title: Bacterial concentration and diversity in fresh tropical shrimps (Penaeus notialis) and the surrounding brackish waters and sediment.
abstract: This study aimed at determining bacterial concentration and diversity in fresh tropical shrimps (Penaeus notialis) and their surrounding brackish waters and sediment. Freshly caught shrimp, water and sediment samples were collected in Lakes Nokoue and Aheme in Benin (West Africa) during two periods with different water salinity and temperature. We used complementary culture-dependent and culture-independent methods for microbiota analysis. During both sampling periods, total mesophilic aerobic counts in shrimp samples ranged between 4.4 and 5.9 log CFU/g and were significantly higher than in water or sediment samples. In contrast, bacterial diversity was higher in sediment or water than in shrimps. The dominant phyla were Firmicutes and Proteobacteria in shrimps, Firmicutes, Proteobacteria, and Actinobacteria in water, and Proteobacteria and Chloroflexi in sediment. At species level, distinct bacterial communities were associated with sediment, water and shrimps sampled at the same site the same day. The study suggests that the bacterial community of tropical brackish water shrimps cannot be predicted from the microbiota of their aquatic environment. Thus, monitoring of microbiological quality of aquatic environments might not reflect shrimp microbiological quality.
authors.affiliation: Laboratoire de Biochimie Microbienne et de Biotechnologie Alimentaire, University of Abomey-Calavi, 01 B.P. 526 Cotonou, Benin; Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands.
authors.forename: D Sylvain
authors.initials: DS
authors.lastname: Dabadé
authors.affiliation: Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands.
authors.forename: Judith C M
authors.initials: JC
authors.lastname: Wolkers-Rooijackers
authors.affiliation: Laboratoire de Biochimie Microbienne et de Biotechnologie Alimentaire, University of Abomey-Calavi, 01 B.P. 526 Cotonou, Benin.
authors.forename: Paulin
authors.initials: P
authors.lastname: Azokpota
authors.affiliation: Laboratoire de Biochimie Microbienne et de Biotechnologie Alimentaire, University of Abomey-Calavi, 01 B.P. 526 Cotonou, Benin.
authors.forename: D Joseph
authors.initials: DJ
authors.lastname: Hounhouigan
authors.affiliation: Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands.
authors.forename: Marcel H
authors.initials: MH
authors.lastname: Zwietering
authors.affiliation: Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands.
authors.forename: M J Rob
authors.initials: MJ
authors.lastname: Nout
authors.affiliation: Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands. Electronic address: Heidy.denBesten@wur.nl.
authors.forename: Heidy M W
authors.initials: HM
authors.lastname: den Besten
mesh_terms: D039903:Actinobacteria / Q000235:genetics / Q000302:isolation & purification; D000354:Africa, Western; D000818:Animals; D015373:Bacterial Typing Techniques; D001541:Benin; D041862:Chloroflexi / Q000235:genetics / Q000302:isolation & purification; D000068536:Bacillota / Q000235:genetics / Q000302:isolation & purification; D019015:Geologic Sediments / Q000382:microbiology*; D064307:Microbiota / Q000235:genetics*; D008969:Molecular Sequence Data; D033561:Penaeidae / Q000382:microbiology*; D020560:Proteobacteria / Q000235:genetics / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S; D000068357:Saline Waters; D012758:Shellfish / Q000382:microbiology*; D012988:Soil Microbiology; D014871:Water Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: Clone libraries analysis; Invertebrates microbiota; PCR-DGGE; Tropical fishery products