Publications

suitability of different mapping algorithms for genome-wide polymorphism scans with pool-seq data.	the cost-effectiveness of sequencing pools of individuals (pool-seq) provides the basis for the popularity and wide-spread use of this method for many research questions, ranging from unravelling the genetic basis of complex traits to the clonal evolution of cancer cells. because the accuracy of pool-seq could be affected by many potential sources of error, several studies determined, for example, the influence of the sequencing technology, the library preparation protocol, and mapping parameter ...	2016	27613752
saccharomyces cerevisiae metabolism in ecological context.	the architecture and regulation of saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry. yet, several recent studies have revealed notable limitations in explaining genotype-metabolic phenotype relations in this yeast, especially when concerning multiple genetic/environmental perturbations. apparently unexpected genotype-phenotype relations may originate in the evolutionarily shaped cellular operating principles bei ...	2016	27634775
complete genome sequencing and comparative genomic analysis of the thermotolerant acetic acid bacterium, acetobacter pasteurianus sku1108, provide a new insight into thermotolerance.	acetobacter pasteurianus sku1108 is a typical thermotolerant acetic acid bacterium. in this study, the complete genome sequence of the sku1108 strain was elucidated, and information on genomic modifications due to the thermal adaptation of sku1108 was updated. in order to obtain a clearer understanding of the genetic background responsible for thermotolerance, the sku1108 genome was compared with those of two closely related complete genome strains, thermotolerant a. pasteurianus 386b and mesoph ...	2016	27667143
new insights into the mechanisms of acetic acid resistance in acetobacter pasteurianus using itraq-dependent quantitative proteomic analysis.	acetobacter pasteurianus is the main starter in rice vinegar manufacturing due to its remarkable abilities to resist and produce acetic acid. although several mechanisms of acetic acid resistance have been proposed and only a few effector proteins have been identified, a comprehensive depiction of the biological processes involved in acetic acid resistance is needed. in this study, itraq-based quantitative proteomic analysis was adopted to investigate the whole proteome of different acidic titer ...	2016	27681379
ethanol production in brazil: a bridge between science and industry.	in the last 40 years, several scientific and technological advances in microbiology of the fermentation have greatly contributed to evolution of the ethanol industry in brazil. these contributions have increased our view and comprehension about fermentations in the first and, more recently, second-generation ethanol. nowadays, new technologies are available to produce ethanol from sugarcane, corn and other feedstocks, reducing the off-season period. better control of fermentation conditions can ...	2016	27818090
microbial succession and flavor production in the fermented dairy beverage kefir.	kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. metagenomic sequencing revealed that lactobacillus kefiranofaciens was the dominant bacterial species i ...	2016	27822552
whole-genome sequence analysis of bombella intestini lmg 28161t, a novel acetic acid bacterium isolated from the crop of a red-tailed bumble bee, bombus lapidarius.	the whole-genome sequence of bombella intestini lmg 28161t, an endosymbiotic acetic acid bacterium (aab) occurring in bumble bees, was determined to investigate the molecular mechanisms underlying its metabolic capabilities. the draft genome sequence of b. intestini lmg 28161t was 2.02 mb. metabolic carbohydrate pathways were in agreement with the metabolite analyses of fermentation experiments and revealed its oxidative capacity towards sucrose, d-glucose, d-fructose and d-mannitol, but not eth ...	2016	27851750
ancestral population reconstitution from isofemale lines as a tool for experimental evolution.	experimental evolution is a powerful tool to study adaptation under controlled conditions. laboratory natural selection experiments mimic adaptation in the wild with better-adapted genotypes having more offspring. because the selected traits are frequently not known, adaptation is typically measured as fitness increase by comparing evolved populations against an unselected reference population maintained in a laboratory environment. with adaptation to the laboratory conditions and genetic drift, ...	2016	27895897
stable host gene expression in the gut of adult drosophila melanogaster with different bacterial mono-associations.	there is growing evidence that the microbes found in the digestive tracts of animals influence host biology, but we still do not understand how they accomplish this. here, we evaluated how different microbial species commonly associated with laboratory-reared drosophila melanogaster impact host biology at the level of gene expression in the dissected adult gut and in the entire adult organism. we observed that guts from animals associated from the embryonic stage with either zero, one or three b ...	2016	27898741
antioxidant and antibacterial activity of the beverage obtained by fermentation of sweetened lemon balm (melissa officinalis l.) tea with symbiotic consortium  of bacteria and yeasts.	kombucha is a fermented tea beverage which is traditionally prepared by fermenting sweetened black or green tea (camellia sinensis l.) with symbiotic consortium of bacteria and yeasts (scoby). in this study, lemon balm (melissa officinalis l.) was used as the only nitrogen source for kombucha fermentation. during the seven-day fermentation process, ph value, titratable acidity (ta), total phenolic content, phenolic compounds, and antioxidant activity against hydroxyl (˙oh) and 1,1-diphenyl-2-pic ...	2014	27904315
16s rrna in situ hybridization followed by flow cytometry for rapid identification of acetic acid bacteria involved in submerged industrial vinegar production.	acetic acid bacteria are involved in many biotechnological processes such as vitamin c, gluconic acid, miglitol or acetic acid production, and others. for a technologist trying to control the industrial process, the ability to follow the microbiological development of the process is thus of importance. during the past few years hybridization in a combination with flow cytometry has often been used for this purpose. since vinegar is a liquid, it is an ideal matrix for flow cytometry analysis. in ...	2016	27904400
comparison of cultivable acetic acid bacterial microbiota in organic and conventional apple cider vinegar.	organic apple cider vinegar is produced from apples that go through very restricted treatment in orchard. during the first stage of the process, the sugars from apples are fermented by yeasts to cider. the produced ethanol is used as a substrate by acetic acid bacteria in a second separated bioprocess. in both, the organic and conventional apple cider vinegars the ethanol oxidation to acetic acid is initiated by native microbiota that survived alcohol fermentation. we compared the cultivable ace ...	2016	27904401
improving fermented quality of cider vinegar via rational nutrient feeding strategy.	this work aimed to find a rational nutrient feeding strategy for cider vinegar fermentation based on adequate information on the nutritional requirement of acetic acid bacteria. through single nutrient lack experiment assay, necessary nutrient recipe for acetobacter pasteurianus cicim b7003 in acetous fermentation was confirmed. compounds from the essential nutrient recipe were tested further to find out the key substrates significantly influencing cider vinegar fermentation. the findings showed ...	2017	28159272
a perspective study of koumiss microbiome by metagenomics analysis based on single-cell amplification technique.	koumiss is a traditional fermented dairy product and a good source for isolating novel bacteria with biotechnology potential. in the present study, we applied the single-cell amplification technique in the metagenomics analysis of koumiss. this approach aimed at detecting the low-abundant bacteria in the koumiss. briefly, each sample was first serially diluted until reaching the level of approximately 100 cells. then, three diluted bacterial suspensions were randomly picked for further study. by ...	2017	28223973
fermentation process for production of apple-based kefir vinegar: microbiological, chemical and sensory analysis.	the aim of this study was to develop a kefir apple-based vinegar and evaluate this fermentation process using new methodology with biospeckle laser. brazilian kefir grains were inoculated in apple must for vinegar production. in this study, the microbial community present in kefir, and correspondent vinegar, was investigated using matrix assisted laser desorption/ionization - time of flight mass spectrometry (maldi-tof ms) technique. saccharomyces cerevisiae, lactobacillus paracasei, lactobacill ...	2017	28283415