed with the LNHR diet, which was numerically confirmed with an ELISA. Further, as determined by ELISA, the LPL concentration was significantly higher in the milk from the cows fed with the LNHR diet at 0430 h sampling point, suggesting that LPL concentration may indicate dietary carbohydrate-induced ruminal changes. The results of this study suggest that diet-induced rumen changes can be reflected in milk in a diurnal pattern, further highlighting the need to consider sampling time points for using milk proteins as a representative biomarker of rumen microbial activity.

Screening macroalgae for mitigation of enteric methane in vitro

This study investigated the effects of 67 species of macroalgae on methanogenesis and rumen fermentation in vitro. Specimens were analyzed for their effect on ruminal fermentation and microbial community profiles. Incubations were carried out in an automated gas production system for 24-h and macroalgae were tested at 2% (feed dry matter basis) inclusion rate. Methane yield was decreased 99% by Asparagopsis taxiformis (AT) when compared with the control. Colpomenia peregrina also decreased methane yield 14% compared with control; no other species influenced methane yield. Total gas production was decreased 14 and 10% by AT and Sargassum horneri compared with control, respectively. Total volatile fatty acid (VFA) concentration was decreased between 5 and 8% by 3 macroalgae, whereas AT reduced it by 10%. Molar proportion of acetate was decreased 9% by AT, along with an increase in propionate by 14%. Asparagopsis taxiformis also increased butyrate and valerate molar proportions by 7 and 24%, respectively, whereas 3 macroalgae species decreased molar proportion of butyrate 3 to 5%. Vertebrata lanosa increased ammonia concentration, whereas 3 other species decreased it. Inclusion of AT decreased relative abundance of Prevotella, Bacteroidales, Firmicutes and Methanobacteriaceae, whereas Clostridium, Anaerovibrio and Methanobrevibacter were increased. Specific gene activities for Methanosphaera stadtmane and Methanobrevibacter ruminantium were decreased by AT inclusion. In this in vitro study, Asparagopsis taxiformis was most effective in decreasing methane concentration and yield, but also decreased total gas production and VFA concentration which indicates overall inhibition of ruminal fermentation. No other macroalgae were identified as potential mitigants of enteric methane.

Dietary supplementation of Allium mongolicum modulates rumen-hindgut microbial community structure in Simmental calves

Compared to traditional herbage, functional native herbage is playing more important role in ruminant agriculture through improving digestion, metabolism and health of livestock; however, their effects on rumen microbial communities and hindgut fermentation are still not well understood. The objective of present study was to evaluate the effects of dietary addition of Allium mongolicum on bacterial communities in rumen and feces of claves. Sixteen 7-month-old male calves were randomly divided into four groups (n = 4). All calves were fed a basal ration containing roughage (alfalfa and oats) and mixed concentrate in a ratio of 60:40 on dry matter basis. In each group, the basal ration was supplemented with Allium mongolicum 0 (SL0), 200 (SL200), 400 (SL400), and 800 (SL800) mg/kg BW. The experiment lasted for 58 days. Rumen fluid and feces in rectum were collected, Rumen fluid and hindgut fecal were collected for analyzing bacterial community. In the rumen, Compared with SL0, there was a greater relative abundance of phylum Proteobacteria (p < 0.05) and genera Rikenellaceae_RC9_gut_group (p < 0.01) in SL800 treatment. In hindgut, compared with SL0, supplementation of A. mongolicum (SL200, SL400, or SL800) decreased in the relative abundances of Ruminococcaceae_UCG-014 (p < 0.01), Ruminiclostridium_5 (p < 0.01), Eubacterium_coprostanoligenes_group (p < 0.05), and Alistipes (p < 0.05) in feces; Whereas, the relative abundances of Christensenellaceae_R-7_group (p < 0.05), and Prevotella_1 (p < 0.01) in SL800 were higher in feces, to maintain hindgut stability. This study provided evidence that A. mongolicum affects the gastrointestinal of calves, by influencing microbiota in their rumen and feces.

Symposium review: The impact of absorbed nutrients on energy partitioning throughout lactation

Most nutrition models and some nutritionists view ration formulation as accounting transactions to match nutrient supplies with nutrient requirements. However, diet and stage of lactation interact to alter the partitioning of nutrients toward milk and body reserves, which, in turn, alters requirements. Fermentation and digestion of diet components determine feeding behavior and the temporal pattern and profile of absorbed nutrients. The pattern and profile, in turn, alter hormonal signals, tissue responsiveness to hormones, and mammary metabolism to affect milk synthesis and energy partitioning differently depending on the physiological state of the cow. In the fresh period (first 2 to 3 wk postpartum), plasma insulin concentration and insulin sensitivity of tissues are low, so absorbed nutrients and body reserves are partitioned toward milk synthesis. As lactation progresses, insulin secretion and sensitivity increase, favoring deposition instead of mobilization of body reserves. High-starch diets increase ruminal propionate production, the flow of gluconeogenic precursors to the liver, and blood insulin concentrations. During early lactation, the glucose produced will preferentially be used by the mammary gland for milk production. As lactation progresses and milk yield decreases, glucose will increasingly stimulate repletion of body reserves. Diets with less starch and more digestible fiber increase ruminal production of acetate relative to propionate and, because acetate is less insulinogenic than propionate, these diets can minimize body weight gain. High dietary starch concentration and fermentability can also induce milk fat depression by increasing the production of biohydrogenation intermediates that inhibit milk fat synthesis and thus favor energy partitioning away from the mammary gland. Supplemental fatty acids also impact energy partitioning by affecting insulin concentration and insulin sensitivity of tissues. Depending on profile, physiological state, and interactions with other nutrients, supplemental fatty acids might increase milk yield at the expense of body reserves or partition energy to body reserves at the expense of milk yield. Supplemental protein or AA also can increase milk production but there is little evidence that dietary protein directly alters whole-body partitioning. Understanding the biology of these interactions can help nutritionists better formulate diets for cows at various stages of lactation.

Comparison of milk and grass composition from grazing Irish dairy herds with and without milk fat depression

BACKGROUND

This study investigated the factors relating to pasture chemical and fatty acid (FA) composition that influence the milk fat percentage of spring calving, grazing dairy cows. The relationship between milk fat percentage and FA composition of the milk in these herds was also investigated.

RESULTS

Milk protein percentage, milk casein percentage and cheddar cheese yield were increased in milk from HMF herds. Cows from LMF herds did not have negatively altered milk processability including rennet coagulation time (RCT), pH and ethanol stability. Crude protein, NDF, ADF, ether extract and total FA content of pasture was not different between LMF and HMF herds. Milk fat concentration of conjugated linoleic acid (CLA) t10, c12 was not different between HMF and LMF herds. Pre-grazing herbage mass and pasture content of crude protein, neutral detergent fibre (NDF) and total FA were similar between HMF and LMF herds. Pasture offered to LMF herds had a higher concentration of monounsaturated fatty acids (MUFA). A strong negative relationship (r = -0.40) was evident between milk fat percentage and pasture crude protein content for MMF herds (3.31-3.94% milk fat).

CONCLUSIONS

This research reports improved milk protein percentage, milk casein percentage and cheddar cheese yield from HMF herds compared to LMF herds. Milk processability was not impacted by low milk fat percentage. Pasture NDF and total fatty acid content was similar in HMF herds and LMF herds. Milk fat percentage had a strong negative association (r = -0.40) with pasture crude protein content in MMF herds (MF 3.31-3.94%). Correlation values between pasture chemical and FA composition and milk fat percentage in LMF herds and HMF herds were low, indicating that diet is not the only causative factor for variation in milk fat of grazing dairy cows. Comparison of milk fatty acid composition from herds with and without milk fat depression suggests that there may be other fatty acids apart from CLA t10, c12 that contribute to the inhibition of milk fat synthesis during milk fat depression in grazing herds.

Integrating data from spontaneous and induced trans-10 shift of ruminal biohydrogenation reveals discriminant bacterial community changes at the OTU level

Introduction

Microbial digestion is of key importance for ruminants, and disturbances can affect efficiency and quality of products for human consumers. Ruminal biohydrogenation of dietary unsaturated fatty acids leads to a wide variety of specific fatty acids. Some dietary conditions can affect the pathways of this transformation, leading to trans-10 fatty acids rather than the more usual trans-11 fatty acids, this change resulting in milk fat depression in dairy cows.

Materials and methods

We combined data from an induced and spontaneous trans-10 shift of ruminal biohydrogenation, providing new insight on bacterial changes at different taxonomic levels. A trans-10 shift was induced using dietary addition of concentrate and/or unsaturated fat, and the spontaneous milk fat depression was observed in a commercial dairy herd.

Results and discussion

Most changes of microbial community related to bacteria that are not known to be involved in the biohydrogenation process, suggesting that the trans-10 shift may represent the biochemical marker of a wide change of bacterial community. At OTU level, sparse discriminant analysis revealed strong associations between this change of biohydrogenation pathway and some taxa, especially three taxa belonging to [Eubacterium] coprostanoligenes group, Muribaculaceae and Lachnospiraceae NK3A20 group, that could both be microbial markers of this disturbance and candidates for studies relative to their ability to produce trans-10 fatty acids.

Subacute ruminal acidosis in dairy herds: Microbiological and nutritional causes, consequences, and prevention strategies

Dairy cattle are frequently fed high-concentrate (HC) diets in modern intensive feeding systems, especially in the transition period. During this period, cows face many alterations that include hormonal changes and shifting to a lactating state. Switching to a HC diet that may disrupt the ruminal microbiota balance can lead to subacute ruminal acidosis (SARA). Moreover, the main factor shaping the rumen microbiota is dietary composition, especially the ratio of starch to fibrous carbohydrates. Feeding highly fermentable carbohydrate diets after adaptation to forage diets leads to a rumen fermentation rate that exceeds rumen absorption and buffering rates, resulting in a reduction in ruminal pH. As a result of Gram-negative bacterial cell lysis, an increase in harmful ruminal bacterial metabolites, including lipopolysaccharide, lactic acid, and histamine, is observed. The interactions between the host immune system and the ruminal microbiota play an essential role in many physiological processes and the development of the disorder. Progress in DNA sequencing and bioinformatics platforms provides new opportunities to investigate the composition of ruminal microbes and yields unique advances in understanding ecology of the rumen. Subacute ruminal acidosis is linked with a change in the ruminal microbiota structure and richness and with other metabolic disorders; such as rumenitis, milk fat depression, laminitis, and liver abscesses. Therefore, this review aims to explore a better understanding of the crosstalk between diet and microbiota in the prevalence of rumen acidosis and its consequences, which is crucial for control strategies such as feeding management, and supplementation with thiamine, prebiotics, and probiotics.

Periodical Changes of Feces Microbiota and Its Relationship with Nutrient Digestibility in Early Lambs

Early mammal gut microorganism colonization affects host health, the feed conversion rate, and production performance. Herein, we explored how fecal microbiota develops and the interactions between microorganisms and nutrients. The lambs were separated from ewes at 7 days old, artificial feeding with milk replacer completely replaced lactation, and the starter diet was added. At 21 days old, the lambs were fed with complete starter and milk replacer was stopped. At day 7, 21, 35, and 49 after birth, fecal samples were collected. Then 16S rRNA gene sequencing in the fecal samples revealed that the alpha diversity increased significantly with age. Principal coordinates analysis showed clear clustering by age (p < 0.05). At the genus level, the relative abundance of 8 genera declined, 12 genera increased (p < 0.1), and 4 genera changed dramatically with age (p < 0.05). The apparent digestibility of dry matter, protein, fat, neutral detergent fiber, and acid detergent fiber significantly decreased by 21.77%, 23.15%, 23.62%, 19.38%, and 45.24%, respectively, from 7 to 35 days of age (p < 0.05), but not thereafter (p > 0.05). Fecal nutrient contents affected the abundance of bacterial genera (p < 0.05). Enterobacteriaceae_unclassified, Clostridium XlVb, Bifidobacterium, and other genera had no relationship with the fecal nutrient content; however, they were closely related to nutrient intake and digestibility, possibly promoting nutrient digestion. Our results suggested that nutrient digestion of young lambs changed rapidly, which was closely related to intestinal microbial colonization.

Consumption of Supplementary Inulin Modulates Milk Microbiota and Metabolites in Dairy Cows with Subclinical Mastitis

The milk microbiota and mediated metabolites directly affect the health of the udder in dairy cows. Inulin, a dietary prebiotic, can modulate the profile of gastrointestinal microbiota. However, whether the inulin intake affects the milk microbial population and metabolites remains unknown. In this study, 40 subclinical mastitis (SCM) cows were randomly divided into 5 groups. Five inulin addition doses, 0, 100, 200, 300, and 400 g/day per cow, based on the same basal diet, were supplemented. The experiments lasted for 8 weeks. The results showed lower relative abundance of mastitis-causing and proinflammation microbes in milk (i.e., Escherichia-Shigella, Pseudomonas, Rhodococcus, Burkholderia-Caballeronia-Paraburkholderia, etc.) and higher abundances of probiotics and commensal bacteria, such as Lactobacillus, Bifidobacterium, etc., in the cows fed 300 g/day inulin compared to that in the control group. Meanwhile, the levels of arachidonic acid proinflammatory mediators (leukotriene E3, 20-carboxy-leukotriene B4, and 12-Oxo-c-LTB3) and phospholipid metabolites were reduced, and the levels of compounds with antibacterial and anti-inflammatory potential (prostaglandin A1, 8-iso-15-keto-prostaglandin E2 [PGE2], etc.) and participating energy metabolism (citric acid, l-carnitine, etc.) were elevated. These data suggested that inulin intake might modulate the microflora and metabolite level in extraintestinal tissue, such as mammary gland, which provided an alternative for the regulation and mitigation of SCM. IMPORTANCE The profile of the microbial community and metabolic activity in milk are the main determinants of udder health status and milk quality. Recent studies have demonstrated that diet could directly modulate the mammary gland microbiome. Inulin is a probiotic dietary fiber which can improve the microbiota population in the gastrointestinal tract. However, whether inulin intake can further regulate the profile of the microbiota and metabolic activities in milk remains unclear. In subclinical mastitic cows, we found that inulin supplementation could reduce the abundance of Escherichia-Shigella, Pseudomonas, Rhodococcus, and Burkholderia-Caballeronia-Paraburkholderia and the levels of (±)12, 13-DiHOME, leukotriene E3 and 20-carboxy-leukotriene B4 etc., while it elevated the abundance of Lactobacillus, Bifidobacterium, and Muribaculaceae, as well as the levels of prostaglandin A1 (PGA1), 8-iso-15-keto-PGE2, benzoic acid, etc. in milk. These data suggest that inulin intake affects the profile of microorganisms and metabolites in milk, which provides an alternative for the regulation of mastitis.

Effects of vegetable oil supplementation on rumen fermentation and microbial population in ruminant: a review

Understanding the nature of ruminant nutrition and digestion is essential to improve feeding management and animal production. Among many approaches, manipulating ruminant nutrition and fermentation through feed supplementation is being practised and researched. Over the last decade, the utilization of vegetable oils in feed formulation and their effects on various aspects of ruminants have been reported by many researchers. It is important to understand the lipid metabolism in ruminants by microorganisms because it affects the quality of ruminant-derived products such as meat and milk. Majority of vegetable oil supplementation could reduce rumen protozoa population in ruminants due to the effects of medium-chain fatty acids (FAs). However, vegetable oil also contains unsaturated FAs that are known to have a negative effect on cellulolytic bacteria which could show inhibitory effects of the fibre digestion. In this paper, the physiology of nutrient digestion of ruminants is described. This paper also provides a current review of studies done on improvement and modification of rumen fermentation and microbial population through vegetable oil supplementation.

Long-Term Effects of Dietary Supplementation with Olive Oil and Hydrogenated Vegetable Oil on the Rumen Microbiome of Dairy Cows

Dietary lipids increase energy density in dairy cow diets and in some cases can increase beneficial fatty acids (FA) in milk and dairy products. However, the degree of FA saturation may affect the rumen microbiome. The objective of this study was to determine the long-term effects of feeding saturated (hydrogenated vegetable oil; HVO) or unsaturated (olive oil; OO) fatty acid (FA) sources on the rumen microbiome of dairy cows. For 63 days, 15 mid-lactating cows were fed with either a basal diet (no fat supplement), or the basal diet supplemented with 3% dry matter (DM), either HVO or OO. Rumen contents were collected on days 21, 42 and 63 for 16S rRNA gene sequencing using the Illumina MiSeq platform. The results reveal dominance of the phyla Firmicutes (71.5%) and Bacteroidetes (26.2%), and their respective prevalent genera Succiniclasticum (19.4%) and Prevotella (16.6%). Succiniclasticum increased with both treatments at all time points. Prevotella was reduced on day 42 in both diets. Bacterial diversity alpha or beta were not affected by diets. Predicted bacterial functions by CowPI showed changes in energy and protein metabolism. Overall, 3% DM of lipid supplementation over 63 days can be used in dairy cow diets without major impacts on global bacterial community structure.

Protected or Unprotected Fat Addition for Feedlot Lambs: Feeding Behavior, Carcass Traits, and Meat Quality

Simple Summary

The use of lipids in ruminant diets aims to increase energy density without affecting the animal’s performance; however, its use can be toxic to the ruminal microbiota, which can be avoided with the use of protected fats. Diets with the inclusion of different fat sources (whole soybean grain, corn germ, calcium salt of fatty acids, and soybean oil) were tested to evaluate the effects of unprotected or protected fats on feeding behavior, carcass characteristics, and quality of the meat of feedlot lambs. The use of calcium salts from fatty acids in feedlot lambs’ diets improves the quantitative and qualitative characteristics of the carcass and meat.

Abstract

This study aimed to evaluate the effect of the inclusion of protected or unprotected fats in the diet of feedlot lambs on feeding behavior, productive characteristics, carcass traits, and meat quality. Forty male Dorper × Santa Inês lambs (22.27 ± 2.79 kg) were randomly assigned to treatments in a completely randomized design. The experimental treatments consisted of five diets: no added fat (NAF), whole soybeans (WSB), calcium salts of fatty acids (CSFA), soybean oil (SO), and corn germ (CG). The total intake of dry matter (DMI) (p < 0.001) and neutral detergent fiber (NDFI) (p = 0.010) were higher in the CSFA and NAF diets. Feeding behavior, morphometric measurements, physicochemical characteristics, and centesimal composition of the Longissimus lumborum muscle were similar between treatments (p > 0.05). The CSFA diet provided higher production (p < 0.05) and better-quality carcasses. The inclusion of fat sources increased the concentration of polyunsaturated fatty acids (p < 0.05). The use of calcium salts of fatty acids in feedlot lambs’ diets provides better quantitative and qualitative characteristics of the meat and carcass.

Comparison of Two Sampling Techniques for Evaluating Ruminal Fermentation and Microbiota in the Planktonic Phase of Rumen Digesta in Dairy Cows

The objective of this experiment was to compare ruminal fluid samples collected through rumen cannula (RC) or using an oral stomach tube (ST) for measurement of ruminal fermentation and microbiota variables. Six ruminally cannulated lactating Holstein cows fed a standard diet were used in the study. Rumen samples were collected at 0, 2, 4, 6, 8, and 12 h after the morning feeding on two consecutive days using both RC and ST techniques. Samples were filtered through two layers of cheesecloth and the filtered ruminal fluid was used for further analysis. Compared with RC, ST samples had 7% greater pH; however, the pattern in pH change after feeding was similar between sampling methods. Total volatile fatty acids (VFA), acetate and propionate concentrations in ruminal fluid were on average 23% lower for ST compared with RC. There were no differences between RC and ST in VFA molar proportions (except for isobutyrate), ammonia and dissolved hydrogen (dH₂) concentrations, or total protozoa counts, and there were no interactions between sampling technique and time of sampling. Bacterial ASV richness was higher in ST compared with RC samples; however, no differences were observed for Shannon diversity. Based on Permanova analysis, bacterial community composition was influenced by sampling method and there was an interaction between sampling method and time of sampling. A core microbiota comprised of Prevotella, S24-7, unclassified Bacteroidales and unclassified Clostridiales, Butyrivibrio, unclassified Lachnospiraceae, unclassified Ruminococcaceae, Ruminococcus, and Sharpea was present in both ST and RC samples, although their relative abundance varied and was influenced by an interaction between sampling time and sampling method. Overall, our results suggest that ruminal fluid samples collected using ST (at 180 to 200 cm depth) are not representative of rumen pH, absolute values of VFA concentrations, or bacterial communities >2 h post-feeding when compared to samples of ruminal fluid collected using RC. However, ST can be a feasible sampling technique if the purpose is to study molar proportions of VFA, protozoa counts, dH₂, and ammonia concentrations.

Changes in the faecal bacterial microbiota during hospitalisation of horses with colic and the effect of different causes of colic

BACKGROUND

Previous studies have identified alterations in the faecal microbiota of horses with colic; however, further work is needed to interpret these findings.

OBJECTIVES

To compare the faecal microbiota of horses presenting for colic at hospital admission, day 1 and day 3/discharge and with different colic duration and lesion locations.

STUDY DESIGN

Prospective observational clinical study.

METHODS

Faecal samples were collected from 17 colic cases at hospital admission, on day 1 and on day 3 post-admission or at the time of hospital discharge if prior to 72 hours. Faecal samples were extracted for genomic DNA, PCR-amplified, sequenced and analysed using QIIME. Species richness and Shannon diversity (alpha diversity) were estimated. The extent of the relationship between bacterial communities (beta diversity) was quantified using pairwise UniFrac distances, visualised using principal coordinate analysis (PCoA) and statistically analysed using permutational multivariate analysis of variance (PERMANOVA). The relative abundance of bacterial populations at the different time points and in different types of colic was compared using ANCOM.

RESULTS

There was a decrease in species richness from admission to day 3/hospital discharge (P < .05), and a lower species richness (P = .005) and Shannon diversity (P = .02) in horses with colic ≥60 h compared to <60 h. Based on PCoA and PERMANOVA, there was a significant difference in bacterial community composition for horses with different colic duration (P = .001) and lesion location (P = .006). Several differences in bacterial phyla and genera were observed at different time points and with different types of colic.

MAIN LIMITATIONS

Relatively low numbers and a diverse population of horses.

CONCLUSIONS

The microbiota change from hospital admission to day 3/discharge in horses with colic and horses with colic ≥60 h and large colon lesions have a distinct bacterial population compared to horses with colic <60 h and small intestinal lesions.

Phytogenic Additives Can Modulate Rumen Microbiome to Mediate Fermentation Kinetics and Methanogenesis Through Exploiting Diet-Microbe Interaction

Ruminants inhabit the consortia of gut microbes that play a critical functional role in their maintenance and nourishment by enabling them to use cellulosic and non-cellulosic feed material. These gut microbes perform major physiological activities, including digestion and metabolism of dietary components, to derive energy to meet major protein (65-85%) and energy (ca 80%) requirements of the host. Owing to their contribution to digestive physiology, rumen microbes are considered one of the crucial factors affecting feed conversion efficiency in ruminants. Any change in the rumen microbiome has an imperative effect on animal physiology. Ruminal microbes are fundamentally anaerobic and produce various compounds during rumen fermentation, which are directly used by the host or other microbes. Methane (CH4) is produced by methanogens through utilizing metabolic hydrogen during rumen fermentation. Maximizing the flow of metabolic hydrogen in the rumen away from CH4 and toward volatile fatty acids (VFA) would increase the efficiency of ruminant production and decrease its environmental impact. Understanding of microbial diversity and rumen dynamics is not only crucial for the optimization of host efficiency but also required to mediate emission of greenhouse gases (GHGs) from ruminants. There are various strategies to modulate the rumen microbiome, mainly including dietary interventions and the use of different feed additives. Phytogenic feed additives, mainly plant secondary compounds, have been shown to modulate rumen microflora and change rumen fermentation dynamics leading to enhanced animal performance. Many in vitro and in vivo studies aimed to evaluate the use of plant secondary metabolites in ruminants have been conducted using different plants or their extract or essential oils. This review specifically aims to provide insights into dietary interactions of rumen microbes and their subsequent consequences on rumen fermentation. Moreover, a comprehensive overview of the modulation of rumen microbiome by using phytogenic compounds (essential oils, saponins, and tannins) for manipulating rumen dynamics to mediate CH4 emanation from livestock is presented. We have also discussed the pros and cons of each strategy along with future prospective of dietary modulation of rumen microbiome to improve the performance of ruminants while decreasing GHG emissions.

Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet

The development of a robust microbiome is critical to the health of dairy calves, but relatively little is known about the progression of the microbiome through the weaning transition. In this study, fecal samples were obtained from ten female Holstein calves at 6 timepoints between 2–13 weeks of age. Calves were fed acidified milk until weaning at 8 weeks old and had access to starter grain throughout the study. Fecal samples were extracted for genomic DNA, PCR-amplified for the V1-V2 region of the 16S rRNA bacterial gene, sequenced on the Illumina MiSeq platform, and analyzed using the QIIME2 pipeline. Bacterial richness, estimated by number of observed species, and bacterial diversity, estimated by Shannon diversity index, both differed significantly between timepoints and both increased over time (P <0.05), with the largest increases occurring during weaning. Weighted and unweighted UniFrac analysis showed significant differences (P <0.05) between bacterial communities across timepoints; betadisper analysis revealed that the microbiomes of individual calves became more similar with time. Throughout the study, Firmicutes was the dominant phylum, followed by Bacteroidetes. Thirteen bacterial genera were found to be significantly influenced by time, including Faecalibacterium, Clostridium, unclassified S24-7, Collinsella, Sharpea, and Treponema. Unclassified Ruminococcaceae was the most prevalent genus at timepoints 1, 3, 5, and 6, but different amplicon sequence variants were detected at each timepoint suggesting the presence of different species of Ruminococcaceae at different times. Bacteroides was the most prevalent genus at timepoint 2, and Prevotella was most prevalent at timepoint 4. Our results indicate that there is considerable variation in the calf microbiome pre-weaning, but the microbial community stabilizes and becomes similar to the adult microbiome at weaning. Further studies to describe the phylogeny and functionality of core microbiota through the weaning transition are needed to improve health and reduce diarrhea in the neonatal period.

Identifying and exploring biohydrogenating rumen bacteria with emphasis on pathways including trans-10 intermediates

Background

Bacteria involved in ruminal formation of trans-10 intermediates are unclear. Therefore, this study aimed at identifying rumen bacteria that produce trans-10 intermediates from 18-carbon unsaturated fatty acids.

Results

Pure cultures of 28 rumen bacterial species were incubated individually in the presence of 40 μg/mL 18:3n-3, 18:2n-6 or trans-11 18:1 under control or lactate-enriched (200 mM Na lactate) conditions for 24 h. Of the 28 strains, Cutibacterium acnes (formerly Propionibacterium acnes) was the only bacterium found to produce trans-10 intermediates from 18:3n-3 and 18:2n-6, irrespective of the growth condition. To further assess the potential importance of this species in the trans-11 to trans-10 shift, different biomass ratios of Butyrivibrio fibrisolvens (as a trans-11 producer) and C. acnes were incubated in different growth media (control, low pH and 22:6n-3 enriched media) containing 40 μg/mL 18:2n-6. Under control conditions, a trans-10 shift, defined in the current study as trans-10/trans-11 ≥ 0.9, occurred when the biomass of C. acnes represented between 90 and 98% of the inoculum. A low pH or addition of 22:6n-3 inhibited cis-9, trans-11 CLA and trans-10, cis-12 CLA formation by B. fibrisolvens and C. acnes, respectively, whereby C. acnes seemed to be more tolerant. This resulted in a decreased biomass of C. acnes required at inoculation to induce a trans-10 shift to 50% (low pH) and 90% (22:6n-3 addition).

Conclusions

Among the bacterial species studied,C. acnes was the only bacterium that have the metabolic ability to produce trans-10 intermediates from 18:3n-3 and 18:2n-6. Nevertheless, this experiment revealed that it is unlikely that C. acnes is the only or predominant species involved in the trans-11 to trans-10 shift in vivo.

Invited review: Role of rumen biohydrogenation intermediates and rumen microbes in diet-induced milk fat depression: An update

To meet the energy requirements of high-yielding dairy cows, grains and fats have increasingly been incorporated in ruminant diets. Moreover, lipid supplements have been included in ruminant diets under experimental or practical conditions to increase the concentrations of bioactive n-3 fatty acids and conjugated linoleic acids in milk and meat. Nevertheless, those feeding practices have dramatically increased the incidence of milk fat depression in dairy cattle. Although induction of milk fat depression may be a management tool, most often, diet-induced milk fat depression is unintended and associated with a direct economic loss. In this review, we give an update on the role of fatty acids, particularly originating from rumen biohydrogenation, as well as of rumen microbes in diet-induced milk fat depression. Although this syndrome seems to be multi-etiological, the best-known causal factor remains the shift in rumen biohydrogenation pathway from the formation of mainly trans-11 intermediates toward greater accumulation of trans-10 intermediates, referred to as the trans-11 to trans-10 shift. The microbial etiology of this trans-11 to trans-10 shift is not well understood yet and it seems that unraveling the microbial mechanisms of diet-induced milk fat depression is challenging. Potential strategies to avoid diet-induced milk fat depression are supplementation with rumen stabilizers, selection toward more tolerant animals, tailored management of cows at risk, selection toward more efficient fiber-digesting cows, or feeding less concentrates and grains.

Dietary energy sources and levels shift the multi-kingdom microbiota and functions in the rumen of lactating dairy cows

Background

Dietary energy source and level in lactation diets can profoundly affect milk yield and composition. Such dietary effects on lactation performance are underpinned by alteration of the rumen microbiota, of which bacteria, archaea, fungi, and protozoa may vary differently. However, few studies have examined all the four groups of rumen microbes. This study investigated the effect of both the level and source of dietary energy on rumen bacteria, archaea, fungi, and protozoa in the rumen of lactating dairy cows. A 2 × 2 factorial design resulted in four dietary treatments: low and high dietary energy levels (LE: 1.52–1.53; and HE: 1.71–1.72 Mcal/kg dry matter) and two dietary energy sources (GC: finely ground corn; and SFC: steam-flaked corn). We used a replicated 4 × 4 Latin square design using eight primiparous Chinese Holstein cows with each period lasting for 21 d. The rumen microbiota was analyzed using metataxonomics based on kingdom-specific phylogenetic markers [16S rRNA gene for bacteria and archaea, 18S rRNA gene for protozoa, and internally transcribed spacer 1 (ITS1) for fungi] followed with subsequent functional prediction using PICRUSt2.

Results

The GC resulted in a higher prokaryotic (bacterial and archaeal) species richness and Faith’s phylogenetic diversity than SFC. For the eukaryotic (fungi and protozoa) microbiota, the LE diets led to significantly higher values of the above measurements than the HE diets. Among the major classified taxa, 23 genera across all the kingdoms differed in relative abundance between the two dietary energy levels, while only six genera (none being protozoal) were differentially abundant between the two energy sources. Based on prokaryotic amplicon sequence variants (ASVs) from all the samples, overall functional profiles predicted using PICRUSt2 differed significantly between LE and HE but not between the two energy sources. FishTaco analysis identified Ruminococcus and Coprococcus as the taxa potentially contributing to the enriched KEGG pathways for biosynthesis of amino acids and to the metabolisms of pyruvate, glycerophospholipid, and nicotinate and nicotinamide in the rumen of HE-fed cows. The co-occurrence networks were also affected by the dietary treatments, especially the LE and GC diets, resulting in distinct co-occurrence networks. Several microbial genera appeared to be strongly correlated with one or more lactation traits.

Conclusions

Dietary energy level affected the overall rumen multi-kingdom microbiota while little difference was noted between ground corn and steam-flaked corn. Some genera were also affected differently by the four dietary treatments, including genera that had been shown to be correlated with lactation performance or feed efficiency. The co-occurrence patterns among the genera exclusively found for each dietary treatment may suggest possible metabolic interactions specifically affected by the dietary treatment. Some of the major taxa were positively correlated to milk properties and may potentially serve as biomarkers of one or more lactation traits.

Association between Rumen Microbiota and Marbling Score in Korean Native Beef Cattle

Simple Summary

The ruminal microbiome affects various metabolic processes associated with animal development; however, few studies have focused on its correlation with marbling. Results of the present study show differences in ruminal microbiomes among Hanwoo Korean beef cattle, which have low or high marbling scores. By elucidating the effect of the ruminal microbiome on the marbling of Hanwoo, differentially abundant microbial taxa, ruminal taxonomic drivers of lipid metabolism, and the correlation with meat quality indices, the present study provides insights into the potential effects of microbial factors on marbling in beef cattle.

Abstract

This study demonstrated the potential effects of the rumen microbiota on the deposition of intramuscular fat, known as marbling. Previous studies on fatty acid metabolism in beef cattle have mostly focused on biohydrogenating rumen bacteria, whereas those on the overall rumen microbiota—to understand their roles in marbling—have not been systematically performed. The rumen microbiota of 14 Korean beef cattle (Hanwoo), which showed similar carcass characteristics and blood metabolites but different marbling scores, were analyzed by 16S rRNA gene sequencing. The rumen samples were grouped into two extreme marbling score groups of host animals as follows: LMS, marbling score≤ 4 or HMS, marbling score ≥7. Species richness tended to be higher in the HMS group, whereas the overall microbiota differed between LMS and HMS groups. RFP12, Verrucomicrobia, Oscillospira, Porphyromonadaceae, and Paludibacter were differentially abundant in the HMS group, whereas Olsenella was abundant in the LMS group. Some marbling-associated bacterial taxa also contributed to the enrichment of two lipid metabolic pathways including “alpha-linolenic acid metabolism” and “fatty acid biosynthesis” in the HMS microbiome. Taxonomic drivers of fatty acid biosynthesis, particularly in the rumen microbiome of high-marbled meat, could thus be further studied to increase the intramuscular fat content.

Effect of 2-hydroxy-4-(methylthio) butanoate (HMTBa) supplementation on rumen bacterial populations in dairy cows when exposed to diets with risk for milk fat depression

Diet-induced milk fat depression (MFD) is a condition marked by a reduction in milk fat yield experimentally achieved by increasing dietary unsaturated fatty acids and fermentable carbohydrates. 2-Hydroxy-4-(methylthio) butanoate (HMTBa) is a methionine analog observed to reduce diet-induced MFD in dairy cows. We hypothesize that the reduction in diet-induced MFD by HMTBa is due to changes in the rumen microbiota. To test this, 22 high-producing cannulated Holstein dairy cows were placed into 2 groups using a randomized block design and assigned to either control or HMTBa supplementation (0.1% of diet dry matter). All cows were then exposed to 3 different diets with a low risk (32% neutral detergent fiber, no added oil; fed d 1 to 7), a moderate risk (29% neutral detergent fiber and 0.75% soybean oil; fed d 8 to 24), or a high risk (29% neutral detergent fiber and 1.5% soybean oil; fed d 25 to 28) for diet-induced MFD. Rumen samples were collected on d 0, 14, 24, and 28, extracted for DNA, PCR-amplified for the V1-V2 region of the 16S rRNA gene, sequenced on an Illumina MiSeq (Illumina, San Diego, CA), and subjected to bacterial diversity analysis using the QIIME pipeline. The α diversity estimates (species richness and Shannon diversity) were decreased in the control group compared with the HMTBa group. Bacterial community composition also differed between control and HMTBa groups based on both weighted UniFrac (relative abundance of commonly detected bacteria) and unweighted UniFrac (presence/absence) distances. Within the HMTBa group, no differences were observed in bacterial community composition between d 0 and d 14, 24, and 28; however, in the control group, d 0 samples were different from d 14, 24, and 28. Certain bacterial genera including Dialister, Megasphaera, Lachnospira, and Sharpea were increased in the control group compared with the HMTBa group. Interestingly, these genera were positively correlated with milk fat trans-10,cis-12 conjugated linoleic acid and trans-10 C18:1, fatty acid isomers associated with biohydrogenation-induced MFD. It can be concluded that diet-induced MFD is accompanied by significant alterations in the rumen bacterial community and that HMTBa supplementation reduces these microbial perturbations.

A Nutrigenomics Approach Using RNA Sequencing Technology to Study Nutrient-Gene Interactions in Agricultural Animals

Thorough understanding of animal gene expression driven by dietary nutrients can be regarded as a bottom line of advanced animal nutrition research. Nutrigenomics (including transcriptomics) studies the effects of dietary nutrients on cellular gene expression and, ultimately, phenotypic changes in living organisms. Transcriptomics can be applied to investigate animal tissue transcriptomes at a defined nutritional state, which can provide a holistic view of intracellular RNA expression. As a novel transcriptomics approach, RNA sequencing (RNA-Seq) technology can monitor all gene expressions simultaneously in response to dietary intervention. The principle and history of RNA-Seq are briefly reviewed, and its 3 principal steps are described in this article. Application of RNA-Seq in different areas of animal nutrition research is summarized. Lastly, the application of RNA-Seq in swine science and nutrition is also reviewed. In short, RNA-Seq holds significant potential to be employed for better understanding the nutrient-gene interactions in agricultural animals.

The Ruminal Microbiome and Metabolome Alterations Associated with Diet-Induced Milk Fat Depression in Dairy Cows

Milk fat depression (MFD) syndrome represents a significant drawback to the dairy industry. The aim of this study was to unravel the ruminal metabolome-microbiome interaction in response to diet-induced MFD in dairy cows. Twelve healthy second parity Holstein dairy cows (days in milk (DIM) = 119 ± 14) were randomly assigned into control (CON, n = 6) group and treatment (TR, n = 6) group. Cows in TR group received a high-starch total mixed ration (TMR) designed to induce an MFD syndrome. Decreased milk fat yield and concentration in TR cows displayed the successful development of MFD syndrome. TR diet increased the relative abundance of Prevotella and decreased the relative abundance of unclassified Lachnospiraceae, Oribacterium, unclassified Veillonellaceae and Pseudobutyrivibrio in ruminal fluid. Metabolomics analysis revealed that the ruminal fluid content of glucose, amino acids and amines were significantly increased in TR cows compared with CON cows. Correlation analysis revealed that the concentration of amines and amino acids were highly correlated with the abundance of Oribacterium, Pseudobutyrivibrio, RC9_gut_group, unclassified BS11_gut_group and Selenomonas. In general, these findings revealed that TR diet reduced the rumination time and altered rumen fermentation type, which led to changes in the composition of ruminal microbiota and metabolites, and caused MFD.

Screening and Bioprospecting of Anaerobic Consortia for Biofuel Production Enhancement from Sugarcane Bagasse

The genera Dysgonomonas, Coprococcus, Sporomusa, Bacteroides, Sedimentibacter, Pseudomonas, Ruminococcus, and Clostridium predominate in compost residue, and vadimCA02, Anaerobaculum, Tatlockia, Caloramator, and Syntrophus prevail in soil used as inoculum in batch rectors. This mixed consortium was used as inoculum for biogas production using different concentrations of sugarcane bagasse (SCB) (from 1.58 to 4.42 g/L) and yeast extract (YE) (from 0.58 to 3.42 g/L) according to a composite central design. The maximum ethanol production (20.11 mg L^-1) was observed using 2.0 and 3.0 g L^-1 of YE and SCB, respectively (C6). Likewise, the highest hydrogen production (0.60 mmol L^-1) was observed using 3.0 and 4.0 g L^-1 of YE and SCB, respectively (C1). Methane was also observed, reaching the maximum production (1.44 mmol L^-1) using 1.0 and 4.0 g L^-1 of YE and SCB, respectively (C2). The archaeal similarity between these conditions was above 90%; however, the richness and diversity were higher in the C2 (12 and 2.42, respectively) than in C1 (5 and 1.43, respectively) and C6 (11 and 2.29, respectively). Equally, the bacterial similarity between C1 and C6 was 60% while richness of 24 and 17 and diversity of 3.13 and 2.81 were observed in C1 and C6, respectively.

Ruminal microbiota composition associated with ruminal fermentation parameters and milk yield in lactating buffalo in Guangxi, China-A preliminary study

The ruminal microbiota of 15 dairy buffalo was characterized using high-throughput 16S rRNA gene amplicon sequencing. Results showed that Bacteroidetes was the dominant bacterial phylum in all rumen samples, followed by Firmicutes, Proteobacteria, Tenericutes and Verrucomicrobia. Butyrivibrio was positively correlated with average milk fat yield (R = 0.55; p = 0.03), average milk total solid yield (R = 0.56; p = 0.03) and standard milk yield (R = 0.52; p = 0.05). Acinetobacter were positively correlated with average milk protein yield (R = 0.56; p = 0.03), average milk total solid yield (R = 0.60; p = 0.02) and standard milk yield (R = 0.57; p = 0.03). Acetobacter was positively correlated with acetate (R = 0.63; p = 0.01), propionate content (R = 0.55; p = 0.03), butyrate content (R = 0.61; p = 0.02) and total VFA (R = 0.62; p = 0.01). The phyla Proteobacteria (R = 0.53; p = 0.04) and genus Prevotella (R = 0.52; p = 0.05) were positively correlated with butyrate content. Correlation analysis suggested that increased Butyrivibrio and Acinetobacter residing in the buffalo rumen could improve milk performance.

Invited review: Advances and challenges in application of feedomics to improve dairy cow production and health

Dairy cattle science has evolved greatly over the past century, contributing significantly to the improvement in milk production achieved today. However, a new approach is needed to meet the increasing demand for milk production and address the increased concerns about animal health and welfare. It is now easy to collect and access large and complex data sets consisting of molecular, physiological, and metabolic data as well as animal-level data (such as behavior). This provides new opportunities to better understand the mechanisms regulating cow performance. The recently proposed concept of feedomics could help achieve this goal by increasing our understanding of interactions between the different components or levels and their impact on animal production. Feedomics is an emerging field that integrates a range of omics technologies (e.g., genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, and metatranscriptomics) to provide these insights. In this way, we can identify the best strategies to improve overall animal productivity, product quality, welfare, and health. This approach can help research communities elucidate the complex interactions among nutrition, environment, management, animal genetics, metabolism, physiology, and the symbiotic microbiota. In this review, we summarize the outcomes of the most recent research on omics in dairy cows and highlight how an integrated feedomics approach could be applied in the future to improve dairy cow production and health. Specifically, we focus on 2 topics: (1) improving milk yield and milk quality, and (2) understanding metabolic physiology in transition dairy cows, which are 2 important challenges faced by the dairy industry worldwide.

Conjugated Linoleic Acid Effects on Cancer, Obesity, and Atherosclerosis: A Review of Pre-Clinical and Human Trials with Current Perspectives

Obesity and its comorbidities, including type 2 diabetes and cardiovascular disease, are straining our healthcare system, necessitating the development of novel strategies for weight loss. Lifestyle modifications, such as exercise and caloric restriction, have proven effective against obesity in the short term, yet obesity persists because of the high predilection for weight regain. Therefore, alternative approaches to achieve long term sustainable weight loss are urgently needed. Conjugated linoleic acid (CLA), a fatty acid found naturally in ruminant animal food products, has been identified as a potential anti-obesogenic agent, with substantial efficacy in mice, and modest efficacy in obese human populations. Originally described as an anti-carcinogenic fatty acid, in addition to its anti-obesogenic effects, CLA has now been shown to possess anti-atherosclerotic properties. This review summarizes the pre-clinical and human studies conducted using CLA to date, which collectively suggest that CLA has efficacy against cancer, obesity, and atherosclerosis. In addition, the potential mechanisms for the many integrative physiological effects of CLA supplementation will be discussed in detail, including an introduction to the gut microbiota as a potential mediator of CLA effects on obesity and atherosclerosis.

A collection of rumen bacteriome data from 334 mid-lactation dairy cows

With the help of the bacteria in the rumen, ruminants can effectively convert human inedible plant fiber to edible food (meat and milk). However, the understanding of rumen bacteriome in dairy cows is still limited, especially in a large population under the same diet, breed, and milking period. Here we described the sequencing data of 16S rRNA gene of rumen bacteriome from 334 mid-lactation Holstein dairy cows generated using the Illumina HiSeq 2500 (PE250) platform. A total of 24,030,828 raw reads with an average of 71,946 ± 13,450 sequences per sample were obtained. The top ten genera with highest relative abundance accounted for 60.65% of total bacterial sequences. We observed 4,460 overall operational taxonomic units (1,827 ± 94 per sample) based on a 97% nucleotide sequence identity between reads. Totally 6,082 amplicon sequence variants (672 ± 131 per sample) were identified in 334 samples. The shareable datasets can be re-used by researchers to assess other rumen bacterial-related biological functions in dairy cows towards the improvement of animal production and health.

Symposium review: Understanding diet-microbe interactions to enhance productivity of dairy cows

Ruminants are dependent on the microbiota (bacteria, protozoa, archaea, and fungi) that inhabit the reticulo-rumen for digestion of feedstuffs. Nearly 70% of energy and 50% of protein requirements for dairy cows are met by microbial fermentation in the rumen, emphasizing the need to characterize the role of microbes in feed breakdown and nutrient utilization. Over the past 2 decades, next-generation sequencing technologies have allowed for rapid expansion of knowledge concerning microbial populations and alterations in response to forages, concentrates, supplements, and probiotics in the rumen. Advances in gene sequencing and emerging bioinformatic tools have allowed for increased throughput of data to aid in our understanding of the functional relevance of microbial genomes. In particular, metagenomics can identify specific genes involved in metabolic pathways, and metatranscriptomics can describe the transcriptional activity of microbial genes. These powerful approaches help untangle the complex interactions between microbes and dietary nutrients so that we can more fully understand the physiology of feed digestion in the rumen. Application of genomics-based approaches offers promise in unraveling microbial niches and respective gene repertoires to potentiate fiber and nonfiber carbohydrate digestion, microbial protein synthesis, and healthy biohydrogenation. New information on microbial genomics and interactions with dietary components will more clearly define pathways in the rumen to positively influence milk yield and components.

Adaptation responses in milk fat yield and methane emissions of dairy cows when wheat was included in their diet for 16 weeks

Short-term studies have shown that feeding dairy cows diets containing a high proportion (>40%) of wheat may result in reduced milk fat concentration and reduced CH₄ emissions (g of CH₄/cow per d), but no long-term studies have been done on these responses. This study compared the milk production and CH₄ responses when 24 dairy cows were fed diets containing high proportions of either wheat or corn over 16 wk. Cows were assigned to 2 groups and offered a diet (CRN) containing 10.0 kg of dry matter/d of crushed corn grain, 1.8 kg of dry matter/d of canola meal, 0.2 kg of dry matter/d of minerals, and 11.0 kg of dry matter/d of chopped alfalfa hay or a similar diet (WHT) in which wheat replaced the corn. Dry matter intake and milk yields of individual cows were measured daily. Methane emissions from individual cows were measured using controlled climate respiration chambers over 2 consecutive days during each of wk 4, 10, and 16. Milk composition was measured on the 2 d when cows were in chambers during wk 4, 10, and 16. Over the 16-wk experimental period, total dry matter intake remained relatively constant and similar for the 2 dietary treatment groups. At wk 4, CH₄ emission, CH₄ yield (g of CH₄/kg of dry matter intake), milk fat yield, and milk fat concentration were substantially less in cows fed the WHT diet compared with the same metrics in cows fed the CRN diet; but these differences were not apparent at wk 10 and 16. The responses over time in these metrics were not similar in all cows. In 4 cows fed the WHT diet, CH₄ yield, milk fat concentration, and milk fat yield remained relatively constant from wk 4 to 16, whereas for 5 fed the WHT diet, their CH₄ emissions, milk fat yields, and milk fat concentrations almost doubled between wk 4 and 16. In the short term (4 wk), the inclusion of approximately 45% wheat instead of corn in the diet of cows resulted in reductions of 39% in CH₄ yield, 35% in milk fat concentration, and 40% in milk fat yield. However, these reductions did not persist to wk 10 or beyond. Our data indicate that cows do not all respond in the same way with some "adaptive" cows showing a marked increase in CH₄ yield, milk fat concentration, and milk fat yield after wk 4, whereas in other "nonadaptive" cows, these metrics were persistently inhibited to 16 wk. This research shows that short-term studies on dietary interventions to mitigate enteric CH₄ emissions may not always predict the long-term effects of such interventions.

Symposium review: Microbial endocrinology-Why the integration of microbes, epithelial cells, and neurochemical signals in the digestive tract matters to ruminant health

The union of microbiology and neurobiology, which has been termed microbial endocrinology, is defined as the study of the ability of microorganisms to produce and respond to neurochemicals that originate either within the microorganisms themselves or within the host they inhabit. It serves as the basis for an evolutionarily derived method of communication between a host and its microbiota. Mechanisms elucidated by microbial endocrinology give new insight into the ways the microbiota can affect host stress, metabolic efficiency, resistance to disease, and other factors that may prove relevant to the dairy industry.