Project description:Coculturing experiments involving three microbial species: Aspergillus (A), Trichoderma (T), and Bacillus (B), representing fungi (A, T) and bacteria (B), respectively. These experiments encompassed various interaction levels, including dual cultures (AB, AT, TB) and triple cultures (ATB). Metabolic profiling by LC-QTOFMS revealed the effect of interaction level on the productivity and diversity of microbial specialized metabolites.
Project description:Interventions: healthy people, intestinal polyp group and intestinal cancer group.:Nil
Primary outcome(s): bacteria;fungi;phages
Study Design: Factorial
Project description:Microbial consortia consist of a multitude of prokaryotic and eukaryotic microorganisms. Their interaction is critical for the functioning of ecosystems. Until now, there is limited knowledge about the communication signals determining the interaction between bacteria and fungi and how they influence microbial consortia. Here, we discovered that bacterial low molecular weight arginine-derived polyketides trigger the production of distinct natural products in fungi. These compounds are produced by actinomycetes found on all continents except Antarctica and are characterized by an arginine-derived positively charged group linked to a linear or cyclic polyene moiety. Producer bacteria can be readily isolated from soil as well as fungi that decode the signal and respond with the biosynthesis of natural products. Both arginine-derived polyketides and the compounds produced by fungi in response shape microbial interactions.
Project description:We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. In blinded lab testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR. Testing of microbial detection array with mixtures of known viruses, blinded clinical samples and viral cell culture samples.
Project description:We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. In blinded lab testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR. Testing of microbial detection array with mixtures of known viruses, blinded clinical samples and viral cell culture samples.
Project description:We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. In blinded lab testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR.
Project description:We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. In blinded lab testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR.
Project description:This study explores the use of short settling times as a strategy to enhance microbial selection and prevent bulking induced by nutrient shortage in an aerobic dynamic feeding (ADF) process using mixed microbial cultures (MMCs) for polyhydroxyalkanoate (PHA) production from fermentation digestate. A 5.0-L aerobic reactor was operated under three conditions: Long Settling (LS, 30 minutes), Short Settling (SS, 10 minutes), and Short Settling under Nutrient Shortage (SS-NS, 10 minutes with reduced nutrient load). Short settling significantly improved biomass settleability, reducing the Sludge Volume Index (SVI) from 126 to 25 mL g⁻¹, and promoted the formation of dense flocs enriched in PHA-accumulating bacteria, as confirmed by transmission electron microscopy. Process kinetics revealed enhanced substrate uptake rates and improved storage yields under SS conditions, despite an elevated C/P ratio. Notably, nutrient shortage conditions were inadvertently reached by the proliferation of Polytoma mirum in the feeding tank. Although Polytoma mirum did not affect VFA composition, its presence significantly reduced nitrogen and phosphorus concentrations. These nutrient shortage conditions were maintained for at least 30 days until the system began to exhibit stress, as demonstrated by an increased SVI (178.6 mL g⁻¹). Microbial community analyses indicated marked shifts: the eukaryotic assemblage transitioned from sessile to motile ciliates under SS, while bacterial diversity within the PHA‐accumulating fraction remained high, with key taxa such as Sphaerotilus and Neomegalonema becoming more prevalent under phosphorus-limited conditions. Overall, short settling not only improved microbial selection but also prevented bulking by retaining well-aggregated biomass, thereby mitigating nutrient shortage conditions.