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Tag: fungi

Published on Leave a comment on Fungi and Bacteria in Household Dust

Another article from results of the crowdsourced study in which household dust samples were sent to researchers at the University of Colorado from approximately 1200 homes across the United States. Some findings after the dust was analyzed: differences were found in the dust of households that were occupied by more males than females and vice versa, indoor fungi mainly comes from the outside and varies with the geographical location of the house, bacteria is determined by the house's inhabitants (people, pets, and insects), clothes do not prevent the spread of bacteria from our bodies, and dogs and cats had a dramatic influence on bacteria in the home. In other words: where you live determines the fungi in the house and who you live with determines the bacteria in the house. From Discovery News:

Household Dust Packed With Thousands of Microbes

Household dust is full of living organisms that are determined, in large part, by where the home is located and who is living in it, finds a new study that includes some surprising revelations. Homes with a greater ratio of male occupants, for example, were found to contain large amounts of skin and fecal-associated bacteria, while women-dominated households contained an abundance of vaginally shed bacteria that somehow wound up in dust.

He and his colleagues used DNA sequencing and high tech imaging to analyze dust samples from approximately 1,200 homes across the United States. They used volunteers to help collect the material. They discovered that indoor fungi mostly originates outside of the home, such that the geographical location of any home strongly predicts the types of fungi existing within dust.“If you want to change the types of fungi you are exposed to in your home, then it is best to move to a different home, preferably one far away,” Fierer and his team said.

Bacteria, on the other hand, were largely predicted by the home’s possible inhabitants, including humans, pets and even insects. Fierer said, “Our bodies are clearly the source for many bacteria that end up in our homes.” The researchers suspect that body size, relative abundance, and hygiene practices are why men tend to shed more Corynebacterium and Dermabacter (the skin-associated species), as well as the poop-associated Roseburia.

The vaginal-linked bacteria Lactobacillus, discovered in homes with a larger ratio of women, provides evidence that clothes do not fully contain the spread of microorganisms produced by our bodies. Members of this genus are actually thought to protect against allergies and asthma, based on earlier research, but further studies are needed to confirm how this, and other bacteria found in dust, impact human health.

Dogs and cats had such a dramatic effect on dust bacterial communities that the researchers could predict, with around 92 percent accuracy, whether or not such animals were in the home, just based on bacteria alone....So far, the news is good for dog lovers, as he pointed out that “previous work conducted by other groups has shown that living with a dog at a young age can actually reduce allergies.”

Published on Leave a comment on The Fungi That Live On Our Skin

This article discusses the fungi living on our skin. Recent research (using state of the art genetic analysis) has found that healthy people have lots of diversity in fungi living on their skin. Certain areas seem to have the greatest populations of fungi: in between toes (average of 40 species), the heel (average of 80 species), toenails (average of 80 species), and the genitals. Currently it is thought that there are "intricate interactions between fungi and immune cells on the skin surface", and that often this mutualistic relationship is beneficial, but at other times dysbiosis (when the microbial community is unbalanced or out of whack) can lead to diseases. If the populations get too unbalanced (e.g., antibiotics can kill off bacteria, and then an increase in fungi populations take their place) then ordinarily non-harmful fungi can become pathogenic. Note that: Mutualistic relationship is a relationship between two different species of organisms in which both benefit from the association. From E-Cronicon:

From Head to Toe: Mapping Fungi across Human Skin

The human microbiota refers to the complex aggregate of fungi, bacteria and archaea, found on the surface of the skin, within saliva and oral mucosa, the conjunctiva, the gastrointestinal. When microbial genomes are accounted for, the term microbiome is deployed. In recent years the first in-depth analysis, using sophisticated DNA sequencing, of the human microbiome has taken place through the U.S. National Institutes of Health led Human Microbiome Project. 

Many of the findings have extended, or even turned upside down, what was previously known about the relationship between humans and microorganisms. One of the most interesting areas related to fungi, especially in advancing our understanding about fungal types, locations and numbers and how this affects health and disease....some parts of the body have a greater prevalence of bacteria (such as the arms) whereas fungi are found in closer association with feet.  

A variety of bacteria and fungi are found on the typical 2 square meters that represent the surface of the skin, and within the deeper layers, of a typical adult. These can be considered as ‘residential’ (that is ordinarily found) or ‘transient’ (carried for a period of time by the host.) The resident microorganism types vary in relation to skin type on the human body; between men and women; and to the geographical region in which people live.

The first observation is that many locations across the skin contain considerable populations of fungi. Prime locations, as reported by Findley and colleagues, were inside the ear canal and behind the ear, within the eyebrows, at the back of the head; with feet: on the heel, toenails, between the toes; and with the rest of the body notable locations were the forearm, back, groin, nostrils, chest, palm, and the elbow.

The second observation is that several different species are found, and these vary according to different niches. Focusing on one ecological niche, a study by Oyeka found that the region between toes, taken from a sample of 100 people, discovered 14 genera of fungi. In terms of the individual species recovered, a relatively high number were observed (an average of 40 species.)....the greatest varieties of fungi are to be found on the heel (approximately 80 different species.) The second most populous area is with the toes, where toe nails recover around 80 different species.....With the genitals, where early investigations had suggested that Candida albicans was the most commonly isolated yeasts. However, an investigation of 83 patients by Bentubo., et al.  showed more variety, with high recoveries of Candida parapsilosis, Rhodotorulamucilaginos, Rhodotorulaglutinis, Candida tropicalis and Trichosporoninkin.

The importance of the investigative work into the human skin fungi helps medical researchers understand more fully the connections between the composition of skin-fungi and certain pathologies. Here the intricate interactions between fungi and immune cells on the skin surface is of importance; often this mutualistic relationship is beneficial, at other times dysbiosis can lead to the manifestation of diseases especially when there is a breakdown of the mutualistic relationship.

Changes to fungal diversity can be associated with several health conditions, including atopic dermatitis, psoriasis, acne vulgaris and chronic wounds. Diversity can alter through the over-use of antibiotics, where a decline in bacterial numbers can lead to a rise in fungal populations occupying the same space.

Moreover, research has indicted that patients who have a primary immunodeficiency are host to more populous fungal communities than healthy people. Here it is suggested that the weaknesses in the immune system allow higher numbers of fungi to survive, and, in turn these weaknesses can lead some ordinarily non-harmful species to become pathogenic. Such opportunistic fungi include species of Aspergillus and Candida.

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Guess what? Our microbiome (the collection of microbes living within and on us) also normally contains fungi. This is our mycobiome.  Very little is known about the mycobiome. (in contrast, much, much more is known about the bacteria within us) The fungi within us may be as low as 0.1% of the total microbiota (all our microbes). But what is known is because advanced genetic analyses have been done (specifically "next-generation” sequencing") or culturing of the fungi.

In some studies of fungi in healthy adults, nothing at all is known about up to 50% of the species found. And each human has a diversity or variety of fungi living within them, and these seem to vary between different parts of the body. What little is known is that fungi that we may have thought of as pathogenic (or no good) and involved in diseases (think Candida and Aspergillus) are also found normally in healthy individuals. For example, Candida were found in the mouth or oral microbiome of healthy adults as well as the gut of many healthy adults (thus part of a healthy microbial ecosystem). Some studies suggest that our diet influences which fungi species are present in the gut.

Fungi are both part of health and disease. They interact with the other microbes within us. Some fungi appear to prevent disease by competing with pathogenic organisms (bad bugs).They have functions in our body that we know very little about. We don't know much about disruptions to the fungi in our bodies or even how fungi come to live within us. The following excerpts are from a scholarly article summarizing what is known about our fungi or mycobiome. Written by Patrick C. Seed, from the Cold Spring Harbor Perspectives in Medicine:

The Human Mycobiome

Fungi are fundamental to the human microbiome, the collection of microbes distributed across and within the body... Here, a comprehensive review of current knowledge about the mycobiome, the collective of fungi within the microbiome, highlights methods for its study, diversity between body sites, and dynamics during human development, health, and disease. Early-stage studies show interactions between the mycobiome and other microbes, with host physiology, and in pathogenic and mutualistic phenotypes. Current research portends a vital role for the mycobiome in human health and disease.

In particular, the diversity and dynamics of the so-called mycobiome, the fungi distributed on and within the body, is poorly understood, particularly in light of the considerable association of fungi with infectious diseases and allergy (Walsh and Dixon 1996). Despite being as low as ≤0.1% of the total microbiota (Qin et al. 2010), the fungal constituents of the microbiome may have key roles in maintaining microbial community structure, metabolic function, and immune-priming frontiers, which remain relatively unexplored. Further questions exist as to how fungi interact cooperatively and noncooperatively with nonfungal constituents of the microbiome.

Fungal colonization of the term infant remains poorly characterized. Although it is known that fungi, such as Candida, are prevalent constituents of the vagina through which most infants are delivered, transmission to the newborn is not well documented, and assembly of additional environmental fungi into the microbiome has not been monitored in the otherwise healthy infant.

Although the microbiome of the healthy term infant remains poorly understood, more effort has been placed on understanding fungal colonization of preterm infants. Infants born 8 or more weeks before term and weighing ≤1500 g at birth are at significantly increased risk for invasive fungal disease, primarily with Candida species (spp.) these infants at risk of Candida colonization and infection.

Based on culture-dependent or genus/species-focused culture-independent methods of identification, the fungi of the oral cavity were previously believed to be few and relatively nondiverse. The genera Candida, Saccharomyces, Penicillium,Aspergillus, Scopulariopsis, and Genotrichum were among those previously reported.... In the oral samples from 20 participants, most had ∼15 fungal genera present...To put this level of diversity into context, prior studies have identified more than 50–100 bacterial genera in the healthy oral microbiome.

Of the oral fungal genera noted among each of the healthy subjects from the Ghannoum study (Ghannoum et al. 2010), Candida and Cladosporium were most common, present in 75% and 65% of participants, respectively. Fungal genera associated with local oral and invasive diseases, including Aspergillus,Cryptococcus, Fusarium, and Alternaria were also identified, indicating that these genera are present in the oral microbiome even during a state of health....The discovery of previously unidentified fungi is a reminder that the oral microbiome remains underexplored.

Although the bacterial constituents of the gut-associated microbiome have been intensely studied, the diversity and function of gut-associated fungi is understudied and lags far behind other aspects of microbiome studies.Only recently have larger studies specifically focused on the gut mycobiome been performed. Hoffmann et al. (2013).... from 98 healthy individuals without known gastrointestinal disease. In total, the researchers identified 66 fungal genera with 13 additional taxa for which a genus-level classification was not possible. An estimated 184 species were present in total. Eighty-nine percent of the samples had Saccharomyces present. Candida and Cladosporium were the second and third most prevalent, present in 57% and 42% of samples, respectively. The research was not able to definitively determine whether certain taxa were resident fungal microbota or transient as part of dietary intake.

Mutualism between fungi and humans is generally not well understood and has not been well studied. However, several examples related to the gut microbiome provide evidence of a beneficial relationship. S. boulardii, closely related to Saccharomyces cerevisiae, has been studied in controlled trials for the prevention and mitigation of antibiotic-associated diarrhea, including diarrhea caused by Clostridium difficile...These studies show the potency of fungi to compete with pathogenic organisms, modify intestinal function, and attenuate inflammation, presumably because of an interaction with the intestinal microbiota....A recent retrospective data review suggested an inverse relationship between Candida and C. difficile, pointing to some common impact of yeast on the gut microbiome and the exclusion of C. difficle outgrowth and/or toxin production (Manian and Bryant 2013).

Humans have a lifelong interaction with complex microbial communities distributed across the body, which fundamentally contributes to the development and physiology of the macro-organism. Only recently has the diversity of fungi within the human microbiome begun to be determined, with early studies showing that, although relatively nonabundant, fungi are diverse within the microbiome as a whole. Although still in the early stage, studies suggest complex interactions between fungal and bacterial constituents of the microbiome.

Microspcopic image of intestinal fungus. Credit: Iliyan Iliev

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Every time you inhale, you suck in thousands of microbes. And depending on where you live, the microbes will vary. From Wired:

An Atlas of the Bacteria and Fungi We Breathe Every Day

EVERY TIME YOU inhale, you suck in thousands of microbes. (Yes, even right then. And just then, too.) But which microbes? Scientists mostly assumed that the living components of air—at the tiniest scales, anyway—were the same no matter where you went.

And? Not true, it turns out. Thanks to a 14-month citizen-science project that sampled and analyzed airborne dust around the country, researchers have constructed the first atlas of airborne bacteria and fungi across the continental US. And airborne microscopic life is really diverse.

More than 1,400 volunteers swabbed surfaces in 1,200 houses around the country, focusing on the places people don’t usually clean. The dust there passively collects microbes. In the end those swabs revealed about 112,000 bacterial and 57,000 fungal phylotypes (i.e. familial groups).

Most of these little guys were harmless. The few pathogens and allergens ended up being location-specific. Alternaria, a fungal genus that’s also a common allergen, is ubiquitous but concentrates most in the midwest. The fungus Cladosporium has smaller hotspots scattered all over the country east of Texas, most frequently in the South and Mid-Atlantic. Meanwhile, the bacterial genus Cellulomonas, an normally harmless microbe (but an emerging pathogen according to one study), is much more common in the west.

The two biggest factors that shape this airborne environment, according to study author and University of Colorado microbial ecologist Noah Fierer, are the types of soil and plants that are located in the area (affecting the acidity in the environment), and the climate (humidity, temperature, etc.) Cities, for example, tended to be more like other cities than the rural areas nearby, which Fierer attributes to urban areas tending to plant the same types of trees and flowers and playing host to the same types of wildlife (pigeons, rats, etc).

Clasdosporium is a genus of fungi including some of the most common indoor and outdoor molds. Credit: Wikipedia.

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This nice general summary of what scientists know about the microbial community within us was just published by a division of the NIH (National Institutes of Health). Very simple and basic. From the National Institute of General Medical Sciences (NIGMS):

Facts about our microbial menagerie

Trillions of microorganisms inhabit us -- inside and out. Scientists are surveying these microbial metropolises to learn more about their role in health. Microbiologists Darren Sledjeski of the National Institutes of Health (NIH) and Andrew Goodman of Yale University share a few details of what researchers have learned so far.

1. The majority of the microbes that inhabit us are bacteria. The rest of the microbial menagerie is fungi and viruses, including ones that infect the bacteria! Collectively, our resident microorganisms are referred to as the human microbiota, and their genomes are called the human microbiome.

2. Our bodies harbor more bacterial cells than human ones. Even so, the microbiota accounts for less than 3 percent of a person's body mass. That's because our cells are up to 10,000 times bigger in volume than bacterial cells.

3. Your collection of bacteria has more genes than you do. Scientists estimate that the genomes of gut bacteria contain 100-fold or more genes than our own genomes. For this reason, the human microbiome is sometimes called our second genome.

4. Most of our microbes are harmless, and some are helpful. For example, harmless microbes on the skin keep infectious microbes from occupying that space. Microbes in the colon break down lactose and other complex carbohydrates that our bodies can't naturally digest.

5. Different microbes occupy different parts of the body. Some skin bacteria prefer the oily nooks near the nose, while others like the dry terrain of the forearm. Bacteria don't all fare well in the same environment and have adapted to live in certain niches.

6. Each person's microbiota is unique. The demographics of microbiota differ among individuals. Diet is one reason. Also, while a type of microbe might be part of one person's normal microbial flora, it might not be part of another's, and could potentially make that person sick.

7. Host-microbial interactions are universal. Microbial communities may vary from person to person, but everyone's got them, including other creatures. For this reason, researchers can use model organisms to tease apart the complexities of host-microbial interactions and develop broad principles for understanding them. The mouse is the most widely used animal model for microbiome studies.

8. The role of microbiota in our health isn't entirely clear. While it's now well accepted that the microbial communities that inhabit us are actively involved in a range of conditions -- from asthma to obesity -- research studies have not yet pinpointed why or how. In other words, the results may suggest that the presence of a bacterial community is associated with a disease, but they don't show cause and effect.

9. Most of our microbes have not been grown in the lab. Microbes require a certain mix of nutrients and other microbes to survive, making it challenging to replicate their natural environments in a petri dish. New culturing techniques are enabling scientists to study previously uncultivated microbes.

10. The impact of probiotic and prebiotic products isn't clear. Fundamental knowledge gaps remain regarding how these products may work and what effects they might have on host-microbial interactions. A new NIH effort to stimulate research in this area is under way.

11. There's even more we don't know! Additional areas of research include studying the functions of microbial genes and the effects of gut microbes on medicines. The more we learn from these and other studies, the more we'll understand how our normal microbiota interacts with us and how to apply that knowledge to promote our health.

Lactobacilli. Credit: Wikipedia.