Supplementing peptides and B vitamins led to significant
presence of lactic acid bacteria and more microbial diversity
Clostridium and Ethanoligenens were the dominant OTUs in
the mineral medium enrichment culture (Figure 3). FISH analysis showed a
very different result and demonstrated dominance in biovolume ofRuminococcaceae using the Rums278 probe, to which the genus ofEthanoligenens belongs. Only a minor biovolume ofClostridium was detected using the Chis150 probe.Lactobacillus was present as a very minor population (Figure S4)
in the mineral medium enrichment. The discrepancy between sequencing
results and FISH evaluation shows that complementary observations of the
microbial community structure are needed when analysing a microbial
community, referred to as the “full cycle rRNA analysis” by Amannet al. (Schleifer et al., 1995).
Lactococcus and Lactobacillus were dominant OTUs in the
complex medium enrichment (Figure 3). Their dominance was confirmed by
FISH analysis using the Lactococcus4 (Lactococcus ) and Lacto722
(Lactobacillus ) probes. The presence of Megasphaera and
minor presence of Clostridium was also confirmed using the Mega-X
(Megasphaera ) and the Chis150 (Clostridium ) probes.
The diversity of the obtained microbial community structures using 16S
rRNA amplicon sequencing can be calculated using the Shannon index for
the observed genera with a presence > 3% of the total
OTU’s. For the mineral medium the Shannon index was 0.94 (sample at 32
SRTs) and for the complex medium this was 1.34 (sample taken at 41
SRTs). Thus, more microbial diversity was observed in the complex medium
enrichment compared to the mineral medium enrichment on the basis of the
number of genera found (Figure 3).