In vitro evaluation of effects of gut region and fiber structure on the intestinal dominant bacterial diversity and functional bacterial species

Association of fibre degradation with ruminal dissolved hydrogen in growing beef bulls fed with two types of forages

The present study investigated the association between fibre degradation and the concentration of dissolved molecular hydrogen (H2) in the rumen. Napier grass (NG) silage and corn stover (CS) silage were compared as forages with contrasting structures and degradation patterns. In the first experiment, CS silage had greater 48-h DM, neutral-detergent fibre (NDF) and acid-detergent fibre degradation, and total gas and methane (CH4) volumes, and lower 48-h H2 volume than NG silage in 48-h in vitro incubations. In the second experiment, twenty-four growing beef bulls were fed diets including 55 % (DM basis) NG or CS silages. Bulls fed the CS diet had greater DM intake (DMI), average daily gain, total-tract digestibility of OM and NDF, ruminal dissolved methane (dCH4) concentration and gene copies of protozoa, methanogens, Ruminococcus albus and R. flavefaciens, and had lower ruminal dH2 concentration, and molar proportions of valerate and isovalerate, in comparison with those fed the NG diet. There was a negative correlation between dH2 concentration and NDF digestibility in bulls fed the CS diet, and a lack of relationship between dH2 concentration and NDF digestibility with the NG diet. In summary, the fibre of CS silage was more easily degraded by rumen microorganisms than that of NG silage. Increased dCH4 concentration with the CS diet presumably led to the decreased ruminal dH2 concentration, which may be helpful for fibre degradation and growth of fibrolytic micro-organisms in the rumen.

Effect of replacing conventional feeds with tropical agricultural by-products on the growth performance, nutrient digestibility and ruminal microbiota of water buffaloes

This study investigated the effect of replacing corn grain, soybean meal and wheat bran with tropical agricultural by-products, such as palm kernel cake (PKC), cassava residue and dried distiller's grain with solubles (DDGS), on the dry matter intake (DMI), growth performance, apparent nutrient digestibility, ruminal short-chain fatty acids (SCFA) and ruminal microbial communities of water buffaloes. Thirty healthy 15-month-old crossbred water buffaloes with a similar initial body weight of 353.1 ± 23.7 kg were randomly allocated into three dietary experimental groups, and they were fed with same forage but three different concentrates for 50 days fattening. The dietary treatments were as following: typical concentrate (TC, 65% corn + 15% wheat bran + 15% soybean meal), partial replacement concentrate Ⅰ (PRC I, 50% corn + 22.5% corn gluten + 22.5% PKC) and partial replacement concentrate Ⅱ (PRC II, 50% corn + 22.5% cassava residue + 22.5% DDGS). The results showed that the average daily gain of the PRC II group was the highest, and the DMI, acid detergent fibre digestibility and neutral detergent fibre digestibility value of the three groups were different and in the following order: PRC II group > TC group > PRC I group. The crude protein digestibility of PRC II was higher than that of the TC and PRC I groups (p < .05). The ruminal concentrations of total SCFA, acetate, propionate and butyrate of TC group were higher than the other two groups (p < .05). The PRC I group had the highest Bacteroidetes-to-Firmicutes ratio (B/F) and relative abundance of the genus Prevotella, while the PRC II group had the lowest B/F and relative abundance of Prevotella. In conclusion, using PKC and corn gluten to completely replace common feed ingredients in the buffalo concentrate ration decreased, while using cassava residue and DDGS increased animal growth performance, mainly due to the different combination influenced nutrient digestibility and ruminal microbial community composition was shifted.

Comparison of Faecal versus Rumen Inocula for the Estimation of NDF Digestibility

Simple Summary

The evaluation of fibre digestibility is very important for the formulation of ruminant diets. Fibre digestibility is usually determined in lab with rumen inoculum obtained from cannulated cows. The research of alternative and less invasive inoculum sources is a critical issue that should be addressed. The present study evaluated the potential of faecal inocula, obtained from cows fed different diets, to assess fibre digestibility of different substrates at different incubation times (48, 240 and 360 h). At short incubation time, fibre digestibility obtained with rumen fluid was always higher than those obtained with faecal inocula, confirming a lower activity of the faecal inocula compared with rumen fluid. However, the type of diets fed to the donor animals had a significant effect on fibre digestibility, with a more active faecal inoculum for cows fed a diet based on maize silage. Despite the differences obtained at the short incubation time, the digestibility values at longer intervals showed that faecal inoculum could replace rumen inoculum. As a consequence, faeces may replace rumen fluid as inoculum for end-point measures, avoiding the use of cannulated animals and decreasing the analytical costs.

Abstract

Cow faeces have been investigated as alternative inoculum to replace rumen fluid to determine neutral detergent fibre (NDF) digestibility (NDFD). Aims of this study were to estimate: (1) the NDFD (48 h) of feed ingredients using a rumen inoculum in comparison with faecal inocula from cows fed diets with different forage basis; (2) the undigestible NDF (uNDF) at 240 and 360 h with ruminal fluid and faecal inocula from lactating cows fed two different diets. At 48 h incubation, the NDFD was affected both by feed and type of inoculum (p < 0.01) and by their interaction (p = 0.03). Overall, the mean NDFD was higher for rumen inoculum than for faecal inocula (585 vs. 389 g/kg NDF, p < 0.05), and faecal inoculum obtained from cows fed hay-based diets gave lower NDFD than those from cows fed maize silage (367 vs. 440 g/kg, p < 0.05). At long incubation times, the average uNDF was affected by substrate, inoculum and incubation time (p < 0.01), but not by their interactions. For each inoculum, significantly lower values were obtained at 360 than at 240 h. Regressions between uNDF with rumen and with the tested faecal inocula resulted in r² ≥ 0.98. Despite the differences at 48 h, the uNDF showed that faecal inoculum could replace rumen fluid at longer incubation times.

Ruminal microbiota composition associated with ruminal fermentation parameters and milk yield in lactating buffalo in Guangxi, China-A preliminary study

The ruminal microbiota of 15 dairy buffalo was characterized using high-throughput 16S rRNA gene amplicon sequencing. Results showed that Bacteroidetes was the dominant bacterial phylum in all rumen samples, followed by Firmicutes, Proteobacteria, Tenericutes and Verrucomicrobia. Butyrivibrio was positively correlated with average milk fat yield (R = 0.55; p = 0.03), average milk total solid yield (R = 0.56; p = 0.03) and standard milk yield (R = 0.52; p = 0.05). Acinetobacter were positively correlated with average milk protein yield (R = 0.56; p = 0.03), average milk total solid yield (R = 0.60; p = 0.02) and standard milk yield (R = 0.57; p = 0.03). Acetobacter was positively correlated with acetate (R = 0.63; p = 0.01), propionate content (R = 0.55; p = 0.03), butyrate content (R = 0.61; p = 0.02) and total VFA (R = 0.62; p = 0.01). The phyla Proteobacteria (R = 0.53; p = 0.04) and genus Prevotella (R = 0.52; p = 0.05) were positively correlated with butyrate content. Correlation analysis suggested that increased Butyrivibrio and Acinetobacter residing in the buffalo rumen could improve milk performance.

In vitro fermentation of arabinoxylan from oat (Avena sativa L.) by Pekin duck intestinal microbiota

Arabinoxylan (AX) is abundant in cereal grains used as feed for ducks. However, the duck intestinal microbes responsible for the degradation of AX are not fully understood. In this study, oat AX was degraded and utilized by different duck intestinal microbiota in vitro. Changes in short-chain fatty acids (SCFAs), branch-chain fatty acids, and the pH resulted from a 72-h AX fermentation in intestinal samples were measured. The addition of AX increased the concentration of isobutyric acid and decreased the concentrations of SCFAs. The pH values decreased significantly in the intestinal samples. Gut microbiota were assessed using high-throughput sequencing of the 16S ribosomal RNA gene, and the results indicated that AX stimulated the growth of Megamonas and Bifidobacterium species, with Megamonas exhibiting the greatest stimulation. Overall, the results suggest that oat AX is utilized by specific bacteria in duck intestines, providing the theoretical basis for the impacts of AX on animal health.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Dietary starch and rhubarb supplement increase ruminal dissolved hydrogen without altering rumen fermentation and methane emissions in goats

Hydrogen is an important intermediate that is produced during carbohydrate fermentation to volatile fatty acid and utilized by methanogens to produce methane in the rumen. Ruminal volatile fatty acid and dissolved methane concentrations are more than 500 times greater than dissolved hydrogen concentration. Therefore, we hypothesized that dissolved hydrogen might have a higher sensitivity in response to dietary changes compared with volatile fatty acid and dissolved methane. Using goats, we investigated the effects of increasing dietary starch content (maize replaced with wheat bran) and supplementing with rhubarb rhizomes and roots on the relationships among dissolved hydrogen, dissolved methane and other fermentation end products. The study was conducted in a replicated 4×4 Latin square with a 2×2 factorial arrangement of four treatments: two starch levels (220 v. 320 g/kg dry matter (DM)), without and with rhubarb supplement (0% v. 2.8% of total mixed ration). Increased dietary starch and rhubarb supplementation did not alter volatile fatty acid concentrations or methane emissions in terms of g/day, g/g DM intake and g/g organic matter digested. However, goats fed the high-starch diet had greater dissolved hydrogen (P=0.005) and relative abundance of Selenomonas ruminantium (P&lt;0.01), and lower (P=0.02) copy number of protozoa than those fed the low-starch diet. Rhubarb increased ruminal dissolved H2 (P=0.03) and total volatile fatty acid concentration (P&lt;0.001), but decreased copies of bacteria (P=0.002). In conclusion, dissolved hydrogen appears to be more sensitive to dietary changes with starch content and rhubarb supplementation, when compared with volatile fatty acid concentrations and methane production.

Nitrate improves ammonia incorporation into rumen microbial protein in lactating dairy cows fed a low-protein diet

Generation of ammonia from nitrate reduction is slower compared with urea hydrolysis and may be more efficiently incorporated into ruminal microbial protein. We hypothesized that nitrate supplementation could increase ammonia incorporation into microbial protein in the rumen compared with urea supplementation of a low-protein diet fed to lactating dairy cows. Eight multiparous Chinese Holstein dairy cows were used in a crossover design to investigate the effect of nitrate or an isonitrogenous urea inclusion in the basal low-protein diet on rumen fermentation, milk yield, and ruminal microbial community in dairy cows fed a low-protein diet in comparison with an isonitrogenous urea control. Eight lactating cows were blocked in 4 pairs according to days in milk, parity, and milk yield and allocated to urea (7.0 g urea/kg of dry matter of basal diet) or nitrate (14.6 g of NO₃^-/kg of dry matter of basal diet, supplemented as sodium nitrate) treatments, which were formulated on 75% of metabolizable protein requirements. Nitrate supplementation decreased ammonia concentration in the rumen liquids (-33.1%) and plasma (-30.6%) as well as methane emissions (-15.0%) and increased dissolved hydrogen concentration (102%), microbial N (22.8%), propionate molar percentage, milk yield, and 16S rRNA gene copies of Selenomonas ruminantium. Ruminal dissolved hydrogen was positively correlated with the molar proportion of propionate (r = 0.57), and negatively correlated with acetate-to-propionate ratio (r = -0.57) and estimated net metabolic hydrogen production relative to total VFA produced (r = -0.58). Nitrate reduction to ammonia redirected metabolic hydrogen away from methanogenesis, enhanced ammonia incorporation into rumen microbial protein, and shifted fermentation from acetate to propionate, along with increasing S. ruminantium 16S rRNA gene copies, likely leading to the increased milk yield.

Ruminal fermentation and microbial community differently influenced by four typical subtropical forages in vitro

The present study evaluated the effects of 4 typical subtropical forages on ruminal microbial community composition to formulate a better diet for buffalo. Corn straw silage, elephant grass, cassava residues and sugarcane tail silage were used as substrates for in vitro fermentation. Eight replicates were set up for every substrate, and fermentation was carried out in a 100-mL glass syringe, using buffalo rumen inoculum. Every replicate was anaerobically dispensed with 10 mL of rumen inoculum, 20 mL of McDougall's buffer and 200 mg of dried substrate, and placed in a water bath at 39 °C. Gas production was recorded at 0, 2, 6, 12, 24, 36, 48 and 72 h of incubation. After 24 h, fermentation was ceased for 4 replicates and samples were collected. Volatile fatty acids (VFA) concentrations were measured using gas chromatography. Microbial populations were quantified using quantitative real-time PCR (qRT-PCR), and microbial community was analyzed using high throughput sequencing technology. The results showed, cassava residues as substrate had the highest gas production, acetate, propionate and total VFA concentrations (P < 0.05), and corn straw silage had the lowest acetate:propionate ratio (P < 0.05). The lowest numbers of fungi, Ruminococcus albus and Fibrobacter succinogenes, and the highest number of protozoa were observed with cassava residues (P < 0.05). The least abundances of bacterial phyla Firmicutes, Bacteroidetes and genus Prevotella, and substantially higher abundance of phylum proteobacteria (56%) and genus Succinivibrio (52%) were observed with cassava residues. The most abundances of Methanobrevibacter gottschalkii and Entodinium were observed with cassava residues. Spearman's correlations analysis showed, Succinivibrio had strong positive correlations with propionate, butyrate, Metadinium and M. gottschalkii, indicating fermentation products were related to microbial community. In conclusion, incubation with cassava residues resulted in lower number of fiber degrading microbes but higher protozoal population because of its low fiber contents. The microbial community was highly altered by in vitro incubation with cassava residues, whereas remained similar for the other 3 high fiber containing substrates.

Molecular hydrogen generated by elemental magnesium supplementation alters rumen fermentation and microbiota in goats

We tested the hypotheses that supplementation of a diet with elemental Mg increases ruminal dissolved H2 (dH2) in rumen fluid, which in turn alters rumen fermentation and microbial community in goats. In a randomised block design, twenty growing goats were allocated to two treatments fed the same basal diet with 1·45 % Mg(OH)2 or 0·6 % elemental Mg. After 28 d of adaptation, we collected total faeces to measure total tract digestibility, rumen contents to analyse fermentation end products and microbial groups, and measured methane (CH4) emission using respiration chambers. Ruminal Mg2+ concentration was similar in both treatments. Elemental Mg supplementation increased dH2 at 2·5 h post morning feeding (+180 %, P<0·001). Elemental Mg supplementation decreased total volatile fatty acid concentration (-8·6 %, P<0·001), the acetate:propionate ratio (-11·8 %, P<0·03) and fungal copy numbers (-63·6 %, P=0·006), and increased propionate molar percentage (+11·6 %, P<0·001), methanogen copy numbers (+47·9 %, P<0·001), dissolved CH4 (+35·6 %, P<0·001) and CH4 emissions (+11·7 %, P=0·03), compared with Mg(OH)2 supplementation. The bacterial community composition in both treatments was overall similar. Ruminal dH2 was negatively correlated with acetate molar percentage and fungal copy numbers (P<0·05), and positively correlated with propionate molar percentage and methanogen copy numbers (P<0·05). In summary, elemental Mg supplementation increased ruminal dH2 concentration, which inhibited rumen fermentation, enhanced methanogenesis and seemed to shift fermentation pathways from acetate to propionate, and altered microbiota by decreasing fungi and increasing methanogens.

Microbial community composition along the digestive tract in forage- and grain-fed bison

BACKGROUND

Diversity and composition of microbial communities was compared across the 13 major sections of the digestive tract (esophagus, reticulum, rumen, omasum, abomasum, duodenum, jejunum, ileum, cecum, ascending colon, transverse colon, descending colon, and rectum) in two captive populations of American bison (Bison bison), one of which was finished on forage, the other on grain.

RESULTS

Microbial diversity fell to its lowest levels in the small intestine, with Bacteroidetes reaching their lowest relative abundance in that region, while Firmicutes and Euryarchaeota attained their highest relative abundances there. Gammaproteobacteria were most abundant in the esophagus, small intestine, and colon. The forage-finished bison population exhibited higher overall levels of diversity, as well as a higher relative abundance of Bacteroidetes in most gut sections. The grain-finished bison population exhibited elevated levels of Firmicutes and Gammaproteobacteria. Within each population, different sections of the digestive tract exhibited divergent microbial community composition, although it was essentially the same among sections within a given region of the digestive tract. Shannon diversity was lowest in the midgut. For each section of the digestive tract, the two bison populations differed significantly in microbial community composition.

CONCLUSIONS

Similarities among sections indicate that the esophagus, reticulum, rumen, omasum, and abomasum may all be considered to house the foregut microbiota; the duodenum, jejunum, and ileum may all be considered to house the small intestine or midgut microbiota; and the cecum, ascending colon, transverse colon, descending colon, and rectum may all be considered to house the hindgut microbiota. Acid from the stomach, bile from the gall bladder, digestive enzymes from the pancreas, and the relatively low retention time of the small intestine may have caused the midgut's low microbial diversity. Differences in microbial community composition between populations may have been most strongly influenced by differences in diet (forage or grain). The clinical condition of the animals used in the present study was not evaluated, so further research is needed to establish whether the microbial profiles of some bison in this study are indeed indicative of dysbiosis, a predisposing factor to ruminal acidosis and its sequelae.

Composition of Ileal Bacterial Community in Grazing Goats Varies across Non-rumination, Transition and Rumination Stages of Life

The establishment of gut microbiota is increasingly recognized as a crucial action in neonatal development, host health and productivity. We hypothesized that the ileal microbiome shifted as goats matured, and this colonization process would be associated with host fermentation capacity. To this end, 18 Liuyang black grazing goats were randomly slaughtered at d 0, 7, 28, 42, and 70. Ileal microbiota was profiled by Miseq sequencing of 16S rRNA gene of bacteria, and fermentation capacity [volatile fatty acid, activities of amylase, carboxymethylcellulase (CMCase) and xylanase] was determined using digesta sample. Principal coordinate analysis revealed that each age group harbored its distinct bacteria. Total bacteria copy number and most alpha diversity indexes increased (P < 0.01) from d 0 to 70. At the phylum level, abundances of Cyanobacteria (P = 0.018) and TM7 (P = 0.010) increased linearly, abundances of Bacteroidetes (P = 0.075) and Fibrobacteres (P = 0.076) tended to increase linearly, whist Proteobacteria abundance tended to decline quadratically (P = 0.052) with age. At the genus level, Enterococcus (30.9%), Lactobacillus (32.8%), and Escherichia (2.0%) dominated at d 0, while Prevotella, Butyrivibrio, Ruminococcus, SMB53, and Fibrobacter surged in abundance after day 20. The highest amylase activity was observed at day 42, while xylanase activity increased quadratically (P = 0.002) from days 28 to 70. Correlation analysis indicated that abundances of Bacteroides, Clostridium, Lactobacillus, Propionibacterium, Enterococcus, and p-75-a5 positively correlated with enzyme activity. Collectively, ileal bacteria in grazing goats assemble into distinct communities throughout development, and might participate in the improvement of host fermentation capacity.

Shifts in Rumen Fermentation and Microbiota Are Associated with Dissolved Ruminal Hydrogen Concentrations in Lactating Dairy Cows Fed Different Types of Carbohydrates

BACKGROUND

Different carbohydrates ingested greatly influence rumen fermentation and microbiota and gaseous methane emissions. Dissolved hydrogen concentration is related to rumen fermentation and methane production.

OBJECTIVES

We tested the hypothesis that carbohydrates ingested greatly alter the rumen environment in dairy cows, and that dissolved hydrogen concentration is associated with these changes in rumen fermentation and microbiota.

METHODS

Twenty-eight lactating Chinese Holstein dairy cows [aged 4-5 y, body weight 480 ± 37 kg (mean ± SD)] were used in a randomized complete block design to investigate effects of 4 diets differing in forage content (45% compared with 35%) and source (rice straw compared with a mixture of rice straw and corn silage) on feed intake, rumen fermentation, and microbial populations.

RESULTS

Feed intake (10.7-12.6 kg/d) and fiber degradation (0.584-0.692) greatly differed (P ≤ 0.05) between cows fed the 4 diets, leading to large differences (P ≤ 0.05) in gaseous methane yield (27.2-37.3 g/kg organic matter digested), dissolved hydrogen (0.258-1.64 μmol/L), rumen fermentation products, and microbiota. Ruminal dissolved hydrogen was negatively correlated (r < -0.40; P < 0.05) with molar proportion of acetate, numbers of fungi, abundance of Fibrobacter succinogenes, and methane yield, but positively correlated (r > 0.40; P < 0.05) with molar proportions of propionate and n-butyrate, numbers of methanogens, and abundance of Selenomonas ruminantium and Prevotella spp. Ruminal dissolved hydrogen was positively correlated (r = 0.93; P < 0.001) with Gibbs free energy changes of reactions producing greater acetate and hydrogen, but not correlated with those reactions producing more propionate without hydrogen.

CONCLUSIONS

Changes in fermentation pathways from acetate toward propionate production and in microbiota from fibrolytic toward amylolytic species were closely associated with ruminal dissolved hydrogen in lactating dairy cows. An unresolved paradox was that greater dissolved hydrogen was associated with greater numbers of methanogens but with lower gaseous methane emissions.

Effects of microcystin-LR on gut microflora in different gut regions of mice

To reveal the toxicological effects of the hepatotoxic microcystin-leucine arginine (MC-LR) on gut microbial community composition in different gut regions, we conducted a subchronic exposure of BALB/c mice to MC-LR via intragastric administration. Denaturing gradient gel electrophoresis (DGGE) was employed to profile the shifts of microbes after MC-LR treatment in the jejuno-ileum, caecum and colon. DGGE profiles analysis showed that MC-LR increased the microbial species richness (number of microbial bands) in the caecum and colon as well as microbial diversity (Shannon-Wiener index) in the caecum. The cluster analysis of DGGE profiles indicated that the microbial structures in the caecum and colon shifted significantly after MC-LR treatment, while that in the jejuno-ileum did not. All the relatively decreased gut microbes belonged to Clostridia in the Firmicutes phylum, and most of them were Lachnospiraceae. The increased ones derived from a variety of microbes including species from Porphyromonadaceae and Prevotellaceae in the Bacteroidetes phylum, as well as Lachnospiraceae and Ruminococcaceae in the Firmicutes phylum, and among which, the increase of Barnesiella in Porphyromonadaceae was most remarkable. In conclusion, subchronic exposure to MC-LR could disturb the balance of gut microbes in mice, and its toxicological effects varied between the jejuno-ileum and the other two gut regions.