title: PCR screening of an African fermented pearl-millet porridge metagenome to investigate the nutritional potential of its microbiota.
abstract: Cereals are staple foods in most African countries, and many African cereal-based foods are spontaneously fermented. The nutritional quality of cereal products can be enhanced through fermentation, and traditional cereal-based fermented foods (CBFFs) are possible sources of lactic acid bacteria (LAB) with useful nutritional properties. The nutritional properties of LAB vary depending on the species and even on the strain, and the microbial composition of traditional CBFFs varies from one traditional production unit (TPU) to another. The nutritional quality of traditional CBFFs may thus vary depending on their microbial composition. As the isolation of potentially useful LAB from traditional CBFFs can be very time consuming, the aim of this study was to use PCR to assess the nutritional potential of LAB directly on the metagenomes of pearl-millet based fermented porridges (ben-saalga) from Burkina Faso. Genes encoding enzymes involved in different nutritional activities were screened in 50 metagenomes extracted from samples collected in 10 TPUs in Ouagadougou. The variability of the genetic potential was recorded. Certain genes were never detected in the metagenomes (genes involved in carotenoid synthesis) while others were frequently detected (genes involved in folate and riboflavin production, starch hydrolysis, polyphenol degradation). Highly variable microbial composition - assessed by real-time PCR - was observed among samples collected in different TPUs, but also among samples from the same TPU. The high frequency of the presence of genes did not necessarily correlate with in situ measurements of the expected products. Indeed, no significant correlation was found between the microbial variability and the variability of the genetic potential. In spite of the high rate of detection (80%) of both genes folP and folK, encoding enzymes involved in folate synthesis, the folate content in ben-saalga was rather low (median: 0.5μg/100g fresh weight basis). This work highlighted the limit of evaluating the nutritional potential of the microbiota of traditional fermented foods by the only screening of genes in metagenomes, and suggests that such a screening should be completed by a functional analysis.
authors.affiliation: Institute of Research for Development (IRD), UMR 204 Food and Nutrition Research in the Global South (NUTRIPASS), IRD/University of Montpellier/SupAgro, BP 64501, 911 Avenue Agropolis, 34394 Montpellier Cedex 5, France.
authors.forename: Fabien
authors.initials: F
authors.lastname: Saubade
authors.affiliation: Institute of Research for Development (IRD), UMR 204 Food and Nutrition Research in the Global South (NUTRIPASS), IRD/University of Montpellier/SupAgro, BP 64501, 911 Avenue Agropolis, 34394 Montpellier Cedex 5, France.
authors.forename: Christèle
authors.initials: C
authors.lastname: Humblot
authors.affiliation: Institute of Research for Development (IRD), UMR 204 Food and Nutrition Research in the Global South (NUTRIPASS), IRD/University of Montpellier/SupAgro, BP 64501, 911 Avenue Agropolis, 34394 Montpellier Cedex 5, France.
authors.forename: Youna M
authors.initials: YM
authors.lastname: Hemery
authors.affiliation: Institute of Research for Development (IRD), UMR 204 Food and Nutrition Research in the Global South (NUTRIPASS), IRD/University of Montpellier/SupAgro, BP 64501, 911 Avenue Agropolis, 34394 Montpellier Cedex 5, France. Electronic address: jean-pierre.guyot@ird.fr.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Guyot
mesh_terms: D019149:Bioreactors; D002050:Burkina Faso; D002338:Carotenoids / Q000096:biosynthesis; D002523:Edible Grain / Q000382:microbiology*; D005285:Fermentation; D005492:Folic Acid / Q000096:biosynthesis; D005516:Food Microbiology; D006868:Hydrolysis; D052197:Limosilactobacillus fermentum / Q000235:genetics* / Q000378:metabolism; D054892:Metagenome / Q000235:genetics*; D064307:Microbiota / Q000235:genetics*; D009753:Nutritive Value; D031782:Pennisetum / Q000382:microbiology*; D059808:Polyphenols / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D012256:Riboflavin / Q000096:biosynthesis; D013213:Starch / Q000378:metabolism; D015003:Yeasts / Q000235:genetics* / Q000378:metabolism
chemical_list: D059808:Polyphenols; D002338:Carotenoids; D013213:Starch; D005492:Folic Acid; D012256:Riboflavin
keywords: Lactobacillus fermentum; Real-time PCR; Starch metabolism; Vitamin B9; Yeasts, Pennisetum glaucum