Microbes and Multiple Stable Community Types

Unique clusters of microbial community composition are often observed in samples from highly similar environments. This makes associating the abundance of any one group of microbes or community type with an environmental driver difficult. New research suggest that alternative stable states could be the reason for these observed clusters of community types.

This hypothesis, called “multi-stability,” was developed in macro-ecology to explain why different plant and animal communities – for example, a forest ecosystem vs a Savannah ecosystem – exist under similar climate conditions. These community types can be switched by a disturbance, and the community remains in the new state even after conditions return to normal.  Using computer simulations, researchers showed that this process can occur in microbial communities. While multi-stability still needs to be observed in real microbiomes, this provides one possible explanation for why multiple community types can be observed under similar conditions.


Sublease Agreement – Bacterial strain exchange in hospital rooms

High-resolution metagenomics makes it possible to distinguish between pathogenic and non-pathogenic strains of similar bacteria, and also reveals that premature infants share, and can exchange, bacterial strains with their environment. Bacteria can form “room microbiomes” in hospitals and persist in the same location, colonizing numerous patients over a long period of time. In this process antibiotic resistant strains might be transmitted among patients without the need to ever meet each other or even being in the hospital at the same time. Understanding how these microbiomes operate is crucial to successfully eliminating pathogens premature infants and other patients pick up in institutional settings.

Link: https://www.nature.com/articles/s41467-017-02018-w


Microbiome Transplants Work for Flora as Well as Fauna

The endangered Hawaiian plant Phyllostegia kaalaensis, a member of the mint family, is critically endangered and highly susceptible to fungal infection.  Current attempts to propagate P. kaalaensis in greenhouses involve fungicides; but after being treated with fungicides, the plants do not thrive when they are returned to a natural environment.  Researchers found that treating P. kaalaensis with leaf slurries from wild plants covered with beneficial fungi was more effective at preventing fungal disease in the greenhouse than chemicals that killed all the fungi in their microbiome, and the plants also did well when they were transferred back to their native habitat. This cheap and simple method of disease prevention may be the key to saving an endangered plant species.

Phyllostegia kaalaensis

Sequence the World!

The goal of the Earth Microbiome Project is to characterize microbial life on our planet using sequencing data.  This ambitious effort relies heavily on collaboration with hundreds of labs around the world so all ecosystems are represented.  Recently, a study was published that presented a compilation of 30,000 samples from the Earth Microbiome Project that can be used as a reference database of Earth’s microbial diversity.  Putting this dataset together was a truly monumental task, and is described in the accompanying “Behind the Paper” article.

My samples from Wisconsin bog lakes are part of the new Earth Microbiome reference database, and both I and my advisor, Trina McMahon, appreciate both the sequencing support provided by the Earth Microbiome Project and the honor of contributing to this massive effort.

Sequencing the Microbiomes of Sponges Around the World


If asked about the connection between sponges and bacteria, most of us would probably  think about the soggy cleaning implement on our kitchen counter; but living sponges – the animal, not the scrubbing aid – have close relationships with many different microorganisms that help them with a wide variety of tasks. Most studies on the microbiomes of sponges have focused on one individual species at a time, but a new, large-scale study by Moitinho-Silva, et al has greatly expanded the available data. The team sequenced a section of the 16S rRNA phylogenetic marker gene of the bacteria on over 3,000 sponges, which represented 268 different sponge species. This data can be used for comparative studies and is accessible on a public server called SpongeEMP (http://www.spongeemp.com/main), where researchers can search for sponge-associated bacteria by their sequences.

Caption: Carteriospongia foliascens, from the Maldives. One of the sponge species whose bacterial community was sequenced in this project.
Credit: Ahmed Abdul Rahman for MDC Seamarc Maldives (Own work) [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons


Citation: Moitinho-Silva, L., et al. (2017) The sponge microbiome project. Gigascience 6 (10): 1-7. http://dx.doi.org/10.1093/gigascience/gix077

The Microbiome Can Influence Experimental Results in Mice

Are microbiomes an unknown variable in mouse studies? The mouse is the model system of choice for studying many diseases and potential treatments before moving to clinical trials in humans. However, a new study suggests that difference in microbiomes between lab-raised mice and their wild cousins may impact their response to infection.  Laboratory mice who received a wild-type microbiome transplant had a much better chance of surviving the flu than mice who did not receive the transplant (92%, vs. 17%, respectively), which demonstrates that the microbiome is involved in resistance to infection and is a variable that needs to be taken into account in other mouse studies.


Human Microbiome Project Expanded

The fact that most bacterial species cannot be cultured and studied in the lab makes metagenomics an essential tool to understand function and diversity of natural microbial populations. In humans, large-scale metagenomics studies open doors to understand the microbiota associated with healthy human beings and possibly help us prevent or treat diseases.

A recent study provides fascinating insides into strain diversity and population structure in microbial communities not only in the gut, but from a total of 6 body-sides in more than 250 human beings over time. Unlike the gut, all other body sides showed a greater strain diversity. Confirming previous findings, the strain profiles were quite stable over time, while there is a much greater difference between individuals. Intriguingly, the study finds that many strains tend to associate with specific body sites. Community assembly seems to be rather driven by functional capabilities of the microbial communities than the taxonomic affiliation, indicating that the environment of different body parts (or simply being associated with a human) selects for specific functions.

The gut microbiome seems to be a special case, as it appears to be highly individual specific when compared to any other body site.

This study builds the foundations for a lot of future studies that can use these data to explain the patterns observed at a fine and broad scale that will enlighten the functions and implications of the human microbiome for our health.

Link: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature23889.html

The Importance of Biodiversity in Microbiomes

Biodiversity is the number of unique organisms in an ecosystem, and because it is straightforward to calculate diversity from a single sample, biodiversity is widely measured in microbiome studies. For example, studies of the human microbiome have found that healthy people tend to have higher biodiversity, or “richness,” than sick people, leading to the hypothesis that richness is essential for human health (see this recent study on seasonal changes diversity in the microbiomes of early hunter-gathers). However, no one has determined exactly why biodiversity should be beneficial, and the biodiversity of one small sample may not accurately reflect the biodiversity of an entire community.

In the field of ecology, the importance of biodiversity in ecosystems is hotly debated, and entire books have been written on the subject.  Richness is often correlated with productivity – think of the biomass produced by the incredibly diverse Amazon rainforest compared to the Sahara – but the counter argument is that a field of corn, which contains just one species of plant life, is more productive than a diverse native prairie.

In addition, adding diversity is not always beneficial, especially when an invasive species disrupts an established ecosystem.  A study on biodiversity and productivity in microbial communities found diminishing returns: after a certain number of taxa were present, each unique microbe added to the community had a smaller impact on productivity.

Another argument for the importance of biodiversity is that it is necessary for ecosystem resilience and serves as a buffer against outside disturbances.  The counter-argument is that by increasing the number of interconnected taxa in a community, you increase the chances that a disturbance acting on a subset of microbes will ripple through an entire community.

It’s difficult to design an experiment to test these competing hypotheses that completely mimics the true conditions of an ecosystem, so study results are often mixed.

On top of the ambiguity surrounding the importance of diversity, there are limitations with how we measure microbial biodiversity. A new study tested this by calculating richness in mock communities – mixtures of pure microbial cultures that can be used to benchmark methods for studying microbiomes. Using standard methods, the author found that richness was overestimated by factors of 10-100 in 16S rRNA gene amplicon sequencing. Differences in richness between samples were often inflated as well. These overestimates in diversity appear to be caused by sequencing and amplification errors – such as incorrect base pairs and chimeras (sequences that are combinations of two or more different pieces of DNA).

Methods that weight unique taxa by abundance and take phylogenetic similarity into account estimate diversity more accurately, as do sequence error-filtering methods, such as denoising or deblurring.  The presence of sequencing errors that mimic diversity may mean that we cannot distinguish between closely related microbes using 16S sequencing.

Finally, the diversity of a single sample is not necessarily representative of the diversity of the ecosystem from which the sample was taken. Looking only at a small portion of the community results in unknown amounts of error.

That’s not to say that we shouldn’t calculate the richness of microbiomes at all.  As this paper asserts, richness is an important property of a microbiome that reflects the forces acting within the community. However, biodiversity alone cannot tell us whether a microbiome is healthy or diseased.

Thanks to Cristina Herren and Robin Rohwer for their help with this article!

“Ancient” Bacteria With Patchwork Genomes Are Younger Than They Seem

A few groups of modern bacteria use anoxygenic photosynthesis (photosynthesis that does not produce oxygen) as an energy source, and the scientific community has assumed that these groups are ancient lineages that evolved when the Earth’s atmosphere was largely devoid of oxygen and oxygen species.

The green, non-sulfur bacteria called Chloroflexi, commonly found in microbial mat communities, is one of these groups of ancient anoxygenic phototrophs, but the authors of this study found that anoxygenic photosynthesis in Chloroflexi only evolved after the oxygenation of the Earth’s atmosphere. Moreover, several of the genes for both photosynthesis and Chloroflexi’s unique mechanism for fixing CO2 (called the 3-hydroxyproprionate bi-cycle) were acquired from other bacteria through horizontal transfer to make a “patchwork” genome. This study highlights how both the genomes and metabolism of bacteria are much more plastic than we thought.

The original article can be found here.

Author: Albatros4825 (Own work) [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons
Caption: Microbial mat at Yellowstone National Park with growths of green Chloroflexus bacteria.


Citation: Shih, P. M., Ward, L. M., and Fischer, W. W. (2017). Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi. Proceedings of the National Academy of Sciences, U.S.A. published online before print. http://dx.doi.org/10.1073/pnas.1710798114


The Influence of C-sections, Formula Feeding, and Antibiotics on the Infant Gut Microbiome

Researchers at the University of Alberta in Canada have discovered that the gut microbiomes of formula-fed or Caesarian-born infants do not develop the in the same way or on the same schedule as vaginally born, breast-fed babies, and the bacterial colonies they develop are often linked to food allergies and rapid weight gain.

The team, led by Anita Kozyrskyj, used the Significance Analysis of Microarray method to study the gut microbiome composition of 166 infants through the first year of their lives.  Although previous research has established what bacteria are seen in growing infants, Kozyrskyj and her colleagues are the first to link the rates of colonization for each of these bacteria with infant age, creating a roadmap for microbial evolution in the developing gut.

The authors explained that over one thousand types of bacteria live in the intestines.  In infants, these bacteria not only help them digest food, they train the baby’s developing immune system.

“We hope this research will help clinicians and parents understand that Caesarean section increases the chance of antibiotic treatment or formula-feeding of newborns, which can affect the development of gut microbiota in later infancy [and affect the future health] of the child,” said Kozyrskyj.

For more information, go to Frontiers in Pediatrics; DOI: 10.3389/fped.2017.00200.