Microbiota analysis, which is the study of microbial communities, is a quickly growing and developing area of scientific interest, with broad implications in human health and disease. These communities consist of bacteria, archaea, protists, fungi and viruses. The majority of non-pathogenic microbiome species form a commensal (mutually non-harmful) relationship with their human host. Others have mutualistic or symbiotic relationships; for instance, by producing vitamins used by the host. On the other hand, some non-pathogenic species are known to produce metabolites that are harmful to the host.

Research has only begun to unravel the effects and importance of microbiome composition on human health and disease, some of which have been unexpected. In addition to digestive and intestinal conditions, the human microbiome has been implicated in a diverse range of health issues such as metabolic conditions, cardiovascular disease, kidney disease, cancer and even psychiatric health.

The area receiving the most research and clinical attention is the microbial community living in the gastrointestinal tract, known as the gut microbiome, of which over one thousand bacterial species have been identified thus far. Other tissues on which microbiomes reside include skin, lungs, saliva, placenta and the female reproductive tract.

Gut microbiome testing services are rapidly gaining popularity. Following the trend set by genetic testing services, the majority of testing companies offer direct-to-consumer services, without requiring physician approval. Consumers or patients submit a stool sample for analysis in the hopes of gaining insights into health conditions. Some companies also provide personalized dietary and lifestyle recommendations for health and weight loss based on gut microbiome analyses. While the gut microbiome is by far the most frequently commercially tested, services can also test skin, an oral swab or saliva.

There are varying opinions within the medical community as to the value of microbiome testing for most patients and consumers, and clinicians have voiced concerns about patients left to interpret results without medical guidance and how meaningful the data are. The cost and level of analysis provided by commercial testing services can vary widely, depending on the testing method being used.

There are several approaches used for research, clinical diagnostic and direct-to-consumer testing to either identify or profile the microbial composition present in a sample. Identification determines whether a microbial species is present or absent in a sample, while profiling determines the relative expression levels of microbes under experimental conditions. NGS methods are the most common approach, but microarrays are also used. There are two common NGS-based methods for analyzing the human microbiome: shotgun metagenomic sequencing and 16S rRNA sequencing.

Shotgun metagenomic sequencing randomly shears the total DNA of all organisms in a microbiome sample into short fragments, sequences the fragments and relies on bioinformatics to reconstruct them into a consensus sequence, yielding genes present in the sample. This provides information not only about microbiome species composition, but also the possible metabolic processes encoded by the genes present in the community. Shotgun metagenomic sequencing is the most in-depth of the commonly used profiling methods, and the most expensive to perform. Because of the huge amount of sequencing data generated, this method requires a large-scale NGS sequencer or a higher-end benchtop sequencer.

16S rRNA sequencing takes advantage of the 16S ribosomal RNA gene sequence, thought to be present in all bacteria. The gene has highly conserved regions that are targeted by sequencing primers, as well as hypervariable regions that provide species-specific signatures by which bacterial species can be identified. This is the quickest and most inexpensive method for identifying bacterial members of a microbiome sample. However, this method has several limitations. Compared to shotgun metagenomic sequencing, 16S rRNA sequencing has lower resolution and sensitivity, capturing less diversity. Also, the technique is limited to identifying bacteria, and cannot detect viruses or fungi. 16S rRNA sequencing can be conducted using a benchtop NGS sequencer.

Microbiome arrays are collections of DNA probes, consisting of species-specific sequences from known microorganisms, fixed onto a glass slide. DNA from a microbiome sample is hybridized to the array, creating a signal if binding has occurred, which indicates the presence of a specific microbial species. Microbiome arrays are more sensitive than 16S rRNA sequencing, allowing detection of greater diversity. Comprehensive coverage includes archaea, bacteria, fungi, protozoa and viruses, encompassing over 11,000 species. However, detection is limited to known species that are specifically included on the array. Unknown species and species that have not been included cannot be detected.

The human microbiome has become a hot area of interest for researchers, clinicians and the general public, contributing to the strong demand for high-throughput sequencing and microarray technologies. As research continues to uncover how the microbiome affects health and disease, consumer demand will only grow.

Microbiome Testing at a Glance:

Leading Vendors

• Illumina
• Thermo Fisher Scientific
• QIAGEN

Largest Markets

• Hospital and Clinical
• Direct-to-consumer
• Academia

Instrument and Array Costs

• Microbiome Arrays: $2,000/plate (24 arrays per plate)
• Microarray Scanner Instrument: $35,000–$175,000
• Benchtop Sequencer: $80,000–$250,000
• Large-scale Sequencer: $125,000–$400,000