Microbiome Researchers Win 2017 Massry Prize

The Massry Prize, awarded by the Meira and Shaul G. Massry Foundation, recognizes researchers who have made outstanding contributions to biomedical science and human health.  Three microbiome researchers were honored this year: Rob Knight, Norman Pace, and Jeffrey Gordon.  Not only does this highlight the excellent work done by these scientists, it also highlights the growing importance of microbiome research.

Norman Pace is a Distinguished Professor Emeritus at the University of Colorado at Boulder whose research was instrumental in the development of 16S rRNA gene amplicon sequencing, a common and powerful technique for classifying members of microbial communities.  Read more here.

Rob Knight is a professor in the Department of Pediatrics at the University of California at San Diego.  He is a founding member of the American Gut Project and the Earth Microbiome Project, and uses next-generation sequencing techniques, such as 16S rRNA gene amplicon sequencing, to investigate a stunningly diverse array of scientific questions about microbiomes.  Read more here.

Jeffrey Gordon is the Dr. Robert J. Glaser Distinguished University Professor at Washington University School of Medicine.  He is well known for using twin studies and animal models, including germ-free mice, to experimentally test the impact of different gut microbiome compositions.  Read more here.

Cohabiting Couples Have Similar Microbiomes

If you’ve ever wondered if you and your significant other are swapping microbes, the answer is yes.  A new study compared the skin microbiomes of cohabiting couples at 17 different body locations and found that the microbiomes of partners were more similar than those of other people in the study.  Here are some research highlights:

Staying Together or Seeing Other People?

Scientists have long thought that the bacterial symbionts inside the gills of the clam Solemya velum are vertically transmitted from parent to offspring because they are also found in the ovaries and embryos of their hosts.  The genome of symbionts usually becomes smaller when it is vertically transmitted, but when the bacterium’s genome was sequenced, it was close in size to its free-living relatives.  To find out why, Russell, Corbett-Detig, and Cavanaugh of Harvard University sequenced the genomes of symbiont and host mitochondria from 61 S. velum clams collected along the east coast of the United States and found many signs that pointed to horizontal transmission.  These included the facts that the evolutionary histories of the partners were decoupled within geographical sites and that both recombination and horizontal gene transfer were found in symbiont genomes.  The phenomena suggest that symbiont populations in S. velum have been mixing and have also been exposed to the environment. The symbionts are therefore likely to have a mixed mode of transmission: vertically passed to host offspring via host eggs and horizontally exchanged through environmental exposure.

The original article can be found here.

Citation: Russell, S. L., Corbett-Detig, R. B., & Cavanaugh, C. M. (2017). Mixed transmission modes and dynamic genome evolution in an obligate animal–bacterial symbiosis. The ISME Journal 11, 1359-1371. https://dx.doi.org/10.1038/ismej.2017.10

Climate warming impacts the lizard gut microbiome

The Earth’s increasing temperatures are likely to impact animals and plants in myriad ways. In this article, Bestion, Cote, and their colleagues show that when lizards are exposed to temperatures elevated no more than 2-3°C, the animals had fewer types of bacterial species in their guts, which can lower their chances of survival.


Original article can be found here.

Ebola RNA Found in Semen Two Years After Infection – Should the WHO Guidelines be Changed?


Researchers at the University of North Carolina (UNC) at Chapel Hill, Ohio-based Clinical Research Management, and the ELWA Hospital in Liberia have found Ebola RNA in the semen of men two years after infection.  The semen of some of these men had previously tested negative for the virus.

The World Health Organization’s 2016 guidelines on the sexual transmission of Ebola asks men who have survived Ebola to either abstain from sexual activity or use condoms for at least 12 months after the onset of their Ebola infection or until their semen has tested negative for Ebola RNA at least twice.  The researchers are thinking about recommending that that period be longer if further research confirms their findings, but stressed that this research must be conducted in way that empowers the Ebola survivor community and does not increase any kind of social stigmatism.

The study was led by William A. Fischer II and David Wohl from UNC, and involved 149 men in Monrovia, Liberia who survived Ebola during the epidemic of 2014-2015.  Thirteen of these men tested positive for Ebola virus RNA, 11 of them two years after the onset of their Ebola infection.

“Our finding of long-term persistence and intermittent detection of viral RNA in semen suggests we need to change how we think about Ebola,” said Fischer.  “It is no longer only an acute illness, but also one with potential long-term effects.  It is becoming clear that, in some survivors, evidence of the virus can linger in the male genital tract for long periods of time with important potential implications for transmission.”

Fischer noted that, while Ebola has been sexually transmitted less than two years after acute infection, no one knows whether the presence of Ebola RNA two years after the onset of the disease means that transmission is still possible.

The team reported that the men whose semen was positive were more likely to be older than those with a negative result, and they complained of vision problems more often than RNA-negative survivors.

For more information, go to the July 22 issue of Open Forum Infectious Diseases.

The Microbiology of Sourdough Starters

If you bake sourdough, starter cultures are a big deal.  This mix of live yeasts and bacteria is what gives sourdough its distinctive taste.  There are even heirloom starters that have supposedly been passaged for over 100 years!  A group of researchers have crowd-sourced samples of sourdough starters from all over the world to study the variations between starters and their impact on finished sourdough bread, and to study the principles of microbial ecology in a relatively simple microbiome.  Stay tuned for results from this ongoing project!

Original Articles can be found here:



It’s not easy having a disrupted microbiome

The link between microbiome diversity and resistance to disease is often talked about, but is difficult to research.  A new study investigated this topic by disrupting the exterior microbiomes of tadpoles and measuring their resistance to parasites later in life.  Tadpoles were reared in either regular pond water, sterilized pond water, or sterilized pond water with long- or short-acting antibiotics.  All the tadpoles were exposed to parasitic gut worms once they reached adulthood.

Tadpoles raised in sterile pond water with long-acting antibiotics took longer to reach adulthood and weighed less as adults. They also had the lowest diversity in their skin and gut microbiomes of all the experimental groups.  Tadpoles raised in regular pond water had the greatest skin and gut microbial diversity.

When the frogs were exposed to parasitic worms, the same number of worms penetrated the guts of individuals in every experimental group, but the frogs that were raised in sterile pondwater or sterile pondwater with antibiotics ended up with significantly higher parasitic gut infestations.  Frogs with higher gut microbiome diversity were more resistant to parasitic worms than frogs who had lower gut microbiome diversity.

Original article can be found here: https://www.nature.com/articles/s41467-017-00119-0

Getting used to a new job: endosymbiotic algae that ferment, not photosynthesize

Many invertebrate animals, like green freshwater hydras, have symbiotic algae that live inside their cells; but only one species of vertebrate has algal symbionts: the salamander Ambystoma maculatum. Burns et al., from the American Museum of Natural History, compared gene expression patterns in Oophila amblystomatis algae that were 1) inside the salamanders’ egg capsules but still extracellular and 2) inside the cells of salamander embryos. They found that algae that were inside embryo cells showed signs of stress and had converted from an oxidative metabolism to fermentation, and additionally used host glutamine as a source of nitrogen. In contrast, the salamander host cells did not exhibit a stress response. They also increased expression of some regulatory genes that are known to suppress immune responses, and the few immunity-related genes that were differentially expressed were mostly involved in innate immunity.

Image attribution: By Fredlyfish4 (Own work) CC BY-SA 3.0  via Wikimedia Commons

Original article can be found here.

Are Wastewater Treatment Plants a “Hot Bed” For Antibiotic Resistance?


A portion of the antibiotics we consume are flushed down the toilet, either directly (not a good idea…) or by way of the human gastrointestinal tract. The antibiotics we increasingly feed to our meat sources may also end up at our local wastewater treatment facility. A recent metagnomic analysis reveals that bacteria containing a large number of antibiotic resistance genes (ARGs) and mobile elements (MEs) accumulate in our wastewater treatment plants, both in the activated sludge and anaerobic digestion processes. The ability of anaeorbic digestion to deactivate antibiotic resistant bacteria prior to biosolids utilization has been debated, and this study shows mixed results: anaeorbic digestion both increased and changed the overall abundance of ARGs but the number of MEs decreased. We should continue to monitor ARGs at our wastewater plants as we rely more heavily on antibiotics to protect and feed an ever growing human population.

Original article can be found here: http://www.sciencedirect.com/science/article/pii/S0043135417305651?via%3Dihub


Not Time Sensitive: the microbiome throughout earth’s history

When we talk about microbiomes, most people think of host-associated microbial communities. This makes sense because the term was first made popular by the Human Microbiome Project.  Now, however, it has a broader meaning and refers to microbial communities everywhere, from buildings to natural hot springs.  Microbial life can be found in the strangest places, and microbiome research is as diverse as the subjects it addresses.

Between June 17th and July 22nd, 2017, an international group of students will learn about the microbiome in yet another context: the earth’s history.  For most of the time our planet has been in existence, only microbial life could thrive.  How microbes survived and influenced the conditions of early earth is one of the key questions in the field of geobiology.

Caltech and USC’s Wrigley Institute are hosting the Agouron International Geobiology course, to give graduate students and postdocs the tools to reach beyond their own field and tackle this interdisciplinary problem.  To chart our world’s history accurately, we must examine rock records and the biomarkers we find in them.

Taking water chemistry and microbiome samples at Mono Lake, CA

Curious?  Check out more here or follow along with #GeoBio17 on twitter for ongoing updates!