Methodological Approaches Used to Assess Fish Gastrointestinal Communities - Aquaculture Nutrition: Gut Health, Probiotics and Prebiotics - page 108

Table 5.2 (continued)

Method Advantages Disadvantages References

Gut microbiota Probiotic study

Culture-independent

16S rRNA gene clone
libraries

Culture-independent,
16S rRNA sequence analysis,
can extrapolate microbial
diversity analysis

Some bias in the PCR process, loss
of diversity

Shiina et al . (2006), Kim
et al . (2007), Navarrete
et al. (2009), Ward
et al . (2009), Han et al .
(2010)

Zhou et al . (2012)

Denaturing gradient gel
electrophoresis (DGGE);
temperature gradient gel
electrophoresis (TTGE)

Culture-independent,
16S rRNA sequence analysis,
can extrapolate microbial
diversity analysis

Some bias in the PCR process, loss of
diversity, semi-quantitative, possible
migration of similar phylotypes to
same gel point

Zhou et al . (2007; 2009a;
2009b), Liu et al .
(2008), Merrifield et al .
(2009b), Navarette et al .
(2009; 2010)

Kim and Austin
(2006), Ferguson
et al . (2010), He
et al . (2011),
Zhou et al . (2012)

rRNA intergenic spacer
analysis (RISA)

Culture-independent,
16S rRNA sequence analysis,
can extrapolate microbial
diversity analysis, not as sensitive
as DGGE/TTGE

Some bias in the PCR process, loss of
diversity, semi-quantitative, possible
migration of similar phylotypes to
same point

Navarette et al . (2009) NR

LH-PCR Culture-independent,

16S rRNA sequence analysis,
can extrapolate microbial
diversity analysis, not as sensitive
as DGGE/TTGE

Some bias in the PCR process, loss of
diversity, semi-quantitative, possible
migration of similar phylotypes to
same point

Heikkinen et al . (2006) NR

Terminal restriction
fragment length
polymorphism (T-RFLP)

Culture-independent,
can extrapolate microbial
diversity analysis, not as sensitive
as DGGE/TTGE

Some bias in the PCR process, loss of
diversity, semi-quantitative, no
phylogenetic information

Moran et al . (2005),
Fjellheim et al . (2012)

NR

Fluorescence in situ
hybridization (FISH)

Culture-independent, in situ ,
quantitative

Can probe only for known bacterial
groups, time consuming for multiple
species, difficulty detecting low
metabolically active cells

Spanggaard et al. (2000),
Asfie et al . (2003),
Huber et al . (2004),
Sugita et al . (2005)

Salinas et al .
(2008), Del'Duca
et al . (2013)