Microbial Metabolism in Fermentation Process

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 17384

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Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
Interests: microbiology; fermentation; microbial metabolism; bioreactors and fermenter; bacteria
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Special Issue Information

Dear Colleagues,

The compounds obtained from the fermentative metabolism of microorganisms have been intensively studied for their technological implications in the agri-food, pharmaceutical, and chemical industries. Microorganisms can be divided into

  • Obligate anaerobes, with fermentation metabolism or anaerobic respiration;
  • Obligate aerobes, with aerobic respiration and part of fermentation metabolism;
  • Facultative anaerobes, with aerobic respiration and anaerobic pathways (anaerobic respiration or fermentation metabolism).

Furthermore, they may also be differentiated by their fermentation pathways, end-products, and for the substrate that can ferment. Fermentation begins with glycolysis in the same way as cellular respiration, but the formed pyruvate does not continue through the citric acid cycle. Two examples of typical metabolism in the fermentation process are lactic acid fermentation and ethanol fermentation.

In lactic acid fermentation, pyruvate accepts electrons from NADH and is reduced to lactic acid; in the homolactic fermentation, the end-product is only lactic acid, while the heterolactic fermentation contains a mixture of lactic acid, ethanol and/or acetic acid, and CO2.

During ethanol fermentation, pyruvate is decarboxylated to acetaldehyde and CO2, and then accepts electrons from NADH, reducing acetaldehyde to ethanol. Other common microbial fermentation pathways are

  • Acetone–butanol–ethanol fermentation, with acetone, butanol, ethanol, and CO2 as end-products;
  • Butanediol fermentation, with ethanol, formic and lactic acid, acetoin, 2,3 butanediol, CO2, and hydrogen gas as end-products;
  • Butyric acid fermentation, with butyric acid, CO2, and hydrogen gas as end-products;
  • Mixed acid fermentation, with acetic, formic, lactic, and succinic acids; and ethanol, CO2, and hydrogen gas as end-products;
  • Propionic acid fermentation, with acetic acid, propionic acid, and CO2 as end-products.

This Special Issue seeks but is not limited to original research articles or reviews; the impact of various microbial metabolisms on the fermentation process, highlighting the enzymes involved; natural and engineering metabolic pathway optimization; and the reduction of microbial stress conditions.

Dr. Alessandro Robertiello
Guest Editor

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Keywords

  • Microbial metabolism
  • Fermentation process
  • Enzymes
  • Metabolic engineering
  • Microbial stress

Published Papers (6 papers)

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Research

11 pages, 2041 KiB  
Article
Transcriptomic Analysis of Staphylococcus equorum KM1031, Isolated from the High-Salt Fermented Seafood Jeotgal, under Salt Stress
by Sojeong Heo, Junghyun Park, Eungyo Lee, Jong-Hoon Lee and Do-Won Jeong
Fermentation 2022, 8(8), 403; https://doi.org/10.3390/fermentation8080403 - 19 Aug 2022
Cited by 2 | Viewed by 1527
Abstract
Staphylococcus equorum is a potential starter for Korean high-salt fermented foods because of its salt tolerance and enzymatic activities that contribute to enhanced sensory properties of the food products. However, the mechanisms of salt tolerance of S. equorum are not fully understood. Here, [...] Read more.
Staphylococcus equorum is a potential starter for Korean high-salt fermented foods because of its salt tolerance and enzymatic activities that contribute to enhanced sensory properties of the food products. However, the mechanisms of salt tolerance of S. equorum are not fully understood. Here, RNA sequencing was performed on S. equorum strain KM1031 exposed to 7% NaCl (w/v) for 2 and 4 h to determine global gene expression changes. Salt pressure for 2 and 4 h resulted in significant differential expression of 4.8% (106/2209) and 6.1% (134/2209) of S. equorum KM1031 genes, respectively. Twenty-five core genes were differentially expressed on salt treatment for both 2 and 4 h, seven of which were related to osmoprotectant uptake and synthesis. We analyzed the genome of strain KM1031 and identified osmoprotectant uptake (Opu) systems, potassium importers, sodium exporters, and the glycine betaine synthesis system. The RNA sequencing results indicated that the OpuD system and glycine betaine synthesis might play the main roles in the salt tolerance of strain KM1031. Finally, the results of RNA sequencing were validated by quantitative real-time PCR of likely salt stress-related genes. This transcriptomic analysis provides evidence regarding the osmotic stress responses of S. equorum strain KM1031. Full article
(This article belongs to the Special Issue Microbial Metabolism in Fermentation Process)
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18 pages, 3737 KiB  
Article
Production and Potential Genetic Pathways of Three Different Siderophore Types in Streptomyces tricolor Strain HM10
by Medhat Rehan, Hassan Barakat, Ibtesam S. Almami, Kamal A. Qureshi and Abdullah S. Alsohim
Fermentation 2022, 8(8), 346; https://doi.org/10.3390/fermentation8080346 - 22 Jul 2022
Cited by 5 | Viewed by 2611
Abstract
Siderophores are iron-chelating low-molecular-weight compounds that bind iron (Fe3+) with a high affinity for transport into the cell. The newly isolated strain Streptomyces tricolor HM10 secretes a pattern of secondary metabolites. Siderophore molecules are the representatives of such secondary metabolites. S. [...] Read more.
Siderophores are iron-chelating low-molecular-weight compounds that bind iron (Fe3+) with a high affinity for transport into the cell. The newly isolated strain Streptomyces tricolor HM10 secretes a pattern of secondary metabolites. Siderophore molecules are the representatives of such secondary metabolites. S. tricolor HM10 produces catechol, hydroxamate, and carboxylate types of siderophores. Under 20 μM FeCl3 conditions, S. tricolor HM10 produced up to 6.00 µg/mL of catechol siderophore equivalent of 2,3-DHBA (2,3-dihydroxybenzoic acid) after 4 days from incubation. In silico analysis of the S. tricolor HM10 genome revealed three proposed pathways for siderophore biosynthesis. The first pathway, consisting of five genes, predicted the production of catechol-type siderophore similar to petrobactin from Bacillus anthracis str. Ames. The second proposed pathway, consisting of eight genes, is expected to produce a hydroxamate-type siderophore similar to desferrioxamine B/E from Streptomyces sp. ID38640, S. griseus NBRC 13350, and/or S. coelicolor A3(2). The third pathway exhibited a pattern identical to the carboxylate xanthoferrin siderophore from Xanthomonas oryzae. Thus, Streptomyces strain HM10 could produce three different types of siderophore, which could be an incentive to use it as a new source for siderophore production in plant growth-promoting, environmental bioremediation, and drug delivery strategy. Full article
(This article belongs to the Special Issue Microbial Metabolism in Fermentation Process)
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24 pages, 4165 KiB  
Article
Analysis of the Composition of Substrate for Industrial Fermentation of Agaricus bisporus Based on Secondary and Tertiary Fermentation Mode Composition Analysis of Industrial Fermentation Substrates of A. bisporus
by Jiaxiang Juan, Qian Wang, Zhaoliang Gao, Tingting Xiao, Hui Chen, Jinjing Zhang, Xiaoxia Song and Jianchun Huang
Fermentation 2022, 8(5), 222; https://doi.org/10.3390/fermentation8050222 - 12 May 2022
Viewed by 2005
Abstract
In this study, changes in metabolites during the fermentation of Agaricus bisporus compost under the Shanghai Lianzhong secondary fermentation method and Jiangsu Yuguan tertiary fermentation method were analysed by applying gas chromatography–mass spectrometry (GC–MS) to understand the differences in metabolites under different fermentation [...] Read more.
In this study, changes in metabolites during the fermentation of Agaricus bisporus compost under the Shanghai Lianzhong secondary fermentation method and Jiangsu Yuguan tertiary fermentation method were analysed by applying gas chromatography–mass spectrometry (GC–MS) to understand the differences in metabolites under different fermentation methods and find metabolic markers at different fermentation stages in different fermentation methods. The results showed that 1002 compounds were identified. Based on the differential metabolites from pathways of significant enrichment, it was found that L-aspartic acid and 5-aminobenzolevulinic acid could be used as potential metabolic markers to evaluate the phase 2 fermentation method of Shanghai Lianzhong and the phase 3 fermentation method of Jiangsu Yuguan, respectively. This study provides a reference for the preparation of quality-stable fermentation materials and further understanding of the cultivation of A. bisporus with fermentation materials. Full article
(This article belongs to the Special Issue Microbial Metabolism in Fermentation Process)
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14 pages, 8100 KiB  
Article
NTH2 1271_1272delTA Gene Disruption Results in Salt Tolerance in Saccharomyces cerevisiae
by Alejandro Hernández-Soto, José Pablo Delgado-Navarro, Miguel Benavides-Acevedo, Sergio A. Paniagua and Andres Gatica-Arias
Fermentation 2022, 8(4), 166; https://doi.org/10.3390/fermentation8040166 - 05 Apr 2022
Viewed by 3224
Abstract
Trehalose is a common energy reservoir, and its accumulation results in osmotic protection. This sugar can accumulate through its synthesis or slow degradation of the reservoir by trehalase enzymes. Saccharomyces cerevisiae contains two neutral trehalases, NTH1 and NTH2, responsible for 75% and [...] Read more.
Trehalose is a common energy reservoir, and its accumulation results in osmotic protection. This sugar can accumulate through its synthesis or slow degradation of the reservoir by trehalase enzymes. Saccharomyces cerevisiae contains two neutral trehalases, NTH1 and NTH2, responsible for 75% and 25% of the enzymatic metabolism. We were interested in the loss-of-function of both enzymes with CRISPR/Cas9. The later NTH2 was of great importance since it is responsible for minor metabolic degradation of this sugar. It was believed that losing its functionality results in limited osmotic protection. We constructed an osmotolerant superior yeast capable of growing in 0.85 M NaCl after independent nth21271_1272delTA mutation by CRISPR/Cas9 technology, compared with nth1 893_894insT and wild type. We suggest that this yeast model could give clues to breeding commercial yeast resulting in non-GMO salinity-tolerant strains. Full article
(This article belongs to the Special Issue Microbial Metabolism in Fermentation Process)
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12 pages, 1098 KiB  
Article
High-Gossypol Whole Cottonseed Exhibited Mediocre Rumen Degradability and Less Microbial Fermentation Efficiency than Cottonseed Hull and Cottonseed Meal with an In Vitro Gas Production Technique
by Weikang Wang, Qichao Wu, Wenjuan Li, Yanlu Wang, Fan Zhang, Liangkang Lv, Shengli Li and Hongjian Yang
Fermentation 2022, 8(3), 103; https://doi.org/10.3390/fermentation8030103 - 28 Feb 2022
Cited by 11 | Viewed by 2460
Abstract
To explore whether or not the gossypol varied in cottonseed by-products affect rumen degradability and fermentation efficiency, an in vitro cumulative gas production experiment was applied with mixed rumen microorganism to compare rumen fermentation characteristics of whole cottonseed (WCS, n = 3 samples), [...] Read more.
To explore whether or not the gossypol varied in cottonseed by-products affect rumen degradability and fermentation efficiency, an in vitro cumulative gas production experiment was applied with mixed rumen microorganism to compare rumen fermentation characteristics of whole cottonseed (WCS, n = 3 samples), cottonseed meal (CSM, n = 3 samples), and cottonseed hull (CSH, n = 2 samples). The five-replicate fermentation per sample per incubation time continuously lasted for 0.5, 1.5, 3, 6, 12, 24, 36, and 48 h with an automated gas production recording system. Regardless of distinct nutrient differences, the free gossypol level in these cottonseed by-products ranked: WCS > CSH > CSM. After 48 h of incubation, the in vitro dry matter degradability and ammonia N concentration ranked as: CSM > WCS > CSH. The cumulative gas production and total volatile fatty acid (VFA) levels in the culture fluids ranked: CSM > CSH > WCS, in which the average production rate ranked: CSM > WCS > CSH. Regarding the molar VFA pattern, WCS in comparison with CSH and CSM presented the lowest production of non-glucogenic acids (e.g., acetate) and exhibited the highest fermentation efficiency of energy from carbohydrates to VFAs. There was a significant negative correlation between the gossypol content and cumulative gas and total VFA production, suggesting that the greater gossypol in cottonseed by-products, the more detrimental effect occurred for rumen fermentation. In a brief, WCS exhibited mediocre rumen degradability and less microbial fermentation efficiency than CSH and CSM, depending on their gossypol levels. Full article
(This article belongs to the Special Issue Microbial Metabolism in Fermentation Process)
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16 pages, 3267 KiB  
Article
Supplementing Glycerol to Inoculum Induces Changes in pH, SCFA Profiles, and Microbiota Composition in In-Vitro Batch Fermentation
by Qingtao Gao, Kai Li, Ruqing Zhong, Cheng Long, Lei Liu, Liang Chen and Hongfu Zhang
Fermentation 2022, 8(1), 18; https://doi.org/10.3390/fermentation8010018 - 31 Dec 2021
Cited by 4 | Viewed by 3001
Abstract
Glycerol was generally added to the inoculum as a cryoprotectant. However, it was also a suitable substrate for microbial fermentation, which may produce more SCFAs, thereby decreased pH of the fermentation broth. This study investigated the effect of supplementing glycerol to inoculum on [...] Read more.
Glycerol was generally added to the inoculum as a cryoprotectant. However, it was also a suitable substrate for microbial fermentation, which may produce more SCFAs, thereby decreased pH of the fermentation broth. This study investigated the effect of supplementing glycerol to inoculum on in vitro fermentation and whether an enhanced buffer capacity of medium could maintain the pH stability during in vitro batch fermentation, subsequently improving the accuracy of short chain fatty acids (SCFAs) determination, especially propionate. Two ileal digesta were fermented by pig fecal inoculum with or without glycerol (served as anti-frozen inoculum or frozen inoculum) in standard buffer or enhanced buffer solution (served as normal or modified medium). Along with the fermentation, adding glycerol decreased the pH of fermentation broth (p < 0.05). However, modified medium could alleviate the pH decrement compared with normal medium (p < 0.05). The concentration of total propionic acid production was much higher than that of other SCFAs in anti-frozen inoculum fermentation at 24 and 36 h, thereby increasing the variation (SD) of net production of propionate. The α-diversity analysis showed that adding glycerol decreased Chao1 and Shannon index under normal medium fermentation (p < 0.05) compared to modified medium (p < 0.05) along with fermentation. PCoA showed that all groups were clustered differently (p < 0.01). Adding glycerol improved the relative abundances of Firmicutes, Anaerovibrio, unclassified_f_Selenomonadaceae, and decreased the relative abundance of Proteobacteria (p < 0.05). The relative abundances of Firmicutes, such as Lactobacillus, Blautia and Eubacterium_Ruminantium_group in modified medium with frozen inoculum fermentation were higher than (p < 0.05) those in normal medium at 36 h of incubation. These results showed that adding glycerol in inoculum changed the fermentation patterns, regardless of substrate and medium, and suggested fermentation using frozen inoculum with modified medium could maintain stability of pH, improve the accuracy of SCFA determination, as well as maintain a balanced microbial community. Full article
(This article belongs to the Special Issue Microbial Metabolism in Fermentation Process)
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