You and Your Microbiome – Part 3

  • Top 10 Cited Microbiome Publications are Summarized
  • Welcome to the New World-View of “Holobionts”
  • TriLink Products Cited in Numerous Microbiome Publications

It’s been almost two-and-a-half years since posting Part 2 in this series on microbiomes, which I first began in 2013, and the publication rate keeps accelerating, with about 7,000 articles indexed in PubMed in 2016—way more than the mere 35 in 1996. This vast amount of new microbiome information being published annually led me to use the following search strategy to guide my selection of what’s trending in importance for microbiomes.

Basically, I used Google Scholar to search for publications since 2015 that had the term “microbiome” in the title and, among those items found, used the number of citations as a quantitative indicator of interest, importance, and/or impact. But before summarizing my findings for these Top 10 Most Cited Microbiome articles, here’s what you can read in my previous two postings on microbiomes in case you missed them or want to refresh your memory:

Proportion of cells in the human body. You are comprised of much more than what you think you are! Taken from

Meet Your Microbiome: The Other Part of You

  • What’s in your microbiome? Why does it matter?
  • Next-generation sequencing is revealing that you and your bacterial microbiome have a biological relationship.

You and Your Microbiome – Part 2

  • Global obesity epidemic is linked to gut microbiome.
  • Investments in microbiome-based therapies are increasing.

Top 10 Cited Microbiome Publications 

The following articles, which were all published in 2015, are listed in decreasing order of the number of citations in Google Scholar. Titles are linked to original documents for interested readers to consult, and synopses represent my attempt to capture essential findings.

1. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile (369 citations)

C. difficile (From

Many antibiotics destroy intestinal microbial communities and increase susceptibility to intestinal pathogens such as Clostridium difficile, which is a major cause of antibiotic-induced diarrhea in hospitalized patients. It was found that Clostridium scindens, a bile acid 7-dehydroxylating intestinal bacterium, is associated with resistance to C. difficile infection and, upon administration as a probiotic, enhances resistance to C. difficile infection.

2. Dynamics and stabilization of the human gut microbiome during the first year of life (298 citations)

Applying metagenomic sequencing analysis on fecal samples from a large cohort of Swedish infants and their mothers, the gut microbiome during the first year of life was characterized to assess the impact of mode of delivery and feeding. In contrast to vaginally delivered infants, the gut microbiota of infants delivered by C-section showed significantly less resemblance to their mothers. Nutrition had a major impact on early microbiota composition and function, with cessation of breast-feeding, rather than introduction of solid food, being required for maturation into an adult-like microbiota.

Graphical abstract by Bäckhed et al. Cell Host & Microbe (2015)

3. Structure and function of the global ocean microbiome (238 citations)

Taken from Sunagawa et al. Science (2015)

Metagenomic sequencing data from 243 ocean samples from 68 locations across the globe was used to generate an ocean microbial reference gene catalog with >40 million novel sequences from viruses, prokaryotes, and picoeukaryotes. This ocean microbial core community has 73% of its abundance shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.

4. Serotonin, tryptophan metabolism and the brain-gut-microbiome axis (200 citations)

Taken from

The brain-gut axis is a bidirectional communication system between the central nervous system and the gastrointestinal tract. Serotonin functions as a key neurotransmitter at both terminals of this network. Accumulating evidence points to a critical role for the gut microbiome in regulating normal functioning of this axis. The developing serotonergic system may be vulnerable to differential microbial colonization patterns prior to the emergence of a stable adult-like gut microbiota. At the other extreme of life, the decreased diversity and stability of the gut microbiota may dictate serotonin-related health problems in the elderly. Therapeutic targeting of the gut microbiota might be a viable treatment strategy for serotonin-related brain-gut axis disorders.

5. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes (184 citations)

Taken from

Colonization of the fetal and infant gut microbiome results in dynamic changes in diversity, which can impact disease susceptibility. To examine the relationship between human gut microbiome dynamics throughout infancy and type 1 diabetes (T1D), a cohort of 33 infants genetically predisposed to type 1 diabetes (T1D) was examined to model trajectories of microbial abundances through infancy. A marked drop in diversity was observed in T1D progressors in the time window between seroconversion and T1D diagnosis, accompanied by spikes in inflammation-favoring organisms, gene functions, and serum and stool metabolites. These trends in the human infant gut microbiome thus distinguish T1D progressors from nonprogressors.

6. The microbiome of uncontacted Amerindians (150 citations)

Taken from

Sequencing of fecal, oral, and skin bacterial samples was used to characterize microbiomes and antibiotic resistance genes (resistome) of members of an isolated Yanomami Amerindian village in the Amazon with no documented previous contact with Western people. These Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group. Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, and no known exposure to antibiotics, they harbor bacteria that carry functional antibiotic resistance (AR) genes, including those that confer resistance to synthetic antibiotics. These results suggest that westernization significantly affects human microbiome diversity and that functional AR genes appear to be a feature of the human microbiome even in the absence of exposure to commercial antibiotics.

7. Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology (136 citations)

Taken from

Individuals with obesity and type 2 diabetes differ from lean and healthy individuals in their abundance of certain gut microbial species and microbial gene richness. This study in humans found that, at baseline, A. muciniphila was inversely related to fasting glucose, waist-to-hip ratio and subcutaneous adipocyte diameter. Subjects with higher gene richness and A. muciniphila abundance exhibited the healthiest metabolic status. Individuals with higher baseline A. muciniphila displayed greater improvement in insulin sensitivity markers and other clinical parameters. A. muciniphila is therefore associated with a healthier metabolic status and better clinical outcomes for overweight/obese adults.

8. Host biology in light of the microbiome: ten principles of holobionts and hologenomes (132 citations)

Today, animals and plants are no longer viewed as autonomous entities, but rather as “holobionts“, composed of the host plus all of its symbiotic microbes. The term “holobiont” refers to symbiotic associations throughout a significant portion of an organism’s lifetime, with the prefix holo- derived from the Greek word holos, meaning whole or entire. Holobiont is now generally used to mean every macrobe and its numerous microbial associates, and the term importantly fills the gap in what to call such assemblages. Symbiotic microbes are fundamental to nearly every aspect of host form, function, and fitness, including traits that once seemed intangible to microbiology: behavior, sociality, and the origin of species. Microbiology thus has a central role of in the life sciences, as opposed to a “bit part.”

Taken from

9. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development (131 citations)

The nasopharynx (NP) is a reservoir for microbes associated with acute
respiratory infections (ARIs). Lung inflammation resulting from ARIs during infancy is linked
to asthma development. The NP microbiome examination during the first year of life in a cohort of 234 children led to characterization of viral and bacterial communities, and documenting all incidents of ARIs. Most infants were initially colonized with Staphylococcus or Corynebacterium before stable colonization with Alloiococcus or Moraxella. Transient incursions of Streptococcus, Moraxella, or Haemophilus marked virus-associated ARIs. Early asymptomatic colonization with Streptococcus was a strong asthma predictor, and antibiotic usage disrupted asymptomatic colonization patterns.

10. Insights into the role of the microbiome in obesity and type 2 diabetes (128 citations)

Obesity and type 2 diabetes (T2D) are associated with changes in the composition of the intestinal microbiota, and the obese microbiome seems to be more efficient in harvesting energy from the diet. Lean male donor fecal microbiota transplantation (FMT) in males with metabolic syndrome resulted in a significant improvement in insulin sensitivity and increased intestinal microbial diversity, including a distinct increase in butyrate-producing bacterial strains. Such differences in gut microbiota composition might function as early diagnostic markers for the development of T2D. The rapid development of FMTs provides hope for novel therapies in the future.

TriLink Products Cited in Microbiome Publications

It always amazes me to learn about the many ways TriLink products are used in basic and applied science. When I searched Google Scholar for publications containing “TriLink [and] microbiome” I found 21 items, among which the following were selected to illustrate diversity of these product types and uses:

Takeaway Messages

In summary, several takeaways should now be apparent to you. The first takeaway is that there is continuing explosive growth of microbiome publications in all manner of life-related research, as evidenced by both the introductory PubMed graph and wide spectrum of subjects covered by the Top 10 Cited Publications mentioned above.

The second takeaway is best summarized in publication #8 above, “[t]oday, animals and plants are no longer viewed as autonomous entities, but rather as ‘holobionts’, composed of the host plus all of its symbiotic microbes.” Each of us is indeed inextricably comprised of our human cells and symbiotic microbiota in or on us—like it or not, and for better or worse.

The final takeaway is that TriLink products play a contributing role in elucidating and applying this new world-view of halobionts.

As usual, your comments are welcomed.

Frightening Fungus Among Us

  • Clinical Alert for Candida auris (C. auris) Issued by CDC
  • US Concerned About C. auris Misidentification and Drug Resistance
  • Sequencing C. auris DNA in Clinical Samples is Preferred for Identification
Strain of C. auris cultured in a petri dish at CDC. Credit Shawn Lockhart, CDC. Taken from

Strain of C. auris cultured in a petri dish at CDC. Credit Shawn Lockhart, CDC. Taken from

When I was a kid and didn’t know better, there was a supposedly funny rhyme that “there’s fungus among us.” While this saying is thankfully passé nowadays, the growing number of infections by a formerly obscure but deadly fungus is frightening. This so-called “superbug” is an antibiotic-resistant fungus called Candida auris (C. auris) that’s worth knowing about, and is the fungal focus of this blog.

First, Some Fungus Facts

Fungi are so distinct from plants and animals that they were allotted a biological ‘kingdom’ of their own in classification of life on earth, although that was only relatively recently, i.e. 1969. There are 99,000 know fungi, which exist in a wide diversity of sizes, shapes and complexity that extends from relatively simple unicellular microorganisms, such as yeasts and molds, to much more complex multicellular fungi, such as mushrooms and truffles.

It was previously thought that genomes of all fungi are derived from the genome of the model fungus Saccharomyces cerevisae, which has been used in winemaking, baking and brewing since ancient times. However, genome sequencing of more than 170 fungal species has revealed that, while the genome size of S. cerevisae is only ~12 Mb, seven species of fungus have genome sizes larger than 100 Mb. This is attributed to various evolutionary pressure-factors generating transposable elements, short sequence repeats, microsatellites, and genome duplication, and noncoding DNA.

Fungal cell walls are made up of intertwined fibers mostly comprised of long chains of chitosan, the same tough compound found in the exoskeletons of animals such as spiders, beetles and lobsters. The chitin in fungal cells is entangled with glucans and other wall components, such as proteins, forming a mass that protects the cell membrane behind it—and posing a formidable barrier against antifungal drugs.

Taken from

Taken from

In researching whether there are any nucleic acid drugs against fungi, I found one early patent by Isis (now Ionis) Pharmaceuticals for use of antisense phosphorothioate-modified oligonucleotides for the treatment of Candida infections, but virtually no other reports. I suspect that will change in the future as pathogenic fungi and other disease-causing microbes become more resistant to conventional drugs.

Fungal infections of the skin are very common and include athlete’s foot, jock itch, ringworm, and yeast infections. While these can usually be readily treated, infections caused by pathogenic fungi have reportedly risen drastically over the past few decades. Moreover, with the increase in the number of immunocompromised (burn, organ transplant, chemotherapy, HIV) patients, fungal infections have led to alarming mortality rates due to ever increasing phenomenon of multidrug resistance.

Segue to a Serious Situation

Emergence of drug-resistant fungi is, in part, the segue to the serious story of the present blog. The other part being incorrect identification of a certain fungus as being a common candida yeast, which is not only scary but seemingly inexcusable in today’s era of highly accurate PCR-based assays to accurately identify microorganisms. Here’s the situation in a nutshell.

  1. auris infection, which is associated with high mortality and is often resistant to multiple antifungal drugs, was first described in 2009 in Japan but has since been reported in countries throughout the world. Unlike many Candida infections, C auris is a hospital-acquired infection that is contracted from the environment or staff of a healthcare facility, and it can spread very quickly.

To determine whether C. auris is present in the United States and to prepare for the possibility of transmission, the Centers for Disease Control (CDC) and Prevention issued a clinical alert in June 2016 requesting that C. auris cases be reported.

(A) MALDI-TOF schematic; (B) mass spectra from three C. parapsilosis; and (C) two C. bracarensis isolates. Taken from researchgate

(A) MALDI-TOF schematic; (B) mass spectra from three C. parapsilosis; and (C) two C. bracarensis isolates. Taken from researchgate

This official alarm bell, if you will, was triggered by the following facts:

  • Many isolates are resistant to all three major classes of antifungal medications, a feature not found in other clinically relevant Candida
  • auris identification requires specialized methods such as a MALDI-TOF mass spectrometry or sequencing the 28s ribosomal DNA, as pictured below.
  • Using common methods, auris is often misidentified as other yeasts, which could lead to inappropriate treatments.

The CDC subsequently found that seven cases were identified in Illinois, Maryland, New York and New Jersey. Five of seven isolates were either misidentified initially as C. haemulonii or not identified beyond being Candida. Five of seven isolates were resistant to fluconazole; one of these isolates was resistant to amphotericin B, and another isolate was resistant to echinocandins. While no isolate was resistant to all three classes of antifungal medications, emergence of a new strain of C. auris that is would pose a serious public health issue.

Sequencing 28s ribosomal DNA. Taken from

Sequencing 28s ribosomal DNA. Taken from

Based on currently available information, the CDC concluded that these cases of C. auris were acquired in the U.S., and several findings suggest that transmission occurred:

  • First, whole-genome sequencing results demonstrate that isolates from patients admitted to the same hospital in New Jersey were nearly identical, as were isolates from patients admitted to the same Illinois hospital.
  • Second, patients were colonized with auris on their skin and other body sites weeks to months after their initial infection, which could present opportunities for contamination of the health care environment.
  • Third, auris was isolated from samples taken from multiple surfaces in one patient’s health care environment, which further suggests that spread within health care settings is possible.

A related Fox News story adds that C. auris was found on a patient’s mattress, bedside table, bed rail, chair, and windowsill. Yikes!

While the above situation in the U.S. might not seem particularly worrisome to you, the potential for emergence of more infectious C. auris strains with higher lethality should be of concern. That has already reportedly occurred in several Asian countries and South Africa. Obviously, deployment of the best available methods for pathogen identification can, in principle, lessen the likelihood of the emergence and/or spread of C. auris in the U.S. and other countries.

Case for Point-of-Care C. auris Nanopore Sequencing?

Taken from 

Taken from

Regular readers of my previous blogs know that I’m an enthusiastic fan of the Oxford Nanopore Technologies minION sequencer, which is proving to be quite useful for characterizing pathogens in very remote regions on Earth—and even on the International Space Station to diagnose astronaut infections! Notwithstanding various current limitations for minION sequencing of microbes, it seems to me that it would be relatively straightforward to generate minION data for many available samples of pathogenic fungi and genetically related microbes to assess the feasibility using minION for faster, cheaper, better unambiguous identification of C. auris minION in centralized or Point-of-Care applications.

Taken from

Taken from

If you think this suggestion is farfetched, think again, after checking out these 2016 publications using minION:

The 51.4-Mb genome sequence of Calonectria pseudonaviculata for fungal plant pathogen diagnosis was obtain using minION.

The first report of the ~54 Mb eukaryotic genome sequence of Rhizoctonia solani, an important pathogenic fungal species of maize, was derived using minION.

Sequence data is generated in ~3.5 hours, and bacteria, viruses and fungi present in the sample of marijuana are classified to subspecies and strain level in a quantitative manner, without prior knowledge of the sample composition.

CDC on C. auris Status and FAQs

In the interest of concluding this blog with the most up-to-date and authoritative information, I consulted the CDC website and found statements and replies to FAQs that are well worth reading at this link.

As a scientist, my overriding question concerns the lack of adoption of improved microbiological methods by hospitals and clinics. The above noted misidentifications of C. auris infections resulting from use of flawed lab analyses seems unacceptable. Although I don’t know all the facts or statistics to generalize, I suspect that there are other incorrect lab analyses due to use of outdated methods. On the other hand, I’m hopeful that, with the FDA’s widely touted Strategic Plan for Moving Regulatory Science into the 21st Century, the section entitled Ensure FDA Readiness to Evaluate Innovative Emerging Technologies—think nanopore sequencing—becomes actionable, sooner rather than later.

Changing established—dare I say entrenched—clinical lab tests is not simple or easy, but if it doesn’t begin it won’t happen, about which I’m quite certain. I can only wonder why development of infectious disease analytical methods and treatments seem to require a crisis. Sadly, I think it boils down to the complexities and socio-political dynamics of who pays.

Frankly, it’s my personal opinion that maybe it’s time Thomas Jefferson’s philosophy about hammering guns into plows is directed to health care.


After writing this blog, I learned that T2 Biosystems has received FDA approval to market in the U.S. the first direct blood test for detection of five yeast pathogens that cause bloodstream infections: Candida albicans and/or Candida tropicalis, Candida parapsilosis, Candida glabrata and/or Candida krusei.

Yeast bloodstream infections are a type of fungal infection that can lead to severe complications and even death if not treated rapidly. Traditional methods of detecting yeast pathogens in the bloodstream can require up to six days, and even more time to identify the specific type of yeast present. The T2Candida Panel and T2Dx Instrument (T2Candida) can identify these five common yeast pathogens from a single blood specimen within 3-5 hours.

T2Candida incorporates technologies that break the yeast cells apart, releasing the DNA for PCR amplification for detection by greatly simplified, miniaturized nuclear magnetic resonance (NMR) technology, as can be seen in this video.

In my opinion, this fascinating new technology is another example of what could be rapidly deployed toward detecting C. auris.

You and Your Microbiome – Part 2

  • Global Obesity Epidemic is Linked to Gut Microbiome
  • DNA Sequence-Based Microbiomes Accurately Associate with Obesity
  • Blue Agave Margaritas Contain Beneficial Gut Microbes
  • Investments in Microbiome-based Therapies on the Rise, but is there Hype?

Last August, my post entitled Meet Your Microbiome: The Other Part of You dealt with growing recognition that trillions of microbes—mostly bacteria but also fungus—reside in and on each of us, and influence our health status. Moreover, the compositions of these microbiomes change with our diet, what we drink or breath, and who we contact—family, pets, and close friends.

Since then, I’ve collected a string of microbiome articles delving into the implications of this dynamic, symbiotic relationship, and selected some topics that I thought were “blogworthy.” This Part 2, as it were, focuses on overweight/obesity, microbiome therapy, and burgeoning business opportunities.

Continue reading

Meet Your Microbiome: The Other Part of You

  • Like it or not, and for better or worse, next-generation sequencing is revealing that you and your bacterial microbiome have an inextricable biological relationship.
  • “RePOOPulating” the gut:  a clinical study of “synthetic stool” as a better alternative to fecal transplant.
  • Microbiome movies, fungus too, and much more.

What’s in your microbiome? Why does it matter?

Writing this blog was inspired by reading Michael Pollan’s recent article in The NY Times Magazine entitled “Some of my best friends are bacteria,” which is an engaging story about Michael having his microbiome sequenced as part of the American Gut project. He notes at the beginning that each of us has several hundred microbial species with whom we share our body, and that these bacteria—numbering ~100 trillion—are living (and dying) right now on the surface of our skin, mouth, and intestine “where the largest contingent of them will be found, a pound or two of microbes together forming a vast, largely uncharted interior wilderness that scientists are just beginning to map.” The sheer numbers of these microbes, he adds, makes us only ~10% human—for every human cell there are ~10 resident microbes—most being “harmless freeloaders” or “favor traders” (i.e. symbiotic), and only a tiny number of pathogens. Furthermore, “[t]his humbling new way of thinking about the self has large implications for human and microbial health, which turn out to be inextricably linked.”


If you want to know what’s in your gut, you can participate in this world wide study by registering at According to the website, you’ll be asked to ‘fill out a diet & lifestyle questionnaire (online) with such things as age, gender, weight, have you taken antibiotics lately, any conditions we should know about it, and so on.’ Anyone over the age of 3 months can participate in the study, and you will have the opportunity to provide a stool, tongue and/or palm sample via an at-home sample kit.

Microbes and Your Health

As more microbiome data is obtained from the American Gut project and analogous studies, correlations with each person’s health status can be made. Having the “wrong” kind of microbes may be associated with predisposition to obesity or certain chronic diseases, for example. Such information may then be used to prescribe dietary or other sources supplemental probiotics. An extreme outcome could involve “fecal transplants” (i.e., fecal microbiota transplantation or fecal bacteriotherapy) wherein a healthy person’s fecal microbiota are installed into a sick person’s gut.

My PubMed searches of these terms led to a number of publications, such as that by Christopher. R. Kelly et al. at Women and Infant’s Hospital, Brown University Alpert School of Medicine, who reported promising results for relapsing Clostridium difficile infection in a small study of 26 patients. Coincidentally, on June 18th there was a report that the US Food & Drug Administration (FDA) is “dropping plans to tightly control” fecal transplants that are “becoming increasingly popular for treating people stricken by life-threatening infections of the digestive system.” This report went on to say that, in the FDA’s view, “such a treatment should only be given to patients who have exhausted other treatment options and who have given consent and been informed that it is an experimental procedure with risks.”

RePOOPulating the gut:  a better alternative?

Among the concerns for fecal transplants are pathogen transmission, patient acceptance and inability to standardize the treatment regime, states Elaine O. Petrof and her colleagues in a study entitled Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut, recently published in Microbiome (2013). This online, open-access article is well worth a quick read if you’re interested in the experimental details, which take advantage of next-generation sequencing as a key method for quite sophisticated identification and analysis of microbes. In brief, a stool substitute preparation—made from 33 purified intestinal bacterial cultures derived from a single healthy donor—was used to treat two patients who had failed at least three courses of metronidazole or vancomycin. Pre-treatment and post-treatment stool samples were analyzed by 16S rRNA sequencing using the Ion Torrent platform. Both patients were infected with a hyper virulent C. difficile strain, but following treatment each reverted to their normal bowel pattern within 2-3 days and remained symptom-free at 6 months. Analysis demonstrated that rRNA sequences found in the stool substitute were rare in the pre-treatment stool samples, but constituted >25% of the sequences 6 months after treatment.


Bacteria on the gut lining. Image: Cardiff University

Microbiome Movies

Relatively low-cost deep-sequencing technology has enabled novel studies aimed at obtaining, in effect,  “moving pictures of the human microbiome,” which is the attention-grabbing title of a study by J. Gregory Caparaso et al. in Genome Biology. This landmark publication in 2011 presented the largest human microbiota time-series analysis to date, covering two individuals each at 4 body sites over 396 time-points. One male and one female each provided gut (feces), mouth, left palm, and right palm samples over 15-mo and 6-mo periods, respectively, Variable regions of 16S ribosomal RNA (rRNA) in each sample were amplified by PCR and sequenced on an Illumina instrument. The following stated results and conclusions may surprise you, as they did me:

“We find that despite stable differences between body sites and individuals, there is pronounced variability in an individual’s microbiota across months, weeks and even days. Additionally, only a small fraction of the total taxa found within a single body site appear to be present across all time points, suggesting that no core temporal microbiome exists at high abundance (although some microbes may be present but drop below the detection threshold). Many more taxa appear to be persistent but non-permanent community members.”

“Because of the immense subject-to-subject variability in the microbiome, studies examining temporal variability, which give a view of dynamics beyond the static pictures previously available, have the potential to transform our understanding of what is ‘normal’ in the human body, and, perhaps, to develop predictive models for the effects of clinical interventions.”

If you’re questioning whether the above study of only two individuals—albeit for many time points—reflects a wider population, rest assured that it apparently does. The recently completed 5-yr Human Microbiome Project (HMP) launched in 2008 involved 242 volunteers, more than 5,000 samples were collected from tissues from 15 (men) and 18 (women) at body sites such as mouth, nose, skin, lower intestine (stool) and vagina. According to the HMP wiki site, this project’s discoveries include:

  • Microbes contribute more genes responsible for human survival than humans’ own genes. It is estimated that bacterial protein-coding genes are 360 times more abundant than human genes.
  • Microbial metabolic activities—for example, digestion of fats—are not always provided by the same bacterial species. The presence of the activities seems to matter more.
  • Components of the human microbiome change over time, affected by a patient disease state and medication. However, the microbiome eventually returns to a state of equilibrium, even though the composition of bacterial types has changed.

Consequently, defining what is “normal” and whether a “core” community of microbes exists is quite complicated, and will likely remain a topic of great interest and debate. In this regard, I found an overview by Dirk Gevers et al. well worth reading. Here’s one section of text that reiterates what I think are important points, and elaborates upon the above second bullet point about microbial metabolic activities, i.e. functional core:

“A potentially more universal ‘core’ human microbiome emerged during the consideration of microbial genes and pathways carried throughout communities’ metagenomes. While microbial organisms varied among subjects as described above, metabolic pathways necessary for human-associated microbial life were consistently present, forming a functional ‘core’ to the microbiome at all body sites. Although the pathways and processes of this core were consistent, the particular genes that implemented them again varied. Microbial sugar utilization, for example, was enriched for metabolism of simple sugars in the oral cavity, complex carbohydrates in the gut, and glycogen/peptidoglycan degradation in the vaginal microbiome. The healthy microbiome may thus achieve a consistent balance of function and metabolism that is maintained in health, but with fine-grained details personalized by genetics, early life events, environmental factors such as diet, and a lifetime of pharmaceutical and immunological exposures.”

Lest you think that such data are collections of facts devoid of utility, think again after reading the following excerpts from the abstract of a publication by Fredrik H. Karlsson et al. in Nature 2013 entitled Gut metagenome in European women with normal, impaired and diabetic glucose control.

“Type 2 diabetes (T2D) is a result of complex gene–environment interactions, and several risk factors have been identified, including age, family history, diet, sedentary lifestyle and obesity. Statistical models that combine known risk factors for T2D can partly identify individuals at high risk of developing the disease. However, these studies have so far indicated that human genetics contributes little to the models, whereas socio-demographic and environmental factors have greater influence.…Here we use shotgun sequencing to characterize the fecal metagenome of 145 European women with normal, impaired or diabetic glucose control. We observe compositional and functional alterations in the metagenomes of women with T2D, and develop a mathematical model based on metagenomic profiles that identified T2D with high accuracy.”

Microbiomes in Homes and Hospitals

Mapping the great indoors—an engaging NY Times article by Peter A. Smith—tells about microbiologists who are using sequencing to “take a census” of what lives in our homes with us and how we “colonize” spaces with other species — viruses, bacteria, microbes. One group has sampled the “microbial wildlife” in 1,400 homes across the USA in a project called The Wild Life of Our Home, which relies on volunteers to swab pillowcases, cutting boards and doorjambs, then send samples in for analysis. Although data are still being analyzed, an earlier study of 40 homes in 9 locations around the Raleigh-Durham area of North Carolina has been published by Robert R. Dunn et al. in PLoS ONE entitled Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes. Among their findings were the following.

“[E]ach of the sampled locations harbored bacterial communities that were distinct from one another” [and that] “the presence of dogs had a significant effect on bacterial community composition in multiple locations within homes as the homes occupied by dogs harbored more diverse communities and higher relative abundances of dog-associated bacterial taxa. Furthermore, we found a significant correlation between the types of bacteria deposited on surfaces outside the home and those found inside the home, highlighting that microbes from outside the home can have a direct effect on the microbial communities living on surfaces within our homes.”

Your dirty dog? (Bing Images)

Your dirty dog? (Bing Images)

Some of you might be wondering what microbes your dog is depositing in your home, while others might be asking about cats. I haven’t a clue about your dog, but cats weren’t directly assessed in this study. Thirteen of the houses had only dogs as pets and the influence of dogs is likely to be greater than cats because of their large size and need to go outdoors. Only three houses had cats but not dogs (three houses had both), and the investigators judged this to be too small a sample size for cats.

The figure shown below taken from the aforementioned Dunn et al. publication tracks 9 sites sampled with 5 sources of microbes. The authors note that “[t]hese results show changes in the relative importance of individual sources across sites, not comparisons across sources within sites. For example, these results show that soil is a more important source of bacteria on door trims than on cutting boards, but these results cannot be used to directly compare the relative importance of soil versus leaves as sources of bacteria at individual locations.” By the same token, the results show that human skin is a more important source of bacteria on toilet seats than on cutting boards.


Source tracking analysis showing relative proportion of bacteria at each sampling site associated with given sources. Values represent median percentages. Warmer colors indicate greater influences of particular sources across the sites (Robert R. Dunn et al. PLoS ONE 2013).

Microbial fingerprints

Roughly 1.7 million hospital-associated infections are reported each year in the USA, and the pathogens that cause them must come from somewhere. Beth Mole (too bad she wasn’t named Millie!) in Nature-News 2013 notes that patients leave a microbial mark on hospitals. This attention getting punch line refers to preliminary findings from the Hospital Microbiome Project that, according to its website, “aims to collect microbial samples from surfaces, air, staff, and patients from the University of Chicago’s new hospital pavilion in order to better understand the factors that influence bacterial population development in healthcare environments.”

According to Beth Mole, “…even in areas with long-term inhabitants, [Jack] Gilbert’s team has found no lingering pathogens. ‘Over the first four months of observations, we’ve seen nothing that concerns us,’ he says.” However, “Gilbert and his team found significant differences between microbial communities in individual hospital rooms. Patients who stayed for only short periods, such as those undergoing elective surgery, had a transient influence on their rooms’ microbial communities; after cleaning, the rooms reverted to a pre-patient state.” In contrast, and of concern, ‘[m]icrobes from long-term patients—including people with cancer or those who had received organ transplants—had time to settle into the rooms. The patients’ microbial fingerprints lingered after they checked out of the hospital, even after their rooms were cleaned.” But even in areas with long-term inhabitants, Gilbert’s team has found no lingering pathogens. “Over the first four months of observations, we’ve seen nothing that concerns us,” he says.”

Thinking Big: The Global Microbiome

If you now muse about greatly expanding the scope of the aforementioned studies to a global scale, you’d be thinking about something that has already been proposed. The Earth Microbiome Project is a “massively multidisciplinary effort to analyze microbial communities across the globe” that proposes to “characterize the Earth by environmental parameter space into different biomes and then explore these using samples currently available from researchers across the globe.” The project intends to “analyze 200,000 samples from these communities using metagenomics, metatranscriptomics and amplicon sequencing to produce a global Gene Atlas describing protein space, environmental metabolic models for each biome, approximately 500,000 reconstructed microbial genomes, a global metabolic model, and a data-analysis portal for visualization of all information.” We’ll all have to stay tuned on this rather ambitious project to learn what is found and, more importantly, what are the conclusions—and whether time-dependent variability is accounted for.

By the way, if you’re wondering about the total global microbiome, Addy Pross’ book entitled What is Life? How Chemistry Becomes Biology states that the earth’s bacterial biomass is estimated to be 2 × 1014 tons, which is sufficient to cover the earth’s land surface to a depth of 1.5 meters!

Microbiome-mania & Toilet-phobia

There seems to be a surge in extending microbiome analysis to many other contexts. Some of these findings are surprising—and prompting jokes—or might scare you about microorganisms present in various places or on things that we come into contact with, whether we know it or not.

Initial, a UK-based provider of hygiene services to businesses and organizations, announced in an April 2013 press release, its research that “…lifts the lid on the grimy state of Britain’s office kitchens.” Being a provider of cleaning services, Initial was presumably quite pleased to inform the public about the following findings.

“Swab testing of a sample of communal workplace kitchens showed that 75% of work surfaces were home to more bacteria than an average feminine sanitary bin. Half also harboured dangerously high levels of coliforms, bacteria present in feces, which can lead to outbreaks of gastrointestinal disease. Over a quarter of the draining boards tested registered more than four times the level of coliforms considered to be safe.”

“The handles of shared fridge-freezers were also shown to be bacteria-rife, with a third carrying high levels of coliforms, whilst 30% of shared microwaves were also shown to be contaminated around the handles and buttons.”

“Tea drinkers were no more hygienic, with over 40% of kettle handles found to be carrying high levels of bacteria, and significantly exceeding the bacteria levels on toilet doors. Also, tested were cupboard, dishwasher and waste bin handles, with the cleanest appliance in the kitchen proving to be the water cooler.”

Speaking of toilets, they seem to be in vogue in metabolome studies. For example, Emma Innes reported online that women’s handbags contain more bacteria than the average toilet seat. The dirtiest item in an average handbag is hand cream—it carries more bacteria than the average toilet seat. Leather handbags carry the most bacteria because the spongy texture provides “perfect growing conditions.” An online article by Harold Maass noted that British researchers found that the average barbecue grill in the UK has more than twice as many germs as the typical toilet seat. Maybe someone has already invented a disposable barbeque grill cover similar to what’s used to cover toilet seats, but obviously nonflammable.

Sanitor Mfg Co. began producing toilet seat covers and dispensers in the USA in 1931.  Seems they are working as your handbag and your barbeque may both harbor more germs than a toilet seat.

Sanitor Mfg Co. began producing toilet seat covers and dispensers in the USA in 1931. Seems they are working as your handbag and your barbeque may both harbor more germs than a toilet seat.

Although humorously entitled as Lifting the lid on toilet plume aerosol, this review article recently published the American Journal of Infection Control examines the evidence regarding toilet plume bioaerosol generation and infectious disease transmission. Here’s a quote of the results of this review of existing literature. “The studies demonstrate that potentially infectious aerosols may be produced in substantial quantities during flushing. Aerosolization can continue through multiple flushes to expose subsequent toilet users. Some of the aerosols desiccate to become droplet nuclei and remain adrift in the air currents. However, no studies have yet clearly demonstrated or refuted toilet plume-related disease transmission, and the significance of the risk remains largely uncharacterized.” Like many investigations, the stated conclusions call for more data: “[a]dditional research in multiple areas is warranted to assess the risks posed by toilet plume, especially within health care facilities.

By the way, the internet has various references to a 6-foot diameter (dare I say) zone wherein toilet aerosol may spread, so keep your toothbrush at a safe distance or consider purchasing a toothbrush sanitizer—of which there are many—after doing your homework on which devices have been validated, and against what, as I did by searching PubMed for “toothbrush sanitizer” etc.

Mycobiome:   Fungus In, On and Among Us

Oh…let’s not forget about fungus—a member of a large group of microorganisms that includes yeasts and molds, as well as mushrooms. These organisms are classified as a kingdom, Fungi, and the discipline of biology devoted to the study of fungi is known as mycology. My PubMed search of “mycobiome” gave only 10 hits, which is far less than ~4,000 found for “microbiome.” The earliest mycobiome publication was entitled “Characterization of the oral fungal microbiome (mycobiome) in healthy individuals” by Mahmoud A. Ghannoum et al. (PLoS Pathogens 2010). This study—which used pyrosequencing to characterize fungi present in the oral cavity of 20 healthy individuals—revealed the “basal” oral mycobiome profile of the enrolled individuals and showed that across all the samples studied, the oral cavity contained 74 culturable and 11 non-culturable fungal genera. The oral mycobiome of at least 20% of the enrolled individuals included the four most common pathogenic fungi—Candida (present in 75% of the cohort; mostly C. albicans), Aspergillus (35%), Fusarium (30%), and Cryptococcus (20%). The authors said that “[i]t is possible that the pathogenicity of these fungi is controlled in healthy individuals by other fungi in the oral mycobiome, as well as a functional immune system.”

Candida albicans (Wikipedia via Bing Images)

Candida albicans (Wikipedia via Bing Images)

More recently, Heidi H. Kong and coworkers in Nature 2013 published a report entitled Topographic diversity of fungal and bacterial communities in human skin. This study involved 10 healthy individuals and used sequencing to analyze fungal and bacterial communities sampled from 14 skin sites that included face, chest, arms, ears, nostrils, head, and feet. Some salient points taken from the abstract are as follows.

“Eleven core-body and arm sites were dominated by fungi of the genus Malassezia, with only species-level classifications revealing fungal-community composition differences between sites. By contrast, three foot sites—plantar heel, toenail and toe web—showed high fungal diversity. Concurrent analysis of bacterial and fungal communities demonstrated that physiologic attributes and topography of skin differentially shape these two microbial communities. These results provide a framework for future investigation of the contribution of interactions between pathogenic and commensal fungal and bacterial communities to the maintenance of human health and to disease pathogenesis.”

Lastly, Who was First?

Who was “first-to-publish” and what was envisaged have always been of interest to me. In researching this posting, I became curious about who introduced the term “microbiome” to generally describe concepts of the type represented in the various aforementioned articles. It’s not easy to be find or establish “first-ever” publications, so I took the easy way out by doing a PubMed search wherein “microbiome” is in the title and/or abstract. Of the ~1,400 articles found, the earliest was entitled New technologies, human-microbe interactions, and the search for previously unrecognized pathogens by David A. Relman at Stanford University, and appeared in Journal of Infectious Diseases in 2002. The following conclusion from his abstract is quite prescient, and I’m amazed by how far and fast microbiome science has progressed since then.

“The development and clinical application of molecular methods have led to the discovery of novel members of the endogenous normal flora as well as putative disease agents. Current challenges include the establishment of criteria for disease causation and further characterization of the human microbiome during states of health. These challenges and the goal of understanding microbial contributions to inflammatory disease may be addressed effectively through the thoughtful integration of modern technologies and clinical insight.”

As always, your comments are welcome—especially if you know of a particularly interesting “microbiome” report that you’d like to share with me and other readers of this blog.


After writing this blog, GenomeWeb reported on August 8th that The Wellcome Trust has awarded $2 million to fund Lindsay Hall, a researcher at the University of East Anglia and the Institute of Food Research, who will seek to find out how bacteria that are beneficial to humans help protect against diseases in the early phases of life, using high-throughput sequencing tools to find out more about the microbial communities that colonize the human body soon after birth. “We are planning to use 16S rRNA-based microbiota community analysis, metagenome, and whole genome sequencing to define and characterize early-life microbiota samples,” Hall told GenomeWeb Daily News in an e-mail. The earliest parts of human life are a critical period in terms of the microbiome because at birth the human gut is completely bacteria-free, Hall explained, noting that the processes that follow birth and lead to microbial colonization are not fully understood. Having a better understanding of these processes could lead to treatments for diseases such as bacterial gastroenteritis, she said. This infectious disease is an increasing cause of infant death in the developing world, and the treatment involves antibiotics, but resistance to antibiotics is increasing and antibiotics also may reduce natural defenses against infection. Under this project, she will look to understand how antibiotics can disrupt these microbial communities, and search for probiotic bacteria.