High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis framew...

Traditional cheeses harbour complex microbial consortia that play an important role in shaping typical sensorial properties. However, the microbial metabolism is considered difficult to control. Microbial community succession and the related gene expression were analysed during ripening of a traditional Italian cheese, identifying parameters that could be modified to accelerate ripening. Afterw...

This review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High-throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most expl...

Urban agriculture has been recently highlighted with the increased importance for recreation in modern society; however, soil quality and public health may not be guaranteed because of continuous exposure to various pollutants. The objective of this study was to evaluate the soil quality of urban agriculture by soil microbial assessments. Two independent variables, organic and inorganic fertili...

Bio-organic fertilizers (BOFs) combine functional microbes with a suitable substrate and have been shown to effectively suppress soil-borne diseases and promote plant growth. Here, we developed a novel bio-organic fertilizer (BOF) by fermentation of a cow plus chicken manure (M) compost using Fen-liquor Daqu (FLD) as a fermentation starter and compared the compositions of bacterial and fungal c...

The short-term responses of soil microbial processes and community structure to perturbation constitute one aspect of soil quality. Such responses are often associated with an increase in the emissions of greenhouse gases (i.e., CO2, NO, or N2O) and the accumulation and potential loss of nitrate by leaching. Here we describe our recent work on responses of soil carbon and nitrogen dynamics, mic...

Domestication took plants from natural environments to agro-ecosystems, where resources are generally plentiful and plant life is better buffered against environmental risks such as drought or pathogens. We hypothesized that predictions derived from the comparison of low vs high resource ecosystems (faster-growing plants promoting faster nutrient cycling in the latter) extrapolate to the proces...

[1] The production of CO2 by soil microorganisms is an important component of the global carbon cycle, and its temperature sensitivity is poorly constrained in global models. To improve our understanding of the factors controlling the temperature dependence of soil microbial respiration, we analyzed the temperature sensitivity of labile soil organic carbon decomposition for 77 soils collected f...

freezing causes changes on chemical and microbial quality of butter. in this research, effects of two different temperatures -9 and -18oc on changes of moisture, fat, acidity and peroxide value and also coliform and psychrotrophic microorganisms in frozen butter were studied. results showed that values of moisture and fat during 7 months of frozen storage at two temperatures decreased 1.8% and ...

With readily applicable hybridization assays, mainly based on rRNA-targeted nucleic acid probes, and direct, cultivation-independent sequence retrieval, microbiologists can for the first time determine the true composition of microbial communities. Phylogenetic identification and exact spatiotemporal quantification of microorganisms will in the future become prerequisites for high quality studi...