Pharyngula

I'm one of those dreadful animal-centric zoologically inclined biologists. Plants? What are those? Fungi? They're related to metazoans somehow. Lichens? Not even on the radar. The first step in fixing a problem, though, is recognizing that you have one. So I confess to you, O Readers, that my name is PZ, and I am a metazoaphile. But I can get better.

My path to opening up to wider horizons is to focus on what I find most interesting about animals, and that is that they are networks of cells driven by networks of genes that generate patterned responses of expression by cell signaling, or communication. See? I'm already a little weird. Show me a baby bunny, and I don't just see a cute little furry pal with an adorable twitchy nose, I see an organized and coherent array of differentiated tissues that arose by a temporal sequence of cell-cell interactions, and I just wanna open him up and play with his widdle epithelial sheets and dismantle his pwetty ducts and struts and fibers and fluids, oochy coo. And ultimately, I want to take apart each cell and ask why it has its particular assortment of genes switched off and on, and how its state affects its neighbors and the whole of the organism.

Which means, lately, that I've acquired a growing interest in bacteria. If I were 30 years younger, I could probably be seduced into a career in microbiology.

There are a couple of reasons why an animal-centric biologist would be interested in bacteria. One is the principle of it; the mechanisms that animal cells use to build complex arrangements of tissues were all first pioneered in single-celled organisms. We have elaborated and added details to gene- and cell-level phenomena, but it's a collection of significant quantitative differences, with nothing known that is essentially new in metazoan cells. All the cool stuff was worked out by evolution in the 3-4billion years before the Cambrian, a potential that simply blossomed in the past half-billion years into big conglomerations of cells. Understanding how the building blocks of multicellularity work individually ought to be a prerequisite to understanding how the assemblages work.

But there's another reason, too, a difference in perspective. It is our conceit to regard ourselves as individuals of Homo sapiens, a body of cells clonally derived from a single human cell. It's not true. It turns out that each one of us is actually a whole population of species, linked by our evolutionary history and lumbering through the world as a team. Genus Homo is also genera Escherichi and Bacteroidetes and Firmicutes and many others.

Physiology

Let's begin with the most widely known factor: we're mostly bacterial in cell numbers, with about ten times as many bacterial cells as human cells. Most of these are nestled deep in our guts, where they are indispensible. In mammals, they help break down complex polysaccharides which we can then absorb through the wall of the digestive tract — these are compounds that would be simply lost without bacterial assistance. Even more dramatically, termite guts contain colonies of bacteria that produce enzymes to break down cellulose. Another insect, aphids, live in plant saps which have negligible protein components, and they rely on gut bacteria that can synthesize nine essential amino acids. One cool feature is that the bacteria can't complete the synthesis of leucine; the last step is carried out by aphid enzymes. The synthetic pathway is split acros two different species!

Another weird twist is that gut bacteria can affect morphology (or vice versa; physiology influences which gut bacteria thrive). Mice with a genetic predisposition to obesity were found to have a different distribution of gut bacteria; fat mice are full of Firmicutes, while lean mice are loaded with Bacteroidetes. Something in the genetics of the obese mice seems to favor the proliferation of that one species. Cause and effect is not so easily separated, though, since doing a fecal transplant and inoculating the guts of germ free mice with the bacteria from obese mice vs. lean mice has a surprising effect: the mice given obese mouse fecal enemas subsequently increased their body fat by 60%. The bacteria promoted more fat storage in the host animal.

So what, you may be thinking, it's mice. However, it turns out that obese humans tend to have reduced amounts of Bacteroidetes species in their guts than lean people, and weight loss is accompanied by an increase in Bacteroidetes. Fecal transplants are not recommended as a weight loss technique…at least not yet.

They have worked for some other problems. Crohn's disease and ulcerative colitis are diseases that involve intestinal inflammation, and they're also associated with imbalances in the species distribution of gut bacteria. Some promising treatments have involved collecting feces from healthy individuals, and using a nasogastric tube to inoculate the guts of Crohn's patients with the stuff. Ick, I know, but it seems to have worked surprisingly well in a small number of patients.

Development

Bacteria are present in the gut from a very early age, and populate the digestive epithelia. There must be interactions going on, and it appears that the bacteria are actually regulating the growth of the gut lining.

Germ-free zebrafish lines have no gut bacteria, and they also have problems. The intestinal lining arrests its development and fails to fully differentiate; the lining also grows much more slowly. They also have difficulty absorbing some nutrients. Add bacteria, though, and growth and differentiation resume. This is a case where the developmental program and the bacterial influences are interdependent, and it makes sense — they've co-evolved.

It's not just fish, either — these are conserved interactions across the vertebrates. Mice exhibit the same dependence on gut flora for development of the intestinal lining.

The very best example of a developmental dependence on bacteria, though, is in squid. The bobtail squid has a light-emitting organ that relies on colonization by a luminescent bacterium, Vibrio fischeri. The animal gleans the bacteria from the water with a special ciliated epithelium and secreted mucus that seems to be just the right flavor for Vibrio, and the bacteria migrate deep into the light-emitting organ. Once colonized, the squid dismantles the harvesting cilia and downregulates the secretion of mucus. If no bacteria of the right species are present, it maintains the cilia. If the bacteria in the organ die, resumes mucus production.

Bacterial symbionts induce light-organ morphogenesis in squid. A Adult squid (E scolopes). SEM images of epithelial fields before B and after C regression of ciliated appendage. Scale bar, 50 mm. Ciliated appendages are marked by an orange dashed line.

Evolution

If something affects development and physiology, it affects evolution, so evolutionary importance is simply rather unavoidable. However, there's also one somewhat surprising observation (to me, at least — microbiologists probably expect it): different species of related organisms can have different microbial populations, even when raised in identical conditions. Different Hydra species in the lab under controlled conditions have recognizably different populations of bacteria living on their epithelia, and Hydra of the same species collected in the wild have similar distributions of species. The properties of each Hydra species uniquely favor different distributions of bacteria, and the bacteria are also preferentially colonizing particular species of Hydra.

Hydra are wonderful experimental animals in that one can ablate stem cells for a particular tissue type, and still get an animal that develops and lives; do the same thing to a vertebrate, for instance knocking out the mesodermal lineage in the embryo, and you get an aborted blob. In Hydra, you get a tissue that survives and is colonized by bacteria…but the kinds of bacteria populating it is different from the populations in the intact animal. The animal and the bacteria are swapping molecular signals that specify favored relationships. Again, these are coevolved populations that recognize molecular properties of the host and symbiont.

This is all getting very complicated. I'm used to thinking in terms of networks of genes: there are regulatory interactions between genes in a single cell that establish cell-type specific patterns of gene activity; all express a common core of genes, but different cell types, such as a neuron vs. a cell of the digestive epithelia, will also have their own unique special-purpose genes switched on. I'm also comfortable thinking of networks of cells: cells are in constant negotiations with their neighbors, mainting a common pattern of expression within a tissue, and defining interacting edges with other tissues. Cells are continually sending out messages about their state into the system and responding to local and global signals. All this is part of the normal process of thinking developmentally.

Now, though, there's another layer: we have to think in terms of networks of species that cooperate in the development and physiology of individual multi-cellular organisms. Purity is compromised. My precious animalia — they're inconceivable without bringing bacteria into the picture.

Fraune S, Bosch TCG (2010) Why bacteria matter in animal development and evolution. Bioessays 32:571-580.