From Penguins to Frogs: The new frontier of wildlife microbiomes

With recent technological advances in DNA sequencing investigating microbiomes from all areas of life has become possible as PLOS ONE Publication Assistant Maija Mallula finds out. With the advancement of DNA sequencing technology, our ability

Who Let the Microbes Out: A Paw Print of Doggy Skin Bacteria

A house is not a home without a dog, and a dog isn’t a “D-O-double-G” without its microbial “crew.” Human microbiome research is progressing rapidly, and we are always learning how the bacteria living on and inside of us contribute … Continue reading »

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Fecal Matters: A Stepping Stool to Understanding Indigenous Cultures


Humans differ by opinions, traits, and baseball team preferences. But one constant factor unifies all humans–we excrete feces, and scientists have recognized that number 2 is number 1 in terms of material for ancient population studies. Humans expel hundreds of … Continue reading »

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In the deep, bioluminescent bacteria bloom bright


Imagine swimming to the bottom of the sea, the water growing impossibly deep and dark the farther you travel. At these depths, beyond the reach of the sun, live strange new sources of light. Fish, jellyfish, and even bacteria light up these midnight waters.

According to new research in PLOS ONE, the light of this deep-sea bioluminescence waxes and wanes with seasonal changes on earth’s surface. In the Mediterranean winter, cold winds cause surface water to cool. As the surface cools, it becomes denser than the water beneath it, and begins to sink. Convection can also cause this layer to expand, potentially extending it to the Mediterranean Sea’s basin floor. When these phenomena occur side by side, as they can in the northwestern part of the Mediterranean Sea, carbon matter from the surface circulates into deeper waters. Think of it as Nature’s way of stirring the pot.

This wintry stir spreads a wave of changing temperatures, water composition and organic matter into the depths of the ocean, which correlates with a burst of bioluminescence activity. Over the course of two and a half years, the researchers recorded two water stirring incidents, followed by periods of bioluminescent activity. In each instance, winter stirring resulted in bioluminescent blooms lasting several weeks in the following spring or summer.

That being said, this phenomenon is likely to change in the coming years. According to the researchers, as climate change continues to affect the sea, convection activity which helps stir the waters and introduce much-needed carbon to the deep sea may decrease by the end of the 21st century. In the meantime, it is important to document deep-sea activity to better understand any actual or forecasted changes.


Citation: Tamburini C, Canals M, Durrieu de Madron X, Houpert L, Lefèvre D, et al. (2013) Deep-Sea Bioluminescence Blooms after Dense Water Formation at the Ocean Surface. PLoS ONE 8(7): e67523. doi:10.1371/journal.pone.0067523

Image: Biolumplate, from Wikimedia Commons.

Resisting Antibiotics: Some Bacteria Get By With a Little Help From Their Friends


Antibiotic resistance is often in the news, as it threatens the effectiveness of one of the foundations of modern medicine. Usually, the concern is about resistance that is inherent to the bacteria, or else develops in bacteria through genetic changes. A paper published today in PLOS ONE suggests another possibility.

In “Chemical communication of antibiotic resistance by a highly resistant subpopulation of bacterial cells,” authors Omar El-Halfawy and Miguel Valvano reveal that some species of bacteria may help others in surviving an antibiotic attack. In addition, they were able to provide insight into the mechanics of how the bacteria perform this action.

The study began with an observation of the bacterial species Burkholderia cenopecia, which typically grows in the soil but can infect people who have cystic fibrosis and those with compromised immune systems. The authors noted that a subpopulation of the species was more resistant to the antibiotic polymyxin B than other bacteria of the species. In other words, these resistant bacteria were more likely to survive after treatment with polymyxin B, and levels of antibiotics that killed the less resistant bacteria did not harm this (more resistant) subpopulation.

When the authors grew the more-resistant B. cenopecia with another strain of bacteria called Pseudomonas aeruginosa (a disease-causing bacterium that can co-exist with B. cenopecia), the P. aeruginosa were much more resistant to the antibiotic than when they grew in isolation.

Why might the P. aeruginosa be more resistant when they were in the presence of B. cenopecia?

The authors suspected that the B. cenopecia were releasing something into their environment that interfered with the action of the antibiotic, making it less potent. Experiments revealed that the bacteria were indeed secreting two proteins associated with increased antibiotic resistance: putrescine (named for its putrid odor!) and Ycel, a protein whose function was previously unknown.

cartoon 3

The large amounts of secreted putrescine blocked the antibiotics’ binding to the surface of the bacteria, and could make both B. cenopecia and P.aeruginosa more resistant to polymyxin B when grown together.

Ycel, on the other hand, was able to bind to the antibiotic directly, presumably decreasing its potency. Ycel is predicted to bind amphiphilic molecules (such as detergents, which  are attracted to both water and oil). Consistent with this prediction, the authors showed that Ycel had a protective effect against amphiphilic antibiotics and less of an effect against others.

These results have implications for combating the growing problem of antibiotic resistance. If we could prevent bacteria from making putrescine or Ycel, antibiotic treatments might be more effective, helping us eventually outflank resistance.

Citations: El-Halfawy OM, Valvano MA (2013) Chemical Communication of Antibiotic Resistance by a Highly Resistant Subpopulation of Bacterial Cells. PLoSONE 8(7): e68874. doi:10.1371/journal.pone.0068874

Bragonzi A, Farulla I, Paroni M, Twomey KB, Pirone L, et al. (2012) Modelling Co-Infection of the Cystic Fibrosis Lung by Pseudomonas aeruginosa and Burkholderia cenocepacia Reveals Influences on Biofilm Formation and Host Response. PLoS ONE 7(12): e52330. doi:10.1371/journal.pone.0052330

Images: Pseudomonas aeruginosa doi:10.1371/journal.pone.0066257

Malaria, tuberculosis caused death on the ancient Nile



Southwest of Cairo, the Nile branches into a network of canals that feed Fayum, a fertile agricultural basin that was a center of civilization and royal pyramid-building for several centuries. The unusual geology responsible for Fayum’s rich terrain may have also led to the prevalence of malaria and tuberculosis in the region during these ancient times.

Ancient DNA (aDNA) from sixteen mummified heads recovered from the region reveals that at least four of these individuals suffered both these infections simultaneously. Many of the others showed signs of infection with either malaria or tuberculosis, as scientists report in a recent PLOS ONE study.

DNA extracted from muscle tissue samples was tested for the presence of two genes specific to Plasmodium falciparum, the malarial parasite, and another gene specific to Mycobacteria, which cause tuberculosis. Two samples tested positive for DNA specific to Plasmodium, one tested positive for the mycobacterial gene, and four individuals tested positive for DNA from both infectious agents, suggesting they suffered both infections together while alive. A previous study suggests that both malaria and tuberculosis were rampant in the Fayum region in the early 19th century, but the age of these mummified samples extends evidence of these diseases in Lower Egypt as far back as approximately 800 B.C.

The World Health Organization estimates that malaria is almost non-existent in the Fayum basin and the rest of Egypt now, but before its eradication, high levels of infection were seen in certain parts of the country, and were strongly linked to certain geological features. The lakes and canals that made the Fayum region so fertile also served as breeding grounds for the mosquito that carries the malarial parasite.

The heads tested here (all were missing bodies) were recovered from a village cemetery on the west bank of the lower Nile, and date from about 1064 BC to 300 AD, a period marked by an agricultural boom and dense crowding in the region, especially under the rule of the Ptolemies. These conditions may have increased the chances of tuberculosis incidence and spread of the disease. As the aDNA from these mummified heads attests, these living conditions and the unique irrigation of the Fayum basin likely created a harbor for both malaria and tuberculosis in ancient populations of this region.

Citation: Lalremruata A, Ball M, Bianucci R, Welte B, Nerlich AG, et al. (2013) Molecular Identification of Falciparum Malaria and Human Tuberculosis Co-Infections in Mummies from the Fayum Depression (Lower Egypt). PLoS ONE 8(4): e60307. doi:10.1371/journal.pone.0060307

Image: Sailing on the Nile by David Corcoran

Opportunistic pathogens evolve mostly harmlessly in healthy humans


Humans interact with bacteria almost every minute of our lives. Of the millions of these interactions, only a handful result in disease, and some bacteria only cause infections under certain conditions. In a recent PLOS ONE study, researchers probe these healthy human-bacterial relations  in one particularly notorious pathogen as it spends the majority of its time in our bodies, doing no harm.

Staphylococcus aureus can cause endocarditis, toxic shock syndrome and other diseases, killing approximately 1 in 100,000 infected people in the US each year. Strains like MRSA have also evolved to carry multiple antibiotic resistance genes, making infections extremely difficult to treat. If human-bacterial interactions are to be described as a ‘genetic arms race’, it may be tempting to cast S. aureus as an enemy that carries every available genetic weapon.

Yet despite a few sporadic skirmishes, the majority of our interactions remain peaceful, as these bacteria thrive in healthy human hosts.  In fact, about a third of healthy adults carry S. aureus in our noses at some point in our lives.  In the article, researchers analyzed the genetic changes in S. aureus carried in such hosts by sequencing the genomes of 130 strains of S. aureus from the nasal passages of 13 healthy adults, five of whom carried strains of MRSA (which is often harmless when carried nasally). Despite the arms race metaphors, they found that S. aureus strains in healthy hosts are not incessantly beefing up their genetic arsenal of antibiotic resistance or pathogenesis genes.

They found bacterial genomes were changed by processes of ‘micro-mutation’, i.e.: small bits of genetic material being added or removed, or changes in a single letter in the genetic code. Large insertions and deletions (macro-mutation) were also common, as were changes caused by bacteria-infecting viruses or small, independently moving rings of DNA called plasmids. Overall, the constant changes in S. aureus genomes were geared toward keeping bacterial genomes healthy by clearing erroneous or harmful mutations. Only on rare occasions did these bacteria acquire distinctive surface proteins or an enterotoxin that could alter their pathogenic potential. In addition, their research also analyzed changes in specific genes used to assess bacterial diversity and relatedness, and developed a new method to detect transmission of bacterial strains among human carriers. Read the full study to learn more about these interesting results.

Many of the changes identified in this study may not directly increase the virulence of disease-causing S. aureus. However, previous work by these researchers demonstrated that mutations arising in bacteria carried by healthy hosts may play an important role in tipping the balance between human health and disease. Here, the authors begin to paint a picture of what these mutations are and how they may occur.

Citation: Golubchik T, Batty EM, Miller RR, Farr H, Young BC, et al. (2013) Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage. PLoS ONE 8(5): e61319. doi:10.1371/journal.pone.0061319

Image: Scanning electron micrograph of S.aureus with increased resistance to vancomycin. Credit CDC/ Matthew J. Arduino, DRPH


PLOS ONE Goes to the Mile-High City for ASM 2013

Bacillus anthracis - three color

PLOS ONE is looking forward to connecting with our editors, authors, reviewers, and readers at the 113th General Meeting of the American Society for Microbiology in Denver, Colorado. Representing PLOS ONE will be Damian Pattinson, Executive Editor; Lindsay Kelley, Editorial Board Manager; Camron Assadi, Product Marketing Manager; and myself (Meg Byrne, Associate Editor).

PLOS ONE continues to publish many high-profile papers in microbiology. Some of the most highly cited articles published since 2011 include a genomic characterization of a deadly Escherichia coli strain; a “field guide” to more than 3000 isolates of methicillin-resistant Staphylococcus aureus found around the world; the genome sequence of a novel ammonia-oxidizing archaeon (a member of the recently discovered third domain of life); and an analysis of the lung microbiomes in smokers with chronic obstructive pulmonary disease, smokers without COPD, and non-smokers.

In the last month, a number of publications have caught our readers’ eyes.  These include an article showing that a breast-milk protein can help fight antibiotic-resistant bacteria; a report of a new antibiotic developed from a bacteria-killing virus; a super-phylogeny of the over 3000 bacterial and archaeal genomes that have been sequenced to date; and an analysis of the immune response to a bacterial lung infection in a 500-year-old mummy.

Come find us at the meeting: We’d love to hear your thoughts about PLOS and science publishing, in general. We’ll be at booth #350 from Sunday, May 19th through Tuesday, May 21st.

For authors: Let us show you your article level metrics (ALMs) and give you a special author t-shirt.  We can also show off one of our latest features, Relative Metrics (Beta), which allows you to compare your paper’s usage to the average usage of articles in related subject areas.

For prospective authors: Please come ask us any questions you have about publishing in PLOS ONE and the family of PLOS journals. We can enumerate the many advantages of publishing in our open access journals, including free readership rights, reuse and remixing rights, unrestricted copyright, automatic posting of the article, and machine accessibility of the published article.

For PLOS ONE academic editors: We are looking forward to seeing you at our Editorial Board Reception on Monday May 20th from 5:30 to 7:30 PM at the Hyatt Regency.  We would love to fill you in on our plans for the future, get your feedback, and say a huge “Thank you!” It’s also a great opportunity to meet other academic editors. Please contact Lindsay Kelley or Camron Assadi for further information.

Also, PLOS Biology is looking forward to catching up with their academic editors at a “Meet the Editors” event on Sunday May 19th between 12:30 and 2:30 PM at the PLOS Booth.

We’re looking forward to seeing many microbiologists in Denver and discussing the small but mighty microbe.


Bacillus anthracis with the cell wall labelled red, the division septa labelled green, and the DNA labelled blue (Schuch et al. PLOS ONE 2013).


Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR (2011) Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis. PLoS ONE 6(2): e16626. doi:10.1371/journal.pone.0016626

Corthals A, Koller A, Martin DW, Rieger R, Chen EI, et al. (2012) Detecting the Immune System Response of a 500 Year-Old Inca Mummy. PLoS ONE 7(7): e41244. doi:10.1371/journal.pone.0041244

Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, et al. (2011) Analysis of the Lung Microbiome in the “Healthy” Smoker and in COPD. PLoS ONE 6(2): e16384. doi:10.1371/journal.pone.0016384

Lang JM, Darling AE, Eisen JA (2013) Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices. PLoS ONE 8(4): e62510. doi:10.1371/journal.pone.0062510

Marks LR, Clementi EA, Hakansson AP (2013) Sensitization of Staphylococcus aureus to Methicillin and Other Antibiotics In Vitro and In Vivo in the Presence of HAMLET. PLoS ONE 8(5): e63158. doi:10.1371/journal.pone.0063158

Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, et al. (2011) Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology. PLoS ONE 6(7): e22751. doi:10.1371/journal.pone.0022751

Monecke S, Coombs G, Shore AC, Coleman DC, Akpaka P, et al. (2011) A Field Guide to Pandemic, Epidemic and Sporadic Clones of Methicillin-Resistant Staphylococcus aureus. PLoS ONE 6(4): e17936. doi:10.1371/journal.pone.0017936

Schuch R, Pelzek AJ, Raz A, Euler CW, Ryan PA, et al. (2013) Use of a Bacteriophage Lysin to Identify a Novel Target for Antimicrobial Development. PLoS ONE 8(4): e60754. doi:10.1371/journal.pone.0060754

Antarctic bacteria float through winter

As the Northern Hemisphere shivers through winter, bacteria in Antarctica are employing an inventive strategy to survive the extreme cold: they use a specialized antifreeze protein to latch onto the ice and stay afloat.

Antifreeze proteins generally protect their hosts from freezing by controlling the growth of destructive ice crystals. They were first found in fish swimming in icy waters (see this paper about the evolution and transfer of these proteins between different fish species), and have also been found in plants and bacteria.

The bacterial case now has an interesting twist, published earlier this winter. The authors of the recent study isolated and characterized the antifreeze protein from Marinomonas primoryensis, found in ice-covered Ace Lake in Antarctica. They determined that the bacteria display the protein on their surface, where it can bind directly to ice crystals and anchor the microorganism to the ice. This behavior is a significant departure from what is known about similar proteins, which act inside cells to protect against internal ice crystallization. The image above shows the results from one of the experiments that confirmed the protein is found on the bacterial surface, rather than the interior.

It may not be immediately obvious how binding to ice benefits the bug, but the researchers suggest that it helps the bacteria stay closer to the water surface, where oxygen and nutrients are more abundant. Instead of requiring protection from freezing, these bacteria take advantage of the ice, essentially turning lemons into lemonade – although that may be a metaphor for a different season.


Graham LA, Lougheed SC, Ewart KV, Davies PL (2008) Lateral Transfer of a Lectin-Like Antifreeze Protein Gene in Fishes. PLoS ONE 3(7): e2616. doi:10.1371/journal.pone.0002616

Guo S, Garnham CP, Whitney JC, Graham LA, Davies PL (2012) Re-Evaluation of a Bacterial Antifreeze Protein as an Adhesin with Ice-Binding Activity. PLoS ONE 7(11): e48805. doi:10.1371/journal.pone.0048805

Greetings from Lake Socompa! A Diversity of Life in Extreme Conditions

The photo above comes to us from a remote part of the Andes, at the base of the active volcano Socompa. Lake Socompa is situated here and its whitish stomatolites (a type of layered sediment deposit created by microorganisms) are home to an unexpected diversity of bacterial life.

In research published this week in PLOS ONE, scientists from Argentina and Germany travelled to this remote location, 3570 meters above sea level, to study the lake’s stomatolites and the harsh environment in which they are formed. Stomatolites were found only on the southern shore, where a hydrothermal spring feeds acidic water into the lake. This region of the Andes mountain range receives very little annual rainfall and, due to its high elevation, experiences high levels of ultraviolet radiation. Yet, rather than being inhospitable to life, scientists found that the region’s extreme environmental conditions actually helped to foster “rich, diverse and active ecosystems” within the lake’s stomatolites.  According to the research, the Lake Socompa site is the highest altitude, thus far, where stomatolites are found to form.

Citation: Farías ME, Rascovan N, Toneatti DM, Albarracín VH, Flores MR, et al. (2013) The Discovery of Stromatolites Developing at 3570 m above Sea Level in a High-Altitude Volcanic Lake Socompa, Argentinean Andes. PLoS ONE 8(1): e53497. doi:10.1371/journal.pone.0053497

Plunging into the Unknown: Belly Button Bacteria and You

Have you ever looked up at the night sky and wondered what kinds of life might exist out there? Well, you can look down – at your belly button that is – and wonder the exact same thing.

According to research published today in PLOS ONE, the belly button is home to an array of bacterial life ranging from the common (like Staphylococci) to the rare (like Archaea which have never been found before on human skin). Some bacteria, like those belonging to the Bacillus genus (pictured above), are feisty – they battle against fungi and viruses. Other bacteria, like those in the Micrococcus genus, are responsible for body odor!

All of this and more were found in the belly buttons of various participants in the study. The authors, led by Dr. Robert Dunn, identified over 2000 phylotypes (i.e., different types or species) of bacteria, most of which were rare and found in less than a tenth of the study’s sixty participants. No one particular phylotype was found in every person, but those that were common were shared by over seventy percent of belly buttons swabbed. What a bacterial ball!

We invited Dr. Dunn, the corresponding author of the study, to help give us some insight on the aptly named “A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable”.


What was the impetus behind your research?

We originally started this project as pure outreach, to help people understand the wonderful ecological system that covers them from head to toe, inside and out. We found that people were very interested in seeing cultures of what lived on them but as we looked at the cultures it became clear there were more species (and simply more interesting things) growing on people than we expected. At some point the project went from outreach to science. […] Darwin got to […] go to the Galapagos, we decided to travel to the navel of the hair[y] guy who we see in the elevator sometimes.

Why choose belly buttons?

In our experience, the belly button is among the most ridiculous parts of the body. It is ridiculous enough that people who don’t necessarily like nature, say for example birds, can still be convinced to sample their belly button. […] The other reasons were more technical. The belly button is relatively less disturbed than, say, your hands. It is less exposed to all the chemicals and other people we bump up against during an ordinary day. In that way it is the closest thing we might find to an “old growth” sample of skin. Finally, it is worth noting that there are other body parts that are ecologically interesting but that we have found, and maybe this is just us being too old-fashioned, are awkward to sample at public science events.

What kinds of lessons do you hope the public takes away from the research?

That we know very little about the species on our bodies and around us in our daily lives. The species in your belly button or armpits, they are an important part of your first line of immune defense, and yet right now no one can explain to you why you have the species you have on your body. I know of no single study that is able to explain the differences in skin bacteria from one person to the next. That is a big mystery, not quite the pyramids of Egypt big, but big, and it is living and dividing on you right now. I’d like people to be more aware of that mystery and that the unknown, biologically speaking, is not just something far away, it is also the funny place that lint accumulates.

It is worth saying, in this context, that while we can now predict which bacteria tend to be frequent and common in belly buttons, we are  totally unable to predict which of the common species will be found on any particular person. Gender doesn’t seem to matter, nor does age, nor does innie/outie, nor does where you live now or where you were born. So that is what we are moving toward, trying to understand what governs the species that are found on any particular person […] and how we might alter our behavior in ways to favor species that keep us healthy and disfavor those that do us harm.

If others are interested in taking part or learning more about it, how would you recommend that they proceed?

Sign up at our mailing list and you can get emails about our next projects. Right now people can participate in projects on ants in their backyards, camel crickets in their basements and microbes in their kitchen, but as new mysteries turn up there will be more. Armpits, for example, are on the horizon. Oh, the armpits….

Participants in this study came from many walks of life: People curious about their spouse’s belly buttons, teachers wanting to find ways to engage their students in the microbial world around them, researchers, museum visitors, science writers and others. Read more of their stories at the links below:

If you would like to learn more about future projects you can visit the project’s home page: Belly Button Biodiversity.



Hulcr J, Latimer AM, Henley JB, Rountree NR, Fierer N, et al. (2012) A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable. PLoS ONE 7(11): e47712. doi:10.1371/journal.pone.0047712

The image above can be found on the project’s home page.