Browsing by Subject "Gut microbiota"

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Analyse komplexer Merkmale beim Schwein mittels SNP-Chip Genotypen, Darmmikrobiota- und Genexpressionsdaten
(2017) Maushammer, Maria; Bennewitz, Jörn
In the present scientific research, SNP chip genotypes, gut microbiota and gene expression data were used for analysing complex traits in a Piétrain population. These data were collected from around 200 performance tested sows and were used for genetic and microbial analyses of complex trait as well as for structural and functional meat quality traits. The gut microbiome plays a major role in the immune system development, state of health and energy supply of the host. Quantitative-genetic methods were applied to analyse the interrelationship between pig gut microbiota compositions, complex traits (daily gain, feed conversion and feed intake) and pig genomes. The specific aims were to characterize the gut microbiota of the pigs, to analyse the effects of host genetics on gut microbial composition, and to investigate the role of gut microbial composition on the host’s complex traits. The pigs were genotyped with a standard 60K SNP chip. Microbial composition was characterized by 16S rRNA gene amplicon sequencing technology. Ten out of 51 investigated bacterial genera showed a significant host heritability, ranging from 0.32 to 0.57. Conducting genome wide association analysis showed associations of 22 SNPs and six bacterial genera. The potential candidate genes identified are involved in the immune system, mucosa structure and secretion of digestive juice. These results show, that parts of the gut microbiota are heritable and that the gut microbiome can be seen as quantitative trait. Microbial mixed linear models were applied to estimate the microbiota variance for each of the investigated traits. The fraction of phenotypic variance explained by the microbial variance was 0.28, 0.21, and 0.16 for daily gain, feed conversion, and feed intake, respectively. The SNP data and the microbiota data were used to predict the phenotypes of the traits using both, genomic best linear unbiased prediction (G-BLUP) and microbial best linear unbiased prediction (M-BLUP) methods. The prediction accuracies of G-BLUP were 0.35, 0.23, and 0.20 for daily gain, feed conversion, and feed intake, respectively. The corresponding prediction accuracies of M-BLUP were 0.41, 0.33, and 0.33. Thus, the gut microbiota can be seen as an explaining variable for complex traits like daily gain, feed conversion and feed intake. In addition, in combination with meat quality traits, transcript levels of muscle tissue were analysed at time of slaughtering. This study should give an insight into the biological processes involved in meat quality characteristics. The aims were to functionally characterise differentially expressed genes, to link the functional information with structural information obtained from GWAS, and to identify potential candidate genes based on these results. An important meat quality trait is the intramuscular fat content, since it affects the juiciness, the taste and the tenderness of the meat. Another important trait is drip loss which causes not only a loss of weight but also a loss of important proteins. Both traits have an impact on the consumer acceptance of fresh meat products. For each of the two traits, eight discordant sibling pairs were selected out of the Piétrain sample and were used for genome-wide gene expression analyses. Thirty five and 114 genes were identified as differentially expressed and trait correlated genes for intramuscular fat content and drip loss, respectively. On the basis of functional annotation, gene groups belonging to the energy metabolism of the mitochondria, the immune response and the metabolism of fat, were associated with intramuscular fat content. Gene groups associated with protein ubiquitination, mitochondrial metabolism, and muscle structural proteins were associated with drip loss. Furthermore, genome-wide association analyses were carried out for these traits and their results were linked to the genome-wide expression analysis by functional annotation. In this context, intramuscular fat was related to muscle contraction, transmembrane transport and nucleotide binding. Drip loss was characterized by the endomembrane system, the energy generation of cells, and phosphorus metabolic processes. Three and four potential candidate genes were identified for intramuscular fat content and drip loss, respectively.
Correction: Schubert et al. Microencapsulation of bacteriophages for the delivery to and modulation of the human gut microbiota through milk and cereal products. Appl. Sci. 2022, 12, 6299
(2023) Schubert, Christina; Fischer, Sabina; Dorsch, Kathrin; Teßmer, Lutz; Hinrichs, Jörg; Atamer, Zeynep
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.
Effects of diets with different phosporus availability on the intestinal microbiota of chickens and pigs
(2019) Tilocca, Bruno; Seifert, Jana
In the research works of the present thesis, 16S rRNA gene sequencing and metaproteomics were employed to investigate the gut microbiota of chickens and pigs kept at experimental diets with varying amount of calcium-phosphorus (CaP) and supplemented MP. This represents a valuable approach to investigate the bacterial specimens involved in the P absorption, allowing for a comprehensive understanding of how the intestinal bacteria adapt to a new diet and which metabolic routes are affected by changing levels of supplemented P and/or MP. Two major experimental trials were performed during the investigation. The first one was conducted on chickens operating a modulation in the dietary levels of Ca, P and MP. This trial highlighted a shift in the composition of the crop and ceca-associated microbial community depending on the composition of the diet fed. Also, investigated protein inventory revealed that the stress condition due to the reduced P availability is mirrored in the gastrointestinal tract (GIT)-associated microbiota. Marked differences were observed in the functions of the bacterial community in the case of P-available diets versus P-deficient ones. Protein repertoire of the first case draws a thriving microbial community focused on complex and anabolic functions. Contrariwise, the bacterial community in the case of P-lacking diets appears to deal with catabolic functions and stress response. The second trial was conducted on pigs and attempts to define the dynamics featuring the microbiota adaptation to a new challenging diet composed of different protein sources and varying levels of Ca and P. Statistical evidences reveal a stepwise adaptation of the fecal microbiota to the experimental diets fed. Both DNA-based approach and metaproteomics independently reveal three main adaptation phases: -before the feeding of the experimental trial (i.e. Zero), -the response of the microbial community to the challenging factor (i.e. MA) and, finally, - the newly achieved homeostatic balance (i.e. EQ). As observed in the first trial, feeding of the experimental diets impairs the overall fecal microbiota composition, stimulating the presence of phase-specific bacterial specimens and a characteristic relative abundance of the shared ones. Bacterial families responsible for the phase-specific architecture of the fecal microbiota are also active in the biochemical pathways driving the functional peculiarities of each adaptation phase. A deeper investigation of the identified protein repertoire revealed that the observed statistical differences among the adaptation phases are uniquely due to the Ca and P composition of the diets fed. None of the observed effects can be attributed to the diverse protein sources supplemented with the diets. Functional categorization of the identified protein inventory depicts three diverse functional assets of the microbial community. Specifically, prior the feeding of the experimental diets, bacteria are hypothesized to live under homeostatic condition, since they appear to be involved in complex and highly-specialized functions. Following the administration of the experimental diets microbial community changes its functional priority and reduce the expression of highly specialized functions to focus on more essential ones. Proteins involved in complex functions such as widening the substrates array and facing complex sugars tend to increase in abundance while the new homeostatic balance is achieved. Altogether, data from both trials provide useful information for future studies aimed to design effective breeding strategies finalized to reduce the P supplementation in the routinely breeding of livestock and maintain a balanced microbial activity in the animal GIT. Investigation of the dynamics of the porcine microbiota provides instructions on the minimal exposure time required from the intestinal microbiota to adapt to a new dietary composition. This is of fundamental importance for the design of future studies aimed to confirm and/or continue our results. Moreover, the anatomical and physiological similarities occurring between humans and pigs, make our findings of interest for future human nutritional studies, where the mechanisms and lasts of the microbiota adaptation process is still object of discussion.