Integrating Dietary Data into Microbiome Studies: A Step Forward for Nutri-Metaomics

Diet is recognised as the main driver of changes in gut microbiota. However, linking habitual dietary intake to microbiome composition and activity remains a challenge, leaving most microbiome studies with little or no dietary information. To fill this knowledge gap, we conducted two consecutive studies (n = 84: a first pilot study (n = 40) to build a web-based, semi-quantitative simplified FFQ (sFFQ) based on three 24-h dietary recalls (24HRs); a second study (n = 44) served to validate the newly developed sFFQ using three 24HRs as reference method and to relate gut microbiome profiling (16S rRNA gene) with the extracted dietary and lifestyle data. Relative validation analysis provided acceptable classification and agreement for 13 out of 24 (54%) food groups and 20 out of 29 nutrients (69%) based on intraclass correlation coefficient, cross-classification, Spearman’s correlation, Wilcoxon test, and Bland–Altman. Microbiome analysis showed that higher diversity was positively associated with age, vaginal birth, and intake of fruit. In contrast, microbial diversity was negatively associated with BMI, processed meats, ready-to-eat meals, sodium, and saturated fat. Our analysis also revealed a correlation between food groups or nutrients and microbial composition. Overall, we provide the first dietary assessment tool to be validated and correlated with microbiome data for population studies.

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Reproducibility and validity of dietary patterns identified using factor analysis among Chinese populations

British Journal Of Nutrition ◽

10.1017/s000711451600249x ◽

2016 ◽

Vol 116 (5) ◽

pp. 842-852 ◽

Cited By ~ 5

Author(s):

Xin Hong ◽

Qing Ye ◽

Zhiyong Wang ◽

Huafeng Yang ◽

Xupeng Chen ◽

...

Keyword(s):

Factor Analysis ◽

Dietary Patterns ◽

Dietary Pattern ◽

Protein Pattern ◽

Dietary Assessment ◽

Intraclass Correlation ◽

Correlation Coefficients ◽

Reference Method ◽

Plant Protein ◽

Food Groups

AbstractIn the present study, we evaluated the reproducibility and validity of dietary patterns among Chinese adult populations. A random subsample of 203 participants (aged 31–80 years) from a community-based nutrition and health survey was enrolled. An eighty-seven-item FFQ was administered twice (FFQ1 and FFQ2) 1 year apart; four 3 consecutive day, 24-h dietary recalls (24-HDR, as a reference method) were performed between the administrations of the two FFQ every 3 months. Dietary patterns from three separate dietary sources were derived using factor analysis based on twenty-eight predefined food groups. Comparisons between dietary pattern scores were made by using Pearson’s or intraclass correlation coefficients (ICC), cross-classification analysis, weighted κ statistic and Bland–Altman plots; the four major dietary patterns identified from FFQ1, FFQ2 and 24-HDR were similar. Regarding reproducibility, ICC for z-scores between FFQ1 and FFQ2 were all >0·6 for dietary patterns. The ‘animal and plant protein’ pattern had the highest ICC of 0·870. For validity, the adjusted Pearson’s correlation coefficients for dietary pattern z-scores between two FFQ and the mean of four 3 consecutive day 24-HDR ranged from 0·387 for the ‘Chinese traditional’ pattern to 0·838 for the ‘animal and plant protein’ pattern. More than 75 % of the participants were classified into the same or adjacent quartile, and <5 % were misclassified into opposite quartiles. The weighted κ ranged from 0·259 to 0·680. Bland–Altman plots indicated that no significant deviation was found between two dietary assessment methods. Our findings indicate a good reasonable reproducibility and a reasonable validity of dietary patterns derived by factor analysis in China.

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Validity and Reliability of a Short Diet Questionnaire to Estimate Dietary Intake in Older Adults in a Subsample of the Canadian Longitudinal Study on Aging

Nutrients ◽

10.3390/nu10101522 ◽

2018 ◽

Vol 10 (10) ◽

pp. 1522 ◽

Cited By ~ 4

Author(s):

Anne Gilsing ◽

Alexandra Mayhew ◽

Hélène Payette ◽

Bryna Shatenstein ◽

Sharon Kirkpatrick ◽

...

Keyword(s):

Longitudinal Study ◽

Assessment Tool ◽

Dietary Assessment ◽

Intraclass Correlation ◽

Correlation Coefficients ◽

Food Groups ◽

Validity And Reliability ◽

Retest Reliability ◽

System Usability Scale ◽

Test Retest Reliability

This study assessed test-retest reliability and relative validity of the Short Diet Questionnaire (SDQ) and usability of an online 24 h recall among 232 participants (62 years ± 9.1; 49.6% female) from the Canadian Longitudinal Study on Aging (CLSA). Participants were asked to complete four 24 h dietary recalls (24HRs) using the Automated Self-Administered 24-h Dietary Assessment Tool (ASA24-Canada-2014), two SDQ administrations (prior to recalls one and four), and the System Usability Scale (SUS) for ASA24. For the SDQ administrations, Intraclass Correlation Coefficients ranged from 0.49 to 0.57 for nutrients and 0.35 to 0.72 for food groups. Mean intakes estimated from the SDQ were lower compared than those from the 24HRs. For nutrients, correlation coefficients were highest for fiber, calcium, and vitamin D (45–64 years: 0.59, 0.50, 0.51; >65 years: 0.29, 0.38, 0.49, p < 0.01); Kappas ranged from 0.14 to 0.37 in those 45–64 years and 0.17 to 0.32 in participants >65 years. Among the 70% who completed all recalls independently, the SUS indicated poor usability, though the majority reported feeling confident using ASA24. Overall, the SDQ captures intake with varying test-retest reliability and accuracy by nutrient and age. Further research is needed to inform use of a more comprehensive dietary measure in the CLSA.

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A Dietary Assessment App for Hospitalized Patients at Nutritional Risk: Development and Evaluation of the MyFood App (Preprint)

10.2196/preprints.9953 ◽

2018 ◽

Author(s):

Mari Mohn Paulsen ◽

Martina Lovise Lindhart Hagen ◽

Marte Hesvik Frøyen ◽

Rikke Julie Foss-Pedersen ◽

Dagfinn Bergsager ◽

...

Keyword(s):

Assessment Tool ◽

Dietary Assessment ◽

Hospital Setting ◽

Reference Method ◽

Hospitalized Patients ◽

Assessment System ◽

University Hospital ◽

Nutritional Risk ◽

Food Groups ◽

Food And Beverage

BACKGROUND Disease-related malnutrition is a common challenge among hospitalized patients. There seems to be a lack of an effective system to follow-up nutritional monitoring and treatment of patients at nutritional risk after risk assessment. We identify a need for a more standardized system to prevent and treat disease-related malnutrition. OBJECTIVE We aimed to develop a dietary assessment app for tablets for use in a hospital setting and to evaluate the app’s ability to measure individual intake of energy, protein, liquid, and food and beverage items among hospitalized patients for two days. We also aimed to measure patients’ experiences using the app. METHODS We have developed the MyFood app, which consists of three modules: 1) collection of information about the patient, 2) dietary assessment function, and 3) evaluation of recorded intake compared to individual needs. We used observations from digital photography of the meals, combined with partial weighing of the meal components, as a reference method to evaluate the app’s dietary assessment system for two days. Differences in the intake estimations of energy, protein, liquid, and food and beverage items between MyFood and the photograph method were analyzed on both group and individual level. RESULTS Thirty-two patients hospitalized at Oslo University Hospital were included in the study. The data collection period ran from March to May 2017. About half of the patients had ≥90% agreement between MyFood and the photograph method for energy, protein, and liquid intake on both recording days. Dinner was the meal with the lowest percent agreement between methods. MyFood overestimated patients’ intake of bread and cereals and underestimated fruit consumption. Agreement between methods increased from day 1 to day 2 for bread and cereals, spreads, egg, yogurt, soup, hot dishes, and desserts. Ninety percent of participants reported that MyFood was easy to use, and 97% found the app easy to navigate. CONCLUSIONS We developed the MyFood app as a tool to monitor dietary intake among hospitalized patients at nutritional risk. The recorded intake of energy, protein, and liquid using MyFood showed good agreement with the photograph method for the majority of participants. The app’s ability to estimate intake within food groups was good, except for bread and cereals which were overestimated and fruits which were underestimated. The app was well accepted among study participants and has the potential to be a dietary assessment tool for use among patients in clinical practice.

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A cross-sectional assessment of food- and nutrient-based standards applied to British schoolchildren’s packed lunches

Public Health Nutrition ◽

10.1017/s1368980016002251 ◽

2016 ◽

Vol 20 (3) ◽

pp. 565-570 ◽

Cited By ~ 4

Author(s):

Charlotte EL Evans ◽

Janet E Cade

Keyword(s):

Primary Schools ◽

Assessment Tool ◽

Dietary Assessment ◽

Quality Score ◽

Food Groups ◽

Multilevel Regression ◽

Optimal Model ◽

Cross Sectional ◽

The Uk ◽

Dietary Data

AbstractObjectiveIn England, standards for school meals included both foods and nutrients until 2015. School policies for packed lunches are generally food based; research is needed to determine whether these are adequate or whether a small number of nutrients would potentially improve their quality.DesignFrom dietary data obtained using a weighed dietary assessment tool, a diet quality score (DQS) for packed lunches was calculated using the number of standards met out of twenty-one (eight foods and thirteen nutrients). Multilevel regression analysis determined the foods and nutrients contributing to variation in the DQS.SettingEighty-nine primary schools across the four regions of the UK (England, Wales, Scotland and Northern Ireland).SubjectsBritish schoolchildren (n 1294), aged 8–9 years, taking a packed lunch.ResultsThe optimal model included all eight foods and seven of the thirteen nutrients, explaining 72 % of the variance in DQS. Folate, Fe and vitamin C, together with the eight food groups, explained 70 % of DQS variation.ConclusionsIdeally, policies for school packed lunches should include food-based standards plus recommendations based on a small number of nutrients.

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Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content

Microbial Ecology ◽

10.1007/s00248-021-01944-z ◽

2021 ◽

Author(s):

Artur Trzebny ◽

Anna Slodkowicz-Kowalska ◽

Johanna Björkroth ◽

Miroslawa Dabert

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

Gut Microbiome ◽

Bacterial Communities ◽

Bacterial Species ◽

Rrna Gene ◽

Microbial Composition ◽

Microbiome Composition ◽

Microsporidian Infection ◽

Functional Content

AbstractThe animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.

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Acculturation and dietary habits of Korean Americans

British Journal Of Nutrition ◽

10.1079/bjn20031068 ◽

2004 ◽

Vol 91 (3) ◽

pp. 469-478 ◽

Cited By ~ 31

Author(s):

Jeongseon Kim ◽

Mabel M. Chan

Keyword(s):

New York ◽

Dietary Habits ◽

Assessment Tool ◽

Dietary Assessment ◽

Korean Americans ◽

Food Groups ◽

Validity And Reliability ◽

Nutrient Intakes ◽

Brown Sugar ◽

Total Fat

This is the first study to investigate how food and nutrient intakes vary with the levels of acculturation of Korean Americans using a dietary assessment tool tested for validity and reliability. The respondents were Korean Americans (n 486) resident in the Greater New York metropolitan area, USA. They were divided into two groups according to the total score of acculturation: low- and high-acculturated groups. Using a food-frequency questionnaire and a modified Suinn-Lew Asian self-identity acculturation scale, differences in the frequencies of food items, food groups and nutrient intakes consumed were analysed by level of acculturation. The low-acculturated group tended to consume significantly more rice, mixed rice, soyabean paste chigae (pot stew), saengsun (fish) chigae, kimchi chigae, other fish broiled or baked, eggs, kimchi, spinach, persimmons, and white or brown sugar in coffee or tea. The high-acculturated group demonstrated a statistically greater tendency to consume bread, cereal, spaghetti, ham, green salad, sweetcorn, chocolate, candies and diet soft drinks. The more acculturated an individual, the more significant was the tendency to consume sweets. The more acculturated group had significantly (P<0·05) higher intakes of % energy from total fat, thiamin, vitamin E and folate, while the low-acculturated group consumed greater amounts of Na, niacin and dietary fibre. The information from the present study can be used to describe dietary habits according to various aspects of acculturation, and allows a better understanding of the dynamics of acculturation and dietary habits.

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Analysis of Hindgut Microbiome of Sheep and Effect of Different Husbandry Conditions

Animals ◽

10.3390/ani11010004 ◽

2020 ◽

Vol 11 (1) ◽

pp. 4

Author(s):

Giulietta Minozzi ◽

Filippo Biscarini ◽

Emanuela Dalla Costa ◽

Matteo Chincarini ◽

Nicola Ferri ◽

...

Keyword(s):

Animal Health ◽

Control Group ◽

P Value ◽

Rrna Gene ◽

Microbial Composition ◽

Core Microbiome ◽

Fecal Microbiome ◽

Microbiome Composition ◽

The Core ◽

Wide Range

The microbiome is now seen as an important resource to understand animal health and welfare in many species. However, there are few studies aiming at identifying the association between fecal microbiome composition and husbandry conditions in sheep. A wide range of stressors associated with management and housing of animals increases the hypothalamic–pituitary axis activity, with growing evidence that the microbiome composition can be modified. Therefore, the purpose of the present study was to describe the core microbiome in sheep, characterized using 16S rRNA gene sequencing, and to explore whether exposure to stressful husbandry conditions changed sheep hindgut microbiome composition. Sheep (n = 10) were divided in two groups: isolated group (individually separated for 3 h/day) and control group (housed in the home pen for the entire trial period). Sheep core microbiome was dominated by Firmicutes (43.6%), Bacteroidetes (30.38%), Proteobacteria (10.14%), and Verrucomicrobia (7.55%). Comparative results revealed few operational taxonomic units (OTUs) with significantly different relative abundance between groups. Chao1, abundance-based coverage estimator (ACE), and Fisher’s alpha indices did not show differences between groups. OTU-based Bray–Curtis distances between groups were not significant (p-value = 0.07). In conclusion, these results describing the core microbiome of sheep do not suggest a strong effect of stressful husbandry conditions on microbial composition.

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Agreement between an Image-Based Dietary Assessment Method and a Written Food Diary among Adolescents with Type 1 Diabetes

Nutrients ◽

10.3390/nu13041319 ◽

2021 ◽

Vol 13 (4) ◽

pp. 1319

Author(s):

Laura Heikkilä ◽

Marja Vanhala ◽

Raija Korpelainen ◽

Päivi Tossavainen

Keyword(s):

Type 1 Diabetes ◽

Dietary Intake ◽

Assessment Tool ◽

Dietary Assessment ◽

Intraclass Correlation ◽

Correlation Coefficients ◽

Assessment Method ◽

Food Diary ◽

Total Carbohydrate

Valid and useful dietary assessment methods for adolescents with type 1 diabetes (T1D) are needed. In this study, we compared an image-based method with a written food diary for dietary intake estimation among adolescents with T1D and evaluated the adolescents’ experiences of the methods. Adolescents with T1D aged 13 to 18 years (n = 13) photographed their meals (n = 264) with a mobile phone camera and simultaneously kept a written food diary for four consecutive days. The participants filled out electronic background and feedback questionnaires. The agreement between the methods was evaluated using intraclass correlation coefficients (ICCs) and Bland–Altman plot analyses. The agreement between the methods was moderate to excellent for the energy intake (ICC = 0.91, 95% confidence interval (CI): 0.66 to 0.97, p < 0.001) and good to excellent for total carbohydrate intake (ICC = 0.95, 95% CI: 0.84 to 0.99, p < 0.001). The adolescents considered photographing easier and faster than keeping a food diary. In conclusion, the image-based method appeared comparable to the food diary for dietary intake estimation among adolescents with T1D. The photographing of meals may become a useful dietary assessment tool for adolescents with T1D, but must be further developed and validated.

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The potential of a Web-based, Self-Administered Dietary Assessment Tool (Foodbook24) for National Nutrition Surveillance. (Preprint)

10.2196/preprints.22759 ◽

2020 ◽

Author(s):

Claire M. Timon ◽

Janette Walton ◽

Albert Flynn ◽

Eileen R. Gibney

Keyword(s):

Dietary Intake ◽

Nutrient Intake ◽

Assessment Tool ◽

Dietary Assessment ◽

Demographic Characteristics ◽

Food Groups ◽

Nutrition Survey ◽

Web Based ◽

24 Hour Recall ◽

Daily Intakes

BACKGROUND There are many constraints to conducting national food consumption surveys for the purposes of national nutrition surveillance including cost, time and participant burden. Validated Web-based dietary assessment technologies offer a potential solution to many if these constraints. OBJECTIVE This study investigated the feasibility of using a previously validated, Web-based 24-hour recall dietary assessment tool (Foodbook24) for the purposes of nutrition surveillance by comparing the demographic characteristics and the quality of dietary intake data collected from an online cohort of participants in Ireland to the most recent Irish National Adult Nutrition Survey (NANS). METHODS Irish adult participants (aged 18 and over) were recruited to use Foodbook24 (Web-based tool). Demographic and dietary intake (by means of 2 non-consecutive self-administered 24-hour recalls) data was collected using Foodbook24. Following completion of the study, the dietary intake data collected were statistically weighted to represent the population of participants that completed the National Adult and Nutrition Survey (NANS) (2011) to facilitate the controlled comparison of intake data. Demographic characteristics of survey respondents were investigated using descriptive statistics in SPSS V20. The controlled comparison of weighted mean daily nutrient intake data collected from the Foodbook24 Web-based study (n= 329 plausible reporters) and the mean daily nutrient intake data collected from NANS (n=1051 plausible reporters) was conducted using the Wilcoxon-Mann–Whitney U-test in Creme Nutrition® software. RESULTS The results of this analysis highlight many differences between the demographic characteristics between both sets of survey participants. Notable differences included a lower proportion of adults aged 65 years and over and a higher proportion of females participated in the Web-based Foodbook24 study relative to the NANS study. Similar ranges of mean daily intakes for the majority of nutrients and food groups were observed (e.g. Energy (kcal/day) and Carbohydrate (g/day)), although significant differences for some nutrient (e.g. Riboflavin (mg/10MJ) and Vitamin B12 (µg/10MJ)) and food groups were identified. A high proportion of participants (47%) reported a willingness to continue to use Foodbook24 for an additional 6-month period. CONCLUSIONS These findings suggest that by using targeted recruitment strategies in the future to ensure the recruitment of a more representative sample, there is potential for Web-based methodologies such as Foodbook24 to be used for nutrition surveillance efforts in Ireland. CLINICALTRIAL n/a

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Gut Microbiome Biomarkers in Adolescent Obesity: a Regional Study

10.1101/745489 ◽

2019 ◽

Cited By ~ 1

Author(s):

Xuefeng Gao ◽

Binbin Wu ◽

Yonglong Pan ◽

Shaoming Zhou ◽

Ming Zhang ◽

...

Keyword(s):

Signaling Pathway ◽

Gut Microbiome ◽

Blood Pressure Measurement ◽

Rrna Gene ◽

Case Control Studies ◽

Regional Study ◽

Microbial Composition ◽

Bacterial Gene ◽

Fecal Microbiome ◽

Microbiome Composition

ABSTRACTPurposeThis study aimed to characterize the gut microbiota in obese Shenzhen adolescents, and evaluate the influence of gender on BMI-related differences in the gut microbiome.MethodsPhysical examinations, blood pressure measurement, serological assay, and body composition evaluation were conducted on two-hundred and five adolescents from Shenzhen. Fecal microbiome composition was profiled via 16S rRNA gene sequencing. A Random Forest (RF) classifier model was built to distinguish the BMI categories based on the gut bacterial composition.ResultsFifty-six taxa consisting mainly of Firmicutes were identified that having significant associations with BMI; two OTUs belonging to Ruminococcaceae and one belonging to Lachnospiraceae had relatively strong positive correlations with body fate rate, waistline, and most of serum biochemical parameters. Based on the 56 BMI-associated OTUs, the RF model showed a robust classification accuracy (AUC 0.96) for predicting the obese phenotype. Gender-specific differences in the gut microbiome composition was obtained, and a lower relative abundance of Odoribacter was particularly found in obese boys. Functional analysis revealed a deficiency in bacterial gene contents related to PPAR signaling pathway in obese subjects for both genders; significantly lower levels of adipocytokine signaling pathway and ethylbenzene degradation were particularly detected in obese girls.ConclusionsThis study revealed unique features of gut microbiome in terms of microbial composition and metabolic functions in obese Shenzhen adolescents. The effect of geographical location, age and gender on the gut microbiome should be carefully considered in case–control studies.

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