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Physically effective neutral detergent fiber (peNDF) is a concept that accounts for the particle length of NDF in a feed, sustaining the normal chewing behavior and rumen fermentation of ruminants. This study aimed to elucidate the effects of dietary peNDF on growth performance and bacterial communities in the rumen of goats through a high-throughput sequencing technique. A total of 30 male Lezhi black goats were randomly assigned to five groups, corresponding to five diets with identical compositions and nutrient levels but with varying forage lengths (the peNDF1.18 contents of the diets were 33.0, 29.9, 28.1, 26.5, and 24.8%, respectively). The whole trial lasted for 44 days. As results show, feed intake and average daily gain were highest when peNDF1.18 content was 26.5%, in which the papilla length of the dorsal sac in rumen was the highest. Chao1 and ACE indexes were similar among the treatments, while Shannon and Simpson indexes of the peNDF1.18 = 28.1% group were the highest (p < 0.05). As the level of dietary peNDF1.18 decreased, the dominant phylum transitioned from Bacteroidetes to Firmicutes. The top three dominant genera of rumen bacteria were Prevotella 1 , Ruminococcaceae NK4A214 group , and Christensenellaceae R-7 group. They all showed a quadratic correlation with dietary peNDF1.18 level (p < 0.05). The relative abundance of Ruminococcaceae UCG-011 was positively correlated, while that of Prevotella 1 was negatively correlated, with amino acid metabolism and energy metabolism (p < 0.01). In conclusion, dietary peNDF level influenced goat growth performance, rumen development, and rumen bacterial community structures, and a peNDF1.18 level between 26.5 and 28.1% was considered optimal for goat diet. [ABSTRACT FROM AUTHOR]

Cellulose is considered to be an alternative form of energy, and has recently gained significance representing millions of dollars for countries that have the opportunity to obtain energy from it. At the same time, cellulosic biomaterials are attractive since they are both cheap and abundant. To use this important resource, its stubborn structure must be broken down. Rumen bacteria are regarded as unique for this job. In this study, 17 cellulolytic bacteria were isolated from rumen samples collected from Erzurum slaughterhouses. Three bacteria (OZ2, OZ5, OZ17) with maximum enzyme activity were identified by sequencing the 16S rRNA gene region. As a result of the sequence analysis, it was determined that isolates belong to Streptomyces ambofaciens OZ2, Cytobacillus oceanisediminis OZ5, and Streptomyces violaceochromogenes OZ17. Then, cellulase production potentials of these identified bacteria were investigated as single and co-cultures. The co-culture of OZ2 and OZ5 demonstrated the best cellulase activity (26 U/mL). As a result of the optimization studies for the co-culture of OZ2 and OZ5, the best culture conditions were 3 g/L yeast extract, 60 h incubation time, pH 6, and temperature 35 °C. Under optimized conditions, the cellulase enzyme activity increased approximately 3.5-fold to 56 U/mL. [ABSTRACT FROM AUTHOR]

Physically effective neutral detergent fiber (peNDF) is a concept that accounts for the particle length of NDF in a feed, sustaining the normal chewing behavior and rumen fermentation of ruminants. This study aimed to elucidate the effects of dietary peNDF on growth performance and bacterial communities in the rumen of goats through a high-throughput sequencing technique. A total of 30 male Lezhi black goats were randomly assigned to five groups, corresponding to five diets with identical compositions and nutrient levels but with varying forage lengths (the peNDF1.18 contents of the diets were 33.0, 29.9, 28.1, 26.5, and 24.8%, respectively). The whole trial lasted for 44 days. As results show, feed intake and average daily gain were highest when peNDF1.18 content was 26.5%, in which the papilla length of the dorsal sac in rumen was the highest. Chao1 and ACE indexes were similar among the treatments, while Shannon and Simpson indexes of the peNDF1.18 = 28.1% group were the highest (p < 0.05). As the level of dietary peNDF1.18 decreased, the dominant phylum transitioned from Bacteroidetes to Firmicutes. The top three dominant genera of rumen bacteria were Prevotella 1, Ruminococcaceae NK4A214 group, and Christensenellaceae R-7 group. They all showed a quadratic correlation with dietary peNDF1.18 level (p < 0.05). The relative abundance of Ruminococcaceae UCG-011 was positively correlated, while that of Prevotella 1 was negatively correlated, with amino acid metabolism and energy metabolism (p < 0.01). In conclusion, dietary peNDF level influenced goat growth performance, rumen development, and rumen bacterial community structures, and a peNDF1.18 level between 26.5 and 28.1% was considered optimal for goat diet.

There is growing interest in the utilization of plant polysaccharides for the modulation of the rumen bacterial community and enhancement of growth performance in ruminants. Fermented wheat bran polysaccharides (FWBPs), plant polysaccharides, have been shown to improve the growth performance of lambs, but little is known about their effect on rumen bacteria. The aim of this study was to investigate the effects of FWBPs supplementation to milk replacer (MR) on the growth performance, blood metabolites, weight and morphology of rumen, rumen fermentation, and rumen bacterial community which were investigated in lambs. Twelve 1.5-month-old crossbred lambs (Dorper × Small-tailed Han Sheep) with an initial body weight (BW) of 11.38 ± 0.19 kg were randomly divided into two groups, namely, the control group and FWBPs group. Compared with the control group, the FWBPs group had a higher average daily weight gain and serum total protein concentrations, and a lower feed: gain ratio. A tendency of increase in final BW and carcass BW was also observed. Administration of FWBPs increased the ruminal papillae width and ruminal butyrate proportion and decreased the concentration of ammonia nitrogen and the proportion of isobutyrate and isovalerate. In addition, the epithelial cell thickness had an increased trend in the FWBPs group. High-throughput sequencing data showed that the relative abundance of Lachnospiraceae_NK3A20_group and Solobacterium was enhanced by FWBP treatment; meanwhile, the relative abundance of NK4A214_group, Megasphaera, and Treponema showed a tendency to be higher than that of the control group. Furthermore, Spearman's correlation analysis revealed that the relative abundances of NK4A214_group, Treponema, and Lachnospiraceae_NK3A20_group were positively correlated with butyrate proportion. Collectively, FWBPs supplementation to MR on lambs altered the rumen bacterial community, promoted rumen development, and improved growth performance.

Efficient feed utilization in dairy cows is crucial for economic and environmental reasons. The rumen microbiota plays a significant role in feed efficiency, but studies utilizing microbial data to predict host phenotype are limited. In this study, 87 primiparous Nordic Red dairy cows were ranked for feed efficiency during their early lactation based on residual energy intake, and the rumen liquid microbial ecosystem was subsequently evaluated using 16S rRNA amplicon and metagenome sequencing. The study used amplicon data to build an extreme gradient boosting model, demonstrating that taxonomic microbial variation can predict efficiency (rtest = 0.55). Prediction interpreters and microbial network revealed that predictions were based on microbial consortia and the efficient animals had more of the highly interacting microbes and consortia. Rumen metagenome data was used to evaluate carbohydrate-active enzymes and metabolic pathway differences between efficiency phenotypes. The study showed that an efficient rumen had a higher abundance of glycoside hydrolases, while an inefficient rumen had more glycosyl transferases. Enrichment of metabolic pathways was observed in the inefficient group, while efficient animals emphasized bacterial environmental sensing and motility over microbial growth. The results suggest that inter-kingdom interactions should be further analyzed to understand their association with the feed efficiency of animals.

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Paper mulberry (Broussonetia papyrifera) is widely ensiled to feed sheep in southwestern China, as unconventional woody forage. Feeding lambs with paper mulberry silage (PMS) may improve certain feeding characteristics, thereby affecting the growth performance and meat quality. The aim of this study is to investigate the effects of four diets of PMS on growth performance, rumen microbial composition, and muscle fatty acids profile in Hu lambs. The results showed that 30% and 40% PMS increased the dry matter intake and average daily gain of Hu lambs compared to the control group. PMS30 and PMS40 increased the content of C24:1, and PMS40 increased the content of C20:5n-3. The content of microbial protein (MCP) was higher in PMS40 than in others, but PMS30 and PMS40 reduced the total volatile fatty acid in rumen. PMS30 significantly increased the ratio of acetic acid to propionic acid. The abundance of ruminal Christensenellaceae_R-7_group and norank_f_Eubacterium_coprostanoligenes_group was significantly higher in PMS30 and PMS40 groups. Moreover, Christensenellaceae_R-7_group had a significant positive correlation with n3-polyunsaturated fatty acid. PMS40 might lead to a relatively high content of unsaturated fatty acids in longissimus dorsi muscle by increasing the relative abundance of Christensenellaceae_R-7_group in rumen. [ABSTRACT FROM AUTHOR]

The continuous trend for a narrowing margin between feed cost and milk prices across dairy farms in the United States highlights the need to improve and maintain feed efficiency. Yeast culture products are alternative supplements that have been evaluated in terms of milk performance and feed efficiency; however, less is known about their potential effects on altering rumen microbial populations and consequently rumen fermentation. Therefore, the objective of this study was to evaluate the effect of yeast culture supplementation on lactation performance, rumen fermentation profile, and abundance of major species of ruminal bacteria in lactating dairy cows. Forty mid-lactation Holstein dairy cows (121 ± 43 days in milk; mean ± standard deviation; 32 multiparous and 8 primiparous) were used in a randomized complete block design with a 7-d adaptation period followed by a 60-d treatment period. Cows were blocked by parity, days in milk, and previous lactation milk yield and assigned to a basal total mixed ration (TMR; 1.6 Mcal/kg of dry matter, 14.6% crude protein, 21.5% starch, and 38.4% neutral detergent fiber) plus 114 g/d of ground corn (CON; n = 20) or basal TMR plus 100 g/d of ground corn and 14 g/d of yeast culture (YC; n = 20; Culture Classic HD, Cellerate Yeast Solutions, Phibro Animal Health Corp.). Treatments were top-dressed over the TMR once a day. Cows were individually fed 1 × /d throughout the trial. Blood and rumen fluid samples were collected in a subset of cows (n = 10/treatment) at 0, 30, and 60 d of the treatment period. Rumen fluid sampled via esophageal tubing was analyzed for ammonia-N, volatile fatty acids (VFA), and ruminal bacteria populations via quantitative PCR amplification of 16S ribosomal DNA genes. Milk yield was not affected by treatment effects. Energy balance was lower in YC cows than CON, which was partially explain by the trend for lower dry matter intake as % body weight in YC cows than CON. Cows fed YC had greater overall ruminal pH and greater total VFA (m M) at 60 d of treatment period. There was a contrasting greater molar proportion of isovalerate and lower acetate proportion in YC-fed cows compared with CON cows. Although the ruminal abundance of specific fiber-digesting bacteria, including Eubacterium ruminantium and Ruminococcus flavefaciens , was increased in YC cows, others such as Fibrobacter succinogenes were decreased. The abundance of amylolytic bacteria such as Ruminobacter amylophilus and Succinimonas amylolytica were decreased in YC cows than CON. Our results indicate that the yeast culture supplementation seems to promote some specific fiber-digesting bacteria while decreasing amylolytic bacteria, which might have partially promoted more neutral rumen pH, greater total VFA, and isovalerate. [ABSTRACT FROM AUTHOR]

The purpose of the study was to assess the artificial saliva (AS) pH on ruminal fermentation and rumen bacteria community in the rumen simulation technique (RUSITEC) system. The experiment was performed in two treatments (low AS pH vs. high AS pH) with four replicates. The low AS pH was sustained by altering the composition of the AS (NaHCO3 from 9.8 to 1.96 g/L, Na2HPO4 from 9.3 to 1.86 g/L) according to McDougall's method. The diets were supplemented with 16 g basic diets with forage to the concentrate ratio of 50:50. The experiments were conducted over 13-day incubation periods, with 9 days adaption and 4 days sample collection. The results showed low AS pH decreased dry matter (DM) degradability (64.37 vs. 58.67%), organic matter (OM) degradability (64.38 vs. 59.32%), neutral detergent fiber (NDF) degradability (46.87 vs. 39.94%), acid detergent fiber (ADF) degradability (38.16 vs. 31.13%), and crude protein (CP) degradability (70.33 vs. 62.99%), respectively. Compared with the high AS pH, the low AS pH increased the proportion of butyrate (P = 0.008) and decreased the proportion of propionate (P < 0.001). At the bacteria community, the low AS pH increased the abundances of Spirochaetes (P = 0.001) and Synergistetes (P = 0.004) and decreased the Verrucomicrobia abundance (P = 0.004) in solid-associated bacteria. At the genus level, the low AS pH increased the abundance of Lactobacillus (P = 0.050) and decreased the abundance of Schwartzia (P = 0.002) in solid-associated bacteria. The abundances of Prevotellaceae_YAB2003_group (P = 0.040), Schwartzia (P = 0.002), and Ruminobacter (P = 0.043) were lower in the low AS pH group compared with the high AS pH group in liquid-associated bacteria. Low AS pH decreased the number of Ruminococcus albus, Ruminococcus flavefaciens, Fibrobacter succinogenes (P < 0.001) both in the solid- and liquid-associated bacteria, respectively. The results of the present study included three groups of bacteria communities according to the different sensitives to rumen pH: the abundances of Lactobacillus, Succinivibrio, and Prevotella_7 are increased with decreasing AS pH; the amounts of R. albus, R. flavefaciens, F. succinogenes as well as the abundances of Schwartzia and Ruminobacter decreased with the reducing AS pH; the abundances of Selenomonas_1, Rikenellaceae_RC9_gut_group, and Succiniclasticum were not affected by the AS pH in RUSTITEC.

Context: Nitrate salts can be utilised by the rumen bacteria as a nitrogen source. Nitrate salts can induce a methaemoglobinaemia in cattle if consumed in sufficient quantities. Methaemoglobinaemia is the principal factor that leads to the onset of clinical signs for nitrate toxicity in cattle. A methaemoglobin concentration ≥20% is considered unsafe for cattle. There are, however, limited studies on the longer-term effects of nitrate supplementation on methaemoglobin formation in Bos indicus steers consuming forage that is reflective of northern Australia's poor quality, native pasture in the dry season. Aims: We hypothesised that the Australian government's recommended daily dose of nitrate salts given to Bos indicus cattle would not cause a methaemoglobinaemia in the blood >20% throughout a 70 day treatment period. Methods: A 70 day study was conducted to determine the methaemoglobin, carboxyhaemoglobin, total haemoglobin, growth rate and forage intakes of cattle supplemented with a non-protein-nitrogen treatment containing nitrate (6.48 g NO3/kg dry matter intake (DMI) or no nitrate and consuming a chaffed Flinders grass hay (Iseilema spp.), a C4 species. The dose rate of nitrate was selected to match the Australian government guidelines. Ten 3-year-old fistulated Bos indicus steers (mean liveweight ± s.d., 400.7 ± 26.2 kg) were randomly allocated into two groups (n = 5). Blood samples were collected at 0, 2, 4 and 6 h after treatment with nitrate or no nitrate on days 10, 30, 50 and 70 to measure haemoglobin fractions in the blood. Key Results: Nitrate treatment caused the mean methaemoglobin (P < 0.001), peak methaemoglobin (P < 0.001) and carboxyhaemoglobin (P = 0.008) concentration to be greater in the blood of steers compared with steers given no nitrate. Nitrate treatment had no general effect on the total haemoglobin, DMI or bodyweight of steers. Conclusions: Bos indicus steers treated with 6.48 g NO3/kg DMI develop a methaemoglobinaemia that does not exceed 20% of total haemoglobin for 70 days. This data supports the Australian government's recommended feeding rate of nitrate to sedentary Bos indicus steers. Implications: The Australian government's method for feeding nitrate to cattle is safe under the conditions of this study. Within the conditions of the study, Bos indicus steers treated with nitrate develop a methaemoglobinaemia that does not exceed 20% of total haemoglobin for 70 days. Although the data in the current study supports the Australian government's recommended dose rate as safe for cattle the data represents Bos indicus steers in a sedentary state. Further research is required to validate the dose rate of nitrate for cattle in an active state. [ABSTRACT FROM AUTHOR]

Feeding yeast culture fermentation products has been associated with improved feed intake and milk yield in transition dairy cows. These improvements in performance have been further described in terms of rumen characteristics, metabolic profile, and immune response. The objective of this study was to evaluate the effects of a commercial yeast culture product (YC; Culture Classic HD, Phibro Animal Health) on performance, blood biomarkers, rumen fermentation, and rumen bacterial population in dairy cows from −30 to 50 d in milk (DIM). Forty Holstein dairy cows were enrolled in a randomized complete block design from −30 to 50 DIM and blocked according to expected calving day, parity, previous milk yield, and genetic merit. At −30 DIM, cows were assigned to either a basal diet plus 114 g/d of ground corn (control; n = 20) or a basal diet plus 100 g/d of ground corn and 14 g/d of YC (n = 20), fed as a top-dress. Cows received the same close-up diet from 30 d prepartum until calving [1.39 Mcal/kg of dry matter (DM) and 12.3% crude protein (CP)] and lactation diet from calving to 50 DIM (1.60 Mcal/kg of DM and 15.6% CP). Blood samples and rumen fluid were collected at various time points from −30 to 50 d relative to calving. Cows fed YC compared with control showed a trend for increased energy-corrected milk (+3.2 kg/d). Lower somatic cell counts were observed in YC cows than in control. We detected a treatment × time interaction in nonesterified fatty acids (NEFA) that could be attributed to a trend for greater NEFA in YC cows than control at 7 DIM, followed by lower NEFA in YC cows than control at 14 and 30 DIM. In the rumen, YC contributed to mild changes in rumen fermentation, mainly increasing postpartal valerate while decreasing prepartal isovalerate. This was accompanied by alterations in rumen microbiota, including a greater abundance of cellulolytic (Fibrobacter succinogenes) and lactate-utilizing bacteria (Megasphaera elsdenii). These results describe the potential benefits of supplementing yeast culture during the late pregnancy through early lactation, at least in terms of rumen environment and performance. [ABSTRACT FROM AUTHOR]

Context. Rumen fermentation modulation with feed additives during the transition period to high-concentrate diets might help to avoid bacterial dysbiosis. Aims. Assessing the effects of the addition of tannins and medium-chain fatty acids (MCFA) to the adaptation diet of beef calves to a high-concentrate ration on the rate of intake, animal performance and rumen bacterial composition. Methods. Eighteen 7-month-old beef calves were abruptly weaned and transitioned over a 28-day period from a milk/grass regime to one of the following diets: a non-supplemented high-concentrate diet plus wheat straw, both given ad libitum (C); C plus 20 g/kg of a 65:35 chestnut and quebracho tannin extract; and C plus 6 g/kg of a commercial mixture of MCFA. Concentrate and straw rate of intake were recorded. Rumen fluid was collected on Days 0, 1, 7, 14, 21 and 28 at 0, 3, 6 and 9 h after feeding to characterise rumen fermentation. Samples from 0 h were analysed to assess the bacterial population using Ion Torrent sequencing. Key results. The rate of intake of concentrates and straw, as well as daily gains and final weights, were similar (P > 0.05) among diets. The addition of tannins or MCFA did not modify (P = 0.98) the rumen bacterial population, which was affected by sampling day (P < 0.001). The additives inclusion did not affect relative abundances of the main bacterial taxa (P < 0.05), most of them differing across days (P < 0.001). Diversity indexes (Shannon and richness) declined over sampling days (P < 0.05), although some genera emerged after concentrate inclusion. Conclusions. At the doses used in the present experiment, tannins and MCFA did not exert any effect on intake, animal performance and bacterial population. Abrupt transition to high-concentrate diets modified the rumen environment and bacterial community, indicating bacterial adaptation to new environmental conditions. Implications. Abrupt transition of 7-month-old calves from milk/pasture to a high-concentrate diet did not impair rumen microbiota or performance; therefore, the use of feed additives seems unnecessary. [ABSTRACT FROM AUTHOR]

A greater understanding of the rumen microbiota and its function may help find new strategies to improve feed efficiency in cattle. This study aimed to investigate whether the cattle breed affects specific ruminal taxonomic microbial groups and functions associated with feed conversion ratio (FCR), using two genetically related Angus breeds as a model. Total RNA was extracted from 24 rumen content samples collected from purebred Black and Red Angus bulls fed the same forage diet and then subjected to metatranscriptomic analysis. Multivariate discriminant analysis (sparse partial least square discriminant analysis (sPLS-DA)) and analysis of composition of microbiomes were conducted to identify microbial signatures characterizing Black and Red Angus cattle. Our analyses revealed relationships among bacterial signatures, host breeds and FCR. Although Black and Red Angus are genetically similar, sPLS-DA detected 25 bacterial species and 10 functions that differentiated the rumen microbial signatures between those two breeds. In Black Angus, we identified bacterial taxa Chitinophaga pinensis, Clostridium stercorarium and microbial functions with large and small subunits ribosomal proteins L16 and S7 exhibiting a higher abundance in the rumen microbiome. In Red Angus, nonetheless, we identified the poorly characterized bacterial taxon Oscillibacter valericigenes with a higher abundance and pathways related to carbohydrate metabolism. Analysis of composition of microbiomes revealed that C. pinensis and C. stercorarium exhibited a higher abundance in Black Angus compared to Red Angus associated with FCR, suggesting that these bacterial species may play a key role in the feed conversion efficiency of forage-fed bulls. This study highlights how the discovery of signatures of bacterial taxa and their functions can be used to harness the full potential of the rumen microbiome in Angus cattle.

This study was aimed to evaluate the potential of a herbal mixture (HM) to improve production performance, rumen fermentation, and milk fatty acid profile in water buffaloes. Sixteen Murrah buffaloes (in four groups) were fed for 10 weeks with the same basal diet supplemented with 0 (control); 20 (HM20), 30 (HM30), and 40 (HM40) g/buffalo per day. The herbal mixture contained an equal quantity of black pepper (fruit), ginger (tubers), cinnamon (bark), peppermint (leaves), ajwain (seeds) and garlic (bulbs). After two weeks of adaptation, daily milk yield, and weekly milk composition were recorded. On the last day of the experiment, rumen contents were collected to determine rumen fermentation parameters and bacterial diversity through 16S rRNA sequencing. Results revealed no effect of treatment on dry matter intake (DMI), rumen fermentation parameters, and daily milk yield. However, milk fat (%) showed a tendency to increase (p = 0.07) in HM20 as compared with the control group. A significant increase in mono and polyunsaturated fatty acids (C14:1, C16:1, C18:2n6 and C18:3) whereas a decrease in saturated fatty acids (C18:0) in milk was observed in HM20 as compared with the control group. No significant change in bacterial diversity parameters (alpha and beta diversity) was observed in response to the treatment. Despite the substantial variation observed in the relative abundance of bacteria among treatment groups, no significant effect of treatment was observed when compared with the control group. Correlation analysis revealed several positive and negative correlations of rumen bacteria with rumen volatile fatty acids (VFA) and milk yield traits. Bacterial genera including Succinivibrionaceae, Butyrivibrio, Pseudobutyrivibrio, and Lachnospiraceae showed a positive correlation with VFA and milk yield traits. Overall, we observed 52 positive and 10 negative correlations of rumen bacteria with milk fatty acid contents. Our study revealed the potential of the herbal mixture at a lower supplemental level (20 g/day) to increase milk fat (%) and unsaturated fatty acid content in buffalo.

Three experiments assessed branched-chain volatile fatty acid (BCVFA) stimulation of neutral detergent fiber (NDF) disappearance after 24 h of incubation in batch cultures derived from ruminal fluid inocula that were enriched with particulate-phase bacteria. In experiment 1, a control was compared with 3 treatments with isomolar doses of all 3 BCVFA (plus valerate), all 3 branched-chain AA (BCAA), or half of each BCVFA and BCAA mix with either alfalfa or grass hays (50%) and ground corn grain (50%). A portion of the BCAA and BCVFA doses were enriched with 13C, and valerate (also enriched with 13C) was added with BCVFA. Although BCAA yielded a similar production of BCVFA compared with dosing BCVFA, equimolar substitution of BCVFA for BCAA decreased the percentage of N in bacterial pellets when alfalfa hay was fed but increased N when grass hay was fed. Substituting BCVFA for BCAA increased total fatty acid (FA) concentration with alfalfa hay. Dosing of BCAA or BCVFA did not affect total branched-chain FA, iso -FA, or anteiso -FA percentages in bacterial total FA, whereas numerous individual FA isomers and their 13C enrichments were affected by these treatments. Increasing recovery of the 13C dose from respective labeled BCVFA primers indicated facilitated BCVFA uptake and incorporation into FA compared with BCAA, whereas increased recovery of 13C from labeled BCAA in the bacteria pellet but not in the FA fraction suggested direct assimilation into bacterial protein. The BCVFA and valerate were dosed in varying combinations that either summed to 4 m M (experiment 2) or had only 1 m M no matter what combination (experiment 3). In general, grass hay was more responsive to stimulation in NDF digestibility by BCVFA than was alfalfa hay, which was attributed to the higher degradable protein in the latter. The net production of the BCVFA (after subtracting dose) was affected by source and combination of BCVFA. Isovalerate dosing tended to increase its own net production; in contrast, isobutyrate seemed to be used more when it was added alone, but 2-methylbutyrate seemed to be preferred over isobutyrate when 2-methylbutyrate was added. Results supported potential interactions, including potential feedback in production from feed BCAA or increased concentration-dependent competition for dosed BCVFA into cellular products. Under our conditions, the BCVFA appear to be more readily available than BCAA, probably because of regulated BCAA transport and metabolism. Valerate consistently provided no benefit. Using nonparametric ranking, all 3 BCVFA or either isovalerate or isobutyrate (both yielding iso -FA) should be combined with 2-methylbutyrate (yielding anteiso -FA) as a potential opportunity to improve NDF digestibility when rumen-degraded BCAA are limited in diets to decrease environmental impact from N in waste. [ABSTRACT FROM AUTHOR]

This study was aimed to evaluate the potential of a herbal mixture (HM) to improve production performance, rumen fermentation, and milk fatty acid profile in water buffaloes. Sixteen Murrah buffaloes (in four groups) were fed for 10 weeks with the same basal diet supplemented with 0 (control); 20 (HM20), 30 (HM30), and 40 (HM40) g/buffalo per day. The herbal mixture contained an equal quantity of black pepper (fruit), ginger (tubers), cinnamon (bark), peppermint (leaves), ajwain (seeds) and garlic (bulbs). After two weeks of adaptation, daily milk yield, and weekly milk composition were recorded. On the last day of the experiment, rumen contents were collected to determine rumen fermentation parameters and bacterial diversity through 16S rRNA sequencing. Results revealed no effect of treatment on dry matter intake (DMI), rumen fermentation parameters, and daily milk yield. However, milk fat (%) showed a tendency to increase (p=0:07) in HM20 as compared with the control group. A significant increase in mono and polyunsaturated fatty acids (C14:1, C16:1, C18:2n6 and C18:3) whereas a decrease in saturated fatty acids (C18:0) in milk was observed in HM20 as compared with the control group. No significant change in bacterial diversity parameters (alpha and beta diversity) was observed in response to the treatment. Despite the substantial variation observed in the relative abundance of bacteria among treatment groups, no significant effect of treatment was observed when compared with the control group. Correlation analysis revealed several positive and negative correlations of rumen bacteria with rumen volatile fatty acids (VFA) and milk yield traits. Bacterial genera including Succinivibrionaceae, Butyrivibrio, Pseudobutyrivibrio, and Lachnospiraceae showed a positive correlation with VFA and milk yield traits. Overall, we observed 52 positive and 10 negative correlations of rumen bacteria with milk fatty acid contents. Our study revealed the potential of the herbal mixture at a lower supplemental level (20 g/day) to increase milk fat (%) and unsaturated fatty acid content in buffalo. [ABSTRACT FROM AUTHOR]

Better characterization of changes in the rumen microbiota in dairy cows over the lactation period is crucial for understanding how microbial factors may potentially be interacting with host phenotypes. In the present study, we characterized the rumen bacterial and archaeal community composition of 60 lactating Holstein dairy cows (33 multiparous and 27 primiparous), sampled twice within the same lactation with a 122 days interval. Firmicutes and Bacteroidetes dominated the rumen bacterial community and showed no difference in relative abundance between samplings. Two less abundant bacterial phyla (SR1 and Proteobacteria) and an archaeal order (Methanosarcinales), on the other hand, decreased significantly from the mid-lactation to the late-lactation period. Moreover, between-sampling stability assessment of individual operational taxonomic units (OTUs), evaluated by concordance correlation coefficient (C-value) analysis, revealed the majority of the bacterial OTUs (6,187 out of 6,363) and all the 79 archaeal OTUs to be unstable over the investigated lactation period. The remaining 176 stable bacterial OTUs were mainly assigned to Prevotella, unclassified Prevotellaceae, and unclassified Bacteroidales. Milk phenotype-based screening analysis detected 32 bacterial OTUs, mainly assigned to unclassified Bacteroidetes and Lachnospiraceae, associated with milk fat percentage, and 6 OTUs, assigned to Ruminococcus and unclassified Ruminococcaceae, associated with milk protein percentage. These OTUs were only observed in the multiparous cows. None of the archaeal OTUs was observed to be associated with the investigated phenotypic parameters, including methane production. Co-occurrence analysis of the rumen bacterial and archaeal communities revealed Fibrobacter to be positively correlated with the archaeal genus vadinCA11 (Pearson r = 0.76) and unclassified Methanomassiliicoccaceae (Pearson r = 0.64); vadinCA11, on the other hand, was negatively correlated with Methanobrevibacter (Pearson r = –0.56). In conclusion, the rumen bacterial and archaeal communities of dairy cows displayed distinct stability at different taxonomic levels. Moreover, specific members of the rumen bacterial community were observed to be associated with milk phenotype parameters, however, only in multiparous cows, indicating that dairy cow parity could be one of the driving factors for host–microbe interactions.

Velvet antler is a regeneration organ of sika deer (Cervus nippon) and an important Chinese medicine, and nutrient metabolism affects its growth. Here, we investigated the effects of arginine supplementation on antler growth, serum biochemical indices, and the rumen bacterial community of sika deer during the antler growth period. Fifteen male sika deer (6 years old) were randomly assigned to three dietary groups, which were supplemented with 0 (n = 5, CON), 2.5 (n = 5, LArg), or 5.0 g/d (n = 5, HArg) L-arginine. The IGF-1, ALT and AST concentrations in the serum of LArg sika deer were significantly higher than those in the serum of CON (P < 0.05) and HArg deer (P < 0.05). The phyla Bacteroidetes, Firmicutes, and Proteobacteria were dominant in the rumen of sika deer among the three groups. Comparison of alpha diversities showed that the ACE and Chao1 indices significantly increased in the LArg and HArg groups compared with those in the CON group. PCoA and ANOSIM results showed that the bacterial community was significantly changed between the CON and LArg groups. Moreover, the relative abundances of Fibrobacter spp. and Prevotellaceae UCG-003 increased, but those of Clostridium sensu stricto 1 and Corynebacterium 1 decreased in the LArg and HArg groups compared with those in the CON group. Additionally, the relative abundances of 19 OTUs were significantly different between the LArg and HArg groups. These results revealed that arginine supplementation affected the sika deer rumen bacterial community and serum biochemical indices.

Better characterization of changes in the rumen microbiota in dairy cows over the lactation period is crucial for understanding how microbial factors may potentially be interacting with host phenotypes. In the present study, we characterized the rumen bacterial and archaeal community composition of 60 lactating Holstein dairy cows (33 multiparous and 27 primiparous), sampled twice within the same lactation with a 122 days interval. Firmicutes and Bacteroidetes dominated the rumen bacterial community and showed no difference in relative abundance between samplings. Two less abundant bacterial phyla (SR1 and Proteobacteria) and an archaeal order (Methanosarcinales), on the other hand, decreased significantly from the mid-lactation to the late-lactation period. Moreover, between-sampling stability assessment of individual operational taxonomic units (OTUs), evaluated by concordance correlation coefficient (C-value) analysis, revealed the majority of the bacterial OTUs (6,187 out of 6,363) and all the 79 archaeal OTUs to be unstable over the investigated lactation period. The remaining 176 stable bacterial OTUs were mainly assigned to Prevotella , unclassified Prevotellaceae, and unclassified Bacteroidales. Milk phenotype-based screening analysis detected 32 bacterial OTUs, mainly assigned to unclassified Bacteroidetes and Lachnospiraceae, associated with milk fat percentage, and 6 OTUs, assigned to Ruminococcus and unclassified Ruminococcaceae, associated with milk protein percentage. These OTUs were only observed in the multiparous cows. None of the archaeal OTUs was observed to be associated with the investigated phenotypic parameters, including methane production. Co-occurrence analysis of the rumen bacterial and archaeal communities revealed Fibrobacter to be positively correlated with the archaeal genus vadinCA11 (Pearson r = 0.76) and unclassified Methanomassiliicoccaceae (Pearson r = 0.64); vadinCA11 , on the other hand, was negatively correlated with Methanobrevibacter (Pearson r = –0.56). In conclusion, the rumen bacterial and archaeal communities of dairy cows displayed distinct stability at different taxonomic levels. Moreover, specific members of the rumen bacterial community were observed to be associated with milk phenotype parameters, however, only in multiparous cows, indicating that dairy cow parity could be one of the driving factors for host–microbe interactions. [ABSTRACT FROM AUTHOR]

Objective: The objective of this study was to compare fenugreek (FG) with alfalfa (Alf) in ruminal fermentation and methane (CH4) production in vitro. Methods: Whole-plant FG harvested at 11- and 15-wk and Alf harvested at early and mid-bloom maturities, alone or as 50:50 mixture of FG and Alf at the respective maturity, were assessed in a series of 48-h in vitro batch culture incubations. Total fermentation gas and methane gas production, dry matter (DM) disappearance, volatile fatty acids, microbial protein and 16S RNA gene copy numbers of total bacteria and methanogens were determined. Results: Compared to early bloom Alf, FG harvested at 11-wk exhibited higher (p<0.05) in vitro DM and neutral detergent fibre disappearance, but this difference was not observed between the mid-bloom Alf and 15-wk FG. Regardless plant maturity, in vitro ruminal fermentation of FG produced less (p<0.001) CH4 either on DM incubated or on DM disappeared basis than that of Alf during 48-h incubation. In vitro ruminal fermentation of FG yielded similar amount of total volatile fatty acids with higher (p<0.05) propionate percentage as compared to fermentation of Alf irrespective of plant maturity. Microbial protein synthesis was greater (p<0.001) with 11-wk FG than early bloom Alf as substrate and 16S RNA gene copies of total bacteria was higher (p<0.01) with 15-wk FG than mid-bloom Alf as substrate. Compared to mid-bloom Alf, 15-wk FG had lower (p<0.05 to 0.001) amount of 16S RNA methanogen gene copies in the whole culture during 48-h incubation. Conclusion: In comparison to Alf, FG emerges as a high quality forage that can not only improve rumen fermentation in vitro, but can also remarkably mitigate CH4 emissions likely due to being rich in saponins. [ABSTRACT FROM AUTHOR]

BACKGROUND: Rumen bacteria play a critical role in feed degradation and productivity. This study evaluated the impact of feeding regimen on the rumen microbial populations and fatty acid composition of the meat of sheep. Twenty‐four Sunit sheep were raised on a grass pasture from birth to 9 months of age, at which time they were randomly divided into two feeding groups: pasture feeding (PF) and barn feeding (BF). Sheep in the PF group were allowed to graze freely on wild grassland for 3 months. Sheep in the BF group were confined for 3 months to a dry barn, in which they roamed freely with corn straw and corn. RESULTS: Sheep in the PF group had greater rumen bacteria diversity. The relative abundances of the genera Butyrivibrio_2, Saccharofermentans and Succiniclasticum were increased, and that of the genus RC9_gut_group was decreased, in the PF compared to the BF sheep. The n‐3 polyunsaturated fatty acid contents were greater in meat from PF sheep than from BF sheep. In addition, the α‐linolenic acid (C18:3 n‐3, ALA) and conjugated linoleic acid (CLA) contents were positively correlated with the abundance of Butyrivibrio_2. CONCLUSION: Grazing may improve the diversity of rumen bacteria and increase the proportion of ALA and CLA in sheep meat. © 2020 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

This study was aimed to evaluate the effect of a mixed phytogenic (MP) on rumen bacteria and their potential association with rumen fermentation and milk yield parameters in water buffaloes. Twenty Murrah buffaloes were fed a basal diet (consisting of maize silage, brewers' grains, and concentrate mixture) for 6 weeks supplemented with 0 (control), 15 (MP15), 25 (MP25), and 35 (MP35) g of mixed phytogenic/buffalo per d. The mixed phytogenic contained fennel (seeds), ajwain (seeds), ginger (tubers), Swertia chirata (leaves), Citrullus colocynthis (fruit), turmeric, fenugreek (seeds), Terminalia chebula (fruit), licorice (roots), and Phyllanthus emblica (fruit) in equal quantities. After 2 weeks of adaptation, daily milk yield, and weekly milk composition were recorded. On the last day of the experiment (d 42), rumen contents were collected to determine rumen fermentation parameters and bacterial diversity through 16S rRNA sequencing. Results revealed no change in dry matter intake, milk yield and rumen fermentation parameters except pH, which increased (P = 0.029) in response to MP supplementation. The mixed phytogenic increased (P < 0.01) milk fatty acids (C4 to C14:0) in MP15 only. The milk C16:1 content and its unsaturation index were higher (P < 0.05) in MP35 as compared to the control and other treatments. Furthermore, C18:3n3 was higher (P < 0.05) in the control, MP15, and MP25, as compared to MP35. Supplementation of MP tended to increase (P = 0.095) the Shannon index of bacterial alpha diversity and a difference (P < 0.05) among treatment groups was observed in beta diversity. Feeding MP increased the Firmicutes, Proteobacteria, and Spirochaetes but decreased Bacteroidetes numerically. In addition, the dominant genus Prevotella decreased in all treatment groups while Pseudobutyrivibrio, Butyrivibrio, and Succinivibrioanceae increased numerically in MP25 and MP35. The mixed phytogenic promoted groups of rumen bacteria positively associated with milk and fat yield. Overall, our study revealed 14 positive correlations of rumen bacteria with milk yield and eight with rumen fermentation parameters. Our findings reveal substantial changes in the rumen bacteriome composition and milk fatty acid content in response to MP but these results should be interpreted carefully, as the sample size of our study was relatively small.

This preliminary investigation was designed to study the effects of different mixed orchard hays on meat quality, fatty acids, amino acids, rumen intestinal microflora, and the relationship between rumen bacteria and fatty acids in the longissimus dorsi muscle of Saanen dairy goats. In this preliminary investigation, goats were separately fed crop straws (corn and wheat straws) and alfalfa (Medicago sativa L.) (CK group), alfalfa + oats (Avena sativa L.) (group I), alfalfa + perennial ryegrass (Lolium perenne L.) (group II), and hairy vetch (Vicia villosa Roth.) + perennial ryegrass (group III). There were differences in shear force and cooking loss between treatments. The contents of saturated fatty acids (SFAs) C14:0, C16:0, and C18:0 in the CK group were significantly higher than those in other three groups (p < 0.001). The 16S rDNA sequencing results showed that the relative abundance of Proteobacteria in group II were higher than those in other three groups (p < 0.05). Association analysis showed that Prevotella_1 was negatively correlated with C18:0 and significantly positively correlated with C16:1, while Clostridium and Romboutsia showed a positive correlation with monounsaturated fatty acids (MUFAs) and polyunsaturated fatty acids (PUFAs). Therefore, feeding mixed hays can increase beneficial fatty acids and the percentages of associated bacteria in rumen and intestines.

Abstract Background Residual feed intake (RFI) in dairy cattle typically calculated at peak lactation is a measure of feed efficiency independent of milk production level. The objective of this study was to evaluate differences in ruminal bacteria, biopolymer hydrolyzing enzyme activities, and overall performance between the most- and the least-efficient dairy cows during the peripartal period. Twenty multiparous Holstein dairy cows with daily ad libitum access to a total mixed ration from d − 10 to d 60 relative to the calving date were used. Cows were classified into most-efficient (i.e. with low RFI, n = 10) and least-efficient (i.e. with high RFI, n = 10) based on a linear regression model involving dry matter intake (DMI), fat-corrected milk (FCM), changes in body weight (BW), and metabolic BW. Results The most-efficient cows had ~ 2.6 kg/d lower DMI at wk 4, 6, 7, and 8 compared with the least-efficient cows. In addition, the most-efficient cows had greater relative abundance of total ruminal bacterial community during the peripartal period. Compared with the least-efficient cows, the most-efficient cows had 4-fold greater relative abundance of Succinivibrio dextrinosolvens at d − 10 and d 10 around parturition and tended to have greater abundance of Fibrobacter succinogenes and Megaspheara elsdenii. In contrast, the relative abundance of Butyrivibrio proteoclasticus and Streptococcus bovis was lower and Succinimonas amylolytica and Prevotella bryantii tended to be lower in the most-efficient cows around calving. During the peripartal period, the most-efficient cows had lower enzymatic activities of cellulase, amylase, and protease compared with the least-efficient cows. Conclusions The results suggest that shifts in ruminal bacteria and digestive enzyme activities during the peripartal period could, at least in part, be part of the mechanism associated with better feed efficiency in dairy cows.

Objective This study was conducted to isolate the cellulolytic microorganism from the rumen of Holstein steers and characterize endoglucanase gene (Cel5A) from the isolated microorganism. Methods To isolate anaerobic microbes having endoglucanase, rumen fluid was obtained from Holstein steers fed roughage diet. The isolated anaerobic bacteria had 98% similarity with Eubacterium cellulosolvens (E. cellulosolvens) Ce2 (Accession number: AB163733). The Cel5A from isolated E. cellulolsovens sp. was cloned using the published genome sequence and expressed through the Escherichia coli BL21. Results The maximum activity of recombinant Cel5A (rCel5A) was observed at 50°C and pH 4.0. The enzyme was constant at the temperature range of 20°C to 40°C but also, at the pH range of 3 to 9. The metal ions including Ca2+, K+, Ni2+, Mg2+, and Fe2+ increased the endoglucanase activity but the addition of Mn2+, Cu2+, and Zn2+ decreased. The Km and Vmax value of rCel5A were 14.05 mg/mL and 45.66 μmol/min/mg. Turnover number, Kcat and catalytic efficiency, Kcat/Km values of rCel5A was 96.69 (s−1) and 6.88 (mL/mg/s), respectively. Conclusion Our results indicated that rCel5A of E. cellulosolvens isolated from Holstein steers had a broad pH range with high stability under various conditions, which might be one of the beneficial characteristics of this enzyme for possible industrial application.

A greater understanding of the rumen microbiota and its function may help find new strategies to improve feed efficiency in cattle. This study aimed to investigate whether the cattle breed affects specific ruminal taxonomic microbial groups and functions associated with feed conversion ratio (FCR), using two genetically related Angus breeds as a model. Total RNA was extracted from 24 rumen content samples collected from purebred Black and Red Angus bulls fed the same forage diet and then subjected to metatranscriptomic analysis. Multivariate discriminant analysis (sparse partial least square discriminant analysis (sPLS-DA)) and analysis of composition of microbiomes were conducted to identify microbial signatures characterizing Black and Red Angus cattle. Our analyses revealed relationships among bacterial signatures, host breeds and FCR. Although Black and Red Angus are genetically similar, sPLS-DA detected 25 bacterial species and 10 functions that differentiated the rumen microbial signatures between those two breeds. In Black Angus, we identified bacterial taxa Chitinophaga pinensis , Clostridium stercorarium and microbial functions with large and small subunits ribosomal proteins L16 and S7 exhibiting a higher abundance in the rumen microbiome. In Red Angus, nonetheless, we identified the poorly characterized bacterial taxon Oscillibacter valericigenes with a higher abundance and pathways related to carbohydrate metabolism. Analysis of composition of microbiomes revealed that C. pinensis and C. stercorarium exhibited a higher abundance in Black Angus compared to Red Angus associated with FCR, suggesting that these bacterial species may play a key role in the feed conversion efficiency of forage-fed bulls. This study highlights how the discovery of signatures of bacterial taxa and their functions can be used to harness the full potential of the rumen microbiome in Angus cattle. [ABSTRACT FROM AUTHOR]

Yeast α-mannan (YM) is a densely branched N-linked glycan that decorates the surface of yeast cell walls. Owing to the high degree of branching, cleavage of the backbone of YM appears to rely on the coupled action of side-chain-cleaving enzymes. Upon examining the genome sequences of bovine-adapted Bacteroides thetaiotaomicron strains, isolated for their ability to degrade YM, we have identified a tandem pair of genes inserted into an orphan pathway predicted to be involved in YM metabolism. Here, we investigated the activity of one of these enzymes, a predicted endo-mannanase from glycoside hydrolase (GH) family 76 (BtGH76-MD40). Purified recombinant BtGH76-MD40 displayed activity on structurally distinct YMs from Saccharomyces cerevisiae and Schizosaccharomyces pombe. Linkage analysis of released oligosaccharide products from S. cerevisiae and S. pombe mannan determined BtGH76-MD40 targets a specific linkage that is conserved in structurally diverse YM substrates. In addition, using two differential derivatization methods, we have shown that there is an absolute requirement for undecorated d -mannopyranose in the −1 subsite. Determination of the BtGH76-MD40 X-ray crystal structure and structural superimposition and molecular docking of a branched alpha-mannopentatose substrate supported these findings. In contrast, BtGH76-MD40 can accommodate extended side chains in the +1 and −2 subsites, highlighting that a single alpha-1,6-mannosyl residue is a prerequisite for activity, and cleavage occurs at the reducing end of the undecorated monosaccharide. Collectively these results demonstrate how acquisition of new enzymes within extant pathways contributes to the functional abilities of saccharolytic bacteria persisting in complex digestive ecosystems. Image 1 • Yeast mannan (YM) is a highly branched polysaccharide with species-dependent structural diversity. • An enzyme has been found within the bovine rumen that cleaves the backbone of YM. • Cleavage requires the presence of an unbranched 6-linked mannose. • Glycosidic linkage analysis and crystallography elucidate the nature of interactions. [ABSTRACT FROM AUTHOR]

This study was conducted to examine the effects of clay (CL) and Saccharomyces cerevisiae fermentation product (SCFP) on the ruminal bacterial community of Holstein dairy cows challenged with aflatoxin B1 (AFB1). A second objective was to examine correlations between bacterial abundance and performance measures. Eight lactating dairy cows stratified by milk yield and parity were randomly assigned to 4 treatments in a 4 × 4 Latin square design with 2 replicate squares, four 33-d periods, and a 5-d washout between periods. The treatments included (1) control (basal diet, no additive); (2) T (control + 63.4 µg/kg AFB1, oral dose); (3) CL (T + 200 g/head per day of sodium bentonite clay, top-dress); and (4) CL+SCFP [CL + 19 g/head per day Diamond V NutriTek (Diamond V Inc., Cedar Rapids, IA) + 16 g/head per day MetaShield (Diamond V Inc.), top-dress]. Cows were adapted to diets containing no AFB1 from d 1 to 25 (predosing period). From d 26 to 30 (dosing period), AFB1 was orally dosed and then withdrawn for d 31 to 33 (withdrawal period). During the predosing period, compared with the control, feeding CL and CL+SCFP increased the relative abundance of the most dominant phylum, Bacteroidetes (55.1 and 55.8 vs. 50.6%, respectively), and feeding CL+SCFP increased Prevotella abundance (43.3 and 43.6 vs. 40.0%, respectively). During the dosing period, feeding AFB1 did not affect the ruminal bacterial community, but the relative abundance of Fibrobacteraceae increased with CL+SCFP compared with T (1.45 vs. 0.97%); Fibrobacter abundance also tended to increase with CL+SCFP compared with T and control, respectively (1.45 vs. 0.97 and 1.05%, respectively). Feeding AFB1 with or without CL or CL+SCFP did not affect ruminal pH or concentrations of NH3-N, total volatile fatty acids, or individual volatile fatty acids. Milk yield and milk component yields were positively correlated with the relative abundance of unclassified Succinivibrionaceae, unclassified YS2, or Coprococcus. Feed efficiency was positively correlated (r ≥ 0.30) with the relative abundance of unclassified YS2, Coprococcus, or Treponema. Feeding aflatoxin at 63 µg/kg, a common contamination level on farms, did not affect the abundance of dominant bacteria or rumen fermentation. When aflatoxin was fed, CL+SCFP increased the abundance of Fibrobacter, a major fibrolytic bacteria genus. Milk yield and DMI were positively correlated with abundance of Succinivibrionaceae and Coprococcus. Feed efficiency was positively correlated with abundance of Coprococcus, Treponema, and YS2. Future studies should speciate culture and determine the functions of the bacteria to elucidate their roles in the rumen and potential contribution to increasing the performance of dairy cows. [ABSTRACT FROM AUTHOR]

Hybridization in bovines is practiced with the main aim of improving production performance, which may imply the microbial variations in the rumen from the parental breed cross to their progeny. Besides, the interactions of offspring breed with sex in terms of rumen bacteria are not clear. This study aims to evaluate the variations in rumen bacterial communities in different breeds and sexes, and the correlations among fattening performance, serum biochemical parameters, and rumen fermentation. Forty-two 19.2 ± 0.67-month-old beef cattle (390 ± 95 kg of initial body weight) comprising two genetic lines (Yiling and Angus × Yiling) and two sexes (heifers and steers) were raised under the same high-grain diet for 120 d. On the last two days, blood samples were collected from each animal via the jugular vein before morning feeding for analyzing serum biochemical parameters; rumen fluid samples were obtained via esophageal intubation 2 h after morning feeding for analyzing rumen fermentation parameters and bacterial communities. The results show that both breed and sex had a certain impact on fattening performance, serum biochemical parameters, and rumen fermentation. No differences in the diversity and structure of rumen bacterial communities were observed. Significant interactions (p < 0.05) of breed and sex were observed for Succinivibrionaceae UCG-002 and Prevotellaceae UCG-001. The relative abundances of the Rikenellaceae RC9 gut group, Prevotellaceae UCG-003, and Succinivibrio were different (p < 0.05) between breeds. Heifers had a higher (p = 0.008) relative abundance of the Rikenellaceae RC9 gut group than steers. Correlation analysis showed a significant relationship (p < 0.05) of rumen bacteria with serum biochemical parameters, rumen pH, and rumen fermentation patterns. Additionally, only two genera, Prevotellaceae UCG-003 and Prevotellaceae UCG-001, had positive correlations with feed efficiency. In conclusion, serum biochemical parameters, rumen fermentation, and rumen bacterial communities are partly driven by the breed and sex of cattle fed a high-grain diet.

Natural, non-toxic feed additives can potentially replace chemical medications and antibiotics that are offered sheep to improve performance. In the present study, Tibetan sheep were supplemented with the root of Astragalus membranaceus (AMT), a traditional herb used widely in China. Twenty-four male Tibetan sheep (31 ± 1.4 kg; 9-month-old) were assigned randomly to one of four levels of supplementary AMT: 0 g/kg (A0), 20 g/kg (A20), 50 g/kg (A50) and 80 g/kg (A80) dry matter intake (DMI). The A50 and A80 groups increased the diversity of rumen bacteria on d 14 and the relative abundances of fiber decomposing bacteria. Supplementary AMT upregulated the metabolism of vitamins, nucleotides, amino acids and glycan, and downregulated the metabolism of lipids and carbohydrates. In addition, supplementary AMT enriched rumen bacteria for drug resistance, and reduced bacteria incurring cell motility. In general, AMT supplementation increased the concentrations of catalase (CAT), superoxide dismutase (SOD) total antioxidant capacity (T-AOC) and secretory immunoglobulin A (sIgA) in the small intestinal mucosa and CAT and SOD in meat tissue. The liver tissue metabolome response showed that AMT in the A80 lambs compared to the A0 lambs upregulated the metabolites for energy synthesis. It was concluded that supplementary A. membranaceus increased the relative abundances of fiber decomposing bacteria and improved the antioxidant capacities and immunity indices of small intestinal mucosa and meat tissue in Tibetan sheep.

Feeding condensed tannin (CT)-containing diets such as sericea lespedeza (Lespedeza cuneata) and reducing stress have been reported to improve meat quality and food safety in goats. In a completely randomized design with split-plot, thirty-six uncastrated male Spanish goats were assigned to 3 dietary treatments (n = 12/treatment): ground ‘Serala’ sericea lespedeza hay (SER), bermudagrass (Cynodon dactylon) hay (BG), or bermudagrass hay—dewormed goats (BG-DW; Control) at 75% of intake, with a corn-based supplementation (25%) for 8 weeks. Prior to slaughter, goats were either transported for 90 min to impose stress or held in pens. Basophil counts were lower (p < 0.01) in the SER group compared to BG or BG-DW groups suggesting a better anti-inflammatory capacity due to polyphenols in the SER diet. Compared to BG-DW group, cortisol level was higher (p < 0.05) and norepinephrine was lower (p < 0.05) in the SER group. The SER group had the lowest aerobic plate counts (APC) in both rumen and rectum (p < 0.01). Longissimus dorsi muscle initial pH was not affected by diet or stress. Feeding sericea hay to goats may have beneficial effects, such as enhanced antioxidant and anti-inflammatory properties during stress and reduced gut microbial counts, without changing meat quality characteristics.

To understand the effects of diet and age on the rumen bacterial community and function, forty-eight dairy cattle at 1.5 (M1.5), 6 (M6), 9 (M9), 18 (M18), 23 (M23), and 27 (M27) months old were selected. Rumen fermentation profile, enzyme activity, and bacteria community in rumen fluid were measured. The acetate to propionate ratio (A/P) at M9, M18, and M23 was higher than other ages, and M6 was the lowest (p < 0.05). The total volatile fatty acid (TVFA) at M23 and M27 was higher than at other ages (p < 0.05). The urease at M18 was lower than at M1.5, M6, and M9, and the xylanase at M18 was higher than at M1.5, M23, and M27 (p < 0.05). Thirty-three bacteria were identified as biomarkers of the different groups based on the linear discriminant analysis (LDA) when the LDA score >4. The variation partitioning approach analysis showed that the age and diet had a 7.98 and 32.49% contribution to the rumen bacteria community variation, respectively. The richness of Succinivibrionaceae_UCG-002 and Fibrobacter were positive correlated with age (r > 0.60, p < 0.01) and positively correlated with TVFA and acetate (r > 0.50, p < 0.01). The Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans has a positive correlation (r > 0.80, p < 0.05) with diet fiber and a negative correlation (r < −0.80, p < 0.05) with diet protein and starch, which were also positively correlated with the acetate and A/P (r > 0.50, p < 0.01). The genera of Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans could be worked as the target bacteria to modulate the rumen fermentation by diet; meanwhile, the high age correlated bacteria such as Succinivibrionaceae_UCG-002 and Fibrobacter also should be considered when shaping the rumen function.

Abstract Background Cashew nut shell liquid (CNSL) is an agricultural byproduct containing alkylphenols that has been shown to favorably change the rumen fermentation pattern only under experimentally fixed feeding conditions. Investigation of CNSL potency in rumen modulation under a variety of feeding regimens, and evidence leading to the understanding of CNSL action are obviously necessary for further CNSL applications. The objective of this study was to evaluate the potency of CNSL for rumen modulation under different dietary conditions, and to visually demonstrate its surfactant action against selected rumen bacteria. Methods Batch culture studies were carried out using various diets with 5 different forage to concentrate (F:C) ratios (9:1, 7:3, 5:5. 3:7 and 1:9). Strained rumen fluid was diluted with a buffer and incubated with each diet. Gas and short chain fatty acid (SCFA) profiles were characterized after 18 h incubation at 39 °C. Monensin was also evaluated as a reference additive under the same conditions. Four species of rumen bacteria were grown in pure culture and exposed to CNSL to determine their morphological sensitivity to the surfactant action of CNSL. Results CNSL supplementation decreased total gas production in diets with 5:5 and 3:7 F:C ratios, whereas the F:C ratio alone did not affect any gas production. Methane decrease by CNSL addition was more apparent in diets with 5:5, 3:7, and 1:9 F:C ratios. An interactive effect of CNSL and the F:C ratio was also observed for methane production. CNSL supplementation enhanced propionate production, while total SCFA production was not affected. Monensin decreased methane production but only in a diet with a 1:9 F:C ratio with increased propionate. Studies of pure cultures indicated that CNSL damaged the cell surface of hydrogen- and formate-producing bacteria, but did not change that of propionate-producing bacteria. Conclusion CNSL can selectively inhibit rumen bacteria through its surfactant action to lead fermentation toward less methane and more propionate production. As CNSL is effective over a wider range of dietary conditions for such modulation of rumen fermentation in comparison with monensin, this new additive candidate might be applied to ruminant animals for various production purposes and at various stages.

This study aimed to evaluate the effect of replacement of ground corn by soybean hulls associated or not to whole soybean grain in the feed supplement on intake, nutrient digestibility, rumen microbial population, and fermentation parameters of growing Nellore steers grazing Brachiaria brizantha cv. Xaraés during rainy season. Were used eight castrated Nellore steers (425 ± 36 kg of body weight (BW)) fitted with ruminal and duodenal cannulas in a replicated 4 × 4 Latin square with a 2 × 2 factorial arrangement, allocated into 4 paddocks of 0.25 ha each, consisting of Brachiaria brizantha cv. Xaraés and supplemented with: (1) ground corn combined with whole soybean grain (SG); (2) ground corn without SG; (3) soybean hulls (SH) combined with SG; and (4) SH without SG. Supplement intake was no affected by SG or SH (mean 2.12 kg-1 d, P > 0.05). There were no interactions between SH and SG on DM and nutrients intake (P > 0.05). The addition of SG reduced the dry matter (DM) intake expressed as % of BW and Kg-1 d, as well forage DM, organic matter (OM), crude protein (CP), neutral detergent fiber (aNDF), and gross energy (GE) intake (P ? 0.01). Animals supplemented with SH without SG had greater digestibility of DM (74.52), OM (77.62), CP (77.51), NDF (71.93) and GE (72.90) than animals supplemented with SH with SG (DM =69.01, OM = 71.92, CP = 72.81, NDF = 66.01, GE =68.01) expressed as % (P ? 0.01). The addition of SG in the supplements declined the ruminal pH and NH3-N (P=0.02). Animals supplemented without SH without SG showed greater Entodinium counts (6.01 n x 104 ml-1, P=0.04), and SG supplementation decreased the numbers of Dasytricha, Isotricha, and ruminal total protozoa (P < 0.01). The abundance of Ruminococcus albus, R. flavefaciens, and Archaeas were higher for SH without SG supplement. Additionally, animals supplemented with SG had lower numbers of Fibrobacter succinogenes. The use of soybean hulls without whole soybean grain in the supplement may be effective to increase fiber digestibility, N retained, R. albus and R. flavefaciens in the rumen of Nellore steers grazing Brachiaria brizantha cv. Xaraés during the rainy season.

The taxonomy and associated nomenclature of many taxa of rumen bacteria are poorly defined within databases of 16S rRNA genes. This lack of resolution results in inadequate definition of microbial community structures, with large parts of the community designated as incertae sedis, unclassified, or uncultured within families, orders, or even classes. We have begun resolving these poorly-defined groups of rumen bacteria, based on our desire to name these for use in microbial community profiling. We used the previously-reported global rumen census (GRC) dataset consisting of >4.5 million partial bacterial 16S rRNA gene sequences amplified from 684 rumen samples and representing a wide range of animal hosts and diets. Representative sequences from the 8,985 largest operational units (groups of sequence sharing >97% sequence similarity, and covering 97.8% of all sequences in the GRC dataset) were used to identify 241 pre-defined clusters (mainly at genus or family level) of abundant rumen bacteria in the ARB SILVA 119 framework. A total of 99 of these clusters (containing 63.8% of all GRC sequences) had no unique or had inadequate taxonomic identifiers, and each was given a unique nomenclature. We assessed this improved framework by comparing taxonomic assignments of bacterial 16S rRNA gene sequence data in the GRC dataset with those made using the original SILVA 119 framework, and three other frameworks. The two SILVA frameworks performed best at assigning sequences to genus-level taxa. The SILVA 119 framework allowed 55.4% of the sequence data to be assigned to 751 uniquely identifiable genus-level groups. The improved framework increased this to 87.1% of all sequences being assigned to one of 871 uniquely identifiable genus-level groups. The new designations were included in the SILVA 123 release (https://www.arb-silva.de/documentation/release-123/) and will be perpetuated in future releases.

Pineapple stem starch (PS) was evaluated for its suitability as a new starch source in concentrate for fattening cattle, based on the growth performance, blood profile, and rumen parameters of 36 steers in a 206-day feeding study. PS was formulated as a 40% concentrate and fed with forage in comparison with ground corn (GC) and ground cassava (CA) formulated at the same level. PS feeding improved weight gain and feed conversion ratio without affecting feed intake. PS did not obviously influence blood lipid profiles throughout the experiment. Ruminal concentration of total short-chain fatty acids (SCFA) increased with PS without affecting SCFA composition throughout the feeding study. Rumen amylolytic group, especially Ruminococcus bromii, was dominant in the rumen microbial community, and showed increased abundance by PS feeding throughout the experiment. These results clearly indicate the potential of PS as a useful starch source for fattening cattle in terms of rumen fermentation and growth performance. [ABSTRACT FROM AUTHOR]

In vitro and in vivo experiments were conducted to determine the metabolism of rumen-protected or unprotected l-citrulline (Cit) plus l-glutamine (Gln) by ruminal microbes. In the in vitro experiment, whole ruminal fluid (3 mL, containing microorganisms) from steers was incubated at 37 ºC with 5 mM Cit plus 6 mM Gln (in a rumen-protected or unprotected form) for 0, 0.5, 2, or 4 h after which times 50 µL samples were collected for AA and ammonia analyses. In the in vivo experiment, at 0.5 h before and 0, 0.5, 1, 2, 4, and 6 h after cannulated adult steers consumed 0.56 kg drieddistillers’ grain mixed with 70 g Cit plus 70 g Gln (in a rumen-protected or unprotected form), samples of ruminal fluid and jugular venous blood were obtained for AA analyses. Results from both in vitro and in vivo experiments demonstrated extensive hydrolysis of rumen-unprotected Gln into glutamate, but little degradation of the rumen-protected Gln or rumenprotected and unprotected Cit by ruminal microbes. Concentrations of Cit and arginine in the plasma of steers consuming rumen-protected or unprotected AA increased at 1 and 2 h after the meal, respectively, when compared with values at 0 h. Collectively, these novel findings indicate that ruminal microbes of adult steers do not degrade extracellular Cit in a rumenprotected or unprotected form. Our results refute the view that all dietary AAs are extensively catabolized by ruminal microorganisms and also have important implications for dietary supplementation with Cit to ruminants to enhance the concentration of arginine in their plasma and their productivity. [ABSTRACT FROM AUTHOR]

Bovicin is a type AII lantibiotic, possessing two β-methyllanthionine and a disulfide bridge encoded by bovA gene hitherto unknown a couple of decades ago. Bacteriocins can be useful in directly inhibiting methanogens and/or redirecting H2 to other reductive microorganisms, in particular, propionate producers or reductive acetogens. So far, the role of nisin and bovicin to suppress greenhouse gas (GHG) production under in vitro conditions has been documented. GHG emissions from ruminants are a threat to the environment, because of their role in global warming as well as in climate change. Methane (CH4) produced from livestock farming practices is a potent GHG, comprising 18% of total GHG emissions in the world. Therefore, minimizing enteric CH4 production is quite essential from both the economical livestock production as well as environment perspectives. Strategies for the abatement of CH4 have provided two-way opportunities, viz., improved livestock productivity and reduced GHG emissions. In the past, different strategies have been proposed and tested to mitigate CH4, such as the dietary composition of feeds, ionophores, antibiotics, vaccines, analogues, probiotics, and secondary metabolites of plants and fungi. However, quite a few of these strategies have been adopted at farm level due to their varied effect on animal health and/or residues on animal products. The use of bacteriocins might have potential in inhibiting methanogens in the rumen. A bacteriocin produced by Streptococcus bovis (an isolate from rumen) named bovicin HC5 has been exhibited to decrease CH4 production to an extent of 50%. In this review, authors intend to discuss the sources, structure, biochemical properties, and antimicrobial spectra of bovicins, besides the potential applications with special reference to CH4 mitigation. [ABSTRACT FROM AUTHOR]

The dietary energy level can affect ruminal microbiota, and further can affect rumen fermentation and fatty acid (FA) synthesis. In this study, we investigated the correlations between rumen bacteria and rumen fermentation parameters and intramuscular fat (IMF) FA profiles of Holstein bulls fed different energy diets via using 16S rRNA high-throughput sequencing and gas chromatography. The results showed that the improved dietary energy increased propionate, isobutyrate and isovalerate concentrations, and decreased acetate concentration and the acetate/propionate ratio. Increased dietary energy improved beef IMF content and had no effects on cooking loss, Warner-Bratzler shear force, water holding capacity, or drip loss. Increase dietary energy also decreased C18:0, C18:1 trans, C22:0, C20:3n-3, C22:6n-3, and saturated fatty acids, and increased C18:1 cis-9, C18:2n-6 trans, and monounsaturated fatty acids. 16S rRNA high-throughput sequencing analysis revealed that dietary energy had no impact on alpha diversity or the relative abundance of most of the major phyla and genera in rumen. In all dietary treatment groups, the dominant microbial phyla were Bacteroidetes (54.91%) and Firmicutes (33.60%), and the major microbial genus was Prevotella_1 (21.75%). Improved dietary energy decreased the abundances of Firmicutes and Tenericutes and increased that of Proteobacteria at the phylum level, while decreasing those of RC9_gut_group, and increased Prevotellaceae_UCG-004, Phocaeicola, Acetitomaculum, Lachnoclostridium_1, Prevotellaceae_UCG-003, and Anaerovibrio at the genus level. Spearman correlation analysis showed high correlations between rumen bacteria and fermentation parameters/IMF FA profiles. Collectively, our data indicated that dietary energy affects the ruminal microbiota, and further affects ruminal fermentation and IMF FA composition. [ABSTRACT FROM AUTHOR]

Rumen digesta was obtained from wild Hokkaido sika deer to compare bacterial flora between summer and winter. Bacterial flora was characterized with molecular‐based approaches and enrichment cultivation. Bacteroidetes was shown as a major phylum followed by Firmicutes, with similar proportions in both seasons. However, two phylogenetically unique groups in Bacteroidetes were found in each season: unknown group A in winter and unknown group B in summer. The ruminal abundance of unknown group A was the highest followed by Ruminococcus flavefaciens in winter. Moreover, the abundance of these two was higher in winter than in summer. In contrast, the abundance of unknown group B was higher in summer than in winter. In addition, this group showed the highest abundance in summer among the bacteria quantified. Unknown group A was successfully enriched by cultivating with oak bark and sterilized rumen fluid, particularly that from deer. Bacteria of this group were distributed in association with the solid rather than the liquid rumen fraction, and were detected as small cocci. Accordingly, unknown group A is assumed to be involved in degradation of fibrous materials. These results suggest that wild Hokkaido sika deer develop a rumen bacterial flora in response to changes in dietary conditions. [ABSTRACT FROM AUTHOR]

The present study was conducted to assess rumen bacteria in lactating cows with different milk protein yield, aiming to understand the role of rumen bacteria in this trait. Cows with high milk protein yield (high milk yield and high milk protein content, HH; n = 20) and low milk protein yield (low milk yield and low milk protein content, LL; n = 20) were selected from 374 mid-lactation Holstein dairy cows fed a high-grain diet. Measurement of the rumen fermentation products showed that the concentrations of ruminal total volatile fatty acids, propionate, butyrate, and valerate and the proportion of isobutyrate were higher in the HH cows than in the LL cows. Amplicon sequencing analysis of the rumen bacterial community revealed that the richness (Chao 1 index) of rumen microbiota was higher in the LL cows than in the HH cows. Among the 10 predominant bacterial phyla (relative abundance being >0.10%, present in >60% of animals within each group), the relative abundance of Proteobacteria was 1.36-fold higher in the HH cows than in the LL cows. At the genus level, the relative abundance of Succinivibrio was significantly higher and that of Clostridium tended to be higher in the LL cows than in the HH cows. Sharpea was 2.28-fold enriched in the HH cows compared with the LL cows. Different relationships between the relative abundances of rumen microbial taxa and volatile fatty acid concentrations were observed in the HH and the LL animals, respectively. Succinivibrio and Prevotella were positively correlated with acetate, propionate, and valerate in the LL cows, whereas Sharpea was positively correlated with propionate and valerate concentrations in the HH cows. Collectively, our results revealed that rumen bacterial richness and the relative abundances of several bacterial taxa significantly differed between dairy cows with high and low milk protein yields, suggesting the potential roles of rumen microbiota contributing to milk protein yield in dairy cows. [ABSTRACT FROM AUTHOR]

Intake in sugar-rich diets can be limited either via rumen fill or excessive rumen fermentation and source of non-fibre carbohydrate (NFC) in the diet can affect both factors. The aim of the current study was to quantify the effect of partially replacing ground maize (GM) with steam-rolled maize (SRM) or pelleted citrus pulp (PCP) at two concentrate levels in sugarcane-based diets on digestibility, rumen ecosystem and metabolism of Nellore steers. Six rumen-cannulated steers were assigned to a 6 × 6 Latin square, replicated in time, in a 2 × 3 factorial arrangement of treatments with two levels of concentrate (600 or 800 g concentrate/kg dry matter [DM]) and three NFC sources. Each steer within a period was considered an experimental unit. Feeding more concentrate increased total tract digestibility of organic matter and decreased fibre intake and passage rate. It also reduced rumen populations of Fibrobacter succinogenes and Streptococcus bovis and increased Ruminococcus flavefaciens. Substituting PCP for GM increased rumen pH, acetic acid and organic matter digestibility. Feeding PCP also reduced R. flavefaciens and R. amylophilus rumen populations. Substituting SRM for GM increased starch digestibility and rumen propionic acid, but decreased rumen ammonia concentration. Feeding SRM increased rumen populations of Megasphaera elsdenii with the high-concentrate diet but reduced Ruminococcus albus populations at both concentrate levels. In conclusion, partial replacement of GM by PCP decreased intake in sugar-rich diets, while increasing total tract neutral detergent fibre digestibility. Replacement of GM with SRM increases rumen fermentation and total tract digestibility of starch. [ABSTRACT FROM AUTHOR]

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Highlights • pH, extruded linseed and grain source effects are studied in a continuous culture. • They modify the biohydrogenation processes of polyunsaturated fatty acids. • They modify the individual fatty acid content of the ruminal bacteria. • They affect content and outflow of odd- and branched-chain fatty acids differently. Abstract Using 6 continuous cultures of rumen microorganisms, we studied the effects of pH (low vs. high) and extruded linseed supplementation (10% of DM) in association with rapidly or slowly degraded starch sources (wheat vs. corn grains) 1) on fatty acid (FA) outflows and PUFA biohydrogenation (BH) processes 2) on FA microbial composition and its contribution to FA outflows, in two replicated periods of 10d (7d adaptation and 3d sampling). The control diet contained wheat. The buffer solutions infused in low or high pH cultures differed by the addition of 10 mL of 5 N H 2 SO 4 or NaOH so as to allow fermentation medium pH fluctuations with diets and time after feeding. The fermentation pattern, daily amounts of hexoses fermented (HF), efficiency of microbial protein synthesis (EMPS), and specific production of gases (CH 4 and H 2) were measured. FA compositions were determined in total effluents and bacterial pools isolated from effluents. Lowering pH (from 6.46 to 6.16 measured just before feeding) increased the VFA concentration in the control diet whereas it decreased it in all linseed supplemented diets. Lowering pH tended to decrease CH 4 specific production as well as acetate and propionate proportions and to increase butyrate and valerate proportions but did not alter HF and EMPS. Linseed but not grain source increased pH by 0.08 and did not modify fermentative parameters. Apparent BH of C18:3 9c,12c,15c and C18:2 9c,12c decreased at low pH but increased with linseed supplementation. Corn associated to linseed increased 18:3 9c,12c,15c BH compared to wheat. Consequently, C18:3 9c,12c,15c outflows increased at low pH and with linseed, and were higher with linseed-wheat diet than linseed-corn diet. For all treatments, the proportions of C18:0 (% of C18-FA outflows) remained low associated with high levels of BH intermediates (C18:2 11t, 15c and C18:1 11t) suggesting that BH did not proceed to completion. Lowering pH decreased C16:1 9c and C18:1 11c bacteria contents and tended to increase anteiso-FA. Linseed supplementation increased C18:0, C18:1 9c, C18:1 9t, C18:2 9c,12c bacteria contents without modifying the C18:3 9c,12c,15c and decreased their odd-FA content and anteiso-FA in tendency. Compared to wheat, corn decreased branched-FA bacteria content, as well as even-saturated FA. Lowering pH decreased the bacterial FA outflow whereas linseed increased it. Both decreased the bacterial FA contribution to total FA outflow. Results indicate that pH and diets modified PUFA BH while differing in their effect on odd- and branched-chain FA bacteria content and outflows. [ABSTRACT FROM AUTHOR]

The taxonomy and associated nomenclature of many taxa of rumen bacteria are poorly defined within databases of 16S rRNA genes. This lack of resolution results in inadequate definition of microbial community structures, with large parts of the community designated as incertae sedis, unclassified, or uncultured within families, orders, or even classes. We have begun resolving these poorly-defined groups of rumen bacteria, based on our desire to name these for use in microbial community profiling. We used the previously-reported global rumen census (GRC) dataset consisting of >4.5 million partial bacterial 16S rRNA gene sequences amplified from 684 rumen samples and representing a wide range of animal hosts and diets. Representative sequences from the 8,985 largest operational units (groups of sequence sharing >97% sequence similarity, and covering 97.8% of all sequences in the GRC dataset) were used to identify 241 pre-defined clusters (mainly at genus or family level) of abundant rumen bacteria in the ARB SILVA 119 framework. A total of 99 of these clusters (containing 63.8% of all GRC sequences) had no unique or had inadequate taxonomic identifiers, and each was given a unique nomenclature. We assessed this improved framework by comparing taxonomic assignments of bacterial 16S rRNA gene sequence data in the GRC dataset with those made using the original SILVA 119 framework, and three other frameworks. The two SILVA frameworks performed best at assigning sequences to genus-level taxa. The SILVA 119 framework allowed 55.4% of the sequence data to be assigned to 751 uniquely identifiable genus-level groups. The improved framework increased this to 87.1% of all sequences being assigned to one of 871 uniquely identifiable genus-level groups. The new designations were included in the SILVA 123 release (https://www.arb-silva.de/documentation/release-123/) and will be perpetuated in future releases. [ABSTRACT FROM AUTHOR]

Abstract The effects of plant metabolites on rumen metabolism vary greatly depending on their antimicrobial spectrum and applied doses. In this study, the minimum inhibitory concentrations (MICs) of commercial aldehydes, trans -2-hexenal (T2H), cis -3-hexenal (C3H), trans -2-nonenal (T2N), and trans -2-decenal (T2D) from green leaf volatiles, were tested on rumen bacteria. These compounds were found more effective on Gram-positive rumen bacteria than the Gram-negatives, and C3H was the most effective compound. Then, for 14 days, the in vitro effects of C3H compared with monensin (5 mg/day) on the rumen microbial population and ruminal fermentation at 187.5, 375 and 750 mg/day doses were tested based on the MIC value (500 μg/mL) by using the rumen simulation technique (Rusitec). Supplementation with C3H at 375 mg/day increased the cell numbers of Butyrivibrio fibrisolvens significantly. The addition of C3H at 375 and 750 mg/day doses also increased Streptecoccus bovis cell counts. The use of monensin did not affect the cell numbers of these bacteria. On the other hand, C3H did not change the counts of total bacteria, methanogens, or hyper-ammonia-producing (HAP) bacteria like monensin. The numbers of Ruminococcus albu s and Ruminococcus flavefaciens were also stable in the presence of C3H but decreased significantly with the addition of monensin (P < 0.05). Fibrobacter succinogenes, Megasphaera elsdenii, and Selenomonas ruminantium cell counts were not affected by either application. In addition, C3H increased the acetate and methane production along with the acetate-to-propionate ratio at all tested concentrations, unlike monensin. Supplementation with C3H decreased propionate production significantly, except at the 187.5 mg/day dose. Butyrate production increased (P < 0.05) only in the presence of 187.5 and 375 mg/day doses of C3H. Production of total volatile fatty acids (VFA) and dry matter digestibility (DMD) did not change in treatment groups. Also, the total protozoa numbers and ammonia-N concentrations significantly decreased (P < 0.05) in C3H-treated samples, similar to monensin. Although C3H did not have favorable effects on energy efficiency, it suppressed rumen protozoa and mitigated rumen ammonia without adversely effecting ruminal fermentation in all applied doses. Based on the result, C3H has the potential to improve protein utilization in the rumen. Highlights • MIC values of green leaf volatiles on rumen bacteria were determined initially. • Cis-3-hexenal was the most effective compound on Gram-positive rumen bacteria. • The effects of cis-3-hexenal in Rusitec were differed from that in pure cultures. • Cis-3-hexenal suppressed rumen protozoa and mitigated rumen ammonia. • Cis-3-hexenal did not depress ruminal fermentation. [ABSTRACT FROM AUTHOR]