• BLV
• Bovine leukemia virus
• Breast cancer

• Animals
• Cattle
• Female
• Humans
• Breast Neoplasms/virology
• Breast Neoplasms/epidemiology
• Enzootic Bovine Leukosis/virology
• Enzootic Bovine Leukosis/epidemiology
• Leukemia Virus, Bovine/isolation & purification
• Leukemia Virus, Bovine/pathogenicity
• Odds Ratio
• Risk Factors

• Aging
• Long-term care facility
• Randomized controlled trial
• Sarcopenia
• Skeletal muscle
• Soy protein

• Humans
• Soybean Proteins/administration & dosage
• Female
• Male
• Long-Term Care/methods
• Muscle, Skeletal/physiology
• Muscle, Skeletal/drug effects
• Aged, 80 and over
• Meals
• Aged
• Body Composition
• Sarcopenia/prevention & control
• Diet/methods
• Diet/statistics & numerical data
• Muscle Strength/drug effects

• airag
• koumiss
• lactic acid bacteria
• mare milk
• yeasts

• Behavioral lifestyle
• Chronic diseases
• Kyrgyz
• Literacy

• Humans
• Cross-Sectional Studies
• Health Literacy
• China
• Life Style
• Cities
• Surveys and Questionnaires

Health is influenced by how the gut microbiome develops as a result of external and internal factors, such as nutrition, the environment, medication use, age, sex, and genetics. Alpha and beta diversity metrics and (enterotype) clustering methods are commonly employed to perform population studies and to analyse the effects of various treatments, yet, with the continuous development of (new) sequencing technologies, and as various omics fields as a result become more accessible for investigation, increasingly sophisticated methodologies are needed and indeed being developed in order to disentangle the complex ways in which the gut microbiome and health are intertwined. Diseases of affluence, such as type 2 diabetes (T2D) and cardiovascular diseases (CVD), are commonly linked to species associated with the Bacteroides enterotype(s) and a decline of various (beneficial) complex microbial trophic networks, which are in turn linked to the aforementioned factors. In this review, we (1) explore the effects that some of the most common internal and external factors have on the gut microbiome composition and how these in turn relate to T2D and CVD, and (2) discuss research opportunities enabled by and the limitations of some of the latest technical developments in the microbiome sector, including the use of artificial intelligence (AI), strain tracking, and peak to trough ratios.

• diet pattern
• human health
• machine learning
• microbiome
• omics

• AoE/M-403/16 Research Grants Council, University Grants Committee (RGC, UGC)

• European dogs
• lactase persistence
• milk-drinking cultures
• population genomics

• Animals
• Dogs
• Gene Frequency
• Humans
• Lactase/genetics
• Lactase/metabolism
• Lactose/metabolism
• Polymorphism, Single Nucleotide
• Selection, Genetic
• White People

• National Natural Science Foundation of China
• Innovative Research Team
• Science and Technology
• National Key R&D Program of China
• Strategic Priority Research Program
• Chinese Academy of Sciences
• Key Research Program of Frontier Sciences of the CAS
• National Youth Talent Support Program
• Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences
• Large Research Infrastructure Funding

• BLV
• HTLV
• bovine leukemia virus
• breast cancer

• Adult
• Animals
• Breast Neoplasms
• Cattle
• Female
• Humans
• Leukemia Virus, Bovine/genetics

• Animals
• Asia
• DNA, Ancient
• Ethnicity/genetics
• Europe
• Fermentation
• Gene Frequency/genetics
• Genotype
• Humans
• Lactase/genetics
• Milk
• Selection, Genetic
• Time Factors

Gastrointestinal (GI) discomforts are common in the elderly population; however, whether such discomforts are associated with dietary intake has not been studied.

To evaluate GI discomforts in Chinese urban elders and the associated factors.

The gastrointestinal symptom rating scale (GSRS) was used to identify GI discomforts in 688 elders from eight cities of China. The semi-quantitative food frequency questionnaire and one time of 24 h dietary recall were used to access the food intake, identify dietary pattern, and calculate the nutrients intake.

About 83% of studied elders experienced at least one of GI discomforts in the past 6 mo; dyspepsia was the most commonly reported (66.7%), followed by reflux (44.8%), abdominal pain (35.9%), constipation (35.8%), and diarrhea (34.7%). Female gender, lower education level, and lower family income were associated with a higher GSRS score. Participants who were diagnosed with a GI-related disease had a higher score of constipation, but a lower score of reflux. Chronic diseases were positively associated with certain GI discomforts. Three dietary patterns were identified by the method of principal component analysis, which were characterized as high intake of salt and tea; more frequent intake of tubers, fruits, aquatic products, and soybeans; and high intake of cereal, vegetables, and meat, respectively. However, no associations between dietary patterns and GSRS score were found. The elders with a higher GSRS score had significantly lower intake of bean products. The elders whose GSRS score was ≥ 21 and 18-20 decreased their bean production intake by 7.2 (0.3, 14.3) g/d and 14.3 (1.2, 27.3) g/d, respectively, compared with those who had a GSRS score ≤ 17. There were no differences in other food categories, calories, or nutrients intake among elders with different GSRS scores.

GI discomforts are common in Chinese urban elders. GI discomforts might be associated with the choice of food.

• Gastrointestinal discomforts
• Nutrition
• Dietary intake
• Nutrients
• Elderly population

• Abdominal Pain
• Aged
• Aged, 80 and over
• China/epidemiology
• Cities
• Cross-Sectional Studies
• Diet
• Eating
• Energy Intake
• Female
• Fruit
• Gastroesophageal Reflux
• Gastrointestinal Diseases/physiopathology
• Humans
• Male
• Meat
• Middle Aged
• Nutrition Surveys
• Principal Component Analysis
• Social Class
• Surveys and Questionnaires
• Urban Population
• Vegetables

The aim of this study was to compare the impact of whole milk supplementation on gut microbiota and cardiometabolic biomarkers between lactose malabsorbers (LM) and absorbers (LA). We performed a pair-wise intervention study of 31 LM and 31 LA, 1:1 matched by age, sex, body mass index, and daily dairy intake. Subjects were required to add 250 mL/day whole milk for four weeks in their routine diet. At the beginning and the end of the intervention period, we collected data on gut microbiota and cardiometabolic biomarkers. Whole milk supplementation significantly increased Actinobacteria (P < 0.01), Bifidobacterium (P < 0.01), Anaerostipe (P < 0.01), and Blautia (P = 0.04), and decreased Megamonas (P = 0.04) in LM, but not LA. Microbial richness and diversity were not affected. The fecal levels of short-chain fatty acids (SCFAs) remained stable throughout the study. Body fat mass (P < 0.01) and body fat percentage (P < 0.01) reduced in both groups, but the changes did not differ between groups. No significant differences in other cardiometabolic markers were found between LM and LA. When compared with LA, whole milk supplementation could alter the intestinal microbiota composition in LM, without significant changes in fecal SCFAs and cardiometabolic biomarkers.

• Bifidobacterium
• gut microbiota
• lactose malabsorption
• milk
• short-chain fatty acids

• Actinobacteria/isolation & purification
• Adult
• Animals
• Bifidobacterium/isolation & purification
• Biomarkers/blood
• Diet/methods
• Feces/microbiology
• Female
• Gastrointestinal Microbiome/physiology
• Humans
• Lactose Intolerance/blood
• Lactose Intolerance/microbiology
• Male
• Milk/chemistry
• Milk/metabolism
• Young Adult

• Asia, Southeastern
• Breath Tests/methods
• Carbohydrate Metabolism/physiology
• Fermentation/physiology
• Gastrointestinal Diseases/diagnosis
• Gastrointestinal Diseases/physiopathology
• Humans
• Hydrogen/analysis
• Reproducibility of Results

Genomic regions of autozygosity (ROA) arise when an individual is homozygous for haplotypes inherited identical-by-descent from ancestors shared by both parents. Over the past decade, they have gained importance for understanding evolutionary history and the genetic basis of complex diseases and traits. However, methods to infer ROA in dense genotype data have not evolved in step with advances in genome technology that now enable us to rapidly create large high-resolution genotype datasets, limiting our ability to investigate their constituent ROA patterns.

We report a weighted likelihood approach for inferring ROA in dense genotype data that accounts for autocorrelation among genotyped positions and the possibilities of unobserved mutation and recombination events, and variability in the confidence of individual genotype calls in whole genome sequence (WGS) data.

Forward-time genetic simulations under two demographic scenarios that reflect situations where inbreeding and its effect on fitness are of interest suggest this approach is better powered than existing state-of-the-art methods to infer ROA at marker densities consistent with WGS and popular microarray genotyping platforms used in human and non-human studies. Moreover, we present evidence that suggests this approach is able to distinguish ROA arising via consanguinity from ROA arising via endogamy. Using subsets of The 1000 Genomes Project Phase 3 data we show that, relative to WGS, intermediate and long ROA are captured robustly with popular microarray platforms, while detection of short ROA is more variable and improves with marker density. Worldwide ROA patterns inferred from WGS data are found to accord well with those previously reported on the basis of microarray genotype data. Finally, we highlight the potential of this approach to detect genomic regions enriched for autozygosity signals in one group relative to another based upon comparisons of per-individual autozygosity likelihoods instead of inferred ROA frequencies.

This weighted likelihood ROA inference approach can assist population- and disease-geneticists working with a wide variety of data types and species to explore ROA patterns and to identify genomic regions with differential ROA signals among groups, thereby advancing our understanding of evolutionary history and the role of recessive variation in phenotypic variation and disease.

The online version of this article (doi:10.1186/s12864-017-4312-3) contains supplementary material, which is available to authorized users.

• Autozygosity
• Consanguinity
• Homozygosity
• Human populations
• Identity by descent
• Inbreeding

• China
• diet quality
• dietary index
• general population
• sociodemographic determinants

Insufficient intake of dairy products is a nutritional problem of concern in China. However, the knowledge, attitude, and practice of consuming dairy products in the Chinese population remain unknown. A total of 1739 subjects from eight cities in China participated in this study. A questionnaire was used to measure knowledge of and attitude toward dairy. A semi-food intake frequency questionnaire was used to obtain the frequencies and amount of different kinds of dairy product intake. Calcium and protein intake were investigated within one 24-hour period of dietary recall. The results showed that questions related to lactose intolerance had the highest unknown rate and the lowest accuracy. Males, subjects with a lower education level, lower monthly family income (<3000 yuan), lower monthly family food expenditure (<1000 yuan), and lower personal monthly expenditure on dairy products (<10 yuan) had a significantly lower knowledge score. For attitude, 42.7 percent of subjects had self-perceived insufficient intake of dairy. While 15.2 percent of subjects reported experiencing lactose intolerance symptoms, 29.5 percent did not know the reasons. In practice, the median (25th, 75th) intake of dairy products was 71.4 (0.0, 200.0) g/day. A significantly lower intake of dairy and low-fat or fat-free dairy products was shown in subjects with poor dairy knowledge. For the perception of lactose intolerance, the lowest intake was shown in the “unsure” group. In conclusion, knowledge gaps and self-perception bias regarding dairy products exist in Chinese urban adults and these are associated with the quantity and quality of dairy intake.

• Sintashta
• dairy products
• life histories
• paleodiet
• stable isotope analysis

The calcium supplementation status during the postpartum period among Chinese lactating women is still unclear. The objective of this study is to utilize data from two population-based prospective cohort studies to examine the calcium supplementation status and to identify whether breastfeeding is associated with increased calcium supplementation among Chinese mothers after child birth. Information from 1540 mothers on breastfeeding and calcium supplementation measured at discharge, 1, 3, and 6 months postpartum were extracted to evaluate the association between breastfeeding and calcium supplementation postpartum. A generalized linear mixed model was applied to each study initially to account for the inherent correlation among repeated measurements, adjusting for socio-demographic, obstetric factors and calcium supplementation during pregnancy. In addition, breastfeeding status measured at different follow-up time points was treated as a time dependent variable in the longitudinal analysis. Furthermore, the effect sizes of the two cohort studies were pooled using fixed effect model. Based on the two cohort studies, the pooled likelihood of taking calcium supplementation postpartum among breastfeeding mothers was 4.02 times (95% confidence interval (2.30, 7.03)) higher than that of their non-breastfeeding counterparts. Dietary supplementation intervention programs targeting different subgroups should be promoted in Chinese women, given currently a wide shortage of dietary calcium intake and calcium supplementation postpartum.

• China
• breastfeeding
• calcium supplementation
• generalized linear mixed model
• infant
• nutrients
• pooled analysis
• postpartum
• time dependent variable

• Adult
• Asian People
• Breast Feeding
• Calcium/administration & dosage
• Cohort Studies
• Dietary Supplements
• Female
• Humans
• Postpartum Period
• Pregnancy
• Young Adult

Cows’ milk generally contains two types of β-casein, A1 and A2 types. Digestion of A1 type can yield the peptide β-casomorphin-7, which is implicated in adverse gastrointestinal effects of milk consumption, some of which resemble those in lactose intolerance. This study aimed to compare the effects of milk containing A1 β-casein with those of milk containing only A2 β-casein on inflammation, symptoms of post-dairy digestive discomfort (PD3), and cognitive processing in subjects with self-reported lactose intolerance.

Forty-five Han Chinese subjects participated in this double-blind, randomized, 2 × 2 crossover trial and consumed milk containing both β-casein types or milk containing only A2 β-casein. Each treatment period was 14 days with a 14-day washout period at baseline and between treatment periods. Outcomes included PD3, gastrointestinal function (measured by smart pill), Subtle Cognitive Impairment Test (SCIT), serum/fecal laboratory biomarkers, and adverse events.

Compared with milk containing only A2 β-casein, the consumption of milk containing both β-casein types was associated with significantly greater PD3 symptoms; higher concentrations of inflammation-related biomarkers and β-casomorphin-7; longer gastrointestinal transit times and lower levels of short-chain fatty acids; and increased response time and error rate on the SCIT. Consumption of milk containing both β-casein types was associated with worsening of PD3 symptoms relative to baseline in lactose tolerant and lactose intolerant subjects. Consumption of milk containing only A2 β-casein did not aggravate PD3 symptoms relative to baseline (i.e., after washout of dairy products) in lactose tolerant and intolerant subjects.

Consumption of milk containing A1 β-casein was associated with increased gastrointestinal inflammation, worsening of PD3 symptoms, delayed transit, and decreased cognitive processing speed and accuracy. Because elimination of A1 β-casein attenuated these effects, some symptoms of lactose intolerance may stem from inflammation it triggers, and can be avoided by consuming milk containing only the A2 type of beta casein.

ClinicalTrials.gov/NCT02406469

The online version of this article (doi:10.1186/s12937-016-0147-z) contains supplementary material, which is available to authorized users.

• Cognitive processing
• Cows’ milk
• Gastrointestinal function
• Lactose intolerance
• β-casein

• calcium
• dairy products
• lactose intolerance
• milk

• Animals
• Dairy Products/adverse effects
• Dairy Products/history
• Diet/adverse effects
• Diet/history
• Diet/trends
• Evolution, Molecular
• Food Industry/history
• Food Industry/trends
• Food Labeling
• Genetic Predisposition to Disease
• History, Ancient
• Humans
• Lactase/genetics
• Lactase/metabolism
• Lactose Intolerance/diet therapy
• Lactose Intolerance/enzymology
• Lactose Intolerance/epidemiology
• Lactose Intolerance/genetics
• Lactose Intolerance/history
• Mutation
• Phenotype
• Risk Factors

• Adult
• Aged
• Animals
• Bayes Theorem
• Beverages/analysis
• Dietary Carbohydrates
• Feeding Behavior
• Female
• Fruit and Vegetable Juices
• Global Health
• Humans
• Male
• Middle Aged
• Milk
• Nutrition Surveys
• Sweetening Agents
• Young Adult

• R01-HD38700 NICHD NIH HHS
• R01 HD038700 NICHD NIH HHS
• 1K99HL124321 NHLBI NIH HHS
• K99 HL124321 NHLBI NIH HHS
• 100693 Wellcome Trust
• T32 DK007703 NIDDK NIH HHS
• R24 HD050924 NICHD NIH HHS
• 5 R24 HD050924 NICHD NIH HHS

• evolution
• inflammatory bowel disease
• lactase
• latitude
• ultraviolet B exposure

• abdominal bloating
• chronic diarrhea
• functional bowel disease
• lactose malabsorption
• milk intolerance

• Adult
• Animals
• Breath Tests/methods
• Dose-Response Relationship, Drug
• Female
• Follow-Up Studies
• Genotype
• Humans
• Hydrogen/metabolism
• Irritable Bowel Syndrome/complications
• Irritable Bowel Syndrome/diagnosis
• Irritable Bowel Syndrome/diet therapy
• Irritable Bowel Syndrome/genetics
• Lactase-Phlorizin Hydrolase/genetics
• Lactose/administration & dosage
• Lactose Intolerance/complications
• Lactose Intolerance/diagnosis
• Lactose Intolerance/diet therapy
• Lactose Intolerance/genetics
• Male
• Middle Aged
• Milk
• Polymorphism, Genetic
• Prognosis
• Sensitivity and Specificity

• Asia
• Constipation
• Management
• Physicians, primary care

• Adult
• Age of Onset
• Animals
• Calcium/metabolism
• Europe/epidemiology
• Genes, Recessive
• Humans
• Lactase
• Lactose Intolerance/epidemiology
• Lactose Intolerance/genetics
• Prevalence
• beta-Galactosidase/deficiency

• Forecasting
• Genetic Counseling/trends
• Genetic Testing/trends
• Hong Kong
• Humans
• Personnel Staffing and Scheduling/trends
• Prenatal Diagnosis/trends