Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost

Compost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing analysis showed that 41% of variation in the rhizosphere bacterial community was explained by compost, in contrast to 23% by plant species. Proteobacterial genera were commonly recruited by all three plant species with specific selections for Ralstonia by tomato and Enterobacteria by maize. These findings were confirmed by analysis of 16S rRNA retrieved from the shotgun metagenomics library. Approximately 70% of functional gene clusters differed more than sevenfold in abundance between rhizosphere and compost. Functional groups associated with the sensing and up-taking of C3 and C4 carboxylic acids, amino acids, monosaccharide, production of antimicrobial substances, and antibiotic resistance were over-represented in the rhizosphere. In summary, compost and plant species synergistically shaped the composition of the rhizosphere microbiome and selected for functional traits associated with the competition on root exudates.

Microbiological services delivered by the pig gut microbiome

The gut microbiome plays a fundamental role in regulating pig health and growth. Understanding the functions performed by the microbiome is vital when considering it as a target to improve pig health and growth, a pursuit driven by the increasing regulation of traditional means of disease control and growth promotion. This chapter explores the structure, diversity and functions of the pig gut microbiome, focusing on the role of the resident bacterial communities. It examines their relationships, interactions, and contributions to the host, ranging from the production of antimicrobial substances and prevention of pathogen colonisation to improvement of nutrient digestibility and the production of volatile fatty acids (VFAs) and vitamins. The chapter also reviews bacterial communication and the antibiotic resistome of the pig gut, outlining how they may be targeted/manipulated to reduce antibiotic resistance and promote improved gut health.

Efflux-Mediated bile Resistance in Gram-Positive Pathogens

Gram-positive pathogens are causing many serious infections that affect humans and result in mild to severe diseases worldwide. In order to survive and initiate infection, enteric pathogens must resist the physiochemical defence factors in the human intestinal tract. One of these defence factors is bile, a potent antibacterial like compound in the intestine. Efflux pumps are the important mechanism by which bacteria resist antibacterial agents such as bile. Efflux of antimicrobial substances outside the bacterial cell is considered as a key factor for intestinal colonization and virulence of enteric pathogens. This paper will review the research conducted on efflux–mediated bile resistance in Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecalis and Clostridium perfringens. These bacteria colonize in the human & animal gastrointestinal tract and they have a multiple mechanism to resist the innate defences in the gut and antibacterial activity of bile. However, bile resistance in these bacteria is not fully understood. The evidence from this review suggests that Gram-positive pathogens have the ability to active transport of bile. Further research is needed to know how these pathogens sense bile and how bile regulates its virulence factor. In general, therefore, it seems that understanding the specific mechanism of bile resistance in enteric bacteria including gram-positive pathogens may involve in the development of novel strategies to control and treatment of gastrointestinal infections.

Non-Antibiotics Strategies to Control Salmonella Infection in Poultry

Salmonella spp. is a facultative intracellular pathogen causing localized or systemic infections, involving economic and public health significance, and remains the leading pathogen of food safety concern worldwide, with poultry being the primary transmission vector. Antibiotics have been the main strategy for Salmonella control for many years, which has allowed producers to improve the growth and health of food-producing animals. However, the utilization of antibiotics has been reconsidered since bacterial pathogens have established and shared a variety of antibiotic resistance mechanisms that can quickly increase within microbial communities. The use of alternatives to antibiotics has been recommended and successfully applied in many countries, leading to the core aim of this review, focused on (1) describing the importance of Salmonella infection in poultry and the effects associated with the use of antibiotics for disease control; (2) discussing the use of feeding-based (prebiotics, probiotics, bacterial subproducts, phytobiotics) and non-feeding-based (bacteriophages, in ovo injection, vaccines) strategies in poultry production for Salmonella control; and (3) exploring the use of complementary strategies, highlighting those based on -omics tools, to assess the effects of using the available antibiotic-free alternatives and their role in lowering dependency on the existing antimicrobial substances to manage bacterial infections in poultry effectively.

The use and control of antimicrobial substances in animal feed – EU regulations and the risks related to their presence

Animal feeds are routinely subject to contamination from diverse sources, including environmental pollution, activities of microbes, and veterinary drug residues. Contamination of feed with chemical substances such as coccidiostats or antibiotics can occur at the stage of production, transport and storage, and their presence may have a negative impact on the health of animals consuming feed contaminated with certain chemicals. This study presents the legal requirements for the production of feed, the presence of antimicrobial substances in feed, and the problem of contamination of feed with antibacterial substances as well as the possible transfer of these compounds to the animal tissues and the natural environment.

Plant metabolite 5-pentadecyl resorcinol is produced by the Amazonian fungus Penicillium sclerotiorum LM 5679

Since the classic studies of Alexander Flemming, Penicillium strains have been known as a rich source of antimicrobial substances. Recent studies have identified novel metabolites produced by Penicillium sclerotiorum that have antibacterial, antifouling and pharmaceutical activities. Here, we report the isolation of a P. sclerotiorum (LM 5679) from Amazonian soil and carry out a culture-based study to determine whether it can produce any novel secondary metabolite(s) that are not thus-far reported for this genus. Using a submerged culture system, secondary metabolites were recovered by solvent extract followed by thin-layer chromatography, nuclear magnetic resonance, and mass spectroscopy. One novel secondary metabolite was isolated from P. sclerotiorum (LM 5679); the phenolic compound 5-pentadecyl resorcinol widely known as an antifungal, that is produced by diverse plant species. This metabolite was not reported previously in any Penicillium species and was only found once before in fungi (that time, in a Fusarium). Here, we discuss the known activities of 5-pentadecyl resorcinol in the context of its mode-of-action as a hydrophobic (chaotropicity-mediated) stressor.

Anti-microbial and Wound Healing Properties of Leaf Extracts of Spermacoce verticillata L

The Rubiaceae family is one of the most important medicinal families that are found in the tropical region of the world. There are many species under the Rubiaceae family such as Coffea arabica, Cinchona officinalis, Spermacoce verticillate. There are several plant parts used to extract the metabolites from, such as the leaf, bark, root, seed, or fruit. The leaf of Spermacoce verticillata has many medicinal values as it contains metabolites which help to reduce microbial activity and help to heal the wound. The microbial activity can lead to skin infections and internal disease. The plant metabolites can act via inhibition of cell wall formation or inhibition of protein synthesis. Wound healing is referred to as the repair of cuts and infections of the human skin. Leaf extracts may help to increase the fibrin formation to clot the blood, and the metabolic compounds may also help to reduce the microbial load in the wound to reduce the chance of infection. Plant leaves contain many metabolites that can act as antimicrobial substances for humans such as minimoidiones A, Cytochalasin D, multiforicin I, and xylarenones E.. Some of those factors can disrupt the sequence of wound healing such as factors of controlling blood sugar level which seriously affect the wound healing and external factors such as contamination of microbes in the wound. The wound healing properties of leaf extract help the immune system to fight the microbes which slow down the wound healing process by the release of harmful metabolites.

The Dynamics of Mycobiota Development in Various Types of Wood Dust Depending on the Dust Storage Conditions

Solid or processed wood, and wood waste in particular (dust, shavings, etc.) are the source of a number of health hazards for workers in the wood industry. One of the many negative health effects of exposure to fungi is allergic diseases caused by hypersensitivity reactions. The aim of this study was to investigate the effect of wood species and the degree of dust fragmentation, resulting from processing conditions and storage conditions on the level of wood dust contamination with microscopic fungi during 1 year of storage. An additional aspect of the research was the assessment of the influence of the antioxidant wood bioactive compounds on the development of A. alternata microscopic fungi. It was found that the conditions in which wood dust is stored significantly affect the development of microscopic fungi, especially fungi of the genus Alternaria. The results indicate that temperature is the determining factor, not the relative humidity of the air. The degree of dust fragmentation resulting from the sanding paper grit also has a significant impact on the development of microscopic fungi. Finer dust is more susceptible to the development of microscopic fungi. The antioxidant activity of the wood from which the dust was formed was found to have a significant impact on the development of microscopic fungi. An inverse relationship was observed, indicating the strong activity of antimicrobial substances. Gaining comprehensive knowledge of how all factors affect each other is a key step in understanding the risk and implementing measures to prevent and protect the work environment.

Discovery of Antimicrobials By Mex : Massively Parallelized Growth Assays

The number of newly approved antimicrobial compounds has been steadily decreasing over the past 50 years emphasizing the need for novel antimicrobial substances. Here we present Mex, a method for the high-throughput discovery of novel antimicrobials, that relies on E.coli self-screening to determine the bioactivity of more than ten thousand naturally occurring peptides. Analysis of thousands of E. coli growth curves using next-generation sequencing enables the identification of more than 1,000 previously unknown antimicrobial peptides. Additionally, by incorporating the kinetics of growth inhibition, a first indication of the mode of action is obtained, which has implications for the ultimate usefulness of the peptides in question. The most promising peptides of the screen are chemically synthesized and their activity is determined in standardized susceptibility assays. Ten out of 15 investigated peptides efficiently eradicate bacteria at a minimal inhibitory concentration in the lower µm or upper nm range. This work represents a step-change in the high-throughput discovery of functionally diverse antimicrobials.