Tomaž Accetto

The clade Gluconacetobacter comprises eleven species originating from various sources such as rhizosphere soil, pink sugarcane mealybug, and vinegar. During sampling of organic vinegars, we isolated strain Hr-1-5, which exhibits high 16S rRNA gene sequence identities (≤98.6%) and low 16S-23S rRNA gene internal transcribed spacer (ITS) sequence identities (≤92.1%) with Gluconacetobacter species. Further genome analysis confirmed that strain Hr-1-5 is a distinct species, supported by an average nucleotide identity (ANIb) of ≤90.6% and an in silico DNA–DNA hybridization (dDDH) value of ≤46% compared with other recognized Gluconacetobacter species. Strain Hr-1-5 darkens the growth medium to a deep brown after 4–5 days of submerged cultivation and similarly colors agar medium after 5–6 days. In silico genome analysis suggests that the strain synthesizes pyomelanin. Phenotypically, it is distinguished from its closest Gluconacetobacter relatives by its ability to produce 5-keto-D-gluconic acid, but not 2-keto-D-gluconic acid, and by its capacity to grow on D-ribose, among other traits. These findings support the classification of strain Hr-1-5 as a novel species, for which we propose the name Gluconacetobacter brunescens sp. nov. Hr-1-5^T (=ZIM B1168^T = LMG 33629^T). Strain Hr-1-5 is of biotechnological interest for its pigment production and enables the in situ production of colored cellulose in a co-culture with a cellulose-producing acetic acid bacterium.

The genera Komagataeibacter and Novacetimonas comprise industrially important species that produce various foods, nanocellulose, acetan-like polysaccharides, enantioselective sugars, and other valuable products. Here, we describe two novel strains, Hr1 and Jurk4, isolated from pear and apple-grape organic vinegars that showed very high (≥99.39%) 16S rRNA gene sequence identities to species of the Komagataeibacter and Novacetimonas genera, respectively. However, analysis of the 16S-23S rRNA gene internal transcribed spacer (ITS) sequences revealed only 92.6% sequence identity between the Hr1 strain and its closest relative, Komagataeibacter sucrofermentans LMG 18788^T, and 93.8% sequence identity between the Jurk4 strain and its closest relative, Novacetimonas cocois JCM 31140^T. Further whole-genome analysis showed for both strains an average nucleotide identity (ANI) below 94% and an in silico DNA–DNA hybridization (dDDH) value of less than 70% to their closest species, supporting their distinction as novel species. The strain Hr1 can be phenotypically differentiated from its closest Komagataeibacter species based on its ability to utilize (NH₄)₂SO₄ as the sole nitrogen source in Asai medium with D-glucose and its inability to grow with 1-propanol as a sole carbon source. The strain Jurk4 can be differentiated from other Novacetimonas type strains based on its ability to produce 5-keto-D-gluconic acid, its growth in a medium with glycerol as the sole carbon source, and its inability to grow in an Asai medium with D-glucose. Both strains produce cellulose and possess clusters for acetane-like polysaccharide production, although of different types, which makes them industrially relevant. Based on these findings, we propose Komagataeibacter piraceti sp. nov. Hr1^T (=ZIM B1167^T = LMG 33628^T) and Novacetimonas labruscae sp. nov. Jurk4^T (=ZIM B1166^T = LMG 33630^T) as two novel members of the acetic acid bacteria group.

Background: Phages are critical components of the gut microbiome, influencing bacterial composition and function as predators, parasites, and modulators of bacterial phenotypes. Prophages, integrated forms of these phages, are prevalent in many bacterial genomes and play a role in bacterial adaptation and evolution. However, the diversity and stability of prophages within gut commensals, particularly in the genera Bacteroides and Phocaeicola , remain underexplored. This study aims to screen and characterize prophages in these genera, providing insights into their diversity, host range, and temporal dynamics in the human gut. Results: Using a combination of three bioinformatic tools—Cenote-Taker 3, Vibrant, and PHASTER—we conducted a comprehensive analysis of prophages in Bacteroides and Phocaeicola . Cenote-Taker 3 identified the most diverse set of prophages, with significant overlaps observed between the tools. After clustering high-quality prophages, we identified 22 unique viral operational taxonomic units (vOTUs). Notably, comparisons between prophages identified in isolated bacterial genomes, metaviromes, and large public gut virome databases revealed a broader host range than initially observed in single isolates. Certain prophages were consistent across time points and individuals, suggesting temporal stability. All identified prophages belonged to the Caudoviricetes class and contained genes related to antibiotic resistance, toxin production, and metabolic processes. Conclusions: The combined use of multiple prophage detection tools allowed for a more comprehensive assessment of prophage diversity in Bacteroides and Phocaeicola . The identified prophages were not only prevalent but also exhibited broad host ranges and temporal stability. The presence of antibiotic resistance and toxin genes suggests that these prophages may significantly influence bacterial community structure and function in the gut, with potential implications for human health. These findings highlight the importance of using diverse detection tools to accurately assess prophage diversity and dynamics.

Bacteria of the genera Xylanibacter and Segatella are among the most dominant groups in the rumen microbiota. They are characterized by the ability to utilize different hemicelluloses and pectin of plant cell-wall as well as plant energy storage polysaccharides. The degradation is possible with the use of cell envelope bound multiprotein apparatuses coded in polysaccharide utilization loci (PULs), which have been shown to be substrate specific. The knowledge of PUL presence in rumen Xylanibacter and Segatella based on bioinformatic analyses is already established and transcriptomic and genetic approaches confirmed predicted PULs for a limited number of substrates. In this study, we transcriptomically identified additional different PULs in Xylanibacter ruminicola KHP1 and Segatella bryantii TF1-3. We also identified substrate preferences and found that specific growth rate and extent of growth impacted the choice of substrates preferentially used for degradation. These preferred substrates were used by both strains simultaneously as judged by their PUL upregulation. Lastly, β-glucan and xyloglucan were used by these strains in the absence of bioinformatically and transcriptomically identifiable PUL systems.

The huge amounts of keratin-rich waste generated daily by various industries, slaughterhouses, and processing plants need to be properly managed. Most keratin degradation-related research focuses on keratin from bird feathers, but a vast minority focuses on keratin from sheep wool, which also presents a serious environmental problem. In this article, we describe the isolation, identification, and characterization of new keratinolytic microorganisms capable of sheep wool degradation from sheep wool and soil enriched with wool keratin. We isolated four bacterial species from the genus Bacillus (B. subtilis, B. altitudinis, B. mycoides, and B. wiedmannii), one streptomycete species Streptomyces coelicoflavus identified by whole genome sequencing, and a fungal species Aphanoascus reticulisporus. In some of the isolated microorganisms, we detected keratinolytic activity for the first time, and for most of them, the ability to degrade sheep wool has not been previously demonstrated. The keratinases of the new isolates are active in a wide range of temperatures (25–85 °C) and pH (6.0–10.0), so all isolates show great potential for further biotechnological use in industry and in various environmental and agricultural applications to reduce and recycle keratin-rich wastes such as sheep wool and waste woollen textiles.

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.

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 Bacteroidesuniformis. 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.