Metagenomic Analysis of the Rumen Microbiome of Steers with Wheat-Induced Frothy Bloat

Rumen microbiota succession throughout the perinatal period and its association with postpartum production traits in dairy cows: A review

The transition period for dairy cows usually refers to the 3 weeks pre-calving to the 3 weeks post-calving. During this period, dairy cows undergo metabolic and physiological adaptations because of their susceptibility to metabolic and infectious diseases. Poor feeding management under these circumstances may adversely affect the health and subsequent production performance of the cows. Owing to long-term adaptation and evolution, the rumen has become a unique ecosystem inhabited by a complex microbial community closely associated with its natural host. Dietary components are metabolized by the rumen microbiota, and volatile fatty acids and microbial protein products can be used as precursor substances for synthesizing meat and milk components. The successful transition of perinatal dairy cows includes changes in diet, physiology, and the rumen microbiota. Rumen microbial profiles have been confirmed to be heritable and repairable; however, adverse circumstances affect rumen microbial composition, host digestion and metabolism, as well as postpartum production traits of dairy cows for a certain period. Preliminary evidence indicates a close relationship between the rumen microbiota and animal performance. Therefore, changes in rumen microbes during the transition period and the intrinsic links between the microbiota and host postpartum phenotypic traits need to be better understood to optimize production performance in ruminants.

Moringa leaf meal exerts growth benefits in small ruminants through modulating the gastrointestinal microbiome

This study investigated the impact of feeding 17% moringa leaf meal (MLM) on the ruminal and fecal microbial composition and body weight gain (BWG) performance of lambs (Ovis aries) and kids (Capra hircus). A total of n = 28 lambs (n = 14, no-moringa, n = 14, 17% moringa) and 24 kids (n = 12, no-moringa, n = 12, 17% moringa) were involved in the experiment and body weight was recorded fortnightly. Metagenomic shotgun sequencing was performed on 28, 22, and 26 ruminal solid, liquid fraction, and fecal samples from lambs, and 23, 22, and 23 samples from kids. Moringa supplementation significantly increased BWG in lambs (21.09 ± 0.78 to 26.12 ± 0.81 kg) and kids (14.60 ± 1.29 to 18.28 ± 1.09 kg) (p-value ≤ 0.01). Microbiome analysis revealed an elevated Firmicutes:Bacteroidetes ratio in the moringa diet group. Moringa-fed animals exhibited increased microbial genera associated with volatile fatty acids (VFAs) production (Prevotella, Anaerovibrio, Lachnospiraceae, Butyrivibrio, Christensenella) and starch and fiber digesters (Proteobacteria, Ruminococcus). The increase in the bacterial genus Sharpea suggested possible methane reduction and decreased proportion of pathogens, Aliarcobacter_ID28198, Campylobacter_ID194 and Campylobacter_ID1660076 suggest health benefits. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant alterations in microbial gene pool and metabolic pathways related to carbohydrate, protein, lipid and energy metabolism, indicating potential improvements in animal health. Overall, moringa feeding showed higher energy recovery, improved growth, and potential benefits in methane reduction and reduced pathogenic bacteria.

Rumen microbiota helps Tibetan sheep obtain energy more efficiently to survive in the extreme environment of the Qinghai-Tibet Plateau

Introduction

T-sheep and H-sheep exhibit different environmental adaptability and production performance. The rumen microbiome has co-evolved with hosts and plays a vital role in nutrient digestion and energy metabolism. In our previous study, we found that T-sheep have a higher efficiency in energy metabolism than H-sheep, but the rumen microbial community remains unclear.

Methods

In this study, we determined the rumen bacterial profile and rumen fermentation parameters to reveal the bacterial profiles and predictive functions among breeds and diets with four different energy levels, as well as the correlation between bacterial profiles and rumen fermentation characteristics.

Results

The results showed that the rumen total volatile fatty acids (VFAs), acetate, butyrate, total branched-chain VFAs, iso-butyrate, and iso-valerate were higher in T-sheep than H-sheep. The alpha diversity of ruminal bacteria is not affected by dietary energy, but it shows a distinction between the sheep breeds. Specifically, T-sheep rumen bacteria exhibit higher alpha diversity than H-sheep. The beta diversity of ruminal bacteria is not influenced by dietary energy or sheep breeds, indicating similar communities of ruminal bacteria between different diets and sheep breeds. The phyla of Bacteroidetes and Firmicutes predominate in the rumen, with a higher relative abundance of Firmicutes observed in T-sheep than H-sheep. The two most abundant genera in the rumen were Prevotella 1 and Rikenellaceae RC9 gut group. Prevotella 1 is the predominant bacterial genus in the rumen of H-sheep, while the Rikenellaceae RC9 gut group dominates in the rumen of T-sheep. Microbial co-occurrence network analysis reveals that variations in rumen fermentation characteristics result from differences in module abundance, with a higher abundance of VFA-producing modules observed in the rumen of T-sheep. Microbial function prediction analysis showed that dietary energy rarely alters the functional composition of rumen bacteria. However, there were differences in the functions of rumen bacteria between sheep breeds, with T-sheep showing a greater emphasis on energy metabolism-related functions, while H-sheep showed a greater emphasis on protein metabolism-related functions.

Discussion

These findings provide evidence of the special rumen microbial community that helps T-sheep efficiently obtain energy from low-protein and low-energy diets, enabling them to survive in the extreme environment of the Qinghai-Tibet Plateau.

Differences in Milk Fatty Acids Profile of Two Breeds of Water Buffaloes Explained by Their Gastrointestinal Microbiota

This experiment investigated gastrointestinal microbes' role in milk fatty acid differences between Murrah and Nili-Ravi buffaloes. After 30 days of a basal diet, rumen microbial diversity was similar, but Murrah buffaloes had greater partially unsaturated fatty acids like C18:2c9t11. Rumen bacteria like Acetobacter, Ruminococcus, and Prevotellaceae_YAB2003_group correlated positively with milk fatty acids C22:5n-6 and C18:3 in Murrah. Fecal microbial beta diversity differed, with UCG-005 and Prevolla positively correlated with C18:2c9t11 and C22:5n-6. The greater quantity of milk fatty acids C18:3, C18:2c9t11, and C22:5n-6 in Murrah milk was linked to rumen and fecal microbes. This suggests that gastrointestinal microbes like Acetobacter, Ruminococcus, and UCG_005 regulate milk fatty acid concentrations in buffaloes.

Responses of nutrient utilization, rumen fermentation and microorganisms to different roughage of dairy buffaloes

Dairy buffaloes are typically fed a high-forage, low-quality diet with high fiber. These conditions result in an inherent energy and protein inefficiency. In order to make full and rational use of feed resources and improve the production level and breeding efficiency of dairy buffaloes, the effects of various roughages on nutrient digestibility, ruminal fermentation parameters, and microorganisms in dairy buffaloes were studied in this experiment. Three ternary hybrid buffaloes, with an average body weight of 365 ± 22.1 kg, were selected and fitted with permanent rumen fistulas. They were fed six different diets, each consisting of 1 kg concentrate supplement and one of six types of roughage, including alfalfa hay (A diet), oat hay (O diet), whole corn silage (W diet), king grass (K diet), sugarcane shoot silage (S diet), and rice straw hay (R diet) according to an incomplete Latin square design of 3 × 6, respectively. The pre-feeding period of each period was 12 d. From day 13 to 15 was the official experimental period. During the prefeeding period, free feed intake for each roughage was determined, and during the experiment, the roughage was fed at 90% of the voluntary feed intake. Digestion and metabolism tests were carried out using the total manure collection method to determine the feed intake and fecal output of each buffalo, and to collect feed and fecal samples for chemical analysis. On day 15, rumen fluid samples were collected two hours after morning feeding to determine rumen fermentation parameters and bacterial 16 S rRNA high-throughput sequencing was performed. The results showed that DM and OM digestibility were greatest for the W diet and lowest for the S diet. The rumen pH of the O diet was significantly greater than that of the W diet. The concentration of rumen fluid NH3-N (mg/dL) increased with increased CP content. The concentration of total volatile fatty acids (mmol/L) in the rumen decreased with increased NDF content but increased with increased NFC content. The relative abundances of Bacteroidetes, Firmicutes, and Spirochaetes were 57.03-74.84%, 14.29-21.86%, and 0.44-1.43% in the different quality roughage groups. Bacteroidetes were mainly Prevotellaceae1 and Rikenellaceae RC_gut_group with relative abundances of 30.17-45.75% and 3.23-7.82%. The relative abundance of Patescibacteria and Spirochaetes decreased with increasing roughage quality. These results provide a theoretical and practical basis for evaluating the nutritional value of dairy buffalo feed, utilizing feed resources, matching rations, feeding scientifically, and protecting animal health.

Changes in Rumen Microbiology and Metabolism of Tibetan Sheep with Different Lys/Met Ratios in Low-Protein Diets

In ruminants, supplementing appropriate amounts of amino acids improves growth, feed utilization efficiency, and productivity. This study aimed to assess the effects of different Lys/Met ratios on the ruminal microbial community and the metabolic profiling in Tibetan sheep using 16S rDNA sequencing and non-target metabolomics. Ninety-two-month-old Tibetan rams (initial weight = 15.37 ± 0.92 kg) were divided into three groups and fed lysine/methionine (Lys/Met) of 1:1 (LP-L), 2:1 (LP-M), and 3:1 (LP-H) in low-protein diet, respectively. Results: The T-AOC, GSH-Px, and SOD were significantly higher in the LP-L group than in LP-H and LP-M groups (p < 0.05). Cellulase activity was significantly higher in the LP-L group than in the LP-H group (p < 0.05). In the fermentation parameters, acetic acid concentration was significantly higher in the LP-L group than in the LP-H group (p < 0.05). Microbial sequencing analysis showed that Ace and Chao1 indicators were significantly higher in LP-L than in LP-H and LP-M (p < 0.05). At the genus level, the abundance of Rikenellaceae RC9 gut group flora and Succiniclasticum were significantly higher in LP-L than in LP-M group (p < 0.05). Non-target metabolomics analyses revealed that the levels of phosphoric acid, pyrocatechol, hydrocinnamic acid, banzamide, l-gulono-1,4-lactone, cis-jasmone, Val-Asp-Arg, and tropinone content were higher in LP-L. However, l-citrulline and purine levels were lower in the LP-L group than in the LP-M and LP-H groups. Banzamide, cis-jasmone, and Val-Asp-Arg contents were positively correlated with the phenotypic contents, including T-AOC, SOD, and cellulase. Phosphoric acid content was positively correlated with cellulase and lipase activities. In conclusion, the Met/Lys ratio of 1:1 in low-protein diets showed superior antioxidant status and cellulase activity in the rumen by modulating the microbiota and metabolism of Tibetan sheep.

Intensive feeding alters the rumen microbiota and its fermentation parameters in natural grazing yaks

Introduction

Amidst the challenging environmental conditions characterized by low oxygen levels and cold temperatures on the plateau, alterations in nutrient supply emerge as pivotal factors influencing the survival and reproduction of yaks. Intensive feeding stands out as a substantial mechanism for nutrient provision, initiating discernible changes in the host's rumen flora. Within the extreme natural conditions prevailing in the plateau area of northwest Yunnan, China, there exists a con-strained comprehension of the variations in rumen microflora, fermentation parameters, and growth responses exhibited by yaks subjected to intensive feeding.

Methods

This study employs 16S rRNA and ITS sequencing methods to scrutinize the rumen flora of yaks engaged in both natural grazing (G) and intensive feeding (F) on the plateau.

Results

The outcomes unveil that, during the severe winter season, yaks adeptly modulate the abundance and diversity of rumen flora in response to dietary modifications under intensive feeding, aiming to optimize the efficient utilization of dietary fiber and energy. Principal Coordinate Analysis (PCoA) illustrates a substantial alteration in the rumen microbial community of naturally grazing yaks when exposed to intensive feeding. The natural grazing group manifests a higher prevalence of Firmicutes and Bacteroidetes, while the intensive feeding group exhibits heightened levels of Prevotella in the rumen. The Rikenellaceae _ RC9 _ gut_ group, associated with mycobacteria, prevails more abundantly in the natural grazing setting. PICRUSt2 analysis indicates that intensive feeding induces bacterial gene overexpression linked to protein metabolism. Rumen fungi showcase heightened diversity under intensification. Intensive feeding results in an augmented abundance of non-fiber-degrading bacteria and semi-fiber-degrading bacteria, accompanied by elevated concentrations of Volatile Fatty Acids (VFA).

Discussion

These findings yield novel insights into the shifts in the rumen microflora of yaks acclimated to intensive feeding in high-altitude environments, provide an important reference for the nutritional regulation of supplemental feeding of natural grazing yaks in the cold season, ultimately contributing to their enhanced growth.

Effects of Grape Pomace on Growth Performance, Nitrogen Metabolism, Antioxidants, and Microbial Diversity in Angus Bulls

Polyphenol-rich grape pomace (GP) represents a valuable processing by-product with considerable potential as sustainable livestock feed. This study aimed to investigate the effects of different levels of GP on the growth performance and nitrogen utilization efficiency, antioxidant activity, and rumen and rectum microbiota of Angus bulls. Thirty Angus bulls were allocated three dietary treatments according to a completely randomized design: 0% (G0), 10% (G10), and 20% (G20) corn silage dry matter replaced with dried GP dry matter. The results showed that the average daily gain (ADG) of the G0 group and G10 group was higher than that of the G20 group (p < 0.05); urinary nitrogen levels decreased linearly with the addition of GP (linear, p < 0.05). In terms of antioxidants, the levels of catalase (CAT) in the G10 group were higher than in the G0 and G20 groups (p < 0.05), and the total antioxidative capacity (T-AOC) was significantly higher than that in the G20 group (p < 0.05). In addition, in the analysis of a microbial network diagram, the G10 group had better microbial community complexity and stability. Overall, these findings offer valuable insights into the potential benefits of incorporating GP into the diet of ruminants.

Understanding the Diversity and Roles of the Ruminal Microbiome

The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.

Characterization of the ruminal microbiota in sheep and goats fed different levels of tannin-rich Sericea lespedeza hay

Understanding ruminal microbiota and diet-host breed interactions under forage feeding conditions is essential for optimizing rumen fermentation and improving feed efficiency in small ruminants. This study aimed to investigate the effects of different ratios of condensed tannin-rich Sericea lespedeza (SL; Lespedeza cuneata) in the diets on changes and interactions of ruminal microbiota and host species (i.e., sheep and goats). Katahdin sheep (n = 12) and Alpine goats (n = 12) at approximately 10 to 12 mo of age were blocked by body weight (BW = 30.3 and 25.5 kg, respectively) and randomly assigned to one of the 3 treatments. Diets contained 75% coarsely ground forage and 25% concentrate. The forages were 1) 100% alfalfa hay (AL), 2) 100% SL, and 3) 50% AL + 50% SL (ASL). In the present study, the diversity and composition of ruminal microbiota differed between sheep and goats fed similar diets. Based on the taxonomic analysis, there was a distinct clustering pattern (P < 0.05) for sheep by diets, but such a pattern was not observed for goats (P > 0.1). The most predominant phyla were Firmicutes, Bacteroidetes, Ascomycota, and methanogen species of Methanobrevibactor sp. in the rumen of sheep and goats, regardless of diets. The Bacteroidetes and Ascomycota were enriched in sheep fed AL and ASL. In contrast, these microbial phyla were enhanced in goats fed tannin-rich SL diets, with the diet-by-host species interaction (P < 0.02) for the Bacteroidetes phylum. Sheep rumen fluid samples showed a higher degree of variability in microbial community composition compared to goat rumen fluid samples. The relative proportion of the Aspergillus fungi population was reduced to 90.7% in the SL group compared with the AL group, regardless of host species. The antimicrobial activity of tannins and greater sensitivities of selected microbiota species to these tannin compounds during SL feeding in sheep and goats perhaps caused this difference. The results from this study suggest that differences in the microbiota were associated with differences in diets and host species. Therefore, this study provides a better understanding of ruminal microbiota and diet-host species interactions under various tannin-rich diets, which could advance consolidative information on rumen microbiome community diversity changes and may improve sheep and goat production.

Differences in composition and diversity of rumen fungi in buffalo fed different diets

The rumen is a complex ecosystem containing a variety of fungi, which are crucial for the digestive activities of ruminants. Previous research on rumen fungi has mainly focused on anaerobic fungi, given the rumen's reputation as a mainly anaerobic environment. The objective of this study was to investigate rumen fungal diversity and the presence of aerobic fungi in buffalo fed on different diets. Three adult buffaloes were used as experimental animals. Alfalfa hay, oat hay, whole corn silage, sugarcane shoot silage, fresh king grass, dried rice straw, and five kinds of mixed diets with concentrate to roughage ratios of 20:80, 35:65, 50:50, 65:35, and 80:20 were used as the experimental diets. The experimental animals were fed different diets for 22 days. Rumen fluid was collected from the rumen fistula for ITS (Internal Transcribed Spacer) sequencing 2 h after feeding on the morning of day 22. The results indicate the presence of large quantities of aerobic fungi in the rumen of the buffaloes 2 h after feeding and suggest that Ascomycota and Basidiomycota are the dominant fungal groups under different feeding conditions. The study also identified 62 different fungal types, which showed significant differences among the 11 experimental diets.

Physical, Metabolic, and Microbial Rumen Development in Goat Kids: A Review on the Challenges and Strategies of Early Weaning

The digestive system of newborn ruminant functions is similar to monogastric animals, and therefore milk flows into the abomasum instead of rumen for digestion. The rumen undergoes tremendous changes over time in terms of structure, function, and microbiome. These changes contribute to the smooth transition from the dependence on liquid diets to solid diets. Goat kids are usually separated at early ages from their dams in commercial intensive systems. The separation from dams minimizes the transfer of microbiota from dams to newborns. In this review, understanding how weaning times and methodologies could affect the normal development and growth of newborn goats may facilitate the development of new feeding strategies to control stress in further studies.

Differences in Faecal Microbiome Taxonomy, Diversity and Functional Potential in a Bovine Cohort Experimentally Challenged with Mycobacterium avium subsp. paratuberculosis (MAP)

Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, a chronic enteritis which results in emaciation and eventual loss of the animal. Recent advances in metagenomics have allowed a more in-depth study of complex microbiomes, including that of gastrointestinal tracts, and have the potential to provide insights into consequences of the exposure of an animal to MAP or other pathogens. This study aimed to investigate taxonomic diversity and compositional changes of the faecal microbiome of cattle experimentally challenged with MAP compared to an unexposed control group. Faecal swab samples were collected from a total of 55 animals [exposed group (n = 35) and a control group (n = 20)], across three time points (months 3, 6 and 9 post-inoculation). The composition and functional potential of the faecal microbiota differed across time and between the groups (p < 0.05), with the primary differences, from both a taxonomic and functional perspective, occurring at 3 months post inoculation. These included significant differences in the relative abundance of the genera Methanobrevibacter and Bifidobacterium and also of 11 other species (4 at a higher relative abundance in the exposed group and 7 at a higher relative abundance in the control group). Correlations were made between microbiome data and immunopathology measurements and it was noted that changes in the microbial composition correlated with miRNA-155, miR-146b and IFN-ɣ. In summary, this study illustrates the impact of exposure to MAP on the ruminant faecal microbiome with a number of species that may have relevance in veterinary medicine for tracking exposure to MAP.

Recent advances in research in the rumen bloat of ruminant animals fed high-concentrate diets

Rumen bloat is the most common digestive disorder in fattening ruminants, which is responsible for around 2-3 % of deaths in the ruminants industry and is therefore considered to be a serious threat to ruminant farming. The root cause of rumen bloat caused by feeding high concentrate dies would be attributed to the production of a large amount of stable foam during the fattening period. The exact mechanism of rumen foam formation has yet to be investigated. Proteins, polysaccharides and carboxylates derived from feed, and synthesized by microbes during the rumen fermentation may act as foaming agents or stabilizers in the formation progress of rumen foam. Supplementation of condensed tannins and other additives can be an effective way to prevent feedlot bloat induced by feeding high concentrate diets.

Effects of Sodium Nitrate and Coated Methionine on Lactation Performance, Rumen Fermentation Characteristics, Amino Acid Metabolism, and Microbial Communities in Lactating Buffaloes

Sodium nitrate is used as a non-protein nitrogen supplement while methionine is considered as a common methionine additive for ruminants. This study investigated the effects of sodium nitrate and coated methionine supplementation on milk yield, milk composition, rumen fermentation parameters, amino acid composition, and rumen microbial communities in lactating buffaloes. Forty mid-lactation multiparous Murrah buffaloes within the initial days in milk (DIM) = 180.83 ± 56.78 d, milk yield = 7.63 ± 0.19 kg, body weight = 645 ± 25 kg were selected and randomly allocated into four groups (N = 10). All of animals received the same total mixed ratio (TMR) diet. Furthermore, the groups were divided into the control group (CON), 70 g/d sodium nitrate group (SN), 15 g/d palmitate coated L-methionine group (MET), and 70 g/d sodium nitrate +15 g/d palmitate coated L-methionine group (SN+MET). The experiment lasted for six weeks, including two weeks of adaption. The results showed that most rumen-free amino acids, total essential amino acids, and total amino acids in Group SN increased (p < 0.05), while the dry matter intake (DMI) and rumen acetate, propionate, valerate, and total volatile fatty acids (TVFA) in Group MET decreased (p < 0.05). However, there was no significant difference in milk yield, milk protein, milk fat, lactose, total solid content, and sodium nitrate residue in milk among groups (p > 0.05). Group SN+MET had a decreased rumen propionate and valerate (p < 0.05), while increasing the Ace, Chao, and Simpson indices of alpha diversity of rumen bacteria. Proteobacteria and Actinobacteriota were significantly increased (p < 0.05) in Group SN+MET, but Bacteroidota, and Spirochaetota were decreased (p < 0.05). In addition, Group SN+MET also increased the relative abundance of Acinetobacter, Lactococcus, Microbacterium, Chryseobacterium, and Klebsiella, which were positively correlated with cysteine and negatively correlated with rumen acetate, propionate, valerate, and TVFA. Rikenellaceae_RC9_gut_group was identified as a biomarker in Group SN. Norank_f__UCG-011 was identified as a biomarker in Group MET. Acinetobacter, Kurthia, Bacillus, and Corynebacterium were identified as biomarkers in Group SN+MET. In conclusion, sodium nitrate increased rumen free amino acids, while methionine decreased dry matter intake (DMI) and rumen volatile fatty acids. The combined use of sodium nitrate and methionine enriched the species abundance of microorganisms in the rumen and affected the composition of microorganisms in the rumen. However, sodium nitrate, methionine, and their combination had no significant effect on the milk yield and milk composition. It was suggested that the combined use of sodium nitrate and methionine in buffalo production was more beneficial.

Forages and pastures symposium: forage biodegradation: advances in ruminal microbial ecology

The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate-active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography and mass spectrometry that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.

Inclusion of Yucca schidigera extract into finishing diets: impacts on ruminal, physiological, and productive responses of feedlot cattle

This experiment compared ruminal, physiological, and productive responses of feedlot cattle receiving Yucca schidigera extract to replace or fed in conjunction with monensin + tylosin. Angus-influenced steers (n = 120) were ranked by body weight (BW; 315 ± 3 kg) and allocated to 4 groups of 30 steers each. Groups were housed in 1 of 4 drylot pens (30 × 12 m) equipped with GrowSafe feeding systems (4 bunks/pen) during the experiment (day -14 to slaughter). On day 0, groups were randomly assigned to receive a diet containing (2 × 2 factorial): 1) no inclusion or inclusion of monensin + tylosin (360 mg and 90 mg/steer daily, respectively) and 2) no inclusion or inclusion of Y. schidigera extract (4 g/steer daily). Steers were slaughtered in 3 groups balanced by treatment combination (36 steers on day 114, 36 steers on day 142, and 48 steers on day 169). Blood was sampled on days 0, 28, 56, and 84, and the day before shipping to slaughter. On day 41, eight rumen-cannulated heifers (BW = 590 ± 15 kg) were housed with steers (1 pair/pen). Pairs rotated among groups every 21 d, resulting in a replicated 4 × 4 Latin square (n = 8/treatment combination) with 14-d washout intervals. Heifers were sampled for blood and rumen fluid at the beginning and end of each 21-d period. Monensin + tylosin inclusion decreased (P < 0.01) feed intake and improved (P = 0.02) feed efficiency of steers, but did not alter (P ≥ 0.17) steer BW gain or carcass merit traits. Inclusion of Y. schidigera extract did not impact (P ≥ 0.30) steer performance and carcass characteristics. Plasma glucose, insulin, insulin-like growth factor-I, and urea-N concentrations were not affected (P ≥ 0.16) by monensin + tylosin, nor by Y. schidigera extract inclusion in steers and heifers. Ruminal pH in heifers was increased (P = 0.04) by monensin + tylosin, and also by (P = 0.03) Y. schidigera extract inclusion. Rumen fluid viscosity was reduced (P = 0.04) by Y. schidigera extract, and rumen protozoa count was increased (P < 0.01) by monensin + tylosin inclusion. The proportion of propionate in the ruminal fluid was increased (P = 0.04) by monensin + tylosin, and tended (P = 0.07) to be increased by Y. schidigera extract inclusion. Hence, Y. schidigera extract yielded similar improvements in rumen fermentation compared with monensin + tylosin, but without increasing performance and carcass quality of finishing cattle. No complimentary effects were observed when combining all these additives into the finishing diet.

First Steps into Ruminal Microbiota Robustness

Despite its central role in ruminant nutrition, little is known about ruminal microbiota robustness, which is understood as the ability of the microbiota to cope with disturbances. The aim of the present review is to offer a comprehensive description of microbial robustness, as well as its potential drivers, with special focus on ruminal microbiota. First, we provide a briefing on the current knowledge about ruminal microbiota. Second, we define the concept of disturbance (any discrete event that disrupts the structure of a community and changes either the resource availability or the physical environment). Third, we discuss community resistance (the ability to remain unchanged in the face of a disturbance), resilience (the ability to return to the initial structure following a disturbance) and functional redundancy (the ability to maintain or recover initial function despite compositional changes), all of which are considered to be key properties of robust microbial communities. Then, we provide an overview of the currently available methodologies to assess community robustness, as well as its drivers (microbial diversity and network complexity) and its potential modulation through diet. Finally, we propose future lines of research on ruminal microbiota robustness.

Dietary forage to concentrate ratios impact on yak ruminal microbiota and metabolites

To improve the rumen fermentation function and growth performance of yaks (Bos grunniens), better understanding of the effect of different dietary forage to concentrate ratios on rumen microbiota and metabolites is needed. In the present study, three diets with different dietary forage to concentrate ratios (50:50, 65:35, and 80:20) were fed to 36 housed male yaks. The changes in the distribution of rumen microorganisms and metabolites and the interactions between them were studied by 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC–MS). The diversity and richness of microorganisms in the rumen varied according to diet. The most abundant phyla were Firmicutes and Bacteroidetes. Firmicutes was the most abundant in the C50 group, and the relative abundance of Bacteroidetes was significantly lower in the C65 group than in the C80 group (p < 0.05). The Christensenellaceae_R-7_group, Rikenellaceae_RC9_gut_group, and Methanobrevibacter had the highest relative abundances at the genus level. Among them, Christensenellace_R-7_group had the highest relative abundance in the C50 group. The Rikenellaceae_RC9_gut_group was significantly abundant in the C80 group compared with the C50 group. The Methanobrevibacter content was higher in the C65 group than in the other two groups. Both the concentration and metabolic pathways of rumen metabolites were influenced by the dietary concentrate ratio; lipids, lipid-like molecules, organic acid metabolites, and organic oxide-related metabolites differed between the groups. Significant changes were found for six metabolic pathways, including arginine and proline metabolism; glycine, serine, and threonine metabolism; glyoxylate and dicarboxylate metabolism; arginine biosynthesis; glycerophospholipid metabolism; glycerolipid metabolism; and nitrogen metabolism.

Mixed Fermentation of Lactiplantibacillus plantarum and Bacillus licheniformis Changed the Chemical Composition, Bacterial Community, and Rumen Degradation Rate of Tea Residue

Tea residue, as a byproduct in tea processing, is highly nutritious and can be used as a good raw material for ruminant feed. This study aimed to investigate the effects of Lactiplantibacillus plantarum (L. plantarum) and Bacillus licheniformis (B. licheniformis) mixed fermentation of tea residue mixture (tea residue:wheat bran, 7:3) on chemical composition, bacterial community, and rumen degradation rate. Changes in chemical composition and bacterial community were evaluated after 0 (F0), 1 (F1), 3 (F3), and 5 (F5) days of fermentation. The rumen degradation rate was studied by the in situ nylon bag method. Compared with group F0, acid soluble protein in other groups increased while pH and neutral detergent fiber decreased (p < 0.05). The group F5 was the best. The diversity of bacterial communities in group F0 was significantly lower than those in the other groups (p < 0.05). The relative abundance of phylum Firmicutes and the genus Lactobacillus increased with increasing fermentation time. The rumen degradation rates of dry matter, crude protein, neutral detergent fiber, and acid detergent fiber were increased after fermentation. In conclusion, mixed fermentation of tea residue by L. plantarum and B. licheniformis can ameliorate chemical composition, reduce bacterial community diversity, and improve the rumen degradation rate.

The Bacterial and Fungal Gut Microbiota of the Greater Wax Moth, Galleria mellonella L. Consuming Polyethylene and Polystyrene

Plastic production has been increasing exponentially in the last 60 years, but plastic disposal is out of control, resulting in the pollution of all ecosystems on Earth. Finding alternative environmentally sustainable choices, such as biodegradation by insects and their associated gut microbiota, is crucial, however we have only begun to characterize these ecosystems. Some bacteria and one fungus have been previously identified in the gut of Greater Wax Moth larvae (Galleria mellonella L., Lepidoptera, Pyralidae) located mainly in the Northern hemisphere. The aim of this study was to describe changes in the gut microbiota associated with the consumption of polyethylene and polystyrene by the Greater Wax Moth in Argentina, considering both bacteria and fungi. Larvae were fed polyethylene, polystyrene and beeswax as control for 7 days. Next generation sequencing revealed changes in the bacterial gut microbiome of the wax moth larvae at the phyla and genus levels, with an increase in two Pseudomonas strains. The fungal communities showed no differences in composition between diets, only changing in relative abundance. This is the first report of both bacterial and fungal communities associated with a plastivore insect. The results are promising and call for more studies concerning a potential multi-kingdom synergy in the plastic biodegradation process.

Metagenomic Analysis Revealed Differences in Composition and Function Between Liquid-Associated and Solid-Associated Microorganisms of Sheep Rumen

The rumen microbiota plays a key role in the utilization of plant materials by ruminants, yet little is known about the key taxa and their genetic functions of the rumen sub-environment involved in the ruminal degradation process. Understanding the differences in the composition and function of ruminal microbiota in the liquid-associated (LA) and solid-associated (SA) systems is needed to further study and regulate rumen function and health. In this study, rumen contents of nine sheep were collected to separate LA and SA systems with elution and centrifugal precipitation. Metagenome sequencing was used to investigate the differences in microbial composition and genetic functions of LA and SA systems, with special emphasis on their degradational potential toward carbohydrates. Results showed that the dominant species composition was similar between the two systems, but SA microorganisms had a higher relative abundance than LA microorganisms in all taxa. The concentration of fiber-degrading bacteria, such as Ruminococcus, Treponema, and Fibrobacter, was higher and Prevotella was lower in the SA vs. LA system. Additionally, SA microorganisms dominated in cellulose degradation, while LA microorganisms were more important in starch utilization based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO)'s functional categories and Carbohydrate-Active Enzymes (CAZymes). In general, SA microorganisms are more abundant and important in metabolic functions than LA, such as carbohydrate and amino acid metabolisms. In summary, the key differential biomarkers between LA and SA systems were Prevotella, Ruminococcus, Treponema, and Fibrobacter. Ruminal microbes degraded carbohydrates synergistically with SA, thus, more focusing on cellulose and hemicellulose, while LA is more important to starch.

Meta-analysis of the effects of monensin on growth and bloat of cattle on pasture

Monensin has been part of the beef production landscape for over 45 years. Although first approved for use in finishing cattle, it has since been approved for cattle in extensive production systems and has been an economical way to increase performance of forage-fed animals. This meta-analysis investigated the impacts of monensin on performance of stocker cattle on high-forage diets. The stocker performance analysis resulted from 38 experiments with 73 mean comparisons; bloat analysis was conducted with 12 experiments with 23 mean comparisons. The metaphor package (version 2.4-0) for R (version 4.0.3; www.r-project.org) was used to determine the overall effect size of monensin compared to a negative control. Each study's n, means, and SEM or P-value was used to calculate the mean difference and estimate of within-study variance for responses of interest. Moderators of monensin response considered in the analysis were delivery method, dose, study duration, initial calf BW, diet ME and CP, and forage category. Initial BW and basal ADG averaged 236 ± 45.9 kg and 0.72 ± 0.28 kg, respectively. In the ADG analysis, the only significant moderator of those considered was length of the study (P < 0.01); as duration of the study increased, the ADG response to monensin decreased by 0.0007 kg/day. For the average 112-day length of study, the average monensin response was estimated to be 0.0784 kg/day increase in ADG, approximately 10% above controls. Sufficient information was presented in 18 citations representing 40 mean comparisons for determining the effect of monensin on BW at the end of the experiment. The response model (P < 0.01) for ending BW, kg = 22.3-0.05 (initial calf BW, kg). Thus, for the average initial BW of 235 kg the average monensin response was estimated to be 10.6 kg increase in average ending BW. The incidence (-20%) and severity (-0.7 bloat score) of bloat was found to be reduced in bloat-prone pastures. There is ample evidence that monensin increases performance of growing calves on high forage diets along with reducing the incidence and severity of bloat.

Intestinal Microbial Diversity of Free-Range and Captive Yak in Qinghai Province

BACKGROUND

The gut microbiome is a large and complex organic assemblage with subtle and close relationships with the host. This symbiotic mechanism is important for the health and adaptability of the host to the environment. Compared with other ruminants, there are few studies on yak intestinal microbes. The study of the gut microbiota of the yak will help us better understand the correlation between the microbiota and the environmental adaptability of the host. In this study, we adapted 16S rDNA sequencing technology to investigate the diversity and composition of the intestinal microbial community in free-range yaks and captive yaks living on the Qinghai-Tibet Plateau (QTP).

RESULTS

Sequencing results showed that the intestinal microbial community diversity was significantly different between free-range yaks and captive yaks. Firmicutes and Bacteroidetes were the dominant bacteria in both free-range and captive yaks. However, there were differences between the microbes of the two analyzed feeding styles in different classification levels. Compared with the captive type, free-range yaks had a higher abundance of Ruminococcaceae, Eubacteriaceae, Desulfovibrionaceae, Elusimicrobium, and Oscillibacter, while the abundance of Succinivibrionaceae, Clostridiales, Lachnospiraceae, Prevotellaceae, Roseburia, and Barnesiella was relatively low. The feeding method may be the key factor for the formation of intestinal flora differences in yaks, while altitude did not significantly affect Qinghai yak.

CONCLUSIONS

In this study, we used 16S rDNA sequencing technology to investigate the composition of intestinal flora in free-range and captive yaks living on the QTP. The exploration of dietary factors can provide a theoretical basis for scientifically and rationally breeding yaks and provides a new direction for the development of prebiotics and microecological agents.

Comparison of Microbial Community and Metabolites in Four Stomach Compartments of Myostatin-Gene-Edited and Non-edited Cattle

Myostatin (MSTN), a major negative regulator of skeletal muscle mass and an endocrine factor, can regulate the metabolism of various organisms. Inhibition of the MSTN gene can improve meat production from livestock. Rumen microorganisms are associated with production and health traits of cattle, but changes in the microbial composition and metabolome in the four stomach compartments of MSTN gene-edited cattle have not previously been studied. Our results indicated that microbial diversity and dominant bacteria in the four stomach compartments were very similar between MSTN gene-edited and wild-type (WT) cattle. The microbiota composition was significantly different between MSTN gene-edited and WT cattle. Our results show that the relative abundance of the phylum Proteobacteria in the reticulum of MSTN gene-edited cattle was lower than that of WT cattle, whereas the relative abundance of the genus Prevotella in the omasum of MSTN gene-edited cattle was significantly higher than that of WT cattle. Metabolomics analysis revealed that the intensity of L-proline and acetic acid was significantly different in the rumen, reticulum, and abomasum between the two types of cattle. Meanwhile, pathway topology analysis indicated that the differential metabolites were predominantly involved in arginine biosynthesis and glutamate metabolism in the rumen, reticulum, and omasum but were mainly involved in pyruvate metabolism and glycolysis/gluconeogenesis in the abomasum. Spearman correlation network analysis further demonstrated that there was a significant correlation between microflora composition and metabolic pathways. These findings provide clues for studying nutrient digestion and absorption ability of MSTN gene-edited cattle.

Effects of Mulberry Branch and Leaves Silage on Microbial Community, Rumen Fermentation Characteristics, and Milk Yield in Lactating Dairy Cows

This study investigated the effects of mulberry branch and leaves (MBL) silage on milk yield, ruminal fermentation, and bacteria composition in dairy cows. Thirty-six mid-lactation cows were selected and randomly allocated into three groups. The control group (C) was fed on a total mixed ratio (TMR) diet, while the experimental groups were fed on TMR supplemented with 5% (L) and 10% (H) MBL silage. The experiment lasted for eight weeks, including two weeks of adaption. The results showed that Group H had an increased milk yield, milk fat content (p < 0.05), and 4% feed conversion ratio (p = 0.10). In addition, rumen propionic acid was significantly increased (p < 0.05), while acetate/propionate was significantly decreased (p < 0.05) in the high MBL silage group. The microbiome analysis showed that Bacteroides, Firmicutes, and Proteobacteria were the predominant phyla. Compared with Group C, the abundance of Bacteroides was significantly decreased (p < 0.01), while the Firmicutes and Proteobacteria were increased but not significantly different in Groups L and H. Prevotella was significantly decreased (p < 0.05) in the MBL silage groups, and Succinivibrionaceae_UCG-001 was increased in Group H. The correlation analysis showed that eight bacterial species belonging to Firmicutes were positively correlated with propionic acid. However, four bacterial species belonging to the Bacteroides group were negatively correlated with propionic acid. In conclusion, feed supplementation with about 5–10% of MBL silage could modulate the rumen microbiota and fermentation, and increase the abundance of fiber-digesting, propionic acid synthesis and milk fat-related microorganisms, thus improving milk yield in dairy cows.

Applications of Metagenomics for Unrevealing the Extended Horizons of Microbiota Prevalence from Soil to Human Health

Phylogenetic analysis of different ecosystems has shown that the number of microbial communities in a single sample exceeds their cultured counterparts. Microbes have been found throughout nature and can thrive in adverse conditions. Besides inhabiting diverse environments, they also play a key role in the maintenance of the ecosystem. Most of these microbes are either unculturable or difficult to culture with conventional culturing methods. Metagenomics is an emerging field of science that has been in the light for a decade and offers a potential way to assess microbial diversity. The development of metagenomics opens new ways to study genetic material directly from the environmental samples. DNA sequencing and synthesis technologies are making it possible to read and write entire genomes. The huge amount of data obtained from genome sequencing inevitably requires bioinformatics tools to handle and further process them for analysis. Advances in DNA sequencing and high-performance computing have brought about exemplar improvement in metagenomics, allowing in-depth study of the largely unexplored frontier of microbial life. This culture-independent method provides extensive information regarding the structure, composition, and function of the diverse assemblages of the environmental microbes. The current review presents an overview of the technical aspects of metagenomics along with its diverse applications.

Rumen Fermentation-Microbiota-Host Gene Expression Interactions to Reveal the Adaptability of Tibetan Sheep in Different Periods

Simple Summary

The Qinghai-Tibet Plateau has a unique ecological environment, involving high altitude, low oxygen levels, strong ultraviolet rays, and severe imbalances in seasonal forage supply, which poses a serious threat to the livestock that feeds on natural pastures to maintain their survival. We have carried out a long-term follow-up study on rumen fermentation characteristics, the microbiota, and rumen epithelial gene expression of local Tibetan sheep. Correlation analysis showed that there were interactions among rumen fermentation characteristics, the microbiota, and host gene expression, mainly by adjusting the amino acid metabolism pathway and energy metabolism pathway to improve energy utilization. At the same time, we adjusted the balance of the rumen “core microbiota”, which was regulated to promote the development of rumen and maintain the homeostasis of rumen environment (which relies Tibetan sheep can better adapt to the harsh environment in different periods of the Qinghai-Tibet Plateau). This provides a theoretical basis for the breeding and management of Tibetan sheep on the Qinghai-Tibet Plateau.

Abstract

As an important ruminant on the Qinghai-Tibet Plateau, Tibetan sheep can maintain their population reproduction rate in the harsh high-altitude environment of low temperature and low oxygen, which relies on their special plateau adaptations mechanism that they have formed for a long time. Microbiomes (known as “second genomes”) are closely related to the nutrient absorption, adaptability, and health of the host. In this study, rumen fermentation characteristics, the microbiota, and rumen epithelial gene expression of Tibetan sheep in various months were analyzed. The results show that the rumen fermentation characteristics of Tibetan sheep differed in different months. The total SCFAs (short-chain fatty acids), acetate, propionate, and butyrate concentrations were highest in October and lowest in June. The CL (cellulase) activity was highest in February, while the ACX (acid xylanase) activity was highest in April. In addition, the diversity and abundance of rumen microbes differed in different months. Bacteroidetes (53.4%) and Firmicutes (27.4%) were the dominant phyla. Prevotella_1 and Rikenellaceae_RC9_gut_group were the dominant genera. The abundance of Prevotella_1 was highest in June (27.8%) and lowest in December (17.8%). In addition, the expression of CLAUDIN4 (Claudin-4) and ZO1 (Zonula occludens 1) was significantly higher in April than in August and December, while the expression of SGLT1 (Sodium glucose linked transporter 1) was highest in August. Correlation analysis showed that there were interactions among rumen fermentation characteristics, the microbiota, and host gene expression, mainly by adjusting the amino acid metabolism pathway and energy metabolism pathway to improve energy utilization. At the same time, we adjusted the balance of the rumen “core microbiota” to promote the development of rumen and maintain the homeostasis of rumen environment, which makes Tibetan sheep better able to adapt to the harsh environment in different periods of the Qinghai-Tibet Plateau.

Comparing noninvasive sampling techniques with standard cannula sampling method for ruminal microbial analysis

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Ruminal cannula is the gold standard for sampling rumen contents but is limited to few animals.

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Noninvasive methods are needed as proxy for cannula to enable sampling larger numbers of cows.

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Saliva, rumination bolus, tube-derived rumen samples, and feces were compared with cannula samples.

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Microbial community in the solid fraction of tube samples mirrored that of cannula samples.

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Rumination bolus may serve as a proxy for cannula samples under certain conditions.

Rumen microbes play an important role in the conversion of indigestible plant material to energy and protein in dairy cows. Sampling for ruminal contents via cannula is considered the gold standard technique for microbial analysis, but the technique requires ruminally cannulated animals and specialized animal facilities. The purpose of this study was to determine whether other sampling methods and locations along the digestive tract may serve as noninvasive proxies to the cannula method for microbial analysis. Six ruminally cannulated lactating Holstein dairy cows were adapted to a standard total mixed ration for 2 wk and sampled during the third week. Sampling locations and methods included salivary content, rumination bolus (regurgitated digesta collected from the cow's mouth), feces, and rumen contents via stomach tube and cannula. Stomach tube and cannula samples differ in proportions of solid and liquid material and were therefore separated into whole (as collected), liquid, and solid fractions. Samples were collected at 0 (before feeding), 2, 4, 6, 8, and 12 h after feeding over 2 d. All samples were extracted for total genomic DNA and selected samples for metabolically active DNA (RNA), PCR-amplified for the V1-V2 region of the 16S rRNA bacterial gene, and analyzed for bacterial diversity using the QIIME2 pipeline followed by statistical analysis in R (https://www.R-project.org/). In DNA-based analysis, at the community level, saliva, rumination bolus, and fecal samples clustered in separate groups, whereas all fractions of stomach tube and cannula samples clustered together, indicating that microbial communities of stomach tube and cannula samples were homogeneous. Rumination bolus samples at 6, 8, and 12 h after feeding clustered with stomach tube and cannula samples, indicating that rumination bolus samples may be an alternative for cannula samples; however, time of sampling is critical for sampling of bolus digesta. Results of the RNA-based analysis of rumination bolus samples and solid samples from cannula and stomach tube at 0 and 6 h after feeding were similar. We concluded that the solid fraction of samples obtained via the stomach tube method may serve as a proxy for the solid fraction of whole ruminal contents obtained via cannula for DNA-based microbial investigations. Both rumination bolus and stomach tube solid samples may serve as proxies for cannula solid samples for RNA-based microbial analysis.

Effects of Condensed Tannins Supplementation on Animal Performance, Phylogenetic Microbial Changes, and In Vitro Methane Emissions in Steers Grazing Winter Wheat

Simple Summary

Grazing wheat pasture is a common practice throughout the southeastern and south-central United States; however, the practice is limited by concerns regarding the occurrence of bloat. In addition, there are few reports concerning methane production by cattle grazing wheat pasture. Naturally occurring plant secondary compounds, including condensed tannins (CT), saponins, and essential oils, are extensively evaluated as natural alternatives to control bloat and to mitigate methane production. However, the effects of CT supplementation on ruminal gas production, rumen microflora community changes, and animal performance in stocker cattle grazing wheat forage are not fully defined. Supplementation with CT induced changes in ruminal bacteria, reduced methane emissions, and increased animal performance. These data indicate that CT supplementation may benefit stocker producers grazing wheat pasture by decreasing the incidence of bloat and increasing animal performance by changing rumen fermentation.

Abstract

Eighteen growing rumen-cannulated steers, with initial body weight (BW) of 167.4 ± 7.10 kg, were randomly allocated to one of three treatments that included a control (0% CT) and two CT treatment levels (0.05% and 0.07% condensed tannins (CT)/kg BW) with two replicates each. Both in vivo and in vitro experiments were conducted. In Exp. 1, final BW and average daily gain were greater (p < 0.05) for the 0.07% CT treatment compared to either 0.05% CT or control groups. Rumen bacterial populations in steers fed winter wheat in the absence of CT represented large proportions of the moderate-guanines and cytosines (GC) containing bacterial clusters with similarity coefficient (SC) ranging from 64% to 92% In the presence of CT on day 0, day 20, and day 60, however, the SC was 60% or greater (90% SC) with multiple bacterial band clusters as shown by the denaturing gel gradient electrophoresis banding patterns. In Exp. 2, in vitro total gas, potential gas, and CH₄ productions decreased (p < 0.01) as CT supplementation increased in steers grazing wheat forage. These results suggested that the administration of CT improved BW gain and induced bacterial community changes in the rumen of steers grazing wheat forage.

Selenium Yeast Dietary Supplement Affects Rumen Bacterial Population Dynamics and Fermentation Parameters of Tibetan Sheep (Ovis aries) in Alpine Meadow

Selenium (Se) deficiency is a widespread and seasonally chronic phenomenon observed in Tibetan sheep (Ovis aries) traditionally grazed on the Qinghai-Tibet Plateau (QTP). Effects of the dietary addition of Se-enriched yeast (SeY) on the bacterial community in sheep rumen and rumen fermentation were evaluated with the aim of gaining a better understanding of the rumen prokaryotic community. Twenty-four yearling Tibetan rams [initial average body weight (BW) of 31.0 ± 0.64 kg] were randomly divided into four treatment groups, namely, control (CK), low Se (L), medium Se (M), and high Se (H). Each group comprised six rams and was fed a basic diet of fresh forage cut from the alpine meadow, to which SeY was added at prescribed dose rates. This feed trial was conducted for over 35 days. On the final day, rumen fluid was collected using a transesophageal sampler for analyzing rumen pH, NH3-N content, volatile fatty acid (VFA) level, and the rumen microbial community. Our analyses showed that NH3-N, total VFA, and propionate concentrations in the M group were significantly higher than in the other groups (P < 0.05). Both the principal coordinates analysis (PCoA) and the analysis of similarities revealed that the bacterial population structure of rumen differed among the four groups. The predominant rumen bacterial phyla were found to be Bacteroidetes and Firmicutes, and the three dominant genera in all the samples across all treatments were Christensenellaceae R7 group, Rikenellaceae RC9 gut group, and Prevotella 1. The relative abundances of Prevotella 1, Rikenellaceae RC9 gut group, Ruminococcus 2, Lachnospiraceae XPB1014 group, Carnobacterium, and Hafnia-Obesumbacterium were found to differ significantly among the four treatment groups (P < 0.05). Moreover, Tax4fun metagenome estimation revealed that gene functions and metabolic pathways associated with carbohydrate and other amino acids were overexpressed in the rumen microbiota of SeY-supplemented sheep. To conclude, SeY significantly affects the abundance of rumen bacteria and ultimately affects the rumen microbial fermentation.

Temporal changes in total and metabolically active ruminal methanogens in dairy cows supplemented with 3-nitrooxypropanol

The purpose of this study was to investigate the effect of 3-nitrooxypropanol (3-NOP), a potent methane inhibitor, on total and metabolically active methanogens in the rumen of dairy cows over the course of the day and over a 12-wk period. Rumen contents of 8 ruminally cannulated early-lactation dairy cows were sampled at 2, 6, and 10 h after feeding during wk 4, 8, and 12 of a randomized complete block design experiment in which 3-NOP was fed at 60 mg/kg of feed dry matter. Cows (4 fed the control and 4 fed the 3-NOP diet) were blocked based on their previous lactation milk yield or predicted milk yield. Rumen samples were extracted for microbial DNA (total) and microbial RNA (metabolically active), PCR amplified for the 16S rRNA gene of archaea, sequenced on an Illumina platform, and analyzed for archaea diversity. In addition, the 16S copy number and 3 ruminal methanogenic species were quantified using the real-time quantitative PCR assay. We detected a difference between DNA and RNA (cDNA)-based archaea communities, revealing that ruminal methanogens differ in their metabolic activities. Within DNA and cDNA components, methanogenic communities differed by sampling hour, week, and treatment. Overall, Methanobrevibacter was the dominant genus (94.3%) followed by Methanosphaera, with the latter genus having greater abundance in the cDNA component (14.5%) compared with total populations (5.5%). Methanosphaera was higher at 2 h after feeding, whereas Methanobrevibacter increased at 6 and 10 h in both groups, showing diurnal patterns among individual methanogenic lineages. Methanobrevibacter was reduced at wk 4, whereas Methanosphaera was reduced at wk 8 and 12 in cows supplemented with 3-NOP compared with control cows, suggesting differential responses among methanogens to 3-NOP. A reduction in Methanobrevibacter ruminantium in all 3-NOP samples from wk 8 was confirmed using real-time quantitative PCR. The relative abundance of individual methanogens was driven by a combination of dietary composition, dry matter intake, and hydrogen concentrations in the rumen. This study provides novel information on the effects of 3-NOP on individual methanogenic lineages, but further studies are needed to understand temporal dynamics and to validate the effects of 3-NOP on individual lineages of ruminal methanogens.

Supplementing Yucca schidigera extract to mitigate frothy bloat in beef cattle receiving a high-concentrate diet

This experiment compared incidence of frothy bloat, as well as ruminal, physiological, and performance responses of beef heifers receiving a bloat-provoking diet and supplemented with Yucca schidigera extract. Sixteen ruminally cannulated Angus-influenced heifers were ranked by body weight (BW) and assigned to 4 groups of 4 heifers each. Groups were enrolled in a replicated 4 × 4 Latin square design containing 4 periods of 28 d, and a 21-d washout interval between periods. Groups were assigned to receive no Y. schidigera extract (CON), or Y. schidigera extract at (as-fed basis) 1 g/heifer daily (YS1), 2 g/heifer daily (YS2), or 4 g/heifer daily (YS4). During each period, heifers (n = 16/treatment) were housed in individual pens, and fed a sorghum (Sorghum bicolor L.)-based bloat-provocative diet at 2% of their BW. Diet and treatments were individually fed to heifers, twice daily in equal proportions (0700 and 1600 hours). Heifers were assessed for bloat score (0 to 5 scale, increasing according to bloat severity) 3 hr after the morning feeding. Blood samples were collected on days 0, 7, 14, 21, and 28 prior to (0 hr) and at 3, 6, and 9 hr relative to the morning feeding. Rumen fluid samples were collected at the same time points on days 0 and 28. Orthogonal contrasts were tested to determine whether inclusion of Y. schidigera extract (0, 1, 2, or 4 g/heifer daily) yielded linear or quadratic effects, and explore an overall effect of Y. schidigera extract supplementation (CON vs. YS1 + YS2 + YS4). Rumen fluid viscosity was impacted quadratically by Y. schidigera extract inclusion (P = 0.02), being greatest in YS1, followed by YS2, and equivalent between CON and YS4 heifers. Heifers receiving Y. schidigera extract had greater (P ≤ 0.05) rumen propionate, iso-valerate, and valerate concentrations, as well as less (P < 0.01) acetate : propionate ratio compared with CON heifers. Inclusion of Y. schidigera extract linearly increased (P ≤ 0.04) average daily gain and feed efficiency. No other treatment effects were noted (P ≥ 0.19) including bloat score (1.07 ± 0.03 across treatments), ruminal protozoa count, plasma concentrations of cortisol, haptoglobin, urea N, total protein, and rumen concentration of total volatile fatty acids. Supplementing Y. schidigera extract up to 4 g/d favored rumen propionate concentrations and linearly increased growth and feed efficiency but failed to mitigate incidence of frothy bloat in beef heifers consuming a grain-based bloat-provocative diet.

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.

Comparative study of the bacterial communities throughout the gastrointestinal tract in two beef cattle breeds

Investigation of the compositional and functional characteristics of the gastrointestinal bacterial community in beef cattle breeds can improve our understanding of the influence of gastrointestinal tract (GIT) regions and host breeds on the bacterial community. In this study, 16S ribosomal RNA (16S rRNA) gene amplicon sequencing was used to characterize the bacterial communities in the rumen, duodenum, jejunum, ileum, caecum, and colon of Xuanhan yellow cattle (XHC) and Simmental crossbred cattle (SXC). The results showed that the diversity of the bacterial population was different in GIT regions of XHC and SXC (P < 0.05). In total, ten bacterial phyla, sixteen bacterial genera, and nine metabolic pathways were identified in the core bacteria. The phyla Firmicutes, Bacteroidetes, and Proteobacteria were predominant, but their proportions were different in GIT regions (P < 0.05). The diversity, structure, and composition of the bacteria in the rumen were similar between the breeds (P > 0.05), and the indices in the intestine showed significant differences (P < 0.05). Moreover, the composition and structure of the bacterial communities in the rumen, small intestine, and large intestine were different regardless of the breed. Thus, the bacterial communities were different among the gastrointestinal regions in each breed, and the bacterial community in the rumen had more stable characteristics than that in the intestine between two breeds. Further studies may focus on the minor microbial communities and the functions of GIT bacteria to better understand gut-microbe interactions. KEY POINTS: • Differences in bacteria among gastrointestinal regions differ in cattle breeds. • Differences between the breeds in the ruminal bacteria are less pronounced than differences in the intestinal bacteria.

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.

Exploring the Rumen and Cecum Microbial Community from Fetus to Adulthood in Goat

Simple Summary

The rumen and cecum are two important fermentation organs in ruminants. The acquisition and development of the neonatal microbiome, as well as the difference between these two organs, was important. We performed 16S rRNA gene sequencing to study the diversity, structure and composition of the goat microbial communities between the rumen and cecum from fetus to adulthood. The results revealed the microbial transmission routes from the mother to fetus, and also revealed the establishment and dynamic fluctuations of the gut microbiome from fetus to adulthood in goats.

Abstract

The present study aimed to investigate the colonization process of epithelial bacteria attached to the rumen and intestinal tract tissue during the development of goats after birth. However, this process from fetus to adulthood was very limited. In goats, the rumen and cecum are two important fermentation organs, and it is important to study the acquisition and development of the neonatal microbiome, as well as the difference between these two organs. To characterize the microbial establishment and dynamic changes in the rumen and cecum from fetus to adulthood, we performed 16S rRNA gene sequencing for 106 samples from 47 individuals of nine pregnant mother–fetus pairs and 16 kids from birth up to 6 months. The diversity, structure and composition of the microbial communities were distinct between the rumen and cecum after birth, while they were similar in the fetal period. The study showed a rapid loss and influx of microbes at birth, followed by slight selection after drinking colostrum, and then a strong selection after weaning, suggesting that the establishment and dynamic fluctuations of the gut microbiome undergoes three distinct phases of microbiome progression in life: a conserved phase (during late pregnancy in the fetus), a transitional phase (newborn until weaning), and a stable phase (from weaning to adulthood). The results supported the view that microbes exist in the fetus, and revealed the establishment and dynamic fluctuations of the gut microbiome from fetus to adulthood in goats.

Influence of probiotics on biofilm formation and diversity of bacteria colonising crop sorghum ensiled with unsalable vegetables

The objective of this study was to characterise in situ digestion kinetics and bacterial colonisation of crop sorghum ensiled with unsalable carrot or pumpkin at 0, 20 or 40% dry matter (DM). Silages with or without the application of a commercial probiotic were incubated in situ for 0, 3, 6, 9, 24 and 48 h. Calculation of in situ digestion kinetics was conducted for DM, organic matter and neutral detergent fibre (aNDF). The V4 region of the 16S rRNA gene was sequenced to determine the composition and diversity of bacteria colonising the silage. Organic matter and DM digestion kinetics indicated that greater vegetable inclusion increased (P < 0.05) the soluble fraction and effective degradability. Bacterial richness at 48 h incubation was greater (P = 0.02) in 20% carrot and 40% pumpkin treatments, compared with the control. An effect of level × probiotic was observed with increased Shannon diversity (P = 0.01) for 40% carrot and 20% pumpkin probiotic treatments, respectively. Primary colonising bacteria were members of the Prevotella genus, dominating after 3 and 6 h of incubation. The abundance of Prevotella increased by 4.1% at 3 h (P < 0.01) and by 4.7% at 9 h incubation with probiotics, compared with the control. Secondary biofilm colonisers included members of Treponema, Saccharofermentans, Fibrobacter, Ruminobacter and Anaerosporobacter genera, dominant from 9 h incubation onward. This study demonstrated that including unsalable vegetables at 20 or 40% DM increases the soluble fraction and effective degradability of sorghum silage during in situ digestion and increases diversity of bacteria colonising ensiled vegetables within the rumen. KEY POINTS: • Ensiling unsalable vegetables is a viable strategy to reduce food waste. • Ensiled vegetables increased in situ soluble fraction and effective degradability. • Bacterial richness at 48 h incubation improved with 20% carrot or 40% pumpkin. • Diversity of colonising rumen bacteria increased with carrot or pumpkin inclusion.

Comparative Analysis of Microbial Community Structure and Function in the Gut of Wild and Captive Amur Tiger

It has been well acknowledged that the gut microbiome is important for host health, composition changes in these microbial communities might increase susceptibility to infections and reduce adaptability to environment. Reintroduction, as an effective strategy for wild population recovery and genetic diversity maintenance for endangered populations, usually takes captive populations as rewilding resource. While, little is known about the compositional and functional differences of gut microbiota between captive and wild populations, especially for large carnivores, like Amur tiger. In this study, high throughput sequencing of the 16S ribosomal RNA (rRNA) gene (amplicon sequencing) and metagenomics were used to analyze the composition and function variations of gut microbiota communities between captive and wild Amur tiger populations based on total 35 fecal samples (13 from captive tigers and 22 from wild tigers). Our results showed that captive Amur tigers have higher alpha diversity in gut microbiota, but that the average unweighted UniFrac distance of bacterial taxa among wild Amur tigers was much larger. The function differences involve most aspects of the body functions, especially for metabolism, environmental information processing, cellular processes, and organismal systems. It was indicated that the diet habit and environment difference between captive and wild populations lead to composition differences of gut microbiota and then resulted in significant differences in functions. These contrasts of functional and compositional variations in gut microbiota between wild and captive Amur tigers are essential insights for guiding conservation management and policy decision-making, and call for more attention on the influence of gut microbiota on the ability of captive animals to survive in the wild.

The gut bacterial diversity of sheep associated with different breeds in Qinghai province

Background

Gut microbiota play important roles in their co-evolution with mammals. However, little is understood about gut bacterial community of Tibetan sheep compared with other sheep breeds. In this study, we investigated the gut bacterial community in 4 different sheep breeds living in the Qinghai-Tibetan Plateau (QTP) of China using high-throughput sequencing (HTS) technique.

Results

The results suggested that bacterial community abundance and breeds diversity of Tibetan sheep (TS) were significantly lower than that of the other three breeds of sheep [Dorset sheep (DrS), Dorper sheep (DrS) and Small Tail Han sheep (STHS)] (p < 0.05). Principal coordinates analysis (PCoA) and nonmetric multidimensional scaling (NMDS) analysis indicated that microbiome composition of TS was significantly different from that of other three sheep breeds (p < 0.01). Firmicutes was the most predominant microbial phylum in the gut, followed by Bacteroidetes. The gut bacterial community of TS showed higher proportions of phylum Spirochaetes, Proteobacteria and Verrucomicrobia, compared to the other three sheep breeds, but the Deferribacteres was absent in TS. At the genus level, Treponema, Succinivibrio, 5-7 N15 and Prevotella showed significantly higher abundance in TS than in the other three sheep breeds (p < 0.05).

Conclusions

In this study, we first employed HTS to understand the gut microbiomes among different sheep breeds in QTP of China.

Identification of Microbial Genetic Capacities and Potential Mechanisms Within the Rumen Microbiome Explaining Differences in Beef Cattle Feed Efficiency

In this study, Bos Taurus cattle offered one high concentrate diet (92% concentrate-8% straw) during two independent trials allowed us to classify 72 animals comprising of two cattle breeds as "Low" or "High" feed efficiency groups. Digesta samples were taken from individual beef cattle at the abattoir. After metagenomic sequencing, the rumen microbiome composition and genes were determined. Applying a targeted approach based on current biological evidence, 27 genes associated with host-microbiome interaction activities were selected. Partial least square analysis enabled the identification of the most significant genes and genera of feed efficiency (VIP > 0.8) across years of the trial and breeds when comparing all potential genes or genera together. As a result, limited number of genes explained about 40% of the variability in both feed efficiency indicators. Combining information from rumen metagenome-assembled genomes and partial least square analysis results, microbial genera carrying these genes were determined and indicated that a limited number of important genera impacting on feed efficiency. In addition, potential mechanisms explaining significant difference between Low and High feed efficiency animals were analyzed considering, based on the literature, their gastrointestinal location of action. High feed efficiency animals were associated with microbial species including several Eubacterium having the genetic capacity to form biofilm or releasing metabolites like butyrate or propionate known to provide a greater contribution to cattle energy requirements compared to acetate. Populations associated with fucose sensing or hemolysin production, both mechanisms specifically described in the lower gut by activating the immune system to compete with pathogenic colonizers, were also identified to affect feed efficiency using rumen microbiome information. Microbial mechanisms associated with low feed efficiency animals involved potential pathogens within Proteobacteria and Spirochaetales, releasing less energetic substrates (e.g., acetate) or producing sialic acid to avoid the host immune system. Therefore, this study focusing on genes known to be involved in host-microbiome interaction improved the identification of rumen microbial genetic capacities and potential mechanisms significantly impacting on feed efficiency in beef cattle fed high concentrate diet.

Effects of Dietary Energy on Growth Performance, Rumen Fermentation and Bacterial Community, and Meat Quality of Holstein-Friesians Bulls Slaughtered at Different Ages

Simple Summary

Beef tenderness, flavour and juiciness are quality characteristics of consumer eating satisfaction. Marbling level of beef could determine quality characteristics by concentrating water soluble flavour molecules and releasing low fat-solubility volatiles faster. Increasing number of Holstein-Friesians bulls are used for beef production, and this breed is considered to have lower meat quality than purebred and crossbred beef cattle. Therefore, in this study we designed different dietary energy levels and slaughter ages to find ways to improve the meat quality of Holstein-Friesians bulls in beef production. We found that Holstein-Friesians bulls fed with 10.90 and 11.68 MJ/kg metabolizable energy diets, compared to a diet with 10.12 MJ/kg of metabolizable energy, had higher average daily gain, dressing percentage, intramuscular fat content and water holding capacity at 23 or 26 months of age. This study provides a basis to use bulls to produce beef by providing indicators of growth performance, rumen fermentation and ruminal bacteria community, and meat quality.

Abstract

The objective of this study was to evaluate the effects of dietary energy levels on growth performance, rumen fermentation and bacterial community, and meat quality of Holstein-Friesians bulls slaughtered at different ages. Thirty-six Holstein-Friesians bulls (17 months of age) were divided into a 3 × 3 factorial experiment with three energy levels (LE, ME and HE; metabolizable energy is 10.12, 10.90 and 11.68 MJ/kg, respectively) of diets, and three slaughter ages (20, 23 and 26 months). Results indicated that bulls fed with ME and HE diets had higher dry matter intake, average daily gain, and dressing percentage at 23 or 26 months of age. The ME and HE diets also reduced bacterial diversity, altered relative abundances of bacteria and produced lower concentrations of acetate, but higher butyrate and valerate concentrations in rumen fluid. Increasing in dietary energy and slaughter age increased the intramuscular fat (IMF) and water holding capacity. In summary, Holstein-Friesians bulls fed with ME and HE diets, slaughtered at 23 and 26 months of age could be a good choice to produce beef with high IMF. Slaughter age may have less influence than dietary energy in altering fermentation by increasing amylolytic bacteria and decreasing cellulolytic bacteria, and thus, further affecting meat quality.

Dynamic Variations in Fecal Bacterial Community and Fermentation Profile of Holstein Steers in Response to Three Stepwise Density Diets

Simple Summary

The gastrointestinal microbial ecosystem of cattle impacts their health and productivity. Collection of fecal samples provides a non-invasive and practicable way to explore the relationships between fecal microbiota and host productivity or health. Fecal bacteria are influenced by diet, feeding regime, animal age, and health status. However, dynamic variations in the fecal fermentation profile and microbiota composition of finishing steers in response to variable diets are limited. In the current study, we conducted an 11-month tracking investigation to uncover the dynamic variations in fecal fermentation profile and bacterial community in steers fed three stepwise density diets. We found that fecal bacterial diversity decreased as dietary density increased and as the fattening phase continued. Our results revealed that fecal organic acids and bacterial composition were influenced by diet and fattening period. Our results also indicated that time-dependent variations of fecal fermentation profile and microbiota composition exist in the long-term fattening of steers in addition to diet stimulation. This study will be beneficial to reducing fecal contamination from the origin by optimizing diet and fattening time.

Abstract

The objective of this study was to track the dynamic variations in fecal bacterial composition and fermentation profile of finishing steers in response to three stepwise diets varied in energy and protein density. A total of 18 Holstein steers were divided into three groups in such a way that each group contained six animals and received one of three stepwise dietary treatments. Dietary treatments were C = standard energy and protein diet, H = high energy and protein diet, and L = low energy and protein diet. Animals were fattened for 11 months with a three-phase fattening strategy. Fecal samples were collected to evaluate the dynamics of fecal fermentation and bacterial composition in response to dietary treatments and fattening phases using 16S rRNA gene sequencing. Fecal acetate, propionate, and butyrate increased with increasing density of diet and as the fattening phase continued. The relative abundances of Firmicutes and Bacteroidetes dominated and showed 56.19% and 33.58%, respectively. Higher dietary density decreased the fecal bacterial diversity, Firmicutes to Bacteroidetes ratio, and the relative abundances of Ruminococcaceae_UCG-005, Rikenellaceae_RC9_gut_group, and Bacteroides, whereas higher dietary density increased the abundance of Prevotella_9. Our results indicated that both fecal fermentation profile and bacterial composition share a time-dependent variation in response to different dietary densities. This knowledge highlights that both diet and fattening phase impact fecal fermentation profile and bacterial composition, and may provide insight into strategies to reduce fecal contamination from the origin by optimizing diet and fattening time.

The Association Between Inflammaging and Age-Related Changes in the Ruminal and Fecal Microbiota Among Lactating Holstein Cows

Inflammaging is well understood in the study of humans; however, it is rarely reported for dairy cows. To understand the changing pattern of the gut microbiota, inflammatory status and milk production performance during the aging process in cows, we grouped 180 cows according to their lactation period: L1 (n = 60, 1st lactation), L3 (n = 60, 3rd lactation), and L5+ (n = 60, at least 5th lactation) and analyzed their milk components and daily milk yields to evaluate the changing pattern of milk production. The microbiota was analyzed using high-throughput sequencing of amplicons of 16S rRNA, which also allowed us to predict the functions of microbes and then study the changing pattern of the ruminal and fecal microbiota. Serum cytokines, including TNF-α, IL-6, IL-10, and TGF-β were measured to study the progress of inflammaging in the cows. We found that old cows (L5+) suffered from a long-term and low-level chronic inflammation, as indicated by significantly higher levels of inflammatory cytokines IL-10, TNF-α, and TGF-β in the L5+ group (p < 0.001). We also observed a significant decrease in daily milk yield and milk lactose, as well as a significant increase in somatic cell score, among the cows in the L5+ group. For the gut microbiota, most of the genera belonging to Prevotellaceae and Lachnospiraceae, which had a higher abundance among cows of both the L1 and L3 groups (LEfSe, LDA > 2), showed a similar change pattern during the aging process, both in the rumen and in feces, and across the six farms. Beneficial bacteria, like Bacteroidaceae, Eubacterium, and Bifidobacterium, displayed lower abundance in the feces of the L5+ group (LEfSe, LDA > 2). Reconstruction of the fecal bacteria community indicated transformation of the fermenting pattern of older cows' (L5+) feces microbiota, with increased functions related the protein metabolism and fewer functions related to carbohydrate and lipid metabolism compared with those in L1 (p < 0.05). Finally, the connections among these changing patterns were revealed using redundancy analysis and network analysis. The results support the hypothesis of prolonging a cows' productive life and improve dairy cow milk productive performances by manipulating the gut microbiota.

Rumen bacterial diversity of Tibetan sheep (Ovis aries) associated with different forage types on the Qinghai-Tibetan Plateau

Diet is the great determinant of bacterial composition in the rumen. However, little is known about the rumen bacterial community of Tibetan sheep living in the special ecological environment of the Qinghai-Tibetan Plateau (QTP) of China. In the present study, we used high-throughput sequencing to investigate the rumen bacterial community of Tibetan sheep associated with two primary diets: alpine pasture diet (a continuation of the sheep's natural grazing diet) and oat (Avena sativa) hay diet on the QTP. The results showed that bacterial community richness and species diversity of the oat hay diet group were significantly greater than that of the native pasture diet group (p < 0.05). Principal co-ordinate analysis and analysis of similarities revealed that the bacterial community of the oat hay diet group was distinctly different from that of the native pasture diet group (p < 0.05). Bacteroidetes and Firmicutes were the predominant microbial phyla in the rumen. The rumen of oat-hay-fed sheep had higher proportions of Proteobacteria and novel bacteria species than the rumen of native-pasture-fed sheep. Actinobacteria, an uncommon bacterial phylum, occurred only in the oat-hay-fed group. At the genus level, Komagataeibacter, Ruminococcaceae_UCG-014, and Ruminococcaceae_NK4A214 showed significantly higher relative abundance in the oat-hay-fed sheep than in the native-pasture-fed sheep (p < 0.05). This study is the first of the QTP to employ high-throughput sequencing to examine the influence of diet on the rumen microbiome of Tibetan sheep.

Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants

Ruminants are unique among livestock due to their ability to efficiently convert plant cell wall carbohydrates into meat and milk. This ability is a result of the evolution of an essential symbiotic association with a complex microbial community in the rumen that includes vast numbers of bacteria, methanogenic archaea, anaerobic fungi and protozoa. These microbes produce a diverse array of enzymes that convert ingested feedstuffs into volatile fatty acids and microbial protein which are used by the animal for growth. Recent advances in high-throughput sequencing and bioinformatic analyses have helped to reveal how the composition of the rumen microbiome varies significantly during the development of the ruminant host, and with changes in diet. These sequencing efforts are also beginning to explain how shifts in the microbiome affect feed efficiency. In this review, we provide an overview of how meta-omics technologies have been applied to understanding the rumen microbiome, and the impact that diet has on the rumen microbial community.