Antibiotic Resistance Genes Found in Medieval Human Dung

Centuries before antibiotics were put into use for human health, genes for antibiotic resistance already existed in viruses found in human coprolites, new research shows.

The American Society for Microbiology (ASM) states that antibiotic resistance genes in the human body are not new.  They have existed for at least centuries.  Fossilized dung (coprolite) from a 14th-century latrine uncovered in Belgium was examined by French researcher and her team.  The press release explains:

The viruses in the fecal sample are phages, which are viruses that infect bacteria, rather than infecting eukaryotic organisms such as animals, plants, and fungi. Most of the viral sequences the researchers found in the ancient coprolite (fossil fecal sample) were related to viruses currently known to infect bacteria commonly found in stools (and hence, in the human gastrointestinal tract), including both bacteria that live harmlessly, and even helpfully in the human gut, and human pathogens, says corresponding author Christelle Desnues of Aix Marseille Université.

The communities of phage within the coprolite were different, taxonomically, from communities seen within modern human fecal samples, but the functions they carry out appear to be conserved, says Desnues. That reinforces the hypothesis that the viral community plays a fundamental role within the human gastrointestinal tract, and one which remains unchanged after centuries, even while the human diet and other human conditions have been changing.

Over the last five years, considerable evidence has emerged that bacteria inhabiting the gut play an important role in maintaining human health, for example, as part of the human metabolic system, says Desnues. Her own research suggests that the bacteriophage infecting the gut bacteria may help maintain these bacteria. Among the genes found in the phage are antibiotic resistance genes and genes for resistance to toxic compounds. Both toxins and antibiotics are common in nature, and Desnues suggests that the resistance genes may simply be protecting the gut bacteria from them.

An Oregon State scientist, commenting on the study, called it the “first paper to analyze an ancient DNA viral metagenome.”

Antibiotic resistance has been used as an illustration of evolution by many defenders of Darwinism.  They portray it as an example of the creative power of evolution.  Here is survival of the fittest at work right in front of us, they point out.  We hit germs with antibiotics, and before we know it, the germs have “evolved” resistance to them.

What this study shows, though, is that resistance to antibiotics was already present centuries ago.  When harmful bacteria in the gut are decimated by an antibiotic medicine, bacteriophage viruses are there with the genetic information to resist it.  No new genetic information is manufactured by evolution.  The bacteriophages provide the information to the bacteria, allowing them to proliferate in spite of the presence of antibiotics.

The study suggests that antibiotics and resistance genes are part of a complex, dynamic design.  Many factors in cells and the human body act as pushes and pulls that counter each other’s effects, in order to maintain homeostasis (dynamic equilibrium).  The elements to maintain homeostasis are already present but sometimes get out of balance.  See also 11/20/13 about how bacteria can recover “dead DNA” from the environment, 11/01/13 (“Overcoming Natural Evil with Good”), and 9/04/11 about antibiotic resistance claimed to be 30,000 years old.

Update 2/28/14: Science Magazine gave a fairly detailed account of this research, ending with this:

Interestingly, Desnues’s team’s research reveals that the phages also carried metabolic genes that equip host bacteria with the ability to process fats and amino acids, which may be the traits that made them so useful to our intestines in the first place. Members of the human microbiome help us digest food, temper inflammation, and may fight obesity—so their resistance to antibiotics actually benefits us.

“It’s as if we need these phages as part of our microbiome,” says Vincent Racaniello, a microbiologist at Columbia University who was not involved in the research. He says that though the species of gut phages have changed over time, the key genes that they swap have remained the same. “We evolved as humans to house [gut phages] for the functions they provide—that’s the coolest part.”

If evolution were not assumed, this would look designed.

This finding also suggests that some viruses are beneficial.  Could it be that they were designed to deliver environmental information to cells?  If an animal moves into a new environment, the viruses could deliver genetic information on how to counteract new upsets to homeostasis, like unfamiliar antibiotics.  Some creation scientists have pointed to evidence of design in these dynamic interactions.  It becomes apparent that disease is a disruption of homeostasis.  Dr. Joe Francis at The Master’s College, for instance, has a thesis on how cholera bacteria (one of the really nasty human pathogens) performs a good function in its normal marine environment.  It’s only when there is a breakdown of normal interactions that the agent is able to overwhelm the defenses of the host.  This would suggest that disease bacteria and viruses are good things gone bad: designed benefits that have gone viral, so to speak.  Ongoing research from a design perspective might be able to explore this possibility.  What seems clear right now is that a major illustration of Darwinian evolution has been undermined.

Interestingly, Desnues’s team’s research reveals that the phages also carried metabolic genes that equip host bacteria with the ability to process fats and amino acids, which may be the traits that made them so useful to our intestines in the first place. Members of the human microbiome help us digest food, temper inflammation, and may fight obesity—so their resistance to antibiotics actually benefits us.

“It’s as if we need these phages as part of our microbiome,” says Vincent Racaniello, a microbiologist at Columbia University who was not involved in the research. He says that though the species of gut phages have changed over time, the key genes that they swap have remained the same. “We evolved as humans to house [gut phages] for the functions they provide—that’s the coolest part.”