Trends in Microbiome Analysis

The microbiome, a complex ecology of billions of bacteria that inhabit the bodies, has received considerable attention in recent years. Bacteria, viruses, fungi, and other microbes are essential to overall health and well-being. The methods and techniques used to investigate the microbiome evolve in tandem with understanding it.

The microbiota is responsible for the well-being, and sicknesses have been featured in various examinations since its disclosure. Depending on the localized regions, microbiota can be categorized into gut, oral, respiratory, and skin microbiota. The microbial networks interact advantageously with the host, adding to homeostasis and directing safe capability. Notwithstanding, microbiota dysbiosis can prompt dysregulation of ordinary physical processes and sicknesses, including cardiovascular illnesses (CVDs), malignant growths, respiratory infections, and so on.

Omics Approach

Omics approaches for microbiome analysis  Microbiomes are comprehensively analyzed by simultaneously assessing thousands of molecules within biological samples, including DNA, RNA, proteins, and metabolites. This is accomplished through various -omics technologies like metagenomics, metatranscriptomics, metaproteomics, and metabolomics. There’s a growing trend of employing two or more of these -omics technologies in tandem, a practice now referred to as “trans-omics analysis.”

Sequencing Method

16s rRNA amplification identifies and validates the type of microorganisms present in a sample, and total DNA sequencing is performed to identify the community’s functions. Sequencing can be categorized by type and technology; a few are discussed below.

16S and Internal Transcribed Spacer (ITS) ribosomal RNA (rRNA) sequencing are prevalent amplicon sequencing techniques employed for the identification and comparison of bacteria and fungi present in a given sample.

Shotgun metagenomic sequencing has the capability to merge numerous microbial sequencing samples into a single operation while achieving extensive sequence coverage for each sample. This method detects extremely low-abundance microbial community members, which might need to be noticed when employing alternative techniques.

In contrast to hybridization-based techniques like microarrays, microbial RNA sequencing allows for an impartial and strand-specific identification of well-known and newly discovered transcripts.

Next-generation sequencing (NGS)–based, whole-genome sequencing (WGS) empowers microbiology researchers to sequence numerous organisms simultaneously through the advantages of multiplexing. This approach eliminates the need for labour-intensive cloning steps that are typically associated with traditional methods.

Key Findings: Microbiome Sampling Collection and Analysis

• Smart Toilet: Biomesense has introduced GutLab^TM, an automated laboratory system compact enough to be placed next to a household toilet. It conducts daily analysis of an individual’s gut microbiome.
• Smart Toilet Paper: Harvard University has developed a groundbreaking project that uses smart, disposable toilet paper to change the way of tracking gut health. Unlike traditional methods, which can be costly and complicated, this approach offers a simple and affordable way to monitor the gut microbiome. It helps users to make more precise adjustments for treatments and dosages. The goal of this project is to create a practical, easy-to-use tool that makes managing gut health more accessible to everyone.
• Wipes: Thorne has transformed stool collection for its Gut Health Test with an innovative wipe-based method. The dissolvable polymer wipe works like regular toilet paper and is placed in a DNA-stabilizing solution after use. This simple, user-friendly approach makes gut health testing more convenient and accessible, encouraging broader adoption of microbiome analysis.
• Ingestible Sensor: Atmo Biosciences has developed an Atmo® Gas Capsule, which is an unprecedented ingestible gas-sensing capsule offering distinctive insights into gut health and the functioning of the microbiome.
• Ingestible pill: Researchers recently announced in ACS Nano that they’ve created an ingestible capsule. When tested in rats, this capsule successfully collected bacteria and other biological samples as it traversed the gastrointestinal (GI) tract. BioMe has created a technology that enables the collection of gut microbiome samples in a minimally invasive and affordable way. It is achieved using a pill-sized medical device designed for precise and non-invasive sampling of the human gut microbiome.
• Patches: Inc. has developed a sample collection kit featuring adhesive patches. These patches are applied to the skin, where they effectively gather layers of epidermal cells along with any microbiome present on or between these skin cells.
• AI: Cargill and Agxio have developed an AI-based microbiome rules-based analytics engine that compares any combination of biomarkers to target ranges using an automated, rules-based methodology. The engine can then identify probable disease risks and recommend preventative or corrective activities as part of an automated report system to improve individual human or animal health and performance.
• Personalized Microbiome Testing: DayTwo offers microbiome sequencing to provide personalized nutrition guidance. It combines microbiome insights with metabolic data, its platform delivers customized dietary recommendations for optimizing blood sugar levels, enhancing metabolic health, and supporting individual wellness objectives.

Microbiome Modulation Solutions

• FMT: One method for restoring the dysbiotic gut is fecal microbiota transplantation (FMT) from healthy donors. Therapeutic candidates for the microbiome are likely to be approved in early 2023, opening the door to future biologics license applications (formal documentation necessary by the FDA to commercialize a novel medication).

• Ferring Pharmaceuticals (Switzerland) has won FDA permission to treat Clostridium difficile with a fecal microbiota therapy, beating out Seres Therapeutics, which is set for an FDA decision in April 2023.

• CRISPR: SNIPR Biome is developing CRISPR-based microbiome therapeutics for human trials. Their patented adaption of natural CRISPR systems enables accurate targeting of the targeted bacterial species while minimizing the development of treatment resistance. Another company, Eligo Biosciences,  has developed a primary therapeutic candidate, EB003, using the company’s patented Sequence- Specific Anti- Microbials (SSAM) platform. SSAM is based on delivering a non-replicative DNA payload encoding an exogenous Cas nuclease directed towards a specific genomic sequence.

• Next-generation Probiotics: The development of genetically engineered probiotics, often called “next-generation probiotics,” uses modified strains of bacteria to target specific health conditions, such as inflammatory bowel disease (IBD) or metabolic disorders. Pendulum Therapeutics creates microbiome therapies that can directly affect metabolic pathways.

• Other Ingredients/Technologies: Other ingredients and technologies which are used for microbiome modulation are prebiotics, organic acids, phytogenic or essential oils, gut health enzymes, postbiotics, biome-actives, stimbiotic, synbiotics, precision glycan, engineered microbes, phage therapy, feed ingredients (seaweed), etc.

Key Innovations

These market players are bringing innovative solutions in microbiome analysis and modulation solutions:

Market Activities

By 2030, the global microbiome market is anticipated to be worth USD 15.55 billion, growing at a CAGR of 11.4%. The microbiome industry can be categorized into various segments based on its applications, including human therapeutics, human diagnostics, agriculture, environmental, food and feed, and others. In 2020, the agriculture and environmental sector held the most significant share of the microbiome market by end-use, making up 39.2% of the total. In the future, it is projected that the human diagnostics sector will experience the highest growth rate within the microbiome market by end-use, with a compound annual growth rate (CAGR) of 18.0% anticipated during the period from 2020 to 2025.

Conclusion

As mentioned in this article, the microbiome study is a rapidly developing and dynamic field that continues to provide ground-breaking insights into human biology and health. More innovative applications and discoveries in microbiome analysis have the potential to transform healthcare and enhance comprehension of the intricate relationship between the body and its microbial companions. With customized medication, psychological well-being, resistance, ongoing sicknesses, natural microbiomes, and maturing at the very front of exploration, the future of microbiome science holds an extraordinary commitment to improving human well-being and prosperity.