Fermentation pattern of several carbohydrate sources incubated in an in vitro semicontinuous system with inocula from ruminants given either forage or concentrate-based diets

The fermentation pattern of several carbohydrate sources and their interaction with the nature of microbial inoculum was studied. Barley (B), maize (M), sorghum, (S), sugarbeet pulp (BP), citrus pulp (CP) and wheat bran (WB) were tested in an in vitro semicontinuous system maintaining poorly buffered conditions from 0 to 6 h, and being gradually buffered to 6.5 from 8 to 24 h to simulate the rumen pH pattern. Rumen fluid inoculum was obtained from lambs fed with either concentrate and barley straw (CI) or alfalfa hay (FI). The extent of fermentation was higher with CI than FI throughout the incubation (p < 0.05). Among the substrates, S, BP and M maintained the highest pH (p < 0.05), whereas CP recorded the lowest pH with both inocula. Similarly, CP recorded the highest gas volume throughout the incubation, followed by WB and B, and S recorded the lowest volume (p < 0.05). On average, the total volatile fatty acid (VFA), as well as lactic acid concentration, was higher with CP than in the other substrates (p < 0.05). The microbial structure was more affected by the animal donor of inoculum than by the substrate. The in vitro semicontinuous system allows for the study of the rumen environment acidification and substrate microbial fermentation under intensive feeding conditions. © 2020 by the authors. Licensee MDPI, Basel, Switzerland

In vitro fermentation pattern and acidification potential of different sources of carbohydrates for ruminants given high concentrate diets

The in vitro fermentation pattern of five sources of carbohydrates of differing nature (maize grain, MZ; sucrose, SU; wheat bran, WB; sugarbeet pulp, BP; and citrus pulp, CT) under conditions of high concentrate diets for ruminants was studied. A first 8 h incubation trial was performed under optimal pH using inoculum from ewes given a fibrous diet, to compare fermentative characteristics of substrates. As planned, incubation pH ranged within 6.3 to 6.6. The gas produced from CT was higher than MZ, SU and BP from 4 and 6 h onwards, and at 8 h, respectively (p0.05) on total volatile fatty acid (VFA) concentration, nor on acetate or propionate proportions, but butyrate was lowest (p<0.05) with CT and BP. The second incubation trial was performed in a poorly-buffered medium, with inoculum from ewes given a concentrate diet. All substrates showed a gradual drop of pH, being lowest with SU after 4 h (p<0.05). Throughout the incubation, gas production was highest with CT and lowest with MZ and BP (p<0.05). Total 8 h VFA concentration was higher with CT than BP, SU and MZ (p<0.05). Acetate proportion was higher, and that of propionate lower, with BP than WB (p<0.05), butyrate proportion being higher with MZ and WB than with BP and CT (p<0.05). Lactic acid concentration was higher (p<0.05) with SU than WB and BP. Fermentation characteristics and acidification potential of feeds depend on the nature of their carbohydrate fraction, and must be considered for practical applications

In vitro acidification potential and fermentation pattern of cereal grains incubated with inoculum from animals given forage or concentrate based diets

This work aimed to study the acidification and fermentation pattern of maize (M1, M2, M3), barley (B1, B2, B3) and sorghum (S1, S2, S3) varieties depending on the rumen environment (inoculum from forage or concentrate diets, FI or CI), in 10 h incubation series with a low buffered medium. With CI, gas volume from barley was similar to maize (P > 0.05) except at 4 and 6 h, when M2 and M1 were lower. Barley or maize varieties did not differ in gas production (P > 0.05). After 10 h, barley and maize produced on average 82.5 and 73.0 mL/g organic matter (OM), whereas S1, S2 and S3 rendered 68.4, 31.1 and 39.7 mL/g. With FI, differences between barley and maize were detected after 6 h (61.0, 35.3 and 14.1 mL/g OM at 10 h for barley, maize and sorghum). Among inocula, pH with CI was lower than with FI (P < 0.001). Incubation pH at 10 h was 5.51, 5.21 and 5.00 with CI, and 5.52, 5.85 and 5.91 with FI, for sorghum, maize and barley varieties. Gas production and total volatile fatty acid (VFA) concentration were higher (P < 0.001) with CI than FI (67.3 vs 36.8 mL/g and 31.0 vs 19.9 mmol/L at 10 and 8 h). Butyrate and valerate proportions were higher with CI (P < 0.001), whereas acetate and branched chain VFA were lower (P < 0.001). Fermentative activity against vitreous starch such as maize or sorghum was lower for forage than concentrate inoculum. Study of fermentation of starch-rich substrates in a low buffered medium gives a more realistic picture than conventionally buffered conditions

Growth and bacterial dynamics of beef calves during transition from milk/pasture to a high-concentrate diet added with tannins or medium-chain fatty acids

Context. Rumen fermentation modulation with feed additives during the transition period to high-concentrate diets might help to avoid bacterial dysbiosis. Aims. Assessing the effects of the addition of tannins and medium-chain fatty acids (MCFA) to the adaptation diet of beef calves to a high-concentrate ration on the rate of intake, animal performance and rumen bacterial composition. Methods. Eighteen 7-month-old beef calves were abruptly weaned and transitioned over a 28-day period from a milk/grass regime to one of the following diets: a non-supplemented high-concentrate diet plus wheat straw, both given ad libitum (C); C plus 20 g/kg of a 65:35 chestnut and quebracho tannin extract; and C plus 6 g/kg of a commercial mixture of MCFA. Concentrate and straw rate of intake were recorded. Rumen fluid was collected on Days 0, 1, 7, 14, 21 and 28 at 0, 3, 6 and 9 h after feeding to characterise rumen fermentation. Samples from 0 h were analysed to assess the bacterial population using Ion Torrent sequencing. Key results. The rate of intake of concentrates and straw, as well as daily gains and final weights, were similar (P > 0.05) among diets. The addition of tannins or MCFA did not modify (P = 0.98) the rumen bacterial population, which was affected by sampling day (P < 0.001). The additives inclusion did not affect relative abundances of the main bacterial taxa (P < 0.05), most of them differing across days (P < 0.001). Diversity indexes (Shannon and richness) declined over sampling days (P < 0.05), although some genera emerged after concentrate inclusion. Conclusions. At the doses used in the present experiment, tannins and MCFA did not exert any effect on intake, animal performance and bacterial population. Abrupt transition to high-concentrate diets modified the rumen environment and bacterial community, indicating bacterial adaptation to new environmental conditions. Implications. Abrupt transition of 7-month-old calves from milk/pasture to a high-concentrate diet did not impair rumen microbiota or performance; therefore, the use of feed additives seems unnecessary. © 2021 CSIRO. All rights reserved

In vitro fermentation of barley according to the inclusion of levels of fatty acid additives in diets for intensive beef production

En dietas para rumiantes en cebo intensivo, así como para vacuno lechero, la adición de grasa en el concentrado permite aumentar la concentración energética y modificar el perfil de ácidos grasos absorbidos, además de atenuar la actividad fermentativa (Palmquist y Jenkins, 1980), contribuyendo a reducir el riesgo de acidosis ruminal.Trabajo financiado con el Proyecto AGL 2013-46820 (MINECO), con la ayuda del Departamento de Industria e Innovación) y el Fondo Social Europeo. S. Yuste disfrutó de una beca FPU (Ministerio de Educación, Cultura y Deporte).Unpublishe

Effect of adding essential oil compounds in diets for intensive beef production on in vitro barley fermentation

La intensificación de los sistemas de producción de carne en rumiantes supone la aparición frecuente de procesos de acidosis (Nagaraja y Titmeyer, 2007), pero un buen manejo alimentario puede prevenir la aparición de estos trastornos digestivos.Trabajo financiado con el Proyecto AGL 2013-46820 (MINECO), con la ayuda del Departamento de Industria e Innovación (Gobierno de Aragón) y el Fonso Social Europeo. S. Yuste disfrutó de una beca FPU (Ministerio de Educación, Cultura y Deporte).Publishe

In vitro assessment of nutritive value of date palm by-products as feed for ruminants

Date-palm leaves, pedicels, date-pits and waste dates are date-palm by-products (DPBP), routinely used as a feed resource by oasis farmers. This work aims to assess in vitro the chemical composition and nutritional value of these DPBP, including waste dates from three varieties (Bouarus, Harchaya and Kentichi). Vetch-oat hay was used as a reference feed material. Palm leaves showed the highest NDF, ADF, lignin and crude protein contents (609, 435, 84, 64 g kg DM, respectively). Cumulative gas production at 144 h of incubation was greatest for Kentichi dates (330 mL gDM) and lowest for date-pits (69 mL gDM). Regardless of the variety, waste dates showed the highest DM effective ruminal degradability (ED=0.48-0.49; estimated for a passage rate of 0.03 h) and organic matter digestibility (OMD), whereas date-pits seemed to be a poorly degradable material, with an ED coefficient of 0.09 g g DM. The lowest total VFA production from ruminal fermentation was with date-pits and the highest with waste dates of the Bouarus variety. These results suggest that waste dates, albeit their low protein content, should be considered highly digestible with energy concentrations as high as that of vetch-oat hay. Palm leaves and pedicels can be considered as highly fibrous emergency roughages for low-producing animals. When DPBP are used as feedstuffs, protein supplements will be necessary to balance the ruminant diets.Peer Reviewe

Effect of preweaning diet on rumen fermentation and blood metabolites in beef calves

El consumo de alimentos sólidos (forrajes o pienso) durante la lactación es vital para alcanzar una correcta transición de pre-rumiante a rumiante adulto (Coverdale et al., 2004). La naturaleza de estos alimentos juega un papel importante en el desarrollo del rumen, provocando una mejor adaptación del animal a la posterior dieta de cebo, con altos niveles de carbohidratos rápidamente fermentables, y ayudando a prevenir la posterior aparición de problemas de acidosis (Khan et al., 2011). El objetivo de este experimento fue determinar el manejo nutricional más adecuado durante la lactación para conseguir una buena adaptación al posterior periodo de cebo en ganado vacuno de carne.Thirty calves of two breeds (Parda de Montaña and Pirenaica) were used to assess !he most suitable feeding strategy (milk only, milk + grass hay or milk + concentrate) during lactation to achieve an adequate adaptation of beef calves to the fattening period, when a high-concentrate die! is offered. Rumen fermentation parameters were affected by supplementation, resulting in a more developed rumen when concentrate was offered. Glucosa and P-hidroxybutyrate concentrations in plasma were not influenced by die! bu! showed a shift in metabolic pathways and fue! used by !he animal, except far animals supplemented with grass hay. Supplementing with concentrates during lactation seems a recommendable practica sinca it improvas ruman farmantation with a carry-ovar effact during transition when cattle will be fed a high-concentrate diet.Financiación procedente de Gobierno de Aragón, INIA-FEOER (RZP2012-02), MINECO (AGL2013-46820P), INIA-FSE (Contrato de M. Blanco) y MECO (beca FPU de S. Yuste, Ref.15/01960).Unpublishe

TOGGLE : toolbox for generic NGS analyses

Background: The explosion of NGS (Next Generation Sequencing) sequence data requires a huge effort in Bioinformatics methods and analyses. The creation of dedicated, robust and reliable pipelines able to handle dozens of samples from raw FASTQ data to relevant biological data is a time-consuming task in all projects relying on NGS. To address this, we created a generic and modular toolbox for developing such pipelines. Results: TOGGLE (TOolbox for Generic nGs anaLysEs) is a suite of tools able to design pipelines that manage large sets of NGS softwares and utilities. Moreover, TOGGLE offers an easy way to manipulate the various options of the different softwares through the pipelines in using a single basic configuration file, which can be changed for each assay without having to change the code itself. We also describe one implementation of TOGGLE in a complete analysis pipeline designed for SNP discovery for large sets of genomic data, ready to use in different environments (from a single machine to HPC clusters). Conclusion: TOGGLE speeds up the creation of robust pipelines with reliable log tracking and data flow, for a large range of analyses. Moreover, it enables Biologists to concentrate on the biological relevance of results, and change the experimental conditions easily