scholarly journals Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
John Leech ◽  
Raul Cabrera-Rubio ◽  
Aaron M. Walsh ◽  
Guerrino Macori ◽  
Calum J. Walsh ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Fermented Food ◽  
Food Type ◽  
Fermented Foods ◽  
Microbial Composition ◽  
Potential Health ◽  
Dairy Foods ◽  
Primary Driver ◽  
Health Promoting ◽  
Insight Into

ABSTRACT Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that consumption of these foods helps to address the negative consequences of “industrialization” of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented-food microbiota to better harness desirable traits. Here, we considerably expand the understanding of fermented-food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity, and functional potential (including antimicrobial resistance and carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from a number of countries. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined data set, 127 high-quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Companilactobacillus, Leuconostoc, and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than nonfermented equivalents, with water kefirs, sauerkrauts, and kvasses containing the greatest numbers of potentially health-associated gene clusters. Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date and yields novel information regarding their relative health-promoting potential. IMPORTANCE Fermented foods are regaining popularity worldwide due in part to a greater appreciation of the health benefits of these foods and the associated microorganisms. Here, we use state-of-the-art approaches to explore the microbiomes of 58 of these foods, identifying the factors that drive the microbial composition of these foods and potential functional benefits associated with these populations. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity and, notably, potential health promoting attributes were more common in fermented foods than nonfermented equivalents. The information provided here will provide significant opportunities for the further optimization of fermented-food production and the harnessing of their health-promoting potential.

scholarly journals Fermented food metagenomics reveals substrate-associated differences in taxonomy, health-associated- and antibiotic resistance-determinants

2020 ◽  
Author(s):  
John Leech ◽  
Raul Cabrera-Rubio ◽  
Aaron M Walsh ◽  
Guerrino Macori ◽  
Calum J Walsh ◽  
...  
Keyword(s):  
Fermented Food ◽  
Molecular Techniques ◽  
Food Type ◽  
Western Society ◽  
Fermented Foods ◽  
Metagenomic Sequencing ◽  
Microbial Composition ◽  
Potential Health ◽  
Health Promoting ◽  
Insight Into

AbstractFermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that the consumption of these foods that help to address the negative consequences of ‘industrialization’ of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented food microbiota to better harness desirable traits. Here we considerably expand the understanding of fermented food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity and functional potential (including antimicrobial resistance, carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from around the Globe. Food type, i.e., dairy-, sugar- or brine-type fermented foods, was to be the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined dataset, 127 high quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Lactobacillus, Leuconostoc and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than non-fermented equivalents, with waterkefirs, sauerkrauts and kvasses containing the greatest numbers of potentially health-associated gene clusters (PHAGCs). Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date, and yields novel information regarding their relative health-promoting potential.ImportanceFermented foods are regaining popularity in Western society due in part to an appreciation of the potential for fermented food microbiota to positively impact on health. Many previous studies have studied fermented microbiota using classical culture-based microbiological methods, older molecular techniques or, where deeper analyses have been performed, have involved a relatively small number of one specific food type. Here, we have used a state-of-the-art shotgun metagenomic approach to investigate 58 different fermented foods of different type and origin. Through this analysis, we were able to identify the differences in the microbiota across these foods, the factors that drove their microbial composition, and the relative potential functional benefits of these microbes. The information provided here will provide significant opportunities for the further optimisation of fermented food production and the harnessing of their health promoting potential.

Recent Insight Into Fermented Foods and Production

2019 ◽  
pp. 83-115
Author(s):  
Dixit V. Bhalani ◽  
Arvind Kumar Singh Chandel ◽  
Poonam Singh Thakur
Keyword(s):  
Value Added ◽  
Vital Role ◽  
Fermented Foods ◽  
Fermented Beverages ◽  
Health Promoting ◽  
Fermentation Technology ◽  
Waste Food ◽  
Domestic Level ◽  
Insight Into ◽  
Value Added Products

The fermented beverages and foods either of plant or animal source play a vital role in the food of society in several parts of the world. The fermented of foods not only afford vital sources of nutrients but also have abundant potential in maintaining health and also preventing various diseases. The bacteria and yeasts are the major groups of microorganisms related to traditional fermented of the foods. Numerous diverse types of traditional fermented beverages and foods are formed at domestic level in the various countries. The advancement of fermentation technology provides value addition to waste food by their complete conversion into the different value-added products. The recent research suggests that the biological functions of fermented foods affect the health due to functional microbes involved during fermentation which provides several health-promoting benefits to the consumers. The emphasis of this chapter is to describe the fermentation technology and their potential to minimize the wastage of foods by conversion of value-added products and their benefits.

scholarly journals Microbiota and Metabolite Modifications after Dietary Exclusion of Dairy Products and Reduced Consumption of Fermented Food in Young and Older Men

Nutrients ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1905
Author(s):  
Jinyoung Kim ◽  
Kathryn J. Burton-Pimentel ◽  
Charlotte Fleuti ◽  
Carola Blaser ◽  
Valentin Scherz ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Dairy Products ◽  
Fermented Food ◽  
Fermented Foods ◽  
Microbiota Composition ◽  
Microbial Composition ◽  
Age Related ◽  
The Impact ◽  
Effect Of Age ◽  
Gut Microbiota Composition

The gut microbiota adapts to age-related changes in host physiology but is also affected by environmental stimuli, like diet. As a source of both pre- and probiotics, dairy and fermented foods modulate the gut microbiota composition, which makes them interesting food groups to use for the investigation of interactions between diet and ageing. Here we present the effects of excluding dairy products and limiting fermented food consumption for 19 days on gut microbiota composition and circulating metabolites of 28 healthy, young (YA) and older (OA) adult men. The intervention affected gut microbial composition in both groups, with significant increases in Akkermansia muciniphila and decreases in bacteria of the Clostridiales order. Lower fasting levels of glucose and insulin, as well as dairy-associated metabolites like lactose and pentadecanoic acid, were observed after the intervention, with no effect of age. The intervention also decreased HDL and LDL cholesterol levels. Dairy fat intake was positively associated with the HDL cholesterol changes but not with the LDL/HDL ratio. In conclusion, restricting the intake of dairy and fermented foods in men modified their gut microbiota and blood metabolites, while the impact of the dietary restrictions on these outcomes was more marked than the effect of age.

scholarly journals Health-Promoting Role of Lactiplantibacillus plantarum Isolated from Fermented Foods

2021 ◽  
Vol 9 (2) ◽  
pp. 349
Author(s):  
Natalia Garcia-Gonzalez ◽  
Natalia Battista ◽  
Roberta Prete ◽  
Aldo Corsetti
Keyword(s):  
Fermented Food ◽  
Starter Cultures ◽  
In Vivo Studies ◽  
Fermented Foods ◽  
Adhesion Ability ◽  
Probiotic Strains ◽  
Health Promoting ◽  
Gastro Intestinal Tract

Fermentation processes have been used for centuries for food production and preservation. Besides the contribution of fermentation to food quality, recently, scientific interest in the beneficial nature of fermented foods as a reservoir of probiotic candidates is increasing. Fermented food microbes are gaining attention for their health-promoting potential and for being genetically related to human probiotic bacteria. Among them, Lactiplantibacillus (Lpb.) plantarum strains, with a long history in the food industry as starter cultures in the production of a wide variety of fermented foods, are being investigated for their beneficial properties which are similar to those of probiotic strains, and they are also applied in clinical interventions. Food-associated Lpb. plantarum showed a good adaptation and adhesion ability in the gastro-intestinal tract and the potential to affect host health through various beneficial activities, e.g., antimicrobial, antioxidative, antigenotoxic, anti-inflammatory and immunomodulatory, in several in vitro and in vivo studies. This review provides an overview of fermented-associated Lpb. plantarum health benefits with evidence from clinical studies. Probiotic criteria that fermented-associated microbes need to fulfil are also reported.

scholarly journals Table Olives More than a Fermented Food

Foods ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 178 ◽  
Author(s):  
Giorgia Perpetuini ◽  
Roberta Prete ◽  
Natalia Garcia-Gonzalez ◽  
Mohammad Khairul Alam ◽  
Aldo Corsetti
Keyword(s):  
Lactic Acid ◽  
Mediterranean Area ◽  
Fermented Food ◽  
Starter Cultures ◽  
Fermented Foods ◽  
Table Olives ◽  
Food Industries ◽  
Health Promoting ◽  
The Mediterranean

Table olives are one of the oldest vegetable fermented foods in the Mediterranean area. Beside their economic impact, fermented table olives represent also an important healthy food in the Mediterranean diet, because of their high content of bioactive and health-promoting compounds. However, olive fermentation is still craft-based following traditional processes, which can lead to a not fully predictable final product with the risk of spontaneous alterations. Nowadays, food industries have to face consumer demands for safe and healthy products. This review offers an overview about the main technologies used for olive fermentation and the role of lactic acid bacteria and yeasts characterizing this niche during the fermentation. Particular attention is offered to the selection and use of microorganisms as starter cultures to fasten and improve the safety of table olives. The development and implementation of multifunctional starter cultures in order to obtain heath-oriented table olives is also discussed.

scholarly journals Microbial Community Structure and Diversity of Shrimp Paste at Different Fermentation Stages

2018 ◽  
Author(s):  
Lingying Dai ◽  
Limei Wang ◽  
Jiang Sun ◽  
Lixue Zheng ◽  
Bin Qi
Keyword(s):  
Microbial Diversity ◽  
High Throughput Sequencing ◽  
Microbial Composition ◽  
Shrimp Culture ◽  
Bacterial Populations ◽  
Three Stages ◽  
Dominant Bacteria ◽  
The Relationship ◽  
Insight Into

AbstractHigh-throughput sequencing was used to reveal the highly diverse bacterial populations in shrimp paste at different fermentation stages. We studied three stages of fermentation and obtained 448,916 reads. Using this approach, we revealed the presence of 30 phyla, 55 classes, 86 orders, 206 families and 695 genera of bacteria in the shrimp paste. Shrimp paste in fermentation metaphase had a more diverse microbiota than that in fermentation prophase and fermentation anaphase. Diversity appeared greatest in fermentation anaphase. The four dominant phyla were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The most common genera were Psychrobacter, Halomonas, Bacillus, Alteribacillus, and Lactococcus. Their content varied at different stages of fermentation. All the microbiome presented a variety of changes in the microbial diversity of shrimp paste.ImportanceMost research on the microbial diversity of shrimp paste has focused on the shrimp culture environment, or the chemical composition and sensory attributes of the paste. Little research has been conducted on the microbial diversity and composition of shrimp paste. The relationship between microbes and the flavor and quality of shrimp paste has thus been unknown. We therefore analyzed the microbial composition and variation of shrimp paste at different stages of fermentation. The dominant bacteria in fermentation prophase, metaphase, and anaphase were identified. Our preliminary findings give some insight into which microbes contribute to the flavor of shrimp paste and suggest how to improve its flavor. In addition, our findings are relevant to optimizing the production of shrimp paste and guaranteeing its quality and safety.

scholarly journals The relationship between fermented food intake and mortality risk in the European Prospective Investigation into Cancer and Nutrition-Netherlands cohort

2015 ◽  
Vol 113 (3) ◽  
pp. 498-506 ◽  
Author(s):  
Jaike Praagman ◽  
Geertje W. Dalmeijer ◽  
Yvonne T. van der Schouw ◽  
Sabita S. Soedamah-Muthu ◽  
W. M. Monique Verschuren ◽  
...  
Keyword(s):  
Food Intake ◽  
Proportional Hazards ◽  
Smoking Habit ◽  
Cox Proportional Hazards ◽  
Fermented Food ◽  
Fermented Foods ◽  
Dairy Foods ◽  
Fermented Dairy ◽  
The Relationship ◽  
Prospective Investigation

The objective of the present study was to investigate the relationship between total and subtypes of bacterial fermented food intake (dairy products, cheese, vegetables and meat) and mortality due to all causes, total cancer and CVD. From the European Prospective Investigation into Cancer and Nutrition-Netherlands cohort, 34 409 Dutch men and women, aged 20–70 years who were free from CVD or cancer at baseline, were included. Baseline intakes of total and subtypes of fermented foods were measured with a validated FFQ. Data on the incidence and causes of death were obtained from the national mortality register. Cox proportional hazards models were used to analyse mortality in relation to the quartiles of fermented food intake. After a mean follow-up of 15 (sd2·5) years, 2436 deaths occurred (1216 from cancer and 727 from CVD). After adjustment for age, sex, total energy intake, physical activity, education level, hypertension, smoking habit, BMI, and intakes of fruit, vegetables and alcohol, total fermented food intake was not found to be associated with mortality due to all causes (hazard ratio upperv. lowest quartile (HRQ4 v. Q1) 1·00, 95 % CI 0·88, 1·13), cancer (HRQ4 v. Q11·02, 95 % CI 0·86, 1·21) or CVD (HRQ4 v. Q11·04, 95 % CI 0·83, 1·30). Bacterial fermented foods mainly consisted of fermented dairy foods (78 %) and cheese (16 %). None of the subtypes of fermented foods was consistently related to mortality, except for cheese which was moderately inversely associated with CVD mortality, and particularly stroke mortality (HRQ4 v. Q10·59, 95 % CI 0·38, 0·92,Ptrend= 0·046). In conclusion, the present study provides no strong evidence that intake of fermented foods, particularly fermented dairy foods, is associated with mortality.

scholarly journals Microbiota identified from preserved Anopheles

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Bianca E Silva ◽  
Zvifadzo Matsena Zingoni ◽  
Lizette L. Koekemoer ◽  
Yael L. Dahan-Moss
Keyword(s):  
Microbial Diversity ◽  
Vector Competence ◽  
Mosquito Species ◽  
Anopheles Funestus ◽  
Cost Effective ◽  
Diversity Indices ◽  
Malaria Vectors ◽  
Microbial Composition ◽  
Culture Independent ◽  
Culture Dependent

Abstract Background Mosquito species from the Anopheles gambiae complex and the Anopheles funestus group are dominant African malaria vectors. Mosquito microbiota play vital roles in physiology and vector competence. Recent research has focused on investigating the mosquito microbiota, especially in wild populations. Wild mosquitoes are preserved and transported to a laboratory for analyses. Thus far, microbial characterization post-preservation has been investigated in only Aedes vexans and Culex pipiens. Investigating the efficacy of cost-effective preservatives has also been limited to AllProtect reagent, ethanol and nucleic acid preservation buffer. This study characterized the microbiota of African Anopheles vectors: Anopheles arabiensis (member of the An. gambiae complex) and An. funestus (member of the An. funestus group), preserved on silica desiccant and RNAlater® solution. Methods Microbial composition and diversity were characterized using culture-dependent (midgut dissections, culturomics, MALDI-TOF MS) and culture-independent techniques (abdominal dissections, DNA extraction, next-generation sequencing) from laboratory (colonized) and field-collected mosquitoes. Colonized mosquitoes were either fresh (non-preserved) or preserved for 4 and 12 weeks on silica or in RNAlater®. Microbiota were also characterized from field-collected An. arabiensis preserved on silica for 8, 12 and 16 weeks. Results Elizabethkingia anophelis and Serratia oryzae were common between both vector species, while Enterobacter cloacae and Staphylococcus epidermidis were specific to females and males, respectively. Microbial diversity was not influenced by sex, condition (fresh or preserved), preservative, or preservation time-period; however, the type of bacterial identification technique affected all microbial diversity indices. Conclusions This study broadly characterized the microbiota of An. arabiensis and An. funestus. Silica- and RNAlater®-preservation were appropriate when paired with culture-dependent and culture-independent techniques, respectively. These results broaden the selection of cost-effective methods available for handling vector samples for downstream microbial analyses.

scholarly journals Suitability Analysis of 17 Probiotic Type Strains of Lactic Acid Bacteria as Starter for Kimchi Fermentation

Foods ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1435
Author(s):  
Hee Seo ◽  
Jae-Han Bae ◽  
Gayun Kim ◽  
Seul-Ah Kim ◽  
Byung Hee Ryu ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Growth Rates ◽  
Principal Component ◽  
Fermented Foods ◽  
Suitability Analysis ◽  
Moderate Growth ◽  
Health Promoting ◽  
Highly Correlated ◽  
Type Strains

The use of probiotic starters can improve the sensory and health-promoting properties of fermented foods. This study aimed to evaluate the suitability of probiotic lactic acid bacteria (LAB) as a starter for kimchi fermentation. Seventeen probiotic type strains were tested for their growth rates, volatile aroma compounds, metabolites, and sensory characteristics of kimchi, and their characteristics were compared to those of Leuconostoc (Le.) mesenteroides DRC 1506, a commercial kimchi starter. Among the tested strains, Limosilactobacillus fermentum, Limosilactobacillus reuteri, Lacticaseibacillus rhamnosus, Lacticaseibacillus paracasei, and Ligilactobacillus salivarius exhibited high or moderate growth rates in simulated kimchi juice (SKJ) at 37 °C and 15 °C. When these five strains were inoculated in kimchi and metabolite profiles were analyzed during fermentation using GC/MS and 1H-NMR, data from the principal component analysis (PCA) showed that L. fermentum and L. reuteri were highly correlated with Le. mesenteroides in concentrations of sugar, mannitol, lactate, acetate, and total volatile compounds. Sensory test results also indicated that these three strains showed similar sensory preferences. In conclusion, L. fermentum and L. reuteri can be considered potential candidates as probiotic starters or cocultures to develop health-promoting kimchi products.

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