Complex Microbial Communities as Part of Fermented Food Ecosystems and Beneficial Properties

2012 ◽  
Author(s):  
Muhammad Imran ◽  
Nathalie Desmasures ◽  
Jean-Paul Vernoux
Keyword(s):  
Microbial Communities ◽  
Fermented Food

scholarly journals Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead

mSystems ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Benjamin E. Wolfe
Keyword(s):  
Microbial Communities ◽  
Taxonomic Diversity ◽  
Fermented Food ◽  
Trophic Levels ◽  
Intraspecific Diversity ◽  
Sequencing Data ◽  
Molecular Approaches ◽  
Model Community ◽  
Microbiome Assembly

ABSTRACTAs troves of microbiome sequencing data provide improved resolution of patterns of microbial diversity, new approaches are needed to understand what controls these patterns. Many microbial ecologists are using cultivated model microbial communities to address this challenge. These systems provide opportunities to identify drivers of microbiome assembly, but key challenges and limitations need to be carefully considered in their development, implementation, and interpretation. How well do model microbial communities mimicin vitrocommunities in terms of taxonomic diversity, trophic levels, intraspecific diversity, and the abiotic environment? What are the best ways to manipulate and measure inputs and outputs in model community experiments? In this perspective, I briefly address some of these challenges on the basis of our experience developing fermented food model communities. Future work integrating genetic and molecular approaches with cultivated model microbial communities will allow microbial ecology to develop a more mechanistic understanding of microbiome diversity.

scholarly journals IDENTIFICATION AND PROBIOTIC CHARACTERIZATION OF MICROBIAL COMMUNITIES FROM FERMENTED RICE WATER AND ASSOCIATION OF ENTEROCOCCUS HIRAE WITH PEPTIC ULCER CAUSING HELICOBACTER PYLORI

2021 ◽  
Vol 10 (5) ◽  
pp. 3578-3587
Author(s):  
S. Umamaheswari
Keyword(s):  
Helicobacter Pylori ◽  
Peptic Ulcer ◽  
Microbial Communities ◽  
Probiotic Strain ◽  
Antagonistic Activity ◽  
Fermented Food ◽  
Causative Organism ◽  
Enterococcus Hirae ◽  
H Pylori ◽  
Rice Water

Fermented rice water is a classic example of fermented food known for nutritional values. The microbiome of fermented rice water is not yet completely revealed. Helicobacter pylori, the causative organism of peptic ulcer and gastric cancer is considered as a WHO priority-2 due to the nature of resisting antibiotics necessitating the research to rule out regiments to avoid H. pylori infections. Probiotics are considered as an emerging alternative to eradicate and manage this pathogen, making it more prominent to have the means to evaluate their effectiveness against this pathogen. The present work is focused on revealing the microbial communities of fermented rice water and to characterize the isolates for their probiotic efficiency along with its antagonistic activity against H. pylori. Three natural inhabitants of fermented rice water were isolated and characterized morphologically and biochemically and were identified using 16s rRNA sequencing. The isolates were further tested for their probiotic efficiency and their antagonistic activity against H. pylori isolated from the gastric endoscopic ulcer samples. The present study highlights Enterococcus hirae as a probiotic strain with potent anti-H. pylori activity.

scholarly journals Microbial Community Succession and Metabolite Changes During Fermentation of BS Sufu, the Fermented Black Soybean Curd by Rhizopus microsporus, Rhizopus oryzae, and Actinomucor elegans

2021 ◽  
Vol 12 ◽  
Author(s):  
Di Yao ◽  
Lei Xu ◽  
Mengna Wu ◽  
Xiaoyu Wang ◽  
Kun Wang ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Solid Phase Microextraction ◽  
Rhizopus Oryzae ◽  
Solid Phase ◽  
Fermented Food ◽  
Gas Chromatography Mass Spectrometry ◽  
Rhizopus Microsporus ◽  
High Throughput Dna Sequencing ◽  
Fermentation Stage

BS Sufu is a fermented food that is made by mixed black soybeans and soybeans. Microbial communities and metabolites play an important role for the final product. We characterized microbial diversity of BS Sufu during fermentation by high-throughput DNA sequencing. Meanwhile, volatile compounds were investigated by solid-phase microextraction (SPME) coupled with gas chromatography–mass spectrometry (GC-MS). The results showed that bacterial diversity was higher than that of fungi in BS Sufu. We found the existence of bacterial and fungal core communities, including Enterococcus, Enterobacter, Rhizopus, and Monascus. Network analysis indicated that bacterial and fungal communities maintain positive and negative interactions, which are important to shape the resident microbial communities in Sufu. In addition, 17 free amino acids (FAAs) were detected at the post-fermentation stage, and umami amino acid mainly contributed to taste of BS Sufu. Furtherly, a total of 79 volatile constituents in BS Sufu, including nine alcohols, 31 esters, and four aldehydes, form synergistically the unique odor of Sufu. Additionally, the correlations between microbiota and metabolites were analyzed. Our results suggested that these microbial taxa and metabolites contribute to the taste and flavor of BS Sufu. This study provided information for analysis of BS Sufu at different fermentation periods in terms of the microbial diversity and metabolites, and this information was important to understand the properties of mixed soybeans Sufu.

scholarly journals Silica/Lignin Carrier as a Factor Increasing the Process Performance and Genetic Diversity of Microbial Communities in Laboratory-Scale Anaerobic Digesters

Energies ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4429
Author(s):  
Agnieszka A. A. Pilarska ◽  
Agnieszka Wolna-Maruwka ◽  
Alicja Niewiadomska ◽  
Krzysztof Pilarski ◽  
Mariusz Adamski ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microbial Communities ◽  
Dehydrogenase Activity ◽  
Operation Mode ◽  
Bacterial Count ◽  
Fermented Food ◽  
Parameter Analysis ◽  
Total Bacterial Count ◽  
Process Performance ◽  
Biogas Yield

The article aims to present results of research on anaerobic digestion (AD) of waste wafers (WF-control) and co-substrate system–waste wafers and cheese (WFC-control), combined with digested sewage sludge, as inoculum. The purpose of this paper is to confirm the outcome of adding silica/lignin (S/L; 4:1) material, as a microbial carrier, on the process performance and genetic diversity of microbial communities. The experiment was conducted in a laboratory under mesophilic conditions, in a periodical operation mode of bioreactors. Selected physicochemical parameters of the tested carrier, along with the microstructure and thermal stability, were determined. Substrates, batches and fermenting slurries were subjected to standard parameter analysis. As part of the conducted analysis, samples of fermented food were also tested for total bacterial count, dehydrogenase activity. Additionally, DNA extraction and next-generation sequencing (NGS) were carried out. As a result of the conducted study, an increase in the volume of produced biogas was recorded for samples fermented with S/L carrier: in the case of WF + S/L by 18.18% to a cumulative biogas yield of 833.35 m3 Mg−1 VS, and in the case of WFC + S/L by 17.49% to a yield of 950.64 m3 Mg−1 VS. The largest total bacterial count, during the process of dehydrogenase activity, was maintained in the WFC + S/L system. The largest bacterial biodiversity was recorded in samples fermented with the addition of cheese, both in the case of the control variant and in the variant when the carrier was used. In contrast, three phyla of bacteria Firmicutes, Proteobacteria and Actinobacteria predominated in all experimental facilities.

scholarly journals Fate of influent microbial populations during medium chain carboxylic acid recovery from brewery and pre-fermented food waste streams

2022 ◽  
Author(s):  
Shilva Shrestha ◽  
Brittany Colcord ◽  
Xavier Fonoll ◽  
Lutgarde Raskin
Keyword(s):  
Carboxylic Acid ◽  
Microbial Communities ◽  
Food Waste ◽  
Fermented Food ◽  
Chain Elongation ◽  
Microbial Populations ◽  
Waste Streams ◽  
Medium Chain ◽  
Acid Recovery

Waste streams continuously introduce active and inactive microbial populations that can influence assembly of microbial communities in chain elongation systems.

scholarly journals Coproporphyrin III Produced by the Bacterium Glutamicibacter arilaitensis Binds Zinc and Is Upregulated by Fungi in Cheese Rinds

mSystems ◽  
2018 ◽  
Vol 3 (4) ◽  
Author(s):  
Jessica L. Cleary ◽  
Shilpa Kolachina ◽  
Benjamin E. Wolfe ◽  
Laura M. Sanchez
Keyword(s):  
Trace Metals ◽  
Microbial Communities ◽  
Molecular Mechanisms ◽  
Chemical Species ◽  
Fermented Food ◽  
Pigment Production ◽  
Microbial Succession ◽  
Content Type ◽  
Bacteria And Fungi ◽  
Pink Pigment

ABSTRACT Microbial communities of fermented food microbiomes typically exhibit predictable patterns of microbial succession. However, the biochemical mechanisms that control the diversity and dynamics of these communities are not well described. Interactions between bacteria and fungi may be one mechanism controlling the development of cheese rind microbiomes. This study characterizes a specific bacterium-fungus interaction previously discovered on cheese rinds between the bacterium Glutamicibacter arilaitensis (formerly Arthrobacter arilaitensis) and fungi of the genus Penicillium and identifies the specialized metabolites produced during cocultures. G. arilaitensis was previously shown to produce an unknown pink pigment in response to the presence of Penicillium. Using a combination of mass spectrometry, nuclear magnetic resonance (NMR), and transcriptome sequencing (RNA-seq), we determined that this pigment production is associated with production of coproporphyrin III. The discovery that coproporphyrin III preferentially bound zinc over other trace metals found in cheese curds highlights the value of using analytical chemistry to confirm identity of predicted chemical species. IMPORTANCE Bacterium-fungus interactions play key roles in the assembly of cheese rind microbial communities, but the molecular mechanisms underlying these interactions are poorly characterized. Moreover, millions of people around the world enjoy eating cheeses and cheese rinds, but our understanding of the diversity of microbial metabolites ingested during cheese consumption is limited. The discovery of zinc coproporphyrin III as the cause of pink pigment production by Glutamicibacter arilaitensis suggests that secretion of this molecule is important for microbial acquisition of trace metals.

scholarly journals Identification of Microbial Communities in Fermented Food using DNA Barcoding Technique and Development of Novel Method for DNA Isolation from Food Products

2021 ◽  
Vol 9 (3) ◽  
pp. 391-397
Author(s):  
Karukuvel Raja Raja ◽  
Sanjay Prasad Selvaraj ◽  
Rekha Shanmugam ◽  
Bharadwaj Revuru ◽  
Sathishkumar Ramalingam
Keyword(s):  
Microbial Communities ◽  
Dna Barcoding ◽  
Dna Isolation ◽  
Food Products ◽  
Fermented Food ◽  
Novel Method

scholarly journals Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

2021 ◽  
Vol 18 (19) ◽  
pp. 10093
Author(s):  
Anna Y. Alekseeva ◽  
Anneloes E. Groenenboom ◽  
Eddy J. Smid ◽  
Sijmen E. Schoustra
Keyword(s):  
Microbial Communities ◽  
Evolutionary Dynamics ◽  
Experimental Testing ◽  
Large Body ◽  
Fermented Food ◽  
Model Systems ◽  
Fermented Foods ◽  
Evolutionary Processes ◽  
Evolutionary Forces ◽  
Laboratory Setup

Eco-evolutionary forces are the key drivers of ecosystem biodiversity dynamics. This resulted in a large body of theory, which has partially been experimentally tested by mimicking evolutionary processes in the laboratory. In the first part of this perspective, we outline what model systems are used for experimental testing of eco-evolutionary processes, ranging from simple microbial combinations and, more recently, to complex natural communities. Microbial communities of spontaneous fermented foods are a promising model system to study eco-evolutionary dynamics. They combine the complexity of a natural community with extensive knowledge about community members and the ease of manipulating the system in a laboratory setup. Due to rapidly developing sequencing techniques and meta-omics approaches incorporating data in building ecosystem models, the diversity in these communities can be analysed with relative ease while hypotheses developed in simple systems can be tested. Here, we highlight several eco-evolutionary questions that are addressed using microbial communities from fermented foods. These questions relate to analysing species frequencies in space and time, the diversity-stability relationship, niche space and community coalescence. We provide several hypotheses of the influence of these factors on community evolution specifying the experimental setup of studies where microbial communities of spontaneous fermented food are used.

scholarly journals Experimental approaches to tracking mobile genetic elements in microbial communities

2020 ◽  
Vol 44 (5) ◽  
pp. 606-630 ◽  
Author(s):  
Christina C Saak ◽  
Cong B Dinh ◽  
Rachel J Dutton
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microbial Communities ◽  
Mobile Genetic Elements ◽  
Mobile Elements ◽  
Microbial Evolution ◽  
Fermented Food ◽  
Chromosome Conformation ◽  
Genetic Elements ◽  
Experimental Approaches

ABSTRACT Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.

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