Systematic analysis of microbiota in pregnant Chinese women and its association with miscarriage.

Background: Miscarriage is the most common adverse pregnancy outcome and more than 50% of its incidence remains unexplained. Earlier studies have suggested that maternal microbiota might be associated with miscarriage, but the association is insufficiently understood. Methods: We used 16S ribosomal RNA (rRNA) amplicon sequencing and metagenomic sequencing technology to characterize the bacterial composition of three sites including the rectum, vagina, and cervix of a case group of 63 pregnant women who had miscarried compared to a control group of 24 pregnant women who underwent voluntary elective abortion. Results: The alpha-diversity from the rectum and cervix was significantly decreased in the case group relative to the control group. However, we did not find significant differences in microbial diversity of vaginal samples between the two groups. Lactobacillus was the most predominant genus in the cervix and vaginal samples. Gestational age at the time of surgery was positively associated with the rectum microbiota diversity, with an effect size of 10% (P=0.004). Host factors including gestational age and red blood count (RBC) were associated with the rectal microbiota diversity. Conclusions: We detected a significantly lower rectal microbiota diversity and a pro-inflammatory tendency in the miscarriage group. This is the first study to investigate the association of microbiota from samples collected from three sites and miscarriage. Further studies are warranted to explore further the role of microbiota in miscarriage.

Highly precise breakpoint detection of chromosome balanced translocation in chronic myelogenous leukaemia: Case series.

Chronic myelogenous leukaemia (CML) has a special phenomenon of chromosome translocation, which is called Philadelphia chromosome translocation. However, the detailed connection of this structure is troublesome and expensive to be identified. Low-coverage whole genome sequencing (LCWGS) could not only detect the previously unknown chromosomal translocation, but also provide the breakpoint candidate small region (with an accuracy of ±200 bases). Importantly, the sequencing cost of LCWGS is about US$300. Then, with the Sanger DNA sequencing, the precise breakpoint can be determined at a single base level. In our project, with LCWGS, BCR and ABL1 are successfully identified to be disrupted in three CML patients (at chr22:23,632,356 and chr9:133,590,450; chr22:23,633,748 and chr9:133,635,781; chr22: 23,631,831 and chr9:133,598,513, respectively). Due to the reconnection after chromosome breakage, classical fusion gene (BCR::ABL1) was found in bone marrow and peripheral blood. The precise breakpoints were helpful to investigate the pathogenic mechanism of CML and could better guide the classification of CML subtypes. This LCWGS method is universal and can be used to detect all diseases related to chromosome variation, such as solid tumours, liquid tumours and birth defects.

A de novo 10q11.23q22.1 deletion detected by whole genome mate-pair sequencing: a case report.

BACKGROUND: Interstitial deletions of chromosome band 10q11-q22 was a genomic disorder distinguished by developmental delay, congenital cleft palate and muscular hypotonia. The phenotypes involved were heterogeneous, hinge on the variable breakpoints and size. CASE PRESENTATION: Here, we presented a patient with soft palate cleft, growth and development delay. The patient was a 2 years and 5 months girl who was not able to walk unless using a children's crutches to support herself. Whole-exome sequencing (WES) and whole-genome mate-pair sequencing (WGMS) were both performed by next generation sequencing (NGS). A 20.76 Mb deletion at 10q11.23q22.1 (seq[GRCh37/hg19]del(10)(50,319,387-71,083,899) × 1) was revealed by the WGMS, which was verified as de novo by quantitative polymerase chain reaction (QPCR). CONCLUSION: Children with 10q11-q22 deletions greater than 20 MB have never been reported before, and we are the first to report and provide a detailed clinical phenotype, which brings further knowledge of 10q11-q22 deletions.

A genome-wide association study for gut metagenome in Chinese adults illuminates complex diseases.

The gut microbiome has been established as a key environmental factor to health. Genetic influences on the gut microbiome have been reported, yet, doubts remain as to the significance of genetic associations. Here, we provide shotgun data for whole genome and whole metagenome from a Chinese cohort, identifying no <20% genetic contribution to the gut microbiota. Using common variants-, rare variants-, and copy number variations-based association analyses, we identified abundant signals associated with the gut microbiome especially in metabolic, neurological, and immunological functions. The controversial concept of enterotypes may have a genetic attribute, with the top two loci explaining 11% of the Prevotella-Bacteroides variances. Stratification according to gender led to the identification of differential associations in males and females. Our two-stage metagenome genome-wide association studies on a total of 1295 individuals unequivocally illustrates that neither microbiome nor GWAS studies could overlook one another in our quest for a better understanding of human health and diseases.

A case report of congenital idiopathic hypogonadotropic hypogonadism caused by novel mutation of GNRHR gene.

RATIONALE: This study aimed to investigate the genetic mutation characteristics of congenital idiopathic hypogonadotropic hypogonadism (IHH) through the clinical features and genetic analysis of 2 patients with IHH in 1 pedigree. PATIENT CONCERNS: A 23-year-old girl presented with primary amenorrhea, sparse pubic hair, lack of breast development, and delayed sexual development. DIAGNOSES: Combined with the clinical characteristics, auxiliary examinations, and molecular genetic analysis, the patient was diagnosed as IHH. INTERVENTIONS: Whole exome and Sanger sequencing were performed to validate the mutation in family members. OUTCOMES: A novel homozygous missense mutation c.521A > G (p.Q174R) in the GNRHR gene was identified in the 2 affected sisters. Familial segregation showed that the homozygous variant was inherited from their parents respectively and the eldest sister was the carrier without correlative symptom. LESSONS: We reported a novel GNRHR mutation in a pedigree with congenital idiopathic hypogonadotropic hypogonadism. Glutamine at amino acid position 174 was highly conserved among various species. The molecular structure of GNRHR protein showed that p.Q174R mutation brought in a new stable hydrogen bond between position 174 and 215, may impede conformational mobility of the TMD4 and TMD5. It suggests that the missense mutation c.521A > G related to congenital idiopathic hypogonadotropic hypogonadism was probably a causative factor for both sisters. Through high-throughput sequencing and experimental verification, we had basically determined the patient's pathogenic mutation and inheritance, which could better guide doctors for treatment.

Sex- and age-related trajectories of the adult human gut microbiota shared across populations of different ethnicities.

Lifelong sex- and age-related trajectories of the human gut microbiota remain largely unexplored. Using metagenomics, we derived the gut microbial composition of 2,338 adults (26-76 years) from a Han Chinese population-based cohort where metabolic health, hormone levels and aspects of their lifestyles were also recorded. In this cohort, and in three independent cohorts distributed across China, Israel and the Netherlands, we observed sex differences in the gut microbial composition and a shared age-related decrease in sex-dependent differences in gut microbiota. Compared to men, the gut microbiota of premenopausal women exhibited higher microbial diversity and higher abundances of multiple species known to have beneficial effects on host metabolism. We also found consistent sex-independent, age-related gut microbial characteristics across all populations, with the presence of members of the oral microbiota being the strongest indicator of older chronological age. Our findings highlight the existence of sex- and age-related trajectories in the human gut microbiota that are shared between populations of different ethnicities and emphasize the pivotal links between sex hormones, gut microbiota and host metabolism.

A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment.

BACKGROUND: The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. RESULTS: Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes. CONCLUSIONS: These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.

[Application of Mindfulness-Based Health-Promotion Behavior in People With Chronic Diseases: SMILE Strategy].

Chronic diseases often impact the quality of life of the patient, causing complications and increased mortality and medical costs. The World Health Organization proposed applying mindfulness as an important strategy to help transform the situation faced by chronic disease cases and to promote their mental flexibility and adaptability. The author reviewed the related literature on mindfulness and introduces the "SMILE" strategy in this article. This strategy includes several stages, including 1) Starting where I am, 2) Motivating patients to become self-aware of the experience of self and internal and external environment interactions, 3) Developing individual health beliefs, 4) Learning mindfulness-based health-promotion behaviors, 5) Evaluating the efficacy of mindfulness-based health-promotion behaviors and self-regulation. SMILE is a powerful strategy with the potential to promote patient wellbeing, acceptance of the need to coexist with chronic disease, and freedom. Mindfulness is an abstract concept. This article provides a reference on mindfulness intervention for healthcare providers.

Alterations in the human gut microbiome associated with Helicobacter pylori infection.

Helicobacter pylori infection (HPI) is a prevalent infectious disease associated with gastric ulcer, gastric cancer, and many nongastrointestinal disorders. To identify genes that may serve as microbial markers for HPI, we performed shotgun metagenomic sequencing of fecal samples from 313 Chinese volunteers who had undergone a C14 breath test. Through comparing differences in intestinal microbial community structure between H. pylori-positive and H. pylori-negative individuals, we identified 58 HPI-associated microbial species (P < 0.05, Wilcoxon test). A classifier based on microbial species markers showed high diagnostic ability for HPI (AUC = 0.84). Furthermore, levels of gut microbial vitamin B12 (VB12) biosynthesis and plasma VB12 were significantly lower in H. pylori-positive individuals compared with H. pylori-negative individuals (P < 0.05, Wilcoxon test). This study reveals that certain alterations in gut microbial species and functions are associated with HPI and shows that gut microbial shift in HPI patients may indirectly elevate the risk of VB12 deficiency.

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.

Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes.

MetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networks.

Pangenome analyses facilitate the interpretation of genetic diversity and evolutionary history of a taxon. However, there is an urgent and unmet need to develop new tools for advanced pangenome construction and visualization, especially for metagenomic data. Here, we present an integrated pipeline, named MetaPGN, for construction and graphical visualization of pangenome networks from either microbial genomes or metagenomes. Given either isolated genomes or metagenomic assemblies coupled with a reference genome of the targeted taxon, MetaPGN generates a pangenome in a topological network, consisting of genes (nodes) and gene-gene genomic adjacencies (edges) of which biological information can be easily updated and retrieved. MetaPGN also includes a self-developed Cytoscape plugin for layout of and interaction with the resulting pangenome network, providing an intuitive and interactive interface for full exploration of genetic diversity. We demonstrate the utility of MetaPGN by constructing Escherichia coli pangenome networks from five E. coli pathogenic strains and 760 human gut microbiomes,revealing extensive genetic diversity of E. coli within both isolates and gut microbial populations. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data, MetaPGN provides advantages in expanding pangenome analysis to uncultured microbial taxa.

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment.

We carried out metagenomic shotgun sequencing and a metagenome-wide association study (MGWAS) of fecal, dental and salivary samples from a cohort of individuals with rheumatoid arthritis (RA) and healthy controls. Concordance was observed between the gut and oral microbiomes, suggesting overlap in the abundance and function of species at different body sites. Dysbiosis was detected in the gut and oral microbiomes of RA patients, but it was partially resolved after RA treatment. Alterations in the gut, dental or saliva microbiome distinguished individuals with RA from healthy controls, were correlated with clinical measures and could be used to stratify individuals on the basis of their response to therapy. In particular, Haemophilus spp. were depleted in individuals with RA at all three sites and negatively correlated with levels of serum autoantibodies, whereas Lactobacillus salivarius was over-represented in individuals with RA at all three sites and was present in increased amounts in cases of very active RA. Functionally, the redox environment, transport and metabolism of iron, sulfur, zinc and arginine were altered in the microbiota of individuals with RA. Molecular mimicry of human antigens related to RA was also detectable. Our results establish specific alterations in the gut and oral microbiomes in individuals with RA and suggest potential ways of using microbiome composition for prognosis and diagnosis.

Establishing a model to assess the effects of school support and self-care behaviors on life satisfaction in adolescents with type 1 diabetes in Taiwan.

BACKGROUND: Life satisfaction is associated with positive development in adolescents. Understanding a path model of life satisfaction can help healthcare providers design interventions to improve positive development in adolescents with type 1 diabetes. PURPOSE: The aim of this study was to construct a model that assesses the effects of school support and self-care behaviors on life satisfaction in adolescents with type 1 diabetes in Taiwan. METHODS: This study used a cross-sectional design. One hundred and thirty-nine adolescents aged 10-18 years and diagnosed with type 1 diabetes were recruited. Participants completed questionnaires that assessed perceived school support, self-care behaviors, and life satisfaction. The hypothesized model was tested using structural equation modeling. RESULTS: School support significantly and directly affected self-care behaviors (ß = .46, p = .022) and life satisfaction (ß = .39, p = .034), self-care behaviors directly affected life satisfaction (ß = .56, p = .048), and school support indirectly affected life satisfaction (ß = .26, p = .015) through the mediation of self-care behaviors. The fix indices were as follows: χ2 = 8.141, df = 11, p = .701, goodness of fit index = .984, normed fit index = .949, and root mean square residual = .001. The model explained 66.1% of total life satisfaction variance. CONCLUSIONS: School support and self-care behaviors positively influence the life satisfaction of adolescents with type 1 diabetes. Improvements in school support and self-care behaviors are necessary to improve life satisfaction in this vulnerable group.

Depressive symptoms in Taiwanese women during the peri- and post-menopause years: associations with demographic, health, and psychosocial characteristics.

OBJECTIVE: The purpose of this study was to evaluate the prevalence of depressive symptoms in peri- and post-menopausal Taiwanese women, and to investigate the relation between depressive symptoms and demographic variables, chronic disease status, health habits, stress management, menopausal symptoms, and attitudes toward menopause and aging. STUDY DESIGN: Cross-sectional study, using a purposive sample of 566 women between 45 and 60 years of age from a medical center and residential community in Southern Taiwan. MAIN OUTCOME MEASURES: Demographic and health habits questionnaire, Women's Health Initiative Symptom Scale, Attitudes Toward Menopause and Aging Scale, and Center for Epidemiological Studies-Depression Scale (CES-D). RESULTS: The prevalence of depressive symptoms (CES-D score≥16) was 38.7% in peri- and post-menopausal Taiwanese women. Bivariate correlations and analyses of variance indicated that higher CES-D scores were related to lower family income, younger age, smoking for a greater number of years, consuming more alcohol, having multiple chronic diseases, not exercising regularly, consulting with a specialist for stress management, having more severe menopausal symptoms, and more negative attitudes toward menopause and aging. A stepwise multiple regression analysis indicated that the key predictors, accounting for 33.7% of the variance, were menopausal symptoms, attitudes toward menopause and aging, family income, and chronic disease status. CONCLUSIONS: Results highlight the importance of considering psychosocial factors, life style, and chronic disease management in providing health guidance for peri- and post-menopausal women to enhance their quality of life and reduce the risk of depressive symptoms.

The relationship between selected developmental assets and health-promoting behaviours of adolescents in Southern Taiwan.

AIMS AND OBJECTIVES: To examine the relationship between selected developmental assets and health-promoting behaviours of adolescents. BACKGROUND: Developmental assets can be considered as potential health assets for adolescents. Understanding the relationship between developmental assets and health-promoting behaviours among adolescents could provide nurses with a new approach to design intervention programmes for adolescent health-promoting behaviours. DESIGN: A cross-sectional study design. METHODS: Anonymous questionnaires were administered to 453 adolescents aged between 13-16 years. Canonical correlation analysis was used to examine the relationship between selected developmental assets and health-promoting behaviours. RESULTS: Canonical correlation analysis indicated two significantly meaningful variate pairs between selected developmental assets and health-promoting behaviour sets. The first pair variate accounted for 51.3% of the total variance, which showed that adolescents who had better self-esteem, future aspirations, responsible choices, family communication, non-parental adult role models, peer role models and community involvement had better behaviours of life appreciation, health responsibility, social support, stress management, nutrition and exercise. The second pair variate accounted for 9.6% of the total variance, which showed that adolescents who had better responsible choices had better stress management behaviours. CONCLUSION: Developmental assets are important to adolescents' health-promoting behaviours. Interventions focusing on strengthening developmental assets can potentially provide an innovative approach for nurses to improve health-promoting behaviours of adolescents. RELEVANCE TO CLINICAL PRACTICE: Strengthening developmental assets can potentially improve the health-promoting behaviours of adolescents. Individual and sociopolitical domains should be incorporated into programmes for enhancement of developmental assets. School nurses can cooperate with family and community and provide environments improving adolescents' developmental assets. Nurses should actively engage in developmental asset programmes for adolescents. The tools for measuring developmental assets modified and developed in this study were valid and reliable. They can be used for further examination of the developmental assets for adolescents in various subset populations.

Diabetes Empowerment Process Scale: development and psychometric testing of the Chinese version.

AIM: This paper is a report of the development and psychometric testing of the Chinese version of the Diabetes Empowerment Process Scale. BACKGROUND: In people living with diabetes, empowerment can improve metabolic and psychosocial outcomes. A scale for measuring empowerment processes can also help healthcare professionals to optimize their empowering actions and would improve their interactions with people living with diabetes. METHOD: Based on literature reviews and interviews with people living with diabetes, a 27-item Chinese Diabetes Empowerment Process Scale was developed. Fifteen items were produced after item analysis and content validity testing. To test construct validity, concurrent validity and internal consistency, 211 outpatients living with diabetes completed the Chinese Diabetes Empowerment Process Scale, a Self-care Behaviour Scale and a Diabetes Empowerment Scale. Test-retest reliability was also analysed with 30 patients. The study was conducted in 2008 and 2009 in Taiwan. RESULTS: Confirmatory factor analysis indicated that a second-order factorial model with four subscales and 15 items best fitted the data. The four subscales were Mutual participation, Raising awareness, Providing necessary information and Open communication. Scores on the Chinese Diabetes Empowerment Process Scale correlated statistically significantly with those on the Self-care Behaviour Scale (r=0.21-0.40; P<0.01) and Diabetes Empowerment Scale (r=0.35-0.65; P<0.01). Reliability was supported by acceptable Cronbach's α (range: 0.73-0.91) and test-retest reliability scores (range: 0.75-0.83). CONCLUSION: The Chinese Diabetes Empowerment Process Scale has satisfactory validity and reliability for measuring the empowerment process of health professionals. Further studies are needed to test the applicability of the scale to other populations.

[Applying the transtheoretical model to tobacco prevention education in adolescence: a literature review].

The Transtheoretical Model (TTM) is a contemporary psychological model of behavioral change employed to develop efficient interventions to promote healthy behavioral changes. Interventions can be individualized to the needs of individuals in order to achieve optimal results. No integrated plan currently exists in Taiwan for reducing cigarette use among children. This article presents a systematic review of TTM, with the goal of constructing a model for protecting teenagers against tobacco-related health risks. Analysis results are hoped to be useful as a reference for developing systematic interventions aimed at reducing the health risks posed to teenagers by cigarette smoking.

[An experience using the transtheoretical model of health behavior change to promote exercise in a type 2 diabetes patient].

This case report shares our experience using the transtheoretical model of health behavior change to promote exercise in a type 2 diabetes patient. The patient was under our care from May through July 2006, during which time the patient was under regular observation and interviewed to collect data. A total of two outpatient consultations and five telephone interviews were conducted. An analysis of results showed the subject to be in the preparation stage of behavior change. To help move the subject into the action stage, the author promoted regular exercise through a variety of strategies, including self-reevaluation, self-change plan development, self-liberation, contingency management, social support search and environmental reevaluation. After nursing intervention, the subject maintained an exercise journal and arranged his own exercise plan. His exercise regimen gradually increased the frequency and intensity of exercise and further extended the scope of exercise to include regular exercise with family members. The author hopes that this case report may provide a reference for health professionals on the use of the transtheoretical model of health behavior change in the care of this type of patient.