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Analysis of Anoxybacillus Genomes from the Aspects of Lifestyle Adaptations, Prophage Diversity, and Carbohydrate Metabolism  [PDF]
Kian Mau Goh, Han Ming Gan, Kok-Gan Chan, Giek Far Chan, Saleha Shahar, Chun Shiong Chong, Ummirul Mukminin Kahar, Kian Piaw Chai
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0090549
Abstract: Species of Anoxybacillus are widespread in geothermal springs, manure, and milk-processing plants. The genus is composed of 22 species and two subspecies, but the relationship between its lifestyle and genome is little understood. In this study, two high-quality draft genomes were generated from Anoxybacillus spp. SK3-4 and DT3-1, isolated from Malaysian hot springs. De novo assembly and annotation were performed, followed by comparative genome analysis with the complete genome of Anoxybacillus flavithermus WK1 and two additional draft genomes, of A. flavithermus TNO-09.006 and A. kamchatkensis G10. The genomes of Anoxybacillus spp. are among the smaller of the family Bacillaceae. Despite having smaller genomes, their essential genes related to lifestyle adaptations at elevated temperature, extreme pH, and protection against ultraviolet are complete. Due to the presence of various competence proteins, Anoxybacillus spp. SK3-4 and DT3-1 are able to take up foreign DNA fragments, and some of these transferred genes are important for the survival of the cells. The analysis of intact putative prophage genomes shows that they are highly diversified. Based on the genome analysis using SEED, many of the annotated sequences are involved in carbohydrate metabolism. The presence of glycosyl hydrolases among the Anoxybacillus spp. was compared, and the potential applications of these unexplored enzymes are suggested here. This is the first study that compares Anoxybacillus genomes from the aspect of lifestyle adaptations, the capacity for horizontal gene transfer, and carbohydrate metabolism.
RESEARCH OF CARBOHYDRATE UTILIZATION BY YEAST MICROFLORA OF FERMENTED MILK PRODUCTS Исследование утилизации углеводов молочного сырья дрожжевой микрофлорой кисломолочных продуктов
Oleshkevich O. I.,Kulikova I. K.,Zhigulina O. V.,Podsvirova I. A.
Polythematic Online Scientific Journal of Kuban State Agrarian University , 2013,
Abstract: In the article, we present the results of the researches of carbohydrate utilization by yeast microflora of fermented milk products
Complex Carbohydrate Utilization by the Healthy Human Microbiome  [PDF]
Brandi L. Cantarel, Vincent Lombard, Bernard Henrissat
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0028742
Abstract: The various ecological habitats in the human body provide microbes a wide array of nutrient sources and survival challenges. Advances in technology such as DNA sequencing have allowed a deeper perspective into the molecular function of the human microbiota than has been achievable in the past. Here we aimed to examine the enzymes that cleave complex carbohydrates (CAZymes) in the human microbiome in order to determine (i) whether the CAZyme profiles of bacterial genomes are more similar within body sites or bacterial families and (ii) the sugar degradation and utilization capabilities of microbial communities inhabiting various human habitats. Upon examination of 493 bacterial references genomes from 12 human habitats, we found that sugar degradation capabilities of taxa are more similar to others in the same bacterial family than to those inhabiting the same habitat. Yet, the analysis of 520 metagenomic samples from five major body sites show that even when the community composition varies the CAZyme profiles are very similar within a body site, suggesting that the observed functional profile and microbial habitation have adapted to the local carbohydrate composition. When broad sugar utilization was compared within the five major body sites, the gastrointestinal track contained the highest potential for total sugar degradation, while dextran and peptidoglycan degradation were highest in oral and vaginal sites respectively. Our analysis suggests that the carbohydrate composition of each body site has a profound influence and probably constitutes one of the major driving forces that shapes the community composition and therefore the CAZyme profile of the local microbial communities, which in turn reflects the microbiome fitness to a body site.
Sara Gregory,Richard Wood,Tracey Matthews,Deborah VanLangen
Journal of Sports Science and Medicine , 2011,
Abstract: The present study compared the metabolic responses between a single low-carbohydrate (LC) and low-fat (LF) meal followed by an aerobic exercise bout in females. Subjects included 8 active, premenopausal females. Subjects completed a LC and LF testing session. Respiratory gas exchange (RER) measurements were taken for 20 min fasted, for 55 min postprandial (PP), and during 30 min of exercise. Blood was collected for assessment of glucose (G), insulin (IN), triglycerides (TG), and free fatty acids (FFA) during the final 10 min of each time period. The LF meal provided 396 kcal (78% carbohydrate, 7% fat, and 15% protein). The LC meal provided 392 kcal (15% carbohydrate, 68% fat, and 18% protein). No significant differences existed between test meals for fasting blood measurements. PP IN (μU·mL-1) levels were significantly lower following LC compared to LF [10.7 (6.1) vs. 26.0 (21.0)]. Postexercise (PE) FFA (mEq·L-1) levels were significantly greater following LC [1.1 (0.3) vs. 0.5 (0.3)]. PE TG (mg·dL-1) levels were significantly greater following LC [152.0 (53.1) vs. 114.4 (40.9)]. RER was significantly lower at all time points following LC compared to LF. In moderately active adult females, ingestion of a single LC meal resulted in greater lipid oxidation at rest and during exercise as compared to a single LF meal. Although macronutrient distribution appears to have dictated substrate utilization in the present study, more research is needed regarding the long-term effects of macronutrient redistribution with and without exercise on substrate utilization.
Carbohydrate-active enzymes from pigmented Bacilli: a genomic approach to assess carbohydrate utilization and degradation
Nicola Manzo, Enrica D'Apuzzo, Pedro M Coutinho, Simon M Cutting, Bernard Henrissat, Ezio Ricca
BMC Microbiology , 2011, DOI: 10.1186/1471-2180-11-198
Abstract: We report the annotation of carbohydrate active enzymes (CAZymes) of two pigmented Bacilli isolated from the human GI-tract and belonging to the Bacillus indicus and B. firmus species. A high number of glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) were found in both isolates. A detailed analysis of CAZyme families, was performed and supported by growth data. Carbohydrates able to support growth as the sole carbon source negatively effected carotenoid formation in rich medium, suggesting that a catabolite repression-like mechanism controls carotenoid biosynthesis in both Bacilli. Experimental results on biofilm formation confirmed genomic data on the potentials of B. indicus HU36 to produce a levan-based biofilm, while mucin-binding and -degradation experiments supported genomic data suggesting the ability of both Bacilli to degrade mammalian glycans.CAZy analyses of the genomes of the two pigmented Bacilli, compared to other Bacillus species and validated by experimental data on carbohydrate utilization, biofilm formation and mucin degradation, suggests that the two pigmented Bacilli are adapted to the intestinal environment and are suited to grow in and colonize the human gut.Spore-forming Bacilli are aerobic, Gram positive organisms sharing a common attribute of being able to differentiate into an endospore (spore), a quiescent cell form characterized by several protective layers surrounding a dehydrated cytoplasm [1]. This structural organization makes the spores extremely resistant to external physical and chemical insults and able to survive almost indefinitely in the absence of water and nutrients [1].The soil is generally indicated as the main habitat of aerobic spore-formers, however, spores have been found in diverse environments including rocks, dust, aquatic environments, and the gut of various insects and animals [2]. Recent reports have highlighted the fact that large numbers of aerobic spore-formers can be isolated from fecal and i
Increasing Protein at the Expense of Carbohydrate in the Diet Down-Regulates Glucose Utilization as Glucose Sparing Effect in Rats  [PDF]
Magdalena Stepien,Claire Gaudichon,Gilles Fromentin,Patrick Even,Daniel Tomé,Dalila Azzout-Marniche
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0014664
Abstract: High protein (HP) diet could serve as a good strategy against obesity, provoking the changes in energy metabolic pathways. However, those modifications differ during a dietary adaptation. To better understand the mechanisms involved in effect of high protein diet (HP) on limiting adiposity in rats we studied in parallel the gene expression of enzymes involved in protein and energy metabolism and the profiles of nutrients oxidation. Eighty male Wistar rats were fed a normal protein diet (NP, 14% of protein) for one week, then either maintained on NP diet or assigned to a HP diet (50% of protein) for 1, 3, 6 and 14 days. mRNA levels of genes involved in carbohydrate and lipid metabolism were measured in liver, adipose tissues, kidney and muscles by real time PCR. Energy expenditure (EE) and substrate oxidation were measured by indirect calorimetry. Liver glycogen and plasma glucose and hormones were assayed. In liver, HP feeding 1) decreased mRNA encoding glycolysis enzymes (GK, L-PK) and lipogenesis enzymes(ACC, FAS), 2) increased mRNA encoding gluconeogenesis enzymes (PEPCK), 3) first lowered, then restored mRNA encoding glycogen synthesis enzyme (GS), 4) did not change mRNA encoding β-oxidation enzymes (CPT1, ACOX1, βHAD). Few changes were seen in other organs. In parallel, indirect calorimetry confirmed that following HP feeding, glucose oxidation was reduced and fat oxidation was stable, except during the 1st day of adaptation where lipid oxidation was increased. Finally, this study showed that plasma insulin was lowered and hepatic glucose uptake was decreased. Taken together, these results demonstrate that following HP feeding, CHO utilization was increased above the increase in carbohydrate intake while lipogenesis was decreased thus giving a potential explanation for the fat lowering effect of HP diets.
Effects of Dietary Carbohydrate-to-Lipid Ratio on the Growth Performance and Feed Utilization of Juvenile Turbot(Scophthalmus maximus) Effects of Dietary Carbohydrate-to-Lipid Ratio on the Growth Performance and Feed Utilization of Juvenile Turbot(Scophthalmus maximus)  [PDF]
MIAO Shuyan,NIE Qin,MIAO Huijun,ZHANG Wenbing,MAI Kangsen
- , 2016,
Abstract: A 9-week feeding trial was conducted to investigate the effects of dietary carbohydrate to lipid ratio(CHO:LIP) on the growth performance and feed utilization of juvenile turbot Scophthalmus maximus(initial body weight 8.75 g ± 0.04 g). Four isonitrogenous and isoenergetic low protein level(39%) diets were formulated with increasing ratios of dietary carbohydrate to lipid(2:18, 6:18, 18:12 and 28:6). A high protein level(50%) diet with the 2:12 ratio of carbohydrate to lipid was used as the control. Results showed that the survival rate, contents of moisture, crude protein and ash in muscle were not significantly affected by dietary treatments. With the dietary CHO:LIP ratio increased from 2:18 to 18:12, weight gain rate significantly increased(P < 0.05). Higher dietary CHO:LIP ratio(28:6) resulted in the significantly decreased weight gain rate(P < 0.05). Meanwhile, this treatment also resulted in the highest daily feed intake and liver glycogen content, as well as the lowest feed efficiency(P < 0.05). Muscle glycogen content in fish fed the diet with 2:12 or 2:18 CHO:LIP ratio was significantly lower than those fed with the other three diets(P < 0.05). The present results confirmed that the juvenile turbot can utilize carbohydrate. Furthermore, the appropriate ratio of dietary carbohydrate to lipid was important to the growth and feed utilization of turbot. The proper CHO:LIP ratio based on the growth performance in the present study was determined to be 18:12 when the dietary protein level was 39%
Evaluation of the Cornell Net Carbohydrate and Protein System (CNCPS) in predicting the nutrient utilization and milk production of buffaloes
D.L. Aquino,J.S. Botas
Italian Journal of Animal Science , 2010, DOI: 10.4081/ijas.2007.s2.465
Abstract: The Cornell Net Carbohydrate and Protein System was used to predict the nutrient utilization and milk production of buffaloes under complete confinement system of management. There were 243 lactation records involving the age of the animals, live weight, body condition score (BCS), milk production, % milk fat, % milk protein; climatic conditions and the actual feed ration. Simulation results showed that age, number of lactation, body weight and calving interval had no direct effect on the actual milk production and nutrient utilization of the dairy buffaloes. Significantly higher metabolizable energy (ME) and metabolizable protein (MP) allowable milk were predicted by the model compared to the actual milk production of the buffaloes. Using the actual ration, the model predicted 91 days for the buffaloes to gain one BCS while 70 days was needed when the CNCPS feed library is used. The model predicted significantly lower DMI (12.8 vs. I6kg/d) and forage intake (9.10 vs. I0.3 kg/d) with a difference of 21 % and 16 % than the actual ration. Significantly lower ME, (33.85 vs. 36.13 Mcal/ d) was supplied by the actual ration but on the contrary, the MP supply (1,655 vs. 1,556 g/d) was higher than the CNCPS feed library. Significantly higher ME, MP and mineral (Ca, P, and K) balances were observed from the two rations indicating that more nutrients were supplied than what is required by the dairy buffaloes. The estimated manure and urine excretions were not significantly affected by the model predictions.
Studies on Vigna mungo L. Effect of Processing on Carbohydrate Fractionation and Influence of Grain Starch on Protein Utilization in Albino Rats
Amer Jamil,Lubna Bashir,Hamid Yaqoob
Pakistan Journal of Biological Sciences , 1999,
Abstract: The effect of black gram starch on the utilization of casein was also tested in albino rats using PER, digestibility coefficient, biological value and net protein utilization as parameters. Soaking reduced the levels of sugars, starch and oligosaccharides but starch digestibility was improved significantly. Cooking increased the level of sugars while starch and verbascose content was decreased. Starch digestibility was also improved on cooking. Stachyose and raffinose contents were increased when unsoaked seeds were cooked, but decreased when the seeds were soaked before cooking. Germination decreased starch and oligosaccharide contents thereby raising the level of the soluble sugars. Starch digestibility was increased appreciably on germination. On cooking, the black gram starch promoted growth similar to corn starch as no difference was noticed in the parameters studied in albino rats.
Implications of various phosphoenolpyruvate-carbohydrate phosphotransferase system mutations on glycerol utilization and poly(3-hydroxybutyrate) accumulation in Ralstonia eutropha H16
Chlud Kaddor, Alexander Steinbüchel
AMB Express , 2011, DOI: 10.1186/2191-0855-1-16
Abstract: Biodiesel (fatty acid methyl esters) is currently beside ethanol the major renewable energy source for substitution of petroleum. During production of biodiesel glycerol occurs as a main by-product (about 10%, w/w), thus saturating the glycerol market. Due to the huge surplus of glycerol that lowers its value, it is important to enlarge the field of its application e.g. as substrate for microbial growth and production of biodegradable polymers which in turn reduces the high production costs of polyhydroxyalkanoates (PHA) in industrial fermentation processes.Ralstonia eutropha H16 serves as model organism to study the hydrogen-based chemolithoautotrophic metabolism and has a great potential in industrial applications because of its ability to produce different biodegradable thermoplastics (PHAs). R. eutropha is a non-pathogenic, Gram-negative, H2-oxidizing β-proteobacterium. The tripartite genome consists of two chromosomes and the megaplasmid pHG1, and its nucleotide sequence was published in 2006 and 2003, respectively (Schwartz et al. 2003; Pohlmann et al. 2006). Autotrophic CO2 fixation proceeds via the Calvin-Benson-Bassham (CBB) cycle. Organic carbon and energy sources for heterotrophic growth comprise sugar acids, fatty acids, alcohols, tricarboxylic acid cycle (TCC) intermediates and other compounds. The utilization of sugars is restricted to the amino sugar N-acetylglucosamine and to fructose. The latter is taken up by an ATP binding cassette (ABC)-type transporter (frcACB) and is then metabolized via the Entner-Doudoroff (ED) pathway (Gottschalk et al. 1964). The uptake of N-acetylglucosamine in R. eutropha is mediated by a sugar-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTSNag consisting of EINag-HPrNag-EIIANag [nagF] and EIIBCNag [nagE]) that functions independently from the two general components of the bacterial PEP-PTS, histidine phosphocarrier protein (HPr, ptsH) and enzyme I component (EI, ptsI). The PEP-PTS is widespread a
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