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In-Depth Information
5 Methodological Approaches Used
to Assess Fish Gastrointestinal
Communities
Zhigang Zhou 1 , Bin Yao 1 , Jaime Romero 2 , Paul Waines 3 ,
Einar Ringø 4 , Matthew Emery 3 ,MarkR.Liles 5 and
Daniel L. Merrifield 3
1 Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, PR China
2 Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile,
Santiago, Chile
3 School of Biological Sciences, Plymouth University, UK
4 Norwegian College of Fishery Science, UiT The Arctic University of Norway,
Tromsø, Norway
5 Department of Biological Sciences, Auburn University, Alabama, USA
ABSTRACT
For historical reasons, much of the information available on the intestinal microbiota of
fish is based on the use of conventional culture-dependent methods. This has consisted
of sampling gut material and spreading gut homogenates on selective or general purpose
agar, followed by incubation, colony counting and subsequent identification, typically by
phenotypic/biochemical tests or during the last decade 16S rRNA sequencing. As is often the
case with microbial communities from environmental samples, the gut microbiota of fish has
been reported to be of low cultivability: cultivability using general purpose culture media has
been reported to represent
0.1% of the total microbial community in the gastrointestinal (GI)
tract of some fish species. A wide range of molecular ecology techniques are available based
on the sequence variability of the 16S and 23S rRNA genes, and over the last 10-12 years
such approaches have become more commonly used to investigate the gut microbiomes of
fish species. The molecular based approaches used have depended on the aim of the studies:
(1) clone libraries have been used to identify the microbiota composition; (2) fingerprinting
methods such as denaturing gradient gel electrophoresis (DGGE) and temporal temperature
gradient electrophoresis (TTGE) have been used to analyse microbial community structure
and diversity; (3) quantitative real-time PCR (qPCR) or fluorescent in situ hybridization
(FISH) have been used to determine the abundance of particular taxa or total microbial levels;
and (4) FISH and immunohistochemistry have been used to assess bacterial-host interactions
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