Food Protection Trends - May/June 2018 - 229

damage to the microbiome that occurs with conventional
antibiotic therapy. In other work, inactive bacteriocins
buried within the genomes of Lactobacillus spp. were resurrected in a quest for new bacteriocins effective against a
broader range of bacteria. The bacteriocin nisin was also intelligently engineered to resist gastric proteases and even to
expand its specificity so that it can destroy Listeria monocytogenes. Hill predicts that, in addition to bacteriocins, other
bacterial agents borrowed from nature, the bacteriophages,
will find increasing use as therapeutics and food additives.
Andrea Ottesen (FDA) described how genomic and
microbiome research on plants and elsewhere is being
used to make food safer. FDA, together with the National Center for Biotechnology Information, is developing
a public library of chloroplast DNA from plant species
(23), dubbed "GenomeTrakrCP." Chloroplast DNA, like
genomic DNA, can be used to identify plant species and
may allow closely related species to be better distinguished
than is possible by standard genomic DNA barcoding (22).
GenomeTrakrCP may soon help identify falsely labeled or
adulterated foods as well as pinpoint the source of plants
associated with foodborne disease outbreaks. Another new
program, Metagenome TrakR, generates a fingerprint of all
of the organisms present in an environment: host, bacterial, fungal, viral, etc. This combined information can help
identify the source of pathogens in food beyond simply
sequencing the pathogen.
Drawing upon the recent ice cream listeriosis outbreak
(11) and the Salmonella outbreak associated with papayas,
Ottesen gave examples of how microbiome knowledge can
improve enrichment strategies, especially for low-abundance pathogens. Other work done in collaboration with
Bob Sanderson ( Jonathan's Sprouts) demonstrated that
protists can accumulate in the water used to grow sprouts.
These protists could serve as "Trojan Horses," quietly
harboring and releasing bacteria, potentially including
pathogens, while sprouts are grown. The potential of air
to introduce microbes (including pathogens) that can
colonize a plant was also discussed. Plastic plants (as a
control) and tomato plants exposed to the same air were
associated with similar bacterial taxa over time, suggesting
that the environment, including air, plays an important
role in determining the microbial composition of the plant
phyllosphere (12).
How are the food industry and regulators using
microbiome/metagenomic analyses now?
Food industry leaders and government regulators
discussed how they are currently using microbiome and
metagenomics analyses (and knowledge obtained from
these efforts).
John O'Brien (Nestle) discussed the impact of recent
high-profile reports on the negative effects of artificial
sweeteners (17) and emulsifiers (5) on the mouse microbi-

ota and their associated impacts on glucose tolerance and
colitis/metabolic syndrome, leading food companies to
examine their use of these additives. On the positive side,
Miguel Freitas (Danone) commented that there is strong
continued interest in using probiotics to improve the
healthfulness of foods.
Microbiome and metagenomic testing are also impacting
food and environmental testing. Greg Siragusa pointed out
the dilemma that a company using whole genome sequencing on environmental samples faces: what should they do
if they find a pathogen? Mark Allard (FDA) said that FDA
is not currently collecting regulatory microbiome samples.
They are screening for antibiotic resistance genes in ground
meats, however, and will be performing metagenomic analyses during water sampling.
Regulatory agencies are conducting microbiome-related
research to directly address significant food safety concerns. Joelle Salazar (FDA) discussed research projects
demonstrating that storage of bagged spinach at abusive
temperatures for several weeks greatly increases the relative
abundance of E. coli. In response to the 2010 outbreak of
E. coli O157:H7 associated with raw milk Gouda cheese,
Salazar also described efforts to better understand how
native microbes influence pathogen survival in cheese by
studying how bacterial composition of cheese is affected
by milk pasteurization, by location within cheese (near the
rind or not), and by aging.
Andrew Benson (Metagenome Analytics and University
of Nebraska-Lincoln) discussed work that is addressing
how the food industry can enter the genomic and metagenomic era. As director of the Nebraska Food for Health
Center, Benson described efforts to understand how
genetic variations in grains (bred from ancestral strains to
improve crop yield, hardiness, etc. but not nutrition) affect
utilization by the human gut microbiome, thereby impacting consumer health.
Benson believes the food industry has been slow to use
next-generation sequencing (NGS)-based diagnostics
because of technical and skill-related challenges as well as
negative perceptions driven by regulatory agency efforts

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