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Institute of dairy science & probiotics

Technical expertise

  • Physical, chemical and microbiological analysis of milk and dairy products;
  • Bacterial isolation, cultivation, identification, biochemical characterisation, microscopy;
  • Evaluation of antimicrobial activity (antibiotics, antimicrobials, bacteriocins);
  • Cultivation of cell cultures, immunological techniques, ELISA;
  • DNA and RNA isolation, real-time PCR, conventional PCR, expression studies;
  • Isolation and characterisation of milk proteins, of bacteriocins;
  • Analyses of microbiota/microbiome composition (microbiological methods, NGS sequencing) in different environments: milk (animal, human), dairy products, gut, clinical samples (feces, biopsies..);
  • Bioreactor processes: cultivation of lactic acid bacteria and bifidobacteria, production of metabolites;
  • Bioinformatic analyses of whole genomes of bacteria, of 16S rDNA metagenomic data..
  • Isolation and analysis of proteins and peptides from milk and dairy products, bacteriocins…
  • Bioreaktorski procesi: gojenje mlečnokislinskih bakterij in bifidobakterij, proizvodnja metabolitov;
  • Bioinformacijske analize genomov bakterij, metagenomskih podatkov 16S rDNA..;
  • Izolacija in analitika proteinov in peptidov iz mleka in mlečnh izdelkov, bakteriocinov…

 

Collection of bacterial isolates

Bacteria are isolated from various environments (fermented foods, milk, human milk, feces, human intestinal mucosa, etc....) and stored in our own collection of microorganisms, which is part of the Slovenian national collection ZIM - Culture Collection of Industrial Microorganisms (https://www.zim-collection.si/about), also registered as WDCM810 (WFCC-MIRC World Data Centre for Microorganisms (WDCM)). Our best studied strain is Lactobacillus paragasseri K7. The results of studies on this strain have been published in numerous scientific articles. Its entire genome has already been sequenced. In collaboration with industrial partners, we have developed the products in powder form or oily suspension containing viable K7 cells. Isolates of particular interest include those from the intestinal mucosa of children, obtained in collaboration with the industrial partner (Medis) as part of the project KC-BRIN - The competence centre for Biotechnological Development and Innovation. Individual isolates are capable of anti-inflammatory activity and/or affecting the intestinal barrier function, and are therefore useful for the prevention or support in the treatment of inflammatory bowel disease. The collection also includes isolates capable of producing metabolites of commercial interest (bacteriocins, vitamin B12) that were tested in collaboration with industry partner Arhel in the LIFE4AcidWhey and LAKTIKA projects.

BF_43

 

Determination of safety and functionality of probiotic and starter bacteria

Determination of safety and functionality of probiotic bacteria can be performed in vitro – using cultivation methods, on cell cultures (Caco2 - epithelial cell model, THP-1 - macrophage model, ...) and in vivo on animals and humans. The main features that are tested include the following:

  • phenotypic and genotypic resistance to clinically relevant antibiotics;
  • species confirmation – probiotics belong belong to species considered safe (EFSA QPS status);
  • inhibition of pathogenic or spoilage bacteria;
  • effects on the host immune system (influence on the expression and secretion of cytokines, effects on the transcriptome of host immune cells, ...) and on the intestinal barrier function;
  • resistance to stress factors (technological processes, passage through the gastrointestinal tract), stability during storage;
  • resistomes of starter cultures, probiotic cultures / products and fermented dairy products.

Representative publications in the field:

  • ROZMAN, V., MOHAR LORBEG, P., TREVEN, P., ACCETTO, T., JANEŽIČ, S., RUPNIK, M., BOGOVIČ MATIJAŠIĆ, B., 2023. Genomic insights into antibiotic resistance and mobilome of lactic acid bacteria and bifidobacteria. Life science alliance 6, 202201637. doi: 10.26508/lsa.202201637
  • ROZMAN, V., MOHAR LORBEG, P., TREVEN, P., ACCETTO, T., GOLOB, M., ZDOVC, I., BOGOVIČ MATIJAŠIĆ, B., 2022. Lactic acid bacteria and bifidobacteria deliberately introduced into the agro-food chain do not significantly increase the antimicrobial resistance gene pool. Gut microbes 2127438. doi: 10.1080/19490976.2022.2127438
  • ROZMAN, V., MOHAR LORBEG, P., ACCETTO, T., BOGOVIČ MATIJAŠIĆ, B., 2020. Characterization of antimicrobial resistance in lactobacilli and bifidobacteria used as probiotics or starter cultures based on integration of phenotypic and in silico data. International Journal of Food Microbiology 314. doi: 10.1016/j.ijfoodmicro.2019.108388
  • ROZMAN, V., MOHAR LORBEG, P., CHANISHVILI, N., ACCETTO, T., KAKABADZE, E., GRDZELISHVILI, N., RUPNIK, M., BOGOVIČ MATIJAŠIĆ, B., 2023. Genomic insights into the safety and bacteriocinogenic potential of isolates from artisanal fermented milk Matsoni. Lwt 185, 115183. doi:10.1016/j.lwt.2023.115183
  • PAVELJŠEK, Diana, IVIČAK-KOCJAN, Karolina, TREVEN, Primož, BENČINA, Mojca, JERALA, Roman, ROGELJ, Irena. Distinctive probiotic features share common TLR2-dependent signalling in intestinal epithelial cells. Cellular microbiology, ISSN 1462-5822, 2021, vol. 23, no. 1 , e13264, str. 1-12, doi: 10.1111/cmi.13264. 
  • PAVELJŠEK, Diana, JUVAN, Peter, KOŠIR, Rok, ROZMAN, Damjana, HACIN, Biljana, IVIČAK-KOCJAN, Karolina, ROGELJ, Irena. Lactobacillus fermentum L930BB and Bifidobacterium animalis subsp. animalis IM386 initiate signalling pathways involved in intestinal epithelial barrier protection. Beneficial microbes, ISSN 1876-2883, 2018, vol. 9, no. 3, str. 515-525, doi: 10.3920/BM2017.0107.
  • SAGAYA, F. M., HACIN, Biljana, TOMPA, Gorazd, IHAN, Alojz, ŠKRAJNAR, Špela, ČERNE, Manica, HURRELL, Richard, BOGOVIČ MATIJAŠIĆ, Bojana, ROGELJ, Irena, VERGÈRES, G. Lactobacillus gasseri K7 modulates the blood cell transcriptome of conventional mice infected with Escherichia coli O157:H7. Journal of applied microbiology, 2014, vol. 116, issue 5, str. 1282-1296. doi:10.1111/jam.12440.
  • TREVEN, Primož, TURKOVÁ, Kristýna, TRMČIĆ, Aljoša, OBERMAJER, Tanja, ROGELJ, Irena, BOGOVIČ MATIJAŠIĆ, Bojana. Detection and quantification of probiotic strain Lactobacillus gasseri K7 in faecal samples by targeting bacteriocin genes. Folia microbiologica, 2013, vol. 58, no. 6, str. 623-630, doi:10.1007/s12223-013-0252-8.
  • BOGOVIČ MATIJAŠIĆ, Bojana, ROGELJ, Irena. Bacteriocins of probiotics and enteric cytoprotection. V: MALAGO, J.J. (ur.), KONINKX, J.F.J.G. (ur.), MARINŠEK-LOGAR, Romana (ur.). Probiotic bacteria and enteric infections : cytoprotection by probiotic bacteria. Dordrecht [etc.]: Springer, cop. 2011, str. 313-354. doi:10.1007/978-94-007-0386-5.
  • MAVRIČ, Anja, TOMPA, Gorazd, TRMČIĆ, Aljoša, ROGELJ, Irena, BOGOVIČ MATIJAŠIĆ, Bojana. Bacteriocins of Lactobacillus gasseri K7-Monitoring of gassericin K7 A and B genesʼ expression and isolation of an active component. Process biochemistry, 2014, vol. 49, no. 8, str. 1251-1259. doi:10.1016/j.procbio.2014.04.022.
  • ČITAR, Manuela, HACIN, Biljana, TOMPA, Gorazd, ŠTEMPELJ, Mateja, ROGELJ, Irena, DOLINŠEK, Jernej, NARAT, Mojca, BOGOVIČ MATIJAŠIĆ, Bojana. Human intestinal mucosa-associated Lactobacillus and Bifidobacterium strains with probiotic properties modulate IL-10, IL-6 and IL-12 gene expression in THP-1 cells. Beneficial microbes, 2015, vol. 6, no. 3, str. 326-336, doi:10.3920/BM2014.0081.Slika 8 - zbirka

Development of methods for quality control of milk and probiotic products

We are developing new methods for determination of the quality of dairy and probiotic products based on conventional microbiological and molecular techniques. For conventional plate counting of microorganisms, different selective and non-selective media are used. The selectivity of media is tested by PCR and gel electrophoresis. We are developing methods for specific detection and quantification of bacterial strains (probiotics) in the products, based on the specific targets in their genomes. We have experiences with the use of PCR and real-time PCR to detect the presence or quantify of individual bacterial strains, species, genera, or broader taxonomic groups in various products such as fermented foods, pharmaceutical formulations containing lyophilized or microencapsulated bacteria, and others. We are evaluating different approaches for determination of the viability of probiotics (determination of the number of colony forming units, quantification of all bacteria or viable bacteria by real-time PCR, the discrimination between damaged and undamaged bacteria by differential staining with fluorescent dyes, ...).

Representative publications in the field:

  • MOHAR LORBEG, Petra, GOLOB, Majda, KRAMER, Mateja, TREVEN, Primož, BOGOVIČ MATIJAŠIĆ, Bojana. Evaluation of dietary supplements containing viable bacteria by cultivation/MALDI-TOF mass spectrometry and PCR identification. Frontiers in microbiology, ISSN 1664-302X, 2021, vol. 12, art. 700138, str. 1-14, doi: 10.3389/fmicb.2021.700138.
  • KOLENC, Borut, MOHAR LORBEG, Petra, ČANŽEK MAJHENIČ, Andreja, CIVIDINI, Angela, SIMČIČ, Mojca, TREVEN, Primož. Influence of two feed supplements on technological properties of goatʼs milk. Mljekarstvo : proizvodnja proučavanje i tehnologija mlijeka i mliječnih proizvoda, ISSN 0026-704X, 2020, vol. 70, no. 3, str. 162-170, doi: 10.15567/mljekarstvo.2020.0303. 
  • MOHAR LORBEG, Petra, BOGOVIČ MATIJAŠIĆ, Bojana. Kakovost probiotičnih prehranskih dopolnil na slovenskem trgu v luči zakonodaje o zdravstvenih trditvah na živilih = Quality of probiotic supplements on the Slovenian market in the light of legislation on health claims on foodstuffs. Farmacevtski vestnik : strokovno glasilo slovenske farmacije, ISSN 0014-8229. [Tiskana izd.], 2017, letn. 68, št. 5, str. 332-344, preglednice. [
  • MONNET, Christophe, BOGOVIČ MATIJAŠIĆ, Bojana. Application of PCR-based methods to dairy products and to non-dairy probiotic products. V: HERNÁNDEZ-RODRÍGUEZ, Patricia (ur.), RAMIREZ GOMEZ, Arlen Patricia (ur.). Polymerase chain reaction. [Rijeka: Intech, cop. 2012], str. 11-50. doi:10.5772/36897.
  • BOGOVIČ MATIJAŠIĆ, Bojana, ZORIČ PETERNEL, Metoda, ROGELJ, Irena. Ugotavljanje deklariranih bakterij v probiotičnih prehranskih dopolnilih in zdravilih na slovenskem trgu = Determination of labeled bacteria in probiotic food supplements and medicinal products (OTC) on Slovenian market. Farmacevtski vestnik, 2010, letn. 61, št. 5/6, str. 263-269. UDK 615
  • BOGOVIČ MATIJAŠIĆ, Bojana, OBERMAJER, Tanja, ROGELJ, Irena. Quantification of Lactobacillus gasseri, Enterococcus faecium and Bifidobacterium infantis in a probiotic OTC drug by Real-time PCR. Food control, 2010, issue 4, vol. 24, str. 419-425. doi:10.1016/j.foodcont.2009.07.001.
  • KRAMER, Mateja, OBERMAJER, Tanja, BOGOVIČ MATIJAŠIĆ, Bojana, ROGELJ, Irena, KMETEC, Vojko. Quantification of live and dead probiotic bacteria in lyophilised product by real-time PCR and by flow cytometry. Applied microbiology and biotechnology, 2009, issue 6, vol. 84, str. 1137-1147. doi:10.1007/s00253-009-2068-7.Slika 10

Study of microbiota in different environments

We study the microbiomes or microbiota, with emphasis on lactic acid bacteria and bifidobacteria, in different environments where these bacterial groups are present: animal milk, human milk, fermented foods, human and animal gut, clinical samples - intestinal mucosa, faeces,... The composition of the microbiota or microbiome is studied using conventional and molecular methods, including high-throughput methods of next-generation sequencing…, in collaboration with researchers from other research groups. 

Representative publications in the field:

TREVEN, P., PAVELJŠEK, D., KOSTANJŠEK, R., GOLOB, M., BOGOVIČ MATIJAŠIĆ, B., MOHAR LORBEG, P. In vitro model of human mammary gland microbial colonization (MAGIC) demonstrates distinctive cytokine response to imbalanced human milk microbiota, 2024. Microbiology spectrum. 2024, doi: 10.1128/spectrum.02369-23

TREVEN, Primož, MAHNIČ, Aleksander, RUPNIK, Maja, GOLOB, Majda, PIRŠ, Tina, BOGOVIČ MATIJAŠIĆ, Bojana, MOHAR LORBEG, Petra. Evaluation of human milk microbiota by 16S rRNA gene next-generation sequencing (NGS) and cultivation/MALDI-TOF mass spectrometry identification. Frontiers in microbiology, ISSN 1664-302X, 2019, vol. 10, art. no. 2612, str. 1-12, doi: 10.3389/fmicb.2019.02612. 

TREVEN, Primož, MRAK, Vesna, BOGOVIČ MATIJAŠIĆ, Bojana, HORVAT, Simon, ROGELJ, Irena. Administration of probiotics Lactobacillus rhamnosus GG and Lactobacillus gasseri K7 during pregnancy and lactation changes mouse mesenteric lymph nodes and mammary gland microbiota. Journal of dairy science, 2015, vol. 98, in press. doi:10.3168/jds.2014-8519.

BOGOVIČ MATIJAŠIĆ, Bojana, OBERMAJER, Tanja, LIPOGLAVŠEK, Luka, GRABNAR, Iztok, AVGUŠTIN, Gorazd, ROGELJ, Irena. Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia. European journal of nutrition, 2014, vol. 53, issue 4, str. 1051-1064, doi:10.1007/s00394-013-0607-6.

OBERMAJER, Tanja, GRABNAR, Iztok, BENEDIK, Evgen, TUŠAR, Tina, ROBIČ PIKEL, Tatjana, FIDLER MIS, Nataša, BOGOVIČ MATIJAŠIĆ, Bojana, ROGELJ, Irena. Microbes in infant gut development : placing abundance within environmental, clinical and growth parameters. Scientific reports, ISSN 2045-2322, 11. sep. 2017, vol. 7, art. no. 11230, str. 1-14, doi: 10.1038/s41598-017-10244-x.

VARDJAN, Tinkara, MOHAR LORBEG, Petra, ČANŽEK MAJHENIČ, Andreja. Stability of prevailing lactobacilli and yeasts in kefir grains and kefir beverages during ten weeks of propagation. International journal of dairy technology, ISSN 1364-727X, 2018, vol. 71, no. S1, str. 51-60, doi: 10.111/1471-0307.12463. 

VARDJAN, Tinkara, MOHAR LORBEG, Petra, ROGELJ, Irena, ČANŽEK MAJHENIČ, Andreja. Characterization and stability of lactobacilli and yeast microbiota in kefir grains. Journal of dairy science, 2013, vol. 96, no. 5, str. 2729-2736. doi: 10.3168/jds.2012-5829.

TRMČIĆ, Aljoša, MONNET, C., ROGELJ, Irena, BOGOVIČ MATIJAŠIĆ, Bojana. Expression of nisin genes in cheese : a quantitative real-time polymerase chain reaction approach. Journal of dairy science, 2011, vol. 94, no. 1, str. 77-85. doi:10.3168/jds.2010-3677.

Slika 11

Studies of milk proteins and peptides in milk and dairy products, bacteriocins and other metabolites

We study proteins and peptides in milk and their degradation products (bioactive peptides) or products of bacterial metabolism (bacteriocins...) after fermentation with lactic acid bacteria. We develop chromatographic methods for proteins (milk proteins, whey proteins, bacteriocins...) on preparative and analytical level.

Representative publications in the field:

BOGOVIČ MATIJAŠIĆ, Bojana, OBERČKAL, Jernej, MOHAR LORBEG, Petra, PAVELJŠEK, Diana, SKALE, Nina, KOLENC, Borut, GRUDEN, Špela, POKLAR ULRIH, Nataša, KETE, Marko, ZUPANČIČ JUSTIN, Maja. Characterisation of lactoferrin isolated from acid whey using pilot-scale monolithic ion-exchange Chromatography. Processes, ISSN 2227-9717. [Online ed.], 2020, vol. 8, art. no. 804, str. 1-19, doi: 10.3390/pr8070804.

ZADRAVEC, Petra, MAVRIČ, Anja, BOGOVIČ MATIJAŠIĆ, Bojana, ŠTRUKELJ, Borut, BERLEC, Aleš. Engineering BmpA as a carrier for surface display of IgG-binding domain on Lactococcus lactis. Protein engineering, design & selection, 2014, vol. 27, no. 1, str. 21-27. doi:10.1093/protein/gzt059.

TOMPA, Gorazd, LAINE, Aire, PIHLANTO, Anne, KORHONEN, Hannu, ROGELJ, Irena, MARNILA, Pertti. Chemiluminescence of non-differentiated THP-1 promocytes : developing an assay for screening anti-inflammatory milk proteins and peptides. Luminescence, 2011, vol. 26, no. 4, str. 251-258. doi:10.1002/bio.1220.

TOMPA, Gorazd, ROGELJ, Irena, MARNILA, Pertti, PIHLANTO; Anne. Bioaktivni peptidi v mleku, fermentiranem z Lactobacillus helveticus BGRA43. V: 27. Bitenčevi živilski dnevi 2012 = 27th Food Technology Days 2012 dedicated to prof. F. Bitenc, 26. september 2012, Ljubljana. DEMŠAR, Lea (ur.), ŽLENDER, Božidar (ur.). Nanotehnologije in nanoživila = Nanotechnologies and nanofoods. Ljubljana: Biotehniška fakulteta, Oddelek za živilstvo, 2012, str. 173-180. [COBISS.SI-ID 3169416]