- Volume 2, Issue 7A, 2020

Promyelocytic leukaemia (PML) bodies are nuclear organelles implicated in post-translational modification by small ubiquitin-like modifier (SUMO) proteins and in the antiviral host cell response to infection. The 72-kDa immediate-early protein 1 (IE1) is considered the principal antagonist of PML bodies encoded by the human cytomegalovirus, one of eight human herpesviruses. Previous work has suggested that the interaction between IE1 and PML proteins, the central organisers of PML bodies, and the subsequent disruption of these organelles serve a critical role in viral replication by counteracting intrinsic antiviral immunity and the induction of interferon (IFN)-stimulated genes. However, this picture has emerged largely from studying mutant IE1 proteins known or predicted to be globally misfolded und metabolically unstable. We systematically screened for stable IE1 mutants by clustered charge-to-alanine scanning. We identified a mutant protein (IE1cc172-176) selectively defective for PML interaction. Functional comparisons between the mutant and wild-type protein revealed that IE1 can undergo modification by mixed polymeric SUMO chains and that it targets PML and Sp100, the two main constituents of PML bodies, via distinct mechanisms. Unexpectedly, IE1cc172-176 supported viral replication almost as efficiently as wild-type IE1. Moreover, lower instead of higher (as expected) levels of tumor necrosis factor alpha, IFN-beta, IFN-lambda and IFN-stimulated gene expression were observed with the mutant compared to the wild-type protein and virus. These results suggest that the disruption of PML bodies is linked to induction rather than inhibition of antiviral gene expression. Our findings challenge current views regarding the role of PML bodies in viral infection.

Air pollution is a major global health problem, with around 91% of the world’s population living in areas that exceed the WHO air pollution guidelines. This complex mix of pollutants almost always includes particulate matter (PM), and this has the greatest impact on human health. PM exposure contributes to a range of diseases such as COPD, heart disease and respiratory infections. Our recent publication was the first to document that as well as damaging the host, PM has a direct impact on bacteria that can cause respiratory infections. We showed that Black Carbon (BC) exposure results in species-specific alterations in biofilm structure in both Streptococcus pneumoniae and Staphylococcus aureus, altered biofilm protectivity against antibiotic exposure, and S. pneumoniae bacterial colonisation in vivo.

Following on from this ground-breaking work, our current data show that the bacterial response to BC occurs at the genetic level, altering the transcription of key genes involved in biofilm formation, colonisation and virulence. Bacterial adhesion to and invasion of human epithelial cells is significantly increased when S. aureus are pre-exposed to BC prior to infection compared to naïve S. aureus cells. In a murine respiratory colonisation model, both S. aureus co-infected alongside BC, and crucially S. aureus pre-exposed to BC, show increased colonisation of the nasopharynx and lungs. These data suggest that the bacteria are responding and adapting to exposure to air pollution, and this has an impact on how the bacteria infect the host.

Coccolithophores are calcifying microalgae that carry characteristic calcite platelets (coccoliths) on their surfaces. Most coccolithophore species exhibit diploid and haploid life cycle stages, each adjusted to different environmental conditions. The diploid life cycle stage of the coccolithophore C. braarudii is heavily calcifying with calcification rates that exceed the rates of photosynthesis. Haploid life-cycle stages are often weakly calcifying, generating significantly less H+ from the intracellular calcification reaction. We show how these different cellular “H+ burdens” require substantially different physiological molecular strategies to regulate intracellular pH under changing environmental conditions. Voltage-gated H+ channels (Hv) have been shown to play a role in the release of H+ in the diploid life cycle previously (Taylor et al. 2011). Combining scanning electron microscopy, electrophysiology, gene expression approaches and physiological measurements, we here show a direct link between the function of proton channels and coccolith formation of the diploid but not the haploid life-cycle stage. Our data also indicate how the different mechanisms for acid-base regulation of the diploid and haploid life-cycle stages may result in different sensitivities towards ocean acidification.

A major challenge in microbial ecology is to understand the stability of interspecies interactions when progressing from pairs of interacting species to multispecies interaction networks. A lack of direct evidence, and a conceptual framework to explore how direct and indirect effects shape cellular responses in species-rich networks has hindered progress in our understanding of these combined effects. Here we aimed to investigate whether higher-order interactions shape community dynamics and transcriptional profiles of all interacting partners in a simplified microbial community that includes a primary producer (Nannochloropsis oceanica CCAP849/10) and two heterotrophic bacteria (Marinobacter sp. FDB33 and Alteromonas sp. FDB36). By combining co-cultivation assays, quantification of absolute abundances, nutrient analysis, and simultaneous RNA-sequencing, we reveal genome-wide transcriptional responses in all binary co-cultivation partners and show that the third partner can profoundly alter binary interactions at the phenotypic and transcription level. Our study demonstrates the context-dependency of binary interactions, whereby environmental conditions and the presence of specific organisms can affect the cellular physiology of the interacting partners and ultimately the stability of the community. Furthermore, our approach provides a powerful tool for probing the molecular basis of emergent properties in more complex systems.

The Tup1-Cyc8 (Ssn6) complex is a powerful epigenetic repressor of genes in the yeast Saccharomyces cerevisiae. The highly conserved complex brings about a repressive chromatin structure at regulatory regions of its target genes or prevents the recruitment of factors needed for activation of transcription. A gap in the current understanding is whether each of the subunits contribute differently to repression. The FLO family of genes are repressed by the Tup1-Cyc8 complex, these genes encode the proteins required for flocculation, a stress response in yeast where the cells aggregate, or form flocs, to protect cells within the floc. Interestingly, each mutant strain has a distinct flocculant phenotype. The tup1Δ strain displays large, dense flocs compared to smaller, more dispersed flocs associated with the cyc8Δ strain. RT-qPCR showed that FLO1 is highly de-repressed in the tup1Δ strain whereas it is de-repressed to a significantly lower level in the cyc8Δ strain. Using the Anchor Away (AA) technique, which allows for a nuclear protein to be conditionally sequestered to the cytoplasm, I am investigating differences in the sequence of events at the FLO1 promoter when Tup1p or when Cyc8p is removed from the nucleus. Six hours after Cyc8p is removed from the nucleus transcription of FLO1 almost reaches the maximum transcription seen in the cyc8Δstrain. However, six hours after removing Tup1p the level of transcription of FLO1 is still over ten times lower than the maximum transcription in tup1Δ. This difference indicates that each of the subunits have independent functions within the complex.

Production of polyhydroxyalkanoates (PHAs) as bio-alternative to petroleum-based plastics is an important field in the biorefinery to move forward in the development of the circular economy. PHAs are bioplastics stored inside microbial cells as carbon reservoirs and can be produced from a broad range of renewable resources such as waste streams. One important waste stream is food waste that can be converted into volatile fatty acids (VFAs) by anaerobic digestion. The produced effluent from food waste is not only rich in VFAs but also, other nutrients such as nitrogen and phosphorus that can be used by the microorganisms to produce PHAs. The aim of this research is to convert VFAs produced from food waste into PHAs, in which two approaches have been studied. The first approach was to use microbial mixed cultures (MMCs) while the second used microbial pure cultures.

The MMCs were enriched in sequencing batch bioreactor cultivations, where nitrogen and carbon starvation were combined to enhance the selection phase. PHA accumulation of the selected cultures was studied in nitrogen-limited fed-batch cultivations. The second approach studied five different PHA producing bacteria: Cupriavidus necator, Burkholderia cepacea, Bacillus megaterium, Bacillus cereus and Bacillus cereus. To select the most promising bacteria, synthetic medium with the same VFAs composition as in MMCs study was used for pre-screening experiments. Both, pure and mixed culture studies, resulted in the production of PHAs containing (R)-3-hydroxybutyrate, (R)-3-hydroxyvalerate and (R)-3-hydroxyhexanoate as monomers and VFAs were consumed with a high rate by the microorganisms.

The Human Gut Microbiota (HGM) comprises two major phyla, the Bacteroidetes and Firmicutes, although important members of the Actinobacteria (Bifidobacterium) and Verrucomicrobia (Akkemansia) also make an important contribution to this ecosystem.

Accumulating datasupport the notionthat the HGM can be modulated by probiotics and prebiotics to prevent or revert common diseases of the gastrointestinal tract (GIT) such as Inflammatory Bowel Disease. Because it is believed that these GIT diseases are linked to the fact that current Western populations follow a more fat-based diet, significant efforts have been made to search for novel prebiotics/probiotics in order to restore and improve gut health.

So far, no publications have described probiotic properties of Bacteroidetes. Nonetheless, a case can be made that certain Bacteroides species present primary glycan degraders that interact in a syntrophic manner with other members of the microbiota, such as bifidobacteria, which are considered beneficial members of the microbiota.

In this study, we present the simbiotic interactions between Bacteroides and Bifidobacterium spp. acting on yeast beta-glucan (1,3/1,6 mixed linkage beta-glucan). Bacteroides cellulosilyticus and Bacteroides ovatus act as keystone organism to share beta-1,3/1,6-glucooligosaccharides with other members of the HGM, including Bifidobacterium breve UCC2003 and Bifidobacterium bifidum. We show in these Bifidobacterium spp. a specific beta-1,3-glucosidase, which degrade some of these sharing oligosaccharides. Also, we have identified the specific sugar symporter, which incorporate these oligosaccharides into the cytoplasm of B. breve UCC2003. With the help of RT-qPCR, we have quantified and monitored how these two members of the HGM are able to symbioticly use this dietary glycan.

The propensity of pathogens to evolve resistance to antibiotics used in clinical infectious disease therapeutics has been an increasing concern in recent decades. Acquisition of resistance often translates into treatment failure and puts patients at risk of serious adverse outcomes. Current laboratory testing of antibiotic susceptibility does not account for the different microenvironments that bacteria encounter within the human body, providing results that often do not translate into the clinic. Our goal is to better understand evolutionary strategies employed by Staphylococcus aureus in development of resistance in distinct environments.

We used adaptive laboratory evolution (ALE) to generate isogenic strains resistant to several antibiotics. Different media were used to mimic distinct environments and multi-omics approaches applied in the understanding of resistance mechanisms.

Evolved strains presented phenotypes similar to those observed in clinical resistant isolates. Mutational analysis indicated that resistance was specific and condition-dependent. Distinct mutations led to resistance phenotypes under a particular environmental condition, but these mutations did not necessarily translate into resistance under a different environmental condition. Furthermore, resistant strains possessed distinct transcriptional landscapes, even when the same systems were mutated, suggesting that similar evolutionary paths translate into distinct resistance mechanisms.

We identified several resistance mechanisms employed by S. aureus that were not only environment-dependent, but also environment specific. Additionally, we showed that ALE can be applied in pathogens of interest to study antibiotic resistance evolution and prediction of clinical resistance mechanisms, as supported by the significant overlap of mutations identified via ALE and those reported in clinical isolates.

Large-scale mining and analysis of bacterial datasets contribute to the comprehensive characterization of complex microbial dynamics within a microbiome and among different bacterial strains, e.g., during disease outbreaks. The study of large-scale bacterial evolutionary dynamics poses many challenges. These include data-mining steps, such as gene annotation, ortholog detection, sequence alignment, and phylogeny reconstruction. These steps require the use of multiple bioinformatics tools and ad-hoc programming scripts, making the entire process cumbersome, tedious and error-prone due to manual handling. This motivated us to develop the M1CR0B1AL1Z3R web server, a ‘one-stop shop’ for conducting microbial genomics data analyses via a simple graphical user interface (Avram, et al., Nucleic Acids Res., 2019). Some of the features implemented in M1CR0B1AL1Z3R are: (i) extracting putative open reading frames and comparative genomics analysis of gene content; (ii) extracting orthologous sets and analyzing their size distribution; (iii) analyzing gene presence-absence patterns; (iv) reconstructing a phylogenetic tree based on the extracted orthologous set; (v) inferring GC-content variation among lineages. M1CR0B1AL1Z3R facilitates the mining and analysis of dozens of bacterial genomes using advanced techniques, with the click of a button. M1CR0B1AL1Z3R is freely available at https://microbializer.tau.ac.il/ [https://microbializer.tau.ac.il/].

The secretion of extracellular enzymes by soil microbes is rate-limiting in the global recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant bacterial phylum, just like in human and animal intestines. The enzymology of Bacteroidetes in the dynamic and competitive soil environment is under-explored compared to their cousins from the human and ruminant gut ecosystems. We are exploring carbohydrate binding and deconstruction by Chitinophaga pinensis. This species was isolated from the leaf litter of a pine forest, and our ongoing microbiological, biochemical, and proteomic analyses show that C. pinensis has a marked metabolic preference for carbohydrates (glycans) of microbial, rather than plant, origin. The species has a repertoire of enzymes that degrade components of the fungal cell wall, and we are characterising several important enzyme activities, including some with unusual substrate specificity.

Several features of the C. pinensis “cazome” make it note-worthy. In particular, there is a significantly reduced reliance on the Polysaccharide Utilisation Loci that define glycan acquisition in most well-studied gut symbiont Bacteroidetes. Instead, C. pinensis produces some large multi-modular enzymes that convey multiple complementary carbohydrate-binding and -degrading functions, and which are often secreted via the phylum-specific Type IX Secretion System.

This presentation will highlight our latest enzyme characterisation data, discussed in the context of the environmental functions of soil bacteria, as well as the use of enzymes for industrial biotechnology.

Fermented foods are consumed by a very large population in Africa but the products have many drawbacks ranging from shelf life instability to contamination and toxicity. These foods therefore require an upgrade through improved fermentation processes. This work determined the phenotypic characteristics of the fermenting microorganisms and microbial ecological succession during fermentation of cassava and maize to determine the predominant fermenting microorganisms. Cassava roots and maize grains were fermented using the traditional method of processing them into fufu and ogi for 72 h and 48 h respectively. Samples were drawn every 12 h for analysis. Enumeration and characterization of lactic acid bacteria were carried out on MRS medium with subsequent microscopic examination, physiological, biochemical reaction tests and API 50 CH gallery. Yeast isolates were identified by their morphological characteristics. Thirteen lactic acid bacteria were isolated from the fermenting cassava and 6 from the fermenting maize. The Isolates were Gram positive and catalase negative. Lactobacillus plantarum, L. fermentum and L. pentusus predominated in both fermentations while Candida tropicalis, C. krusei and Saccharomyces cerevisae also predominated in both fermentations. Candida inconspicuo was found only in cassava fermentation. The results of this work revealed the microbial ecology of fermented cassava and maize which is a prerequisite to the understanding needed to develop a multifunctional starter culture for these fermentations for their upgrade.

Keywords: Cassava, Maize, Fermentation, lactic acid bacteria, Yeasts.

Gonorrhea is the second most commonly reported notifiable sexually transmitted disease in the world. Neisseria gonorrhoeae causes 78 million cases annually of gonorrhoea worldwide. There are no vaccines and antibiotic-resistant organisms are circulating rapidly. The estradiol-treated female mouse model is the only animal model available for studying the host response against gonococci and biological significance of host-restricted bacterial-host cell interactions observed in vitro. However, mouse models have limitations such as cost, time and ethics. Therefore, there is an urgent need for the development of new alternative in vivo models. The Galleria mellonella larval model is a simple, widely available, cost-effective, and powerful tool for studying microbial infections prior to any vertebrate animal testing. Here we report, for the first time, that G. mellonella can be used as an infection model for Neisseria spp., focusing particularly on N. gonorrhoeae. We demonstrated dose-dependent larval death and recovery of viable gonococci from the host, visualised host-pathogen interactions using histopathology and confirmed the importance of insect haemocytes as an innate immune cell during infection. The model was also used to test the efficacy of antibiotics used to treat gonorrhoea. Our results demonstrate that G. mellonella can be used as a model to study pathogenesis and virulence of gonococcal infection in addition to rapid in vivo testing of antimicrobials.

Since the last influenza pandemic in 2009, H1N1pdm has been introduced into the swine population in Europe where, in combination with swine influenza A virus (IAV) lineages, it started to generate a variety of reassortant viruses of unknown zoonotic risk for humans. To study these reassortment events, we isolated a wild swine lung cell clone (C22) susceptible to IAV infection. We established conditions for co-infection and passaging of H1N1pdm and swine avian-like H1N1. After 7 passages, we plaque-purified C22-adapted strains, characterized their genome composition by next-generation sequencing and analysed replication abilities in swine and human lung cell lines as well as in human lung tissue ex vivo.

Among C22-adapted viruses isolated from co-infection, we revealed reassortants carrying PB1/PA/NA or only PB1/PA from H1N1pdm. We also detected exclusively swine H1N1-derived strains. All isolates carried distinct mutations. As expected, adapted viruses reached higher titers compared to both parental strains in swine lung cells. Furthermore, all C22-adapted viruses were able to replicate in human lung A549 cells without any prior adaptation to the human host. Strikingly, all reassortants were able to infect and efficiently replicate in human lung tissue ex vivo, indicating that these viruses might pose a zoonotic risk.

To summarize, we successfully established an in vitro swine-like model to study reassortment and adaptation of IAVs currently circulating in swine. Our results indicate that our model might be a useful tool to prospectively evaluate the compatibility of different IAV strains to generate reassortants, which might represent a threat to the human population.

Phosphorus (P) is an essential macronutrient for all living organisms and is applied as fertilizer in agroecosystems to improve crop growth. Recycling-derived fertilizers (RDFs) have been developed for nutrient recovery from Europe’s largest waste streams as a sustainable alternative to this finite resource. The impact of four RDFs (two ashes, two struvites) on the soil microbiome in comparison with a P-free control and triple super phosphate (TSP) as mineral fertilizer was investigated in a pot trial and a subsequent microcosm trial (subset of samples). For both experiments perennial ryegrass was cultivated for 54 days. The pot trial was conducted at P fertilization rates of 20 and 60 kg P ha-1 in quadruplicates. After the pot harvest the bulk soil was stored until the microcosm trial was conducted, using the control, TSP and the two ashes at 60 kg P ha-1 in six replicates. Pot trial results showed highest P bioavailability from struvites at high P rates, also resulting in higher biomass yield on average. Furthermore, P solubilization capabilities from tri-calcium phosphate was enhanced in the RDFs treatments, while the TSP treatments were negatively affected. For the microcosm trial, most probable number (MPN) analysis showed that phytate-utilizing bacterial abundance was significantly increased in one of the ashes and had also remained higher in the RDF treatments after storage. Understanding the effects of recycling-derived fertilizer application on the soil P cycle is vital for developing a more sustainable agriculture.

BK polyomavirus (BKPyV) is a small, non-enveloped dsDNA virus that infects 70-90% of the world's population and causes a lifelong, silently persistent infection. In immunocompromised individuals, BKPyV replication can result in serious pathology. Bone marrow transplant patients can develop a haemorrhagic cystitis, and in kidney transplant patients BKPyV replication can provoke a nephropathy that leads to deterioration of allograft function and eventual loss of the transplanted organ. There are currently no antiviral treatments with clinical efficacy against BKPyV associated nephropathy.

While the life cycles of non-enveloped viruses are often assumed to require cell lysis to release progeny virions, we have evidence to suggest that BKPyV exits the cell via non-lytic means using an unconventional secretory pathway. We have investigated the effects of knocking out cellular genes thought to be involved in unconventional secretory pathways that bypass the Golgi apparatus on the release of BKPyV. We observe decreased BKPyV release from cells that have undergone CRISPR-mediated knockout of Golgi Reassembly Stacking Protein (GORASP) 1 or 2. Investigation of BKPyV-induced changes to the plasma membrane of infected cells demonstrated increased cell surface expression of transmembrane proteins normally resident in the endoplasmic reticulum. This appears to be inhibited by the knockout of GORASP1 or 2, suggesting that virions and ER markers are secreted via a common pathway in infected cells. These experiments are uncovering novel virus-host interactions that, when targeted, could help prevent BKPyV-associated nephropathy and allograft loss.

The Group A carbohydrate (GAC), a bacterial surface polysaccharide, is an essential virulence factor of Streptococcus pyogenes required for growth and infection of humans.In terms of its chemical composition, this peptidoglycan-anchored polymer is mainly formed by a string of rhamnose sugars, with alternated modifications of N-acetylglucosamine and glycerolphosphate. The rhamnose polysaccharide (RhaPS) that forms the backbone chain is synthesised intracellularly by the sequential action of three rhamnosyltransferases named GacB, GacC and GacG. Importantly, deletion of any of these rhamnosyltransferases causes bacterialdeath.

In this work, we used an interdisciplinary approach to demonstrate that: 1) GacB is a novel enzyme that initiates the RhaPS biosynthesis; 2) GacC catalyses the formation of a unique stem; 3) GacG elongates the RhaPS string by adding a yet unknown number of rhamnoses. Here, we also show that homologs from different streptococcal species can substitute GacB and GacC in the RhaPS production. In particular, we demonstrate that several human pathogens from the Streptococcus genus encompassed in the Lancefield serotyping scheme, and the dental pathogen Streptococcus mutans can replace S. pyogenes’ enzymes. In contrast, the homologs from S. pneumoniae sp. D39 did not, suggesting a different structural arrangement for its surface carbohydrate. Our results highlight the importance of the group carbohydrate biosynthesis pathways in the Streptococcus genus and open the door for the future development of multi-target compounds that could inhibit these enzymes in Streptococcus pyogenes and other pathogenic streptococci of clinical and veterinary importance.

Bacterial spores are of concern in food processing due to their ubiquity and resistance. This study seeks to determine the effect of ultraviolet C (UV-C) in the inactivation of spores of Bacillus subtilis and Bacillus velezensis that can result in enzymatic spoilage in foods using PBS as the suspension medium. Purified spore samples were treated under 1 pass in a UV-C reactor using 10 mL of spore inoculum with one dose of the radiation (410 mJ/cm2) for 10secs at room temperature. Aliquots of the treated samples were plated on tryptone soy agar supplemented with 0.6% glucose and the colonies counted. Flow cytometry analysis was done using 500 μL of both treated and control samples with a cell concentration of a ≥106 CFU/ml with propidium iodide (15 μM) and SYTO 9 (500 nM) used as live/dead stains. Samples were processed for microscopy (SEM and Raman-AFM Imaging). The maximum lethality is 2.5 for B. velezensis and the minimum is 0.1 for B. subtilis. Microscopic imaging of treated spores shows significant morphological disruption of the spore structure. The Raman spectroscopy analysis reveals the B. subtilis isolates to have the highest concentrations of dipicolnic acid (Ca+2DPA) as well as other compounds belonging to other functional groups. Flow cytometric analysis of treated spores reveals sub-populations unaccounted for by plate count. UV-C shows a promising application in the inactivation of resistant spores during processing of liquid foods such as milk.

It is estimated that £5 billion are invested yearly into chronic wound management by the NHS. Whilst the demand for treatment rises every year, it has become harder to treat wounds given the burden of antimicrobial resistance. Chronic wounds can easily become harbouring grounds for polymicrobial biofilms in which species interact in specific ways.

This study assessed the interactions between two commonly co-isolated chronic wound pathogens: Pseudomonas aeruginosa (ATCC 9027) and Staphylococcus aureus (EMRSA 15), whose biofilm relation initiates a Gram-negative shift. During this phenomenon, P. aeruginosa takes over the majority of the bacterial community, at the detriment of S. aureus. The Gram-negative shift marks the turning point from an acute to a chronic wound. The pH of a chronic wound is typically alkaline, and it was hypothesised that topical dressings with an acidic pH could disrupt the onset of the Gram negative shift, and therefore chronicity. Six different topical dressings with low pH were used in achronic wound model to assess their ability to reverse or delay the Gram-negative shift. It was found that they did not have an impact on the onset of the Gram-negative shift, despite their low pH values. However, the lower the pH of the dressings, the more frequently small colony variant (SCV) bacteria were observed in the biofilm. SCVs are known for causing persistent or chronic infections. It was therefore concluded that low pH dressings alone may not be favourable for managing chronic wound infection.

The contribution of the gut microbiota to health and disease is becoming ever more apparent in the last number of years, due to developments in DNA sequencing technology and more well-defined cultivation techniques. This has resulted in the identification of health-promoting bacteria. Until recently, prebiotics, non-digestible food substrates which are selectively utilised by beneficial bacteria, were employed with a view to increasing the growth of well-established health promoting bacteria, namely Lactobacillus and Bifidobacterium. However, other beneficial bacteria recently revealed may also be targeted to enhance their growth as they establish themselves as the next generation of health-promoting microbes. These include anaerobes such as Akkermansia muciniphila, Faecalibacterium prausnitzii and Eubacterium rectale. Identification of growth substrates/bioactives through the analysis of genome sequence data can aid in elucidating which substrates may best enhance the growth of these microbes which are often difficult to grow.

The phenotypic microbial trait analyser, Traitar, can predict 67 phenotypes based on the genome sequence inputted. Some of these traits include substrates that could potentially be utilised by the bacteria. Another tool, CarveMe, which has been created with the aim of making metabolic modelling more user-friendly, was also used with the same genomes. A select number of substrates identified in both tools have been chosen to be evaluated in vitro in order to establish the accuracy of these predictive tools as well as giving an indication as to how these beneficial microbes can be modulated through dietary components.