Table 3.

Biopsy specimen processing

Specimen	Recipient fluid	Processing	Purpose
Biopsy #1	RNAlater	Nucleic acid extraction	Transcriptomics
Biopsy #2	HBSS	FACS	Cell isolation
Biopsy #3	None	Flash frozen	Culture-independent and culture-based assays of mucosa-associated microbial community
Biopsy #4	None	Flash frozen	Archiving for validation of drug targets
Biopsies #5 and #6*	Formalin	Paraffin embedded	Histochemistry (H&E) and immunohistochemistry; Morphometric analyses and EED scoring
Duodenal Aspirate	Microbiota: glycerol/cysteine solution Other: Nil	Precharged N2 dry shipper to −80 freezer	Culture-independent and culture-based assays

*Biopsy site: biopsy #6 from duodenal bulb, all others distal to the ampulla of Vater.

EED, environmental enteric dysfunction; FACS, fluorescence-activated cell sorting; HBSS, Hank’s balanced salt solution.