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

Integrating 16S rRNA Sequencing and LC-MS-Based Metabolomics to Evaluate the Effects of Dietary Crude Protein on Ruminal Morphology, Fermentation Parameter and Digestive Enzyme Activity in Tibetan Sheep

The dietary crude protein level could affect ruminal fermentation parameters and the microflora of ruminants. The present study's aim was to investigate the effects of different protein level diets on ruminal morphology, fermentation parameters, digestive enzyme activity, microflora and metabolites of Tibetan sheep. Ninety weaned lambs (initial weight of 15.40 ± 0.81 kg, 2 months old) were selected and randomly divided into three groups (six pens/treatment, five rams/pen). Dietary treatments were formulated with 13.03% (high protein, HP), 11.58% (moderate protein, MP) and 10.20% (low protein, LP), respectively. Compared with LP, both papillae length and papillae width were significantly promoted in HP and MP (p < 0.05). The concentrations of ammonia nitrogen, total VFAs, propionic acids and butyric acids in HP were significantly increased compared to those in MP and LP (p < 0.05). The activities of protease and α-amylase in HP were significantly greater than those of LP (p < 0.05). For the ruminal microbial community, higher proportions of phylum Prevotella 1 and Succiniclasticum and genus Rikenellaceae RC9 gut group and Ruminococcus 1 were observed in HP (p < 0.05). A total of 60 differential metabolites (DMs) (28 up, 32 down) between HP and MP; 73 DMs (55 up, 18 down) between HP and LP; and 65 DMs (49 up, 16 down) between MP and LP were identified. Furthermore, four pathways of the biosynthesis of unsaturated fatty acids, tryptophan metabolism, bile secretion and ABC transporters were significantly different (p < 0.05). The abundance of phylum Prevotella 1 was negatively associated with stearic acid and palmitic acid but positively associated with the taurine. The abundance of genus Ruminococcus 1 was negatively associated with stearic acid, oleic acid, erucic acid, Indole-3-acetamide and palmitic acid but positively associated with 6-hydroxymelatonin. In conclusion, a 13.03% CP level improved ruminal morphology, fermentation parameters and digestive enzyme activities through modulating the microbial community and regulating metabolism in Tibetan sheep.

Effects of Combined Live Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus Cereus Tablets on the Structure and Function of the Intestinal Flora in Rabbits Undergoing Hepatic Artery Infusion Chemotherapy

Few studies have explored the biological mechanism by which probiotics alleviate adverse reactions to chemotherapy drugs after local hepatic chemotherapy perfusion by regulating the intestinal flora. This study investigates the effects of Combined Live Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus Cereus Tablets on the intestinal microbial structure and intestinal barrier function, as well as the potential mechanism in rabbits after local hepatic chemotherapy infusion. Eighteen New Zealand White rabbits were randomly divided into a control group, a hepatic local chemotherapy perfusion group, and a hepatic local chemotherapy perfusion + Combined Live Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus Cereus Tablets group to assess the effects of Combined Live Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus Cereus Tablets on the adverse reactions. The administration of Combined Live Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus Cereus Tablets alleviated the intestinal flora disorder caused by local hepatic perfusion chemotherapy, promoted the growth of beneficial bacteria, and inhibited the growth of harmful bacteria. The Combined Live Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus Cereus Tablets also reduced the levels of serum pro-inflammatory cytokines and liver injury factors induced by local hepatic perfusion chemotherapy. Our findings indicate that Combined Live Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus Cereus Tablets can ameliorate the toxicity and side effects of chemotherapy by regulating intestinal flora, blocking pro-inflammatory cytokines, reducing liver injury factors, and repairing the intestinal barrier. Probiotics may be used as a potential alternative therapeutic strategy to prevent the adverse reactions caused by chemotherapy with local hepatic perfusion.

Impact of Dietary Regime and Seasonality on Hindgut's Mycobiota Diversity in Dairy Cows

We describe and discuss the intestinal mycobiota of dairy cows reared in France following variations in dietary regimes and two seasons. Two groups of 21 animals were followed over a summer and winter period, and another group of 28 animals was followed only during the same summer season. The summer diet was based on grazing supplemented with 3-5 kg/d of maize, grass silage and hay, while the winter diet consisted of 30% maize silage, 25% grass silage, 15% hay and 30% concentrate. A total of 69 DNA samples were extracted from the feces of these cows. Amplification and sequencing of the ITS2 region were used to assess mycobiota diversity. Analyses of alpha and beta diversity were performed and compared statistically. The mycobiota changed significantly from summer to winter conditions with a decrease in its diversity, richness and evenness parameters, while beta diversity analysis showed different mycobiota profiles. Of note, the Geotrichum operational taxonomic unit (OTU) was prevalent in the winter group, with a mean relative abundance (RA) of 65% of the total mycobiota. This Geotrichum OTU was also found in the summer group, but to a lesser extent (5%). In conclusion, a summer grazing diet allowed a higher fecal fungal diversity. These data show, for the first time, that a change in diet associated with seasonality plays a central role in shaping hindgut fungal diversity.

Effects of Thymbra capitata essential oil on in vitro fermentation end-products and ruminal bacterial communities

An in vitro trial was carried out to investigate the effects of natural Thymbra capitata essential oil (NEO) and its main compounds [including carvacrol, p-cymene, γ-terpinene given alone or in a synthetic combination (SEO)] on ruminal fermentation and the bacterial community using batch cultures inoculated with ruminal digesta and incubating two different basal diets [high-forage (F) and high-concentrate (C) diet]. After 24 h of incubation, primary fermentation end-products [gas, methane, volatile fatty acids (VFAs) and ammonia] and rumen microbial diversity were determined. NEO reduced the total VFA concentration (P < 0.05) only in the C diet. In contrast, SEO and carvacrol decreased the total VFA concentration (P < 0.05) only in the F diet. Methane production was not affected (P > 0.05) by any of the experimental treatments or diets evaluated. Microbial diversity analysis showed only a moderate effect of carvacrol and SEO on 13 genera, including, mainly, Atopobium and Blautia (involved in subacute ruminal acidosis) or Candidatus Saccharimonas (related to laminitis). In conclusion, T. capitata EO has a limited potential to attain nutritional or environmental benefits, but further research should be carried out to clarify its effects on animal health and microbial food safety.

Evaluation of stirring time through a rumen simulation technique: Influences on rumen fermentation and bacterial community

Introduction

Rumen motility is a key element that influences ruminant nutrition, whereas little is known about the effects of rumen contraction duration on rumen fermentation and ruminal microbiome. We previously reported that proper rotation speed of a rumen simulation technique (RUSITEC) system enhanced rumen fermentation and microbial protein (MCP) production. In the present study, different contraction durations and intervals were simulated by setting different stirring times and intervals of the stirrers in a RUSITEC system. The objective of this trial was to evaluate the influences of stirring time on rumen fermentation characteristics, nutrient degradation, and ruminal bacterial microbiota in vitro.

Methods

This experiment was performed in a 3 × 3 Latin square design, with each experimental period comprising 4 d for adjustment and 3 d for sample collection. Three stirring time treatments were set: the constant stir (CS), the intermittent stir 1 (each stir for 5 min with an interval of 2 min, IS1), and the intermittent stir 2 (each stir for 4 min with an interval of 3 min, IS2).

Results

The total volatile fatty acid (TVFA) concentration, valerate molar proportion, ammonia nitrogen level, MCP density, protozoa count, disappearance rates of dry matter, organic matter, crude protein, neutral detergent fiber, and acid detergent fiber, emissions of total gas and methane, and the richness index Chao 1 for the bacterial community were higher (p < 0.05) in the IS1 when compared to those in the CS. The greatest TVFA, MCP, protozoa count, nutrient disappearance rates, gas productions, and bacterial richness indices of Ace and Chao 1 amongst all treatments were observed in the IS2. The relative abundance of the genus Treponema was enriched (p < 0.05) in CS, while the enrichment (p < 0.05) of Agathobacter ruminis and another two less known bacterial genera were identified in IS2.

Discussion

It could be concluded that the proper reduction in the stirring time might help to enhance the feed fermentation, MCP synthesis, gas production, and the relative abundances of specific bacterial taxa.

Tannic acid supplementation in the diet of Holstein bulls: Impacts on production performance, physiological and immunological characteristics, and ruminal microbiota

This study was conducted to evaluate the influences of supplementing tannic acid (TA) at different doses on the production performance, physiological and immunological characteristics, and rumen bacterial microbiome of cattle. Forty-eight Holstein bulls were randomly allocated to four dietary treatments: the control (CON, basal diet), the low-dose TA treatment [TAL, 0.3% dry matter (DM)], the mid-dose TA treatment (TAM, 0.9% DM), and the high-dose TA treatment (TAH, 2.7% DM). This trial consisted of 7 days for adaptation and 90 days for data and sample collection, and samples of blood and rumen fluid were collected on 37, 67, and 97 d, respectively. The average daily gain was unaffected (P > 0.05), whilst the ruminal NH3-N was significantly decreased (P < 0.01) by TA supplementation. The 0.3% TA addition lowered (P < 0.05) the levels of ruminal isobutyrate, valerate, and tumor necrosis factor alpha (TNF-α), and tended to (P < 0.1) increase the gain to feed ratio. The digestibility of DM, organic matter (OM), and crude protein, and percentages of butyrate, isobutyrate, and valerate were lower (P < 0.05), while the acetate proportion and acetate to propionate ratio in both TAM and TAH were higher (P < 0.05) than the CON. Besides, the 0.9% TA inclusion lessened (P < 0.05) the concentrations of glucagon and TNF-α, but enhanced (P < 0.05) the interferon gamma (IFN-γ) level and Simpson index of ruminal bacteria. The 2.7% TA supplementation reduced (P < 0.05) the intake of DM and OM, and levels of malondialdehyde and thyroxine, while elevated (P < 0.05) the Shannon index of the rumen bacterial populations. Moreover, the relative abundances of the phyla Fibrobacteres and Lentisphaerae, the genera Fibrobacter and Bradyrhizobium, and the species Bradyrhizobium sp., Lachnospiraceae bacterium RM29, and Lachnospiraceae bacterium CG57 were highly significantly (q < 0.01) or significantly (q < 0.05) raised by adding 2.7% TA. Results suggested that the TA addition at 0.3% is more suitable for the cattle, based on the general comparison on the impacts of supplementing TA at different doses on all the measured parameters.

Tannic acid reduced apparent protein digestibility and induced oxidative stress and inflammatory response without altering growth performance and ruminal microbiota diversity of Xiangdong black goats

The present study was performed to evaluate the impacts of tannic acid (TA) supplementation at different levels on the growth performance, physiological, oxidative and immunological metrics, and ruminal microflora of Xiangdong black goats. Twenty-four goats were randomly assigned to four dietary treatments: the control (CON, basal diet), the low-dose TA group [TAL, 0.3 % of dry matter (DM)], the mid-dose TA group (TAM, 0.6 % of DM), and the high-dose TA group (TAH, 0.9 % of DM). Results showed that the growth performance was unaffected (P > 0.05) by adding TA, whilst the 0.3 % and 0.6 % TA supplementation significantly decreased (P < 0.05) the apparent digestibility of crude protein (CP) and ruminal NH3-N concentration, and raised (P < 0.05) the level of total volatile fatty acid (TVFA) in rumen. The increments of alanine aminotransferase (ALT), triglyceride (TG), cortisol (CORT), total antioxidant capacity (T-AOC), interleukin (IL)-1β, IL-6, and serumamyloid A (SAA), and decrements of globulin (GLB), immunoglobulin G (IgG), cholinesterase (CHE), glutathione reductase (GR), creatinine (CRE), growth hormone (GH), high-density lipoprotein cholesterol (HDLC), and insulin-like growth factor 1 (IGF-1) to different extents by TA addition were observed. Although the Alpha and Beta diversity of rumen bacterial community remained unchanged by supplementing TA, the relative abundance of the predominant genus Prevotella_1 was significantly enriched (P < 0.05) in TAL. It could hence be concluded that the TA supplementation in the present trial generally decreased CP digestion and caused oxidative stress and inflammatory response without influencing growth performance and ruminal microbiota diversity. More research is needed to explore the premium dosage and mechanisms of effects for TA addition in the diet of goats.

Bifidobacterium breve Alleviates DSS-Induced Colitis in Mice by Maintaining the Mucosal and Epithelial Barriers and Modulating Gut Microbes

This study was designed to explore the different intestinal barrier repair mechanisms of Bifidobacterium breve (B. breve) H4-2 and H9-3 with different exopolysaccharide (EPS) production in mice with colitis. The lipopolysaccharide (LPS)-induced IEC-6 cell inflammation model and dextran sulphate sodium (DSS)-induced mice colitis model were used. Histopathological changes, epithelial barrier integrity, short-chain fatty acid (SCFA) content, cytokine levels, NF-κB expression level, and intestinal flora were analyzed to evaluate the role of B. breve in alleviating colitis. Cell experiments indicated that both B. breve strains could regulate cytokine levels. In vivo experiments confirmed that oral administration of B. breve H4-2 and B. breve H9-3 significantly increased the expression of mucin, occludin, claudin-1, ZO-1, decreased the levels of IL-6, TNF-α, IL-1β and increased IL-10. Both strains of B. breve also inhibited the expression of the NF-κB signaling pathway. Moreover, B. breve H4-2 and H9-3 intervention significantly increased the levels of SCFAs, reduced the abundance of Proteobacteria and Bacteroidea, and increased the abundance of Muribaculaceae. These results demonstrate that EPS-producing B. breve strains H4-2 and H9-3 can regulate the physical, immune, and microbial barrier to repair the intestinal damage caused by DSS in mice. Of the two strains, H4-2 had a higher EPS output and was more effective at repair than H9-3. These results will provide insights useful for clinical applications and the development of probiotic products for the treatment of colitis.

Rhubarb Alleviates Acute Lung Injury by Modulating Gut Microbiota Dysbiosis in Mice

Intestinal microbiota disorders can aggravate pulmonary inflammation during acute lung injury (ALI). As a traditional Chinese herb, Rhubarb can regulated the gut microbiota. Therefore, this study was conducted to test the hypothesis that rhubarb alleviates gut microbiota dysbiosis and inflammation. Feces were collected from patients with ALI to detect the gut microbiota using 16S rDNA sequencing. Subsequently, a mouse model of ALI was established using lipopolysaccharide to investigate changes in the gut microbiota, the peripheral blood was attained for detecting the Th17/Treg cell ratio and the serum level of HDAC6 and HDAC9, and the effect of rhubarb treatment on the gut microbiota and Th17/Treg ratio were also evaluated. The results indicated that both the Firmicutes phylum decreased and the Bacteroidetes phylum increased were identified in patients with ALI, which induced the alternation of histone metabolites. The mice models also showed a similar imbalance in the Firmicutes/Bacteroidetes ratio at phylum of level. Rhubarb treatment alleviated the damaged lung tissue, accelerated Alistipes, Clostridium, and Lactobacillus proliferation at the level of genus, increased the level of HDAC6 in both the mice lung tissue and serum, and markedly reduced the Treg cells and increased the Th17 cells in the spleen tissue. The study suggested that both patients and mouse models with ALI presented gut microbiota dysbiosis, and lead to a Th17/Treg cell imbalance in ALI mouse. Rhubarb promoted Alistipes, Clostridium, and Lactobacillus proliferation, increased the HDAC6 concentration, restored the Th17/Treg cell balance, and protected against ALI.

Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics

Muskox (Ovibos moschatus), as the biggest herbivore in the High Arctic, has been enduring the austere arctic nutritional conditions and has evolved to ingest and digest scarce and high lignified forages to support the growth and reproduce, implying probably harbor a distinct microbial reservoir for the deconstruction of plant biomass. Therefore, metagenomics approach was applied to characterize the rumen microbial community and understand the alteration in rumen microbiome of muskoxen fed either triticale straw or brome hay. The difference in the structure of microbial communities including bacteria, archaea, fungi, and protozoa between the two forages was observed at the taxonomic level of genus. Further, although the highly abundant phylotypes in muskoxen rumen fed either triticale straw or brome hay were almost the same, the selective enrichment different phylotypes for fiber degrading, soluble substrates fermenting, electron and hydrogen scavenging through methanogenesis, acetogenesis, propionogenesis, and sulfur-reducing was also noticed. Specifically, triticale straw with higher content of fiber, cellulose selectively enriched more lignocellulolytic taxa and electron transferring taxa, while brome hay with higher nitrogen content selectively enriched more families and genera for degradable substrates-digesting. Intriguingly, the carbohydrate-active enzyme profile suggested an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on triticale straw. The majority of the cellulases belonged to fiver GH families (i.e., GH5, GH6, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus, Piromyces, Neocallimastix, and Fibrobacter. Abundance of major genes coding for hemicellulose digestion was higher than cellulose mainly including GH8, GH10, GH16, GH26, and GH30, and these enzymes were produced by members of the genera Fibrobacter, Ruminococcus, and Clostridium. Oligosaccharides were mainly of the GH1, GH2, GH3, and GH31 types and were associated with the genera Prevotella and Piromyces. Our results strengthen metatranscriptomic evidence in support of the understanding of the microbial community and plant polysaccharide response to changes in the feed type and host animal. The study also establishes these specific microbial consortia procured from triticale straw group can be used further for efficient plant biomass hydrolysis.

Effect of Divergent Feeding Regimes During Early Life on the Rumen Microbiota in Calves

The objective of this study was to determine whether divergent feeding regimes during the first 41 weeks of the life of a calf are associated with long-term changes in the rumen microbiota and the associated fermentation end-products. Twenty-four calves (9 ± 5 days of age) were arranged in a 2 × 2 factorial design with two divergent treatments across three dietary phases. In phase 1 (P01), calves were offered a low-milk volume/concentrate starter diet with early weaning (CO) or high-milk volume/pasture diet and late weaning (FO). In phase 2 (P02), calves from both groups were randomly allocated to either high-quality (HQ) or low-quality (LQ) pasture grazing groups. In phase 3 (P03), calves were randomly allocated to one of two grazing groups and offered the same pasture-only diet. During each dietary phase, methane (CH₄) and hydrogen (H₂) emissions and dry matter intake (DMI) were measured in respiration chambers, and rumen samples for the evaluation of microbiota and short-chain fatty acid (SCFA) characterizations were collected. In P01, CO calves had a higher solid feed intake but a lower CH₄ yield (yCH₄) and acetate:propionate ratio (A:P) compared with FO calves. The ruminal bacterial community had lower proportions of cellulolytic bacteria in CO than FO calves. The archaeal community was dominated by Methanobrevibacter boviskoreani in CO calves and by Mbb. gottschalkii in FO calves. These differences, however, did not persist into P02. Calves offered HQ pastures had greater DMI and lower A:P ratio than calves offered LQ pastures, but yCH₄ was similar between groups. The cellulolytic bacteria had lower proportions in HQ than LQ calves. In all groups, the archaeal community was dominated by Mbb. gottschalkii. No treatment interactions were observed in P02. In P03, all calves had similar DMI, CH₄ and H₂ emissions, SCFA proportions, and microbial compositions, and no interactions with previous treatments were observed. These results indicate that the rumen microbiota and associated fermentation end-products are driven by the diet consumed at the time of sampling and that previous dietary interventions do not lead to a detectable long-term microbial imprint or changes in rumen function.

Effect of Methane Inhibitors on Ruminal Microbiota During Early Life and Its Relationship With Ruminal Metabolism and Growth in Calves

The present study aimed to determine whether dietary supplementation with methanogen inhibitors during early life may lead to an imprint on the rumen microbial community and change the rumen function and performance of calves to 49-weeks of rearing. Twenty-four 4-day-old Friesian x Jersey cross calves were randomly assigned into a control and a treatment group. Treated calves were fed a combination of chloroform (CF) and 9,10-anthraquinone (AQ) in the solid diets during the first 12 weeks of rearing. Afterward, calves were grouped by treatments until week 14, and then managed as a single group on pasture. Solid diets and water were offered ad libitum. Methane measurements, and sample collections for rumen metabolite and microbial community composition were carried out at the end of weeks 2, 4, 6, 8, 10, 14, 24 and 49. Animal growth and dry matter intake (DMI) were regularly monitored over the duration of the experiment. Methane emissions decreased up to 90% whilst hydrogen emissions increased in treated compared to control calves, but only for up to 2 weeks after treatment cessation. The near complete methane inhibition did not affect calves’ DMI and growth. The acetate:propionate ratio decreased in treated compared to control calves during the first 14 weeks but was similar at weeks 24 and 49. The proportions of Methanobrevibacter and Methanosphaera decreased in treated compared to control calves during the first 14 weeks; however, at week 24 and 49 the archaea community was similar between groups. Bacterial proportions at the phylum level and the abundant bacterial genera were similar between treatment groups. In summary, methane inhibition increased hydrogen emissions, altered the methanogen community and changed the rumen metabolite profile without major effects on the bacterial community composition. This indicated that the main response of the bacterial community was not a change in composition but rather a change in metabolic pathways. Furthermore, once methane inhibition ceased the methanogen community, rumen metabolites and hydrogen emissions became similar between treatment groups, indicating that perhaps using the treatments tested in this study, it is not possible to imprint a low methane microbiota into the rumen in the solid feed of pre-weaned calves.

Lignocelluloytic activities and composition of bacterial community in the camel rumen

The camel is well-adapted to utilize the poor-quality forages in the harsh desert conditions as the camel rumen sustains fibrolytic microorganisms, mainly bacteria that are capable of breaking down the lignocellulosic biomass efficiently. Exploring the composition of the bacterial community in the rumen of the camel and quantifying their cellulolytic and xylanolytic activities could lead to understanding and improving fiber fermentation and discovering novel sources of cellulases and xylanases. In this study, Illumina MiSeq sequencing of the V4 region on 16S rRNA was applied to identify the bacterial and archaeal communities in the rumen of three camels fed wheat straw and broom corn. Furthermore, rumen samples were inoculated into bacterial media enriched with xylan and different cellulose sources, including filter paper (FP), wheat straw (WS), and alfalfa hay (AH) to assess the ability of rumen bacteria to produce endo-cellulase and endo-xylanase at different fermentation intervals. The results revealed that the phylum Bacteroidetes dominated the bacterial community and Candidatus Methanomethylophilus dominated the archaeal community. Also, most of the bacterial community has fibrolytic potential and the dominant bacterial genera were Prevotella, RC9_gut_group, Butyrivibrio, Ruminococcus, Fibrobacteres, and Treponema. The highest xylanase production (884.8 mU/mL) was observed at 7 days. The highest cellulase production (1049.5 mU/mL) was observed when rumen samples were incubated with Alfalfa hay for 7 days.

Disentangling the Complexity of the Rumen Microbial Diversity Through Fractionation Using a Sucrose Density Gradient

The ruminal microbial community is an important element in health, nutrition, livestock productivity, and climate impact. Despite the historic and current efforts to characterize this microbial diversity, many of its members remain unidentified, making it challenging to associate microbial groups with functions. Here we present a low-cost methodology for rumen sample treatment that separates the microbial community based on cell size, allowing for the identification of subtle compositional changes. In brief, the sample is centrifuged through a series of sucrose density gradients, and cells migrate to their corresponding density fraction. From each fraction, DNA is extracted and 16S rRNA gene amplicons are sequenced. We tested our methodology on four animals under two different conditions, fasting, and post-feeding. Each fraction was examined by confocal microscopy showing that the same sucrose fraction consistently separated similar cell-sized microorganisms independent of the animal or treatment. Microbial composition analysis using metabarcoding showed that our methodology detected low abundance bacterial families and population changes between fasting and post-feeding treatments that could not be observed by bulk DNA analysis. In conclusion, the sucrose-based method is a powerful low-cost approximation to untwine, enrich, and potentially isolate uncharacterized members of the ruminal microbiome.

Lactobacillus ruminis Alleviates DSS-Induced Colitis by Inflammatory Cytokines and Gut Microbiota Modulation

Lactobacillus ruminis can stimulate the immune response in vitro, but previous studies were only carried out in vitro and the anti-inflammatory effects of L. ruminis needs more in vivo evidences. In this study, the immune regulation and potential mechanisms of L. ruminis was investigated in DSS-induced colitis mice. L. ruminis FXJWS27L3 and L. ruminis FXJSW17L1 relieved the symptoms of colitis, including inhibition of colon shortening and colon tissue damage. L. ruminis FXJWS27L3 significantly reduced the pro-inflammatory cytokines IL-1β, TNF-α, and IL-17, while L. ruminis FXJSW17L1 significantly increased short chain fatty acids in mice feces. Moreover, L. ruminis FXJWS27L3 and L. ruminis FXJSW17L1 treatments significantly increased the gut microbiota diversity and balance the intestine microbiota profiles, which improved the imbalance of intestine microbiota composition to a certain extent. The results showed that L. ruminis can alleviate DSS-induced colitis, which possibly was related to promoting the expression of pro-inflammatory cytokines, up-regulating SCFAs and restoring the imbalance of gut microbiota.

Fermented Soybean Meal Replacement in the Diet of Lactating Holstein Dairy Cows: Modulated Rumen Fermentation and Ruminal Microflora

This study was conducted to examine the influences of replacing soybean meal (SBM) with fermented soybean meal (FSBM) in the diet of lactating Holstein cattle on rumen fermentation and ruminal bacterial microbiome. Twenty-four lactating Chinese Holstein dairy cattle were assigned to each of the two treatments in a completely randomized design: the SBM group [the basal total mixed ration (TMR) diet containing 5.77% SBM] and the FSBM group (the experimental TMR diet containing 5.55% FSBM). This trial lasted for 54 days (14 days for adjustment and 40 days for data and sample collection), and samples of rumen liquid were collected on 34 d and 54 d, respectively. The results showed that replacing SBM with FSBM significantly increased the molar percentages of propionate (P < 0.01) and valerate (P < 0.05), but reduced the total volatile fatty acid (TVFA) concentration (P < 0.05), butyrate molar proportion (P < 0.05), and the acetate to propionate ratio (P < 0.01). The copy numbers of total bacteria (P < 0.05), Fibrobacter succinogenes (P < 0.01), Selenomonas ruminantium (P < 0.01), and Prevotella spp. (P < 0.05) in the FSBM group were greater, while the density of Prevotella ruminicola (P < 0.05) was lower than those in the SBM treatment. Additionally, Succiniclasticum ruminis and Saccharofermentans acetigenes were significantly enriched (P < 0.05) in the rumen fluid of FSBM-fed cows, despite the fact that there was no remarkable difference in the Alpha diversity indexes, structure and KEGG pathway abundances of the bacterial community across the two treatments. It could hence be concluded that the substitution of FSBM for SBM modulated rumen fermentation and rumen bacterial microbiota in lactating Holstein dairy cows. Further research is required to elucidate the relevant mechanisms of FSBM, and provide more insights into the application of FSBM in dairy cattle.

Dietary Supplementation with Sugar Beet Fructooligosaccharides and Garlic Residues Promotes Growth of Beneficial Bacteria and Increases Weight Gain in Neonatal Lambs

The proper development of the early gastrointestinal tract (GIT) microbiota is critical for newborn ruminants. This microbiota is susceptible to modification by diverse external factors (such as diet) that can lead to long-lasting results when occurring in young ruminants. Dietary supplementation with prebiotics, ingredients nondigestible and nonabsorbable by the host that stimulate the growth of beneficial GIT bacteria, has been applied worldwide as a potential approach in order to improve ruminant health and production yields. However, how prebiotics affect the GIT microbiota during ruminants' early life is still poorly understood. We investigated the effect of milk supplementation with a combination of two well-known prebiotics, fructooligosaccharides (FOS) from sugar beet and garlic residues (all together named as "additive"), exerted on preweaned lamb growth and the composition of their fecal microbiota, by using 16S rRNA gene amplicon high-throughput sequencing. The results showed a significant increase in the mean daily weight gain of lambs fed with the additive. Lamb fecal microbiota was also influenced by the additive intake, as additive-diet lambs showed lower bacterial diversity and were significantly more abundant in Bifidobacterium, Enterococcus, Lactobacillus and Veillonella. These bacteria have been previously reported to confer beneficial properties to the ruminant, including promotion of growth and health status, and our results showed that they were strongly linked to the additive intake and the increased weight gain of lambs. This study points out the combination of FOS from sugar beet and garlic residues as a potential prebiotic to be used in young ruminants' nutrition in order to improve production yields.

Lizhong decoction ameliorates ulcerative colitis in mice via modulating gut microbiota and its metabolites

Ulcerative colitis (UC), a kind of inflammatory bowel disease, is generally characterized by chronic, persistent, relapsing, and nonspecific ulceration of the bowel, which is widespread in the world. Although the pathogenesis of UC is multifactorial, growing evidence has demonstrated that gut microbiota and its metabolites are closely related to the development of UC. Lizhong decoction (LZD), a well-known classical Chinese herbal prescription, has been used to clinically treat UC for long time, but its mechanism is not clear. In this study, 16S rRNA gene sequencing combining with untargeted metabolomics profiling was used to investigate how LZD worked. Results indicated that LZD could shape the gut microbiota structure and modify metabolic profiles. The abundance of opportunistic pathogens such as Clostridium sensu stricto 1, Enterobacter, and Escherichia-Shigella correlated with intestinal inflammation markedly decreased, while the levels of beneficial bacteria including Blautia, Muribaculaceae_norank, Prevotellaceae UCG-001, and Ruminiclostridium 9 elevated in various degrees. Additionally, fecal metabolite profiles reflecting microbial activities showed that adenosine, lysoPC(18:0), glycocholic acid, and deoxycholic acid notably decreased, while cholic acid, α-linolenic acid, stearidonic acid, and L-tryptophan significantly increased after LZD treatment. Hence, based on the systematic analysis of 16S rRNA gene sequencing and metabolomics of gut flora, the results provided a novel insight that microbiota and its metabolites might be potential targets for revealing the mechanism of LZD on amelioration of UC.Key Points • The potential mechanism of LZD on the amelioration of UC was firstly investigated.• LZD could significantly shape the structure of gut microbiota.• LZD could notably modulate the fecal metabolic profiling of UC mice. Graphical abstract.

Supplementation of live yeast based feed additive in early life promotes rumen microbial colonization and fibrolytic potential in lambs

Rumen microbiota is of paramount importance for ruminant digestion efficiency as the microbial fermentations supply the host animal with essential sources of energy and nitrogen. Early separation of newborns from the dam and distribution of artificial milk (Artificial Milking System or AMS) could impair rumen microbial colonization, which would not only affect rumen function but also have possible negative effects on hindgut homeostasis, and impact animal health and performance. In this study, we monitored microbial communities in the rumen and the feces of 16 lambs separated from their dams from 12 h of age and artificially fed with milk replacer and starter feed from d8, in absence or presence of a combination of the live yeast Saccharomyces cerevisiae CNCM I-1077 and selected yeast metabolites. Microbial groups and targeted bacterial species were quantified by qPCR and microbial diversity and composition were assessed by 16S rDNA amplicon sequencing in samples collected from birth to 2 months of age. The fibrolytic potential of the rumen microbiota was analyzed with a DNA microarray targeting genes coding for 8 glycoside hydrolase (GH) families. In Control lambs, poor establishment of fibrolytic communities was observed. Microbial composition shifted as the lambs aged. The live yeast supplement induced significant changes in relative abundances of a few bacterial OTUs across time in the rumen samples, among which some involved in crucial rumen function, and favored establishment of Trichostomatia and Neocallimastigaceae eukaryotic families. The supplemented lambs also harbored greater abundances in Fibrobacter succinogenes after weaning. Microarray data indicated that key cellulase and hemicellulase encoding-genes were present from early age in the rumen and that in the Supplemented lambs, a greater proportion of hemicellulase genes was present. Moreover, a higher proportion of GH genes from ciliate protozoa and fungi was found in the rumen of those animals. This yeast combination improved microbial colonization in the maturing rumen, with a potentially more specialized ecosystem towards efficient fiber degradation, which suggests a possible positive impact on lamb gut development and digestive efficiency.

Bacterial communities in the solid, liquid, dorsal, and ventral epithelium fractions of yak (Bos grunniens) rumen

Yak (Bos grunniens) is an important and dominant livestock species in the challenging environment of the Qinghai–Tibetan Plateau. Rumen microbiota of the solid, liquid, and epithelium fractions play key roles in nutrient metabolism and contribute to host adaptation in ruminants. However, there is a little knowledge of the microbiota in these rumen fractions of yak. Therefore, we collected samples of solid, liquid, dorsal, and ventral epithelium fractions from five female yaks, then amplified bacterial 16S rRNA gene V4 regions and sequenced them using an Illumina MiSeq platform. Principal coordinates analysis detected significant differences in bacterial communities between the liquid, solid, and epithelium fractions, and between dorsal and ventral epithelium fractions. Rikenellaceae RC9, the families Lachnospiraceae and Ruminococcaceae, and Fibrobacter spp. were the abundant and enriched bacteria in solid fraction, while the genera Prevotella and Prevotellaceae UCG 003 were higher in the liquid fraction. Campylobacter spp., Comamonas spp., Desulfovibrio spp., and Solobacterium spp. were significantly higher in dorsal epithelium, while Howardella spp., Prevotellaceae UCG 001, Ruminococcaceae UCG 005, and Treponema 2 were enriched in the ventral epithelium. Comparison of predictive functional profiles among the solid, liquid, and dorsal, and ventral epithelium fractions also revealed significant differences. Microbiota in the ventral fraction of yak rumen also significantly differ from reported microbiota of cattle. In conclusion, our results improve our knowledge of the taxonomic composition and roles of yak rumen microbiota.

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

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

Effect of Acid/Ethanol Ratio on Medium Chain Carboxylate Production with Different VFAs as the Electron Acceptor: Insight into Carbon Balance and Microbial Community

Medium chain carboxylates (MCCs) are important precursors for biodiesel production. Using chain elongation to produce MCCs is an emerging bioenergy technology. In this study, batch tests were conducted to investigate fermentative MCC production through chain elongation from acetate, propionate, n-butyrate, and ethanol. The effect of the acid/ethanol ratio on MCC production by mixed culture was investigated. Better MCC production, especially n-caproate production, was achieved at optimal acid/ethanol ratios of 1:4, 1:3, and 1:2 with acetate, propionate, and n-butyrate as the electron acceptor, respectively. The n-caproate concentration was high, up to 41.54 mmol/L, and the highest n-caproate production efficiency was 57.96% with the n-butyrate/ethanol ratio of 1:2. The higher concentration of ethanol might stimulate the growth of chain elongation bacteria to promote chain elongation. The highest MCC production efficiency with different electron acceptors corresponded to less carbon loss and a higher chain elongation degree. In addition, with the optimal acid/ethanol ratio, the substrate was maximally utilized for chain elongation. The microbial community analysis confirmed the carbon balance analysis with the maximum relative abundance of 52.66–60.55% of the n-caproate producer Clostridium_sensu_stricto_12 enriched by the optimal acid/ethanol ratios with different volatile fatty acids (VFAs) as electron acceptors.

Feeding modes shape the acquisition and structure of the initial gut microbiota in newborn lambs

Early gut microbial colonization is important for postnatal metabolic and immune development. However, little is known about the effects of different feeding modes (suckling versus bottle-feeding) or microbial sources on this process in farm animals. We found that suckled and bottle-fed newborn lambs had their own distinct gut microbiota. Results from 16S rRNA gene sequencing and qPCR showed that, compared with suckling, bottle feeding significantly increased the abundances of Escherichia/Shigella, Butyricicoccus, and Clostridium XlVa, while significantly decreased the abundance of Clostridium XI. The higher levels of Escherichia/Shigella in bottle-fed lambs suggest that artificial feeding may increase the number of potential pathogens and delay the establishment of the anaerobic environment and anaerobic microbes. Feeding modes also affected the direct transmission of bacteria from the mother and the environment to newborns. The SourceTracker analysis estimated that the early gut microbes of suckled lambs were mainly derived from the mother's teats (43%) and ambient air (28%); whereas those of bottle-fed lambs were dominated by bacteria from the mother's vagina (46%), ambient air (31%), and the sheep pen floor (12%). These findings advance our understanding of gut microbiota in early life and may help design techniques to improve gut microbiota and health.

Heterogeneous development of methanogens and the correlation with bacteria in the rumen and cecum of sika deer (Cervus nippon) during early life suggest different ecology relevance

BACKGROUND

Enteric methane from the ruminant livestock is a significant source in global greenhouse gas emissions, which is mainly generated by the methanogens inhabiting the rumen and cecum. Sika deer (Cervus nippon) not only produces less methane than bovine, but they also harbor a distinct methanogen community. Whereas, knowledge of methanogens colonization in the rumen and cecum of sika deer is relatively still unknown, which could provide more insights to the manipulation of gut microbiota during early life.

RESULTS

Here, we examined the development of bacteria and methanogens in the rumen and cecum of juvenile sika deer from birth to post-weaning (1 day, 42 days and 70 days, respectively) based on next generation sequencing. The results showed that the facultative anaerobic bacteria were decreased and the cellulolytic bacteria were increased. However, methanogens established soon after birth thrived through the whole developmental period, indicating a different succession process than bacteria in the GIT, and the limited role of age and dietary change on GIT methanogens. We also found Methanobrevibacter spp. (Mean relative abundance = 44.2%) and Methanocorpusculum spp. (Mean relative abundance = 57.5%) were dominated in the rumen and cecum, respectively. The methanogens also formed specific correlations with bacteria under different niches, suggesting a role of ecology niche on methanogen community.

CONCLUSIONS

This study contributes to our knowledge about the microbial succession in GIT of sika deer, that may facilitate the development of targeted strategies to improve GIT function of sika deer.

A Rhizosphere-Derived Consortium of Bacillus subtilis and Trichoderma harzianum Suppresses Common Scab of Potato and Increases Yield

The ability of a rhizosphere-derived microbial product (composed of a consortium of a strain of Bacillus subtilis and a strain of Trichoderma harzianum) to suppress common scab disease in potato caused by Streptomyces spp. was examined over a two-year period. Relative to the condition in which 0 kg·ha^-1 of the designated microbial product was applied (control), the disease index decreased by 30.6%-46.1%, and yield increased by 23.0%-32.2% in treatments in which 225 or 300 kg·ha^-1 of the microbial product was administered, respectively. The bacterial communities present in the rhizosphere were assessed at an early stage of tuber formation, a time at which tubers are susceptible to common scab. Potato plants in which soils were treated with 225 or 300 kg·ha^-1 of the microbial product harbored rhizospheric microbiota with lower α-diversity and an increased relative abundance of taxa representing the beneficial bacteria. In summary, a select microbial product composed of a consortium of Bacillus subtilis and Trichoderma harzianum effectively suppressed common scab disease and increased tuber yield by establishing a high relative abundance of beneficial bacteria in the rhizosphere.

Characterizing the bacterial community across the gastrointestinal tract of goats: Composition and potential function

The composition and function of the microbial community in the gastrointestinal tract (GIT) have increasingly captured the attention of nutritionists because these traits affect the nutrient utilization efficiency and health of host animals. Little information has been reported on these aspects of the goat GIT. This study used 12 female goats (weighing 20.70 ± 1.60 kg and 10 months of age) to examine the composition and function of the microbiota in the rumen, abomasum, jejunum, cecum, and colon. Total genomic DNA was extracted from chyme samples from different sections of the GIT, and the hypervariable region of the 16S rRNA gene was amplified by PCR using bacterial universal primers. The amplicons were sequenced on an Illumina MiSeq platform, and the biological information was analyzed using QIIME software. A total of 857 genera that belonged to 39 phyla were observed across the goat GIT, with Bacteroidetes and Firmicutes dominating. Our results revealed significant differences in the composition, diversity, and species abundance of the bacterial communities in the different sections of the GIT. However, the compositions of the bacterial communities in adjacent GIT segments showed similarities in addition to differences. The study indicated that there were significant differences in microbial function among the GIT regions. In particular, the relative abundances of genes involved in energy metabolism, amino acid metabolism, nucleotide metabolism, and glycan metabolism were overrepresented in samples from the forestomach, and genes related to energy metabolism, amino acid metabolism, and glycan metabolism were mainly enriched in samples from the small intestine. Additionally, the relative abundances of bacteria at the phylum and genus levels were significantly correlated with these metabolic functions. In general, there were significant differences in composition and potential function among the bacterial communities in the goat GIT.

Rumen microbiome in dairy calves fed copper and grape-pomace dietary supplementations: Composition and predicted functional profile

The rumen microbiome is fundamental for the productivity and health of dairy cattle and diet is known to influence the rumen microbiota composition. In this study, grape-pomace, a natural source of polyphenols, and copper sulfate were provided as feed supplementation in 15 Holstein-Friesian calves, including 5 controls. After 75 days of supplementation, genomic DNA was extracted from the rumen liquor and prepared for 16S rRNA-gene sequencing to characterize the composition of the rumen microbiota. From this, the rumen metagenome was predicted to obtain the associated gene functions and metabolic pathways in a cost-effective manner. Results showed that feed supplementations did alter the rumen microbiome of calves. Copper and grape-pomace increased the diversity of the rumen microbiota: the Shannon's and Fisher's alpha indices were significantly different across groups (p-values 0.045 and 0.039), and Bray-Curtis distances could separate grape-pomace calves from the other two groups. Differentially abundant taxa were identified: in particular, an uncultured Bacteroidales UCG-001 genus and OTUs from genus Sarcina were the most differentially abundant in pomace-supplemented calves compared to controls (p-values 0.003 and 0.0002, respectively). Enriched taxonomies such as Ruminiclostridium and Eubacterium sp., whose functions are related to degradation of the grape- pomace constituents (e.g. flavonoids or xyloglucan) have been described (p-values 0.027/0.028 and 0.040/0.022 in Pomace vs Copper and Controls, respectively). The most abundant predicted metagenomic genes belonged to the arginine and proline metabolism and the two- component (sensor/responder) regulatory system, which were increased in the supplemented groups. Interestingly, the lipopolysaccharide biosynthetic pathway was decreased in the two supplemented groups, possibly as a result of antimicrobial effects. Methanogenic taxa also responded to the feed supplementation, and methane metabolism in the rumen was the second most different pathway (up-regulated by feed supplementations) between experimental groups.

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

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