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Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial and archaeal members of complex biogas-producing microbial communities. In the present study, the microbiomes of three industrial-scale biogas digesters, each fed with different substrates, were analysed using a machine-learning guided genome-centric metagenomics framework complemented with metatranscriptome data. This data permitted us to elucidate the relationship between abundant core methanogenic communities and their syntrophic bacterial partners. In total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, the assembled 16 S rRNA gene profiles of these nrMAGs showed that the phylum Firmicutespossessed the highest copy number, while the representatives of the archaeal domain had the lowest. Further investigation of the three anaerobic microbial communities showed characteristic alterations over time but remained specific to each industrial-scale biogas plant. The relative abundance of various microorganisms as revealed by metagenome data was independent from corresponding metatranscriptome activity data. Archaeashowed considerably higher activity than was expected from their abundance. We detected 51 nrMAGs that were present in all three biogas plant microbiomes with different abundances. The core microbiome correlated with the main chemical fermentation parameters, and no individual parameter emerged as a predominant shaper of community composition. Various interspecies H2/electron transfer mechanisms were assigned to hydrogenotrophic methanogens in the biogas plants that ran on agricultural biomass and wastewater. Analysis of metatranscriptome data revealed that methanogenesis pathways were the most active of all main metabolic pathways.

The aim of this study was to examine clinically healthy cow’s udder milk microbiota and presence of cytokines in different seasons. Milk samples taken from the cows were checked for the presence of Gram-positive and Gram-negative bacteria, and the somatic cell count was detected. Immunohistochemistry methods were performed to detect interleukin (IL) -2, IL-4, IL-8, IL-10, IL-12, IL-17a, ß-defensin-3, transforming growth factor (TGF)-a1, interferon-c and nuclear factor (NF)-zB presence in the milk. S. agalactiae, S. uberis, S. aureus, E. coli,and Klebsiella, Enterobacter, Citrobacterspp. were found in healthy cow’s milk. In the first round, the highest prevalence was observed for S. aureus. In the second round, the highest mean levels were observed for S. uberis, then followed S. aureus. IL-4, IL-17a and TGF-a1 demonstrated the highest expression in the milk samples. NF-zB had the lowest expression among all factors. The presence of a rich bacterial microbiome (mostly S.aureus, S.uberis) in the milk of healthy animals, as well as changing bacterial species between in spring and autumn seasons occur as a result of both the immune state of the animal and many external factors, which consequently affects the amount of expressed cytokines.

Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial and archaeal members of complex biogas-producing microbial communities. In the present study, the microbiomes of three industrial-scale biogas digesters, each fed with different substrates, were analysed using a machine-learning guided genome-centric metagenomics framework complemented with metatranscriptome data. This data permitted us to elucidate the relationship between abundant core methanogenic communities and their syntrophic bacterial partners. In total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, the assembled 16?S rRNA gene profiles of these nrMAGs showed that the phylum Firmicutespossessed the highest copy number, while the representatives of the archaeal domain had the lowest. Further investigation of the three anaerobic microbial communities showed characteristic alterations over time but remained specific to each industrial-scale biogas plant. The relative abundance of various microorganisms as revealed by metagenome data was independent from corresponding metatranscriptome activity data. Archaeashowed considerably higher activity than was expected from their abundance. We detected 51 nrMAGs that were present in all three biogas plant microbiomes with different abundances. The core microbiome correlated with the main chemical fermentation parameters, and no individual parameter emerged as a predominant shaper of community composition. Various interspecies H2/electron transfer mechanisms were assigned to hydrogenotrophic methanogens in the biogas plants that ran on agricultural biomass and wastewater. Analysis of metatranscriptome data revealed that methanogenesis pathways were the most active of all main metabolic pathways.

The aim of this study was to examine clinically healthy cow’s udder milk microbiota and presence of cytokines in different seasons. Milk samples taken from the cows were checked for the presence of Gram-positive and Gram-negative bacteria, and the somatic cell count was detected. Immunohistochemistry methods were performed to detect interleukin (IL) -2, IL-4, IL-8, IL-10, IL-12, IL-17a, β-defensin-3, transforming growth factor (TGF)-ā1, interferon-ć and nuclear factor (NF)-źB presence in the milk. S. agalactiae, S. uberis, S. aureus, E. coli,and Klebsiella, Enterobacter, Citrobacterspp. were found in healthy cow’s milk. In the first round, the highest prevalence was observed for S. aureus. In the second round, the highest mean levels were observed for S. uberis, then followed S. aureus. IL-4, IL-17a and TGF-ā1 demonstrated the highest expression in the milk samples. NF-źB had the lowest expression among all factors. The presence of a rich bacterial microbiome (mostly S.aureus, S.uberis) in the milk of healthy animals, as well as changing bacterial species between in spring and autumn seasons occur as a result of both the immune state of the animal and many external factors, which consequently affects the amount of expressed cytokines.

Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SPβ recombines with low copy number phi3Ts phage DNA present within the B. subtilispopulation. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillussp. strains suggests that SPβ and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillussp. genomes indicates that similar diversification of SPβ-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.

Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPß prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SPß recombines with low copy number phi3Ts phage DNA present within the B. subtilispopulation. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillussp. strains suggests that SPß and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillussp. genomes indicates that similar diversification of SPß-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.

Biofilms are closely packed cells held and shielded by extracellular matrix composed of structural proteins and exopolysaccharides (EPS). As matrix components are costly to produce and shared within the population, EPS-deficient cells can act as cheaters by gaining benefits from the cooperative nature of EPS producers. Remarkably, genetically programmed EPS producers can also exhibit phenotypic heterogeneity at single-cell level. Previous studies have shown that spatial structure of biofilms limits the spread of cheaters, but the long-term influence of cheating on biofilm evolution is not well understood. Here, we examine the influence of EPS nonproducers on evolution of matrix production within the populations of EPS producers in a model biofilm-forming bacterium, Bacillus subtilis. We discovered that general adaptation to biofilm lifestyle leads to an increase in phenotypical heterogeneity of epsexpression. However, prolonged exposure to EPS-deficient cheaters may result in different adaptive strategy, where epsexpression increases uniformly within the population. We propose a molecular mechanism behind such adaptive strategy and demonstrate how it can benefit the EPS producers in the presence of cheaters. This study provides additional insights on how biofilms adapt and respond to stress caused by exploitation in long-term scenario.

Biofilms are closely packed cells held and shielded by extracellular matrix composed of structural proteins and exopolysaccharides (EPS). As matrix components are costly to produce and shared within the population, EPS-deficient cells can act as cheaters by gaining benefits from the cooperative nature of EPS producers. Remarkably, genetically programmed EPS producers can also exhibit phenotypic heterogeneity at single-cell level. Previous studies have shown that spatial structure of biofilms limits the spread of cheaters, but the long-term influence of cheating on biofilm evolution is not well understood. Here, we examine the influence of EPS nonproducers on evolution of matrix production within the populations of EPS producers in a model biofilm-forming bacterium, Bacillus subtilis. We discovered that general adaptation to biofilm lifestyle leads to an increase in phenotypical heterogeneity of epsexpression. However, prolonged exposure to EPS-deficient cheaters may result in different adaptive strategy, where epsexpression increases uniformly within the population. We propose a molecular mechanism behind such adaptive strategy and demonstrate how it can benefit the EPS producers in the presence of cheaters. This study provides additional insights on how biofilms adapt and respond to stress caused by exploitation in long-term scenario.

Biomethane has gained increasing attention in the recent years as an alternative, local energy source option. Biogas is generated during the anaerobic digestion of organic materials via a multistep process catalyzed by complex microbial communities. This review aims at providing a concise summary of recent studies on the microbial communities in various biogas reactors. The effects of acid composition, C/N ratio, mixing and the geometry of the anaerobic digester on the microbial ecosystem is discussed. Recent studies demonstrated the extensive fluctuations in the biogas microbial communities in response to changes in temperature, substrate type, pH, type of volatile fatty acids, organic loading rate, etc. The goals to ensure the stability of the anaerobic degradation process and to maximize the biogas production require the better understanding of these metabolic changes, since functional stability strongly correlates with the state and composition of microbial communities. The safe and controlled intensification of biogas production would be an important step to make biogas a real competitor of fossil fuels.