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Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (n = 24), root (n = 24), and fruit (n = 24) composite samples were subjected to DNA extraction and high-throughput 16SrRNA gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, Bacillaceae, Microbacteriaceae, Nocardioidaceae, Pseudomonadaceae, Rhodobacteraceae, and Sphingomonadaceae, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Enterobacteriaceae, Erythrobacteraceae, Flavobacteriaceae, Nocardioidaceae, Rhodobacteraceae, and Streptomycetaceae. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs.

Adaptations of eukaryotic cells to environmental changes are important for their survival. However, under some circumstances, microenvironmental changes promote that eukaryotic cells utilize a metabolic signature resembling a unicellular organism named the Warburg effect. Most cancer cells share the Warburg effect displaying lactic fermentation and high glucose uptake. The Warburg effect also induces a metabolic rewiring stimulating glutamine consumption and lipid synthesis, also considered cancer hallmarks. Amino acid metabolism alteration due to the Warburg effect increases plasma levels of proline and branched-chain amino acids in several cancer types. Proline and lipids are probably used as electron transfer molecules in carcinogenic cells. In addition, branched-chain amino acids fuel the Krebs cycle, protein synthesis, and signaling in cancer cells.This review covers how metabolomics studies describe changes in some metabolites and proteins associated with the Warburg effect and related metabolic pathways.In this review, we analyze the metabolic signature of the Warburg effect and related phenotypes and propose some Warburg effect-related metabolites and proteins (lactate, glucose uptake, glucose transporters, glutamine, branched-chain amino acids, proline, and some lipogenic enzymes) as promising cancer biomarkers.

The antioxidant phenotype caused by resveratrol has been recognized as a key piece in the health benefits exerted by this phytochemical in diseases related to aging. It has recently been proposed that a mitochondrial pro-oxidant mechanism could be the cause of resveratrol antioxidant properties. In this regard, the hypothesis that resveratrol impedes electron transport to complex III of the electron transport chain as its main target suggests that resveratrol could increase reactive oxygen species (ROS) generation through reverse electron transport or by the semiquinones formation. This idea also explains that cells respond to resveratrol oxidative damage, inducing their antioxidant systems. Moreover, resveratrol pro-oxidant properties could accelerate the aging process, according to the free radical theory of aging, which postulates that organism's age due to the accumulation of the harmful effects of ROS in cells. Nonetheless, there is no evidence linking the chronological lifespan (CLS) shorten occasioned by resveratrol with a pro-oxidant mechanism. Hence, this study aimed to evaluate whether resveratrol shortens the CLS of Saccharomyces cerevisiae due to a pro-oxidant activity. Herein, we provide evidence that supplementation with 100 μM of resveratrol at 5% glucose: (1) shortened the CLS of ctt1Δ and yap1Δ strains; (2) decreased ROS levels and increased the catalase activity in WT strain; (3) maintained unaffected the ROS levels and did not change the catalase activity in ctt1Δ strain; and (4) lessened the exponential growth of ctt1Δ strain, which was restored with the adding of reduced glutathione. These results indicate that resveratrol decreases CLS by a pro-oxidant mechanism.

Enterobacteriaceae is one of the most important bacterial groups within the Proteobacteria phylum. This bacterial group includes pathogens, commensal and beneficial populations. Numerous 16S rRNA gene PCR-based assays have been designed to analyze Enterobacteriaceae diversity and relative abundance, and, to the best of our knowledge, 16 primer pairs have been validated, published and used since 2003. Nonetheless, a comprehensive performance analysis of these primer sets has not yet been carried out. This information is of particular importance due to the recent taxonomic restructuration of Enterobacteriaceae into seven bacterial families. To overcome this lack of information, the identified collection of primer pairs (n = 16) was subjected to primer performance analysis using multiple bioinformatics tools. Herein it was revealed that, based on specificity and coverage of the 16S rRNA gene, these 16 primer sets could be divided into different categories: Enterobacterales-, multi-family-, multi-genus- and Enterobacteriaceae-specific primers. These results highlight the impact of taxonomy changes on performance of molecular assays and data interpretation. Moreover, they underline the urgent need to revise and update the molecular tools used for molecular microbial analyses.

Acidovorax avenae causes red stripe disease, which is characterised by red stripe and top rot symptoms in sugarcane (Saccharum spp. hybrids). The incidence of one or both these symptoms in the sugarcane fields was up to 30% in the Chiapas and Veracruz states of Mexico between 2015 and 2016. This study aimed to identify the causative agent of these symptoms and to determine the distribution and incidence of the disease in sugarcane-producing agroecological regions. Eleven bacterial isolates with phenotypic characteristics similar to those of A. avenae were isolated from the symptomatic tissue. Phylogenetic reconstruction based on the 16S rDNA sequence identified these 11 isolates as A. avenae with 99% identity. A. avenae infection was identified in three of the seven agroecological regions of Mexico (Cordoba-Gulf, Papaloapan-Gulf, and Southern region) with incidences ranging between 1 and 55%. The highest incidence of A. avenae infection was in the COLMEX 94-8 variety in the Cordoba-Gulf region (55%), whereas the lowest (1%) incidence was in the CP 72-2086 variety in the Papaloapan-Gulf region. The inoculation of these 11 strains resulted in the development of necrosis and wilting of the youngest leaves, dead of inoculated leave, and stem rot symptoms in the susceptible variety CP 72-2086. This is the first study to report the distribution and incidence of A. avenae in sugarcane plantations of Mexico.

The Crabtree effect molecular regulation comprehension could help to improve ethanol production with biotechnological purposes and a better understanding of cancer etiology due to its similarity with the Warburg effect. Snf1p/Hxk2p/Mig1p pathway has been linked with the transcriptional regulation of the hexose transporters and phenotypes associated with the Crabtree effect. Nevertheless, direct evidence linking the genetic control of the hexose transporters with modulation of the Crabtree effect phenotypes by the Snf1p/Hxk2p/Mig1p pathway is still lacking. In this sense, we provide evidence that SNF1 and HXK2 genes deletion affects exponential growth, mitochondrial respiration, and transcript levels of hexose transporters in a glucose-dependent manner. The Vmax of the hexose transporters with the high transcript levels was correlated positively with the exponential growth and negatively with the mitochondrial respiration. HXT2 gene transcript levels were the most affected by the deletion of the SNF1/HXK2/MIG1 pathway. Deleting the orthologous genes SNF1 and HXK2 in Kluyveromyces marxianus (Crabtree negative yeast) has an opposite effect compared to Saccharomyces cerevisiae in growth and mitochondrial respiration. Overall, these results indicate that the SNF1/HXK2/MIG1 pathway regulates transcript levels of the hexose transporters, which shows an association with the exponential growth and mitochondrial respiration in a glucose-dependent manner.

Storage of guava fruit cv ‘Media china’ at temperatures below 8 °C causes chilling injury associated with changes in cell membrane lipids. The aim of the present study was to evaluate the effects of two temperatures (4 and 10 °C) and three controlled atmospheres (air; 10 kPa O2; 5 kPa CO2 and 10 + 5 kPa of O2 and CO2) on microsomal lipid profiles in ripened fruit or fruit storage during three weeks. The study revealed that chilling injury is associated with a decrease in microsomal membrane volume and microsomal protein and phospholipids content (5%, 47% and 22%; respectively). Also, it was observed a decrease in Monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG), Phosphatidylinositol (PI), phosphatidic acid (PA), cardiolipin (CL) contents and a substitution of saturated fatty acids (FA) for unsaturated FA in the microsomal membrane. Importantly, it was found that storing guava fruit 'Media China' at 10 °C under 5 kPa CO2 reduced chilling injury prevalence and increased shelf life, suggesting that these storage conditions maintained membrane functionality. Overall, these results indicate that CI is associated to deep alterations in membrane lipids pathway.

The Crabtree effect occurs under high-glucose concentrations and is characterized by the increase of the growth and a decrease in mitochondrial respiration of yeasts. Regulation of the Crabtree effect could enhance ethanol production with biotechnological purposes and a better understanding of the etiology of cancer due to its similitude with the Warburg effect. Nonetheless, the conclusive molecular mechanism of the Crabtree effect is still on debate. The pathway Snf1p/Hxk2p/Mig1p has been linked with the transcriptional regulation of the hexose transporters and has also been identified in the modulation of phenotypes related to the Crabtree effect. Nevertheless, it has not been directly identified the genetic regulation of the hexose transporters with modulation of the Crabtree effect phenotypes by Snf1p/Hxk2p/Mig1p pathway. In this sense, we provide evidence that the deletion of the SNF1 and HXK2 genes affects the exponential growth, mitochondrial respiration, and the transcription of hexose transporters in a glucose-dependent manner in Saccharomyces cerevisiae. The Vmax of the main hexose transporters transcribed showed a positive correlation with the exponential growth and a negative correlation with the mitochondrial respiration. Transcription of the gene HXT2 was the most affected by the deletion of the pathway SNF1/HXK2/MIG1. Deletion of the orthologous genes SNF1 and HXK2 in the Crabtree negative yeast, K. marxianus, has a differential effect in exponential growth and mitochondrial respiration in comparison with S. cerevisiae. Overall, these results indicate that the SNF1/HXK2/MIG1 pathway transcriptionally regulates the hexose transporters having an influence in the exponential growth and mitochondrial respiration in a glucose-dependent manner.

Background: Differences in gut microbiota composition have been associated with obesity and metabolic alterations in children. The aim of this study was to analyze the abundance of the main bacterial families of the gut among children according to their body composition and metabolic markers. Methods: A cross-sectional study was conducted with 93 school-aged children (8.4 ± 1.6 years old). Anthropometric and body composition variables were measured and a blood sample was collected to determine glucose, insulin, lipid profile, C-reactive protein, leptin, and cytokines [interleukin 6, interleukin 10 (IL-10), tumor necrosis factor α (TNFα)]. DNA was extracted from stool samples and the abundance of bacterial families (Bacteroidaceae-Porphyromonadaceae-Prevotellaceae, Lactobacillaceae, Enterococcaceae, and Lachnospiraceae-Ruminococcaceae) was determined by qPCR assays. Results: Children with obesity and high waist/height ratio had lower Bacteroidaceae-Porphyromonadaceae-Prevotellaceae and higher abundance of Lactobacillaceae when compared with normal-weight children. TNFα was negatively associated and IL-10 was positively associated with Bacteroidaceae-Porphyromonadaceae-Prevotellaceae. Triglycerides showed a positive relationship with Lachnospiraceae-Ruminococcaceae whereas high-density lipoprotein-cholesterol was negatively associated with Lactobacillaceae. Conclusion: In rural Mexican school-aged children, a low abundance of Bacteroidaceae-Porphyromonadaceae-Prevotellaceae and a high abundance of Lactobacillaceae are associated with obesity and metabolic disturbances.

Poultry meat deterioration is caused by environmental conditions, as well as proliferation of different bacterial groups, and their interactions. It has been proposed that meat spoilage involves two bacterial groups: one group that initiates the deterioration process, known as specific spoilage organisms (SSOs), and the other known as spoilage associated organisms (SAOs) which represents all bacteria groups recovered from meat samples before, during, and after the spoilage process. Numerous studies have characterized the diversity of chicken meat SAOs, nonetheless, the identification of the SSOs remains a long-standing question. Based on recent genomic studies, it is suggested that the SSOs should possess an extensive genome size to survive and proliferate in raw meat, a cold, complex, and hostile environment. To evaluate this hypothesis, we performed comparative genomic analyses in members of the meat microbiota to identify microorganisms with extensive genome size and ability to cause chicken meat spoilage. Our studies show that members of the Pseudomonadaceae family have evolved numerous biological features such as large genomic size, slow-growing potential, low 16S rRNA copy number, psychrotrophic, and oligotrophic metabolism to initiate the spoilage of poultry meat. Moreover, inoculation experiments corroborated that these biological traits are associated with the potential to cause chicken meat deterioration. Together, these results provide new insights into the identification of SSO. Further studies are in progress to elucidate the impact of the SSO on meat quality and microbiota diversity.

Red Drupelet Reversion (RDR) in blackberry is a physiological disorder where numerous fruit drupelets regress to red from black color during post-harvest handling. The specific mechanism causing RDR is still unknown; however, numerous studies have suggested that anthocyanin contents could be involved in this phenomenon. Recently, it has been reported that RDR in cultivars ‘Ouachita’, ‘Triple Crown’ and ‘Apache’ could be associated with a reduction (56–63 %) in anthocyanin contents after 24 h of storage. Interestingly, other studies have observed that RDR could be linked to fruit mechanical damage during transportation; specifically, due to fruit vibration (10 Hz and acceleration of 0.5 g). Based on this notion, the main goal of the present study was to establish a fruit vibration model to evaluate the relationship between mechanical damage, anthocyanin content and RDR appearance. Blackberry clamshells cv. ‘APF-122′ (170 g) were subjected to vibration (10 Hz and acceleration of 0.5 g) during 1, 3, and 5 min to induce RDR. Color and anthocyanin content were evaluated at 0, 24, 48, 72, 96 and 120 h of storage at 1 °C. RDR was observed immediately after fruit was subjected to 5 min vibration; however, no changes were observed in anthocyanin concentration. Multiphoton microscopy revealed that reverted fruit possessed anthocyanins dispersed within the cells; in contrast, no reverted fruit held anthocyanins in spherical agglomerates. Also, it was observed that anthocyanin fluorescence emission was reduced in reverted drupelet, suggesting changes in intermolecular interactions between anthocyanins. Interestingly, a reduction in anthocyanin concentration in reverted fruit was observed only after 72 h of storage; indicating that anthocyanin content may not be involved in the RDR process. Taken together, these results suggest that blackberry color reversion could be associated with changes in anthocyanin intermolecular interactions. Further studies are in progress to corroborate this hypothesis.

A broad range of health benefits have been attributed to resveratrol (RSV) supplementation in mammalian systems, including the increases in longevity. Nonetheless, despite the growing number of studies performed with RSV, the molecular mechanism by which it acts still remains unknown. Recently, it has been proposed that inhibition of the oxidative phosphorylation activity is the principal mechanism of RSV action. This mechanism suggests that RSV might induce mitochondrial dysfunction resulting in oxidative damage to cells with a concomitant decrease of cell viability and cellular life span. To prove this hypothesis, the chronological life span (CLS) of Saccharomyces cerevisiae was studied as it is accepted as an important model of oxidative damage and aging. In addition, oxygen consumption, mitochondrial membrane potential, and hydrogen peroxide (H2O2) release were measured in order to determine the extent of mitochondrial dysfunction. The results demonstrated that the supplementation of S. cerevisiae cultures with 100 μM RSV decreased CLS in a glucose-dependent manner. At high-level glucose, RSV supplementation increased oxygen consumption during the exponential phase yeast cultures, but inhibited it in chronologically aged yeast cultures. However, at low-level glucose, oxygen consumption was inhibited in yeast cultures in the exponential phase as well as in chronologically aged cultures. Furthermore, RSV supplementation promoted the polarization of the mitochondrial membrane in both cultures. Finally, RSV decreased the release of H2O2 with high-level glucose and increased it at low-level glucose. Altogether, this data supports the hypothesis that RSV supplementation decreases CLS as a result of mitochondrial dysfunction and this phenotype occurs in a glucose-dependent manner.

The aim of the present study was to evaluate extractable (EPP), non-extractable polyphenols (NEPP) and organic acid in Roselle by-product, as well as its potential health beneficial effects in obesity control and their complication in rats fed with high caloric diet. Roselle by-product showed a higher content of dietary fiber and NEPP than Roselle calix, which was was a better source of EPP (P .05). The UPLC-QTOF MS

Background: Salmonella surveillance relies on invA polymerase chain reaction (PCR) assays for the rapid detection of Salmonella; however, false-positive results have been reported using this method. Objectives: To evaluate the performance and specificity of the published and validated PCR protocols targeting invA gene for the detection of Salmonella. Methods: The performance and specificity of 11 different PCR primer sets were evaluated using Salmonella type strains and Citrobacter spp., Escherichia coli and Serratia spp. isolates recovered during a Salmonella surveillance program. Results: It was revealed that the published PCR protocols using validated primers targeting invA and 16S rRNA genes generated false-positive signals. Importantly, a protocol targeting the ttrA/C genes was able to discriminate Salmonella and non-Salmonella isolates. Conclusions: Detection of Salmonella spp. by means of invA PCR amplification is not reliable. In fact, false-positive results are commonly obtained from Citrobacter, E. coli and Serratia isolates. It is recommended to use other loci, such as ttrA/C genes, for the accurate and reliable detection of Salmonella.

The aim of the present study was to evaluate extractable (EPP), non-extractable polyphenols (NEPP) and organic acid in Roselle by-product, as well as its potential health beneficial effects in obesity control and their complication in rats fed with high caloric diet. Roselle by-product showed a higher content of dietary fiber and NEPP than Roselle calix, which was was a better source of EPP (P

Background Global public concerns about “industrial agriculture” have widely disseminated amongst consumers the myth that chickens are fed growth hormones to produce meat more efficiently. This misleading information regarding the use of hormones in chickens is now a growing health concern among consumer groups. Scope and Approach Worldwide, the poultry industry relies on science and technology to define new strategies to improve the health, welfare and performance of animals in production. In this report, we performed a detailed analysis of the poultry science literature and provide the scientific bases explaining why chickens are not feed hormones. Key Findings and Conclusions The use of growth hormones in poultry meat production does not occur because: i) they are too expensive to be used in chickens, ii) they do not promote growth in poultry and iii) their use is illegal in many countries. Therefore, health providers, policy makers, food professionals, consumer advocates, food producers and veterinarians can use this information to educate consumers and eliminate negative concerns related to hormone use in the poultry industry.

The metabolic effects induced by resveratrol have been associated mainly with the consumption of high-calorie diets; however, its effects with standard or low-calorie diets remain unclear. To better understand the interactions between resveratrol and cellular energy levels, we used Saccharomyces cerevisiae as a model. Herein it is shown that resveratrol: (a) decreased cell viability in an energy-dependent manner; (b) lessening of cell viability occurred specifically when cells were under cellular respiration; and (c) inhibition of oxygen consumption in state 4 occurred at low and standard energy levels, whereas at high energy levels oxygen consumption was promoted. These findings indicate that the effects of resveratrol are dependent on the cellular energy status and linked to metabolic respiration. Importantly, our study also revealed that S. cerevisiae is a suitable and useful model to elucidate the molecular targets of resveratrol under different nutritional statuses. Copyright © 2016 John Wiley & Sons, Ltd.

Worldwide, chicken meat is considered one of the main sources of Salmonella enterica in humans. To protect consumers from this foodborne pathogen, international health authorities recommend the establishment of continuous Salmonella surveillance programs in meat. However, these programs are scarce in many world regions; thus, the goal of the present study was to perform a longitudinal surveillance of S. enterica in chicken meat in Mexico. A total of 1160 samples were collected and analyzed monthly from 2016 to 2018 in ten chicken meat retailers (supermarkets and wet markets) located in central Mexico. The isolation and identification of S. enterica was carried out using conventional and molecular methods. Overall, S. enterica was recovered from 18.1% (210/1160) of the chicken meat samples. Remarkably, during the three years of evaluation, S. enterica was more prevalent (P < 0.0001) in supermarkets (27.2%, 158/580) than in wet markets (9.0%, 52/580). The study was 3.8 times more likely (odds ratio = 3.8, P < 0.0001) to recover S. enterica from supermarkets than wet markets. Additionally, a higher prevalence (P < 0.05) of this pathogen was observed during the spring, summer, autumn, and winter in supermarkets compared with wet markets. Moreover, the recovery rate of S. enterica from supermarkets showed a gradual increase from 20.78% to 42% (P < 0.0001) from 2016 to 2018. Interestingly, no correlation (P > 0.05) was observed between the S. enterica recovery rate in chicken meat and reported cases of Salmonella infections in humans. Higher levels of S. enterica in chicken meat retailed in supermarkets are not unusual; this phenomenon has also been reported in some European and Asian countries. Together, these results uncover an important health threat that needs to be urgently addressed by poultry meat producers and retailers.

Due to recent outbreaks of cyclosporiasis associated with consumption of fresh berries, producers are demanding modern microbiological tools for the rapid and accurate identification of the human pathogen Cyclospora cayetanensis in berries and environmental samples. The aim of the present work was to develop a molecular tool based on a PCR approach for the rapid and accurate detection of C. cayetanensis. A nested PCR assay was validated for the amplification of a 294 bp size region of the 18S rRNA gene from C. cayetanensis. The limit of detection for the nested PCR assay was validated using 48 berry samples spiked with ~0, 10, 100, and 1000 oocyst per gram of sample. With this assay, it was possible to detect as few as 1 oocyst per gram of berry, in a 50 g sample. Sanger DNA sequencing and phylogenetic analysis were carried out to confirm the presence of C. cayetanensis in berry (n = 17) and soil (n = 5) samples. The phylogenetic analysis revealed that the C. cayetanensis sequences obtained from Mexico clustered within a group recovered from China, Peru, Guatemala-Haiti, and Japan. The PCR protocol designed in the present study could be an important tool for the rapid and accurate detection of this human pathogen in environmental and food samples.

An important priority of poultry producers is to guarantee animal welfare during animal production; however, broilers are exposed to unavoidable chronic stress (also known as allostasis) when they are captured, caged, and transported to the processing plant. This antemortem management causes allostatic load, animal injuries, and poor carcass quality. The aim of the present study was to evaluate the effects of an allostatic modulator (AM) on antemortem stress by measuring the appearance and microbiological quality of broiler carcasses. The AM consisted of a liquid formula containing ascorbic acid, acetyl salicylic acid, and electrolytes, administered orally 48 h before shipment to the processing plant. A total of 600 chickens (49-days-old) were used under a factorial arrangement 2 × 2 × 2 [2 commercial hybrid lines, 2 feed withdrawal programs (10 and 16 h), and 2 water treatments (control and AM)]. Each treatment included 25 chickens per pen and was carried out in triplicate. The broilers were shipped, slaughtered, and processed in a commercial processing plant where carcass defects (bruises and broken bones caused by antemortem management), crop pH, and carcass bacterial counts were evaluated in all experimental groups. Broilers under AM treatment showed a reduction in carcass defects (P = 0.015), crop pH (P = 0.0001), coliforms counts (P = 0.014), and total aerobic mesophilic bacteria (P = 0.0001) when compared to the control treatment. The present study indicates that the AM can be used to improve carcass quality in broilers. Our study provides a novel and economic alternative to reduce the allostatic load in broilers.

Several studies have observed that use of a conventional PCR protocol with primers LM1 and LM2 for the identification of the hlyA gene of Listeria monocytogenes generates non-specific PCR amplifications and false positives. For this reason, in this study we provide a modified PCR protocol that improves the specificity of the results obtained with LM1 and LM2 primers.

Reduced susceptibility to sporadic colorectal cancer in native Africans (NA) is correlated with low consumption of animal products and greater microbial production of colonic methane. In this context, two hydrogenotrophic microbial groups are of interest, methanogenic Archaea (MA) utilizing H2 to produce methane and sulfate-reducing bacteria (SRB) generating hydrogen sulfide, which has been linked with chronic inflammatory disorders of the colon. In the present study, stool samples from NA, consuming a diet high in resistant starch and low in animal products, and from African Americans (AA) and European Americans (EA), both consuming a typical Western diet, were examined for genetic diversity and structure of Archaea, MA and SRB communities. In general, a greater proportion of NA than AA and EA harboured the full range of targeted hydrogenotrophic groups. Terminal restriction fragment length polymorphism analysis of 16S rRNA genes and specific functional genes, combined with multivariate statistical analyses, revealed that NA harboured more diverse and different Archaea and MA populations than AA and EA. Also, NA harboured significantly distinct SRB populations compared with AA and EA. Taken together, these data are consistent with diet selecting for distinct hydrogenotrophic microbiota.

Inflammatory bowel disease (IBD) is thought to occur in genetically susceptible individuals. However, environmental factors, potentially including shifts in commensal microbiota, are also required to trigger disease. This review discusses some of the recent discoveries in host susceptibility and interaction with the microbial environment, and pinpoints key areas for advancement in our understanding of IBD pathogenesis.Meta-analyses of genome-wide association studies have uncovered many new exciting genes associated with susceptibility loci for IBD. In addition, improved methods to analyze the commensal microbiota pave the way to better define dysbiosis and its potential role in disease. Lastly, identification of viral triggers in experimental systems suggests a potential role for viral infection in IBD.Understanding the precise microbial and immune triggers of IBD in a genetic context will hopefully lead to a better understanding of the pathogenesis of this disease and the discovery of novel therapeutic approaches, including vaccination against specific viruses.

A trial was conducted to evaluate the influence of dietary Aspergillus Meal (AM) prebiotic on intestinal development, morphology in turkey poults. Day-old Nicholas poults (n = 100) were randomly assigned to two groups. Poults in each group were divided and placed in floor pens with 50 poults each. One group served as a control and received a ration containing no added AM prebiotic. Poults in the treatment group were provided a ration supplemented with 0.2% AM prebiotic. Each dietary regimen and water were provided ad libitum to 30 days of age. Poults were humanely killed by CO2 inhalation and specimens of duodenum and distal ileum were collected at 10, 20 and 30 days. Histology sections were cut (5 μm) and stained with haematoxylin and eosin and combinations of either of periodic acid-Schiff with alcian blue, or high iron diamine with alcian blue stains to evaluate 20 intact villi on each section. The morphometric variables analyzed included villi height, villi surface area and crypt depth. In addition, goblet cells, classified as neutral, acidic or sulpho mucin cells, respectively, were quantitative for each treatment group. At all times of evaluation, AM prebiotic significantly increased the number of acid mucin cells in the duodenum, neutral mucin cells in the ileum and sulpho mucin cells in the duodenum and ileum. Villi height and villi surface area of both duodenum and ileum were significantly increased at days 10 and 30 compared to control. The present study suggest that AM prebiotic has an impact on the mucosal architecture and goblet cells proliferation in the duodenum and ileum of neonate poults.

Supplementation of infant formulas with prebiotic ingredients continues the effort to mimic functional properties of human milk. In this double-blind, controlled, 28-day study, healthy term infants received control formula (control group; n = 25) or control formula supplemented with polydextrose (PDX) and galactooligosaccharide (GOS) (4 g/liter) (PG4 group; n = 27) or with PDX, GOS, and lactulose (LOS) (either 4 g/liter [PGL4 group; n = 27] or 8 g/liter [PGL8 group; n = 25]). A parallel breast-fed group (BF group) ( n = 30) was included. Stool characteristics, formula tolerance, and adverse events were monitored. Fecal bacterial subpopulations were evaluated by culture-based selective enumeration ( Enterobacteriaceae ), quantitative real-time PCR ( Clostridium clusters I, XI, and XIV, Lactobacillus , and Bifidobacterium ), and fluorescence in situ hybridization (FISH) ( Bifidobacterium ). Fecal bacterial community profiles were examined by using 16S rRNA gene PCR-denaturing gradient gel electrophoresis. The daily stool consistency was significantly softer or looser in the BF group than in all of the groups that received formula. The formulas were well tolerated, and the incidences of adverse events did not differ among feeding groups. Few significant changes in bacterial subpopulations were observed at any time point. The bacterial communities were stable; individual profiles tended to cluster by subject rather than by group. Post hoc analysis, however, demonstrated that the bacterial community profiles for subjects in the BF, PG4, PGL4, and PGL8 groups that first received formula at a younger age were less stable than the profiles for subjects in the same groups that received formula at an older age, but there was no difference for the control group. These data indicate that formulas containing PDX, GOS, and LOS blends are more likely to influence gut microbes when administration is begun in early infancy and justify further investigation of the age-related effects of these blends on fecal microbiota.

The human genome is approximately 3 billion basepairs long. An estimated 2--3% of DNA codes for genes; the remaining 97--98% is noncoding DNA [11]. Although the noncoding regions in DNA were once called "junk DNA" (with the assumption that these regions were not serving a purpose) it is now understood that within noncoding DNA are functional regions that affect the expression of genes [34]. However, we are still far from understanding the breadth of function in the noncoding regions, and identification of functional elements is a complex problem, difficult to study in vitro because of the enormous number of possibilities. In this project, we are searching in silico for candidate functional elements in noncoding DNA. These candidates will then be studied at the bench to assess function. Our guiding principle is that regions of noncoding DNA that have been conserved across evolutionary time are good candidates as functional elements; we use a genetic algorithms approach to search for these candidate elements, called motifs. Our system is thus called GAMI, Genetic Algorithms for Motif Inference. GAMI has been demonstrated to be a successful approach to this task, as will be described below.

Resistant maltodextrin has been shown to increase fecal bulk by resisting digestion and being partially fermented by colonic bacteria to short-chain fatty acids (SCFA). The objective of this experiment was to determine potential prebiotic effects, gastrointestinal tolerance, and fecal characteristics of free-living humans fed a novel resistant maltodextrin or a normal maltodextrin control.Subjects (n = 38) were enrolled in a randomized, double-blind study where they were assigned to one of three daily treatments: 15 g maltodextrin; 7.5 g maltodextrin plus 7.5 g resistant maltodextrin (Fibersol-2; Matsutani Chemical Company, Hyogo, Japan); and 15 g resistant maltodextrin. The experiment lasted 7 wk and consisted of a 2 wk baseline period, a 3 wk treatment period, and a 2 wk washout period. During wk 3 to 5 (treatment period), subjects consumed their assigned treatments.Resistant maltodextrin supplementation tended to increase (p = 0.12) fecal Bifidobacterium populations during the treatment period, altered (p0.05) bacterial populations from baseline to treatment, and resulted in very minor effects in gastrointestinal tolerance. There was a shift (p0.05) in molar proportions of SCFA towards butyrate, the preferred energy substrate of colonocytes.Resistant maltodextrin supplementation was well tolerated, resulted in favorable fermentation characteristics in the large bowel, and also resulted in a change in bacterial populations.

The gastrointestinal tract is a dynamic ecosystem composed of an organized matrix of host eukaryotic cells, including a fully functional immune system, and numerous microbial habitats normally colonized by a diverse array of microbes. Recent analyses of the gastrointestinal microbiota by use of molecular-based methods indicate that bacterial populations vary substantially among but appear relatively stable within individuals. These observations raise many important questions about the role of the normal microbiota in the development of both the innate and the adaptive immune systems of the host and about how perturbations in this relationship may contribute to various intestinal or immunologic disorders. Here, 3 critical issues pertaining to the intestinal microbiota are briefly reviewed: what are the microbes, where are the microbes, and what controls the composition of the microbiota.

In previous work, we presented GAMI [1], an approach to motif inference that uses a genetic algorithms search. GAMI is designed specifically to find putative conserved regulatory motifs in noncoding regions of divergent species, and is designed to allow for analysis of long nucleotide sequences. In this work, we compare GAMI's performance when run with its original fitness function (a simple count of the number of matches) and when run with information content, as well as several variations on these metrics. Results indicate that information content does not identify highly conserved regions, and thus is not the appropriate metric for this task, while variations on information content as well as the original metric succeed in identifying putative conserved regions.

The metabolic effects induced by resveratrol have been associated mainly with the consumption of high-calorie diets; however, its effects with standard or low-calorie diets remain unclear. To better understand the interactions between resveratrol and cellular energy levels, we used Saccharomyces cerevisiae as a model. Herein it is shown that resveratrol: (a) decreased cell viability in an energy-dependent manner; (b) lessening of cell viability occurred specifically when cells were under cellular respiration; and (c) inhibition of oxygen consumption in state 4 occurred at low and standard energy levels, whereas at high energy levels oxygen consumption was promoted. These findings indicate that the effects of resveratrol are dependent on the cellular energy status and linked to metabolic respiration. Importantly, our study also revealed that S. cerevisiae is a suitable and useful model to elucidate the molecular targets of resveratrol under different nutritional statuses. Copyright © 2016 John WileySons, Ltd.

The intestinal mucosa represents the most active defense barrier against the continuous challenge of food antigens and pathogenic microorganisms present in the intestinal lumen. Protection against harmful agents is conferred by factors such as gastric acid, peristalsis, mucus, intestinal proteolysis, and the intestinal biota. The establishment of beneficial bacterial communities and metabolites from these complex ecosystems has varying consequences for host health. This hypothesis has led to the introduction of novel therapeutic interventions based on the consumption of beneficial bacterial cultures. Mechanisms by which probiotic bacteria affect the microecology of the gastrointestinal tract are not well understood, but at least three mechanisms of action have been proposed: production/presence of antibacterial substances (e.g., bacteriocins or colicins), modulation of immune responses and specific competition for adhesion receptors to intestinal epithelium. The rapid establishment of bacterial communities has been thought to be essential for the prevention of colonization by pathogenic bacteria. Some animal models suggest that the reduction in bacterial translocation in neonatal animals could be associated with an increase in intestinal bacterial communities and bacteriocin-like inhibitory substances produced by these species. This review emphasizes the role of the intestinal microbiota in the reduction of the gastrointestinal infections and draws heavily on studies in poultry.

Currently, standard protocols for microbial DNA extraction from intestinal tissues do not exist. We assessed the efficiency of a commercial kit with and without mechanical disruption. Better quality DNA was obtained without mechanical disruption. Thus, it appears that bead-beating is not required for efficient microbial DNA extraction from intestinal biopsies.

Reduced susceptibility to sporadic colorectal cancer in native Africans (NA) is correlated with low consumption of animal products and greater microbial production of colonic methane. In this context, two hydrogenotrophic microbial groups are of interest, methanogenic Archaea (MA) utilizing H2 to produce methane and sulfate-reducing bacteria (SRB) generating hydrogen sulfide, which has been linked with chronic inflammatory disorders of the colon. In the present study, stool samples from NA, consuming a diet high in resistant starch and low in animal products, and from African Americans (AA) and European Americans (EA), both consuming a typical Western diet, were examined for genetic diversity and structure of Archaea, MA and SRB communities. In general, a greater proportion of NA than AA and EA harboured the full range of targeted hydrogenotrophic groups. Terminal restriction fragment length polymorphism analysis of 16S rRNA genes and specific functional genes, combined with multivariate statistical analyses, revealed that NA harboured more diverse and different Archaea and MA populations than AA and EA. Also, NA harboured significantly distinct SRB populations compared with AA and EA. Taken together, these data are consistent with diet selecting for distinct hydrogenotrophic microbiota.

Background The small intestinal epithelium is highly sensitive to radiation and is a major site of injury during radiation therapy and environmental overexposure. Objective To examine probiotic bacteria as potential radioprotective agents in the intestine. Methods 8-week-old C57BL/6 wild-type or knockout mice were administered probiotic by gavage for 3 days before 12 Gy whole body radiation. The intestine was evaluated for cell-positional apoptosis (6 h) and crypt survival (84 h). Results Gavage of 5×107 Lactobacillus rhamnosus GG (LGG) improved crypt survival about twofold (p

Hydrogenotrophic microbiota have a significant impact on colonic health; however, little is known about their diversity and ecology in situ. Here, molecular-based methods and multivariate analyses were used to examine the abundance and diversity of mucosa-associated hydrogenotrophic microbes in 90 biopsies collected from right colon, left colon and rectum of 25 healthy subjects. Functional genes of all three hydrogenotrophic groups were detected in at least one colonic region of all subjects. Methanogenic archaea (MA) constituted approximately one half of the hydrogenotrophic microbiota in each colonic region. Sulfate-reducing bacteria (SRB) were more abundant than acetogens in right colon, while acetogens were more abundant than SRB in left colon and rectum. MA genotypes exhibited low diversity, whereas SRB genotypes were diverse and generally similar across the three regions within subject but significantly variable among subjects. Multivariate cluster analysis defined subject-specific patterns for the diversity of SRB genotypes; however, neither subject- nor region-specific clusters were observed for the abundance of hydrogenotrophic functional genes. Sequence analyses of functional gene clones revealed that mucosa-associated SRB were phylogenetically related to Desulfovibrio piger, Desulfovibrio desulfuricans and Bilophila wadsworthia; whereas MA were related to Methanobrevibacter spp., Mb. smithii and the order Methanomicrobiales. Together these data demonstrate for the first time that the human colonic mucosa is persistently colonized by all three groups of hydrogenotrophic microbes, which exhibit segmental and interindividual variation in abundance and diversity.

The colonic mucus layer is comprised primarily of acidomucins, which provide viscous properties and can be broadly classified into sialomucins or sulfomucins based on the presence of terminating sialic acid or sulfate groups. Differences in acidomucin chemotypes have been observed in diseases such as colorectal cancer and inflammatory bowel disease, and variation in sialo- and sulfomucin content may influence microbial colonization. For example, sulfate derived from sulfomucin degradation may promote the colonization of sulfate-reducing bacteria (SRB), which through sulfate respiration generate the genotoxic gas hydrogen sulfide. Here, paired biopsies from right colon, left colon, and rectum of 20 subjects undergoing routine screening colonoscopies were collected to enable parallel histochemical and microbiological studies. Goblet cell sialo- and sulfomucins in each biopsy were distinguished histochemically and quantified. Quantitative PCR and multivariate analyses were used to examine the abundance of hydrogenotrophic microbial groups and SRB genera relative to acidomucin profiles. Regional variation was observed in sialomucins and sulfomucins with the greatest abundance of each found in the rectum. Mucin composition did not appear to influence the abundance of SRB or other hydrogenotrophic microbiota but correlated with the composition of different SRB genera. A higher sulfomucin proportion correlated with higher quantities of Desulfobacter, Desulfobulbus and Desulfotomaculum, relative to the predominant Desulfovibrio genus. Thus, acidomucin composition may influence bacterial sulfate respiration in the human colon, which may in turn impact mucosal homeostasis. These results stress the need to consider mucus characteristics in the context of studies of the microbiome that target intestinal diseases.

A longstanding hypothesis in intestinal microbial ecology is that autochthonous microbes (resident) play a role that is distinct from allochthonous microbes (transient microbes in the fecal stream). A challenge has been to identify this pool of microbes. We used laser capture microdissection to collect microbes from the mouse ascending colon. This area contains transverse folds that mimic human intestinal folds and contains a distinct population of intestinal microbes that is associated with the mucosa. Our analysis of bacterial 16S rRNA genes showed that this area was enriched for Lachnospiraceae and Ruminococcaceae. In this addendum, we further compare this community to studies of mucosa-associated microbes in humans. This analysis reveals common phylogenetic groups of bacteria that are present in both mouse and human. However, we found microorganisms at the genus and species levels including Faecalibacterium prausnitzii which appears to be specific for humans. We propose that that examination of the mucosa-associated microbes in wild type and genetically modified mice will be a valuable component to define host microbial interactions that are essential for homeostasis.