Browsing by Subject "16S rRNA"

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Comparison of plant cell wall degrading community in the rumen of N’Dama and N’Dama x Jersey crossbred cattle in relation to in vivo and in vitro cell wall degradation
(2004) Nouala-Fonkou, Simplice; Becker, Klaus
This thesis presents a unique combination of an in vivo feeding trial, the analysis of the microbial community structure in the rumen, and in vitro fermentation studies, in order to assess the impact of breeds and diets on animal performance in a West African production setting. Pure N?Dama and N?Dama x Jersey crossbred cattle were fed two basal diets, baby corn and groundnut hay, supplemented with graded levels of either conventional concentrate or moringa leaf meal, to compare animal responses in productivity. In this context, Moringa oleifera leaf meal constitutes a locally available, potential alternative to commercial concentrate for cattle production. The cell wall digesting community of N?Dama and its crosses was analysed using phylogenetically based hybridisation probes to account for the contribution of rumen microbes to differences in fermentation patterns and animal response. In vitro fermentation studies were carried out using the same diets and supplementation levels as fed in vivo, to test the accuracy of the in vitro gas production technique in predicting the optimum level of supplementation. The in vivo feeding experiment focussed on the comparison of breed performance with diets relevant for local production conditions. Six N?Dama and six N?Dama x Jersey (crossbred) animals were used in a cross over design. They were fed consecutively three combinations of roughage and supplement, baby corn stover and concentrate (BCS:Co), groundnut hay and concentrate (GNH:Co) and groundnut hay and moringa meal (GNH:Mo), each at 5 levels of supplementation (0, 10, 20, 30 and 40%). Results from this study showed that there was a clear difference in animal response to different feeding regimes between the two breeds. When averaged over all diets organic matter intake (OMI) was higher in crossbred compared to N?Dama (94 and 87.6 g/kg 0.75 d-1, respectively). When analyzed for the diets and averaged over the breeds OMI was higher when animals were fed the baby corn based diet compared to groundnut based diets (95 against 88 g/kg 0.75 d-1). Only when the diet consisted of BCS:Co, and at low levels of supplementation, N?Dama ingested more than crossbred, but the difference was not significant. With GNH:Co crossbred ingested significantly more at levels of supplementation less or equal to 20%. With GNH:Mo crossbred ingested more, whatever the level of supplementation. The optimum level of supplementation in vivo, estimated with the single slope broken line model, was 10% and 20% for both breeds when they were fed BCS:Co and GNH:Co respectively, but 30% for N?Dama and 10% for the crossbreds when animals were fed GNH:Mo. Organic matter digestibility (OMD) was higher in N?Dama (64.6% against 60.7% in crossbreds) when animals were fed BCS:Co and supplementation had no effect on OMD of BCS:Co whatever the breed. When animals were fed groundnut hay as basal diet, OMD was also significantly higher in N?Dama at low levels of supplementation, but the differences became insignificant beyond 10% and 20% of concentrate or moringa, respectively. With GNH:Co OMD showed a quadratic response (p<0.001) with increasing level of supplementation when it was fed to crossbreds and was not affected when it was fed to N?Dama. Increasing levels of moringa meal supplementation increased OMD in both breeds up to a peak at 20 and 30% for N?Dama and crossbred, respectively. Average daily weight gain (ADG) was not affected by the breed, however it was higher on BCS:Co compared to other diets. On BCS:Co ADG increased with the level of supplementation, reaching a peak at 30%, whereas supplementation had no effect on ADG when animals were fed groundnut hay based diets. As N?Dama could take in and digest more of the low quality BCS:Co diet, they were less efficient in feed conversion under this feeding regime (FCE: 14 vs. 9 for the crossbreds). On GNH based diets, however, N?Dama surpassed the crossbreds in feed conversion efficiency with ratios of 11 vs. 13 for GNH:Co and 9 vs. 27 on GNH:Mo. Rumen microbes play the key role for the digestibility of a given feed and thus also for feed intake and finally animal performance. Obviously, the community composition and activity is highly dependent on the diet. With the present set-up, however, with identical external conditions and three different, well defined diets fed to both, N?Dama and crossbred cattle, a comparison of the microbial community structure between breeds could be attempted. The in vivo and in vitro data taken in the other parts of the study allow a sensible interpretation of potential changes in microbial composition. Rumen fluid was collected from three fistulated N?Dama and three crossbred animals adapted to the experimental diets at medium supplementation level. The cell wall degrading community was analyzed using the phylogenetically based 16S rRNA hybridisation probes. The results showed that on BCS:Co diet the Fibrobacter and R. flavefaciens RNA concentrations were higher in rumen fluid of N?Dama compared to crossbred. These concentrations were also significantly affected by the diet, such that they were higher on baby corn stover compared to groundnut hay based diets. The results of the microbial community analysis suggested that the differences between breeds observed in digestibility could be partially explained by the composition of the cell wall degrading community. Parallel to the in vivo experiment, in vitro fermentation studies were undertaken to evaluate the predictability of the in vivo response to supplementation by the in vitro data. Rumen fluid from 3 N?Dama and 3 crossbred donor animals was used for 24 hour in vitro fermentations. The donor animals were fed consecutively the same three diets used in vivo (BCS:Co, GNH:Co and GNH:Mo) at 20% level of supplementation. Each of these inocula was incubated with in vitro substrates consisting of all the combinations tested in vivo (i.e. 3 diets, 5 levels of supplementation) plus supplement alone. This design should allow to analyze for both, the impact of donor breed as well as that of the donor diet and to conclude which factors may be varied while maintaining predictability. The breed of the donor animals did not significantly affect 24 hour gas production, but short chain fatty acid concentration was higher with rumen fluid from crossbreds when donors were fed BCS:Co and GNH:Mo. Moringa meal as supplement to donor animals changed the fermentation pattern of all the substrates, such that gas production and SCFA increased substantially in groundnut hay based substrates, whereas gas production of BCS:Co substrates decreased and SCFA did not substantially change. In vitro digestibility was higher with rumen fluid from N?Dama whatever the diet of donor animals and the substrate incubated. GNH:Mo as donor diet also increased IVTD of all the substrates. Even though there was no clear response in vivo, this indicates a general stimulation of microbial activity in the rumen and renders moringa leaf meal a promising supplement. Averaged over all data there was a positive correlation (r2=0.53 p<0.001) between IVTD and in vivo OMD. This correlation was much stronger when calculated for a specific diet (e.g. r2=0.90 p<0.001 for BCS:Co, averaged over the breeds). Analyzing the data for the individual breeds affected correlations only to a minor degree. Thus, when testing a supplementation strategy in vitro, it should be important that donor animals are fed the same components (roughage and supplement) that will be combined at different levels in vitro, whilst the breed of donor animals may be of second importance. This work provides conclusive evidence that in vitro incubations may be used to design supplementation strategies, thus reducing the need for in vivo experiments. Moringa leaf meal is a promising local resource to substitute for conventional concentrate. Differences in productivity between breeds could be correlated to (and may be partially manifested through) a divergent community structure of rumen microbes. That, in turn, indicates that animals of different breeds might have a ?genetic background? that favours the establishment of a certain community, even if the animals are kept under identical conditions. This relationship should be investigated by more advanced molecular techniques.
Effect of a diet rich in galactose or fructose, with or without fructooligosaccharides, on gut microbiota composition in rats
(2022) Mhd Omar, Nor Adila; Dicksved, Johan; Kruger, Johanita; Zamaratskaia, Galia; Michaëlsson, Karl; Wolk, Alicja; Frank, Jan; Landberg, Rikard
Recent studies suggest that a diet rich in sugars significantly affects the gut microbiota. Adverse metabolic effects of sugars may partly be mediated by alterations of gut microbiota and gut health parameters, but experimental evidence is lacking. Therefore, we investigated the effects of high intake of fructose or galactose, with/without fructooligosaccharides (FOS), on gut microbiota composition in rats and explored the association between gut microbiota and low-grade systemic inflammation. Sprague–Dawley rats (n = 6/group) were fed the following isocaloric diets for 12 weeks (% of the dry weight of the sugars or FOS): (1) starch (control), (2) fructose (50%), (3) galactose (50%), (4) starch+FOS (15%) (FOS control), (5) fructose (50%)+FOS (15%), (6) galactose (50%)+FOS (15%), and (7) starch+olive (negative control). Microbiota composition in the large intestinal content was determined by sequencing amplicons from the 16S rRNA gene; 341F and 805R primers were used to generate amplicons from the V3 and V4 regions. Actinobacteria, Verrucomicrobia, Tenericutes, and Cyanobacteria composition differed between diets. Bifidobacterium was significantly higher in all diet groups where FOS was included. Modest associations between gut microbiota and metabolic factors as well as with gut permeability markers were observed, but no associations between gut microbiota and inflammation markers were observed. We found no coherent effect of galactose or fructose on gut microbiota composition. Added FOS increased Bifidobacterium but did not mitigate potential adverse metabolic effects induced by the sugars. However, gut microbiota composition was associated with several metabolic factors and gut permeability markers which warrant further investigations.
Metaomic studies of the dietary impact on the structural and functional diversity of the rumen microbiome
(2018) Deusch, Simon; Seifert, Jana
Ruminant production efficiency and related emission of greenhouse gases are mainly determined by the rumen microbiome. The structure and activity of the microbial communities in turn are mostly influenced by the animal’s feed intake. The most widely used forage sources for ruminant production in Europe are corn silage, grass silage and grass hay. Progress in animal production requires optimized feeding strategies which presuppose an improved understanding of the dietary impact on the complex bionetwork residing in the rumen. A broad range of different methods are applicable to investigate archaea and bacteria which represent the most active members of the rumen microbiome. Most rumen studies available are restricted to nucleic acid-based approaches with limited functional insights. To improve knowledge about the prokaryotic communities and their adaptation responses to different animal feeds, it is essential to focus on the actual functions out of numerous possibilities that are encoded by the genomes of the rumen microbiome. Therefore proteins are best suited since representing the actual function of investigated cells combined with phylogenetic information. The major aim of this project was the feasible, first-time establishment of a metaproteomics-based characterization of the ruminal prokaryotic communities to further investigate the dietary impact on the prokaryotic rumen metaproteome. The first part was providing an overview about research that used state of the art technologies to investigate the microbiome of the gastrointestinal tract of farm animals. Yet, Omics-technologies and their combination are rarely employed in livestock science. The considered studies relied mainly on stand-alone, DNA-based molecular methods which clearly emphasized the importance of introducing contemporary methods such as shotgun metaproteomics to study the rumen microbiome and to gain deeper, more complete insights into the actual functions carried out by the specific members of the prokaryotic communities. The second part of the current project focused on a suitable, mass spectrometry-based analysis of the prokaryotic communities in the rumen ecosystem. Metaproteomic studies are challenged by the heterogeneity of the rumen sample matter that contains, besides archaeal and bacterial cells, also eukaryotic cells of rumen fungi and protozoa as well as enormous amounts of plant cells from ingested feed and epithelial cells of the animals. Shotgun metaproteomic studies require the extraction of proteins preferably of the desired target organisms to increase the coverage of the respective metaproteome and the reliability of subsequent protein identifications. This entails the avoidance of undesired proteins present in the rumen samples. In contrast to nucleic acids, proteins cannot be enriched or amplified by PCR thus, optimized sample preparation protocols are necessary in order to retrieve enhanced amounts of prokaryotic instead of plant-derived or other eukaryotic cells before protein extraction and subsequent LC-MS/MS analysis. The final step and the major aim of this project was the in depth analysis of the metaproteome of archaea and bacteria and their adaptive response to the most common forages, corn silage, grass silage and grass hay accessing as well host-related influences and variations between different ecological niches within the rumen. Improved mass-spectrometric measurements and the construction of a customized, sample-specific in-house database for enhanced bioinformatic quantification of proteins yielded comprehensive datasets comprising 8,163 bacterial and 358 archaeal proteins that were identified across 27 samples from three different rumen fractions of three Jersey cows, fed rotationally with three different diets. The functional and structural data of the metaproteomic analysis was further flanked by 16S rRNA gene-based analyses of the archaeal and bacterial community structures and the metabolomes of the rumen fluid fractions were quantified by nuclear magnetic resonance. So far, to the best of our knowledge, there are no studies investigating the metaproteome expressed by the entirety of archaeal and bacterial communities in the different phases of the rumen ecosystem under varying dietary influence. Dietary treatments revealed significant variations in the metaproteome composition and community structures of ruminal bacteria. Host-related effects were not significant. In conclusion, within this project the application of shotgun metaproteomics to characterize the prokaryotic rumen metaproteome was successfully implemented and the obtained results clearly emphasized the benefits of using complementary, state of the art methods to study the microbiome of complex ecosystems like the rumen. Considering the specific functional niches of the rumen microbiome have been shown to be of great importance.
The porcine intestinal microbiota : studies on diversity and dietary impact
(2018) Burbach, Katharina; Seifert, Jana
The entirety of microbial communities within the gastrointestinal tract is referred to as intestinal microbiota and is predominantly composed of bacteria. Interactions between the microbiota, the host and the diet are essential for maintaining a healthy and functional intestinal ecosystem. The overarching aim of this thesis was the characterization of the porcine intestinal microbiota and further to enhance knowledge about the effects of varying diets. High-throughput sequencing of the 16S rRNA gene facilitates exploration of the taxonomic composition of the microbiota. However, the respective findings may be impaired by methodological variations. Thus, within this thesis, commercial DNA extraction kits are evaluated for their suitability in porcine microbiota analysis. The tested extractions yield into variations of quantity and quality of DNA. The DNA extracts are further used to elucidate the structure of the microbiota by a rapid fingerprinting (Terminal Restriction Fragment Length Polymorphism) and high-resolution sequencing (Illumina amplicon sequencing). While different variable regions of the 16S rRNA gene vary in the taxonomical resolution, sequencing analyses exhibit a good comparability of the two regions V1-V2 and the V5-V6. Furthermore, the microbiota profiles reveal a high consistency by the fingerprinting and sequencing approach but are distinguished by the different DNA extraction kits. Based on criteria of DNA extraction and the depicted microbiota composition, it is recommended to use the FastDNA SPIN Kit for Soil for further analysis of porcine intestinal microbiota. Subsequently, these methodological findings are applied to investigate the impact of varying diets. Illumina amplicon sequencing of the V1-V2 region of the 16S rRNA gene reveals different microbiota structures when diets are solely composed of rye or triticale. Besides the taxonomic analyses of ileal digesta and fecal samples, the concentrations of bacterial metabolites in feces are determined. In summary, rye promotes an increased abundance of saccharolytic bacteria like Lactobacillus, Bifidobacterium, and Prevotella and results in higher concentrations of bacterial metabolites in fecal samples. In contrast, a diet based on triticale is associated with an increased abundance of Clostridium sensu stricto, which may indicate an enhanced cellulolytic potential of the microbiota. When the crude protein content is increased (18%), compared to a lower content (14%), an increased abundance of Lactobacillus is demonstrated in microbiota of ileal digesta samples. However, the content of crude protein did not affect the overall microbiota significantly. In addition, dietary supplementation with probiotic Bacillus spp. shows no effect. In conclusion, these dietary effects on microbiota are considered together with results of a protein digestibility analysis. Moreover, an impact of dietary calcium and phosphorus in combination with different sources of dietary protein is analyzed by fingerprinting approach of digesta samples. Here, the content of calcium-phosphorus shows significant effects on the microbiota of caecal digesta and the putative identities of discriminative variables are determined by a cloning-sequencing approach. Similar, 16S rRNA gene sequencing reveals a significant impact of dietary calcium-phosphorus on the overall fecal microbiota without indicating specific discriminating variables. In combination with the results of a meta-proteomic approach, a gradual adaptation on dietary changes is indicated and consequently, a prolonged adaptation time of three to four weeks is recommended for diet-microbiota studies. This thesis includes a comprehensive analysis of the microbiota across and along the gastrointestinal tract of piglets and explores the dietary inclusion of four levels of insect larvae meal. Feeding insects represent an alternative source of dietary protein, whereby the increased content of chitin indicates a potential shift in microbiota composition compared to a control diet. However, in this case, the structural analysis demonstrates no effects on the overall microbiota’s structure. However, a pairwise comparison between diets reveals significant effects on the microbiota of digesta samples of the small intestine. Dietary inclusion of 5% insect meal increases the abundance of Lactobacillus, whereas the control treatment promotes Bifidobacterium. In conclusion, the results of the present thesis emphasize the importance of standardization within 16S rRNA gene based studies of the porcine intestinal microbiota. Furthermore, the necessity of studying various sampling sites combined with multidisciplinary approaches is demonstrated.