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PubMed1979

Mating pheromones of Saccharomyces kluyveri: pheromone interactions between Saccharomyces kluyveri and Saccharomyces cerevisiae.

Saccharomyces kluyveri is a heterothallic yeast with two allelic mating types denoted as a-k and alpha-k by analogy with Saccharomyces cerevisiae and from the work described here. S. kluyveri produces mating pheromones analogous to those of S. cerevisiae, but which appear to have different specificity. S. kluyveri thus differs from S. cerevisiae, Hansenula wingei, and Schizosaccharomyces pombe in that it exhibits both strong constitutive agglutination and mating pheromones. alpha-k cells produce a pheromone ("alpha-k-factor") which causes a-k cells to arrest in the G1 phase of the cell cycle and to undergo a morphological change. After a period of time dependent on the concentration of alpha-k-factor, cells exposed to the factor resume cell division. alpha-k-factor has no effect on a-k/alpha-k diploids or on alpha-k cells, but at high concentration does induce G1 arrest of S. cerevisiaea cells (a-c). a-k cells produce a pheromone ("a-k-factor") which causes alpha-k cells to exhibit a morphological change. In addition, a-k cells exhibit the Bar phenotype with respect to alpha-k-factor. Partially purified preparations of S. cerevisiae alpha-factor are more active in inducing G1 arrest of a-k cells than of a-c cells. A more purified preparation of alpha-c-factor is less active against a-k cells than a-c cells, suggesting that an additional factor (KRE, kluyveri response enhancer) may be lost during purification. Attempts to mate S. kluyveri and S. cerevisiae cells by prototroph selection and by cell-to-cell mating have been unsuccessful with all combinations of mating types. Thus, S. cerevisiae and S. kluyveri are incompatible for mating even though their pheromones exhibit some physiological cross-reaction.

Crosses, Genetic↗
PubMed2025

Genomic and phenotypic comparison of Saccharomyces cerevisiae and Saccharomyces boulardii.

Saccharomyces boulardii is a widely used probiotic yeast with clinical efficacy against certain gastrointestinal disorders. Although genomically related to S. cerevisiae, the extent to which S. boulardii harbors distinct probiotic-relevant traits remains incompletely defined, particularly across commercially distributed strains. Here, we performed comparative genomic, physiological, and functional analyses of five S. boulardii strains and three S. cerevisiae strains, including baker's and laboratory variants. S. boulardii strains shared conserved genetic features and exhibited a conserved chromosomal inversion on chromosome XVI, lower copy numbers of CAZyme genes, and lineage-specific amino acid substitutions in central and tryptophan catabolism pathways-potentially underlying elevated production of immunomodulatory metabolites. S. boulardii strains also exhibited enhanced acid tolerance, elevated acetate and succinate production, and robust immunomodulatory activity, including suppression of IL-8 secretion and NF-κB, and consistent activation of the aryl hydrocarbon receptor (AhR) compared to S. cerevisiae. In contrast, S. cerevisiae strains displayed greater bile salt tolerance and faster growth under aerobic and anaerobic conditions at both 30°C and 37°C but lacked consistent anti-inflammatory effects or AhR agonism. Metabolic and immunological phenotypes varied with oxygen availability and strain background. Despite high genomic similarity, S. cerevisiae and S. boulardii exhibit distinct functional capacities relevant to probiotic efficacy. These findings help define speciesand strain-specific features that inform the development and regulatory evaluation of next-generation yeast probiotics.

AhR activation↗
PubMed1976

Control of fatty-acid synthetase levels by exogeneous long-chain fatty acids in the yeasts Candida lipolytica and Saccharomyces cerevisiae.

Endogeneous fatty acid biosynthesis in the two yeast species, Saccharomyces cerevisiae and Candida lipolytica is completely repressed by the addition of long-chain fatty acids to the growth medium. In Candida lipolytica, this repression is accompanied by a corresponding loss of fatty acid synthetase activity in the cell homogenate, when the cells were grown on fatty acids as the sole carbon source. The activity of the Saccharomyces cerevisiae fatty acid synthetase, however, remains unaffected by the addition of fatty acids to a glucose-containing growth medium. From fatty-acid-grown Candida lipolytica cells no fatty acid synthetase complex can be isolated, nor is there any immunologically cross-reacting fatty acid synthetase protein detectable in the crude cell extract. From this it is concluded that Candida lipolytica, but not Saccharomyces cerevisiae, is able to adapt to the growth on fatty acids either by repression of fatty acid synthetase biosynthesis or by a fatty-acid-induced proteolytic degradation of the multienzyme complex. Similarly, the fatty acid synthetase complex disappears rapidly from stationary phase Candida lipolytica cells even after growth in fatty-acid-free medium. Finally, it was found that the fatty acid synthetase complexes from Saccharomyces cerevisiae and Candida lipolytica, though very similar in size and subunit composition, were immunologically different and had no common antigenic determinants.

Acetyl-CoA Carboxylase↗
PubMed1977

Proteolysis of L-(+)-lactate cytochrome c oxidoreductase (cytochrome b2) extracted from Saccharomyces cerevisiae and Hansenula anomala yeasts.

The L-(+)-Lactate:cytochrome c oxidoreductase or cytochrome b2 from the yeasts Saccharomyces cerevisiae and Hansenula anomala were partially hydrolysed in various concentrations of trypsin. Conditions were found which allowed the isolation from the Hansenula enzyme of a 140 000 +/- 10 000-dalton flavoprotein. The prosthetic flavin groups were still reducible by substrate (spectroscopic evidence) but the flavoprotein was unable to form a complex with cytochrome c, the physiological acceptor in the enzymatic reaction. No such flavoprotein units could be found during proteolysis of the Saccharomyces enzyme. The heme prosthetic group of the Hansenula enzyme remained bound to a 15 500 +/- 1000-dalton protein unit which was larger than, but very similar to, the well known 'cytochrome b2 core' of the Saccharomyces enzyme. Moreover, the degradation of different enzyme samples by contaminated proteases allowed the isolation of a particular form of Hansenula enzyme: each tetramer had, on the mean, four bound flavins and only two heme groups. These molecules completely retained their ability to form a complex with cytochrome c.

Ascomycota↗
PubMed1978

Characterization of two forms of asparaginase in Saccharomyces cerevisiae.

Saccharomyces cerevisiae X2180-1A synthesizes two forms of asparaginase: L-asparaginase I, an internal constitutive enzyme, and asparaginase II, an external enzyme which is secreted in response to nitrogen starvation. The two enzymes are biochemically and genetically distinct. The structural gene for asparaginase I (asp 1) is closely linked to the trp 4 gene on chromosome IV. The gene controlling the synthesis of asparaginase II is not linked to either the trp 4 or asp 1 genes. The rate of biosynthesis of asparaginase II is unaltered in yeast strains carrying the structural gene mutation for asparaginase I. Asparaginase II has been purified approximately 300-fold from crude extracts of Saccharomyces by heat and pH treatment, ethanol fractionation, ammonium sulfate fractionation followed by Sephadex G-25 chromatography, and DEAE-cellulose chromatography. Multiple activity peaks were obtained which, upon gas chromatographic analysis, exhibit varying mannose to protein ratios. Asparaginase I has been purified approximately 100-fold from crude extracts of Saccharomyces by protamine sulfate treatment, ammonium sulfate fractionation, gel permeation chromatography, and DEAE-cellulose chromatography. No carbohydrate component was observed upon gas chromatographic analysis. Comparative kinetic and analytic studies show the two enzymes have little in common except their ability to hydrolyze L-asparagine to L-aspartic acid and ammonia.

Asparaginase↗
PubMed2019

Unique genetic basis of the distinct antibiotic potency of high acetic acid production in the probiotic yeast Saccharomyces cerevisiae var. boulardii.

The yeast Saccharomyces boulardii has been used worldwide as a popular, commercial probiotic, but the basis of its probiotic action remains obscure. It is considered conspecific with budding yeast Saccharomyces cerevisiae, which is generally used in classical food applications. They have an almost identical genome sequence, making the genetic basis of probiotic potency in S. boulardii puzzling. We now show that S. boulardii produces at 37°C unusually high levels of acetic acid, which is strongly inhibitory to bacterial growth in agar-well diffusion assays and could be vital for its unique application as a probiotic among yeasts. Using pooled-segregant whole-genome sequence analysis with S. boulardii and S. cerevisiae parent strains, we succeeded in mapping the underlying QTLs and identified mutant alleles of SDH1 and WHI2 as the causative alleles. Both genes contain a SNP unique to S. boulardii (sdh1 F317Y and whi2 S287*) and are fully responsible for its high acetic acid production. S. boulardii strains show different levels of acetic acid production, depending on the copy number of the whi2 S287* allele. Our results offer the first molecular explanation as to why S. boulardii could exert probiotic action as opposed to S. cerevisiae They reveal for the first time the molecular-genetic basis of a probiotic action-related trait in S. boulardii and show that antibacterial potency of a probiotic microorganism can be due to strain-specific mutations within the same species. We suggest that acquisition of antibacterial activity through medium acidification offered a selective advantage to S. boulardii in its ecological niche and for its application as a probiotic.

Acetic Acid↗
PubMed2026

The Saccharomyces Genome Database-a history of ideas and accomplishments, 1994-2026.

The Saccharomyces Genome Database (SGD) is one of the longest-running and most consequential biological databases in the world. Founded in the early 1990s at Stanford University under the visionary leadership of David Botstein and developed under the long-term technical direction of J. Michael Cherry, SGD has served for more than three decades not only as the authoritative knowledge center for the budding yeast Saccharomyces cerevisiae, but also as the source for much of the fundamentals of eukaryotic biology. This history traces the arc of a remarkable intellectual and scientific project: beginning with the challenge of building the very first integrated eukaryotic genome database and evolving across 30 years into a global knowledge hub for genetics, functional genomics, and human disease research. The history is organized chronologically, with each section highlighting the central ideas, technical developments, and concrete accomplishments of that period.

Databases, Genetic↗
PubMed2026

The Tor pathway, ribosome concentration, and wobble decoding mediate inhibitory effects of the Leu-Pro CUC-CCG codon pair in Saccharomyces cerevisiae.

Translation elongation and efficiency are modulated by the genetic code, with reduced translation efficiency and slow translation caused by 17 inhibitory codon pairs in the yeast Saccharomyces cerevisiae Nine of these inhibitory pairs are functionally important as they are disproportionately strongly conserved within orthologous genes in Saccharomyces sensu stricto For three pairs, including CGA-CGA, inhibition is triggered by ribosome collisions followed by known quality control responses, but the mechanisms by which nine other pairs cause inhibition are unknown. Here, our examination of the molecular basis of inhibition by one such pair, the highly conserved Leu-Pro CUC-CCG codon pair, yielded four findings. First, inhibition is mediated by tRNALeu(UAG), which decodes CUC by a U•C wobble interaction and effectively competes with the nonessential Watson-Crick base-pairing tRNALeu(GAG) Second, despite nearly universal conservation of U33 in tRNAs, the C33 alteration in tRNALeu(GAG) does not significantly impair its function. Third, inhibition likely is mediated by ribosome collisions, as many suppressors bear mutations known or predicted to reduce ribosome concentration, and as local reduction in ribosome concentration suppresses inhibition. Thus, differences between CUC-CCG and CGA-CGA inhibition likely occur downstream from ribosome collisions. Fourth, we find a link between the metabolic state and CUC-CCG inhibition, as we find six suppressor mutations in SCH9, a downstream effector of TORC1 that mediates ribosome production. As Sch9 is inactive during starvation, causing reduced ribosome concentration, one biological function of inhibitory pairs may be to mediate a change in relative expression during starvation conditions.

Ribosomes↗
PubMed1975

The regulated catabolism of endogenous and exogenous phosphatidylinositol by Saccharomyces cerevisiae leading to extracellular glycerophosphorylinositol and inositol.

It was previously shown that phosphatidylinositol catabolism leads to the accumulation of glycerophosphorylinositol in the culture medium of Saccharomyces cerevisiae. We now find that lack of an energy source (glucose) reduces the formation of glycerophosphorylinositol and increases extra-cellular inositol. This situation is reversed by refeeding glucose. [3H]Phosphatidylinositol is the precursor of extra-cellular [3H]inositol with energy-starved cells. Extracellular glycerophosphorylcholine and glycerophosphorylethanolamine accumulate more slowly than glycerophosphorylinositol in the growth medium and do not appear to be a strongly affected by energy starvation. Phosphatidylinositol deacylation appears to occur at the cell surface in a regulated manner. Exogenously added phosphatidylinositol apparently does not mix randomly with the endogenous pool since it is not converted to either inositol-containing sphingolipid or to diphosphoinositide, both previously shown to be derived in part from cellular phosphatidylinositol. Labeled exogenous phosphatidylinositol is, however, quantitatively converted to glycerophosphorylinositol with the probable intermediat formation of monoacyl-glycerophosphorylinositol. Breakdown of exogenous phosphatidylinositol requires an energy source and does not lead to free inositol. Deacylation of exogenously added 1-acyl-glycerophosphorylinositol occurs much faster than deacylation of phosphatidylinositol and does not require an energy source. Glycerophosphorylethanolamine formation from exogenous phosphatidylethanolamine occurs about as fast as the breakdown of phosphatidylinositol and is also inhibited in the absence of energy source. The much slower deacylation of exogenous phosphatidylcholine was also affected by an energy source. Glycerophosphorylinosiyolaccumulates in the culture medium of Kloeckera apiculata, Saccharomyces carlsbergenis, and Neurospora crassa.

Biological Transport↗
PubMed1978

S-adenosyl methionine requiring mutants in Saccharomyces cerevisiae: evidences for the existence of two methionine adenosyl transferases.

Mutants requiring S-adenosyl methionine (SAM) for growth have been selected in Saccharomyces cerevisiae. Two classes of mutants have been found. One class corresponds to the simultaneous occurrence of mutations at two unlinked loci SAM1 and SAM2 and presents a strict SAM requirement for growth on any medium. The second class corresponds to special single mutations in the gene SAM2 which lead to a residual growth on minimal medium but to normal growth on SAM supplemented medium or on a complex medium like YPGA not containing any SAM. These genetic data can be taken as an indication that Saccharomyces cerevisiae possesses two isoenzymatic methionine adenosyl transferases (MAT). In addition, SAM1 and SAM2 loci have been identified respectively with the ETH-10 and ETH2 loci previously described. Biochemical evidences corroborate the genetic results. Two MAT activities can be dissociated in a wild type extract (MATI and MATII) by DEAE cellulose chromatography. Mutations at the SAM1 locus lead to the absence or to the modification of MATII whereas mutations at the SAM2 locus lead to the absence or to the modification of MATI. Moreover, some of our results seem to show that MATI and MATII are associated in vivo.

Bicarbonates↗
PubMed1977

Induction of mitotic crossing over in Saccharomyces by p-Toluidine.

p-Toluidine, a carcinogen for rats, does not cause genetic damage when tested directly in Saccharomyces cerevisiae; however, certain chemical derivatives of p-toluidine do induce gene conversion when tested directly. It may be suspected by analogy with other aromatic amines that p-toluidine, a monocyclic aromatic amine, requires conversion to breakdown products which are then the genetically active and carcinogenic entities. The Udenfriend hydroxylation medium, which has been used previously to show the genetic activity of certain other aromatic amines and nitrosamines, was used in the incubation of p-toluidine with Saccharomyces cerevisiae. The resulting breakdown products, but not the parent compound, induced reciprocal mitotic recombination in a diploid strain D-3. Recombination was monitored by using induced homozygosity of the red ade 2 marker, and the reciprocal nature of the event was confirmed by observing the simultaneous homozygosity of two peripheral markers.

Biotransformation↗
PubMed1977

Active transport of L-sorbose and 2-deoxy-D-galactose in Saccharomyces fragilis.

Sorbose and 2-deoxy-D-galactose are taken up in Saccharomyces fragilis by an active transport mechanism, as indicated by the energy requirement of the process and the accumulation of free sugar against the concentration gradient. There are no indications for transport-associated phosphorylation as mechanism of energy coupling with these two sugars. The measured sugar-proton cotransport and the influx inhibition by uncouplers suggest a chemiosmotic coupling mechanism. Thus there are at least two different active transport mechanisms operative in Saccharomyces fragilis: transport-associated phosphorylation in the case of 2-deoxy-D-glucose and chemiosmotic coupling in the case of sorbose and 2-deoxy-D-galactose. The differences between the two mechanisms are discussed. Uncouplers do not stimulate downhill sorbose transport in energy-depleted cells and evoke an almost complete inhibition of efflux and of exchange transport. The differences between this sugar-proton cotransport system and similar systems in bacteria and Chlorella are discussed.

Adenosine Triphosphate↗
PubMed1979

Transcription maps of mtDNAs of two strains of saccharomyces: transcription of strain-specific insertions; Complex RNA maturation and splicing.

We have developed a two-dimensional method for simultaneously mapping on the yeast mtDNA genome all the transcripts representing more than 0.01% of mtRNA. In two yeast strains, Saccharomyces carlsbergensis NCYC-74 and Saccharomyces cerevisiae KL14-4A, about 25 discrete transcripts were found apart from tRNAs. The mtDNAs of these strains differ by the absence (NCYC-74) or presence (KL 14-4A) of various large insertions located within genetically active regions. The transcripts can all be related to known loci on the genetic map. In nearly all cases the RNAs are much longer than required to specify the known protein product of the locus concerned. The organization of the transcripts is similar in the two strains except at the positions of the large insertions (500-3300 bp) in the oxi-3 and cob loci. The sequences of these insertions are present in RNA species larger than 25S, but are absent from smaller transcripts of the same regions. This is probably due to splicing, since the coding sequences for most of these smaller transcripts are noncontiguous. The smaller transcripts of other loci also seem to arise from processing of larger RNA species. The oxi-3 locus, containing the structural gene for cytochrome c oxidase subunit l, is transcribed in a very complex fashion that suggests differential splicing into partially overlapping transcripts. This may indicate that oxi-3 has additional genetic functions, including possible control of the biosynthesis of cytochrome c oxidase holoenzyme or its assembly into the mitochondrial inner membrane. As in the case of the eucaryote nucleus, the regulation of mitochondrial gene expression seems to occur more at the level of RNA processing than has been recognized thus far.

Chromosome Mapping↗
PubMed2025

Quorum sensing in Saccharomyces cerevisiae brewing strains: effects of 2-phenylethanol on proteomic, lipidomic, and metabolomic profile.

Quorum sensing (QS) is a known mechanism by which microbial populations adjust gene expression and coordinate community-wide social behaviors based on the proximate population density. This regulatory system has garnered significant interest in both scientific research and the food industry. However, a central question remains whether industrial strains of Saccharomyces cerevisiae, the yeast species predominantly utilized in brewing, employ quorum signalling mechanisms similar to those observed in laboratory strains and other fungi. Despite the potential relevance of microbial social behavior regulators to brewing practices, studies examining QS in Saccharomyces spp. are limited. In this investigation, three industrial brewing strains of S. cerevisiae were cultivated on SLAD (nitrogen-restrictive) and SHAD (nitrogen-sufficient) agar media supplemented with 200 μM of the aromatic alcohol 2-phenylethanol (2-PE) over 72 h at 24°C. Subsequent analyses of the harvested biomass included proteomic, lipidomic, and metabolomic assessments. Results indicated that two of the industrial strains showed minimal differences in their profiles upon exposure to 2-PE, while the third strain exhibited significant differences. These findings imply that the impact of the QS molecule 2-PE on the proteome, lipidome, and metabolome of industrial S. cerevisiae may be strain-specific rather than universally applicable to the species.

Quorum Sensing↗
PubMed2026

Gene expression is stable despite widespread cis and trans regulatory divergence in Saccharomyces yeasts.

Regulatory evolution can alter phenotypes, but cis- and trans-regulatory mechanisms may also diverge extensively while total transcript abundance remains stable. Comparisons of parental expression with allele-specific expression in F1 hybrids provide a framework for separating cis- and trans-regulatory effects because both parental alleles are measured in a shared trans-regulatory environment. Here, we analyzed RNA sequencing data from Saccharomyces cerevisiae, Saccharomyces paradoxus, and their F1 hybrid. Among the 4,164 genes with sufficient allele-specific support for strict classification, 2,134 (51.2%) showed detectable cis and/or trans regulatory divergence. However, hybrid expression remained largely conserved, with 81.5% of genes not significantly different from either parent. Compensatory cis-trans divergence predominated over reinforcing divergence; cross-replicate estimation reduced the apparent magnitude of this excess, but opposite-sign effects remained predominant in all 20 non-overlapping replicate comparisons. To connect gene expression to genome sequence, we analyzed the strongly cis-diverged locus LYS2 and found species differences in promoter architecture, including an S. cerevisiae-specific AT-rich insertion, altered spacing among candidate regulatory features, and a promoter-proximal TATA-like element unique to S. cerevisiae. Sequence-based nucleosome prediction suggests that these differences create a broader promoter-proximal nucleosome-depleted region in S. cerevisiae than in S. paradoxus. We also quantified allele-resolved intron retention and found that allele-resolved intron retention was broadly conserved, with only rare locus-specific hybrid-associated shifts. Together, these results show that regulatory divergence is widespread but often buffered in the hybrid, whereas intron-retention divergence is comparatively limited.

Saccharomyces↗
PubMed2026

Moderate expression and activity of flocculins underlie the characteristic flocculation phenotype of Saccharomyces pastorianus.

Flocculation is a key technological trait in lager brewing, governing fermentation performance, yeast recovery, and beer quality. In the allo-aneuploid hybrid yeast Saccharomyces pastorianus, the genetic basis of flocculation remains poorly resolved due to its complex dual sub-genome architecture. Here, we systematically re-annotated and functionally characterized the complete FLO gene repertoire of the Group II strain CBS 1483. Thirteen FLO genes were identified, including allelic variants and a previously uncharacterized adhesin, Flo12, containing a Hyphal_reg_CWP domain instead of the canonical PA14 lectin-binding domain. Structural modeling revealed strong conservation of Ca²+-binding residues in PA14 domains, alongside repeat-region diversification likely contributing to functional variability. Using optogenetic expression in a FLO-null background, we demonstrated that SpcI-FLO9-1 and SpcI-FLO9-2_1 are the strongest drivers of flocculation, exhibiting NewFlo-like sugar sensitivity. Transcriptomic analysis during 17°P wort fermentation showed dynamic induction of these genes coinciding with flocculation onset. Surprisingly, deletion of both loci in CBS 1483 did not abolish but only delayed sedimentation in wort, accompanied by improved maltose utilization and attenuation. These findings reveal functional redundancy and compensatory mechanisms within the FLO network of lager yeast, highlighting the genetic complexity underlying flocculation, and providing a molecular framework to inform yeast selection, strain development, and optimization of the lager fermentation processes.IMPORTANCEFlocculation, the process by which yeast cells aggregate and settle, is essential for producing clear, high-quality lager beer, and for efficient yeast recovery during brewing. However, the genetic basis of this trait in lager yeast has remained poorly understood because these strains possess unusually complex hybrid genomes. In this study, we systematically identified and characterized the complete set of flocculation genes in the industrial lager yeast Saccharomyces pastorianus CBS 1483. We demonstrated that lager yeast flocculation is not controlled by a single dominant gene, but instead emerges from the combined action of several moderately active adhesion proteins that are expressed at low levels during fermentation. Surprisingly, deleting the two strongest candidate genes only delayed, rather than eliminated, sedimentation, revealing a robust compensatory network that preserves brewing performance. These findings refine the current understanding of yeast flocculation and provide a molecular framework for developing brewing strains with improved fermentation efficiency, product consistency, and flavor quality.

Saccharomyces pastorianus↗
PubMed2026

Effect of Saccharomyces cerevisiae fermentation postbiotic supplementation on metagenomics of digital dermatitis lesions in lactating Holstein cows.

Digital dermatitis (DD) is the leading cause of lameness in cattle, posing major animal welfare and economic concerns. Effective prevention strategies are increasingly important given emerging antimicrobial resistance associated with common DD treatments. Supplementation with Saccharomyces cerevisiae fermentation postbiotics (SCFP) has been shown to enhance innate immunity and reduce DD lesion development. This study evaluated the effect of a commercial SCFP supplement on the microbial composition of DD lesions using shotgun metagenomic sequencing to characterize microbial communities and associated antimicrobial resistance genes. Beta diversity analysis revealed that stage M4 DD lesions from SCFP-supplemented cows had a trend for different microbial compositions compared with controls (P = 0.051). At the genus level, M2 lesions were found to have statistically significant lower abundance of the genera Desulfovibrio, Pseudomonas, Staphylococcus, Anaerotignum, Caproicibacterium, and Bacteroides in the SCFP treatment group compared with the control (P < 0.05). M2 lesions from the SCFP treatment group were also found to have statistically significant higher abundance of the genera Fusobacterium, Citricoccus, Listeria, and Fundicoccus as compared with the control (P < 0.05). M4 lesions were found to have statistically significant lower abundance of the genera Blautia and Petrimonas in the SCFP treatment group compared with the control (P < 0.05). At the species level, M2 lesions were found to have statistically significant lower abundance of the species Desulfovibrio sp. G11, Anaerotignum sp. MB30-C6, Caproicibacterium argilliputei, and Prevotella intermedia in the SCFP treatment group compared with the control (P < 0.05). M2 lesions from the SCFP treatment group were also found to have statistically significant higher abundance of the species Fundicoccus culcitae and Helcococcus ovis as compared with the control (P < 0.05). Metagenomic analysis identified antimicrobial resistance genes associated with multiple antibiotics commonly used for DD treatment, including tetracyclines, lincosamides, and pleuromutilins. These findings demonstrate the potential for SCFP supplementation to alter the microbial composition of DD lesions while highlighting the ongoing concerns regarding antimicrobial resistance in DD management.IMPORTANCEDigital dermatitis (DD) causes substantial economic loss and welfare concerns in cattle production systems worldwide. Our findings show that dietary supplementation with Saccharomyces cerevisiae fermentation postbiotics (SCFP) has the potential to alter the microbial ecology of DD lesions. Importantly, this work identifies antimicrobial resistance genes within DD lesions, underscoring the limitations of antibiotic-based control strategies. By linking nutritional supplementation to changes in microbial communities and resistance gene profiles, this study advances understanding of non-antibiotic approaches to disease mitigation and supports the development of sustainable, microbiome-informed management practices in food animal production.

Animals↗
PubMed2026

Gene expression is stable despite widespread cis and trans regulatory divergence in Saccharomyces yeasts.

Regulatory evolution can alter phenotypes, but cis- and trans-regulatory mechanisms may also diverge extensively while total transcript abundance remains stable. Comparisons of parental expression with allele-specific expression in F1 hybrids provide a framework for separating cis- and trans-regulatory effects because both parental alleles are measured in a shared trans-regulatory environment. Here, we analyzed RNA sequencing data from Saccharomyces cerevisiae, Saccharomyces paradoxus, and their F1 hybrid. Regulatory divergence was widespread, with 61.3% of tested orthologs showing significant divergence in at least one cis or trans component. However, hybrid expression remained largely conserved, with 81.6% of genes not significantly different from either parent. Compensatory cis-trans divergence predominated over reinforcing divergence, consistent with widespread buffering of transcript abundance. To connect genome-wide patterns to mechanism, we analyzed the strongly cis-diverged locus LYS2 and found species differences in promoter architecture, including an S. cerevisiae-specific AT-rich insertion, altered spacing among candidate regulatory features, and a promoter-proximal TATA-like element unique to S. cerevisiae. Sequence-based nucleosome prediction suggests that these differences create a broader promoter-proximal nucleosome-depleted region in S. cerevisiae than in S. paradoxus. We also quantified allele-resolved intron retention and found that splicing was broadly conserved, with only rare locus-specific hybrid-associated shifts. Together, these results show that regulatory divergence is widespread but often buffered in the hybrid, whereas post-transcriptional divergence is comparatively limited.

Gene expression↗