Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species

The human microbiome influences human health in both negative and positive ways. Studies on the transportomes of these organisms yield information that may be utilized for various purposes, including the identification of novel drug targets and the manufacture of improved probiotic strains. Moreover, these genomic analyses help to improve our understanding of the physiology and metabolic capabilities of these organisms. The present study is a continuation of our studies on the transport proteins of the major gut microbes. <i>Bifidobacterium</i> species are essential members of the human gut microbiome, and they initiate colonization of the gut at birth, providing health benefits that last a lifetime. In this study we analyze the transportomes of nine bifidobacterial species: <i>B. adolescentis, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. longum</i> subsp. <i>infantis, B. longum</i> subsp. <i>longum, and B. pseudocatenulatum</i>. All of these species have proven probiotic characteristics and exert beneficial effects on human health. Surprisingly, we found that all nine of these species have similar pore-forming toxins and drug exporters that may play roles in pathogenesis. These species have transporters for amino acids, carbohydrates, and proteins, essential for their organismal lifestyles and adaption to their respective ecological niches. The strictly probiotic species, <i>B. bifidum</i>, however, contains fewer such transporters, thus indicative of limited interactions with host cells and other gut microbial counterparts. The results of this study were compared with those of our previous studies on the transportomes of multiple species of <i>Bacteroides, Escherichia coli/Salmonella</i>, and <i>Lactobacillus</i>. Overall, bifidobacteria have larger transportomes (based on percentages of total proteins) than the previously examined groups of bacterial species, with a preference for primary active transport systems over secondary carriers. Taken together, these results provide useful information about the physiologies and pathogenic potentials of these probiotic organisms as reflected by their transportomes.

Colonization and Development of the Fecal Microflora of South China Tiger Cubs (Panthera tigris amoyensis) by Sequencing of the 16S rRNA Gene

Postnatal colonization and development of the gut microbiota is linked to health and growth. A comprehensive understanding of the postnatal compositional changes and development of the microbial community is helpful to understand the gut health and improve the survival rate of South China tiger cubs (<i>Panthera tigris amoyensis</i>). Fecal samples from three tiger cubs were collected on the day of birth in 2018 (June 17–21 [G0], July 18 [G1], July 31 [G2], and August 7 [G3]). The 16S rRNA genes of the fecal microflora were sequenced. Results showed that 38 phyla, 58 classes, 134 orders, 272 families, and 636 genera of bacteria from 3,059 operational taxonomic units were identified from 12 fecal samples. The diversity and abundance of species of group G0 were significantly higher (<i>p</i> &#x3c; 0.05 or 0.01) than those of groups G2 and G3. The predominant phylum was Proteobacteria in groups G0 and G1 (38.85% and 48%, respectively) and Firmicutes in groups G2 and G3 (71.42% and 75.29%, respectively). At the phylum level, the abundance of Deinococcus-Thermus was significantly decreased in groups G1, G2, and G3 as compared to group G0 (<i>p</i> &#x3c; 0.05), while that of Firmicutes was significantly increased in groups G2 and G3 (<i>p</i> &#x3c; 0.05). At the genus level, the abundance of <i>Faecalibacterium</i>, <i>Ralstonia</i>, and unidentified <i>Rickettsiales</i> was significantly decreased in groups G1, G2, and G3 as compared with group G0 (<i>p</i> &#x3c; 0.05), while that of <i>Pseudomonas</i> was significantly decreased in groups G2 and G3 (<i>p</i> &#x3c; 0.05). The composition and structure of fecal microbiota of South China tiger cubs changed after birth.

The Formation of Spore-Like Akinetes: A Survival Strategy of Filamentous Cyanobacteria

Some cyanobacteria of the order Nostocales can form akinetes, spore-like dormant cells resistant to various unfavorable environmental fluctuations. Akinetes are larger than vegetative cells and contain large quantities of reserve products, mainly glycogen and the nitrogen storage polypeptide polymer cyanophycin. Akinetes are enveloped in a thick protective coat containing a multilayered structure and are able to germinate into new vegetative cells under suitable growth conditions. Here, we summarize the significant morphological and physiological changes that occur during akinete differentiation and germination and present our investigation of the physiological function of the storage polymer cyanophycin in these cellular processes. We show that the cyanophycin production is not required for formation and germination of the akinetes in the filamentous cyanobacterium <i>Anabaena variabilis</i> ATCC 29413.

Contribution of the Clp Protease to Bacterial Survival and Mitochondrial Homoeostasis

Fast adaptation to environmental changes ensures bacterial survival, and proteolysis represents a key cellular process in adaptation. The Clp protease system is a multi-component machinery responsible for protein homoeostasis, protein quality control, and targeted proteolysis of transcriptional regulators in prokaryotic cells and prokaryote-derived organelles of eukaryotic cells. A functional Clp protease complex consists of the tetradecameric proteolytic core ClpP and a hexameric ATP-consuming Clp-ATPase, several of which can associate with the same proteolytic core. Clp-ATPases confer substrate specificity by recognising specific degradation tags, and further selectivity is conferred by adaptor proteins, together allowing for a fine-tuned degradation process embedded in elaborate regulatory networks. This review focuses on the contribution of the Clp protease system to prokaryotic survival and summarises the current state of knowledge for exemplary bacteria in an increasing degree of interaction with eukaryotic cells. Starting from free-living bacteria as exemplified by a non-pathogenic and a pathogenic member of the Firmicutes, i.e., <i>Bacillus subtilis</i> and <i>Staphylococcus aureus</i>, respectively, we turn our attention to facultative and obligate intracellular bacterial pathogens, i.e., <i>Mycobacterium tuberculosis, Listeria monocytogenes,</i> and <i>Chlamydia trachomatis</i>, and conclude with mitochondria. Under stress conditions, the Clp protease system exerts its pivotal role in the degradation of damaged proteins and controls the timing and extent of the heat-shock response by regulatory proteolysis. Key regulators of developmental programmes like natural competence, motility, and sporulation are also under Clp proteolytic control. In many pathogenic species, the Clp system is required for the expression of virulence factors and essential for colonising the host. In accordance with its evolutionary origin, the human mitochondrial Clp protease strongly resembles its bacterial counterparts, taking a central role in protein quality control and homoeostasis, energy metabolism, and apoptosis in eukaryotic cells, and several cancer cell types depend on it for proliferation.

Secondary Metabolites Governing Microbiome Interaction of Staphylococcal Pathogens and Commensals

Various <i>Staphylococcus</i> species colonize skin and upper airways of warm-blooded animals. They compete successfully with many other microorganisms under the hostile and nutrient-poor conditions of these habitats using mechanisms that we are only beginning to appreciate. Small-molecule mediators, whose biosynthesis requires complex enzymatic cascades, so-called secondary metabolites, have emerged as crucial components of staphylococcal microbiome interactions. Such mediators belong to a large variety of compound classes and several of them have attractive properties for future drug development. They include, for instance, bacteriocins such as lanthipeptides, thiopeptides, and fibupeptides that inhibit bacterial competitor species; signaling molecules such as thiolactone peptides that induce or inhibit sensory cascades in other bacteria; or metallophores such as staphyloferrins and staphylopine that scavenge scant transition metal ions. For some secondary metabolites such as the aureusimines, the exact function remains to be elucidated. How secondary metabolites shape the fitness of <i>Staphylococcus</i> species in the complex context of other microbial and host defense factors remains a challenging field of future research. A detailed understanding will help to harness staphylococcal secondary metabolites for excluding the pathogenic species <i>Staphylococcus aureus</i> from the nasal microbiomes of at-risk patients, and it will be instrumental for the development of advanced anti-infective interventions.

A Novel Enrichment Culture Highlights Core Features of Microbial Networks Contributing to Autotrophic Fe(II) Oxidation Coupled to Nitrate Reduction

Fe(II) oxidation coupled to nitrate reduction (NRFO) has been described for many environments. Yet very few autotrophic microorganisms catalysing NRFO have been cultivated and their diversity, as well as their mechanisms for NRFO <i>in situ</i> remain unclear. A novel autotrophic NRFO enrichment culture, named culture BP, was obtained from freshwater sediment. After more than 20 transfers, culture BP oxidized 8.22 mM of Fe(II) and reduced 2.42 mM of nitrate within 6.5 days under autotrophic conditions. We applied metagenomic, metatranscriptomic, and metaproteomic analyses to culture BP to identify the microorganisms involved in autotrophic NRFO and to unravel their metabolism. Overall, twelve metagenome-assembled genomes (MAGs) were constructed, including a dominant <i>Gallionellaceae</i> sp. MAG (≥71% relative abundance). Genes and transcripts associated with potential Fe(II) oxidizers in culture BP, identified as a <i>Gallionellaceae</i> sp., <i>Noviherbaspirillum</i> sp., and <i>Thiobacillus</i> sp., were likely involved in metal oxidation (e.g., <i>cyc2</i>, <i>mtoA</i>), denitrification (e.g., <i>nirK</i>/<i>S</i>, <i>norBC</i>), carbon fixation (e.g., <i>rbcL</i>), and oxidative phosphorylation. The putative Fe(II)-oxidizing protein Cyc2 was detected for the <i>Gallionellaceae</i> sp. Overall, a complex network of microbial interactions among several Fe(II) oxidizers and denitrifiers was deciphered in culture BP that might resemble NRFO mechanisms <i>in situ</i>. Furthermore, 16S rRNA gene amplicon sequencing from environmental samples revealed 36 distinct <i>Gallionellaceae</i> taxa, including the key player of NRFO from culture BP (approx. 0.13% relative abundance <i>in situ</i>). Since several of these <i>in situ</i>-detected <i>Gallionellaceae</i> taxa were closely related to the key player in culture BP, this suggests that the diversity of organisms contributing to NRFO might be higher than currently known.

CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes

Being frequently exposed to foreign nucleic acids, bacteria and archaea have developed an ingenious adaptive defense system, called CRISPR-Cas. The system is composed of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) array, together with CRISPR (<i>cas</i>)-associated genes. This system consists of a complex machinery that integrates fragments of foreign nucleic acids from viruses and mobile genetic elements (MGEs), into CRISPR arrays. The inserted segments (spacers) are transcribed and then used by cas proteins as guide RNAs for recognition and inactivation of the targets. Different types and families of CRISPR-Cas systems consist of distinct adaptation and effector modules with evolutionary trajectories, partially independent. The origin of the effector modules and the mechanism of spacer integration/deletion is far less clear. A review of the most recent data regarding the structure, ecology, and evolution of CRISPR-Cas systems and their role in the modulation of accessory genomes in prokaryotes is proposed in this article. The CRISPR-Cas system&apos;s impact on the physiology and ecology of prokaryotes, modulation of horizontal gene transfer events, is also discussed here. This system gained popularity after it was proposed as a tool for plant and animal embryo editing, in cancer therapy, as antimicrobial against pathogenic bacteria, and even for combating the novel coronavirus – SARS-CoV-2; thus, the newest and promising applications are reviewed as well.

Natural Products from Nocardia and Their Role in Pathogenicity

<i>Nocardia</i> spp. are filamentous Actinobacteria of the order Corynebacteriales and mostly known for their ability to cause localized and systemic infections in humans. However, the onset and progression of nocardiosis is only poorly understood, in particular the mechanisms of strain-specific presentations. Recent genome sequencing has revealed an extraordinary capacity for the production of specialized small molecules. Such secondary metabolites are often crucial for the producing microbe to survive the challenges of different environmental conditions. An interesting question thus concerns the role of these natural products in <i>Nocardia-</i>associated pathogenicity and immune evasion in a human host. In this review, a summary and discussion of <i>Nocardia</i> metabolites is presented, which may play a part in nocardiosis because of their cytotoxic, immunosuppressive and metal-chelating properties or otherwise vitally important functions. This review also contains so far unpublished data concerning the biosynthesis of these molecules that were obtained by detailed bioinformatic analyses.

The Role of hlb-Converting Bacteriophages in Staphylococcus aureus Host Adaption

As an opportunistic pathogen of humans and animals, <i>Staphylococcus aureus</i> asymptomatically colonizes the nasal cavity but is also a leading cause of life-threatening acute and chronic infections. The evolution of <i>S. aureus</i> resulting from short- and long-term adaptation to diverse hosts is tightly associated with mobile genetic elements<i>. S. aureus</i> strains can carry up to four temperate phages, many of which possess accessory genes encoding staphylococcal virulence factors. More than 90% of human nasal isolates of <i>S. aureus</i> have been shown to carry Sa3int phages, whereas invasive <i>S. aureus</i> isolates tend to lose these phages. Sa3int phages integrate as prophages into the bacterial <i>hlb</i> gene, disrupting the expression of the sphingomyelinase Hlb, an important virulence factor under specific infection conditions. Virulence factors encoded by genes carried by Sa3int phages include staphylokinase, enterotoxins, chemotaxis-inhibitory protein, and staphylococcal complement inhibitor, all of which are highly human specific and probably essential for bacterial survival in the human host. The transmission of <i>S. aureus</i> from humans to animals is strongly correlated with the loss of Sa3int phages, whereas phages are regained once a strain is transmitted from animals to humans. Thus, both the insertion and excision of prophages may confer a fitness advantage to this bacterium<i>.</i> There is also growing evidence that Sa3int phages may perform “active lysogeny,” a process during which prophages are temporally excised from the chromosome without forming intact phage particles. The molecular mechanisms controlling the peculiar life cycle of Sa3int phages remain largely unclear. Nevertheless, their regulation is likely fine-tuned to ensure bacterial survival within different hosts.