on e h e a l t h: f o o d metagenometrakr · me (andrea) padmini liz errol seth sasha mark reiter...
TRANSCRIPT
1
ON E H E A L T H: F O O DMetagenomeTrakr
2
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
3
GenomeTrakr
(Whole Genome Sequencing)5 million bases
WGS
4
GenomeTrakr
5
Host Insect
Bacteria
Fungi
Virus
Protist
Archaea
AMR
Metagenomes MetagenomeTrakr
6
MetagenomeTrakr
7
Farm to Fork Continuum
How will Metagenometrakr help this continuum?
S P O I L A G E
9
Identifying Risk Factors
Amendments
Transportation
Water
Soil
Air
Plants
Plants
Soil
Air
Water
Monitor/Control True Phyllo
95% shared taxonomy (OTUs) between Controls and Phyllo samples
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.
Diversity of Microbial Communities in Air Samples
collected from Vegetable Fields and Poultry Farms
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
Enriching Listeria monocytogenes from ice cream
Genomes from different hours of enrichment (H20, H36, & H40) cluster with WGS of pure isolates from Blue Bell ice cream listeriosis outbreak
(quasi-metagenomic source tracking)
20
Enriching Salmonella from Papayas
Enriching Salmonella from Kratom
Metagenometrakr - Synthesis of Trakrs
TrakrCP, MicroChemTrakr Mitochontrakr, Insects in food,Fungal species
TrakrProtista, Cyclotrakr
25
IMPACT OF METHYL BROMIDE ON SOIL MICROBIOTAGLOBAL SYMPOSIUM ON SOIL POLLUTION MAY 2018, ROME ITALY
26
B A C T E R I A
CONTROL METHYL BROMIDE
Actinobacteria: ThermomonosporaceaeActinomadura and Actinoallomurus
Sphingobacteria: SphingobacteriaceaeMucilaginibacter (recently proposed novel genus)
27
P R O T I S T S
CONTROL METHYL BROMIDE
500 million reads
28
Loss
29
Other genera < 3%
Bacillus
IN THE GREY
30
31
Christensenella minuta
32
? ?
? ?
“my backyard”
About 6-8 woody species
per hectare.
Amazonian rainforest
300 woody species per hectaire.
34
The effect of infections on susceptibility toautoimmune and allergic diseases
N Engl J Med. 2002
Obesity
35
Autism
Obesity
IBS (Irritable Bowel Syndrome)
Cardiovascular
CDIC.difficile infectionDiabetes
36
39 trillion microbial cells
57%
30 trillion human cells
43%
37
2-20 million microbial genes
20,000 human genes
1000x
38
Ottesen, Ramachandran,Timme (ORS) Jarvis, Grim, (OARSA) Tadesse (CVM), Morin (ORA)
40
41
• 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
T0 T1 T2 T3 T4
PI Bob Sanderson
74 hours, Control top, CE bottom
3M Petri Films – noticing a suppressive effect
17 hours, Control top, CE bottom
Bacteria found in sprout water over 4 days
Fungi found in sprout water over 4 days
Protists found in sprout water over 4 days
Enterobacteriaceae
48
BMC Microbiology 2013
49