579 Mikroorganismen, Pilze, Algen
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Introduction: Land-based cultivation using alternative water resources, such as saline groundwater (brine), offers a promising strategy for the sustainable production of the green macroalga Ulva compressa. Because Ulva growth and morphogenesis depend strongly on associated bacteria, understanding microbiome dynamics during acclimatization to brine is essential for stable biomass production. This study compared the growth performance and microbiome composition of two U. compressa cultivars with contrasting cultivation histories: a recently isolated strain from Helgoland (C2019) and a long-term laboratory cultivar originating from Ria Formosa (C1952).
Methods: Two experiments were conducted. In the first, growth performance and microbiome composition of the two cultivars were compared using different substrates under brine conditions. In the second, the stepwise acclimatization of best-performing cultivar C2019 from artificial seawater to brine was investigated, tracking specific growth rates, core microbiome composition, and fatty acid profiles over the course of acclimatization.
Results: In the substrate experiment, cultivar identity explained most of the variation in microbiome composition. Under laboratory cultivation in brine C2019, maintained a more diverse core microbiome and in the scaled-up experiment this cultivar exhibited higher specific growth rates than C1952 on PET and PA substrates. Bacterial genera previously identified as producers of algal growth- and morphogenesis-promoting factors (AGMPFs) - including Roseobacter, Maribacter, Zobellia, Sulfitobacter, and Marivita - remained consistently associated with C2019 throughout brine cultivation in all conducted experiments despite substantial microbiome restructuring. The transition from artificial seawater to brine induced transient changes in fatty acid composition during acclimatization, which stabilized after prolonged exposure.
Discussion: Together, these findings demonstrate that cultivar-specific host–microbiome interactions are closely associated with successful acclimatization to inland brine cultivation. They highlight the importance of considering the algal holobiont when developing resilient land-based Ulva production systems.
This study investigated how fruit matrices and the probiotic strain Lacticaseibacillus paracasei subsp. paracasei F19 (F19) interact with Saccharomyces cerevisiae US-05 to shape volatile formation, microbial viability, and sensory outcomes during the fermentation of Catharina sour beer. The central objective was to fill the current knowledge gap regarding dynamic flavor development in mixed fermentations, particularly in systems where probiotic LAB may contribute both functional and aromatic benefits. Microbial viability was monitored using propidium monoazide quantitative PCR (PMA-qPCR); volatile compounds were profiled by headspace solid-phase microextraction coupled to gas chromatography–mass spectrometry (HS-SPME/GC–MS); and sensory acceptance was evaluated with 62 untrained panelists using a 9-point hedonic scale. F19 displayed strong viability throughout fermentation (5–7 log CFU/mL), with significant increases after 58 days in the control and passion fruit formulations (p < 0.05), achieving the recommended daily intake level in 350-mL servings. HS-SPME/GC–MS identified 143 volatile compounds, including key aroma contributors, such as 3-methylbutyl acetate, ethyl hexanoate, and ethyl octanoate, as well as 23 core volatiles persistent across all stages. Sensory evaluation revealed a clear preference for the passion fruit beer (6.94 ± 2.01), linked to 18 unique volatiles including 6-methylhept-5-en-2-one and benzaldehyde, while the peach beer—despite containing honey-like 2-phenylacetaldehyde—showed lower acceptance (5.72 ± 1.91). Overall, this first integrated volatilomic, microbial, and sensory analysis demonstrates that L. paracasei F19 enhances aroma diversity and remains viable in fruit-based sour beers, with passion fruit providing the most promising sensory and functional profile for innovative probiotic craft beer development.
Microbiome research, the study of microbial communities in diverse environments, has seen significant advances due to the integration of deep learning (DL) methods. These computational techniques have become essential for addressing the inherent complexity and high-dimensionality of microbiome data, which consist of different types of omics datasets. Deep learning algorithms have shown remarkable capabilities in pattern recognition, feature extraction, and predictive modeling, enabling researchers to uncover hidden relationships within microbial ecosystems. By automating the detection of functional genes, microbial interactions, and host-microbiome dynamics, DL methods offer unprecedented precision in understanding microbiome composition and its impact on health, disease, and the environment. However, despite their potential, deep learning approaches face significant challenges in microbiome research. Additionally, the biological variability in microbiome datasets requires tailored approaches to ensure robust and generalizable outcomes. As microbiome research continues to generate vast and complex datasets, addressing these challenges will be crucial for advancing microbiological insights and translating them into practical applications with DL. This review provides an overview of different deep learning models in microbiome research, discussing their strengths, practical uses, and implications for future studies. We examine how these models are being applied to solve key problems and highlight potential pathways to overcome current limitations, emphasizing the transformative impact DL could have on the field moving forward.
Catharina sour, the first internationally recognized Brazilian beer, is characterized by fermentation with lactic acid bacteria (LAB), which may have probiotic potential, and the addition of fruit juice. This study aimed to evaluate the use of the starter Streptococcus thermophilus TH‐4 (TH‐4) and the probiotics Lacticaseibacillus paracasei F19 and 431, associated with Saccharomyces cerevisiae US-05, in the absence (control)/presence of passion fruit or peach juices. Evaluation proceeded during fermentation and storage by enumeration using pour-plate and qPCR; gene expressions of hop resistance; proteome by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS); and odor, flavor, and metabolome by Headspace Solid-Phase Microextraction (HS-SPME), coupled with the gas chromatography–mass spectrometry (GC–MS) analysis. We concluded that the strains studied are recommended for applications in sour beers, due to the presence of defense mechanisms like membrane adhesion and H+ pump. Furthermore, HS-SPME/GC-MS indicated that the strains may contribute to the beer flavor and odor.
This study evaluated the potential of red pitaya pulp fermented with Lacticaseibacillus paracasei subsp. paracasei F-19 (F-19) as a base for probiotic products. Physicochemical parameters, sugar, betacyanin, and phenolic contents, and antioxidant activity were analyzed over 28 days at 4 °C and compared to a non-fermented pulp, and to a pulp fermented with Bifidobacterium animalis subsp. lactis BB-12 (BB-12). Volatile compounds were identified using HS-SPME/GC–MS. Probiotic viability during storage and survival through in vitro-simulated gastrointestinal tract (GIT) stress were assessed. Red pitaya pulp, rich in moisture (85.83 g/100 g), carbohydrates (11.65 g/100 g), and fibers (2.49 g/100 g), supported fermentation by both strains. F-19 and BB-12 lowered pH, with F-19 showing stronger acidification, and maintained high viability (8.85–8.90 log CFU/mL). Fermentation altered sugar profiles and produced unique volatile compounds, enhancing aroma and sensory attributes. F-19 generated 2-phenylethanol, a unique flavor compound, absent in BB-12. Phenolic content initially increased but antioxidant activity decreased during storage. Betacyanin remained stable for up to 14 days. Red pitaya improved F-19 viability through the simulated GIT, while BB-12 populations significantly decreased (p < 0.05). These results suggest red pitaya pulp is a promising plant-based matrix for F-19, offering protection during digestion and highlighting its potential as a functional food with enhanced bioactive compound bioavailability and sensory attributes.
This study aimed to evaluate the probiotic strain Lacticaseibacillus (L.) paracasei subsp. paracasei F19 (F19) with the yeast Saccharomyces cerevisiae US-05 (US-05), using Spondias mombin L. (‘taperebá’ or ‘cajá’) juice and by-product, in four sour-type beer formulations: control, with bagasse, juice, and juice and bagasse. The viability of F19 was evaluated by pour-plating and PMA-qPCR. Fermentability, in addition to physicochemical and sensory parameters, and aroma and flavor, were evaluated during brewery by using Headspace Solid-Phase Microextraction (HS-SPME) coupled with gas chromatography–mass spectrometry (GC–MS). F19 was successful in fermenting bagasse in a MRS medium (9.28 log CFU/mL in 24 h) but had a low viability in hopped wort, growing better in formulations without bagasse or juice. No difference between formulations was observed regarding sensory acceptability, and the HS-SPME/GC-MS revealed different flavors and aroma compounds. In conclusion, the production of a potential probiotic sour beer with F19 and US-05 is feasible regarding probiotic viability. However, S. mombin, as juice or bagasse, threatened probiotic survival. Different flavors and aroma compounds were detected, whereas no difference between formulations was found regarding sensory acceptability. The moderate alcohol content achieved is important for bacterial survival and for the development of a probiotic beer with health claims.
Endophytic fungi that colonize the plant root live in an environment with relative high concentrations of different sugars. Analyses of genome sequences indicate that such endophytes can secrete carbohydrate-related enzymes to compete for these sugars with the surrounding plant cells. We hypothesized that typical plant sugars can be used as carbon source by root endophytes and that these sugars also serve as signals to induce the expression and secretion of glycolytic enzymes. The plant-growth-promoting endophytes Serendipita indica and Serendipita herbamans were selected to first determine which sugars promote their growth and biomass formation. Secondly, particular sugars were added to liquid cultures of the fungi to induce intracellular and extracellular enzymatic activities which were measured in mycelia and culture supernatants. The results showed that both fungi cannot feed on melibiose and lactose, but instead use glucose, fructose, sucrose, mannose, arabinose, galactose and xylose as carbohydrate sources. These sugars regulated the cytoplasmic activity of glycolytic enzymes and also their secretion. The levels of induction or repression depended on the type of sugars added to the cultures and differed between the two fungi. Since no conventional signal peptide could be detected in most of the genome sequences encoding the glycolytic enzymes, a non-conventional protein secretory pathway is assumed. The results of the study suggest that root endophytic fungi translocate glycolytic activities into the root, and this process is regulated by the availability of particular plant sugars.
Aus mitteleuropäischer Sicht ist die durch Parasiten verursachte und von Sandmücken übertragene Leishmaniose eine in Ländern tropischer und subtropischer Regionen auftretende Infektionskrankheit. In zunehmendem Maße werden jedoch autochthone Fälle in Mitteleuropa, insbesondere in Süddeutschland, verzeichnet. Dies ist vermutlich auf die globale Erwärmung und die Ausdehnung des Verbreitungsgebietes der Sandmücken nach Norden zurückzuführen. Die vorliegende Arbeit befasst sich mit der Identifizierung und phylogenetischen Charakterisierung der Erreger dieser Fälle. Dazu wurden verschiedene Marker im Leishmaniengenom sequenziert und mit bekannten Arten verglichen. Die untersuchte DNA stammte von autochthonen kutanen Leishmaniosen bei Pferden und einem Rind, die in den letzten zehn Jahren in Deutschland und der Schweiz auftraten. Aufgrund identischer Sequenzen konnten die Parasiten als L. siamensis identifiziert bzw. verifiziert werden, eine erst im Jahr 2008 neu beschriebene Art, die in Thailand humane viszerale Leishmaniose verursacht. Die phylogenetischen Analysen zeigten die Ähnlichkeit von L. siamensis mit weiteren bisher nicht identifizierten Stämmen aus Martinique und Ghana, die kutane Leishmaniose bei Menschen verursachen. Um die Frage zu beantworten, ob sich die Leishmaniose zu einer in Mitteleuropa endemischen zoonotischen Krankheit entwickeln könnte, müssen weitere Studien über kompatible Vektoren, mögliche Reservoire und zur Virulenz durchgeführt werden.
Etablierung von Hochdurchsatz-Kultivierungs- und -Screeningmethoden für phototrophe Einzeller
(2012)
Mit Hochdurchsatz-Kultivierungs- und -Screeningmethoden können viele Proben parallel, miniaturisiert und kostengünstig bearbeitet werden. Für phototrophe Organismen wie Mikroalgen und Cyanobakterien sind Hochdurchsatz-Kultivierungsverfahren jedoch bis heute kaum etabliert. Im Rahmen dieser Arbeit wurden diese Verfahren beispielhaft für das Cyanobakterium Synechocystis sp. PCC 6803 etabliert. Die benötigte technische Automatisierung wurde hierbei durch den Einsatz eines Tecan Genesis RSP 150 Pipettierroboters erreicht. Die Kultivierung erfolgte in Deepwell-Mikrotiterplatten innerhalb einer speziell angefertigten Kammer mit programmierbaren Schüttlern, einstellbarer Belichtung und CO2-Atmosphäre. Die in diesem System erreichten Wachstumsraten sind vergleichbar mit publizierten Kultivierungsmethoden. Das Hochdurchsatz-Screening wurde mit Hilfe eines in den Roboter integrierten Tecan Genios Plus Plattenreaders durchgeführt. Es wurden beispielhaft Methoden zur Bestimmung von optischer Dichte und Chlorophyllgehalt etabliert. Die hier vorgestellte Plattform kann vielseitig zur Analyse phototropher Organismen eingesetzt werden und ist durch entsprechende Assays leicht zur Messung anderer Parameter erweiterbar.
