1. Nisin-loaded gelatin microparticles for the enhanced bioactivity of bacterial nanocelluloseMaša Hren, Janja Trček, Aleksandra Šakanović, Hristina Obradović, Mateja Erdani-Kreft, Silvo Hribernik, Selestina Gorgieva, 2025, izvirni znanstveni članek Opis: Bacterial nanocellulose (BnC) is of immense importance in medicine, although its lack of bioactivity present intriguing issue. We propose a method to modify BnC with gelatin and nisin biomolecules, and explore their synergistic effect on the antimicrobial activity. Gelatin microparticles (without/with nisin loading) with a size ~0.5 μm and ~ 1.3 μm were prepared by spray drying and stabilised by dehydrothermal treatment. Modified BnC-based membranes supported the formation of biologically relevant minerals and were non-cytotoxic to human gingival fibroblast cells (HGF). The presence of gelatin microparticles improved the viability of HGF by approximately 20 %, due to the effect of gelatin alone, independent of the addition of nisin. BnC coated with a nisin/gelatin solution reduces the viability of HGF by about 20 %, but this negative effect is not observed by nisin coated gelatin microparticles. The cell viability of BnC membranes was above 90 % in both porcine and human urothelial cells. The antimicrobial activity study confirmed an inhibitory effect of membranes modified with nisin-coated microparticles or a gelatin/nisin solution against Staphylococcus aureus at a non-cytotoxic nisin dose (150 μg/mL). The study demonstrates the structural effects of gelatin and gelatin/nisin mixtures on the bioactivity of BnC and provides a rationale for the modification procedure.
Ključne besede: bacterial nanocellulose, gelatin, nisin, spray-drying, antimicrobial function, bioactivity
Objavljeno v DKUM: 10.03.2025; Ogledov: 0; Prenosov: 6
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2. In silico characterization of sirtuins in acetic acid bacteria reveals a novel phylogenetically distinctive groupIgor Jugović, Janja Trček, 2025, izvirni znanstveni članek Opis: Acetic acid bacteria are single-celled organisms well-known for their ability to convert ethanol into acetic acid. Still, recent research suggests they may harbor another attractive characteristic - the production of proteins with remarkable similarities to sirtuins. Sirtuins have been linked to lifespan extension in various organisms, raising intriguing questions about the potential connection between acetic acid bacteria and the biology of aging. This article delves into the characterization of sirtuin homologs in acetic acid bacteria. Up to three types of sirtuin homologs have been identified in 21% of acetic acid bacteria genomes deposited in NCBI. All three types were present only in the genera Acetobacter and Novacetimonas, which are known to survive in the harshest environmental conditions (high concentrations of acetic acid and ethanol). Interestingly, two types of these sirtuin homologs (SirAAB-L and SirAAB-S) constitute a separate group (SirAAB), distinctive from all other presently known sirtuins. The results obtained in silico thus encourage further studies into the function of these types of sirtuins and their interplay with metabolic pathways in these industrially important bacteria.
Ključne besede: acetic acid bacteria, Acetobacter, Novacetimonas, aging, sirtuins, SirAAB, SirAAB-L, SirAAB-S
Objavljeno v DKUM: 14.02.2025; Ogledov: 0; Prenosov: 5
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3. Customized 16S-23S rDNA ITS amplicon metagenomics for acetic acid bacteria species identification in vinegarsand kombuchasAlja Ribič, Janja Trček, 2024, izvirni znanstveni članek Opis: Acetic acid bacteria (AAB) are involved in food and beverage production bioprocesses, like
those in vinegar and kombucha. They oxidize sugars and alcohols into various metabolites, resulting
in the final products’ pleasant taste and aroma. The 16S rDNA amplicon metagenomics using
Illumina technology is usually used to follow the microbiological development of these processes.
However, the 16S rRNA gene sequences among different species of AAB are very similar, thus not
enabling a reliable identification down to the species level but only to the genus. In this study, we
have constructed primers for amplifying half of the 16S-23S rRNA gene internal transcribed spacer
(ITS) for library construction and further sequencing using Illumina technology. This approach was
successfully used to estimate the relative abundance of AAB species in defined consortia. Further
application of this method for the analysis of different vinegar and kombucha samples proves
it suitable for assessing the relative abundance of AAB species when these bacteria represent a
predominant part of a microbial community.
Ključne besede: ITS metagenomics, microbiota, consortia, Acetobacter, Komagataeibacter, Novacetimonas
Objavljeno v DKUM: 04.02.2025; Ogledov: 0; Prenosov: 7
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4. Low occurrence of Acinetobacter baumannii in gulls and songbirdsAndżelina Łopińska, Piotr Indykiewicz, Evelyn Skiebe, Y Pfeifer, Janja Trček, Leszek Jerzak, Piotr Minias, Jacek Nowakowski, Mateusz Ledwoń, Jacek Betleja, Gottfried Wilharm, 2020, izvirni znanstveni članek Opis: Acinetobacter baumannii is a worldwide occurring nosocomial pathogen, the natural habitats of which remain to be defined. Recently, white stork nestlings have been described as a recurring source of A. baumannii. Here, we challenged the hypothesis of a general preference of A. baumannii for avian hosts. Taking advantage of campaigns to ring free-living birds, we collected cloacal swab samples from 741 black-headed gulls (Chroicocephalus ridibundus) in Poland, tracheal and cloacal swabs from 285 songbirds in Poland as well as tracheal swabs from 25 songbirds in Slovenia and screened those for the growth of A. baumannii on CHROMagar™ Acinetobacter. Of the 1,051 samples collected only two yielded A. baumannii isolates. Each carried one variant of the bla OXA-51-like gene, i.e. OXA-71 and OXA-208, which have been described previously in clinical isolates of A. baumannii. In conclusion, our data do not support a general preference of A. baumannii for avian hosts.
Ključne besede: Acinetobacter baumannii, seagulls, songbirds, Erithacus rubecula, Chroicocephalus ridibundus, free-living birds, nosocomial pathogen
Objavljeno v DKUM: 28.01.2025; Ogledov: 0; Prenosov: 5
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5. A cyclic di-GMP network is present in gram-positive Streptococcus and gram-negative Proteus speciesYing Liu, Changhan Lee, Fengyang Li, Janja Trček, Heike Bähre, Rey-Ting Guo, Chun-Chi Chen, Alexey Chernobrovkin, Roman Zubarev, Ute Römling, 2020, izvirni znanstveni članek Opis: The ubiquitous cyclic di-GMP (c-di-GMP) network is highly redundant with numerous GGDEF domain proteins as diguanylate cyclases and EAL domain proteins as c-di-GMP specific phosphodiesterases comprising those domains as two of the most abundant bacterial domain superfamilies. One hallmark of the c-di-GMP network is its exalted plasticity as c-di-GMP turnover proteins can rapidly vanish from species within a genus and possess an above average transmissibility. To address the evolutionary forces of c-di-GMP turnover protein maintenance, conservation, and diversity, we investigated a Gram-positive and a Gram-negative species, which preserved only one single clearly identifiable GGDEF domain protein. Species of the family Morganellaceae of the order Enterobacterales exceptionally show disappearance of the c-di-GMP signaling network, but Proteus spp. still retained one diguanylate cyclase. As another example, in species of the bovis, pyogenes, and salivarius subgroups as well as Streptococcus suis and Streptococcus henryi of the genus Streptococcus, one candidate diguanylate cyclase was frequently identified. We demonstrate that both proteins encompass PAS (Per-ARNT-Sim)-GGDEF domains, possess diguanylate cyclase catalytic activity, and are suggested to signal via a PilZ receptor domain at the C-terminus of type 2 glycosyltransferase constituting BcsA cellulose synthases and a cellulose synthase-like protein CelA, respectively. Preservation of the ancient link between production of cellulose(-like) exopolysaccharides and c-di-GMP signaling indicates that this functionality is even of high ecological importance upon maintenance of the last remnants of a c-di-GMP signaling network in some of today’s free-living bacteria.
Ključne besede: cellulose biosynthesis, cyclic di-GMP signaling, EAL domain, GGDEF domain, Proteus mirabilis, Streptococcus gallolyticus subsp. gallolyticus
Objavljeno v DKUM: 28.01.2025; Ogledov: 0; Prenosov: 13
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6. Why? - Successful Pseudomonas aeruginosa clones with a focus on clone CChanghan Lee, Jens Klockgether, Sebastian Fischer, Janja Trček, Burkhard Tümmler, Ute Römling, 2020, pregledni znanstveni članek Opis: The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.
Ključne besede: disaggregase, FtsH, genomic island, protein homeostasis, pulsed field gel electrophoresis, whole genome sequencing
Objavljeno v DKUM: 28.01.2025; Ogledov: 0; Prenosov: 5
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7. Razvoj bioaktivnih membran na osnovi bakterijske nanoceluloze za uporabo pri opeklinah : doktorska disertacijaUrška Jančič, 2024, doktorska disertacija Opis: V doktorski disertaciji smo se osredotočili na razvoj novih bioaktivnih membran na osnovi bakterijske nanoceluloze (BnC), in situ, modificirane s karboksimetil celulozo (CMC), in ex situ, modificirane s proteolitskim encimom bromelainom (Br) in/ali protimikrobnim peptidom nizinom (N) za nekirurško odstranitev mrtvega kožnega tkiva (mrtvine) pri opeklinah ter hitrejše, učinkovitejše in netoksično celjenje opeklin. Membrane BnC smo producirali s pred kratkim opisano novo vrsto ocetnokislinske bakterije Komagataeibacter melomenusus AV436T, saj je bila ta izmed testiranih ocetnokislinskih bakterij najproduktivnejša. Za učinkovito odstranitev ostankov bakterij in komponent gojišča smo optimizirali alkalno obdelavo membran (1 h 0,5 M NaOH), s CMC-Br konjugati pa smo določili optimalno masno razmerje zamreževalca EDC/NHS (2/1) za najvišjo ohranitev specifične proteolitske aktivnosti bromelaina. In situ modifikacijo membran BnC smo izvedli z dodajanjem CMC v gojišče RAE za namnoževanje bakterij, kar je vodilo v nastanek membran BnC-CMC s karboksilnimi skupinami, gostejšo razporeditvijo fibrilov in izboljšanim rehidracijskim razmerjem v primerjavi z membrano BnC. Bromelain smo ex situ imobilizirali na (modificirane) membrane BnC z adsorpcijo in kovalentno vezavo z uporabo zamreževalca EDC/NHS, pri čemer smo za identifikacijo optimalne kombinacije procesnih parametrov (koncentracije CMC, bromelaina in zamreževalca EDC/NHS) z maksimalno specifično proteolitsko aktivnostjo bromelaina uporabili metodologijo odzivnih površin (RSM). S koimobilizacijo bromelaina in nizina smo proučevali sinergistični učinek obeh komponent s ciljem razširitve protimikrobnega delovanja in pridobitve proteolitskega delovanja. Optimalne bioaktivne membrane in njihove reference smo okarakterizirali s fizikalno-kemijskimi analiznimi metodami, kar je vključevalo ATR-FTIR in mikroanalizo FTIR, SEM, EDS, XPS, XRD, stične kote, kapaciteto zadrževanja vode, rehidracijsko razmerje, vsebnost vode, zeta potencial, TGA, mehanske lastnosti in specifično proteolitsko aktivnost. Biološko aktivnost membran smo analizirali s testiranjem protimikrobne aktivnosti in z različnimi in vitro (celična viabilnost in morfologija celic NHDF in HaCaT, celjenje ran) in ex vivo metodami (testiranje bioadhezije na modelu piščančje kože, testiranja toksičnosti na ekspantatih človeške kože – histološke študije, aktivnost LDH, sproščanje IL-8). Optimalni imobilizacijski pogoji (9 mg/mL CMC in 10 mg/mL bromelaina) so omogočili hiperaktivacijo encima s specifično proteolitsko aktivnostjo 2,3 U/mg in 39,1 % učinkovitostjo imobilizacije. Imobilizacija bromelaina in/ali nizina na membrano BnC-CMC je povečala povprečen premer nanovlaken, rehidracijsko razmerje in vsebnost vode ter izboljšala protimikrobno delovanje in adhezijske lastnosti. Membrani BnC-CMC in BnC-CMC-N sta bili in vitro citokompatibilni za celice NHDF in HaCaT ter sta povzročili hitrejšo proliferacijo celic HaCaT in/ali migracijo celic NHDF kot komercialni produkt Vivamel. Ex vivo analiza na ekspantatih človeške kože je za membrano BnC-CMC pokazala citokompatibilnost brez akutne toksičnosti in iritacije kože, membrana BnC-CMC-N je bila prav tako citokompatibilna brez akutne toksičnosti, vendar z zmernim dražilnim učinkom. Membrana BnC-CMC-Br je na ekspantatih človeške kože izkazovala aktivnost, ki se je odražala v razgradnji medceličnih stikov v epidermisu, vendar ni povzročila inducirajoče akutne toksičnosti in iritacije kože. Pripravljene membrane BnC-CMC, BnC-CMC-Br in BnC-CMC-N izkazujejo potencial za uporabo v različnih fazah zdravljenja opeklin.
Ključne besede: bakterijska nanoceluloza, bioaktivnost, bromelain, nizin, protimikrobna aktivnost, proteolitska aktivnost, membrana, opekline
Objavljeno v DKUM: 14.01.2025; Ogledov: 0; Prenosov: 38
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8. Analiza uporabnosti medgenske regije 16S-23S rDNA za neposredno identifikacijo vrst ocetnokislinskih bakterij iz mikrobiot kisa in kombuče s tehnologijo sekvenciranja Illumina : magistrsko deloAlja Ribič, 2024, magistrsko delo Opis: V magistrskem delu smo razvili metodološki pristop za neposredno identifikacijo vrst ocetnokislinskih bakterij iz kisa in kombuče na osnovi sekvenciranja odseka medgenske regije 16S-23S rDNA s tehnologijo Illumina. Do sedaj uporabljena tarčna molekula, to je gen za 16S rRNA, je namreč v primeru ocetnokislinskih bakterij evolucijsko zelo ohranjena, zato zagotavlja zanesljivo identifikacijo le do nivoja rodu. S tem namenom smo konstruirali dva para začetnih oligonukleotidov za pomnoževanje polovice medgenske regije 16S-23S rDNA, in ju uporabili za konstrukcijo knjižnic in sekvenciranje s tehnologijo Illumina. Z obema paroma začetnih oligonukleotidov smo najprej analizirali relativno abundanco vrst ocetnokislinskih bakterij v laboratorijsko pripravljenih bakterijskih združbah. Par začetnih oligonukleotidov, ki je omogočil boljšo oceno vrstne sestave bakterijske združbe, smo nadalje uporabili za analizo mikrobiot jabolčnega, bezgovega in vinskega kisa ter napitka kombuča. Preiskani vzorci so bili proizvedeni s tradicionalnim statičnim in submerznim postopkom. Postavljena metoda je uporabna za hitro identifikacijo vrst ocetnokislinskih bakterij iz substratov, kjer te bakterije predstavljajo prevladujoči del bakterijske združbe.
Ključne besede: ocetnokislinske bakterije, medgenska regija 16S-23S rDNA, Illumina, kis, kombuča
Objavljeno v DKUM: 08.10.2024; Ogledov: 0; Prenosov: 14
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9. Opis fenotipskih lastnosti in primerjalna analiza genomov bakterije Gluconacetobacter entanii : magistrsko deloKarin Jelenko, 2024, magistrsko delo Opis: Gluconacetobacter entanii je vrsta iz skupine ocetnokislinskih bakterij in taksonomsko spada v družino Acetobacteraceae. Opisana je bila leta 2000 po izolaciji, fenotipski karakterizaciji in analizi osnovnih DNA-taksonomskih markerjev sevov iz industrijskih bioreaktorjev za proizvodnjo alkoholnega kisa v južni Nemčiji. Vsi opisani sevi so tolerirali visoke odstotke ocetne kisline (do 14,6 %). Od vseh sevov je bil le tipski sev LTH 4560T shranjen v mednarodne zbirke mikroorganizmov, a se je kasneje pokazalo, da ni preživel dolgotrajnega shranjevanja v liofilizirani obliki. Taksonomija ocetnokislinskih bakterij je bila v zadnjih letih deležna več sprememb. Med drugim je bila skupina filogenetsko bližnjih sevov znotraj rodu Gluconacetobacter leta 2013 reklasificirana v rod Komagataeibacter, znotraj tega rodu pa je bil leta 2022 osnovan nov rod Novacetimonas. Vrsta G. entanii bi tej reklasifikaciji morala slediti, a zaradi pravil bakterijske taksonomije, ki dovoljuje spremembe samo za kultivabilne vrste, njeno ime ostaja nespremenjeno. V magistrskem delu smo preučili več sevov vrste G. entanii iz zbirke mikroorganizmov Laboratorija za mikrobiologijo, Oddelka za biologijo, na Fakulteti za naravo-slovje in matematiko, Univerze v Mariboru. Sevi so bili pridobljeni v predhodnih raziskavah iz bioreaktorjev za industrijsko proizvodnjo jabolčnega kisa iz različnih kisarn v Sloveniji. Sevom smo sistematično pregledali fenotipske lastnosti in s primerjalno genomiko preiskali podobnost njihovih genomov z genomom tipskega seva G. entanii. Na podlagi funkcijske anotacije genomov smo identificirani gena gmhB in psp, specifična za vrsto G. entanii. S tedenskim precepljanjem seva AV429 na gojišču RAE v prisotnosti 1 vol % ocetne kisline in 1 vol % etanola v obdobju 43 mesecev smo preiskali njegovo genomsko stabilnost. Rezultati so odkrili le točkovne mutacije, ne pa insercij in delecij. Opravljena karakterizacija novih kultivabilnih sevov bakterije G. entanii je odkrila slabo ujemanje fenotipskih lastnostih s tipskim sevom G. entanii, zaradi česar ti sevi ne morejo nadomestiti obstoječega tipskega seva kot neotipska vrsta. V želji poenotenja nadaljnjih raziskav na področju taksonomije rodu Novacetimonas predlagamo, da se sev G. entanii AV429 uporablja kot referenčni sev za bakterijsko vrsto G. entanii.
Ključne besede: Gluconacetobacter entanii, Novacetimonas, ocetnokislinske bakterije, taksonomija
Objavljeno v DKUM: 23.09.2024; Ogledov: 0; Prenosov: 9
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10. Production efficiency and properties of bacterial cellulose membranes in a novel grape pomace hydrolysate by Komagataeibacter melomenusus ▫$AV436^T$▫ and Komagataeibacter xylinus LMG 1518Selestina Gorgieva, Urška Jančič, Eva Cepec, Janja Trček, 2023, izvirni znanstveni članek Opis: The microbial production of cellulose using different bacterial species has been extensively examined for various
industrial applications. However, the cost-effectiveness of all these biotechnological processes is strongly related to the culture medium for bacterial cellulose (BC) production. Herein, we examined a simple and modified
procedure for preparing grape pomace (GP) hydrolysate, without enzymatic treatment, as a sole growth medium
for BC production by acetic acid bacteria (AAB). The central composite design (CCD) was used to optimise the GP
hydrolysate preparation toward the highest reducing sugar contents (10.4 g/L) and minimal phenolic contents
(4.8 g/L). The experimental screening of 4 differently prepared hydrolysates and 20 AAB strains identified the
recently described species Komagataeibacter melomenusus AV436T as the most efficient BC producer (up to 1.24 g/
L dry BC membrane), followed by Komagataeibacter xylinus LMG 1518 (up to 0.98 g/L dry BC membrane). The
membranes were synthesized in only 4 days of bacteria culturing, 1 st day with shaking, followed by 3 days of
static incubation. The produced BC membranes in GP-hydrolysates showed, in comparison to the membranes
made in a complex RAE medium 34 % reduction of crystallinity index with the presence of diverse cellulose
allomorphs, presence of GP-related components within the BC network responsible for the increase of hydrophobicity, the reduction of thermal stability and 48.75 %, 13.6 % and 43 % lower tensile strength, tensile
modulus, and elongation, respectively. Here presented study is the first report on utilising a GP-hydrolysate
without enzymatic treatment as a sole culture medium for efficient BC production by AAB, with recently
described species Komagataeibacter melomenusus AV436T as the most efficient producer in this type of food-waste
material. The scale-up protocol of the scheme presented here will be needed for the cost-optimisation of BC
production at the industrial levels.
Ključne besede: grape pomace hydrolysate, bacterial cellulose, acetic acid bacteria, Komagataeibacter melomenusus
Objavljeno v DKUM: 26.07.2024; Ogledov: 98; Prenosov: 13
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