Changes in bacterial diversity associated with epithelial tissue in the beef cow rumen during the transition to a high-grain diet

Comparative analysis of intestinal microbiota composition between free-ranged captive yak populations in Nimu County

The intestinal microbiota assumes a pivotal role in modulating host metabolism, immune responses, overall health, and additional physiological dimensions. The structural and functional characteristics of the intestinal microbiota may cause alterations within the host's body to a certain extent. The composition of the gut microbiota is associated with environmental factors, dietary habits, and other pertinent conditions. The investigation into the gut microbiota of yaks remained relatively underexplored. An examination of yak gut microbiota holds promise in elucidating the complex relationship between microbial communities and the adaptive responses of the host to its environment. In this study, yak were selected from two distinct environmental conditions: those raised in sheds (NS, n=6) and grazed in Nimu County (NF, n=6). Fecal samples were collected from the yaks and subsequently processed for analysis through 16S rDNA and ITS sequencing methodologies. The results revealed that different feeding styles result in significant differences in the Alpha diversity of fungi in the gut of yaks, while the gut microbiota of captive yaks was relatively conserved. In addition, significant differences appeared in the abundance of microorganisms in different taxa, phylum Verrucomicrobiota was significantly enriched in group NF while Firmicutes was higher in group NS. At the genus level, Akkermansia, Paenibacillus, Roseburia, Dorea, UCG_012, Anaerovorax and Marvinbryantia were enriched in group NF while Desemzia, Olsenella, Kocuria, Ornithinimicrobium and Parvibacter were higher in group NS (P<0.05 or P<0.01). There was a significant difference in the function of gut microbiota between the two groups. The observed variations are likely influenced by differences in feeding methods and environmental conditions both inside and outside the pen. The findings of this investigation offer prospective insights into enhancing the yak breeding and expansion of the yak industry.

Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review

Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.

Integrating Omics Technologies for a Comprehensive Understanding of the Microbiome and Its Impact on Cattle Production

Ruminant production holds a pivotal position within the global animal production and agricultural sectors. As population growth escalates, posing environmental challenges, a heightened emphasis is directed toward refining ruminant production systems. Recent investigations underscore the connection between the composition and functionality of the rumen microbiome and economically advantageous traits in cattle. Consequently, the development of innovative strategies to enhance cattle feed efficiency, while curbing environmental and financial burdens, becomes imperative. The advent of omics technologies has yielded fresh insights into metabolic health fluctuations in dairy cattle, consequently enhancing nutritional management practices. The pivotal role of the rumen microbiome in augmenting feeding efficiency by transforming low-quality feedstuffs into energy substrates for the host is underscored. This microbial community assumes focal importance within gut microbiome studies, contributing indispensably to plant fiber digestion, as well as influencing production and health variability in ruminants. Instances of compromised animal welfare can substantially modulate the microbiological composition of the rumen, thereby influencing production rates. A comprehensive global approach that targets both cattle and their rumen microbiota is paramount for enhancing feed efficiency and optimizing rumen fermentation processes. This review article underscores the factors that contribute to the establishment or restoration of the rumen microbiome post perturbations and the intricacies of host-microbiome interactions. We accentuate the elements responsible for responsible host-microbiome interactions and practical applications in the domains of animal health and production. Moreover, meticulous scrutiny of the microbiome and its consequential effects on cattle production systems greatly contributes to forging more sustainable and resilient food production systems, thereby mitigating the adverse environmental impact.

The Colonization of Rumen Microbiota and Intervention in Pre-Weaned Ruminants

In pre-weaned ruminants, the microbiota colonizes rapidly in the rumen after birth and constantly interacts with the host to sustain health and metabolism. The developing microbial community is more malleable, so its manipulation may improve ruminant health and productivity as well as may have long-term effects on ruminants. Hence, understanding the process of rumen microbiota establishment is helpful for nutritional interventions of rumen microbiota in pre-weaned ruminants. This paper reviews the latest advances in the colonization of rumen microbiota while providing insights into the most suitable time for manipulating rumen microbial colonization in early life. In addition, different factors that affect rumen microbiota establishment during the pre-weaned ruminants are discussed in the current manuscript. The purpose of this review is to aid in the development of guidelines for manipulating rumen microbiota to improve animal productivity and health.

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.

Diversity of growth performance and rumen microbiota vary with feed types

Diet is a major factor in influencing the growth performance and the microbial community of lambs. This study aimed to investigate how diverse diets influence their growth performance and rumen microbiota. Ninety male lambs were randomly allocated into three groups in a completely randomized design with equal lambs: non-pelleted native grass hay (HA) as the control diet and pelleted native grass hay (GP) and pelleted native grass hay with concentrate (GPC) as experimental diets. The rumen fluid samples of the lambs in the HA, GP, and GPC groups were used to study rumen microbiota diversity through 16S rDNA high-throughput sequencing. In the present study, the final body weight, dry matter intake, and average daily gain differed significantly (p &lt; 0.05) among the HA, GP, and GPC groups. Compared to the HA group, higher final body weight, dry matter intake, and average daily gain were found in the GP group. Similarly, better animal performance was observed in the GPC group than in the GP group. The principal coordinates analysis displayed that the composition of the rumen microbiota in the three groups was distinctly separated from each other. Bacteroidetes and Firmicutes were the dominant members of the community in the HA and GP groups, while Bacteroidetes, Firmicutes, and Proteobacteria became the predominant members in the GPC group. The comparison among these groups showed significant (p &lt; 0.05) differences in Rikenellaceae_RC9_gut_group, Prevotella_1, Ruminococcaceae_NK4A214_group, and Succiniclasticum. These results suggest that the GP and GPC diets are more beneficial for growth performance than the HA diet and also indicate that the rumen microbiota varied in response to different feed types. In conclusion, these results could provide strategies to influence rumen microbiota for better growth and a healthier ecosystem on the Mongolian Plateau and lay the theoretical groundwork for feeding the pelleted native grass diet.

Comparative research of intestinal microbiota diversity and body mass regulation in Eothenomys miletus from different areas of Hengduan mountain regions

In order to investigate the effects of different areas on intestinal bacterial diversity and body mass regulation in Eothenomys miletus from Hengduan mountain regions, and to explore the community structure and diversity of intestinal microflora and their role in body mass regulation. E. miletus was collected from five areas including Deqin (DQ), Xianggelila (XGLL), Lijiang (LJ), Jianchuan (JC), and Dali (DL), we used 16S rRNA sequencing technology combined with physiological and morphological methods to study the intestinal microbiota diversity, abundance and community structure of the intestinal bacteria in winter, and to explore the influence of geographical factors, physiological indicators including food intake, resting metabolic rate (RMR), non-shivering thermogenesis (NST), neuropeptide Y (NPY), Agouti-Related Protein (AgRP), proopiomelanocortin (POMC), cocaine and amphetamine regulated transcription peptide (CART), and morphological indicators including body mass, body length and other nine indicators on the intestinal microflora diversity in E. miletus. The results showed that there were significant differences in metabolic indexes such as RMR, NST, NPY, AgRP, and morphological indexes such as body length, tail length and ear length among the five regions. Bacterial community in intestinal tract of E. miletus mainly includes three phyla, of which Firmicutes is the dominant phyla, followed by Bacteroidetes and Tenericutes. At the genus level, the dominant bacterial genera were S24-7(UG), Clostridiales (UG), and Lachnospiraceae (UG), etc. α diversity of intestinal microorganisms in DL and JC were significantly different from that in the other three regions. Genera of intestinal microorganisms in DL and JC were also the most. Moreover, Bacteroides, Ruminococcus, and Treponema could affect energy metabolism in E. miletus, which were closely related to the environment in which they lived. All of these results indicated that different areas in Hengduan Mountain had certain effects on the structure of intestinal microbial community in E. miletus, which were responded positively to changes in food abundance and other environmental factors. Furthermore, Firmicutes and Bacteroidetes play an important role in the body mass regulation in E. miletus.

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.

Ruminal bacterial community is associated with the variations of total milk solid content in Holstein lactating cows

Total milk solid (TMS) content directly reflects the quality of milk. Rumen bacteria ferment dietary components, the process of which generates the precursors for the synthesis of milk solid, therefore, the variation in rumen bacterial community could be associated with milk solid in dairy cows. In this study, 45 healthy mid-lactation Holstein dairy cows with the similar body weight, lactation stage, and milk yield were initially used for the selection of 10 cows with high TMS (HS) and 10 cows with low TMS (LS). All those animals were under the same feeding management, and the individual milk yield was recorded for 14 consecutive days before milk and rumen fluid were sampled. Rumen fluid was used to determine bacterial community by 16S rRNA gene sequencing technique. The HS cows had significantly greater feed intake and milk TMS, fat, protein content than LS cows (P < 0.05). Among the volatile fatty acids (VFA), propionic acid and valeric acid concentrations were significantly greater in HS cows than those in LS cows (P < 0.05). There was no significant difference in the concentrations of acetate, butyrate, isobutyrate, valerate, and the total VFA (P > 0.05), nor was the acetate-to-propionate ratio, pH value, ammonia nitrogen and microbial crude protein concentrations (P > 0.05). Significant differences in the relative abundances of some bacterial genera were found between HS and LS cows. Spearman’s rank correlation analysis revealed that TMS content was correlated positively with the abundances of Ruminococcaceae UCG-014, Ruminococcaceae NK4A214 group, Prevotellaceae UCG-001, Butyrivibrio 2, Prevotellaceae UCG-003, Candidatus Saccharimonas, Ruminococcus 2, Lachnospiraceae XPB1014 group, probable genus 10, Eubacterium ventriosum group, but negatively correlated with Pyramidobacte. In addition, Ruminococcaceae UCG-014, Ruminococcus 2, Ruminococcaceae UCG001, probable genus 10 and Eubacterium ventriosum group might boost the total VFA production in the rumen. In conclusion, the dry matter intake of dairy cows and some special bacteria in rumen were significantly associated with TMS content, which suggests the potential function of rumen bacteria contributing to TMS content in dairy cows.

Effects of Dietary Supplementation With Clostridium butyricum on Growth Performance, Apparent Digestibility, Blood Metabolites, Ruminal Fermentation and Bacterial Communities of Fattening Goats

Clostridium butyricum (C. butyricum) is currently widely used to improve the body health and productive performance of monogastric animals. However, there have been few reports on the effects and specific mechanism of action of Clostridium butyricum in ruminants. This study aimed to investigate the effects of Clostridium butyricum supplementation on the growth performance and digestive microbiota of fattening goats. Twenty-four healthy male Albas goats (body weight = 22 ± 2.03 kg) were randomly divided into 3 treatment groups with eight goats in each group. The treatments were as follows: control group (CON) (basal diet, concentrate to forage ratio = 65:35); low-dose Clostridium butyricum (LCB) (basal diet plus 2.0 × 10⁸ CFU/kg Clostridium butyricum); and high-dose Clostridium butyricum (HCB) (basal diet plus 1.0 × 10⁹ CFU/kg Clostridium butyricum). The experiment lasted for 8 weeks after a 2-week adaptation period. Therefore, growth performance and rumen and rectum microbiota were evaluated in goats supplemented with Clostridium butyricum and its metabolites. The results showed that dietary supplementation with Clostridium butyricum significantly increased the pH (P < 0.05), but had no significant effect on growth performance (P > 0.05). Compared with the control group, dietary Clostridium butyricum supplementation significantly increased the relative abundance of Prevotella_1, Christensenellaceae AE_R-7_Group and Prevotellaceae AE_UCG-003 (P < 0.05), and significantly decreased Succiniclasticum and Muribaculaceae_unclassified (P < 0.05). The relative abundance of Clostridium in the rumen was <1.0%. Moreover, 16S rDNA analysis showed that the fecal Clostridium or Clostridium butyricum count was significantly decreased (P < 0.05), and the relative abundance of Alistipes and Akkermansia was increased (P < 0.10) in the low-dose group compared with the control group. Supplementing Clostridium butyricum in a high-concentrate diet did not significantly affect the performance of goats, while regulation of the gastrointestinal microbiota and related metabolites was associated with rumen fermentation.

Comparisons of Corn Stover Silages after Fresh- or Ripe-Corn Harvested: Effects on Digestibility and Rumen Fermentation in Growing Beef Cattle

Both waxy corn stover after fresh- (CF) and ripe-corn (CR) harvested are important byproducts of corn cropping system and have 20 d difference in harvest time. The study aimed to investigate the effects of prolonging harvest time on the nutritive value of corn stover silage by comparing CF with CR silages. In vitro ruminal experiment was firstly performed to investigate substrate degradation and fermentation of CF and CR silages. The CR diet was formulated by replacing 50% forage of CF silage with CR silage on a dry matter (DM) basis. Fourteen crossbred steers (Simmental × Limousin × local Chinese) aged 13 months with an average weight of 318.1 ± 37.1 kg were selected and randomly allocated into two dietary treatment groups. Although the CR silage had greater DM and fiber contents than CF silage, it did not alter in vitro degradation (p > 0.05), but with lower molar percentage of propionate and acetate to propionate ratio (p < 0.05). The cattle fed CR diet had a higher DM intake and lower fiber digestibility with reduction in 18S rRNA gene copies of protozoa and fungi and 16S rRNA gene copies of Fibrobacter succinogenes (p < 0.05). Further 16S rRNA gene amplicon analysis indicated a similar diversity of bacteria community between CR and CF treatments (p > 0.05). Few differences were observed in the abundance of genera larger than 1% (p > 0.05), except for the reduction in abundance of genera Ruminococcaceae_NK4A214_group in CR treatment (p < 0.05). In summary, prolonging 20 d harvest time of corn stover silage increases the forage fiber and DM content, which promotes feed intake with decreased fiber degradation, although rumen fermentation and growth performance are not changed in growing beef cattle.

Comparison of gut microbiome in the Chinese mud snail (Cipangopaludina chinensis) and the invasive golden apple snail (Pomacea canaliculata)

Background

Gut microbiota play a critical role in nutrition absorption and environmental adaptation and can affect the biological characteristics of host animals. The invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) are two sympatric freshwater snails with similar ecological niche in southern China. However, gut microbiota comparison of interspecies remains unclear. Comparing the difference of gut microbiota between the invasive snail P. canaliculata and native snail C. chinensis could provide new insight into the invasion mechanism of P.canaliculata at the microbial level.

Methods

Gut samples from 20 golden apple snails and 20 Chinese mud snails from wild freshwater habitats were collected and isolated. The 16S rRNA gene V3-V4 region of the gut microbiota was analyzed using high throughput Illumina sequencing.

Results

The gut microbiota dominantly composed of Proteobacteria, Bacteroidetes, Firmicutes and Epsilonbacteraeota at phylum level in golden apple snail. Only Proteobacteria was the dominant phylum in Chinese mud snail. Alpha diversity analysis (Shannon and Simpson indices) showed there were no significant differences in gut microbial diversity, but relative abundances of the two groups differed significantly (P < 0.05). Beta diversity analysis (Bray Curtis and weighted UniFrac distance) showed marked differences in the gut microbiota structure (P < 0.05). Unique or high abundance microbial taxa were more abundant in the invasive snail compared to the native form. Functional prediction analysis indicated that the relative abundances of functions differed significantly regarding cofactor prosthetic group electron carrier and vitamin biosynthesis, amino acid biosynthesis, and nucleoside and nucleotide biosynthesis (P < 0.05). These results suggest an enhanced potential to adapt to new habitats in the invasive snail.

Effects of the higher concentrate ratio on the production performance, ruminal fermentation, and morphological structure in male cattle-yaks

Background

The present study evaluated the effects of the different concentrate‐to‐forage ratio on the parameters of production, ruminal fermentation, blood biochemical indices, and ruminal epithelial morphological structure of the male cattle‐yaks.

Methods

Eight male cattle‐yaks (280 ± 10 kg of body weight) were randomly divided into the high concentrate (HighC, 70% concentrate feeds on a dry matter basis) and low concentrate (LowC, 50% concentrate feeds on a dry matter basis) groups. All the animals were regularly provided rations twice a day at 08:00 and 16:00 h and had free access to water. The experiment lasted for 37 days.

Results

The dry matter intake and average daily gain of the HighC group were higher (p < 0.05) than those of LowC group. Moreover, a high concentrate diet was found to significantly increase (p < 0.05) the total volatile fatty acid (TVFA) production, and the ratio of propionate and butyrate in TVFA. On the contrary, the ruminal pH, the ratio of isobutyrate and isovalerate, and the acetate‐to‐propionate were significantly decreased (p < 0.05) after high concentrate feeding. The lipopolysaccharide concentrations of the ruminal fluid and plasma in the HighC group were higher (p < 0.05) than those of the LowC group. The results of the ruminal histomorphology showed the rumen to possess an inflammatory reaction.

Conclusion

These findings revealed that upon higher dry matter intake and average daily gain, high concentrate feeding altered the rumen fermentation and morphology, inducing the ruminal inflammation of the cattle‐yak.

Distinctive roles between rumen epimural and content bacterial communities on beef cattle feed efficiency: A combined analysis

Rumen content-associated (RC) and epithelial tissue-attached (RT) bacterial communities are composed of different phylotypes and play distinctive roles. This study aimed to compare the composition of the RT and RC bacterial communities of steers differing in feed efficiency. The microbiota of RT and RC samples collected from sixteen beef steers with high or low residual feed intake (RFI) were analyzed through sequencing of partial 16S rRNA gene amplicons. Bacteroidetes, Proteobacteria and Firmicutes were the predominant phyla and Prevotella was the most abundant genus in both RC and RT bacterial communities. In total, 19 OTUs of the RC samples and 19 OTUs of the RT samples were differentially abundant (DA) between H-RFI and l-RFI steers. Among them, a common DA OTU belonged to Prevotella genus was identified in both RC and RT samples, making it the potential key microbial marker for indicating feed efficiency of steers. The co-occurrence of the DA OTUs among RT and RC samples suggest the importance of these two communities function as a complete system in influencing host feed efficiency.

Identifying active rumen epithelial associated bacteria and archaea in beef cattle divergent in feed efficiency using total RNA-seq

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The most active archaea in the epimural community were different from that of the liquid and content-associated community, but the exact taxonomy requires further identification.

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Rumen epithelial attached methanogens may not contribute to differences in CH₄ production and variations in feed efficiency.

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Families Campylobacteraceae and Neisseriaceae, which contain oxygen scavenging bacteria were significantly more active on the epithelium of efficient cattle.

To date, the role of ruminal epithelial attached microbiota in cattle feed efficiency is undefined. In this study, we aimed to characterize transcriptionally active bacteria and archaea attached to the rumen epithelial wall and to determine whether they differ in cattle with varied feed efficiency. RNA-sequencing was performed to obtain the rumen epithelial transcriptomes from 9 of the most efficient (low RFI) and 9 of the most inefficient (high RFI) animals. The bacteria and archaea 16S rRNA transcripts were identified using an in-house developed pipeline, enriched from filtered reads that did not map to the bovine genome. Archaea from unclassified genera belonging to the Euryarchaeota phylum showed the most activity on the rumen epithelium of low RFI (81.3 ± 1.9%) and high RFI (76.4 ± 3.0%) steers. Bacteria from the Succinivibrionaceae family showed the greatest activity of bacteria on the low RFI (28.7 ± 9.0%) and high RFI (33.9± 8.8%) epithelium. Of the bacterial families, Campylobacteraceae and Neisseriaceae had significantly greater activity on the low RFI epithelium (p < 0.05) and are known to play a role in oxygen scavenging. Greater activity of rumen epithelial attached oxygen scavenging bacteria may provide more optimal feed fermentation conditions, which contributes to high fermentation efficiency in the rumen.

Dynamics of the ruminal microbial ecosystem, and inhibition of methanogenesis and propiogenesis in response to nitrate feeding to Holstein calves

It is known that nitrate inhibits ruminal methanogenesis, mainly through competition with hydrogenotrophic methanogens for available hydrogen (H₂) and also through toxic effects on the methanogens. However, there is limited knowledge about its effects on the others members of ruminal microbiota and their metabolites. In this study, we investigated the effects of dietary nitrate inclusion on enteric methane (CH₄) emission, temporal changes in ruminal microbiota, and fermentation in Holstein calves. Eighteen animals were maintained in individual pens for 45 d. Animals were randomly allocated to either a control (CTR) or nitrate (NIT, containing 15 g of calcium nitrate/kg dry matter) diets. Methane emissions were estimated using the sulfur hexafluoride (SF₆) tracer method. Ruminal microbiota changes and ruminal fermentation were evaluated at 0, 4, and 8 h post-feeding. In this study, feed dry matter intake (DMI) did not differ between dietary treatments (P > 0.05). Diets containing NIT reduced CH₄ emissions by 27% (g/d) and yield by 21% (g/kg DMI) compared to the CTR (P < 0.05). The pH values and total volatile fatty acids (VFA) concentration did not differ between dietary treatments (P > 0.05) but differed with time, and post-feeding (P < 0.05). Increases in the concentrations of ruminal ammonia nitrogen (NH₃–N) and acetate were observed, whereas propionate decreased at 4 h post-feeding with the NIT diet (P < 0.05). Feeding the NIT diet reduced the populations of total bacteria, total methanogens, Ruminococcus albus and Ruminococcus flavefaciens, and the abundance of Succiniclasticum, Coprococcus, Treponema, Shuttlewortia, Succinivibrio, Sharpea, Pseudobutyrivibrio, and Selenomona (P < 0.05); whereas, the population of total fungi, protozoa, Fibrobacter succinogenes, Atopobium and Erysipelotrichaceae L7A_E11 increased (P < 0.05). In conclusion, feeding nitrate reduces enteric CH₄ emissions and the methanogens population, whereas it decreases the propionate concentration and the abundance of bacteria involved in the succinate and acrylate pathways. Despite the altered fermentation profile and ruminal microbiota, DMI was not influenced by dietary nitrate. These findings suggest that nitrate has a predominantly direct effect on the reduction of methanogenesis and propionate synthesis.

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.

Effects of early high nutrition related to metabolic imprinting events on growth, carcass characteristics, and meat quality of grass-fed Wagyu (Japanese Black cattle)

The study was conducted to clarify how early high plane of nutrition related to metabolic imprinting affected growth, carcass characteristics, and meat quality of grass-fed Wagyu (Japanese Black cattle). Wagyu steers were allocated randomly into 2 dietary groups: (1) steers fed milk replacer (crude protein 26.0%, crude fat 25.5%; maximum intake 0.6 kg/d) until 3 mo of age and then fed roughage (orchard grass hay) ad libitum from 4 to 10 mo of age (roughage group, RG; n = 11); (2) steers fed milk replacer (maximum intake of 1.8 kg/d) until 3 mo of age and then fed a high-concentrate diet from 4 to 10 mo of age (early high nutrition, EHN; n = 12). After 11 mo of age, all steers were fed roughage ad libitum until 31 mo of age and then slaughtered. Growth performance, carcass traits, longissimus muscle (LM) meat quality and intramuscular fat (IMF) content, plasma insulin-like growth factor I (IGF-I) concentration, and bone mineral density were measured. Body weight was greater in EHN steers (571 kg) than RG steers (520 kg; P < 0.01). Plasma IGF-I levels were higher in EHN steers than in RG steers at 3, 10, and 14 mo of age (P < 0.01, P < 0.005, P < 0.001, respectively); however, plasma IGF-I levels were lower in EHN steers compared with RG steers at 30 mo of age (P < 0.01). The total weight of the muscles and bones of the left half of the carcass was not different between the 2 groups (P = 0.065). Five of the 19 muscles investigated (semimembranosus, P = 0.036; infraspinatus, P = 0.024; supraspinatus, P = 0.0019; serratus ventralis cervicis, P = 0.032; serratus ventralis thoracis, P = 0.027) were heavier in EHN steers. Total fat weight in the left half of the carcass was 30% greater (P = 0.025) in HNE carcasses. Subcutaneous and perirenal fat weights were 53% and 84% greater (P = 0.008, P = 0.002, respectively) in EHN carcasses. The LM IMF content was greater in EHN loins (13.2%) compared with RG loins (9.4%) at 31 mo of age (P = 0.038); however, no differences were found for shear force, tenderness, and cook loss. These results suggested early high-nutrition affected the growth and meat quality of livestock.

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.

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.

Interactions between Cryptosporidium, Enterocytozoon, Giardia and Intestinal Microbiota in Bactrian Camels on Qinghai-Tibet Plateau, China

Cryptosporidium spp., Enterocytozoon bieneusi, and Giardia duodenalis are zoonotic pathogens commonly found in the intestinal tract of mammalian hosts including livestock and humans. The prevalence of these eukaryote microorganisms in domestic animals and their interaction with intestinal microbiota are not yet fully recognized. We analyzed the intestinal microbiota composition with metagenomics and functional characterization with Cluster of Orthologous (COG) in Bactrian camels, which were raised on Qinghai-Tibet Plateau, Northwest China. Thus, fecal samples were collected from the animals to determine the parasite infection and the profile of microbiota. Analysis of intestinal microbiota at genus level revealed important features of interaction between parasites infection and bacterial community. Coprococcus and Prevotella were more abundant while Akkermansia had lower relative abundance with E. bieneusi infection. Bacteria of Akkermansia, Lactococcus, Oxalobacter, Sphaerochaeta, Paludibacter, Fibrobacter, Anaerovibrio, Pseudomonas, Mogibacterium, Pseudoramibacter_Eubacterium, YRC22, Flexispira, SMB53, AF12, and Roseburia genera were found under-presented and Oscillospira genus over-presented when G. duodenalis infection was present. Meanwhile, Cryptosporidium spp. and E. bieneusi co-infected animals showed lower relative abundance of Allobaculum, Rikenella, Shuttleworthia, Epulopiscium, Bilophila, Dorea, Fibrobacter, and TG5. Results demonstrate important interaction between the intestinal parasites and microbiota, and provide informative link for understanding the co-evolution of zoonotic pathogens and bacteria in domestic animals.

Rumen Epithelial Communities Share a Core Bacterial Microbiota: A Meta-Analysis of 16S rRNA Gene Illumina MiSeq Sequencing Datasets

In this meta-analysis, 17 rumen epithelial 16S rRNA gene Illumina MiSeq amplicon sequencing data sets were analyzed to identify a core rumen epithelial microbiota and core rumen epithelial OTUs shared between the different studies included. Sequences were quality-filtered and screened for chimeric sequences before performing closed-reference 97% OTU clustering, and de novo 97% OTU clustering. Closed-reference OTU clustering identified the core rumen epithelial OTUs, defined as any OTU present in ≥ 80% of the samples, while the de novo data was randomly subsampled to 10,000 reads per sample to generate phylum- and genus-level distributions and beta diversity metrics. 57 core rumen epithelial OTUs were identified including metabolically important taxa such as Ruminococcus, Butyrivibrio, and other Lachnospiraceae, as well as sulfate-reducing bacteria Desulfobulbus and Desulfovibrio. Two Betaproteobacteria OTUs (Neisseriaceae and Burkholderiaceae) were core rumen epithelial OTUs, in contrast to rumen content where previous literature indicates they are rarely found. Two core OTUs were identified as the methanogenic archaea Methanobrevibacter and Methanomethylophilaceae. These core OTUs are consistently present across the many variables between studies which include different host species, geographic region, diet, age, farm management practice, time of year, hypervariable region sequenced, and more. When considering only cattle samples, the number of core rumen epithelial OTUs expands to 147, highlighting the increased similarity within host species despite geographical location and other variables. De novo OTU clustering revealed highly similar rumen epithelial communities, predominated by Firmicutes, Bacteroidetes, and Proteobacteria at the phylum level which comprised 79.7% of subsampled sequences. The 15 most abundant genera represented an average of 54.5% of sequences in each individual study. These abundant taxa broadly overlap with the core rumen epithelial OTUs, with the exception of Prevotellaceae which were abundant, but not identified within the core OTUs. Our results describe the core and abundant bacteria found in the rumen epithelial environment and will serve as a basis to better understand the composition and function of rumen epithelial communities.

Rumen epithelial transcriptome and microbiome profiles of rumen epithelium and contents of beef cattle with and without liver abscesses

Abscess is the highest cause of liver condemnation and is estimated to cost the beef industry US$64 million annually. Fusobacterium necrophorum, commonly found in the bovine rumen, is the primary bacteria associated with liver abscess in cattle. Theoretically, damage to the rumen wall allows F. necrophorum to invade the bloodstream and colonize the liver. The objective of this study was to determine the changes in gene expression in the rumen epithelium and microbial populations adherent to the rumen epithelium and in the rumen contents of beef cattle with liver abscesses compared with those with no liver abscesses. Rumen epithelial tissue and rumen content were collected from 31 steers and heifers with liver abscesses and 30 animals with no liver abscesses. Ribonucleic acid (RNA) sequencing was performed on the rumen epithelium, and a total of 221 genes were identified as differentially expressed in the animals with liver abscesses compared with animals with no abscesses, after removal of genes that were identified as a result of interaction with sex. The nuclear factor kappa-light-chain enhancer of activated B cells signaling and interferon signaling pathways were significantly enriched in the differentially expressed gene (DEG) set. The majority of the genes in these pathways were downregulated in animals with liver abscesses. In addition, RNA translation and protein processing genes were also downregulated, suggesting that protein synthesis may be compromised in animals with liver abscesses. The rumen content bacterial communities were significantly different from the rumen wall epimural bacterial communities. Permutational multivariate analysis of variance (PERMANOVA) analysis did not identify global differences in the microbiome of the rumen contents but did identify differences in the epimural bacterial communities on the rumen wall of animals without and with liver abscesses. In addition, associations between DEG and specific bacterial amplicon sequence variants of epimural bacteria were observed. The DEG and bacterial profile on the rumen papillae identified in this study may serve as a method to monitor animals with existing liver abscesses or to predict those that are more likely to develop liver abscesses.

Comparing the Bacterial Community in the Gastrointestinal Tracts Between Growth-Retarded and Normal Yaks on the Qinghai-Tibetan Plateau

In ruminants, the bacterial community in the gastrointestinal tract (GIT) has an essential role in healthy growth. Examining the bacterial composition in the GIT between growth-retarded and normal yaks could improve our understanding of the role of microorganisms in yaks with growth retardation. In this study, eight male yaks with growth retardation were used as the growth-retarded yak (GRY) group, and another eight male growth normal yaks (GNYs) with the same breed and age were used as the GNY group. We compared the bacterial community in the rumen, duodenum, jejunum, ileum, cecum, and colon between GRY and GNY groups based on the 16S ribosomal RNA gene sequencing. Alpha-diversity revealed that the Shannon index in the duodenum and ileum of the GNY group was higher (P < 0.05) than that of the GRY group. However, the opposite trend was found in the jejunum and cecum. The principal coordinates analysis (PCoA) showed that the bacterial structure in all segments of GIT differed from each other between two groups. In the rumen, the relative abundances of Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-014, and Treponema 2 were higher (P < 0.05) in the GNY group as compared with the GRY group. However, the Christensenellaceae R-7 group exhibited an opposite trend. In the jejunum, compared with the GNY group, the unclassified Chitinophagaceae was enriched significantly (P < 0.05) in the GRY group. However, the unclassified Peptostreptococcaceae, Christensenellaceae R-7 group, and Lachnospiraceae NK3A20 group were enriched (P < 0.05) in the GNY group. In the ileum, the relative abundances of the Rikenellaceae RC9 gut group and Prevotellaceae UCG-004 were higher (P < 0.05) in the GNY group than those in the GRY group. In the cecum, the GNY group showed a higher (P < 0.05) relative abundance of Prevotellaceae UCG-003 as compared with the GRY group. In the colon, the relative abundances of Treponema 2 and unclassified Lachnospiraceae were slightly higher (0.05 < P < 0.10) in the GNY group than those in the GRY group. Overall, these results improve our knowledge about the bacterial composition in the GIT of growth-retarded and normal yaks, and regulating the bacterial community may be an effective solution to promote the compensatory growth of GRYs.

Ruminal microbiota-host interaction and its effect on nutrient metabolism

Rumen microbiota has a close and intensive interaction with the ruminants. Microbiota residing in the rumen digests and ferments plant organic matters into nutrients that are subsequently utilized by the host, making ruminants a unique group of animals that can convert plant materials indigestible by humans into high-quality animal protein as meat and milk. Many studies using meta-omics technologies have demonstrated the relationships between rumen microbiome and animal phenotypes associated with nutrient metabolism. Recently, the causality and physiological mechanisms underpinning the host-microbiota interactions have attracted tremendous research interest among researchers. This review discusses the host-microbiota interactions and the factors affecting these interactions in ruminants and provides a summary of the advances in research on animal husbandry. Understanding the microbiota composition, the functions of key bacteria, and the host-microbiota interaction is crucial for the development of knowledge-based strategies to enhance animal productivity and host health.

PacBio and Illumina MiSeq Amplicon Sequencing Confirm Full Recovery of the Bacterial Community After Subacute Ruminal Acidosis Challenge in the RUSITEC System

The impact of subacute rumen acidosis (SARA) on the rumen bacterial community has been frequently studied in in vivo trials. Here we investigated whether these alterations can be mirrored by using the rumen simulation technique (RUSITEC) as an in vitro model for this disease. We hypothezised that the bacterial community fully recovers after a subacute ruminal acidosis challenge. We combined a PacBio nearly full-length 16S rRNA gene analysis with 16S rRNA gene Illumina MiSeq sequencing of the V4 hypervariable region. With this hybrid approach, we aimed to get an increased taxonomic resolution of the most abundant bacterial groups and an overview of the total bacterial diversity. The experiment consisted of a control period I and a SARA challenge and ended after a control period II, of which each period lasted 5 d. Subacute acidosis was induced by applying two buffer solutions, which were reduced in their buffering capacity (SARA buffers) during the SARA challenge. Two control groups were constantly infused with the standard buffer solution. Furthermore, the two SARA buffers were combined with three different feeding variations, which differed in their concentrate-to-hay ratio. The induction of SARA led to a decrease in pH below 5.8, which then turned into a steady-state SARA. Decreasing pH values led to a reduction in bacterial diversity and richness. Moreover, the diversity of solid-associated bacteria was lower for high concentrate groups throughout all experimental periods. Generally, Firmicutes and Bacteroidetes were the predominant phyla in the solid and the liquid phase. During the SARA period, we observed a decrease in fibrolytic bacteria although lactate-producing and -utilizing families increased in certain treatment groups. The genera Lactobacillus and Prevotella dominated during the SARA period. With induction of the second control period, most bacterial groups regained their initial abundance. In conclusion, this in vitro model displayed typical bacterial alterations related to SARA and is capable of recovery from bouts of SARA. Therefore, this model can be used to mimic SARA under laboratory conditions and may contribute to a reduction in animal experiments.

Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment

Simple Summary

Recently, it has become apparent that the microbiome is essential to health and affects practically every aspect of physiology. The rumen contains highly dense and diverse microbial communities, which can impact health through their composition, diversity, and assembly. Nevertheless, the diversity and function of rumen microbes have not been fully described. Therefore, this study aims to identify differences in the functional attributes and metabolites of rumen microbiota to heat stress by metagenomics and metabolomics analyses. We observed differences in biological changes, as well as changes in rumen metabolites and metabolic pathways depending on the breed of cow. In addition, significant changes in rumen bacterial taxa and functional gene abundance were observed. Overall, the findings of this study improve our understanding of heat-vulnerable ruminal bacteria and related genes.

Abstract

The microbial community within the rumen can be changed and shaped by heat stress. Accumulating data have suggested that different breeds of dairy cows have differential heat stress resistance; however, the underlying mechanism by which nonanimal factors contribute to heat stress are yet to be understood. This study is designed to determine changes in the rumen microbiome of Holstein and Jersey cows to normal and heat stress conditions. Under heat stress conditions, Holstein cows had a significantly higher respiration rate than Jersey cows. Heat stress increased the rectal temperature of Holstein but not Jersey cows. In the Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis, Jersey cows had a significantly higher proportion of genes associated with energy metabolism in the normal condition than that with other treatments. Linear discriminant analysis effect size (LEfSe) results identified six taxa as distinguishing taxa between normal and heat stress conditions in Holstein cows; in Jersey cows, 29 such taxa were identified. Changes in the rumen bacterial taxa were more sensitive to heat stress in Jersey cows than in Holstein cows, suggesting that the rumen mechanism is different in both breeds in adapting to heat stress. Collectively, distinct changes in rumen bacterial taxa and functional gene abundance in Jersey cows may be associated with better adaptation ability to heat stress.

Effects of Dietary Energy Levels on Rumen Fermentation, Microbial Diversity, and Feed Efficiency of Yaks (Bos grunniens)

The microbial community of the yak (Bos grunniens) rumen plays an important role in surviving the harsh Tibetan environment where seasonal dynamic changes in pasture cause nutrient supply imbalances, resulting in weight loss in yaks during the cold season. A better understanding of rumen microbiota under different feeding regimes is critical for exploiting the microbiota to enhance feed efficiency and growth performance. This study explored the impact of different dietary energy levels on feed efficiency, rumen fermentation, bacterial community, and abundance of volatile fatty acid (VFA) transporter transcripts in the rumen epithelium of yaks. Fifteen healthy castrated male yaks were divided into three groups and fed with low (YL), medium (YM), and high energy (YH) levels diet having different NEg of 5.5, 6.2, and 6.9 MJ/kg, respectively. The increase in feed efficiency was recorded with an increase in dietary energy levels. The increase in dietary energy levels decreased the pH and increased the concentrations of acetate, propionate, butyrate, and valerate in yak rumens. The increase in the mRNA abundance of VFA transporter genes (MCT1, DRA, PAT1, and AE2) in the rumen epithelium of yaks was recorded as dietary energy level increased. High relative abundances of Firmicutes and Bacteroidetes were recorded with the increase in dietary energy levels. Significant population shifts at the genus level were recorded among the three treatments. This study provides new insights into the dietary energy-derived variations in rumen microbial community.

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.

Groundwater microbial diversity and antibiotic resistance linked to human population density in Yucatan Peninsula, Mexico

Microbial community composition in selected karst groundwater sites in the Yucatan Peninsula, Mexico, was assessed to determine the environmental variables influencing groundwater microbial diversity. The karst aquifer system is a groundwater-dependent ecosystem and is the world’s second largest underwater karst cave system. The area’s geology allows precipitation to infiltrate into the groundwater system and prevents accumulation of surface water; as such, groundwater is the only source of fresh water on the peninsula. The sampling locations consisted of three karst sinkholes that extend through the freshwater zone into the saline water, and an abandoned drinking water well of an ocean-side resort, during the dry and rainy seasons. The analysis showed that highly diverse microbial communities are present in the Yucatan groundwater, sustained by permanently warm temperatures and high nutrient input from human activity. Proximity to densely populated areas, such as tourist resorts, is the most important factor influencing both the diversity and presence of fecal bacteria and the antibiotic resistance profile.

Effect of extruded grain feed, with the preliminary germination of rapeseed, on the cicatricial digestion of dairy cows and calves

This article describes the scientific and production experience conducted in the Druzhba LLC, of the Buinsky district of the Republic of Tatarstan. The purpose of the scientific and production experiment is to study the effect of extruded feed, with the preliminary germination of rapeseed in a 0.05 % nicotinic acid solution, on the cicatricial digestion of calves and dairy cows. During the experiment, it is found that feeding calves and dairy cows with extruded feed with preliminary germination of rapeseed in a 0.05 % nicotinic acid solution had a positive effect on cicatricial digestion, contributing to an increase in ammonia to 8.7 and 7.9 %, acetic acid – 12, 6 and 11.5 % and propionic – 13.4 and 12.6 % acids, with a decrease in butyric acid – 12.8 and 10.4 %, an increase in the total microbial number – 8 4.0 and 16.3 %, in including cellulolytic bacteria – 11.6 and 14.3 %, ciliates – 13.4 and 12.9 %, as well as the enzymatic activity of cicatricial microflora, respectively accordingly, in comparison with the control and the group where the grain feed is subjected to only one extrusion. Thus, the use of extruded feed with pre-germinated rapeseed in feeding calves and dairy cows improved the underlying indices of cicatricial digestion compared with the control group of animals fed with non-extruded feed and the group of animals fed with extruded feed.

Temporal Dynamics in Rumen Bacterial Community Composition of Finishing Steers during an Adaptation Period of Three Months

The objective of this study was to explore whether collecting rumen samples of finishing steers at monthly intervals differed, and whether this difference or similarity varied with diets. For these purposes, 12 Chinese Holstein steers were equally divided into two groups. The dietary treatments were either standard energy and standard protein (C) or low energy and low protein (L). Rumen samples were obtained on day 30, day 60 and day 90 from both dietary treatments and were analyzed by using 16S rRNA gene sequencing. The results showed that monthly intervals had no effect on the richness and evenness of the rumen bacterial community in the two diets. However, taxonomic difference analysis (relative abundance >0.5%) revealed that the relative abundance of three phyla (Proteobacteria, Fibrobacteres and Cyanobacteria) and six genera (Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, Fibrobacter, Eubacterium_coprostanoligenes_group, Ruminococcaceae_UCG-010 and Ruminobacter) were significantly different between monthly sampling intervals, and the difference was prominent between sampling in the first month and the subsequent two months. Moreover, the differences in abundances of phyla and genera between monthly sampling intervals were affected by diets. Analysis of similarity (ANOSIM) showed no significant differences between monthly sampling intervals in the C diet. However, ANOSIM results revealed that significant differences between the first month and second month and between the first month and third month were present in the L diet. These results indicated that temporal dynamics in rumen bacterial community composition did occur even after an adaptation period of three months. This study tracked the changes in rumen bacterial populations of finishing cattle after a shift in diet with the passage of time. This study may provide insight into bacterial adaptation time to dietary transition in finishing steers.

Comparison of gut microbiota diversity between wild and captive bharals (Pseudois nayaur)

Background

Gastrointestinal microbiota play an important role in animal host immunity, nutrient metabolism, and energy acquisition, and have therefore drawn increasing attentions. This study compared the diversity of the gut microbiota of both wild and captive bharals, which is an ungulate herbivore of caprid from the Qinghai-Tibet plateau.

Results

The sequencing of the V4-V5 region of the 16S rRNA gene via high-throughput sequencing technology showed that the dominant bacterial phyla are Firmicutes and Bacteroides both in wild and captive bharals. However, their abundance differed significantly between groups. Firmicutes were significantly higher in wild bharals, while Bacteroides were significantly higher in captive bharals. Different diets are likely a key influencing factor in the diversity and abundance of gut microbiota in bharals.

Conclusions

Changes in diets affect the diversity of gut microbiota and the relative abundance of pathogenic bacteria, increasing the risk of diseases outbreak in captive bharals. The results of this study suggest that the structure and function of the gut microbiota should be regulated via dietary intervention, accurate provision of an individualized diet, and optimization of the functional network of gut microbiota and its interaction with the host. This will improve the ex situ protection of wild animals.

Temporal Stability of the Ruminal Bacterial Communities in Beef Steers

Nutritional studies involving ruminants have traditionally relied on relatively short transition or wash-out periods between dietary treatments, typically two to four weeks. However, little is known about adequate adaptation periods required to reach stabilization of the rumen microbiome that could provide more accurate results from nutritional studies in ruminants. This study determined the rumen bacterial communities and rumen environment parameters over ten weeks following transition from a forage-based to concentrate-based diet. Several α-diversity metrics, including observed OTUs and Simpson’s Evenness fluctuated throughout the trial, but were typically either greatest (observed OTUs) or lowest (Simpson’s) at week 5 of the trial contrasted from weeks 1 and 10 (P < 0.05). At week 4, several orders associated with the shift to the final bacterial community composition, including Pasteurellales, Aeromonadales, and Bacteroidales. At week 5, rumen pH was correlated with α-diversity (P = 0.005) and predictive of the rumen microbiome signature at week 10 (R² = 0.48; P = 0.04). Rumen microbiome stability did not occur until approximately 9 weeks following adaptation to the diet and was associated with changes in specific bacterial populations and rumen environment. The results of this study suggest that adaptation and wash-out periods must be re-evaluated in order to accommodate necessary rumen microbiome acclimation.

β-Defensins: Farming the Microbiome for Homeostasis and Health

Diverse commensal populations are now regarded as key to physiological homeostasis and protection against disease. Although bacteria are the most abundant component of microbiomes, and the most intensively studied, the microbiome also consists of viral, fungal, archael, and protozoan communities, about which comparatively little is known. Host-defense peptides (HDPs), originally described as antimicrobial, now have renewed significance as curators of the pervasive microbial loads required to maintain homeostasis and manage microbiome diversity. Harnessing HDP biology to transition away from non-selective, antibiotic-mediated treatments for clearance of microbes is a new paradigm, particularly in veterinary medicine. One family of evolutionarily conserved HDPs, β-defensins which are produced in diverse combinations by epithelial and immune cell populations, are multifunctional cationic peptides which manage the cross-talk between host and microbes and maintain a healthy yet dynamic equilibrium across mucosal systems. They are therefore key gatekeepers to the oral, respiratory, reproductive and enteric tissues, preventing pathogen-associated inflammation and disease and maintaining physiological normality. Expansions in the number of genes encoding these natural antibiotics have been described in the genomes of some species, the functional significance of which has only recently being appreciated. β-defensin expression has been documented pre-birth and disruptions in their regulation may play a role in maladaptive neonatal immune programming, thereby contributing to subsequent disease susceptibility. Here we review recent evidence supporting a critical role for β-defensins as farmers of the pervasive and complex prokaryotic ecosystems that occupy all body surfaces and cavities. We also share some new perspectives on the role of β-defensins as sensors of homeostasis and the immune vanguard particularly at sites of immunological privilege where inflammation is attenuated.

Urea plus nitrate pretreatment of rice and wheat straws enhances degradation and reduces methane production in in vitro ruminal culture

BACKGROUND

Urea pretreatment of straw damages fiber structure, while nitrate supplementation of ruminal diets inhibits enteric methane production. The study examined the combined effects of these treatments on ruminal substrate biodegradation and methane production using an in vitro incubation system. Rice and wheat straws were pretreated with urea (40 g kg^-1 straw dry matter, DM) and urea + ammonium nitrate (34 + 6 g kg^-1 dry matter (DM), respectively), and each straw (control, urea, urea+nitrate) was used in batch culture incubations in three replications (runs).

RESULTS

Urea pretreatment increased (P < 0.05) neutral-detergent solubles (NDS) content (+17%) and in vitro DM degradation of rice straw, in comparison with control. Urea+nitrate pretreatment of rice and wheat straws had higher (P < 0.05) NDS content, in vitro DM degradation and propionate molar proportion, and lower (P < 0.05) acetate:propionate ratio and lower methane production with a decline of methanogens, in comparison to control.

CONCLUSIONS

Urea+nitrate pretreatment combines positive effects of urea pretreatment and nitrate supplementation, and can be a potential strategy to improve ruminal biodegradation, facilitate propionate production and reduce methane production from lignified straws. © 2018 Society of Chemical Industry.

Comparisons of bacterial and archaeal communities in the rumen and a dual-flow continuous culture fermentation system using amplicon sequencing

Dual-flow continuous culture (CC) fermenters are commonly used to study rumen fermentation in vitro. Research using culture-based and oligonucleotide techniques has shown that certain microbial populations within fermenters may be maintained at abundances similar to those observed in vivo. In this study, bacterial and archaeal communities in the rumen of dairy cattle and in a dual-flow CC fermentation system were compared using high-throughput amplicon sequencing targeting the V4 hypervariable region of 16S rRNA. We hypothesized that the in vitro system harbored a comparable bacterial and archaeal community to that observed in the rumen. Members of the Bacteroidetes and Firmicutes made up the 2 most abundant phyla in the rumen, inoculum, and fermenters and did not differ among sample types (P > 0.10). Similarly, Prevotellaceae, the most abundant family in all 3 sample types, did not differ based on source (P = 0.80). However, beta diversity analyses revealed that bacterial and archaeal communities differed between fermenters and rumen samples (P ≤ 0.001), but fermenter bacterial and archaeal communities stabilized by day 4 of each period. While the overall bacterial and archaeal community differs between natural rumens and those detected in in vitro fermenter systems, several prominent taxa were maintained at similar relative abundances suggesting that fermenters may provide a suitable environment in which to study shifts among the predominant members of the microbial community.

Influence of short-term dietary starch inclusion on the equine cecal microbiome

The objective of this study was to determine bacterial community profiles of the equine cecum in response to abrupt inclusion of varying levels of dietary starch. Seven cecally cannulated Quarter Horse geldings (497 to 580 kg) were used in a crossover design with two 28-d periods and a 28-d washout between each. Horses were randomly assigned to dietary treatments consisting of a commercial concentrate offered as fed at either 0.6 (low starch [LS]) or 1.2% BW (high starch [HS]) daily that was divided into 2 meals at 12-h intervals. Prior to the start of each period, horses were allowed ad libitum access to coastal bermudagrass () hay. Concentrate was fed on d 1 with no adaptation. Cecal fluid was collected on d 1 at h 0 and at 3, 6, 9, and 12 h relative to the initial concentrate meal on d 1. Additional samples were collected 6 h after feeding on d 2, 3, and 7 of each period. Cecal contents were used to determine pH and VFA concentrations and extract microbial DNA. The V4 through V6 region of 16S rRNA gene was amplified using PCR and sequenced on the Roche 454 FLX platform. Sequence analysis was performed with QIIME, and data were analyzed using the MIXED procedure of SAS. Cecal pH tended to decrease ( = 0.09) in horses fed HS in the first 12 h after the first concentrate meal and remained lower ( ≤ 0.05) the following 7 d. Total VFA were greater ( ≤ 0.05) in horses fed HS in the initial 12 h and 7 d after addition of concentrate. Species richness determined using the Chao1 index was unchanged ( > 0.20) over the initial 12 h and decreased ( = 0.01) over 7 d for both treatments. Community diversity determined using the Shannon index tended to decrease ( = 0.06) over the 7 d. Relative abundances of Paraprevotellaceae were greater ( ≤ 0.05) in HS in the first 12 h. Over 7 d, relative abundances of Paraprevotellaceae, Veillonellaceae, and Succinivibrionaceae were greater ( ≤ 0.05) in HS compared with LS. Abrupt and short-term exposure to dietary starch does alter cecal fermentation and microbial community structure in horses, but the impact on horse health is unknown.

Rhubarb Supplementation Promotes Intestinal Mucosal Innate Immune Homeostasis through Modulating Intestinal Epithelial Microbiota in Goat Kids

The abuse and misuse of antibiotics in livestock production pose a potential health risk globally. Rhubarb can serve as a potential alternative to antibiotics, and several studies have looked into its anticancer, antitumor, and anti-inflammatory properties. The aim of this study was to test the effects of rhubarb supplementation to the diet of young ruminants on innate immune function and epithelial microbiota in the small intestine. Goat kids were fed with a control diet supplemented with or without rhubarb (1.25% DM) and were slaughtered at days 50 and 60 of age. Results showed that the supplementation of rhubarb increased ileal villus height (P = 0.036), increased jejujal and ileal anti-inflammatory IL-10 production (P < 0.05), increased jejunal and ileal Claudin-1 expression at both mRNA and protein levels (P < 0.05), and decreased ileal pro-inflammatory IL-1β production (P < 0.05). These changes in innate immune function were accompanied by shifts in ileal epithelial bacterial ecosystem in favor of Blautia, Clostridium, Lactobacillus, and Pseudomonas, and with a decline in the relative abundance of Staphylococcus (P < 0.001) when rhubarb was supplemented. Additionally, age also affected (P < 0.05) crypt depth, cytokine production, Claudin-1 expression and relative abundances of specific genera in epithelial bacteria. Collectively, the supplementation of rhubarb could enhance host mucosal innate immune homeostasis by modulating intestinal epithelial microbiota during the early stages of animal development.

Transcriptome analysis of ruminal epithelia revealed potential regulatory mechanisms involved in host adaptation to gradual high fermentable dietary transition in beef cattle

Background

The transition from a high forage to a highly fermentable diet can induce digestive disorders in the rumen. To date, the host mechanisms that regulate the adaption to such dietary transition are largely unknown. To understand the molecular mechanisms involved in such phenomena, RNA-sequencing was performed to identify the changes in the transcriptome of ruminal epithelia during gradual transition from a diet containing 0% to 89% grain.

Results

In total, the expression of 11,044, 11,322 and 11,282 genes were detected in ruminal epithelia of beef heifers (n = 15) fed 0%, 72% and 89% barley grain diet, respectively. The transcriptome profiles of rumen epithelia differed between low grain diet (LGD) (0% grain) and high grain diet (HGD) (72% and 89%), and HGD tended to reduce the expression of genes involved in epithelial catalytic and binding activities. When diet was changed from 72% to 89% grain, the mean ruminal pH change was significantly different among individual heifers with five of them decreased (down group (DG); from 6.30±0.09 to 5.87±0.15, P < 0.01) and five of them increased (up group (UG); from 5.84±0.42 to 6.35±0.37, P < 0.05). The functional analysis of differentially expressed (DE) genes revealed inhibited “Immune response of leukocytes”, “Attraction of phagocytes”, and “Cell movement of leukocytes” (P < 0.05) functions (Z-score = −2.2, −2.2 and −2.0, respectively) in DG, and inhibited “Concentration of lipid” and “Proliferation of epithelial cells” functions in UG (Z-score = −2.0, and −1.8, respectively). In addition, the expression of genes involved in ketogenesis (HMGCL) and lipid synthesis (SREBF2, FABP4) was increased in DG, while the expression of ketogenesis (ACAT2, HMGCS) and cholesterol synthesis related genes (HMGC and FDPS) were deceased in UG. Furthermore, the upstream regulators were found to be involved in the regulation of immune response and cell cycle progress, and SNP (g.46834311A > G) in FABP4 was identified between two groups of animals (P < 0.1).

Conclusion

The identified genes, upstream regulators, and SNP could be potential genetic markers that may account for the varied individual ruminal pH responses to the dietary transition stress.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4317-y) contains supplementary material, which is available to authorized users.

The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle

BACKGROUND

The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal gut will have a major role in reducing the contribution of animal production to this problem. Here, the influence of diet on the ruminal resistome and abundance of pathogenicity genes was assessed in ruminal digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions of concentrate.

RESULTS

Two hundred and four genes associated with antimicrobial resistance (AMR), colonisation, communication or pathogenicity functions were identified from 4966 metagenomic genes using KEGG identification. Both the diversity and abundance of these genes were higher in concentrate-fed animals. Chloramphenicol and microcin resistance genes were dominant in samples from forage-fed animals (P < 0.001), while aminoglycoside and streptomycin resistances were enriched in concentrate-fed animals. The concentrate-based diet also increased the relative abundance of Proteobacteria, which includes many animal and zoonotic pathogens. A high ratio of Proteobacteria to (Firmicutes + Bacteroidetes) was confirmed as a good indicator for rumen dysbiosis, with eight cases all from concentrate-fed animals. Finally, network analysis demonstrated that the resistance/pathogenicity genes are potentially useful as biomarkers for health risk assessment of the ruminal microbiome.

CONCLUSIONS

Diet has important effects on the complement of AMR genes in the rumen microbial community, with potential implications for human and animal health.

A High Grain Diet Dynamically Shifted the Composition of Mucosa-Associated Microbiota and Induced Mucosal Injuries in the Colon of Sheep

This study investigated the dynamic shifts in mucosa-associated microbiota composition and mucosal morphology in the colon of sheep fed a high grain (HG) diet. A total of 20 male sheep were randomly assigned to four groups (n = 5 for each). The sheep in first group received hay diet. The animals in other 3 groups were fed an HG diet for 7 (HG7), 14 (HG14), or 28 (HG28) days, respectively. Colonic digesta samples were collected to determine the pH and the concentrations of volatile fatty acid (VFA) and lactate. The colonic mucosa was sampled to characterize the bacterial communities using Illumina MiSeq sequencing and to determine mRNA expression levels of cytokines and tight junction protein genes using quantitative real-time PCR. As time advanced, results revealed that colonic pH linearly decreased (P = 0.007), and the concentrations of total VFA linearly increased (P < 0.001). Microbial analysis showed that an HG diet linearly reduced (P < 0.050) the diversity and richness of the colonic microbiota. The principal coordinate analysis results showed that the colonic mucosa-associated bacterial communities of the four groups significantly shifted with number of days fed an HG diet. At the genus level, HG feeding significantly increased the relative abundance of some taxa including Prevotella, Coprococcus, Roseburia, and Clostridium_sensu_stricto_1, and decreased the proportion of Treponema, and the percentage of these taxa was not affected by days fed an HG diet. The microscopic examination showed that HG feeding caused the mucosal epithelial injury. The RT-PCR results showed that the mRNA expression of claudin-1 (P = 0.038), IL-1β (P = 0.045), IL-6 (P = 0.050), and TNF-α (P = 0.020) increased linearly with number of days fed an HG diet. The correlation analysis revealed significant correlation between the colonic mucosal mRNA expression of cytokines and mucosal bacterial composition. Generally, HG feeding increased colonic fermentation and altered colonic mucosal bacterial communities, which eventually caused colonic mucosal damage and led to colonic dysfunction, and these changes occurred gradually over at least 4 weeks.

Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method

Advances in high throughput, next generation sequencing technologies have allowed an in-depth examination of biological environments and phenomena, and are particularly useful for culture-independent microbial community studies. Recently the use of RNA for metatranscriptomic studies has been used to elucidate the role of active microbes in the environment. Extraction of RNA of appropriate quality is critical in these experiments and TRIzol reagent is often used for maintaining stability of RNA molecules during extraction. However, for studies using rumen content there is no consensus on (1) the amount of rumen digesta to use or (2) the amount of TRIzol reagent to be used in RNA extraction procedures. This study evaluated the effect of using various quantities of ground rumen digesta and of TRIzol reagent on the yield and quality of extracted RNA. It also investigated the possibility of using lower masses of solid-phase rumen digesta and lower amounts of TRIzol reagent than is used currently, for extraction of RNA for metatranscriptomic studies. We found that high quality RNA could be isolated from 2 g of ground rumen digesta sample, whilst using 0.6 g of ground matter for RNA extraction and using 3 mL (a 5:1 TRIzol : extraction mass ratio) of TRIzol reagent. This represents a significant savings in the cost of RNA isolation. These lower masses and volumes were then applied in the RNA-Seq analysis of solid-phase rumen samples obtained from 6 Angus X Hereford beef heifers which had been fed a high forage diet (comprised of barley straw in a forage-to-concentrate ratio of 70:30) for 102 days. A bioinformatics analysis pipeline was developed in-house that generated relative abundance values of archaea, protozoa, fungi and bacteria in the rumen and also allowed the extraction of individual rRNA variable regions that could be analyzed in downstream molecular ecology programs. The average relative abundances of rRNA transcripts of archaea, bacteria, protozoa and fungi in our samples were 1.4 ± 0.06, 44.16 ± 1.55, 35.38 ± 1.64, and 16.37 ± 0.65% respectively. This represents the first study to define the relative active contributions of these populations to the rumen ecosystem and is especially important in defining the role of the anaerobic fungi and protozoa.

High-grain diets altered rumen fermentation and epithelial bacterial community and resulted in rumen epithelial injuries of goats

This study evaluated the effects of high-grain diets on the rumen fermentation, epithelial bacterial community, morphology of rumen epithelium, and local inflammation of goats during high-grain feeding. Twelve 8-month-old goats were randomly assigned to two different diets, a hay diet or a high-grain diet (65% grain, HG). At the end of 7 weeks of treatment, samples of rumen content and rumen epithelium were collected. Rumen pH was lower (P < 0.05), but the levels of volatile fatty acids and lipopolysaccharides were higher (P < 0.05) in the HG group than those in the hay group. The principal coordinate analysis indicated that HG diets altered the rumen epithelial bacterial community, with an increase in the proportion of genus Prevotella and a decrease in the relative abundance of the genera Shuttleworthia and Fibrobacteres. PICRUSt analysis suggested that the HG-fed group had a higher (P < 0.05) relative abundance of gene families related to energy metabolism; folding, sorting, and degradation; translation; metabolic diseases; and immune system. Furthermore, HG feeding resulted in the rumen epithelial injury and upregulated (P < 0.05) the gene expressions of IL-1β and IL-6, and the upregulations were closely related to the rumen pH, LPS level, and rumen epithelial bacteria abundance. In conclusion, our results indicated that the alterations in the rumen environment and epithelial bacterial community which were induced by HG feeding may result in the damage and local inflammation in the rumen epithelium, warranting further study of rumen microbial-host interactions in the HG feeding model.

Changes in Metabolically Active Bacterial Community during Rumen Development, and Their Alteration by Rhubarb Root Powder Revealed by 16S rRNA Amplicon Sequencing

The objective of this present study was to explore the initial establishment of metabolically active bacteria and subsequent evolution in four fractions: rumen solid-phase (RS), liquid-phase (RL), protozoa-associated (RP), and epithelium-associated (RE) through early weaning and supplementing rhubarb root powder in 7 different age groups (1, 10, 20, 38, 41, 50, and 60 d) during rumen development. Results of the 16S rRNA sequencing based on RNA isolated from the four fractions revealed that the potentially active bacterial microbiota in four fractions were dominated by the phyla Proteobacteria, Firmicutes, and Bacteroidetes regardless of different ages. An age-dependent increment of Chao 1 richness was observed in the fractions of RL and RE. The principal coordinate analysis (PCoA) indicated that samples in four fractions all clustered based on different age groups, and the structure of the bacterial community in RE was distinct from those in other three fractions. The abundances of Proteobacteria decreased significantly (P < 0.05) with age, while increases in the abundances of Firmicutes and Bacteroidetes were noted. At the genus level, the abundance of the predominant genus Mannheimia in the Proteobacteria phylum decreased significantly (P < 0.05) after 1 d, while the genera Quinella, Prevotella, Fretibacterium, Ruminococcus, Lachnospiraceae NK3A20 group, and Atopobium underwent different manners of increases and dominated the bacterial microbiota across four fractions. Variations of the distributions of some specific bacterial genera across fractions were observed, and supplementation of rhubarb affected the relative abundance of various genera of bacteria.

Understanding host-microbial interactions in rumen: searching the best opportunity for microbiota manipulation

Ruminants utilize a wide variety of dietary substrates that are not digestible by the mammals, through microbial fermentation taking place in the rumen. Recent advanced molecular based approaches have allowed the characterization of rumen microbiota and its compositional changes under various treatment conditions. However, the knowledge is still limited on the impacts of variations in the rumen microbiota on host biology and function. This review summarizes the information to date on host-microbial interactions in the rumen and how we can apply such information to seek the opportunities to enhance the animal performance through manipulating the rumen function.