Fungi have been used since ancient times in food and beverage-making processes and, more recently, have been harnessed for the production of antibiotics and in processes of relevance to the bioeconomy. Moreover, they are starting to gain attention as a key component of the human microbiome. However, fungi are also responsible for human infections. The incidence of community-acquired and nosocomial fungal infections has increased considerably in recent decades. Antibiotic resistance development, the increasing number of immunodeficiency-and/or immunosuppression-related diseases and limited therapeutic options available are triggering the search for novel alternatives. These new antifungals should be less toxic for the host, with targeted or broader antimicrobial spectra (for diseases of known and unknown etiology, respectively) and modes of actions that limit the potential for the emergence of resistance among pathogenic fungi. Given these criteria, antimicrobial peptides with antifungal properties, i.e., antifungal peptides (AFPs), have emerged as powerful candidates due to their efficacy and high selectivity. In this review, we provide an overview of the bioactivity and classification of AFPs (natural and synthetic) as well as their mode of action and advantages over current antifungal drugs. Additionally, natural, heterologous and synthetic production of AFPs with a view to greater levels of exploitation is discussed. Finally, we evaluate the current and potential applications of these peptides, along with the future challenges relating to antifungal treatments.

Bacteria, Archaea, Eukarya and viruses coexist in the human gut, and this coexistence is functionally balanced by symbiotic or antagonistic relationships. Antagonism is often characterized by the production of antimicrobials against other organisms occupying the same environmental niche. Indeed, close co-evolution in the gut has led to the development of specialized antimicrobials, which is attracting increased attention as these may serve as novel alternatives to antibiotics and thereby help to address the global problem of antimicrobial resistance. The gastrointestinal (GI) tract is especially suitable for finding novel antimicrobials due to the vast array of microbes that inhabit it, and a considerable number of antimicrobial producers of both wide and narrow spectrum have been described. In this review, we summarize some of the antimicrobial compounds that are produced by bacteria isolated from the gut environment, with a special focus on bacteriocins. We also evaluate the potential therapeutic application of these compounds to maintain homeostasis in the gut and the biocontrol of pathogenic bacteria.

The metabolism of S. Typhimurium within infected host cells plays a fundamental role in virulence since it enables intracellular proliferation and dissemination and affects the innate immune response. An essential requirement for the intracellular replication of S. Typhimurium is the need to regenerate ATP. The metabolic route used to fulfil this requirement is the subject of the present study. For infection models we used human and murine epithelial and macrophage cell lines. The epithelial cell lines were mICc12, a transimmortalised murine colon enterocyte cell line that shows many of the characteristics of a primary epithelial cell line, and HeLa cells. The model macrophage cell lines were THP-1A human monocyte/macrophages and RAW 264.7 murine macrophages. Using a mutational approach combined with an exometabolomic analysis, we showed that neither fermentative metabolism nor anaerobic respiration play major roles in energy generation in any of the cell lines studied. Rather, we identified overflow metabolism to acetate and lactate as the foremost route by which S. Typhimurium fulfils its energy requirements.

There is increasing evidence suggesting a link between the autism spectrum disorder (ASD) and the gastrointestinal (GI) microbiome. Experimental and clinical studies have shown that patients diagnosed with ASD display alterations of the gut microbiota. These alterations do not only extend to the gut microbiota composition but also to the metabolites they produce, as a result of its connections with diet and the bidirectional interaction with the host. Thus, production of metabolites and neurotransmitters stimulate the immune system and influence the central nervous system (CNS) by stimulation of the vagal nerve, as an example of the gut-brain axis pathway. In this review we compose an overview of the interconnectivity of the different GI-related elements that have been associated with the development and severity of the ASD in patients and animal models. We review potential biomarkers to be used in future studies to unlock further connections and interventions in the treatment of ASD.

Guide RNA molecules (crRNA) produced from clustered regularly interspaced short palindromic repeat (CRISPR) arrays, altogether with effector proteins (Cas) encoded by cognate cas (CRISPR associated) genes, mount an interference mechanism (CRISPR-Cas) that limits acquisition of foreign DNA in Bacteria and Archaea. The specificity of this action is provided by the repeat intervening spacer carried in the crRNA, which upon hybridization with complementary sequences enables their degradation by a Cas endonuclease. Moreover, CRISPR arrays are dynamic landscapes that may gain new spacers from infecting elements or lose them for example during genome replication. Thus, the spacer content of a strain determines the diversity of sequences that can be targeted by the corresponding CRISPR-Cas system reflecting its functionality. Most Escherichia coli strains possess either type I-E or I-F CRISPR-Cas systems. To evaluate their impact on the pathogenicity of the species, we inferred the pathotype and pathogenic potential of 126 strains of this and other closely related species and analyzed their repeat content. Our results revealed a negative correlation between the number of I-E CRISPR units in this system and the presence of pathogenicity traits: the median number of repeats was 2.5-fold higher for commensal isolates (with 29.5 units, range 0–53) than for pathogenic ones (12.0, range 0–42). Moreover, the higher the number of virulence factors within a strain, the lower the repeat content. Additionally, pathogenic strains of distinct ecological niches (i.e., intestinal or extraintestinal) differ in repeat counts. Altogether, these findings support an evolutionary connection between CRISPR and pathogenicity in E. coli.

Nisin P is a natural nisin variant, the genetic determinants for which were previously identified in the genomes of two Streptococcus species, albeit with no confirmed evidence of production. Here we describe Streptococcus agalactiae DPC7040, a human faecal isolate, which exhibits antimicrobial activity against a panel of gut and food isolates by virtue of producing nisin P. Nisin P was purified, and its predicted structure was confirmed by nanoLC-MS/MS, with both the fully modified peptide and a variant without rings B and E being identified. Additionally, we compared its spectrum of inhibition and minimum inhibitory concentration (MIC) with that of nisin A and its antimicrobial effect in a faecal fermentation in comparison with nisin A and H. We found that its antimicrobial activity was less potent than nisin A and H, and we propose a link between this reduced activity and the peptide structure.Nisin is a small peptide with antimicrobial activity against a wide range of pathogenic bacteria. It was originally sourced from a Lactococcus lactis subsp. lactis isolated from a dairy product 1 and is classified as a class I bacteriocin, as it is ribosomally synthesised and post-translationally modified 2 . Nisin has been studied extensively and has a wide range of applications in the food industry, biomedicine, veterinary and research fields 3-6 . It is approved as a food preservative by the Food and Agriculture Organization and is Generally Recognized As Safe (GRAS) by the United States Food and Drug Administration 4 .Structurally, nisin is classified as a lantibiotic because it contains lanthionine (Lan), an unusual amino acid formed by two alanine residues linked by a sulphur atom through their β-carbon 4 . Other unusual amino acids present in nisin are dehydroalanine (Dha), dehydrobutyrine (Dhb) and β-methyl-lanthionine 4 . Nisin activity and stability are closely related to its structure and can be altered by pH changes. Increasing pH results in decreasing activity as a consequence of alterations in structure, therefore, nisin is more stable at lower pH. Nisin is heat-stable and also exhibits high stability at low temperatures, which makes it suitable for freeze-storage 7 .Nisin has nine reported natural variants (Fig. 1, Table 1). Nisin A is the most studied nisin as it was the first one purified 8 . Nisin Z is considered the first natural variant of nisin A; it differs in the presence of an asparagine amino acid in position 27 instead of a histidine residue 9 . This substitution has very little effect on antimicrobial activity, thermal and pH stability compared to nisin A, but affects the solubility of the molecule, with nisin Z being more soluble at neutral pH 10 . A study of its distribution also revealed that nisin Z is more widespread than nisin A 10 . Nisin F, produced by L. lactis isolated from a fish gut, also has asparagine and valine in positions 21 and 30 11 . Nisin Q was identified in an environmental L. lactis isolate and differs from nisin A due to the presence of valine, leucine, asparagine and va...

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Fusobacterium nucleatum is an emerging human pathogen associated with a number of intestinal conditions including colorectal cancer (CRC) development. Screening for gut-derived strains that exhibit anti-F. nucleatum activity revealed Streptococcus salivarius DPC6487 as a strain of interest. Whole genome sequencing analysis of DPC6487 resulted in the identification of a gene predicted to encode a novel nisin variant designated nisin G. The structural nisin G peptide differs from the prototypical nisin A with respect to seven amino acids (Ile4Tyr, Ala15Val, Gly18Ala, Asn20His, Met21Leu, His27Asn and His31Ile), including differences that have not previously been associated with a natural nisin variant. The nisin G gene cluster consists of nsgGEFABTCPRK with transposases encoded between the nisin G structural gene (nsgA) and nsgF. The cluster lacked an equivalent to the nisI immunity determinant. S. salivarius DPC6487 exhibited a narrower spectrum of activity compared to the nisin A producer, Lactococcus lactis NZ9700, when assessed through deferred antagonism-based assays. Such narrow spectrum activity is desirable as it is less likely to lead to collateral damage to gut commensals. Ultimately, this is the first report of a nisin variant produced by a representative of a species that is frequently a focus for probiotic development. The production of this bacteriocin by a gut-derived S. salivarius and its narrow spectrum activity against F. nucleatum indicates that this strain merits further attention to determine its potential for probiotic-related applications.