scholarly journals Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Rebecca L. Walker ◽  
Hera Vlamakis ◽  
Jonathan Wei Jie Lee ◽  
Luke A. Besse ◽  
Vanessa Xanthakis ◽  
...  
Keyword(s):  
Metabolic Syndrome ◽  
Microbial Diversity ◽  
Gut Microbiome ◽  
Large Scale ◽  
Rrna Gene ◽  
Cvd Risk ◽  
Taxonomic Assignment ◽  
Association Analyses ◽  
Microbial Species ◽  
Cardiometabolic Traits

Abstract Background The human gut harbors trillions of microbes that play dynamic roles in health. While the microbiome contributes to many cardiometabolic traits by modulating host inflammation and metabolism, there is an incomplete understanding regarding the extent that and mechanisms by which individual microbes impact risk and development of cardiovascular disease (CVD). The Framingham Heart Study (FHS) is a multi-generational observational study following participants over decades to identify risk factors for CVD by correlating genetic and phenotypic factors with clinical outcomes. As a large-scale population-based cohort with extensive clinical phenotyping, FHS provides a rich landscape to explore the relationships between the gut microbiome and cardiometabolic traits. Methods We performed 16S rRNA gene sequencing on stool from 1423 participants of the FHS Generation 3, OMNI2, and New Offspring Spouse cohorts. Data processing and taxonomic assignment were performed with the 16S bioBakery workflow using the UPARSE pipeline. We conducted statistical analyses to investigate trends in overall microbiome composition and diversity in relation to disease states and systematically examined taxonomic associations with a variety of clinical traits, disease phenotypes, clinical blood markers, and medications. Results We demonstrate that overall microbial diversity decreases with increasing 10-year CVD risk and body mass index measures. We link lifestyle factors, especially diet and exercise, to microbial diversity. Our association analyses reveal both known and unreported microbial associations with CVD and diabetes, related prescription medications, as well as many anthropometric and blood test measurements. In particular, we observe a set of microbial species that demonstrate significant associations with CVD risk, metabolic syndrome, and type 2 diabetes as well as a number of shared associations between microbial species and cardiometabolic subphenotypes. Conclusions The identification of significant microbial taxa associated with prevalent CVD and diabetes, as well as risk for developing CVD, adds to increasing evidence that the microbiome may contribute to CVD pathogenesis. Our findings support new hypothesis generation around shared microbe-mediated mechanisms that influence metabolic syndrome, diabetes, and CVD risk. Further investigation of the gut microbiomes of CVD patients in a targeted manner may elucidate microbial mechanisms with diagnostic and therapeutic implications.

scholarly journals Microbial Diversity Analysis of Sediment from Nakdong River Estuary in the Republic of Korea Using 16S rRNA Gene Amplicon Sequencing

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Kyunghoi Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Large Scale ◽  
Sediment Quality ◽  
River Estuary ◽  
Republic Of Korea ◽  
Rrna Gene ◽  
Nakdong River ◽  
The Republic

Deterioration of sediment quality has been found in the Nakdong River Estuary after large-scale reclamations. Here, I report microbial diversity in sediments of Nakdong River Estuary in the Republic of Korea based on 16S rRNA gene sequencing by next-generation sequencing (NGS) techniques.

scholarly journals The association between the maternal diet and the maternal and infant gut microbiome: a systematic review

2020 ◽  
pp. 1-29 ◽  
Author(s):  
Siofra E. Maher ◽  
Eileen C. O’Brien ◽  
Rebecca L. Moore ◽  
David F. Byrne ◽  
Aisling A. Geraghty ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Gut Microbiome ◽  
Dietary Intervention ◽  
Maternal Diet ◽  
Rrna Gene ◽  
High Fat ◽  
High Fat Diets ◽  
Culture Independent ◽  
Infant Gut Microbiome ◽  
Fat Diets

Abstract During pregnancy, changes occur to influence the maternal gut microbiome, and potentially the fetal microbiome. Diet has been shown to impact the gut microbiome. Little research has been conducted examining diet during pregnancy with respect to the gut microbiome. To meet inclusion criteria, dietary analyses must have been conducted as part of the primary aim. The primary outcome was the composition of the gut microbiome (infant or maternal), as assessed using culture-independent sequencing techniques. This review identified seven studies for inclusion, five examining the maternal gut microbiome and two examining the fetal gut microbiome. Microbial data were attained through analysis of stool samples by 16S rRNA gene-based microbiota assessment. Studies found an association between the maternal diet and gut microbiome. High-fat diets (% fat of total energy), fat-soluble vitamins (mg/day) and fibre (g/day) were the most significant nutrients associated with the gut microbiota composition of both neonates and mothers. High-fat diets were significantly associated with a reduction in microbial diversity. High-fat diets may reduce microbial diversity, while fibre intake may be positively associated with microbial diversity. The results of this review must be interpreted with caution. The number of studies was low, and the risk of observational bias and heterogeneity across the studies must be considered. However, these results show promise for dietary intervention and microbial manipulation in order to favour an increase of health-associated taxa in the gut of the mother and her offspring.

scholarly journals Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

2014 ◽  
Vol 80 (12) ◽  
pp. 3677-3686 ◽  
Author(s):  
Jun Liu ◽  
Zheng-Shuang Hua ◽  
Lin-Xing Chen ◽  
Jia-Liang Kuang ◽  
Sheng-Jin Li ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Community Composition ◽  
Environmental Conditions ◽  
Mine Tailings ◽  
Large Scale ◽  
Hot Springs ◽  
Mine Drainage ◽  
Rrna Gene ◽  
Content Type ◽  
Geochemical Parameters

ABSTRACTRecent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within theAlphaproteobacteria,Deltaproteobacteria, andFirmicuteswere attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.

scholarly journals Major Lipids, Apolipoproteins, and Alterations of Gut Microbiota

2020 ◽  
Vol 9 (5) ◽  
pp. 1589
Author(s):  
Kyung Eun Yun ◽  
Jimin Kim ◽  
Mi-hyun Kim ◽  
Eunkyo Park ◽  
Hyung-Lae Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Large Scale ◽  
Blood Lipids ◽  
Density Lipoprotein ◽  
Lipoprotein Cholesterol ◽  
Control Group ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Lipid Markers

The gut microbiota has been linked to blood lipids. However, the relationship between the gut microbiome and other lipid markers like apolipoproteins A1 (apoA1) and B (apoB) as well as classical lipid markers in Asians remain unclear. Here, we examined the associations between gut microbial diversity and taxonomic compositions with both apolipoproteins and lipid markers in a large number of Korean patients. The fecal 16S rRNA gene sequencing data from 1141 subjects were analyzed and subjects were categorized into control group (G0) or abnormal group (G1) according to blood lipid measurements. The microbial diversity and several taxa of the gut microbiota were significantly associated with triglyceride, apoA1, and apoB levels, but not with total cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol levels. The alpha diversity of the gut microbiota was inversely associated with high triglyceride level. Interestingly, G1 of apoA1 showed increased microbial richness and distinct microbial community compared with G0 of apoA1. A high abundance of Fusobacteria and low abundance of Oscillospira were found in the hypertriglyceridemia group. In this large-scale study, we identified associations of gut microbiota with apolipoproteins and classical lipid markers, indicating that the gut microbiota may be an important target for regulating blood lipids.

scholarly journals Large-scale association analyses identify host factors influencing human gut microbiome composition

2021 ◽  
Vol 53 (2) ◽  
pp. 156-165
Author(s):  
Alexander Kurilshikov ◽  
Carolina Medina-Gomez ◽  
Rodrigo Bacigalupe ◽  
Djawad Radjabzadeh ◽  
Jun Wang ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Large Scale ◽  
Host Factors ◽  
Human Gut ◽  
Association Analyses ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
Factors Influencing

scholarly journals Metagenomics Analysis of Race and Age influence on the Vaginal Microbiome in Pregnant and Non-pregnant Healthy Women

2021 ◽  
Author(s):  
Zahra Golestani ◽  
Samira Ghaedmohammadi ◽  
Najmeh Mozdoori
Keyword(s):  
Large Scale ◽  
Chinese Women ◽  
Meta Analysis ◽  
Relative Number ◽  
Vaginal Microbiota ◽  
Rrna Gene ◽  
Body Parts ◽  
Vaginal Microbiome ◽  
Microbial Species ◽  
Healthy Women

Abstract Various human body parts are host to many microbial species and have a mutualistic relationship with them. The presence of these microbial species in reproductive tubes plays an essential protective role against the proliferation of harmful organisms and is an important factor in reproductive health. The vaginal microbiota during pregnancy plays a vital role in the health of the mother and the infant. Microbiota imbalance during pregnancy is associated with many complications. As a result, the detection of vaginal microbiota during pregnancy can reduce the risk of these problems. High-throughput culture-independent technologies allow the study of vaginal microbiome on a large scale. This study aimed to compare the vaginal microbiota between pregnant and non-pregnant healthy women of different age or race using the meta-analysis method. The results from 7 articles having 16S rRNA gene sequences, were extracted and analyzed by CLC. Data from 898 pregnant and 702 non-pregnant women showed that the Bacilli, Clostridia, Actinobacteria and Coriobacteria were the dominant classes in pregnancy. The vaginal microbiota in normal non-pregnancy is also predominated by Bacilli. Still, beta diversity maps demonstrated that non-pregnant vaginal microbiome is more variable than that in the pregnant state. This study reveals new insights into age and ethnic effects on the pregnant and non-pregnant vaginal microbiome and found that the microbiome of Chinese women was more distinct than the other races. It was also detected that the relative number of bacterial classes is dramatically lower in women above the age of 35 relative to younger ones.

scholarly journals METAWORKS: A flexible, scalable bioinformatic pipeline for multi-marker biodiversity assessments

2020 ◽  
Author(s):  
Teresita M. Porter ◽  
Mehrdad Hajibabaei
Keyword(s):  
Large Scale ◽  
Ad Hoc ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Taxonomic Assignment ◽  
Protein Coding ◽  
Domains Of Life ◽  
Reference Databases ◽  
Marker Studies ◽  
Assignment Approach

AbstractBackgroundMulti-marker metabarcoding is increasingly being used to generate biodiversity information across different domains of life from microbes to fungi to animals such as in ecological and environmental studies. Current popular bioinformatic pipelines support microbial and fungal marker analysis, while ad hoc methods are used to process animal metabarcode markers from the same study. The purpose of this paper is to introduce MetaWorks, a ‘meta’barcode pipeline that does ‘the works’ and supports the bioinformatic processing of various metabarcoding markers including rRNA and their spacers as well as protein coding loci.ResultsMetaWorks provides a Conda environment to quickly gather most of the programs and dependencies for the pipeline. MetaWorks is automated using Snakemake to ensure reproducibility and scalability. We have supplemented existing RDP-trained classifiers for SSU (prokaryotes), ITS (fungi), and LSU (fungi) with trained classifiers for COI (eukaryotes), rbcL (diatoms or eukaryotes), SSU (diatoms or eukaryotes), and 12S (fish). MetaWorks can process rRNA genes, but it can also properly handle ITS spacers by trimming flanking conserved rRNA gene regions, as well as handle protein coding genes by removing obvious pseudogenes.ConclusionsAs far as we are aware, MetaWorks is the first flexible multi-marker metabarcode pipeline that can accommodate rRNA genes, spacer, and protein coding markers in the same pipeline. This is ideal for large-scale, multi-marker studies to provide a harmonized processing environment, pipeline, and taxonomic assignment approach. Updates to MetaWorks will be made as needed to reflect advances in the underlying programs, reference databases, or hidden Markov model (HMM) profiles for pseudogene filtering. Future developments will include support for additional metabarcode markers, RDP trained reference databases, and HMM profiles for pseudogene filtering.

Metabolic Syndrome Alone Raises CVD Risk

2010 ◽  
Vol 43 (17) ◽  
pp. 63
Author(s):  
HEIDI SPLETE
Keyword(s):  
Metabolic Syndrome ◽  
Cvd Risk

Metabolic Syndrome Fails to Predict CVD Risk

2008 ◽  
Vol 38 (17) ◽  
pp. 21
Author(s):  
LORINDA BULLOCK
Keyword(s):  
Metabolic Syndrome ◽  
Cvd Risk

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.

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