Exploring microbial succession and diversity during solid-state fermentation of Tianjin duliu mature vinegar
TL;DR: The composition and succession of microbial communities in the entire solid-state fermentation were investigated, including starter daqu and acetic acid fermentation (AAF), indicating that lactic acid bacteria (LAB) had important influences on the flavor and taste of vinegar.
About: This article is published in Bioresource Technology.The article was published on 2013-11-01. It has received 72 citations till now. The article focuses on the topics: Acetic acid bacteria & Acetobacter.
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TL;DR: A perspective for bridging the gap between the phenotype and genotype of ecological system is provided, and understanding of MSSF mechanisms in Zhenjiang aromatic vinegar is advanced, showing bacteria made more contribution to flavour formation than fungi.
Abstract: Multispecies solid-state fermentation (MSSF), a natural fermentation process driven by reproducible microbiota, is an important technique to produce traditional fermented foods. Flavours, skeleton of fermented foods, was mostly produced by microbiota in food ecosystem. However, the association between microbiota and flavours and flavour-producing core microbiota are still poorly understood. Here, acetic acid fermentation (AAF) of Zhenjiang aromatic vinegar was taken as a typical case of MSSF. The structural and functional dynamics of microbiota during AAF process was determined by metagenomics and favour analyses. The dominant bacteria and fungi were identified as Acetobacter, Lactobacillus, Aspergillus, and Alternaria, respectively. Total 88 flavours including 2 sugars, 9 organic acids, 18 amino acids, and 59 volatile flavours were detected during AAF process. O2PLS-based correlation analysis between microbiota succession and flavours dynamics showed bacteria made more contribution to flavour formation than fungi. Seven genera including Acetobacter, Lactobacillus, Enhydrobacter, Lactococcus, Gluconacetobacer, Bacillus and Staphylococcus were determined as functional core microbiota for production of flavours in Zhenjiang aromatic vinegar, based on their dominance and functionality in microbial community. This study provides a perspective for bridging the gap between the phenotype and genotype of ecological system, and advances our understanding of MSSF mechanisms in Zhenjiang aromatic vinegar.
149 citations
TL;DR: Canonical correspondence analysis revealed microbial structure transition happened at thermophilic stages under environmental stress of moisture, pH, acidity, and pile temperature, which might help to effectively control the traditional Daqu SSF process by adjusting relevant environmental parameters.
Abstract: In this study, we investigated the microbiota dynamics during two industrial-scale traditional solid-state fermentation (SSF) processes of Daqu starters. Similar evolution profiles of environmental parameters, enzymatic activities, microbial amounts and communities were observed during the medium temperature SSF (MTSSF) and low temperature SSF (LTSSF) processes. Orders of Rickettsiales and Streptophyta only dominated the initial two days, and Eurotiales only predominated from days 10 to 24, however, phylotypes of Enterobacteriales, Lactobacillales, Bacillales, Saccharomycetales and Mucorales both prevailed throughout the MTSSF and LTSSF processes. Nevertheless, the pH in MTSSF process on day 5 were 5.28, while in LTSSF process (4.87) significantly lower (P < 0.05). The glucoamylase activities in MTSSF process dropped from 902.71 to 394.33 mg glucose g-1 h-1 on days 5 to 24, while significantly lower (P < 0.05) in LTSSF process and decreased from 512.25 to 268.69 mg glucose g-1 h-1. The relative abundance of Enterobacteriales and Lactobacillales in MTSSF process constituted from 10.30% to 71.73% and 2.34% to 16.68%, while in LTSSF process ranged from 3.16% to 41.06% and 8.43% to 57.39%, respectively. The relative abundance of Eurotiales in MTSSF process on days 10 to 24 decreased from 36.10% to 28.63%, while obviously higher in LTSSF process and increased from 52.00% to 72.97%. Furthermore, lower bacterial richness but higher fungal richness were displayed, markedly differences in bacterial communities but highly similarities in fungal communities were exhibited, during MTSSF process comparatively to the LTSSF process. Canonical correspondence analysis revealed microbial structure transition happened at thermophilic stages under environmental stress of moisture, pH, acidity and pile temperature. These profound understanding might help to effectively control the traditional Daqu SSF process by adjusting relevant environmental parameters.
89 citations
Cites methods from "Exploring microbial succession and ..."
...The V4 regions of bacterial 16S rRNA gene and ITS1 regions of fungal rRNA genes were amplified used the specific primers 515f/806r (Peiffer et al., 2013) and ITS5-1737F/ITS2-2043R (Huang et al., 2016) with the barcodes, respectively....
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TL;DR: The dominant microorganism species involved in the stages of alcoholic fermentation and acetic acid fermentation of dissimilar vinegars were summarized and various physicochemical properties and crucial compounds in disparate types of vinegar were summarized.
Abstract: Vinegar is one of the oldest acetic acid-diluted solution products in the world. It is produced from any fermentable sugary substrate by various fermentation methods. The final vinegar products possess unique functions, which are endowed with many kinds of compounds formed in the fermentation process. The quality of vinegar is determined by many factors, especially by the raw materials and microbial diversity involved in vinegar fermentation. Given that metabolic products from the fermenting strains are directly related to the quality of the final products of vinegar, the microbial diversity and features of the dominant strains involved in different fermentation stages should be analyzed to improve the strains and stabilize fermentation. Moreover, although numerous microbiological studies have been conducted to examine the process of vinegar fermentation, knowledge about microbial diversity and their roles involved in fermentation is still fragmentary and not systematic enough. Therefore, in this review, the dominant microorganism species involved in the stages of alcoholic fermentation and acetic acid fermentation of dissimilar vinegars were summarized. We also summarized various physicochemical properties and crucial compounds in disparate types of vinegar. Furthermore, the merits and drawbacks of vital fermentation methods were generalized. Finally, we described in detail the relationships among microbial diversity, raw materials, fermentation methods, physicochemical properties, compounds, functionality, and final quality of vinegar. The integration of this information can provide us a detailed map about the microbial diversity and function involved in vinegar fermentation.
86 citations
Cites background from "Exploring microbial succession and ..."
...T. delbreuckii Kaur et al. (2011), Lončar et al. (2006), Malbaša et al. (2009), Sievers et al. (1995), Solieri and Giudici (2009), Sreeramulu et al. (2000), Steinkraus et al. (1996), Teoh et al. (2004) Red vinegar RV 1....
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...Organic acids, including lactic acid and acetic acid, are the major sources of total acids and dominant flavor components of vinegar that are mainly produced during the AAF process (Nie et al. 2013; Tesfaye et al. 2002b)....
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...Thus, the dynamic changes in a microbial community during AAF are different from those during other fermentation stages (Nie et al. 2013)....
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TL;DR: The recent applications of meta-omics in cheese, vinegar, fermented alcoholic beverage, fermented vegetables, fermented tea, and soybean products explore the underlying mechanism of food fermentation and reveal fermented foods as rich sources of valuable genes and bioactive substances.
Abstract: Background Food fermentation is an important pillar of societal traditions, but also crucial in terms of economy for numerous regional products, as well as rich microbiological resources awaiting exploration. During the past few years, tremendous efforts have been made to provide important and deeper insights into the underlying molecular mechanisms of fermented foods through amplicon analysis, metagenomic and metatranscriptomic sequencing, as well as metaproteomic investigation, and integrated with metabolomics analysis. Scope and approach In this review the meta-omic tools applied in fermented foods are summarized. Then the recent meta-omic studies in cheese, vinegar, fermented alcoholic beverage, fermented vegetables, fermented tea, and soybean products are reviewed and emphasized. Key findings and conclusions Mainly based on high-throughput DNA sequencing, amplicon analysis, metagenomics and metatranscriptomics, together with metaproteomics and high-resolution metabolomics have allowed exploration of microbial community dynamics and functional characterization in traditional fermented foods in astonishing scale and speed during the past few years. The recent applications of meta-omics in cheese, vinegar, fermented alcoholic beverage, fermented vegetables, fermented tea, and soybean products explore the underlying mechanism of food fermentation and reveal fermented foods as rich sources of valuable genes and bioactive substances. Though there is limitation, promising clues exist for future investigation. Further integration of multiple meta-omic tools, together with powerful statistical analysis methods will assuredly lead to more detailed functional characterization and more efficient and sustainable production practices in fermented foods worldwide.
84 citations
TL;DR: In this paper, a review of the nutrients and bioactive components in different types of vinegars and their functional properties is presented, including amino acids, sugars, vitamins, and minerals.
84 citations
References
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TL;DR: Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment.
Abstract: We describe a new molecular approach to analyzing the genetic diversity of complex microbial populations. This technique is based on the separation of polymerase chain reaction-amplified fragments of genes coding for 16S rRNA, all the same length, by denaturing gradient gel electrophoresis (DGGE). DGGE analysis of different microbial communities demonstrated the presence of up to 10 distinguishable bands in the separation pattern, which were most likely derived from as many different species constituting these populations, and thereby generated a DGGE profile of the populations. We showed that it is possible to identify constituents which represent only 1% of the total population. With an oligonucleotide probe specific for the V3 region of 16S rRNA of sulfate-reducing bacteria, particular DNA fragments from some of the microbial populations could be identified by hybridization analysis. Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment. The results we obtained demonstrate that this technique will contribute to our understanding of the genetic diversity of uncharacterized microbial populations.
11,380 citations
"Exploring microbial succession and ..." refers methods in this paper
...The V3 region of the 16S rDNA gene amplified using primers 338f and 518r was selected for bacterial community analysis (Muyzer et al., 1993)....
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TL;DR: This work sequences a diverse array of 25 environmental samples and three known “mock communities” at a depth averaging 3.1 million reads per sample to demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature.
Abstract: The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known “mock communities” at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.
6,767 citations
"Exploring microbial succession and ..." refers background in this paper
...Unlike a diversity estimates, b diversity is a measure of the degree of similarity (e.g., phylogenetic relatedness) between pairs of communities (Caporaso et al., 2011)....
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..., phylogenetic relatedness) between pairs of communities (Caporaso et al., 2011)....
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...The b diversity metrics are useful for documenting shifts in the membership and structure of communities that may occur between sample categories or across environmental gradients (Caporaso et al., 2011)....
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...…sequencing technologies have opened new frontiers in microbial community analysis by providing a cost-effective means for exploring composition, diversity, and distribution of microbial communities in fermented foods (Caporaso et al., 2011; Huse et al., 2008; Jung et al., 2011; Kim et al., 2011)....
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TL;DR: Forest Vegetation of Higher Elevations on Diorite and the Two-Phase Ef fect .......... .............. . 299 Forest Vegetation in Transects.
Abstract: II. PROCEDURE .................................. 285 Study Areas ................................. 285 Vegetation Samples and Soil Data ..... ..... 286 Arrangement of Samples in Transects .... . 286 Evaluation of Transect Techniques . ..... . 288 Transect Tables ................... ....... 289 III. VEGETATION DESCRIPTION ...... ............. 291 Low Elevations on Diorite . ... ......... .. 291 Low Elevations on Gabbro ..... ........ 297 Low Elevations on Serpentine and the Two-Phase Ef fect .......... .............. . 299 Forest Vegetation of Higher Elevations on Diorite ......................... ....... 302 Vegetation of Higher Elevations on Serpentine . . 305
3,332 citations
"Exploring microbial succession and ..." refers methods in this paper
...To indicate the microbial diversity in AAF process, the a diversity indices (including Chao1, ACE, Simpson, and Shannon–Weaver indices) were quantified in terms of OTU richness, and b diversity of different samples was analyzed using Whittaker’s method (Whittaker, 1960)....
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TL;DR: It is indicated that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.
Abstract: Mammals are metagenomic in that they are composed of not only their own gene complements but also those of all of their associated microbes. To understand the coevolution of the mammals and their indigenous microbial communities, we conducted a network-based analysis of bacterial 16S ribosomal RNA gene sequences from the fecal microbiota of humans and 59 other mammalian species living in two zoos and in the wild. The results indicate that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.
3,072 citations
"Exploring microbial succession and ..." refers background in this paper
...It is shown that b diversity metrics are far less sensitive to effects such as sequencing errors and chimeras (Ley et al., 2008)....
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TL;DR: It is shown that a 2% single- linkage preclustering methodology followed by an average-linkage clustering based on pairwise alignments more accurately predicts expected OTUs in both single and pooled template preparations of known taxonomic composition.
Abstract: Summary Deep sequencing of PCR amplicon libraries facilitates the detection of low-abundance populations in environmental DNA surveys of complex microbial communities. At the same time, deep sequencing can lead to overestimates of microbial diversity through the generation of low-frequency, error-prone reads. Even with sequencing error rates below 0.005 per nucleotide position, the common method of generating operational taxonomic units (OTUs) by multiple sequence alignment and complete-linkage clustering significantly increases the number of predicted OTUs and inflates richness estimates. We show that a 2% single-linkage preclustering methodology followed by an average-linkage clustering based on pairwise alignments more accurately predicts expected OTUs in both single and pooled template preparations of known taxonomic composition. This new clustering method can reduce the OTU richness in environmental samples by as much as 30‐60% but does not reduce the fraction of OTUs in long-tailed rank abundance curves that defines the rare biosphere.
1,260 citations
"Exploring microbial succession and ..." refers methods in this paper
...All V3 tags were aligned together and pre-clustered at 98% similarity by singlelinkage preclustering (SLP) tool (Huse et al., 2010)....
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