How Ancient Microbes Can Change the Future of Science.


Breaking down the microbiology world one bite at a time

How Ancient Microbes Can Change the Future of Science.

Launched in 2017, the Human Microbiome Project was a research initiative to improve understanding of the role of microbes in the human body. With tons of generated data and fascinating discoveries, this project drastically changed the way people perceive microorganisms. Technological advances in the field of molecular biology and genetics allowed microbiologists to sequence and amplify microbial DNA material, construct trees of life, and study even the smallest genes present in a cell. Scientists were able not only to re-discover pathogenic characteristics of microorganisms but also to explore potential benefits they bring by mutually co-existing with humans. 

Nowadays, in 2021, microbes and people are “friends”, rather than “enemies”. Society is aware of those great things that microorganisms do. “Include probiotics in your diet to have better digestion!”, “Eat more fermented foods to improve your health!”, “Microbes boost our immune system, protect against diseases, and keep us happy!”. The list can go on and on, and all of these things are absolutely correct. Microorganisms are, indeed, in constant service to people. Scientists look into the future with excitement ready to provide more evidence to support an existing relationship between humans and microbes. 

However, more and more researchers think that it is important not only to continue exploring beneficial properties of microbes but also to go back in time and study ancient microorganisms. Paleomicrobiology, a study of ancient microorganisms, can uncover information about the evolution of microorganisms, ancient diseases, cultural customs, and major historic events. 

Now, how and where can we find these prehistoric microbes? Remember, these are specimens that are thousands of years old! It turns out, there are different natural environments/structures, serving as sources of ancient microorganisms: 

  1. Extreme environments, such as permafrost;
  2. Amber;
  3. Dental calculus;
  4. Coprolites.

Extreme environments 
Extreme environments, like permafrost or fossil ice, promote preservation of ancient microbial forms and their DNA. The reason is quite simple: organisms that live in these conditions have very unique survival mechanisms that allow cells to enter a “state of dormancy”, a state where normal biological functions are suspended or slowed down. Plus, these environments are rarely subject to change. One of the most recent examples involves the resurrection of a 30,000-year-old Pithovirus sibericum sample from Siberian permafrost. It is the oldest isolated eukaryote-infecting virus, and, interestingly enough, it still retained its infectivity despite such an extended dormant state! Studying microbial communities of ancient permafrosts will shed more light on proteins and adaptation techniques used by these microbes for their survival.

30,000-year-old virus Pithovirus sibericum. The image is taken from the original research article by Legendre et al. 

Amber is a fossilized tree resin. Its low water activity and abundance of natural sugars represent a perfect environment for the preservation of ancient bacterial species. Many bacteria that were isolated from amber belong to the genus Bacillus1, which is famous for its spore-forming abilities. Spores are the most dormant form of bacteria because they exhibit minimal biological activity. This characteristic of spores has been attributed to the action of small, acid-soluble proteins (SASPs)2. While still viable, metabolism of spore-forming bacteria becomes so slow that they can survive for thousands of years! 

Dental calculus 
Dental calculus is a fossilized bacterial biofilm that forms on the surfaces of teeth. What is unique about this “preservation site” is that dental calculus does not shed and does not change its structure over time (and by “over time” I mean thousands of years!). In his paper, Turner-Walker proposed several factors that contribute to an excellent preservation of genetic material in dental calculus. Firstly, it is not a material that is easily colonized by environmental bacteria. Teeth lack biological channels that typically provide points of entry and movement for bacteria that are not already present in the body. Secondly, dental calculus also lacks a rich nutrient source that can potentially attract and support bacterial growth and promote decomposition. Finally, once fossilized, dental calculus becomes extremely firm, making it resistant to decay.

The recovery of ancient bacteria from dental DNA is usually associated with disease. By identifying a certain disease, scientists can propose a possible lifestyle of a human or an animal. Moreover, disease determination allows researchers to find a causing agent of this disease, which, in most cases, are bacteria and opportunistic pathogens. For example, studies have detected bacteria Yersinia pestis3 and Salmonella enterica serovar typhi4 present in ancient teeth. 

Bacteria Salmonella enterica serovar typhi (left, and bacteria Yersinia pestis (right,

The Justinianic Plague that lasted for over 200 years originated from Y. pestis, which was spread from Asia over the Alps and throughout Europe5. Some scientists even suggest that the modern strains of this bacteria derived from the strain that caused Bubonic Plague in Europe in the 14th century. These observations demonstrate how the analyses of ancient DNA can help to understand evolutionary patterns and forces of mutation in bacterial genomes.

Last, but definitely not least, are coprolites – fossilized remains of feces – that, undoubtedly, represent the richest source of ancient microorganisms. It is a widely known fact that stool contains billions of microorganisms, and therapies such as fecal transplantation, are used to transfer microorganisms from one organism to another. Thus, with the hope to discover ancient microorganisms, scientists decided to study coprolites from a “microbiological” perspective. 

Reinhard and his colleagues conducted the study, in which they examined coprolites found on the Colorado Plateau (Utah, USA)6. They identified bacterial DNA samples that belonged to the Alpha-, Beta-, and Gammaproteobacteria, Bacteroides, Clostridia, Eubacterium spp. and even Vibrio spp. It is easy to see how microbiologically diverse ancient coprolites are! 

If studied carefully, recovered coprolites could contain an enormous amount of information about lifestyles, dietary habits, and even certain cultural norms of ancient people. And because composition of a microbiome is highly dependable on a lifestyle and dietary preferences, scientists can get a better understanding of a prehistoric world. Although it is interesting to learn about ancient microorganisms, studies in the area of paleomicrobiology can help scientists to establish a link between the past, the present, and the future. By determining the composition of ancient microbiomes, it becomes easy to trace evolutionary changes that occurred due to industrialization, globalization, and modern sanitation practices1. It is intuitive that people have drastically changed their relationship with microbes, and this change is literally recorded in the body. 

Link to the original post: Rivera-Perez, J.I., Santiago-Rodriguez, T.M., Toranzos, G.A. 2016. Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology. Microbiol Spectr. 4(4). doi:10.1128/microbiolspec.EMF-0006-2015

Featured image: and Created in Biorender.

  1.  Rivera-Perez, J.I., Santiago-Rodriguez, T.M., Toranzos, G.A. 2016. Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology. Microbiol Spectr. 4(4). doi:10.1128/microbiolspec.EMF-0006-2015
  2.  Cano RJ. 1997. Isolation, characterization, and diversity of microorganisms from amber. Proceedings of SPIE. 3111: 444-451. doi:10.1117/12.278799
  3. Drancourt, M., Aboudharam, G., Signoli, M., Dutour, O., Raoult, D. 1998. Detection of 400-year-old Yersinia pestis DNA in human dental pulp: an approach to the diagnosis of ancient septicemia. Proc Natl Acad Sci USA. 95:12637–12640.
  4. Papagrigorakis, M.J., Synodinos, P.N., Yapijakis, C. 2007. Ancient typhoid epidemic reveals possible ancestral strain of Salmonella enterica serovar Typhi. Infect Genet Evol. 7:126–127.
  5. Harbeck, M. et al. 2013. Yersinia pestis DNA from skeletal remains from the 6(th) century AD reveals insights into Justinianic Plague. PLoS Pathog.
  6.  Reinhard, K.J., Hevly, R.H., Anderson, G.A. 1987. Helminth remains from prehistoric Indian coprolites on the Colorado Plateau. J Parasitol. 73:630–639.