nutrients Article Gut Microbiota Functional Dysbiosis Relates to Individual Diet in Subclinical Carotid Atherosclerosis Andrea Baragetti 1,† , Marco Severgnini 2,† , Elena Olmastroni 3 , Carola Conca Dioguardi 4 , Elisa Mattavelli 1 , Andrea Angius 5 , Luca Rotta 6 , Javier Cibella 7 , Giada Caredda 1 , Clarissa Consolandi 2 , Liliana Grigore 8,9 , Fabio Pellegatta 8,9 , Flavio Giavarini 1 , Donatella Caruso 1 , Giuseppe Danilo Norata 1 , Alberico Luigi Catapano 1,9, * and Clelia Peano 4,7   Citation: Baragetti, A.; Severgnini, M.; Olmastroni, E.; Dioguardi, C.C.; Mattavelli, E.; Angius, A.; Rotta, L.; Cibella, J.; Caredda, G.; Consolandi, C.; et al. Gut Microbiota Functional Dysbiosis Relates to Individual Diet in Subclinical Carotid Atherosclerosis. Nutrients 2021, 13, 304. https://doi.org/ 10.3390/nu13020304 Received: 9 December 2020 Accepted: 15 January 2021 Published: 21 January 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1 Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy; andrea.baragetti@unimi.it (A.B.); elisa.mattavelli@unimi.it (E.M.); giada.caredda@unimi.it (G.C.); flavio.giavarini@unimi.it (F.G.); donatella.caruso@unimi.it (D.C.); danilo.norata@unimi.it (G.D.N.) 2 Institute of Biomedical Technologies, National Research Council, 20090 Segrate, Milan, Italy; marco.severgnini@itb.cnr.it (M.S.); clarissa.consolandi@itb.cnr.it (C.C.) 3 Epidemiology and Preventive Pharmacology Service (SEFAP), Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy; olmastronielena92@gmail.com 4 Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, Rozzano, 20125 Milan, Italy; carola.conca_dioguardi@humanitas.it (C.C.D.); clelia.peano@humanitasresearch.it (C.P.) 5 Institute of Genetic and Biomedical Research, National Research Council, 09042 Cagliari, Italy; andrea.angius@irgb.cnr.it 6 Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy; luca.rotta@ieo.it 7 Genomic Unit, IRCCS, Humanitas Clinical and Research Center, 20090 Rozzano, Milan, Italy; Huge@humanitasresearch.it 8 S.I.S.A. Center for the Study of Atherosclerosis, Bassini Hospital, 20092 Cinisello Balsamo, Milan, Italy; grigore.centroatero@gmail.com (L.G.); fabio.pellegatta@guest.unimi.it (F.P.) 9 MultiMedica IRCCS, 20092 Cinisello Balsamo, Milan, Italy * Correspondence: alberico.catapano@unimi.it; Tel.: +39-0250-318-302 † These authors equally contributed. Abstract: Gut Microbiota (GM) dysbiosis associates with Atherosclerotic Cardiovascular Diseases (ACVD), but whether this also holds true in subjects without clinically manifest ACVD represents a challenge of personalized prevention. We connected exposure to diet (self-reported by food diaries) and markers of Subclinical Carotid Atherosclerosis (SCA) with individual taxonomic and functional GM profiles (from fecal metagenomic DNA) of 345 subjects without previous clinically manifest ACVD. Subjects without SCA reported consuming higher amounts of cereals, starchy vegetables, milky products, yoghurts and bakery products versus those with SCA (who reported to consume more mechanically separated meats). The variety of dietary sources significantly overlapped with the separations in GM composition between subjects without SCA and those with SCA (RV coefficient between nutrients quantities and microbial relative abundances at genus level = 0.65, p-value = 0.047). Additionally, specific bacterial species (Faecalibacterium prausnitzii in the absence of SCA and Escherichia coli in the presence of SCA) are directly related to over-representation of metagenomic pathways linked to different dietary sources (sulfur oxidation and starch degradation in absence of SCA, and metabolism of amino acids, syntheses of palmitate, choline, carnitines and Trimethylamine n-oxide in presence of SCA). These findings might contribute to hypothesize future strategies of personalized dietary intervention for primary CVD prevention setting. Keywords: Atherosclerotic Cardiovascular Diseases; Gut Microbiota; next generation sequencing 1. Introduction Atherosclerotic Cardiovascular Diseases (ACVD) still contribute significantly to ex- cessive mortality, despite pharmacological weapons substantially improving their treat- Nutrients 2021, 13, 304. https://doi.org/10.3390/nu13020304 https://www.mdpi.com/journal/nutrients