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Advances in high-throughput DNA sequencing have propelled research into the human microbiome and its link to metabolic health. We explore microbiome analysis methods, specifically emphasizing metabolomics, how dietary choices impact the production of microbial metabolites, providing an overview of studies examining the connection between enterotypes and diet, and thus, improvement of personalized dietary recommendations. Acetate, propionate, and butyrate constitute more than 95% of the collective pool of short-chain fatty acids. Conflicting data on acetate’s effects may result from its dynamic signaling, which can vary depending on physiological conditions and metabolic phenotypes. Human studies suggest that propionate has overall anti-obesity effects due to its well-documented chemistry, cellular signaling mechanisms, and various clinical benefits. Butyrate, similar to propionate, has the ability to reduce obesity by stimulating the release of appetite-suppressing hormones and promoting the synthesis of leptin. Tryptophan affects systemic hormone secretion, with indole stimulating the release of GLP-1, which impacts insulin secretion, appetite suppression, and gastric emptying. Bile acids, synthesized from cholesterol in the liver and subsequently modified by gut bacteria, play an essential role in the digestion and absorption of dietary fats and fat-soluble vitamins, but they also interact directly with intestinal microbiota and their metabolites. One study using statistical methods identified primarily two groupings of enterotypes Bacteroides and Ruminococcus. The Prevotella-dominated enterotype, P-type, in humans correlates with vegetarians, high-fiber and carbohydrate-rich diets, and traditional diets. Conversely, individuals who consume diets rich in animal fats and proteins, typical in Western-style diets, often exhibit the Bacteroides-dominated, B-type, enterotype. The P-type showcases efficient hydrolytic enzymes for plant fiber degradation but has limited lipid and protein fermentation capacity. Conversely, the B-type features specialized enzymes tailored for the degradation of animal-derived carbohydrates and proteins, showcasing an enhanced saccharolytic and proteolytic potential. Generally, models excel at predictions but often struggle to fully elucidate why certain substances yield varied responses. These studies provide valuable insights into the potential for personalized dietary recommendations based on enterotypes
Diet can influence healthy aging through anti- or proinflammatory effects, partly by modulating the gut microbiome composition. This study investigated the relationships between the Dietary Inflammatory Index (DII), the gut microbiome, and nutritional status in elderly individuals. Methods: This cross-sectional analysis included 114 home-dwelling individuals aged over 70 years. The Energy-adjusted DII (E-DII) was calculated from 3-day food diaries, and blood samples were taken to measure micronutrient status, glucose, and lipid metabolism. Body composition was assessed using bioimpedance, and fecal gut microbiome composition was analyzed through 16S rRNA gene sequencing. The participants were categorized into maintaining an anti-inflammatory diet (AD) and a pro-inflammatory diet (PD) based on the median E-DII score. The associations of E-DII groups with blood markers and microbial diversity and composition were examined using the analysis of covariance, permutational analysis of variance, and multivariate linear models. Results: The AD (n = 57, 76 ± 3.83 years) and PD (n = 57, 75 ± 5.21 years) groups were similar in age but differed in sex distribution, with a higher proportion of females in the AD group (p = 0.02). When compared to the PD group and adjusted for sex, the AD group had a lower body mass index, fat mass, fasting insulin level, HOMA-IR (Homeostasis Model Assessment of Insulin Resistance), fasting triglycerides, and serum uric acid concentration (all p < 0.05), with higher concentrations of high-density lipoprotein, red-blood-cell folate (RBC), and Omega-3 index (all p < 0.05). While the microbial diversity and composition did not differ between the DII groups, folate concentrations were negatively associated with Agathobacter and positively associated with Bacteroides abundance (both q = 0.23). Lower uric acid concentrations were associated with a higher abundance of Bifidobacterium (q = 0.09) and lower abundance of Phocaeicola (q = 0.11). Discussion: The study suggests that following an anti-inflammatory diet is associated with improved nutritional status in the elderly. Dietary blood markers, rather than E-DII, were found to be associated with the gut microbiome, suggesting a potential link between the microbiome and changes in nutritional markers independent of diet. Further studies are needed to explore the causal relationship between dietary inflammatory potential, gut microbiome, and healthy aging.
Hyperhydricity (HH) is one of the most important physiological disorders that negatively affects various plant tissue culture techniques. The objective of this study was to characterize optical features to allow an automated detection of HH. For this purpose, HH was induced in two plant species, apple and Arabidopsis thaliana, and the severity was quantified based on visual scoring and determination of apoplastic liquid volume. The comparison between the HH score and the apoplastic liquid volume revealed a significant correlation, but different response dynamics. Corresponding leaf reflectance spectra were collected and different approaches of spectral analyses were evaluated for their ability to identify HH-specific wavelengths. Statistical analysis of raw spectra showed significantly lower reflection of hyperhydric leaves in the VIS, NIR and SWIR region. Application of the continuum removal hull method to raw spectra identified HH-specific absorption features over time and major absorption peaks at 980 nm, 1150 nm, 1400 nm, 1520 nm, 1780 nm and 1930 nm for the various conducted experiments. Machine learning (ML) model spot checking specified the support vector machine to be most suited for classification of hyperhydric explants, with a test accuracy of 85% outperforming traditional classification via vegetation index with 63% test accuracy and the other ML models tested. Investigations on the predictor importance revealed 1950 nm, 1445 nm in SWIR region and 415 nm in the VIS region to be most important for classification. The validity of the developed spectral classifier was tested on an available hyperspectral image acquisition in the SWIR-region.
Within the consortium “Experimentation Field Agro-Nordwest”, a practical concept for knowledge and technology transfer of digital competence in agriculture was created. For this purpose, the web-based e-learning system “SensX” was set up, consisting of videos, presentations and instructions. In addition, the classical e-learning concept was extended by data sets, student experiments and sensor data of plants acquired by a remote phenotyping robot. This resulted in a massive open online course (MOOC), which was tested with agricultural and biotechnology students in higher education at the University of Applied Sciences Osnabrück over two years. The evaluation process of “SensX” included an empirical survey, qualitative interviews of the participating students by an external institution and an evaluation of the concept by the lecturers.
Background
The current development of sensor technologies towards ever more cost-effective and powerful systems is steadily increasing the application of low-cost sensors in different horticultural sectors. In plant in vitro culture, as a fundamental technique for plant breeding and plant propagation, the majority of evaluation methods to describe the performance of these cultures are based on destructive approaches, limiting data to unique endpoint measurements. Therefore, a non-destructive phenotyping system capable of automated, continuous and objective quantification of in vitro plant traits is desirable.
Results
An automated low-cost multi-sensor system acquiring phenotypic data of plant in vitro cultures was developed and evaluated. Unique hardware and software components were selected to construct a xyz-scanning system with an adequate accuracy for consistent data acquisition. Relevant plant growth predictors, such as projected area of explants and average canopy height were determined employing multi-sensory imaging and various developmental processes could be monitored and documented. The validation of the RGB image segmentation pipeline using a random forest classifier revealed very strong correlation with manual pixel annotation. Depth imaging by a laser distance sensor of plant in vitro cultures enabled the description of the dynamic behavior of the average canopy height, the maximum plant height, but also the culture media height and volume. Projected plant area in depth data by RANSAC (random sample consensus) segmentation approach well matched the projected plant area by RGB image processing pipeline. In addition, a successful proof of concept for in situ spectral fluorescence monitoring was achieved and challenges of thermal imaging were documented. Potential use cases for the digital quantification of key performance parameters in research and commercial application are discussed.
Conclusion
The technical realization of “Phenomenon” allows phenotyping of plant in vitro cultures under highly challenging conditions and enables multi-sensory monitoring through closed vessels, ensuring the aseptic status of the cultures. Automated sensor application in plant tissue culture promises great potential for a non-destructive growth analysis enhancing commercial propagation as well as enabling research with novel digital parameters recorded over time.
Computer-image processing becomes more and more important in the analysis of data in biological and agricultural research and practice. However, robust image processing is highly de pendent on the histogram analysis algorithms used and the quality of the data being processed. The algorithm presented here aims to improve the accuracy of the classification of image data generated under complex boundary situations and inconsistent lighting conditions. Using the example of the determination of nitrogen content of tomato leaves and the qualitative determination of starch con tent of apples on the basis of color image processing, we showed that the developed algorithm is able to perform a robust classification and represents an improvement to simple histogram analysis.
Dairy farming has been the subject of public debate on animal welfare for a number of years now. Animal welfare discussions on dairy farming often include the demand for more nature connectedness in this area. This study focuses on the divergent perspectives of consumers and scientists on the importance of more nature connectedness for animal welfare strategies in German dairy farming. Within Europe, Germany is the main producer of cow’s milk and an important industry in many rural areas in Germany is dairy farming. The insights presented are based on qualitative interviews with dairy farming and livestock researchers from Germany and Austria. A key finding of this study is that we need to look more closely at the actual content of nature claims in animal welfare debates. The scientists interviewed tend to see idealized conditions in animal welfare discussions with images of nature which in fact seldom lead to improved conditions in dairy farming and, even then, only to a limited extent. The scientists interviewed rate calls for more nature connectedness in dairy farming from the nonagricultural public as anti-modern, complexity-reducing, and normative. Nevertheless, some of the scientists interviewed did have valuable insights into the nonagricultural public’s criticism of dairy farming practices. These scientists argued, however, that animal welfare needs to differentiate between nature connectedness and the innate needs of cattle when it comes to animal welfare strategies. An important conclusion of the study is that more discussion formats are needed to promote the exchange of ideas between different social groups attempting to understand animal welfare in dairy farming.