A rapid shift to high-grain diet results in dynamic changes in rumen epimural microbiome in sheep

Prevalence, Antimicrobial Resistance, and Diversity of Campylobacter Isolated from U.S. Goat Feces: 2019 NAHMS Survey

Goats are often asymptomatic carriers of Campylobacter, including the foodborne pathogen Campylobacter jejuni. Infections can have significant and economically detrimental health outcomes in both humans and animals. The primary objective of this study was to estimate the prevalence of Campylobacter in U.S. goat herds. Campylobacter species were isolated from 106 of 3,959 individual animals and from 42 of 277 goat operations that participated in fecal sample collection as part of the National Animal Health Monitoring System Goat 2019 study. Weighted animal-level prevalence was 2.3% (SE = 0.5%) and operation prevalence was 13.0% (SE = 3.2%). Animal-level prevalence ranged widely from 0 to 70.0%, however, 52.4% of positive operations (22/42) had only a single isolate. C. jejuni was the most frequently isolated species (68.9%; 73/106), followed by C. coli (29.3%, 31/106). A total of 46.2% (36/78) of viable isolates were pan-susceptible to 8 antimicrobials. Resistance to tetracycline (TET) was observed in 44.9% (35/78) of isolates, while 12.8% (10/78) were resistant to ciprofloxacin (CIP) and nalidixic acid (NAL). Among all isolates, a single resistance profile CIP-NAL-TET was observed in 3.8% (3/78) of isolates. A total of 35 unique sequence types (STs) were identified, 11 of which are potentially new. Multiple C. jejuni STs were observed in 48.1% (13/27) of positive operations. Goats with access to surface water, operations reporting antibiotics in the feed or water (excluding ionophores and coccidiostats), and operations reporting abortions and without postabortion management tasks had significantly greater odds of being Campylobacter positive. This snapshot of the U.S. goat population enriches the limited pool of knowledge on Campylobacter species presence in U.S. goats.

Impact of deoxynivalenol on rumen function, production, and health of dairy cows: Insights from metabolomics and microbiota analysis

Deoxynivalenol contamination in feed and food, pervasive from growth, storage, and processing, poses a significant risk to dairy cows, particularly when exposed to a high-starch diet; however, whether a high-starch diet exacerbates these negative effects remains unclear. Therefore, we investigated the combined impact of deoxynivalenol and dietary starch on the production performance, rumen function, and health of dairy cows using metabolomics and 16 S rRNA sequencing. Our findings suggested that both high- and low-starch diets contaminated with deoxynivalenol significantly reduced the concentration of propionate, isobutyrate, valerate, total volatile fatty acids (TVFA), and microbial crude protein (MCP) concentrations, accompanied by a noteworthy increase in NH3-N concentration in vitro and in vivo (P < 0.05). Deoxynivalenol altered the abundance of microbial communities in vivo, notably affecting Oscillospiraceae, Lachnospiraceae, Desulfovibrionaceae, and Selenomonadaceae. Additionally, it significantly downregulated lecithin, arachidonic acid, valine, leucine, isoleucine, arginine, and proline metabolism (P < 0.05). Furthermore, deoxynivalenol triggered oxidative stress, inflammation, and dysregulation in immune system linkage, ultimately compromising the overall health of dairy cows. Collectively, both high- and low-starch diets contaminated with deoxynivalenol could have detrimental effects on rumen function, posing a potential threat to production performance and the overall health of cows. Notably, the negative effects of deoxynivalenol are more pronounced with a high-starch diet than a low-starch diet.

Microbiota and Nutrient Portraits of European Roe Deer (Capreolus capreolus) Rumen Contents in Characteristic Southern German Habitats

Roe deer (Capreolus capreolus) are found in various habitats, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants still needs to be improved. There are only a few publications for individual species with a low number of samples. This study aims to identify a core microbiota for Bavarian roe deer and present nutrient and microbiota portraits of the individual habitat types. This study investigated the roe deer's rumen (reticulorumen) content from seven different characteristic Bavarian habitat types. The focus was on the composition of nutrients, fermentation products, and the rumen bacterial community. A total of 311 roe deer samples were analysed, with the most even possible distribution per habitat, season, age class, and gender. Significant differences in nutrient concentrations and microbial composition were identified for the factors habitat, season, and age class. The highest crude protein content (plant protein and microbial) in the rumen was determined in the purely agricultural habitat (AG), the highest value of non-fibre carbohydrates in the alpine mountain forest, and the highest fibre content (neutral detergent fibre, NDF) in the pine forest habitat. Maximum values for fibre content go up to 70% NDF. The proportion of metabolites (ammonia, lactate, total volatile fatty acids) was highest in the Agriculture-Beech-Forest habitat (ABF). Correlations can be identified between adaptations in the microbiota and specific nutrient concentrations, as well as in strong fluctuations in ingested forage. In addition, a core bacterial community comprising five genera could be identified across all habitats, up to 44% of total relative abundance. As with all wild ruminants, many microbial genera remain largely unclassified at various taxonomic levels. This study provides a more in-depth insight into the diversity and complexity of the roe deer rumen microbiota. It highlights the key microorganisms responsible for converting naturally available nutrients of different botanical origins.

Seasonal shifts in pronghorn antelope (Antilocapra americana) diets under a new lens: Examining diet composition using a molecular technique

Foraging is one of the most fundamental activities contributing to the maximization of an animal's fitness, and thus herbivores must optimize their diet selection and intake to meet their nutrient demands for survival, growth, and reproduction. Using plant DNA barcoding, we determined diet composition of five subpopulations of adult female pronghorn antelope (Antilocapra americana) grazing rangelands in southern and southeastern Idaho, USA. Fecal samples were collected for two years (2018-2019), and across metabolically-important adult female life history stages (late gestation, early lactation, breeding season). Plant DNA barcoding yielded 137 detected species within pronghorn diets across subpopulations and sampling periods with forbs being the most abundant. Pronghorn dietary functional group composition ranged from 52.2-60.3% from forbs followed by shrubs (22.6-28.2%), graminoids (8.7-15.7%), and legumes (5.5-9.6%). Dietary protein intake was also highest from forbs and ranged from 32.4-62.4% followed by graminoids (1.2-43.1%), shrubs (18.7-21.3%), and legumes (2.6-7.4%). We found significant intra- and interannual differences in the mean number of genera-based plant detections in pronghorn diets. Dietary protein intake of cultivated legumes (e.g., alfalfa [Medicago sativa] and sainfoin [Onobrychis viciifolia]) was lower than expected, ranging from <1.0-30.8%, suggesting that even within an agricultural-dominated landscape, factors other than plant nutritional composition contributed to pronghorn diets. Although the plant DNA barcoding technique exhibits limitations, it demonstrated potential for elucidating pronghorn dietary species richness, particularly for plants consumed in small proportions, as well as for observing temporal fluctuations in functional group composition and dietary protein intake explained through the interplay between environmental factors, plant chemical composition, and the animals' physiological needs.

Effect of replacing corn straw by sweet sorghum silage or whole plant corn silage in sheep diets on rumen fermentation and bacterial flora

Sweet sorghum silage (SS; Sorghum dochna 'Dochna') has been extensively studied in recent years as a supplementary forage-to-corn silage (CS; Zea mays L.), but there are still relatively few studies on its effects on the rumen environment of sheep. Determining the short-term impact of converting roughage from corn straws to SS compared to CS on rumen fermentation and bacterial population dynamics was the main goal of the current study. Twelve female thin-tailed Han sheep (29.8 ± 1.34 kg) were randomly divided into one of two treatments: concentrate supplemented with SS or CS, respectively. During the 15-day pretest period, concentrate was fed in two separate feedings at 0800 h and 1800 h, and ensure that the animals were all consumed within an hour of being fed. Thereafter, the animals had free access to corn straw. The feeding procedures during the pretest period were the same as during the measurement period. Rumen fluid was collected via sheep esophageal tube on the last day of adaptation phase (1-7 days) and stabilisation phase (8-30 days), respectively. The results showed that there was a similarity in the total concentration of VFA (volatile fatty acid) and the proportions of acetate, propionate, butyrate, and branched-chain VFA (P > 0.05) and microbial diversity indices (P > 0.05) between the two silage groups throughout the experimental period. The concentration of Ammonia nitrogen (P = 0.001) and proportion of valerate (P = 0.028) decreased in the CS and SS groups, respectively. The abundance and predicted function of rumen bacteria in the SS group did not differ significantly (P > 0.05) between the two measurement phases. However, the abundance of Prevotella_1 (P = 0.038) was higher in the CS group than in the SS group at 7 d. The abundances of Firmicutes (P = 0.005) and Ruminococcaceae_NK4A214_group (P = 0.002) increased, while the abundances of Bacteroidetes (P = 0.044), Proteobacteria (P = 0.046), and Prevotella_1 (P = 0.009) decreased in the CS group at 30 d. Genes related to pyruvate metabolism (P = 0.020) were significantly higher at 30 d than at 7 d, whereas purine metabolism (P = 0.007), pyrimidine metabolism (P = 0.007), and metabolic pathways (P = 0.010) were lower at 30 d in the CS group. In conclusion, this study indicated that SS maintained a steady rumen environment, while CS caused high fluctuations in bacterial abundance and predicted function for sheep.

Effects of supplementation of sodium acetate on rumen fermentation and microbiota in postpartum dairy cows

The primary product of rumen fermentation is acetic acid, and its sodium salt is an excellent energy source for post-partum cows to manage negative energy balance (NEB). However, it is unknown how adding sodium acetate (NAc) may affect the rumen bacterial population of post-partum cows. Using the identical nutritional total mixed ration (TMR), this research sought to characterize the impact of NAc supplementation on rumen fermentation and the composition of bacterial communities in post-partum cows. After calving, 24 cows were randomly assigned to two groups of 12 cows each: a control group (CON) and a NAc group (ACE). All cows were fed the same basal TMR with 468 g/d NaCl added to the TMR for the CON group and 656 g/d NAc added to the TMR for the ACE group for 21 days after calving. Ruminal fluid was collected before morning feeding on the last day of the feeding period and analyzed for rumen bacterial community composition by 16S rRNA gene sequencing. Under the identical TMR diet conditions, NAc supplementation did not change rumen pH but increased ammonia nitrogen (NH3-N) levels and microbial crude protein (MCP) concentrations. The administration of NAc to the feed upregulated rumen concentrations of total volatile fatty acids (TVFA), acetic, propionic, isovaleric and isobutyric acids without affecting the molar ratio of VFAs. In the two experimental groups, the Bacteroidota, Firmicutes, Patescibacteria and Proteobacteria were the dominant rumen phylum, and Prevotella was the dominant rumen genus. The administration of NAc had no significant influence on the α-diversity of the rumen bacterial community but upregulated the relative abundance of Prevotella and downregulated the relative abundance of RF39 and Clostridia_UCG_014. In conclusion, the NAc supplementation in the post-peripartum period altered rumen flora structure and thus improved rumen fermentation in dairy cows. Our findings provide a reference for the addition of sodium acetate to alleviate NEB in cows during the late perinatal period.

A short exposure to a semi-natural habitat alleviates the honey bee hive microbial imbalance caused by agricultural stress

Honeybee health and the species' gut microbiota are interconnected. Also noteworthy are the multiple niches present within hives, each with distinct microbiotas and all coexisting, which we termed "apibiome". External stressors (e.g. anthropization) can compromise microbial balance and bee resilience. We hypothesised that (1) the bacterial communities of hives located in areas with different degrees of anthropization differ in composition, and (2) due to interactions between the multiple microbiomes within the apibiome, changes in the community of a niche would impact the bacteria present in other hive sections. We characterised the bacterial consortia of different niches (bee gut, bee bread, hive entrance and internal hive air) of 43 hives from 3 different environments (agricultural, semi-natural and natural) through 16S rRNA amplicon sequencing. Agricultural samples presented lower community evenness, depletion of beneficial bacteria, and increased recruitment of stress related pathways (predicted via PICRUSt2). The taxonomic and functional composition of gut and hive entrance followed an environmental gradient. Arsenophonus emerged as a possible indicator of anthropization, gradually decreasing in abundance from agriculture to the natural environment in multiple niches. Importantly, after 16 days of exposure to a semi-natural landscape hives showed intermediate profiles, suggesting alleviation of microbial dysbiosis through reduction of anthropization.

The Potential Use of Endophyte-Free inebrians as Sheep Feed Evaluated with In Vitro Fermentation

Endophytic fungal infection is the major reason for intoxication of animals caused by drunken horse grass. Fortunately, it has been established that seed detoxification techniques and isolation of endophytic fungi infect non-endophytic fungi populations with the same genetic background as endophyte-infected Achnatherum inebrians. Moreover, sheep can use endophyte-free Achnatherum inebriants (EF) without obvious toxicity symptoms. The present study selected EF as a representative grass, consisting of five different replacement levels, EF0, EF25, EF50, EF75, and EF100, corresponding to 0%, 25%, 50%, 75%, and 100% of the fermentation substrate, respectively. Simultaneously, in vitro fermentation and the 16S rRNA amplicon sequencing method was used to explore the effect of EF on sheep ruminal fermentation and microbial diversity. The results revealed that EF100 had the highest values for pH, acetate: propionate, the Patescibacteria, Kiritimatiellaeota, and Synergistetes phylum levels, Ruminococcaceae, Prevotellaceae, and Saccharofermentans genus levels than the other treatments (p < 0.05). In contrast, EF25 was associated with higher levels of abundance-based coverage estimator (ACE), Chaol index of the phyla Synergistetes and Bacteroidetes, and of the genus Erysipelotrichaceae, Rikenellaceae, and Prevotella as compared with other treatments (p < 0.05). EF50 resulted in the greatest values for the genus Christensenellaceae and Lachnospiraceae as compared with other treatments (p < 0.05). EF75 resulted in the greatest values for the Shannon index as compared with other treatments (p < 0.05). EF0 resulted in the greatest values for gas production (GP), ammonia nitrogen (NH3-N), total volatile fatty acid (TVFA), acetate, propionate, butyrate, valerate, isobutyrate, isovalerate, and the phyla Firmicutes, Proteobacteria, and Spirochaetes, and the genus Succiniclasticum, Ruminobacter, Family_XIII and Treponema as compared with other treatments (p < 0.05). PICRUSt2 analysis indicated that most of the functional prediction pathways were involved in Carbohydrate metabolism and, Amino acid metabolism. Therefore, the recommended ratio of EF in sheep diet should range from 25% to 50%, and the maximum proportion should not exceed 75%.

Metabolomics approach reveals high energy diet improves the quality and enhances the flavor of black Tibetan sheep meat by altering the composition of rumen microbiota

This study aims to determine the impact of dietary energy levels on rumen microbial composition and its relationship to the quality of Black Tibetan sheep meat by applying metabolomics and Pearson's correlation analyses. For this purpose, UHPLC-QTOF-MS was used to identify the metabolome, whereas 16S rDNA sequencing was used to detect the rumen microbiota. Eventually, we observed that the high energy diet group (HS) improved the carcass quality of Black Tibetan sheep and fat deposition in the longissimus lumborum (LL) compared to the medium energy diet group (MS). However, HS considerably increased the texture, water holding capacity (WHC), and volatile flavor of the LL when compared to that of MS and the low energy diet group (LS). Metabolomics and correlation analyses revealed that dietary energy levels mainly affected the metabolism of carbohydrates and lipids of the LL, which consequently influenced the content of volatile flavor compounds (VOCs) and fats. Furthermore, HS increased the abundance of Quinella, Ruminococcus 2, (Eubacterium) coprostanoligenes, and Succinivibrionaceae UCG-001, all of which participate in the carbohydrate metabolism in rumen and thus influence the metabolite levels (stachyose, isomaltose, etc.) in the LL. Overall, a high-energy diet is desirable for the production of Black Tibetan sheep mutton because it improves the mouthfeel and flavor of meat by altering the composition of rumen microbiota, which influences the metabolism in the LL.

Calcium Propionate Supplementation Has Minor Effects on Major Ruminal Bacterial Community Composition of Early Lactation Dairy Cows

Calcium propionate is one kind of good source for preventing and treating hypocalcemia and ketosis for dairy cows in early lactation. However, little is known about the effects of different feeding levels of calcium propionate on the ruminal bacterial community of early lactation dairy cows. This study aimed to explore the effects of different calcium propionate feeding levels on the ruminal fermentation and bacterial community composition of early lactation dairy cows. Twenty-four multiparous cows were randomly allocated into control (CON), low calcium propionate (LCaP), medium calcium propionate (MCaP), and high calcium propionate (HCaP) groups with six cows per group after calving. The CON group cows were fed the normal total mixed ration (TMR), and the cows of the LCaP, MCaP, and HCaP groups were fed TMR supplemented with 200, 350, and 500 g/day calcium propionate for 35 days after calving, respectively. The rumen fermentation parameters were measured every week, and the ruminal bacterial community composition of the last week was analyzed by 16S rRNA gene sequencing. Under the same diet, the rumen pH showed no difference among the four groups, but the content of microbial crude protein (MCP) and ammonia nitrogen quadratically decreased and linearly increased with calcium propionate supplementation, respectively. The feeding of calcium propionate linearly increased the concentrations of total volatile fatty acid (VFA), acetate, propionate, butyrate, iso-valerate, and valerate in the rumen. In all the treatment groups, Bacteroidetes, Firmicutes, and Proteobacteria were the dominant phyla, and Prevotella_1 and Succiniclasticum were the dominant genera in the rumen. Compared with the CON group, the addition of calcium propionate to the early lactation dairy cows quadratically improved the alpha diversity index of Chao1 estimator and observed species, but had little effect on the relative abundance of the major bacterial at phyla and genera level. These results suggested different levels of calcium propionate supplementation improved the rumen fermentation and the ruminal bacterial diversity but had little impact on the major ruminal bacterial community composition of dairy cows in early lactation.

O efeito de probióticos fúngicos adicionados a uma dieta rica em grãos no trato gastrointestinal de ovinos

Resumo Objetivou-se avaliar as características microbiológicas e físico-químicas do fluido ruminal e histológicas do trato gástrico intestinal (TGI) de ovinos sob dieta de alto grão com probiótico fungos Aspergillus terreus e/ou Rhizomucor spp. Analisou-se quatro probióticos (sem inóculos, com Rhizomucor spp., com Aspergillus terreus e com mistura dos dois fungos) e dois processamentos de milho (moído/inteiro), em fatorial 4x2 em em Delineamento Inteiramente Casualizados (DIC). Borregos Santa Inês/Dorper foram alojados em oito baias com cinco borregos em cada, durante 75 dias. Coletou-se fluido ruminal para o estudo do perfil microbiológico do rúmen, da característica macroscópica, da concentração de nitrogênio amoniacal e da atividade microbiológica, além dos fragmentos do TGI para análises histológicas. Pelas análises dos fluidos, os animais apresentaram baixo índice de acidose. O odor aromático e a cor castanho-enegrecido predominaram, o que caracteriza ambiente com pH neutro. As amostras do fluido apresentaram alta atividade microbiana. O pH ruminal diferenciou-se (P<0,05) quanto ao tipo de processamento, sendo maior para milho grão moído (MGM). Não houve diferença para nenhuma das comunidades microbiológicas analisadas (P>0,05) (bactérias Lac+ e Lac-, fungos, leveduras e protozoários). Seis gêneros de fungos anaeróbicos facultativos foram identificados num total de 15 observações. O Cladosporium spp. foi o gênero mais prevalente (46,66%), seguido do Aspergillus spp. (26,66%). A largura da base das papilas ruminais apresentou interação significativa, sendo maior para MGM (P<0,05) com Rhizomucor e o controle (P<0,05). O fluido ruminal de ovinos sob dieta de alto concentrado de grão com adição dos fungos Aspergillus terreus e Rhizomucor spp. não tiveram afetadas as características microbiológicas e físico-químicas.

The effect of fungal probiotics added to a high-grain diet on the gastrointestinal tract of sheep

Abstract This study aimed to evaluate the microbiological and physicochemical characteristics of the ruminal fluid and histological characteristics of the gastrointestinal tract (GIT) of sheep on a high-grain diet containing the probiotic fungi Aspergillus terreus and Rhizomucor spp. The study included four treatment groups (without probiotic, with Rhizomucor spp., with Aspergillus terreus, and with a mixture of both fungi), and two types of corn (ground/whole), in a Completely Randomized Design (CRD) arranged in 4 x 2 factorial design. Santa Inês x Dorper lambs were housed in eight pens with five lambs each for 75 days. Rumen fluid was collected to study the rumen microbiological profile, macroscopic characteristics, ammonia nitrogen concentration, and microbiological activity. In addition, GIT samples were taken for histological analysis. Fluid analyses showed that the animals presented a low acidosis index. The samples presented a predominantly aromatic odor and blackish-brown color, indicating a neutral pH and high microbial activity. The rumen pH differed (P < 0.05) according to the level of processed corn consumed, being higher for ground grain corn (GGC). There was no difference for any of the microbiological communities analyzed (P > 0.05) (Lac+ and Lac- bacteria, fungi, yeasts, and protozoa). Six genera of facultative anaerobic fungi were identified in 15 observations. Cladosporium spp. was the most prevalent genus (46.66%), followed by Aspergillus spp. (26,66%). The width of the base of rumen papillae showed significant correlation being greater for GCG (P < 0.05) with Rhizomucor and for the control (P < 0.05). The rumen fluid of sheep on a high-grain diet with added Aspergillus terreus and Rhizomucor spp. showed no microbiological and physicochemical changes.

Changes in the Fermentation and Bacterial Community by Artificial Saliva pH in RUSITEC System

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.

Metagenomic Sequencing Reveals that High-Grain Feeding Alters the Composition and Metabolism of Cecal Microbiota and Induces Cecal Mucosal Injury in Sheep

The cecum serves as an additional fermentation site for ruminants, but it lacks buffering capacity and has a relatively simple epithelial structure compared to the rumen. The role of high-grain (HG) diets in manipulating the rumen microbiome has been well elucidated, yet the microbial response to such diets in the cecum and the subsequent microbe-host interactions remain largely unexplored. Here, we describe the modification of the cecal microbiome and host epithelial gene expression based on data from 20 sheep grouped to feed an HG diet for 7, 14, and 28 days. Our data indicate that the alteration of cecal microbial fermentation was manifested by a decrease in luminal pH and an increase in acetate and butyrate concentrations following the diet change to HG. We further demonstrate that the alteration of the microbiome was driven by microbes that are likely acetate producers (e.g., Blautia spp. and Akkermansia spp.) and butyrate producers (e.g., Anaerostipes spp. and Roseburia spp.). Moreover, the core microbiota in the cecal microbiome was predominantly maintained after HG diet feeding, while the specific populations of the cecal microbiomes adaptively varied at the species and genomic levels time dependently. Association analysis suggests that the perturbations of the cecal microbiome under the HG diet were closely linked to the variations in the two key enzymes that catalyze the conversion of pyruvate to acetyl-CoA and urease enzymes that hydrolyze urea into ammonia, alongside mucosal inflammatory responses. Overall, our findings here provide novel insights into understanding microbiome-host interactions in the hindgut of ruminants.

IMPORTANCE High-grain (HG) diets are known to alter the rumen microbiome. However, the responses of the hindgut microbiota and its epithelial function need further investigation in ruminants. Using 20 sheep as the experimental model, we found that the microbial fermentation pattern of the cecum changed after switching to the HG diet. The taxa of the acetate and butyrate producers increased with the feeding time. Moreover, enzymes engaged in carbon and nitrogen metabolisms of the cecal microbiome are altered. The expression of epithelial genes related to volatile fatty acid (VFA) absorption and metabolism, cytokines, and tight junction proteins, alongside light microscopy visualization of epithelial tissue, suggested that the HG diet may induce cecal mucosal inflammatory responses. Our findings reveal cecal microbial and metabolic perturbations in response to HG diets in sheep and provide a new reference for the research on hindgut microbial homeostasis and host health in ruminants.

Effects of Dietary Energy Levels on Rumen Fermentation, Gastrointestinal Tract Histology, and Bacterial Community Diversity in Fattening Male Hu Lambs

This study investigated rumen fermentation and histological and microbial diversity in male Hu lamb fed diets with different metabolizable energy (ME) levels (MEA, 9.17 MJ/kg, MEB, 10.00 MJ/kg, and MEC, 10.82 MJ/kg). Thirty-six male Hu lambs were randomly allotted to three treatments, and the feeding trial lasted for 67 days. Rumen fermentation results suggest that the iso-valerate had a significant effect on dietary energy level. The papillary height (PH) of rumen was the highest in the MEB group, the crypt depth (CD) was significantly increased in the duodenum and jejunum, and the villus height (VH)-to-CD ratio (VH/CD) was significantly decreased in the duodenum by increasing dietary energy levels; the VH, villus width (VW), and VH/CD also had significant differences in the ileum. 16S rRNA sequencing results showed that the operational taxonomic units (OTUs) number, the ACE, and Chao1 indices were linearly decreased by increasing dietary energy level; 24 phyla including 124 genera were identified, and the relative abundance of Papillibacter and Quinella linearly decreased by increasing the dietary energy level. Compared to MEA and MEB groups, the relative abundance of unidentified_Veillonellaceae and Anaerovibrio was significantly increased in the MEC group at the genus level. The relative abundance of the carbohydrate metabolism pathway predicted by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was linearly increased by increasing the dietary energy levels. Three metabolic pathways identified in Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 were significantly influenced as the dietary energy level increased. In summary, these results demonstrated that the dietary energy levels affected the rumen fermentation parameters, morphological structures of the gastrointestinal tract (GIT), and the composition and function of rumen microflora in male Hu sheep.

Mucosal Microbiota and Metabolome in the Ileum of Hu Sheep Offered a Low-Grain, Pelleted or Non-pelleted High-Grain Diet

Alterations in mucosal microbiota and metabolites are critical to intestinal homeostasis and host health. This study used a combination of 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC/MS) to investigate mucosal microbiota and their metabolic profiles in the ileum of Hu sheep fed different diets. Here, we randomly allocated 15 Hu sheep to three diets, a non-pelleted low-grain diet (control diet; CON), a non-pelleted high-grain diet (HG), and a pelleted high-grain diet (HP). After 60 days of treatment, ileal mucosal samples were collected for microbiome and metabolome analysis. The results of principal coordinate analysis and permutation multivariate analysis showed that there was a tendency for microbial differentiation between the CON and HG groups (P < 0.1), although no significant difference between the HG and HP groups was observed (P > 0.05). Compared with the CON diet, the HG diet decreased (P < 0.05) the abundance of some probiotic species (e.g., Sphingomonas and Candidatus Arthromitus) and increased (P < 0.05) the abundance of acid-producing microbiota (e.g., Succiniclasticum, Nesterenkonia, and Alloprevotella) in the ileal mucosa. Compared with the HG diet, the HP diet decreased (P < 0.05) the abundance of Alloprevotella and increased (P < 0.05) the abundance of Mycoplasma in the ileal mucosa. Furthermore, partial least squares discriminant analysis and orthogonal partial least-squared discriminant analysis indicated that different dietary treatments resulted in different metabolic patterns in the ileal mucosa of the CON, HG, and HP groups. The HG diet altered (VIP > 1 and P < 0.05) the metabolic patterns of amino acids, fatty acids, and nucleotides/nucleosides (such as increased amounts of ornithine, tyrosine, cis-9-palmitoleic acid, and adenosine) compared with the CON diet. However, 10 differential metabolites (VIP > 1 and P < 0.05; including tyrosine, ornithine, and cis-9-palmitoleic acid) identified in the HG group exhibited a diametrically opposite trend in the HP group, suggesting that the HP diet could partially eliminate the changes brought upon by the HG diet. Collectively, our findings demonstrate that different diets altered the ileal mucosal microbiota and metabolites and provide new insight into the effects of high-grain diets on the intestinal health of ruminant animals.

Solid diet manipulates rumen epithelial microbiota and its interactions with host transcriptomic in young ruminants

Solid diet supplementation in the early life stages of ruminants could improve rumen microbiota and tissue development. However, most studies focus on bacteria in the rumen content community. The microbiota attached on rumen epithelium are rarely investigated, and their correlations with rumen content bacteria and host transcripts are unknown. In this study, rumen digesta attached in the epithelium from goats in three diet regimes (milk replacer only, milk replacer supplemented concentrate and milk replacer supplemented concentrate plus alfalfa pellets) were collected for measurement of the epithelial microbiota using next generation sequencing. Correspondingly, the rumen tissues of the same animals were measured with the host transcriptome. The distinct microbial structures and compositions between rumen content and epithelial communities were associated with solid diet supplementation. Regarding rumen development in pre‐weaning ruminants, a solid diet, especially its accompanying neutral detergent fibre nutrients, was the most significant driver that influenced the rumen microbiota and epithelium gene expression. Compared with content bacteria, rumen epithelial microbiota had a stronger association with the host transcriptome. The host transcriptome correlated with host phenotypes were associated with rumen epithelial microbiota and solid diet. This study reveals that the epithelial microbiota is crucial for proper rumen development, and solid diet could improve rumen development through both the rumen content and epithelial microbiota.

Response of sheep rumen fermentation and microbial communities to feed infected with the endophyte Epichloë gansuensis as evaluated with rumen-simulating technology

Achnatherum inebrians, a perennial grass, is widely distributed in China. When infected by the endophyte Epichloë gansuensis, A. inebrians produces an abundance of alkaloids that enhance plant survival but are toxic to animals. Here we used in vitro fermentation to study the impact of endophyte- infected A. inebrians (E+) addition on rumen fermentation characteristics and on microbial community and diversity as assessed with amplicon sequencing technology. We examined E+ addition at five levels, E0, E25, E50, E75, and E100, corresponding to 0%, 25%, 50%, 75%, and 100% of the fermentation substrate, respectively. Both the fermentation characteristics and rumen microbial community structure differed significantly among treatments. E100 resulted in the highest values for pH, the Shannon index, Kiritimatiellaeota, and Lentisphaerae levels relative to the other treatments. In contrast, E25 was associated with higher levels of ammonia nitrogen, total volatile fatty acid, propionate, butyrate, isobutyrate, valerate, of the phyla Bacteroidetes and Firmicutes, and of the genus Prevotella_1, Succiniclasticum, Family_XIII_AD3011_group, Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG-001, and Pyramidobacter as compared with other treatments. E50 resulted in the greatest values for the abundance-based coverage estimator (ACE) and the Chao1 index as compared with other treatments. E0 resulted in the greatest values for digestibility of dry matter, gas production, acetate, and Ruminobacter as compared with other treatments. This approach avoided animal toxicity experiments and confirmed that rumen fermentation characteristics and rumen microbiota were affected by E+ toxin. Therefore, E25 showed higher abundance in Prevotella_1, Prevotellaceae_ UCG-001, and Lachnospiraceae_XPB1014_group that implied they should play significant roles in E+ alkaloids degradation. And then, we can infer that rumen microorganisms should function as an antidote with respect to this poisoning reaction at moderate dietary percentages of E+.

The Rumen Epithelial Microbiota: Possible Gatekeepers of the Rumen Epithelium and Its Potential Contributions to Epithelial Barrier Function and Animal Health and Performance

Ruminants are characterized by their unique mode of digesting cellulose-rich plant material in their forestomach, the rumen, which is densely populated by diverse microorganisms that are crucial for the breakdown of plant material. Among ruminal microbial communities, the microorganisms in the rumen fluid or attached to feed particles have attracted considerable research interest. However, comparatively less is known about the microorganisms attached to the rumen epithelium. Generally, the tissue lining the gastrointestinal tract serves the dual role of absorbing nutrients while preventing the infiltration of unwanted compounds and molecules as well as microorganisms. The rumen epithelium fulfills critical physiological functions for the ruminant host in energy absorption, metabolism, and nutrient transport. Essential host metabolites, such as short-chain fatty acids, ammonia, urea, and minerals, are exchanged across the rumen wall, thereby exposing the rumen epithelial microbiota to these nutrients. The integrity of the gastrointestinal barrier is central to animal health and productivity. The integrity of the rumen epithelium can be compromised by high ruminal microbial fermentation activity resulting in decreased rumen pH or by stress conditions such as heat stress or feed restriction. It is important to keep in mind that feeding strategies in cattle have changed over the last decades in favor of energy- and nutrient-rich concentrates instead of fiber-rich forages. These dietary shifts support high milk yields and growth rates but raised concerns regarding a possibly compromised rumen function. This paper will provide an overview of the composition of rumen epithelial microbial communities under physiological and disease conditions and will provide insights into the knowledge about the function and in situ activity of rumen epithelial microorganisms and their relevance for animal health and production. Given that an impaired intestinal barrier will negatively affect economically significant phenotypes, a better understanding of rumen wall microbiota is urgently needed.

Comparison of the fermentation and bacterial community in the colon of Hu sheep fed a low-grain, non-pelleted, or pelleted high-grain diet

Microbial fermentation in the hindgut is likely an important contributor to energy availability in ruminants, except for the rumen. This study aimed to investigate commensal bacteria in the colon influenced by diverse dietary niches. Fifteen male sheep were randomly allotted into three feeding groups: non-pelleted low-grain (CON, n = 5), non-pelleted high-grain (HG, n = 5), and pelleted high-grain (HP, n = 5) diets. The HG and HP groups had higher fermentation parameters than the CON group, especially acetate concentration (CON = 46.91; HG = 61.66; HP = 77.99). The HG diet altered the composition of commensal bacteria in the colon in comparison to the CON group, including the increase of genera related to acetate production (e.g., Acetitomaculum spp.), butyrate production (e.g., Coprococcus spp. and Subdoligranulum spp.), and starch degradation (e.g., Prevotella spp., Roseburia spp., and Oscillibacter spp.). The colon functional compendium had co-alteration with taxonomic changes that indicated non-pelleted HG diet caused a detrimental colonic niche. The HP diet specifically promoted the abundance of Ruminococcus, Olsenella, and Alloprevotella genera to achieve the highest acetate concentration and decreased the starch-degrader Roseburia spp. and Oscillibacter spp. in contrast to the HG group. Our results provide a systematic view of the microbial fermentation, community, and functional guilds in colonic digesta and mucosa in regard to using an HP diet to maintain colonic niche homeostasis under the adverse influence of the HG diet.Key Points• Non-pelleted and pelleted high-grain diets altered sheep colonic fermentation.• Non-pelleted and pelleted high-grain diets resulted in diverse microbial composition.• The pelleted method ameliorated microbial functions compared with the high-grain diet.

Effects of dietary energy levels on rumen fermentation, microbiota, and gastrointestinal morphology in growing ewes

This study investigated whether dietary metabolizable energy (ME) could generate dynamical effects on rumen fermentation, gastrointestinal tract (GIT) morphology, and microbial composition of growing ewes. A total of twenty-eight female Hu lambs were randomly allotted to two treatments with different dietary ME levels: 9.17 (FEA) and 10.41 MJ/kg (FEB). These lambs were further made ready for a 67-day feeding trial. Results showed that the molar proportions of butyrate (p = .020), iso-valerate (p = .028), and valerate (p = .005) were significantly higher in the FEB group than those in the FEA group. The results of the GIT morphologic properties showed that the villus height (VH) (p = .005) was significantly higher and crypt depth was significantly deeper (CD) (p = .005) in the duodenum and that the rumen papillary height (PH) was significantly higher (p = .020) in FEB group compared with the FEA group. High-throughput sequencing results showed that 1826 operational taxonomic units (OTUs) were obtained and that the OTU number (p = .039), the ACE (p = .035), and Chao1 indices (p = .005) were lower in the FEB group. Moreover, 76 genera belonging to 21 phyla were detected in all samples; the relative abundance of Papillibacter (p = .036) and Flexilinea (p = .046) was significantly lower in the high energy group, whereas the relative abundance of unidentified Lachnospiraceae (p = .019), Acetitomaculum (p = .029), unidentified Veillonellaceae (p = .017), Anaerovibrio (p = .005), and Succinivibrio (p = .035) was significantly higher in the FEB group at the genus level. Furthermore, the relative abundance of genes and metabolic pathways were predicted by PICRUSt. The relative abundance of gene families related to carbohydrate metabolism was particularly higher (p = .027) in the FEB group. In summary, these results reveal that the dietary energy levels altered the composition and function of rumen microbiota and GIT morphology in growing female Hu sheep and provide a reference for optimizing diet formula and 10.41MJ/kg of ME level has been recommended in the growing period.

Effect of different glucogenic to lipogenic nutrient ratios on rumen fermentation and bacterial community in vitro

Aims

This study was to investigate the effect of different ratios of glucogenic to lipogenic nutrients on rumen fermentation and the corresponding ruminal bacterial communities.

Methods and Results

Four diets, including glucogenic diet (G), lipogenic diet (L), two mixed diets: GL1 (G: L = 2 : 1) and GL2 (G:L = 1 : 2), served as substrates and were incubated with rumen fluid in vitro. The results revealed that the gas production, dry matter digestibility and propionate proportion were significantly increased by the G diet than others. The G diet increased the bacterial genera of Succinivibrionaceae_UCG_002, Succinivibrio, Selenomonas_1 and Ruminobacter but decreased some cellulolytic bacteria including the Eubacterium and several genera in family Ruminococcaceae than others.

Conclusions

When the glucogenic nutrient was above 1/3 of the dietary energy source among the four diets, the in vitro incubation had a higher feed digestibility and lower acetate to propionate ratio. Bacterial genera, including Selenomonas, Succinivibrio, Ruminobacter, certain genera in Ruminococcaceae, Christensenellaceae_R‐7_group and Eubacterium, were more sensitive to the glucogenic to lipogenic nutrients ratio.

Significance and Impact of the Study

The present study provides a new perspective about the effect of dietary glucogenic to lipogenic ingredient ratios on rumen metabolism by comparing end‐products, gas production and bacterial composition via an in vitro technique.

Microbiome-host co-oscillation patterns in remodeling of colonic homeostasis during adaptation to a high-grain diet in a sheep model

BACKGROUND

Ruminant gastrointestinal tract homeostasis deploys interactive microbiome-host metabolic communication and signaling axes to underpin the fitness of the host. After this stable niche is destroyed by environmental triggers, remodeling of homeostasis can occur as a spontaneous physiological compensatory actor.

RESULTS

In this study, 20 sheep were randomly divided into four groups: a hay-fed control (CON) group and a high-grain (HG) diet group for 7, 14, or 28 days. Then, we examined 16S rRNA gene sequences and transcriptome sequences to outline the microbiome-host co-oscillation patterns in remodeling of colonic homeostasis in a sheep model during adaptation to a HG diet. Our data revealed that with durations of an HG diet, the higher starch levels directly affected the colonic lumen environment (lower pH and higher fermentation parameters), which in turn filtered lumen-specific functional taxonomic groups (HG-sensitive and HG-tolerant taxa). The colonic epithelium then gave rise to a new niche that triggered endoplasmic reticulum stress to activate unfolded protein response, if the duration of endoplasmic reticulum stress was overlong, this process would regulate cell apoptosis (Caspase-3, Caspase-8, and TNFRSF21) to achieve a functional transformation.

CONCLUSIONS

Our results provide a holistic view of the colonic microbial assemblages and epithelium functional profile co-oscillation patterns in remodeling of colonic homeostasis during adaptation to an HG diet in a sheep model. These findings also provide a proof of concept that the microbe-host collaboration is vital for maintaining hindgut homeostasis to adapt to dietary dichotomies.

Gut Microbiome of Chinese Forest Musk Deer Examined across Gender and Age

Animal gut microbiota begins to colonize after birth and is functionally indispensable for maintaining the health of the host. It has been reported that gender and age influence the composition of the intestinal microbiome. However, the effects of gender and age on the intestinal microorganism of forest musk deer (FMD) remain unclear. The aim of this study was to establish the relationship between the structure and composition of fecal microbiota of male and female forest musk deer with age. Here, Illumina Miseq 300PE sequencing platform targeting 16S rRNA V3–V4 hypervariable region applied to define the fecal microbiota of male and female FMD with two age groups, juvenile (age 1–2 years) and adult (age 4–10 years). Alpha diversity index did not show significant difference in bacterial diversity between the males and females or among age groups. The intestinal microbiota of FMD was dominated by three phyla, the Firmicutes, Proteobacteria and Bacteroidetes regardless of gender and different ages. Higher proportions of Proteobacteria were found in adult male and juvenile female individuals. The composition of Bacteroidetes was stable with the gender and age of FMD. Interestingly, the relative abundance of genera Clostridiales and Bacteroidales were higher in the juvenile FMD. Conversely, proportions of Pseudomonas and Lachnospiraceae were abundant in the adult FMD. Higher proportions of Ruminococcaceae, Dore, and 5-7N15 were found in the juvenile male groups. They may reflect the different immune resistance of male and female individuals at different stages of development. This study explored the fecal microbiota composition of forest musk deer in relation to gender and age, which may provide an effective strategy for developing intestinal microecological preparations and potential musk deer breeding.