Phylogenomics of a Saccharomyces cerevisiae cocoa strain reveals adaptation to a West African fermented food population

Díaz-Muñoz, Cristian; Verce, Marko; Vuyst, Luc De; Weckx, Stefan

doi:10.1016/j.isci.2022.105309

Cited by 5 publications

(5 citation statements)

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“…The current study dealt with the microbial diversity (cocoa pulp-bean mass) and VOC and non-VOC dynamics (cocoa pulps, cocoa beans during fermentation, and drying cocoa beans) of a spontaneous (NC) and five SCI CFPs, differing in the participating yeasts, carried out in duplicate with Trinitario cocoa in plastic vessels in Costa Rica. Besides a well-characterized S. cerevisiae strain, IMDO 050523 ( Lefeber et al, 2012 ; Moens et al, 2014 ; Díaz-Muñoz et al, 2022 ), strains of H. opuntiae (IMDO 020003) and P. kudriavzevii (IMDO 060005) were involved, which were different from those used previously, namely H. opuntiae IMDO 040108 ( Díaz-Muñoz et al, 2023 ) and P. kudriavzevii IMDO 020508 ( Díaz-Muñoz et al, 2021 ). Based on the total cocoa pulp-bean mass DNA, a suitable high-resolution ASV approach, taking into account the full-length 16S rRNA gene (bacteria) and the ITS1 region of the fungal rRNA transcribed unit (yeasts), allowed to monitor the starter culture strains added along the fermentation courses.…”

Section: Discussionmentioning

confidence: 99%

“…Additionally, it is challenging to determine the real number of rRNA genes present in fungal genomes, as most of them are highly fragmented. Even with highly contiguous fungal genomes, assembled using third-generation sequencing technologies, it is possible that the number of rRNA genes is underestimated during the assembly, as is the case for the S. cerevisiae IMDO 050523 genome ( Díaz-Muñoz et al, 2022 ). However, the approximate number can be estimated using the sequencing coverage information ( Ganley and Kobayashi, 2007 ; C. Díaz-Muñoz, Q. Vanderauwera, L. De Vuyst, and S. Weckx, unpublished results).…”

Section: Discussionmentioning

confidence: 99%

“…For a more accurate monitoring of the starter culture strains applied, the basic local alignment search tool (BLAST, version 2.2.30; Altschul et al, 1997 ) was used to align the ASVs obtained and belonging to the species corresponding with the strains used (except for Hanseniaspora for which the genus was used), to the known genome sequences of the inoculated strains [ Liml. fermentum IMDO 0611222 ( Verce et al, 2020 ), A. pasteurianus IMDO 0506386 ( Illeghems et al, 2013 ), S. cerevisiae IMDO 050523 ( Díaz-Muñoz et al, 2022 ), H. opuntiae IMDO 020003 (unpublished), and P. kudriavzevii IMDO 060005 (unpublished)] that contained the 16S rRNA gene(s) (bacteria) and ITS1 region (yeasts).…”

Section: Methodsmentioning

confidence: 99%

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Yeast strains do have an impact on the production of cured cocoa beans, as assessed with Costa Rican Trinitario cocoa fermentation processes and chocolates thereof

et al. 2023

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The microbiological and metabolic outcomes of good cocoa fermentation practices can be standardized and influenced through the addition of starter culture mixtures composed of yeast and bacterial strains. The present study performed two spontaneous and 10 starter culture-initiated (SCI) cocoa fermentation processes (CFPs) in Costa Rica with local Trinitario cocoa. The yeast strains Saccharomyces cerevisiae IMDO 050523, Hanseniaspora opuntiae IMDO 020003, and Pichia kudriavzevii IMDO 060005 were used to compose starter culture mixtures in combination with the lactic acid bacterium strain Limosilactobacillus fermentum IMDO 0611222 and the acetic acid bacterium strain Acetobacter pasteurianus IMDO 0506386. The microbial community and metabolite dynamics of the cocoa pulp-bean mass fermentation, the metabolite dynamics of the drying cocoa beans, and the volatile organic compound (VOC) profiles of the chocolate production were assessed. An amplicon sequence variant approach based on full-length 16S rRNA gene sequencing instead of targeting the V4 region led to a highly accurate monitoring of the starter culture strains added, in particular the Liml. fermentum IMDO 0611222 strain. The latter strain always prevailed over the background lactic acid bacteria. A similar approach, based on the internal transcribed spacer (ITS1) region of the fungal rRNA transcribed unit, was used for yeast strain monitoring. The SCI CFPs evolved faster when compared to the spontaneous ones. Moreover, the yeast strains applied did have an impact. The presence of S. cerevisiae IMDO 050523 was necessary for successful fermentation of the cocoa pulp-bean mass, which was characterized by the production of higher alcohols and esters. In contrast, the inoculation of H. opuntiae IMDO 020003 as the sole yeast strain led to underfermentation and a poor VOC profile, mainly due to its low competitiveness. The P. kudriavzevii IMDO 060005 strain tested in the present study did not contribute to a richer VOC profile. Although differences in VOCs could be revealed in the cocoa liquors, no significant effect on the final chocolates could be obtained, mainly due to a great impact of cocoa liquor processing during chocolate-making. Hence, optimization of the starter culture mixture and cocoa liquor processing seem to be of pivotal importance.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Yeast strains do have an impact on the production of cured cocoa beans, as assessed with Costa Rican Trinitario cocoa fermentation processes and chocolates thereof

et al. 2023

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“…The advancement of high-throughput sequencing technology has made it possible to profile the genomic evolution of S. cerevisiae on a larger scale. Over the past decade, amounts of genome sequencing have been performed to characterize the genetic diversity of S. cerevisiae strains sampled from a wide range of habitats, such as wine, plants and human-guts [11][12][13][14][15][16][17] . Notably, Peter et al reported the whole genome sequencing for 1,011 S. cerevisiae strains worldwide, successfully delineating the global evolutionary portrait of the species 9 .…”

Section: Introductionmentioning

confidence: 99%

Yeast adapts to diverse ecological niches driven by genomics and metabolic reprogramming

Wang,

Nielsen,

Zhou

et al. 2024

Preprint

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The famous model organism -Saccharomyces cerevisiaeis widely present in a variety of natural and human-associated habitats. Despite extensive studies of this organism, the metabolic mechanisms driving its adaptation to varying niches remain elusive. We here gathered genomic resources from 1,807S. cerevisiaestrains and assembled them into a high-quality pan-genome, facilitating the comprehensive characterization of genetic diversity across isolates. Utilizing the pan-genome, 1,807 strain-specific genome-scale metabolic models (ssGEMs) were generated, which performed well in quantitative predictions of cellular phenotypes, thus helping to examine the metabolic disparities among allS. cerevisiaestrains. Integrative analyses of fluxomic and transcriptomics with ssGEMs showcased the ubiquitous transcriptional regulation in certain metabolic sub-pathways (i.e., amino acid synthesis) at a population level. Additionally, the gene/reaction loss analysis through the ssGEMs refined by transcriptomics showed thatS. cerevisiaestrains from various ecological niches had undergone reductive evolution at both the genomic and metabolic network levels when compared to wild isolates. Finally, the compiled analyses of the pan-genome, transcriptome, and metabolic fluxome revealed remarkable metabolic differences amongS. cerevisiaestrains originating from distinct oxygen-limited niches, including human gut and cheese environments, and identified convergent metabolic evolution, such as downregulation of oxidative phosphorylation pathways. Together, these results illustrate how yeast adapts to distinct niches modulated by genomic and metabolic reprogramming, and provide computational resources for translating yeast genotype to fitness in future studies.

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“…The fermentation process plays an active role in the physical, nutritional, and organoleptic modifications of the starting material (Ao et al, 2011;Jung et al, 2011;Kim et al, 2012). Fermentation is one of the oldest forms of food processes in the world (Díaz-Muñoz et al, 2022). Plentiful microorganisms, including yeasts involved in the fermentation processes, as a consequence, are liable for converting sugars into alcohols along with secondary metabolites, which have an effect on the fermented beverages taste.…”

Section: Introductionmentioning

confidence: 99%

Saccharomyces cerevisiae - Fermented Garlic Attenuates Gamma-irradiation Induced Brain and Liver Toxicity Via Regulation of the NF-κB and STAT3 Signaling Pathway

El-Sonbaty,

Abd Elhameed,

Ismail

2023

Egypt. J. Rad.Sci.

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T HE PRESENT study was designed to evaluate the radio-protective effects of Saccharomyces cerevisiae-fermented garlic extract (FGE) on γ-irradiation-induced acute toxicity in rats' brain and liver. The rats were divided into four groups, Group I (C; control group), Group II (FGE), III (R: irradiated rats), Group IV (FGE+R). In C, and R groups rats were administered orally with 1 ml of water, and in FGE, and FGE+R groups, rats administered orally with 1 ml of FGE. At day 21, R and FGE+R groups were exposed to a single shot of whole-body gamma irradiation (6 Gy). The results showed that γ-irradiation significantly increased the activity of the hepatic enzymes; ALT, AST, ALP, GGT, and the levels of total-cholesterol (TC), and triglycerides (TG) in the serum. In addition, the activity of SOD, and GSH-Px were significantly decreased, with alteration in the trace elements levels were observed in the brain and liver cytosolic fractions. Moreover, the levels of MDA, and the pro-inflammatory markers; TNF-α, IL-1β, IL-6 and caspase-3 activity were significantly elevated, GSH content was significantly decreased (P<0.001), the gene expression ratios of NF-κB and STAT3 showed significant up-regulation (P<0.001), as well as, DNA fragmentations were observed in brain and liver tissues. FGE pre-treatment has significantly ameliorated the changes in all these studied parameters. The histopathological investigations confirmed these biochemical changes in the brain and liver tissues. These findings could suggest that the bioactivities of FGE showed neuro-hepato-protective effects on acute toxicity of gamma irradiation, by improving the antioxidant, anti-inflammatory and anti-apoptotic activities associated with regulation of the NF-κB and STAT3 signaling pathway in rats' brain and liver.

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Phylogenomics of a Saccharomyces cerevisiae cocoa strain reveals adaptation to a West African fermented food population

Cited by 5 publications

References 108 publications

Yeast strains do have an impact on the production of cured cocoa beans, as assessed with Costa Rican Trinitario cocoa fermentation processes and chocolates thereof

Yeast strains do have an impact on the production of cured cocoa beans, as assessed with Costa Rican Trinitario cocoa fermentation processes and chocolates thereof

Yeast adapts to diverse ecological niches driven by genomics and metabolic reprogramming

Saccharomyces cerevisiae - Fermented Garlic Attenuates Gamma-irradiation Induced Brain and Liver Toxicity Via Regulation of the NF-κB and STAT3 Signaling Pathway

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