Gut bacteria

Human gut bacteria convert the secondary bile acid lithocholic acid with 3alfa-Hydroxysteroid Dehydrogenase into 3-Oxol-lithocholic acid (3-oxoLCA) as well as the abundant gut metabolite Isolithocholic acid (isoLCA))
Paik et al. 2022 Nature 603: 907

Gut bacteria play a crucial role in maintaining the health of the gastrointestinal tract. They:

• Secrete neurotransmitters


• Synthesize metabolites and endotoxins


• Regulate the permeability, structure, and function of the mucosa

These activities help normalize the functioning of the gastrointestinal tract. However, gut dysbiosis - an imbalance in gut bacteria - can disrupt one or more of these parameters, leading to disturbances in normal gut function.
Rajput et al. 2021

In addition:

• They have evolved with the host to resist pathogens.


• They are essential for immune system development.


• They help synthesize vitamins.


• They degrade complex carbohydrates in food. This process provides up to 10% of food energy. Complex glycans in dietary fibers are degraded only by bacteria.

McNeil 1984 Am J Clin Nutr 39(2): 338-342
Muegge et al. 2011 Science 332: 970-974
Groussin et al. 2017 Nat Commun 8: 14319
Pickard et al. 2017 Immunol Rev. 279(1): 70-89
Rowland et al. 2018 Eur. J. Nutr. 57: 1-24
Cheng et al. 2019 Front Immunol 10: 60
Caruso et al. 2020 Nat Rev Immunol 20: 411-426

Bacteria adapt to their local host genotype
Batstone et al. 2020 Science 370: 476-478

Reference genomes for gut bacteria are underrepresented
Zou et al. 2019b Nat Biotechnol 37: 179-185

It is estimated that <4% of the bacterial genomes in the US National Center for Biotechnology Information (NCBI) database belong to the human gut microbiota
Zou et al. 2019b Nat Biotechnol 37: 179-185

The total density of bacteria is greater in the colon than the small intestine
Kim et al. 2017 Immunol Rev. 279(1): 90-105

It is more important to ask "what are the intestinal bacteria doing" than "which intestinal bacteria are there."
Donia & Fischbach 2015 Science 349: 1254766

Less than 20% of All Gastrointestinal Bacteria Are Able to Be Cultured by Conventional Methodologies
Yan et al. 2011 Hepatology 53: 96-105

see also:
Culturable Genome Reference (CGR)
Defending & Pathogens / Pathobionts / Pathogenic Bacteria
Gut microbiota
Host - Microbiota interactions