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Rey (University of Wisconsin-Madison) illustrated how
microbial metabolism can affect host nutrition, using gut
microbial metabolism of choline as an example. Besides
serving as a key methyl group donor involved in 1-carbon
metabolism (and therefore epigenetic regulation), choline
is also important in cell membrane integrity and serves as
a precursor to the neurotransmitter acetylcholine. Choline
intake is particularly important during the perinatal period,
with deficiencies in utero associated with cognitive and
behavioral problems in offspring.
Gut bacteria can convert choline into trimethylamine
(TMA), depleting plasma choline levels. When germ-free
mice are colonized with recombinant bacteria lacking the
enzyme needed to convert choline to TMA, the mice have
higher plasma levels of choline. Rey's group demonstrated that reduced plasma choline levels resulting from gut
microbial choline utilization can trigger problems similar
to those associated with dietary choline deficiency. Current
dietary recommendations for choline do not take into
account microbial metabolism of the nutrient.
TMA produced from choline by gut bacteria can be converted by the host to trimethylamine N-oxide (TMAO),
a proatherogenic metabolite linked to cardiovascular atherosclerosis, diabetes, and other diseases. Rey commented
that in some stages of life (for example, during perinatal
development) choline depletion may be more problematic
than TMAO accumulation.
Perturbations in the microbiome can perturb health
When alterations in the microbiome are linked to
negative health consequences, the shift is referred to as
dysbiosis. André Marette (Université Laval, Québec City,
Canada) described how dysbiosis can cause obesity-linked
cardiometabolic diseases. Gut microbiota from obese
donors (mice or humans) can also transfer metabolic syndrome to germ-free mice (15, 19). Maintaining integrity of
the gut mucosal layer appears critical: emulsifiers (found
in some processed foods) may cause dysbiosis leading to
colitis and metabolic syndrome by perturbing the microbial composition of the gut mucosal layer (5).
Anne Marie Singh (University of Wisconsin-Madison)
described how the gut microbiome influences immune
system development, thereby impacting the development
of food allergies. Increased levels of Staphylococcus aureus
were found in fecal samples from children with food
allergies. An association between atopic dermatitis and
colonization with S. aureus has also been noted, suggesting
that certain S. aureus proteins may act as "super antigens"
that trigger broad immune responses, subverting the
development of oral tolerance to foods. Studies in mice
strengthen the hypothesis: oral tolerance can be elicited
by oral administration of peanut or egg protein, but such
tolerance is prevented when Staphylococcal enterotoxin B is
given concurrently.

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Food Protection Trends May/June

Studying the microbiome
Techniques used to study the microbiome were addressed throughout the day. Several speakers, including
Rey, described studies in which germ-free mice were
colonized with defined species of microbes. An important
strength of these types of studies is that they allow both
host and microbial genetics to be manipulated.
Paul Morley (Colorado State University) discussed the
microbial ecology of antibiotic resistance in cattle. The lack
of consistent correlation between administration of antibiotics and antimicrobial resistance is a puzzle. In a recent
study by Morley's group, beef cattle raised without antibiotics did not show substantially different abundances of
antibiotic resistance genes in their microbiome compared
with cattle raised conventionally with antibiotics (20).
Morley's research integrates a genomic approach to find
out "who is there" with a transcriptome approach to see
which microbes are active and a metabolomic approach to
identify what microbial products are generated. Significant
nasopharyngeal microbiota changes occur in cattle from
the time of weaning to arrival at (and during the time at)
a feedlot. Microbiome changes precede illness, suggesting
that times when the microbiota are in rapid flux are opportunities for pathogenic infection (18). Morley provided
evidence that the "resistome," or collection of genomic
sequences encoding antibiotic resistance genes, varies
greatly among the feces, soil, and water in a feedlot. The
abundance of antibiotic resistance genes decreases through
the time of slaughter (10), with no resistance genes found
in samples collected after slaughter.
Microbiome research being conducted now is predicted
to drive significant health-related benefits
Personalized nutrition may someday be based on an individual's unique microbiome. A recent study cited by Cindy
Davis described how an individual's glycemic response to a
food can now be predicted based on his or her microbiome
(21). Dietary requirements may change to reflect colonic
microbial requirements to maximize host health.
Microbiome-based anti-infectives are being investigated,
as discussed in detail by Colin Hill. The microbiome plays
an important role in preventing infection with foodborne
pathogens, as germ-free mice are exquisitely sensitive to
infection. Hill described a recent clinical study in which
oral administration of a probiotic plus a prebiotic prevented sepsis among infants in rural India (13). Hill's group has
developed probiotics that are efficacious against a variety of
microbial diseases in various animal species, including porcine salmonellosis, bovine mastitis, and murine listeriosis.
Probiotics may function as anti-infectives through a
variety of mechanisms, including the production of bacteriocins that kill or inhibit other bacteria. Hill's group identified
thuricin as efficacious against Clostridium difficile (14),
selectively attacking the pathogen while preventing collateral

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