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.

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 Phenotypic and molecular characterization of different isolates of Lactobacillus plantarum from four Nigerian fermented foods for use as probiotics in aquaculture

2018 ◽  
Vol 5 (10) ◽  
pp. 329-337
Author(s):  
Daniel Olusegun Diyaolu ◽  
Fatuyi Olanipekun Ekundayo ◽  
Emmanuel Adedayo Fasakin ◽  
Olabode Thomas Adebayo
Keyword(s):  
16S Rrna ◽  
Lactobacillus Plantarum ◽  
Biochemical Characterization ◽  
Bacterial Species ◽  
Fermented Food ◽  
Rrna Gene ◽  
Fermented Foods ◽  
Slight Variation ◽  
16S Rna

This study aimed at identifying Lactobacillus plantarum from fermented maize, sorghum, soyabeans and cassava, using both phenotypic method and 16S RNA sequencing, as well as determining similarity or otherwise among recovered isolates. Biochemical characterization of isolates recovered from these fermented foods revealed that L. plantarum occurred in all fermented food examined, with slight variation in their abilities to ferment some sugars (arabinose, dulbitol and mannitol). These phenotypically identified isolates were also confirmed to be L. plantarum by 16S rRNA sequencing, having close relatedness (> 95%) with other isolates available in the gene bank. However, intragenomic heterogeneity of the 16S rRNA gene was observed among these L. plantarum isolates. The result obtained in this finding pinpoints the need to evaluate the beneficial effects each strain of L. plantarum may possess as promising probiotics, rather than generalising common effects for all strains of this bacterial species.

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.

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.

Microbial Profiling of Malera and Phab: Starters Used for Preparing Traditional Fermented Foods and Beverages in Himachal Pradesh, India

2019 ◽  
Vol 15 (7) ◽  
pp. 707-711
Author(s):  
Vipasha Sharma ◽  
Sampan Attri ◽  
Rishi Mahajan ◽  
Gunjan Goel
Keyword(s):  
16S Rrna ◽  
Himachal Pradesh ◽  
Fermented Food ◽  
Alcoholic Beverages ◽  
Careful Examination ◽  
Rrna Gene ◽  
Fermented Foods ◽  
Dgge Profile ◽  
Shannon Diversity ◽  
Microbial Profiling

Background: Traditional fermented food preparation uses customary processing methods passed on from generation to generation under natural conditions. These fermented foods use native flora without being aware of the significant role of microbes involved in the fermentation process. Therefore, the present study aimed to determine the bacterial composition of traditional starters used in different fermented food preparations in Himachal Pradesh region India. Methods: The study investigated the bacterial DGGE (Denaturating Gradient Gel Electrophoresis) profile targeting V3 region of 16S rRNA of two traditional starters known as Malera and Phab. The starters are used in the preparation of fermented cereals product known as bhaturoo and alcoholic beverages. The Shannon diversity and richness were calculated from DGGE profile. The 16S rRNA gene sequences of identified bacterial species were deposited in NCBI database. Results: The DGGE profile identified eleven and seven different bacterial strains in Malera and Phab, respectively. The Shannon diversity index of 1.07 and 0.94 was obtained for Malera and Phab, respectively. The bacterial population was dominated by different strains of Bifidobacterium sp. in both the starters along with the presence of non lactic enterobacteriacae members such as Klebsiella sp. and a pathogenic strain of Dickeya chrysanthemi. Conclusion: The study is the first report on microbial profiling of microflora of starters. A careful examination of individual components and method of preparation of the starters should be taken to avoid contamination by pathogens.

scholarly journals Bacterial compositions of indigenous Lanna (Northern Thai) fermented foods and their potential functional properties

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242560
Author(s):  
Chonthicha Pakwan ◽  
Thararat Chitov ◽  
Panuwan Chantawannakul ◽  
Manop Manasam ◽  
Sakunnee Bovonsombut ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Functional Properties ◽  
Food Samples ◽  
Fermented Food ◽  
Fermented Foods ◽  
Food Groups ◽  
Northern Thailand ◽  
Pork Sausage ◽  
Culture Independent

Many indigenous fermented foods of Northern Thailand and neighbouring regions have traditionally been known for their health benefits. In this study, we explored the communities of bacteria in selected fermented foods which are commonly consumed among ethnic groups around Northern Thailand, for which information on their microbial compositions or their functional properties is still limited. The selected food groups included Thua Nao (alkaline fermented soybean product), Nham (fermented pork sausage/loaf), Nam phak (fermented Chinese cabbage) and Miang (fermented leaves from Miang Tea trees). Bacteria in these fermented foods were isolated and enumerated. Bacterial communities were determined using a culture-independent (pyrosequencing) approach. Lactic acid bacteria were recovered from all of these fermented food samples, with levels ranging from 3.1 to 7.5 log CFU/g throughout the fermentation processes. Analysis of the 16S rRNA gene from the fermented food samples using 454-pyrosequencing resulted in 113,844 sequences after quality evaluation. Lactic acid bacteria were found in high proportions in Nham, Nam phak and Miang. Bacillus was predominant in Thua nao, in which significant proportions of Lactic acid bacteria of the family Leuconostocaceae were also found. Groups of lactic acid bacteria found varied among different food samples, but three genera were predominant: Lactococcus, Lactobacillus and Leuconostoc, of which many members are recognised as probiotics. The results showed that these traditional Thai fermented food products are rich sources of beneficial bacteria and can potentially be functional/probiotic foods.

scholarly journals ACTIVE PROBIOTIC ANALYSIS OF FERMENTED CEREAL AND LEGUMES COMMONLY CONSUMED IN NIGERIA

2021 ◽  
Vol 9 (10) ◽  
pp. 913-917
Author(s):  
Moses O. Omale ◽  
Keyword(s):  
Human Health ◽  
Castor Oil ◽  
Food Samples ◽  
Primary Objective ◽  
Fermented Food ◽  
Bacillus Species ◽  
Fermented Foods ◽  
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.

scholarly journals Isolation and Biochemical Characterization of Lactic Acid Bacteria from Fermented Foods

2021 ◽  
Vol 10 (10) ◽  
pp. 584-600
Author(s):  
Sirisha J. Lakshmi ◽  
K. Lakshmi A. Vijaya Gopal
Keyword(s):  
Biochemical Characterization ◽  
Food Samples ◽  
Fermented Food ◽  
Fermented Foods ◽  
Biochemical Tests ◽  
Test Reaction ◽  
Negative Results ◽  
Oxidase Test ◽  
Positive Results

Probiotics are considered as successful major category of food supplements. Probiotics can be functional foods because their health benefits are essentially higher than traditional nutritional products. Probiotic bacteria was collected from home made and commercial fermented food samples. A total of 30 food samples were collected from local areas of Guntur in Andhra Pradesh. Bacteria were isolated on MRS agar medium after observation of growth and pure culture was obtained by sub-culturing on the same medium. Purity of each culture was confirmed by morphological investigation, Gram’s staining and further identification by specific biochemical tests. The isolates from both dairy and non-dairy fermented foods were identified as rods, bacilli, cocci and chain shape. While some isolates showed positive results some showed negative results for catalase test, methyl red test, oxidase test, aescualin fermentation, starch hydrolysis, arginine hydrolysis, citrate utilization and voges prausker’s test reaction. Based on morphological, cultural and biochemical characterization of 16 bacterial isolates out of 30 were identified as Lactobacillus spp.

scholarly journals A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Adrienn Gréta Tóth ◽  
István Csabai ◽  
Gergely Maróti ◽  
Ákos Jerzsele ◽  
Attila Dubecz ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Pathogenic Bacteria ◽  
Gene Diversity ◽  
Fermented Food ◽  
Practical Significance ◽  
Fermented Foods ◽  
Bacterial Strains ◽  
Genetic Components ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene

AbstractAntimicrobial resistance (AMR) is a global threat gaining more and more practical significance every year. The main determinants of AMR are the antimicrobial resistance genes (ARGs). Since bacteria can share genetic components via horizontal gene transfer, even non-pathogenic bacteria may provide ARG to any pathogens which they become physically close to (e.g. in the human gut). In addition, fermented food naturally contains bacteria in high amounts. In this study, we examined the diversity of ARG content in various kefir and yoghurt samples (products, grains, bacterial strains) using a unified metagenomic approach. We found numerous ARGs of commonly used fermenting bacteria. Even with the strictest filter restrictions, we identified ARGs undermining the efficacy of aminocoumarins, aminoglycosides, carbapenems, cephalosporins, cephamycins, diaminopyrimidines, elfamycins, fluoroquinolones, fosfomycins, glycylcyclines, lincosamides, macrolides, monobactams, nitrofurans, nitroimidazoles, penams, penems, peptides, phenicols, rifamycins, tetracyclines and triclosan. In the case of gene lmrD, we detected genetic environment providing mobility of this ARG. Our findings support the theory that during the fermentation process, the ARG content of foods can grow due to bacterial multiplication. The results presented suggest that the starting culture strains of fermented foods should be monitored and selected in order to decrease the intake of ARGs via foods.

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