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Image result for moldy wallpaper How many people know this? That wallpaper could have fungi (mold) living on it, and this fungi can release toxins (mycotoxins) that can pollute the air and sicken people when people inhale the toxins. The releasing of toxins from the fungi (mold) into the air is called aerosolization - and when this indoor air pollution causes people  living or working in the building to become sick, it is called sick building syndrome. This study looked at 3 common indoor fungal species: Penicillium brevicompactum, Aspergillus versicolor, and Stachybotrys chartarum, and the mycotoxins they produce after growing on wallpaper.

Why does fungi grow on some wallpaper?  The researchers write that: "Many fungi can develop on building material in indoor environments if moisture is high enough". So either high humidity in the home (especially when the weather is hot) or water damage can result in mold growth. It is estimated that in Northern Europe and North America about 20 to 40 % of buildings have visible fungal growth on surfaces. How do the mycotoxins get into the air and move around inside the home? Ordinary living, with people moving around rooms, slamming doors, air drafts from opening windows, and ceiling fans all cause "air velocities" that move around the toxins. Please note that we normally breathe in fungi and bacteria, but inhaling an overload of mycotoxins from moldy wallpaper can sicken a person. From News-Medical:

Fungal toxins from wallpaper source of illness says new research

According to a new study, there are several toxins from fungi that could be released into the air indoors and the source could be fungi living in the wall papers. These may lead to serious health problems say researchers. These ordinary fungi that live with the household wallpaper are basically of three types found the study researchers. They can grow and eventually spread to the air. This leads to serious health consequences. These effects of transmission of the airborne fungi and their toxins on human health have not been studied or considered with importance till date say researchers.

The toxins released from the fungi are called mycotoxins. They can pollute the indoor air and lead to indoor air pollution – a condition called sick building syndrome. Sick building syndrome is a condition where the residents start to feel ill according to the time they have spent in a building.... Study co-author Jean-Denis Bailly, a professor of food hygiene at the National Veterinary School of Toulouse in France in a statement explained that these mycotoxins are released from moldy material of growth of the fungi. They are eventually inhaled by the inhabitants of the home. While investigating the quality of air indoors especially at homes that have higher fungal contamination, the indoor air quality also needs to be tested for fungal toxins, he explained.

According to researchers, there has been extensive study of fungal contamination of food. However there has been little work in terms of fungal toxins in air. For this study they looked at three fungi that commonly also contaminated foods - Penicillium brevicompactum, Aspergillus versicolor and Stachybotrys chartarum. A piece of wallpaper was found to be contaminated with these three fungi. A flowing stream of air was allowed over the wallpaper and samples of air of the room were then collected for testing.

On analysis of the indoor air the researchers found that the small particles of dust floating around in the house which could then be inhaled easily, contained toxins from these fungi. Also all fungi did not spread the toxins at the same rates they found. Some spread more toxins than others and this could help researchers to decide on which fungi species to concentrate on in terms of disease prevention they said.

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20131201_101300 Last week a person told an amazing story in the comments section after a post on this site. After suffering from a "constant runny nose and a bad smell" in the nose for 2 years - which was diagnosed as "fungi and staph" in the sinuses - the person started doing "kimchi treatments" (as discussed in the Sinusitis Treatment Summary page). After 2 weeks a fungal ball was loosened, which came out of the sinuses and into the mouth, and was then spit out. About an inch in size - a smelly, grey/green, round fungal ball. Wow. Which leads to the question: Are any of the microbes in live kimchi anti-fungal?

Kimchi is an amazing live fermented food, typically made with cabbage and other vegetables and a variety of seasonings. Kimchi is the national dish of Korea and so there is tremendous interest in Korea in studying kimchi to learn about the many different microbial species in kimchi, including how they change over the course of fermentation. It turns out that kimchi contains many species of bacteria, including various species of Lactobacillus - which are considered beneficial. Of course one of the species found in kimchi over the course of fermentation is Lactobacillus sakei - the bacteria that successfully treats sinusitis, and which I have written about extensively. L. sakei predominates over pathogenic bacteria (antibacterial) - which is why it is also used as a sausage starter culture (to kill off bacteria such as Listeria). One study found that the garlic, ginger, and leek used in making kimchi were the sources of L. sakei bacteria found in fermented kimchi.

Studies show that a number of the Lactobacillus species found in kimchi are antifungal against a number of different kinds of fungi.  Some of these antifungal bacteria are: Lactobacillus plantarum, L. cruvatus, L. lactis, L. casei, L. pentosus, L. acidophilus, and L. sakei (here, here.

A study from 2005 found that some Lactobacillus species found in kimchi are predominant over a fungi known to cause health problems in humans - Aspergillus fumigatus, a mold (fungi) which is the most common cause of Aspergillus infections. Aspergillus (of which there are many species) is very common both indoors and outdoors (on plants, soil, rotting plants, household dust, etc.), so people typically breathe in these fungal spores daily and without any negative effects. However, sometimes Aspergillus can cause allergic reactions, infections in the lungs and sinuses (including fungal balls), and other infections. (more information at CDC site). The study found that 5 bacterial species in kimchi were also antifungal against other species of fungi (Aspergillus flavus, Fusarium moniliforme, Penicillium commune, and Rhizopus oryzae). The 5 bacterial species in kimchi that they found to be antifungal were: Lactobacillus cruvatus, L. lactis subsp. lactis, L. casei, L. pentosus, and L. sakei.

Just keep in mind that fungi are everywhere around us, and even part of the microbes that live in and on us - this is our mycobiome (here and here). We also breathe in a variety of fungi (mold spores) every day. In healthy individuals (even babies) all the microbes (bacteria, viruses, fungi, etc) live in balanced microbial communities, but the communities can become "out of whack" (dysbiosis) for various reasons, and microbes that formerly co-existed peacefully can multiply and become problematic.  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. Or other pathogenic microbes can enter the community (e.g., through infection), and the person becomes ill.

IN SUMMARY: Kimchi has beneficial bacteria in it that are effective not just against bacteria (antibacterial), but also against some kinds of fungi (antifungal). One 2016 review study went so far as to say: "Kimchi possesses anti-inflammatory, antibacterial, antioxidant, anticancer, antiobesity, probiotic properties, cholesterol reduction, and antiaging properties." Experiences of my family and people writing suggest that the L. sakei in kimchi (and other products) is also antibiofilm. Hopefully, there will be some research on this in the future. But in the meantime, please keep writing to me about fungal complications of sinusitis, and especially if kimchi, L. sakei products, or other probiotics helped.

 A new study has summarized what we know about fungi that live in and on babies - and yes, we all have fungi both on and within us. It's called the mycobiome. In healthy individuals all the microbes (bacteria, viruses, fungi, etc) live in balanced microbial communities, but the communities can become "out of whack" (dysbiosis) for various reasons, and microbes that formerly co-existed peacefully can multiply and become problematic. Or other pathogenic microbes can enter the community, and the person becomes ill.

In healthy adults, approximately 0.1% of the microbes in the adult intestine are fungi, from approximately 60 unique species. Most species live peacefully in the body, and some fungi even have health benefits (e.g., Saccharomyces boulardii prevents gastrointestinal disease). Some fungi that many view as no good and involved with diseases (e.g., Candida and Aspergillus) are also found normally in healthy people. Studies show that normally infants also have fungi. Some fungi that live in the baby's gut (thus detected in fecal samples) are Candida (including C. albicans), Saccharomyces, and Cladosporium. The researchers (from the Univ. of Minnesota) point out that the study of fungi in babies has been neglected and much more research needs to be done.

Whether an infant is born vaginally or through cesarean delivery (C-section) affects the composition of the baby's bacterial communities over the first 6 months of life. And similarly, it looks like when the baby passes through the birth canal, the baby is exposed to the mother's mycobiota (fungi), and then these colonize in the infant's gut. Babies born by C-section have some differences in their fungi, such as being colonized by the mother's skin fungi (such as Malassezia fungi). After birth, a parent kissing and touching the baby (skin to skin contact) also transmits microbes, including fungi, to the baby.

Whether a baby drinks breast milk or formula strongly affects the infant's bacteria within the GI tract. For example, breast-fed infants have more Bifidobacteria and Labctobacilli in their gut compared to formula-fed infants. One study found about 700 species of bacteria in breast milk. Thus, scientists think that human breast milk also influences the infant gut mycobiota (fungi), although this research still needs to be done.

Whether a baby is born prematurely or at term (gestational age) is important. For infants born prematurely, intestinal fungi can cause big problems, such as an overgrowth in the gut. For example, 10% of premature babies get invasive, systemic Candidiasis, and about 20% die. Some factors leading to this are: a naïve immune system, bacterial communities out of whack (dysbiosis) due to antibiotic exposure, and use of parenteral nutrition (because this doesn't contain all the microbes from the mother that are in breast milk). In premature infants, beneficial fungi such as S. boulardii, may help to regulate the growth of opportunistic fungal colonizers such as Candida.

it is clear that whether the baby received antibiotics is important. The bacterial community of infants is altered by exposure to antibiotics in both term and preterm infants. For example, in a lengthy study over the first 3 years of life, infants receiving multiple courses of antibiotics had bacterial community changes following antibiotics and their gut bacterial microbiome became less diverse (fewer species). Although most commonly used antibiotics do not directly act on fungi, anti-bacterial antibiotic exposure is associated with alterations to the mycobiota (fungi) -  such as increased rates of fungal colonization, fungal overgrowth, and changes in the fungal community. For ex., premature infants exposed to cephalosporin antibiotics have an increased risk for invasive Candidiasis (a fungal overgrowth).

Out of whack (dysbiotic) microbial communities, incuding fungi, are found in IBD (intestinal bowel diseases) in children. They have more of some fungi (e.g. Pichia jadinii and Candida parapsilosis) and less of Cladosporium cladosporiodes, and an overall decrease in fungal diversity in the gut, as compared to healthy children.

From BMC Medicine: Infant fungal communities: current knowledge and research opportunities

The microbes colonizing the infant gastrointestinal tract have been implicated in later-life disease states such as allergies and obesity. Recently, the medical research community has begun to realize that very early colonization events may be most impactful on future health, with the presence of key taxa required for proper immune and metabolic development. However, most studies to date have focused on bacterial colonization events and have left out fungi, a clinically important sub-population of the microbiota. A number of recent findings indicate the importance of host-associated fungi (the mycobiota) in adult and infant disease states, including acute infections, allergies, and metabolism, making characterization of early human mycobiota an important frontier of medical research. This review summarizes the current state of knowledge with a focus on factors influencing infant mycobiota development and associations between early fungal exposures and health outcomes. We also propose next steps for infant fungal mycobiome research....

Could this be? Fungal infection being the cause of Alzheimer's disease? Noteworthy from this study: all the Alzheimer's disease (AD) patients had evidence of fungal infections in their brains, central nervous systems, and vascular systems, but none were found in the control subjects (those without Alzheimer's disease). Many of the symptoms of AD (such as inflammation of the central nervous system and activation of the immune system) match those with long-lasting fungal infections. A "microbial cause" has long been suggested as a cause of AD, and interestingly other studies have also found fungal infections in AD patients. The research so far has found several fungal species in AD patients (including Candida albicans). The researchers mention that in one study anti-fungal treatment reversed clinical symptoms of AD in 2 patients (but it was written off  as misdiagnosis).

Another possibility that immediately occurs to  explain the findings is that perhaps Alzheimer's disease somehow results in fungal infections - that the AD makes them more prone to fungal infection. In case you're wondering - all the AD patients and control patients studied had died - this is why their brain tissue could be studied so thoroughly. From Nature:

Different Brain Regions are Infected with Fungi in Alzheimer’s Disease

The possibility that Alzheimer’s disease (AD) has a microbial aetiology has been proposed by several researchers. Here, we provide evidence that tissue from the central nervous system (CNS) of AD patients contain fungal cells and hyphae. Fungal material can be detected both intra- and extracellularly using specific antibodies against several fungi. Different brain regions including external frontal cortex, cerebellar hemisphere, entorhinal cortex/hippocampus and choroid plexus contain fungal material, which is absent in brain tissue from control individuals. Analysis of brain sections from ten additional AD patients reveals that all are infected with fungi. Fungal infection is also observed in blood vessels, which may explain the vascular pathology frequently detected in AD patients. Sequencing of fungal DNA extracted from frozen CNS samples identifies several fungal species. Collectively, our findings provide compelling evidence for the existence of fungal infection in the CNS from AD patients, but not in control individuals.

Neurodegenerative diseases constitute a heterogeneous group of disorders of the central nervous system (CNS) that are characterised by a slow and irreversible loss of neuronal functions. The aetiology of primary neurodegenerative diseases, such as Alzheimer’s disease (AD), multiple sclerosis (MS), Parkinson’s disease (PD) and amyotrophic lateral sclerosis (ALS), remains largely unknown. A common feature of many neurodegenerative diseases is the presence of aggregates of misfolded proteins (intracellular inclusions) in regions of the CNS that can serve as neuropathological hallmarks for disease diagnosis1,2. ....The prevailing dogma to explain the pathogenesis of AD is that the accumulation of amyloid deposits formed by Aβ pepetide may induce intracellular tangles of tau protein that in turn leads to neuronal death11. However, the so-called “amyloid hypothesis” has been questioned by several findings including the failure of clinical trials aimed to lower amyloid deposits or tau tangles12,13,14. Moreover, many elderly people with normal cognitive function have substantial amyloid burden in their CNS11. At present, there is no therapy to stop or reverse the symptoms of AD.

Aside from cognitive decline, the vast majority of AD patients present clear signs of inflammation and damage to blood vessels15,16. Inflammation of the CNS and immune activation play a major role in the pathophysiology of AD. Indeed, a number of cytokines, such as interleukins (IL-1 and IL-6), tumor necrosis factor α and interferon γ, are elevated in the brain of AD patients, suggesting an increased immune response17,18,19. These observations have led to the speculation that AD has an autoimmune aetiology20. Many investigators have also considered the idea that AD is an infectious disease, or at least that infectious agents constitute a risk factor for AD21,22,23. Accordingly, genetic material from several viruses and bacteria have been reported in brains from AD patients. In particular, herpes simplex type 1 (HSV-1) and Chlamydophila pneumoniae have been suggested as potential aetiological agents of AD. In addition, brain infection by several pathogens may induce amyloid formation24,25,26. Furthermore, Αβ peptide exhibits antimicrobial activity and shows particularly strong inhibitory activity againstCandida albicans27.

Recently, we provided strong evidence for fungal infection in AD patients28,29. Fungal DNA and proteins were found in frozen brain tissue from AD patients, but not from control patient tissue. .....No fungal material was observed in brain tissue from ten control individuals, whereas fungal infection was clearly present in brains from ten additional AD patients. Moreover we were able to amplify fungal DNA from frozen tissue of different AD brain regions. Collectively, our findings provide compelling evidence for the presence of fungal infection in brains from all AD patients analysed.

Because most of the above results were obtained from only one AD patient and one control individual, it was of interest to examine CNS sections from additional AD patients and controls. To this end, we analysed ERH tissue sections from a further ten AD patients and ten controls by double immunostaining with anti-fungal (green) and anti-tubulin (red) antibodies. Notably, fungal infection was evident in all AD patients studied (Fig. 4), whereas no fungal cells were detected in tissue sections from control individuals.... The existence of different fungal morphologies reinforces the idea that several species can be present, supporting the concept of mixed fungal infections. In conclusion, fungal cells and/or hyphae were found in all AD patients analysed although the morphological characteristics may be different for each patient, thus implying that the fungal species present in each patient may also differ. 

..... In conclusion, fungal structures can be observed also in the vascular system of AD patients..... Of note, several species could be detected from the same region, supporting the concept of mixed fungal infection. Conversely, no single fungal species was present in all four regions of the CNS examined. Of note, some of the species detected, such as Malasezzia spp., Phoma and S. cerevisiae, have been previously identified in AD brains40. Significantly, the majority of the species listed in Table 1 are described as human pathogens42,43. The possibility that different fungal species or a combination of species serves as a risk factor or represents the cause of AD might explain the diversity observed in the evolution and severity of clinical symptoms in each AD patient. 

The possibility that AD is a fungal disease, or that fungal infection is a risk factor for the disease, opens new perspectives for effective therapy for these patients. The present findings demonstrate that fungi can be detected in brain tissue from different regions of the AD CNS. In all eleven patients (plus three additional CP samples) described in this study, as well as in four patients previously analysed, there is clear evidence for fungal cells inside neurons or extracellularly29. Therefore, 100% of the AD patients analysed thus far by our laboratory present fungal cells and fungal material in brain sections.....Observations from other laboratories also support the possibility of fungal infections in AD patients. .... Moreover, antifungal treatment in two patients diagnosed with AD reversed clinical symptoms51,52. The interpretation of these results was that perhaps these patients were misdiagnosed.

Proceeding on the assumption that fungi are the aetiological agent of AD, all of the symptoms observed in AD patients can be readily explained. ....It is quite possible that the existence of one fungal infection may facilitate the colonisation by other fungal species that can affect other areas of the CNS, giving rise to mixed fungal infections.

The existence of fungal infection in AD patients may be due to its involvement in the aetiology of this disease, but it could also be possible that, for reasons yet unknown, these patients are more prone to this type of infection. The fact that they are elderly and may have a poor adaptive immune response, or possibly changes in the diet and hygiene habits, may contribute to the emergence of fungal infections. It is evident that clinical trials will be necessary to establish a causal effect of fungal infection in AD. There are at present a number of highly effective antifungal compounds with little toxicity58,59,60,61

Candida albicans (Credit: Josef Reischig, Wikimedia Commons)

 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.”

  This article discusses the fungi living on our skin. Recent research (using state of the art genetic analysis) has found that normal, 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. 

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.

Microscope image of intestinal fungus.     Image: Iliyan Iliev

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).

Cladosporium sp conidia.jpgCladosporium is a genus of fungi including some of the most common indoor and outdoor molds  Photo: Wikipedia

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.

Lactobacillus sp 01.pngLactobacillus (the rods) near a squamous epithelial cell      Photo from CDC