Strain-specific Characteristics Research Articles

E. coli catheter-associated urinary tract infections are associated with distinctive virulence and biofilm gene determinants.

Urinary catheterization facilitates urinary tract colonization by E. coli and increases infection risk. Here, we aimed to identify strain-specific characteristics associated with the transition from colonization to infection in catheterized patients. In a single-site study population, we compared E. coli isolates from patients with catheter-associated asymptomatic bacteriuria (CAASB) to those with catheter-associated urinary tract infection (CAUTI). CAUTI isolates were dominated by a phylotype B2 subclade containing the multidrug-resistant ST131 lineage relative to CAASB isolates, which were phylogenetically more diverse. A distinctive combination of virulence-associated genes was present in the CAUTI-associated B2 subclade. Catheter-associated biofilm formation was widespread among isolates and did not distinguish CAUTI from CAASB strains. Preincubation with CAASB strains could inhibit catheter colonization by multiple ST131 CAUTI isolates. Comparative genomic analysis identified a group of variable genes associated with high catheter biofilm formation present in both CAUTI and CAASB strains. Among these, ferric citrate transport (Fec) system genes were experimentally associated with enhanced catheter biofilm formation using reporter and fecA deletion strains. These results are consistent with a variable role for catheter biofilm formation in promoting CAUTI by ST131-like strains or resisting CAUTI by lower-risk strains that engage in niche exclusion.

Transcriptomic profiling reveals differences in the adaptation of two Tetragenococcus halophilus strains to a lupine moromi model medium

BackgroundTetragenococcus (T.) halophilus is a common member of the microbial consortia of food fermented under high salt conditions. These comprises salty condiments based on soy or lupine beans, fish sauce, shrimp paste and brined anchovies. Within these fermentations this lactic acid bacterium (LAB) is responsible for the formation of lactic and other short chain acids that contribute to the flavor and lower the pH of the product. In this study, we investigated the transcriptomic profile of the two T. halophilus strains TMW 2.2254 and TMW 2.2256 in a lupine moromi model medium supplied with galactose. To get further insights into which genomic trait is important, we used a setup with two strains. That way we can determine if strain dependent pathways contribute to the overall fitness. These strains differ in the ability to utilize L-arginine, L-aspartate, L-arabinose, D-sorbitol, glycerol, D-lactose or D-melibiose. The lupine moromi model medium is an adapted version of the regular MRS medium supplied with lupine peptone instead of casein peptone and meat extract, to simulate the amino acid availabilities in lupine moromi.ResultsThe transcriptomic profiles of the T. halophilus strains TMW 2.2254 and TMW 2.2256 in a lupine peptone-based model media supplied with galactose, used as simulation media for a lupine seasoning sauce fermentation, were compared to the determine potentially important traits. Both strains, have a great overlap in their response to the culture conditions but some strain specific features such as the utilization of glycerol, sorbitol and arginine contribute to the overall fitness of the strain TMW 2.2256. Interestingly, although both strains have two non-identical copies of the tagatose-6P pathway and the Leloir pathway increased under the same conditions, TMW 2.2256 prefers the degradation via the tagatose-6P pathway while TMW 2.2254 does not. Furthermore, TMW 2.2256 shows an increase in pathways required for balancing out the intracellular NADH/NADH+ ratios.ConclusionsOur study reveals for the first time, that both versions of tagatose-6P pathways encoded in both strains are simultaneously active together with the Leloir pathway and contribute to the degradation of galactose. These findings will help to understand the strain dependent features that might be required for a starter strain in lupine moromi.

ThermusQ: Toward the cell simulation platform for Thermus thermophilus.

ThermusQ is a website that aims to gather all the molecular information on Thermus thermophilus and to provide a platform to easily access the whole view of the bacterium. ThermusQ comprises the genome sequences of 22 strains from T. thermophilus and T. oshimai strains, plus the sequences of known Thermus phages. ThermusQ also contains information and map diagrams of pathways unique to Thermus strains. The website provides tools to retrieve sequence data in different ways. By gathering the whole data of T. thermophilus strains, the strainspecific characteristics was found. This bird's-eye view of the whole data will lead the research community to identify missing important data and the integration will provide a platform to conduct future biochemical simulations of the bacterium.

494. Enteric bacteria are immune-reactive in patients with Crohn's disease with extraintestinal manifestations

Abstract Background Bacterial constituents of the intestinal microbiota can contribute to local and systemic inflammatory diseases. Crohn's disease (CD), a type of inflammatory bowel disease, can result in extraintestinal manifestations (EIM) including peripheral (CD-SpA) and axial spondyloarthritis (CD-AxSpA). Microbial contributors to CD pathogenesis can be identified by flow cytometric sorting and 16S sequencing of bacteria recognized by mucosal IgA. We expand this technique by incubating fecal samples with autologous sera, capturing bacterial species recognized by circulating IgG in a process called IgG-seq. We hypothesize that these systemically-recognized enteric bacteria are linked to development of CD-EIM. Methods Fecal samples from individuals with CD were sorted into IgG-positive and negative populations. DNA was extracted from each population, 16S sequencing performed, and sequences processed with QIIME2. Intestinal coating index (ICI) was calculated at the genus level. Serum cell-free DNA sequencing (cfDNA) was performed for a subset of samples. Results IgG-seq was conducted on 86 CD, 41 CD-SpA, and 16 CD-AxSpA samples. PCoA analysis demonstrates significant differences in microbiome composition in the three groups (P = 0.013, PERMANOVA). Relative abundances of Escherichia-Shigella and Ruminococcus are positively correlated with joint disease activity. Analysis of IgG ICI for genera present in > 10% of patients demonstrates overrepresentation of Ruminococcus, Escherichia-Shigella, and Bacteroides in IgG-recognized fractions. IgG recognition of bacteria does not cluster specifically by CD or EIM severity. cfDNA sequencing demonstrates no Ruminococcus DNA in serum, whereas E. coli DNA was detected in multiple patient sera. Conclusion IgG-seq is a robust method for identifying immune-reactive enteric bacteria; our results highlight the link between immune response to enteric bacterial genera, such as Escherichia-Shigella and Ruminococcus, and joint disease activity in CD-SpA and CD-AxSpA. While Escherichia-Shigella may induce immunity by breaching the mucosal barrier, the absence of Ruminococcus in serum cfDNA suggests immune activation at barrier sites. Further studies are needed to characterize the strain-specific features that underlie our findings. Disclosures Fardina Malik, MD, Pfizer: Advisor/Consultant Iwijn de Vlaminck, PhD, GenDX: Advisor/Consultant|GenDX: Board Member|Kanvas Biosciences: Board Member|Kanvas Biosciences: Ownership Interest|Karius Inc.: Board Member|Karius Inc.: Ownership Interest|Viracor Eurofins: Advisor/Consultant Randy S. Longman, MD, PhD, Pfizer: Advisor/Consultant.

Changes to the upper gastrointestinal microbiotas of children with reflux oesophagitis and oesophageal metaplasia.

Little is known of the relationships among paediatric upper gastrointestinal microbiotas, and the impact of medication use and disease on their diversity. Here, we investigated the diversity of three microbiotas in the upper gastrointestinal tract of paediatric patients in relation to each other and to host factors. Oral, oesophageal and gastric microbiotas from a prospective paediatric cohort (n=54) were profiled using the 16S rRNA gene and ITS2 amplicon sequencing. 16S rRNA gene amplicon sequencing of oesophageal biopsies from a retrospective paediatric cohort (n=96) and shotgun metagenomics data from oesophageal brushings (n=88) were employed for genomic signature validation. Bacterial diversity and composition showed substantial differences across oral, oesophageal and gastric fluid samples that were not replicated for fungi, and the presence of reflux led to increased homogeneity in the bacterial component of these three microbiotas. The oral and oesophageal microbiotas were associated with age, sex, history of oesophageal atresia and presence of oesophageal metaplasia, with the latter characterized by Prevotella enrichment. Proton pump inhibitor use was associated with increased oral bacterial richness in the gastric fluid, and this correlated with increased levels of gastric pro-inflammatory cytokines. Profiling of oesophageal biopsies from a retrospective paediatric cohort confirmed an increased Prevotella prevalence in samples with metaplasia. Analysis of metagenome-derived oesophageal Prevotella melaninogenica genomes identified strain-specific features that were significantly increased in prevalence in samples with metaplasia. Prevotella enrichment is a signature associated with paediatric oesophageal metaplasia, and proton pump inhibitor use substantially alters the paediatric gastric microenvironment.

Insights into the biodegradation and heavy metal resistance potential of the genus Brevibacillus through comparative genome analyses

Members of the genus Brevibacillus belonging to the familyPaenibacillaceae are Gram-positive/variable, endospore-forming, and rod-shaped bacteria that dwell in various environmental habitats. Brevibacillus spp. have a wide range of enzyme activities such as degradation of various carbohydrates, plastics, and they possess resistance against heavy metals. These characteristics make them encouraging contenders for biotechnological applications.In this work, we analyzed the reference genomes of 19Brevibacillusspecies, focusing on discovering the biodegradation and heavy metal resistance capabilities of this little studied genus from genomic data. The results indicate that several strain specific traits were identified. For example Brevibacillus halotolerans s-14, and Brevibacillus laterosporus DSM 25 have more glycoside hydrolases (GHs) compared to other carbohydrate-active enzymes, and therefore might be more suitable for biodegradation of carbohydrates. In contrast, strains such as Brevibacillus antibioticus TGS2-1, with a higher number of glycosyltransfereases (GTs) may aid in the biosynthesis of complex carbohydrates. Our results also suggest some correlation between heavy metal resistance and polyurethane degradation, thus indicating that heavy metal resistance strains (e.g. Brevibacillus reuszeri J31TS6) can be a promising source of enzymes for polyurethane degradation. These strain specific features make the members of this bacterial group potential candidates for further investigations with industrial implications. This work also represents the first exhaustive study of Brevibacillus at the genome scale.

Impact of <i>Candida spp.</i> metabolites on human skin fibroblasts

Micromycetes spp. have been increasingly involved in the etiology of infectious diseases guiding to consider them not as important as bacterial and viral pathogens. Nowadays, a lot of severe forms of candidiasis are caused by C. auris, C. albicans, whereas C. glabrata and C. krusei are of similar importance. Members of these species were selected to investigate related metabolite action on human skin fibroblasts. Candida spp. being continuously found on the epithelium and mucosal membranes resulting in to sustained interaction between microbiota and human cells. Potential to produce metabolites containing pathogenicity factors is one of the crucial events for transition to invasive candidiasis, wherein human epithelial cells build up the front line of defense barrier preventing Candida spp. invasion into deeper host tissues. The study was aimed at assessing data on metabolite effects derived from epidemiologically relevant Candida spp. on primary human skin fibroblast culture in vitro. In particular, there were analyzed Candida spp. metabolites acting on fibroblast monolayer integrity and viability in cell suspension. It was found that Candida spp. metabolites might directly cause fibroblast death so that biocidal activity was exhibited as a strain-specific feature. A direct biocidity against dermal cells was more typical for strains C. glabrata и C. krusei, less pronounced for C. albicans and very weak for C. auris. In addition, a mechanism for secretory product-related biocidal activity derived from various Candida spp. on dermal fibroblasts in vitro revealed that it resulted in fibroblasts death 1 hour after exposure that peaked at 3 hrs. Cell death was equally proceeded via apoptosis and necrosis. Of note, biocidal effect of fungal metabolites showed no correlation with Candida-related potential to cleave intercellular junctions. It was found that C. auris metabolites showing weak biocidity against some fibroblasts simultaneously resulted in more marked disruption of cell monolayer compared to other Candida spp. Perhaps, it is just a feature of C. auris that might account for its higher invasiveness potential allowing to destroy tight human tissues more effectively compared to other Candida spp.

Misfolded amyloid-β strains and their potential roles in the clinical and pathological variability of Alzheimer's disease.

Misfolded amyloid-β strains and their potential roles in the clinical and pathological variability of Alzheimer's disease.

Discriminating cell line specific features of antibiotic-resistant strains of Escherichia coli from Raman spectra via machine learning analysis.

While Raman spectroscopy can provide label-free discrimination between highly similar biological species, the discrimination is often marginal, and optimal use of spectral information is imperative. Here, we compare two machine learning models, an artificial neural network and a support vector machine, for discriminating between Raman spectra of 11 bacterial mutants of Escherichia coli MDS42. While we find that both models discriminate the 11 bacterial strains with similarly high accuracy, sensitivity and specificity, it is clear that the models form different class boundaries. By extracting strain-specific (and function-specific) spectral features utilized by the models, we find that both models utilize a small subset of high intensity peaks while separate subsets of lower intensity peaks are utilized by only one method or the other. This analysis highlights the need for methods to use the complete spectral information more effectively, beginning with a better understanding of the distinct information gained from each model.

Role of sialylation of N-linked glycans in prion pathogenesis.

Mammalian prion or PrPSc is a proteinaceous infectious agent that consists of a misfolded, self-replicating state of the prion protein or PrPC. PrPC and PrPSc are posttranslationally modified with N-linked glycans, which are sialylated at the terminal positions. More than 30years have passed since the first characterization of the composition and structural diversity of N-linked glycans associated with the prion protein, yet the role of carbohydrate groups that constitute N-glycans and, in particular, their terminal sialic acid residues in prion disease pathogenesis remains poorly understood. A number of recent studies shed a light on the role of sialylation in the biology of prion diseases. This review article discusses several mechanisms by which terminal sialylation dictates the spread of PrPSc across brain regions and the outcomes of prion infection in an organism. In particular, relationships between the sialylation status of PrPSc and important strain-specific features including lymphotropism, neurotropism, and neuroinflammation are discussed. Moreover, emerging evidence pointing out the roles of sialic acid residues in prion replication, cross-species transmission, strain competition, and strain adaptation are reviewed. A hypothesis according to which selective, strain-specified recruitment of PrPC sialoglycoforms dictates unique strain-specific disease phenotypes is examined. Finally, the current article proposes that prion strains evolve as a result of a delicate balance between recruiting highly sialylated glycoforms to avoid an "eat-me" response by glia and limiting heavily sialylated glycoforms for enabling rapid prion replication.

Modeling tauopathy using human-like pathogenic tau seeds.

Compared with traditional transgenic models of tauopathy, there is no confounding effect from the insertion of the exogenous gene and overexpression of the human mutant tau in the tau spreading models. By strategically choosing the location and time of the inoculation, we can spatiotemporally determine the starting point of tau pathology in the model mimicking the development of tauopathy. Moreover, they recapitulate the strain-specific features of tau pathology. Regardless of these advantages, human-like tau spreading models are very much confined due to the limitation on quantity and quality of tau seeds. In vitro seeding assay has shown its great potential of amplifying the pathogenic tau seeds to expand their quantity and increase their quality. In the study, we used biochemically enriched, human-derived, tau aggregates as seeds to template recombinant tau (rT40) in vitro. Using biochemistry and electron microscopy, we examined the biophysical properties of the amplified materials and the human-derived tau seeds. We also interrogated the pathogenicity of the amplified human-like tau strains with orthogonal spreading models of tauopathy. As a result, we observed elongated tau filaments with recombinant T40 attached to the seeds. Compared with the seeds control, the amplified tau strains showed increased pathogenic tau species after seeding. The amplified tau strains recapitulate the pathogenicity and biophysical property of the original seeds. Our data suggest that the in vitro seeded recombinant tau can be recruited onto the seeds and converted into the confirmation of pathological tau seeds in a strain-dependent manner. Along with the conversion, the pathogenicity of different tau strains can be conferred and conserved into the recombinant tau. The study provides an authentic way of amplifying tau strains in vitro as well as a tool to expand our ability to understand tau fibrillization and transmission.

Universal and strain specific structure features of segment 8 genomic RNA of influenza A virus—application of 4-thiouridine photocrosslinking

RNA structure in the influenza A virus (IAV) has been the focus of several studies that have shown connections between conserved secondary structure motifs and their biological function in the virus replication cycle. Questions have arisen on how to best recognize and understand the pandemic properties of IAV strains from an RNA perspective, but determination of the RNA secondary structure has been challenging. Herein, we used chemical mapping to determine the secondary structure of segment 8 viral RNA (vRNA) of the pandemic A/California/04/2009 (H1N1) strain of IAV. Additionally, this long, naturally occurring RNA served as a model to evaluate RNA mapping with 4-thiouridine (4sU) crosslinking. We explored 4-thiouridine as a probe of nucleotides in close proximity, through its incorporation into newly transcribed RNA and subsequent photoactivation. RNA secondary structural features both universal to type A strains and unique to the A/California/04/2009 (H1N1) strain were recognized. 4sU mapping confirmed and facilitated RNA structure prediction, according to several rules: 4sU photocross-linking forms efficiently in the double-stranded region of RNA with some flexibility, in the ends of helices, and across bulges and loops when their structural mobility is permitted. This method highlighted three-dimensional properties of segment 8 vRNA secondary structure motifs and allowed to propose several long-range three-dimensional interactions. 4sU mapping combined with chemical mapping and bioinformatic analysis could be used to enhance the RNA structure determination as well as recognition of target regions for antisense strategies or viral RNA detection.

Mechanisms of antibiotic resistance of Clostridioides difficile.

Clostridioides difficile (CD) is one of the top five urgent antibiotic resistance threats in USA. There is a worldwide increase in MDR of CD, with emergence of novel strains which are often more virulent and MDR. Antibiotic resistance in CD is constantly evolving with acquisition of novel resistance mechanisms, which can be transferred between different species of bacteria and among different CD strains present in the clinical setting, community, and environment. Therefore, understanding the antibiotic resistance mechanisms of CD is important to guide optimal antibiotic stewardship policies and to identify novel therapeutic targets to combat CD as well as other bacteria. Epidemiology of CD is driven by the evolution of antibiotic resistance. Prevalence of different CD strains and their characteristic resistomes show distinct global geographical patterns. Understanding epidemiologically driven and strain-specific characteristics of antibiotic resistance is important for effective epidemiological surveillance of antibiotic resistance and to curb the inter-strain and -species spread of the CD resistome. CD has developed resistance to antibiotics with diverse mechanisms such as drug alteration, modification of the antibiotic target site and extrusion of drugs via efflux pumps. In this review, we summarized the most recent advancements in the understanding of mechanisms of antibiotic resistance in CD and analysed the antibiotic resistance factors present in genomes of a few representative well known, epidemic and MDR CD strains found predominantly in different regions of the world.

Novel Pharmacokinetic/Pharmacodynamic Parameters Quantify the Exposure-Effect Relationship of Levofloxacin against Fluoroquinolone-Resistant Escherichia coli.

Minimal inhibitory concentration-based pharmacokinetic/pharmacodynamic (PK/PD) indices are commonly applied to antibiotic dosing optimisation, but their informative value is limited, as they do not account for bacterial growth dynamics over time. We aimed to comprehensively characterise the exposure–effect relationship of levofloxacin against Escherichia coli and quantify strain-specific characteristics applying novel PK/PD parameters. In vitro infection model experiments were leveraged to explore the exposure–effect relationship of three clinical Escherichia coli isolates, harbouring different genomic fluoroquinolone resistance mechanisms, under constant levofloxacin concentrations or human concentration–time profiles (≤76 h). As an exposure metric, the ‘cumulative area under the levofloxacin–concentration time curve’ was determined. The antibiotic effect was assessed as the ‘cumulative area between the growth control and the bacterial-killing and -regrowth curve’. PK/PD modelling was applied to characterise the exposure–effect relationship and derive novel PK/PD parameters. A sigmoidal Emax model with an inhibition term best characterised the exposure–effect relationship and allowed for discrimination between two isolates sharing the same MIC value. Strain- and exposure-pattern-dependent differences were captured by the PK/PD parameters and elucidated the contribution of phenotypic adaptation to bacterial regrowth. The novel exposure and effect metrics and derived PK/PD parameters allowed for comprehensive characterisation of the isolates and could be applied to overcome the limitations of the MIC in clinical antibiotic dosing decisions, drug research and preclinical development.

Unraveling the Central Role of Sulfur-Oxidizing Acidiphilium multivorum LMS in Industrial Bioprocessing of Gold-Bearing Sulfide Concentrates.

Acidiphilium multivorum LMS is an acidophile isolated from industrial bioreactors during the processing of the gold-bearing pyrite-arsenopyrite concentrate at 38–42 °C. Most strains of this species are obligate organoheterotrophs that do not use ferrous iron or reduced sulfur compounds as energy sources. However, the LMS strain was identified as one of the predominant sulfur oxidizers in acidophilic microbial consortia. In addition to efficient growth under strictly heterotrophic conditions, the LMS strain proved to be an active sulfur oxidizer both in the presence or absence of organic compounds. Interestingly, Ac. multivorum LMS was able to succeed more common sulfur oxidizers in microbial populations, which indicated a previously underestimated role of this bacterium in industrial bioleaching operations. In this study, the first draft genome of the sulfur-oxidizing Ac. multivorum was sequenced and annotated. Based on the functional genome characterization, sulfur metabolism pathways were reconstructed. The LMS strain possessed a complicated multi-enzyme system to oxidize elemental sulfur, thiosulfate, sulfide, and sulfite to sulfate as the final product. Altogether, the phenotypic description and genome analysis unraveled a crucial role of Ac. multivorum in some biomining processes and revealed unique strain-specific characteristics, including the ars genes conferring arsenic resistance, which are similar to those of phylogenetically distinct microorganisms.

Vaccine Quality Is a Key Factor to Determine Thermal Stability of Commercial Newcastle Disease (ND)Vaccines.

Vaccination against Newcastle disease (ND), a devastating viral disease of chickens, is often hampered by thermal inactivation of the live vaccines, in particular in tropical and hot climate conditions. In the past, “thermostable” vaccine strains (I-2) were proposed to overcome this problem but previous comparative studies did not include formulation-specific factors of commercial vaccines. In the current study, we aimed to verify the superior thermal stability of commercially formulated I-2 strains by comparing six commercially available ND vaccines. Subjected to 37 °C as lyophilized preparations, two vaccines containing I-2 strains were more sensitive to inactivation than a third I-2 vaccine or compared to three other vaccines based on different ND strains. However, reconstitution strains proved to have a comparable tenacity. Interestingly, all vaccines still retained a sufficient virus dose for protection (106 EID50) after 1 day at 37 °C. These results suggest that there are specific factors that influence thermal stability beyond the strain-specific characteristics. Exposing ND vaccines to elevated temperatures of 51 and 61 °C demonstrated that inactivation of all dissolved vaccines including I-2 vaccine strains occurred within 2 to 4 h. The results revealed important differences among the vaccines and emphasize the importance of the quality of a certain vaccine preparation rather than the strain it contains. These data highlight that regardless of the ND strain used for vaccine preparation, the appropriate cold chain is mandatory for keeping live ND vaccines efficiency in hot climates.

Rapid strain-specific identification of two Lactobacillus rhamnosus strains using PCR based on gene family analysis

Because the probiotic and growth characteristics of probiotics are strain-specific features, it is crucial to be able to distinguish the probiotic strains from the other strains in the same species. To rapidly identify Lactobacillus rhamnosus at the strain level through PCR, a method for searching for several strain-specific sequences in the genome of a strain was investigated. The whole genomes of L. rhamnosus hsryfm 1301 and L. rhamnosus LV108 were sequenced, and gene family analysis was performed with using L. rhamnosus GG and L. rhamnosus Lc705 as reference strains. Thirty-one and 19 strain-specific open reading frames (ORFs) were found in L. rhamnosus hsryfm 1301 and L. rhamnosus LV108, respectively. Thus, strain-specific primer pairs could be designed in a more rational and controllable manner. Concatenation of several strain-specific primer pairs designed from the strain-specific ORFs (and their adjacent regions) were able to distinguish L. rhamnosus LV108 (primer pairs V2, V4, V5, and V9) or L. rhamnosus hsryfm 1301 (primer pairs H1, H2, H3, and H4) from 12 other L. rhamnosus strains. This strain-specific identification method was determined to be accurate, rapid, economical, reproducible and easy to perform.

The Probiotic Strain Lactobacillus fermentum 39: Biochemical Properties, Genomic Features, and Antiviral Activity

Lactobacillus fermentum 39 is a well-known probiotic strain, which is widely used for production of pharmacopoeial probiotic preparations, dietary supplements, and foodstuffs enriched with probiotic microorganisms. In the course of analysis by transmission electron microscopy, the cell morphology was studied, biochemical properties of the strain and strain-specific characteristics of sugar metabolism were thoroughly analyzed, its full genome was sequenced, and the cluster of genes responsible for exopolysaccharide synthesis was characterized. The cells of Lactobacillus fermentum 39 were shown to be capable of adsorbing rotavirus particles, which allows us to substantiate a new aspect of application of probiotics, including this strain, in acute gastroenteritis caused by human rotaviruses.

Distinctive chemical and aromatic composition of red wines produced by Saccharomyces cerevisiae co-fermentation with indigenous and commercial non-Saccharomyces strains

The use of Saccharomyces cerevisiae and non-Saccharomyces yeast species as mixed starters has advantages over pure culture fermentation because of increased wine sensory characteristics. The aim of the present study was to evaluate the divergences of wine compositions fermented by indigenous non-Saccharomyces strains (Torulaspora delbrueckii TD12 and Lachancea thermotolerans LT9) or commercial non-Saccharomyces strains (T. delbrueckii Prelude and L. thermotolerans Concerto) combined with S. cerevisiae D254, respectively. Results evidenced that although belong to the same species, the content of chemical and aromatic compounds of red wines produced by indigenous and commercial strains was significantly different after alcoholic fermentation (ALF) and malolactic fermentation (MLF). TD12/D254 was characterized with a higher amount of glycerol, ethyl esters, and volatile acids, whilst Prelude/D254 was distinguished by a higher intensity of isoamyl acetate and a lower production of acetic acid. LT9/D254 increased the intensity of higher alcohols, esters, and β-damascenone compared with Concerto/D254. After MLF, the diversities variation of glycerol and lactic acid were increased, but acetic acid and most volatile compounds were reduced. TD12/D254 obtained better aromatic quality as assessed by calculating the odor activity values (OAVs). Our results highlighted the strain-specificity of non-Saccharomyces strains in shaping the aromatic characteristic of wine, and suggested that more attention should be paid to the strain-specific characteristics when selecting non-Saccharomyces strains to improve aroma diversity and quality of the wine. In this regard, the indigenous strain is a suitable choice because of better adaptation to fermentation conditions and generating typical sensory characteristics specific to the wine region.

Draft Genome Resources for Plant-Beneficial Fungi Clonostachys rosea Strains ACM941 and 88-710.

Clonostachys rosea strains ACM941 and 88-710 are beneficial microbes recognized for their plant disease control and growth promotion properties, respectively, when applied to economically important crops. In addition to their geographical and functional overlap, the two strains also share a high degree of genetic similarity. In an effort to identify the subtleties that underlie their strain-specific applications, their genomic sequence is reported here. The genome size of ACM941 was estimated to be 56.9 Mb, encoding 17,585 putative genes, while strain 88-710 was estimated to have a 55.5 Mb genome size, containing 17,188 predicted genes. Overall, ACM941 and 88-710 share >96% of their encoded genomes, such that their strain-specific characteristics are likely encoded in either the remaining variable 4% or differentially regulated shared genes or both. These genomic sequences form a foundation for future studies aimed at identifying the genomic and metabolic machinery driving their respective beneficial properties.