1. Novel Siphoviridae Bacteriophages infecting Bacteroides uniformis contain diversity generating retroelementStina Hedžet, Maja Rupnik, Tomaž Accetto, 2021, original scientific article Abstract: Intestinal phages are abundant and important components of gut microbiota, yet the isolated and characterized representatives that infect abundant gut bacteria are sparse. Here we describe the isolation of human intestinal phages infecting Bacteroides uniformis. Bacteroides is one of the most common bacterial groups in the global human gut microbiota; however, to date not many Bacteroides specific phages are known. Phages isolated in this study belong to a novel viral genus, Bacuni, within the Siphoviridae family. Their genomes encode diversity-generating retroelements (DGR), which were shown in other bacteriophages to promote phage adaptation to rapidly changing environmental conditions and to broaden their host range. Three isolated phages showed 99.83% genome identity but one of them infected a distinct B. uniformis strain. The tropism of Bacuni phages appeared to be dependent on the interplay of DGR mediated sequence variations of gene encoding putative phage fimbrial tip proteins and mutations in host genes coding for outer-membrane proteins. We found prophages with up to 85% amino acid similarity over two-thirds of the Bacuni phage genome in the B. acidifaciens and Prevotella sp. genomes. Despite the abundance of Bacteroides within the human microbiome, we found Bacuni phages only in a limited subset of published gut metagenomes.
Keywords: gut, Bacteroides, virome, prophage, diversity-generating retroelement, uniformis, Siphoviridae
Published in DKUM: 19.08.2024; Views: 64; Downloads: 5
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2. Genomic insights into antibiotic resistance and mobilome of lactic acid bacteria and bifidobacteriaVita Rozman, Petra Mohar Lorbeg, Primož Treven, Tomaž Accetto, Sandra Janežič, Maja Rupnik, Bojana Bogovič Matijašić, 2023, original scientific article Abstract: Lactic acid bacteria (LAB) and Bifidobacterium sp. (bifidobacteria) can carry antimicrobial resistance genes (ARGs), yet data on resistance mechanisms in these bacteria are limited. The aim of our study was to identify the underlying genetic mechanisms of phenotypic resistance in 103 LAB and bifidobacteria using whole-genome sequencing. Sequencing data not only confirmed the presence of 36 acquired ARGs in genomes of 18 strains, but also revealed wide dissemination of intrinsic ARGs. The presence of acquired ARGs on known and novel mobile genetic elements raises the possibility of their horizontal spread. In addition, our data suggest that mutations may be a common mechanism of resistance. Several novel candidate resistance mechanisms were uncovered, providing a basis for further in vitro studies. Overall, 1,314 minimum inhibitory concentrations matched with genotypes in 92.4% of the cases; however, prediction of phenotype based on genotypic data was only partially efficient, especially with respect to aminoglycosides and chloramphenicol. Our study sheds light on resistance mechanisms and their transferability potential in LAB and bifidobacteria, which will be useful for risk assessment analysis.
Published in DKUM: 17.07.2024; Views: 112; Downloads: 5
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3. Broad host range may be a key to long-term persistence of bacteriophages infecting intestinal Bacteroidaceae speciesStina Hedžet, Maja Rupnik, Tomaž Accetto, 2022, original scientific article Abstract: The longitudinal studies have found that the human gut microbiota is stable over time with some major bacterial lineages or even strains persisting for years. This was recently extended to gut bacteriophages using the metagenomic data. Here, we focused on cultivation of the major Bacteroidetes of human gut, the Bacteroides and Phocaeicola strains, and their bacteriophages from two healthy donors. The persistence of Bacteroides and Phocaeicola species and strains was confirmed. We isolated 28 genetically different phages grouped into seven distinct clusters, two of these were new. Moreover, the bacteriophages from several groups, although being genetically quite homogeneous, had the ability to infect the strains belonging to different species isolated from several sampling time-points and different donors. We propose that the ability to infect several host species, which differ in their nutritional niches, may promote long-term persistence of dominant gut bacteriophage groups.
Published in DKUM: 17.06.2024; Views: 128; Downloads: 8
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4. Description of Komagataeibacter melaceti sp. nov. and Komagataeibacter melomenusus sp. nov. isolated from apple cider vinegarLeon Marič, Ilse Cleenwerck, Tomaž Accetto, Peter Vandamme, Janja Trček, 2020, original scientific article Abstract: Two novel strains AV382 and AV436 were isolated from a submerged industrial bioreactor for production of apple cider vinegar in Kopivnik (Slovenia). Both strains showed very high (≥98.2%) 16S rRNA gene sequence similarities with Komagataeibacter species, but lower 16S–23S rRNA gene internal transcribed spacer (ITS). The highest similarity of the 16S–23S rRNA gene ITS of AV382 was to Komagataeibacter kakiaceti LMG 26206$^T$ (91.6%), of AV436 to Komagataeibacter xylinus LMG 1515$^T$ (93.9%). The analysis of genome sequences confirmed that AV382 is the most closely related to K. kakiaceti (ANIb 88.2%) and AV436 to K. xylinus (ANIb 91.6%). Genome to genome distance calculations exhibit for both strains ≤47.3% similarity to all type strains of the genus Komagataeibacter. The strain AV382 can be differentiated from its closest relatives K. kakiaceti and Komagataeibacter saccharivorans by its ability to form 2-keto and 5-keto-D-gluconic acids from glucose, incapability to grow in the presence of 30% glucose, formation of C$_{19:0}$ cyclo ω8c fatty acid and tolerance of up to 5% acetic acid in the presence of ethanol. The strain AV436 can be differentiated from its closest relatives K. xylinus, Komagataeibacter sucrofermentans, and Komagataeibacter nataicola by its ability to form 5-keto-D-gluconic acid, growth on 1-propanol, efficient synthesis of cellulose, and tolerance to up to 5% acetic acid in the presence ethanol. The major fatty acid of both strains is C$_{18:1}$ ω7c. Based on a combination of phenotypic, chemotaxonomic and phylogenetic features, the strains AV382$^T$ and AV436$^T$ represent novel species of the genus Komagataeibacter, for which the names Komagataeibacter melaceti sp. nov. and Komagataeibacter melomenusus are proposed, respectively. The type strain of Komagataeibacter melaceti is AV382$^T$ (= ZIM B1054$^T$ = LMG 31303$^T$ = CCM 8958$^T$) and of Komagataeibacter melomenusus AV436$^T$ (= ZIM B1056$^T$ = LMG 31304$^T$ = CCM 8959$^T$).
Keywords: Acetic acid bacteria, Acetobacteraceae, Komagataeibacter, Komagataeibacter melaceti, Komagataeibacter melomenusus, vinegar
Published in DKUM: 02.09.2022; Views: 498; Downloads: 16
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5. Acetan and acetan-like polysaccharides: genetics, biosynthesis, structure, and viscoelasticityJanja Trček, Iztok Dogša, Tomaž Accetto, David Stopar, 2021, review article Abstract: Bacteria produce a variety of multifunctional polysaccharides, including structural, intracellular, and extracellular polysaccharides. They are attractive for the industrial sector due to their natural origin, sustainability, biodegradability, low toxicity, stability, unique viscoelastic properties, stable cost, and supply. When incorporated into different matrices, they may control emulsification, stabilization, crystallization, water release, and encapsulation. Acetan is an important extracellular water-soluble polysaccharide produced mainly by bacterial species of the genera Komagataeibacter and Acetobacter. Since its original description in Komagataeibacter xylinus, acetan-like polysaccharides have also been described in other species of acetic acid bacteria. Our knowledge on chemical composition of different acetan-like polysaccharides, their viscoelasticity, and the genetic basis for their production has expanded during the last years. Here, we review data on acetan biosynthesis, its molecular structure, genetic organization, and mechanical properties. In addition, we have performed an extended bioinformatic analysis on acetan-like polysaccharide genetic clusters in the genomes of Komagataeibacter and Acetobacter species. The analysis revealed for the first time a second acetan-like polysaccharide genetic cluster, that is widespread in both genera. All species of the Komagataeibacter possess at least one acetan genetic cluster, while it is present in only one third of the Acetobacter species surveyed.
Keywords: extracellular polysaccharide, acetan, acetan genetic cluster, acetan synthesis, acetan viscoelasticity, applications of acetan, Komagataeibacter, Acetobacter
Published in DKUM: 02.09.2022; Views: 605; Downloads: 11
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