The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health.

Food and human health are inextricably linked. As such, revolutionary impacts on health have been derived from advances in the production and distribution of food relating to food safety and fortification with micronutrients. During the past two decades, it has become apparent that the human microbiome has the potential to modulate health, including in ways that may be related to diet and the composition of specific foods. Despite the excitement and potential surrounding this area, the complexity of the gut microbiome, the chemical composition of food, and their interplay in situ remains a daunting task to fully understand. However, recent advances in high-throughput sequencing, metabolomics profiling, compositional analysis of food, and the emergence of electronic health records provide new sources of data that can contribute to addressing this challenge. Computational science will play an essential role in this effort as it will provide the foundation to integrate these data layers and derive insights capable of revealing and understanding the complex interactions between diet, gut microbiome, and health. Here, we review the current knowledge on diet-health-gut microbiota, relevant data sources, bioinformatics tools, machine learning capabilities, as well as the intellectual property and legislative regulatory landscape. We provide guidance on employing machine learning and data analytics, identify gaps in current methods, and describe new scenarios to be unlocked in the next few years in the context of current knowledge

Tolerance to Glutaraldehyde in Escherichia coli Mediated by Overexpression of the Aldehyde Reductase YqhD by YqhC

Glutaraldehyde is a widely used biocide on the market for about 50 years. Despite its broad application, several reports on the emergence of bacterial resistance, and occasional outbreaks caused by poorly disinfection, there is a gap of knowledge on the bacterial adaptation, tolerance, and resistance mechanisms to glutaraldehyde. Here, we analyze the effects of the independent selection of mutations in the transcriptional regulator yqhC for biological replicates of Escherichia coli cells subjected to adaptive laboratory evolution (ALE) in the presence of glutaraldehyde. The evolved strains showed improved survival in the biocide (11–26% increase in fitness) as a result of mutations in the activator yqhC, which led to the overexpression of the yqhD aldehyde reductase gene by 8 to over 30-fold (3.1–5.2 log2FC range). The protective effect was exclusive to yqhD as other aldehyde reductase genes of E. coli, such as yahK, ybbO, yghA, and ahr did not offer protection against the biocide. We describe a novel mechanism of tolerance to glutaraldehyde based on the activation of the aldehyde reductase YqhD by YqhC and bring attention to the potential for the selection of such tolerance mechanism outside the laboratory, given the existence of YqhD homologs in various pathogenic and opportunistic bacterial species

Enzyme production by filamentous fungus for lignocellulose hydrolysis

Orientadores: Aline Carvalho da Costa, José Geraldo da Cruz PradellaDissertação (mestrado) - Universidade Estadual de Campoinas, Faculdade de Engenharia QuímicaResumo: A produção de enzimas lignocelulolíticas por Trichoderma reesei RUT-C30 foi otimizada em frascos agitados e bioreatores de 0,5 e 3L visando maximizar os títulos enzimáticos e produtividade volumétrica. Para isso, foram testadas como fontes de carbono (1% m/v) bagaço de cana-de-açúcar pré-tratado por processo hidrotérmico (BH) ou por explosão a vapor, com (BED) e sem (BEX) deslignificação, em meio contendo proteose peptona, tween 80 e solução salina. Celulose comercial Celufloc200 (CE) foi testada para comparação. Maior produção de enzimas celulolíticas foi obtida com a utilização de BED (1,38 ± 0,11 FPU/mL) quando em comparação com CE (0,78 ± 0,14 FPU/mL) em frascos agitados, sendo esse material utilizado como fonte de carbono nos demais ensaios. A produção de hemicelulases (xilanases) foi similar para os dois meios (em U/mL): 18,03 ± 1,56 para BED e 20,04 ± 1,50 para CE. A variação da concentração da solução salina, da fonte de carbono e dos nutrientes permitiu aumento da produção de enzimas celulolíticas para 1,89 ± 0,12 (meio com o dobro de solução salina) e 2,73 ± 0,09 (meio com 2% m/v de BED e nutrientes proporcionais) em frascos agitados. A suplementação da fonte de carbono com farelo de soja, sacarose, licor de pré-tratamento, lactose e glicerol foi estudada e farelo de soja foi selecionado como suplemento do meio. A elaboração de um meio de mistura contendo o dobro de solução salina, farelo de soja e nutrientes proporcionais à concentração da fonte de carbono (meio MIX) permitiu o aumento da produção de enzimas para, em FPU/mL: 3,33 ± 0,10 (MIX15: contém 1,5% m/v de BED), 3,78 ± 0,33 (MIX20) e 3,67 ± 0,34 (MIX30) em frascos agitados. As atividades de xilanases foram superiores a 130 U/Ml utilizando os meios de mistura. Em bioreator de 3L a produção de enzimas celulolíticas utilizando o meio MIX15 atingiu 2,29 ± 0,20 FPU/mL. Para o meio padrão (BED 1% m/v) o pico de atividade obtido foi de 1,14 ± 0,32 FPU/mL. O aumento da concentração da fonte de carbono em bioreator para 3% (m/v) a partir do meio MIX15 resultou no aumento da atividade celulolítica para 4,20 ± 0,34 FPU/mL. Os picos de atividade de xilanases atingiram valores superiores a 180 U/mL em bioreator. O desempenho do coquetel enzimático produzido no meio MIX15 foi avaliado na hidrólise de BED e BH, e comparado ao coquetel produzido no meio padrão e a um coquetel comercialmente disponível (Sigma). Os valores de conversão de celulose em glicose foram superiores para o coquetel MIX15 em relação aos demais coquetéis ao se utilizar 3 ou 5% de sólidos, com ou sem adição de beta-glucosidase comercial (Novozym 188)Abstract: The production of lignocellulolytic enzymes by Trichoderma reesei RUT-C30 was optimized in shake flasks and 0.5 and 3L bioreactors to maximize the enzymatic titles and volumetric productivity. The carbon sources considered were sugar cane bagasse (1% w/v) pretreated by the hydrothermal process (BH) or steam explosion, with (BED) and without (BEX) delignification. The medium contained proteose peptone, Tween 80 and saline solution. Commercial cellulose Celufloc200 (CE) was used for comparison. Increased production of cellulolytic enzymes in flasks was obtained with BED as carbon source (1.38 ± 0.11 FPU / ml) when compared to CE (0.78 ± 0.14 FPU / ml), and this material was selected as carbon source for further studies. The production of hemicellulases (xylanases) was similar for the two carbon sources (U / mL): 18.03 ± 1.56 with BED and 20.04 ± 1.50 with CE. Variation of the concentration of the salt solution, carbon source and nutrients led to an increased production of cellulolytic enzymes: 1.89 ± 0.12 (medium with doubled saline solution concentration) and 2.73 ± 0.09 (medium with 2% w/v BED and nutrients proportional to the carbon source) in shake flasks. Supplementation of the carbon source with soybean meal, sucrose, pretreatment liquor, lactose and glycerol was studied and soybean meal has been selected as supplement. The preparation of a mixture medium containing doubled saline solution, soybean meal and nutrients proportional to the concentration of the carbon source allowed increasing the production of enzymes for (in FPU / ml): 3.33 ± 0.10 (MIX15 - containing 1.5% w/v BED) , 3.78 ± 0.33 (MIX20) and 3.67 ± 0.34 (MIX30) in shake flasks. Xylanase activities were higher than 130 U/mL. In a 3L bioreactor, production of cellulolytic enzymes using MIX15 medium reached 2.29 ± 0.20 FPU / mL. For the standard medium (BED 1% w/v) the peak activity was 1.14 ± 0.32 FPU / mL. Increasing the concentration of the carbon source in the bioreactor to 3% w/v starting from MIX15 resulted in a cellulolytic activity of 4.20 ± 0.34 FPU / mL. Xylanase activity reached values higher than 180 U/mL in the bioreactor. The performance of the enzyme cocktail produced in MIX15 medium was evaluated for the hydrolysis of BED and BH, and compared to the cocktail produced in the standard medium and to a cocktail commercially available (Sigma). The values of conversion of cellulose to glucose were higher for the cocktail MIX15 compared to the other cocktails when using 3 or 5% solids, with or without adding commercial beta-glucosidase (Novozym 188)MestradoDesenvolvimento de Processos QuímicosMestra em Engenharia Químic

Benzalkonium Chlorides: Uses, Regulatory Status, and Microbial Resistance.

Benzalkonium chlorides (BACs) are chemicals with widespread applications due to their broad-spectrum antimicrobial properties against bacteria, fungi, and viruses. This review provides an overview of the market for BACs, as well as regulatory measures and available data on safety, toxicity, and environmental contamination. We focus on the effect of frequent exposure of microbial communities to BACs and the potential for cross-resistant phenotypes to emerge. Toward this goal, we review BAC concentrations in consumer products, their correlation with the emergence of tolerance in microbial populations, and the associated risk potential. Our analysis suggests that the ubiquitous and frequent use of BACs in commercial products can generate selective environments that favor microbial phenotypes potentially cross-resistant to a variety of compounds. An analysis of benefits versus risks should be the guidepost for regulatory actions regarding compounds such as BACs

Short- and Long-Term Transcriptomic Responses of Escherichia coli to Biocides: a Systems Analysis.

The mechanisms of the bacterial response to biocides are poorly understood, despite their broad application. To identify the genetic basis and pathways implicated in the biocide stress response, we exposed Escherichia coli populations to 10 ubiquitous biocides. By comparing the transcriptional responses between a short-term exposure (30 min) and a long-term exposure (8 to 12 h) to biocide stress, we established the common gene and pathway clusters that are implicated in general and biocide-specific stress responses. Our analysis revealed a temporal choreography, starting from the upregulation of chaperones to the subsequent repression of motility and chemotaxis pathways and the induction of an anaerobic pool of enzymes and biofilm regulators. A systematic analysis of the transcriptional data identified a zur-regulated gene cluster to be highly active in the stress response against sodium hypochlorite and peracetic acid, presenting a link between the biocide stress response and zinc homeostasis. Susceptibility assays with knockout mutants further validated our findings and provide clear targets for downstream investigation of the implicated mechanisms of action.IMPORTANCE Antiseptics and disinfectant products are of great importance to control and eliminate pathogens, especially in settings such as hospitals and the food industry. Such products are widely distributed and frequently poorly regulated. Occasional outbreaks have been associated with microbes resistant to such compounds, and researchers have indicated potential cross-resistance with antibiotics. Despite that, there are many gaps in knowledge about the bacterial stress response and the mechanisms of microbial resistance to antiseptics and disinfectants. We investigated the stress response of the bacterium Escherichia coli to 10 common disinfectant and antiseptic chemicals to shed light on the potential mechanisms of tolerance to such compounds