Effects of dietary supplementation of active dried yeast on fecal methanogenic archaea diversity in dairy cows

Holistic View and Novel Perspective on Ruminal and Extra-Gastrointestinal Methanogens in Cattle

Despite the extensive research conducted on ruminal methanogens and anti-methanogenic intervention strategies over the last 50 years, most of the currently researched enteric methane (CH4) abatement approaches have shown limited efficacy. This is largely because of the complex nature of animal production and the ruminal environment, host genetic variability of CH4 production, and an incomplete understanding of the role of the ruminal microbiome in enteric CH4 emissions. Recent sequencing-based studies suggest the presence of methanogenic archaea in extra-gastrointestinal tract tissues, including respiratory and reproductive tracts of cattle. While these sequencing data require further verification via culture-dependent methods, the consistent identification of methanogens with relatively greater frequency in the airway and urogenital tract of cattle, as well as increasing appreciation of the microbiome-gut-organ axis together highlight the potential interactions between ruminal and extra-gastrointestinal methanogenic communities. Thus, a traditional singular focus on ruminal methanogens may not be sufficient, and a holistic approach which takes into consideration of the transfer of methanogens between ruminal, extra-gastrointestinal, and environmental microbial communities is of necessity to develop more efficient and long-term ruminal CH4 mitigation strategies. In the present review, we provide a holistic survey of the methanogenic archaea present in different anatomical sites of cattle and discuss potential seeding sources of the ruminal methanogens.

Chocolate byproducts and protected fats enriched with chromium to replace corn in diets of early lactation Holstein cows: feed utilization, blood profile, and lactational performance

The present experiment aimed to evaluate the partial replacement of corn with chocolate byproducts or protected fats in the diet of lactating cows on feed utilization, blood profile and lactation performance. Fifty multiparous Holstein cows (560±22 kg BW, 3±1 parity, 7±1 days in milk, and previous milk production of 34±3 kg/d), were randomly assigned to 5 treatments in a completely randomized design for 90 days. The control diet contained a concentrate feed mixture containing (per kg DM 412 g concentrate feed mixture, 412 g corn silage, and 176 g berseem hay). The control diet contained 17.6% crushed corn (DM basis). In another treatment, the control diet was supplemented with 1 g chromium daily (Chromium diet). In the other diets, each kg of crushed corn grain was replaced with 600 g chocolate byproducts (CH diet), 400 g protected fats (PF diet), or 500 g of chocolate byproducts and protected fats mixture (1:1 DM basis) (CHPF diet), DM basis, and each of the diets was also supplemented with 1 g chromium daily. Both amounts of protected fats and chocolate byproducts had the same energy concentration as 1 kg of corn. Without affecting feed intake, the replacement increased (P<0.01) milk production, milk fat concentration, and feed efficiency. The replacement (P<0.05) increased the concentrations of serum total proteins, albumin, glucose, cholesterol, triglyceride, and chromium in comparison with the control diet. Higher (P<0.001) nutrient digestibility was observed with CH, PF, and CHPF treatments. It is concluded that chromium supplementation did not affect feed utilization or cows performance; however, partial replacement of corn with chromium supplemented protected fat, chocolate byproducts or their mixture improved milk production and feed efficiency.

Comparison of Fecal Microbiota Communities between Primiparous and Multiparous Cows during Non-Pregnancy and Pregnancy

Imbalances in the gut microbiota composition may lead to several reproductive disorders and diseases during pregnancy. This study investigates the fecal microbiome composition between primiparous and multiparous cows during non-pregnancy and pregnancy to analyze the host-microbial balance at different stages. The fecal samples obtained from six cows before their first pregnancy (BG), six cows during their first pregnancy (FT), six open cows with more than three lactations (DCNP), and six pregnant cows with more than three lactations (DCP) were subjected to 16S rRNA sequencing, and a differential analysis of the fecal microbiota composition was performed. The three most abundant phyla in fecal microbiota were Firmicutes (48.68%), Bacteroidetes (34.45%), and Euryarchaeota (15.42%). There are 11 genera with more than 1.0% abundance at the genus level. Both alpha diversity and beta diversity showed significant differences among the four groups (p < 0.05). Further, primiparous women were associated with a profound alteration of the fecal microbiota. The most representative taxa included Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG_003, Christensenellaceae_R_7_group, Ruminococcaceae UCG-005, Ruminococcaceae UCG-013, Ruminococcaceae UCG-014, Methanobrevibacter, and [Eubacterium] coprostanoligenes group, which were associated with energy metabolism and inflammation. The findings indicate that host-microbial interactions promote adaptation to pregnancy and will benefit the development of probiotics or fecal transplantation for treating dysbiosis and preventing disease development during pregnancy.

Insights into the biotechnology potential of Methanosarcina

Methanogens are anaerobic archaea which conserve energy by producing methane. Found in nearly every anaerobic environment on earth, methanogens serve important roles in ecology as key organisms of the global carbon cycle, and in industry as a source of renewable biofuels. Environmentally, methanogenic archaea play an essential role in the reintroducing unavailable carbon to the carbon cycle by anaerobically converting low-energy, terminal metabolic degradation products such as one and two-carbon molecules into methane which then returns to the aerobic portion of the carbon cycle. In industry, methanogens are commonly used as an inexpensive source of renewable biofuels as well as serving as a vital component in the treatment of wastewater though this is only the tip of the iceberg with respect to their metabolic potential. In this review we will discuss how the efficient central metabolism of methanoarchaea could be harnessed for future biotechnology applications.

Yeast Products Mediated Ruminal Subenvironmental Microbiota, and Abnormal Metabolites and Digestive Enzymes Regulated Rumen Fermentation Function in Sheep

Yeast products (YP) are commonly used as rumen regulators, but their mechanisms of action are still unclear. Based on our previous studies, we questioned whether yeast products would have an impact on rumen solid-associated (SA) and liquid-associated (LA) microorganisms and alter rumen fermentation patterns. Thirty 3-month-old male sheep weighing 19.27 ± 0.45 kg were selected and randomized into three groups for 60 days: (1) basal diet group (CON group), (2) basal diet add 20 g YP per day (low YP, LYP group) and (3) basal diet add 40 g YP per day (high YP, HYP group). The results demonstrated that the addition of YP increased rumen cellulase activity, butyrate and total volatile fatty acid (TVFA) concentrations (p < 0.05), while it decreased rumen amylase activity and abnormal metabolites, such as lactate, lipopolysaccharides (LPS) and histamine (HIS) (p < 0.05). Metagenomic analysis of rumen microorganisms in three groups revealed that YP mainly influenced the microbial profiles of the SA system. YP increased the relative abundance of R. flavefaciens and decreased methanogens in the SA system (p < 0.05). With the addition of YP, the abundance of only a few lactate-producing bacteria increased in the SA system, including Streptococcus and Lactobacillus (p < 0.05). However, almost all lactate-utilizing bacteria increased in the LA system, including Megasphaera, Selenomonas, Fusobacterium and Veillonella (p < 0.05). In addition, YP increased the abundance of certain GHs family members, including GH43 and GH98 (p < 0.05), but decreased the abundance of some KEGG metabolic pathways involved in starch and sucrose metabolism, biosynthesis of antibiotics and purine metabolism, among others. In conclusion, the addition of YP to high-concentrate diets can change the abundance of major functional microbiota in the rumen, especially in the solid fraction, which in turn affects rumen fermentation patterns and improves rumen digestibility.

Contrasting Fecal Methanogenic and Bacterial Profiles of Organic Dairy Cows Located in Northwest Washington Receiving Either a Mixed Diet of Pasture and TMR or Solely TMR

Currently, little is known regarding fecal microbial populations and their associations with methanogenic archaea in pasture-based dairy cattle. In this study, we assessed the fecal microbiome of organic dairy cows across different time points receiving a mixed diet of pasture and total mixed ration (TMR) or TMR only. We hypothesized that the fecal methanogenic community, as well as co-occurrence patterns with bacteria, change across diets. To test these hypotheses, we analyzed TMR and pasture samples, as well as the V3-V4 region of 16S rRNA of fecal samples collected over the course of a one-year study period from 209 cows located on an organic dairy in Northwest Washington. The inherent variability in pasture quality, quantity, availability, and animal preference can lead to diverse dietary intakes. Therefore, we conducted a k-means clustering analysis to identify samples from cows that were associated with either a pasture-based diet or a solely TMR diet. A total of 4 clusters were identified. Clusters 1 and 3 were mainly associated with samples primarily collected from cows with access to pasture of varying quality and TMR, cluster 2 was formed by samples from cows receiving only TMR, and cluster 4 was a mix of samples from cows receiving high-quality pasture and TMR or TMR only. Interestingly, we found little difference in the relative abundance of methanogens between the community clusters. There was evidence of differences in diversity between pasture associated bacterial communities and those associated with TMR. Cluster 4 had higher diversity and a less robust co-occurrence network based on Spearman correlations than communities representing TMR only or lower-quality pasture samples. These findings indicate that varied bacterial communities are correlated with the metabolic characteristics of different diets. The overall good pasture and TMR quality in this study, combined with the organic allowance for feeding high levels of TMR even during the grazing season, might have contributed to the lack of differences in the fecal archaeal community from samples associated with a mixed pasture and TMR diet, and a TMR only diet. Mitigation strategies to decrease methane emissions such as increasing concentrate to forage ratio, decreasing pasture maturity and adopting grazing systems targeting high quality pasture have been shown to be efficient for pasture-based systems. However, the allowance for organic dairy producers to provide up to an average of 70% of a ruminant's dry matter demand from dry matter fed (e.g., TMR), suggests that reducing enteric methane emissions may require the development of novel dietary strategies independent of pasture management.

Effects of Autolyzed Yeast Supplementation in a High-Starch Diet on Rumen Health, Apparent Digestibility, and Production Variables of Lactating Holstein Cows

Fifteen multiparous rumen-cannulated Holstein cows were assigned to one of five treatments in a replicated 5 × 5 Latin square design. The treatments were low-starch (LS) (22.8 ± 1% of dry matter; DM) without autolyzed yeast (AY; LS0, control), high-starch (HS) (31.2 ± 4% of DM) without AY (HS0), and HS with either 15 g (HS15), 30 g (HS30), or 45 g (HS45) of AY supplementation. Cows in HS0 had increased (p < 0.03) dry matter intake (DMI; 24.9 kg/d) and energy-corrected milk (ECM; 34.4 kg/d) compared to cows in LS0 (19.9 and 31.3 kg/d, respectively). There was a tendency for a quadratic treatment effect for feed efficiency (ECM/DMI, p = 0.07) and crude protein (CP) apparent digestibility (AD) (p = 0.09). Cows in HS45 tended (p = 0.09) to have increased DMI (25.6 kg/d) compared to cows in HS0 (24.9 kg/d). Cows in HS0 had greater (p < 0.04) milk protein nitrogen (N; 166 g/d) and microbial N production (161 g/d) than those in LS0 (140 and 138 g/d, respectively). In conclusion, the addition of AY tended to improve DMI, feed efficiency, and CP AD when cows were fed the HS diet.

Camelina sativa L. Oil Mitigates Enteric in vitro Methane Production, Modulates Ruminal Fermentation, and Ruminal Bacterial Diversity in Buffaloes

This study was aimed to evaluate the effects of Camelina sativa oil (CO) on fermentation kinetics and methane (CH₄) production in rations with different roughage (R) to concentrate (C) ratios. Three total mixed rations (TMRs) were used as substrates (R70:C30, R50:C50, and R30:C70) supplemented with different levels of CO (0, 2, 4, 6, and 8% on dry matter basis) in an in vitro batch culture system. The enteric CH₄ production was determined at different times of incubation while fermentation parameters were measured at the end of incubation. Results revealed that CO significantly decreased (P < 0.05) CH₄ production at 48 h in medium (R50:C50) and low- (R30:C70) roughage diets than control. Camelina oil at all levels significantly (P < 0.05) affected ammonia nitrogen (NH₃-N) and microbial protein (MCP) in all rations. Propionate concentration was increased by supplementing 8% CO to R70:C30 TMR, but it decreased with increasing levels of CO for low- and medium-roughage diets. Acetate concentration was significantly (P < 0.05) higher at 4% CO supplementation, but it decreased with 8% CO level in R30:C70 TMR. For all rations, CO decreased (P < 0.001) total bacteria, protozoa, and methanogens. Total fungi counts were affected by CO in all rations, especially with a 6% level in two rations (R30:C70 and R50:C50) and 8% level with high-roughage ration (R70:C30). Supplementation of CO in medium-roughage ration (R50:C50) showed a linear (P < 0.05) decrease in bacterial richness and evenness indices along with Shannon diversity as compared to the control. Moreover, CO also increased Firmicutes to Bacteroidetes ratio in all TMRs more effectively at higher levels. Camelina oil also affected the relative abundance of Prevotella in both low- and medium-roughage diets while increasing the abundance of Ruminobacter and Pseudobutyrivibrio. The present study concluded that CO enhanced fermentation kinetics while decreasing enteric in vitro CH₄ production from fibrous diets. Thus, it may be considered as a potentially effective and environmentally friendly way of mitigating CH₄ emission from livestock.

Quantifying non-fibrous carbohydrates, acid detergent fiber and cellulose of forage through an in vitro gas production technique

BACKGROUND

The in vitro gas production (GP) technique has been useful for evaluating the potential degradability of feedstuffs in ruminal environments; GP is related to the components of feedstuff ingredients.

RESULTS

Linear models were generated and validated as alternatives of quantifying neutral detergent-soluble fiber, starch (St)/hemicellulose (Hem) and cellulose (Cel) through GP. Residuals of models obtained from the peaks of GP [0-8 h (GP-8), > 8-24 h (GP-24), > 24-48 h (GP-48) and > 24-81 h (GP-81)] of 0.02, 0.04, 0.08, 0.12 and 0.20 g of glucose (Glu), St and Cel respectively. The incubations were analyzed in mixtures of Glu, St and Cel. The best fitting models (r² from 0.709 to 0.935) were tested on corn stover (CS) to quantify rapid fermentation fractions (RF; equivalent to Glu), medium fermentation fractions (MF; equivalent to St) and low fermentation fractions (LF48; equivalent to Cel); in CS, RF, MF and LF models had standardized residuals < 0.09. The analysis with Leucaena (Leucaena leucocephala Lam. de Wit) and star grass (Cynodon nlemfuensis Vanderyst) consider high-protein ingredients.

CONCLUSION

The in vitro GP of RF, MF and LF48 fractions equivalent to Glu, St and Cel are affected by maturity and harvest time even when the chemical composition remains similar, and so RF, MF and LF48 should be considered during the design of ruminant diets. In vitro GP could be used to quantify the components of some forages, although further studies are necessary. © 2020 Society of Chemical Industry.

Potential use of chromium to combat thermal stress in animals: A review

Heat stress (HS) has adverse effects on the body: it decreases body weight, feed efficiency, feed intake, carcass quality, and nutrient digestibility. Chromium (Cr) can prevent lipid peroxidation induced by HS through its strong antioxidant activities, especially when it is added to the poultry diet. It improves the action of insulin and nutrient metabolism (of lipids, proteins, nucleic acid, and carbohydrates) through activation of enzymes associated with such pathways. The results of the studies on Cr added to diets with concentrations of 0.05 mg Cr/kg of Cr-methionine led to improved feed efficiency and DM intake by cows and Holstein dairy calves exposed to high environmental temperatures. Moreover, calves that received Cr at levels of 0.05 mg/kg of body weight tended to have higher serum concentrations of glucose and higher ratios of insulin to glucose. In heat-stressed pigs, Cr addition (200 ppb) increased blood neutrophils by about 37%. Several studies have asserted that Cr can inhibit inflammation in lactating cows by promoting the release of Hsp72, assisting production of IL-10 and inhibiting degradation of IκBα in HS conditions. In addition, Cr supplementation was observed to possibly have positive impacts on both cell-mediated and humeral immunity in heat-stressed buffalo calves. Studies over the last two decades have shown with certainty that chromium supplementation has an impact on many variables in chickens. Moreover, Cr is believed to increase insulin action in insulin-sensitive tissues (i.e., adipose and muscles), resulting in increased farm animal productivity through the improvement of feed intake, growth rate, carcass quality, reproductive parameters and immune functions.

The structure of microbial populations in Nelore GIT reveals inter-dependency of methanogens in feces and rumen

Background

The success of different species of ruminants in the colonization of a diverse range of environments is due to their ability to digest and absorb nutrients from cellulose, a complex polysaccharide found in leaves and grass. Ruminants rely on a complex and diverse microbial community, or microbiota, in a unique compartment known as the rumen to break down this polysaccharide. Changes in microbial populations of the rumen can affect the host’s development, health, and productivity. However, accessing the rumen is stressful for the animal. Therefore, the development and use of alternative sampling methods are needed if this technique is to be routinely used in cattle breeding. To this end, we tested if the fecal microbiome could be used as a proxy for the rumen microbiome due to its accessibility. We investigated the taxonomic composition, diversity and inter-relations of two different GIT compartments, rumen and feces, of 26 Nelore (Bos indicus) bulls, using Next Generation Sequencing (NGS) metabarcoding of bacteria, archaea and ciliate protozoa.

Results

We identified 4265 Amplicon Sequence Variants (ASVs) from bacteria, 571 from archaea, and 107 from protozoa, of which 143 (96 bacteria and 47 archaea) were found common between both microbiomes. The most prominent bacterial phyla identified were Bacteroidetes (41.48%) and Firmicutes (56.86%) in the ruminal and fecal microbiomes, respectively, with Prevotella and Ruminococcaceae UCG-005 the most relatively abundant genera identified in each microbiome. The most abundant archaeal phylum identified was Euryarchaeota, of which Methanobrevibacter gottschalkii, a methanogen, was the prevalent archaeal species identified in both microbiomes. Protozoa were found exclusively identified in the rumen with Bozasella/Triplumaria being the most frequent genus identified. Co-occurrence among ruminal and fecal ASVs reinforces the relationship of microorganisms within a biological niche. Furthermore, the co-occurrence of shared archaeal ASVs between microbiomes indicates a dependency of the predominant fecal methanogen population on the rumen population.

Conclusions

Co-occurring microorganisms were identified within the rumen and fecal microbiomes, which revealed a strong association and inter-dependency between bacterial, archaeal and protozoan populations of the same microbiome. The archaeal ASVs identified as co-occurring between GIT compartments corresponded to the methanogenic genera Methanobrevibacter and Methanosphaera and represented 26.34% of the overall archaeal sequencesdiversity in the rumen and 42.73% in feces. Considering that these archaeal ASVs corresponded to a significant part of the overall diversity of both microbiomes, which is much higher if one includes the interactions of these co-occurring with other rumen archaea ASVs, we suggest that fecal methanogens could be used as a proxy of ruminal methanogens.

Effects of particle size of ground alfalfa hay on caecal bacteria and archaea populations of rabbits

This work was aimed to investigate the effects of the different particle size of ground alfalfa hay on caecal microbial and archeal communities of rabbits. One hundred-twenty New Zealand rabbits (950.3 ± 8.82 g) were allocated into four treatments, with five replicates in each treatment and six rabbits in each replicate. The particle sizes of the alfalfa meal in the four treatment diets were 2,500, 1,000, 100 and 10 µm respectively, while the other ingredients were ground through a 2.5 mm sieve. High-throughput sequencing technology was applied to examine the differences in bacteria and methanogenic archaea diversity in the caecum of the four treatment groups of rabbits. A total of 745,946 bacterial sequences (a mean of 31,081 ± 13,901 sequences per sample) and 539,227 archaeal sequences (a mean of 22,468 ± 2,443 sequences per sample) were recovered from twenty-four caecal samples, and were clustered into 9,953 and 2,246 OTUs respectively. A total of 26 bacterial phyla with 465 genera and three archaeal phyla with 10 genera were identified after taxonomic summarization. Bioinformatic analyses illustrated that Firmicutes (58.69% ∼ 68.50%) and Bacteroidetes (23.96% ∼ 36.05%) were the two most predominant bacterial phyla and Euryarchaeota (over 99.9%) was the most predominant archaeal phyla in the caecum of all rabbits. At genus level, as the particle size of alfalfa decreased from 2,500 to 10 µm, the relative abundances of Ruminococcaceae UCG-014 (P < 0.001) and Lactobacillus (P = 0.043) were increased and Ruminococcaceae UCG-005 (P = 0.012) was increased first and then decreased when the alfalfa particle size decreased, while Lachnospiraceae NK4A136 group (P = 0.016), Ruminococcaceae NK4A214 (P = 0.044), Christensenellaceae R-7 group (P = 0.019), Lachnospiraceae other (Family) (P = 0.011) and Ruminococcaceae UCG-013 (P = 0.021) were decreased. The relative abundance of Methanobrevibacter was increased from 62.48% to 90.40% (P < 0.001), whereas the relative abundance of Methanosphaera was reduced from 35.47% to 8.62% (P < 0.001). In conclusion, as the particle size of alfalfa meal decreased, both the bacterial and archaeal population in the caecum of rabbit experienced alterations, however archaea response earlier than bacteria to the decrease of alfalfa meal particle size.

Dynamic role of single-celled fungi in ruminal microbial ecology and activities

In ruminants, high fermentation capacity is necessary to develop more efficient ruminant production systems. Greater level of production depends on the ability of the microbial ecosystem to convert organic matter into precursors of milk and meat. This has led to increased interest by animal nutritionists, biochemists and microbiologists in evaluating different strategies to manipulate the rumen biota to improve animal performance, production efficiency and animal health. One of such strategies is the use of natural feed additives such as single-celled fungi yeast. The main objectives of using yeasts as natural additives in ruminant diets include; (i) to prevent rumen microflora disorders, (ii) to improve and sustain higher production of milk and meat, (iii) to reduce rumen acidosis and bloat which adversely affect animal health and performance, (iv) to decrease the risk of ruminant-associated human pathogens and (v) to reduce the excretion of nitrogenous-based compounds, carbon dioxide and methane. Yeast, a natural feed additive, has the potential to enhance feed degradation by increasing the concentration of volatile fatty acids during fermentation processes. In addition, microbial growth in the rumen is enhanced in the presence of yeast leading to the delivery of a greater amount of microbial protein to the duodenum and high nitrogen retention. Single-celled fungi yeast has demonstrated its ability to increase fibre digestibility and lower faecal output of organic matter due to improved digestion of organic matter, which subsequently improves animal productivity. Yeast also has the ability to alter the fermentation process in the rumen in a way that reduces methane formation. Furthermore, yeast inclusion in ruminant diets has been reported to decrease toxins absorption such as mycotoxins and promote epithelial cell integrity. This review article provides information on the impact of single-celled fungi yeast as a feed supplement on ruminal microbiota and its function to improve the health and productive longevity of ruminants.

Effect of Dietary Supplementation of Moringa Oleifera on the Production Performance and Fecal Methanogenic Community of Lactating Dairy Cows

Simple Summary

High-quality forages such as protein-rich ingredients are essential to maximize production performance in dairy production. However, enteric methane produced by methanogenesis represents a substantial waste of feed energy for ruminants. Thus, it is important to evaluate the environmental effect when such feed ingredients are used to provide necessary nutrients. The aim of the present study was to examine the effects of dietary supplementation of Moringa oleifera on the production performance and fecal methanogenic community in lactating cows. The study’s main results suggest that inclusion of Moringa oleifera improved milk fat content and changed the composition and diversity of methanogens. This study indicates that secondary metabolites from Moringa oleifera may regulate fermentation conditions and associations between some methanogens and other microbes. These findings provide basic information on the utilization of alternative forage resources for dairy cows and can help to better understand the regulation of microbial metabolic function and methane emissions.

Abstract

Development of alternative forage resources is of great importance to provide necessary nutrients and minimize greenhouse gas emissions in ruminant production. The aim of this study was to examine the effects of dietary supplementation of Moringa oleifera on the production performance and fecal methanogenic community in dairy cows using methyl-coenzyme M reductase α-subunit gene. Sixty-four cows were allocated to one of four treatments: basal diet without M. oleifera (control) or low (3% w/w, M3), medium (6%, M6), or high (9%, M9) supplementation with M. oleifera. This study demonstrated that different supplementation levels of Moringa oleifera in the diet achieved similar feed intake and milk production, but adding 6% of Moringa oleifera improved milk fat content. Two families, two phyla, three genera, and three species in total were identified among the four treatments. The fecal archaeal community in the control treatment was predominated by Methanobrevibacter (39.1% of the total sequence reads) followed by Methanosphaera and Methanocorpusculum at the genus level. The increased abundance of the Methanosphaera genus and Methanosphaera sp. ISO3-F5 species was induced by secondary metabolites of Moringa oleifera in the diet. Results indicated that Moringa oleifera supplementation not only improved dairy product quality but could also potentially reduce methane emissions.

Bacterial Community Diversity Associated With Different Utilization Efficiencies of Nitrogen in the Gastrointestinal Tract of Goats

The objective of this study was to examine the association between bacterial community structure and the utilization efficiency of nitrogen (UEN) phenotypes by determining the bacterial community in the gastrointestinal tract (GIT) of goats that differ in UEN using high-throughput 16S rRNA gene sequencing. Thirty Nubian goats were selected as experimental animals, and their UEN was determined in a metabolic experiment. Subsequently, eight individuals were grouped into the high nitrogen utilization (HNU) phenotype, and seven were grouped into the low nitrogen utilization (LNU) phenotype. The bacterial 16S rRNA gene amplicons from the rumen, abomasum, jejunum, cecum and colon contents of these animals were sequenced using next-generation high-throughput sequencing technology. Two hundred thirty-nine genera belonging to 23 phyla in the rumen, 319 genera belonging to 30 phyla in the abomasum, 248 genera belonging to 36 phyla in the jejunum, 248 genera belonging to 25 phyla in the colon and 246 genera belonging to 23 phyla in the cecum were detected, with Bacteroidetes and Firmicutes predominating. In addition, a significant correlation was observed between the UEN and the genera Succiniclasticum, Bacteroides, Ruminobacter, Methanimicrococcus, Mogibacterium, Eubacterium_hallii_group and Ruminococcus_1 in the rumen; Bacteroidales_S24-7_group, Bacteroidales_RF16_group, Bacteroidales_UCG-001 and Anaerovibrio in the abomasum; Ruminococcus_2, Candidatus_Saccharimonas, Candidatus_Arthromitus and Coprococcus_1 in the jejunum; Erysipelotrichaceae_UCG-004, Akkermansia, Senegalimassilia, Candidatus_Soleaferrea and Methanocorpusculum in the colon; and Ruminococcaceae_UCG-002, Anaerovibrio and Ruminococcaceae_UCG-007 in the cecum. Furthermore, the real-time PCR results showed that the ruminal copies of Fibrobacter_succinogenes, Butyrivibrio_fibrisolvens, Ruminococcus_sp._HUN007, Prevotella ruminicola and Streptococcus bovis in the HNU animals were significantly higher than those in the LNU animals. This study suggests an association of GIT microbial communities as a factor that influences UEN in goats.

Effect of Limit-Fed Diets With Different Forage to Concentrate Ratios on Fecal Bacterial and Archaeal Community Composition in Holstein Heifers

Limit-feeding of a high concentrate diet has been proposed as an effective method for improving feed efficiency and reducing total manure output of dairy heifers; meanwhile the effects of this method on hindgut microbiota are still unclear. This study investigated the effects of a wide range of dietary forage:concentrate ratios (F:C) on the fecal composition of bacteria and archaea in heifers using next-generation sequencing. Four diets with different F:C (80:20, 60:40, 40:60, and 20:80) were limit-fed to 24 Holstein heifers, and the fecal fermentation parameters and bacterial and archaeal communities were investigated. With increasing dietary concentrate levels, the fecal dry matter output, neutral detergent fiber (NDF) content, and proportion of acetate decreased linearly (P < 0.01), while the fecal starch content and proportions of propionate, butyrate, and total branched-chain volatile fatty acids (TBCVFAs) were increased (P ≤ 0.05). An increased concentrate level linearly increased (P = 0.02) the relative abundance of Proteobacteria, and linearly decreased (P = 0.02) the relative abundance of Bacteroidetes in feces. At the genus level, the relative abundance of unclassified Ruminococcaceae and Paludibacter which may have the potential to degrade forage decreased linearly (q ≤ 0.02) with increasing dietary concentrate levels, while the relative abundance of Roseburia and Succinivibrio which may be non-fibrous carbohydrate degrading bacteria increased linearly (q ≤ 0.05). Some core microbiota operational taxonomic units (OTUs) also showed significant association with fecal VFAs, NDF, and/or acid detergent fiber (ADF) content. Meanwhile, the relative abundance of most detected taxa in archaea were similar across different F:C, and only Methanosphaera showed a linear decrease (P = 0.01) in high concentrate diets. Our study provides a better understanding of fecal fermentation parameters and microbiota under a wide range of dietary F:C. These findings support the potential for microbial manipulation by diet, which could enhance feed digestibility and relieve environmental problems associated with heifer rearing.