Pekka Varmanen

University of Helsinki | HY · Department of Food and Nutrition

Propionibacterium freudenreichii ( PFR ) DSM 20271 is a bacterium known for its ability to thrive in diverse environments and to produce vitamin B12. Despite its anaerobic preference, recent studies have elucidated its ability to prosper in the presence of oxygen, prompting a deeper exploration of its physiology under aerobic conditions. Here, we i...

Mycobacterium marinum, a slow-growing Actinobacterium, typically induces tuberculosis-like disease in fish. Here, we report a new reference sequence for M. marinum ATCC 927T, along with its DNA methylome. This aims to maximize the research potential of this type strain and facilitates investigations into the pathomechanisms of human tuberculosis.

Inhibiting quorum sensing (QS), a central communication system, is a promising strategy to combat bacterial pathogens without antibiotics. Here, we designed novel hybrid compounds targeting the PQS (Pseudomonas quinolone signal)-dependent quorum sensing (QS) of Pseudomonas aeruginosa that is one of the multidrug-resistant and highly virulent pathog...

Inhibition of quorum sensing (QS)-dependent biofilm formation and virulence is extensively investigated as a novel approach to combat bacterial pathogens by impeding their ability to cause antibiotic-tolerant diseases. Such strategies are considered a promising alternative to conventional antibacterial therapy since interrupting the central cell-to...

Abstract Copper shows a high promise in developing biomedical materials with antibacterial effect. The antibacterial effect can be enhanced by nanostructured surfaces with superhydrophobic properties, which reduce the solid contact area available for bacterial adhesion and adherent growth. Here, three structured surfaces are fabricated to test the...

Disrupting bacterial quorum sensing (QS) signaling is a promising strategy to combat pathogenic biofilms without the development of antibiotic resistance. Here, we report that food-associated bacteria can interfere with the biofilm formation of a Gram-negative pathogenic bacterium by targeting its AHL (acyl-homoserine lactone) QS system. This was d...

Anoplocephala perfoliata is a common tapeworm in horses causing colic and even mortalities. Current diagnostic tests to detect A. perfoliata infections have their limitations and an improved method is needed. Immunoreactive excretory/secretory proteins (E/S proteome) of this parasite can provide promising candidates for diagnostic tests. We compare...

In the present study, we report the design and synthesis of novel amide-type hybrid molecules based on anthranilic acid and quinoline or β-carboline heterocyclic scaffolds. Three types of biological screenings were performed: (i) in vitro antiproliferative screening against a panel of solid tumor and leukemia cell lines, (ii) antiviral screening ag...

The bioaccessibility of vitamin B12 (B12) in plant-based products fortified using wheat bran extract fermented with B12-producing food-grade Propionibacterium freudenreichii was studied by applying a standard static in vitro model. At first, a culture of P. freudenreichii, fresh or heat-treated, was subjected to in vitro assays. Then, food ingredie...

The present study investigated the in situ production of vitamin B12 in eleven cereal, pseudo-cereal and legume materials by fermentation with Propionibacterium freudenreichii DSM 20271 and Levilactobacillus brevis (formerly Lactobacillus brevis) ATCC 14869. P. freudenreichii was used as the vitamin producer and L. brevis was selected to improve th...

Cutibacterium acnes is a member of the normal human skin microbiome. However, it is also associated with skin disorders and persistent infections of orthopedic implants. Here, we announce complete genome sequences and methylomes of the C. acnes subsp. acnes strains DSM 1897 T and DSM 16379 together with their active restriction-modification systems...

The present study investigated Staphylococcus aureus ATCC25923 surfaceomes (cell surface proteins) during prolonged growth by subjecting planktonic and biofilm cultures (initiated from exponential or stationary cells) to label-free quantitative surfaceomics and phenotypic confirmations. The abundance of adhesion, autolytic, hemolytic, and lipolytic...

The novel Acidipropionibacterium genus encompasses species of industrial importance but also those associated with food spoilage. In particular, Acidipropionibacterium acidipropionici, Acidipropionibacterium thoenii, and Acidipropionibacterium jensenii play an important role in food fermentation, as biopreservatives, or as potential probiotics. Not...

The present study investigated the effect of co-fermentation on vitamin B12 content and microbiological composition of wheat bran. Propionibacterium freudenreichii DSM 20271 was used as the producer of vitamin while Lactobacillus brevis ATCC 14869 was selected to ensure the microbial safety of the bran dough. Fermentation trials were conducted in b...

Bacterial biofilms have clear implications in disease and in food applications involving probiotics. Here, we show that switching the carbohydrate source from glucose to fructose increased the biofilm formation and the total surface-antigenicity of a well-known probiotic, Lactobacillus rhamnosus GG. Surfaceomes (all cell surface-associated proteins...

Bacterial biofilms have clear implications in disease and in food applications involving probiotics. Here, we show that switching the carbohydrate source from glucose to fructose increased the biofilm formation and the total surface-antigenicity of a well-known probiotic, Lactobacillus rhamnosus GG. Surfaceomes (all cell surface-associated proteins...

A Gram-stain-positive, catalase-positive and pleomorphic rod organism was isolated from malted barley in Finland, classified initially by partial 16S rRNA gene sequencing and originally deposited in the VTT Culture Collection as a strain of Propionibacterium acidipropionici (currently Acidipropionibacterium acidipropionici). The subsequent comparis...

Vitamin B12 is a micronutrient naturally existing in animal products. A growing interest and need to replace animal protein with plant protein sources have resulted in increased attention to developing vitamin B12-fortified plant-based food. Natural fortification by Propionibacterium freudenreichii is a promising alternative to chemical fortificati...

Fig. S3. Adherence of JS22 cells cultured in the absence and presence of 300 mM NaCl to porcine mucus (PM) and Polysorp (PS, hydrophobic surface).

Fig. S4. Comparison of the identified InlA peptides in comparison with the predicted full‐size InlA (146‐kDa) orthologue from P. freudenreichii ITG P20.

Table S2. Identification of the strain‐specific 1‐DE differences (Fig. 1A) from the selected P. freudenreichii and Acidipropionibacterium strains.

Table S3. Phosphopeptides identified from the tryptic peptide digests of the RpfB containing protein spots cut out from the 2‐DE secretome gels of JS14 and JS22.

Fig. S1. Representative growth curves of all P. freudenreichii and Acidipropionibacterium strains in PPA as a function of time (A). Time points used for sample withdrawal and the respective ODs of each strain at 600 nm (B).

Fig. S2. Protein database composed of all predicted protein sequences from JS14 and JS22.

Table S1. Bacterial strains used in this study.

This study compared the secretomes (proteins exported out of the cell) of Propionibacterium freudenreichii of different origin to identify plausible adaptation factors. Phylosecretomics indicated strain-specific variation in secretion of adhesins/invasins (SlpA, InlA), cell-wall hydrolysing (NlpC60 peptidase, transglycosylase), protective (RpfB) an...

The in situ production of active vitamin B12 was investigated in aqueous cereal-based matrices with three strains of food-grade Propionibacterium freudenreichii. Matrices prepared from malted barley flour (33% w/v; BM), barley flour (6%; BF), and wheat aleurone (15%; AM) were fermented. The effect of cobalt and the lower ligand 5,6-dimethylbenzimid...

Background Propionibacterium freudenreichii is an industrially important bacterium granted the Generally Recognized as Safe (the GRAS) status, due to its long safe use in food bioprocesses. Despite the recognized role in the food industry and in the production of vitamin B12, as well as its documented health-promoting potential, P. freudenreichii r...

Certain strains of lactic acid bacteria have been reported to inhibit fungal growth and may so be potential as biocontrol agents. In this study, 171 LAB strains were isolated from traditional fermented Kenyan milk and maize products and tested against aflatoxin-producing A. flavus fungi. The three LAB strains showing highest antifungal activity wer...

Propionibacterium freudenreichii is a traditional dairy bacterium and a producer of short chain fatty acids (propionic and acetic acids) as well as vitamin B12. In food applications, it is a promising organism for in situ fortification with B12 vitamin since it is generally recognized as safe (GRAS) and it is able to synthesize biologically active...

SUMMARY Lactic acid bacteria (LAB) are important starter, commensal, or pathogenic microorganisms. The stress physiology of LAB has been studied in depth for over 2 decades, fueled mostly by the technological implications of LAB robustness in the food industry. Survival of probiotic LAB in the host and the potential relatedness of LAB virulence to...

We analysed the response of the model bacterium Lactococcus lactis to abrupt depletion of glucose after several generations of exponential growth. Glucose depletion resulted in a drastic drop in the energy charge accompanied by an extremely low GTP level and an almost total arrest of protein synthesis. Strikingly, the cell prioritized the continued...

Unlabelled: Lipoteichoic acid (LTA) is an important cell wall component of Gram-positive bacteria and a promising target for the development of vaccines and antimicrobial compounds against Staphylococcus aureus Here we demonstrate that mutations in the conditionally essential ltaS (LTA synthase) gene arise spontaneously in an S. aureus mutant lack...

Microscopic analysis of the wild-type, clpX-inactivated, and LTA-negative strains. The S. aureus SA564 wild type, the SA564 clpX strain, and the 564-25-2 (SA564 clpX ltaSH476Q) strain were grown in TSB to the log phase at either 30°C or 37°C, samples were prepared for microscopy analysis, and bacteria were stained with vancomycin-BODIPY. Left panel...

(A) Growth curves of S. aureus 8325-4 and derived strains. Overnight cultures of S. aureus strains 8325-4 (WT), 8325-4-ΔclpX, 8325-4-ΔclpX ltaSstop, 8325-4-iltaS (WT-iltaS), and 8325-4ΔclpX-iltaS were harvested, washed, and diluted 1:1,000 into TSB substituted with 1 mM IPTG. Cultures were incubated at 37°C, and OD600 values were recorded. To maint...

Fluorescence microscopic analysis of strain 8325-4-iltaS grown to exponential phase at 37°C in the presence of 1 mM IPTG, and stained with BODIPY-vancomycin. Bacteria were grown and prepared for fluorescence microscopy as described in Materials and Methods. Download

Fluorescence microscopic analysis of strain 8325-4-clpX-iltaS grown to exponential phase at 37°C in the presence of 1 mM IPTG and stained with BODIPY-vancomycin. Bacteria were grown and prepared for fluorescence microscopy as described in Materials and Methods. Download

Supplementary Materials and Methods. Download

Effect of size and growth phase of inoculum on growth of clpX mutant. S. aureus strains 8325-4 and 8325-4 clpX were grown to exponential (OD, ~0.1; “exp”) or stationary (overnight culture; “stat”) phase at 37°C and diluted (1:10 or 1:1,000) as indicated into 300 µl TSB, and growth was measured at 30°C in a Bioscreen C instrument. Values represent m...

Fluorescence microscopic analysis of strain 8325-4-iltaS grown to exponential phase at 37°C in the absence of IPTG and stained with BODIPY-vancomycin. Bacteria were grown and prepared for fluorescence microscopy as described in Materials and Methods. Download

Fluorescence microscopic analysis of strain 8325-4-clpX-iltaS grown to exponential phase at 37°C in the absence of IPTG and stained with BODIPY-vancomycin. Bacteria were grown and prepared for fluorescence microscopy as described in Materials and Methods. Download

Bacterial strains, plasmids, and primers used in this study.

List of all identified surface-associated proteins from SA564 and its mutant derivatives (strains ΔclpX and ΔclpX-ltsA) cultured at 30°C or 37°C. All trypsin digestions were conducted with duplicate cells. Relevant information related to protein functions, physicochemical characteristics, and subcellular location are described in Text S1. EC, extra...

Propionibacterium freudenreichii is the only generally recognized safe (GRAS) bacterium known to synthesize active vitamin B12 and offers previously untapped potential for naturally fortifying foods with vitamin B12. Biosynthesis of the lower ligand 5,6-dimethylbenizimidazole (DMBI) is often a key limiting factor in the production of active vitamin...

The present study reports the effect of Penicillin G (PenG) on the proteome dynamics of the Staphylococcus aureus strain Newman during biofilm mode of growth. The viability of the 18-h-old biofilm cells challenged with PenG at the concentration of 1mgmL(-1) was first assessed by plate counting, resazurin and LIVE/DEAD fluorescence staining, which i...

Background Propionibacterium freudenreichii is a food grade bacterium that has gained attention as a producer of appreciable amounts of cobalamin, a cobamide with activity of vitamin B12. Production of active form of vitamin is a prerequisite for attempts to naturally fortify foods with B12 by microbial fermentation. Active vitamin B12 is distingui...

Propionibacterium freudenreichii subsp. freudenreichii DSM 20271(T) is the type strain of species Propionibacterium freudenreichii that has a long history of safe use in the production dairy products and B12 vitamin. P. freudenreichii is the type species of the genus Propionibacterium which contains Gram-positive, non-motile and non-sporeforming ba...

The present study reports the identification and comparison of all expressed cell-surface exposed proteins from the well-known probiotic L. rhamnosus GG and a related dairy strain, Lc705. To obtain this information, the cell-surface bound proteins were released from intact cells by trypsin shaving under hypertonic conditions with and without DTT. L...

AimsThe environmental pathogen Streptococcus uberis causes intramammary infections in dairy cows. Because biofilm growth might contribute to Strep. uberis mastitis, we conducted a biological screen to identify genes potentially involved in the regulation of biofilm growth.Methods and ResultsBy screening a transposon mutant library of Strep. uberis,...

The present study reports comparative proteome cataloging of a bovine mastitis- and a human-associated Staphylococcus epidermidis (SE) strain with a specific focus on surfome (cell-wall bound and extracellular) proteins. Protein identification by GeLC-MS/MS analyses resulted in 1400 and 1287 proteins from the bovine (PM221) and human (ATCC12228) st...

The present study reports comparative genomics and proteomics of Staphylococcus epidermidis (SE) strains isolated from bovine intramammary infection (PM221) and human hosts (ATCC12228 and RP62A). Genome-level profiling and protein expression analyses revealed that the bovine strain and the mildly infectious ATCC12228 strain are highly similar. Thei...

Staphylococcus epidermidis (SE) includes commensal and pathogenic strains capable of infecting humans and animals. This study reports global exoproteome profiling of bovine mastitis strain PM221 and two human strains, commensal-type ATCC12228 and sepsis-associated RP62A. We identified 451, 395 and 518 proteins from culture supernatants of PM221, AT...

Diabetic nephropathy is a complication of diabetes and a major cause of end-stage renal disease. To characterize the early pathophysiological mechanisms leading to glomerular podocyte injury in diabetic nephropathy, we performed quantitative proteomic profiling of glomeruli isolated from rats with streptozotocin-induced diabetes and controls. Fluor...

Trichinellosis is a zoonotic disease in humans caused by Trichinella spp. The present study was undertaken to discover excretory-secretory (E-S) proteins from T. spiralis and T. britovi muscle larvae (ML) that hold promise for species-specific diagnostics. To that end, the purified E-S proteins were analyzed by fluorescent two-dimensional differenc...

Table S2. Identification of T. britovi and T. spiralis E-S proteins showing differential abundance in 2-D DIGE gels. The grey or white backgrounds correspond to proteins that are produced more in T. britovi or T. spiralis, respectively.

The evolutionary success of bacteria depends on their excellent genetic flexibility that promotes adaptation in diverse environmental niches and different host organisms. The economically important group of bacteria well-adapted to milk-environment include species of the genera like Staphylococcus, Streptococcus and Lactobacillus. Some of these spe...

Gram-positive staphylococci include commensal and pathogenic bacteria that are adapted to different mammalian species, particularly to humans and cattle[1]. Among these species, Staphylococcus epidermidis is considered an opportunistic pathogen that ranks first among the causative agents of nosocomial infections and is the most common source of inf...