Lichens and their bacterial microbiome – a thinglink exploration

General summary:

See those spots on the rock face? Those are lichens! These are plants made of algae and fungi living and working together to maintain the health of the whole organism. Frequently, however, lichens contain many different kinds of bacteria that can perform different metabolic processes that can help the lichen thrive. We don’t know a lot about the bacteria that live with lichen, or how and why they associate with lichen. Bates et al. explores the diversity of the bacterial community living with lichen, and their potential contributions to the overall health of a lichen community.

The researchers primarily looked at the bacterial communities to see if they vary based on the species of lichen. Do certain species benefit from certain additional metabolic process? In order to do this, the researchers used both traditional culture based methods – a method which grows the bacteria in a lab –  and modern genetic techniques, which can more accurately describe bacterial communities than culturing.

After collecting and analyzing samples from 4 different species of lichens, the researchers compared the results and discovered that, while some bacterial species were present in all the lichens sampled, there were also certain bacterial species that associated only with certain species of lichen. Bacterial species associated with all the lichens were more likely to be nitrogen fixing bacteria, which provide crucial nitrogen to plants. This research allows us to fill in one small piece of the puzzle that is symbiotic lichens. Do these unique bacterial species contribute to the specific lichen species they associate with? Did they coevolve with the lichen, as the human gut microbiome has coevolved with our species? All these questions remain to be answered by microbiologists in the future.

In-depth, technical summary:

While we traditionally understand lichens to be symbiotic communities of algae and fungi or cyanobacteria, we don’t think of them as organisms having significant microbiomes. This, as it turns out, is false. Bates et al. (2011)  set out to characterize the bacterial microbiomes of 4 species of lichens on 3 different rock outcroppings.

Using both traditional culture based methods, and 16S rRNA gene amplicon pyrosequencing, Bates et al. (2011)  analyzed the lichen microbiome. They found no trace of archeal 16S rRNA genes, and their sequencing results yielded much more diversity than their culturing results, as can be expected. Using Bray-Curtis NMDS, they discovered that the bacterial communities cluster based on lichen species, rather than outcropping, suggesting that certain bacterial species do associate with certain lichen species. Among the bacteria ubiquitous in the lichen samples, most were potential nitrogen fixing bacteria of the Alphaproteobacteria. This suggests that lichen associate with nitrogen fixing bacteria, however the results are not definitive due to the low accuracy of their species identification, as well as the fact that they did not target functional genes in the lichen microbiome.

This research shows that, while there are certain bacteria present in all lichens just as there are in humans, there are species specific associations between lichen species and the lichen microbiome. Further research into the coevolution and specialized roles of bacteria in the lichen microbiome is required to understand the lichen microbiome, and to understand the full extent of their symbiotic relationships.

Thinglink Ind. Post A.W


We have long known about the microbial presence within clouds but until recently most of our data has been a result of cell culturing which as we all know: may not be representative of the microbial community. This study via the use of 16s amplicon sequencing sought to define both the taxonomic identity and microbial activity via extracted DNA and RNA respectively. Atmospheric samples were taken periodically above France via a modified weather probes. Each sample was screened for the relative amount of industrial contaminants to serve as a comparison to the negative control. This study found that on average 11000 to 21000 distinct OTUs which is comparable to that of a typical soil sample. Prokaryotes made up the majority of the sample with low amounts of eukaryotic fungal populations also being present. The source of this diversity has been attributed to aerosols particulate products that resulted from saphorytes. The Microbial richness of the aforementioned microbes was more pronounced in the contaminated samples. Between all the samples it was evident that the metabolic functions of these microbes were important for many hydrological mechanisms such as ice nucleation and ion mediated chemistry reactions which aid in both the formation of water droplets and the act of precipitation respectively. The microbiome of the cloud was found to be variable depending on the location and sensitive to changes in resources (such as industrial contaminants, temperature and topography) so further study should be allocated to defining, and in the far future, altering the clouds’ microbiome.


Recent studies have suggested that clouds could could act as a catalyst for environmental change. In fact the sheer abundance of microbes housed within a typical cloud is comparable to your everyday sample of dirt. Many of these microbes are important for key functions of the water cycle such as: aiding in the formation of water droplets, the initiation of precipitation and others. In fact, some of these microbial players have been shown to be partly responsible for the acceleration of climate change via the depletion of ozone. Indeed even bacteria which are responsible for creating methane, a potent greenhouse gas, were found in the clouds themselves, further aggravating climate change. While we have always known that there are microbes in the air, and by extension the clouds, we were ignorant as a species to the sheer magnitude and richness of the cloud microbiome. Above us in the skies are basically wastewater treatment plants that filter and control the flow of Earth’s lifeblood: water. Equipped with a better understanding of the microbial presence and hydrological implication there-in, mankind has made a significant step towards altering our weather and water cycles and perhaps in the far future this research could serve as the backbone of space exploration as we flush out variables involved in terraforming.

Pictures on my thing-link: compliments of Sophie

Hand-Phone Microbiome Connection – Individual Thinglink Communities Project Post   General Audience Most people on planet Earth own a mobile cell phone. In fact, more people worldwide own mobile phones than have access to working toilets. But did you know that  we share more than just an emotional connection with our phones? That they carry our personal microbiome? The human microbiome is defined …

Microbial Interactions- Your Home and You!


General audience:

Do you think of your body as a habitat? Have you ever considered the multitudes of microscopic organisms that colonize your skin? Most of us don’t, but the truth is that you are a teeming ecosystem of bacteria and other microbes. Even more, each person has a distinctive ‘fingerprint’ associated with their own unique microbiome, or the ecosystem found on their person.
However, you also impact the environment you occupy; your house is covered in your own microbes, and so is anyone else who lives with you- even your pets. In fact, you’re also covered in their bacteria. Entire families can be linked by the microbial communities found on their skin, and their houses associated by finding the same communities on inanimate objects. About 77% of the time, a person’s bacterial signature can be matched to their house accurately!
A person’s individual microbial signature is most distinct within the nose and least on the hands. On average, about a third of a person’s skin microbiome is the same as that of surfaces within their house, though this can rise or fall depending on the individuals and areas sampled. Merely by existing in a space, you spread your own microbial fingerprint. Conversely, the longer you are away from an area, the weaker this fingerprint is on an area.
Of course, the big question- can any of the bacteria in my house hurt me? This study found that your hands actually have the highest chance of carrying microbes that can make you sick, and that’s because your hands touch the most surfaces in your house. Countertops were found to have more potentially harmful types of bacteria than any other surface in a house.
Knowing this, scientists can apply knowledge of microbes to assess the spread of disease, individual health, and the impact of humans on bacterial diversity. Since an increasing number of people are spending time indoors and at home, understanding the spread of bacteria in the context of health in our homes and how our actions serve to spread our signature to our environment and to others.


Recent investigations into the microbial communities in human-made environments have revealed the composition of such environments to be directly linked to the occupants of each space, human and animal alike. Utilizing 16S rRNA amplicon sequencing, the microbial communities from numerous surfaces within homes and on human occupants were characterized and compared to identify patterns.
In this study, 1625 samples yielded 21,997 OTUs over a 4-6 week period. Several of the families moved during the period of the study; when this occurred, samples were obtained from both the old and new spaces. Analysis of similarities (ANOSIM) differentiation was used to compare differences between surfaces, humans, and pets within and between the homes studied.
Within each study area, humans were the greatest contributors to bacteria found on surfaces. Actinobacteria and Proteobacteria, two major components of human skin flora, dominated such samples. Between humans, the soles of the feet were found to contain the most unique OTUs, while the palms of the hands were least distinct.
It was found that a person’s skin sample could be matched to commonly accessed surfaces within their house 76.7% of the time, demonstrating not only that microbial communities in homes are significantly more similar to those of their occupants, but that colonization can occur rapidly. Additionally, the longer an occupant was not within the area, the less their own microbial signature could be detected in samples. This may indicate rapid turnover of bacteria or demonstrate how significant the contribution of microbial transfer from skin to surfaces is within a space.
The study also looked briefly into microbes with pathogen potential by utilizing shallow shotgun metagenomic sequencing. Corynebacterium was found on all humans, with Enhydrobacter-, Streptococcus-, and Enterobacter-like bacteria found on surfaces around the house, especially on countertops. Close matches for Pantoea agglomerans and Acinetobacter baumannii were also observed in kitchen samples. Hand samples were found to have the greatest potential for pathogenic bacteria, sharing the greatest similarity with countertops.
Better understanding the impact of humans upon the microbiome in environment they occupy and how these microbes are distributed and spread is a crucial and understudied facet of human health. This study works to look into the origins and patterns of such communities, with intriguing discoveries with applications in healthcare and microbial analysis.


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Presence of microbes on utensils.

Layman’s Term:

Microscopic organisms are everywhere. Even in places where you would think they are not. Like clean clothes, clean kitchen counters or even washed utensils. Remember those advertisements which claim that they kill 99.9% bacteria. You might think still 0.1% are left there even after using antibacterial disinfectants. In Ontario, they have a standard that on a cleaned utensil there should not be more than 100 bacterial colonies! Imagine what happens to utensils cleaned by us in dishwashers which does not even use those kinds of disinfectants! A study was done by scientists in Ontario, Canada on the dishwashers which did not handle a lot of utensils at an instance. So if you are living in a family daycare services, or residential care home, this article is for you. Along with disinfectants, high temperature is also needed to kill microorganisms which the dishwashers actually use. But in places where the utensils are not that much, the dishwashers cannot achieve that temperature. Also, if low temperature is used to treat utensils then sanitizer has to be used at a set time and concentration but normal dishwashers do not have this function. So, if you live in any of these places then you might ask that they install a commercial sized dishwasher instead of domestic dishwasher. The study found that 83% of these dishwashers actually worked within the prescribed limits but still there are 17%, that is, more than 1 out of 6 instances that your utensils are actually not clean and contain a lot of unwanted stuff.


Technical Explanation:

This paper aimed at the study of cleaning ability of domestic dishwashers employed in residential care homes. The researchers picked these places because they know that dishwashers do not work that good if there are less utensils cleaned at a time. This happens due to low temperature that water reaches when cleaning occurs. A temperature of 82oC for 10 seconds or chemical sanitization at 24oC is required to properly sanitize the utensils. For samples, they chose 4 establishments with different number of dishwashing units to a total of 103 units. 4 different types of utensils were selected for the study and were swabbed after one full cycle was over. Standard operating procedures laid out by United States Public Health Service’s (USPHS) were followed. Of the 103 domestic dishwashers evaluated, 85 (83%) yielded results that fell within the prescribed limit of no more than 100 bacterial colonies per utensil as determined by heterotrophic plate count (HPC). Dishwashers that contained utensils classified as somewhat soiled or very soiled before washing were more likely to fail (P < 0.05) than those that were classified as very clean or somewhat clean before washing, when all other characteristics and operating parameters and the number of plastic items were controlled for. With increasing maximum rinse temperature, dishwashers were less likely to fail (P < 0.05) while the same characteristics were controlled for. Also, dishwashers were more likely to fail when chlorinated detergents were used (P < 0.05).



ThingLink Soil Microbiology Technical Summary


As environments globally become subjected to urban infrastructure, the biodiversity of flora and fauna have visibly plummeted, yet microbes are often overlooked. To see if urbanization has any effects on soil microbial diversity, researchers in Beijing studied microbial samples from the Forbidden City and the surrounding 5 ring roads. These ring roads were each constructed during different periods of time, following mass urbanization starting from 1970, and serve as a temporal gradient for comparing microbial samples. The further out from the Forbidden City a ring road is, the more recently it was built. Soil samples were taken across a transect from the forbidden city out into the surrounding ring roads and the 16s rRNA genes were sequenced. Alpha and beta diversity tests showed that samples from outer and inner roads displayed the highest diversity values. This observation rejected the idea that diversity levels could be explained by an urbanization age based gradient but it was found that acidity may partially explain the variance values of the microbial samples. Overall, their major findings were that variances in diversity can only partially be explained by urbanization and pH, leaving most of the variation related to the unexplained complexity of urban environments.

ThingLink Soil Microbiology Non-Technical Summary


Research has shown that the diversity of life has diminished with increased urbanization, but the focus has mainly been on plants and animals. This study focuses on the changes to soil microbial diversity in city or human-altered environments, because human alteration of the environment (pollution, construction, landscaping, etc)can drastically influence living conditions of local microorganisms. Focusing on Beijing, a city that rapidly urbanized from 1970 onwards, the study examined soils relating to how long ago the part of the city was build. Centered on the Forbidden City as the oldest point, moving outwards are ring roads that were added at different times outward with a total number of 5 roads. These researchers took samples from the different road levels to compare how microbial samples differ across different levels of urbanization. Overall, the main bacterial groups stayed the same across all samples, but microbial diversity differed. Analyses showed that differences in microbial communities could be explained by changes in soil acidity and these differences were not related to the age of the city area. The conclusion was that urbanization in Beijing has complex effects on the microbial diversity and these effects varied based on the layout of specific locations.

Microorganisms in the Mouth-Individual Thinglink Communities Project Post


General Audience:

We all know that it is important to brush our teeth, but did you know that even with excellent hygiene there is still an estimated 500,000 bacteria on each tooth? This may sound alarming and maybe even concerning, but don’t worry because most of the bacteria that are in your mouth cause no harm and some even have a beneficial effect. The first bacteria were viewed by Antonie Van Leeuwenhoek in 1683. He took cells from his cheek and examined the sample under his homemade microscope (Avila et al. 2008). As previously mentioned microorganisms can have a wide variety of relationships with its host. In the oral microbiome most cells either don’t affect its host or can be helpful, however there are cases where bacteria can be pathogenic and dangerous to its host, often times causing disease. The exact trigger of what causes bacteria to go from having no effect to being dangerous is unknown, however there are two main theories. Theory one says that the bacteria associated with a host present in the mouth have always been in the pathogenic state but have been outnumbered by non-harmful bacteria and never had the opportunity to grow, until they did. Theory two says that the bacteria change due to an environmental change.  There is currently an estimated 750 unknown microbial cells living in the human mouth waiting to be discovered but studying the oral microbiome is challenging because it is difficult to replicate the environment accurately. There is however a technique for studying the microorganisms in the mouth called metagenomics. This process is able to analyze large amounts of microbial families. Metagenomic sequencing is much faster and more accurate than grow individual communities to study. Previous studies have found a positive health correlation between a high concentration of P. gingivalis, Tannerella forsythia, and Actinobacillus in healthy mouths. Knowing the microorganisms that inhabit a person’s mouth is crucial for understanding what interactions are taking place and can lead to improving medical and health practices.  



There is the same amount of prokaryotic organisms living in/on a person as the amount of eukaryotic cells that make up the human body. There are many different types of cells in the human oral microbiome, some are commensal, some are beneficial and some are pathogenic. Studies are currently looking at why cells become pathogenic and have come up with two theories. The first one theorizes that certain host associated cells in the oral environment have always been pathogenic, however they were overpopulated by commensal cells and were held at bay until they had the opportunity to grow. The second theory states that an environmental change occurs which triggers the bacteria the change into pathogenic cells. Since the oral microbiome is extremely difficult to replicate, studying the environment and cells that live in it can be challenging. However metagenomic sequencing has made a large difference in the ability to identify large communities of microbes at once. This is much more accurate and time efficient than isolating the different microorganisms. Isolating individual microbes can also be challenging since only a small amount will show up on swab plates. Studies previously performed have found a correlation between people with good hygiene and a healthy microbiome, having high concentrations of P. gingivalis, Tannerella forsythia, and actinobacillus. There is still so much to be discovered about the human oral microbiome, there is an estimated additional 750 host associated microbial cells yet to be discovered in the human mouth.

Microbial Communities: Built Environment Non-Technical Summary

Non-Technical Summary

Humans spend most of their time inside buildings- that includes the time they spend in the hospital. Hospitals are a hub for not only sick patients, but healthcare workers and visitors. As a high-traffic area, the types of bacteria growing in a hospital are constantly fluctuating. This growth is only exacerbated by the bacteria lent to the environment by the sick patients. The conditions that impact how microbes spread in a hospital are important to understand so a patient doesn’t come down with a new disease while being treated for something unrelated. Researchers from the University of Chicago spent over a year sampling what bacteria were growing throughout a new hospital and on patients- and they found some surprising results.  When a new patient was admitted to the hospital, the bacteria of the room they were staying in quickly came to resemble the patient. This trend was most obvious on surfaces that a patient would often touch- like a bedrail. Results from DNA sequencing showed that antimicrobial resistance was also present. However, bacteria with resistances to drugs were more likely to be found on the hospital surfaces rather than living on the skin of patients or staff. Researchers also found that certain patients had fewer microbes on themselves and their surroundings. In particular, chemotherapy patients had fewer different types of microbes. This study concluded that humans are the biggest factor for what microbes are living in buildings. Further research should spend more time looking for trends in microbial transfer within hospitals and for deciding what can be done to present a healthy hospital.

S. Lax, et al., Bacterial colonization and succession in a newly opened hospital. Sci. Transl. Med. 9, eaah6500, (2017),