What does a typical gut microbe look like and do?

Shape

The picture below is from a real stool sample (Figure 1), which has been stained and viewed under a light microscope. There's evidence of rods, spheres (cocci), elipses (ovoid or coccobacilli) and things in between.

Of the ~500 important gut colonisers, 64% are rods (straight, curved, pleomorphic), 20% are cocci, 5% coccobacilli, 4% oval-shaped and 8% unreported/miscellaneous shapes. In reality, even cocci bacterial cells have lumps and bumps, and rods are rarely the classic Lactobacillus straight rod.  So, a typical average bug could be rod-shaped, maybe with rounded ends and a little stunted; something like the image below (Figure 2), which shows two joined rod/coccobacillus bacteria.

If this is the shape of a prototypical gut microbe, what are its likely physiological attributes?

Mobility

It would be useful for an opportunistic pathogen to be mobile in the competitive ecosystem of the gut, especially if it intends to attack and penetrate the epithelial cells. But the tendency for mutualistic microbes would be to evolve away from the need to be mobile.

It appears that being sessile is the trend in the gut environment: of the important gut bacteria, 72% are not motile, 16% swim (flagella) and most others are not reported (10%) but are likely to be non-motile as well. So, our typical average bug is now rod-shaped and stationary, and it relies on the motion of the bowels and secretions from the epithelium to move food to its location - or it just goes with the flow.

Oxygen tolerance

More oxygen is present the higher up the GI tract we go. This is why aerobes (Bacillus) and facultative anaerobes (Lactobacillus) can exist in the small intestine and caecum. As the organisms reach the bowel the amount of oxygen is heavily depleted. Facultative anaerobes tend to use up any residual oxygen before resorting to anaerobic fermentative metabolism.

The anoxic conditions encourage the growth of anaerobes: of the important gut bacteria, 67% are anaerobic and don't grow in the presence of oxygen; 25% tolerate oxygen or deoxygenated environments, 2% are microaerophilic and only 2% are aerobic (3% not reported).

Gram stain

A Gram stain has historically been used to divide the world of bacteria roughly in two. Gram positive bacteria include most of the Firmicutes and the Actinobacteria, while the Gram negative microbes can come from mainly Bacteroidetes and Proteobacteria, but also the Verrucomicrobia, Fusobacteria, Spirochaetes, Synergistetes and Tenericutes. Archae seem to be a mixture of both, which seems fitting since the top 500 are split pretty evenly as well: 51% Gram +, 44% Gram neg. So, our typical average microbe could be either.

Spores

Endospores are produced by some Firmicutes and exospores can come from Actinobacteria. 

For our set of bacteria, only 13% produce spores, while 81% don't. A single microbe, Schaalia odontolytica, produces exospores. 5% were not reported (but are probably non-spore producing).

Your average microbe

In conclusion, we could say that our prototypical average bug is an anaerobic, non-motile, asporogenous, (distorted) rod. Gram stain could be + or neg. Well, it turns out that 33% of the top 500 indeed share all these attributes.

Table 1. Summary of a typical gut microbe.

OK, but what is this bug likely to do for you?

Chances are, our prototypical microbe is interested in the carbohydrates we ingest. Whether these are derived from vegetables, fibre or resistant starches, the microbe is more than likely capable of breaking down those parts of the carbohydrate meal we can't digest ourselves. Of the top 500 microbes, 74% have at least some strains that are able to utilise, ferment or oxidise glucose, while 11% can't (16% not reported). In order to get to free glucose, the bugs must hydrolyse a variety of recalcitrant carbohydrate polymers.

In return, fermenting bacteria can often produce acetate, propionate and butyrate, which are consumed by the body as an energy source and promote the health of the intestinal lining. Our average bug might also consume the mucin released by the epithelium, in which case it probably plays a role in regulating inflammatory responses and helps exclude pathogens.