. 2023 May 16;47(3):fuad022. doi: 10.1093/femsre/fuad022

Table 4.

Bacterial genera described in the human small intestine luminal and mucosal regions. The table includes the top five genera (or higher level if not described down to genus level) detected in each study.

	Bacillota	Pseudomonadota	Bacteroidota	Actinomycetota	Fusobacteriota	Other
*Duodenum*
Lumen	Carnobacteriaceae ^3b, Gemella², Gemellaceae^3b, Lactobacillaceae^3b, Streptococcaceae^3b, Streptococcus^1,2,3a, Veillonellaceae^3b, Veillonella²,^3a	Enterobacteriaceae ^1,3a, Escherichia–Shigella¹, Haemophilus¹, Pasteurellaceae²	Prevotella ²	Rothia ^3a	Fusobacterium ^1,3a
Mucosa	Faecalibacterium ⁶, Lactobacillus^6b, Streptococcaceae⁴, Streptococcus^5,6a, Veillonellaceae⁴, Veillonella⁵	Acinetobacter ^6b, Bradyrhizobiaceae⁴, Escherichia⁵, Haemophilus⁵, Pseudomonadaceae⁴, Stenotrophomonas^6a	Bacteroides ⁶, Prevotellaceae⁴, Prevotella^5,6
*Jejunum*
Lumen	Carnobacteriaceae ^3b, Clostridiaceae^3b, Gemella^2a,2c, Lactobacillaceae^2,3b, Streptococcaceae^3b, Streptococcus²,⁷,^3a, Veillonellaceae^3b, Veillonella²,⁷,^3a	Enterobacteriaceae ^2b,2c,3a, Escherichia⁷, Pasteurellaceae^2a,2b, Pseudomonas^3a	Prevotella ⁷	Rothia ^3a	Fusobacterium ⁷
Mucosa	Clostridium IX ⁹, Clostridium XI⁹, Lactobacilli¹⁰, Streptococcaceae⁴, Streptococci¹⁰, Streptococcus^5,8,9 , Veillonellaceae⁴, Veillonella^5,8	Actinobacillus ¹⁰, Bradyrhizobiaceae⁴, Enterococcus¹⁰, Escherichia⁵, Haemophilus^5,8, Klebsiella¹⁰, Pseudomonadaceae⁴, Proteobacteria⁹	Bacteroidetes ⁹, Prevotellaceae⁴, Prevotella⁸	Actinomyces ⁵, Rothia⁸	Fusobacteria ⁹
*Proximal Ileum*
Lumen*	Clostridium I ¹¹, Streptococcus¹¹, Veillonella¹¹	Enterococcus ¹¹, Oxalobacter¹¹
Mucosa	Streptococcaceae⁴, Streptococcus ⁵, Veillonellaceae⁴, Veillonella⁵	Comamonadaceae ⁴, Escherichia⁵, Haemophilus⁵, Pseudomonadaceae⁴	Bacteroides ⁵	Micrococcaceae ⁴
*Terminal ileum*
Lumen	(no data)
Mucosa	Clostridium XIVa^5,9, Clostridium IV⁹, Clostridium IX⁹, Clostridium XIVb⁹, Granulicatella¹³, Lachnospiraceae⁴, Ruminocacceae⁴, Streptococcus^5,13, Veillonellaceae⁴	Acinetobacter ¹², Aeromonadaceae¹², Cupriavidus¹², Enterobacteriaceae^4,12, Escherichia⁵	Bacteroidaceae ⁴, Bacteroidetes⁹, Bacteroides⁵	Actinomyces ¹³, Rothia¹³	Cetobacterium ¹², Fusobacterium⁵	Verrucomicrobiaceae ⁹, TM7(G-1)¹³

References:

¹Barlow et al. (2021), ^2aSeekatz et al. (2019) (proximal jejunum), ^2bSeekatz et al. (2019) (mid jejunum), ^2cSeekatz et al. (2019) (distal jejunum), ^3aLeite et al. (2020b) (group 2), ^3bLeite et al. (2020b) (group 3), ⁴Vuik et al. (2019), ⁵Nagasue et al. (2022), ^6aLi et al. (2015) (Mucus – luminal fluid), ^6bLi et al. (2015) (Mucosal biopsies); ⁷Sundin et al. (2017); ⁸Dlugosz et al. (2014), ⁹Wang et al. (2005), ¹⁰Hayashi et al. (2005), ¹¹Booijink et al. (2010), ¹²Fan et al. (2020), and ¹³Villmones et al. (2018).

*(Based on ileostomy samples)