Dataset Information

The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens.

ABSTRACT: The rumen simulation technique (RUSITEC) is a well-established semicontinuous in vitro model for investigating ruminal fermentation; however, information on the stability of the ruminal bacterial microbiota and metabolome in the RUSITEC system is rarely available. The availability of high resolution methods, such as high-throughput sequencing and metabolomics improve our knowledge about the rumen microbial ecosystem and its fermentation processes. Thus, we used Illumina MiSeq 16S rRNA amplicon sequencing and a combination of direct injection mass spectrometry with a reverse-phase LC-MS/MS to evaluate the dynamics of the bacterial community and the concentration of several metabolites in a RUSITEC experiment as a function of time and in response to a challenge with a pathogenic Clostridium perfringens (C. perfringens) strain. After four days of equilibration, samples were collected on days 5, 6, 7, 10, 12 and 15 of the steady-state and experimental period. From a total of six fermenters, three non-infected fermenters were used for investigating time-dependent alterations; three fermenters were incubated with C. perfringens and compared with the non-infected vessels at days 10, 12 and 15. Along the time-line, there was no statistically significant change of the overall bacterial community, however, some phylotypes were enriched at certain time points. A decrease in Fibrobacter and Elusimicrobia over time was followed by an increase in Firmicutes and Actinobacteria. In contrast, classical fermentation measurements such as pH, redox potential, NH3-N, short chain fatty acids and the concentrations of metabolites determined by metabolomics (biogenic amines, hexoses and amino acids) remained stable throughout the experiment. In response to C. perfringens addition the concentrations of several amino acids increased. Although the overall bacterial community was not altered here either, some minor changes such as an enrichment of Synergistetes and Bacteroidetes were detectable over time. In conclusion, both, the bacterial community composition and the metabolome in the RUSITEC system were relatively stable during the experiment.

SUBMITTER: Wetzels SU

PROVIDER: S-EPMC5802913 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens.

Wetzels Stefanie U SU Eger Melanie M Burmester Marion M Kreienbrock Lothar L Abdulmawjood Amir A Pinior Beate B Wagner Martin M Breves Gerhard G Mann Evelyne E

PloS one 20180207 2

The rumen simulation technique (RUSITEC) is a well-established semicontinuous in vitro model for investigating ruminal fermentation; however, information on the stability of the ruminal bacterial microbiota and metabolome in the RUSITEC system is rarely available. The availability of high resolution methods, such as high-throughput sequencing and metabolomics improve our knowledge about the rumen microbial ecosystem and its fermentation processes. Thus, we used Illumina MiSeq 16S rRNA amplicon s ...[more]

PMID: 29415046

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Project description:A decrease in methanogenesis is expected to improve ruminant performance by allocating rumen metabolic hydrogen ([2H]) to more energy-rendering fermentation pathways for the animal. However, decreases in methane (CH4) emissions of up to 30% are not always linked with greater performance. Therefore, the aim of this study was to understand the fate of [2H] when CH4 production in the rumen is inhibited by known methanogenesis inhibitors (nitrate, NIT; 3-nitrooxypropanol, NOP; anthraquinone, AQ) in comparison with a control treatment (CON) with the Rumen Simulation Technique (RUSITEC). Measurements started after 1 week adaptation. Substrate disappearance was not modified by methanogenesis inhibitors. Nitrate mostly seemed to decrease [2H] availability by acting as an electron acceptor competing with methanogenesis. As a consequence, NIT decreased CH4 production (-75%), dissolved dihydrogen (H2) concentration (-30%) and the percentages of reduced volatile fatty acids (butyrate, isobutyrate, valerate, isovalerate, caproate and heptanoate) except propionate, but increased acetate molar percentage, ethanol concentration and the efficiency of microbial nitrogen synthesis (+14%) without affecting gaseous H2. Nitrooxypropanol decreased methanogenesis (-75%) while increasing both gaseous and dissolved H2 concentrations (+81% and +24%, respectively). Moreover, NOP decreased acetate and isovalerate molar percentages and increased butyrate, valerate, caproate and heptanoate molar percentages as well as n-propanol and ammonium concentrations. Methanogenesis inhibition with AQ (-26%) was associated with higher gaseous H2 production (+70%) but lower dissolved H2 concentration (-76%), evidencing a lack of relationship between the two H2 forms. Anthraquinone increased ammonium concentration, caproate and heptanoate molar percentages but decreased acetate and isobutyrate molar percentages, total microbial nitrogen production and efficiency of microbial protein synthesis (-16%). Overall, NOP and AQ increased the amount of reduced volatile fatty acids, but part of [2H] spared from methanogenesis was lost as gaseous H2. Finally, [2H] recovery was similar among CON, NOP and AQ but was largely lower than 100%. Consequently, further studies are required to discover other so far unidentified [2H] sinks for a better understanding of the metabolic pathways involved in [2H] production and utilization.

Project description:Plant based by-products (BP) produced from food and bioethanol industries are human inedible, but can be recycled into the global food chain by ruminant livestock. However, limited data is available on the methanogenesis potential associated with supplementing a solely BP formulated concentrate to a pastoral based diet. Therefore the objective of this in vitro study was to investigate the effects of BP inclusion rate (in a formulated concentrate) to a pasture based diet on dietary digestibility, rumen fermentation patterns, methane production and the prokaryotic microbial community composition. Diets consisted of perennial ryegrass and one of two supplementary concentrates, formulated to be isonitrogenous (16% CP) and isoenergetic (12.0 MJ/ME/kg), containing either 35% BP, barley and soybean meal (BP35) or 95% BP (BP95) offered on a 50:50 basis, however, starch, NDF and fat content varied. The BPs, included in equal proportions on a DM basis, were soyhulls, palm kernel expeller and maize dried distillers grains. The BP35 diet had greater (P < 0.05) digestibility of the chemical constituents DM, OM, CP, NDF, ADF. Greater total VFA production was seen in the BP35 diet (P < 0.05). Daily methane production (mmol/day; +22.7%) and methane output per unit of total organic matter digested (MPOMD; +20.8%) were greatest in the BP35 diet (P < 0.01). Dietary treatment influenced microbial composition (PERMANOVA; P = 0.023) with a greater relative abundance of Firmicutes (adj P < 0.01) observed in the BP35. The Firmicutes:Bacteroidetes ratio was significantly reduced in the BP95 diet (P < 0.01). The relative proportions of Proteobacteria (adj P < 0.01), Succinivibrionaceae (adj P < 0.03) and Succinivibrio (adj P = 0.053) increased in the BP95 diet. The abundance of Proteobacteria was found to be negatively associated with daily methane production (rs, -0.71; P < 0.01) and MPOMD (rs, -0.65; P < 0.01). Within Proteobacteria, the relationship of methane production was maintained with the mean abundance of Succinivibrio (rs, -0.69; P < 0.01). The abundance of the Firmicutes phyla was found to be positively correlated with both daily methane production (rs, 0.79; P < 0.001) and MPOMD (rs, 0.75; P < 0.01). Based on in vitro rumen simulation data, supplementation of an exclusively BP formulated concentrate was shown to reduce daily methane output by promoting a favorable alteration to the rumen prokaryotic community.

Dataset Information

The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens.

Publications

The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens.

Similar Datasets

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