Methodological Approaches Used to Assess Fish Gastrointestinal Communities - Aquaculture Nutrition: Gut Health, Probiotics and Prebiotics - page 109

Direct fluorescence staining
(e.g. nucleic acid/
protein stains such as
DAPI, acradine orange,
TRITC etc.)

Culture-independent,
inexpensive, quantitative

Possible binding of cells/stain to
extracellular material can make
quantification difficult, careful
optimization may be required for
effective staining, detection of
eukaryotic cells

Asfie et al . (2003), Sugita
et al . (2005), Navarette
et al . (2009; 2010)

Tovar et al . (2002),
Salinas et al .
(2008)

qPCR Culture-independent,

quantitative

Probes only for known bacterial groups He et al . (2010), Kopecný

et al . (2010), Li et al .
(2013)

Avella et al . (2010;
2012)

Histochemistry Culture-independent,

in situ , quantitative

Probes only for known bacterial groups NR Gildberg and

Mikkelsen (1998),
Planas et al .
(2006)

ELISA Culture-independent,

quantitative

Requirement of polyclonal antisera Ringø et al . (1996) Ringø et al . (1996),

Ringø and
Vadstein (1998),
Ringø (1999)

Electron microscopy
(SEM and TEM)

Culture-independent,
visualization of
colonization patterns and
interactions with
enterocytes

Time consuming, only applicable for
epithelium associated cells, no
phylogenetic information,
semi-quantitative

Ringø et al . (2006b),
Merrifield et al . (2009a;
2009b), Ghosh et al.
(2010)

Andlid et al . (1995),
Merrifield
et al . (2010;
2011), Zhou et al .
(2012)

Community libraries using
NGS

Culture-independent,
can extrapolate
microbial abundance
and diversity analysis,
quantitative

Expensive, time consuming, some bias in
the PCR process

Roeselers et al . (2011), van
Kessel et al . (2011),
Desai et al . (2012), Wu
et al . (2012)

Peggs et al . (2014),
Rodiles et al .
(2014)

NR = to the authors' knowledge, not reported.