scholarly journals Identification and Characterization of Human Observational Studies in Nutritional Epidemiology on Gut Microbiomics for Joint Data Analysis

Nutrients ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 3292
Author(s):  
Mariona Pinart ◽  
Katharina Nimptsch ◽  
Sofia K. Forslund ◽  
Kristina Schlicht ◽  
Miguel Gueimonde ◽  
...  
Keyword(s):  
Data Sharing ◽  
Gut Microbiome ◽  
Observational Studies ◽  
Data Access ◽  
Nutritional Epidemiology ◽  
Rrna Gene ◽  
Specific Information ◽  
Related Factors ◽  
Cross Sectional ◽  
Health And Disease

In any research field, data access and data integration are major challenges that even large, well-established consortia face. Although data sharing initiatives are increasing, joint data analyses on nutrition and microbiomics in health and disease are still scarce. We aimed to identify observational studies with data on nutrition and gut microbiome composition from the Intestinal Microbiomics (INTIMIC) Knowledge Platform following the findable, accessible, interoperable, and reusable (FAIR) principles. An adapted template from the European Nutritional Phenotype Assessment and Data Sharing Initiative (ENPADASI) consortium was used to collect microbiome-specific information and other related factors. In total, 23 studies (17 longitudinal and 6 cross-sectional) were identified from Italy (7), Germany (6), Netherlands (3), Spain (2), Belgium (1), and France (1) or multiple countries (3). Of these, 21 studies collected information on both dietary intake (24 h dietary recall, food frequency questionnaire (FFQ), or Food Records) and gut microbiome. All studies collected stool samples. The most often used sequencing platform was Illumina MiSeq, and the preferred hypervariable regions of the 16S rRNA gene were V3–V4 or V4. The combination of datasets will allow for sufficiently powered investigations to increase the knowledge and understanding of the relationship between food and gut microbiome in health and disease.

scholarly journals Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Robert C. Kaplan ◽  
Zheng Wang ◽  
Mykhaylo Usyk ◽  
Daniela Sotres-Alvarez ◽  
Martha L. Daviglus ◽  
...  
Keyword(s):  
Community Health ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Shannon Index ◽  
Health Study ◽  
Rrna Gene ◽  
Cross Sectional ◽  
Hispanic Community ◽  
The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

Alterations of gut microbiome in autoimmune hepatitis

Gut ◽  
2019 ◽  
Vol 69 (3) ◽  
pp. 569-577 ◽  
Author(s):  
Yiran Wei ◽  
Yanmei Li ◽  
Li Yan ◽  
Chunyan Sun ◽  
Qi Miao ◽  
...  
Keyword(s):  
Autoimmune Hepatitis ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Disease Status ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Healthy Controls ◽  
Microbial Composition ◽  
Cross Sectional ◽  
Treatment Naïve

ObjectiveThe significance of the liver-microbiome axis has been increasingly recognised as a major modulator of autoimmunity. The aim of this study was to take advantage of a large well-defined corticosteroids treatment-naïve group of patients with autoimmune hepatitis (AIH) to rigorously characterise gut dysbiosis compared with healthy controls.DesignWe performed a cross-sectional study of individuals with AIH (n=91) and matched healthy controls (n=98) by 16S rRNA gene sequencing. An independent cohort of 28 patients and 34 controls was analysed to validate the results. All the patients were collected before corticosteroids therapy.ResultsThe gut microbiome of steroid treatment-naïve AIH was characterised with lower alpha-diversity (Shannon and observed operational taxonomic units, both p<0.01) and distinct overall microbial composition compared with healthy controls (p=0.002). Depletion of obligate anaerobes and expansion of potential pathobionts including Veillonella were associated with disease status. Of note, Veillonella dispar, the most strongly disease-associated taxa (p=8.85E–8), positively correlated with serum level of aspartate aminotransferase and liver inflammation. Furthermore, the combination of four patients with AIH-associated genera distinguished AIH from controls with an area under curves of approximately 0.8 in both exploration and validation cohorts. In addition, multiple predicted functional modules were altered in the AIH gut microbiome, including lipopolysaccharide biosynthesis as well as metabolism of amino acids that can be processed by bacteria to produce immunomodulatory metabolites.ConclusionOur study establishes compositional and functional alterations of gut microbiome in AIH and suggests the potential for using gut microbiota as non-invasive biomarkers to assess disease activity.

scholarly journals Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Joan Mas-Lloret ◽  
Mireia Obón-Santacana ◽  
Gemma Ibáñez-Sanz ◽  
Elisabet Guinó ◽  
Miguel L. Pato ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Complex Structure ◽  
High Coverage ◽  
Cross Sectional ◽  
Microbiome Analysis ◽  
Hypervariable Regions ◽  
16S Gene ◽  
Faecal Samples ◽  
Health And Disease ◽  
And Function

AbstractThe gut microbiome has a fundamental role in human health and disease. However, studying the complex structure and function of the gut microbiome using next generation sequencing is challenging and prone to reproducibility problems. Here, we obtained cross-sectional colon biopsies and faecal samples from nine participants in our COLSCREEN study and sequenced them in high coverage using Illumina pair-end shotgun (for faecal samples) and IonTorrent 16S (for paired feces and colon biopsies) technologies. The metagenomes consisted of between 47 and 92 million reads per sample and the targeted sequencing covered more than 300 k reads per sample across seven hypervariable regions of the 16S gene. Our data is freely available and coupled with code for the presented metagenomic analysis using up-to-date bioinformatics algorithms. These results will add up to the informed insights into designing comprehensive microbiome analysis and also provide data for further testing for unambiguous gut microbiome analysis.

scholarly journals Dietary quality and the colonic mucosa–associated gut microbiome in humans

2019 ◽  
Vol 110 (3) ◽  
pp. 701-712 ◽  
Author(s):  
Yanhong Liu ◽  
Nadim J Ajami ◽  
Hashem B El-Serag ◽  
Clark Hair ◽  
David Y Graham ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Gut Microbiome ◽  
Colonic Mucosa ◽  
Bacterial Community Composition ◽  
Healthy Eating Index ◽  
Lower Score ◽  
Dietary Quality ◽  
Rrna Gene ◽  
Cross Sectional ◽  
Β Diversity

Abstract Background Despite tremendous interest in modulating the microbiome to improve health, the association between diet and the colonic mucosa–associated gut microbiome in healthy individuals has not been examined. Objective To investigate the associations between Healthy Eating Index (HEI)–2005 and the colonic mucosa–associated microbiota. Methods In this cross-sectional observational study, we analyzed bacterial community composition and structure using 16S rRNA gene (V4 region) sequencing of 97 colonic mucosal biopsies obtained endoscopically from different colon segments of 34 polyp-free participants. Dietary consumption was ascertained using an FFQ. Differences in α- and β-diversity and taxonomic relative abundances between the higher and lower score of total HEI and its components were compared, followed by multivariable analyses. Results The structure of the microbiota significantly differed by the scores for total HEI, total and whole fruits (HEI 1 and HEI 2), whole grains (HEI 6), milk products and soy beverages (HEI 7), and solid fat, alcohol, and added sugar (HEI 12). A lower score for total HEI and HEIs 2, 7, and 12 was associated with significantly lower richness. A lower score for total HEI was associated with significantly reduced relative abundance of Parabacteroides, Roseburia, and Subdoligranulum but higher Fusobacterium. A lower score for HEI 2 was associated with lower Roseburia but higher Bacteroides. A lower score for HEI 7 was associated with lower Faecalibacterium and Fusobacterium but higher Bacteroides. A lower score for HEI 12 was associated with lower Subdoligranulum but higher Escherichia and Fusobacterium (false discovery rate–adjusted P values <0.05). The findings were confirmed by multivariate analysis. Less abundant bacteria such as Alistipes, Odoribacter, Bilophila, and Tyzzerella were also associated with dietary quality. Conclusions A lower score for total HEI–2005 was significantly associated with reduced relative abundance of potentially beneficial bacteria but increased potentially harmful bacteria in the colonic mucosa of endoscopically normal individuals.

Factors Associated With Vaccination Compliance in Southeast Asian Children: A Systematic Review

2021 ◽  
pp. 101053952110146
Author(s):  
Ayers Gilberth Ivano Kalaij ◽  
Michael Sugiyanto ◽  
Ahmad Fadhil Ilham
Keyword(s):  
Systematic Review ◽  
Health Care ◽  
Southeast Asia ◽  
Vaccination Coverage ◽  
Observational Studies ◽  
Childhood Vaccination ◽  
Family Status ◽  
Related Factors ◽  
Cross Sectional ◽  
Factors Associated

Although vaccination coverage has reached a peak of 86% globally, around 19.9 million infants and children are yet to receive routine vaccinations—with Asia holding the highest prevalence of noncompliance. This implies notable gaps in vaccination coverage among some regions in the world. This study aims to analyze the factors associated with compliance toward childhood vaccination in Southeast Asia. A systematic review of observational studies was conducted using the following databases: PubMed, Scopus, and Cochrane. Included studies analyze factors affecting compliance with childhood vaccination in Southeast Asia, and assessed with JBI (Joanna Briggs Institute) and Newcastle-Ottawa Scale’s criteria. Sixteen observational studies were included, with a total of 41 956 subjects, consisting of 15 cross-sectional studies and one case-control study. Our results suggested that parental personal–related, children and family status–related, socioeconomic, and health care–related factors strongly affected subjects’ compliance with immunization. Prominent determinants were older maternal age, higher economics groups, parents in government or health care sectors, and frequent antenatal care visits. On the other hand, noncompliance were associated with younger age, large quantity of family members, lower economic groups, lower education, and unemployed parents. We hope that this comprehensive assessment thoroughly addresses challenges and inform strategies to raise compliance toward childhood vaccination in Southeast Asia.

scholarly journals Impact of Different Exercise Modalities on the Human Gut Microbiome

Sports ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 14
Author(s):  
Dierdra Bycura ◽  
Anthony C. Santos ◽  
Arron Shiffer ◽  
Shari Kyman ◽  
Kyle Winfree ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Sequence Data ◽  
Exercise Program ◽  
Rrna Gene ◽  
Human Gut ◽  
Post Intervention ◽  
Cross Sectional ◽  
Intervention Phase ◽  
Human Gut Microbiome

In this study we examined changes to the human gut microbiome resulting from an eight-week intervention of either cardiorespiratory exercise (CRE) or resistance training exercise (RTE). Twenty-eight subjects (21 F; aged 18–26) were recruited for our CRE study and 28 subjects (17 F; aged 18–33) were recruited for our RTE study. Fecal samples for gut microbiome profiling were collected twice weekly during the pre-intervention phase (three weeks), intervention phase (eight weeks), and post-intervention phase (three weeks). Pre/post VO2max, three repetition maximum (3RM), and body composition measurements were conducted. Heart rate ranges for CRE were determined by subjects’ initial VO2max test. RTE weight ranges were established by subjects’ initial 3RM testing for squat, bench press, and bent-over row. Gut microbiota were profiled using 16S rRNA gene sequencing. Microbiome sequence data were analyzed with QIIME 2. CRE resulted in initial changes to the gut microbiome which were not sustained through or after the intervention period, while RTE resulted in no detectable changes to the gut microbiota. For both CRE and RTE, we observe some evidence that the baseline microbiome composition may be predictive of exercise gains. This work suggests that the human gut microbiome can change in response to a new exercise program, but the type of exercise likely impacts whether a change occurs. The changes observed in our CRE intervention resemble a disturbance to the microbiome, where an initial shift is observed followed by a return to the baseline state. More work is needed to understand how sustained changes to the microbiome occur, resulting in differences that have been reported in cross sectional studies of athletes and non-athletes.

scholarly journals Thigh-worn accelerometry for measuring movement and posture across the 24-hour cycle: a scoping review and expert statement

2020 ◽  
Vol 6 (1) ◽  
pp. e000874
Author(s):  
Matthew L Stevens ◽  
Nidhi Gupta ◽  
Elif Inan Eroglu ◽  
Patrick Joseph Crowley ◽  
Barbaros Eroglu ◽  
...  
Keyword(s):  
Physical Activity ◽  
Data Sharing ◽  
Scoping Review ◽  
Observational Studies ◽  
Data Access ◽  
Research Use ◽  
Movement Behaviour ◽  
Free Living ◽  
Survey Responses ◽  
Monitoring Protocols

IntroductionThe Prospective Physical Activity Sitting and Sleep consortium (ProPASS) is an international collaboration platform committed to harmonise thigh-worn accelerometry data. The aim of this paper is to (1) outline observational thigh-worn accelerometry studies and (2) summarise key strategic directions arising from the inaugural ProPASS meeting.Methods(1) We performed a systematic scoping review for observational studies of thigh-worn triaxial accelerometers in free-living adults (n≥100, 24 hours monitoring protocols). (2)Attendees of the inaugural ProPASS meeting were sent a survey focused on areas related to developing ProPASS: important terminology (Q1); accelerometry constructs (Q2); advantages and distinct contribution of the consortium (Q3); data pooling and harmonisation (Q4); data access and sharing (Q5 and Q6).Results(1) Eighty eligible articles were identified (22 primary studies; n~17 685). The accelerometers used most often were the ActivPAL3 and ActiGraph GT3X. The most commonly collected health outcomes were cardiometabolic and musculoskeletal. (2) None of the survey questions elicited the predefined 60% agreement. Survey responses recommended that ProPASS: use the term physical behaviour or movement behaviour rather than ‘physical activity’ for the data we are collecting (Q1); make only minor changes to ProPASS’s accelerometry construct (Q2); prioritise developing standardised protocols/tools (Q4); facilitate flexible methods of data sharing and access (Q5 and Q6).ConclusionsThigh-worn accelerometry is an emerging method of capturing movement and posture across the 24 hours cycle. In 2020, the literature is limited to 22 primary studies from high-income western countries. This work identified ProPASS’s strategic directions—indicating areas where ProPASS can most benefit the field of research: use of clear terminology, refinement of the measured construct, standardised protocols/tools and flexible data sharing.

scholarly journals A review of data sharing statements in observational studies published in the BMJ: A cross-sectional study

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1708 ◽  
Author(s):  
Laura McDonald ◽  
Anna Schultze ◽  
Alex Simpson ◽  
Sophie Graham ◽  
Radek Wasiak ◽  
...  
Keyword(s):  
Medical Journal ◽  
Data Sharing ◽  
Exploratory Study ◽  
Observational Studies ◽  
Cross Sectional Study ◽  
Research Data ◽  
Observational Research ◽  
Sectional Study ◽  
Cross Sectional ◽  
Current State

In order to understand the current state of data sharing in observational research studies, we reviewed data sharing statements of observational studies published in a general medical journal, the British Medical Journal. We found that the majority (63%) of observational studies published between 2015 and 2017 included a statement that implied that data used in the study could not be shared. If the findings of our exploratory study are confirmed, room for improvement in the sharing of real-world or observational research data exists.

scholarly journals New Insights into Molecular Basis Identification of Three Novel Strains of the Bacillus Subtilis Group Produce Cry Proteins Isolated from Soil Samples in Adana, Turkey

2021 ◽  
Author(s):  
Semih Yilmaz ◽  
Abeer Babiker Idris ◽  
Abdurrahman Ayvaz ◽  
Aysun Cetin ◽  
Funda Ulgen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Evolutionary Relationship ◽  
Cross Sectional Study ◽  
Soil Samples ◽  
Bacillus Species ◽  
Rrna Gene ◽  
Specific Information ◽  
Cross Sectional ◽  
Cry Proteins ◽  
Subtilis Group

Aims: This study aimed to analyze the evolutionary relationship between Bacillus species isolated from agricultural soil using in-silico tools. Methods and Results: A cross-sectional study was conducted in Adana province, in Turkey. A total of 120 Bacillus species were isolated from 80 soil samples. However, the phylogenetic tree diverged into two lineages; one belongs to B. subtilis group while the other belongs to B. cereus group. Interestingly, three native strains (SY27.1A, SY35.3A, and SY58.5A), which produce Cry proteins, shared high similarity with B. subtilis group (over 99%) and less than 95% similarity with known B. thuringiensis and other species of B. cereus group. Furthermore, 11 canonical SNPs (canSNPs) were identified in strains that belong to B. pumilus group when compared with B. subtilis reference sequences. Conclusions: Phylogenetic analysis of 16S rRNA sequences was found valuable for differentiation between Bacillus species isolated from soil samples. In addition, SNPs analysis provided more intra-specific information in the cases of B. subtilis group. Significance and Impact of Study: A detailed analysis was provided for the SNPs present in a conserved region of 16S rRNA gene of Bacillus species. Also, we proposed three novel Bacillus strains that produce Cry proteins and belong to B. subtilis group.

scholarly journals Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of matched stool and colon biopsy samples

2019 ◽  
Author(s):  
Joan Mas-Lloret ◽  
Mireia Obón-Santacana ◽  
Gemma Ibáñez-Sanz ◽  
Elisabet Guinó ◽  
Miguel L Pato ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Complex Structure ◽  
High Coverage ◽  
Cross Sectional ◽  
Microbiome Analysis ◽  
16S Gene ◽  
Faecal Samples ◽  
Colon Biopsy ◽  
Health And Disease ◽  
And Function

AbstractThe gut microbiome has a fundamental role in human health and disease. However, studying the complex structure and function of the gut microbiome using next generation sequencing is challenging and prone to reproducibility problems due to the heterogeneity of sample sets. Here, we obtained cross-sectional colon biopsies and faecal samples from nine participants in our COLSCREEN study and sequenced them in high coverage using Illumina pair-end shotgun (for faecal samples) and IonTorrent 16S (for paired feces and colon biopsies) technologies. The metagenomes consisted of between 47 and 92 million reads per sample and the targeted sequencing covered more than 300K reads per sample across seven hypervariable regions of the 16S gene. Our data is freely available and coupled with code for the presented metagenomic analysis using up-to-date bioinformatics algorithms. These results will add up to the informed insights into designing comprehensive microbiome analysis and also provide data for further testing for unambiguous gut microbiome analysis.

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