Factors that alter rumen microbial ecology

Supplementary feeding of cattle-yak in the cold season alters rumen microbes, volatile fatty acids, and expression of SGLT1 in the rumen epithelium

Cattle-yak, a hybrid offspring of yak (Bos grunniens) and cattle (Bos taurus), inhabit the Qinghai-Tibet Plateau at an altitude of more than 3,000 m and obtain nutrients predominantly through grazing on natural pastures. Severe shortages of pasture in the cold season leads to reductions in the weight and disease resistance of grazing cattle-yak, which then affects their production performance. This study aimed to investigate the effect of supplementary feeding during the cold season on the rumen microbial community of cattle-yak. Six cattle-yak (bulls) were randomly divided into two groups-"grazing + supplementary feeding" (G+S) (n = 3) and grazing (G) (n = 3)-and rumen microbial community structure (based on 16S rRNA sequencing), volatile fatty acids (VFAs), and ruminal epithelial sodium ion-dependent glucose transporter 1 (SGLT1) expression were assessed. There were significant differences in the flora of the two groups at various taxonomic classification levels. For example, Bacteroidetes, Rikenellaceae, and Rikenellaceae_RC9_gut_group were significantly higher in the G+S group than in the G group (P < 0.05), while Firmicutes and Christensenellaceae_R-7_group were significantly lower in the G+S group than in the G group (P < 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) analyses revealed that functions related to carbohydrate metabolism and energy production were significantly enriched in the G+S group (P < 0.05). In addition, the concentration of total VFAs, along with concentrations of acetate, propionate, and butyrate, were significantly higher in the G+S group than in the G group (P < 0.05). Furthermore, SGLT1 expression in ruminal epithelial tissue was significantly lower in the G+S group (P < 0.01). Supplementary feeding of cattle-yak after grazing in the cold season altered the microbial community structure and VFA contents in the rumen of the animals, and decreased ruminal epithelial SGLT1 expression. This indicated that supplementary feeding after grazing aids rumen function, improves adaptability of cattle-yak to the harsh environment of the Qinghai-Tibet Plateau, and enhances ability of the animals to overwinter.

Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle

Domestication and subsequent selection of cattle to form breeds and biological types that can adapt to different environments partitioned ancestral genetic diversity into distinct modern lineages. Genome-wide selection particularly for adaptation to extreme environments left detectable signatures genome-wide. We used high-density genotype data for 42 cattle breeds and identified the influence of Bos grunniens and Bos javanicus on the formation of Chinese indicine breeds that led to their divergence from India-origin zebu. We also found evidence for introgression, admixture, and migration in most of the Chinese breeds. Selection signature analyses between high-altitude (≥1800 m) and low-altitude adapted breeds (<1500 m) revealed candidate genes (ACSS2, ALDOC, EPAS1, EGLN1, NUCB2) and pathways that are putatively involved in hypoxia adaptation. Immunohistochemical, real-time PCR and CRISPR/cas9 ACSS2-knockout analyses suggest that the up-regulation of ACSS2 expression in the liver promotes the metabolic adaptation of cells to hypoxia via the hypoxia-inducible factor pathway. High altitude adaptation involved the introgression of alleles from high-altitude adapted yaks into Chinese Bos taurus taurus prior to their formation into recognized breeds and followed by selection. In addition to selection, adaptation to high altitude environments has been facilitated by admixture and introgression with locally adapted cattle populations.

Transcriptomic analysis reveals the molecular mechanisms of rumen wall morphological and functional development induced by different solid diet introduction in a lamb model

Background

This study aimed to elucidate the molecular mechanisms of solid diet introduction initiating the cellular growth and maturation of rumen tissues and characterize the shared and unique biological processes upon different solid diet regimes.

Methods

Twenty-four Hu lambs were randomly allocated to three groups fed following diets: goat milk powder only (M, n = 8), goat milk powder + alfalfa hay (MH, n = 8), and goat milk powder + concentrate starter (MC, n = 8). At 42 days of age, the lambs were slaughtered. Ruminal fluid sample was collected for analysis of concentration of volatile fatty acid (VFA) and microbial crude protein (MCP). The sample of the rumen wall from the ventral sac was collected for analysis of rumen papilla morphology and transcriptomics.

Results

Compared with the M group, MH and MC group had a higher concentration of VFA, MCP, rumen weight, and rumen papilla area. The transcriptomic results of rumen wall showed that there were 312 shared differentially expressed genes (DEGs) between in “MH vs. M” and “MC vs. M”, and 232 or 796 unique DEGs observed in “MH vs. M” or “MC vs. M”, respectively. The shared DEGs were most enriched in VFA absorption and metabolism, such as peroxisome proliferator-activated receptor (PPAR) signaling pathway, butanoate metabolism, and synthesis and degradation of ketone bodies. Additionally, a weighted gene co-expression network analysis identified M16 (2,052 genes) and M18 (579 genes) modules were positively correlated with VFA and rumen wall morphology. The M16 module was mainly related to metabolism pathway, while the M18 module was mainly associated with signaling transport. Moreover, hay specifically depressed expression of genes involved in cytokine production, immune response, and immunocyte activation, and concentrate starter mainly altered nutrient transport and metabolism, especially ion transport, amino acid, and fatty acid metabolism.

Conclusions

The energy production during VFA metabolism may drive the rumen wall development directly. The hay introduction facilitated establishment of immune function, while the concentrate starter enhanced nutrient transport and metabolism, which are important biological processes required for rumen development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-021-00556-4.

Cnidoscolus aconitifolius leaf pellet can manipulate rumen fermentation characteristics and nutrient degradability

Objective

Chaya (Cnidoscolus aconitifolius) leaf has been found to be an important source of protein, vitamins, minerals, as well as phytonutrients. The present study aimed to evaluate the effect of Chaya leaf pellet (CHYP) with various level of crude protein (CP) in the concentrate on rumen fermentation characteristics and nutrient degradability in in vitro gas production technique.

Methods

In an in vitro rumen fermentation study the dietary treatments were arranged according to a 3×5 factorial arrangement in a completely randomized design, consisting of Factor A: three levels of CP of concentrate mixtures (14%, 16%, and 18% CP, respectively) and Factor B: five levels of CHYP supplementation (at 0%, 2%, 4%, 6%, and 8% of dry matter substrates).

Results

The gas production kinetics, fraction (a) and fraction (b) were lower (p<0.05) with an increasing CHYP addition. Additionally, the fraction (a+b) was found to yield a significant interaction (p<0.05) while the fraction (c) was not impacted by CHYP addition. However, in vitro DM degradability was enhanced and interactive (p<0.05), using 16% CP of concentrate with 6% and 8% CHYP, when compared with 18% CP in the non-addition. Additionally, the treatment with higher CP of the concentrate was higher in NH₃-N concentration (p<0.001) and by CHYP supplementation group (p<0.05). Nevertheless, protozoal counts in the rumen were remarkably decreased (p<0.05) with increasing level of CHYP supplementation. Furthermore, rumen C₂ concentration was lower (p<0.05) in the treatments with CHYP supplementation, while C₃ was significantly increased and interactive (p<0.05) between levels of CP and CHYP supplementation especially at 8% CHYP supplementation.

Conclusion

Based on this study, the results revealed CHYP as a promising feed supplement to enhance rumen fermentation and to mitigate methane production. However, in vivo feeding experiments should be subsequently conducted to elucidate the effect of CHYP supplementation on rumen fermentation, as well as ruminant production efficiency.

Gossypol Exhibited Higher Detrimental Effect on Ruminal Fermentation Characteristics of Low-Forage in Comparison with High-Forage Mixed Feeds

Gossypol is a key anti-nutritional factor which limits the feeding application of cottonseed by-products in animal production. A 2 × 4 factorial in vitro experiment was conducted to determine the effect of gossypol addition levels of 0, 0.25, 0.5, and 0.75 mg/g on ruminal fermentation of a high-forage feed (HF, Chinese wildrye hay/corn meal = 3:2) in comparison with a low-forage feed (LF, Chinese wildrye hay/corn meal = 2:3). After 48 h of incubation, in vitro dry matter disappearance was greater in the LF than the HF group, while the cumulative gas production and asymptotic gas production were greater in the HF than the LF group (p < 0.05). Regardless of whatever ration type was incubated, the increasing gossypol addition did not alter in vitro dry matter disappearance. The asymptotic gas production, cumulative gas production, molar percentage of CO₂ and H₂ in fermentation gases, and microbial protein in cultural fluids decreased with the increase in the gossypol addition. Conversely, the gossypol addition increased the molar percentage of CH₄, ammonia N, and total volatile fatty acid production. More than 95% of the gossypol addition disappeared after 48 h of in vitro incubation. Regardless of whatever ration type was incubated, the real-time PCR analysis showed that the gossypol addition decreased the populations of Fibrobactersuccinogenes, Ruminococcus albus, Butyrivibrio fibrisolvens, Prevotella ruminicola, Selenomonas ruminantium, and fungi but increased Ruminococcus flavefaciens, protozoa, and total bacteria in culture fluids in comparison with the control (p < 0.01). Additionally, the tendency of a smaller population was observed for R. albus, B. fibrisolvens, and fungi with greater inclusion of gossypol, but a greater population was observed for F. succinogenes, R. flavefaciens, S. ruminantium, protozoa, and total bacteria. In summary, the present results suggest that rumen microorganisms indeed presented a high ability to degrade gossypol, but there was an obvious detrimental effect of the gossypol addition on rumen fermentation by decreasing microbial activity when the gossypol inclusion exceeded 0.5 mg/g, and such inhibitory effect was more pronounced in the low-forage than the high-forage group.

Metagenomic analysis reveals significant differences in microbiome and metabolic profiles in the rumen of sheep fed low N diet with increased urea supplementation

Urea is a cost-effective replacement for feed proteins in ruminant diets. However, its metabolism by the rumen microbiome is not fully understood. Here, rumen contents were collected from 18 male sheep fed one of the following three treatments: a low N basal diet with no urea (UC, 0 g/kg dry matter (DM)), low urea (LU, 10 g/kg DM) and high urea (HU, 30 g/kg DM). Principal coordinate analysis showed that the microbial composition and functional profiles of the LU treatment significantly differed from the UC and HU treatments. The genera Prevotella, Succinivibrio, Succinatimonas and Megasphaera were higher in the LU rumen, while the genera Clostridium, Ruminococcus and Butyrivibrio were enriched in the UC and HU rumen. The aspartate-glutamate and arginine-proline metabolic pathways and valine, leucine and isoleucine biosynthesis were higher in the LU rumen. The cysteine and methionine metabolism, lysine degradation and fructose and pentose phosphate metabolism pathways were higher in the UC and HU rumen. The protozoa population in the HU treatment was higher than in the UC and LU treatments. These findings suggest that the rumen microbiome of sheep fed low N diet with different urea supplementation are significantly different.

Effects of Saccharomyces cerevisiae fermentation products and subacute ruminal acidosis on feed intake, fermentation, and nutrient digestibilities in lactating dairy cows

Effects of Saccharomyces cerevisiae fermentation products (SCFP) and subacute ruminal acidosis (SARA) on rumen and hindgut fermentation, feed intake, and total tract nutrient digestibilities were determined in 32 lactating Holstein cows between weeks 4 and 9 of lactation. Treatments included control, 14 g·d−1 Diamond V Original XPC™ (SCFPa; Diamond V, Cedar Rapids, IA, USA), 19 g·d−1 NutriTek® (SCFPb-1X; Diamond V), and 38 g·d−1 NutriTek® (SCFPb-2X; Diamond V). During weeks 5 and 8, SARA challenges were conducted by switching from a 18.6% to a 27.9% dry matter (DM) starch diet. This reduced the rumen and feces pH. The durations of the rumen pH below 5.6 during these challenges averaged 175.0, 233.8, 246.9, and 79.3 min·d−1 for the control, SCFPa, SCFPb-1X, and SCFPb-2X treatments, respectively. Hence, SARA was not induced under the SCFPb-2X treatment. The feces pH during the SARA challenges was lowest during SCFPb-2X, suggesting this treatment shifted fermentation from the rumen to the hindgut. The SARA challenges reduced the total tract digestibility of DM, neutral detergent fiber digestibility (NDFd), and phosphorus, but tended to increase that of starch. The SCFPb-2X treatment increased the NDFd from 52.7% to 61.8% (P < 0.05). The SCFPb-2X treatment attenuated impacts of SARA.

Dynamic progression of the calf's microbiome and its influence on host health

The first year of a calf's life is a critical phase as its digestive system and immunity are underdeveloped. A high level of stress caused by separation from mothers, transportation, antibiotic treatments, dietary shifts, and weaning can have long-lasting health effects, which can reduce future production parameters, such as milk yield and reproduction, or even increase the mortality of calves. The early succession of microbes throughout the gastrointestinal tract of neonatal calves follows a sequential pattern of colonisation and is greatly influenced by their physiological state, age, diet, and environmental factors; this leads to the establishment of region- and site-specific microbial communities. This review summarises the current information on the various potential factors that may affect the early life microbial colonisation pattern in the gastrointestinal tract of calves. The possible role of host-microbe interactions in the development and maturation of host gut, immune system, and health are described. Additionally, the possibility of improving the health of calves through gut microbiome modulation and using antimicrobial alternatives is discussed. Finally, the trends, challenges, and limitations of the current research are summarised and prospective directions for future studies are highlighted.

Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas

BACKGROUND

Adaptive shifts in gut microbiome composition are one route by which animals adapt to seasonal changes in food availability and diet. However, outside of dietary shifts, other potential environmental drivers of gut microbial composition have rarely been investigated, particularly in organisms living in their natural environments.

RESULTS

Here, we generated the largest wild nonhuman primate gut microbiome dataset to date to identify the environmental drivers of gut microbial diversity and function in 758 samples collected from wild Ethiopian geladas (Theropithecus gelada). Because geladas live in a cold, high-altitude environment and have a low-quality grass-based diet, they face extreme thermoregulatory and energetic constraints. We tested how proxies of food availability (rainfall) and thermoregulatory stress (temperature) predicted gut microbiome composition of geladas. The gelada gut microbiome composition covaried with rainfall and temperature in a pattern that suggests distinct responses to dietary and thermoregulatory challenges. Microbial changes were driven by differences in the main components of the diet across seasons: in rainier periods, the gut was dominated by cellulolytic/fermentative bacteria that specialized in digesting grass, while during dry periods the gut was dominated by bacteria that break down starches found in underground plant parts. Temperature had a comparatively smaller, but detectable, effect on the gut microbiome. During cold and dry periods, bacterial genes involved in energy, amino acid, and lipid metabolism increased, suggesting a stimulation of fermentation activity in the gut when thermoregulatory and nutritional stress co-occurred, and potentially helping geladas to maintain energy balance during challenging periods.

CONCLUSION

Together, these results shed light on the extent to which gut microbiota plasticity provides dietary and metabolic flexibility to the host, and might be a key factor to thriving in changing environments. On a longer evolutionary timescale, such metabolic flexibility provided by the gut microbiome may have also allowed members of Theropithecus to adopt a specialized diet, and colonize new high-altitude grassland habitats in East Africa. Video abstract.

Interactions between Anaerobic Fungi and Methanogens in the Rumen and Their Biotechnological Potential in Biogas Production from Lignocellulosic Materials

Anaerobic fungi in the digestive tract of herbivores are one of the critical types of fiber-degrading microorganisms present in the rumen. They degrade lignocellulosic materials using unique rhizoid structures and a diverse range of fiber-degrading enzymes, producing metabolic products such as H2/CO2, formate, lactate, acetate, and ethanol. Methanogens in the rumen utilize some of these products (e.g., H2 and formate) to produce methane. An investigation of the interactions between anaerobic fungi and methanogens is helpful as it provides valuable insight into the microbial interactions within the rumen. During the last few decades, research has demonstrated that anaerobic fungi stimulate the growth of methanogens and maintain methanogenic diversity. Meanwhile, methanogens increase the fiber-degrading capability of anaerobic fungi and stimulate metabolic pathways in the fungal hydrogenosome. The ability of co-cultures of anaerobic fungi and methanogens to degrade fiber and produce methane could potentially be a valuable method for the degradation of lignocellulosic materials and methane production.

Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus)

Studies connecting microbiome composition and functional performance in wildlife have received little attention and understanding their connections with wildlife physical condition are sorely needed. We studied the variation in gut microbiota (hard fecal pellets) between allopatric subspecies of the European wild rabbit in wild populations and in captured individuals studied under captivity. We evaluated the influence of environmental and host-specific factors. The microbiome of wild rabbit populations reduced its heterogeneity under controlled conditions. None of the host-specific factors tested correlated with the microbiota composition. We only observed significant intra-group dispersion for the age factor. The most diverse microbiomes were rich in Ruminococcaceae potentially holding an enriched functional profile with dominance of cellulases and xylanases, and suggesting higher efficiency in the digestion of fiber-rich food. Conversely, low diversity gut microbiomes showed dominance of Enterobacteriaceae potentially rich in amylases. We preliminary noticed geographical variations in field populations with higher dominance of Ruminococcaceae in south-western than in north-eastern Spain. Spatial differences appeared not to be subspecies driven, since they were lost in captivity, but environmentally driven, although differences in social structure and behavior may also play a role that deserve further investigations. A marginally significant relationship between the Ruminococcaceae/Enterobacteriaceae ratio and potential life expectancy was observed in captive rabbits. We hypothesize that the gut microbiome may determine the efficiency of feeding resource exploitation, and can also be a potential proxy for life expectancy, with potential applications for the management of declining wild herbivorous populations. Such hypotheses remain to be explored in the future.

Longitudinal evaluation of fecal microbiota transplantation for ameliorating calf diarrhea and improving growth performance

Calf diarrhea is associated with enteric infections, and also provokes the overuse of antibiotics. Therefore, proper treatment of diarrhea represents a therapeutic challenge in livestock production and public health concerns. Here, we describe the ability of a fecal microbiota transplantation (FMT), to ameliorate diarrhea and restore gut microbial composition in 57 growing calves. We conduct multi-omics analysis of 450 longitudinally collected fecal samples and find that FMT-induced alterations in the gut microbiota (an increase in the family Porphyromonadaceae) and metabolomic profile (a reduction in fecal amino acid concentration) strongly correlate with the remission of diarrhea. During the continuous follow-up study over 24 months, we find that FMT improves the growth performance of the cattle. This first FMT trial in ruminants suggest that FMT is capable of ameliorating diarrhea in pre-weaning calves with alterations in their gut microbiota, and that FMT may have a potential role in the improvement of growth performance.

Ruminal Degradation of Rumen-Protected Glucose Influences the Ruminal Microbiota and Metabolites in Early-Lactation Dairy Cows

Rumen-protected glucose (RPG) plays an important role in alleviating the negative energy balance of dairy cows. This study used a combination of rumen microbes 16S and metabolomics to elucidate the changes of rumen microbial composition and rumen metabolites of different doses of RPG's rumen degradation part in early-lactation dairy cows. Twenty-four multiparous Holstein cows in early lactation were randomly allocated to control (CON), low-RPG (LRPG), medium-RPG (MRPG), or high-RPG (HRPG) groups in a randomized block design. The cows were fed a basal total mixed ration diet with 0, 200, 350, and 500 g of RPG per cow per day, respectively. Rumen fluid samples were analyzed using Illumina MiSeq sequencing and ultrahigh-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. MRPG supplementation increased bacterial richness and diversity, including increasing the relative abundance of cellulolytic bacteria, such as Ruminococcus, Lachnospiraceae_NK3A20_group, Ruminiclostridium, and Lachnospiraceae_UCG-008 MRPG significantly increased the concentrations of acetate, propionate, butyrate, and total volatile fatty acid in the rumen. Ruminal fluid metabolomics analysis showed that RPG supplementation could significantly regulate the synthesis of amino acids digested by protozoa in the rumen. Correlation analysis of the ruminal microbiome and metabolome revealed some potential relationships between major bacterial abundance and metabolite concentrations. Our analysis found that RPG supplementation of different doses can change the diversity of microorganisms in the rumen and affect the rumen fermentation pattern and microbial metabolism and that a daily supplement of 350 g of RPG might be the ideal dose.IMPORTANCE Dairy cows in early lactation are prone to a negative energy balance because their dry matter intake cannot meet the energy requirements of lactation. Rumen-protected glucose is used as an effective feed additive to alleviate the negative energy balance of dairy cows in early lactation. However, one thing that is overlooked is that people often think that rumen-protected glucose is not degraded in the rumen, thus ignoring its impact on the microorganisms in the rumen environment. Our investigation and previous experiments have found that rumen-protected glucose is partially degraded in the rumen. However, there are few reports on this subject. Therefore, we conducted research on this problem and found that rumen-protected glucose supplementation at 350 g/day can promote the development and metabolism of rumen flora. This provides a theoretical basis for the extensive application of rumen bypass glucose at a later stage.

In vitro fermentation characteristics of tropical legumes and grasses of good and poor nutritional quality and the degradability of their neutral detergent fibre

Context Tropical legumes are commonly assumed to share all positive attributes known from temperate legumes such as lucerne. However, increasing evidence exists on the differences between those forages, particularly in terms of their ruminal degradability. Aims Exploring the 24-h rumen in vitro-fermentation characteristics of tropical legumes, their direct comparison with lucerne, and their interactions with grasses depending on their nutritional quality. Methods Arachis and stylosanthes (tropical legumes), pennisetum and andropogon (tropical grasses), and lucerne (lucerne_21 and lucerne_35, harvested 21 and 35 days after emergence respectively) were used for the study. On the basis of the nitrogen and neutral detergent fibre (NDF) concentration, arachis and pennisetum were classified as of good quality, while stylosanthes and andropogon as of poor quality. The following four incubation series were performed: first, forages alone were incubated under iso-nitrogenous conditions; second, forages were incubated under iso-nitrogenous conditions with supplemented starch; third, NDF extract of each forage was incubated alone; fourth, NDF extract of tropical grasses and legumes was incubated combined in grass:legume proportions of 33:67 and 67:33. Key results When incubated alone, gas production (GP) and total short chain fatty acids were higher for temperate legumes, intermediate for tropical legumes and lowest for tropical grasses. Similar trends were observed for GP when the forages were incubated with starch, but the differences between arachis and lucerne_35 disappeared; short chain fatty acids did not differ among all tropical forages. Moreover, acetate:propionate ratio was highest for tropical legumes, intermediate for temperate legumes, and lowest for tropical grasses. Gas production of NDF extracts was highest for the lucerne samples and lowest for the tropical legumes. Improvements in GP were found when the NDF from the poor-quality grass (andropogon) was combined with the legumes, particularly the good-quality legume (arachis). Conclusions On the basis of the gas production, tropical legumes appear to have lower degradability than do temperate ones, while also showing a different fermentation pattern. Fibre of tropical legumes is less degradable than that of tropical grasses, but when combining both fibre sources, there seems to be a synergistic effect on degradability. Implications The current results give important insights on the fermentation characteristics of tropical legumes, helping better understand their role in ruminants’ nutrition, while giving inputs towards improving their utilisation.

Effect of additive fermented residues from factory on rumen fermentation and microbial population in beef cattle

Context Suboptimal beef production resulting from poor growth performance of the animals in Thailand may be due to insufficient energy and protein in the animal feed. Therefore, there is a need to find new, locally available and economical nutrient-rich feed resources. By-products from the agri-industry could be one such alternative to improve livestock feed quality. The aim of the study was to evaluate the feed intake, nutrient digestibility, rumen fermentation and microbial population of additive fermented cassava pulp with residues from noodle factory (CN). Four beef cattle at ~2–3 years of age were randomly assigned according to a 4 × 4 Latin square design. Four feed treatments had cassava pulp:residue ratios of 0:0 (NCN), 70:30 (CN1), 60:40 (CN2), 50:50 (CN3). In conclusion, feeding with CN at 60:40 might be an alternative to improve rumen fermentation efficiency, estimated energy, apparent digestibility and bacteria population. Aims The aim of the present study was to determine feed intake, nutrient digestibility, rumen fermentation and microbial population of cattle fed additive fermented cassava pulp with residues from noodle factory (CN). Methods Four beef cattle of ~2–3 years of age and of initial bodyweight of 150 ± 40 kg were randomly assigned to the following four treatments, according to a 4 × 4 Latin square design: cassava pulp:residue at ratios of 0:0 (NCN), 70:30 (CN1), 60:40 (CN2) and 50:50 (CN3) was added. All animals were fed concentrated 16% crude protein and cassava pulp–residue at 1% of bodyweight of animals. Rice straw, water and mineral salt block were offered ad libitum. Key results Feed intake and bodyweight change were not affected, while estimated energy intake and nutrient digestibilities increased (P &lt; 0.05) after animals were fed CN2 and CN3. Ruminal pH, ruminal temperature, ammonia nitrogen and blood urea nitrogen were not altered by CN, whereas total volatile fatty acids and the proportion of propionate increased with an increasing proportion of residues from noodle factory (P &lt; 0.05). Simultaneously, methane production was reduced by CN. In addition, bacterial population and efficiency of microbial nitrogen synthesis were increased (P &lt; 0.05) by CN. Real-time polymerase chain reaction showed that the populations of total bacterial and F. succinogenes increased (P &lt; 0.05), whereas populations of protozoa, R. flavefaciens and R. albus were not significantly different among the treatments. Conclusions It is concluded that feeding with CN can improve rumen fermentation efficiency, estimated energy, apparent digestibility and bacterial population. Feeding with CN2 is recommended because it showed the best response Implications Agri-industry by-products such as cassava pulp and residues from noodle factory can provide an economical alternative to improve feed quality and, hence, beef animal performace in Thailand.

Subacute Ruminal Acidosis in Zebu Cattle: Clinical and Behavioral Aspects

Simple Summary

Cattle that are fed high levels of concentrates may develop short-term rumen acidity that may occur frequently leading to necrosis of the rumen wall and reduced nutrient absorption, thereby decreasing animal productivity. This condition is known as subacute acidosis. Here, we evaluated an experimental model to induce such a condition in Nelore cattle, a Zebu breed widely used in Brazil, and assessed several clinical and feeding behavioral patterns of affected animals to better understand the disease pathogenesis and clinical outcomes. Subacute acidosis led to a reduction in food consumption and rumination time, and an increase was observed in the time spent in decubitus. Additionally, subacute acidosis caused different degrees of depression that was more pronounced with higher ruminal lactic acid concentrations.

Abstract

We evaluated the clinical aspects and feeding behavior of cattle with subacute ruminal acidosis (SARA) caused by short-chain fatty acids (SCFAs). Ten healthy Nelore heifers were subjected to an adjusted SARA induction protocol using citrus pulp (CP). Clinical examinations were performed at baseline and at 3, 6, 9, 12, 15, 18, and 24 h intervals after induction, with ruminal fluid, blood, and feces sampling. The animals’ feeding behavior was evaluated on, before, and for 3 days after SARA by observing the animals every 5 min for 24 h. The dry matter intake (DMI) was recorded daily. The ruminal pH during SARA was always lower than baseline, with an acidotic duration of 547 ± 215 min, a minimum pH of 5.38 ± 0.16, and an average pH of 5.62 ± 0.1. SARA was mainly caused by SCFAs (maximum 118.4 ± 9.3 mmol/L), with the production of l-lactic acids (7.17 mmol/L) and d-lactic acids (0.56 mmol/L) 6 h after the experiment began. The DMI was reduced by 66% and 48% on days 1 and 2, respectively, and returned to normal levels on day 3. SARA caused a reduction in feed intake and rumination time, as well as an increase in the time spent in decubitus on days 1 and 2. These results were influenced by the ruminal pH, ruminal movement, and osmolarity. Furthermore, SARA caused different degrees of depression, which became more pronounced with higher ruminal lactic acid concentrations.

DHA content in milk and biohydrogenation pathway in rumen: a review

Docosahexaenoic acid (DHA) is an essential human nutrient that may promote neural health and development. DHA occurs naturally in milk in concentrations that are influenced by many factors, including the dietary intake of the cow and the rumen microbiome. We reviewed the literature of milk DHA content and the biohydrogenation pathway in rumen of dairy cows aim to enhance the DHA content. DHA in milk is mainly derived from two sources: α-linolenic acid (ALA) occurring in the liver and consumed as part of the diet, and overall dietary intake. Rumen biohydrogenation, the lymphatic system, and blood circulation influence the movement of dietary intake of DHA into the milk supply. Rumen biohydrogenation reduces DHA in ruminal environmental and limits DHA incorporation into milk. The fat-1 gene may increase DHA uptake into the body but this lacks experimental confirmation. Additional studies are needed to define the mechanisms by which different dietary sources of DHA are associated with variations of DHA in milk, the pathway of DHA biohydrogenation in the rumen, and the function of the fat-1 gene on DHA supply in dairy cows.

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.

Overexpression of miR156 and Silencing SPL6RNAi and SPL13RNAi Genes in Medicago sativa on the Changes of Carbohydrate Physiochemical, Fermentation, and Nutritional Profiles

This study aimed to explore the comparative effects of overexpressing miR156 with individually silencing SPL6RNAi and SPL13RNAi genes on carbohydrate physiochemical, fermentation, and nutritional profiles of alfalfa (Medicago sativa). Three sub-genotypes of miR156 overexpressed (miR156 OE), SPL6RNAi, and SPL13RNAi grown with the wild type (WT) in a greenhouse were harvested 3 times at an early vegetative stage. Samples were freeze-dried, ground, and analyzed for carbohydrate nutritional profiles in terms of chemical composition, CNCPS fractions, energetic values, in vitro degradation, and fermentation characteristics. Results showed that miR156 OE had lower fiber and higher energy compared to all other genotypes. Moreover, miR156 OE had higher starch compared to SPL13RNAi and higher DM degradation compared to WT and SPL13RNAi. In conclusion, overexpression of miR156 decreased the fiber content of alfalfa but increased energy and DM degradation. SPL6RNAi was more similar to miR156 OE alfalfa in chemical composition and degradation, indicating that the SPL6RNAi gene plays an important role in the miR156 overexpression event.

Interactions Between Rumen Microbes, VFAs, and Host Genes Regulate Nutrient Absorption and Epithelial Barrier Function During Cold Season Nutritional Stress in Tibetan Sheep

As one of the important ruminants of the Qinghai-Tibet Plateau, Tibetan sheep are able to reproduce and maintain their population in this harsh environment of extreme cold and low oxygen. However, the adaptive mechanism of Tibetan sheep when nutrients are scarce in the cold season of the Plateau environment is unclear. We conducted comparative analysis rumen fermentation parameters, rumen microbes, and expression of host genes related to nutrient absorption and rumen epithelial barrier function in cold and warm season Tibetan sheep. We found that concentrations of the volatile fatty acids (VFAs) acetate, propionate and butyrate of Tibetan sheep in the cold season were significantly higher than in the warm season (P < 0.05). Microbial 16S rRNA gene analysis revealed significant differences in rumen microbiota between the cold and warm seasons, and the abundance of microbial in the cold season was significantly higher than that in the warm season (P < 0.05), and the lack of nutrients in the cold season led to a significant reduction in the expression of SGLT1, Claudin-4, and ZO-1 genes in the rumen epithelium. Correlation analysis revealed significant associations of some rumen microorganisms with the fermentation product acetate and the rumen epithelial genes SGLT1, Claudin-4, and ZO-1.

Ruminal acidosis, bacterial changes, and lipopolysaccharides

Acute and subacute ruminal acidosis (SARA) are common nutritional problems in both beef and dairy cattle. Therefore, the objective of this review is to describe how ruminal Gram-negative bacteria could contribute to the pathogenesis of ruminal acidoses, by releasing lipopolysaccharides (LPS; a component of their cell wall) in the ruminal fluid. When cattle consume excessive amounts of highly fermentable carbohydrates without prior adaptation, normal fermentation become disrupted. The fermentation of these carbohydrates quickly decreases ruminal pH due to the accumulation of short-chain fatty acids and lactate in the rumen. As a consequence, ruminal epithelium may be damaged and tissue function could be impaired, leading to a possible translocation of pathogenic substances from the rumen into the bloodstream. Such changes in fermentation are followed by an increase in Gram-positive bacteria while Gram-negative bacteria decrease. The lyses of Gram-negative bacteria during ruminal acidosis increase LPS concentration in the ruminal fluid. Because LPS is a highly proinflammatory endotoxin in the circulatory system, past studies have raised concerns regarding ruminal LPS contribution to the pathogenesis of ruminal acidosis. Although animals that undergo these disorders do not always have an immune response, recent studies showed that different Gram-negative bacteria have different LPS composition and toxicity, which may explain the differences in immune response. Given the diversity of Gram-negative bacteria in the rumen, evaluating the changes in the bacterial community during ruminal acidosis could be used as a way to identify which Gram-negative bacteria are associated with LPS release in the rumen. By identifying and targeting ruminal bacteria with possible pathogenic LPS, nutritional strategies could be created to overcome, or at least minimize, ruminal acidosis.

A comparative study of artificial cow and sheep rumen fermentation of corn straw and food waste: Batch and continuous operation

To optimize the artificial rumen microorganism sources and develop a stable artificial rumen system, batch and continuous operation were investigated with corn straw and food waste as substrates. The batch trials evaluated the volatile fatty acid (VFA) yield, biogas production, and lignocellulose degradation efficiency. The continuous test evaluated the performance of the artificial cow and sheep rumen systems using a dynamic membrane bioreactor (DMBR) with a stepwise organic loading rate at mesophilic temperature. The anaerobic digestion (AD) of the lignocellulose biomass after rumen fermentation pretreatment and of the permeate from the artificial rumen system were also evaluated for CH₄ production. The results indicated that the cow rumen microorganisms were more suitable than sheep rumen microorganisms for lignocellulosic biomass pretreatment and maximized the CH₄ yield through the AD process without inhibition. After approximately four months of continuous operation, a stable and continuous artificial rumen system for lignocellulosic biomass degradation was achieved with cow rumen fluid as inoculum. Based on analysis of the core lignocellulose-degrading enzyme levels and gel filtration chromatography, the cow rumen microorganisms could secrete more extracellular multienzyme complexes to hydrolyze lignocellulosic biomass than the sheep rumen microorganisms in vitro. During the batch and continuous operations, a high diversity and similar richness of bacteria and fungi demonstrated that the cow rumen microorganisms can be used as a preferred inoculum for the artificial rumen system. The use of an artificial cow rumen system with a DMBR is a promising way to construct a stable and continuous artificial rumen system to biodegrade lignocellulosic biomass for biogas production.

The Duration of Increased Grain Feeding Affects the Microbiota throughout the Digestive Tract of Yearling Holstein Steers

Effects of the duration of moderate grain feeding on the taxonomic composition of gastrointestinal microbiota were determined in 15 Holstein yearling steers. Treatments included feeding a diet of 92% dry matter (DM) hay (D0), and feeding a 41.5% barley grain diet for 7 (D7) or 21 d (D21) before slaughter. At slaughter, digesta samples were collected from six regions, i.e., the rumen, jejunum, ileum, cecum, colon, and rectum. Extracted DNA from these samples was analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Three distinct PCoA clusters existed, i.e., the rumen, the jejunum/ileum, and the cecum/colon/rectum. Feeding the grain diet for 7 d reduced microbial diversity in all regions, except the ileum. Extending the duration of grain feeding from 7 to 21 d did not affect this diversity further. Across regions, treatment changed the relative abundances of 89 genera. Most of the changes between D0 and D7 and between D7 and D21 were opposite, demonstrating the resilience of gastrointestinal microbiota to a moderate increase in grain feeding. Results show that the duration of a moderate increase in grain feeding affects how gastrointestinal microbiota respond to this increase.

Comparative study of the bacterial communities throughout the gastrointestinal tract in two beef cattle breeds

Investigation of the compositional and functional characteristics of the gastrointestinal bacterial community in beef cattle breeds can improve our understanding of the influence of gastrointestinal tract (GIT) regions and host breeds on the bacterial community. In this study, 16S ribosomal RNA (16S rRNA) gene amplicon sequencing was used to characterize the bacterial communities in the rumen, duodenum, jejunum, ileum, caecum, and colon of Xuanhan yellow cattle (XHC) and Simmental crossbred cattle (SXC). The results showed that the diversity of the bacterial population was different in GIT regions of XHC and SXC (P < 0.05). In total, ten bacterial phyla, sixteen bacterial genera, and nine metabolic pathways were identified in the core bacteria. The phyla Firmicutes, Bacteroidetes, and Proteobacteria were predominant, but their proportions were different in GIT regions (P < 0.05). The diversity, structure, and composition of the bacteria in the rumen were similar between the breeds (P > 0.05), and the indices in the intestine showed significant differences (P < 0.05). Moreover, the composition and structure of the bacterial communities in the rumen, small intestine, and large intestine were different regardless of the breed. Thus, the bacterial communities were different among the gastrointestinal regions in each breed, and the bacterial community in the rumen had more stable characteristics than that in the intestine between two breeds. Further studies may focus on the minor microbial communities and the functions of GIT bacteria to better understand gut-microbe interactions. KEY POINTS: • Differences in bacteria among gastrointestinal regions differ in cattle breeds. • Differences between the breeds in the ruminal bacteria are less pronounced than differences in the intestinal bacteria.

Calcium salts of long-chain fatty acids from linseed oil decrease methane production by altering the rumen microbiome in vitro

Calcium salts of long-chain fatty acids (CSFA) from linseed oil have the potential to reduce methane (CH4) production from ruminants; however, there is little information on the effect of supplementary CSFA on rumen microbiome as well as CH4 production. The aim of the present study was to evaluate the effects of supplementary CSFA on ruminal fermentation, digestibility, CH4 production, and rumen microbiome in vitro. We compared five treatments: three CSFA concentrations-0% (CON), 2.25% (FAL) and 4.50% (FAH) on a dry matter (DM) basis-15 mM of fumarate (FUM), and 20 mg/kg DM of monensin (MON). The results showed that the proportions of propionate in FAL, FAH, FUM, and MON were increased, compared with CON (P < 0.05). Although DM and neutral detergent fiber expressed exclusive of residual ash (NDFom) digestibility decreased in FAL and FAH compared to those in CON (P < 0.05), DM digestibility-adjusted CH4 production in FAL and FAH was reduced by 38.2% and 63.0%, respectively, compared with that in CON (P < 0.05). The genera Ruminobacter, Succinivibrio, Succiniclasticum, Streptococcus, Selenomonas.1, and Megasphaera, which are related to propionate production, were increased (P < 0.05), while Methanobrevibacter and protozoa counts, which are associated with CH4 production, were decreased in FAH, compared with CON (P < 0.05). The results suggested that the inclusion of CSFA significantly changed the rumen microbiome, leading to the acceleration of propionate production and the reduction of CH4 production. In conclusion, although further in vivo study is needed to evaluate the reduction effect on rumen CH4 production, CSFA may be a promising candidate for reduction of CH4 emission from ruminants.

Multi-omics Approaches To Decipher the Impact of Diet and Host Physiology on the Mammalian Gut Microbiome

In recent years, various studies have demonstrated that the gut microbiota influences host metabolism. However, these studies were focused primarily on a single or a limited range of host species, thus preventing a full exploration of possible taxonomic and functional adaptations by gut microbiota members as a result of host-microbe coevolution events. In the current study, the microbial taxonomic profiles of 250 fecal samples, corresponding to 77 host species that cover the mammalian branch of the tree of life, were reconstructed by 16S rRNA gene-based sequence analysis. Moreover, shotgun metagenomics was employed to investigate the metabolic potential of the fecal microbiomes of 24 mammals, and subsequent statistical analyses were performed to assess the impact of host diet and corresponding physiology of the digestive system on gut microbiota composition and functionality. Functional data were confirmed and extended through metatranscriptome assessment of gut microbial populations of eight animals, thus providing insights into the transcriptional response of gut microbiota to specific dietary lifestyles. Therefore, the analyses performed in this study support the notion that the metabolic features of the mammalian gut microbiota have adapted to maximize energy extraction from the host's diet.IMPORTANCE Diet and host physiology have been recognized as main factors affecting both taxonomic composition and functional features of the mammalian gut microbiota. However, very few studies have investigated the bacterial biodiversity of mammals by using large sample numbers that correspond to multiple mammalian species, thus resulting in an incomplete understanding of the functional aspects of their microbiome. Therefore, we investigated the bacterial taxonomic composition of 250 fecal samples belonging to 77 host species distributed along the tree of life in order to assess how diet and host physiology impact the intestinal microbial community by selecting specific microbial players. Conversely, the application of shotgun metagenomics and metatranscriptomics approaches to a group of selected fecal samples allowed us to shed light on both metabolic features and transcriptional responses of the intestinal bacterial community based on different diets.

Apparent total tract digestibility, ruminal fermentation, and blood metabolites in beef steers fed green-chopped cool-season forages

An experiment was conducted during the winter of two consecutive years to evaluate the effects of feeding green-chopped cool-season forages on digestibility, ruminal fermentation, and blood parameters in beef steers. Nine ruminally cannulated Angus crossbred steers (year 1: 359 ± 79 kg; year 2: 481 ± 105 kg) received ad libitum green-chopped forages from pastures planted with one of the following mixtures: 1) OAT = Horizon 201 oats (Avena sativa L.)/Prine annual ryegrass (Lolium multiflorum Lam.) at 95 and 17 kg/ha, respectively; 2) RYE = FL401 cereal rye (Secale cereale L.)/Prine annual ryegrass (Lolium multiflorum Lam.) at 78 and 17 kg/ha, respectively; or 3) TRIT = Trical 342 triticale (X Triticosecale spp.)/Prine annual ryegrass (Lolium multiflorum Lam.) at 95 and 17 kg/ha, respectively. Intake was measured using the GrowSafe system and orts were discarded prior to subsequent feeding. After a 14-d adaptation, feed and fecal samples were collected twice daily for 4 d to determine apparent total tract nutrient digestibility using indigestible neutral detergent fiber (NDF) as an internal marker. On day 19, blood and ruminal fluid samples were collected every 3 h during a 24-h period to analyze plasma urea nitrogen (PUN) and glucose, ruminal pH, and concentration of ruminal ammonia nitrogen (NH3-N) and volatile fatty acids (VFA). Data were analyzed as a generalized randomized block design with repeated measures using the PROC MIX of SAS. No effect of treatment (P > 0.05) was observed for intake of dry matter, organic matter (OM), crude protein, NDF, or acid detergent fiber. Apparent total tract digestibility of nutrients was greater (P < 0.05) for OAT and TRIT when compared with RYE, with OM digestibility being 82.7%, 79.6%, and 69.5%, respectively. An effect of time (P < 0.01) was observed for ruminal pH. Plasma concentration of glucose was greater (P < 0.01) in steers consuming OAT, whereas steers fed RYE had greater (P < 0.05) concentrations of ruminal NH3-N and PUN, and the least concentration of total ruminal VFA (P < 0.05), despite having the greatest (P > 0.05) molar proportion of acetate, branched-chain VFA, and acetate:propionate. Increased nutrient digestibility and favorable ruminal fermentation and blood metabolites of OAT and TRIT are potentially conducive to enhanced growth performance when compared with RYE.

Comparison of the microbial communities of alpacas and sheep fed diets with three different ratios of corn stalk to concentrate

The objective of this study was to investigate the characteristics of ruminal microbial communities of alpacas (Lama pacos) and sheep (Ovis aries) fed three diets with varying ratios of roughage (corn stalk) to concentrate, 3:7 (LS), 5:5 (MS) and 7:3 (HS). Six alpacas (one-year-old and weighing 29.5 ± 7.1 kg) and six sheep (one-year-old and weighing 27.9 ± 2.7 kg) were used in this study, in a replicated 3 × 3 Latin square experiment. Total protozoa concentration was determined under the microscope; total fungi and methanogens were assessed using quantitative polymerase chain reaction and expressed as a percentage of total bacterial 16S rRNA gene copies; bacterial communities were investigated by targeted 16S rRNA gene (V3-V4 region) sequencing. The percentage of fungi was significantly higher in alpacas than in sheep under the LS diet, while the concentration of protozoa was significantly lower in alpacas under HS, MS and LS diets. The alpha diversity including Shannon, Chao l and ACE indices of bacterial communities was higher in alpacas than in sheep, under the LS diet. A total of 299 genera belonging to 22 phyla were observed in the forestomach of alpaca and sheep, with Bacteroidetes and Firmicutes dominating both animal species. Phyla Armatimonadetes and Fusobacteria, as well as 64 genera, were detected only in alpacas, whereas phyla Acidobacteria and Nitrospira, as well as 44 genera, were found only in sheep. The abundance of cellulolytic bacteria, including Butyrivibrio and Pseudobutyrivibrio, was higher in alpacas than in sheep under all three diets. These differences in the forestomach microbial communities partly explained why alpacas displayed a higher poor-quality roughage digestibility, and a lower methane production. Results also revealed that the adverse effects of high-concentrate diets (70%) were lesser in alpacas than in sheep.

Systematic Analysis of Escherichia coli Isolates from Sheep and Cattle Suggests Adaption to the Rumen Niche

The commonly used laboratory bacterium Escherichia coli normally does not produce and secrete cellulases due to its complex bilayer membrane structure and poor secretory apparatus. In our previous study, the cellulolytic E. coli strain ZH-4 with extracellular cellulase activity was found in the bovine rumen. In this study, we demonstrate that the secretion of cellulase is a common feature of E. coli isolates from the rumen of animals such as sheep and cattle. Physiological phenotype characterization of these E. coli isolates, together with genome, transcriptome, and comparative genomics analysis, suggests their adaption to the rumen niche. The higher growth rate of the isolated strains under aerobic conditions meets the competitive requirements of the strains in rumen microecosystem, while anaerobic accumulation of reduced H₂ and succinate is hypothesized to be the results of adaptation to the rumen environment. Cellulase secretion increased significantly when the molecular chaperone genes ibpA and ibpB were overexpressed. This was also revealed by the transcriptomic data. A possible mechanism for cellulase secretion by E. coli isolates was proposed based on the transcriptomic data and molecular experiments.IMPORTANCE As an important intestinal microorganism, E. coli is present in the intestinal tract of animals and in many other environments. However, it normally does not produce and secret cellulases due to its complex bilayer membrane structure and poor secretory apparatus. Here, we proved that E. coli is widely present in the rumen of sheep and cattle. Systematic analysis of the isolates indicated that they have adapted to the rumen niche, with phenotypes that include secretion of cellulase and fermentative accumulation of succinate and H₂ The finding that overexpression of small heat shock protein genes ibpA and ibpB could facilitate cellulase BcsZ secretion, which provides a possible insight into the protein secretion mechanism of rumen-colonizing E. coli.

Disruption of ruminal homeostasis by malnutrition involved in systemic ruminal microbiota-host interactions in a pregnant sheep model

BACKGROUND

Undernutrition is a prevalent and spontaneous condition in animal production which always affects microbiota-host interaction in gastrointestinal tract. However, how undernutrition affects crosstalk homeostasis is largely unknown. Here, we discover how undernutrition affects microbial profiles and subsequently how microbial metabolism affects the signal transduction and tissue renewal in ruminal epithelium, clarifying the detrimental effect of undernutrition on ruminal homeostasis in a pregnant sheep model.

RESULTS

Sixteen pregnant ewes (115 days of gestation) were randomly and equally assigned to the control (CON) and severe feed restriction (SFR) groups. Ewes on SFR treatment were restricted to a 30% level of ad libitum feed intake while the controls were fed normally. After 15 days, all ewes were slaughtered to collect ruminal digesta for 16S rRNA gene and metagenomic sequencing and ruminal epithelium for transcriptome sequencing. Results showed that SFR diminished the levels of ruminal volatile fatty acids and microbial proteins and repressed the length, width, and surface area of ruminal papillae. The 16S rRNA gene analysis indicated that SFR altered the relative abundance of ruminal bacterial community, showing decreased bacteria about saccharide degradation (Saccharofermentans and Ruminococcus) and propionate genesis (Succiniclasticum) but increased butyrate producers (Pseudobutyrivibrio and Papillibacter). Metagenome analysis displayed that genes related to amino acid metabolism, acetate genesis, and succinate-pathway propionate production were downregulated upon SFR, while genes involved in butyrate and methane genesis and acrylate-pathway propionate production were upregulated. Transcriptome and real-time PCR analysis of ruminal epithelium showed that downregulated collagen synthesis upon SFR lowered extracellular matrix-receptor interaction, inactivated JAK3-STAT2 signaling pathway, and inhibited DNA replication and cell cycle.

CONCLUSIONS

Generally, undernutrition altered rumen bacterial community and function profile to decrease ruminal energy retention, promoted epithelial glucose and fatty acid catabolism to elevate energy supply, and inhibited the proliferation of ruminal epithelial cells. These findings provide the first insight into the systemic microbiota-host interactions that are involved in disrupting the ruminal homeostasis under a malnutrition pattern. Video Abstract.

Brisket Disease Is Associated with Lower Volatile Fatty Acid Production and Altered Rumen Microbiome in Holstein Heifers

Simple Summary

Development of the dairy industry in the high-altitude plateau environment through incorporation of Holstein cows is complicated by the risk of brisket disease. While the physiological effects of brisket disease are well-studied, its effects on rumen function and microbial community composition are not. There are clear shifts in volatile fatty acids production and rumen microbial community composition in Holstein heifers suffering from brisket disease. Observed shifts reveal key genera associated with healthy and disease states and suggest that bovine brisket disease is associated with impaired rumen functioning. This work supports further understanding of the roles of key rumen taxa in bovine brisket disease, with particular focus on candidate rumen biomarkers in healthy animals that may be able to reduce economic losses for farmers.

Abstract

Brisket disease is heritable but is also associated with non-genetic risk factors and effects of the disease on the rumen microbiome are unknown. Ten Holstein heifers were exposed to the plateau environment for three months and divided into two groups according to the index of brisket disease, the mean pulmonary arterial pressure (mPAP): brisket disease group (BD, n = 5, mPAP > 63 mmHg) and healthy heifer group (HH, n = 5, mPAP < 41 mmHg). Rumen fluid was collected for analysis of the concentrations of volatile fatty acids (VFAs). Extracted DNA from rumen contents was analyzed using Illumina MiSeq 16S rRNA sequencing technology. The concentration of total VFA and alpha-diversity metrics were significantly lower in BD group (p < 0.05). Ruminococcus and Treponema were significantly decreased in BD heifers (p < 0.05). Correlation analysis indicated that 10 genera were related to the mPAP (p < 0.05). Genera of Anaerofustis, Campylobacter, and Catonella were negatively correlated with total VFA and acetic acid (R < −0.7, p < 0.05), while genera of Blautia, YRC22, Ruminococcus, and Treponema were positively related to total VFA and acetic acid (R > 0.7; p < 0.05). Our findings may be a useful biomarker in future brisket disease work.

Dragon fruit (Hylocereus undatus) peel pellet as a rumen enhancer in Holstein crossbred bulls

Objective

An experiment was conducted to assess the effect of dragon fruit peel pellet (DFPP) as a rumen enhancer of dry matter consumption, nutrient digestibilities, ruminal ecology, microbial protein synthesis and rumimal methane production in Holstein crossbred bulls.

Methods

Four animals, with an average live-weight of 200±20 kg were randomly assigned in a 4×4 Latin square design to investigate the influence of DFPP supplementation. There were four different dietary treatments: without DFPP, and with 200, 300, and 400 g/h/d, respectively.

Results

Results revealed that dry matter consumption of total intake, rice straw and concentrate were not significantly different among treatments (p>0.05). It was also found that ruminal pH was not different among treatments (p>0.05), whilst protozoal group was reduced when DFPP increased (p<0.01). Blood urea nitrogen and NH₃-N concentrations were increased at 400 g of DFPP supplementation (p<0.01). Additionally, volatile fatty acid production of propionate was significantly enhanced by the DFPP supplementation (p<0.05), while production of methane was consequently decreased (p<0.05). Furthermore, microbial protein synthesis and urinary purine derivatives were remarkably increased especially at 400 g of DFPP supplementation (p<0.05).

Conclusion

Plant secondary compounds or phytonutrients (PTN) containing saponins (SP) and condensed tannins (CT) have been reported to influence rumen fermentation. DFPP contains both CT and SP as a PTN. The addition of 400 g of DFPP resulted in improved rumen fermentation end-products especially propionate (C3) and microbial protein synthesis. Therefore, DFPP is a promising rumen enhancer and indicated a significant potential of DFPP as feedstuff for ruminant feed to mitigate rumen methane production.

Heat stress on calves and heifers: a review

The current review is designed with aims to highlight the impact of heat stress (HS) on calves and heifers and to suggest methods for HS alleviation. HS occurs in animals when heat gain from environment and metabolism surpasses heat loss by radiation, convection, evaporation and conduction. Although calves and heifers are comparatively heat resistant due to less production of metabolic heat and more heat dissipation efficiency, they still suffer from HS to some degree. Dry matter intake and growth performance of calves and heifers are reduced during HS because of redistributing energy to heat regulation through a series of physiological and metabolic responses, such as elevated blood insulin and protein catabolism. Enhanced respiration rate and panting during HS accelerate the loss of CO2, resulting in altered blood acid-base chemistry and respiratory alkalosis. HS-induced alteration in rumen motility and microbiota affects the feed digestibility and rumen fermentation. Decreased luteinizing hormone, estradiol and gonadotrophins due to HS disturb the normal estrus cyclicity, depress follicular development, hence the drop in conception rate. Prenatal HS not only suppresses the embryonic development by the impaired placenta, which results in hypoxia and malnutrition, but also retards the growth, immunity and future milk production of newborn calves. Based on the above challenges, we attempted to describe the possible impacts of HS on growth, health, digestibility and reproduction of calves and heifers. Likewise, we also proposed three primary strategies for ameliorating HS consequences. Genetic development and reproductive measures, such as gene selection and embryo transfers, are more likely long-term approaches to enhance heat tolerance. While physical modification of the environment, such as shades and sprinkle systems, is the most common and easily implemented measure to alleviate HS. Additionally, nutritional management is another key approach which could help calves and heifers maintain homeostasis and prevent nutrient deficiencies because of HS.

Seasonal Variation and Sexual Dimorphism of the Microbiota in Wild Blue Sheep (Pseudois nayaur)

Microbiota of the wild blue sheep (Pseudois nayaur) presents a seasonal variation due to different dietary selection and feeding strategies from different ecological niches chosen by different sex in summer. To address those issues, we analyzed the variation of gut microbiota based on the material from the feces, with 16S rRNA and meta-genome aimed to explore seasonal and gender differences. The results indicate that seasonal dietary changes and gender differentiation, as expected, cause the variation in sheep's gut microbiota structure. The variation of the former is more significant than the latter. Dominant Firmicutes exists a significantly higher abundance in summer than that in winter. Subordinate Bacteroides expresses no seasonal difference between the two seasons. Compared with the winter group, the summer group is featured by abundant enzymes digesting cellulose and generating short-chain fatty acids (SCFAs), such as beta-glucosidase (EC: 3.2.1.21) for cellulose digestion, and butyrate kinase (EC:2.7.2.7) in butyrate metabolism, implying that the changes of the composition in intestinal flora allow the sheep to adapt to the seasonalized dietary selection through alternated microbial functions to reach the goal of facilitating the efficiency of energy harvesting. The results also show that the blue sheep expresses a prominent sexual dimorphism in the components of gut microbiota, indicating that the two sexes have different adaptations to the dietary selection, and demands for physical and psychological purposes. Thus, this study provides an example of demonstrating the principles and regulations of natural selection and environmental adaptation.

Comparative Study of the Water-Soluble Antioxidants in Fodder Additives and Sheep Blood Serum by Amperometric and Biochemical Methods

The effects of chitosan as feed additive for animals (FAFAs) on various digestive processes are an important to study because of the animal nutrition and production quality, healthcare and farming. The aims of this study were to evaluate the total amount of water-soluble antioxidants (TAWSA) of chitosan and high protein microbiologically synthesized concentrate as FAFAs; to assess the effect of these FAFAs on TAWSA values, parameters of sheep blood serum and rumen content by biochemical, physical and chemical methods. The laboratory studies of TAWSA values of feed components based on chitosan from different manufacturers or/and a high-protein concentrate were implemented. The animal experiments were carried out on six rumen-fistulated ewes (in three rounds of 14 days each, i.e., three groups) to confirm the results of the laboratory studies. The particular differences of the TAWSA of sheep blood by using both FAFAs by amperometric method were determined. A strong negative correlation -0.67 (or -0.86) was observed between TAWSA and the total protein (globulin's) content in the blood for the Group 3 of animals. A moderate (0.40) or strong (0.73) positive correlation between TAWSA and total protein content in the blood for the Group 2 of animals than weak correlation 0.23 (or 0.26) for the control Group 1. In conclusion, the correlations between the value changes of TAWSA vs. major biochemical parameters of a blood serum of rumen-fistulated ewes (Group 3 > Group 2 > Group 1) or some indicators of the rumen content (ingesta pH, total content of volatile fatty acids, etc.) were found for the first time.

Saccharomyces cerevisiae fermentation products (SCFP) stabilize the ruminal microbiota of lactating dairy cows during periods of a depressed rumen pH

Background

Effects of Saccharomyces cerevisiae fermentation products (SCFP) on rumen microbiota were determined in vitro and in vivo under a high and a depressed pH. The in vitro trial determined the effects of Original XPC and NutriTek (Diamond V, Cedar Rapids, IA) at doses of 1.67 and 2.33 g/L, respectively, on the abundances of rumen bacteria under a high pH (> 6.3) and a depressed pH (5.8–6.0) using quantitative PCR (qPCR). In the in vivo trial eight rumen-cannulated lactating dairy cows were used in a cross-over design. Cows were randomly assigned to SCFP treatments (Original XPC, Diamond V, Cedar Rapids, IA) or control (No SCFP) before two 5-week experimental periods. During the second period, SCFP treatments were reversed. Cows on the SCFP treatment were supplemented with 14 g/d of SCFP and 126 g/d of ground corn. Other cows received 140 g/d ground corn. During the first 4 wk. of each period, cows received a basal diet containing 153 g/kg of starch. During week 5 of both periods, the rumen pH was depressed by a SARA challenge. This included replacing 208 g/kg of the basal diet with pellets of ground wheat and barley, resulting in a diet that contained 222 g/kg DM of starch. Microbial communities in rumen liquid digesta were examined by pyrosequencing, qPCR, and shotgun metagenomics.

Results

During the in vitro experiment, XPC and NutriTek increased the relative abundances of Ruminococcus flavefaciens, and Fibrobacter succinogenes determined at both the high and the depressed pH, with NutriTek having the largest effect. The relative abundances of Prevotella brevis, R. flavefaciens, ciliate protozoa, and Bifidobacterium spp. were increased by XPC in vivo. Adverse impacts of the in vivo SARA challenge included reductions of the richness and diversity of the rumen microbial community, the abundances of Bacteroidetes and ciliate protozoa in the rumen as determined by pyrosequencing, and the predicted functionality of rumen microbiota as determined by shotgun metagenomics. These reductions were attenuated by XPC supplementation.

Conclusions

The negative effects of grain-based SARA challenges on the composition and predicted functionality of rumen microbiota are attenuated by supplementation with SCFP.

Cosubstrate strategy for enhancing lignocellulose degradation during rumen fermentation in vitro: Characteristics and microorganism composition

To enhance the degradation of wheat straw (WS) and corn straw (CS) in rumen fermentation, characterization of degradation and ruminal microorganisms of monosubstrate (WS/CS) groups and a cosubstrate strategy with food waste (FW) group was performed. The cellulose, hemicellulose, and lignin degradation efficiency of WS and CS; soluble chemical oxygen demand; volatile fatty acid yields; and activity of ligninolytic, cellulolytic, and hemicellulolytic enzymes for the cosubstrate group were improved compared with those for the corresponding monosubstrate groups. An accurate and a good of fit of the Weibull kinetic model, decreased crystallinity index values, and characteristic absorbance bands in the Fourier transform-infrared spectra further confirmed that cosubstrate addition with FW decreased the resistance of cellulose and hemicellulose to biodegradation. High-throughput sequencing results suggested that the bacterial diversity in CS rumen fermentation and fungal diversity and richness in WS rumen fermentation were promoted with FW as a cosubstrate. The cosubstrate addition with FW significantly affected the composition of the ruminal bacteria and fungi in rumen fermentation. The relative abundances (RAs) of rumen bacteria were increased in the cosubstrate CS/WS and FW fermentation conditions, and the enhancement of CS degradation with FW supplementation was stronger than that of WS rumen fermentation with FW supplementation. The RAs of the ruminal fungal genera Ustilago and Fusarium were promoted in CS and WS fermentation with FW, respectively. Moreover, the fermentation properties and rumen flora in the FW rumen fermentation also provided some evidence to suggest an enhancement of the cosubstrate strategy compared with the monosubstrate strategy.

Effects of feeding strategy and duration of the dry period on the rumen microbiota of dairy cows

The composition of rumen microbiota during late gestation and early lactation was compared between cows receiving a close-up diet (1.43 Mcal net energy of lactation (NEl) kg−1 dry matter (DM)) throughout a 40 d dry period (SHORT) and cows receiving a far-off diet (1.28 Mcal NEl kg−1 DM) as well as the close-up diet (as above) for 39 and 21 d, respectively, during a conventional 60 d dry period (CONV). Rumen fluid was collected at weeks −2, −1, +1, +2, and +7 relative to calving. Extracted DNA was analyzed for taxonomic composition of the rumen microbiome using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. At week +1, this composition differed (P < 0.05) between treatments. In cows under the CONV treatment, this composition only differed (P < 0.05) between weeks −1 and +1. For SHORT cows, this composition tended to differ between weeks +1 and +2 (P = 0.09) as well as between weeks +2 and +7 (P < 0.03). The change of the taxonomic composition of the rumen microbiota after calving, mainly consisting of increases in the abundance of Firmicutes and decreases in that of Bacteroidites, was comparatively slower and less favourable under the SHORT treatment. This may have been due to more excessive grain intake before calving of cows on the latter treatment.

A meta-analysis of the bovine gastrointestinal tract microbiota

The bovine gastrointestinal (GI) tract microbiota has important influences on animal health and production. Presently, a large number of studies have used high-throughput sequencing of the archaeal and bacteria 16S rRNA gene to characterize these microbiota under various experimental parameters. By aggregating publically available archaeal and bacterial 16S rRNA gene datasets from 52 studies we were able to determine taxa that are common to nearly all microbiota samples from the bovine GI tract as well as taxa that are strongly linked to either the rumen or feces. The methanogenic genera Methanobrevibacter and Methanosphaera were identified in nearly all fecal and rumen samples (> 99.1%), as were the bacterial genera Prevotella and Ruminococcus (≥ 92.9%). Bacterial genera such as Alistipes, Bacteroides, Clostridium, Faecalibacterium and Escherichia/Shigella were associated with feces and Fibrobacter, Prevotella, Ruminococcus and Succiniclasticum with the rumen. As expected, individual study strongly affected the bacterial community structure, however, fecal and rumen samples did appear separated from each other. This meta-analysis provides the first comparison of high-throughput sequencing 16S rRNA gene datasets generated from the bovine GI tract by multiple studies and may serve as a foundation for improving future microbial community research with cattle.

Rapeseed pod meal can replace concentrate and enhance utilization of feed on in vitro gas production and fermentation characteristics

Rapeseed provides multi-products as human food and animal feed especially the oil and meal. Rapeseed oil and meal after extraction are nutritious and have been used in animal feeding. This study aimed at studying the effect of rapeseed pod meal as the replacement of concentrate (RPM) on in vitro gas and fermentation characteristics. Dietary treatments were imposed in a 2 × 6 factorial arrangement according to a completely randomized design (CRD). The first factor was two ratios of roughage to concentrate (R:C at 60:40, and 40:60) and the second factor was six levels of RPM at 0, 20, 40, 60, 80, and 100% of dietary substrate. The results revealed that the R:C ratio and RPM increased kinetics of gas production, in vitro degradability and improved rumen fermentation (P < 0.001). Ratio of R:C influenced (P < 0.05) on both protozoal population and methane production, while level of RPR did not. Both factors had influenced (P < 0.01) a, a + b, and c, as well as total gas production; nevertheless, there were no interactions (P > 0.05). Interestingly, both factors have greatly impacted on TVFA, C₃ (P < 0.01) and tended to reduce methane production as level of RPM replacement increased. In conclusion, RPM improved rumen fermentation and increased in vitro DM degradability, hence is potential for replacement of concentrate and effectively used for ruminant feeding.

Relationship between the True Digestibility of Dietary Calcium and Gastrointestinal Microorganisms in Goats

Simple Summary

The specific enzymes secreted by microorganisms in the gastrointestinal tract (GIT) of ruminants, such as phytase, can catalyze the decomposition of calcium compounds (e.g., phytic acid) and release bound calcium for the absorption of animals. Therefore, we speculate that gastrointestinal microbes could be a factor affecting digestion and absorption of dietary calcium. However, little related research has been reported. In the present study, we found that the true digestibility of calcium (TDC) in goats is related to gastrointestinal bacteria. Some gastro-intestinal bacteria, such as ruminal Prevotella, were beneficial for true host digestibility of dietary calcium.

Abstract

The current study was performed to examine the relationship between the true digestibility of calcium (TDC) in the diet and bacterial community structure in the gastrointestinal tract (GIT) of goats. Twenty-six Nubian healthy female goats were selected as experimental animals, and their TDC was determined using metabolic experiments. Eight goats were grouped into the high digestibility of Calcium (HC) phenotype, and another eight were grouped into the low digestibility of Calcium (LC) phenotype. Their bacterial 16S rRNA gene amplicons from the rumen, abomasum, jejunum, cecum, and colon contents were sequenced using next-generation high-throughput sequencing technology. In the rumen, 239 genera belonging to 23 phyla, 319 genera belonging to 30 phyla in the abomasum, 248 genera belonging to 36 phyla in the jejunum, 248 genera belonging to 25 phyla in the colon and 246 genera belonging to 23 phyla in the cecum were detected. In addition, there was a significant correlation between the TDC and the relative abundance of Candidatus_Saccharimonas, Christensenellaceae_R-7_group, Mogibacterium, Prevotella_1, Prevotella_UCG_004, Ruminococcus_2, Saccharibacteria in the rumen, Eubacterium_coprostanoligens_group, Lachnospiraceae_ND3007_group, Lachnospiraceae_NK3A20_group, p-1088-a5_gut_group, and Planctomycetes in the abomasum, Butyrivibrio in the cecum, and Fibrobacter in the cecum were observed. This study suggests an association of GIT microbial communities as a factor influencing TDC in goats.

Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance

BACKGROUND

Recently, we reported that some dairy cows could produce high amounts of milk with high amounts of protein (defined as milk protein yield [MPY]) when a population was raised under the same nutritional and management condition, a potential new trait that can be used to increase high-quality milk production. It is unknown to what extent the rumen microbiome and its metabolites, as well as the host metabolism, contribute to MPY. Here, analysis of rumen metagenomics and metabolomics, together with serum metabolomics was performed to identify potential regulatory mechanisms of MPY at both the rumen microbiome and host levels.

RESULTS

Metagenomics analysis revealed that several Prevotella species were significantly more abundant in the rumen of high-MPY cows, contributing to improved functions related to branched-chain amino acid biosynthesis. In addition, the rumen microbiome of high-MPY cows had lower relative abundances of organisms with methanogen and methanogenesis functions, suggesting that these cows may produce less methane. Metabolomics analysis revealed that the relative concentrations of rumen microbial metabolites (mainly amino acids, carboxylic acids, and fatty acids) and the absolute concentrations of volatile fatty acids were higher in the high-MPY cows. By associating the rumen microbiome with the rumen metabolome, we found that specific microbial taxa (mainly Prevotella species) were positively correlated with ruminal microbial metabolites, including the amino acids and carbohydrates involved in glutathione, phenylalanine, starch, sucrose, and galactose metabolism. To detect the interactions between the rumen microbiome and host metabolism, we associated the rumen microbiome with the host serum metabolome and found that Prevotella species may affect the host's metabolism of amino acids (including glycine, serine, threonine, alanine, aspartate, glutamate, cysteine, and methionine). Further analysis using the linear mixed effect model estimated contributions to the variation in MPY based on different omics and revealed that the rumen microbial composition, functions, and metabolites, and the serum metabolites contributed 17.81, 21.56, 29.76, and 26.78%, respectively, to the host MPY.

CONCLUSIONS

These findings provide a fundamental understanding of how the microbiome-dependent and host-dependent mechanisms contribute to varied individualized performance in the milk production quality of dairy cows under the same management condition. This fundamental information is vital for the development of potential manipulation strategies to improve milk quality and production through precision feeding. Video Abstract.

Impact of docusate and fauna-free on feed intake, ruminal flora and digestive enzyme activities of sheep

Four Small‐tail Han male hogget sheep, fitted with rumen cannula and fed the same basal diet were used to study the impacts of docusate (DOC) and fauna‐free on the voluntary feed intake (VFI), and ruminal protozoal, bacterial and fungal counts and the digestive enzyme activities. By a 4 × 4 Latin square design, sheep were given no DOC (the control), 2 doses of DOC: 1.2 and 3.0 g/kg diet or oral dose of 6.0 g/d DOC for three days (fauna‐free treatment) in each period of 18 days, the last three days of which were for sampling the rumen fluid. Compared with the control, 1.2 g/kg of DOC supplementation significantly resulted in increases of 18.0% VFI and 44% bacterial count, and no significant change in the fungal number. Supplementing DOC reduced protozoal number in a dose‐dependent manner. The fibre degradation enzyme activity in rumen fluid increased by 17.7% with a concomitant 10% increase in volatile fatty acids (VFA); the protease activity was reduced by 23% with a corresponding reduction in rumen ammonia by 42%. In contrast, supplementing 3.0 g/kg of DOC has adverse effects on those measures compared with 1.2 g/kg of DOC. Defaunation was accompanied with substantial increases in the bacterial and fungal counts, but had no significant influences on VFI and the enzyme activity for starch, protein and pectin digestion, and small changes in fibre digestion enzymes and the total VFA compared with the control. A high correlation (r² = 0.82) was noted between VFI and the total activity of fibre digestion enzymes and VFA. It was proposed that fibre digestion rate in the rumen is a primary factor for determining VFI in sheep, and dietary supplementation of 1.2 g/kg of DOC could partially result in enhanced activity of fibre digestive enzyme in the rumen and increase VFI.

Persistent action of cow rumen microorganisms in enhancing biodegradation of wheat straw by rumen fermentation

Rumen fermentation is known to be effective for lignocellulosic-wastes biodegradation to certain extent but it is still unclear if there exists a termination of the microorganisms' action to further degrade the bio-refractory fractions. In order to illuminate the related microbiological characteristics, experiments were conducted in a prolonged duration of rumen fermentation of mechanically ruptured wheat straw, with inoculation of cow rumen microorganisms in vitro. Although the organic wastes could not be biodegraded quickly, continuous conversion of the lignocellulosic contents to volatile fatty acids and biogas proceeded in the duration of more than three months, resulting in 96-97% cellulose and hemicellulose decomposition, and 42% lignin decomposition. X-ray diffraction and Fourier transform infrared spectroscopy further demonstrated the characteristics of lignocellulosic structure decomposition. Under the actions of cow rumen microorganisms, stable pH was maintained in the fermentation liquid, along with a steady NH₄⁺-N, volatile fatty acids accumulation, and a large buffering ability. It was identified by enzyme analysis and Illumina MiSeq sequencing that the rich core lignocellulolytic enzymes secreted by the abundant and diverse rumen bacteria and fungi contributed to the persistent degradation of lignocellulosic wastes. Members of the Clostridiales order and Basidiomycota phylum were found to be the dominant lignocellulolytic bacteria and fungi, respectively. It could thus be inferred that the main lignocellulose degradation processes were a series of catalytic reactions under the actions of lignocellulolytic enzymes secreted from bacteria and fungi. The dominant hydrogenotrophic methanogens (Methanomassiliicoccus, Methanobrevibacter, Methanosphaera, and Methanoculleus) in the rumen could also assist CH₄ production if the rumen fermentation was followed with anaerobic digestion.

A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle

Analysis of shotgun metagenomic data generated from next generation sequencing platforms can be done through a variety of bioinformatic pipelines. These pipelines employ different sets of sophisticated bioinformatics algorithms which may affect the results of this analysis. In this study, we compared two commonly used pipelines for shotgun metagenomic analysis: MG-RAST and Kraken 2, in terms of taxonomic classification, diversity analysis, and usability using their primarily default parameters. Overall, the two pipelines detected similar abundance distributions in the three most abundant taxa Proteobacteria, Firmicutes, and Bacteroidetes. Within bacterial domain, 497 genera were identified by both pipelines, while an additional 694 and 98 genera were solely identified by Kraken 2 and MG-RAST, respectively. 933 species were detected by the two algorithms. Kraken 2 solely detected 3550 species, while MG-RAST identified 557 species uniquely. For archaea, Kraken 2 generated 105 and 236 genera and species, respectively, while MG-RAST detected 60 genera and 88 species. 54 genera and 72 species were commonly detected by the two methods. Kraken 2 had a quicker analysis time (~4 hours) while MG-RAST took approximately 2 days per sample. This study revealed that Kraken 2 and MG-RAST generate comparable results and that a reliable high-level overview of sample is generated irrespective of the pipeline selected. However, Kraken 2 generated a more accurate taxonomic identification given the higher number of "Unclassified" reads in MG-RAST. The observed variations at the genus level show that a main restriction is using different databases for classification of the metagenomic data. The results of this research indicate that a more inclusive and representative classification of microbiomes may be achieved through creation of the combined pipelines.

How Dietary Diversity Enhances Hedonic and Eudaimonic Well-Being in Grazing Ruminants

Ruminants evolved in diverse landscapes of which they utilized, by choice, a diverse arrangement of plants (grasses, forbs, and trees) for food. These plants provide them with both primary (carbohydrates, protein, etc.) and secondary (phenolics, terpenes, etc.) compounds (PPC and PSC, respectively). As no one plant could possibly constitute a “balanced-diet,” ruminants mix diets so that they can exploit arrangements of PPC to meet their individual requirements. Diet mixing also allows for ruminants to ingest PSC at levels, acquiring their benefits such as antioxidants and reduced gastrointestinal parasites, without overstepping thresholds of toxicity. Meeting dietary requirements is assumed to provide satisfaction through achieving positive internal status and comfort, thereby a sense of hedonic (happiness through pleasure) well-being. Furthermore, choice including dietary choice is a factor influencing well-being of ruminants in a manner akin to that in humans. Choice may facilitate eudaimonic (happiness through pursuit of purpose) well-being in livestock. Nutritional status plays an integral role in oxidative stress, which is linked with illness. Several diseases in livestock have been directly linked to oxidative stress. Mastitis, metritis, hypocalcaemia, and retained placenta occur in animals transitioning from dry to lactating and have been linked to oxidative stress and such a stress has likewise been linked to diseases that occur in growing livestock as well, such as bovine respiratory disease. The link between physiological stress and oxidative stress is not well-defined in livestock but is evident in humans. As dietary diversity allows animals to select more adequately balanced diets (improved nutrition), take advantage of PSC (natural antioxidants), and allows for choice (improved animal well-being) there is a strong possibility for ruminants to improve their oxidative status and thus health, well-being, and therefor production. The purposes of this review are to first, provide an introduction to oxidative and physiological stress, and nutritional status as effected by dietary diversity, with special attention to providing support and on answering the “how.” Second, to provide evidence of how these stresses are connected and influence each other, and finally discuss how dietary diversity provides a beneficial link to all three and enhances both eudaimonic and hedonic well-being.

BIPEP: Sequence-based Prediction of Biofilm Inhibitory Peptides Using a Combination of NMR and Physicochemical Descriptors

Biofilms are biological systems that are formed by a community of microorganisms in which microbial cells are connected on a surface within a self-produced matrix of an extracellular polymeric substance. On some occasions, microorganisms use biofilms to protect themselves against the harmful effects of the host body immune system and the surrounding environment, hence increasing their chances of survival against the various anti-microbial agents. Biofilms play a crucial role in medicine and industry because of the problems they cause. Designing agents that inhibit bacterial biofilm formation is very costly and takes too much time in the laboratory to be discovered and validated. Therefore, developing computational tools for the prediction of biofilm inhibitor peptides is inevitable and important. Here, we present a computational prediction tool to screen the vast number of peptide sequences and select potential candidate peptides for further lab experiments and validation. In this learning model, different feature vectors, extracted from the peptide primary structure, are exploited to learn patterns from the sequence of biofilm inhibitory peptides. Various classification algorithms including SVM, random forest, and k-nearest neighbor have been examined to evaluate their performance. Overall, our approach showed better prediction in comparison with other prediction methods. In this study, for the first time, we applied features extracted from NMR spectra of amino acids along with physicochemical features. Although each group of features showed good discrimination potential alone, we used a combination of features to enhance the performance of our method. Our prediction tool is freely available.