Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome

ABSTRACT Lifestyle factors, such as diet, strongly influence the structure, diversity, and composition of the microbiome. While we have witnessed over the last several years a resurgence of interest in fermented foods, no study has specifically explored the effects of their consumption on gut microbiota in large cohorts. To assess whether the consumption of fermented foods is associated with a systematic signal in the gut microbiome and metabolome, we used a multi-omic approach (16S rRNA amplicon sequencing, metagenomic sequencing, and untargeted mass spectrometry) to analyze stool samples from 6,811 individuals from the American Gut Project, including 115 individuals specifically recruited for their frequency of fermented food consumption for a targeted 4-week longitudinal study. We observed subtle but statistically significant differences between consumers and nonconsumers in beta diversity as well as differential taxa between the two groups. We found that the metabolome of fermented food consumers was enriched with conjugated linoleic acid (CLA), a putatively health-promoting molecule. Cross-omic analyses between metagenomic sequencing and mass spectrometry suggest that CLA may be driven by taxa associated with fermented food consumers. Collectively, we found modest yet persistent signatures associated with fermented food consumption that appear present in multiple -omic types which motivate further investigation of how different types of fermented food impact the gut microbiome and overall health. IMPORTANCE Public interest in the effects of fermented food on the human gut microbiome is high, but limited studies have explored the association between fermented food consumption and the gut microbiome in large cohorts. Here, we used a combination of omics-based analyses to study the relationship between the microbiome and fermented food consumption in thousands of people using both cross-sectional and longitudinal data. We found that fermented food consumers have subtle differences in their gut microbiota structure, which is enriched in conjugated linoleic acid, thought to be beneficial. The results suggest that further studies of specific kinds of fermented food and their impacts on the microbiome and health will be useful.

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Consumption of Fermented Plant Foods Is Associated with Systematic Differences in the Human Gut Microbiome and Metabolome

Current Developments in Nutrition ◽

10.1093/cdn/nzaa062_030 ◽

2020 ◽

Vol 4 (Supplement_2) ◽

pp. 1573-1573

Author(s):

Nicole Litwin ◽

Bryn Taylor ◽

Franck Lejzerowicz ◽

Marion Poirel ◽

Justin Shaffer ◽

...

Keyword(s):

Mass Spectrometry ◽

Food Consumption ◽

Gut Microbiome ◽

Amplicon Sequencing ◽

Fermented Foods ◽

Metagenomic Sequencing ◽

Plant Food ◽

Gut Health ◽

Human Gut ◽

Human Gut Microbiome

Abstract Objectives Fermented foods have gained much attention due to their proposed gut health benefits from recent clinical trials. However, very few studies have explored the effects of fermented foods, especially of plant origin, on gut microbiota composition and functional capacity in large human cohorts. Thus, the objective of this study was to assess whether self-reported fermented plant food consumption is associated with compositional or functional microbiome changes in a subset of individuals in the American Gut Project (AGP) cohort. Methods Using a multi-omics approach (e.g., 16S rRNA amplicon sequencing, metagenomic sequencing, and untargeted mass spectrometry), we analyzed stool samples from 6811 healthy individuals from the AGP including 115 individuals specifically recruited for their fermented plant food consumption for a targeted four-week longitudinal study. Results We observed subtle, yet statistically significant differences between fermented plant food consumers and non-consumers in beta diversity as well as differential taxa between the two groups. We found that the metabolome of fermented plant food consumers was enriched with conjugated linoleic acid (CLA), a putatively health-promoting compound. Cross-omic analyses between metagenomic sequencing and mass spectrometry suggest that CLA may be driven by taxa associated with fermented plant food consumers. Conclusions Collectively, we found modest, yet persistent signatures associated with fermented plant food consumption that appear present in multiple omic types, which motivates further investigation of how different types of fermented foods may impact the human gut microbiome and overall health. Funding Sources Danone Nutricia Research.

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Does Consumption of Fermented Foods Modify the Human Gut Microbiota?

Journal of Nutrition ◽

10.1093/jn/nxaa077 ◽

2020 ◽

Vol 150 (7) ◽

pp. 1680-1692 ◽

Cited By ~ 3

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.

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Gut Microbiota-Targeted Diets Modulate Human Immune Status

10.1101/2020.09.30.321448 ◽

2020 ◽

Author(s):

Hannah C. Wastyk ◽

Gabriela K Fragiadakis ◽

Dalia Perelman ◽

Dylan Dahan ◽

Bryan D Merrill ◽

...

Keyword(s):

Immune System ◽

Gut Microbiota ◽

Gut Microbiome ◽

Fermented Food ◽

Community Diversity ◽

Fermented Foods ◽

Dietary Interventions ◽

High Fiber ◽

Prospective Study Design ◽

Microbiota Diversity

AbstractDiet modulates the gut microbiome, and gut microbes, in turn, can impact the immune system. Here, we used two gut microbiota-targeted dietary interventions, plant-based fiber or fermented foods, to determine how each influences the human microbiome and immune system in healthy adults. Using a 17-week randomized, prospective study design combined with -omics measurements of microbiome and host, including extensive immune profiling, we found distinct effects of each diet. High-fiber consumers showed increased gut microbiome-encoded glycan-degrading CAZymes despite stable community diversity. Three distinct immunological trajectories in high fiber-consumers corresponded to baseline microbiota diversity. Alternatively, the high-fermented food diet steadily increased microbiota diversity and decreased inflammatory markers. The data highlight how coupling dietary interventions to deep and longitudinal immune and microbiome profiling can provide individualized and population-wide insight. Our results indicate that fermented foods may be valuable in countering the decreased microbiome diversity and increased inflammation pervasive in the industrialized society.

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Examination of traditional fermented food consumption and product awareness of university students in Istanbul, Turkey

The North African Journal of Food and Nutrition Research - July-December 2021 ◽

10.51745/najfnr.5.12.122-129 ◽

2021 ◽

Vol 5 (12) ◽

pp. 122-129

Author(s):

Şule Aktaç ◽

Simay Kundakçı ◽

Fatma Esra Güneş

Keyword(s):

University Students ◽

Food Consumption ◽

Cross Sectional Study ◽

Fermented Food ◽

Fermented Foods ◽

Industrial Products ◽

Chi Square ◽

Related Factors ◽

Cross Sectional ◽

Positive Effects

Background: Traditional fermented foods (TFF), which display positive effects on health, constitute a part of the traditions of a region and have continuity over many years. Familiarity with a product and the naturalness of food are positively associated with general attitudes toward traditional food consumption. Aims: To determine university students’ awareness and consumption of TFF and related factors in Turkey. Subjects and Methods: In this descriptive cross-sectional study, the faculties of Marmara University were stratified between January and June 2019, and a questionnaire on TFF consumption and related knowledge and attitudes was administered to 1,233 volunteer students selected using the random sampling method. The normality of data distribution was checked with the Kolmogorov-Smirnov test, and the data were analyzed with the chi-square test. Results: The students were familiar with the majority of TFF, with the most common being yoghurt (91.8%) and cheese (88.7%), while hardaliye (27.1%) and olives (27.1%) were less known TFF products. The majority of the students (60.7-99.2%) consumed cheese, yoghurt, pickled olives, pickle, soudjouk, tarhana, vinegar, and butter. The TFF were habitually consumed as industrial products, except tarhana, pickle, and yoghurt. It was also determined that the TFF consumption did not change according to the season in 76.4% of the students, and it was affected by the consumption of parents, whether they lived with their family or alone (p < 0.05). Conclusions: The students showed high awareness of TTF consumption, which was influenced by parent’s consumption and lifestyles. To ensure the continuity of TFF consumption, positive attitudes and behaviors must be maintained. Keywords: Consumption, familiarity, fermented foods, industrial products, Turkey.

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Species and strain cultivation of skin, oral, and gut microbiota

10.1101/2021.04.01.435439 ◽

2021 ◽

Author(s):

Elizabeth Fleming ◽

Victor Pabst ◽

Amelia Hoyt ◽

Wei Zhou ◽

Rachel Hardy ◽

...

Keyword(s):

Mass Spectrometry ◽

High Resolution ◽

Gut Microbiota ◽

Strain Level ◽

Microbial Consortia ◽

Metagenomic Sequencing ◽

Mechanistic Studies ◽

Microbial Species ◽

Human Microbiota

Genomics-driven discovery of microbial species have provided extraordinary insights into the biodiversity of human microbiota. High resolution genomics to investigate species- and strain-level diversity and mechanistic studies, however, rely on the availability of individual microbes from a complex microbial consortia. Here, we describe and validate a streamlined workflow for cultivating microbes from the skin, oral, and gut microbiota, informed by metagenomic sequencing, mass spectrometry, and strain profiling.

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Yoghurt Consumption is Associated With Transient Changes in the Composition of the Human Gut Microbiome

10.21203/rs.3.rs-99718/v1 ◽

2020 ◽

Author(s):

Caroline Ivanne Le Roy ◽

Alexander Kurilshikov ◽

Emily Leeming ◽

Alessia Visconti ◽

Ruth Bowyer ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

Visceral Fat ◽

Gut Microbiome ◽

Body Weight Gain ◽

Healthy Eating Index ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Sequencing Data ◽

Shotgun Metagenomic Sequencing

Abstract Background: Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits. Results: According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17±0.34; P = 2.72x10-10) and improved metabolic health characterised by reduced visceral fat (beta = -28.18±11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41±0.051; P = 6.14x10-12) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30±0.052; P = 1.49x10-8) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LifeLines-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed that increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation.Conclusions: Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species (i.e. S. thermophilus and B. lactis).

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Relationship between the Japanese-style diet, gut microbiota, and dementia: a cross-sectional study

10.21203/rs.3.rs-255821/v1 ◽

2021 ◽

Author(s):

Naoki Saji ◽

Tsuyoshi Tsuduki ◽

Kenta Murotani ◽

Takayoshi Hisada ◽

Taiki Sugimoto ◽

...

Keyword(s):

Cognitive Function ◽

Gut Microbiota ◽

Cognitive Decline ◽

Gut Microbiome ◽

Cross Sectional Study ◽

Dietary Composition ◽

Microbial Metabolites ◽

Cross Sectional ◽

Fish And Shellfish ◽

Japanese Diet

Abstract Background Previous studies have shown associations between the gut microbiota, microbial metabolites, and cognitive decline. However, the effect of the dietary composition on such associations has not been fully investigated. Methods We performed a cross-sectional sub-analysis of data from our prospective hospital-based cohort study (the Gimlet study) to evaluate the relationships between dietary composition, cognitive decline, and the gut microbiota. All the participants of the Gimlet study had been provided with information regarding this sub-study in 2018. Patients were excluded if they were unable to provide sufficient data in the questionnaire regarding their dietary composition. We assessed their demographics, dietary composition, risk factors, cognitive function, results of brain imaging, gut microbiome, and microbial metabolites. On the basis of previous studies, a nine-component traditional Japanese diet index (JDI9), a 12-component modern JDI (JDI12), and a 12-component revised JDI (rJDI12), were defined. Higher JDI scores indicated greater conformity to the traditional Japanese diet. We then evaluated the relationships between the JDI scores, cognitive function, and the gut microbiome and microbial metabolites using multivariable logistic regression analyses. Results We analyzed data from 85 eligible patients (61% women; mean age: 74.6 ± 7.4 years; mean Mini-Mental State Examination score: 24 ± 5). Compared with participants with dementia, those without dementia were more likely to consume foods in the JDI12, including fish and shellfish (64.5% vs. 39.1%, P = 0.048), mushrooms (61.3% vs. 30.4%, P = 0.015), soybeans and soybean-derived foods (62.9% vs. 30.4%, P = 0.013), and coffee (71.0% vs. 43.5%, P = 0.024). There were non-significant trends towards lower fecal concentrations of gut microbial metabolites in participants with a more traditional Japanese diet. Participants with dementia had lower JDI9, JDI12, and rJDI12 scores than participants without dementia (dementia vs. non-dementia, median JDI9 score: 5 vs. 7, P = 0.049; JDI12: 7 vs. 8, P = 0.017; and rJDI12: 7 vs. 9, P = 0.006, respectively). Conclusions Adherence to a traditional Japanese diet was found to be inversely associated with cognitive decline and tended to be associated with lower concentrations of gut microbial metabolites. Trial registration: UMIN000031851.

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Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples

mSystems ◽

10.1128/msystems.00289-19 ◽

2019 ◽

Vol 4 (5) ◽

Cited By ~ 9

Author(s):

Sonia Tarallo ◽

Giulio Ferrero ◽

Gaetano Gallo ◽

Antonio Francavilla ◽

Giuseppe Clerico ◽

...

Keyword(s):

Colorectal Cancer ◽

Gut Microbiota ◽

Small Rna ◽

Gut Microbiome ◽

Small Rnas ◽

Area Under The Curve ◽

Small Rna Sequencing ◽

Predictive Tool ◽

Cross Sectional ◽

Stool Samples

ABSTRACT Dysbiotic configurations of the human gut microbiota have been linked to colorectal cancer (CRC). Human small noncoding RNAs are also implicated in CRC, and recent findings suggest that their release in the gut lumen contributes to shape the gut microbiota. Bacterial small RNAs (bsRNAs) may also play a role in carcinogenesis, but their role has been less extensively explored. Here, we performed small RNA and shotgun sequencing on 80 stool specimens from patients with CRC or with adenomas and from healthy subjects collected in a cross-sectional study to evaluate their combined use as a predictive tool for disease detection. We observed considerable overlap and a correlation between metagenomic and bsRNA quantitative taxonomic profiles obtained from the two approaches. We identified a combined predictive signature composed of 32 features from human and microbial small RNAs and DNA-based microbiome able to accurately classify CRC samples separately from healthy and adenoma samples (area under the curve [AUC] = 0.87). In the present study, we report evidence that host-microbiome dysbiosis in CRC can also be observed by examination of altered small RNA stool profiles. Integrated analyses of the microbiome and small RNAs in the human stool may provide insights for designing more-accurate tools for diagnostic purposes. IMPORTANCE The characteristics of microbial small RNA transcription are largely unknown, while it is of primary importance for a better identification of molecules with functional activities in the gut niche under both healthy and disease conditions. By performing combined analyses of metagenomic and small RNA sequencing (sRNA-Seq) data, we characterized both the human and microbial small RNA contents of stool samples from healthy individuals and from patients with colorectal carcinoma or adenoma. With the integrative analyses of metagenomic and sRNA-Seq data, we identified a human and microbial small RNA signature which can be used to improve diagnosis of the disease. Our analysis of human and gut microbiome small RNA expression is relevant to generation of the first hypotheses about the potential molecular interactions occurring in the gut of CRC patients, and it can be the basis for further mechanistic studies and clinical tests.

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Trends in Fermented Food Consumption and Sodium Intake from Fermented Foods for Korean Adults Using the Korea National Health and Nutrition Examination Survey (KNHANES) (P18-025-19)

Current Developments in Nutrition ◽

10.1093/cdn/nzz039.p18-025-19 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

Author(s):

Sangyoung Kim ◽

Jeanne Freeland-Graves ◽

Hyun Ja Kim

Keyword(s):

Food Consumption ◽

National Health ◽

Sodium Intake ◽

Fermented Food ◽

Fermented Foods ◽

Nutrition Examination Survey ◽

Men And Women ◽

Korean Adults ◽

Health And Nutrition ◽

Over Time

Abstract Objectives To examine the trends in the consumption of fermented foods and sodium intake over time, using data from the Korean National Health and Nutrition Examination Survey (KNHANES). Methods This research study is a secondary analysis using KNHANES data from 1998 to 2016 which is a cross-sectional survey. The target population was Korean adults, ages ≥19 years and the total number was 76,199, with 32,324 men and 43,875 women. Assessment of fermented food consumption and sodium intake was conducted via analysis of 24-hour dietary recall data. Multivariate linear regressions and logistic regressions were performed to calculate the P for trends by applying strata, cluster, and sampling weights by SAS PROC SURVEY. Age was standardized for all analyses in order to calculate P for trends for education, income, fermented food consumption, and sodium intake. Results A significant decline in fermented food consumption was observed in both men and women (P < 0.0001). Among fermented foods, kimchi consumption was greatly reduced while pickled vegetables consumption showed a marked increase. Similarly, sodium intake from fermented foods significantly declined over time in both men and women (P < 0.0001). Conclusions The consumption of fermented foods and sodium intake from fermented foods by Korean adults significantly decreased over time from 1998 to 2016. Funding Sources N/A.

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