scholarly journals Considerations for the design and conduct of human gut microbiota intervention studies relating to foods

2020 ◽  
Vol 59 (8) ◽  
pp. 3347-3368
Author(s):  
J. R. Swann ◽  
M. Rajilic-Stojanovic ◽  
A. Salonen ◽  
O. Sakwinska ◽  
C. Gill ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Intervention Studies ◽  
Health Claims ◽  
Host Responses ◽  
Human Gut ◽  
Eligibility Criteria ◽  
Functional Changes ◽  
Human Gut Microbiota ◽  
The Impact

AbstractWith the growing appreciation for the influence of the intestinal microbiota on human health, there is increasing motivation to design and refine interventions to promote favorable shifts in the microbiota and their interactions with the host. Technological advances have improved our understanding and ability to measure this indigenous population and the impact of such interventions. However, the rapid growth and evolution of the field, as well as the diversity of methods used, parameters measured and populations studied, make it difficult to interpret the significance of the findings and translate their outcomes to the wider population. This can prevent comparisons across studies and hinder the drawing of appropriate conclusions. This review outlines considerations to facilitate the design, implementation and interpretation of human gut microbiota intervention studies relating to foods based upon our current understanding of the intestinal microbiota, its functionality and interactions with the human host. This includes parameters associated with study design, eligibility criteria, statistical considerations, characterization of products and the measurement of compliance. Methodologies and markers to assess compositional and functional changes in the microbiota, following interventions are discussed in addition to approaches to assess changes in microbiota–host interactions and host responses. Last, EU legislative aspects in relation to foods and health claims are presented. While it is appreciated that the field of gastrointestinal microbiology is rapidly evolving, such guidance will assist in the design and interpretation of human gut microbiota interventional studies relating to foods.

Whole Grains, Dietary Fibers and the Human Gut Microbiota: A Systematic Review of Existing Literature

2020 ◽  
Vol 11 (3) ◽  
pp. 235-248 ◽  
Author(s):  
Hadith Tangestani ◽  
Hadi Emamat ◽  
Hamid Ghalandari ◽  
Sakineh Shab-Bidar
Keyword(s):  
Systematic Review ◽  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Pathogenic Bacteria ◽  
Whole Grains ◽  
Dietary Fibers ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Population Demographic ◽  
The Impact

Background: The health benefits of dietary fibers have been proved for a long time. The importance of microbiota has been identified in human health and there is a growing interest to study the factors affecting it. Objective: This systematic review aimed to investigate the impact of fiber and whole grains (WGs) on human gut microbiota in a patent-based review. Methods: All related clinical trials were systematically searched on PubMed and Scopus search engines from inception up to Feb 2020. Interventional human studies reporting changes in microbiota by using any type of grains/fibers were included. The following information was extracted: date of the publication, location and design of the study, sample size, study population, demographic characteristics, the amount of dietary WGs/fiber, the duration of intervention, the types of grains or fibers, and changes in the composition of the microbiota. Results: Of 138 studies which were verified, 35 studies with an overall population of 1080 participants, met the inclusion criteria and entered the systematic review. The results of interventional trials included in this review suggest some beneficial effects of consuming different amounts and types of WGs and fibers on the composition of intestinal microbiota. Most included studies showed that the intake of WGs and fibers increases bifidobacteria and lactobacilli and reduces the pathogenic bacteria, such as Escherichia coli and clostridia in the human gut. Conclusion: The consumption of WGs/fibers may modify the intestinal microbiota and promote the growth of bifidobacteria and lactobacilli. Nevertheless, further research is warranted in different populations and pathological conditions.

scholarly journals Does Consumption of Fermented Foods Modify the Human Gut Microbiota?

2020 ◽  
Vol 150 (7) ◽  
pp. 1680-1692 ◽  
Author(s):  
Leah T Stiemsma ◽  
Reine E Nakamura ◽  
Jennifer G Nguyen ◽  
Karin B Michels
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Food Consumption ◽  
Intervention Studies ◽  
Fermented Food ◽  
Fermented Foods ◽  
Human Intervention ◽  
Human Gut ◽  
Gut Dysbiosis ◽  
Human Gut Microbiota

ABSTRACT The human microbiota is a key contributor to many aspects of human health and its composition is largely influenced by diet. There is a growing body of scientific evidence to suggest that gut dysbiosis (microbial imbalance of the intestine) is associated with inflammatory and immune-mediated diseases (e.g., inflammatory bowel disease and asthma). Regular consumption of fermented foods (e.g., kimchi, kefir, etc.) may represent a potential avenue to counter the proinflammatory effects of gut dysbiosis. However, an assessment of the available literature in this research area is lacking. Here we provide a critical review of current human intervention studies that analyzed the effect of fermented foods on the composition and/or function of the human gut microbiota. A total of 19 human intervention studies were identified that met this search criteria. In this review, we discuss evidence that consumption of fermented foods may modify the gut microbiota in humans. Further, there is cursory evidence to suggest that gut microbiota compositional changes mediate associations between fermented food consumption and human health outcomes. Although promising, there remains considerable heterogeneity in the human populations targeted in the intervention studies we identified. Larger longitudinal feeding studies with longer follow-up are necessary to confirm and enhance the current data. Further, future studies should consider analyzing microbiota function as a means to elucidate the mechanism linking fermented food consumption with human health. This review highlights methodologic considerations for intervention trials, emphasizing an expanse of research opportunities related to fermented food consumption in humans.

Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota

PROTEOMICS ◽  
2015 ◽  
Vol 15 (20) ◽  
pp. 3474-3485 ◽  
Author(s):  
Alessandro Tanca ◽  
Antonio Palomba ◽  
Salvatore Pisanu ◽  
Maria Filippa Addis ◽  
Sergio Uzzau
Keyword(s):  
Gut Microbiota ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
The Impact

Understanding the impact of chia seed mucilage on human gut microbiota by using the dynamic gastrointestinal model simgi®

2018 ◽  
Vol 50 ◽  
pp. 104-111 ◽  
Author(s):  
Alba Tamargo ◽  
Carolina Cueva ◽  
Laura Laguna ◽  
M.Victoria Moreno-Arribas ◽  
Loreto A. Muñoz
Keyword(s):  
Gut Microbiota ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Chia Seed ◽  
The Impact ◽  
Seed Mucilage

scholarly journals The Impact of a Dynamic Working Environment on Human Gut Microbiota

2021 ◽  
Author(s):  
Lu Ling ◽  
Jun Zhou ◽  
Qianlong Meng ◽  
Ziran Zhang ◽  
Wenkun Li ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Clinical Characteristics ◽  
Dietary Habits ◽  
Living Environment ◽  
Working Environment ◽  
Rrna Gene ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Train Drivers ◽  
The Impact

Gut microbiota dysbiosis is associated with a variety of diseases, such as inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS), metabolic diseases, allergic diseases, neurodevelopmental disorders and cancer. The human gut microbiota can be influenced by a variety of factors, including geography, dietary habits, living environment, age and altered lifestyle etc. This study was conducted to explore the gut microbiota compositions in officials who are in a stable working environment and train drivers who are in a dynamic working environment. Microbiota communities in the feces of 80 officials and 88 train drivers were analyzed using Illumina MiSeq sequencing targeting the V3-V4 region of 16S ribosomal RNA (rRNA) gene and ITS1 region of fungi. There were significant differences between the two groups in diversity and richness of gut microbiota, while the microbial community compositions of the two groups were similar. The relationship between gut microbiota and clinical characteristics was investigated. We found that more bacteria and fungi were positively correlated with clinical characteristics. Functional prediction analysis of the gut microbiota between the two groups by PICRUSt2 revealed significant differences between the official group and the train driver group. Elucidating these differences of the microbiome between the two groups will provide a foundation understanding of the impact of a dynamic environment on gut microbiota.

scholarly journals Does geographical variation confound the relationship between host factors and the human gut microbiota: a population-based study in China

BMJ Open ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. e038163
Author(s):  
Shan Sun ◽  
Huijun Wang ◽  
Matthew CB Tsilimigras ◽  
Annie Green Howard ◽  
Wei Sha ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Geographical Variation ◽  
Population Based ◽  
Host Factors ◽  
Secondary Outcome ◽  
Human Gut ◽  
Population Based Study ◽  
Human Gut Microbiota ◽  
Wide Range ◽  
The Impact

ObjectiveThe human gut microbiota plays important roles in human health but is also known to be highly diverse between populations from different regions. Yet most studies inadequately account for this regional diversity in their analyses. This study examines the extent to which geographical variation can act as a confounding variable for studies that associate the microbiota with human phenotypic variation.DesignPopulation-based study.SettingChina.Participants2164 participants from 15 province-level divisions in China.Primary and secondary outcome measuresWe analysed the impact of geographic location on associations between the human gut microbiota and 72 host factors representing a wide variety of environmental-level, household-level and individual-level factors.ResultsWhile the gut microbiota varied across a wide range of host factors including urbanisation, occupation and dietary variables, the geographic region (province/megacity) of the participants explained the largest proportion of the variance (17.9%). The estimated effect sizes for other host factors varied substantially by region with little evidence of a reproducible signal across different areas as measured by permutational multivariate analysis of variance and random forest models.ConclusionsOur results suggest that geographic variation is an essential factor that should be explicitly considered when generalising microbiota-based models to host phenotype across different populations.

The impact of Crohn's disease genes on healthy human gut microbiota: a pilot study

Gut ◽  
2013 ◽  
Vol 62 (6) ◽  
pp. 952.1-954 ◽  
Author(s):  
Christopher Quince ◽  
Elin E Lundin ◽  
Anna N Andreasson ◽  
Dario Greco ◽  
Joseph Rafter ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Pilot Study ◽  
Crohn's Disease ◽  
Gut Microbiota ◽  
Disease Genes ◽  
Human Gut ◽  
Healthy Human ◽  
Human Gut Microbiota ◽  
The Impact

scholarly journals Quantifying the Impact of Human Leukocyte Antigen on the Human Gut Microbiota

mSphere ◽  
2021 ◽  
Author(s):  
Stijn P. Andeweg ◽  
Can Keşmir ◽  
Bas E. Dutilh
Keyword(s):  
Gut Microbiota ◽  
Human Leukocyte Antigen ◽  
Human Leukocyte ◽  
Colonization Resistance ◽  
Human Gut ◽  
Leukocyte Antigen ◽  
Human Gut Microbiota ◽  
The Impact ◽  
Uptake Of Nutrients

The microorganisms that live in the digestive tracts of humans, known as the gut microbiota, are essential for hosts’ survival, as they support crucial functions. For example, they support the host in facilitating the uptake of nutrients and give colonization resistance against pathogens.

scholarly journals Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi

mBio ◽  
2018 ◽  
Vol 9 (3) ◽  
Author(s):  
Yan Zhang ◽  
Arthur Brady ◽  
Cheron Jones ◽  
Yang Song ◽  
Thomas C. Darton ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Clinical Outcomes ◽  
Salmonella Enterica ◽  
Enteric Pathogens ◽  
Wild Type ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Functional Differences ◽  
And Function ◽  
The Impact

ABSTRACT Insights into disease susceptibility as well as the efficacy of vaccines against typhoid and other enteric pathogens may be informed by better understanding the relationship between the effector immune response and the gut microbiota. In the present study, we characterized the composition (16S rRNA gene profiling) and function (RNA sequencing [RNA-seq]) of the gut microbiota following immunization and subsequent exposure to wild-type Salmonella enterica serovar Typhi in a human challenge model to further investigate the central hypothesis that clinical outcomes may be linked to the gut microbiota. Metatranscriptome analysis of longitudinal stool samples collected from study subjects revealed two stable patterns of gene expression for the human gut microbiota, dominated by transcripts from either Methanobrevibacter or a diverse representation of genera in the Firmicutes phylum. Immunization with one of two live oral attenuated vaccines against S.  Typhi had minimal effects on the composition or function of the gut microbiota. It was observed that subjects harboring the methanogen-dominated transcriptome community at baseline displayed a lower risk of developing symptoms of typhoid following challenge with wild-type S.  Typhi. Furthermore, genes encoding antioxidant proteins, metal homeostasis and transport proteins, and heat shock proteins were expressed at a higher level at baseline or after challenge with S.  Typhi in subjects who did not develop symptoms of typhoid. These data suggest that functional differences relating to redox potential and ion homeostasis in the gut microbiota may impact clinical outcomes following exposure to wild-type S.  Typhi. IMPORTANCE S.  Typhi is a significant cause of systemic febrile morbidity in settings with poor sanitation and limited access to clean water. It has been demonstrated that the human gut microbiota can influence mucosal immune responses, but there is little information available on the impact of the human gut microbiota on clinical outcomes following exposure to enteric pathogens. Here, we describe differences in the composition and function of the gut microbiota in healthy adult volunteers enrolled in a typhoid vaccine trial and report that these differences are associated with host susceptibility to or protection from typhoid after challenge with wild-type S . Typhi. Our observations have important implications in interpreting the efficacy of oral attenuated vaccines against enteric pathogens in diverse populations.

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