Abstract
The Clusters of Orthologous Genes (COG) database, also referred to as the Clusters of Orthologous Groups of proteins, was created in 1997 and went through several rounds of updates, most ...recently, in 2014. The current update, available at https://www.ncbi.nlm.nih.gov/research/COG, substantially expands the scope of the database to include complete genomes of 1187 bacteria and 122 archaea, typically, with a single genome per genus. In addition, the current version of the COGs includes the following new features: (i) the recently deprecated NCBI’s gene index (gi) numbers for the encoded proteins are replaced with stable RefSeq or GenBank\ENA\DDBJ coding sequence (CDS) accession numbers; (ii) COG annotations are updated for >200 newly characterized protein families with corresponding references and PDB links, where available; (iii) lists of COGs grouped by pathways and functional systems are added; (iv) 266 new COGs for proteins involved in CRISPR-Cas immunity, sporulation in Firmicutes and photosynthesis in cyanobacteria are included; and (v) the database is made available as a web page, in addition to FTP. The current release includes 4877 COGs. Future plans include further expansion of the COG collection by adding archaeal COGs (arCOGs), splitting the COGs containing multiple paralogs, and continued refinement of COG annotations.
•Kinetic growth model: Monod, Blackman, Haldane, Tessier, Moser, Contois, Logarithmic, Powell, Han and Levenspiel, Logistic, Luong, Webb, Yano and Koga, and Aiba-Edwards.•The Monod, Moser, Tesseir, ...Contois, and Blackman model do not account for inhibition of cell growth.•The Monod model does not account for the lag and death phase during the growth phase.•The Haldane model is capable of handling both toxic and non-toxic substrate.•The Monod model is the most widely used kinetic growth model.
Bacteria in biological wastewater treatment process play an important role in the removal of substrate concentration. When bacteria removes the substrate, they continuously growth until such time when the substrate concentration is depleted. This paper aims to review the performance of kinetic growth rate models that describe specific bacteria growth rate. The kinetic growth rate models reviewed were: Monod, Blackman, Haldane, Teissier, Moser, Contois, Logarithmic, Powell, Han and Levenspiel, Logistic, Luong, Webb, Yano and Koga, and Aiba-Edwards. The performance review of the models were based on coefficient of determination (R²). Another statistical measure of performance was root mean square error (RMSE). All kinetic growth rate models performed well when subjected to both toxic and non-toxic substrate concentration. The most notable kinetic growth rate model was the Haldane model which was well represented in the literature.
Biological stability of drinking water refers to the concept of providing consumers with drinking water of same microbial quality at the tap as produced at the water treatment facility. However, ...uncontrolled growth of bacteria can occur during distribution in water mains and premise plumbing, and can lead to hygienic (e.g., development of opportunistic pathogens), aesthetic (e.g., deterioration of taste, odor, color) or operational (e.g., fouling or biocorrosion of pipes) problems. Drinking water contains diverse microorganisms competing for limited available nutrients for growth. Bacterial growth and interactions are regulated by factors, such as (i) type and concentration of available organic and inorganic nutrients, (ii) type and concentration of residual disinfectant, (iii) presence of predators, such as protozoa and invertebrates, (iv) environmental conditions, such as water temperature, and (v) spatial location of microorganisms (bulk water, sediment, or biofilm). Water treatment and distribution conditions in water mains and premise plumbing affect each of these factors and shape bacterial community characteristics (abundance, composition, viability) in distribution systems. Improved understanding of bacterial interactions in distribution systems and of environmental conditions impact is needed for better control of bacterial communities during drinking water production and distribution. This article reviews (i) existing knowledge on biological stability controlling factors and (ii) how these factors are affected by drinking water production and distribution conditions. In addition, (iii) the concept of biological stability is discussed in light of experience with well-established and new analytical methods, enabling high throughput analysis and in-depth characterization of bacterial communities in drinking water. We discussed, how knowledge gained from novel techniques will improve design and monitoring of water treatment and distribution systems in order to maintain good drinking water microbial quality up to consumer's tap. A new definition and methodological approach for biological stability is proposed.
Burns are a common health problem worldwide and are highly susceptible to bacterial infections that are difficult to handle with ordinary wound dressings. Therefore, burn wound repair is extremely ...challenging in clinical practice. Herein, a series of self-healing hydrogels (QCS/OD/TOB/PPY@PDA) with good electrical conductivity and antioxidant activity were prepared on the basis of quaternized chitosan (QCS), oxidized dextran (OD), tobramycin (TOB), and polydopamine-coated polypyrrole nanowires (PPY@PDA NWs). These Schiff base cross-links between the aminoglycoside antibiotic TOB and OD enable TOB to be slowly released and responsive to pH. Interestingly, the acidic substances during the bacteria growth process can induce the on-demand release of TOB, avoiding the abuse of antibiotics. The antibacterial results showed that the QCS/OD/TOB/PPY@PDA9 hydrogel could kill high concentrations of Pseudomonas aeruginosa (PA), Staphylococcus aureus, and Escherichia coli in a short time and showed a bactericidal effect for up to 11 days in an agar plate diffusion experiment, while showing good in vivo antibacterial activity. Excellent and long-lasting antibacterial properties make it suitable for severely infected wounds. Furthermore, the incorporation of PPY@PDA endowed the hydrogel with near-infrared (NIR) irradiation assisted bactericidal activity of drug-resistant bacteria, conductivity, and antioxidant activity. Most importantly, in the PA-infected burn wound model, the QCS/OD/TOB/PPY@PDA9 hydrogel more effectively controlled wound inflammation levels and promoted collagen deposition, vascular generation, and earlier wound closure compared to Tegaderm dressings. Therefore, the TOB smart release hydrogels with on-demand delivery are extremely advantageous for bacterial-infected burn wound healing.
In article number 2007993, Haeshin Lee, Hyun Jung Chung, and co‐workers demonstrate the polydopamine–oxygen relationship using a fluorescence coupling strategy during bacterial growth‐induced ...hypoxia. With the exponential growth of bacteria, oxygen is consumed and leads to the inhibition of dopamine polymerization, which is directly measured by fluorescent nanoparticle sensors. The current method can be applied as a simple diagnostic assay to detect bacterial growth and antibiotic resistance.
Droplet microfluidics has revolutionized single-cell analysis, allowing for ultra-high-throughput sorting of droplets to meet the demands of single-cell sorting. However, accurately and efficiently ...dispensing target droplets into specific containers for downstream analysis has remained a challenge. Here, we present an integrated microfluidic droplet dispenser based on the electrohydrodynamic (EHD) principle, capable of on-demand single droplet dispensing with high accuracy. Our system uses optical signal activation and EHD actuation to isolate and dispense droplets. The microfluidic droplet auto dispenser consists of four main modules: a pump-drive chip module, an optical automatic signal recognition module, a high voltage control module, and an automated X-Y translation stage module. By optimizing the chip structure and voltage parameter, this platform successfully isolates single Escherichia coli (E. coli) cells onto a Petri dish for downstream cultivation and heterogeneity analysis. In addition, the dispenser microfluidic system dispenses the sorted droplets in a "one droplet, one well" manner, providing an automated method for droplet interface from the micro- to macro- platform. This dispenser system provides a platform for phenotypic screening of single colony pick and single cell analysis
•An integrated microfluidic droplet dispenser based on the electrohydrodynamic (EHD) principle.•Realize efficient single droplet dispensing with optical signal activation and EHD-based drive.•Provide an automated method for transferring droplets from the microchip to the macroscopic world.
The measurement of potential enzymatic activities has been proposed as an efficient method to infer nutrient limitations for microorganisms in environmental samples. To validate this use, ...confirmation with direct methods of microbial growth responses to resource additions are required. We experimentally manipulated nutrient-poor soils from the afromontane subtropics with relatively low (grassland soils, ca. 4% soil carbon (C)) or high organic matter content (forest soils, ca. 13% soil C) with nutrient additions (plant material added at 8 mg C g−1 soil combined with mineral N and/or P to reach C:N:P mass-ratios of 10:1:1) in a multifactorial design for one month in order to shift the microbial community towards C-, N- or P-limitation. We then measured the responses of the most commonly measured indicator enzymes used to infer growth limiting nutrients, using ß-1,4-glucosidase, ß-1,4-N-acetylglucosaminidase and leucine aminopeptidase, and acid phosphatase as indicators for C-, N- and P-acquiring enzymatic activities, respectively. In the same soil samples, we also determined the responses in bacterial (3H-leucine incorporation) and fungal growth rates (14C-acetate incorporation into ergosterol) to nutrient supplements, and also verified these with biomass responses (microbial PLFA and ergosterol concentrations) to the factorial nutrient loading amendments. Ratios of C-, N-, and P-acquiring enzymes indicated that the grassland soils were primarily P-limited, and secondarily co-limited by C and N, while the forest soils were co-limited by C and P. However, short-term responses in growth rates and respiration to nutrient additions, along with long-term growth rate, respiration and biomass responses to nutrient loading treatments all indicated that bacterial growth, fungal growth and respiration were primarily limited by C in both grassland and forest soils. We conclude that enzymatic ratios do not capture the growth-limiting factors for bacterial growth, fungal growth, or respiration in soil. Furthermore, the addition of C-rich plant material could shift the fungal community into N-limitation, while bacteria were shifted into co-limitation by both C and N, revealing that bacteria and fungi can be limited by different nutrients within the same soil environment.
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•Enzyme assays did not capture the limiting factors for microbial growth or respiration.•Enzyme assays overestimated N- and P-limitation relative to that of C.•Bacteria and fungi can be limited by different nutrients in the same environment.
Microplastics (MPs) are emerging pollutants as vectors for microbial colonization, but their role as nutrients sources for microbial communities has rarely been reported. This study explored the ...impact of six types of MPs on assimilable organic carbon (AOC) and microbial communities over eight weeks. The following were the primary conclusions: (1) MPs contributed to AOC increment and subsequently increased bacterial regrowth potential. The maximum AOC reached 722.03 μg/L. The increase in AOC formation corresponded to AOC NOX, except in PVC samples where AOC P17 primarily increased. (2) The MPs accelerated bacterial growth and changed the bacterial distribution between the biofilm and water phases. A high MP surface-area-to-volume ratio or low MPs density contributed to bacterial accumulation and biofilm formation around the plastisphere, thereby decreasing the relative microbial proportion in the water phase. (3) High-throughput sequencing and scanning electron microscope revealed that different MPs shaped various microbial communities temporally and spatially. (4) Biofilm formatting and formatted models were established and simulated to explain the kinetic interaction between the AOC and bacteria inhabiting the plastisphere. Finally, the challenges that plastic-deprived AOC represent in terms of anti-bacterial measures and chemical safety are discussed.
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•The nutrient-supply effect of microplastics for bacterial growth was explored.•Different MPs contribute various assimilable organic carbon formation and subsequently shaped microbial communities.•MPs’ properties have impacts on bacterial growth and distribution between biofilm and water phase.•Biofilm formatting and formatted phases of biofilm, were defined and simulated.
The objective of this study was to evaluate the effects of NaCl reduction (2.5% 2.0%, 1.5% and 1.0%) on the bacterial growth, physicochemical characteristics, flavour profile and sensory traits of ...fermented dry sausage. The moisture content, water activity and lactic acid bacteria count increased as the NaCl level decreased (P < 0.05), contributing to decreases in pH (P < 0.05). A total of 50 volatile compounds were identified, and increases in volatile compounds, such as acetone, 3-hydroxy-2-butanone, with high odour activity values derived from carbohydrate metabolism and lipid oxidation may contribute to flavour development (P < 0.05). Additionally, the increased Staphylococcus spp. counts in sausages with 2.0% and 2.5% NaCl contributed to the increased contents of ethyl octanoate, ethyl butyrate and ethyl acetate (P < 0.05). Sensory evaluation showed higher scores for taste, chewiness and aroma in sausages with 2.0% and 2.5% NaCl. Therefore, it can be concluded that 2.0% NaCl can be employed as the desired addition level in fermented sausage to achieve better quality and flavour.
•Sausages with reduction in NaCl level had higher moisture content and water activity.•The reduction of NaCl level increased lactic acid bacteria population.•Volatile compounds in fermented sausage during fermentation were identified.•2.0% NaCl can be employed as the desired addition level in fermented sausage.
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