Microbiome Research: Don’t Forget The Fungi
Microbial Interactions In Living Systems
The emerging field of the microbiome is in pursuit of understanding the microbe-microbe and microbe-host interactions that occur in virtually all living systems. This includes interactions critical to plant and animal health. The fundamental question is: What role(s) do the microbes and their functions play in broader systems?
Advancements in technology, such as next generation sequencing, have allowed us to overcome the barriers of culture-dependent methods of identification and classification, providing the ability to sequence and identify a more complete community of microbes in any given sample with a high degree of sensitivity and reproducibility.
It seems, however, that the term ‘microbiome’ tends to implicitly refer to commensal and pathogenic bacteria, with very little attention paid to the role of eukaryotic organisms. As such, the field is heavily utilizing 16S amplicon sequencing to increase our understanding of these bacteria. But what about other amplicons such as 18S or ITS (internal transcribed spacer) that shed light on eukaryotic or fungal communities?
In recent years, there have been more published data elucidating the presence and contribution of fungi in certain disease states. These fungi have been shown to interact with bacterial communities in either a synergistic or competitive manner. In either relationship, these fungi may be a critical component of the progression of such diseases—including hepatitis B, cystic fibrosis, and even inflammatory bowel disease. As a result, researchers have coined the term ‘mycobiome’ to refer to the communities of fungi that may play an interesting role in the system.
The human body is a unique ecosystem, and we have long known mucosal sites are abundant with fungal flora. What we are beginning to identify is how these communities interact with other sites across the body, where bacterial communities reside. Besides the specific diseases associated with fungi, we are seeing evidence that overall gut health is maintained by a degree of fungal-bacterial interaction. Mechanistically, the mycobiome appears to play a role in inflammation and metabolism by modulating the bacterial microbiome.
Environmental microbiomes are also of growing interest in the microbiome field, with a particular focus on ocean microbiomes, air pollutants, and soil microbiomes. In soil microbiomes, where fungi are prevalent, researchers are interested in certain subcategories; studies focus on the soil microbiome, the plant/rhizosphere microbiome, or the point at which these two microbiomes interact, which is called the mycorrhizosphere. The fungal component of these microbial communities plays a critical role in the nutrition and growth of plants as well as in the exclusion of plant diseases. Mycorrhizal fungi have even been shown to mediate signaling between plants.
Amplicon Sequencing: 16S, 18S, & ITS
Unlike other next generation sequencing labs that have exclusively focused on the approaches of molecular biology and genomics, Microbiome Insights also pulls from expertise in microbial ecology and infectious disease to provide a more complete picture of the ecosystem. We have implemented standardized protocols for 16S (Prokaryotic) sequencing and have developed robust workflows for both 18S (Eukaryotic) and ITS2 (fungal) sequencing using the Illumina Miseq. We apply these approaches as necessary to address specific scientific questions, and can build on this data using shotgun metagenomic sequencing. Altogether our expertise allows us to provide our customers with a full suite of tests—without forgetting the fungi.