title: Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors: Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Via Università 100, 80055, Portici, Italy.
authors: Francesca
authors: F
authors: De Filippis
authors: Department of Food Science, University of Parma, Parco Area delle Scienze 48/A, 43124, Parma, Italy.
authors: Nicoletta
authors: N
authors: Pellegrini
authors: Department of Agricultural and Food Sciences, Alma Mater Studiorum University of Bologna, viale Fanin 44, 40127, Bologna, Italy.|Inter-Departmental Centre for Industrial Agri-Food Research, Alma Mater Studiorum University of Bologna, Piazza Goidanich 60, 47521, Cesena, Italy.
authors: Luca
authors: L
authors: Laghi
authors: Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/a, 70126, Bari, Italy.
authors: Marco
authors: M
authors: Gobbetti
authors: Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Via Università 100, 80055, Portici, Italy. ercolini@unina.it.
authors: Danilo
authors: 0000-0002-3474-2884
authors: D
authors: Ercolini
mesh_terms: D001439:Bacteroides / Q000145:classification / Q000254:growth & development / Q000302:isolation & purification*; D004032:Diet; D059305:Diet, High-Fat; D014676:Diet, Vegetarian; D004043:Dietary Fiber / Q000378:metabolism; D004044:Dietary Proteins / Q000378:metabolism; D005243:Feces / Q000382:microbiology; D005247:Feeding Behavior; D000069196:Gastrointestinal Microbiome / Q000502:physiology*; D041981:Gastrointestinal Tract / Q000382:microbiology*; D018720:Prevotella / Q000145:classification / Q000254:growth & development / Q000302:isolation & purification*; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D004043:Dietary Fiber; D004044:Dietary Proteins; D012336:RNA, Ribosomal, 16S
keywords: Gut microbiota; Oligotyping; Omnivore diet; Plant-based diet