Methodological Approaches Used to Assess Fish Gastrointestinal Communities - Aquaculture Nutrition: Gut Health, Probiotics and Prebiotics - page 107

Table 5.2 Overview, and examples, of the main methodologies utilized for the assessment of the gut microbiota of fish.

Method Advantages Disadvantages References

Gut microbiota Probiotic study

Culture-dependent

Culturing on general media
followed by biochemical
characteristics

Easy, inexpensive,
quantitative

Culture-dependent, large number of
isolates required to provide meaningful
data, time consuming, metabolic
plasticity of organisms may introduce
error

Al-Harbi and Uddin (2003;
2004; 2005)

Bagheri et al .
(2008)

Culturing on selective
media

Easy, inexpensive,
quantitative

Culture-dependent, selectivity of media is
not guaranteed

Carnevali et al . (2006),
Rollo et al . (2006), Silvi
et al . (2008), Ghosh
et al . (2010)

Zhou et al . (2007),
Lv et al . (2007),
Ghosh et al .
(2008)

Culturing on general media
followed by 16S rRNA
sequence analysis of
isolates

Confidence of species level
identification of isolates,
quantitative

Culture-dependent, large number of
isolates required to provide meaningful
data, time consuming

Ringø et al. (2006a;
2006b; 2008),
Merrifield et al . (2009a)

Aubin et al .
(2005)

Culturing on media
followed by random
amplified polymorphic
DNA (RAPD) analysis of
isolates

Easy, inexpensive,
quantitative

Culture-dependent, large number of
isolates required to provide meaningful
data, time consuming, low
reproducibility, phylogenetic
information only available with
comparison to RAPD profiles of known
cultures

NR Balcázar et al .

(2007a; 2007b;
2009), Vendrell
et al . (2008)

(continued overleaf )