Category Archives: paleomicrobiology

CFP: Contagions sessions at the International Congress for Medieval Studies 2018

by Michelle Ziegler

Contagions: The Society for Historic Infectious Disease Studies has been given the opportunity of organizing three sessions at next year’s International Congress for Medieval Studies. This is the equivalent of a full day at the congress. The Congress will be held from May 10 to May 13, 2018, at Western Michigan University in Kalamazoo Michigan.  Our sessions next year will be:

Interdisciplinary Approaches to Historic Disease I and II

These two sessions are open to any aspect of study on infectious diseases and nutritional disorders in people and animals from the Late Antique to Late Medieval periods (400-1600 CE). These sessions are intended to be interdisciplinary as sessions, not necessarily as individual papers. Presentations on infectious diseases in literature, history, archaeology, and anthropology are all welcome.

Signs of Resilience in Medieval Populations

Major epidemics and natural disasters are ideal situations to study community resilience. No community is resistant to natural disasters; resilience is the best we can expect. Epidemics like the Black Death hit multiple communities in rapid succession but not all communities were equally affected in the short or long term. There are so many questions that can be asked.

  •  What allows some communities to quickly rebound while others dwindle away?
  • How do people mentally cope with a famine and/or massive epidemic?
  • What changes did communities make to better prepare or prevent a similar disaster in the future? Examples would include rebuilding flood walls or rerouting a river, increasing communal food stores, or building a surveillance system to detect the plague.
  • How did past experiences alter the community response to the next epidemic or another disaster?
  • How did responses differ between types of disaster (epidemic, flood, earthquake)? Flooding, at least, would be expected on a regular basis.
  • How did they prioritize their response? For example, did community leaders prioritize the economy (import/export) over public health?
  • What role did religious institutions play in disaster response?


Presentations are limited to 20 minutes. PowerPoint-like presentations are encouraged.  Participant Information Forms and an abstract are due to Michelle Ziegler by September 15th, contact prior to that date would be appreciated. Initial contact can be made through the form below.


The Microbial Anthropocene


Over the last decade or so, geologists and ecologists have begun to talk about planet earth entering a new geologic period called the Anthropocene, defined as the period when humans became the driving force of change on planet Earth. Debates continue on when the Anthropocene begins; sometime in the late 18th century when the industrial age is underway with the first steam engines, new products appear like plastic that persist in geology, and in medicine, Jenner begins his work on vaccines in the 1790s, would make sense.  I suggest that this also marks the beginning of the microbial Anthropocene — when humans become a driving force in microbial evolution.

Microbiology of the Anthropocene (Gillings and Paulson, 2013). Note the logarithmic time scale.

The graphic above is eye-opening. The Anthropocene is apparent in every level of microbial ecology examined. It is a good reminder that human intervention in microbial evolution goes far beyond infectious disease.

Perhaps most stunning message this graphic brought to me is the logarithmic nature of change. It finally dawned on me looking at this graphic that it also reflects the periods of epidemiological transition theory (ETT). The hunter-gatherer period correlates with the Pleistocene, then the first transition to the farmer-urban period (of epidemics) correlates with the Holocene, and the second transition to the modern third epidemiological phase characterized by longer lifespans and chronic disease is the Anthropocene.  Finally, the time scale of the epidemiologic transitions makes some sense. The logarithmic scale may not bode well for the speed of future transitions.

The changes of the Anthropocene filter down through all living and non-living things. Among living things, there are winners and losers: species whose range and differentiation expands and others are driven to extinction. We can see this on a huge scale in the ocean where we have coral bleaching caused by loss of microbial symbionts, while there is an increasing incidence of toxic blooms and an enlarging dead zone in the Gulf of Mexico both caused by an overgrowth of some microbial species. With each transition, natural selection seems to go into overdrive until a new equilibrium is established (Gilling and Paulsen, 2).

Michael Gillings and Ian Paulsen identified several areas of microbial evolution and ecology impacted during the Anthropocene. The strong selective pressure antibiotics have exerted on infectious agents is the most commonly discussed risk in modern medical microbiology. Changes in the human microbiome are most closely related to diet changes (another feature of the Anthropocene), but our normal flora is also collateral damage of antimicrobial treatment. We often overlook that most antibiotics consumed by humans and livestock are washed through our bodies into the watershed where they alter the microbial ecology of entire ecosystems. Antimicrobial therapy began long before traditional modern antibiotics; mercury was used in medieval medicine to treat syphilis, leprosy and as a topical treatment for lice. Arsenic is still used to poison pests like rats. These early antimicrobials prompted the increase and spread of mercury and arsenic resistance in a wide variety of pathogens and environmental bacteria.

Industrial and agricultural practices have involved bacteria in changes to the global biogeochemistry and played a major role in climate change. The spread of industrialized agriculture has increased the methane production from (bacteria in) livestock, rice patties, and landfills. Crop rotations with legumes with their nitrogen-fixing symbionts increase the agricultural output of the land but in doing so the symbionts have altered the global nitrogen cycle. Gillings and Paulsen observed that the combined effect of burning fossil fuels, cultivating legumes, and industrial nitrogen fixation in fertilizer now accounts for about 45% of global nitrogen fixation. Agriculture on an industrial scale has impacted soil microbiology to the point where it has altered the carbon and nitrogen cycle of the entire planet. Elevated levels of methane and carbon dioxide do more than raise just the global temperature. While some have breathed a sigh of relief that the oceans have acted as a carbon sink, it has not been without cost. An acidic ocean is a price we pay for the carbon sink.  The drop in marine pH will affect all microbial communities down to the depths of the abyss. Coral bleaching due to a loss of their microbial symbionts is just one of the most obvious outcomes.

Disease emergence and dispersal has been more of a mixed bag. New diseases get a great deal of attention but with the exception of HIV, they are not worse than the “age of epidemics”  (plague, typhoid fever, yellow fever, etc.).   Vaccines have still amounted to an overall decrease in infectious disease deaths. The three worst diseases to emerge during the Anthropocene are cholera, influenza, and HIV/AIDS. The greatest concerns today are the speed of dispersal for antibiotic resistant strains of old foes and development of new vaccines. Still, though, there are possibly more infectious organisms than ever.  We have driven only two viruses to extinction — smallpox and rinderpest — while new zoonotic diseases emerge at a steady clip.

Completely synthetic microbes created in a laboratory may well eventually be the primary hallmark of the Anthropocene. We are on the verge of being there now and there are an uncountable number of engineered microbes that produce a variety of products from biofuels to drugs. It will be up to us to manage the use of a technology capable of resurrecting a long-extinct bacterial strain or virus.

Do we really think we are smart enough to manage the tsunami of change occurring the microbial world?



Gillings, M. R., & Paulsen, I. T. (2013). Microbiology of the Anthropocene. Anthropocene, 5, 1-8.

Ötzi’s Lyme Disease in Context

One of the ancient DNA finds that continues to intrigue me is the discovery of Borrelia burgdorferi, the agent of Lyme disease, in Ötzi the 5300-year-old ice mummy from the Italian Alps. As far as I know, this is the only finding of B. burgdorferi in ancient remains of any date.  I discussed the initial report of these findings back in the summer of 2012. 


The more we learn about Ötzi’s environment and lifestyle, the less mysterious it seems. There are no signs of human habitation or land management in these high Alpine regions. Indicators of deforestation, farming, and pasture maintenance are lacking from lake sediment and pollen studies. Festi, Putzer and Oeggl (2013) found the first signs of human land management in the Ötztal Alps to began about 1000 years after Ötzi’s time. During the Copper Age, subsistence occupation of the valley floor was sufficient for the population of Ötzi’s time. They did minimal farming, and breeding of caprines (sheep, goats, and ibex). Festi, Putzer and Oeggl (2013) note that Ötzi’s mummy is the only piece of evidence for humans that high in the Otztal Alps before the Bronze Age.

Before Ötzi’s time, landscape management in the Mesolithic was to support red deer herds that were “in a state of semi-domestication by means of active hunting” (Rollo et al, 2002). (Native Americans managed deer populations in similar ways by promoting a landscape where deer thrive near their hunting grounds.) The importance of deer to Ötzi is underscored by everything about him from the red deer meat in his stomach to the roe deerskin that made up his quiver and antler in some of his tools (Rollo et al, 2012). Two different species of deer have been confirmed by genetic analysis.  Most of his clothing was made of sheep and goat skins (O’Sullivan et al, 2016).

The agent of Lyme disease, B. burgdorferi, is transmitted primarily by the tick Ixodes ricinus, common on deer, sheep, cattle, humans and dogs as adults and feed on rodents and small mammals as nymphs. Ticks often thrive at the forest edge where there are grasses for them to climb up to catch passing deer. It seems likely that they would also thrive in along upland forest edges as well. Ixodes ricinus is found throughout the Alps.  It is feasible that Lyme disease was a greater problem for humans when we relied on deer as a staple food.

Ötzi’s B. burgdorferi has yet to be confirmed by a second group. Interestingly, a recent study of B. burgdorferi’s phylogeny suggests that it originated in Europe and later spread to ‘post-Columbian’ North America (Margos et al, 2008). Although Lyme disease was only recognized in the 20th century, it is apparently an ancient disease caused by multiple Borrelia species. And Ötzi’s sequence has not been added to any phylogeny I’ve found, odd. Overlooked, or a problematic sequence?


Festi, D., Putzer, A., & Oeggl, K. (2013). Mid and late Holocene land-use changes in the Otztal Alps, territory of the Neolithic Iceman “Otzi”. Quaternary International, 353, 1–18.

Margos, G., Gatewood, A. G., Aanensen, D. M., Hanincová, K., Terekhova, D., Vollmer, S. A., et al. (2008). MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi. Proceedings of the National Academy of Sciences, 105(25), 8730–8735.

O’Sullivan, N. J., Teasdale, M. D., Mattiangeli, V., Maixner, F., Pinhasi, R., Bradley, D. G., & Zink, A. (2016). A whole mitochondria analysis of the Tyrolean Iceman’s leather provides insights into the animal sources of Copper Age clothing. Scientific Reports, 6, 1–9.

Rollo, F., Ubaldi, M., Ermini, L., & Marota, I. (2002). Otzi’s last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps. Proceedings of the National Academy of Sciences of the United States of America, 99(20), 12594–12599.