Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae

Background

Wine fermentation is a harsh ecological niche to which wine yeast are well adapted. The initial high osmotic pressure and acidity of grape juice is followed by nutrient depletion and increasing concentrations of ethanol as the fermentation progresses. Yeast’s adaptation to these and many other environmental stresses, enables successful completion of high-sugar fermentations. Earlier transcriptomic and growth studies have tentatively identified genes important for high-sugar fermentation. Whilst useful, such studies did not consider extended growth (>5 days) in a temporally dynamic multi-stressor environment such as that found in many industrial fermentation processes. Here, we identify genes whose deletion has minimal or no effect on growth, but results in failure to achieve timely completion of the fermentation of a chemically defined grape juice with 200 g L⁻¹ total sugar.

Results

Micro- and laboratory-scale experimental fermentations were conducted to identify 72 clones from ~5,100 homozygous diploid single-gene yeast deletants, which exhibited protracted fermentation in a high-sugar medium. Another 21 clones (related by gene function, but initially eliminated from the screen because of possible growth defects) were also included. Clustering and numerical enrichment of genes annotated to specific Gene Ontology (GO) terms highlighted the vacuole’s role in ion homeostasis and pH regulation, through vacuole acidification.

Conclusion

We have identified 93 genes whose deletion resulted in the duration of fermentation being at least 20% longer than the wild type. An extreme phenotype, ‘stuck’ fermentation, was also observed when DOA4, NPT1, PLC1, PTK2, SIN3, SSQ1, TPS1, TPS2 or ZAP1 were deleted. These 93 Fermentation Essential Genes (FEG) are required to complete an extended high-sugar (wine-like) fermentation. Their importance is highlighted in our Fermentation Relevant Yeast Genes (FRYG) database, generated from literature and the fermentation-relevant phenotypic characteristics of null mutants described in the Saccharomyces Genome Database. The 93-gene set is collectively referred to as the ‘Fermentome’. The fact that 10 genes highlighted in this study have not previously been linked to fermentation-related stresses, supports our experimental rationale. These findings, together with investigations of the genetic diversity of industrial strains, are crucial for understanding the mechanisms behind yeast’s response and adaptation to stresses imposed during high-sugar fermentations.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-552) contains supplementary material, which is available to authorized users.

The microbial challenge of winemaking: yeast-bacteria compatibility

The diversity and complexity of wine environments present challenges for predicting success of fermentation. In particular, compatibility between yeast and lactic acid bacteria is affected by chemical and physical parameters that are strain and cultivar specific. This review focuses on the impact of compound production by microbes and physical interactions between microbes that ultimately influence how yeast and bacteria may work together during fermentation. This review also highlights the importance of understanding microbial interactions for yeast-bacteria compatibility in the wine context.

Diffusion-Limited Growth of Microbial Colonies

The emergence of diffusion-limited growth (DLG) within a microbial colony on a solid substrate is studied using a combination of mathematical modelling and experiments. Using an agent-based model of the interaction between microbial cells and a diffusing nutrient, it is shown that growth directed towards a nutrient source may be used as an indicator that DLG is influencing the colony morphology. A continuous reaction–diffusion model for microbial growth is employed to identify the parameter regime in which DLG is expected to arise. Comparisons between the model and experimental data are used to argue that the bacterium Bacillus subtilis can undergo DLG, while the yeast Saccharomyces cerevisiae cannot, and thus the non-uniform growth exhibited by this yeast must be caused by the pseudohyphal growth mode rather than limited nutrient availability. Experiments testing directly for DLG features in yeast colonies are used to confirm this hypothesis.

Quantifying the dominant growth mechanisms of dimorphic yeast using a lattice-based model

A mathematical model is presented for the growth of yeast that incorporates both dimorphic behaviour and nutrient diffusion. The budding patterns observed in the standard and pseudohyphal growth modes are represented by a bias in the direction of cell proliferation. A set of spatial indices is developed to quantify the morphology and compare the relative importance of the directional bias to nutrient concentration and diffusivity on colony shape. It is found that there are three different growth modes: uniform growth, diffusion-limited growth (DLG) and an intermediate region in which the bias determines the morphology. The dimorphic transition due to nutrient limitation is investigated by relating the directional bias to the nutrient concentration, and this is shown to replicate the behaviour observed in vivo Comparisons are made with experimental data, from which it is found that the model captures many of the observed features. Both DLG and pseudohyphal growth are found to be capable of generating observed experimental morphologies.

Yeast bioprospecting versus synthetic biology-which is better for innovative beverage fermentation?

Producers often utilise some of the many available yeast species and strains in the making of fermented alcoholic beverages in order to augment flavours, aromas, acids and textural properties. But still, the demand remains for more yeasts with novel phenotypes that not only impact sensory characteristics but also offer process and engineering advantages. Two strategies for finding such yeasts are (i) bioprospecting for novel strains and species and (ii) genetic modification of known yeasts. The latter enjoys the promise of the emerging field of synthetic biology, which, in principle, would enable scientists to create yeasts with the exact phenotype desired for a given fermentation. In this mini review, we compare and contrast advances in bioprospecting and in synthetic biology as they relate to alcoholic fermentation in brewing and wine making. We explore recent advances in fermentation-relevant recombinant technologies and synthetic biology including the Yeast 2.0 Consortium, use of environmental yeasts, challenges, constraints of law and consumer acceptance.

Quantifying two-dimensional filamentous and invasive growth spatial patterns in yeast colonies

The top-view, two-dimensional spatial patterning of non-uniform growth in a Saccharomyces cerevisiae yeast colony is considered. Experimental images are processed to obtain data sets that provide spatial information on the cell-area that is occupied by the colony. A method is developed that allows for the analysis of the spatial distribution with three metrics. The growth of the colony is quantified in both the radial direction from the centre of the colony and in the angular direction in a prescribed outer region of the colony. It is shown that during the period of 100–200 hours from the start of the growth of the colony there is an increasing amount of non-uniform growth. The statistical framework outlined in this work provides a platform for comparative quantitative assays of strain-specific mechanisms, with potential implementation in inferencing algorithms used for parameter-rate estimation.

In nutrient-depleted environments, it is commonly observed that strains of the yeast Saccharomyces cerevisiae forage by the mechanisms of filamentous and invasive growth. How do we quantify this spatial patterning of outward growth from a yeast colony? Previous studies have primarily relied on measuring the amount of growth, but do not take into account the spatial distribution of this highly non-uniform process. We fill this void by providing a statistical approach that enables the quantification of this important spatial information. This approach enables a more detailed mathematical analysis of the growth process and should allow the precise definition of mutant phenotypes, thus enabling a detailed analysis of the genetic control of morphogenesis.

Evaluation of the ability of commercial wine yeasts to form biofilms (mats) and adhere to plastic: implications for the microbiota of the winery environment

Commercially available active dried wine yeasts are regularly used by winemakers worldwide to achieve reliable fermentations and obtain quality wine. This practice has led to increased evidence of traces of commercial wine yeast in the vineyard, winery and uninoculated musts. The mechanism(s) that enables commercial wine yeast to persist in the winery environment and the influence to native microbial communities on this persistence is poorly understood. This study has investigated the ability of commercial wine yeasts to form biofilms and adhere to plastic. The results indicate that the biofilms formed by commercial yeasts consist of cells with a combination of different lifestyles (replicative and non-replicative) and growth modes including invasive growth, bud elongation, sporulation and a mat sectoring-like phenotype. Invasive growth was greatly enhanced on grape pulp regardless of strain, while adhesion on plastic varied between strains. The findings suggest a possible mechanism that allows commercial yeast to colonise and survive in the winery environment, which may have implications for the indigenous microbiota profile as well as the population profile in uninoculated fermentations if their dissemination is not controlled.

A thin-film extensional flow model for biofilm expansion by sliding motility

In the presence of glycoproteins, bacterial and yeast biofilms are hypothesized to expand by sliding motility. This involves a sheet of cells spreading as a unit, facilitated by cell proliferation and weak adhesion to the substratum. In this paper, we derive an extensional flow model for biofilm expansion by sliding motility to test this hypothesis. We model the biofilm as a two-phase (living cells and an extracellular matrix) viscous fluid mixture, and model nutrient depletion and uptake from the substratum. Applying the thin-film approximation simplifies the model, and reduces it to one-dimensional axisymmetric form. Comparison with Saccharomyces cerevisiae mat formation experiments reveals good agreement between experimental expansion speed and numerical solutions to the model withO ( 1 ) parameters estimated from experiments. This confirms that sliding motility is a possible mechanism for yeast biofilm expansion. Having established the biological relevance of the model, we then demonstrate how the model parameters affect expansion speed, enabling us to predict biofilm expansion for different experimental conditions. Finally, we show that our model can explain the ridge formation observed in some biofilms. This is especially true if surface tension is low, as hypothesized for sliding motility.

A special drop: Characterising yeast isolates associated with fermented beverages produced by Australia's indigenous peoples

Way-a-linah, an alcoholic beverage produced from the fermented sap of Eucalyptus gunnii, and tuba, a fermented drink made from the syrup of Cocos nucifera fructifying bud, are two of several fermented beverages produced by Australian Aboriginal and Torres Strait people. Here we describe the characterisation of yeast isolates from samples associated with the fermentation of way-a-linah and tuba. Microbial isolates were obtained from two different geographical locations in Australia - the Central Plateau in Tasmania, and Erub Island in the Torres Strait. While Hanseniaspora species and Lachancea cidri were the most abundant species in Tasmania, Candida species were the most abundant in Erub Island. Isolates were screened for tolerance to stress conditions found during the production of fermented beverages and for enzyme activities relevant to the appearance, aroma and flavour of these beverages. Based on screening results, eight isolates were evaluated for their volatile profile during the fermentation of wort, apple juice and grape juice. Diverse volatile profiles were observed for beers, ciders and wines fermented with different isolates. These findings reveal the potential of these isolates to produce fermented beverages with unique aroma and flavour profiles and highlight the vast microbial diversity associated with fermented beverages produced by Australia's Indigenous peoples.

Risk of aortic disease in long-distance cross-country skiers; a study of 209,226 patients

Background/Introduction

Aneurysmal dilatation and dissection of the aorta are two facets of aortic disease that can lead to major disability and death. Some risk factors for aortic disease are also risk factors for atherosclerotic disease, but the overall causes of aortic disease are diverse and largely unknown. Persons with aortic aneurysms are advised to limit their physical activity, but associations of physical activity with subsequent incidence of aortic disease are little known. Earlier studies have shown strong association of performance in Vasaloppet with incidence of hypertension, a major risk factor for aortic disease.

Aim

To investigate associations of high levels of physical activity with incidence of aortic disease.

Methods

We studied 209,226 participants in a 30–90 km cross-country skiing event (Vasaloppet) and 536,038 persons from the general population, matched to the skiers on age, sex and residence. The number of completed races during the study period and the fastest relative finishing time in a race was recorded. The main outcomes were: 1) aortic disease (defined as thoracic and abdominal aortic aneurysm and/or aortic dissection); and 2) aortic dissection.

Results

During a median time at risk of 8.8 years, 1,442 aortic disease events and 265 aortic dissections occurred. Skiers had lower incidence of aortic disease than non-skiers (Cox proportional hazards ratio [HR] 0.42; 95% confidence interval [CI] 0.36–0.50). An association of better finishing time with aortic disease was observed, with a dose-response gradient from the fastest third (HR 0.25; 95% CI 0.18–0.35), via the slowest third (HR 0.64; 95% CI 0.49–0.82) to the non-skiers (reference group). Among skiers the number of completed races was not associated with incidence of aortic disease. Skiers also had lower incidence of acute aortic dissection (HR 0.61; 95% CI 0.44–0.85) than non-skiers. Low event rate among skiers made conclusions in subgroups unreasonable. All results are adjusted for age, sex, education and income. Results were similar in models accounting for use of antihypertensive and cholesterol-lowering medicines and genetic syndromes associated with aortic disease.

Conclusion

Participation in a long-distance skiing event was associated with lower risk of aortic disease and aortic dissection. Faster completion of the race was strongly associated with lower incidence of aortic disease. If causal, this study suggests that high physical activity and exercise may be protective against aortic disease.

Kaplan-Meier Aorta disease

Funding Acknowledgement

Type of funding source: None

Blood pressure lowering treatment for prevention of cardiovascular events in patients with atrial fibrillation: an individual-participant data meta-analysis

Background

Randomised evidence showing that pharmacological blood pressure (BP) lowering can reduce cardiovascular risk of patients with atrial fibrillation (AF) is limited.

Purpose

This study aimed to compare the effect of BP-lowering treatment on fatal and non-fatal cardiovascular outcomes in patients with and without AF overall and by major drug classes.

Methods

We extracted individual participant data from all trials with over 1,000 person-years of follow-up that had randomly assigned patients to different classes of BP-lowering drugs, BP-lowering drugs vs placebo, or to more vs less intensive BP-lowering regimens. We investigated the effects of BP-lowering treatment on a composite endpoint of major cardiovascular events (stroke, ischaemic heart disease or heart failure) according to AF status at baseline using fixed-effect one-stage individual participant data meta-analyses based on Cox proportional hazards models stratified by trial.

Findings

Twenty-two trials were included with 188,570 patients, of whom 13,266 (7%) had AF at baseline. Patients with AF had lower BP at baseline than patients without AF (143/84 mmHg, SD 21/12mmHg) versus 155/88 mmHg, SD 21/13 mmHg, respectively). Meta-regression showed that relative risk reductions were proportional to trial-level intensity of BP lowering, both in patients with and without AF. The hazard ratio for major cardiovascular events was 0.91 in patients with AF (95% confidence interval [0.83–1.00]) and 0.91 without AF (95% confidence interval [0.88–0.93]) for each 5-mmHg reduction in systolic BP, with no difference between subgroups (p=0.91) (Figure 1). Similar patterns were observed for individual components of the composite primary outcome. In patients with AF, there was no evidence that treatment effects varied according to baseline systolic BP or use of specific drug classes.

Conclusion

This study demonstrated that BP-lowering treatment reduces the risk of major cardiovascular events in patients with AF to a similar extent to that of patients without AF, even when baseline BP is below recommended treatment thresholds. Owing to their higher absolute cardiovascular risk, treatment in patients with AF is likely to result in greater absolute risk reduction than in patients without AF. Guidelines should be updated to clearly recommend pharmacological BP lowering for prevention of cardiovascular events in patients with AF.

Figure 1. Forest plot

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): British Heart Foundation

An off-lattice discrete model to characterise filamentous yeast colony morphology

We combine an off-lattice agent-based mathematical model and experimentation to explore filamentous growth of a yeast colony. Under environmental stress, Saccharomyces cerevisiae yeast cells can transition from a bipolar (sated) to unipolar (pseudohyphal) budding mechanism, where cells elongate and bud end-to-end. This budding asymmetry yields spatially non-uniform growth, where filaments extend away from the colony centre, foraging for food. We use approximate Bayesian computation to quantify how individual cell budding mechanisms give rise to spatial patterns observed in experiments. We apply this method of parameter inference to experimental images of colonies of two strains of S. cerevisiae, in low and high nutrient environments. The colony size at the transition from sated to pseudohyphal growth, and a forking mechanism for pseudohyphal cell proliferation are the key features driving colony morphology. Simulations run with the most likely inferred parameters produce colony morphologies that closely resemble experimental results.

Long-term incidence of pacemaker implantations and bradycardia among cross-country skiers

Background

Bradycardia is more common among well-trained athletes. The associations of training with pacemaker implantations are less known. We aim to investigate the association of endurance training with incidence of bradycardia and pacemaker implantations in a cohort of endurance athletes. Furthermore, we aim to establish potential sex differences of such associations.

Methods

Swedish skiers (209,072) that completed 1 or more races in the 30 to 90 km cross-country skiing event Vasaloppet (1989–2011) and a matched sample (n=531,949) of nonskiers were followed until first event of bradycardia or pacemaker implantation. The Swedish National Patient Register of in-patient and specialized outpatient care was used to obtain the date of diagnoses. Cox regression was used to investigate associations of number of completed races and finishing time with incidence of bradycardia and pacemaker implantations.

Results

Male skiers had higher incidence of bradycardia (hazard ratio [HR], 1.14; 95% CI, 0.99–1.30) and pacemaker implantations (HR, 1.14; 95% CI, 1.02–1.28) than male nonskiers. Male skiers completing most races or with the fastest finishing times had the highest incidence. The incidence of bradycardia (HR, 0.96; 95% CI, 0.70–1.30) and pacemaker implantations (HR, 0.97; 95% CI, 0.75–1.25) among female skiers in Vasaloppet was not different to that of female nonskiers. There was a trend that female skiers completing most races or with fastest finishing times had lower incidence.

Conclusions

Male skiers had higher incidence of bradycardia and pacemaker implantations. Female skiers in Vasaloppet had non-different incidence of bradycardia and pacemaker implantations. Men with the highest number of races and fastest finishing times had the highest incidence of pacemaker implantations. This indicates that bradycardia associated with training is not always as benign as previously suggested. The response appears to be different between sexes.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): Uppsala UniversityCKF Dalarna

Socioeconomic status, secondary prevention activities during the first year after a myocardial infarction and target attainments

Background

Socioeconomic status (SES) is a strong predictor of recurrent events post-myocardial infarction (MI) with unclear underlying mechanisms. To what extent SES is associated with secondary prevention activities (SPAs) and attainment of quality-of-care treatment goals is unknown.

Purpose

We aimed to assess the association between SES and SPAs during the first year post-MI and attained treatment targets at the 1-year follow-up.

Methods

Nationwide Swedeheart registry-based cohort study on 30,191 18–76 year old 11–15 month survivors of a first MI (8,180 women) 2006–2013. Complementary individual-level clinical data and data on SES (age and gender stratified quintiles of disposable income, level of education, and marital status), were linked from other national registries. Associations between SES and the outcomes were estimated in multivariable logistic regression models with basic adjustment for potential registry-related confounding.

Results

The associations between all indicators of SES and attendance to patient education and physical training programs were strong, moderate for dietary program attendance but absent for participation in smoking cessation program (Table 1). Higher SES was also associated with repeated lipid profile measurements and the highest vs lowest income with intensified statin therapy.

Correspondingly, higher SES was associated with having achieved target levels of LDL-C, blood pressure, and HbA1c as well as with persistence to and being on high intensity statin treatment (Figure 1). Further, higher SES was strongly associated with having quit smoking. No association with income was however observed regarding the weekly physical activity goal.

Conclusions

Higher SES was strongly associated with most SPAs including programs aiming at life style change and risk factor control as well as with attainment of corresponding secondary prevention targets. This may be explanatory for higher long-term risk of recurrent disease.

Figure 1. Target Attainment Forest Plots

Funding Acknowledgement

Type of funding source: Other. Main funding source(s): Stockholm City Council and The Swedish Heart and Lung Association

Effect of blood pressure lowering treatment on the risk of atrial fibrillation: an individual-participant data meta-analysis

Background

Although observational studies have suggested an association between elevated blood pressure (BP) and increased risk of atrial fibrillation (AF), randomised evidence on the effects of pharmacological blood pressure lowering on the risk of new-onset AF remains limited.

Purpose

To investigate the effects of pharmacological BP lowering on the risk of AF overall and stratified by baseline risk of AF and by drug class.

Methods

We extracted individual participant data from trials with over 1,000 person-years of follow-up that had randomly assigned patients to different classes of BP-lowering drugs, BP-lowering drugs vs placebo, or to more vs less intensive BP-lowering regimens. We investigated the effects of BP lowering on the risk of new-onset AF using fixed-effect one-stage individual participant data meta-analyses based on Cox proportional hazards models stratified by trial.

Results

Twenty-one trials were included with a total of 194,041 patients, in whom 6,357 new-onset and 516 recurrent AF events were recorded. The hazard ratio for new-onset AF was 1.01, 95% CI [0.95–1.07] per each 5-mmHg reduction in systolic BP, and meta-regression suggested that treatment effects were similar irrespective of the intensity of systolic BP reduction. Patients were overall at low risk of AF at baseline (median 2.3%, IQR [1.2–3.4%] at 5 years), and there was no evidence of heterogeneity in treatment effects across thirds of risk and 10-mmHg strata of baseline systolic BP (Figure). There was also no clear evidence that treatment effects differed between drug classes when renin-angiotensin-aldosterone system inhibitors and calcium channel blockers were compared with placebo and/or standard treatment.

Conclusion

In a low-risk population, pharmacological BP lowering did not reduce the risk of new-onset AF. Further research is needed to understand whether the effects would be different in high-risk individuals, and to better clarify the existence of class-specific effects.

Figure 1. Forest plot

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): British Heart Foundation

Prevalence of coronary atherosclerosis in individuals with pre-diabetes and diabetes compared to normoglycemic individuals

Background

Patients with type 2 diabetes have a two- to four-fold higher risk of death and cardiovascular events than the general population. Understanding the characteristics of atherosclerosis in people with different stages of dysglycaemia compared to normoglycaemic individuals may be useful for tailored prevention strategies in the future.

Purpose

To characterise the prevalence of coronary artery atherosclerosis in individuals with prediabetes, previously undetected diabetes and previously known diabetes compared with normoglycaemic individuals in a large population-based cohort.

Methods

Data were obtained from the Swedish CArdiopulumonary bioImage Study (SCAPIS), a population-based cohort of participants aged 50–64 years. The 25,553 study participants were categorised according to their glycaemic status: normoglycaemic (glucose: <6.1 mmol/L and HbA1c <6.0% (<42 mmol/mol)), pre-diabetes (6.1–6.9 mmol/L and/or elevated HbA1c 6.0–6.5% (42–47mmol/mol)), previously undetected diabetes (glucose ≥7.0 mmol/L and/or HbA1c >6.5% (≥48 mmol/mol)) or known diabetes. Plaque burden (number of diseased coronary segments) was determined by coronary computed tomography angiography (CCTA) in all 18 coronary artery segments. Total coronary artery atherosclerotic burden was assessed by segment involvement score (SIS) ≥4 and any coronary atherosclerosis. Imaging and analyses were performed using a calcium scoring protocol. The calcium content in each coronary artery was measured and summed to obtain an overall coronary artery calcification score (CACS).

Results

Study participants with dysclycaemia were defined as pre-diabetes (n=3,989, 16%), undetected diabetes (n=648, 2.5%) or known diabetes (n=1,033, 6.5%). The prevalence of CCTA-detected atherosclerosis among study participants, stratified by glycaemic status into four groups, is shown in Figure 1. The distribution of CACS categories by glycaemic status is shown in Figure 2. The association between CACS and glycaemic status, with normoglycemia as reference, was further explored in an adjusted (age, sex and site) ordinal regression: pre-diabetes 1.33 (95% CI 1.25–1.42), undetected diabetes 1.82 (95% CI 1.59–2.09), known diabetes 2.88 (95% CI 2.59–3.20). In a sensitivity analysis excluding people with previous myocardial infarction, coronary artery bypass grafting, percutaneous coronary intervention or with stent (n=693), the results were virtually unchanged, pre-diabetes 1.31 (95% CI 1.23–1.40), undetected diabetes 1.80 (95% CI 1.57–2.07), known diabetes 2.73 (95% CI 2.45–3.05).

Conclusions

The prevalence of coronary atherosclerosis increased substantially with increasing dysglycaemia. Our data suggest that more aggressive screening and/or treatment of individuals with prediabetes and diabetes to prevent cardiovascular disease should be discussed in the future.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): The main funding body of The Swedish CArdioPulmonary bioImage Study (SCAPIS) is the Swedish Heart- and Lung Foundation.