Comparison of culture-dependent and independent approaches to characterize fecal bifidobacteria and lactobacilli.
Different culture-dependent and independent methods were applied to investigate the population of bifidobacteria and lactobacilli in the feces of five healthy subjects. Bacteria were isolated on MRS, a complex medium supporting growth of lactobacilli and bifidobacteria, and on three selective media for bifidobacteria and two for lactobacilli. Taxonomic characterization of the isolates was carried out by RAPD-PCR and partial 16S sequencing. The selectivity of genus-specific media was also investigated by challenging colonies from MRS plates to grow onto each medium. In parallel, a quantitative and qualitative description of bifidobacteria and lactic acid bacteria was obtained by FISH, qPCR, TRFLP, and 16S rRNA gene sequencing. Bifidobacteria did not fail to grow on their specific media and were easily isolated and enumerated, showing comparable quantitative data among culture-dependent and -independent techniques. The Bifidobacterium species identified on plates and those extracted from TRFLP and 16S rRNA gene sequencing were mostly overlapping. Selective media for lactobacilli gave unsuitable results, being too stringent or too permissive. The quantification of lactobacilli through selective plates, qPCR, FISH, and 16S rRNA gene sequencing gave unreliable results. Therefore, unlike bifidobacteria, intestinal lactobacilli are still problematic in terms of quantification and accurate profiling at level of species and possibly of strains by both culture-dependent and culture-independent techniques.
Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
Andrea
A
Quartieri
Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
Marta
M
Simone
Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
Caterina
C
Gozzoli
Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
Mina
M
Popovic
Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, Valencia, Spain.
Giuseppe
G
D'Auria
Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
Alberto
A
Amaretti
Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
Stefano
S
Raimondi
Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy. Electronic address: maddalena.rossi@unimore.it.
Maddalena
M
Rossi
D000328:Adult; D001644:Bifidobacterium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D005243:Feces / Q000382:microbiology*; D006801:Humans; D007778:Lactobacillus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D008297:Male; D058889:Molecular Typing; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D019105:Random Amplified Polymorphic DNA Technique; D060888:Real-Time Polymerase Chain Reaction; D055815:Young Adult
D012336:RNA, Ribosomal, 16S
Bifidobacterium; Count; Fecal microbiota; Lactobacillus; Molecular methods; Selective media