Search

Background Gut microbiota data obtained by DNA sequencing are complex and compositional because of large numbers of detectable taxa, and because microbiota characteristics are described in relative terms. Nutrition researchers use principal component analysis (PCA) to derive dietary patterns from food data. Although compositional PCA methods are not commonly used to describe patterns from complex microbiota data, this approach would be useful for identifying gut microbiota patterns associated with diet and body composition. Objectives To use compositional PCA to describe the principal components (PCs) of gut microbiota in 5-y-old children and explore associations between microbiota components, diet, and BMI z-score. Methods A fecal sample was provided by 319 children aged 5 y. Their primary caregiver completed a validated 123-item quantitative FFQ. Body composition was determined using DXA, and a BMI z-score was calculated. Compositional PCA identified characterizing taxa and weightings for calculation of gut microbiota PC scores at the genus level, and was examined in relation to diet and body size. Results Three gut microbiota PCs were found. PC1 (negative loadings on uncultured Christensenellaceae and Ruminococcaceae) was related to lower BMI z-scores and longer duration of breastfeeding (per month) (β = -0.14; 95% CI: -0.26, -0.02; and β = 0.02; 95% CI: 0.003, 0.34, respectively). PC2 (positive loadings on Fusicatenibacter and Bifidobacterium; negative loadings on Bacteroides) was associated with a lower intake of nuts, seeds, and legumes (β = -0.05 per gram; 95% CI: -0.09, -0.01). When adjusted for fiber intake, PC2 was also associated with higher BMI z-scores (β = 0.12; 95% CI: 0.01, 0.24). PC3 (positive loadings on Faecalibacterium, Eubacterium, and Roseburia) was associated with higher intakes of fiber (β = 0.02 per gram; 95% CI: 0.003, 0.04) and total nonstarch polysaccharides (β = 0.02 per gram; 95% CI: 0.003, 0.04). Conclusions Our results suggest that specific gut microbiota components determined using compositional PCA are associated with diet and BMI z-score.This trial was registered at clinicaltrials.gov as NCT00892983.

Background Our Prevention of Overweight in Infancy (POI) study suggested that a brief sleep intervention in infancy reduced the risk of obesity at age 2 y. In contrast, we observed no benefit from the nutrition and activity intervention. Objective The objective of the study was to determine how these interventions influenced growth at ages 3.5 and 5 y compared with usual care (Control). Design A follow-up of a parallel, 4-arm, single-blind, 2-y, randomized controlled trial in 802 women (86% European, 48% primiparous) recruited in pregnancy (58% response rate) was undertaken. All groups received standard Well-Child care with additional support for 3 intervention groups: FAB (promotion of breastfeeding, healthy eating, physical activity: 8 contacts, antenatal, 18 mo); Sleep (prevention of sleep problems: antenatal, 3 wk); Combination (both interventions). Follow-up measures were collected by staff blinded to group allocation. The primary outcome was child body mass index (BMI) z score, and secondary outcomes were prevalence of obesity (BMI ≥95th percentile), self-regulation (psychological measures), sleep, physical activity (accelerometry, questionnaires), and dietary intake (food-frequency questionnaire). Analyses were conducted through the use of multiple imputation. Results Retention was 77% at age 3.5 y and 69% at age 5 y. Children in the FAB group had significantly higher BMI z scores than did Controls at age 5 y (adjusted difference: 0.25; 95% CI: 0.04, 0.47) but not at age 3.5 y (0.15; 95% CI: -0.04, 0.34). Children who received the Sleep intervention (Sleep and Combination groups) had significantly lower BMI z scores at age 3.5 y (-0.24; 95% CI: -0.38, -0.10) and at age 5 y (-0.23; 95% CI: -0.38, -0.07) than children who did not (Control and FAB groups). Conclusions A conventional intervention had unexpected adverse long-term weight outcomes, whereas positive outcomes from a less conventional sleep intervention remained promising at age 5 y. More intensive or extended sleep intervention might have larger or longer-lasting effects and should be investigated. This trial was registered at clinicaltrials.gov as NCT00892983.

Diets rich in complex carbohydrates that resist digestion in the small bowel can alter large bowel ecology and microbiota biochemistry because the carbohydrates become substrates for bacterial growth and metabolism. Conventional or germ-free weanling rats were fed a control diet or diets containing 1.25, 2.5, or 5% konjac (KJ), a commonly used ingredient in Asian foods, for 28 d. In the absence of bowel microbiota, 5% KJ elicited a significant increase in colonic goblet cell numbers and increased expression of mast cell protease genes and of genes that were overrepresented in the KEGG pathway "Metabolism of xenobiotics by cytochrome P450" relative to the control diet. In contrast, feeding 5% KJ caused few changes in mucosal gene expression in conventional rats. Analysis of the colonic microbiota of conventional rats fed KJ showed modest increases in the proportions of Actinobacteria and Bacteroidetes relative to rats fed the control diet, with a concomitant reduction in Firmicutes, which included a 50% reduction in Lactobacillus abundance. Colonic concentrations of short-chain fatty acids and colonic crypt lengths were increased by feeding KJ. Goblet cell numbers were greater in conventional rats fed KJ relative to the control diet but were lower compared with germ-free animals. Serum metabolite profiles were different in germ-free and conventional rats. Metabolites that differed in concentration included several phospholipids, a bile acid metabolite, and an intermediate product of tryptophan metabolism. Overall, KJ in the diet was potentially damaging to the bowel mucosa and produced a protective response from the host. This response was reduced by the presence of the bowel microbiota, which therefore ameliorated potentially detrimental effects of dietary KJ.

Given the relatively immature state of the neonatal gut and gut-associated immune system, the safety of probiotic strains for use as ingredients in infant milk formulae must be demonstrated in infant populations. As part of a double-blind placebo-controlled clinical trial of two commercially available probiotic strains in the reduction of risk for infant eczema, a number of safety outcomes were measured. Infants received daily doses of Lactobacillus rhamnosus HN001 (6 × 10 9 cfu day −1 ) or Bifidobacterium animalis subsp. lactis HN019 (9 × 10 9 cfu day −1 ), or placebo from birth to 24 months. Mothers received the same treatment from 35 weeks gestation, for up to 6 months postnatally while breastfeeding. No statistically significant differences were observed between the treatment groups for study withdrawal, incidence of adverse events, morphometric data, wheeze, and antibiotic use over the treatment period. We conclude that probiotics strains HN001 and HN019 were safe and well tolerated in infants, and did not affect normal growth.

Monoassociations of germ-free animals with colitogenic and probiotic bacterial strains trigger intestinal epithelial cell (IEC) activation and host-derived feedback mechanisms. To characterize the impact of a single nonpathogenic bacterial strain on the intestinal epithelium in the presence of an established microbiota, we inoculated reconstituted Lacotobacillus-free (RLF) mice at 8 wk of age with Lactobacillus reuteri 100-23. Primary IEC from the small intestine of L. reuteri-inoculated and control RLF mice were isolated 2, 6, and 21 d after inoculation followed by gene expression analysis (real-time PCR; Affymetrix microarrays) as well as 2-dimensional-gel electrophoreses (2D SDS-PAGE) and peptide mass fingerprinting via matrix-assisted laser desorption/ionization time of flight MS. At d 6, gene expression of proinflammatory cytokines and chemokines including interleukin (IL)-1alpha, IL-6, interferon-gamma-inducible protein 10, and macrophage inflammatory protein 2 was transiently induced, whereas gene expression levels of regulatory proteins A20 and Toll-interacting protein decreased. In addition, 8 target proteins with changes in the steady-state protein expression levels were identified at d 2 and 6 of L. reuteri colonization. Consistent with the absence of histopathology, L. reuteri-induced activation of primary IEC returned to control levels by d 21 after inoculation of RLF mice. The capability of L. reuteri 100-23 to directly trigger epithelial cell activation was confirmed in small IEC cultures using the murine cell line Mode-K. These results clearly indicate that the intestinal epithelium is reactive toward environmental changes induced by the commensal bacterial strain L. reuteri even in the presence of an already-established microbiota. The induction of transient IEC activation may help to maintain mucosal homeostasis.

An undisturbed sediment core taken from Round Lake, Hawke's Bay, New Zealand, using a specially designed sterile sampler, has been dated by tephra analysis and radiocarbon and analysed for pollen, charcoal and DNA. It appears to cover the last ca. 3600 years. There are clear indications of Māori effects on vegetation from ca. 800 BP. DNA was extracted from the core and amplified using bacterial and a range of other PCR primers targeting human and other animal mtDNA sequences. Cloned bacterial DNA sequences from just above the Taupo tephra (dated to AD 217-247) produced 98% and 99% similarity matches with human faecal bacteria. The 98% match was to the human gut bacterial genus Prevotella. This genus can, however, be found in a range of animal (including insect) guts. Extracted DNA was matched closely to the New Zealand native fish species Gobiomorphus cotidianus. Further work is needed to establish unequivocally that no DNA movement through the profile is occurring, but these results suggest a new technique of potentially revolutionary importance for Quaternary research. © 2007 Elsevier Ltd and INQUA.

Straight-run broiler chickens were raised either in floor pens or wire-floored cages (trial 1) or in floor pens only (trials 2, 3, and 4). Birds raised in floor pens had lower BW and feed intakes than those raised in cages. The administration of bacitracin in the feed increased feed intake from d 12 to d 35, decreased the feed conversion ratio during the same period in trial 2, and improved the weight gain of broilers from d 0 to 10 in trial 3. The concentrations of conjugated bile salts (taurocholic and taurochenodeoxycholic acids) were higher in the ileal contents of broilers administered the antimicrobials compared with untreated birds. Supplementation of the feed with monensin increased fat digestibility in the ileum of the birds. Although total numbers of bacteria in ileal contents were the same regardless of whether antimicrobials were administered or not, the bacterial community differed qualitatively. Populations of Lactobacillus salivarius were reduced in birds fed antimicrobials relative to untreated broilers. A representative ileal isolate of L. salivarius deconjugated bile salts in pure culture in the laboratory and in the ileal contents of ex-Lactobacillus-free chickens maintained in a protective environment and colonized by the Lactobacillus isolate. These observations provide a link between bile salt deconjugation in the ileum by L. salivarius and decreased weight gain of broilers. Lactobacillus salivarius populations could be targeted in future studies aimed at modification of the ileal bacterial community to achieve growth promotion of broilers without the administration of antimicrobial drugs.

A study was undertaken to test the effect of 2 commercially available probiotics on the production efficiency of broiler chickens hatched from the same breeder flock at 3 different ages (28, 43, and 57 wk). At each of the 3 breeder flock ages, 1,600 broiler chickens were hatched and randomly allocated to 1 of 4 treatments: 1) no probiotics (control), 2) probiotic 1 administered in the drinking water, 3) probiotic 1 administered as a spray, and 4) probiotic 2 administered in the feed. A coccidiostat was included in the feed, but no other antimicrobial agents were given. Broilers were then reared on straw litter in identical floor pens for a period of 6 wk. There were no significant differences in broiler BW, feed conversion, or mortality between the probiotic treatments and the control group in any of the trials. The 43-wk-old breeder flock had the highest fertility and hatchability and the lowest percentage of chicks culled at hatching. Throughout the broiler production period, the broilers from the 43- and 57-wk-old breeder flocks had higher BW and weight gains than the broilers produced at 28 wk of breeder flock age. Broiler feed conversion over the 6-wk production period decreased as the breeder flock aged. Probiotics had no effect on chick quality or production efficiency in broilers produced by the breeder flock ages examined.

The intestinal microflora is composed of numerous bacterial species that inhabit the distal small bowel and the large bowel. This complex microbial collection weilds marked influences on the biochemistry, physiology, immunology and disease resistance of the host. The derivation of scientifically valid probiotic products should be based on knowledge of the intestinal microflora because, by definition, consumption of the probiotic impacts on the microbial community harboured in the digestive tract. Variation in the stability and complexity of bacterial populations harboured by different human subjects may influence the outcome of probiotic administration. An understanding of the colonisation attributes, biochemical activities, and immunostimulatory properties of lactobacilli and bifidobacteria is required so that rational choices can be made in the selection of strains for incorporation into probiotic products.

An important consideration in the genetic manipulation of lactic acid bacteria is whether or not strains retain their normal industrial properties after transformation with plasmid DNA. A survey of plasmid types in various lactic acid bacteria showed that pE194-type rolling circle (RCR) plasmids were present in 24% of 70 commercial Lactococcus lactis cheese starters but not in any of 38 strains representing nine species of Lactobacillus . By contrast, theta plasmids showing homology to the pCI305 rep gene were present in most (though not all) lactococcal strains and not in any of the lactobacilli. Plasmids not belonging to either group were also present in some Lc. lactis and Lactobacillus strains. Six selected Lc. lactis subsp. cremoris strains were transformable with pFX3 (a 4.5 kb pE194-type rolling circle vector), yet four of these strains had significantly lower or zero transformation frequencies with pCI3340 (a 5.7 kb pCI305-based theta vector), possibly due to plasmid incompatibility. However, all transformants maintained full milkcoagulating activity. In addition to Lc. lactis , strains of Lc. garviae , Enterococcus faecalis and Lactobacillus reuteri were able to be transformed with pCI3340, making this a potentially useful vector for these species.

The distal small bowel and the large bowel of humans, even in health, are inhabited by a complex collection of microbes (mostly bacteria) known as the normal microflora. Gram-positive, lactic acid-producing bacteria are represented in this colection (bifidobacteria, lactobacilli, enterococci, eubacteria, peptostreptococci). The influence of the normal microflora as a whole on the host is well known from studies comparing germfree and conventional animals. More recently, using an unique experimental animal system (lactobacillus-free mice), lactobacilli have been shown to influence markedly the biochemistry of the intestinal tract (azoreductase,β-glucuronidase, bile salt hydrolase, proportions of unconjugated/conjugated bile acids). The effect of the consumption of lactic acid-producing bacteria on the normal microflora and the intestinal milieu of humans is therefore of interest. Detailed analysis of the composition, at the level of bacterial strains, of the normal microflora should be possible using DNA probes and ribotyping. These studies are necessary to provide a basis for the study of the effects of ingested lactic acid bacteria on the large bowel ecosystem, and for the derivation and use of genetically modified bacteria that will have a desirable impact on human health.

Lactobacillus reuteri 100-63 contains a 9.8 kb plasmid (pGT633) encoding resistance to the macrolide-lincosamide-streptogramin (MLS) type B antibiotics. The restriction endonucleases AccI, BamHI, BclI, EcoRI, EcoRV, HhaI, HindII, HpaI, KpnI, SalI, and SspI were employed to establish a physical map of pGT633. Next, genetic transfer experiments were conducted to establish the host range of pGT633. The results revealed that pGT633 replicated autonomously and encoded constitutive resistance to erythromycin in a variety of bacterial hosts, including Bacillus subtilis BD170, Streptococcus sanguis DL1, Staphylococcus aureus RN4220, and Enterococcus faecalis 19433, as well as several Lactobacillus spp. A 2.2 kb BamHI fragment of pGT633 containing the genetic determinant (ermGT) encoding resistance to erythromycin was cloned into Escherichia coli. Determination of the nucleotide sequence of ermGT revealed a methylase gene 731 bp in length that was highly related (ca. 81% nucleotide and ca. 78% amino acid identity) to the ermC gene from S. aureus plasmid pE194. The leader sequences of ermGT and ermC were identical except for a single base change at nt 51.

A piston-type mud sampler is described. It is a development of the Livingstone corer and was designed to extract cores for DNA analysis of sediments. Prevention of contamination was paramount. As the entire system is self-contained and the sample is retained in the corer, it was found ideal for extracting very soft sediments which could not be captured by existing corers.

Enteric and diarrheal diseases are a major worldwide cause of death among children under the age of 5. In this age group, diarrhea occurs 2.5 billion times per year [1] and causes 15% of childhood deaths.[2] Diarrheal diseases claim 59 million disability-adjusted life years (DALYs), nearly all from children in low- and middle-income countries.[3] Despite this enormous burden, these numbers fail to capture the full impact of enteric and diarrheal diseases. Early and frequent exposure to intestinal pathogens begins a cycle (Figure 1A) that affects digestion, nutrient absorption, growth, and immunity.[4] Repeated infections, with either overt diarrhea or subclinical enteropathy, produce acute and chronic undernutrition,[5] which leads to more frequent and severe infections.[6] Undernutrition contributes to 53% of childhood deaths [7] and is the leading risk factor for poor health outcomes in childhood;[8] survivors are at risk for developmental deficits in growth, fitness, and cognition that persist into adulthood with devastating consequences.[4] These consequences have a multiplicative effect on calculations of DALYs from diarrheal disease.[9] Open in a separate window Figure 1 The vicious cycle of diarrhea and undernutrition in susceptible children (A) The devastating synergy between enteric infections and undernutrition is influenced by the environment, the human genome, host nutrition, and the human microbiome. Various interventions (red boxes) may inhibit progression to the next step in the cycle, minimizing both acute and chronic morbidities. (B) Employing a spectrum of disease outcome measures would lend greater insight into the pathology underlying enteric and diarrheal diseases, while providing a more complete understanding of interventions targeting basic steps of enteric and diarrheal disease pathogenesis. Adapted with permission from Wiley: Nutrition Reviews,4 copyright 2008. http://www.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1753-4887.