Qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance are assessed. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA was updated with 54 biological agents, received between April and September 2019; 23 already had QPS status, 14 were excluded from the QPS exercise (7 filamentous fungi, 6 Escherichia coli, Sphingomonas paucimobilis which was already evaluated). Seventeen, corresponding to 16 TUs, were evaluated for possible QPS status, fourteen of these for the first time, and Protaminobacter rubrum, evaluated previously, was excluded because it is not a valid species. Eight TUs are recommended for QPS status. Lactobacillus parafarraginis and Zygosaccharomyces rouxii are recommended to be included in the QPS list. Parageobacillus thermoglucosidasius and Paenibacillus illinoisensis can be recommended for the QPS list with the qualification 'for production purposes only' and absence of toxigenic potential. Bacillus velezensis can be recommended for the QPS list with the qualification 'absence of toxigenic potential and the absence of aminoglycoside production ability'. Cupriavidus necator, Aurantiochytrium limacinum and Tetraselmis chuii can be recommended for the QPS list with the qualification 'production purposes only'. Pantoea ananatis is not recommended for the QPS list due to lack of body of knowledge in relation to its pathogenicity potential for plants. Corynebacterium stationis, Hamamotoa singularis, Rhodococcus aetherivorans and Rhodococcus ruber cannot be recommended for the QPS list due to lack of body of knowledge. Kodamaea ohmeri cannot be recommended for the QPS list due to safety concerns.

https://efsa.onlinelibrary.wiley.com/doi/pdf/10.2903/j.efsa.2020.5965

Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 13: suitability of taxonomic units notified to EFSA until September 2020.

The gut microbiota is a dense and diverse ecosystem that is involved in many physiological functions as well as in disease pathogenesis. It is dominated by bacteria, which have been extensively studied in the past 15 years; however, other microorganisms, such as fungi, phages, archaea and protists, are also present in the gut microbiota. Exploration of the fungal component, namely, the mycobiota, is at an early stage, and several specific technical challenges are associated with mycobiota analysis. The number of fungi in the lower gastrointestinal tract is far lower than that of bacteria, but fungal cells are much larger and much more complex than bacterial cells. In addition, a role of the mycobiota in disease, notably in IBD, is indicated by both descriptive data in humans and mechanistic data in mice. Interactions between bacteria and fungi within the gut, their functional roles and their interplay with the host and its immune system are fascinating areas that researchers are just beginning to investigate. In this Review, we discuss the newest data on the gut mycobiota and explore both the technical aspects of its study and its role in health and gastrointestinal diseases. The authors review the newest data on the gut fungal microbiota. They explore technical aspects of its analysis, how the mycobiome is influenced by immune and environmental factors, including fungi–bacteria interactions, and links between the mycobiota and gut diseases.

The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases

SummaryBackground
The concept of an altered collective gut microbiota rather than identification of a single culprit is possibly the most significant development in inflammatory bowel disease research. We have entered the “omics” era, which now allows us to undertake large-scale/high-throughput microbiota analysis which may well define how we approach diagnosis and treatment of inflammatory bowel disease (IBD) in the future, with a strong steer towards personalised therapeutics.

Aim
To assess current epidemiological, experimental and clinical evidence of the current status of knowledge relating to the gut microbiome, and its role in IBD, with emphasis on reviewing the evidence relating to microbial therapeutics and future microbiome modulating therapeutics.

Methods
A Medline search including items ‘intestinal microbiota/microbiome’, ‘inflammatory bowel disease’, ‘ulcerative colitis’, ‘Crohn's disease’, ‘faecal microbial transplantation’, ‘dietary manipulation’ was performed.

Results
Disease remission and relapse are associated with microbial changes in both mucosal and luminal samples. In particular, a loss of species richness in Crohn's disease has been widely observed. Existing therapeutic approaches broadly fall into 3 categories, namely: accession, reduction or indirect modulation of the microbiome. In terms of microbial therapeutics, faecal microbial transplantation appears to hold the most promise; however, differences in study design/methodology mean it is currently challenging to elegantly translate results into clinical practice.

Conclusions
Existing approaches to modulate the gut microbiome are relatively unrefined. Looking forward, the future of microbiome-modulating therapeutics looks bright with several novel strategies/technologies on the horizon. Taken collectively, it is clear that ignoring the microbiome in IBD is not an option.

Review article: the gut microbiome in inflammatory bowel disease-avenues for microbial management.

Gut microbial dysbiosis and altered metabonomics have been implicated in the pathogenesis of Crohn’s disease (CD). The aim of our study was to characterize the gut microbiome structure and metaboli...

https://www.tandfonline.com/doi/pdf/10.1080/19490976.2020.1865708

Microbial and metabolic features associated with outcome of infliximab therapy in pediatric Crohn's disease.

The gut microbiome comprised of microbes from multiple kingdoms, including bacteria, fungi, and viruses. Emerging evidence suggests that the intestinal fungi (the gut "mycobiome") play an important role in host immunity and inflammation. Advances in next generation sequencing methods to study the fungi in fecal samples and mucosa tissues have expanded our understanding of gut fungi in intestinal homeostasis and systemic immunity in health and their contribution to different human diseases. In this review, the current status of gut mycobiome in health, early life, and different diseases including inflammatory bowel disease, colorectal cancer, and metabolic diseases were summarized.

https://journals.sagepub.com/doi/pdf/10.1177/17562848211047130

The role of gut mycobiome in health and diseases.

Background & Aims: although increasing evidence suggests a role for fungi in inflammatory bowel disease (IBD), data are scarce and mostly from adults. Our aim was to define the characteristics of fungal microbiota in newly-diagnosed treatment-naive children with Crohn disease (CD).

Methods: The children referred for colonoscopy were prospectively enrolled in the study at King Khalid University Hospital, King Saud University and Al Mofarreh Polyclinics in Riyadh. Tissue and stool samples were collected and frozen till sequencing analysis. The children with confirmed CD diagnosis were designated as cases and the others as non- IBD controls. 78 samples were collected from 35 children (15 CD and 20 controls). Statistical analysis was performed to investigate CD associations and diversity.

Results: CD-associated fungi varied with the level of phylogenetic tree. There was no significant difference in abundance between normal and inflamed mucosa. Significantly abundant CD-associated taxa included Psathyrellaceae (p=0.01), Cortinariaceae (p= 0.04), Psathyrella (p= 0.004), and Gymnopilus (p=0.03).Monilinia was significantly depleted (p=0.03), whereas other depleted taxa, although not statistically significant, included Leotiomycetes (p= 0.06), Helotiales (p=0.08), Sclerotiniaceae (p=0.07). There was no significant difference in fungal diversity between CD and controls.

Conclusions: We report highly significant fungal dysbiosis in newly diagnosed treatment naive CD children. Depleted and more abundant taxa suggest anti-inflammatory and proinflamatory potentials respectively. Further studies with larger sample size including functional analysis are needed to clarify the significance of the fungal community in the pathogenesis of CD.

/pdf/fungal-microbiota-profile-in-newly-diagnosed-treatment-naive-4u6z0f313z.pdf

Fungal Microbiota Profile in Newly Diagnosed Treatment-naïve Children with Crohn’s Disease

AIM To investigate the accuracy of fungal dysbiosis in mucosa and stool for predicting the diagnosis of Crohn's disease (CD). METHODS Children were prospectively enrolled in two medical centers: one university hospital and one private gastroenterology clinic in the city of Riyadh, Kingdom of Saudi Arabia. The children with confirmed diagnosis of CD by standard guidelines were considered cases, and the others were considered non-inflammatory bowel disease controls. Mucosal and stool samples were sequenced utilizing Illumina MiSeq chemistry following the manufacturer's protocols, and abundance and diversity of fungal taxa in mucosa and stool were analyzed. Sparse logistic regression was used to predict the diagnosis of CD. The accuracy of the classifier was tested by computing the receiver operating characteristic curves with 5-fold stratified cross-validation under 100 permutations of the training data partition and the mean area under the curve (AUC) was calculated. RESULTS All the children were Saudi nationals. There were 15 children with CD and 20 controls. The mean age was 13.9 (range: 6.7-17.8) years for CD children and 13.9 (3.25-18.6) years for controls, and 10/15 (67%) of the CD and 13/20 (65%) of the control subjects were boys. CD locations at diagnosis were ileal (L1) in 4 and colonic (L3) in 11 children, while CD behavior was non-stricturing and non-penetrating (B1) in 12 and stricturing (B2) in 3 children. The mean AUC for the fungal dysbiosis classifier was significantly higher in stools (AUC = 0.85 ± 0.057) than in mucosa (AUC = 0.71 ± 0.067) (P < 0.001). Most fungal species were significantly more depleted in stools than mucosal samples, except for Saccharomyces cerevisiae and S. bayanus, which were significantly more abundant. Diversity was significantly more reduced in stools than in mucosa. CONCLUSION We found high AUC of fungal dysbiosis in fecal samples of children with CD, suggesting high accuracy in predicting diagnosis of CD.

Fungal dysbiosis predicts the diagnosis of pediatric Crohn’s disease

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Fungal Microbiota Profile in Newly Diagnosed Treatment-naïve Children with Crohn’s Disease

Fungal dysbiosis predicts the diagnosis of pediatric Crohn’s disease