Perspective: Human Milk Composition and Related Data for National Health and Nutrition Monitoring and Related Research

National health and nutrition monitoring is an important federal effort in the United States and Canada, and the basis for many of their nutrition and health policies. Understanding of child exposures through human milk (HM) remains out of reach due to lack of current and representative data on HM's composition and intake volume. This article provides an overview of the current national health and nutrition monitoring activities for HM-fed children, HM composition (HMC) and volume data used for exposure assessment, categories of potential measures in HM, and associated variability factors. In this Perspective, we advocate for a framework for collection and reporting of HMC data for national health and nutrition monitoring and programmatic needs, including a shared vision for a publicly available Human Milk Composition Data Repository (HMCD-R) to include essential metadata associated with HMC. HMCD-R can provide a central, integrated platform for researchers and public health officials for compiling, evaluating, and sharing HMC data. The compiled compositional and metadata in HMCD-R would provide pertinent measures of central tendency and variability and allow use of modeling techniques to approximate compositional profiles for subgroups, providing more accurate exposure assessments for purposes of monitoring and surveillance. HMC and related metadata could facilitate understanding the complexity and variability of HM composition, provide crucial data for assessment of infant and maternal nutritional needs, and inform public health policies, food and nutrition programs, and clinical practice guidelines.

A Bayesian method for identifying associations between response variables and bacterial community composition

Determining associations between intestinal bacteria and continuously measured physiological outcomes is important for understanding the bacteria-host relationship but is not straightforward since abundance data (compositional data) are not normally distributed. To address this issue, we developed a fully Bayesian linear regression model (BRACoD; Bayesian Regression Analysis of Compositional Data) with physiological measurements (continuous data) as a function of a matrix of relative bacterial abundances. Bacteria can be classified as operational taxonomic units or by taxonomy (genus, family, etc.). Bacteria associated with the physiological measurement were identified using a Bayesian variable selection method: Stochastic Search Variable Selection. The output is a list of inclusion probabilities ([Formula: see text]) and coefficients that indicate the strength of the association ([Formula: see text]) for each bacterial taxa. Tests with simulated communities showed that adopting a cut point value of [Formula: see text] ≥ 0.3 for identifying included bacteria optimized the true positive rate (TPR) while maintaining a false positive rate (FPR) of ≤ 5%. At this point, the chances of identifying non-contributing bacteria were low and all well-established contributors were included. Comparison with other methods showed that BRACoD (at [Formula: see text] ≥ 0.3) had higher precision and a higher TPR than a commonly used center log transformed LASSO procedure (clr-LASSO) as well as higher TPR than an off-the-shelf Spike and Slab method after center log transformation (clr-SS). BRACoD was also less likely to include non-contributing bacteria that merely correlate with contributing bacteria. Analysis of a rat microbiome experiment identified 47 operational taxonomic units that contributed to fecal butyrate levels. Of these, 31 were positively and 16 negatively associated with butyrate. Consistent with their known role in butyrate metabolism, most of these fell within the Lachnospiraceae and Ruminococcaceae. We conclude that BRACoD provides a more precise and accurate method for determining bacteria associated with a continuous physiological outcome compared to clr-LASSO. It is more sensitive than a generalized clr-SS algorithm, although it has a higher FPR. Its ability to distinguish genuine contributors from correlated bacteria makes it better suited to discriminating bacteria that directly contribute to an outcome. The algorithm corrects for the distortions arising from compositional data making it appropriate for analysis of microbiome data.

NUQUEST-NUtrition QUality Evaluation Strengthening Tools: development of tools for the evaluation of risk of bias in nutrition studies

BACKGROUND

Dietary exposure assessments are a critical issue in evaluating human nutrition studies; however, nutrition-specific criteria are not consistently included in existing bias assessment tools.

OBJECTIVES

Our objective was to develop a set of risk of bias (RoB) tools that integrated nutrition-specific criteria into validated generic assessment tools to address RoB issues, including those specific to dietary exposure assessment.

METHODS

The Nutrition QUality Evaluation Strengthening Tools (NUQUEST) development and validation process included 8 steps. The first steps identified 1) a development strategy; 2) generic assessment tools with demonstrated validity; and 3) nutrition-specific appraisal issues. This was followed by 4) generation of nutrition-specific items and 5) development of guidance to aid users of NUQUEST. The final steps used established ratings of selected studies and feedback from independent raters to 6) assess reliability and validity; 7) assess formatting and usability; and 8) finalize NUQUEST.

RESULTS

NUQUEST is based on the Scottish Intercollegiate Guidelines Network checklists for randomized controlled trials, cohort studies, and case-control studies. Using a purposive sample of 45 studies representing the 3 study designs, interrater reliability was high (Cohen's κ: 0.73; 95% CI: 0.52, 0.93) across all tools and at least moderate for individual tools (range: 0.57-1.00). The use of a worksheet improved usability and consistency of overall interrater agreement across all study designs (40% without worksheet, 80%-100% with worksheet). When compared to published ratings, NUQUEST ratings for evaluated studies demonstrated high concurrent validity (93% perfect or near-perfect agreement). Where there was disagreement, the nutrition-specific component was a contributing factor in discerning exposure methodological issues.

CONCLUSIONS

NUQUEST integrates nutrition-specific criteria with generic criteria from assessment tools with demonstrated reliability and validity. NUQUEST represents a consistent and transparent approach for evaluating RoB issues related to dietary exposure assessment commonly encountered in human nutrition studies.

Inadequate vitamin D status is associated with lower food plus supplemental intake of vitamin D in children of South Asian ethnicity living in the National Capital Region of Canada

Vitamin D status, measured in a Vitamin D Standardization Program certified laboratory, was assessed among children of South Asian and European ethnicity living in the national capital region of Canada to explore factors that may account for inadequate status. Demographic information, dietary and supplemental vitamin D over 30 d prior to measurement of serum 25-hydroxyvitamin D (25OHD), and anthropometry were measured (age 6.0-18.9 y; n = 58/group; February-March 2015). No group related differences in age, height and body mass index (BMI) Z-scores or in food vitamin D intakes were observed. Standardized serum 25OHD was lower in South Asian children (mean ± SD: 39.0 ± 16.8 nmol/L vs. European: 58.4 ± 15.8 nmol/L). A greater proportion of South Asian children had serum 25OHD <40 nmol/L (56.9 vs. 8.6%, P < 0.0001) and fewer took supplements (31 vs. 50%, P = 0.0389). In a multi-factorial model (r2 = 0.54), lower vitamin D status was associated with overweight/obese BMI and older age (14-18 y); no interaction with ethnicity was observed. Lower vitamin D status was associated with lower total vitamin D intake only in South Asian children. This study reinforces the importance of public health actions towards meeting vitamin D intake recommendations among those of high-risk deficiency. Novelty: A higher proportion of South Asian vs. European children had inadequate vitamin D status. Lower vitamin D status was associated with a BMI in the overweight/obese range. Lower vitamin D status was associated with lower total vitamin D intake in South Asian but not European children.

Early prenatal use of a multivitamin diminishes the risk for inadequate vitamin D status in pregnant women: results from the Maternal-Infant Research on Environmental Chemicals (MIREC) cohort study

BACKGROUND

Reports on the adequacy of vitamin D status of pregnant women are not available in Canada.

OBJECTIVES

The objectives of this study were to examine vitamin D status across pregnancy and identify the correlates of vitamin D status of pregnant women in Canada.

METHODS

Pregnant women (≥18 years) from 6 provinces (2008-2011) participating in a longitudinal cohort were studied. Sociodemographic data, obstetrical histories, and dietary and supplemental vitamin D intakes were surveyed. Plasma 25-hydroxyvitamin D (25OHD) was measured using an immunoassay standardized to LC-MS/MS from samples collected during the first (n = 1905) and third trimesters (n = 1649) and at delivery (n = 1543). The proportion of women with ≥40 nmol/L of plasma 25OHD (adequate status) was estimated at each time point, and factors related to achieving this cut point were identified using repeated-measures logistic regression. Differences in 25OHD concentrations across trimesters and at delivery were tested a using repeated-measures ANOVA with a post hoc Tukey's test.

RESULTS

In the first trimester, 93.4% (95% CI: 92.3%-94.5%) of participants had 25OHD ≥40 nmol/L. The mean plasma 25OHD concentration increased from the first to the third trimester and then declined by delivery (69.8 ± 0.5 nmol/L, 78.6 ± 0.7 nmol/L, and 75.7 ± 0.7 nmol/L, respectively; P < 0.0001). A lack of multivitamin use early in pregnancy reduced the odds of achieving 25OHD ≥40 nmol/L (ORadj = 0.33; 95% CI: 0.25-0.42) across all time points. Factors associated with not using a prenatal multivitamin included multiparity (ORadj = 2.08; 95% CI: 1.42-3.02) and a below-median income (ORadj = 1.39; 95% CI: 1.02-1.89).

CONCLUSIONS

The results from this cohort demonstrate the importance of early multivitamin supplement use to achieve an adequate vitamin D status in pregnant women.

Calcium exacerbates the inhibitory effects of phytic acid on zinc bioavailability in rats

BACKGROUND

Complementary feeding of breastfed infants with foods high in bioavailable zinc (Zn) can help meet physiological requirements for Zn. Some infant cereals contain high concentrations of phytic acid (PA) and calcium (Ca) that may reduce absorbable Zn.

OBJECTIVES

This study measured PA, Zn and Ca concentrations in selected infant cereals sold in Canada and investigated the effects of dietary PA and Ca at concentrations present in infant cereals on Zn bioavailability in rats.

METHODS AND RESULTS

Male Sprague-Dawley rats (36-day old) were fed a control diet containing normal Zn (29.1 mg/kg) and Ca (4.95 g/kg) or six test diets (n = 12/diet group). Test diets were low in Zn (8.91-9.74 mg/kg) and contained low (2.16-2.17 g/kg), normal (5.00-5.11 g/kg) or high (14.6-14.9 g/kg) Ca without or with added PA (8 g/kg). After 2 weeks, rats were killed and Zn status of the rats was assessed. PA, Zn and Ca concentrations in infant cereals (n = 20) differed widely. PA concentrations ranged from undetectable to 16.0 g/kg. Zn and Ca concentrations ranged from 7.0-29.1 mg/kg and 0.8-13.4 g/kg, respectively. The [PA]/[Zn] and [PA × Ca]/[Zn] molar ratios in infants cereals with detectable PA (16 of 20 cereals) ranged from 22-75 and 0.9-14.9 mol/kg, respectively, predicting low Zn bioavailability. Body weight, body composition (lean and fat mass), right femur weight and length measurements and Zn concentrations in serum and femur indicated that diets higher in Ca had a more pronounced negative effect on Zn status of rats fed a PA-supplemented diet. Addition of PA to the diet had a greater negative effect on Zn status when Ca concentration in the diet was higher.

CONCLUSION

These results show that, in rats, higher concentrations of dietary Ca and PA interact to potentiate a decrease in bioavailable Zn and may suggest lower Zn bioavailability in infant cereals with higher PA and Ca concentrations.

Proposed Phytic Acid Standard Including a Method for Its Analysis

A method is described that accurately and rapidly quantifies the free and total phosphorous content of a commercially available, purified, phytic acid preparation. This allows its use as a standard for phytic acid determinations in foods. The method involves a wet ashing step followed by phosphorous measurement with a 1-amino-2-naphthol-4-sulfonic acid-molybdate reagent in a microplate reader at 660 nm. The procedure can be performed in 3 h with as little as 50 mg sample.

Fructooligosaccharides and wheat bran fed at similar fermentation levels differentially affect the expression of genes involved in transport, signaling, apoptosis, cell proliferation, and oncogenesis in the colon epithelia of healthy Fischer 344 rats

The influence of the source of fermentable material (FM) on the luminal concentrations of their end products and its effects on colon cell metabolism and disease susceptibility is not well characterized. We hypothesized that total fermentation but not the source (type) of FM would be the main factor in determining cellular /molecular outcomes in the healthy colon epithelia. The main aim of this study was to elucidate the role of two different sources of FM, fructooligosaccharides (FOS) and wheat bran (WB), on the expression of genes involved in short chain fatty acid (SCFA) transport, G-protein signaling, apoptosis, cell proliferation and oncogenesis in colon epithelia of healthy rats. Male Fischer 344 rats (n = 10/group) were fed AIN-93G control (0% FM) or experimental diets containing WB (~1%, 2%, or 5% FM) or FOS (~2%, 5%, or 8% FM). Rats were killed after 6 weeks and the colon mucosa was assessed for the expression of target genes using real-time quantitative polymerase chain reaction. By comparison to the control, dose-related changes of mRNA levels were found in rats fed FOS-based diets, including: (a) upregulation of three SCFA transporters (Smct2, Mct1 and Mct4) but downregulation of Mct2, (b) upregulation of Gpr109a and downregulation of Gpr120, Gpr43, Gprc5a, Rgs2 and Rgs16, (c) upregulation of apoptosis-related genes including Bcl2, Bcl2-like 1, Bak1, Caspase 3, Caspase 8 and Caspase 9, (d) downregulation of the oncogenes and metastasis genes Ros1, Fos, Cd44, Fn1 and Plau, and (e) downregulation of several genes involved in cellular proliferation including Hbegf, Hoxb13, Cgref1, Wfdc1, Tgm3, Fgf7, Nov and Lumican. In contrast, rats fed WB-based diets resulted in dose-related upregulation of mRNA levels of Smct2, Rgs16, Gprc5a, Gpr109a, Bcl2-like 1, Caspase 8, and Fos. Additionally, different gene expression responses were observed in rats fed FOS and WB at 2% and 5% FM. Over all, these gene changes elicited by FOS and WB were independent of the expression of the tumor suppressor Tp53. These results suggest that fermentation alone is not the sole determinant of gene responses in the healthy rat colon.

Housing influences tissue cytokine levels and the fecal bacterial community structure in rats

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Housing impacted the Bacteroidetes/Firmicutes ratio in feces.

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Bedding influenced fecal short chain fatty acid outputs.

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Splenic concentrations of interleukin-4 were higher in bedding-housed rats.

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Fecal bacterial community change was consistent with higher coprophagy in bedding.

Immune measures and the fecal bacterial community were examined in female Biobreeding rats housed in wire bottom cages (wire) or in solid bottom cages containing hardwood chips (bedding). Housing did not affect food intake, weight gain, fecal output or fibre content, serum liver enzymes, or spleen and mesenteric lymph node immune cell populations. Bedding-housed rat feces were enriched in phylotypes aligning within the phylum Firmicutes (families Lactobacillaceae and Erysipelotrichaceae) and had a 2-fold lower content of phylotypes aligning within the phylum Bacteroidetes. Feces from bedding-housed rats also contained significantly more acetic acid and less propionic, isobutyric, valeric and isovaleric acids than those housed on wire. Bedding-housed rats had significantly higher splenic concentrations of interleukin-4 (P < 0.001). These results demonstrate that bedding can indirectly influence systemic and mucosal immune measures, potentially adding additional complexities and confounding results to nutrition studies investigating the health effects of dietary fibres.

Baseline Assessment of 25-Hydroxyvitamin D Reference Material and Proficiency Testing/External Quality Assurance Material Commutability: A Vitamin D Standardization Program Study

The Vitamin D Standardization Program (VDSP) coordinated a study in 2012 to assess the commutability of reference materials and proficiency testing/external quality assurance materials for total 25-hydroxyvitamin D [25(OH)D] in human serum, the primary indicator of vitamin D status. A set of 50 single-donor serum samples as well as 17 reference and proficiency testing/external quality assessment materials were analyzed by participating laboratories that used either immunoassay or LC-MS methods for total 25(OH)D. The commutability test materials included National Institute of Standards and Technology Standard Reference Material 972a Vitamin D Metabolites in Human Serum as well as materials from the College of American Pathologists and the Vitamin D External Quality Assessment Scheme. Study protocols and data analysis procedures were in accordance with Clinical and Laboratory Standards Institute guidelines. The majority of the test materials were found to be commutable with the methods used in this commutability study. These results provide guidance for laboratories needing to choose appropriate reference materials and select proficiency or external quality assessment programs and will serve as a foundation for additional VDSP studies.

An Analysis of Factors Associated with 25-Hydroxyvitamin D Levels in White and Non-White Canadians

Vitamin D status was assessed in 19-79 year old whites (8351 participants of European ancestry) and non-whites (1840 participants encompassing all other ancestries) from cycles 1 to 3 (years 2007-2013) of the Canadian Health Measures Survey. Status was assessed using the U.S. Institute of Medicine (IOM) 25-hydroxyvitamin D [25(OH)D] cut point values of 30 and 40 nmol/L. Overall, median 25(OH)D concentrations were significantly higher in whites [58.9 (28.6, 100.1) nmol/L; 5th and 95th percentile] compared with non-whites [43.5 (19.0, 83.2); P < 0.001]. Values were higher in females [58.5 (27.5, 101.3) nmol/L] when compared with males [53.5 (24.2, 92.7) nmol/L] and increased with age. Non-whites were more likely to have 25(OH)D values below IOM established cut points for optimum bone health with 20.1 (16.0, 24.2) and 42.2% (36.8, 47.7) of non-whites having serum 25(OH)D concentrations <30 and <40 nmol/L, respectively. The corresponding values for whites were 5.9 (4.6, 7.2) and 16.1% (14.0, 18.3). Values were lower during the first quarter when compared with the third quarter. Supplement intake was an important factor in determining 25(OH)D levels, but it did not alone account for the difference in status. Equivalent increases in 25(OH)D levels were observed in whites and non-whites during the summer months, suggesting there was no functional difference in sun exposure response. It is apparent that a complex interaction of factors affect 25(OH)D values in free-living Canadians.

The Vitamin D Standardization Program (VDSP) Manual for Retrospective Laboratory Standardization of Serum 25-Hydroxyvitamin D Data

Low concentrations of total 25-hydroxyvitamin D [25(OH)D], the principal biological measure of vitamin D status, have been associated with clinical and public health outcomes. The determination of levels under which there is an increase in the risk of disease, as well as comparisons across populations, have been difficult to establish due the large assay variability in measuring 25(OH)D. Accordingly, the Vitamin D Standardization Program (VDSP) includes the retrospective standardization of existing 25(OH)D values collected by epidemiological and clinical studies, as well as clinical trials, as one of its main objectives. We introduce methodology developed by the VDSP that can be used to standardize the measurement of time-stable analytes, including 25(OH)D, in samples that have been banked and maintained appropriately. Sample size estimation formulae are first applied to calculate the required number of banked blood samples to be reanalyzed using either of two approaches. In the first approach, existing samples are remeasured using the current measurement procedure, and an equation relating "old" to "current" measurements is obtained. A second set of sera, usually 40-50 single-donor serum samples, are measured with the current measurement procedure and an assay traceable to a reference measurement procedure and/or certified reference materials, which yields a second calibration equation. These two equations are combined to produce standardized levels from the original old values. This approach is necessary when study restrictions prevent serum samples from being shipped to an external laboratory and is illustrated with samples from the Canadian Health Measures Survey. When serum samples are permitted to be shared with other laboratories, or the study investigators can carry out the measurements with a traceable assay, a single calibration equation method is used. Existing samples are selected and remeasured using the available traceable assay. We outline the statistical theory supporting the VDSP protocol and provide implementation examples. The methods proposed are generalizable to any instance in which banked specimens have been properly prepared and stored and the analyte of interest is stable under those conditions.

Standardizing 25-hydroxyvitamin D values from the Canadian Health Measures Survey

BACKGROUND

The Canadian Health Measures Survey (CHMS) is an ongoing cross-sectional national survey that includes a measure of 25-hydroxyvitamin D [25(OH)D] by immunoassay. For cycles 1 and 2, the collection period occurred approximately every 2 y, with a new sample of ∼5600 individuals.

OBJECTIVE

The goal was to standardize the original 25(OH)D CHMS values in cycles 1 and 2 to the internationally recognized reference measurement procedures (RMPs) developed by the US National Institute for Standards and Technology (NIST) and Ghent University, Belgium.

DESIGN

Standardization was accomplished by using a 2-step procedure. First, serum samples corresponding to the original plasma samples were remeasured by using the currently available immunoassay method. Second, 50 serum samples with known 25(OH)D values assigned by the NIST and Ghent reference method laboratories were measured by using the currently available immunoassay method. The mathematical models for each step-i.e., 1) YCurrent = XOriginal and 2) YNIST-Ghent = XCurrent -were estimated by using Deming regression, and the 2 models were solved to obtain a single equation for converting the "original" values to NIST-Ghent RMP values.

RESULTS

After standardization (cycles 1 and 2 combined), the percentage of Canadians with 25(OH)D values <40 nmol/L increased from 16.4% (original) to 19.4% (standardized), and values <50 nmol/L increased from 29.0% (original) to 36.8% (standardized). The 25(OH)D standardized distributions (cycles 1 and 2 analyzed separately) were similar across age and sex groups; slightly higher values were associated with cycle 2 in the young and old. This finding contrasts with the original data, which indicated that cycle 2 values were lower for all age groups.

CONCLUSION

The shifts in 25(OH)D distribution brought about by standardization indicate its importance in drawing correct conclusions about potential population deficiencies and insufficiencies and in permitting the comparison of distributions between national surveys.

Sex differences in gut fermentation and immune parameters in rats fed an oligofructose-supplemented diet

BACKGROUND

Mechanistic data to support health claims is often generated using rodent models, and the influence of prebiotic supplementation has largely been evaluated using male rodents. Given that sex-based differences in immune parameters are well recognized and recent evidence suggests differences in microbiota composition between sexes, validation of the effectiveness of prebiotics merits assessment in both males and females. Here, we have compared the effect of oligofructose (OF) supplementation on the fecal bacterial community, short chain fatty acid profiles, and gut mucosal and systemic immune parameters in male and female rats.

METHODS

Male and female rats were fed rodent chow or chow supplemented with OF (5 % w/w). Fecal community change was examined by analyzing 16S rRNA gene content. To compare effects of OF between sexes at the gut microbial and mucosal immune level, fecal short chain fatty acid and tissue cytokine profiles were measured. Serum lipopolysaccharide levels were also evaluated by the limulus amebocyte lysate assay as an indirect means of determining gut permeability between sexes.

RESULTS

In the fecal community of females, OF supplementation altered community structure by increasing abundance in the Phylum Bacteroidetes. In male rats, no changes in fecal community structure were observed, although fecal butyrate levels significantly increased. Liver Immunoglobulin A (IgA) levels were higher in males relative to females fed OF, and serum LPS concentrations were higher in males independent of diet. Females had higher basal levels of the regulatory cytokine interleukin-10 (IL-10) in the colon and liver, while males had higher basal levels of the pro-inflammatory cytokines IL-6 and cytokine-induced neutrophil chemoattractant-1 (CINC-1) in the cecum and liver.

CONCLUSIONS

We have shown that male and female rat gut communities metabolize an OF-supplemented diet differently. Sex-specific responses in both the fecal community and systemic immune parameters suggest that this difference may result from an increase in the availability of gut peptidyl-nitrogen in the males. These findings demonstrate the importance of performing sex-comparative studies when investigating potential health effects of prebiotics using rodent models.

Spaceflight influences both mucosal and peripheral cytokine production in PTN-Tg and wild type mice

Spaceflight is associated with several health issues including diminished immune efficiency. Effects of long-term spaceflight on selected immune parameters of wild type (Wt) and transgenic mice over-expressing pleiotrophin under the human bone-specific osteocalcin promoter (PTN-Tg) were examined using the novel Mouse Drawer System (MDS) aboard the International Space Station (ISS) over a 91 day period. Effects of this long duration flight on PTN-Tg and Wt mice were determined in comparison to ground controls and vivarium-housed PTN-Tg and Wt mice. Levels of interleukin-2 (IL-2) and transforming growth factor-beta1 (TGF-β1) were measured in mucosal and systemic tissues of Wt and PTN-Tg mice. Colonic contents were also analyzed to assess potential effects on the gut microbiota, although no firm conclusions could be made due to constraints imposed by the MDS payload and the time of sampling. Spaceflight-associated differences were observed in colonic tissue and systemic lymph node levels of IL-2 and TGF-β1 relative to ground controls. Total colonic TGF-β1 levels were lower in Wt and PTN-Tg flight mice in comparison to ground controls. The Wt flight mouse had lower levels of IL-2 and TGF-β1 compared to the Wt ground control in both the inguinal and brachial lymph nodes, however this pattern was not consistently observed in PTN-Tg mice. Vivarium-housed Wt controls had higher levels of active TGF-β1 and IL-2 in inguinal lymph nodes relative to PTN-Tg mice. The results of this study suggest compartmentalized effects of spaceflight and on immune parameters in mice.

Temporal change in the gut community of rats fed high amylose cornstarch is driven by endogenous urea rather than strictly on carbohydrate availability

AIM

To examine change in the gut community of rats fed high amylose maize starch (HAMS).

METHODS AND RESULTS

Rats were fed AIN93G diets containing HAMS (5% resistant starch type 2) or alphacell (control). HAMS increased faecal short-chain fatty acid output, faecal propionate and total bacteria output but reduced gut pH and blood urea concentrations compared with rats ingesting the control diet. Feeding HAMS resulted in a gut community dominated by four phylotypes homologous with Ruminococcus bromii, Bacteroides uniformis and with yet to be cultivated organisms aligning into the Family Porphyromonadaceae. Enrichment of phylotypes aligning within the Bacteroidetes occurred primarily in the caecum, whereas those homologous with R. bromii were found primarily in the faeces. HAMS altered community structure such that the phylum Bacteroidetes represented the dominant gut lineage and progressively reduced faecal community phylotype richness over the duration of feeding.

CONCLUSIONS

Feeding HAMS resulted in a caecal and faecal community dominated by organisms that require ammonia as a primary nitrogen source. Gut ammonia derived from endogenous urea represents an important factor contributing to caecal community composition in addition to the ability to utilize HAMS. Increases in faecal propionate, rather than butyrate as is often observed following resistant starch feeding, reflected a gut community dominated by the Bacteroidetes.

SIGNIFICANCE

Diet-mediated change is often viewed strictly in terms of available carbohydrate. Here, we have shown that ammonia derived from endogenous urea is an important factor contributing to gut community composition and structure in rats fed this substrate.

Summary of an NIH workshop to identify research needs to improve the monitoring of iodine status in the United States and to inform the DRI

The Office of Dietary Supplements (ODS) at the NIH sponsored a workshop on May 12-13, 2011, to bring together representatives from various NIH institutes and centers as a first step in developing an NIH iodine research initiative. The workshop also provided an opportunity to identify research needs that would inform the dietary reference intakes for iodine, which were last revised in 2001. Iodine is required throughout the life cycle, but pregnant women and infants are the populations most at risk of deficiency, because iodine is required for normal brain development and growth. The CDC monitors iodine status of the population on a regular basis, but the status of the most vulnerable populations remains uncertain. The NIH funds very little investigator-initiated research relevant to iodine and human nutrition, but the ODS has worked for several years with a number of other U.S. government agencies to develop many of the resources needed to conduct iodine research of high quality (e.g., validated analytical methods and reference materials for multiple types of samples). Iodine experts, scientists from several U.S. government agencies, and NIH representatives met for 2 d to identify iodine research needs appropriate to the NIH mission.

Molecular methods to measure intestinal bacteria: a review

The intestine is an exceptionally rich ecosystem encompassing a complex interaction among microorganisms, influenced by host factors, ingested food, and liquid. Characterizing the intestinal microbiota is currently an active area of research. Various molecular-based methods are available to characterize the intestinal microbiota, but all methods possess relative strengths, as well as salient weaknesses. It is important that researchers are cognizant of the limitations of these methods, and that they take the appropriate steps to mitigate weaknesses. Here, we discuss methodologies used to monitor intestinal bacteria including: (i) traditional clone libraries; (ii) direct sequencing using next-generation parallel sequencing technology; (iii) denaturing gradient gel electrophoresis and temperature gradient gel electrophoresis; (iv) terminal restriction fragment length polymorphism analysis; (v) fluorescent in situ hybridization; and (vi) quantitative PCR. In addition, we also discuss experimental design, sample collection and storage, DNA extraction, gene targets, PCR bias, and methods to reduce PCR bias.

Dietary fructooligosaccharides and wheat bran elicit specific and dose-dependent gene expression profiles in the proximal colon epithelia of healthy Fischer 344 rats

Proximal colon epithelial gene responses to diets containing increasing levels of dietary fermentable material (FM) from 2 different sources were measured to determine whether gene expression patterns were independent of the source of FM. Male Fischer 344 rats (10/group) were fed for 6 wk a control diet containing 10% (g/g) cellulose (0% FM); or a 2, 5, or 10% wheat bran (WB) diet (1, 2, 5% FM); or a 2, 5, or 8% fructooligosaccharides (FOS) diet (2, 5, 8% FM). WB and FOS were substituted for cellulose to give a final 10% nondigestible material content including FM. Gene responses were relative to expression in rats fed the control diet. The gene response patterns associated with feeding ∼2% FM (5% WB and 2% FOS) were similar (∼10 gene changes ≥ 1.6-fold; P ≤ 0.01) and involved genes associated with transport (Scnn1g, Mt1a), transcription (Zbtb16, Egr1), immunity (Fkbp5), a gut hormone (Retn1β), and lipid metabolism (Scd2, Insig1). These changes were also similar to those associated with 5% FM but only in rats fed the 10% WB diet. In contrast, the 5% FOS diet (~5% FM) was associated with 68 gene expression changes ≥ 1.6-fold (P ≤ 0.01). The diet with the highest level of fermentation (8% FOS, ~8% FM) was associated with 132 changes ≥ 1.6-fold (P ≤ 0.01), including genes associated with transport, cellular proliferation, oncogene and tumor metastasis, the cell cycle, apoptosis, signal transduction, transcript regulation, immunity, gut hormones, and lipid metabolic processes. These results show that both the amount and source of FM determine proximal colon epithelial gene response patterns in rats.

Continuous feeding of antimicrobial growth promoters to commercial swine during the growing/finishing phase does not modify faecal community erythromycin resistance or community structure

AIMS

To investigate the effect of continuous feeding of antimicrobial growth promoters (tylosin or virginiamycin) on the swine faecal community.

METHODS AND RESULTS

The study consisted of two separate on-farm feeding trials. Swine were fed rations containing tylosin (44 or 88 mg kg(-1) of feed) or virginiamycin (11 or 22 mg kg(-1) of feed) continuously over the growing/finishing phases. The temporal impact of continuous antimicrobial feeding on the faecal community was assessed and compared to nondosed control animals through anaerobic cultivation, the analysis of community 16S rRNA gene libraries and faecal volatile fatty acid content. Feeding either antimicrobial had no detectable effect on the faecal community.

CONCLUSIONS

Erythromycin methylase genes encoding resistance to the macrolide-lincosamide-streptogramin B (MLS(B) ) antimicrobials are present at a high level within the faecal community of intensively raised swine. Continuous antimicrobial feeding over the entire growing/finishing phase had no effect on community erm-methylase gene copy numbers or faecal community structure.

SIGNIFICANCE AND IMPACT OF THE STUDY

Antimicrobial growth promoters are believed to function by altering gut bacterial communities. However, widespread MLS(B) resistance within the faecal community of intensively raised swine likely negates any potential effects that these antimicrobials might have on altering the faecal community. These findings suggest that if AGP-mediated alterations to gut communities are an important mechanism for growth promotion, it is unlikely that these would be associated with the colonic community.

Spatial distribution of some microbial trophic groups in a plug-flow-type anaerobic bioreactor treating swine manure

Anaerobic digestion of swine manure is carried out by a consortium of microbial species, including volatile fatty acid (VFA) producers, VFA-degraders and methanogens. The distribution of five phylogenetic groups within a plug-flow-type anaerobic bioreactor consisting of eight serially-connected tanks was examined through the sequential digestion of swine manure. Quantification was carried out using reverse transcription real-time PCR (RT-Q-PCR) assays targeting the 16S rRNA of Clostridium (cluster XIVa), Peptostreptococcus, Syntrophomonas, Methanosaeta, and Methanosarcina spp. The VFA producers Peptostreptococcus spp. and Clostridium spp. were found predominantly in compartments where hydrolysis/acidogenesis took place. The spatial distribution of the aceticlastic methanogens, Methanosaeta and Methanosarcina, within the bioreactor was not correlated with methanogenic activity. In contrast the VFA-degrading genus Syntrophomonas spp. was more abundant in compartments with elevated methanogenic activity. Multivariate statistical analyses of the RT-Q-PCR data have provided new insights into our understanding of how the various trophic groups were distributed within this bioreactor system. While the distribution of clostridia, peptostreptococci and Syntrophomonas corresponded to their known metabolic functions, aceticlastic methanogens were not apparently linked to the methanogenesis stage occurring in latter compartments, suggesting that hydrogenotrophic methanogens were the primary methane generators in this bioreactor. However, aceticlastic methanogens could be involved in compartments related to the hydrolysis/acidogenesis stage.

Diets enriched in oat bran or wheat bran temporally and differentially alter the composition of the fecal community of rats

A clear understanding of how diet alters gastrointestinal communities is important given the suggested link between gut community composition and a wide variety of disease pathologies. To characterize this link for commonly consumed dietary fiber sources, we investigated the change in the fecal community of rats fed diets containing 5% nonnutritive fiber (control), 3% (wt:wt) oat bran plus 2% nonnutritive fiber (OB), or 5% (w/w) wheat bran (WB) over a 28-d feeding trial using both molecular- and cultivation-based methodologies. Pooled fecal samples from 8 rats fed the same diet were analyzed at 4 time points. On d 28, bran-fed rats had approximately twice the total cultivable bacteria than rats fed the control diet. Over the course of feeding, the cultivable community was initially dominated by bacteroides, then by bifidobacteria, lactobacilli, enterococci, and various enterics. In contrast, molecular analysis revealed the appearance of new operational taxonomic units (phylotypes) that were both temporally and inequitably distributed throughout the fecal community. The majority of change occurred in 2 major lineages within the Firmicutes: the Clostridium coccoides group and the Clostridium leptum subgroup. The time course of change depended on the source of bran, with the majority of new phylotypes appearing by d 14 (OB) or d 28 (WB), although adaptation of the fecal community was slow and continued over the entire feeding trial. Bacterial community richness was higher in bran-fed rats than in those fed the control diet. Change within the C. coccoides and C. leptum lineages likely reflect their high abundance within the gut bacterial community and the role of clostridia in fiber digestion. The results illustrate the limitations of relying solely on cultivation to assess bacterial changes and illustrate that community changes are complex in an ecosystem containing high numbers of interdependent and competing species of bacteria.

Dietary fructooligosaccharides alter the cultivable faecal population of rats but do not stimulate the growth of intestinal bifidobacteria

The effect of fructans on the cultivable faecal community of Bio Breeding rats fed diets containing 5% (m/v) food-grade fructooligosaccharide (FOS) was investigated. Culturing of faecal material using chicory inulin as the sole carbohydrate source revealed the presence of a greater diversity of inulin-utilizing bacterial species in FOS-fed rats as compared with the control rats, although both contained species which effectively utilized inulin. The majority of cultivable inulin-utilizing species fell within the Clostridium coccoides group and Clostridium leptum subgroup, some of which were related to previously cultured butyrate-producing bacteria from the intestines of various animals. The impact of FOS on the growth of the indigenous bifidobacteria community and three inulin-utilizing isolates was assessed using real-time polymerase chain reaction. While dietary FOS was found to stimulate the growth of all three inulin-utilizing isolates, no growth stimulation of the indigenous bifidobacteria community occurred over the duration of the feeding trial.

Carbohydrate metabolism in erythrocytes of copper deficient rats

Dietary copper deficiency is known to adversely affect the circulatory system of fructose-fed rats. Part of the problem may lie in the effect of copper deficiency on intermediary metabolism. To test this, weanling male Long-Evans rats were fed for 4 or 8 weeks on sucrose-based diets containing low or adequate copper content. Copper deficient rats had significantly lower plasma and tissue copper as well as lower plasma copper, zinc-superoxide dismutase activity. Copper deficient rats also had a significantly higher heart:body weight ratio when compared to pair-fed controls. Direct measurement of glycolysis and pentose phosphate pathway flux in erythrocytes using (13)C NMR showed no differences in carbon flux from glucose or fructose to pyruvate but a significantly higher flux through the lactate dehydrogenase locus in copper deficient rats (approximately 1.3 times, average of glucose and glucose + fructose measurements). Copper-deficient animals had significantly higher erythrocyte concentrations of glucose, fructose, glyceraldehyde 3-phosphate and NAD(+). Liver metabolite levels were also affected by copper deficiency being elevated in glycogen and fructose 1-phosphate content. The results show small changes in carbohydrate metabolism of copper deficient rats.

Culture-independent phylogenetic analysis of the faecal flora of the rat

The dominant faecal flora of the rat was determined using randomly cloned 16S rDNA comparative sequence analysis. A total of 109 near full-length 16S rDNA clones were sequenced, representing 69 unique 16S rRNA phylotypes or operational taxonomic units (OTUs). Estimates of species richness indicated that approximately 338 species were present in the faeces, suggesting that only 20% of species were identified. Only two of 39 Gram-negative clones aligned with previously cultured species, the remainder fell into a separate lineage within the Bacteroides-Cytophaga phylum. Several clones within this new group were related to 16S rDNA sequences previously identified from mouse faeces. Lactobacilli were the most abundant Gram-positive species, representing 23% of the total clones but only 7% of OTUs. The remaining Gram-positive clones were distributed among the Clostridium coccoides group (9%), the Clostridium leptum subgroup (18%), and throughout the low GC Gram-positive bacteria (13%). The majority of OTUs (63/69 or 91%) were less than 97% homologous to previously cultured bacteria. Faecal samples were also cultured using a variety of anaerobic media. With the exception of the lactobacilli, the cultured isolates demonstrated low species diversity and poorly reflected the population, as defined through comparative sequence analysis.

Folate derived from cecal bacterial fermentation does not increase liver folate stores in 28-d folate-depleted male Sprague-Dawley rats

This study assessed the ability of rats to absorb and store the folate synthesized by cecal bacteria. Male weanling Sprague-Dawley rats were folate depleted by feeding a low folacin AIN93G formulated basal diet for 28 d; they were then fed repletion diets containing folate (0.25-1.0 mg/kg diet), dietary fiber (DF; wheat bran, oat bran, ground corn, wheat germ) or undigested and fermented dietary material (UFDM; polydextrose, inulin) in the presence and absence of an antibiotic (succinylsulfathiazole). Fermentation was stimulated by DF and UFDM and reduced by the antibiotic. In the absence of succinylsulfathiazole, the increase in liver folate (during the repletion phase) was proportional only to the folate content of the diet and did not vary with added DF or UFDM. Adding succinylsulfathiazole lowered total folate excretion from 13.8 +/- 8.2 to 4.8 +/- 2.9 nmol/d (pooled diets, P < 0.00001) in agreement with its role in inhibiting bacterial folate synthesis. In addition, succinylsulfathiazole lowered liver folate in rats fed control and test diets approximately equally with a mean decrease from 11.6 +/- 2.5 to 7.5 +/- 2.5 nmol/g wet liver (pooled diets, P < 0.00001), suggesting that the antibiotic also affected rat folate absorption and/or metabolism. Increased bacterial fermentation and excretion as well as increased bacterial folate production in the presence of added DF and UFDM were demonstrated by increased volatile fatty acid content in cecal and fecal samples (P < 0.000001) and increased diaminopimelic acid, muramic acid and folate in feces (P < 0.00001). The magnitude of these changes depended on the type of DF and UFDM. These results show that bacterially synthesized folate is not substantially absorbed and stored in the liver of Sprague-Dawley male rats.