Tackling the earth’s biggest microbiome, one thousand blueprints at a time

In the early 2000’s a small group of French scientists had a big dream: studying the world’s oceans, all of them, better and in more detail than anyone had done before. They managed to obtain a boat, the schooner Tara, and ran a number of shorter expeditions. In 2009 the time had come for the big one: for three years Tara sailed the world’s oceans, taking thousands of samples for later analysis. The goal of the ‘Tara Oceans’ expedition was to create the most comprehensive dataset describing the oceans, the largest (micro)biome on the planet. Since then, Tara has continued to sail the seas, collecting data, and spreading knowledge. Read more about the scientific fairytale, and follow along with the current expedition at http://oceans.taraexpeditions.org.

Dozens of scientific publications have been written about the data collected during Tara Oceans. The breadth was so unparalleled that the journal Science devoted a special issue to the expedition in 2015. One of the articles in that issue is titled “structure and function of the global ocean microbiome” and describes just that, based on over 40 million genes identified using DNA sequencing. But a gene by itself doesn’t tell the whole story, even if you have 40 million of them. To start getting a deeper understanding, it’s important to find the owner of those genes. Easier said than done, but several labs picked up the gauntlet.

They could do this, because Tara Oceans made all their data publicly available for the community to analyze and build upon. Now, nearly two years later, Delmont and colleagues and Tully and coworkers have released preprint articles describing the reconstruction of 1070 and 2631 draft genomes, respectively, based on the Tara Oceans datasets. These genomes can be seen as blueprints for organisms living in the ocean, many of which we had never seen before. Over the past few years, reconstructing these blueprints has become a staple technique in microbial ecology, but is at such a (planetary) scale it’s still an extraordinary feat.

Tully and colleagues decided to use over 200 individual datasets across all filter size ranges the Tara Oceans team collected water on. As expected, their approach yields more than twice as many genomes as Delmont’s analysis, who used only the smallest filters, from the surface ocean (93 datasets). However, Tully’s analysis of the reconstructed genome data is more limited, sticking to a matter-of-factly reporting about the genomes and their place in the tree of life. In contrast Delmont and colleagues use their genomes to shed more light on nitrogen fixation, a process that could be a factor in controlling primary production in the ocean.

Delmont and colleagues only need 9 of their 1070 genomes to tell this nitrogen fixation story, and explicitly state that they hope that other labs will use their own specific expertise to analyze the reconstructed genomes and help create a better understanding of the ocean microbiome. Tully and coworkers concur, stating in their preprint article that they envision their reconstructed genomes will be a (community) resource.

Both statements emphasize that DNA sequencing is turning the microbiome field more and more into a big-data science, where we need eachothers’ knowledge, skills and expertise to make the most out of the data. As far as I’m concerned, the Tara Oceans project and these two groups are both shining examples of this.

More Information can be found here:

Tara Oceans microbiome paper

Structure and function of the global ocean microbiome http://science.sciencemag.org/content/348/6237/1261359.full

Tully and colleagues

The Reconstruction of 2,631 Draft Metagenome-Assembled Genomes from the Global Oceans

http://www.biorxiv.org/content/early/2017/07/13/162503

Delmont and colleagues

Nitrogen-Fixing Populations Of Planctomycetes And Proteobacteria Are Abundant In The Surface Ocean

http://www.biorxiv.org/content/early/2017/04/23/129791

For a more personal account of the work by Delmont and colleagues:

http://merenlab.org/2017/05/21/thousand-genomes-from-tara/

 

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:

http://www.npr.org/sections/thesalt/2017/07/17/536485684/more-than-bread-sourdough-as-a-window-into-the-microbiome

http://robdunnlab.com/projects/sourdough/#origins

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