Metagenome sequencing to analyze the impacts of thiamine supplementation on ruminal fungi in dairy cows fed high-concentrate diets

Effects of yeast culture on in vitro ruminal fermentation and microbial community of high concentrate diet in sheep

This research aimed to investigate effects of different yeast culture (YC) levels on in vitro fermentation characteristics and bacterial and fungal community under high concentrate diet. A total of 5 groups were included in the experiment: control group without YC (CON), YC1 (0.5% YC proportion of substrate dry matter), YC2 (1%), YC3 (1.5%) and YC4 (2%). After 48 h of fermentation, the incubation fluids and residues were collected to analyze the ruminal fermentation parameters and bacterial and fungal community. Results showed that the ruminal fluid pH of YC2 and YC4 groups was higher (P < 0.05) than that of CON group. Compared with CON group, the microbial protein, propionate and butyrate concentrations and cumulative gas production at 48 h of YC2 group were significantly increased (P < 0.05), whereas an opposite trend of ammonia nitrogen and lactate was observed between two groups. Microbial analysis showed that the Chao1 and Shannon indexes of YC2 group were higher (P < 0.05) than those of CON group. Additionally, YC supplementation significantly decreased (P < 0.05) Succinivibrionaceae_UCG-001, Streptococcus bovis and Neosetophoma relative abundances. An opposite tendency of Aspergillus abundance was found between CON and YC treatments. Compared with CON group, the relative abundances of Prevotella, Succiniclasticum, Butyrivibrio and Megasphaera elsdenii were significantly increased (P < 0.05) in YC2 group, while Apiotrichum and unclassified Clostridiales relative abundances were decreased (P < 0.05). In conclusion, high concentrate substrate supplemented with appropriate YC (1%) can improve ruminal fermentation and regulate bacterial and fungal composition.

Milk Yields and Milk Fat Composition Promoted by Pantothenate and Thiamine via Stimulating Nutrient Digestion and Fatty Acid Synthesis in Dairy Cows

Considering the synergistic effect of pantothenate and thiamine on the regulation of energy metabolism, this study investigated the influences of coated calcium pantothenate (CCP) and coated thiamine (CT) on milk production and composition, nutrients digestion, and expressions of genes involved in fatty acids synthesis in mammary glands. Forty-four multiparous Chinese Holstein cows (2.8 ± 0.19 of parity, 772 ± 12.3 kg of body weight [BW], 65.8 ± 8.6 days in milk [DIM] and 35.3 ± 1.9 kg/d of milk production, mean ± SD) were blocked by parity, BW, DIM, and milk production, and they were allocated into one of four treatments in a 2 × 2 factorial block design. Additional CCP (0 mg/kg [CCP-] or 55 mg/kg dry matter [DM] of calcium pantothenate from CCP [CCP+]) and CT (0 g/kg [CT-] or 5.3 mg/kg DM of thiamine from CT [CT+]) were hand-mixed into the top one-third of total mixed ration. Both CCP and CT additives increased milk production, fat content, true protein, and lactose by promoting nutrient digestibility. The CCP or/and CT supplementation induced the elevation of C11:0, C12:0, C13:0, C14:0, C14:1, C15:0, C15:1, C16:00, C16:1, C24:00, C24:1 fatty acids, saturated fatty acid, and C4-16 fatty acid contents in milk fat; but it decreased C17-22 fatty acid content. Ruminal total VFA content was increased, but pH was decreased by both additives. The ruminal fermentation pattern was altered, and a tendency of acetate formation was implied by the increased acetate-to-propionate ratio after both additives' supplementation. The expressions of PPARγ, SREBPF1, ACACA, FASN, SCD, and FABP3 mRNAs were enhanced by CCP or CT addition, but the relative expression of LPL mRNA was upregulated by CT addition only. Additionally, blood glucose, triglyceride, insulin-like growth factor-1, and total antioxidant capacity were promoted by both additives. The combination of CCP and CT more effectively increased the ruminal total VFA concentration, the acetate to propionate ratio, and blood glucose level, and decreased ammoniacal nitrogen concentration than that achieved by CCP or CT alone. The results suggested that CCP and CT supplementation stimulated lactation performance by promoting nutrient digestion and fatty acid synthesis in the mammary glands.

Effects of ensiling sugarcane tops with bacteria-enzyme inoculants on growth performance, nutrient digestibility, and the associated rumen microbiome in beef cattle

Major challenges when ensiling sugarcane tops include fermentation that results in high quantities of alcohol and decrease in nutrient digestibility due to the accumulation of fiber components. Increased efforts to apply bacteria-enzyme inoculants in silage have the potential to improve nutrient digestibility. This study aimed to evaluate the effects of ensiling sugarcane tops with bacteria-enzyme inoculants or mixed bacterial inoculants on growth performance, nutrient digestibility, and rumen microbiome in beef cattle. Chopped sugarcane tops were ensiled in plastic bags for 60 d after application of 1) no inoculant (control check, CK); 2) bacteria-enzyme inoculants containing Pediococcus acidilactici, Saccharomyces cerevisiae, cellulase, and xylanase (T1, viable colony-forming units of each bacterial strain ≥108 CFU/g; enzyme activity of each enzyme ≥200 U/g); or 3) mixed bacterial inoculants containing Lactobacillus plantarum, Bacillus subtilis, and Aspergillus oryzae (T2, viable colony-forming units of each bacterial strain ≥107 CFU/g). Silages were fed to eighteen Holstein bull calves (n = 6/treatment) weighing 163.83 ± 7.13 kg to determine intake in a 49-d experimental period. The results showed that beef cattle-fed T1 silage or T2 silage had a significantly higher (P < 0.05) average daily gain than those fed CK silage, but the difference in dry matter intake was not significant (P > 0.05). The apparent digestibility of crude protein (CP) and acid detergent fiber (ADF) were higher (P < 0.05) for beef cattle-fed T1 silage or T2 silage than for those fed CK silage. The rumen bacterial community of beef cattle-fed T1 silage or T2 silage had a tendency to increase (P > 0.05) abundance of Firmicutes and Rikenellaceae_RC9_gut_group than those fed CK silage. Rumen fungal communities of beef cattle-fed T1 or T2 silage had a tendency to increase (P > 0.05) abundance of Mortierellomycota and of Mortierella than those fed CK silage. Spearman's rank correlation coefficient showed that the apparent digestibility of ADF for beef cattle was positively correlated with unclassified_p_Ascomycota of the fungal genera (P < 0.05). Neocalimastigomycota of the fungal phyla was strongly positively correlated with the apparent digestibility of neutral detergent fiber (NDF) (P < 0.05). Ruminococcus was positively correlated with the apparent digestibility of CP (P < 0.05). It was concluded that both T1 and T2 improved the growth performance of beef cattle by improving the ruminal apparent digestibility of CP and ADF, and had no significant impact on major rumen microbial communities in beef cattle.

Rumen microbiota responses to the enzymatic hydrolyzed cottonseed peptide supplement under high-concentrate diet feeding process

In current dairy production, dietary energy is always excessively provided with a high-concentrate diet feeding to improve milk production. However, this feeding practice disturbed the rumen microbial ecosystem and the balance between ruminal energy and nitrogen, resulting in decreased nutrient fermentability, which in turn declined the milk yield of dairy cows. Therefore, supplementation of dietary degradable nitrogen may be helpful for high dairy production. In this study, we evaluated the regulatory effects of easily utilized enzymatic hydrolyzed cottonseed peptide (EHP) supplements on rumen microbiota communities and rumen nutrient fermentability under high-concentrate feeding. For this purpose, a gradient concentrate of EHP (from 0.2 to 1.0%) was added to the high-concentrate basal substrates for an in vitro experiment. Each treatment contained three replicates, with three bottles in each replicate. Rumen fermentable parameters included microbial protein content, volatile fatty acids, and ammonia-N; the rumen nutrient degradability of dry matter, crude protein, neutral detergent fiber, acid detergent fiber, ether extracts, calcium, and phosphorus were further investigated after in vitro fermentation for 72 h. Then, rumen microbiota communities and their correlation with ruminal fermentation parameters and rumen nutritional degradability were analyzed to understand the regulatory mechanism of the EHP supplements on rumen fermentability. Results indicate that treatment with 0.6% of EHP supplements had the highest content of acetate, butyrate, and neutral detergent fiber degradability among all treatments. Furthermore, EHP supplements significantly increased the relative abundance of rumen cellulose and starch-degrading bacteria such as Ruminococcus, Bifidobacterium, and Acetitomaculum, and the high nitrogen utilizing bacteria Butyrivibrio and Pseudobutyrivibrio, which may further promote the rumen carbohydrate and nitrogen metabolism. In summary, supplementation of easily degraded small peptides helps reestablish rumen energy and nitrogen balance to promote the rumen fermentable functions and nutritional degradability under high-concentrate diet feeding circumstances. These findings may further promote dairy production.

Metagenomic insights into the rumen epithelial integrity responses to the vitamin B1 supplement under high-concentrate diets treatments

Subacute ruminal acidosis (SARA) becomes the most common nutritional metabolic disease in high-yielding dairy cows and later fatting beef cattle because of the increasing consumption of high-concentrate diets in modern feeding patterns. Our previous research found a certain piece of evidence that adding 180 mg thiamine/kg DMI could increase the rumen pH and regulate the structure of the rumen microbial community in vivo. However, there is still limited experimental data on the effects of SARA on thiamine status, the damage to the structure of rumen epithelial cells, and the underlying mechanism of the epithelium alterations. For this purpose, a total of 18 Angus bulls (average 22.0-months-old) with an average live weight of 567.6 ± 27.4 kg were randomly allocated into a control treatment (CON), a high-concentrate diet treatment (HC), and a high-concentrate diet with the vitamin B1 supplement treatment (HCB). All bulls were conducted with a 7-day adjustment period followed by a 60-day-long main feeding procedure. Results indicated that ADFI and ADG significantly decreased in the HC treatment compared with CON (P < 0.05), while significantly increased after the VB1 supplement (P < 0.05). Besides, ruminal acetate content was significantly downregulated while propionate was significantly upregulated under the HC treatment compared with CON (P < 0.05); however, these alterations showed a completely inverse regulatory effect on the VB1 supplement compared with HC (P < 0.05). These changes causatively induced a significant decrease in the A/P ratio in the HC treatment compared with CON and HCB treatments (P < 0.05). Bacterial communities in the HC treatment could be separated from those in CON through PCoA axes 1 and 2. Meanwhile, the VB1 supplement significantly altered the bacterial communities compared with the HC treatment, except for HCB-3. Furthermore, the HC treatment significantly upregulated the expression of JNK, Bax, Caspase-8, Caspase-3, Caspase-9, and Cyt-C compared with CON, while significantly downregulated the expression of Bcl-2. The VB1 supplement showed a complete converse gene expression compared with HC. In conclusion, the VB1 supplement could effectively attenuate the alterations that occurred when exposed to high-concentrate diets, and help promote production performance through increased fermentability.

Microbial and metabolomic insights into the bovine lipometabolic responses of rumen and mammary gland to zymolytic small peptide supplementation

Small peptides provide the easily utilized nitrogen for rumen microbial and promote acetate generation for milk fat synthesis. However, the impacts of peptide supplements on lipometabolic processes were still unclear. Therefore, a total of 800 multiparous dairy herds (with an average live weight of 667.6 ± 39.4 kg, an average lactation of 89.3 ± 18.8 days, and an average calving parity of 2.76 ± 0.47) were randomly allocated to the control (CON) and the small peptide (SP) supplement (100 g/day for each cow) treatments, respectively. A 35-day-long feeding procedure that includes a 7-day-long pretreatment test and a 28-day-long treatment test was followed for all cows. Dry matter intake (DMI) was recorded every day and calculated by the deviation between the supply and residue, while the daily milk production was automatically recorded through the rotary milking facilities. Milk samples were collected from each replicate on the last day, followed by the milk quality and milk lipid composition measurement. Rumen fluid samples were collected on the last day through esophageal tubing 3 h after morning feeding for the determination of the underlying mechanism of the small peptide on lipid metabolism through the measurement of rumen lipometabolic-related metabolites and rumen bacterial communities. Results indicated that dry matter intake showed an increasing trend, while milk production and the milk fat content remarkably increased after SP supplement (P < 0.05). Further detailed detection showed the mainly increased milk composition focused on monounsaturated fatty acid (MUFA) and polyunsaturated fatty acid (PUFA). Acetate-producing microbes, such as Acetitomaculum, Bifidobacterium, Succiniclasticum, and Succinivibrio, and butyrate-producing microbes, such as Shuttleworthia and Saccharofermentans, significantly proliferated, which causatively brought the increased ruminal content of acetate, isobutyrate, and butyrate after SP supplement (P < 0.05) compared with CON. Lipometabolic metabolites such as phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), phosphatidylserine (PS), triacylglycerol (TG), and Acetyl-CoA also significantly increased after SP supplement. In summary, SP supplements help to increase milk fat content through the proliferation of rumen bacterial communities, which provided more acetate and butyrate for milk fat synthesis combined with the promotion of ruminal lipometabolism.

Diet Supplementation With Sulfur Amino Acids Modulated Fermentation Metabolome and Gut Microbiome in Goats

Dietary amino acids shift hydrogen metabolism to an alternative hydrogen sink consisting of dissolved hydrogen sulfur (dH2S) rather than methanogenesis; and influences the fermentation metabolome and microbiome associated with particles and liquid fractions in gut regions (foregut, small intestine, and hindgut) of goats. A completely randomized block design with a total of 20 goats (5 goats per treatment) was used to conduct the trial. The goats were fed on a diet that consisted of a concentrated mixture with maize stover roughage (50:50, on a dry matter basis) and randomly assigned to one of the four treatments: without amino acid supplementation (a basal diet), a basal diet supplemented with methionine (Met), a basal diet supplemented with lysine (Lys), and a basal diet supplemented with methionine and lysine (ML). Goats fed Met alone or in combination had less acetate, acetate to propionate ratio, and greater propionate (p &lt; 0.05) in the foregut and hindgut than those fed control or Lys. Nonetheless, the goats fed on the amino acid supplements had higher levels of branched-chain VFA (p &lt; 0.05) in the foregut and hindgut than the control goats. Goats fed on ML had the highest ammonia (p &lt; 0.01), followed by Met or Lys, both in the foregut and hindgut, compared with the control. Those fed on Met alone or in combination, had lower dH2, dCH4 (p &lt; 0.01), and higher dH2S (p &lt; 0.01) in the foregut and hindgut than the control or Lys. The goats that were fed on Met alone or in combination, had higher 16S rRNA gene copies of total bacteria, methanogens, and 18S rRNA gene copies of protozoa, fungi, and fiber-utilizing bacterial species (p &lt; 0.01) associated with particles vs. liquid, both in the foregut and hindgut than the control goats. This study gives insights into the use of sulfur-containing amino acids, as an alternative dietary mitigation strategy of methanogenesis in ruminants and highlights the need for further research in this direction.

Alterations of gut microbiome and metabolite profiles in choledocholithiasis concurrent with cholangitis

BACKGROUND AND AIMS

Gut microbiota and their metabolic products might play important roles in regulating the pathogenesis of choledocholithiasis concurrent with cholangitis (CC). The aim of this study was to explore the characteristic gut dysbiosis, metabolite profiles and the possible roles in patients with CC.

METHODS

A case-control study was carried out to analyze the alterations in the intestinal microbiota and their metabolites in patients with CC (n = 25) compared with healthy controls (HCs) (n = 25) by metagenomic sequencing to define the gut microbiota community and liquid chromatography/mass spectrometry (LC/MS) analysis to characterize the metabolite profiles.

RESULTS

Significantly reduced Shannon diversity index (p = 0.043) and differential overall fecal microbiota community in CCs were observed. Twelve dominant altered species were identified and analyzed (LDA score > 3.0, p < 0.05) (Q value < 0.05), including unclassified_f_Enterobacteriaceae, Escherichia_coli, Roseburia_faecis and Eubacterium rectale. Moreover, the levels of KEGG pathways related to biofilm formation of Escherichia coli, lipopolysaccharide (LPS) biosynthesis, and the metabolism of propanoate and glutathione in CCs were significantly altered. Finally, 47 markedly changed metabolites (VIP > 1.0 and p < 0.05), including low level of kynurenic acid (KYNA) and high concentration of N-palmitoylsphingosine involving tryptophan metabolism and sphingolipid signaling pathways, were identified to validate aberrant metabolic patterns in CCs, and multiple correlated metabolic modules involving bile inflammation were altered in CCs.

CONCLUSION

Our study provides novel insights into compositional and functional alterations in the gut microbiome and metabolite profiles in CC and the underlying mechanisms between gut microbiota and bile inflammation.

Potential protective effects of thiamine supplementation on the ruminal epithelium damage during subacute ruminal acidosis

In ruminants, the ruminal epithelium not only has the function of absorbing nutrients but also is an important tissue to prevent harmful substances in the rumen from entering the blood circulation. Thus, the normal function of ruminal epithelium is critical for ruminants. However, subacute ruminal acidosis induced by high-concentrate diets often damages the barrier function of ruminal epithelium in ruminants. Recently, many studies have shown that dietary supplementation with thiamine is an effective method to alleviate subacute ruminal acidosis. In order to provide theoretical reference for the in-depth study of subacute ruminal acidosis and the application of thiamine in the future, this review introduces the effects of subacute ruminal acidosis on morphological structure, inflammatory response, and tight junction of ruminal epithelium. In addition, this paper summarizes the role of thiamine in maintaining ruminal epithelial function of ruminants during subacute ruminal acidosis challenge.

Metagenomic Insight: Dietary Thiamine Supplementation Promoted the Growth of Carbohydrate-Associated Microorganisms and Enzymes in the Rumen of Saanen Goats Fed High-Concentrate Diets

Subacute ruminal acidosis (SARA) is often caused by feeding a high-concentrate diet in intensive ruminant production. Although previous studies have shown that dietary thiamine supplementation can effectively increase rumen pH and modify rumen fermentation, the effect of thiamine supplementation on rumen carbohydrate-related microorganisms and enzymes in goats under SARA conditions remain unclear. Therefore, the objective of the present study was to investigate the effects of dietary thiamine supplementation on carbohydrate-associated microorganisms and enzymes in the rumen of Saanen goats fed high-concentrate diets. Nine healthy mid-lactating Saanen goats in parity 1 or 2 were randomly assigned into three treatments: A control diet (CON; concentrate:forage (30:70)), a high-concentrate diet (HC; concentrate:forage (70:30)), and a high-concentrate diet with 200 mg of thiamine/kg of DMI (HCT; concentrate:forage (70:30)). Compared with the HC group, dietary thiamine supplementation improved ruminal microbes associated with fiber, including Prevotella, Fibrobacter, Neocallimastix, and Piromyces (p < 0.05). In addition, an increase in the relative abundance of enzymes involved in both fiber degradation and starch degradation, such as CBM16, GH3, and GH97, was observed in the HCT treatment. (p < 0.05). Thus, thiamine supplementation can improve carbohydrate metabolism by increasing the abundance of the microorganisms and enzymes involved in carbohydrate degradation. In conclusion, this study revealed the relationship between ruminal microbiota and enzymes, and these findings contributed to solving the problems arising from the high-concentrate feeding in ruminant production and to providing a new perspective on ruminant health.

Anaerobic Fungi: Past, Present, and Future

Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.

Ruminal Methanogenic Responses to the Thiamine Supplementation in High-Concentrate Diets

BACKGROUND

Thiamine supplementation in high-concentrate diets (HC) was confirmed to attenuate ruminal subacute acidosis through promoting carbohydrate metabolism, however, whether thiamine supplementation in HC impacts methane metabolism is still unclear. Therefore, in the present study, thiamine was supplemented in the high-concentrate diets to investigate its effects on ruminal methanogens and methanogenesis process.

METHODS

an in vitro fermentation experiment which included three treatments: control diet (CON, concentrate/forage = 4:6; DM basis), high-concentrate diet (HC, concentrate/forage = 6:4; DM basis) and high-concentrate diet supplemented with thiamine (HCT, concentrate/forage = 6:4, DM basis; thiamine supplementation content = 180 mg/kg DM) was conducted. Each treatment concluded with four repeats, with three bottles in each repeat. The in vitro fermentation was sustained for 48h each time and repeated three times. At the end of fermentation, fermentable parameters, ruminal bacteria and methanogens community were measured.

RESULTS

HC significantly decreased ruminal pH, thiamine and acetate content, while significantly increasing propionate content compared with CON (p < 0.05). Conversely, thiamine supplementation significantly increased ruminal pH, acetate while significantly decreasing propionate content compared with HC treatment (p < 0.05). No significant difference of ruminal methanogens abundances among three treatments was observed. Thiamine supplementation significantly decreased methane production compared with CON, while no significant change was found in HCT compared with HC.

CONCLUSION

thiamine supplementation in the high-concentrate diet (HC) could efficiently reduce CH4 emissions compared with high-forage diets while without causing ruminal metabolic disorders compared with HC treatment. This study demonstrated that supplementation of proper thiamine in concentrate diets could be an effective nutritional strategy to decrease CH4 production in dairy cows.

Metagenomic Insights into Effects of Thiamine Supplementation on Carbohydrate-Active Enzymes' Profile in Dairy Cows Fed High-Concentrate Diets

As the co-enzyme of pyruvate formate-lyase under ruminal anaerobic condition, thiamine plays a critical role in carbohydrate metabolism in dairy cows. The objective of this study was to investigate the impacts of thiamine supplementation on ruminal carbohydrate-active enzymes. Twelve Holstein dairy cows were randomly assigned into three dietary treatments: control diet (CON; 20% starch, dry matter (DM) basis), high-concentrate diet (HC; 33.2% starch, DM basis) and a high-concentrate diet supplemented with 180 mg thiamine/kg DM (HCT; 33.2% starch, DM basis). Dry matter intake and milk production were recorded for 21 days. Rumen fluid samples were collected, and ruminal pH and volatile fatty acids (VFAs) were measured. The metagenome sequencing technique was used to detect the genes in ruminal microorganisms and identify putative carbohydrate-active enzymes. The total abundances of carbohydrate-active enzymes and fiber-degrading enzymes were both reduced by HC with no effect on starch-degrading enzymes compared with CON. However, the fiber-degrading enzymes and starch-degrading enzymes were both increased after thiamine supplementation. These results indicated that 180 mg thiamine /kg DM might effectively improve rumen carbohydrate metabolism through increasing the abundance of ruminal carbohydrate-active enzymes and consequently balanced the rumen volatile fatty acids and rumen pH, providing a practical strategy in preventing subacute ruminal acidosis in cows offered HC.

Characterization of Anaerobic Rumen Fungal Community Composition in Yak, Tibetan Sheep and Small Tail Han Sheep Grazing on the Qinghai-Tibetan Plateau

Simple Summary

Anaerobic rumen fungi play a vital role in fiber degradation. The objective of this study was to compare the anaerobic rumen fungal communities of full grazing ruminants in the Qinghai-Tibetan Plateau. Our results showed that the anaerobic rumen fungal community was affected by host species and the dynamic associations of them were host specific. This is the first study exploring the anaerobic rumen fungi in the full-grazing ruminants, which could lay a solid foundation to really identify fiber degradation fungal taxa using culture-dependent techniques in the future.

Abstract

The anaerobic rumen fungal community play a critical role in fibrous material degradation. However, there is a lack of data describing the composition of anaerobic rumen fungal community of full grazing ruminants in the Qinghai-Tibetan Plateau. For this reason, we employed the next-generation sequencing technique to elucidate the rumen fungal structure composition and evaluate the effects of host species on fungal communities. Community comparisons (Bray–Curtis index) between yak and Tibetan sheep revealed that the rumen fungal community was affected by host species (p < 0.05). The alpha diversity indices in the yak were significantly higher than in the Tibetan sheep and Small Tail Han sheep. Neocallimastigomycota was predominant regardless of host species. Within this phylum, unidentified genus of Neocallimastigaceae was the most dominant in all samples, followed by Piromyces and Orpinomyces. Moreover, the shared and unique OTUs in the rumen were identified and most of them belonged to the Orpinomyces. Co-occurrence network analysis identified that each animal species had their own keystone species and most of them were non-dominant flora. Our data indicate that host breeds override living environment as the key factor that determines fungal community in the rumen of grazing ruminants in the Qinghai-Tibetan Plateau.

Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows

Background

Overfeeding of high-concentrate diet (HC) frequently leads to subacute ruminal acidosis (SARA) in modern dairy cows’ production. Thiamine supplementation has been confirmed to attenuate HC induced SARA by increasing ruminal pH and ratio of acetate to propionate, and decreasing rumen lactate, biogenic amines and lipopolysaccharide (LPS). The effects of thiamine supplementation in HC on rumen bacteria and fungi profile had been detected in our previous studies, however, effects of thiamine supplementation in HC on rumen non-methanogen archaea is still unclear. The objective of the present study was therefore to investigate the effects of thiamine supplementation on ruminal archaea, especially non-methanogens in HC induced SARA cows.

Results

HC feeding significantly decreased dry matter intake, milk production, milk fat content, ruminal pH and the concentrations of thiamine and acetate in rumen fluid compared with control diet (CON) (P < 0.05), while the concentrations of propionate and ammonia-nitrogen (NH₃-N) were significantly increased compared with CON (P < 0.05). These changes caused by HC were inversed by thiamine supplementation (P < 0.05). The taxonomy results showed that ruminal archaea ranged from 0.37 to 0.47% of the whole microbiota. Four characterized phyla, a number of Candidatus archaea and almost 660 species were identified in the present study. In which Euryarchaeota occupied the largest proportion of the whole archaea. Furthermore, thiamine supplementation treatment significantly increased the relative abundance of non-methanogens compared with CON and HC treatments. Thaumarchaeota was increased in HC compared with CON. Thiamine supplementation significantly increased Crenarchaeota, Nanoarchaeota and the Candidatus phyla, however decreased Thaumarchaeota compared with HC treatment.

Conclusions

HC feeding significantly decreased ruminal pH and increased the content of NH₃-N which led to N loss and the increase of the relative abundance of Thaumarchaeota. Thiamine supplementation increased ruminal pH, improved the activity of ammonia utilizing bacteria, and decreased Thaumarchaeota abundance to reduce the ruminal NH₃ content and finally reduced N loss. Overall, these findings contributed to the understanding of thiamine’s function in dairy cows and provided new strategies to improve dairy cows’ health under high-concentrate feeding regime.

Electronic supplementary material

The online version of this article (10.1186/s12917-018-1745-0) contains supplementary material, which is available to authorized users.