Cattle-compost-soil: The transfer of antibiotic resistance in livestock agriculture.

Antibiotic resistance is a major global health threat. Agricultural use of antibiotics is considered to be a main contributor to the issue, influencing both animals and humans as defined by the One Health approach. The purpose of the present study was to determine the abundance of antibiotic-resistant bacterial populations and the overall bacterial diversity of cattle farm soils that have been treated with animal manure compost.

Microbiology at Home (M@H): an Online, Self-Paced Solution To Enhance Practical Skills in Foundation Microbiology.

The online education market share is rapidly increasing, raising the demand to teach sciences outside the laboratory environment. Here, we present Microbiology at Home (M@H), a new approach that integrates hands-on microbiology experimentation with online interactive simulations using authentic scenarios in microbiology in the home environment. The M@H program includes 8 practical activities aligned to the ASM curriculum for practical skills.

The Hydroponic Rockwool Root Microbiome: Under Control or Underutilised?

Land plants have an ancient and intimate relationship with microorganisms, which influences the composition of natural ecosystems and the performance of crops. Plants shape the microbiome around their roots by releasing organic nutrients into the soil. Hydroponic horticulture aims to protect crops from damaging soil-borne pathogens by replacing soil with an artificial growing medium, such as rockwool, an inert material made from molten rock spun into fibres.

Expression of key auxin biosynthesis genes correlates with auxin and starch content of developing wheat (Triticum aestivum) grains.

The effect of auxin on wheat (Triticum aestivum L.) grain size is contentious. Additionally, the contributions to the IAA pool from de novo synthesis versus hydrolysis of IAA-glucose are unclear.

A review of the antimicrobial side of antidepressants and its putative implications on the gut microbiome.

Objective: Serotonin reuptake inhibitors are the predominant treatment for major depressive disorder. In recent years, the diversity of the gut microbiota has emerged to play a significant role in the occurrence of major depressive disorder and other mood and anxiety disorders. Importantly, the role of the gut microbiota in the treatment of such disorders remains to be elucidated.

Storage and handling of human faecal samples affect the gut microbiome composition: A feasibility study.

Human gut microbiome analysis through faecal sampling typically involves five stages: sample collection, storage, DNA extraction, next generation sequencing and bioinformatics analysis. Of these, the first three are considered irreversible. This feasibility study describes an assessment of methodologies used for faecal DNA extraction and sample handling, using the parameters DNA yield, purity and resultant microbial profile.

Gut microbiome and depression: what we know and what we need to know.

Gut microbiome diversity has been strongly associated with mood-relating behaviours, including major depressive disorder (MDD). This association stems from the recently characterised bi-directional communication system between the gut and the brain, mediated by neuroimmune, neuroendocrine and sensory neural pathways. While the link between gut microbiome and depression is well supported by research, a major question needing to be addressed is the causality in the connection between the two, which will support the understanding of the role that the gut microbiota play in depression.

Metabolic Engineering of KT2440 for the Production of -Hydroxy Benzoic Acid.

-Hydroxy benzoic acid (PHBA) is the key component for preparing parabens, a common preservatives in food, drugs, and personal care products, as well as high-performance bioplastics such as liquid crystal polymers. KT2440 was engineered to produce PHBA from glucose the shikimate pathway intermediate chorismate. To obtain the PHBA production strain, chorismate lyase UbiC from and a feedback resistant 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase encoded by gene were overexpressed individually and simultaneously.

Quantitative analysis of aromatics for synthetic biology using liquid chromatography.

The replacement of petrochemical aromatics with bio-based molecules is a key area of current biotechnology research. To date, a small number of aromatics have been produced by recombinant bacteria in laboratory scale while industrial production still requires further strain development. While each study includes some distinct analytical methodology to quantify certain aromatics, a method that can reliably quantify a great number of aromatic products and relevant pathway intermediates is needed to accelerate strain development.

Production of para-aminobenzoic acid from different carbon-sources in engineered Saccharomyces cerevisiae.

Background: Biological production of the aromatic compound para-aminobenzoic acid (pABA) is of great interest to the chemical industry. Besides its application in pharmacy and as crosslinking agent for resins and dyes pABA is a potential precursor for the high-volume aromatic feedstocks terephthalic acid and para-phenylenediamine. The yeast Saccharomyces cerevisiae synthesises pABA in the shikimate pathway: Outgoing from the central shikimate pathway intermediate chorismate, pABA is formed in two enzyme-catalysed steps, encoded by the genes ABZ1 and ABZ2.

Formation of hydrogen sulfide from cysteine in Saccharomyces cerevisiae BY4742: genome wide screen reveals a central role of the vacuole.

Discoveries on the toxic effects of cysteine accumulation and, particularly, recent findings on the many physiological roles of one of the products of cysteine catabolism, hydrogen sulfide (H2S), are highlighting the importance of this amino acid and sulfur metabolism in a range of cellular activities. It is also highlighting how little we know about this critical part of cellular metabolism. In the work described here, a genome-wide screen using a deletion collection of Saccharomyces cerevisiae revealed a surprising set of genes associated with this process.

In vivo instability of chorismate causes substrate loss during fermentative production of aromatics.

Metabolic engineering of microbial strains to produce aromatic compounds deriving from the shikimate pathway is of great interest to the chemical industry as a more sustainable alternative for feedstock production. Chorismate is a significant intermediate in the shikimate pathway. In this study, the formation of phenylalanine and phenylpyruvate as by-products in strains engineered downstream of the chorismate node for increased aromatic production was explored in yeast fermentations.

Fluxomics - connecting 'omics analysis and phenotypes.

In our modern 'omics era, metabolic flux analysis (fluxomics) represents the physiological counterpart of its siblings transcriptomics, proteomics and metabolomics. Fluxomics integrates in vivo measurements of metabolic fluxes with stoichiometric network models to allow the determination of absolute flux through large networks of the central carbon metabolism. There are many approaches to implement fluxomics including flux balance analysis (FBA), (13) C fluxomics and (13) C-constrained FBA as well as many experimental settings for flux measurement including dynamic, stationary and semi-stationary.

In situ high throughput method for H(2)S detection during micro-scale wine fermentation.

An in situ high throughput method for the detection of H(2)S during fermentation was developed. The method utilizes a redox reaction in which sulfide ion reduces methylene blue, leading to its decolourisation. Incorporation of methylene blue into the fermentation media allows real-time detection of H(2)S during fermentation and the generation of an H(2)S production profile.

Effects of rehydration nutrients on H2S metabolism and formation of volatile sulfur compounds by the wine yeast VL3.

In winemaking, nutrient supplementation is a common practice for optimising fermentation and producing quality wine. Nutritionally suboptimal grape juices are often enriched with nutrients in order to manipulate the production of yeast aroma compounds. Nutrients are also added to active dry yeast (ADY) rehydration media to enhance subsequent fermentation performance.

Monitoring autophagy in yeast using FM 4-64 fluorescence.

The original observations and experiments dealing with autophagy were purely morphological in nature. Even though more and more molecular techniques have been introduced, experimenters are often asked to provide visual evidence of autophagic processes in order to back up data obtained via other means. In yeast as well, autophagosomes were initially defined morphologically and indirectly, by observing intravacuolar autophagic bodies that accumulate upon starvation.

Caffeine induces macroautophagy and confers a cytocidal effect on food spoilage yeast in combination with benzoic acid.

Weak organic acids are an important class of food preservatives that are particularly efficacious towards yeast and fungal spoilage. While acids with small aliphatic chains appear to function by acidification of the cytosol and are required at high concentrations to inhibit growth, more hydrophobic organic acids such as sorbic and benzoic acid have been suggested to function by perturbing membrane dynamics and are growth-inhibitory at much lower concentrations. We previously demonstrated that benzoic acid has selective effects on membrane trafficking in Saccharomyces cerevisiae.

Aup1p, a yeast mitochondrial protein phosphatase homolog, is required for efficient stationary phase mitophagy and cell survival.

Autophagy is a catabolic membrane-trafficking process that occurs in all eukaryotic cells and leads to the hydrolytic degradation of cytosolic material in the vacuolar or lysosomal lumen. Mitophagy, a selective form of autophagy targeting mitochondria, is poorly understood at present. Several recent reports suggest that mitophagy is a selective process that targets damaged mitochondria, whereas other studies imply a role for mitophagy in cell death processes.