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Competing Interests: Funding Support and Author Disclosures Dr Di Costanzo is a recipient of a research position under cofunding from the European Union REACT-EU, PON Research and Innovation 2014-2020. Dr Pirona is supported by GenomeUp srl through an industrial PhD scholarship. Dr Bini has received personal fees for public speaking from SOBI; has stock options in Eli Lilly, UnitedHealth, Novo Nordisk, Merck, and Thermo Fisher Scientific; and has received grants for meeting participation from Novartis. Dr D’Erasmo has received personal fees for public speaking or consultancy or grant support from Amryt Pharmaceutical, Akcea Therapeutics, SOBI, AuroraBiopharma, Novartis, Amarin, Daiichi-Sankyo, Bayer, Ultragenyx, and Sandoz. Dr Baratta has received personal fees for public speaking from Sandoz. Dr Arca has received research grant support from Amryt Pharmaceutical, Amgen, IONIS, Akcea Therapeutics, Daiichi-Sankyo, Novartis, Pfizer, and Regeneron; has served as a consultant for Amgen, Akcea Therapeutics, Daiichi-Sankyo, and Ultragenyx; and has received fees for lecturing, congress participation, and advisory board participation from Amgen, Amryt Pharmaceutical, Daiichi-Sankyo, Regeneron, Sanofi, Amarin, and Ultragenyx. All other authors have reported that they have no relationships relevant to the contents of this paper to disclose.

Background: Crohn's disease (CD) is characterized by chronic intestinal inflammation. Diet is a key modifiable factor influencing the gut microbiome (GM) and a risk factor for CD. However, the impact of diet modulation on GM function in CD patients is understudied. Herein, we evaluated the effect of a high-fiber, low-fat diet (the Mi-IBD diet) on GM function in CD patients. All participants were instructed to follow the Mi-IBD diet for 8 weeks. One group of CD patients received one-time diet counseling only (Gr1); catered food was supplied for the other three groups, including CD patients (Gr2) and dyads of CD patients and healthy household controls (HHCs) residing within the same household (Gr3-HHC dyads). Stool samples were collected at baseline, week 8, and week 36, and analyzed by liquid chromatography-tandem mass spectrometry., Results: At baseline, the metaproteomic profiles of CD patients and HHCs differed. The Mi-IBD diet significantly increased carbohydrate and iron transport and metabolism. The predicted microbial composition underlying the metaproteomic changes differed between patients with ileal only disease (ICD) or colonic involvement: ICD was characterized by decreased Faecalibacterium abundance. Even on the Mi-IBD diet, the CD patient metaproteome displayed significant underrepresentation of carbohydrate and purine/pyrimidine synthesis pathways compared to that of HHCs. Human immune-related proteins were upregulated in CD patients compared to HHCs., Conclusions: The Mi-IBD diet changed the microbial function of CD patients and enhanced carbohydrate metabolism. Our metaproteomic results highlight functional differences in the microbiome according to disease location. Notably, our dietary intervention yielded the most benefit for CD patients with colonic involvement compared to ileal-only disease. Video Abstract., (© 2024. The Author(s).)

The present study aimed to investigate the pharyngeal and nasal microbiota composition in children with adenotonsillar hypertrophy (AH) and assess longitudinal alterations in both microbiota after a probiotic oral spray treatment. A cohort of 57 AH patients were enrolled and randomly assigned to the probiotic and placebo groups for a 5-month treatment course. Pharyngeal and nasal swabs were collected before and after treatment and analyzed by 16S rRNA-based metataxonomics and axenic cultures for pathobiont identification. 16S rRNA sequences from pharyngeal and nasal swabs of 65 healthy children (HC) were used as microbiota reference profiles. We found that the pharyngeal and nasal microbiota of AH children were similar. When compared to HC, we observed an increase of the genera Rothia , Granulicatella , Streptococcus , Neisseria , and Haemophilus , as well as a reduction of Corynebacterium , Pseudomonas, Acinetobacter, and Moraxella in both microbiota of AH patients. After probiotic treatment, we confirmed the absence of adverse effects and a reduction of upper respiratory tract infections (URTI). Moreover, the composition of pharyngeal microbiota was positively influenced by the reduction of potential pathobionts, like Haemophilus spp., with an increase of beneficial microbial metabolic pathways. Finally, the probiotic reduced the abundance of the pathobionts Streptococcus mitis and Gemella haemolysans in relation to AH severity. In conclusion, our results highlight the alterations of the pharyngeal and nasal microbiota associated with AH. Moreover, probiotic administration conferred protection against URTI and reduced the presence of potential pathobionts in patients with AH., Importance: Adenotonsillar hypertrophy (AH) is considered the main cause of breathing disorders during sleep in children. AH patients, after significant morbidity and often multiple courses of antibiotics, often proceed to tonsillectomy and/or adenoidectomy. Given the potential risks associated with these procedures, there is a growing interest in the use of nonsurgical adjuvant therapies, such as probiotics, that could potentially reduce their need for surgical intervention. In this study, we investigated the pharyngeal and nasal microbiota in patients with AH compared with healthy children. Furthermore, we tested the effects of probiotic spray administration on both disease symptoms and microbiota profiles, to evaluate the possible use of this microbial therapy as an adjuvant for AH patients., Competing Interests: Authors I.P. and G.M. are employed by GenomeUp SRL, Viale Pasteur, 6, 00144, Rome, Italy. Authors V.D. and L.M. are employed by DMG, Pomezia, Italy. Author L.P. received research support from DMG. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

The relationship between COVID-19 and nasopharyngeal (NP) microbiota has been investigated mainly in the adult population. We explored the NP profile of children affected by COVID-19, compared to healthy controls (CTRLs). NP swabs of children with COVID-19, collected between March and September 2020, were investigated at the admission ( T 0 ), 72 h to 7 days ( T 1 ), and at the discharge ( T 2 ) of the patients. NP microbiota was analyzed by 16S rRNA targeted-metagenomics. Data from sequencing were investigated by QIIME 2.0 and PICRUSt 2. Multiple machine learning (ML) models were exploited to classify patients compared to CTRLs. The NP microbiota of COVID-19 patients ( N = 71) was characterized by reduction of α-diversity compared to CTRLs ( N = 59). The NP microbiota of COVID-19 cohort appeared significantly enriched in Streptococcus , Haemophilus , Staphylococcus , Veillonella , Enterococcus , Neisseria , Moraxella , Enterobacteriaceae, Gemella , Bacillus , and reduced in Faecalibacterium , Akkermansia , Blautia , Bifidobacterium , Ruminococcus , and Bacteroides, compared to CTRLs (FDR < 0.001). Exploiting ML models, Enterococcus, Pseudomonas, Streptococcus, Capnocytopagha, Tepidiphilus, Porphyromonas, Staphylococcus , and Veillonella resulted as NP microbiota biomarkers, in COVID-19 patients. No statistically significant differences were found comparing the NP microbiota profile of COVID-19 patients during the time-points or grouping patients on the basis of high, medium, and low viral load (VL). This evidence provides specific pathobiont signatures of the NP microbiota in pediatric COVID-19 patients, and the reduction of anaerobic protective commensals. Our data suggest that the NP microbiota may have a specific disease-related signature since infection onset without changes during disease progression, regardless of the SARS-CoV-2 VL., Importance: Since the beginning of pandemic, we know that children are less susceptible to severe COVID-19 disease. A potential role of the nasopharyngeal (NP) microbiota has been hypothesized but to date, most of the studies have been focused on adults. We studied the NP microbiota modifications in children affected by SARS-CoV-2 infection showing a specific NP microbiome profile, mainly composed by pathobionts and almost missing protective anaerobic commensals. Moreover, in our study, specific microbial signatures appear since the first days of infection independently from SARS-CoV-2 viral load., Competing Interests: Authors G.M. and V.G. are employed by GenomeUp SRL, Viale Pasteur, Rome, Italy. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.