This is not a new field; Martha Gilliam worked on it from the late 1960s. In fact, she says in 1973:

> When attempting to determine the normal microbial flora of an insect,, one should keep in mind the statement by Boush et al. (1972) : “We are well aware of the near impossibility of definitively determining the normal microflora of a particular insect. Not, only should one consider all life stages, plant hosts, geographical and ecological locations within the range of the species, as well as seasonal variability, but, the nearly infinite possible microbial cultural parameters, all selective to some degree, as well."



The following article nicely summarizes what we know about defensive symbionts in 2013. 

Some key things to look for

1) the frequent use of the word "hypothesized"

2) very little in this field is actually "known"

3) hi-tech tools will never replicate nor predict what happens in the real world

Martin Kaltenpoth and Tobias Engl (2013) Defensive microbial symbionts in Hymenoptera

It has long been hypothesized that an important function
of the native gut microbiota of insects is to competitively
inhibit pathogens from colonizing the gut

As Bacillus strains have been repeatedly isolated
from various bee species including 25 to 40-million-yearold
amber-preserved specimens (Cano et al. 1994; Cano &
Borucki 1995), an intimate association between bees and
protective Bacillus symbionts has been hypothesized (Gilliam 1997). 

It has to be noted, however, that the mechanistic
basis of the protective activity conferred by both the
lactic acid bacteria and the Bacillus strains remains largely
unknown, although the involvement of organic acids as
well as AMPs and fatty acids has been hypothesized
(Gilliam 1997; Vasquez et al. 2012).

bacteria with the
ability to inhibit bee pathogens have been isolated
throughout the bee hive (Gilliam et al. 1988; Anderson
et al. 2011), and Anderson et al. (2011) even hypothesized
that there might be a sub-caste of bees that is best-suited
to nurture the symbiotic bacteria for the aid in food preservation
and protection from disease.

But although high-throughput
sequencing and DNA barcoding provide powerful tools
that can also contribute significantly towards understanding
animal ecology (e.g. Clare et al. 2009), none of these
techniques can act as a substitute for detailed observations
on the natural history of the study organisms.

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