scholarly journals On Pickles: Biological and Sociocultural Links Between Fermented Foods and the Human Gut Microbiome

2021 ◽  
Author(s):  
Andrew Flachs ◽  
Joseph Orkin
Keyword(s):  
Microbial Ecology ◽  
Bacterial Flora ◽  
Human Microbiome ◽  
Food Products ◽  
Food Samples ◽  
Fermented Food ◽  
Fermented Foods ◽  
Stool Samples ◽  
Probiotic Microbes ◽  
Microbiological Data

Abstract BackgroundThe composition of the human microbiome varies considerably in diversity and density across communities as a function of the foods we eat and the places we live. While all foods contain microbes, humans directly shape this microbial ecology through fermentation. Fermented foods are produced from microbial reactions that depend on local environmental conditions, fermentation practices, and the manner in which foods are prepared and consumed. These interactions are of special interest to ethnobiologists because they link investigations of how people shape and know the world around them to local knowledge, food traditions, local flora, and microbial taxa. MethodsIn this manuscript, we report on data collected at a fermentation revivalist workshop in Tennessee. To ask how fermentation traditions are learned and influence macro and micro ecologies, we conducted interviews and participated in a four-day craft fermentation workshop, and then collected both fermented food products and stool samples from workshop participants eating those fermented foods. ResultsWe identified ten major themes comprised of 29 sub-themes drawn from 326 marked codes in the transcripts. In combination, this analysis allowed us to summarize key experiences with fermentation, particularly those related to a sense of authenticity, place, health, and the discovery of tactile work. From the 605 ASVs shared between food and fecal samples, we identified 25 candidate ASVs that are suspected to have been transmitted from fermented food samples to the gut microbiomes of the workshop participants. Our results indicate that many of the foods prepared and consumed during the workshop were rich sources of probiotic microbes. ConclusionsBy combining these qualitative social and quantitative microbiological data, we suggest that variation in culturally-informed fermentation practices introduces variation in bacterial flora even among very similar foods, and that these food products can influence gut microbial ecology.

scholarly journals On pickles: biological and sociocultural links between fermented foods and the human gut microbiome

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Andrew Flachs ◽  
Joseph D. Orkin
Keyword(s):  
Microbial Ecology ◽  
Bacterial Flora ◽  
Human Microbiome ◽  
Food Products ◽  
Food Samples ◽  
Fermented Food ◽  
Fermented Foods ◽  
Stool Samples ◽  
Probiotic Microbes ◽  
Microbiological Data

Abstract Background The composition of the human microbiome varies considerably in diversity and density across communities as a function of the foods we eat and the places we live. While all foods contain microbes, humans directly shape this microbial ecology through fermentation. Fermented foods are produced from microbial reactions that depend on local environmental conditions, fermentation practices, and the manner in which foods are prepared and consumed. These interactions are of special interest to ethnobiologists because they link investigations of how people shape and know the world around them to local knowledge, food traditions, local flora, and microbial taxa. Methods In this manuscript, we report on data collected at a fermentation revivalist workshop in Tennessee. To ask how fermentation traditions are learned and influence macro and micro ecologies, we conducted interviews with eleven people and participated in a four-day craft fermentation workshop. We also collected 46 fermented food products and 46 stool samples from workshop participants eating those fermented foods. Results We identified ten major themes comprised of 29 sub-themes drawn from 326 marked codes in the transcripts. In combination, this analysis allowed us to summarize key experiences with fermentation, particularly those related to a sense of authenticity, place, health, and the discovery of tactile work. From the 605 amplicon sequence variants (ASVs) shared between food and fecal samples, we identified 25 candidate ASVs that are suspected to have been transmitted from fermented food samples to the gut microbiomes of the workshop participants. Our results indicate that many of the foods prepared and consumed during the workshop were rich sources of probiotic microbes. Conclusions By combining these qualitative social and quantitative microbiological data, we suggest that variation in culturally informed fermentation practices introduces variation in bacterial flora even among very similar foods, and that these food products can influence gut microbial ecology.

scholarly journals Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Edoardo Pasolli ◽  
Francesca De Filippis ◽  
Italia E. Mauriello ◽  
Fabio Cumbo ◽  
Aaron M. Walsh ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Gut Microbiome ◽  
Large Scale ◽  
Streptococcus Thermophilus ◽  
Fermented Food ◽  
Fermented Foods ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Stool Samples

Abstract Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.

Assessment of bacterial diversity in selected Philippine fermented food products through PCR-DGGE

2011 ◽  
Vol 2 (4) ◽  
pp. 273-281 ◽  
Author(s):  
L.M. Dalmacio ◽  
A.K. Angeles ◽  
L.L. Larcia ◽  
M. Balolong ◽  
R. Estacio
Keyword(s):  
Bacterial Diversity ◽  
16S Rdna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Acetic Acid Bacteria ◽  
Food Samples ◽  
Fermented Food ◽  
Probiotic Bacteria ◽  
Rrna Gene ◽  
Fermented Foods ◽  
16S Rdna Pcr

The bacterial population in several Philippine fermented food preparations was assessed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) of the 16S rRNA gene (16S rDNA). Genomic DNA was isolated directly from alamang (fermented shrimp paste), burong isda (fermented fish and rice), burong hipon (fermented shrimp and rice), burong mustasa (fermented mustard leaves), tuba (sugar cane wine), suka (vinegar) and sinamak (spiced vinegar) using one of two protocols, namely – MoBio DNA Extraction Kit procedure and a cetyltrimethylammonium bromide-based method. Samples recalcitrant to both methods underwent enrichment in three culture broths prior to DNA isolation. Isolated DNA was amplified using nested primer pairs targeting the bacterial 16S rDNA. PCR products were subjected to DGGE to elucidate the bacterial diversity in each fermented food. 16S rDNA sequence analyses revealed that lactic acid bacteria (LAB) and acetic acid bacteria (AAB) were dominant in the food samples. The LAB identified were Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus panis, Lactobacillus pontis and Weissella cibaria. Identified AAB were Acetobacter pomorum, Acetobacter ghanensis, Acetobacter orientalis, and Acetobacter pasteurianus. Among these, L. fermentum, L. plantarum and W. cibaria are established probiotic bacteria, while L. panis and L. pontis are potential probiotic bacteria. This finding would increase the appeal and significance of local fermented foods to consumers. Furthermore, the majority of the identified bacteria in the study have not been reported before in culture-dependent studies of similar food preparations. As such, some of the bacterial 16S rDNA obtained were cloned to have an initial partial bacterial 16S rDNA library for Philippine fermented foods.

scholarly journals In Vitro Evaluation of Probiotic Properties of Indigenous Yeasts Isolated from Nigerian Fermented Food Products

2021 ◽  
pp. 75-85
Author(s):  
I. A. Adesokan ◽  
A. I. Sanni ◽  
S. S. Kanwar
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Large Subunit ◽  
Food Products ◽  
Fermented Food ◽  
Adhesive Property ◽  
Fermented Foods ◽  
Probiotic Properties ◽  
Bile Tolerance ◽  
Acid And Bile Tolerance ◽  
Indigenous Yeast

Probiotics are living microbial food supplements which beneficially affect the host by improving the intestinal microbial balance. Before an organism can be designated as probiotic there are certain criteria that must be fulfilled. These include acid and bile tolerance, antimicrobial activity, ability to co-aggregate, hydrophobicity etc. One hundred and eighty one indigenous yeast isolates recovered from various fermented food products of Nigeria were characterized and grouped using phenotypic methods. Forty two selected yeast isolates were identified using molecular method which involved sequencing of D1 and D2 domain of the large subunit of ribosomal DNA. Then nine indigenous Saccharomyces cerevisiae were evaluated for their probiotic characteristics such as acid and bile tolerance, transit in simulated gastric and intestinal juices, autoaggregation and hydrophobicity. Saccharomyces cerevisiae SC10 was included as a positive control. The S. cerevisiae were able to grow in the presence of acidic medium with pH as low as 2 and 3. In the minimum inhibitory concentration test with 0-1% ox bile, all the S. cerevisiae tested were able to grow. The growth for 3% bile tolerance test ranged from 4.81 to 5.35 log cfu/ml. These isolates were able to survive in simulated gastro-intestinal transit. All the yeast isolates exhibited bile salt deconjugation activity against sodium glycodeoxycholate and were able to grow in the presence of all other bile salts investigated. Autoaggregation ability (an adhesive property) of the indigenous yeast isolates ranged from 89.80% for S. cerevisiae BK19 to 99.91% for S. cerevisiae OB03. The native yeast isolates also exhibited high percentage hydrophobicity, another adhesive property of probiotics. The values obtained ranged from 31.62 to 83.45% for isolates AG23A and OB 17. These observations indicate that the native yeast isolates from Nigerian fermented foods have the potential of being use as probiotics for making functional foods.

Identification and Antimicrobial Susceptibility of Lactic Acid Bacteria from Retail Fermented Foods

2007 ◽  
Vol 70 (11) ◽  
pp. 2606-2612 ◽  
Author(s):  
BEILEI GE ◽  
PING JIANG ◽  
FEIFEI HAN ◽  
NASREEN K. SALEH ◽  
NIVEDITA DHIMAN ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Antimicrobial Susceptibility ◽  
Food Products ◽  
The United States ◽  
Fermented Food ◽  
23S Rrna ◽  
Fermented Foods ◽  
Intrinsic Resistance ◽  
Safety Criterion

One important safety criterion of using lactic acid bacteria (LAB) in food applications is to ensure that they do not carry transferable antimicrobial resistance (AR) determinants. In this study, 63 LAB belonging to six genera, Streptococcus, Lactobacillus, Lactococcus, Enterococcus, Leuconostoc, and Pediococcus, were recovered from 28 retail fermented food products in Maryland, identified to species with 16S–23S rRNA spacer PCRs, and characterized for antimicrobial susceptibility against eight antimicrobials. Besides intrinsic resistance to ciprofloxacin or vancomycin in some lactobacilli, tetracycline resistance was observed in two Streptococcus thermophilus isolates from one cheese and one sour cream sample and was associated with the presence of a nonconjugative tet(S) gene. The results indicated a low level of AR among naturally occurring and starter LAB cultures in fermented dairy and meat products in the United States; therefore, the probability for foodborne LAB to serve as reservoirs of AR is low. Further studies involving a larger sample size are needed to assess the potential risk of AR gene transfer from LAB in fermented food products.

scholarly journals Thai Fermented Foods as a Versatile Source of Bioactive Microorganisms—A Comprehensive Review

2018 ◽  
Vol 86 (3) ◽  
pp. 37 ◽  
Author(s):  
Bhagavathi Sivamaruthi ◽  
Periyanaina Kesika ◽  
Chaiyavat Chaiyasut
Keyword(s):  
Fermented Food ◽  
Bioactive Molecules ◽  
Fermented Foods ◽  
Spontaneous Fermentation ◽  
Isolation And Characterization ◽  
Probiotic Microbes ◽  
Asian People ◽  
Traditional Fermented Foods

Fermented foods are known for several health benefits, and they are generally used among the Asian people. Microorganisms involved in the fermentation process are most responsible for the final quality of the food. Traditional fermented (spontaneous fermentation) foods are a versatile source of bioactive molecules and bioactive microbes. Several reports are available regarding the isolation and characterization of potent strains from traditional fermented foods. A collection of information for easy literature analysis of bioactive microbes derived from Thai fermented food is not yet available. The current manuscript compiled information on bioactive (antimicrobial- and enzyme-producing probiotic) microbes isolated from naturally fermented Thai foods.

scholarly journals ISOLATION AND CHARACTERIZATION OF ACTIVE PROBIOTIC ORGANISMS IN FERMENTED ZEA MAYS, PENTADETHRA MACROPHYLLA BENTH,AND RICINUS COMMUNIS

2021 ◽  
Vol 9 (4) ◽  
pp. 512-516
Author(s):  
Sunday S. Agbem ◽  
Keyword(s):  
Ricinus Communis ◽  
Food Samples ◽  
Primary Objective ◽  
Fermented Food ◽  
Bacillus Species ◽  
Fermented Foods ◽  
Isolation And Characterization ◽  
Micro Organisms ◽  
Protein Rich

Active probiotic organisms are good bacteria considered to be live micro-organisms that are obtained from fermented foods. Evidence has shown that probiotics are essential in human health. This studys primary objective is to isolate and characterize the active probiotic organisms present in certain fermented food samples. Maize, African oil bean, and castor oil were subjected to analysis. The result found the presence of active probiotic organisms such as Pedioccocus, Lactobacillus, Micrococcus, and Bacillus species. The study concluded that these organisms are responsible for the fermentation of carbohydrates and protein-rich seeds.

Registered Designation of Origin Areas of Fermented Food Products Defined by Microbial Phenotypes and Artificial Neural Networks

1999 ◽  
Vol 65 (10) ◽  
pp. 4484-4489 ◽  
Author(s):  
M. F. S. Lopes ◽  
C. I. Pereira ◽  
F. M. S. Rodrigues ◽  
M. P. Martins ◽  
M. C. Mimoso ◽  
...  
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Raw Materials ◽  
Food Products ◽  
Fermented Food ◽  
Fermented Foods ◽  
Fermented Sausage ◽  
Local Environments ◽  
Artificial Neural ◽  
Counterfeit Products

ABSTRACT Cheese produced from raw ewes’ milk andchouriço, a Portuguese dry fermented sausage, are still produced in a traditional way in certain regions of Portugal by relying on colonization by microbial populations associated with the raw materials, equipment, and local environments. For the purpose of describing the product origins and types of these fermented foods, metabolic phenotypes can be used as descriptors of the product as well as to determine the presence of compounds with organoleptic value. The application of artificial neural networks to the metabolic profiles of bacterial isolates was assayed and allowed the separation of products from different regions. This method could then be used for the Registered Designation of Origin certification process of food products. Therefore, besides test panel results for these traditionally produced food products, another tool for validating products for the marketplace is available to the producers. The method can be improved for the detection of counterfeit products.

scholarly journals African Sorghum-Based Fermented Foods: Past, Current and Future Prospects

Nutrients ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 1111 ◽  
Author(s):  
Oluwafemi Ayodeji Adebo
Keyword(s):  
Rural Communities ◽  
Food Processing ◽  
Food Products ◽  
Fermented Food ◽  
Fermented Foods ◽  
Staple Food ◽  
Future Prospects ◽  
Nutrient Sources ◽  
Commercial Success ◽  
Processing Techniques

Sorghum (Sorghum bicolor) is a well-known drought and climate resistant crop with vast food use for the inhabitants of Africa and other developing countries. The importance of this crop is well reflected in its embedded benefits and use as a staple food, with fermentation playing a significant role in transforming this crop into an edible form. Although the majority of these fermented food products evolve from ethnic groups and rural communities, industrialization and the application of improved food processing techniques have led to the commercial success and viability of derived products. While some of these sorghum-based fermented food products still continue to bask in this success, much more still needs to be done to further explore evolving techniques, technologies and processes. The addition of other affordable nutrient sources in sorghum-based fermented foods is equally important, as this will effectively augment the intake of a nutritionally balanced product.

scholarly journals From Sample to Multi-Omics Conclusions in under 48 Hours

mSystems ◽  
2016 ◽  
Vol 1 (2) ◽  
Author(s):  
Robert A. Quinn ◽  
Jose A. Navas-Molina ◽  
Embriette R. Hyde ◽  
Se Jin Song ◽  
Yoshiki Vázquez-Baeza ◽  
...  
Keyword(s):  
16S Rrna ◽  
Clinical Medicine ◽  
Food Samples ◽  
Fermented Food ◽  
Fermented Foods ◽  
Microbial Culture ◽  
Omics Data ◽  
Industrial Microbiology ◽  
Time Required ◽  
Time Frames

ABSTRACT Polymicrobial infections are difficult to diagnose due to the challenge in comprehensively cultivating the microbes present. Omics methods, such as 16S rRNA sequencing, metagenomics, and metabolomics, can provide a more complete picture of a microbial community and its metabolite production, without the biases and selectivity of microbial culture. However, these advanced methods have not been applied to clinical or industrial microbiology or other areas where complex microbial dysbioses require immediate intervention. The reason for this is the length of time required to generate and analyze omics data. Here, we describe the development and application of a pipeline for multi-omics data analysis in time frames matching those of the culture-based approaches often used for these applications. This study applied multi-omics methods effectively in clinically relevant time frames and sets a precedent toward their implementation in clinical medicine and industrial microbiology. Multi-omics methods have greatly advanced our understanding of the biological organism and its microbial associates. However, they are not routinely used in clinical or industrial applications, due to the length of time required to generate and analyze omics data. Here, we applied a novel integrated omics pipeline for the analysis of human and environmental samples in under 48 h. Human subjects that ferment their own foods provided swab samples from skin, feces, oral cavity, fermented foods, and household surfaces to assess the impact of home food fermentation on their microbial and chemical ecology. These samples were analyzed with 16S rRNA gene sequencing, inferred gene function profiles, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics through the Qiita, PICRUSt, and GNPS pipelines, respectively. The human sample microbiomes clustered with the corresponding sample types in the American Gut Project (http://www.americangut.org ), and the fermented food samples produced a separate cluster. The microbial communities of the household surfaces were primarily sourced from the fermented foods, and their consumption was associated with increased gut microbial diversity. Untargeted metabolomics revealed that human skin and fermented food samples had separate chemical ecologies and that stool was more similar to fermented foods than to other sample types. Metabolites from the fermented foods, including plant products such as procyanidin and pheophytin, were present in the skin and stool samples of the individuals consuming the foods. Some food metabolites were modified during digestion, and others were detected in stool intact. This study represents a first-of-its-kind analysis of multi-omics data that achieved time intervals matching those of classic microbiological culturing. IMPORTANCE Polymicrobial infections are difficult to diagnose due to the challenge in comprehensively cultivating the microbes present. Omics methods, such as 16S rRNA sequencing, metagenomics, and metabolomics, can provide a more complete picture of a microbial community and its metabolite production, without the biases and selectivity of microbial culture. However, these advanced methods have not been applied to clinical or industrial microbiology or other areas where complex microbial dysbioses require immediate intervention. The reason for this is the length of time required to generate and analyze omics data. Here, we describe the development and application of a pipeline for multi-omics data analysis in time frames matching those of the culture-based approaches often used for these applications. This study applied multi-omics methods effectively in clinically relevant time frames and sets a precedent toward their implementation in clinical medicine and industrial microbiology.

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