Epimural bacterial community structure in the rumen of Holstein cows with different responses to a long-term subacute ruminal acidosis diet challenge

Microbial inoculum effects on the rumen epithelial transcriptome and rumen epimural metatranscriptome in calves

Manipulation of the rumen microbial ecosystem in early life may affect ruminal fermentation and enhance the productive performance of dairy cows. The objective of this experiment was to evaluate the effects of dosing three different types of microbial inoculum on the rumen epithelium tissue (RE) transcriptome and the rumen epimural metatranscriptome (REM) in dairy calves. For this objective, 15 Holstein bull calves were enrolled in the study at birth and assigned to three different intraruminal inoculum treatments dosed orally once weekly from three to six weeks of age. The inoculum treatments were prepared from rumen contents collected from rumen fistulated lactating cows and were either autoclaved (control; ARF), processed by differential centrifugation to create the bacterial-enriched inoculum (BE), or through gravimetric separation to create the protozoal-enriched inoculum (PE). Calves were fed 2.5 L/d pasteurized waste milk 3x/d from 0 to 7 weeks of age and texturized starter until euthanasia at 9 weeks of age, when the RE tissues were collected for transcriptome and microbial metatranscriptome analyses, from four randomly selected calves from each treatment. The different types of inoculum altered the RE transcriptome and REM. Compared to ARF, 9 genes were upregulated in the RE of BE and 92 in PE, whereas between BE and PE there were 13 genes upregulated in BE and 114 in PE. Gene ontology analysis identified enriched GO terms in biological process category between PE and ARF, with no enrichment between BE and ARF. The RE functional signature showed different KEGG pathways related to BE and ARF, and no specific KEGG pathway for PE. We observed a lower alpha diversity index for RE microbiome in ARF (observed genera and Chao1 (p < 0.05)). Five microbial genera showed a significant correlation with the changes in host gene expression: Roseburia (25 genes), Entamoeba (two genes); Anaerosinus, Lachnospira, and Succiniclasticum were each related to one gene. sPLS-DA analysis showed that RE microbial communities differ among the treatments, although the taxonomic and functional microbial profiles show different distributions. Co-expression Differential Network Analysis indicated that both BE and PE had an impact on the abundance of KEGG modules related to acyl-CoA synthesis, type VI secretion, and methanogenesis, while PE had a significant impact on KEGGs related to ectoine biosynthesis and D-xylose transport. Our study indicated that artificial dosing with different microbial inocula in early life alters not only the RE transcriptome, but also affects the REM and its functions.

Investigating the impact of feed-induced, subacute ruminal acidosis on rumen epimural transcriptome and metatranscriptome in young calves at 8- and 17-week of age

Introduction

With the goal to maximize intake of high-fermentable diet needed to meet energy needs during weaning period, calves are at risk for ruminal acidosis. Using the calves from previously established model of feed-induced, ruminal acidosis in young calves, we aimed to investigate the changes in rumen epimural transcriptome and its microbial metatranscriptome at weaning (8-week) and post-weaning (17-week) in canulated (first occurred at 3 weeks of age) Holstein bull calves with feed-induced subacute ruminal acidosis.

Methods

Eight bull calves were randomly assigned to acidosis-inducing diet (Treated, n = 4; pelleted, 42.7% starch, 15.1% neutral detergent fiber [NDF], and 57.8% nonfiber carbohydrates), while texturized starter was fed as a control (Control, n = 4; 35.3% starch, 25.3% NDF, and 48.1% nonfiber carbohydrates) starting at 1 week through 17 weeks. Calves fed acidosis-inducing diet showed significantly less (p < 0.01) body weight over the course of the experiment, in addition to lower ruminal pH (p < 0.01) compared to the control group. Rumen epithelial (RE) tissues were collected at both 8 weeks (via biopsy) and 17 weeks (via euthanasia) and followed for whole transcriptome RNA sequencing analysis. Differentially expressed genes (DEGs) analysis was done using cufflinks2 (fold-change ≥2 and p < 0.05) between treated and control groups at 8-week of age, and between 8- and 17-week for the treated group.

Results

At 8-week of age, DEGs between treatment groups showed an enrichment of genes related to the response to lipopolysaccharide (LPS) (p < 0.005). The impact of prolonged, feed-induced acidosis was reflected by the decreased expression (p < 0.005) in genes involved in cell proliferation related pathways in the RE at 17-week of age in the treated group. Unique sets of discriminant microbial taxa were identified between 8-and 17-week calves in the treated group and the treatment groups at 8-week, indicating that active microbial community changes in the RE are an integral part of the ruminal acidosis development and progression.

Rumen Biogeographical Regions and Microbiome Variation

The rumen is a complex organ that is critical for its host to convert low-quality feedstuffs into energy. The conversion of lignocellulosic biomass to volatile fatty acids and other end products is primarily driven by the rumen microbiome and its interaction with the host. Importantly, the rumen is demarcated into five distinct rumen sacs as a result of anatomical structure, resulting in variable physiology among the sacs. However, rumen nutritional and microbiome studies have historically focused on the bulk content or fluids sampled from single regions within the rumen. Examining the rumen microbiome from only one or two biogeographical regions is likely not sufficient to provide a comprehensive analysis of the rumen microbiome and its fermentative capacity. Rumen biogeography, digesta fraction, and microbial rumen–tissue association all impact the diversity and function of the entirety of the rumen microbiome. Therefore, this review discusses the importance of the rumen biographical regions and their contribution to microbiome variation.

Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep

While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have rarely been examined in sheep. In addition, rumen microbial composition can differ between ruminal fractions, and be associated with ruminant feed efficiency and methane emissions. In this study, 16S rRNA amplicon sequencing was used to investigate the effects of breed and ruminal fraction on bacterial and archaeal communities in sheep. Solid, liquid and epithelial rumen samples were obtained from a total of 36 lambs, across 4 different sheep breeds (Cheviot (n = 10), Connemara (n = 6), Lanark (n = 10) and Perth (n = 10)), undergoing detailed measurements of feed efficiency, who were offered a nut based cereal diet ad-libitum supplemented with grass silage. Our results demonstrate that the feed conversion ratio (FCR) was lowest for the Cheviot (most efficient), and highest for the Connemara breed (least efficient). In the solid fraction, bacterial community richness was lowest in the Cheviot breed, while Sharpea azabuensis was most abundant in the Perth breed. Lanark, Cheviot and Perth breeds exhibited a significantly higher abundance of epithelial associated Succiniclasticum compared to the Connemara breed. When comparing ruminal fractions, Campylobacter, Family XIII, Mogibacterium, and Lachnospiraceae UCG-008 were most abundant in the epithelial fraction. Our findings indicate that breed can impact the abundance of specific bacterial taxa in sheep while having little effect on the overall composition of the microbial community. This finding has implications for genetic selection breeding programs aimed at improving feed conversion efficiency of sheep. Furthermore, the variations in the distribution of bacterial species identified between ruminal fractions, notably between solid and epithelial fractions, reveals a rumen fraction bias, which has implications for sheep rumen sampling techniques.

Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome

The activities of different microbes in the cow rumen have been shown to modulate the host's ability to utilize plant biomass, while the host-rumen interface has received little attention. As datasets collected worldwide have pointed to Campylobacteraceae as particularly abundant members of the rumen epithelial microbiome, we targeted this group in a subset of seven cows with meta- and isolate genome analysis. We show that the dominant Campylobacteraceae lineage has recently speciated into two populations that were structured by genome-wide selective sweeps followed by population-specific gene import and recombination. These processes led to differences in gene expression and enzyme domain composition that correspond to the ability to utilize acetate, the main carbon source for the host, at the cost of inhibition by propionate. This trade-off in competitive ability further manifests itself in differential dynamics of the two populations in vivo. By exploring population-level adaptations that otherwise remain cryptic in culture-independent analyses, our results highlight how recent evolutionary dynamics can shape key functional roles in the rumen microbiome.

Liver abscess microbiota of feedlot steers finished in natural and traditional management programs

Liver abscess etiology in feedlot steers involves the escape of bacteria from the digestive tract to form a polymicrobial abscess within or on the external surface of the liver. However, little is known about the effects of feedlot finishing systems on the microbial composition of the liver abscess purulent material. Liver abscesses were collected at the time of harvest from steers originating from a single feedlot managed in either a traditional program (which included tylosin phosphate supplementation) or a natural program (without tylosin phosphate supplementation). The purulent material of liver abscesses from traditionally managed steers (N = 53 abscesses) and that of naturally managed steers (N = 62 abscesses) was characterized using the V4 region of the 16S rRNA gene. Two phyla and three genera were found in greater than 1% relative abundance across all abscesses. The genus Fusobacterium was identified in all liver abscess samples and accounted for 64% of sequencing reads. Bacteroides and Porphyromonas genera accounted for 33% and 1% of reads, respectively. Trueperella was more likely to be found in the liver abscesses of naturally managed steers than traditionally managed steers (P = 0.022). Over 99% of the genus-level bacterial sequences observed across all liver abscesses belonged to Gram-negative genera. Bacteria known to colonize both the rumen and hindgut were identified within liver abscesses. No differences in alpha diversity or beta diversity were detected between liver abscess communities (between the two management programs or individual pens) when tested as richness, Shannon Diversity Index, or weighted UniFrac distances (P > 0.05). These results were consistent with previous identification of Fusobacterium necrophorum as the primary bacteriologic agent within liver abscesses and emphasized the relationship between the gastrointestinal microbiota and liver abscess formation. Though the microbiota of the liver abscess purulent material was similar between steers fed an antibiotic-free diet and those fed an antibiotic-containing diet from the same feedlot, divergence was detected in liver abscess communities with some being dominated by Fusobacterium and others being dominated by Bacteroides.

Characterization of presence and activity of microRNAs in the rumen of cattle hints at possible host-microbiota cross-talk mechanism

MicroRNAs (miRNAs), as important post-transcriptional regulators, are ubiquitous in various tissues. The aim of this exploratory study was to determine the presence of miRNAs in rumen fluid, and to investigate the possibility of miRNA-mediated cross-talk within the ruminal ecosystem. Rumen fluid samples from four cannulated Holstein cows were collected during two feeding regimes (forage and high-grain diet) and DNA and RNA were extracted for amplicon and small RNA sequencing. Epithelial biopsies were simultaneously collected to investigate the co-expression of miRNAs in papillae and rumen fluid. We identified 377 miRNAs in rumen fluid and 638 in rumen papillae, of which 373 were shared. Analysis of microbiota revealed 20 genera to be differentially abundant between the two feeding regimes, whereas no difference in miRNAs expression was detected. Correlations with at least one genus were found for 170 miRNAs, of which, 39 were highly significant (r > |0.7| and P < 0.01). Both hierarchical clustering of the correlation matrix and WGCNA analysis identified two main miRNA groups. Putative target and functional prediction analysis for the two groups revealed shared pathways with the predicted metabolic activities of the microbiota. Hence, our study supports the hypothesis of a cross-talk within the rumen at least partly mediated by miRNAs.

Effects of Barley Starch Level in Diet on Fermentation and Microflora in Rumen of Hu Sheep

This study aimed to explore the effects of different levels of barley starch instead of corn starch on the rumen fermentation and microflora when feeding a corn-based diet to Hu sheep. Thirty-two male Hu sheep equipped with permanent rumen fistulas were selected and fed in individual metabolic cages. All sheep were randomly divided into four groups (eight sheep in each group) and fed with four diets containing a similar starch content, but from different starch sources, including 100% of starch derived from corn (CS), 33% of starch derived from barley + 67% of starch derived from corn (33 BS), 67% of starch derived from barley + 33% of starch derived from corn (67 BS) and 100% of starch derived from barley (100 BS). The experimental period included a 14 d adaptation period and a 2 d continuous data collection period. The results showed that the molar proportions of acetate, isobutyrate, butyrate and isovalerate and the ratio of acetate to propionate in the 67 BS and 100 BS groups decreased compared with the CS and 33 BS groups (p < 0.001), while the molar proportions of propionate and valerate increased (p < 0.001). The combination of 33% barley starch and 67% corn starch in the diet improved the production of TVFAs (p = 0.007). The OTUs and Shannon indexes of the CS and 33 BS groups were higher than the 67 BS and 100 BS groups (p < 0.001), and the Chao1 and Ace indexes were higher than the 100 BS group (p < 0.05). In addition, the 33 BS group had increased the relative abundances of Bacteroidetes, Prevotella and Ruminococcus and the abundances of Fibrobacter succinogenes, Ruminococcus flavefaciens, Streptococcus bovis, Selenomonas ruminantium and Prevotella brevis relative to the CS group (p < 0.05). These results indicate that the substitution of 33% of the CS with BS did not change the rumen fermentation pattern relative to the CS group, and increased the richness and diversity of the rumen microbes in Hu sheep compared with other two starch substitute groups.

Invited review: Effect of subacute ruminal acidosis on gut health of dairy cows

Subacute ruminal acidosis (SARA) is assumed to be a common disease in high-yielding dairy cows. Despite this, the epidemiological evidence is limited by the lack of survey data. The prevalence of SARA has mainly been determined by measuring the pH of ruminal fluid collected using rumenocentesis. This may not be sufficiently accurate, because the symptoms of SARA are not solely due to ruminal pH depression, and ruminal pH varies among sites in the rumen, throughout a 24-h period, and among days. The impact of SARA has mainly been studied by conducting SARA challenges in cows, sheep, and goats based on a combination of feed restriction and high-grain feeding. The methodologies of these challenges vary considerably among studies. Variations include differences in the duration and amount of grain feeding, type of grain, amount and duration of feed restriction, number of experimental cows, and sensitivity of cows to SARA challenges. Grain-based SARA challenges affect gut health. These effects include depressing the pH in, and increasing the toxin content of, digesta. They also include altering the taxonomic composition of microbiota, reducing the functionality of the epithelia throughout the gastrointestinal tract (GIT), and a moderate inflammatory response. The effects on the epithelia include a reduction in its barrier function. Effects on microbiota include reductions in their richness and diversity, which may reduce their functionality and reflect dysbiosis. Changes in the taxonomic composition of gut microbiota throughout the GIT are evident at the phylum level, but less evident and more variable at the genus level. Effects at the phylum level include an increase in the Firmicutes to Bacteroidetes ratio. More studies on the effects of a SARA challenge on the functionality of gut microbiota are needed. The inflammatory response resulting from grain-based SARA challenges is innate and moderate and mainly consists of an acute phase response. This response is likely a combination of systemic inflammation and inflammation of the epithelia of the GIT. The systemic inflammation is assumed to be caused by translocation of immunogenic compounds, including bacterial endotoxins and bioamines, through the epithelia into the interior circulation. This translocation is increased by the increase in concentrations of toxins in digesta and a reduction of the barrier function of epithelia. Severe SARA can cause rumenitis, but moderate SARA may activate an immune response in the epithelia of the GIT. Cows grazing highly fermentable pastures with high sugar contents can also have a low ruminal pH indicative of SARA. This is not accompanied by an inflammatory response but may affect milk production and gut microbiota. Grain-based SARA affects several aspects of gut health, but SARA resulting from grazing high-digestible pastures and insufficient coarse fiber less so. We need to determine which method for inducing SARA is the most representative of on-farm conditions.

Effects of Phragmites australis Shoot Remainder Silage on Growth Performance, Blood Biochemical Parameters, and Rumen Microbiota of Beef Cattle

The objective of the present study was to assess the effects of replacing corn silage with Phragmites australis shoot remainder (PSR) silage on intake, growth performance, serum biochemical parameters, and rumen microbial diversity of growing-finishing beef. Fifteen Angus beef cattle with an average body weight of 253 ± 2.94 kg were randomly divided into three groups (five replicas vs. each group vs. Angus beef cattle). The three treatments were group A fed 60% PSR silage + 40% concentrate, group B fed 30% PSR silage + 30% corn silage + 40% concentrate, and group C fed 60% corn silage + 40% concentrate. The adaptation period was 15 days, and the trial period lasted for 45 days. Results showed that the ADG was significantly higher, and FCR was significantly lower both in groups A and B compared with group C. The results of serum biochemical parameters showed that the concentration of GLU was significantly lower in group B than both groups A and C. Microbial diversity results showed that the OTUs, Shannon, Chao1, and ACE indices were significantly lower in group A compared with groups B and C. At the phyla level, the relative abundances of Tenericutes and Melainabacteria had significant differences among the three groups, and the relative abundances of Papillibacter, Anaeroplasma, and Anaerovorax had significant differences among the three groups at the genus level. Additionally, Rikenellaceae was the unique biomarker among the three groups. Furthermore, the results of function prediction showed that the gene families associated with metabolism of cofactors and vitamins, cellular processes and signaling, metabolism, biosynthesis of other secondary metabolites, infectious diseases, signaling molecules and interaction, nervous system, and digestive system were significantly decreased, while lipid metabolism was dramatically increased from groups A to C at KEGG level 2. At KEGG level 3, 11 metabolic pathways were significantly influenced among the three groups. In summary, these findings indicated that PSR silage substituted the corn silage totally or partially improved the growth performance, and altered the rumen microbial composition and diversity and the corresponding change in prediction function of rumen bacteria in Angus beef cattle.

Effects of Management, Dietary Intake, and Genotype on Rumen Morphology, Fermentation, and Microbiota, and on Meat Quality in Yaks and Cattle

Traditionally, yaks graze only natural grassland, even in harsh winters. Meat from grazing yaks is considered very healthy; however, feedlot fattening, which includes concentrate, has been introduced. We questioned whether this change in management and diet would have an impact on the rumen and meat quality of yaks. This study examined the morphology, fermentation, and microbiota of the rumen and the quality of meat of three groups of bovines: (1) grazing yaks (GYs, 4-year olds), without dietary supplements; (2) yaks (FYs, 2.5-year olds) feedlot-fattened for 5 months after grazing natural pasture; and (3) feedlot-fattened cattle (FC, Simmental, 2-year olds). This design allowed us to determine the role of diet (with and without concentrate) and genotype (yaks vs. cattle) on variables measured. Ruminal papillae surface area was greater in the FYs than in the GYs (P = 0.02), and ruminal microbial diversity was greater but richness was lesser in the GYs than in the FC and FYs. Concentrations of ruminal volatile fatty acids were greater in the yaks than in the cattle. In addition, both yak groups had higher protein and lower fat contents in meat than the FC. Meat of GY had a lower n6:n3 ratio than FY and FC, and was the only group with a ratio below r, which is recommended for healthy food. Essential amino acids (EAA), as a proportion of total AA and of non-essential AA of yak meat, met WHO criteria for healthy food; whereas FC did not.

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.

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.

Analysis of Host Jejunum Transcriptome and Associated Microbial Community Structure Variation in Young Calves with Feed-Induced Acidosis

Diet-induced acidosis imposes a health risk to young calves. In this study, we aimed to investigate the host jejunum transcriptome changes, along with its microbial community variations, using our established model of feed-induced ruminal acidosis in young calves. Eight bull calves were randomly assigned to two diet treatments beginning at birth (a starch-rich diet, Aci; a control diet, Con). Whole-transcriptome RNA sequencing was performed on the jejunum tissues collected at 17 weeks of age. Ribosomal RNA reads were used for studying microbial community structure variations in the jejunum. A total of 853 differentially expressed genes were identified (402 upregulated and 451 downregulated) between the two groups. The cell cycle and the digestion and absorption of protein in jejunal tissue were affected by acidosis. Compared to the control, genera of Campylobacter, Burkholderia, Acidaminococcus, Corynebacterium, and Olsenella significantly increased in abundance in the Aci group, while Lachnoclostridium and Ruminococcus were significantly lower in the Aci group. Expression changes in the AXL gene were associated with the abundance variations of a high number of genera in jejunum. Our study provided a snapshot of the transcriptome changes in the jejunum and its associated meta-transcriptome changes in microbial communities in young calves with feed-induced acidosis.

A Grain-Based SARA Challenge Affects the Composition of Epimural and Mucosa-Associated Bacterial Communities throughout the Digestive Tract of Dairy Cows

The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.

Pseudoprevotella muciniphila gen. nov., sp. nov., a mucin-degrading bacterium attached to the bovine rumen epithelium

A Gram-negative, strictly anaerobic mucin-degrading bacterium, which we designated strain E39^T, was isolated from the rumen epithelium of Korean cattle. The cells were non-motile and had a coccus morphology. Growth of strain E39^T was observed at 30–45°C (optimum, 39°C), pH 6.5–8.5 (optimum, pH 7.5), and in the presence of 0.0–1.0% (w/v) NaCl (optimum, 0.0–0.5%). Strain E39^T contained C_16:0, C_18:0, C_18:1ω9c, iso-C_15:0, and anteiso-C_15:0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine, unidentified aminophospholipid, and unidentified lipids. The major respiratory isoprenoid quinones were MK-8 and MK-9. The major fermented end-products of mucin were acetate and succinate. The G+C content of the genomic DNA was 46.4 mol%. Strain E39^T was most closely related to Alloprevotella rava 81/4-12^T with an 87.3% 16S rRNA gene sequence similarity. On the basis of phenotypic, chemotaxonomic, and molecular properties, strain E39^T represents a novel genus of the family Prevotellaceae; as such, the name Pseudoprevotella muciniphila gen. nov., sp. nov. is proposed. A functional annotation of the whole genome sequences of P. muciniphila E39^T revealed that this bacterium has a putative mucin-degrading pathway and biosynthetic pathways of extracellular polymeric substances and virulence factors which enable bacteria to adhere to the epithelial cells and avoid the host’s immune responses.

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.

Diet Transition from High-Forage to High-Concentrate Alters Rumen Bacterial Community Composition, Epithelial Transcriptomes and Ruminal Fermentation Parameters in Dairy Cows

Effects of changing diet on rumen fermentation parameters, bacterial community composition, and transcriptome profiles were determined in three rumen-cannulated Holstein Friesian cows using a 3 × 4 cross-over design. Treatments include HF-1 (first high-forage diet), HC-1 (first high-concentrate diet), HC-2 (succeeding high-concentrate diet), and HF-2 (second high-forage diet as a recovery period). Animal diets contained Klein grass and concentrate at ratios of 8:2, 2:8, 2:8, and 8:2 (two weeks each), respectively. Ammonia-nitrogen and individual and total volatile fatty acid concentrations were increased significantly during HC-1 and HC-2. Rumen species richness significantly increased for HF-1 and HF-2. Bacteroidetes were dominant for all treatments, while phylum Firmicutes significantly increased during the HC period. Prevotella, Erysipelothrix, and Galbibacter significantly differed between HF and HC diet periods. Ruminococcus abundance was lower during HF feeding and tended to increase during successive HC feeding periods. Prevotellaruminicola was the predominant species for all diets. The RNA sequence analysis revealed the keratin gene as differentially expressed during the HF diet, while carbonic-anhydrase I and S100 calcium-binding protein were expressed in the HC diet. Most of these genes were highly expressed for HC-1 and HC-2. These results suggested that ruminal bacterial community composition, transcriptome profile, and rumen fermentation characteristics were altered by the diet transitions in dairy cows.

Unveiling the Bovine Epimural Microbiota Composition and Putative Function

Numerous studies have used the 16S rRNA gene target in an attempt to characterize the structure and composition of the epimural microbiota in cattle. However, comparisons between studies are challenging, as the results show large variations associated with experimental protocols and bioinformatics methodologies. Here, we present a meta-analysis of the rumen epimural microbiota from 11 publicly available amplicon studies to assess key technical and biological sources of variation between experiments. Using the QIIME2 pipeline, 332 rumen epithelial microbiota samples were analyzed to investigate community structure, composition, and functional potential. Despite having a significant impact on microbial abundance, country of origin, farm, hypervariable region, primer set, animal variability, and biopsy location did not obscure the identification of a core microbiota. The bacterial genera Campylobacter, Christensenellaceae R-7 group, Defluviitaleaceae UCG-011, Lachnospiraceae UCG-010, Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-014, Succiniclasticum, Desulfobulbus, and Comamonas spp. were found in nearly all epithelium samples (>90%). Predictive analysis (PICRUSt) was used to assess the potential functions of the epithelial microbiota. Regularized canonical correlation analysis identified several pathways associated with the biosynthesis of precursor metabolites in Campylobacter, Comamonas, Desulfobulbus, and Ruminococcaceae NK4A214, highlighting key metabolic functions of these microbes within the epithelium.

Sodium butyrate attenuated iE-DAP induced inflammatory response in the mammary glands of dairy goats fed high-concentrate diet

BACKGROUND

Long-term high-concentrate (HC) diet feeding increased bacterial endotoxins, which translocated into the mammary glands of dairy goats and induced inflammatory response. γ-d-Glutamyl-meso-diaminopimelic acid (iE-DAP), bacterial peptidoglycan component, triggered inflammatory response through activating nucleotide oligomerization domain protein 1 (NOD1) signaling pathway. While dietary supplemented with sodium butyrate (SB) relieved inflammatory response and improved animal health and production. To investigate the effects and the mechanisms of action of SB on the inflammatory response in the mammary glands of dairy goats fed HC diet, 12 Saanen dairy goats were randomly assigned into HC group and SB regulated (BHC) group.

RESULTS

The results showed that SB supplementation attenuated ruminal pH decrease caused by HC diet in dairy goats resulting in a decrease of proinflammatory cytokines and iE-DAP plasma concentration and the mRNA expression of NOD1 and other inflammation-related genes. The protein levels of NOD1, NF-κB p65 and NF-κB pp65 were decreased by the SB supplementation. The expression of histone deacetylase 3 (HDAC3) was also inhibited by the SB supplementation. Meanwhile, the chromatin compaction ratios and DNA methylation levels of NOD1 and receptor-interacting protein 2 (RIP2) of BHC group were upregulated.

CONCLUSION

Collectively, the SB supplementation mitigated the inflammatory response in the mammary glands of dairy goats during HC-induced subacute ruminal acidosis (SARA) by inhibiting the activation of the NOD1/NF-κB signaling pathway through the decrease of the iE-DAP concentration in the rumen fluid and plasma and HDAC3 expression. DNA methylation and chromatin remodeling also contributed to the anti-inflammatory effect of SB. © 2020 Society of Chemical Industry.

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

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

Feed Additives Differentially Impact the Epimural Microbiota and Host Epithelial Gene Expression of the Bovine Rumen Fed Diets Rich in Concentrates

The success of nutritional strategies for the prevention of subacute ruminal acidosis (SARA) and the related microbial dysbiosis still remains unpredictable due to the complexity of the rumen ecosystem. The rumen epimural community, due to proximity, has the greatest opportunity to influence host gene expression. The aim of this study was to determine the effect of two separate feed additives on the rumen epimural community and host epithelial gene expression. Eight rumen cannulated Holstein cows were randomly assigned to one of three feeding groups: autolyzed yeast (AY), phytogenics (PHY) and control (CON) using a 3 × 3 Latin square design. Cows were fed an intermittent SARA model that started with 100% forage diet (Baseline) followed by two 65% concentrate-diet induced SARA challenges (SARAI, SARAII), separated by 1 week of forage only feeding. Rumen papillae samples were collected via the cannula during the Baseline, SARAI and SARAII periods. Microbial DNA was extracted and sequenced targeting the 16S rRNA gene and host RNA was analyzed using RT-qPCR. Analysis of the taxonomic composition at the genera level showed a tendency to increase in the relative abundances of Pseudobutyrivibrio (P = 0.06), Selenomonas (P = 0.07) and significantly increase in SHD-231 (P = 0.01) in PHY treated animals, whereas Succiniclasticum tended to decrease in both PHY and AY treated animals compared to the control. Linear discriminant analysis effect size testing was performed and based on treatment × feeding phase interaction, a number of biomarker genera were identified including the previously identified Succiniclasticum. Supplementation with AY correlated positively with CD14 and DRA expression and negatively to CLDN1, MyD88, and MCT4 expression. Supplementation with PHY showed a negative correlation to CLDN4 gene expression. Anaerovibrio showed the highest positive Pearson correlations to biogenic amines tested in the rumen fluid including putrescine (r = 0.67), cadaverine (r = 0.84), and tyramine (r = 0.83). These results show that supplementing feed additives to high grain diets can have a positive influence on the stability of the epimural populations, and that changes in the epimural community are correlated with changes in host epithelial gene expression.

The bovine epimural microbiota displays compositional and structural heterogeneity across different ruminal locations

Dairy cattle are globally important agricultural animals. Central to their biology is the rumen, which houses an essential microbial community, or microbiome, important for providing nutrition from otherwise host-inaccessible dietary components. The rumen environment is noted for its substantial spatial heterogeneity, as illustrated by the stratification into ruminal solid and liquid phases. A third microbiota found directly attached to the ruminal epithelium (the epimural microbiota) also exists but is less well understood because of challenges in sampling the ruminal epithelium. As a result, our understanding of the epimural microbiota is based on analyses of cannulated animals sampled at a single location-the ventral sac-and does not account for other ruminal locations, which may have importance for overall rumen function. To address this knowledge gap, we hypothesize that the epimural microbiota at different ruminal locations differs due to known morphological, physiological, and functional differences across the geographic spread of the rumen epithelium. Here, we characterized bacterial epimural communities at different sites within 8 lactating Holstein dairy cows using 16S rRNA gene sequencing. Four different sites were sampled via rumen tissue biopsy: cranial sac (CS), ventral sac (VS), caudodorsal blind sac (CDBS), and caudoventral blind sac (CVBS). We found that locations differed in both epimural bacterial community structure and composition, with the CDBS community displaying the greatest diversity. Across all sampling sites, epimural bacterial communities were dominated by members of the phyla Bacteroidetes, Firmicutes, and Proteobacteria. Bacteria within Prevotellaceae, Butyrivibrio, Campylobacter, Mogibacterium, and Desulfobulbus all showed high relative sequence abundance and differential distributions according to sample location. There appears to be a core epimural microbiota present across all locations in all cows, although relative abundance was highly variable. The difference in relative abundance in epimural microbial communities, perhaps influenced by host physiology and the diversity within rumen contents, likely has important consequences for nutrition acquisition and general health. To the best of our knowledge, this work represents the first characterization of the ruminal epimural microbiota across different epithelial locations for any bovine ruminant.

The Signature Microbiota Drive Rumen Function Shifts in Goat Kids Introduced to Solid Diet Regimes

The feeding regime of early, supplementary solid diet improved rumen development and production in goat kids. However, the signature microbiota responsible for linking dietary regimes to rumen function shifts are still unclear. This work analyzed the rumen microbiome and functions affected by an early solid diet regime using a combination of machine learning algorithms. Volatile fatty acids (i.e., acetate, propionate and butyrate) fermented by microbes were found to increase significantly in the supplementary solid diet groups. Predominant genera were found to alter significantly from unclassified Sphingobacteriaceae (non-supplementary group) to Prevotella (supplementary solid diet groups). Random Forest classification model revealed signature microbiota for solid diet that positively correlated with macronutrient intake, and linearly increased with volatile fatty acid production. Bacteria associated with carbohydrate and protein metabolism were also identified. Utilization of a Fish Taco analysis portrayed a set of intersecting core species contributed to rumen function shifts by the solid diet regime. The core community structures consisted of the specific, signature microbiota and the manipulation of their symbiotic partners are manipulated by extra nutrients from concentrate and/or forage, and then produce more volatile fatty acids to promote rumen development and functions eventually host development. Our study provides mechanisms of the microbiome governed by a solid diet regime early in life, and highlights the signature microbiota involved in animal health and production.

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

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

Effects of clay mineral supplementation on particle-associated and epimural microbiota, and gene expression in the rumen of cows fed high-concentrate diet

The increased concentrate amounts in cow diets may initiate changes in both particle-associated (PaM) and epimural microbiota (EpM) with the potential for promoting the establishment of pathogens. Clay minerals have shown promising potentials in binding harmful microorganisms and metabolites due to their high adsorption capacity. This study evaluated the effects of a clay-mineral based product (CM) on PaM, EpM, fermentation parameters, and epithelial gene expression in cows fed a high-concentrate diet. Eight rumen-cannulated non-lactating Holstein cows received a concentrate mix supplemented with CM or not (CON) in a change-over design with an initial 100% roughage diet phase (RD, 1 week), followed by intermittent 65%-high-concentrate-diet phases (HC1, HC2; 1 and 2 week duration, respectively), interrupted by 1 week roughage only. Rumen samples for short-chain fatty acids, ammonia, and lactate quantification, as well as PaM, and epithelial biopsies for EpM examination and epithelial gene expression were collected via the cannula once during each feeding phase. Phylogenetic distance analysis of Illumina MiSeq sequencing of the 16S rRNA gene region V345 showed a clear clustering of RD microbiota compared to HC in PaM, showing the impact of the high-concentrate diet on the bacterial community. In the EpM this effect was less pronounced, due to higher variability in RD. In the PaM, a decrease (P < 0.01) of community diversity occurred with the onset of HC feeding, while in the EpM there was an increase in diversity (P < 0.05). In the PaM, CM increased the relative abundance of genus Butyrivibrio (P < 0.01), a commensal bacterium of the rumen, which was, with 6.4%, the second most abundant genus. There, the CM supplementation decreased the genera Lactobacillus, Fusobacterium, and Treponema (P = 0.05), which are potentially either lactate producing or opportunistic pathogens. In the EpM, CM decreased the relative abundance of Succiniclasticum genus (P < 0.01), a possible endotoxin producer, and increased bacteria that are associated with a normobiotic rumen, such as Campylobacter (P = 0.06). Barrier function genes were upregulated in HC2 and nutrient transport genes downregulated in HC1 (P < 0.05); however, there was little effect on pro-inflammatory genes at the epithelium. The CM showed a significant decreasing effect on the cellular metabolism genes HMGCS1 (P = 0.04). Our results suggest that CM supplementation can increase the relative abundance of commensal microbiota and decrease bacteria that could negatively impact the rumen milieu and health during high-concentrate feeding.

Adaptive responses in short-chain fatty acid absorption, gene expression, and bacterial community of the bovine rumen epithelium recovered from a continuous or transient high-grain feeding

The feeding of high-grain diets to dairy cows commonly results in lowered pH and ruminal dysbiosis, characterized by changes in absorption dynamics of short-chain fatty acids (SCFA) across the reticuloruminal wall, epithelial function, and the epithelial bacteria community structure. Therefore, the present study evaluated the effect of high-grain feeding persistence on the absorption kinetics of reticuloruminal SCFA, gene expression in the rumen epithelium, and the associated shifts in the epithelial bacteria in cows recovering from either a long-term continuous high-grain feeding model or a long-term transient high-grain feeding model. In a crossover study design, 8 nonlactating Holstein cows were fed 60% concentrate either continuously for 4 wk (continuous) or with a 1-wk break in the second week of the high-grain feeding (transient). After the high-grain feeding, all animals were fed a diet of 100% forage (recovery) for an additional 8 wk. Rumen papilla biopsies and SCFA absorption measurements were taken at the start of the trial (baseline), after the 4-wk high-grain feeding (49 d), after 2-wk recovery forage feeding (63 d), and after 8-wk recovery forage (105 d). Absorption of SCFA was determined in vivo using the washed and isolated reticulorumen technique. Rumen papillae biopsies were used for adherent bacterial DNA and host RNA extraction. The epithelial bacteria were determined using Illumina MiSeq (Microsynth AG, Balgach, Switzerland) sequencing of the 16S rRNA gene. No significant effects of the high-grain feeding model were seen for bacterial diversity. However, bacterial diversity increased with time spent in the recovery forage feeding period regardless of feeding model. The relative abundance of Acidobacteria phyla and Acetivibrio spp. increased when animals were fed a transient high-grain feeding model. A trend toward increased CLDN4 expression was observed in the continuous model. Furthermore, there were interactions between feeding model and sampling day for gene targets CD14, DRA, NHE2, NHE3, and MCT2. When comparing length of recovery, in the continuous model increased relative absorption of SCFA was sustained at 63 d but dropped to baseline measurements at 105 d. A similar pattern was found with the transient model but it did not reach significance. The only gene target that was found to significantly correlate to relative absorption of SCFA was DRA (correlation coefficient ≤ -0.41). Whereas, genera Alkalibaculum, Anaerorhabdus, Coprococcus, and Dethiobacter all showed positive correlations to gene targets for pH regulation (NHE2 and NHE3) and SCFA uptake (MCT1) but negative correlations to SCFA absorption. We conclude that while the rumen absorption and epithelial bacteria were able to recover to baseline levels after 8 wk of forage feeding, the time needed for re-establishment of homeostasis in host gene expression is longer, especially when high-grain feeding is interrupted.

Linkages between Epithelial Microbiota and Host Transcriptome in the Ileum during High-Grain Challenges: Implications for Gut Homeostasis in Goats

A high-grain (HG) diet can result in ruminal subacute acidosis, which is detrimental to gut health and can lead to decreased productivity. This study investigated the ileal epithelial microbiota and its relationship with host epithelial function in goats fed a HG diet (concentrate/hay, 90:10) and a control diet (concentrate/hay, 55:45), aiming to elucidate the mechanisms involved in ileal adaptation to subacute acidosis. The HG challenge increased the ileal volatile fatty acid concentration ( p = 0.030) and altered the ileal epithelial microbiota by increasing (FDR < 0.05) relative abundances of active carbohydrate and protein degraders Synergistetes, Prevotella, Fibrobacter, Clostridium, Treponema, and unclassified Ruminococcaceae by 20.1-, 6.3-, 16.8-, 8.5-, 19.9-, and 7.1-fold, respectively. However, the HG diet tended to reduce (FDR < 0.10) the relative abundance of Candidatus Arthromitus (38.8 ± 36.1 versus 2.1 ± 3.1). Microbial functional potentials inferred using PICRUSt indicated that the HG challenge elevated abundances of pathways associated with metabolism of amino acid, glycan, cofactors, and vitamins, whereras it decreased pathways associated with signal transduction, xenobiotic biodegradation, and metabolism. Additionally, in the ileal epithelium of HG goats, transcriptome analysis identified the increment (FDR < 0.10) of candidate genes involved in metabolism of carbohydrates, lipids, proteins, vitamins, and the proinflammatory cytokine pathway, while downregulating genes encoding antimicrobials and complements (FDR < 0.05). Collectively, the HG challenge shifted the structure and functional potentials of the ileal microbial community and affected the host responses in the ileum of goats toward increased metabolic activities of macro- and micronutrients, together with an increased risk of gut inflammation.

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

The rapid shift to high-grain (HG) diets in ruminants can affect the function of the rumen epithelium, but the dynamic changes in the composition of the epithelium-associated (epimural) bacterial community in sheep still needs further investigation. Twenty male lambs were randomly allocated to four groups (n = 5). Animals of the first group received hay diet and represented a control group (CON). Simultaneously, animals in the other three groups (HG groups) were rapidly shifted to an HG diet (60% concentrate)which continued for 7 (HG7), 14 (HG14) and 28 (HG28) days, correspondingly. Results showed that ruminal pH dramatically decreased due to the rapid shift to the HG diet (P <0.001), while, the concentrations of butyrate (P <0.001), lactate (P = 0.001), valerate (P = 0.008) and total volatile fatty acids (P = 0.001) increased. Diversity estimators showed a dramatic decrease after the shift without recovering as the HG feeding continued. The principal coordinates analysis showed that CON group clustered separately from all HG groups with the presence of significant difference only between HG7 and HG28 (P = 0.034). The non-parametric multivariate analysis (npmv R-package) deduced that the primary significant differences in phyla and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt)-predicted Kyoto Encyclopedia of Genes and Genomes (KEGGs) was attributed mainly to the diet composition (P <0.001, P = 0.001) compared to its application period (P = 0.140, 0.545) which showed a significant effect only on the genus (P = 0.001) and the operational taxonomic units (OTUs) level (P = 0.011). The Kruskal-Wallis test deduced that six phyla showed a significant effect due to the shift in diet composition. At the genus level, HG feeding altered the abundance of 12 taxa, four of which showed a significant variation due to the duration of the HG diet application. Similarly, we found that 21 OTUs showed significant variations due to the duration of the HG diet application. Furthermore, the genes abundance predicted by PICRUSt revealed that the HG feeding significantly affected seven metabolic pathways identified in the KEGG. Particularly, the abundance of gene families associated with carbohydrates metabolism were significantly higher in HG feeding groups (P = 0.027). Collectively, these results revealed that the rapid transition to an HG diet causes dramatic alterations in ruminal fermentation and the composition and function of ruminal epithelium-associated microbiome in sheep, while, the duration of the HG diet application causes drastic alterations to the abundance of some species.

Impact of high-grain diet feeding on mucosa-associated bacterial community and gene expression of tight junction proteins in the small intestine of goats

The objective of this study was to investigate the impact of a high‐grain (HG) diet on the microbial fermentation, the composition of the mucosa‐associated bacterial microbiota, and the gene expression of tight junction proteins in the small intestine of goats. In the present study, we randomly assigned 10 male goats to either a hay diet (n = 5) or a HG diet (56.5% grain; n = 5) and then examined changes in the bacterial community using Illumina MiSeq sequencing and the expression of tight junction proteins using qRT‐PCR in the mucosa of the small intestine. The results showed that HG diet decreased the luminal pH (p = 0.005) and increased the lipopolysaccharide content (p < 0.001) in the digesta of the ileum, and it increased the concentration of total volatile fatty acids in the digesta of the jejunum (p = 0.015) and ileum (p = 0.007) compared with the hay diet. MiSeq sequencing results indicated that the HG diet increased (FDR = 0.007–0.028) the percentage of the genera Stenotrophomonas, Moraxella, Lactobacillus, and Prevotella in jejunal mucosa but decreased (FDR = 0.016) the abundance of Christensenellaceae R7 group in the ileal mucosa compared with the hay diet. Furthermore, the HG diet caused downregulation of the mRNA expression of claudin‐4, occludin, and ZO‐1 in jejunal and ileal mucosa (p < 0.05). Collectively, our data suggested that the HG diet induced changes in the relative abundance of some mucosa‐associated bacteria, in addition to downregulation of the mRNA expression of tight junction proteins in the small intestine. These findings provide new insights into the adaptation response of the small intestine to HG feeding in ruminants.

Review: The application of omics to rumen microbiota function

Rumen microbiome profiling uses 16S rRNA (18S rRNA, internal transcribed spacer) gene sequencing, a method that usually sequences a small portion of a single gene and is often biased and varies between different laboratories. Functional information can be inferred from this data, but only for those that are closely related to known annotated species, and even then may not truly reflect the function performed within the environment being studied. Genome sequencing of isolates and metagenome-assembled genomes has now reached a stage where representation of the majority of rumen bacterial genera are covered, but this still only represents a portion of rumen microbial species. The creation of a microbial genome (bins) database with associated functional annotations will provide a consistent reference to allow mapping of RNA-Seq reads for functional gene analysis from within the rumen microbiome. The integration of multiple omic analytics is linking functional gene activity, metabolic pathways and rumen metabolites with the responsible microbiota, supporting our biological understanding of the rumen system. The application of these techniques has advanced our understanding of the major microbial populations and functional pathways that are used in relation to lower methane emissions, higher feed efficiencies and responses to different feeding regimes. Continued and more precise use of these tools will lead to a detailed and comprehensive understanding of compositional and functional capacity and design of techniques for the directed intervention and manipulation of the rumen microbiota towards a desired state.

Changes in the Rumen Epithelial Microbiota of Cattle and Host Gene Expression in Response to Alterations in Dietary Carbohydrate Composition

The inclusion of high-quality hay (HQH), in place of concentrates, shifts dietary carbohydrate intake, and the extent to which these shifts effect epimural microbiota and epithelial gene expression of the rumen has not yet been evaluated. Eight ruminally cannulated nonlactating Holstein cows were used in a replicated 4 by 4 Latin square design with four dietary treatments containing HQH, with either 0% concentrate/100% HQH (100HQH), 25% concentrate/75% HQH (75HQH), or 40% concentrate/60% HQH (60HQH). The fourth group (control [CON]) was fed 60% normal fiber-rich hay and 40% concentrate. The data showed that measures of diversity for the rumen epimural population, specifically the Shannon (P = 0.004) and Simpson (P = 0.003) indices, decreased with increasing levels of HQH in the diet. The feeding of HQH shifted the epimural population from predominantly Firmicutes to Proteobacteria Phylogenetic analysis revealed that HQH feeding markedly shifted the abundance of Campylobacter spp. from 7.8 up to 33.5% (P < 0.001), with greater ingestion of protein (r = 0.63) and sugars (r = 0.65) in HQH diet being responsible for this shift. The expression of genes targeting intracellular pH regulation, barrier function, and nutrient uptake of rumen epithelium remained stable regardless of the carbohydrate source. In conclusion, the data suggest strong alterations of the ruminal epimural microbiota in response to changes in the nutritive patterns of the diet. Further research is warranted to evaluate the long-term effects of these significant microbial changes on rumen health and food safety aspects in cattle at a transcriptional level.IMPORTANCE Feeding of forages versus starchy concentrates is a highly debated topic. Hay is believed to be healthier and more ecological sustainable for cattle than are concentrates, although the effects of feeding hay with enhanced sugar and protein content on epimural microbiota and host gene expression have not yet been evaluated. This research provides a report of the role of feeding hay with increased sugar and protein content in place of starchy concentrates in altering epimural microbiota and in generating a host response. Our research shows that the addition of high-quality hay to dairy rations shifted nutrient intake, resulting in strong alterations in the epimural microbiota in cattle. This work provides a background for further long-term research regarding the effects of feeding practices on the host-microbiome interaction and its role in rumen health and food safety in cattle.

Differential Microbial Communities of Omnivorous and Herbivorous Cattle in Southern China

In Hong Kong, cattle were traditionally raised by farmers as draft animals to plough rice fields. Due to urbanization in the 20th century, they were gradually abandoned and became wild cattle straying in suburban Hong Kong. Recently, these cattle were observed to have become omnivorous by eating leftover barbeque food waste in country parks. Microbiome analysis was performed on fecal samples of the omnivorous cattle using deep sequencing and the resulting microbiome was compared with that of traditional herbivorous cattle in Southern China. A more diverse gut microbiome was observed in the omnivorous cattle, suggesting that microbiota diversity increases as diet variation increases. At the genus level, the relative abundance of Anaeroplasma, Anaerovorax, Bacillus, Coprobacillus and Solibacillus significantly increased and those of Anaerofustis, Butyricimonas, Campylobacter, Coprococcus, Dehalobacterium, Phascolarctobacterium, rc4.4, RFN20, Succinivibrio and Turicibacter significantly decreased in the omnivorous group. The increase in microbial community levels of Bacillus and Anaerovorax likely attributes to the inclusion of meat in the diet; while the decrease in relative abundance of Coprococcus, Butyricimonas, Succinivibrio, Campylobacter and Phascolarctobacterium may reflect the reduction in grass intake. Furthermore, an increased consumption of resistant starch likely resulted in the increase in abundance of Anaeroplasma. In conclusion, a significant change in the gut microbial community was observed in the omnivorous cattle, suggesting that diet may be one of the factors that may signal an adaptation response by the cattle to maintain feed efficiency as a consequence of the change in environment.

The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens

The rumen simulation technique (RUSITEC) is a well-established semicontinuous in vitro model for investigating ruminal fermentation; however, information on the stability of the ruminal bacterial microbiota and metabolome in the RUSITEC system is rarely available. The availability of high resolution methods, such as high-throughput sequencing and metabolomics improve our knowledge about the rumen microbial ecosystem and its fermentation processes. Thus, we used Illumina MiSeq 16S rRNA amplicon sequencing and a combination of direct injection mass spectrometry with a reverse-phase LC-MS/MS to evaluate the dynamics of the bacterial community and the concentration of several metabolites in a RUSITEC experiment as a function of time and in response to a challenge with a pathogenic Clostridium perfringens (C. perfringens) strain. After four days of equilibration, samples were collected on days 5, 6, 7, 10, 12 and 15 of the steady-state and experimental period. From a total of six fermenters, three non-infected fermenters were used for investigating time-dependent alterations; three fermenters were incubated with C. perfringens and compared with the non-infected vessels at days 10, 12 and 15. Along the time-line, there was no statistically significant change of the overall bacterial community, however, some phylotypes were enriched at certain time points. A decrease in Fibrobacter and Elusimicrobia over time was followed by an increase in Firmicutes and Actinobacteria. In contrast, classical fermentation measurements such as pH, redox potential, NH3-N, short chain fatty acids and the concentrations of metabolites determined by metabolomics (biogenic amines, hexoses and amino acids) remained stable throughout the experiment. In response to C. perfringens addition the concentrations of several amino acids increased. Although the overall bacterial community was not altered here either, some minor changes such as an enrichment of Synergistetes and Bacteroidetes were detectable over time. In conclusion, both, the bacterial community composition and the metabolome in the RUSITEC system were relatively stable during the experiment.

Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria

Microbiota of the rumen wall constitute an important niche of rumen microbial ecology and their composition has been elucidated in different ruminants during the last years. However, the knowledge about the function of rumen wall microbes is still limited. Rumen wall biopsies were taken from three fistulated dairy cows under a standard forage-based diet and after 4 weeks of high concentrate feeding inducing a subacute rumen acidosis (SARA). Extracted RNA was used for metatranscriptome sequencing using Illumina HiSeq sequencing technology. The gene expression of the rumen wall microbial community was analyzed by mapping 35 million sequences against the Kyoto Encyclopedia for Genes and Genomes (KEGG) database and determining differentially expressed genes. A total of 1,607 functional features were assigned with high expression of genes involved in central metabolism, galactose, starch and sucrose metabolism. The glycogen phosphorylase (EC:2.4.1.1) which degrades (1->4)-alpha-D-glucans was among the highest expressed genes being transcribed by 115 bacterial genera. Energy metabolism genes were also highly expressed, including the pyruvate orthophosphate dikinase (EC:2.7.9.1) involved in pyruvate metabolism, which was covered by 177 genera. Nitrogen metabolism genes, in particular glutamate dehydrogenase (EC:1.4.1.4), glutamine synthetase (EC:6.3.1.2) and glutamate synthase (EC:1.4.1.13, EC:1.4.1.14) were also found to be highly expressed and prove rumen wall microbiota to be actively involved in providing host-relevant metabolites for exchange across the rumen wall. In addition, we found all four urease subunits (EC:3.5.1.5) transcribed by members of the genera Flavobacterium, Corynebacterium, Helicobacter, Clostridium, and Bacillus, and the dissimilatory sulfate reductase (EC 1.8.99.5) dsrABC, which is responsible for the reduction of sulfite to sulfide. We also provide in situ evidence for cellulose and cellobiose degradation, a key step in fiber-rich feed digestion, as well as oxidative stress response and oxygen scavenging at the rumen wall. Archaea, mainly Methanocaldococcus and Methanobrevibacter, were found to be metabolically active with a high number of transcripts matching to methane and carbohydrate metabolism. These findings enhance our understanding of the metabolic function of the bovine rumen wall microbiota.

Rumen Bacteria Communities and Performances of Fattening Lambs with a Lower or Greater Subacute Ruminal Acidosis Risk

Several ruminal cellulolytic bacteria species are sensitive to pH and could therefore be used as biomarkers to determine the risk of sub-acute ruminal acidosis (SARA) in finishing lambs. This study compared a 2–4 h post feeding ruminal pH measurement to abundances of the ruminal pH-sensitive bacteria to evaluate the risk of SARA in a herd of 120 finishing lambs. The lambs were reared in individual units for 50 days. Ruminal fluid was collected by use of an orogastric tube on day 51 2-4 h after feeding. Although the lambs were fed an identical diet, they responded differently in the abundances of four ruminal pH sensitive cellulolytic bacteria (Ruminococcus albus, Ruminococcus flavefaciens and Fibrobacter succinogenes and Butyrivibrio fibrisolvens). Lambs with the most or the least cellulolytic bacteria were then classified as either lower SARA risk (LSR, n = 10) or higher SARA risk group (HSR, n = 10), respectively. Data showed that the ruminal pH and VFA profiles were uncorrelated with the number of cellulolytic bacteria (P > 0.050). Lambs with the HSR showed lower ruminal pH (P = 0.013) and acetate to propionate ratio (P = 0.018), higher concentrations of lactate (P = 0.035) and proportion of propionate (P = 0.033) compared to those with the LSR. The DMI and ADG did not differ in LSR and HSR lambs (P > 0.050). A diversity analysis revealed significantly lower diversity in HSR lambs than in LSR (Simpson index, P = 0.004). The relative abundances of the phyla Bacteroidetes, Fibrobacteres, Verruomicrobia, and Proteobacteria were higher in LSR lambs than in HSR (P < 0.050). The abundances of several phyla including Firmicutes, Tenericutes and Actinobacteria were higher in the HSR than in the LSR group (P < 0.050). The bacterial communities of the LSR and HSR clustered separately in rumen based on the Unifrac distances, indicating distinct bacteria communities at OTU level between the LSR and HSR lambs. Overall, there was no correlation between 2 and 4 h post-feeding ruminal pH and the abundance of pH-sensitive bacteria and the amount of these bacteria could be used as a potential biomarker of SARA in lamb herd.

Invited review: Practical feeding management recommendations to mitigate the risk of subacute ruminal acidosis in dairy cattle

Rumen health is of vital importance in ensuring healthy and efficient dairy cattle production. Current feeding programs for cattle recommend concentrate-rich diets to meet the high nutritional needs of cows during lactation and enhance cost-efficiency. These diets, however, can impair rumen health. The term "subacute ruminal acidosis" (SARA) is often used as a synonym for poor rumen health. In this review, we first describe the physiological demands of cattle for dietary physically effective fiber. We also provide background information on the importance of enhancing salivary secretions and short-chain fatty acid absorption across the stratified squamous epithelium of the rumen; thus, preventing the disruption of the ruminal acid-base balance, a process that paves the way for acidification of the rumen. On-farm evaluation of dietary fiber adequacy is challenging for both nutritionists and veterinarians; therefore, this review provides practical recommendations on how to evaluate the physical effectiveness of the diet based on differences in particle size distribution, fiber content, and the type of concentrate fed, both when the latter is part of total mixed ration and when it is supplemented in partial mixed rations. Besides considering the absolute amount of physically effective fiber and starch types in the diet, we highlight the role of several feeding management factors that affect rumen health and should be considered to control and mitigate SARA. Most importantly, transitional feeding to ensure gradual adaptation of the ruminal epithelium and microbiota; monitoring and careful management of particle size distribution; controlling feed sorting, meal size, and meal frequency; and paying special attention to primiparous cows are some of the feeding management tools that can help in sustaining rumen health in high-producing dairy herds. Supplementation of feed additives including yeast products, phytogenic compounds, and buffers may help attenuate SARA, especially during stress periods when the risk of a deficiency of physically effective fiber in the diet is high, such as during early lactation. However, the usage of feed additives cannot fully compensate for suboptimal feeding management.

Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling

Subacute rumen acidotic (SARA) conditions are a consequence of high grain feeding. Recent work has shown that the pattern of grain feeding can significantly impact the rumen epimural microbiota. In a continuation of these works, the objective of this study was to determine the role of grain feeding patterns on the colonization and associated changes in predicted functional properties of the fiber-adherent microbial community over a 48 h period. Eight rumen-cannulated Holstein cows were randomly assigned to interrupted or continuous 60%-grain challenge model (n = 4 per model) to induce SARA conditions. Cows in the continuous model were challenged for 4 weeks, whereas cows of interrupted model had a 1-wk break in between challenges. To determine dynamics of rumen fiber-adherent microbial community we incubated the same hay from the diet samples for 24 and 48 h in situ during the baseline (no grain fed), week 1 and 4 of the continuous grain feeding model as well as during the week 1 following the break in the interrupted model. Microbial DNA was extracted and 16SrRNA amplicon (V3-V5 region) sequencing was done with the Illumina MiSeq platform. A significant decrease (P < 0.001) in fiber-adherent rumen bacterial species richness and diversity was observed at the end of a 4 week continuous SARA challenge in comparison to the baseline. A total of 159 operational taxonominc units (OTUs) were identified from the microbial population representing > 0.1% relative abundance in the rumen, 18 of which were significantly impacted by the feeding challenge model. Correlation analysis of the significant OTUs to rumen pH as an indicator of SARA showed genus Succiniclasticum had a positive correlation to SARA conditions regardless of treatment. Predictive analysis of functional microbial properties suggested that the glyoxylate/dicarboxylate pathway was increased in response to SARA conditions, decreased between 24h to 48h of incubation, negatively correlated with propanoate metabolism and positively correlated to members of the Veillonellaceae family including Succiniclasticum spp. This may indicate an adaptive response in bacterial metabolism under SARA conditions. This research clearly indicates that changes to the colonizing fiber-adherent rumen microbial population and their predicted functional genes occur in both the short (48 h) and long term (4 wk) under both continuous and interrupted SARA challenge models.