Vanderbilt Researchers Show Some Anaerobic Bacteria Have Surprisingly High Mutation Rates
By Andy Flick, Evolutionary Studies scientific coordinator
Ask any biologist what causes DNA mutations, and oxygen will likely make the shortlist. It is reactive, super-abundant, and has been fingered as a major culprit in genetic damage for decades. So, here is a head-scratcher: if oxygen is such a DNA troublemaker, bacteria that avoid it entirely should have lower mutation rates, right?
New research led by graduate student Owen Hale in the Behringer Lab reveals that one order of anaerobic bacteria does not exhibit lower mutation rates and these findings challenge long-held assumptions about what actually drives mutation in microbes.
The new paper, “Elevated rates and biased spectra of mutations in anaerobically cultured lactic acid bacteria,” was published in mBio. Hale tracked three species of lactic acid bacteria (Lactobacillus acidophilus, Lactobacillus crispatus, and Lactococcus lactis) through more than 1,000 generations in strictly oxygen-free conditions. The experiment revealed exceptionally high mutation rates compared to oxygen-using bacteria.
The mutations were not random, either. They were strongly biased toward a specific type of change called transitions, which result from spontaneous deamination of DNA bases. The bias in mutations is shared by aerobic bacteria highlighting that even without oxygen around to create damaging free radicals, DNA remains inherently fragile and prone to certain types of errors.
According to Hale, the findings point to population demographics rather than environmental oxygen levels as the primary driver of mutation rates in these bacteria. While oxygen does cause DNA damage, the results suggest that mutation rates are shaped more by a species’ population size over time than by whether oxygen is present.
Most of these mutations have little to no effect on the organism, so there is no need to worry about the “mutant bacteria” lurking in that morning yogurt.
The reason population size matters comes down to a balance between natural selection and random genetic drift. “If your population size is really large, then you should be able to maintain lower mutation rates,” Hale explained.
In large populations, natural selection can efficiently weed out even slightly harmful mutations in DNA repair genes. But in smaller populations, random chance (genetic drift) dominates, and these repair genes can be lost simply by bad luck. The bacteria in this study have relatively small effective population sizes, which means their high mutation rates are consistent with what evolutionary theory predicts when drift overpowers selection.
The three bacterial species in this study are more than lab curiosities, they are industrial heavyweights used in probiotics, pharmaceuticals, and dairy fermentation.
Box 1: Understanding Mutation Bias
“The DNA code is made up of four letters: A, C, T, and G. We looked at single nucleotide mutations (SNMs), a kind of ‘typo’ where one letter changes into another. What we found is that the rate at which C’s turn into T’s is generally much higher than the rate of C’s turning into A’s or any other type of ‘typo’. This difference in the rates of specific SNMs is what we mean by bias. The one exception to the trend was the high rates of T to C mutations in L. acidophilus, which is likely due to the loss of a key DNA repair gene. Mutation bias is important for evolution because mutations are the source of evolutionary novelty that other evolutionary forces like natural selection work on, and the bias controls which mutations will come to be.”
The industrial workhorse Lactobacillus acidophilus provided a particularly striking example. This commercial strain has been domesticated for dairy fermentation, and Behringer noted that “the diversity within the commercial strains is all but gone…these commercial strains haven’t been domesticated in this way for that long.”
The team found that L. acidophilus has lost some DNA repair proteins while possibly adding others, suggesting the mutation rate itself may be evolving in real time. Because domestication dramatically reduced the population size of these commercial strains, the bacteria can no longer maintain all their repair machinery as efficiently. Yet even within this relatively short timeframe, the genetic signatures are already visible.
Hale noted, “viral infections can ruin dairy fermentations, and understanding how the bacteria adapt to overcome this challenge not only improved dairy fermentation but completely revolutionized gene editing technology and is already saving patients’ lives. Basic research can have short-term practical applications, but life is full of surprises, and you’ll never find them if you don’t look!”
Citation: Hale, O.F., Yin, M. and Behringer, M.G., 2025. Elevated rates and biased spectra of mutations in anaerobically cultured lactic acid bacteria. Mbio, 16(12), pp.e03054-25.
Funding Statement: Anaerobic culture facilities were provided by the Vanderbilt Institute for Infection, Immunology, and Inflammation. Library prep and genomic sequencing were conducted at the Vanderbilt Technologies for Advanced Genomics (VANTAGE). High-performance computing resources were provided by the Vanderbilt Advanced Computing Center for Research and Education (ACCRE).
This work was supported by National Institute of General Medical Sciences Grant R35GM150625 (M.G.B.), Danone North America Gut Microbiome, Yogurt, and Probiotic Fellowship Program (O.F.H.), as well as additional funds provided by the Evolutionary Studies Initiative at Vanderbilt (O.F.H. and M.G.B.) and the Vanderbilt Undergraduate Summer Research Program (M.Y. and M.G.B.).