Dynamic Gut Microbiome

Welcome,

    Let me begin with a question. What is the most common bacteria in the gut flora? Before reading on, give a small thought and come up with your own answer. If you answered it E coli, you are wrong. You are not the only one to come up with this answer. Often when I ask this question to my students, they come up with the same answer. Reason, almost always when you attempt bacterial culture your routine culture plates grows E coli. So let me explain why it is not the case.

Photo 1: Lactose fermenting pink colonies
E coli. Image source

    Culture media is designed to allow growth of certain group of bacteria. No matter what culture media you have, it will support the growth of limited set of organisms. Suppose, I use a specific culture media, say for example McConkey's agar which supports growth of enteric organisms and my growth conditions is aerobic, near neutral pH so on and so forth. The bacteria that can grow most rapidly in the plate under predefined conditions is at a competitive advantage of growth. The bacteria that fits very easily on to this criterion is E coli. However, this doesn't imply that the species is most predominant there.

McConkey's Agar contains

Enzymatic Digest of Gelatin ................................................. 17 g
Enzymatic Digest of Casein ................................................. 1.5 g
Enzymatic Digest of Animal Tissue....................................... 1.5 g
Lactose .............................................................................. 10 g
Bile Salts Mixture ............................................................... 1.5 g
Sodium Chloride ................................................................. 5 g
Neutral Red ........................................................................ 0.03 g
Crystal Violet ..................................................................... 0.001 g
Agar .................................................................................. 13.5 g

Final pH: 7.1 ± 0.2 at 25 C

   The E coli growth is abundant in this case since it can tolerate the bile salt mixture well and is suited to grow in the conditions. For argument sake, had I tried to grow Staphylococcus here, it simply wouldn't grow no matter how much much quantity of Staphylococcus, I try to add. This is for the simple reason that the Staphylococcus cannot tolerate bile salts.

    So, now that i have impressed you the fact that E coli is not the most common organism in gastro-intestinal tract am obliged to answer the who? The answer now doesn't seem to be so simple. The most accepted fact is that bacterial species making up the human gut microbiota are strict anaerobes, of which predominant organisms are members of the genus Bacteroides. Several species has been documented to inhabit the human gut flora. The list includes- Bacteroides fragilis group, Bacteroides plebeius, Bacteroides coprocola, Bacteroides helcogenes, Bacteroides intestinalis, Bacteroides finegoldii, Bacteroides dorei, Bacteroides cellulosilyticus sp. nov, Bacteroides xylanisolvens sp. nov and Bacteroides thetaiotaomicron.

Photo 2: Intestinal section from a gnotobiotic mouse model inoculated with selected bacterial species found in the human gut. Blue=Bacteroides WH2, green=Bacteroides thetaiotamicron, pink=Bacteroides vulgatus, yellow= Collinsella aerofaciens, red=Ruminococcus torques. Credit: Yuko Hasegawa/MBL Woods Hole. Source

    Other more common bacteria found in the gut flora include Prevotella speciesa and Fusobacterium species. However to quote one particular species or group as normal abundant bacterial community in the human microbiome is misleading. Let me quote from Huse , a researcher in Human Microbiome Project (HMP). “The more closely we look, the more bacterial diversity we find, We can’t even name all these kinds of bacteria we are discovering in human and environmental habitats. It’s like trying to name all the stars. What this means is, there is not just one way to be healthy, There doesn’t have to be one or two ‘just right’ gut communities, but rather a range of ‘just fine’ communities”. Source. As predictable, the gut flora is probably dynamic and most influenced by the diet. As a matter of fact, the type of diet (Vegetarian or Non vegetarian diet decides the percentage count of Bacteroides spp., Bifidobacterium spp etc in the gut flora. (Reference)

Huse, S., Ye, Y., Zhou, Y., & Fodor, A. (2012). A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters PLoS ONE, 7 (6) DOI: 10.1371/journal.pone.0034242

Further Reading

1. Celine Robert, Christophe Chassard,  Paul A. Lawson and Annick Bernalier-Donadille. Bacteroides cellulosilyticus sp. nov., a cellulolytic bacterium from the human gut microbial community. IJSEM (July 2007); 57 (7): 1516-1520. Link