title: Spatial Variation of the Gut Microbiota in Broiler Chickens as Affected by Dietary Available Phosphorus and Assessed by T-RFLP Analysis and 454 Pyrosequencing.
abstract: Molecular fingerprinting and sequencing based techniques have been widely used to characterize microbial communities. Terminal restriction fragment length polymorphism (T-RFLP) and 454-pyrosequencing were used to determine the microorganisms present in the different sections of the chicken gastrointestinal tract (GIT) (crop, jejunum, ileum and caeca). Broilers fed with diets differing in phosphorous (P) and calcium (Ca) as well as in phytase levels were used to study the microbiota of the upper and lower part of the GIT. A database with terminal restriction fragments (T-RF) of the most important organism present in the different gastrointestinal sections was constructed. The analysis revealed a distinct microbial assemblage on each section. Regardless of the diet, crop, jejunum and ileum were mainly colonized by Lactobacillaceae, and caeca were the most diverse site. The correlation between Lactobacillus crispatus and L. reuteri was positive in the crop, but negative in the jejunum. In crop samples, higher P and Ca levels led to a shift in the abundance of L. reuteri and L. crispatus to L. salivarius and L. taiwanensis whereas in the ileum supplementation of phytase favored L. salivarius and L. taiwanensis but resulted in decreased abundance of L. crispatus. Both methods were correlating significantly, being T-RFLP a reliable fingerprinting method to rapidly analyze large numbers of samples in a cost-effective and rapid manner. Results are easy to interpret with no need of deep bioinformatics knowledge and can be integrated with taxonomic information.
authors.affiliation: Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany.
authors.forename: Maren
authors.initials: M
authors.lastname: Witzig
authors.forename: Amelia
authors.initials: A
authors.lastname: Carminha-Silva
authors.affiliation: Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany.
authors.forename: Amelia
authors.initials: A
authors.lastname: Camarinha da Silva
authors.affiliation: Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Green-Engert
authors.affiliation: Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Hoelzle
authors.affiliation: Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany.
authors.forename: Ellen
authors.initials: E
authors.lastname: Zeller
authors.affiliation: Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Seifert
authors.affiliation: Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany.
authors.forename: Ludwig E
authors.initials: LE
authors.lastname: Hoelzle
authors.affiliation: Institut für Nutztierwissenschaften, Universität Hohenheim, Stuttgart, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Rodehutscord
mesh_terms: D000821:Animal Feed; D000824:Animal Nutritional Physiological Phenomena; D000818:Animals; D002118:Calcium / Q000008:administration & dosage; D002645:Chickens / Q000382:microbiology*; D003001:Cloning, Molecular; D004032:Diet; D004063:Digestion; D005260:Female; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000382:microbiology; D020869:Gene Expression Profiling; D006863:Hydrogen-Ion Concentration; D007777:Lactobacillaceae / Q000145:classification; D008969:Molecular Sequence Data; D015999:Multivariate Analysis; D016226:Phosphorus, Dietary / Q000008:administration & dosage; D012150:Polymorphism, Restriction Fragment Length; D025341:Principal Component Analysis; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D016226:Phosphorus, Dietary; D012336:RNA, Ribosomal, 16S; D002118:Calcium