October 30, 2013 –
Nelson: “We know now that we’re covered in microbes. … We’re just starting to understand what these microbes do.”
Over the past couple of decades, research into human biology has revealed some startling information. It turns out, that in addition to our 10 trillion human cells, we are hosts to one hundred trillion microbial cells which greatly contribute to our health (or lack thereof). We are actually individual ecosystems, and those ecosystems vary widely based on where we live, what we eat and our genetic composition.
The DNA of the microbiome, as our collection of hundreds of species of microbial friends is known, contains approximately 3 million genes – over 100 times the 23,000 genes that constitute our human DNA.
Thanks to advances in DNA testing, researchers are learning more about who these microbes are and the services they provide our bodies: they aid in digestion, synthesize vitamins and help to regulate certain bodily functions. It’s also possible that certain diseases can be treated by modifying the microbiome – adding certain microbes to the mix or killing off specific troublemakers, for instance.
In fact, the microbiome may have a tangible link to several auto-immune diseases: diabetes, rheumatoid arthritis, muscular dystrophy, multiple sclerosis, fibromyalgia and maybe even some cancers.
This approach to understanding human well-being was the focus of a symposium last month in the CALIT2 Building. “Microbiome Connections to Health and Disease,” sponsored by CALIT2 and UC Irvine’s Institute for Genomics and Bioinformatics, featured six experts in the field who shared their findings in this relatively new research area.
Karen Nelson is president of the J. Craig Venter Institute, a non-profit genomics research institution in Rockville, Md. (with a branch open soon in La Jolla, Calif.). This “bioneer” led the genetic sequencing in 2006 of the first human gut microbiome, and has sequenced many other parts of the microbiome as well.
From left, Li, Raffatellu, Vaziri and Underhill discussed their research on the human microbiome.
Nelson shared with the audience the progress of high-throughput genetic sequencing in simple terms. In 1996-97, she told the audience, the genome sequencing of the first living organism – Haemophilus influenza – took two years and $2 million to complete. Today, Nelson said, the same project could be completed in an afternoon for a fraction of that cost.
This is good news, since despite their best efforts, scientists still cannot cultivate in a lab the majority of the microbes that live in and on our bodies. But as sequencing techniques improve and costs decrease, researchers are able to extract DNA from almost any environment, gaining a richer understanding of its physiology.
Nelson gave a brief history of the Venter Institute, along with a glimpse into its founder, J. Craig Venter. Among his many accomplishments: In 2002-03 he sequenced 2 million genes from a vial of water he had collected from the Sargasso Sea. “He essentially doubled the number of predicted protein sequences in the GenBank overnight and identified an estimated 1800 species and 1.2 million new genes from a single vial of water,” Nelson said, vastly increasing knowledge about the world’s biodiversity.
Her group at the Venter Institute examines microbial diversity in humans, primarily along the gastro-intestinal tract. While genomic sequencing is “easy and fun,” she said, it’s important to recognize the role of the other ‘omics’ – proteomics, transciptomics, metabolomics, viromics and more – in understanding the metabolic capabilities of the human microbiome.
“We know now that we’re covered in microbes. … We’re just starting to understand what these microbes do – they’re essential to processing plant material, and for functioning of the GI tract, but the majority of the roles of these microbial species are unknown,” she said.
In 2007 NIH launched an initiative seeking to characterize the healthy microbiome. Metagenomes from 300 healthy people were sequenced to form a baseline of the healthy microbiome; to date, nearly 3,000 complete bacterial, viral and fungal reference genomes have been sequenced.
The Venter Institute currently is investigating the interface between the host and the microbiome in more than 24 disease-focused studies. “There are questions about any disease you can imagine: obesity, various cancers, acne, urinary tract infections, autism, various animal models, etc.,” Nelson said, emphasizing the institute’s “systems approach” to understanding disease. “We’re trying to identify new biomarkers that can be used as predictors of disease onset and progression. That’s our major goal.”
She is optimistic about the possibilities. “I think we’re in the early stages of understanding what the microbiome means to health and disease,” she said. “Now that we have technologies available … I think we’re going to be making significant inroads.”
Smarr: “It is clear we have a tightly-coupled, dynamic microbiome/immune system…”
Larry Smarr, founding director of CALIT2, knows a thing or two about the microbiome and its interactions with the human body. For the last five years, he has been self-sampling his own ecosystem – measuring and cataloging over time data from 150 variables present in his blood and fecal samples.
The human immune system in a healthy person, he said, is in constant homeostasis with its microbiome. But in those with autoimmune diseases, this give-and-take microbial ecology fails.
He shared several graphs with the audience that indicated his painstaking efforts and their ultimate result: he discovered he has an enduring – yet episodic – autoimmune disorder called Crohn’s disease. “I’m essentially in a state of chronic inflammation,” he said.
In 2011, after undergoing an MRI, he told his doctor, “Give me my data.” With the help of his CALIT2 virtual reality team, the slice-by-slice view of Smarr’s body became an interactive fly-through video game.
“The UCSD radiologist and I found that along about 10 centimeters of the sigmoid colon, when you look at it in cross-section, the wall is about 15 millimeters thick instead of 3. That’s because of the inflammation.”
Smarr sprang into action. Already a user of “23and me,” a health and ancestry DNA service, he found that he had a well-known genetic predisposition to Crohn’s. Since then he has had his whole human genome sequenced through Harvard’s Public Genome Project and is beginning the research needed to compare it with the microbiome genetic data he was collecting. He sees four-to-six month swings in his immune variables, including some such as lysozyme, a protein which bores holes through the walls of certain gut bacteria. “It is clear we have a tightly-coupled, dynamic microbiome/immune system, which can have oscillations like the El Nino/El Nina oscillations we see in Earth’s coupled ocean/atmosphere system.”
Key to understanding these fluctuations, he said, is measuring changes at different points in time of both the immune variables and the microbiome ecology. “And thanks to Karen [Nelson], who has graciously received my samples and sequenced them in her lab, I can now show you my gut microbial ecology in great detail,” he said to audience laughter. “We’re just now starting to analyze these coupled time series; it hasn’t been possible before.”
Smarr originally had refused any therapy until he could get enough data points to reveal the natural oscillation in his system. But persistent discomfort led him to a month of antibiotics and two months of prednisone, an immunosuppressant. Ever the scientist, he just added to his dataset. “The day after I stopped [the medications] I did another sample. So now I can compare directly the impact of therapy at the detailed strain level of the microbiome.”
Smarr’s FuturePatient team at CALIT2 at UC San Diego then retrieved human gut microbiome genetic information from the National Institutes of Health’s Human Microbiome Program for about 35 healthy patients and a number of IBD patients.
Following the genomic sequencing done at the Venter Institute, complex software pipelines, developed by UCSD’s Weizhong Li, processed 12.5 billion Illumina genomic sequencing “reads” on the San Diego Supercomputer Center’s Gordon supercomputer using about 25 CPU-years; Smarr says because their work was highly parallel, they did it in about 250,000 CPU-hours.
What they found was surprising: in the normal healthy gut microbiome, two main components (or “phyla”) dominate: Firmicutes and Bacteroidetes, whereas in his inflamed gut, Smarr found the Bacteroidetes had been reduced by 20-fold and in their place rarer phyla such as Proteobacteria, Fusobacteria and Euryarchaeota had taken their place.
Smarr compared the results to the aftermath of a forest fire, where certain rare species bloom to replace the primary ecological occupiers. “As medicine begins to include the microbiome in human health, it is going to profit from many decades of research into ecological dynamics,” he said.
Understanding the variation of these dynamics over time and over a wide variety of patients is the next step. Smarr is working with several groups to organize a double-blind clinical trial to study the microbiome in other patients with inflamed guts. “Then you can begin to separate the signal from the noise to start understanding the causal connections in this coupled immune/microbiome system.”
Other presenters in the half day symposium:
• Huiying Li, UCLA assistant professor of molecular & medical pharmacology and faculty affiliate at the California NanoSystems Institute, who discussed the human skin microbiome and its relationship to acne. The human skin microbiome plays important roles in skin health and disease. Bacterial population structure and diversity at the strain level, however, is poorly understood, according to Li. Propionibacterium acnes is a dominant skin commensal, but is also linked to acne vulgaris, one of the most common skin diseases.
Li and her team compared the skin microbiome at the strain level and genome level between acne patients and healthy individuals; metagenomic analysis demonstrated that while the relative abundances of P. acnes are similar, the population structure at the strain level is significantly different in the two cohorts. Certain strains were highly associated with acne and other strains were enriched in healthy skin. By sequencing and comparing a large number of P. acnes genomes, they identified potential genetic determinants of various P. acnes strains in association with acne or health. The study highlighted the importance of strain level analysis of the human microbiome to define the role of commensals in health and disease, she said.
• Manuela Raffatellu, M.D., UCI assistant professor of microbiology & molecular genetics, who explained why some bacteria thrive in the human gut while others don’t. Mucosal surfaces are often the first interface between the host, the commensal microbiota (trillions of bacteria) and pathogenic microorganisms. Among the most complex of these environments is the gut mucosa, where the commensal microbiota coexist with the host in a mutually beneficial equilibrium, she said.
Infection with enteric pathogens like Salmonella Typhimurium disrupts this equilibrium by causing intestinal inflammation, a response that suppresses the growth of the commensal microbiota and favors the growth of S. Typhimurium by several mechanisms. Infection with S. Typhimurium results in the upregulation of antimicrobial proteins that inhibit bacterial growth by limiting the availability of essential nutrients, including metal ions, in a process termed “nutritional immunity.” Dr. Raffatellu’s lab studies the mechanisms by which S. Typhimurium evades nutritional immunity and acquires metal ions in the inflamed gut, allowing this pathogen to successfully compete with the microbiota for these essential nutrients.
• Nick Vaziri, M.D., UCI professor of medicine, described the microbiome’s role in kidney disease and its relationship to seemingly unrelated organ system failures. Chronic kidney disease (CKD), he said, is associated with oxidative stress and inflammation, which contribute to the progression of kidney disease and its numerous complications. Until recently, little attention had been paid to the role of the intestine and its microbial flora in the pathogenesis of the CKD-associated inflammation.
Dr. Vaziri’s presentation provided an overview of the impact of uremia on the structure and function of the gut and its microbial flora, as well as their potential link to the associated systemic inflammation.
• David Underhill, associate director of immunology research, biomedical sciences, Cedars Sinai Medical Center, shared his research into immunity, inflammation and how cells recognize and react to fungi in the gut. Mucosal fungal infections are relatively common in Crohn’s Disease patients, and antibodies against fungal antigens (ASCA) are a well-accepted clinical marker for disease severity. However, what fungi populate the intestine and how immunity to them might play a role in inflammatory disease is currently unknown, he said.
Fungi are sensed by a number of innate immune receptors, among which Dectin-1, expressed on myeloid cells, is critical for host defense. Underhill found that commensal fungi populate the guts of rats and mice, and that Dectin-1-/- mice are more susceptible to experimental colitis characterized by increased infiltration of certain cells in the colon. Interestingly, this pathology is driven by intestinal fungus, and antifungal therapy ameliorated the severity of colitis in these mice. The data also demonstrated that altered interactions between the fungal microflora and the host mucosal immune system can profoundly influence intestinal pathology.
— Anna Lynn Spitzer
