Utjecaj novih fermentiranih proizvoda, koji sadržavaju ekstrudiranu pšenicu, na kakvoću pšeničnoga kruha

Lactobacillus sakei MI806, Pediococcus pentosaceus MI810 and Pediococcus acidilactici MI807, able to produce bacteriocin-like inhibitory substances, were originally isolated from Lithuanian spontaneous rye sourdough and adapted in the novel fermentation medium containing extruded wheat material. The novel fermented products (50 and 65 % moisture content) were stored at the temperatures used in bakeries (15 days at 30–35 °C in the summer period or 20 days under refrigeration conditions at 0–6 °C). The number of lactic acid bacteria (LAB) was determined during the storage of fermented products for 15–20 days. Furthermore, the effect of novel fermented products stored under different conditions on wheat bread quality was examined. Extruded wheat material was found to have a higher positive effect on LAB growth compared to the control medium by lowering the reduction of LAB populations in fermented products with the extension of storage time and increase of temperature. During storage, lower variation and lower decrease in LAB count were measured in the novel fermented products with a moisture content of 65 % compared to those with 50 %. Furthermore, this humidity allows for the production of a product with higher moisture content in continuous production processes. The addition of the new fermented products with 65 % humidity to the wheat bread recipe (10 % of the quantity of flour) had a significant effect on bread quality: it increased the acidity of the crumb and specific volume of the bread, and decreased the fractal dimension of the crumb pores and crumb firmness. Based on the microbiological investigations of fermented products during storage and baking tests, the conditions of LAB cultivation in novel fermentation media were optimized (time of cultivation approx. 20 days at 0–6 °C and approx. 10 days at 30–35 °C).Lactobacillus sakei MI806, Pediococcus pentosaceus MI810 i Pediococcus acidilactici MI807, bakterije koje proizvode inhibitore slične bakteriocinu, izolirane su iz litvanskoga kiselog tijesta što se proizvodi od raženoga brašna, te prilagođene za uporabu u novoj fermentacijskoj podlozi s ekstrudiranom pšenicom. Da bi se ispitala mogućnost njihove primjene u pekarama, ti novi fermentirani proizvodi (s 50 i 65 % vlažnosti) skladišteni su 15 dana pri ljetnim temperaturama od 30 do 35 °C i 20 dana u hladnjaku pri 0 do 6 °C. Tijekom tih 15 do 20 dana ispitivan je broj mliječno-kiselih bakterija u fermentiranim proizvodima, te njihov utjecaj na kakvoću kruha. Dodatak ekstrudirane pšenice bitno je utjecao na rast mliječno-kiselih bakterija, u usporedbi s kontrolnom podlogom, smanjujući njihovo odumiranje u fermentiranim proizvodima tijekom duljeg skladištenja pri povišenoj temperaturi. Tijekom skladištenja primijećene su manje promjene broja mliječno-kiselih bakterija u novim fermentiranim proizvodima sa 65 % vlažnosti nego u onima s 50 % vlažnosti, pa je zaključeno da se njihovim dodatkom u kontinuiranom procesu može proizvesti kruh s većim udjelom vlage. Dodatak 10 % novih fermentiranih proizvoda sa 65 % vlažnosti pšeničnom brašnu bitno je utjecao na kakvoću kruha: povećali su se kiselost krušnih mrvica i specifični volumen kruha, a smanjila fraktalna dimenzija pora te čvrstoća mrvica. Na osnovi mikrobioloških istraživanja fermentiranih proizvoda tijekom skladištenja te pokusnog pečenja kruha optimirani su uvjeti uzgoja mliječno-kiselih bakterija u novim fermentiranim proizvodima (optimalno vrijeme uzgoja bilo je otprilike 20 dana pri 0-6 °C i 10 dana pri 30-35 °C)

16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics.

The prebiotic potential of nervine herbal medicines has been scarcely studied. We therefore used anaerobic human fecal cultivation to investigate whether medicinal herbs commonly used as treatment in neurological health and disease in Ayurveda and other traditional systems of medicine modulate gut microbiota. Profiling of fecal cultures supplemented with either Kapikacchu, Gotu Kola, Bacopa/Brahmi, Shankhapushpi, Boswellia/Frankincense, Jatamansi, Bhringaraj, Guduchi, Ashwagandha or Shatavari by 16S rRNA sequencing revealed profound changes in diverse taxa. Principal coordinate analysis highlights that each herb drives the formation of unique microbial communities predicted to display unique metabolic potential. The relative abundance of approximately one-third of the 243 enumerated species was altered by all herbs. Additional species were impacted in an herb-specific manner. In this study, we combine genome reconstruction of sugar utilization and short chain fatty acid (SCFA) pathways encoded in the genomes of 216 profiled taxa with monosaccharide composition analysis of each medicinal herb by quantitative mass spectrometry to enhance the interpretation of resulting microbial communities and discern potential drivers of microbiota restructuring. Collectively, our results indicate that gut microbiota engage in both protein and glycan catabolism, providing amino acid and sugar substrates that are consumed by fermentative species. We identified taxa that are efficient amino acid fermenters and those capable of both amino acid and sugar fermentation. Herb-induced microbial communities are predicted to alter the relative abundance of taxa encoding SCFA (butyrate and propionate) pathways. Co-occurrence network analyses identified a large number of taxa pairs in medicinal herb cultures. Some of these pairs displayed related culture growth relationships in replicate cultures highlighting potential functional interactions among medicinal herb-induced taxa

Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities

An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more complex multi-species communities based on the assumption that microbes minimize adjustments of pairwise interactions in response to neighbor species. We termed this rule-based inference minimal interspecies interaction adjustment (MIIA). Our critical assessment of MIIA has produced reliable predictions of shifting interspecies interactions that are dependent on the functional role of neighbor organisms. We also show how MIIA has been applied to a microbial community composed of competing soil bacteria to elucidate a new finding that – in many cases – adding fewer competitors could impose more significant impact on binary interactions. The ability to predict membership-dependent community behavior is expected to help deepen our understanding of how microbiomes are organized in nature and how they may be designed and/or controlled in the future

Introduction to fungal physiology

This chapter describes some basic aspects of fungal cell physiology, focusing primarily on nutrition, growth, metabolism in unicellular yeasts and filamentous fungi, and cell death. It considers the most common growth forms, the filamentous fungi and unicellular yeasts. Fungal growth involves transport and assimilation of nutrients, followed by their integration into cellular components, followed by biomass increase and eventual cell division or septation. The physiology of vegetative reproduction and its control in fungi has been most widely studied in two model eukaryotes, the budding yeast, Saccharomyces cerevisiae, and the fission yeast, Schizosaccharomyces pombe. An understanding of the death of fungal cells is important from a fundamental viewpoint because fungi, especially yeasts, represent valuable model systems for the study of cellular aging and apoptosis (programed cell death). Recycling and redeployment of cellular material also helps drive the apical growth of filamentous fungi and the mycelium explores and extends through the environment

A quantitative image analysis pipeline for the characterization of filamentous fungal morphologies as a tool to uncover targets for morphology engineering: a case study using aplD in Aspergillus niger

Background Fungal fermentation is used to produce a diverse repertoire of enzymes, chemicals, and drugs for various industries. During submerged cultivation, filamentous fungi form a range of macromorphologies, including dispersed mycelia, clumped aggregates, or pellets, which have critical implications for rheological aspects during fermentation, gas/nutrient transfer, and, thus, product titres. An important component of strain engineering efforts is the ability to quantitatively assess fungal growth phenotypes, which will drive novel leads for morphologically optimized production strains. Results In this study, we developed an automated image analysis pipeline to quantify the morphology of pelleted and dispersed growth (MPD) which rapidly and reproducibly measures dispersed and pelleted macromorphologies from any submerged fungal culture. It (i) enables capture and analysis of several hundred images per user/day, (ii) is designed to quantitatively assess heterogeneous cultures consisting of dispersed and pelleted forms, (iii) gives a quantitative measurement of culture heterogeneity, (iv) automatically generates key Euclidian parameters for individual fungal structures including particle diameter, aspect ratio, area, and solidity, which are also assembled into a previously described dimensionless morphology number MN, (v) has an in-built quality control check which enables end-users to easily confirm the accuracy of the automated calls, and (vi) is easily adaptable to user-specified magnifications and macromorphological definitions. To concomitantly provide proof of principle for the utility of this image analysis pipeline, and provide new leads for morphologically optimized fungal strains, we generated a morphological mutant in the cell factory Aspergillus niger based on CRISPR-Cas technology. First, we interrogated a previously published co-expression networks for A. niger to identify a putative gamma-adaptin encoding gene (aplD) that was predicted to play a role in endosome cargo trafficking. Gene editing was used to generate a conditional aplD expression mutant under control of the titratable Tet-on system. Reduced aplD expression caused a hyperbranched growth phenotype and diverse defects in pellet formation with a putative increase in protein secretion. This possible protein hypersecretion phenotype could be correlated with increased dispersed mycelia, and both decreased pellet diameter and MN. Conclusion The MPD image analysis pipeline is a simple, rapid, and flexible approach to quantify diverse fungal morphologies. As an exemplar, we have demonstrated that the putative endosomal transport gene aplD plays a crucial role in A. niger filamentous growth and pellet formation during submerged culture. This suggests that endocytic components are underexplored targets for engineering fungal cell factories.DFG, 414044773, Open Access Publizieren 2019 - 2020 / Technische Universität Berli

A Genetic Algorithm for Feeding Trajectory Optimisation of Fed-batch Fermentation Processes

In this work a genetic algorithm is proposed with the purpose of the feeding trajectory optimization during a fed-batch fermentation of E. coli. The feed rate profiles are evaluated based on a number of objective functions. Optimization results obtained for different feeding trajectories demonstrate that the genetic algorithm works well and shows good computational performance. Developed optimal feed profiles meet the defined criteria. The ration of the substrate concentration and the difference between actual cell concentration and theoretical maximum cell concentration is defined as the most appropriate objective function. In this case the final cell concentration of 43 g·l-1 and final product concentration of 125 g·l-1 are achieved and there is not significant excess of substrate