Soil protein as a potential antimicrobial agent against methicillin -resistant Staphylococcus aureus

Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship

Microbes live in diverse habitats (i.e. biomes), yet their species and genes were biome-specific, forming enrichment patterns. These enrichment patterns have mirrored the biome-species-function relationship, which is shaped by ecological and evolutionary principles. However, a grand picture of these enrichment patterns, as well as the roles of external and internal factors in driving these enrichment patterns, remain largely unexamined. In this work, we have examined the enrichment patterns based on 1705 microbiome samples from four representative biomes (Engineered, Gut, Freshwater, and Soil). Moreover, an "enrichment sphere" model was constructed to elucidate the regulatory principles behind these patterns. The driving factors for this model were revealed based on two case studies: (1) The copper-resistance genes were enriched in Soil biomes, owing to the copper contamination and horizontal gene transfer. (2) The flagellum-related genes were enriched in the Freshwater biome, due to high fluidity and vertical gene accumulation. Furthermore, this enrichment sphere model has valuable applications, such as in biome identification for metagenome samples, and in guiding 3D structure modeling of proteins. In summary, the enrichment sphere model aims towards creating a bluebook of the biome-species-function relationships and be applied in many fields.

Isolation and identification of promising antibiotic-producing bacteria

Multiple stresses in waste dumpsite soils can drive antibiotic production as one of the strategies for survival. Bacteria are the most prolific producers of antibiotics. This study investigated the antibiotic production potential of bacteria isolated from Bahir Dar city municipal solid waste dumpsite (MSWDS). Bacteria were isolated from soil collected from the dumpsite on starch casein or nutrient agar. The isolates were carefully screened for antimicrobial activity against six pathogenic bacterial test strains. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were also determined from cell-free metabolites of the most promising isolates. Isolates showing antimicrobial activity were identified using cultural and biochemical methods. A total of 143 distinctive colonies were obtained and tentatively identified to 13 bacterial genera. Twenty-six (18.18%) of the isolates (six Bacillus and 20 actinobacteria related) demonstrated antimicrobial activities at least against one of the tested bacterial strains. These isolates were related to two actinobacterial and 11 other bacterial genera. Seven out of 26 isolates showed a broad-spectrum of antibiotic activities. Two isolates, which showed a wide spectrum, were selected for the MIC and MBC tests against Escherichia coli and Staphylococcus aureus. The MIC and MBC of the isolates were recorded to be 250–500 µg/mL against the test strains. Bahir Dar city MSWDS contained a high incidence of antibiotic-producing bacteria. Strain level identification of the isolates and detailed characterization of the metabolites will give a good insight into the antimicrobial production potential in the waste dumpsite.

Probing Antimicrobial Halloysite/Biopolymer Composites with Electron Microscopy: Advantages and Limitations

Halloysite is a tubular clay nanomaterial of the kaolin group with a characteristic feature of oppositely charged outer and inner surfaces, allowing its selective spatial modification. The natural origin and specific properties of halloysite make it a potent material for inclusion in biopolymer composites with polysaccharides, nucleic acids and proteins. The applications of halloysite/biopolymer composites range from drug delivery and tissue engineering to food packaging and the creation of stable enzyme-based catalysts. Another important application field for the halloysite complexes with biopolymers is surface coatings resistant to formation of microbial biofilms (elaborated communities of various microorganisms attached to biotic or abiotic surfaces and embedded in an extracellular polymeric matrix). Within biofilms, the microorganisms are protected from the action of antibiotics, engendering the problem of hard-to-treat recurrent infectious diseases. The clay/biopolymer composites can be characterized by a number of methods, including dynamic light scattering, thermo gravimetric analysis, Fourier-transform infrared spectroscopy as well as a range of microscopic techniques. However, most of the above methods provide general information about a bulk sample. In contrast, the combination of electron microscopy with energy-dispersive X-ray spectroscopy allows assessment of the appearance and composition of biopolymeric coatings on individual nanotubes or the distribution of the nanotubes in biopolymeric matrices. In this review, recent contributions of electron microscopy to the studies of halloysite/biopolymer composites are reviewed along with the challenges and perspectives in the field.