Nothing in Biology Makes Sense: Stalking the wild holobiont

figure made from dishes containing images of microbes Photo by Pickersgill Reef.

Over at Nothing in Biology Makes Sense!, Sarah Hird introduces us to the concept of the holobiont and its hologenome:

Most evolutionary biologists probably consider the individual as the fundamental unit of natural selection. We think about the genes of one mother or one father being passed on to one descendant. But is this view too constrained? The “hologenome” is all the genomes that belong to the “holobiont” – an organism and all its microbes.

Would natural selection be better understood as acting on organisms together with all the microbes they host? Go read the whole thing and see what you think.◼


Nothing in Biology Makes Sense: Circumcision and microbial ecology

Banana Peel What? Photo by photograφ.

Over at Nothing in Biology Makes Sense!, Sarah Hird describes a new study of what happens to the microbial community of the human penis when you make a … let’s say a certain change to its environment?

They begin by sampling the penile microbiota of 156 uncircumcised men. Approximately half of the men are then circumcised and all subjects are resampled after one year (presumably enough time that behavior is unaffected by the procedure).

Yeah, it’s maybe not surprising that circumcision would change what kinds of bacteria hang out in the region formerly covered by the foreskin. But apparently that change may contribute to the reduced rate of HIV transmission associated with circumcision. To find out how, go read the whole thing.◼


Communities within communes: Do bees’ social lives influence their gut bacteria?

ResearchBlogging.orgAs anyone who’s trying to sell you probiotic yogurt will tell you, what you can eat often depends on what’s living in your gut. For many animals, symbiotic bacterial communities help break down foods that would otherwise be indigestible. Perhaps most famously, termites would be unable to eat wood without specialized microbes in their guts [$a], but many other animals host bacteria that break down cellulose, the tough structural sugar of plant tissue, or to supply nutrients lacking in their diet.

This honeybee is carrying more than pollen. Photo by Danny Perez Photography.

The importance of gut microbes for digesting certain kinds of food has led to the suggestion that acquiring the right microbes can be an evolutionary key innovation—a change that creates access to new resources and spurs adaptive radiation. A 2009 study of gut microbes in ants found that evolutionary transitions to eating plants were associated with acquiring similar gut microbes.

So what about the biggest group of herbivorous hymenoptera, the bees? Bees’ ancestors were most likely predatory wasps, but some time in the Cretaceous Period they began making a living on pollen and nectar instead. A new study of gut microbes in a wide diversity of bees suggests that social organization, not diet, changed what lives inside bees’ bellies [$a].

The study examined the bacteria inside representatives of seven bee families, collecting sequence data from a gene widely used in studies of bacteria. The method employed allowed the authors to identify not just what kinds of bacteria were present, but how abundant each kind was. This microbial profile was specifically compared to the profile for Apis mellifera, the honeybee, whose gut microbes have been studied quite a bit already.

The bees form a monophyletic group—they all share a single common ancestor—and they are overwhelmingly herbivorous. Phylogenetic logic suggests, then, that any changes to the gut microbe community associated with the evolutionary transition to eating pollen and nectar would have occurred once, in the common ancestor. The microbes that facilitated that transition should also be widely shared by herbivorous bees.

In fact, most of the bee families sampled had little in common with the honeybees’ gut bacteria. Close relatives of the bacterial types found in Apis mellifera only turned up in two other Apis species, and bumble bees (genus Bombus). Since herbivory doesn’t explain this pattern of similarity (or lack thereof), the authors suggest that what really matters to bees’ guts is social behavior. Apis and Bombus are eusocial, forming hives of related workers cooperating to support a handful of reproductive individuals; the other bees surveyed in the study live mostly alone.

Life is different in the hive. Photo by stewickie.

As the authors note, eusociality would certainly change the environment offered to symbiotic bacteria. Bees in a hive should transmit bacteria among themselves, especially when feeding larvae. So eusocial bees mostly get their gut bacteria from their sisters. The bacteria in the guts of the solitary bees surveyed were mostly related to strains found in soil and on plants—so solitary bees are probably populating their guts with bacteria from their environment.

The idea that eusociality has shaped bees’ interactions with their symbiotic bacteria is interesting, but the data presented in this study are preliminary at best. The sampling of bee diversity presented here is broad, but not very deep—most of the bee families covered are represented by only one or two species. Understanding the effects of social structure on bees’ gut bacteria will take much finer-grained sampling to focus on evolutionary transitions not from predation to herbivory, but from solitary to eusocial lifestyles.


Kaltenpoth, M. (2011). Honeybees and bumblebees share similar bacterial symbionts. Molecular Ecology, 20 (3), 439-40 DOI: 10.1111/j.1365-294X.2010.04960.x

Martinson, V. G., B. N. Danforth, R. L. Minckley, O. Rueppell, S. Tingek, & N. A. Moran. (2011). A simple and distinctive microbiota associated with honey bees and bumble bees Molecular Ecology, 20 (3), 619-28 DOI: 10.1111/j.1365-294X.2010.04959.x

Ikeda-Ohtsubo, W., & A. Brune (2009). Cospeciation of termite gut flagellates and their bacterial endosymbionts: Trichonympha species and ‘Candidatus Endomicrobium trichonymphae’. Molecular Ecology, 18 (2), 332-42 DOI: 10.1111/j.1365-294X.2008.04029.x

Russell, J., Moreau, C., Goldman-Huertas, B., Fujiwara, M., Lohman, D., & Pierce, N. (2009). Bacterial gut symbionts are tightly linked with the evolution of herbivory in ants. Proc. Nat. Acad. Sci. USA, 106 (50), 21236-41 DOI: 10.1073/pnas.0907926106