Unusual sub-genus associations of fecal Prevotella and Bacteroides with specific dietary patterns

Background: Diet has a recognized effect in shaping gut microbiota. Many studies link an increase in Prevotella to high-fibre diet, while Bacteroides abundance is usually associated with the consumption of animal fat and protein-rich diets. Nevertheless, closely related species and strains may harbour different genetic pools; therefore, further studies should aim to understand whether species of the same genus are consistently linked to dietary patterns or equally responsive to diet variations. Here, we used oligotyping of 16S rRNA gene sequencing data to exploit the diversity within Prevotella and Bacteroides genera in faecal samples of omnivore and non-omnivore subjects from a previously studied cohort. Results: A great heterogeneity was found in oligotype composition. Nevertheless, different oligotypes within the same genus showed distinctive correlation patterns with dietary components and metabolome. We found that some Prevotella oligotypes are significantly associated with the plant-based diet but some are associated with animal-based nutrients, and the same applies to Bacteroides. Therefore, an indiscriminate association of Bacteroidetes genera with specific dietary patterns may lead to an oversimplified vision that does not take into account sub-genus diversity and the different possible responses to dietary components. Conclusions: We demonstrated that Prevotella and Bacteroides oligotypes show distinctive correlation patterns with dietary components and metabolome. These results substantiate a current oversimplification of diet-dependent microbe-host associations and highlighted that sub-genus differences must be taken into account when planning gut microbiota modulation for health benefits

Proteolytic and lipolytic starter cultures and their effect on traditional fermented sausages ripening and sensory traits

In this study, three starter formulations including Lactobacillus curvatus and Staphylococcus xylosus strains selected in vitro on the basis of their lipolytic and proteolytic activities were employed for the manufacture of traditional fermented sausages of southern Italy. Microbial population, proteolysis, lipolysis, changes in free amino acids (FAA) and free fatty acids (FFA) and development of characteristic taste and flavor of the final product were investigated. Proteolysis and lipolysis were observed in sausages inoculated with proteolytic and lipolytic S. xylosus coupled with L. curvatus, while the sausage started with only S. xylosus without lactobacilli was identical to the non-inoculated control, indicating that the proteolysis could be due to both microbial activity and endogenous proteases activated by the decrease in pH. The statistical analysis applied to the instrumental and sensory data showed that there was an effect of the starter used on the characteristics of the sausage obtained. In particular, the control samples showed very close features different from the sausages obtained by adding starter cultures. Finally, analyzing the sensory parameters the sausages ripened without starter addition and those started without the L. curvatus AVL3 showed similar features indicating an influence of the presence of the lactobacilli on the final organoleptic quality of the sausages. An appropriate choice of a combination of strains in a starter formulation is fundamental to obtain products of the expected quality

Environmental microbiome mapping as a strategy to improve quality and safety in the food industry

In food industries, an environmentally-adapted microbiome can colonize the surfaces of equipment and tools and be transferred to the food product or intermediates of production. These complex microbial consortia may include microbial spoilers, pathogens, as well as beneficial microbes. Advances in sequencing technologies and metagenomics provide the opportunity to map the environmental microbiome in food industries at an unprecedented depth, highlighting the importance of the resident microbial communities in influencing food quality and safety, as well as the main factors shaping its composition and activities. However, specific technical issues must be considered. Although microbiome mapping in the food industry has the potential to revolutionize food safety and quality management systems, its application as routine practice is still challenging and technical issues limit the exploitation of the powerful information that can be obtained by the application of such state-of-the-art approaches

Animal rennets as sources of dairy lactic acid bacteria

The microbial composition of artisan and industrial animal rennet pastes was studied by using both culture-dependent and -independent approaches. Pyrosequencing targeting the 16S rRNA gene allowed to identify 361 operational taxonomic units (OTUs) to the genus/species level. Among lactic acid bacteria (LAB), Streptococcus thermophilus and some lactobacilli, mainly Lactobacillus crispatus and Lactobacillus reuteri, were the most abundant species, with differences among the samples. Twelve groups of microorganisms were targeted by viable plate counts revealing a dominance of mesophilic cocci. All rennets were able to acidify ultrahigh-temperature-processed (UHT) milk as shown by pH and total titratable acidity (TTA). Presumptive LAB isolated at the highest dilutions of acidified milks were phenotypically characterized, grouped, differentiated at the strain level by randomly amplified polymorphic DNA (RAPD)-PCR analysis, and subjected to 16S rRNA gene sequencing. Only 18 strains were clearly identified at the species level, as Enterococcus casseliflavus, Enterococcus faecium, Enterococcus faecalis, Enterococcus lactis, Lactobacillus delbrueckii, and Streptococcus thermophilus, while the other strains, all belonging to the genus Enterococcus, could not be allotted into any previously described species. The phylogenetic analysis showed that these strains might represent different unknown species. All strains were evaluated for their dairy technological performances. All isolates produced diacetyl, and 10 of them produced a rapid pH drop in milk, but only 3 isolates were also autolytic. This work showed that animal rennet pastes can be sources of LAB, mainly enterococci, that might contribute to the microbial diversity associated with dairy productions

Gut microbiota as target for innovative strategies against food allergy.

The dramatic increase in food allergy prevalence and severity globally requires effective strategies. Food allergy derives from a defect in immune tolerance mechanisms. Immune tolerance is modulated by gut microbiota function and structure, and microbiome alterations (dysbiosis) have a pivotal role in the development of food allergy. Environmental factors, including a low-fiber/high-fat diet, cesarean delivery, antiseptic agents, lack of breastfeeding, and drugs can induce gut microbiome dysbiosis, and have been associated with food allergy. New experimental tools and technologies have provided information regarding the role of metabolites generated from dietary nutrients and selected probiotic strains that could act on immune tolerance mechanisms. The mechanisms are multiple and still not completely defined. Increasing evidence has provided useful information on optimal bacterial species/strains, dosage, and timing for intervention. The increased knowledge of the crucial role played by nutrients and gut microbiota-derived metabolites is opening the way to a post-biotic approach in the stimulation of immune tolerance through epigenetic regulation. This review focused on the potential role of gut microbiome as the target for innovative strategies against food allergy

Therapeutic Effects of Butyrate on Pediatric Obesity: A Randomized Clinical Trial

Importance: The pediatric obesity disease burden imposes the necessity of new effective strategies. Objective: To determine whether oral butyrate supplementation as an adjunct to standard care is effective in the treatment of pediatric obesity. Design, Setting, and Participants: A randomized, quadruple-blind, placebo-controlled trial was performed from November 1, 2020, to December 31, 2021, at the Tertiary Center for Pediatric Nutrition, Department of Translational Medical Science, University of Naples Federico II, Naples, Italy. Participants included children aged 5 to 17 years with body mass index (BMI) greater than the 95th percentile. Interventions: Standard care for pediatric obesity supplemented with oral sodium butyrate, 20 mg/kg body weight per day, or placebo for 6 months was administered. Main Outcomes and Measures: The main outcome was the decrease of at least 0.25 BMI SD scores at 6 months. The secondary outcomes were changes in waist circumference; fasting glucose, insulin, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglyceride, ghrelin, microRNA-221, and interleukin-6 levels; homeostatic model assessment of insulin resistance (HOMA-IR); dietary and lifestyle habits; and gut microbiome structure. Intention-to-treat analysis was conducted. Results: Fifty-four children with obesity (31 girls [57%], mean [SD] age, 11 [2.91] years) were randomized into the butyrate and placebo groups; 4 were lost to follow-up after receiving the intervention in the butyrate group and 2 in the placebo group. At intention-to-treat analysis (n = 54), children treated with butyrate had a higher rate of BMI decrease greater than or equal to 0.25 SD scores at 6 months (96% vs 56%, absolute benefit increase, 40%; 95% CI, 21% to 61%; P < .01). At per-protocol analysis (n = 48), the butyrate group showed the following changes as compared with the placebo group: waist circumference, -5.07 cm (95% CI, -7.68 to -2.46 cm; P < .001); insulin level, -5.41 μU/mL (95% CI, -10.49 to -0.34 μU/mL; P = .03); HOMA-IR, -1.14 (95% CI, -2.13 to -0.15; P = .02); ghrelin level, -47.89 μg/mL (95% CI, -91.80 to -3.98 μg/mL; P < .001); microRNA221 relative expression, -2.17 (95% CI, -3.35 to -0.99; P < .001); and IL-6 level, -4.81 pg/mL (95% CI, -7.74 to -1.88 pg/mL; P < .001). Similar patterns of adherence to standard care were observed in the 2 groups. Baseline gut microbiome signatures predictable of the therapeutic response were identified. Adverse effects included transient mild nausea and headache reported by 2 patients during the first month of butyrate intervention. Conclusions and Relevance: Oral butyrate supplementation may be effective in the treatment of pediatric obesity. Trial Registration: ClinicalTrials.gov Identifier: NCT04620057

Distribution of antibiotic resistance genes in the saliva of healthy omnivores, ovo-lacto-vegetarians, and vegans

Food consumption allows the entrance of bacteria and their antibiotic resistance (AR) genes into the human oral cavity. To date, very few studies have examined the influence of diet on the composition of the salivary microbiota, and even fewer investigations have specifically aimed to assess the impact of different long-term diets on the salivary resistome. In this study, the saliva of 144 healthy omnivores, ovo-lacto-vegetarians, and vegans were screened by nested PCR for the occurrence of 12 genes conferring resistance to tetracyclines, macrolide-lincosamide-streptogramin B, vancomycin, and \u3b2-lactams. The tet(W), tet(M), and erm(B) genes occurred with the highest frequencies. Overall, no effect of diet on AR gene distribution was seen. Some differences emerged at the recruiting site level, such as the higher frequency of erm(C) in the saliva of the ovo-lacto-vegetarians and omnivores from Bologna and Turin, respectively, and the higher occurrence of tet(K) in the saliva of the omnivores from Bologna. A correlation of the intake of milk and cheese with the abundance of tet(K) and erm(C) genes was seen. Finally, when the occurrence of the 12 AR genes was evaluated along with geographical location, age, and sex as sources of variability, high similarity among the 144 volunteers was seen

Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals

Objectives MicroRNA (miRNA) profiles have been evaluated in several biospecimens in relation to common diseases for which diet may have a considerable impact. We aimed at characterising how specific diets are associated with the miRNome in stool of vegans, vegetarians and omnivores and how this is reflected in the gut microbial composition, as this is still poorly explored. Design We performed small RNA and shotgun metagenomic sequencing in faecal samples and dietary recording from 120 healthy volunteers, equally distributed for the different diets and matched for sex and age. Results We found 49 miRNAs differentially expressed among vegans, vegetarians and omnivores (adj. p 0.22, adj. p <0.05) with the estimated intake of nutrients, particularly animal proteins, phosphorus and, interestingly, lipids. In omnivores, higher Prevotella and Roseburia and lower Bacteroides abundances than in vegans and vegetarians were observed. Lipid metabolism-related miR-425-3p and miR-638 expression levels were associated with increased abundances of microbial species, such as Roseburia sp. CAG 182 and Akkermansia muciniphila, specific of different diets. An integrated analysis identified 25 miRNAs, 25 taxa and 7 dietary nutrients that clearly discriminated (area under the receiver operating characteristic curve=0.89) the three diets. Conclusion Stool miRNA profiles are associated with specific diets and support the role of lipids as a driver of epigenetic changes and host-microbial molecular interactions in the gut