title: Characterization of relative abundance of lactic acid bacteria species in French organic sourdough by cultural, qPCR and MiSeq high-throughput sequencing methods.
abstract: In order to contribute to the description of sourdough LAB composition, MiSeq sequencing and qPCR methods were performed in association with cultural methods. A panel of 16 French organic bakers and farmer-bakers were selected for this work. The lactic acid bacteria (LAB) diversity of their organic sourdoughs was investigated quantitatively and qualitatively combining (i) Lactobacillus sanfranciscensis-specific qPCR, (ii) global sequencing with MiSeq Illumina technology and (iii) molecular isolates identification. In addition, LAB and yeast enumeration, pH, Total Titratable Acidity, organic acids and bread specific volume were analyzed. Microbial and physico-chemical data were statistically treated by Principal Component Analysis (PCA) and Hierarchical Ascendant Classification (HAC). Total yeast counts were 6 log10to 7.6 log10CFU/g while LAB counts varied from 7.2 log10to 9.6 log10CFU/g. Values obtained by L. sanfranciscensis-specific qPCR were estimated between 7.2 and 10.3 log10CFU/g, except for one sample at 4.4 log10CFU/g. HAC and PCA clustered the sixteen sourdoughs into three classes described by their variables but without links to bakers' practices. L. sanfranciscensis was the dominant species in 13 of the 16 sourdoughs analyzed by Next Generation Sequencing (NGS), by the culture dependent method this species was dominant only in only 10 samples. Based on isolates identification, LAB diversity was higher for 7 sourdoughs with the recovery of L. curvatus, L. brevis, L. heilongjiangensis, L. xiangfangensis, L. koreensis, L. pontis, Weissella sp. and Pediococcus pentosaceus, as the most representative species. L. koreensis, L. heilongjiangensis and L. xiangfangensis were identified in traditional Asian food and here for the first time as dominant in organic sourdough. This study highlighted that L. sanfranciscensis was not the major species in 6/16 sourdough samples and that a relatively high LAB diversity can be observed in French organic sourdough.
authors.affiliation: Oniris, Laboratoire de Microbiologie Alimentaire et Industrielle, Rue de la Géraudière CS 82225, 44322 Nantes Cedex 3, France; INRA, UMR Sciences pour l'œnologie, 2 place Pierre Viala, 34060 Montpellier Cedex 01, France.
authors.forename: Elisa
authors.initials: E
authors.lastname: Michel
authors.affiliation: Oniris, Laboratoire de Microbiologie Alimentaire et Industrielle, Rue de la Géraudière CS 82225, 44322 Nantes Cedex 3, France.
authors.forename: Clarisse
authors.initials: C
authors.lastname: Monfort
authors.affiliation: Oniris, Laboratoire de Microbiologie Alimentaire et Industrielle, Rue de la Géraudière CS 82225, 44322 Nantes Cedex 3, France.
authors.forename: Marion
authors.initials: M
authors.lastname: Deffrasnes
authors.affiliation: INRA, UMR Sciences pour l'œnologie, 2 place Pierre Viala, 34060 Montpellier Cedex 01, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Guezenec
authors.affiliation: Oniris, Laboratoire de Microbiologie Alimentaire et Industrielle, Rue de la Géraudière CS 82225, 44322 Nantes Cedex 3, France.
authors.forename: Emilie
authors.initials: E
authors.lastname: Lhomme
authors.affiliation: INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 42 rue Georges Morel, 49007 Beaucouzé Cedex, France.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Barret
authors.affiliation: INRA, UMR Sciences pour l'œnologie, 2 place Pierre Viala, 34060 Montpellier Cedex 01, France.
authors.forename: Delphine
authors.initials: D
authors.lastname: Sicard
authors.affiliation: SECALIM Unit UMR1014, Oniris, INRA, Université Bretagne Loire, Nantes, France; UMR INRA 1014 Secalim, La Chantrerie CS, 40307, Nantes Cedex 3, France. Electronic address: xavier.dousset@oniris-nantes.fr.
authors.forename: Xavier
authors.initials: X
authors.lastname: Dousset
authors.affiliation: Oniris, Laboratoire de Microbiologie Alimentaire et Industrielle, Rue de la Géraudière CS 82225, 44322 Nantes Cedex 3, France. Electronic address: bernard.onno@oniris-nantes.fr.
authors.forename: Bernard
authors.initials: B
authors.lastname: Onno
mesh_terms: D001939:Bread / Q000382:microbiology*; D005285:Fermentation / Q000502:physiology*; D005516:Food Microbiology; D059014:High-Throughput Nucleotide Sequencing; D019344:Lactic Acid / Q000378:metabolism; D007778:Lactobacillus / Q000145:classification* / Q000235:genetics / Q000378:metabolism*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA
chemical_list: D012336:RNA, Ribosomal, 16S; D019344:Lactic Acid
keywords: Lactic acid bacteria; MiSeq; Molecular characterization; Organic sourdough; qPCR