Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome

A metagenomic catalogue of the ruminant gut archaeome

While the ruminant gut archaeome regulates the gut microbiota and hydrogen balance, it is also a major producer of the greenhouse gas methane. However, ruminant gut archaeome diversity within the gastrointestinal tract (GIT) of ruminant animals worldwide remains largely underexplored. Here, we construct a catalogue of 998 unique archaeal genomes recovered from the GITs of ruminants, utilizing 2270 metagenomic samples across 10 different ruminant species. Most of the archaeal genomes (669/998 = 67.03%) belong to Methanobacteriaceae and Methanomethylophilaceae (198/998 = 19.84%). We recover 47/279 previously undescribed archaeal genomes at the strain level with completeness of >80% and contamination of <5%. We also investigate the archaeal gut biogeography across various ruminants and demonstrate that archaeal compositional similarities vary significantly by breed and gut location. The catalogue contains 42,691 protein clusters, and the clustering and methanogenic pathway analysis reveal strain- and host-specific dependencies among ruminant animals. We also find that archaea potentially carry antibiotic and metal resistance genes, mobile genetic elements, virulence factors, quorum sensors, and complex archaeal viromes. Overall, this catalogue is a substantial repository for ruminant archaeal recourses, providing potential for advancing our understanding of archaeal ecology and discovering strategies to regulate methane production in ruminants.

Effects of High-Grain Diet on Performance, Ruminal Fermentation, and Rumen Microbial Flora of Lactating Holstein Dairy Cows

The objectives of the current study were to evaluate the fluctuations in production performance, rumen fermentation, and microbial community in lactating dairy cows fed a high-grain diet (HG). In this study, 16 healthy Holstein lactating dairy cattle with similar milk yields of 16.80 ± 4.30 kg/d, days in milk 171.44 ± 23.25 days, and parity 2.2 ± 1.5 times were selected and randomly allocated into two groups. One group was fed a low-grain diet (LG; 40% concentrate, DM basis; n = 8), and the other group was fed a high-grain diet (HG; 60% concentrate, DM basis; n = 8). The experiment lasted 6 weeks, including 1 week for adaptation. The experimental results showed that the milk fat content in the milk of lactating cows in the HG group was significantly reduced (p < 0.05), and the milk urea nitrogen (MUN) content showed an increasing trend (0.05 < p < 0.10) compared with the LG group. Compared with the LG group, rumen fluid pH was significantly decreased after feeding a high-grain diet, and contents of total volatile fatty acids (TVFA), acetate, propionate, and butyrate were significantly increased (p < 0.05). The acetate/propionate significantly decreased (p < 0.05). HG group significantly increased the abundance of Prevotella and Bacteroides in rumen fluid while significantly reducing the abundance of Methanobrevibacter and Lachnospiraceae ND3007_group (p < 0.05). Microorganisms with LDA scores > 2 were defined as unique, with the bacterial genus Anaerorhabdus_furcosa_group identified as a biomarker for the LG group, and the unique bacterial genus in the HG group were Prevotella, Stenotrophomonas, and Xanthomonadaceae. The prediction results of microbial function showed that a total of 18 KEGG differential pathways were generated between the two treatment groups, mainly manifested in metabolic pathways, signal transduction, and the immune system. In conclusion, the HG group promoted rumen fermentation by altering the microbial composition of lactating cows. Our findings provide a theoretical basis for the rational use of high-grain diets to achieve high yields in intensive dairy farming.

From Food Waste to Sustainable Agriculture: Nutritive Value of Potato By-Product in Total Mixed Ration for Angus Bulls

Raw potato fries are a type of potato by-product (PBP), and they have great potential as a partial replacement of grain in animal feeds to improve the environmental sustainability of food production. This study aimed to investigate the effects of replacing corn with different levels of PBP (0%, 12.84%, 25.65%, and 38.44%) in the total mixed ration (TMR) of Angus bull. Sixty 16-month-old Angus bulls (548.5 ± 15.0 kg, mean ± SD) were randomly assigned to four treatments. The results indicated that with the increase in the substitution amount of PBP, the body weight decreased significantly. The dry matter apparent digestibility and starch apparent digestibility linearly decreased as PBP replacement increased. The feed ingredient composition in the TMR varied, leading to a corresponding change in the rumen microbiota, especially in cellulolytic bacteria and amylolytic bacteria. The abundance of Succiniclasticum in the 12.84% PBP and 38.44% PBP diets was significantly higher than that in the 0% PBP and 25.65% PBP diets. The abundance of Ruminococcus linearly increased. In conclusion, using PBP to replace corn for beef cattle had no negative impact on rumen fermentation, and the decrease in apparent digestibility explained the change in growth performance. Its application in practical production is highly cost-effective and a strategy to reduce food waste.

CcNAC6 Acts as a Positive Regulator of Secondary Cell Wall Synthesis in Sudan Grass (Sorghum sudanense S.)

The degree of forage lignification is a key factor affecting its digestibility by ruminants such as cattle and sheep. Sudan grass (Sorghum sudanense S.) is a high-quality sorghum forage, and its lignocellulose is mostly stored in the secondary cell wall. However, the secondary cell wall synthesis mechanism of Sudan grass has not yet been studied in depth. To further study the secondary cell wall synthesis mechanism of Sudan grass using established transcriptome data, this study found that CcNAC6, a homologous gene of Arabidopsis AtSND2, is related to the secondary cell wall synthesis of Sudan grass. Accordingly, we constructed a CcNAC6-overexpressing line of Arabidopsis to investigate the function of the CcNAC6 gene in secondary cell wall synthesis. The results showed that the overexpression of the CcNAC6 gene could significantly increase the lignin content of Arabidopsis. Based on subcellular localization analysis, CcNAC6 is found in the nucleus. In addition, yeast two-hybridization screening showed that CcCP1, associated with secondary cell wall synthesis, can interact with CcNAC6. Therefore, the above results indicate that CcNAC6 has a positive regulatory effect on the secondary cell wall synthesis of Sudan grass, and it is speculated that CcNAC6 may be the main regulator of the secondary cell wall synthesis of Sudan grass through its interaction with another regulatory protein, CcCP1. This study provides a theoretical basis and new genetic resources for the creation of new Sudan grass germplasm with a low lignin content.

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments

BACKGROUND

Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species.

RESULTS

We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea.

CONCLUSIONS

The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.

CcNAC1 by Transcriptome Analysis Is Involved in Sudan Grass Secondary Cell Wall Formation as a Positive Regulator

Sudan grass is a high-quality forage of sorghum. The degree of lignification of Sudan grass is the main factor affecting its digestibility in ruminants such as cattle and sheep. Almost all lignocellulose in Sudan grass is stored in the secondary cell wall, but the mechanism and synthesis of the secondary cell wall in Sudan grass is still unclear. In order to study the mechanism of secondary cell wall synthesis in Sudan grass, we used an in vitro induction system of Sudan grass secondary cell wall. Through transcriptome sequencing, it was found that the NAC transcription factor CcNAC1 gene was related to the synthesis of the Sudan grass secondary cell wall. This study further generated CcNAC1 overexpression lines of Arabidopsis to study CcNAC1 gene function in secondary cell wall synthesis. It was shown that the overexpression of the CcNAC1 gene can significantly increase lignin content in Arabidopsis lines. Through subcellular localization analysis, CcNAC1 genes could be expressed in the nucleus of a plant. In addition, we used yeast two-hybrid screening to find 26 proteins interacting with CcNAC1. GO and KEGG analysis showed that CcNAC1 relates to the metabolic pathways and biosynthesis of secondary metabolites. In summary, the synthesis of secondary cell wall of Sudan grass can be regulated by CcNAC1.

Fermented cottonseed and rapeseed meals outperform soybean meal in improving performance, rumen fermentation, and bacterial composition in Hu sheep

Background

This study examined the effects of substituting cottonseed meal (CSM) or rapeseed meal (RSM) for soybean meal (SBM) on Hu sheep performance, rumen fermentation, and bacterial composition. 51 four-month-old indigenous male Hu sheep with starting body weights of 22.51 ± 2.84 kg and similar origins were randomly assigned to three treatments; (1) non-fermented total mixed ration (TMR) with SBM (CK), (2) fermented TMR containing CSM (F-CSM group), and (3) fermented TMR containing RSM (F-RSM group).

Results

The three groups’ intake of dry matter differed significantly (p &lt; 0.05). In terms of average daily gain, the F-RSM group outperformed the CK and F-CSM groups (p &lt; 0.05). The pH of the rumen was substantially lower in the CK group than in the F-CSM and F-RSM groups (p &lt; 0.05), and the F-CSM group had greater amounts of volatile fatty acids (VFA) than the F-RSM and CK groups. In comparison to the CK group, the microbial crude protein yield was significantly higher in the F-CSM and F-RSM groups (p &lt; 0.05). The F-CSM group significantly outperformed the F-RSM group of pepsin and cellulose enzyme activity (p &lt; 0.05). The relative abundance of Bacteroidetes was greater in the CK and F-RSM groups compared to the F-CSM group (p &lt; 0.05). In comparison to the other groups, Firmicutes were less abundant in the CK group (p &lt; 0.05). Prevotella was present in a higher relative abundance in the F-CSM and F-RSM groups than in the CK group (p &lt; 0.05). Prevotella was greater in relative abundance in the F-CSM and F-RSM groups than in the CK group (p &lt; 0.05). The relative abundances of Veillonellaceae_UCG-001 and Lachnospiraceae_XPB1014 correlated with rumen butyric acid content and NH3-N content (p &lt; 0.05). Gene function prediction revealed that replacing SBM with F-CSM or F-RSM in the diet of Hu sheep can promote glycan biosynthesis and metabolism.

Conclusion

The replacement of F-CSM and F-RSM for SBM has an influence on the richness and diversity of rumen bacteria at the phylum and genus levels. Replacement of SBM with F-CSM increased VFA yield and further promoted the performance of Hu sheep.

Replacing soybean meal with high-oil pumpkin seed cake in the diet of lactating Holstein dairy cows modulated rumen bacteria and milk fatty acid profile

This research aimed to investigate the effects of replacing soybean meal with high-oil pumpkin seed cake (HOPSC) on ruminal fermentation, lactation performance, milk fatty acid, and ruminal bacterial community in Chinese dairy cows. Six multiparous Chinese Holstein cows at 105.50 ± 5.24 d in milk (mean ± standard deviation) and 36.63 ± 0.74 kg/d of milk yield were randomly allocated, in a 3 × 3 Latin square design, to 3 dietary treatments in which HOPSC replaced soybean meal. Group 1 was the basal diet with no HOPSC (0HOPSC); group 2 was a 50% replacement of soybean meal with HOPSC and dried distillers grains with solubles (DDGS; 50HOPSC), and group 3 was a 100% replacement of soybean meal with HOPSC and DDGS (100HOPSC). We found no difference in the quantity of milk produced or milk composition among the 3 treatment groups. Feed efficiency tended to increase linearly as more HOPSC was consumed. In addition, rumen fermentation was not influenced when soybean meal was replaced with HOPSC and DDGS; the relative abundance of ruminal bacteria at the phylum and genus levels was altered. We also observed that as the level of HOPSC supplementation increased, the relative abundance of Firmicutes and Tenericutes linearly increased, whereas that of Bacteroidetes decreased. However, with increasing HOPSC supplementation, the relative abundance of Ruminococcus decreased linearly at the genus level in the rumen, and the relative abundance of Prevotella showed a linear downward tendency. Changes in dietary composition and rumen bacteria had no significant effect on the fatty acid composition of milk. In conclusion, our results indicated that replacing soybean meal with a combination of HOPSC and DDGS can meet the nutritional needs of high-yielding dairy cows without adversely affecting milk yield and quality; however, the composition of rumen bacteria could be modified. Further study is required to investigate the effects of long-term feeding of HOPSC on rumen fermentation and performance of dairy cows.

Rumen Microbiome Reveals the Differential Response of CO2 and CH4 Emissions of Yaks to Feeding Regimes on the Qinghai-Tibet Plateau

Shifts in feeding regimes are important factors affecting greenhouse gas (GHG) emissions from livestock farming. However, the quantitative values and associated drivers of GHG emissions from yaks (Bos grunniens) following shifts in feeding regimes have yet to be fully described. In this study, we aimed to investigate CH4 and CO2 emissions differences of yaks under different feeding regimes and their potential microbial mechanisms. Using static breathing chamber and Picarro G2508 gas concentration analyzer, we measured the CO2 and CH4 emissions from yaks under traditional grazing (TG) and warm-grazing and cold-indoor feeding (WGCF) regimes. Microbial inventories from the ruminal fluid of the yaks were determined via Illumina 16S rRNA and ITS sequencing. Results showed that implementing the TG regime in yaks decreased their CO2 and CH4 emissions compared to the WGCF regime. The alpha diversity of ruminal archaeal community was higher in the TG regime than in the WGCF regime. The beta diversity showed that significant differences in the rumen microbial composition of the TG regime and the WGCF regime. Changes in the rumen microbiota of the yaks were driven by differences in dietary nutritional parameters. The relative abundances of the phyla Neocallimastigomycota and Euryarchaeota and the functional genera Prevotella, Ruminococcus, Orpinomyces, and Methanobrevibacter were significantly higher in the WGCF regime than in the TG regime. CO2 and CH4 emissions from yaks differed mainly because of the enrichment relationship of functional H2- and CO2-producing microorganisms, hydrogen-consuming microbiota, and hydrogenotrophic methanogenic microbiota. Our results provided a view that it is ecologically important to develop GHG emissions reduction strategies for yaks on the Qinghai-Tibet Plateau based on traditional grazing regime.

Susceptibility of dairy cows to subacute ruminal acidosis is reflected in both prepartum and postpartum bacteria as well as odd- and branched-chain fatty acids in feces

Background

The transition period is a challenging period for high-producing dairy cattle. Cows in early lactation are considered as a group at risk of subacute ruminal acidosis (SARA). Variability in SARA susceptibility in early lactation is hypothesized to be reflected in fecal characteristics such as fecal pH, dry matter content, volatile and odd- and branched-chain fatty acids (VFA and OBCFA, respectively), as well as fecal microbiota. This was investigated with 38 periparturient dairy cows, which were classified into four groups differing in median and mean time of reticular pH below 6 as well as area under the curve of pH below 6. Furthermore, we investigated whether fecal differences were already obvious during a period prior to the SARA risk (prepartum).

Results

Variation in reticular pH during a 3-week postpartum period was not associated with differences in fecal pH and VFA concentration. In the postpartum period, the copy number of fecal bacteria and methanogens of unsusceptible (UN) cows was higher than moderately susceptible (MS) or susceptible (SU) cows, while the genera Ruminococcus and Prevotellacea_UCG-001 were proportionally less abundant in UN compared with SU cows. Nevertheless, only a minor reduction was observed in iso-BCFA proportions in fecal fatty acids of SU cows, particularly iso-C15:0 and iso-C16:0, compared with UN cows. Consistent with the bacterial changes postpartum, the lower abundance of Ruminococcus was already observed in the prepartum fecal bacterial communities of UN cows, whereas Lachnospiraceae_UCG-001 was increased. Nevertheless, no differences were observed in the prepartum fecal VFA or OBCFA profiles among the groups. Prepartum fecal bacterial communities of cows were clustered into two distinct clusters with 70% of the SU cows belonging to cluster 1, in which they represented 60% of the animals.

Conclusions

Inter-animal variation in postpartum SARA susceptibility was reflected in post- and prepartum fecal bacterial communities. Differences in prepartum fecal bacterial communities could alert for susceptibility to develop SARA postpartum. Our results generated knowledge on the association between fecal bacteria and SARA development which could be further explored in a prevention strategy.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-022-00738-8.

Yak rumen microbiome elevates fiber degradation ability and alters rumen fermentation pattern to increase feed efficiency

Rumen microbes play an important role in ruminant energy supply and animal performance. Previous studies showed that yak (Bos grunniens) rumen microbiome and fermentation differ from other ruminants. However, little is understood about the features of the rumen microbiome that make yak adapted to their unique environmental and dietary conditions. This study was to investigate the rumen microbiome and metabolome to understand how yak adapt to the coarse forage and harsh environment in the Qinghai-Tibetan plateau. Nine female Qaidam yellow cattle (Bos taurus), 9 dzomo (hybrids of cattle and yak) and 9 female plateau yak (B. grunniens), about 5 to 6 years old, were used in this study. Rumen fermentation parameters, fibrolytic enzyme activities, and rumen metataxonomic were determined. Then 18 (6 samples per group) were selected for rumen metagenomic and metabolome analysis. Metataxonomic analysis revealed that the rumen microbiota was significantly different among plateau yak, Qaidam yellow cattle, and dzomo (P < 0.05). Metagenomic analysis displayed a larger gene pool encoding a richer repertoire of carbohydrate-active enzymes in the rumen microbiome of plateau yak and dzomo than Qaidam yellow cattle (P < 0.05). Some of the genes encoding glycoside hydrolases that mediate the digestion of cellulose and hemicellulose were significantly enriched in the rumen of plateau yak than Qaidam yellow cattle, but glycoside hydrolase 57 that primarily includes amylases was abundant in Qaidam yellow cattle (P < 0.05). The rumen fermentation profile differed also, Qaidam yellow cattle having a higher molar proportion of acetate but a lower molar proportion of propionate than dzomo and plateau yak (P < 0.05). Based on metabolomic analysis, rumen microbial metabolic pathways and metabolites were different. Differential metabolites are mainly amino acids, carboxylic acids, sugars, and bile acids. Changes in rumen microbial composition could explain the above results. The present study showed that the rumen microbiome of plateau yak helps its host to adapt to the Qinghai-Tibetan plateau. In particular, the plateau yak rumen microbiome has more enzymes genes involved in cellulase and hemicellulase than that of cattle, resulting higher fibrolytic enzyme activities in yak, further providing stronger fiber degradation function.

Taxonomy and Functional Diversity in the Fecal Microbiome of Beef Cattle Reared in Brazilian Traditional and Semi-Intensive Production Systems

The importance of beef production for economy of Brazil and the growing demand for animal protein across the globe warrant an improvement in the beef production system. Although most attention has been on modulation of the rumen microbiome to improve ruminant production, the role of the lower gut microbiome in host health and nutrition remains relatively unexplored. This work aimed to investigate the taxonomy and functional variations in the fecal microbiome of Brazilian beef cattle reared in two different production systems using a metagenomic approach. Sixty male beef cattle from six farms representing semi-intensive (I, n = 2) and traditional (T, n = 4) Brazilian beef production systems were enrolled in the study. Shotgun sequencing was used to characterize taxonomic and functional composition and diversity of the microbiome in fecal samples collected from each animal. Fecal samples were analyzed for copper (Cu), lead (Pb), nitrogen (N), phosphorous (P), selenium (Se), and zinc (Zn) and stable isotopes of carbon (¹³C) and nitrogen (¹⁵N). The fecal microbiome was influenced by the beef production systems with greater functional and lower taxonomic diversity in beef cattle feces from I systems compared with that from T systems. The concentration of N, P, and Zn was higher in beef cattle feces from I systems compared with that from T systems and was associated with taxonomic and functional profile of fecal microbiome in I system, suggesting the role of fecal nutrients in shaping system-specific microbiome. Semi-intensive management practices led to a more complex but less connected fecal microbiome in beef cattle. The microbial community in beef cattle feces from I systems was characterized by greater abundance of beneficial bacteria (phylum Firmicutes and butyrate-producing bacteria family Lachnospiraceae and genera Anaerostipes, Blautia, Butyrivibrio, Eubacterium, Roseburia, and Ruminococcus). In addition, the fecal abundance of microbial genes related to immune system, nutrient metabolism, and energy production was greater in beef cattle raised under I systems compared with that under T systems. Findings of the current study suggest that semi-intensive management practices could facilitate the development of a healthier and more efficient fecal microbiome in beef cattle by driving an increase in the abundance of beneficial bacteria and functional genes.

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

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

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

Characterization of growth phenotypes and gastrointestinal tract microbiota in sheep fed with caragana

AIMS

Using high-protein caragana as an unconventional feed supplement has promising application potential in livestock feeding programmes, and verifying its function is of great importance to guide efficient dietary management of livestock.

METHODS AND RESULTS

This study investigated the resulting changes in the growth, slaughter performance, serum physiological index, physical and chemical characteristics of meat, ruminal and intestine morphology and gastrointestinal tract microbiota in sheep fed with caragana (CAR), corn straw (COR) and alfalfa (ALF) diets. The CAR group showed an increased abundance of Christensenellaceae R-7 group, Marvinbryantia, Ruminococcaceae NK4A214, Lachnospiraceae UCG-002 and Desulfuromonas in the rumen compared with ALF, and CAR group mainly enhanced starch and sucrose metabolism, fructose and mannose metabolism, photosynthesis and d-alanine metabolism in the rumen compared with ALF.

CONCLUSIONS

CAR diet positively changed the fatty acid profile of longissimus dorsi muscle and significantly altered the composition and function of the microbiota in the rumen, ileum and cecum.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study systematically demonstrated the feasibility of CAR as an alternative to ALF for animal fattening in a complete formula granulated feed and provided a fundamental basis for further research and development of CAR as an unconventional feed source for ruminants.

Vaccination against the brown stomach worm, Teladorsagia circumcincta, followed by parasite challenge, induces inconsistent modifications in gut microbiota composition of lambs

Background

Growing evidence points towards a role of gastrointestinal (GI) helminth parasites of ruminants in modifying the composition of the host gut flora, with likely repercussions on the pathophysiology of worm infection and disease, and on animal growth and productivity. However, a thorough understanding of the mechanisms governing helminth-microbiota interactions and of their impact on host health and welfare relies on reproducibility and replicability of findings. To this aim, in this study, we analysed quantitative and qualitative fluctuations in the faecal microbiota composition of lambs vaccinated against, and experimentally infected with, the parasitic GI nematode Teladorsagia circumcincta over the course of two separate trials performed over two consecutive years.

Methods

Two trials were conducted under similar experimental conditions in 2017 and 2018, respectively. In each trial, lambs were randomly assigned to one of the following experimental groups: (i) vaccinated/infected, (ii) unvaccinated/infected and (iii) unvaccinated/uninfected. Faecal samples collected from individual animals were subjected to DNA extraction followed by high-throughput sequencing of the V3-V4 region of the bacterial 16S rRNA gene and bioinformatics and biostatistical analyses of sequence data.

Results

Substantial differences in the populations of bacteria affected by immunisation against and infection by T. circumcincta were detected when comparing data from the two trials. Nevertheless, the abundance of Prevotella spp. was significantly linked to helminth infection in both trials.

Conclusions

Despite the largely conflicting findings between the two trials, our data revealed that selected gut microbial populations are consistently affected by T. circumcincta infection and/or vaccination. Nevertheless, our study calls for caution when interpreting data generated from in vivo helminth-microbiome interaction studies that may be influenced by several intrinsic and extrinsic host-, parasite- and environment-related factors.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04688-4.

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

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

Determination of the optimal priming interval of rumen fluids used as inocula for the in vitro digestibility trials through radial enzyme diffusion method

Context Determination of the neutral detergent fibre digestibility is one of the important parameters to consider when formulating diets. However, the in vitro determination shows low repeatability because of the source of rumen-fluid inoculum. Priming of the rumen fluid inocula, obtained through an oesophageal probe, has been proposed to overcome this issue. Aim The objective of the study was to investigate the evolution of the microbial enzymatic activities of different rumen fluids during a priming procedure, to establish the fermentation interval that minimises the differences among rumen-fluid degradative potentials. Methods Three farms for each type of diet were involved in the study. Rumen fluids were obtained from dry and lactating cows fed the following four diet types: 100% hay or a diet with 80:20 forage:concentrate ratio (F:C) as dry-cow diets, and ad libitum hay and concentrate, or a total mixed ration (both at 60:40 F:C) as lactating-cow diets. On each farm, rumen fluid was collected from three Holstein cows by using an oesophageal probe, and mixed. Two aliquots of each rumen fluid mix were added to the medium containing the same priming substrate in an in vitro batch-fermentation system. During the incubation, the fermentation fluids were sampled in duplicate at 0-, 1-, 2-, 4-, 8-, 24- and 48-h intervals. Enzymatic activities of amylase, cellulase and xylanase were determined by radial enzyme diffusion method. Key results Initial enzymatic activities were quite variable and increased with an increasing incubation time. By 24 h, amylase showed similar values among high-concentrate diet fermentation fluids, and a lower data dispersion in comparison to the other intervals; cellulase was characterised by similar values in all the fermentation fluids derived from diets including concentrates, and xylanase showed similar activity in the fermentation fluids derived from high-concentrate diets. Development of the enzymatic activity of the fermentation fluids derived from the 100% hay diet differed from the others. Conclusions A 24-h priming procedure was needed to stabilise and equalise the enzymatic activity of the rumen fluid from cows fed high-concentrate diets. This was not observed in rumen fluid from cows fed hay-based diets. Implications The 24-h-primed rumen fluid can be used to increase the repeatability of neutral detergent fibre digestibility determination.

Spent Coffee Grounds Alter Bacterial Communities in Latxa Dairy Ewes

Antimicrobial and antioxidant properties of spent coffee grounds (SCG) make them a potential ingredient in a diet for ruminants. This study investigated the effects of SCG on rumen microbiota. For 51 days, 36 dairy ewes were assigned to the experimental treatments (0, 30, 50, and 100 g SCG/kg). Ruminal samples were collected on day 50. DNA was extracted and subjected to paired-end Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA genes. Bioinformatic analyses were performed using QIIME (v.1.9.0). SCG increased dose-dependently bacterial diversity and altered bacterial structure. Further, 60, 78, and 449 operational taxonomic unit (OUT) were different between control and 30, 50 and 100 g/kg SCG groups, respectively. Higher differences were observed between the control and 100 g/kg SCG group, where OTU of the genera Treponema, CF231, Butyrivibrio, BF331, Anaeroplasma, Blautia, Fibrobacter, and Clostridium were enriched with SCG. Correlations between volatile fatty acids (VFA) and bacterial taxa were sparser in the SCG groups and had little overlap. Certain bacterial taxa presented different signs of the correlation with VFA in SCG and control groups, but Butyrivibrio and Blautia consistently correlated with branched-chain VFA in all groups. SCG induced shifts in the ruminal bacterial community and altered the correlation networks among bacterial taxa and ruminal VFA.

Guar gum different from Ganoderma lucidum polysaccharide in alleviating colorectal cancer based on omics analysis

It is unclear if guar gum can alleviate colorectal cancer (CRC). We evaluated the effect of guar gum (unmodified) on the mortality, colon status, serous tumor necrosis factor-alpha (TNF-α) concentration, and gut microbial and colonic epithelial cell gene expression profiles in CRC mice and performed omics analyses to compare these with those of Ganoderma lucidum polysaccharide (GLP), whose main component is β-glucan (>90%). We found that guar gum had a CRC alleviating effect. However, it showed a 20% higher mortality rate, shorter colon length, worse colon status, larger number and size of tumors, higher concentration of serous TNF-α and upregulation of epithelial cell genes (Il10, Cytl1, Igkv7-33, Ighv1-14, Igfbp6 and Foxd3) compared to that of GLP. The higher relative abundance of Akkermansia, the alteration of microbial metabolic pathways, especially those involving chaperones and folding catalysts, fatty acid biosynthesis, glycerophospholipid metabolism, glycolysis/gluconeogenesis, lipid biosynthesis and pyruvate metabolism, and the upregulation of specific genes (Mcpt2, Mcpt9, Des and Sostdc1) were also determined in animals fed a guar gum diet. The results suggested that the alleviating effect of guar gum (an inexpensive polysaccharide) on CRC was inferior to that of GLP (a more expensive polysaccharide). This could potentially be attributed to the increased presence of Akkermansia, the alteration of 10 microbial metabolic pathways and the upregulation of 4 epithelial cell genes.

Use of Integrative Interactomics for Improvement of Farm Animal Health and Welfare: An Example with Fescue Toxicosis

Rapid scientific advances are increasing our understanding of the way complex biological interactions integrate to maintain homeostatic balance and how seemingly small, localized perturbations can lead to systemic effects. The ‘omics movement, alongside increased throughput resulting from statistical and computational advances, has transformed our understanding of disease mechanisms and the multi-dimensional interaction between environmental stressors and host physiology through data integration into multi-dimensional analyses, i.e., integrative interactomics. This review focuses on the use of high-throughput technologies in farm animal research, including health- and toxicology-related papers. Although limited, we highlight recent animal agriculture-centered reports from the integrative multi-‘omics movement. We provide an example with fescue toxicosis, an economically costly disease affecting grazing livestock, and describe how integrative interactomics can be applied to a disease with a complex pathophysiology in the pursuit of novel treatment and management approaches. We outline how ‘omics techniques have been used thus far to understand fescue toxicosis pathophysiology, lay out a framework for the fescue toxicosis integrome, identify some challenges we foresee, and offer possible means for addressing these challenges. Finally, we briefly discuss how the example with fescue toxicosis could be used for other agriculturally important animal health and welfare problems.

Time-restricted feeding alleviates cardiac dysfunction induced by simulated microgravity via restoring cardiac FGF21 signaling

Dietary restriction has been well-described to improve health metrics, but whether it could benefit pathophysiological adaptation to extreme environment, for example, microgravity, remains unknown. Here, we investigated the effects of a daily rhythm of fasting and feeding without reducing caloric intake on cardiac function and metabolism against simulated microgravity. Male rats under ad libitum feeding or time-restricted feeding (TRF; food access limited to 8 hours every day) were subjected to hindlimb unloading (HU) to simulate microgravity. HU for 6 weeks led to left ventricular dyssynchrony and declined cardiac function. HU also lowered pyruvate dehydrogenase (PDH) activity and impaired glucose utilization in the heart. All these were largely preserved by TRF. TRF showed no effects on HU-induced loss of cardiac mass, but significantly improved contractile function of cardiomyocytes. Interestingly, TRF raised liver-derived fibroblast growth factor 21 (FGF21) level and enhanced cardiac FGF21 signaling as manifested by upregulation of FGF receptor-1 (FGFR1) expression and its downstream markers in HU rats. In isolated cardiomyocytes, FGF21 treatment improved PDH activity and glucose utilization, consequently enhancing cell contractile function. Finally, both liver-specific knockdown (KD) of FGF21 and cardiac-specific FGFR1 KD abrogated the cardioprotective effects of TRF in HU rats. These data demonstrate that TRF improves cardiac glucose utilization and ameliorates cardiac dysfunction induced by simulated microgravity, at least partially, through restoring cardiac FGF21 signaling, suggesting TRF as a potential countermeasure for cardioprotection in long-term spaceflight.

Effects of dietary replacement of soybean meal with dried distillers grains with solubles on the microbiota occupying different ecological niches in the rumen of growing Hu lambs

Background

Diet has a profound impact on the rumen microbiota, and the impact can vary among the different rumen ecological niches (REN). This study investigated the effects of dietary replacement of soybean meal (SBM) with dried distillers grains with solubles (DDGS) on the rumen microbiota occupying different REN of growing Hu lambs. After a 9-week feeding trial, 6 lambs from each dietary treatment (SBM vs. DDGS-based diets) were slaughtered for sample collection. The microbiota of the rumen solid, liquid, and epithelium fractions was examined using amplicon sequencing analysis of bacterial 16S rRNA gene, functional prediction, and qPCR.

Results

No interaction of dietary protein source (PS) and REN were detected for virtually all the measurements made in this study. The DDGS substitution resulted in very limited influence on bacterial community structure. However, the metabolic pathways predicted from 16S rRNA gene sequences varied greatly between SBM- and DDGS-based diets. The populations of rumen total bacteria, fungi, sulfate-reducing bacteria (SRB), and methanogens were not influenced by DDGS substitution, but the population of protozoa was reduced. The bacterial communities in rumen solid (RS) and liquid (RL) were similar in taxonomic composition but were different in relative abundance of some taxa. In contrast, the bacterial composition and relative abundance of rumen epithelium (RE) were greatly distinct from those of the RS and the RL. In alignment with the bacterial relative abundance, the metabolic pathways predicted from 16S rRNA genes also varied greatly among the different REN. The populations of total bacteria, protozoa, and methanogens attached to the RE were smaller than those in the RS and RL, and the fungal population on the rumen epithelium was smaller than that in the RS but similar to that in the RL. On the contrary, the SRB population on the RE was greater than that in the RS and RL.

Conclusions

Substitution of SBM with DDGS had greater impact to the protozoa than to the other microbes, and the microbial community structure and functions at different REN are distinct and niche-adapted.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Dietary Bioactive Lipid Compounds Rich in Menthol Alter Interactions Among Members of Ruminal Microbiota in Sheep

This study aimed to investigate the effects of two practically relevant doses of menthol-rich plant bioactive lipid compounds (PBLC) on fermentation, microbial community composition, and their interactions in sheep rumen. Twenty-four growing Suffolk sheep were divided into three treatments and were fed hay ad libitum plus 600 g/d of concentrate containing no PBLC (Control) or PBLC at low dose (80 mg/d; PBLC-L) or high dose (160 mg/d; PBLC-H). After 4 weeks on the diets, samples of ruminal digesta were collected and analyzed for short-chain fatty acid (SCFA), ammonia, and microbiota; microbiota being analyzed in the solid and the liquid digesta fractions separately. Ruminal SCFA and ammonia concentrations were not affected by the PBLC treatments. The microbiota in the solid fraction was more diverse than that in the liquid fraction, and the relative abundance of most taxa differed between these two fractions. In the solid fraction, phylogenetic diversity increased linearly with increased PBLC doses, whereas evenness (lowest in PBLC-L) and Simpson diversity index (greatest in PBLC-H) changed quadratically. In the liquid fraction, however, the PBLC supplementation did not affect any of the microbial diversity measurements. Among phyla, Chloroflexi (highest in PBLC-L) and unclassified_bacteria (lowest in PBLC-L) were altered quadratically by PBLC. Lachnospiraceae, Bacteroidaceae (increased linearly), BS11 (increased in PBLC-L), Christensenellaceae (decreased in PBLC treatments), and Porphyromonadaceae (increased in PBLC treatments) were affected at the family level. Among genera, Butyrivibrio increased linearly in the solid fraction, YRC22 increased linearly in the liquid fraction, whereas Paludibacter increased and BF311 increased linearly with increasing doses of PBLC in both fractions. The PBLC treatments also lowered methanogens within the classes Thermoplasmata and Euryarchaeota. Correlation network analysis revealed positive and negative correlations among many microbial taxa. Differential network analysis showed that PBLC supplementation changed the correlation between some microbial taxa and SCFA. The majority of the predicted functional features were different between the solid and the liquid digesta fractions, whereas the PBLC treatments altered few of the predicted functional gene categories. Overall, dietary PBLC treatments had little influence on the ruminal fermentation and microbiota but affected the associations among some microbial taxa and SCFA.

Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints

The gut microbiome of primates, including humans, is reported to closely follow host evolutionary history, with gut microbiome composition being specific to the genetic background of its primate host. However, the comparative models used to date have mainly included a limited set of closely related primates. To further understand the forces that shape the primate gut microbiome, with reference to human populations, we expanded the comparative analysis of variation among gut microbiome compositions and their primate hosts, including 9 different primate species and 4 human groups characterized by a diverse set of subsistence patterns (n = 448 samples). The results show that the taxonomic composition of the human gut microbiome, at the genus level, exhibits increased compositional plasticity. Specifically, we show unexpected similarities between African Old World monkeys that rely on eclectic foraging and human populations engaging in nonindustrial subsistence patterns; these similarities transcend host phylogenetic constraints. Thus, instead of following evolutionary trends that would make their microbiomes more similar to that of conspecifics or more phylogenetically similar apes, gut microbiome composition in humans from nonindustrial populations resembles that of generalist cercopithecine monkeys. We also document that wild cercopithecine monkeys with eclectic diets and humans following nonindustrial subsistence patterns harbor high gut microbiome diversity that is not only higher than that seen in humans engaging in industrialized lifestyles but also higher compared to wild primates that typically consume fiber-rich diets.IMPORTANCE The results of this study indicate a discordance between gut microbiome composition and evolutionary history in primates, calling into question previous notions about host genetic control of the primate gut microbiome. Microbiome similarities between humans consuming nonindustrialized diets and monkeys characterized by subsisting on eclectic, omnivorous diets also raise questions about the ecological and nutritional drivers shaping the human gut microbiome. Moreover, a more detailed understanding of the factors associated with gut microbiome plasticity in primates offers a framework to understand why humans following industrialized lifestyles have deviated from states thought to reflect human evolutionary history. The results also provide perspectives for developing therapeutic dietary manipulations that can reset configurations of the gut microbiome to potentially improve human health.

Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes

Ruminant animals have a symbiotic relationship with the microorganisms in their rumens. In this relationship, rumen microbes efficiently degrade complex plant-derived compounds into smaller digestible compounds, a process that is very likely associated with host animal feed efficiency. The resulting simpler metabolites can then be absorbed by the host and converted into other compounds by host enzymes. We used a microbial community metabolic network inferred from shotgun metagenomics data to assess how this metabolic system differs between animals that are able to turn ingested feedstuffs into body mass with high efficiency and those that are not. We conducted shotgun sequencing of microbial DNA from the rumen contents of 16 sheep that differed in their residual feed intake (RFI), a measure of feed efficiency. Metagenomic reads from each sheep were mapped onto a database-derived microbial metabolic network, which was linked to the sheep metabolic network by interface metabolites (metabolites transferred from microbes to host). No single enzyme was identified as being significantly different in abundance between the low and high RFI animals (P > 0.05, Wilcoxon test). However, when we analyzed the metabolic network as a whole, we found several differences between efficient and inefficient animals. Microbes from low RFI (efficient) animals use a suite of enzymes closer in network space to the host's reactions than those of the high RFI (inefficient) animals. Similarly, low RFI animals have microbial metabolic networks that, on average, contain reactions using shorter carbon chains than do those of high RFI animals, potentially allowing the host animals to extract metabolites more efficiently. Finally, the efficient animals possess community networks with greater Shannon diversity among their enzymes than do inefficient ones. Thus, our system approach to the ruminal microbiome identified differences attributable to feed efficiency in the structure of the microbes' community metabolic network that were undetected at the level of individual microbial taxa or reactions.

RUMINANT NUTRITION SYMPOSIUM: Tiny but mighty: the role of the rumen microbes in livestock production

The microbes inhabiting the rumen convert low-quality, fibrous, plant material into useable energy for the host ruminant. Consisting of bacteria, protozoa, fungi, archaea, and viruses, the rumen microbiome composes a sophisticated network of symbiosis essential to maintenance, immune function, and overall production efficiency of the host ruminant. Robert Hungate laid the foundation for rumen microbiome research. This area of research has expanded immensely with advances in methodology and technology that have not only improved the ability to describe microbes in taxonomic and density terms but also characterize populations of microbes, their functions, and their interactions with each other and the host. The interplay between the rumen microbiome and the host contributes to variation in many phenotypic traits expressed by the host animal. A better understanding of how the rumen microbiome influences host health and performance may lead to novel strategies and treatments for trait improvement. Furthermore, elucidation of maternal, genetic, and environmental factors that influence rumen microbiome establishment and development may provide novel insights into possible mechanisms for manipulating the rumen microbial composition to enhance long-term host health and performance. The potential for these tiny but mighty rumen microbes to play a role in improving livestock production is appreciated despite being relatively obscure.