Graphical abstract

The viromes of the mammalian lower gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing two groups of stabled horses, and a further group of feral horses that were isolated on an island. Our results indicate that the dsDNA viromes of the horse feces feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes, such as CrAssphage-related viruses found in humans, were identified. Additionally, many bacteriophage genus-level clusters were found to be present in all three geographically isolated populations. The diversity of the horse intestinal bacteriophages is severely undersampled, and so consequently only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways. Therefore, the diversity and structure of the intestinal virome in different animal species needs to be experimentally studied.Short abstract (needed in some journals as eLife)The viromes of the mammalian gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing stabled horses, and feral horses that were isolated on an island. The viromes equine fecal viromes feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes were identified. Additionally, many bacteriophage genus-level clusters were found to be present in geographically isolated populations. Only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways.Importance. (needed for mBio)The study presents the first in depth analysis of the composition and variability of the gut dsDNA bacteriophage community in the mammalian species, other than humans. The study demonstrates that the bacteriophage ecology in the gut is substantially different in different animal species. The results also indicate that the genetic diversity of the equine intestinal bacteriophages is immense and almost totally unexplored by the moment.

Numerous studies confirm the high degree of involvement of the intestinal microbiota in most processes in the human body. There is evidence for the effect of intestinal microbiota on the success of chemo and immunotherapy of oncological diseases. It is assumed that the intestinal microbiota exhibits an indirect effect on the antitumor therapy through such mechanisms as general immunomodulation, an increase in cells that specifically respond to antigens of both microbial and tumor origin, metabolism, degradation (utilization) of drug compounds. The intestinal microbiota is currently considered as an additional, but important target for studying the effective use of antitumor therapy and reducing its toxicity, as well as a predictor of the success of immunotherapy. In this review, we highlight the results of studies published to date that confirm the relationship between gut microbiome and antitumor efficacy of immune checkpoint inhibitors. Despite the promising and theoretically substantiated conclusions, there are still some discrepancies among the existing data that will have to be addressed in order to facilitate the further development of this direction.

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Natural fungal communities are characterized by a high diversity of unique biochemical pathways, including the biosynthesis of antimicrobial substances, organic acids, and even toxins (Branco, 2019). At the same time, individual fungi from one community might significantly differ from each other in terms of their functional capabilities (Wisecaver et al., 2014). This is due to differences in gene content.Functional capabilities are of great interest to modern industrial biotechnology (Chergui et al., 2021;Habibi et al., 2021;Li et al., 2020). Also, information about gene content can be useful to solve ecological problems such as the bioconversion of solid waste (Chilakamarry et al., 2022) or caffeine utilization (Zhou et al., 2018).To get a more complete picture of the functional capabilities of the fungi under study, functional annotation of whole genome assemblies is used.

Fungi are inseparable companions of human life, they can be found in both the environment and human organs including skin, respiratory tract and gut. Studies of fungal communities are of great interest to modern biology, partially due to their specific way of life and the presence of unique biochemical pathways they have. Fungi have been shown to be both producers of useful compounds, such as antibiotics and organic acids, and pathogens of various diseases. When considering the selected fungal community, in a number of cases it is rather difficult to evaluate its functional capabilities, which is partially caused by some technical difficulties in the analysis and annotation of whole eukaryotic genomes. In practice, the taxonomic composition of fungal communities is determined using short marker sequences. The most popular fungal taxonomy markers are ITS (internal transcribed spacer) sequences. Here, we present FunFun, the instrument that allows to evaluate the functional content of an individual fungus or mycobiome based on ITS sequencing data.

Motivation: Nonribosomal peptides (NRPs) are a class of secondary metabolites synthesized by multimodular enzymes named nonribosomal peptide synthetases (NRPSs) and mainly produced by bacteria and fungi. It has been shown that NRPs have a huge structural and functional diversity including antimicrobial activity, therefore, they are of increasing interest for modern biotechnology. Methods such as NMR and LC-MS/MS allow to determine NRP structure precisely, but it is often not a trivial task to find natural producers of them. Today, searches are usually performed manually, mostly with tools such as antiSMASH or Prism. However, there are cases when potential producers should be found among hundreds of strains, for instance, when analyzing metagenomes data. Thus, the development of automated approaches is a high-priority task for further NRP research. Results: We developed BioCAT, a two-side approach to find biosynthesys gene clusters (BGCs) which may produce a given NRP when the structure of interesting NRP has already been found. Formally, the BioCAT unites the antiSMASH software and the rBAN retrosynthesis tool but some improvements were added to both gene cluster and NRP chemical structure analyses. The main feature of the method is PSSM usage to store specificities of NRPS modules, which has increased the alignment quality in comparison with more strict approaches developed earlier. An ensemble model was implemented to calculate the final alignment score. We tested the method on a manually curated NRP producers database and compared it with a competing tool called GARLIC. Finally, we showed the method applicability on a several external examples.