Rumen Bacteria Research Articles

Litter size influences rumen microbiota and fermentation efficiency, thus determining host early growth in goats.

Multiple litters are accompanied by low birth weight, low survival rates, and growth rates in goats during early life. Regulating rumen microbiota structure can indirectly or directly affect host metabolism and animal growth. However, the relationship between high litter size and rumen microbiome, rumen fermentation, and growth performance in goat kids is unclear. In the present study, thirty 6-month-old, female goats were investigated, of which 10 goats were randomly chosen from single, twin and triplet goats respectively, and their birth weight was recorded. From birth, all goats were subjected to the same feed and management practices. Individual weaning and youth body weight were measured, and the rumen fluid samples were collected to characterize the bacterial communities and to determine the ruminal volatile fatty acids (VFA), free amino acids (AA), and free fatty acids (FA) concentration of those young goats. Compared with the single and twin goats, triplet goats have lower weaning and youth body weight and average daily gain (ADG). Ruminal propionate, butyrate, and total VFA were decreased in triplet goats. Meanwhile, ruminal AA, such as branched chain amino acids (BCAA), essential amino acids (EAA), unsaturated fatty acids (UFA), and monounsaturated fatty acids (MUFA) were decreased, while saturated fatty acids (SFA) and odd and branched chain fatty acids (OBCFA) were increased in triplet goats. Our results also revealed that litter size significantly affected the rumen bacterial communities, and triplet goats had a lower the Firmicutes: Bacteroidota ratio, the abundance of Firmicutes phylum, Rikenellaceae family, and Rikenellaceae RC9 gut group, and had a higher proportion of Prevotellaceae family, and several genera of Prevotellaceae, such as Prevotella, and unclassified f Prevotellaceae. Furthermore, Spearman's correlation network analysis showed that the changes in the rumen bacteria were associated with changes in rumen metabolites. In conclusion, this study revealed that high litter size could bring disturbances to the microbial communities and decrease the rumen fermentation efficiency and growth performance, which can be utilized to better understand variation in microbial ecology that will improve growth performance in triplet goats.

Potential role of rumen bacteria in modulating milk production and composition of admixed dairy cows

Cattle milk is an important food for the growing calf and humans because of its concentrated macro and micro nutrients. However, the quantity and quality of milk nutrients vary depending on several factors. This study evaluated the effect of dietary modification on rumen bacteria as well as the potential role of rumen bacteria in modifying milk production and composition profile. Using a 16S rRNA metagenomic approach, the study characterized the rumen bacterial community composition in four dairy cows and their milk production and composition. The results indicated that Bacteroidetes and Firmicutes were the dominant bacteria, totaling ∼83.7% of the rumen bacteria. An increase in concentrate proportion in diet led to an increase in the abundance of Bacteroidetes (P≤0.05) and Proteobacteria while Firmicutes and Fibrobacter decreased. Milk production and composition were highly correlated with the abundance of various rumen bacterial members. Lentispaerae (P=0.010), and Synergistetes (P=0.011) exhibited a positive and significant correlation while Tenericutes (P=0.009) showed a negative correlation with milk protein. Fusobacteria (P=0.016) showed a negative correlation with milk lactose. Similarly, several genera showed correlations with milk parameters. The correlation between microbes with milk parameters implies that the bacterial community possesses the potential to influence milk production and composition.

Effects of waste milk feeding on rumen fermentation and bacterial community of pre-weaned and post-weaned dairy calves.

The objective of this study was to investigate the effect of waste milk with antibiotic residue on rumen fermentation and rumen bacterial composition of dairy calves during pre-weaned and post-weaned periods. A total of 24 Holstein male calves (43.4 ± 0.93 kg body weight, mean ± standard error) were allocated into four blocks based on birth date. Dairy calves were supplied 100% milk replacer (MR, n = 8), 50% milk replacer mixed with 50% waste milk (MM, n = 8), or 100% waste milk (WM, n = 8). Ruminal samples were collected at 49 and 63 days of age and then subjected to determinations of pH value, volatile fatty acids (VFA), ammonia nitrogen (NH3-N) and 16S rRNA gene amplicon sequencing. The results showed that feeding WM had no effect on the pH value, the concentrations of VFA (acetic acid, propionic acid, butyric acid, isovaleric acid, valeric acid), and NH3-N in dairy calves compared to feeding MR. However, from 49 to 63 days of age, the pH value (p < 0.001) was significantly increased, while the levels of total VFA (p = 0.004), acetic acid (p = 0.01), propionic acid (p = 0.003) and valeric acid (p < 0.001) were significantly decreased. For rumen microorganisms, there was no differences in bacterial diversity among the treatments. But the relative abundance of Veillonellaceae was significantly lower (p = 0.05) in the calves fed WM than that from MR group at 49 days of age; however, no difference was detected at 63 days of age. Feeding WM to calves tended to reduce family Veillonellaceae and genus Olsenella in the rumen at 49 days of age (p = 0.049). Analysis of temporal changes in rumen bacteria based on alpha-diversity and beta-diversity as well as the microbial relative abundances did not exhibit any difference. In addition, relative abundances of Clostridia_UCG-014, Prevotella, Syntrophococcus, Eubacterium_nodatum_group, Pseudoramibacter and Solobacterium were correlated with rumen pH value and the concentrations of TVFA, propionic acid, isovaleric acid, valeric acid and NH3-N. In conclusion, compare to MR, calves supplied with WM had little changes on the rumen pH value, NH3-N or VFAs contents. Additionally, limited effects could be found on rumen microbiota in the calves fed WM. However, further studies needed to explore if there exist any long-term effects of early-life rumen microbiota modulation on dairy cows.

Effect of Energy Provision Strategy on Rumen Fermentation Characteristics, Bacterial Diversity and Community Composition.

This study was conducted to explore the rumen fermentation characteristics, bacterial diversity, and community composition of Hu sheep under four energy provision strategies. Ninety-six Hu sheep (body weight: 17.78 ± 1.24 kg) were equally assigned to four energy provision strategies: (1) low-energy diet for the whole finishing stage (LL); (2) high-energy diet for the whole finishing stage (HH); (3) low-energy diet in the early finishing stage and high-energy diet in the late finishing stage (LH); (4) high-energy diet in the early finishing stage and low-energy diet in the late finishing stage (HL). The results showed that the proportion of acetate was lower in the HH group than that in the HL group, whereas the opposite result was observed for the butyrate proportion (p &lt; 0.05). The Chao 1, observed species, PD whole tree, and Shannon index of the rumen bacteria were higher in the LL group than that in the HH group (p &lt; 0.05). The taxonomic annotations revealed that the Patescibacteria, Rikenellaceae RC9 gut group, Christensenellaceae R-7 group, and Anaeroplasma abundances were higher in the HL group than that in the HH group, and the opposite results were observed regarding the relative abundances of Selenomonas and Anaerovibrio (p &lt; 0.05). The relative abundances of Spirochaetota and Treponema were higher in the LH group than that in the HH group (p &lt; 0.05). Moreover, the analysis of similarity (ANOSIM) showed significant differences between groups (R = 0.6792 and p = 0.001). This study indicates that the energy provision strategy had little impact on the rumen fermentation characteristics, while it heavily affected the rumen bacterial diversity and community composition. This study may provide insight into the rumen fermentation characteristics and bacterial community under routine finishing models and contribute to the optimization of energy provision strategies of Hu sheep.

Effects of diet and castration on fatty acid composition and volatile compounds in the meat of Korean native black goats.

This study determined the effects of dietary treatments and castration on meat quality, fatty acids (FAs) profiles, and volatile compounds in Korean native black goats (KNBG, Capra hircus coreanae), including the relationship between the population of rumen microbiomes and meat FA profiles. Twenty-four KNBG (48.6±1.4 kg) were randomly allocated to one of four treatments arranged into a 2×2 factorial structure. The factors were dietary forage to concentrate ratio (high forage [HF, 80:20] and low forage [LF, 20:80]), and a castration treatment (castration [CA] vs non-castration [NCA]). Among meat quality traits, the CA group exhibited a higher percentage of crude fat and water holding capacity (p<0.05). The profiles of the saturated fatty acid (SFA) in meat sample derived from CA KNBG showed a significantly lower percentage compared to NCA individuals, due to the lower proportion of C14:0 and C18:0. Feeding a high-forage diet to KNBG increased the formation of C18:1n7, C18:3n3, C20:1n9, C22:4n6 in meat, and polyunsaturated fatty acid (PUFA) profiles (p<0.05). Consequently, the n6:n3 ratio declined (p<0.05). There was an interaction between dietary treatment and castration for formation of C20:5n3 (p<0.05), while C18:1n9, C22:6n3, monounsaturated fatty acid (MUFA) and the MUFA:SFA ratio were influenced by both diet and castration (p<0.05). Nine volatile compounds were identified and were strongly influenced by both dietary treatments, castration (p<0.05), and their interaction. In addition, principal component analysis (PCA) revealed distinctly different odor patterns in the NCA goats fed LF diets. Spearman correlation analysis showed a high correlation between rumen bacteria and meat PUFAs. These results suggest the essential effects of the rumen microbial population for the synthesis of meat FAs and volatile compounds in KNBG meat, where dietary intake and castration also contribute substantially.

The response of rumen pH, fermentation parameters and rumen bacteria to feeds of different concentrate to roughage ratios in buffalos

This experiment was conducted to study the regularity influence in apparent digestibility, rumen fermentation parameters, and relative bacterial abundance in buffaloes with different concentrate to roughage ratios. Three adult female barren buffaloes with permanent rumen fistulas were fed five diets with concentrate to roughage ratios of 20:80, 35:65, 50:50, 65:35, and 80:20 according to an incomplete Latin square design of 3×5, respectively. The pre-feeding period of each period was 12 d. From day 13 to 15 of the experiment, the feed intake of each buffalo was accurately recorded and all feces were collected. Samples of diet and feces were collected for nutrient analysis. Rumen fluid was collected to determine rumen fermentation parameters, and rumen bacteria were analyzed by 16S rRNA sequencing. After 2 hours of feeding in the morning on the 15th day of the experiment, rumen bacteria were analyzed. The daily gain and DMI (G/kgW0.75) reached the highest at the concentrate to roughage ratio of 50:50, and the apparent digestibility of ADF NDF NDICP ADICP reached the highest at the concentrate to roughage ratio of 35:65. The weight loss of the experimental animals when the concentrate to roughage was 80:20. Rumen pH decreased with the increase of concentrate level, starch content and NFC content. The rumen ammonia nitrogen concentration increased with the increase in the concentrate to roughage ratio and protein content. The concentration of total volatile fatty acids (mmol/L) in the rumen decreased with the increase of NDF but increased with the increase of NFC and CP, and the acetic acid proportion increased with the increase of NDF. There were differences in the relative abundance of rumen bacterial microbiota with the different concentrate to roughage ratios. Moreover, the relative abundance of each bacterial microbiota changed regularly with the change of concentrate to roughage ratio. The relative abundance of Bacteroidetes, Firmicutes, and other rumen core microbiota varied linearly or nonlinearly with the change of concentrate to roughage ratio. This suggests that the relative abundance of the ratio of rumen microbiota can be used to specify or measure rumen health and subacute rumen acidosis/rumen acidosis.

A large database linking the rumen bacterial composition and milk traits in Lacaune sheep

Ruminants are able to produce food for human consumption from plants, thanks to rumen bacteria. Bacteria are able to transform feed to microbial proteins and to biohydrogenate unsaturated fatty acids, contributing directly to fine milk composition. The database consists of daily records of milk yield, somatic cell score and 17 milk components such as fatty acids and proteins from 795 Lacaune dairy ewes. Ruminal samples were extracted from ewes using a gastric tube and sequenced to determine the bacterial composition by metabarcoding 16S rRNA gene on a next-generation sequencing platform. From bioinformatics analysis, 9,536,442 sequences were retained and re-grouped into 2,059 affiliated OTUs, represented by 751 to 168,617 sequences. Overall, 2,059 OTUs from 795 samples were attributed to 11 phyla. The most representative phyla were Bacteroidota (50.6%) and Firmicutes (43.6%), and the most abundant families were Prevotellaceae (37.9%), Lachnospiraceae (18.1%), Ruminococcaceae (8.97%). Both shared datasets will be useful for researchers to study the link between rumen bacteria and milk traits and to propose solutions to improve animal production and health.

Metabolome and microbiome analysis revealed the effect mechanism of different feeding modes on the meat quality of Black Tibetan sheep.

Black Tibetan sheep is one of the primitive sheep breeds in China that is famous for its great eating quality and nutrient value but with little attention to the relationship between feeding regimes and rumen metabolome along with its impact on the muscle metabolism and meat quality. This study applies metabolomics-based analyses of muscles and 16S rDNA-based sequencing of rumen fluid to examine how feeding regimes influence the composition of rumen microbiota, muscle metabolism and ultimately the quality of meat from Black Tibetan sheep. Twenty-seven rams were randomly assigned to either indoor feeding conditions (SG, n = 9), pasture grazing with indoor feeding conditions (BG, n = 9) or pasture grazing conditions (CG, n = 9) for 120 days. The results showed that, compared with BG and CG, SG improved the quality of Black Tibetan sheep mutton by preventing a decline in pH and increasing fat deposition to enhance the color, tenderness and water holding capacity (WHC) of the Longissimus lumborum (LL). Metabolomics and correlation analyses further indicated that the feeding regimes primarily altered amino acid, lipid and carbohydrate metabolism in muscles, thereby influencing the amino acid (AA) and fatty acid (FA) levels as well as the color, tenderness and WHC of the LL. Furthermore, SG increased the abundance of Christensenellaceae R-7 group, [Eubacterium] coprostanoligenes group, Methanobrevibacter, Ruminococcus 2 and Quinella, decreased the abundance of Lactobacillus, Prevotella 1 and Rikenellaceae RC9 gut group, and showed a tendency to decrease the abundance of Succinivibrio and Selenomonas 1. Interestingly, all of these microorganisms participated in the deposition of AAs and FAs and modified the levels of different metabolites involved in the regulation of meat quality (maltotriose, pyruvate, L-ascorbic acid, chenodeoxycholate, D-glucose 6-phosphate, glutathione, etc.). Overall, the results suggest that feeding Black Tibetan sheep indoors with composite forage diet was beneficial to improve the mouthfeel of meat, its color and its nutritional value by altering the abundance of rumen bacteria which influenced muscle metabolism.

Effect of whole oilseeds in the diet on bacterial diversity in the solid fraction of the ruminal content of steers.

Our hypothesis was that different whole oilseeds included in the diet for steers confined could alter the diversity of rumen bacteria compared to a diet without oilseeds or an exclusively forage diet. It was aimed to evaluate the effects of oilseeds inclusion in the diet on bacterial diversity in the solid fraction of the ruminal content of steers, by gene sequences of the conserved 16S rDNA region. Six crossbred steers castrated males, fitted with ruminal cannula were used in a 6 × 6 Latin square design, using 21-day period. At the start of the experiment, the live weight of the animals averaged 416 ± 9.7kg (mean ± SD). A total of 2,180,562 16S rDNA sequences were generated for the Bacteria domain by MiSeq sequencing. The bacterial diversity was composed of 24 bacterial phyla, with the most abundant being Firmicutes, Bacteroidetes, and Proteobacteria. Other phyla with less diversity were also identified including Eurychaeota, Tenericutes, SR1 Absconditalbacteria, Synergistetes, Actinobacteria, Saccharibacteria, Elusimicrobia, Cyanobacteria, Verrucomicrobia, Fusobacteria, Lentisphaerae. The similarity in the bacterial community averaged 50% for all the experimental diets. Steers-fed corn silage exhibited a great diversity of bacteria of the Firmicutes phylum. The steers-fed oilseeds in the diet had a great diversity of bacteria from the phylum Bacteroidetes and Proteobacteria. The inclusion of whole oilseeds in the steer diets can alter the rumen bacteria population by up to 50% of total diversity.

Rumen and cecum bacteria of beef cattle that differ in feed efficiency fed a forage diet.

Most of the research addressing feed efficiency and the microbiota has been conducted in cattle fed grain diets, although cattle evolved to consume forage diets. Our hypothesis was that the bacteria in the rumen and cecum differed in cattle that have a common feed intake but had different ^average daily body weight gains (ADG) on a forage diet. Heifers (n = 134) were 606 ± 1 d of age and weighed 476 ± 3 kg at the start of the 84-d feeding study. Heifers were offered ad libitum access to a totally mixed ration that consisted of 86% ground brome hay, 10% wet distillers grains with solubles, and 4% mineral supplement as dry matter. Feed intake and body weight gain were measured, and gain was calculated. Heifers with the least (n = 8) and greatest (n = 8) ADG within 0.32 SD of the mean daily dry matter intake were selected for sampling. Digesta samples from the rumen and cecum were collected, and subsequent 16S analysis was conducted to identify Amplicon Sequence Variants. There were no differences in Alpha and Beta diversity between ADG classification within sample sites (P > 0.05). Both sample sites contained calculated balances of sister clades using phylogenetic isometric log ratio transferred data that differed across ADG classification. These findings suggest that bacteria did not differ at the community level, but there was structural difference at the clade level.

Effect of supplementation with ruminal probiotics on growth performance, carcass characteristics, plasma metabolites, methane emissions, and the associated rumen microbiome changes in beef cattle.

To evaluate the effect of supplementing beef cattle with a ruminal probiotic consisting of native rumen microbes (NRM; Chordicoccus furentiruminis, Prevotella albensis, and Succinivibrio dextrinosolvens) on methane (CH4) emissions, growth performance, carcass characteristics, and plasma metabolites, Angus × SimAngus-crossbred steers (n = 32; 8 per pen) and heifers (n = 48; 12 per pen) with an initial body weight (BW) of 353 ± 64 kg were used in randomized complete block design. Cattle were blocked by sex and BW and randomly assigned to 1 of 2 treatments (2 pens per treatment). Treatments consisted of diets offered for ad libitum intake with (NRM) or without (CON) the inclusion of the ruminal probiotic. Cattle were fed a growing diet for 49 d followed by a ground corn-based diet for 124 ± 27 d until reaching the targeted final BW (635 kg for steers and 590 kg for heifers). Methane emissions were estimated using the GreenFeed system (n = 12 per treatment) prior to trial commencement (baseline; period 1), and on three (2, 3, and 4), and two (5 and 6) different sampling periods throughout the growing and finishing stage, respectively. All data were analyzed using the PROC MIXED procedure of SAS. For CH4 production (g/d), there was a tendency for an NRM supplementation × period interaction (P = 0.07) where cattle-fed diets with NRM had lower production of methane in periods 3 and 4. Including NRM in the diet decreased CH4 yield (g/kg of dry matter intake (DMI)) by 20%. For CH4 emission intensity (g/kg of average daily gain (ADG)), an interaction (P < 0.01) of NRM supplementation × period occurred. In periods 2 and 3, cattle-fed diets with NRM inclusion had lower CH4 emission intensity than CON cattle. During the 84-d period when all cattle were still on the finishing diet, feeding NRM increased (P = 0.02) ADG and tended to increase (P = 0.10) DMI. At the end of the 84-d period, cattle-fed NRM tended to be heavier (P = 0.06) than CON cattle. Cattle supplemented with NRM required less (P = 0.04) days on feed to reach the targeted final BW. No differences (P ≤ 0.11) were detected for gain-to-feed ratio and carcass characteristics. Cattle-fed NRM had greater abundance of uncultured rumen bacteria that may improve rumen digestion when fed a high grain diet and potentially promote the reduction of enteric CH4 production. Results from this study suggest that daily administration of NRM may be a strategy to mitigate methanogenesis and improve the growth performance of beef cattle.

Influence of dietary organic trace minerals on enteric methane emissions and rumen microbiota of heat-stressed dairy steers

Ruminants are the main contributors to methane (CH4), a greenhouse gas emitted by livestock, which leads to global warming. In addition, animals experience heat stress (HS) when exposed to high ambient temperatures. Organic trace minerals are commonly used to prevent the adverse effects of HS in ruminants; however, little is known about the role of these minerals in reducing enteric methane emissions. Hence, this study aimed to investigate the influence of dietary organic trace minerals on rumen fermentation characteristics, enteric methane emissions, and the composition of rumen bacteria and methanogens in heat-stressed dairy steers. Holstein (n=3) and Jersey (n=3) steers were kept separately within a 3×3 Latin square design, and the animals were exposed to HS conditions (Temperature-Humidity Index [THI], 82.79 ± 1.10). For each experiment, the treatments included a Control (Con) consisting of only basal total mixed rations (TMR), National Research Council (NRC) recommended mineral supplementation group (NM; TMR + [Se 0.1 ppm + Zn 30 ppm + Cu 10 ppm]/kg dry matter), and higher concentration of mineral supplementation group (HM; basal TMR + [Se 3.5 ppm + Zn 350 ppm + Cu 28 ppm]/kg dry matter). Higher concentrations of trace mineral supplementation had no influence on methane emissions and rumen bacterial and methanogen communities regardless of breed (p > 0.05). Holstein steers had higher ruminal pH and lower total volatile fatty acid (VFA) concentrations than Jersey steers (p < 0.05). Methane production (g/d) and yield (g/kg dry matter intake) were higher in Jersey steers than in Holstein steers (p < 0.05). The relative abundances of Methanosarcina and Methanobrevibacter olleyae were significantly higher in Holstein steers than in Jersey steers (p < 0.05). Overall, dietary organic trace minerals have no influence on enteric methane emissions in heat-stressed dairy steers; however, breed can influence it through selective alteration of the rumen methanogen community.

Effect of galangal essential oils on rumen microbial population and biodiversity on in vitro rumen fermentation

The study aimed to evaluate the effect of administering galangal essential oil (EO) on the abundance of rumen bacteria using the 16s rRNA method. The treatments included a control (no EO addition), galangal EO (30, 60, 120 µL), and cineole (5 µL). The treatments were assessed using a 48‐hour in vitro batch culture of rumen fluid containing a 60:40 ratio of forage to concentrate. For amplification of the prokaryotes (bacteria and archaea) in region V4, 16s rRNA primer 5’GTGCCAGCMGCCGCGTAA, GGACTACHVGGGTWTCTAAT3’ was employed. The data for rumen microbial abundance were analysed descriptively, while the data for rumen microbial diversity were obtained from the report on the Next Generation Sequencing Method. The microbial composition of each sample was tested for operational taxonomic units (OTUs) with a 97% identity rate on a valid label. The 16S rRNA gene sequencing yielded a total of 3,977 OTUs. Adding galangal and cineole EOs resulted in the same variation of the Shannon index. The population index (chao1 index) was highest when 60 µL of galangal EO was added, compared to 30 and 120 µL of galangal EO and cineole. In addition, providing 60 µL of galangal EO decreased the abundance of Prevotella ruminicola compared to the control and cineole doses. The addition of galangal EO also led to a decline in the number of Methanobacteriales. The population of the fibre‐degrading bacteria group (Ruminococcus albus and Ruminococcus flavefaciens) was higher in a dose of galangal EO than the control and cineole. Therefore, it can be concluded that the effective dose of galangal EO, i.e. 60 µL/300 mg (DM feed) in vitro, can reduce the abundance of Prevotella bacteria and methanogens.

Effects of Feeding Different Levels of Sprouted Barley on Fermentation Characteristics, Bacterial Quantification, and Rumen Morphology of Growing Lambs.

The objective of the present study was to investigate the effects of sprouted barley inclusion level on the growth performance, digestibility, volatile fatty acids, bacterial quantification, and rumen morphology of growing lambs. Five dietary treatments with sprouted barley (0, 25, 50, 75 and 100%) and nine replicates per dietary treatment were performed on forty-five Awassi lambs (90 days old). The average weight gain, intake, and digestibility of dry and organic matter were recorded. The pH, color, volatile fatty acids, bacterial quantification, and rumen histomorphometry were also determined. The results showed that the average dry and organic matter intake in T2 to T4 and the average weight gain in T4 decreased linearly. In contrast, the digestibility of dry and organic matter by sprouted barley (T2 to T4) was higher. The pH values and rumen color were not affected. Concentrations of formic acid, acetic acid, butyric acid, and the ratio of acetic acid to propionic acid were increased, while lactic acid and total volatile fatty acids were lower in all levels of sprouted barley. In addition, lambs fed T4 had a higher quantification of Anaerovibrio Lipolytica, Butyrivibrio Fibrisolvens, and Streptococcus Bovis quantification. Selenomonas Ruminantium was higher in T1, T2, and T4, whereas Megashpaera Elsdenii was lower in T1 to T3. The rumen histomorphometric was improved by sprouted barley (T2 and T3). Sprouted barley improved digestibility and rumen histomorphometry and increased the concentration of some volatile fatty acids and rumen bacteria but resulted in a decrease in average dry and organic matter intake, which negatively affected weight gain in lambs fed 100 % sprouted barley. Further studies are required to determine the potential effects on growing lambs fed sprouted barley.

Comparative Analysis of Rumen Bacterial Profiles and Functions during Adaption to Different Phenology (Regreen vs. Grassy) in Alpine Merino Sheep with Two Growing Stages on an Alpine Meadow

Phenological periods can affect the growth of forage, the single food source for grazing animals, and its nutrition and the stage of growth of the animals can affect the rumen microbiota. The aim of this study was to evaluate the effects of phenological periods (regreen vs. grassy) and growing stages (hoggets (1.5 years old) vs. rams (3 years old)) on rumen bacteria communities and functions in Alpine Merion sheep. The result showed that the Alpha diversity indices of ACE (p &lt; 0.001), Chao (p &lt; 0.001), and Shannon (p &lt; 0.001) were higher in the regreen stage. At the phylum level, the abundances of Bacteroidetes (p = 0.003) and Firmicutes (p = 0.017) shifted with plant phenology. The abundance of fiber-degrading bacteria altered at the genus level (p &lt; 0.05). Genes related to fatty acid degradation and metabolism increased in both the growing stage sheep (p &lt; 0.05). In the grassy stage, the abundance of vitamin B6 metabolism (p = 0.046) was increased in hoggets. In summary, this study showed that the phenological stage had a significant effect on the rumen bacterial compartment and functions in two growing stages, while the growing stage only tended to change rumen bacterial diversity.

Alterations in the rumen bacterial communities and metabolites of finishing bulls fed high-concentrate diets supplemented with active dry yeast and yeast culture.

This study investigated the effects of active dry yeast (ADY) and yeast culture (YC) supplementation on rumen bacteria and metabolites in finishing bulls fed high-concentrate diets using the full-length 16S rDNA gene sequencing and liquid chromatography-mass spectrometry. Supplementation with ADY improved the alpha diversity and relative abundance of rumen bacteria, while YC only affected relative abundance of rumen bacteria at the genus level. Sixty-three differential metabolites were identified in rumen fluid after ADY supplementation, and 17 after YC. PICRUSt2 functional prediction showed that ADY supplementation improved the capacity of amino acid metabolism, lipid metabolism, carbohydrate metabolism, metabolism of terpenoids and polyketides, and energy metabolism in rumen bacteria (all P < 0.05). Correlation analysis showed that the rumen differential metabolites following ADY supplementation were mainly related to Oligosphaera, Verruc, Mycoplasma, and Anaeroplasma. Supplementation with ADY was more effective than YC in remodeling the rumen bacterial flora structure and metabolite composition under high-concentrate diets.

Mulberry flavonoids modulate rumen bacteria to alter fermentation kinetics in water buffalo.

Mulberry flavonoids can modulate the composition of rumen microbiota in ruminants to improve nutrient digestibility, owing to their strong biological activities. This study aimed to explore the effect of mulberry leaf flavonoids (MLF) on rumen bacteria, fermentation kinetics, and metagenomic functional profile in water buffalo. Forty buffaloes (4 ± 1 lactations) with almost same body weight (av. 600 ± 50 Kg) and days in milk (90 ± 20 d) were randomly allocated to four treatments having different levels of MLF: 0 g/d (control), 15 g/d (MLF15), 30 g/d (MLF30), and 45 g/d (MLF45) supplemented in a basal diet. After 35 days of supplementation, rumen contents were collected to determine rumen fermentation parameters. The 16S rRNA gene sequencing was performed to elucidate rumen bacteria composition. The obtained taxonomic data were analyzed to explore the rumen bacteriome and predict the associated gene functions and metabolic pathways. Results demonstrated a linear increase (p < 0.01) in rumen acetate, propionate, and total VFAs in the MLF45 group as compared to control. No effect of treatment was observed on rumen pH and butyrate contents. Acetate to propionate ratio in the MLF45 group linearly and quadratically decreased (p = 0.001) as compared to MLF15 and control groups. Similarly, MLF45 linearly increased (p < 0.05) the microbial protein (MCP) and NH3-N as compared to other treatments. Treatment adversely affected (p < 0.01) almost all alpha diversity parameters of rumen bacteria except Simpson index. MLF promoted the abundance of Proteobacteria while reducing the relative abundances of Actinobacteria, Acidobacteria, Chloroflexi, and Patescibacteria. The MLF supplementation tended to substantially reduce (0.05 < p < 0.1) the abundance of Actinobacteria, and Patescibacteria while completely eliminating Acidobacteria (p = 0.029), Chloroflexi (p = 0.059), and Gemmatimonadetes (p = 0.03) indicating the negative effect of flavonoids on the growth of these bacteria. However, MLF45 tended to substantially increase (p = 0.07) the abundance (~21.5%) of Acetobacter. The MLF treatment exhibited negative effect on five genera by significantly reducing (Sphingomonas) or eliminating (Arthobactor, unclassified_c__Actinobacteria, norank_c__Subgroup_6, norank_o__Saccharimonadales, and Nocardioides) them from the rumen microbiota. Pearson correlation analysis revealed 3, 5 and 23 positive correlations of rumen bacteria with milk yield, rumen fermentation and serum antioxidant parameters, respectively. A positive correlation of MCP was observed with three bacterial genera (Acetobacter, Enterobacter, and Klebsiella). The relative abundance of Pseudobutyrivibrio and Empedobacter also showed a positive correlation with the ruminal acetate and propionate. The present study indicated 45 g/d as an appropriate dose of MLF which modulated rumen bacteria and its functional profile in water buffalo.

Integrated Transcriptome and Microbiota Reveal the Regulatory Effect of 25-Hydroxyvitamin D Supplementation in Antler Growth of Sika Deer.

The level of plasma 25-hydroxyvitamin D (25(OH)D) is associated with the growth of the antler, a fast-growing bone organ of Cervidae. However, the benefits of 25(OH)D supplementation on antler growth and the underlying mechanisms remain unclear. Here, the antler growth profile and transcriptome, plasma parameters, rumen bacteria, and metabolites (volatile fatty acids and amino acids) were determined in sika deer in a 25(OH)D supplementation group (25(OH)D, n = 8) and a control group (Ctrl, n = 8). 25(OH)D supplementation significantly increased the antler weight and growth rate. The levels of IGF-1,25(OH)D and 1,25-dihydroxyvitamin D were significantly higher in the 25(OH)D group than in the Ctrl group, while the levels of LDL-C were lower. The levels of valerate and branched-chain amino acids in the rumen fluid were significantly different between the 25(OH)D and Ctrl groups. The bacterial diversity indices were not significantly different between the two groups. However, the relative abundances of the butyrate-producing bacteria (families Lachnospiraceae and Succinivibrionaceae) and the pyruvate metabolism pathway were higher in the 25(OH)D group. The transcriptomic profile of the antler was significantly different between the 25(OH)D and Ctrl groups, with 356 up- and 668 down-regulated differentially expressed genes (DEGs) in the 25(OH)D group. The up-regulated DEGs were enriched in the proteinaceous extracellular matrix and collagen, while the down-regulated DEGs were enriched in the immune system and lipid metabolism pathways. Overall, these results provide novel insights into the effects of 25(OH)D supplementation on the host metabolism, rumen microbiota, and antler transcriptome of sika deer.

Detection of Colistin Sulfate on Piglet Gastrointestinal Tract Microbiome Alterations.

The gut microbiome exerts important functions on host health maintenance, whereas excessive antibiotic use may cause gut flora dysfunction resulting in serious disease and dysbiosis. Colistin is a broad-spectrum antibiotic with serious resistance phenomena. However, it is unclear whether colistin alters the gastrointestinal tract microbiome in piglets. In this study, 16s rDNA-based metagenome analyses were used to assess the effects of colistin on the modification of the piglet microbiome in the stomach, duodenum, jejunum, cecum, and feces. Both α- and β-diversity indices showed that colistin modified microbiome composition in these gastrointestinal areas. In addition, colistin influenced microbiome composition at the phylum and genus levels. At the species level, colistin upregulated Mycoplasma hyorhinis, Chlamydia trachomatis, Lactobacillus agilis, Weissella paramesenteroides, and Lactobacillus salivarius abundance, but downregulated Actinobacillus indolicus, Campylobacter fetus, Glaesserella parasuis, Moraxella pluranimalium, Veillonella caviae, Neisseria dentiae, and Prevotella disiens abundance in stomachs. Colistin-fed piglets showed an increased abundance of Lactobacillus mucosae, Megasphaera elsdenii DSM 20460, Fibrobacter intestinalis, and Unidentified rumen bacterium 12-7, but Megamonas funiformis, Uncultured Enterobacteriaceae bacterium, Actinobacillus porcinus, Uncultured Bacteroidales bacterium, and Uncultured Clostridiaceae bacterium abundance was decreased in the cecum. In feces, colistin promoted Mucispirillum schaedleri, Treponema berlinense, Veillonella magna, Veillonella caviae, and Actinobacillus porcinus abundance when compared with controls. Taken together, colistin modified the microbiome composition of gastrointestinal areas in piglets. This study provides new clinical rationalization strategies for colistin on the maintenance of animal gut balance and human public health.

Bacterial species in the ruminal content of steers fed oilseeds in the diet.

The aim of this study was to evaluate bacterial species and diversity of methanogenic Archaea in the solid fraction of the ruminal content, through the gene sequences of the conserved 16S rDNA region, in response to the following diets: canola, cottonseed, sunflower, soybean, corn silage, and control diet. Six rumen-fistulated crossbred steers, with body weight (BW) of 416.33 ± 93.30kg, were distributed in a 6 × 6 Latin square design. Regardless of the diet provided, amylolytic, proteolytic, and lactic bacteria were identified in the rumen fluid. Cellulolytic bacteria were predominant for all diets, reaching 47.75% of operational taxonomic units (OTUs) in animals fed with the cottonseed diet. Amylolytic bacteria reach 62.51% of OTU in animal fed sunflower diet, while proteolytic bacteria correspond to 65.96% of OTU in this same diet. Also, Megasphaera elsdenii bacterium was identified for all diets, with a greater percentage of OTU in steers fed the cottonseed diet. The diversity analysis of the species identified the methanogenic Archaea Methanobrevibacter ruminantium in all diets. We conclude that the control and corn silage diets have the most similar bacterial flora; diets with oilseeds had 47.5% similarity in rumen flora bacteria species. Animals fed with soybean showed a reduced number of methanogenic Archaea in the rumen content, which could be an alternative feed for cattle due to their low potential for energy losses with the production of methane.