Fish gut microbe composition

Spanggaard et al. (2000) The microflora of rainbow trout intestine: a comparison
of traditional and molecular identification. Aquaculture 182, 1–15

The
purpose of this study was to compare classical agar plate counts with direct
microscopic counts to evaluate the culturability of the bacterial population in
the intestinal tract of rainbow trout. Identification of the culturable
flora using seven key characteristics was compared with molecular
identification by 16S rRNA analysis. Samples from 48 rainbow trout from
three different farms and two sampling times from one farm were analyzed with direct
microscopic counts (4x,6-diamidino-2-phenylindole, DAPI) and plate
counts (tryptone soya agar, TSA).

The study
indicates that from an overall point of view, the same groups of bacteria,
typical of the aquatic system, are represented in the intestinal flora and that
slight differences in initial numbers or species in the water and/or feed
decide which particular species of bacteria will dominate the gut flora. The
most interesting findings of this paper were how much the microflora of rainbow
trout varies between individual fish. The variance of dominating bacteria between and
within the fish farms was high. Interestingly the variation in
bacterial counts between the fish farms and time points was lower than the
individual fish-to-fish variation. The bacterial population of healthy fish
reflects their respective aqueous environments dominant bacterial flora and
resides in the lumen. Fish intestine do not have a stable microflora. The
fluctuations detected may be regarded as day-to-day fluctuations and/or
seasonal variations as the samples from each farm were taken at different times
when the temperature was noted to be different.

This study has consequences in a wider context as studies
trying to evaluate the effects of treatments such as probiotics on intestinal
microbiota composition must consider that results may not be consistent for
commercial use because there is not the same community to alter in each farm.
Further this variation between fish of the same treatment may cause statistical
analysis on results of such studies to show variable and therefore insignificant
results when in-fact there is an effect. The authors suggest that samples for
quantitative microbial analysis should be pooled with care. Having this
extensive study as to what to expect to find in the intestinal microbiota of a
rainbow trout is very useful for comparison to other research and what species
to focus on when monitoring the microbiota as a health indicator. However the
identification of the microflora appeared to have been done on a random basis
and therefore is incomplete.

The paper was not clear on which method was best to use for
identification although claims that the classical and molecular identification
had high agreement. Total counts found using culture techniques compared to
DAPI staining were highly similar indicating that culturable organisms
dominated the microflora. The study found that a high percentage of the
microbiota in the intestines of rainbow trout could be cultured but this is
still only on average 50%. There was no
obvious direct comparison between method and groups of species found. In a few
samples from the same farm there were high discrepancies between plate and
direct microscopic counts due to low culturablity. In the conclusion it seems
that direct microscopic analysis using the DAPI stain was best to get total
counts and gene analysis provided the most detailed identification. This paper
was difficult to interpret as it was not clearly fulfilling the objectives and
after saying one thing would say something different!