Category Archives: Mediterranean

Summer reading

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The summer seemed to fly by. Here is some of my reading from the summer. Let me know what you read this summer in the comments or on Twitter. 


Gibson, Abraham. (2016) Feral Animals in the American South: An Evolutionary History. Cambridge University Press.

Hutchison, Dale L (2016) Disease and Discrimination: Poverty and Pestilence in Colonial Atlantic America. University of Florida Press.



Green, M. (2017). The Globalisations of Disease. In N. Boivin, R. Crassard, & M. Petraglia (Eds.), Human Dispersal and Species Movement From Prehistory to the Present (pp. 494–520). Cambridge.

Silva, C. (2008). Miraculous Plagues: Epidemiology on New England’s Colonial Landscape. Early American Literature, 43(2), 249–270.

Newfield, T. P. (2017). Malaria and malaria-like disease in the early Middle Ages. Early Medieval Europe, 25(3), 251–300.

Moodley, Y., Linz, B., Bond, R. P., Nieuwoudt, M., Soodyall, H., Schlebusch, C. M., et al. (2012). Age of the Association between Helicobacter pylori and Man. PLoS Pathogens, 8(5), e1002693.

Maixner, F., Krause-Kyora, B., Turaev, D., Herbig, A., Hoopmann, M. R., Hallows, J. L., et al. (2016). The 5300-year-old Helicobacter pylori genome of the Iceman. Science (New York, NY), 351(6269), 162–165.

Domínguez-Bello, M. G., Pérez, M. E., Bortolini, M. C., Salzano, F. M., Pericchi, L. R., Zambrano-Guzmán, O., & Linz, B. (2008). Amerindian Helicobacter pylori Strains Go Extinct, as European Strains Expand Their Host Range. PLoS ONE, 3(10), e3307–7.

Baeza, A., Santos-Vega, M., Dobson, A. P., & Pascual, M. (2017). The rise and fall of malaria under land-use change in frontier regions. Nature Geosciences, 1(5), 1–7.

Tucker Lima, J. M., Vittor, A., Rifai, S., & Valle, D. (2017). Does deforestation promote or inhibit malaria transmission in the Amazon? A systematic literature review and critical appraisal of current evidence. Philosophical Transactions of the Royal Society B: Biological Sciences, 372(1722), 20160125–11.

Viganó, C., Haas, C., Rühli, F. J., & Bouwman, A. S. (2017). 2,000 Year old β-thalassemia case in Sardinia suggests malaria was endemic by the Roman period. American Journal of Physical Anthropology, 23(1), 147–9.

Calvignac-Spencer, S., & Lenz, T. L. (2017). The One Past Health workshop: connecting ancient DNA and zoonosis research. BioEssays, 39(7), 1700075–4.

Lynteris, C. (2017). Zoonotic diagrams: mastering and unsettling human‐animal relations. Journal of the Royal Anthropological Institute, 42, 713.

Donoghue, H. D. (2017). Insights gained from ancient biomolecules into past and present tuberculosis—a personal perspective. International Journal of Infectious Diseases, 56, 176–180.


Reservoirs of Salt Adapted Yersinia pestis

The Arab Maghreb is one of the most arid environments to host plague reservoirs. The most recent study on the area highlights the proximity of plague foci to salt water, either the Mediterranean Sea, Atlantic Ocean or importantly inland salt lakes (Malek et al, 2016). These inland salt springs, called chotts, are saltier than the ocean. They were specifically able to cultivate Y. pestis from high salt soil and isolate a high salt tolerant strain of Yersinia pestis from Algeria. Plague foci across North Africa were found at an average of 0.89 km from salt water, while the average distance from fresh water is 4.6 km.

Plague sites 1940-2015. Red = plague sites, Blue = salt water lakes, Yellow = fresh water. Cropped from Malek et al, 2016.

They also note the importance of L-form Yersinia pestis in their environmental samples. L-form bacteria are an understudied cell wall deficient state that quite a few bacteria, including Yersinia pestis, use for long term survival. The L-form of Y. pestis may be important in environmental persistence. Because they are believed to have a slower reproduction rate,  the L-form may also play a role in altering the molecular clock of some strains. To date,  publications that focus on L-form Y. pestis have been in either Russian or Chinese. It seems clear that the L-form is found in some instances in Asia as well. Importantly, some L-form bacteria can regain their cell wall and return to active ‘normal’ growth.

Soil osmolarity is the key feature that allows (or requires) the L-form to persist. Withstanding osmotic tensions is the primary role of the cell wall. Without the cell wall, the cell loses its ‘normal’ shape, taking on a spherical shape determined by hydrophobic-hydrophilic interactions (like oil and water). As the cell membrane is primarily made of phospholipid, its the L-form shape resembles a sturdy oil globule or a liposome (B below). This was apparent by gram stain when the normal individual short rod-shaped (coccobacilli) cells transformed into clusters of completely round (cocci) cells. This was confirmed under the electron microscope where the change is very apparent.


They also isolated a strain, Algeria3, a descendant of the third pandemic, from soil containing 4% salt, that can grow in a 15% salt broth. Other Algerian isolates that were not found in high salt soils experimentally survived as well in high salt media if the salt content was ramped up in a step-wise fashion. Growth in high salt conditions altered their protein production to increase those related to osmoregulation, metabolism, outer membrane proteins and others of unknown function.  Osmoregulation genes changes are a direct response to the higher salt concentration. The L-form cells are clearly still metabolically active.

Taken together these protein profiles suggest that it has adapted to survive in the salty soil with the ability to adjust its structure and function as necessary to persist.  They note that other plague reservoirs are in regions of the world with salt lakes or other salty sources, but more environmental sampling will be necessary to determine if this is a universal Y. pestis capability. This all has obviously important implications for plague ecology.


Malek, M. A., Bitam, I., Levasseur, A., Terras, J., Gaudart, J., Azza, S., et al. (2016). Yersinia pestis halotolerance illuminates plague reservoirs. Scientific Reports, 7, 1–10.

A winter’s worth of work

Its well into spring now and my blogging has perhaps hit an all time low. I have been working on a project that I will write about more later this year. I’ve been reading a lot about environmental history, not the usual material for this blog. Some of it is listed below. It’s a sample of the kind of thing that I need to be read to understand disease in the past. I think it will be worth it eventually even if pollen diagrams and geology diagrams are not very exciting. 

I do have quite a few ideas for new posts, so I will be back…soon. 

A sampling of some of my recent reading:

Büntgen, U., Myglan, V. S., Ljungqvist, F. C., McCormick, M., Di Cosmo, N., Sigl, M., et al. (2016). Cooling and societal change during the Late Antique Little Ice Age from 536 to around 660 AD. Nature Geoscience, 1–7.

Mitchell, P. D. (2015). Human Parasites in Medieval Europe: Lifestyle, Sanitation and Medical Treatment. Advances in Parasitology (Vol. 90, pp. 389–420). Elsevier Ltd.

Mitchell, P. D. (2016). Human parasites in the Roman World: health consequences of conquering an empire. Parasitology, 1–11.

Brogolio, G.P. 2015. Flooding in Northern Italy during the Early Middle Ages: resilience and adaption, in Post-Classical Archaeologies. 5: 47-68.

Galassi FM, Bianucci, R., Gorini, G., Giacomo M. Paganotti. G.M., Habicht, M.E., and Rühli, F.J. 2016. The sudden death of Alaric I (c. 370–410AD), the vanquisher of Rome: A tale of malaria and lacking immunity, European Journal of Internal Medicine. [Ahead of Print]

Mensing, S. A., Tunno, I., Sagnotti, L., Florindo, F., Noble, P., Archer, C., et al. 2015. 2700 years of Mediterranean environmental change in central Italy: synthesis of sedimentary and cultural records to interpret past impacts of climate on society, in Quaternary Science Reviews, 116(C), 72–94.

Sadori, L., Giraudi, C., Masi, A., Magny, M., Ortu, E., Zanchetta, G., & Izdebski, A. 2015. Climate,  environment and society in southern Italy during the last 2000 years. A review of the environmental, historical and archaeological evidence, in Quaternary Science Reviews, 1–16.

Li, Y.-F., Li, D.-B., Shao, H.-S., Li, H.-J., & Han, Y.-D. (2016). Plague in China 2014—All sporadic case report of pneumonic plague. BMC Infectious Diseases, 1–8.

Statskiewicz, A. (2007). The early medieval cemetery at Aschheim-Bajuwarenring: A Merovinigan population under the influence of pestilence? In Skeletal series and their socio-economic context (pp. 35–56).