Table 1.

Studies sampling the SI microbiota and their methods.

Study cohort	Sampling method	Location in SI	Microbial analysis	Limitations	Main Species Identified	Reference
54-y-old female, previous good health	Mucosal biopsies via colonoscopy and using a Watson intestinal biopsy capsule	Jejunum Distal ileum	16S rRNA gene amplicon sequencing	Prone to contamination Prior lavage treatment Invasive Low taxonomic resolution Small sample size	Jejunum: Streptococcus & Proteobacteria Distal ileum: Bacteroidetes & Clostridium clusters XIVa and IV	Wang et al. 2005 [3]
26 patients who underwent emergency surgery requiring colonic resection	Mucosal biopsies following colonic resection	Terminal ileum	16S rRNA gene amplicon sequencing	Low taxonomic resolution Invasive Difficult interpretation	Bacteroides, Bifidobacteria, Lactobacilli & Enterobacteria	Ahmed et al. 2007 [4]
3 deceased elderly individuals	Intestinal contents obtained during autopsy	Jejunum Ileum	16S rRNA gene amplicon sequencing	Small sample size Cannot study microbial dynamics	Streptococcus, Lactobacillus, ‘Gammaproteobacteria’, the Enterococcus group & the Bacteroides group	Hayashi et al. 2005 [5]
5 individuals with an ileostomy & 4 healthy individuals	Ileostomy effluent Intestinal fluid using an intraluminal naso-ileal catheter	(Distal) SI Jejunum, ileum & terminal	GI tract-specific phylogenetic microarray HITChip	Altered GI anatomy (Ileostomy samples) Potential exposure to external environment (Ileostomy samples) Disease context (IBD) (Ileostomy samples) Risk of contamination (naso-ileal catheter) Invasive (naso-ileal catheter)	Streptococcus, E.coli, Clostridium, high G+C organisms	Zoetendal et al. 2012 [12]
5 participants undergoing colonoscopy	Mucosal biopsies via colonoscopy	Terminal ileum	Metagenomic shotgun sequencing	Small sample size Prior lavage treatment Large number of human reads, low microbial coverage	B. vulgatus, B. thetaiotaomicron, B. uniformis & B. caccae	Vaga et al. 2020 [6]
Liver disease patients undergoing esophagogastroduodenoscopy	Duodenal aspirate and biopsies during upper endoscopy – novel technique detailed by the authors	Duodenum	16S rRNA gene amplicon sequencing	Limited to the duodenum Invasive Disease context	Aspirate: Veillonella, Streptococcus, Prevotella Biopsy: Streptococcus, S24–7 (Muribaculaceae), Parabacteroides	Dreskin et al. 2021 [14]
49 individuals with an ileostomy 9 individuals with an Ileoanal pouch	Ileostomy effluent Fecal sample	SI	Metagenomic shotgun sequencing	Disease context (IBD) Altered GI anatomy (Ileostomy samples) Potential exposure to external environment (Ileostomy samples) Limited sample population	Streptococcus, Escherichia, Veillonella, Blautia, Actinomyces, Enterococcus, Lactobacillus	Ruigrok et al. 2021 [10]
27 patients undergoing radical cystectomy	Lab cultivation of samples obtained by rubbing a swab against the ileal mucosa 25 cm from the ileocecal valve	Ileum	MALDI-TOF/Biotyper	Limited to cultivable microbes Disease context may have an influence on the microbial composition	viridans streptococci, Candida, Actinomyces, Rothia & Lactobacillus species.	Villmones et al. 2021 [7]
8 fasted healthy individuals	Orally intubation with a four-lumen catheter with multiple aspiration ports – multiple samples	Duodenum Jejunum	16S rRNA gene amplicon sequencing	Invasive Risk of contamination Limited to proximal SI	Firmicutes, Proteobacteria & Bacteroidetes (duodenum)	Seekatz et al. 2019 [15]
Ex vivo study on lamb SI	A novel capsule robot designed by the authors: samples mucosa and intestinal contests	SI	/	Still under development	/	Rehan et al. 2020 [16]
27 patients undergoing radical cystectomy with urinary diversion	Sample obtained valve by rubbing a swab against the luminal wall about 25 cm proximal to the ileocecal during surgery	Distal ileum	16S rRNA gene amplicon sequencing plus targeted sequencing of alternative genes when necessary for higher taxonomic resolution	Disease context may have an influence on the microbial composition	Streptococcus, Granulicatella, Actinomyces, Solobacterium, Rothia, Gemella & TM7(G-1)	Villmones et al. 2018 [8]
6 patients undergoing gastric bypass surgery	Sample obtained valve by rubbing a swab against the luminal wall during surgery	Jejunum	16S rRNA gene amplicon sequencing	Disease context may have an influence on the microbial composition	Streptococcus, Granulicatella, Schaalia odontolytica complex & Gemella	Villmones et al. 2022 [9]
7 individuals with an ileostomy	Ileostomy effluent	SI	HITChip based on SSU rRNA gene sequences	Disease context (IBD) Altered GI anatomy Potential exposure to external environment Limited sample population	Streptococcus, Veillonella & Clostridium cluster I	Booijink et al. 2010 [11]
30 individuals with an ileostomy	Ileostomy effluent	SI	16S rRNA gene amplicon sequencing	Disease context (colorectal cancer) Altered GI anatomy Potential exposure to external environment Limited sample population	Lactobacillus, Clostridium, Streptococcus, Enterococcus, & Veillonella	Yilmaz et al. 2022 [13]

Abbreviations: SI, small intestine.

NB: Includes studies that also sampled the large intestine; however, only the methods used to study the SI and the corresponding results are detailed.