Preterm pigs show many signs of immaturity that are characteristic of preterm infants. In preterm infants, the cerebellum grows particularly rapid and hypoplasia and cellular lesions are associated with motor dysfunction and cognitive deficits. We hypothesized that functional brain delays observed in preterm pigs would be paralleled by both structural and molecular differences in the cerebellum relative to term born piglets. Cerebella were collected from term (n = 56) and preterm (90% gestation, n = 112) pigs at 0, 5, and 26 days after birth for stereological volume estimations, large-scale qPCR gene expression analyses (selected neurodevelopmental genes) and western blot protein expression analysis (Sonic Hedgehog pathway). Memory and learning was tested using a T-maze, documenting that preterm pigs showed delayed learning. Preterm pigs also showed reduced volume of both white and gray matter at all three ages but the proportion of white matter increased postnatally, relative to term pigs. Early initiation of enteral nutrition had limited structural or molecular effects. The Sonic Hedgehog pathway was unaffected by preterm birth. Few differences in expression of the selected genes were found, except consistently higher mRNA levels of Midkine, p75, and Neurotrophic factor 3 in the preterm cerebellum postnatally, probably reflecting an adaptive response to preterm birth. Pig cerebellar development appears more affected by postconceptional age than by environmental factors at birth or postnatally. Compensatory mechanisms following preterm birth may include faster white matter growth and increased expression of selected genes for neurotrophic factors and regulation of angiogenesis. While the pig cerebellum is immature in 90% gestation preterm pigs, it appears relatively mature and resilient toward environmental factors.

Background: Evidence suggests that early life infections, presence of older siblings and furred pets in the household affect the risk of developing allergic diseases through altered microbial exposure. Recently, low gut microbial diversity during infancy has also been linked with later development of allergies. We investigated whether presence of older siblings, furred pets and early life infections affected gut microbial communities at 9 and 18 months of age and whether these differences were associated with the cumulative prevalence of atopic symptoms of eczema and asthmatic bronchitis at 3 years of age. Bacterial compositions and diversity indices were determined in fecal samples collected from 114 infants in the SKOT I cohort at age 9 and 18 months by 16S rRNA gene sequencing. These were compared to the presence of older siblings, furred pets and early life infections and the cumulative prevalence of diagnosed asthmatic bronchitis and self-reported eczema at 3 years of age. Results: The number of older siblings correlated positively with bacterial diversity (p = 0.030), diversity of the phyla Firmicutes (p = 0.013) and Bacteroidetes (p = 0.004) and bacterial richness (p = 0.006) at 18 months. Further, having older siblings was associated with increased relative abundance of several bacterial taxa at both 9 and 18 months of age. Compared to the effect of having siblings, presence of household furred pets and early life infections had less pronounced effects on the gut microbiota. Gut microbiota characteristics were not significantly associated with cumulative occurrence of eczema and asthmatic bronchitis during the first 3 years of life. Conclusions: Presence of older siblings is associated with increased gut microbial diversity and richness during early childhood, which could contribute to the substantiation of the hygiene hypothesis. However, no associations were found between gut microbiota and atopic symptoms of eczema and asthmatic bronchitis during early childhood and thus further studies are required to elucidate whether sibling-associated gut microbial changes influence development of allergies later in childhood.

To assess the microbial influence on postnatal hematopoiesis, we examined the role of early life microbial colonization on the composition of leukocyte subsets in the neonatal spleen. A high number of CD11b(+)Gr-1(+) splenocytes present perinatally was sustained for a longer period in conventionally colonized (CONV) mice than in mono-colonized (MC) and germfree (GF) mice, and the CD4(+) T cell population established faster in CONV mice. At the day of birth, compared to GF mice, the expression of Cxcl2 was up-regulated and Arg1 down-regulated in livers of CONV mice. This coincided with lower abundance of polylobed cells in the liver of CONV mice. An earlier peak in the expression of the genes Tjp1, Cdh1, and JamA in intestinal epithelial cells of CONV mice indicated an accelerated closure of the epithelial barrier. In conclusion, we have identified an important microbiota-dependent neonatal hematopoietic event, which we suggest impacts the subsequent development of the T cell population in the murine spleen.

ABSTRACT Fecal samples were obtained from a cohort of 330 healthy Danish infants at 9, 18, and 36 months after birth, enabling characterization of interbacterial relationships by use of quantitative PCR targeting 31 selected bacterial 16S rRNA gene targets representing different phylogenetic levels. Nutritional parameters and measures of growth and body composition were determined and investigated in relation to the observed development in microbiota composition. We found that significant changes in the gut microbiota occurred, particularly from age 9 to 18 months, when cessation of breastfeeding and introduction of a complementary feeding induce replacement of a microbiota characterized by lactobacilli, bifidobacteria, and Enterobacteriaceae with a microbiota dominated by Clostridium spp. and Bacteroides spp. Classification of samples by a proxy enterotype based on the relative levels of Bacteroides spp. and Prevotella spp. showed that enterotype establishment occurs between 9 and 36 months. Thirty percent of the individuals shifted enterotype between 18 and 36 months. The composition of the microbiota was most pronouncedly influenced by the time of cessation of breastfeeding. From 9 to 18 months, a positive correlation was observed between the increase in body mass index and the increase of the short-chain-fatty-acid-producing clostridia, the Clostridum leptum group, and Eubacterium hallii. Considering previously established positive associations between rapid infant weight gain, early breastfeeding discontinuation, and later-life obesity, the corresponding microbial findings seen here warrant attention.

Dietary carbohydrates improve growth conditions for distinct populations of bacteria that may affect mucosal and systemic immunity. In this study, we fed in a parallel experiment a 10% xylooligosaccharide (XOS)-supplemented diet or a control diet to 2 groups of male C57BL/6NTac mice for 10 wk from weaning. We found that the XOS diet significantly increased Bifidobacterium throughout the intestine compared with control-fed mice, with the highest proportions found in the ileum after XOS feeding (P < 0.001). In the intestinal epithelium, most innate immune-related genes were unaffected by XOS feeding, whereas expression of interleukin 1β (Il1β) (P < 0.01) and interferon γ (Ifnγ) (P < 0.05) was significantly less in blood from XOS-fed mice than from control-fed mice. In vitro treatment of blood with propionate significantly decreased Il1β (P < 0.01), Ifnγ (P < 0.01), and interleukin 18 (Il18) (P < 0.001) expression, supporting our hypothesis that increased production of short-chain fatty acids (SCFAs) in the gut, which are transported across the intestine and into the systemic compartments, results in downregulation of low-grade inflammatory cytokines. The defensin regenerating islet-derived protein 3γ (RegIIIγ) was significantly more highly expressed in the small intestine (P < 0.01) in XOS-fed mice compared with control-fed mice, suggesting only minor contact between bifidobacteria and epithelial cells. In support of this, the SCFA-induced sodium/hydrogen exchanger isoform 3 expression tended to be greater in the XOS group than in the control group (P = 0.06), indicating an indirect SCFA-mediated antiinflammatory effect of XOS. In conclusion, XOS feeding decreases systemic inflammation, and this effect is most likely caused by higher SCFA concentrations as a result of an increased bifidobacterial saccharolytic fermentation in the entire gut and not only in the large intestine.

PURPOSE:Fruit consumption is associated with a decreased risk of CVD in cohort studies and is therefore endorsed by health authorities as part of the '5 or more a day' campaigns. A glass of fruit juice is generally counted as one serving. Fruit may cause protection by affecting common risk factors of CVD.METHODS:Apples are among the most commonly consumed fruits and were chosen for a comprehensive 5 × 4 weeks dietary crossover study to assess the effects of whole apples (550 g/day), apple pomace (22 g/day), clear and cloudy apple juices (500 ml/day), or no supplement on lipoproteins and blood pressure in a group of 23 healthy volunteers.RESULTS:The intervention significantly affected serum total and LDL-cholesterol. Trends towards a lower serum LDL-concentration were observed after whole apple (6.7%), pomace (7.9%) and cloudy juice (2.2%) intake. On the other hand, LDL-cholesterol concentrations increased by 6.9% with clear juice compared to whole apples and pomace. There was no effect on HDL-cholesterol, TAG, weight, waist-to-hip ratio, blood pressure, inflammation (hs-CRP), composition of the gut microbiota or markers of glucose metabolism (insulin, IGF1 and IGFBP3).CONCLUSIONS:Apples are rich in polyphenols and pectin, two potentially bioactive constituents; however, these constituents segregate differently during processing into juice products and clear juice is free of pectin and other cell wall components. We conclude that the fibre component is necessary for the cholesterol-lowering effect of apples in healthy humans and that clear apple juice may not be a suitable surrogate for the whole fruit in nutritional recommendations.

Freezing stool samples prior to DNA extraction and downstream analysis is widely used in metagenomic studies of the human microbiota but may affect the inferred community composition. In this study, DNA was extracted either directly or following freeze storage of three homogenized human fecal samples using three different extraction methods. No consistent differences were observed in DNA yields between extractions on fresh and frozen samples; however, differences were observed between extraction methods. Quantitative PCR analysis was subsequently performed on all DNA samples using six different primer pairs targeting 16S rRNA genes of significant bacterial groups, and the community composition was evaluated by comparing specific ratios of the calculated abundances. In seven of nine cases, the Firmicutes to Bacteroidetes 16S rRNA gene ratio was significantly higher in fecal samples that had been frozen compared to identical samples that had not. This effect was further supported by qPCR analysis of bacterial groups within these two phyla. The results demonstrate that storage conditions of fecal samples may adversely affect the determined Firmicutes to Bacteroidetes ratio, which is a frequently used biomarker in gut microbiology.

BACKGROUND:Postnatal regulation of the small intestinal mucus layer is potentially important in the development of adult gut functionality. We hypothesized that the nature of bacterial colonization affects mucus gene regulation in early life.We thus analyzed the influence of the presence of a conventional microbiota as well as two selected monocolonizing bacterial strains on the transcription of murine genes involved in mucus layer development during the first week of life.Mouse pups (N = 8/group) from differently colonized dams: Germ-free (GF), conventional specific pathogen free (SPF), monocolonized with either Lactobacillus acidophilus NCFM (Lb) or Escherichia coli Nissle (Ec) were analyzed by qPCR on isolated ileal tissue sections from postnatal days 1 and 6 (PND1, PND6) after birth with respect to: (i) transcription of specific genes involved in mucus production (Muc1-4, Tff3) and (ii) amounts of 16S rRNA of Lactobacillus and E. coli. Quantification of 16S rRNA genes was performed to obtain a measure for amounts of colonized bacteria.RESULTS:We found a microbiota-independent transcriptional increase of all five mucus genes from PND1 to PND6. Furthermore, the relative level of transcription of certain mucus genes on PND1 was increased by the presence of bacteria. This was observed for Tff3 in the SPF, Ec, and Lb groups; for Muc2 in SPF; and for Muc3 and Muc4 in Ec and Lb, respectively.Detection of bacterial 16S rRNA genes levels above the qPCR detection level occurred only on PND6 and only for some of the colonized animals. On PND6, we found significantly lower levels of Muc1, Muc2 and Muc4 gene transcription for Lb animals with detectable Lactobacillus levels as compared to animals with Lactobacillus levels below the detection limit.CONCLUSIONS:In summary, our data show that development of the expression of genes encoding secreted (Muc2/Tff3) and membrane-bound (Muc1/Muc3/Muc4) mucus regulatory proteins, respectively, is distinct and that the onset of this development may be accelerated by specific groups of bacteria present or absent at the mucosal site.

Subacute toxicity of 14 nm nanoparticulate silver (Ag-NP) stabilised with polyvinylpyrrolidone and ionic silver in the form of silver acetate (Ag-acetate) was investigated in four-week-old Wistar rats. Animals received orally by gavage the following: vehicle control (10 ♀, 6 ♂); Ag-NP at doses: 2.25 (8 ♀), 4.5 (8 ♀) or 9 mg/kg bw/day (10 ♀, 6 ♂); or Ag-acetate 9 mg silver/kg bw/day (8 ♀) for 28 days. Clinical, haematolological and biochemical parameters, organ weights, macro- and microscopic pathological changes were investigated. Caecal bacterial phyla and their silver resistance genes were quantified. For the Ag-NP groups, no toxicological effects were recorded. For Ag-acetate, lower body weight gain (day 4–7, 11–14, 14–16, P < 0.05; overall, day 1–28, P < 0.01), increased plasma alkaline phosphatase (P < 0.05), decreased plasma urea (P < 0.05) and lower absolute (P < 0.01) and relative (P < 0.05) thymus weight were recorded. In conclusion, these findings indicate toxicity of 9 mg/kg bw/day ionic silver but not of an equimolar Ag-NP dose. This is in accordance with previously reported data showing that oral Ag-acetate, in comparison with an equimolar dose of Ag-NP, resulted in higher silver plasma and organ concentrations.

Alterations in the human gut microbiota caused, for example, by diet, functional foods, antibiotics, or occurring as a function of age are now known to be of relevance for host health. Therefore, there is a strong need for methods to detect such alterations in a rapid and comprehensive manner. In the present study, we developed and validated a high-throughput real-time quantitative PCR-based analysis platform, termed GUt Low-Density Array (GULDA). The platform was designed for simultaneous analysis of the change in the abundance of 31 different microbial 16S rRNA gene targets in fecal samples obtained from individuals at various points in time. The target genes represent important phyla, genera, species, or other taxonomic groups within the five predominant bacterial phyla of the gut, Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobia and also Euryarchaeota. To demonstrate the applicability of GULDA, analysis of fecal samples obtained from six healthy infants at both 9 and 18 months of age was performed and showed a significant increase over time of the relative abundance of bacteria belonging to Clostridial cluster IV (Clostridia leptum group) and Bifidobacterium bifidum and concurrent decrease in the abundance of Clostridium butyricum and a tendency for decrease in Enterobacteriaceae over the 9-month period.

microbial ecosystem DTU Orbit (06/12/2018) Gut Low Density Array (GULDA), a novel qPCR approach to the study of the intestinal microbial ecosystem Causal relationships between the vast numbers of bacterial species present in the human intestines contain a lot of potential information on the regulation of the gut in the healthy as well as in diseased states. Based on the hypothesis that the human gut microbiota constitutes a dynamic ecosystem, interesting correlations between the presences of the given species should exist at any time. However, due to technical restrictions, it has not previously been possible to analyze such intrinsic bacterial patterns and correlations rapidly for a sufficiently large number of samples. To this purpose, we developed GULDA; a qPCR low-density array with particular focus on bacteria of relevance to the human gut microbiota. The output is given as arbitrary bacterial quantities, which for large sample numbers allow for further characterization of the gut microbiota by uniand multivariate statistical methods.

We previously reported that the non-digestible carbohydrates inulin and apple pectin promoted Listeria monocytogenes infection in guinea pigs, whereas xylo- and galacto-oligosaccharides (XOS and GOS), prevented infection by this pathogen. In the present study, mechanisms that could explain the previous in vivo observations were explored. Mixing bacterial cultures with XOS significantly (P < 0.05) decreased the ability of two out of three strains of L. monocytogenes to adhere to Caco-2 cells. Additionally, 2 h incubation with XOS followed by washing of the bacteria significantly (P < 0.05) decreased the ability of all three strains to adhere to Caco-2 cells. Consistently, expression of the adhesion-relevant genes inlA and lap was reduced by the presence of XOS. The observation that XOS inhibit the adhesion of Listeria to the intestinal epithelium in vitro may explain the reported preventive effect of XOS on Listeria infection in guinea pigs in vivo, while the preventive effect of GOS was not explicable by the assays chosen here.

development of the intestinal mucus layer DTU Orbit (09/12/2018) Influence of the gut microbiota on transcriptional regulation of genes involved in early life development of the intestinal mucus layer The interplay between the gut microbiota and the intestinal mucus layer is important both in the maintenance of the epithelial barrier as part of the innate immune defense, and in the conservation of gut homeostasis. Little is known about how the microbiota regulates mucin proteins, which protect the mucosal surfaces of all epithelial linings by physical hindrance or specific binding of pathogenic agents including virus and bacteria. It has been shown that the presence and composition of the microbiota is directly involved in the regulation of gene transcription in the intestinal epithelium. The intestinal mucus layer of germ free mice has been shown to display a distinctly different composition and structure compared to mucus from conventionally bred animals in vitro and in vivo. This points towards an important role of the microbiota in the regulation of mucin production. To which extent expression of all mucin genes are dependent on the presence of microorganisms and whether specific bacteria are capable of regulating mucus production in early life remains, however, to be established. The very first period after birth is believed to be vulnerable for establishment of the gut microbiota and consequently for the health and integrity of the epithelium throughout life. In this period, a development regulated by endogeneous factors such as hormones, in parallel with gene regulation caused by the microorganisms present in the gut, takes place. Although the microflora undoubtedly plays a regulatory role in the regulation of production of mucin, the importance of endogenous regulation as opposed to gut microbiota has not been investigated. Four groups of mouse pups (n=8 in each group) from differently colonized dams were analyzed with respect to expression of genes involved in mucin production (muc1-4, tff3) in ileal segments isolated on Day 1 and Day 6 after birth. Additionally, the presence of Lactobacillus and E. coli in the ileal samples was assessed by 16S rRNA gene quantification. The pups in the groups were born from dams that were either: 1) germ free (GF), 2) conventional specific pathogen free (SPF), 3) monocolonized with Lactobacillus acidophilus NCFM (Lb NCFM), or 4) monocolonized with E. coli Nissle (E. coli). All data was found by quantitative real-time PCR (qPCR) on Applied Biosystems platforms. Results from these studies showed interesting differences between the four tested animal groups and the two different days tested, which will be presented at the meeting. This is the first study to examine effects of different colonizing bacteria on mucus related gene expression levels in new born mice. These results may thus improve our understanding of the complex interplay between the gut microbiota and epithelial development in the very early life phases.

Certain indigestible carbohydrates, known as prebiotics, are claimed to be beneficial for gut health through a selective stimulation of certain gut microbes including bifidobacteria. However, stimulation of such microbes does not necessarily imply a preventive effect against pathogen infection. We recently demonstrated a reduced resistance to Salmonella infection in mice fed diets containing fructo-oligosaccharides (FOS) or xylo-oligosaccharides (XOS). In the present study, faecal and caecal samples from the same mice were analysed in order to study microbial changes potentially explaining the observed effects on the pathogenesis of Salmonella. Denaturing gradient gel electrophoresis revealed that the microbiota in faecal samples from mice fed FOS or XOS were different from faecal samples collected before the feeding trial as well as from faecal profiles generated from control animals. This difference was not seen for caecal profiles. Further analysis of faecal samples by real-time PCR demonstrated a significant increase in the Bacteroidetes phylum, the Bacteroides fragilis group and in Bifidobacterium spp. in mice fed FOS or XOS. The observed bifidogenic effect was more pronounced for XOS than for FOS. The Firmicutes phylum and the Clostridium coccoides group were reduced by both FOS and XOS. Surprisingly, no significant differences were detected between faecal samples collected before and after pathogen challenge in any of the groups. Furthermore, no effect of diets on caecal concentrations of short-chain fatty acids was recorded. In conclusion, diets supplemented with FOS or XOS induced a number of microbial changes in the faecal microbiota of mice. The observed effects of XOS were qualitatively similar to those of FOS, but the most prominent bifidogenic effect was seen for XOS. An increased level of bifidobacteria is thus not in itself preventive against Salmonella infection, since the same XOS or FOS-fed mice were previously reported to be more severely affected by Salmonella than control animals.

Oxygen restriction increases the infection potential of Listeria monocytogenes - a transcriptional analysis. Listeria monocytogenes has been implicated in several food borne outbreaks as well as sporadic cases of disease during the last two decades. Increased understanding of the biology of this organism is important in the prevention of food borne listeriosis. This is highly relevant for safety assessment of this organism in food. We have previously shown (Andersen et al., BMC Microbiology; 2007, 7:55) that the environmental conditions to which L. monocytogenes is exposed prior to ingestion are decisive for its in vivo infective potential in the gastrointestinal tract after passage of the gastric barrier. Infection of Caco-2 cells revealed that Listeria cultivated under oxygen-restricted conditions were approximately 100 fold more invasive than similar cultures grown without oxygen restriction. This means that not only the number of Listeria present in a given food item, but that also the physiological condition of these bacteria is important for food safety. The in vitro and in vivo data suggest that an oxygen-restricted L. monocytogenes cell represents a significantly higher risk than a cell grown without oxygen restriction. In order to identify transcriptional differences contributing to different invasiveness, microarrray gene chip technology was applied to cDNA created from RNA isolated from oxygen restricted and non-restricted cultures. The analysis confirmed several relevant genes to be differentially transcribed in the two environmental conditions e.g. genes related to virulence potential of Listeria monocytogenes.

Our study was part of the large European project ISAFRUIT aiming to reveal the biological explanations for the epidemiologically well-established health effects of fruits. The objective was to identify effects of apple and apple product consumption on the composition of the cecal microbial community in rats, as well as on a number of cecal parameters, which may be influenced by a changed microbiota.