on e h e a l t h: f o o d metagenometrakr · me (andrea) padmini liz errol seth sasha mark reiter...
TRANSCRIPT
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ON E H E A L T H: F O O DMetagenomeTrakr
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t h e e c o l o g y o f p a t h o g e n i c i t ye c o l o g y o f n u t r i t i o n
e c o l o g y o f h e a l t h
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GenomeTrakr
(Whole Genome Sequencing)5 million bases
WGS
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GenomeTrakr
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Host Insect
Bacteria
Fungi
Virus
Protist
Archaea
AMR
Metagenomes MetagenomeTrakr
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MetagenomeTrakr
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Farm to Fork Continuum
How will Metagenometrakr help this continuum?
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S P O I L A G E
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Identifying Risk Factors
Amendments
Transportation
Water
Soil
Air
Plants
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Plants
Soil
Air
Water
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Monitor/Control True Phyllo
95% shared taxonomy (OTUs) between Controls and Phyllo samples
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A. “We live at the bottom of a sea of air”
B. Inanimate surface (plastic plant) for air monitoring and state of the art air sampler.
C. In the field placement of inanimate “monitor” next to live plant.
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Diversity of Microbial Communities in Air Samples
collected from Vegetable Fields and Poultry Farms
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e c o l o g y o f m e t h o d s
e f f i c i e n c y o f m e t h o d s
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Enriching Listeria monocytogenes from ice cream
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Genomes from different hours of enrichment (H20, H36, & H40) cluster with WGS of pure isolates from Blue Bell ice cream listeriosis outbreak
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(quasi-metagenomic source tracking)
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Enriching Salmonella from Papayas
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Enriching Salmonella from Kratom
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Metagenometrakr - Synthesis of Trakrs
TrakrCP, MicroChemTrakr Mitochontrakr, Insects in food,Fungal species
TrakrProtista, Cyclotrakr
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IMPACT OF METHYL BROMIDE ON SOIL MICROBIOTAGLOBAL SYMPOSIUM ON SOIL POLLUTION MAY 2018, ROME ITALY
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B A C T E R I A
CONTROL METHYL BROMIDE
Actinobacteria: ThermomonosporaceaeActinomadura and Actinoallomurus
Sphingobacteria: SphingobacteriaceaeMucilaginibacter (recently proposed novel genus)
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P R O T I S T S
CONTROL METHYL BROMIDE
500 million reads
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Loss
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Other genera < 3%
Bacillus
IN THE GREY
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Christensenella minuta
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? ?
? ?
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“my backyard”
About 6-8 woody species
per hectare.
Amazonian rainforest
300 woody species per hectaire.
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The effect of infections on susceptibility toautoimmune and allergic diseases
N Engl J Med. 2002
Obesity
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Autism
Obesity
IBS (Irritable Bowel Syndrome)
Cardiovascular
CDIC.difficile infectionDiabetes
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39 trillion microbial cells
57%
30 trillion human cells
43%
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2-20 million microbial genes
20,000 human genes
1000x
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Ottesen, Ramachandran,Timme (ORS) Jarvis, Grim, (OARSA) Tadesse (CVM), Morin (ORA)
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• Padmini Ramachandran M.S. CFSAN FDA
• Elizabeth Reed M.S. CFSAN FDA
• Mark Reiter PhD Virginia Tech
• Joshua Freeman PhD Virginia Tech
• Seth Commicheaux PhD U. Maryland
• Sasha Gorham M.S. NIH
• Errol Strain PhD CFSAN FDA
Me (Andrea) Padmini Liz Errol Seth Sasha Mark Reiter
• Marc Allard CFSAN FDA
• Eric Brown CFSAN FDA
• Sandra Tallent CFSAN FDA
• Jie Zheng CFSAN FDA
• Rebecca Bell CFSAN FDA
• Rachel Binet CFSAN FDA
• Bob Sanderson Jonathon’s Sprouts
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T0 T1 T2 T3 T4
PI Bob Sanderson
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74 hours, Control top, CE bottom
3M Petri Films – noticing a suppressive effect
17 hours, Control top, CE bottom
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Bacteria found in sprout water over 4 days
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Fungi found in sprout water over 4 days
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Protists found in sprout water over 4 days
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Enterobacteriaceae
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BMC Microbiology 2013
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