Shitty Treasure Chests
(March 25th, 2014) Despite its rather disgusting nature, poop holds a wealth of secrets and is the source of a myriad of research projects. And you don’t even need a fresh sample. French researchers found that coprolites, fossilised faecal matter, reveal just as much.
Namur, Belgium, 14th century. After a hearty meal, a man has to relieve himself and walks to the village’s latrine. Little did he know that 700 years later, researchers would take an interest in his droppings. In 1996, archaeologists excavated a closed barrel, containing a “121.4g, dark-brown, well preserved coprolite specimen” - research properly began in 2007 and recently spawned two publications.
In the first one, Christelle Desnues from the Aix Marseille Université in Marseille, France, analysed the fossilised faeces’ viral community. Their work provides the earliest evidence of an arms race in the human gut, between bacterial and viral invaders. Desnues and colleagues sequenced viral DNA to determine their most likely affiliation and get to know some of their properties. “We were interested in viruses because these are 100 times more abundant in our body than eukaryotic cells but their diversity is still largely unexplored, especially in ancient samples,” explains Desnues.
The group identified a wide variety of viruses - some known to infect eukaryotes, bacteria and archaea. In addition, Desnues and co. were able to infer some of the likely metabolic functions of these viruses which, apparently, have remained conserved throughout the centuries. They include some key adaptations like antibiotic resistance. Finding these particular genes in an ancient coprolite is of great importance: “The detection of antibiotic resistance genes in a bacteriophage genome before the use of antibiotics by humans indicates that antibiotics are ubiquitous natural weapons used by bacteria in a dynamic environment such as the human gastro-intestinal tract and that phages are long-time active combatants in this battle.”
Even more surprising than the sheer presence of antibiotic resistance genes was the fact that the ancient samples contained even more of them than our modern gut microbes. This reduction may be explained by our modern environment, where efficient sanitation techniques in food and water supplies may have led to the evolution of less resistant gut bacteria. Besides antibiotic resistance genes, the team also detected genes involved in the fat and amino acid metabolisms, key genes present today in our gut´s microbiome supporting the digestion of food, fighting inflammation and maybe even fighting obesity.
In late February, a second paper, by some of the same authors examined the same pile of poop a bit further. Led by Michel Drancourt, from Aix Marseille Université, Marseille, France, the excrement experts used metagenomic and cell culture tools to reconstruct the sample’s microbiotic flora. Among amoebal cysts, plant fibres, seeds, pollens and mold remains, they identified several bacterial species that are typical inhabitants of the human gut, such as Proteobacteria, Gemmatimonadetes, Actinobacteria and Chlamydia. The microbial motley crew also featured intestinal parasites (Trichuris and Ascaris), systemic pathogens like Bartonella, known to be involved in zoonoses, and Bordetella, species causing respiratory tract infections. Both were detected for the first time in a coprolite sample.
Martin Ezcurra, palaeobiologist from the University of Birmingham, not involved with these studies, is impressed: “Gut contents and the diversity of the intestinal fauna and flora are key information to study the evolution of behaviour. Coprolites provide a unique opportunity to gather this information from thousand to million year old animals or ancient humans. They are like an ancient treasure chest with a formidable source of information about past times. Desnues, Drancourt and colleagues conducted multiple analyses to gather all the information that they can and identified several microorganisms that lived hundreds of years ago in the gut of an ancient European. Their data are extremely exciting and can potentially help to understand the evolution of some human diseases and the coevolution of intestinal microbiota with our species.”
All in all, the two studies point to the need of a better understanding of the microbiome of both ancient and modern stool samples, as they may give us some valuable insights into the inner workings of our gut microbes and the role of viruses, “as a reservoir of antibiotic resistance genes and vectors in the rapid emergence of antibiotic resistant bacteria,” explains Desnues.
Photo: Fotolia/dominique szatrowski