40 Microbiome Statistics & Trends Changing the Industry in 2024

The microbiome industry is experiencing rapid growth and transformation, driven by advancements in sequencing technologies, increased funding, and innovative research. This blog article compiles 40 key statistics that highlight the significant changes and trends in the microbiome field in 2024.

Covering aspects from market size and segmentation to machine learning applications and insights from major conferences, this article provides a comprehensive overview of the current state and future potential of microbiome research and its applications in health and disease management.

Whether you’re a researcher, clinician, or industry professional, these statistics offer valuable insights into the evolving landscape of microbiome science.

40 Statistics Changing the Microbiome Industry in 2024

10 Microbiome Sequencing Market & Segment Statistics

From a recent report published by Allied Market Research, we can get a good picture of the state of the microbiome sequencing market in 2024.

 The report provides detailed insights into market valuation, growth rates, and segment performances, highlighting the significant advancements and investments in microbiome sequencing technologies. This data underscores the expanding opportunities and increasing importance of microbiome research in healthcare and disease management.

Key statistics from this report on the current state of the microbiome sequencing market include:

1. The global microbiome sequencing market size was valued at $859.4 million in 2021, and is projected to reach $3,417.09 million by 2031.
2. The market is growing at a compound annual growth rate (CAGR) of 14.8% from 2022 to 2031.
3. The market is segmented into shotgun sequencing, RNA sequencing, targeted gene sequencing, whole-genome sequencing, and others. The RNA sequencing segment accounted for the largest market share segment by technique. The shotgun sequencing segment exhibited the highest growth during the forecast period.
4. The market is bifurcated into outsourced and internal research, with outsourced research accounting for the largest research share in 2021.
5. The market is segmented by end user into pharmaceutical & biopharmaceutical companies and academic centers & research centers, with the academic centers & research centers segment accounting for the largest end user market size in 2021.

Additional research by Global Market Insights digs deeper into specifically the topic of the human microbiome market size and segmentation. Key statistics from this report show that:

1. In 2023, the Human Microbiome market size was valued at $842.36 million, with an estimated market value of $6.47 billion in 2032.
2. The market is expected to grow at a compound annual growth rate (CAGR) of 25.7% from 2024 to 2032.
3. The market segmentation is split into three. These segments include: Digestive Tract, Therapeutics, and Infectious Diseases. 
4. In 2022, the Digestive Tract segment held a 31.9% market share, and the Therapeutics segment held a 65.2% market share.
5. In 2022, the Infectious Diseases Segment was valued at $278.2 million.

10 Human Gut Microbiome Market Trends & Restraints Statistics

The aforementioned Global Market Insights report goes on to highlight some key trends and restraints in human microbiome research. An additional study by Research & Markets includes a market trends report and forecast that also provides some interesting insights into the trends and challenges shaping the industry.

Key statistics from these reports state that:

1. Probiotics will remain the largest segment between 2018 to 2030 due to increasing health concerns; growing awareness of the relationship between nutrition, diet, and health; and increasing penetration of the probiotic market in dairy and other foods.
2. Infectious disease will remain the largest disease type between 2018 to 2030 due to increasing cognizance of the negative effects of antibiotic use on the natural flora (such as disruptions), which has highlighted the need for specific bacterial-targeted therapies for infectious diseases.
3. In 2021, the Federal Government of the U.S. spent USD 864 million on microbiome research and development.
4. The Federal Government of the U.S. is expected to spend USD 903 million on microbiome research and development in 2022.
5. Navigating regulatory processes for microbiome-based therapies involves extended timelines and substantial financial investments.
6. The development of microbiome-based therapies requires comprehensive research and clinical trials, contributing to high development costs.
7. Human Microbiome By Product [Value (By Highest $ Million) from 2018 to 2030]: Prebiotics, Probiotics, Food, Medical Food, Drugs.
8. Human Microbiome By Disease Type [Value (By Highest $M) from 2018 to 2030]: Infectious, Metabolic/ Endocrine, Cancer, Blood, Neurological.
9. Human Microbiome By Research Technology [Value (By Highest $M) from 2018 to 2030]: Proteomics, Metabolomics, Genomics.
10. Human Microbiome By Application [Value (By Highest $M) from 2018 to 2030]: Therapeutics, Diagnostics.

10 Microbiome & Machine Learning Applications Statistics

Figure 2: This figure provides an overview of the microbiome workflow for studying microbial communities using shotgun sequencing, 16S rRNA gene sequencing, metatranscriptomics, metaproteomics, and metabolomics. The figure illustrates the process of sample collection from various sites and then proceeds through different experimental procedures, bioinformatics pipelines, and ML analyses. 

In a recent report published by NCBI titled ‘Microbiome and machine learning applications: categorization, accessibility, and future directions’, researchers explored the latest developments in how machine learning capabilities can integrate with microbiome sequencing methods and microbiome data analysis.

These insights highlight some key examples of successes in ML and microbiome study, across a range of applications.

Key statistics from this report relating to recent developments in the applications of machine learning in microbiome studies include:

1. Mihajlović et al. (2021) employed a random forest (RF) model to classify Inflammatory Bowel Disease (IBD), achieving an average F1 score of 91%.
2. Liñares-Blanco et al. (2022) generated a metagenomic signature using RF, achieving AUC scores of 0.74 and 0.76 for Ulcerative Colitis (UC) and Crohn’s Disease (CD), respectively.
3. Bakir-Gungor et al. (2021) used RF to develop a classification model for Type 2 Diabetes (T2D) diagnosis, highlighting a subset of 15 commonly selected features.
4. Bhattacharya et al. (2022) implemented ML for geospatial microbial provenance with accuracy rates ranging from 85 to 89% for city classification and 90 to 94% for continental classification.
5. Leung et al. (2022) integrated metagenomics, metabolomics, and clinical data to classify participants’ NAFLD status, achieving an overall AUROC score of about 93%.
6. Pasolli et al. (2016) analyzed 2,424 publicly available datasets using an ML-based framework, focusing on species-level abundances and strain-specific markers.
7. Gupta et al. (2020) introduced the Gut Microbiome Health Index (GMHI), which evaluated disease presence likelihood from a dataset of 4,347 publicly available human stool metagenomes.
8. Casimiro-Soriguer et al. (2022) performed a meta-analysis of 1,042 fecal metagenomic samples using an ML pipeline, achieving high accuracy in predicting colorectal cancer (CRC).
9. Lugli et al. (2023) utilized 10,935 metagenomic profiles to study bacterial genetic diversity in the infant gut microbiome, identifying critical bacterial signatures.
10. Nelkner et al. (2023) conducted a meta-analysis using data from 16 primary studies, examining microbial communities in agricultural soils across Europe, emphasizing standardized metadata reporting.

10 Key Statistics From the 2024 Gut Microbiota for Health World Summit

As recent news reports highlight, the 2024 Gut Microbiota for Health World Summit brought with it a number of insights and developments in the world of the microbiome. These findings showcase the latest advancements in microbiome research, therapeutic innovations, and the profound impact of gut health on overall well-being. 

Here are some key statistics and insights from the summit:

1. Eran Elinav, MD, PhD found that Klebsiella pneumoniae strains induced gut inflammation and T helper 1 (Th1) cells in IBD models and identified a 5-phage combination that suppressed gut inflammation in these models.
2. Ken Croitoru, MD & The GEM Project recruited 5,000 healthy first-degree relatives of Crohn’s patients in 2008, and 112 developed Crohn’s disease (80% siblings; 20% offspring). They found that gut microbiome composition, analyzed using 16S ribosomal RNA sequencing, is associated with the future onset of Crohn’s disease. 
3. The GEM Project also discovered that a Mediterranean diet is associated with increased abundance of Faecalibacterium and lower levels of subclinical gut inflammation, defined by fecal calprotectin.
4. Through his company and bio-product, Daniel van der Lelie, PhD, MBA, found that GUT-108 reversed colitis in a humanized chronic T-cell–mediated mouse model and produced metabolites promoting mucosal healing and immunoregulatory responses.
5. In nine randomized controlled studies, Dina Kao, MD, found FMT induced clinical remission in 33% of patients with mild to moderate ulcerative colitis (vs 16% with standard treatment) and endoscopic remission in 15% of FMT patients (vs 9% with standard treatment).
6. Research by Iliyan Iliev, PhD showed that mucosal washings in UC patients contained high levels of Candida spp., with Candida albicans being the most immunogenic and secreting the toxin candidalysin in high-damage strains.
7. Research by Jack Gilbert, PhD found colorectal tumors in 88% of mice fed a Western diet, given antibiotics, and treated with surgery and an enema containing a collagenolytic strain of Enterococcus faecalis, compared to 30% of mice fed a standard diet with the same procedures.
8. A team led by Nathan Price, PhD, found that 45% of the variance in gut microbiome alpha diversity was explained by a subset of 40 plasma metabolites in a cohort from a consumer wellness program.
9. Research by Meng Wu, PhD, showed that complement component 3 (C3) gene expression was found in colon tissue and lymphoid follicles in mice, with the microbiome inducing luminal complement C3 secretion even when transmitted to germ-free mice. Her research indicated that basal C3 levels induced by the gut microbiome are correlated with the susceptibility and severity of infectious diarrhea.
10. In the PREDICT-1 study by Sharon Donovan, PhD, RD, continuous glucose monitoring (CGM) devices showed strong concordance in monitoring glycemic responses, suggesting their potential use in personalized nutrition. 

What You Can Do With This Data

Researchers can leverage these statistical insights in a number of ways to drive future studies and clinical applications in microbiome science. 

By focusing on areas such as disease prediction, dietary interventions, and therapeutic developments, scientists can enhance our understanding of the gut microbiome’s role in health and disease. Additionally, integrating advanced sequencing technologies and machine learning models can lead to more personalized and effective treatments.

Here are some actionable steps and applications based on the data provided:

• Explore opportunities for funding, considering that significant investments are being made (e.g., USD 903 million in 2022 by the U.S. Federal Government). Collaborate with institutions benefiting from such funding to maximize research outcomes.
• Prioritize research in RNA sequencing and shotgun sequencing, the segments showing the largest market share and highest growth. These methodologies are essential for comprehensive microbiome analysis.
• Investigate the potential of novel biotherapeutic products like GUT-108, which have shown efficacy in reversing colitis in mouse models.
• Apply machine learning models, such as Random Forest (RF), for disease classification and biomarker discovery. For example, RF models have achieved F1 scores of 91% for IBD classification and AUC scores of 0.74 and 0.76 for UC and CD, respectively.
• Implement ML for geospatial microbial provenance and personalized nutrition research, leveraging models that integrate metagenomics, metabolomics, and clinical data.
• Employ state-of-the-art sequencing platforms like the CosmosID-HUB for diverse sequencing needs, including deep shotgun metagenomic sequencing, metatranscriptomics, and metabolomics. These technologies enable precise and comprehensive microbiome analysis.
• Investigate the therapeutic potential of fecal microbiota transplantation (FMT) for conditions beyond Clostridioides difficile infection, such as ulcerative colitis. With clinical remission rates of 33% in UC patients, FMT represents a promising treatment avenue.
• Utilize findings from studies like PREDICT-1 to integrate continuous glucose monitoring (CGM) devices into personalized nutrition plans. These devices have shown strong concordance in monitoring glycemic responses, aiding in the development of tailored dietary interventions.
• Plan for extended timelines and substantial financial investments when navigating regulatory pathways for microbiome-based therapies. Engage in comprehensive research and clinical trials to ensure safety and efficacy.
• Study the role of complement component 3 (C3) in gut immunity, as its gene expression is influenced by the microbiome and correlates with susceptibility to infectious diarrhea. Understanding these interactions can inform new therapeutic strategies.

Closing Thoughts

At CosmosID, we are committed to enabling research that pushes the boundaries of our understanding of the microbiome. Statistical analysis of microbiome data and insights gathered from recent studies and market reports highlight the rapid advancements and immense potential in this field. By leveraging cutting-edge sequencing technologies, integrating machine learning, and exploring innovative therapeutic applications, we can uncover new dimensions of health and disease management.

Our mission is to support researchers and clinicians with state-of-the-art tools, next-generation sequencing services, plus comprehensive bioinformatics and data analytics, empowering them to make ground-breaking discoveries and translate them into real-world applications. 

Whether it’s enhancing diagnostic accuracy in human health, developing personalized nutrition plans, or pioneering new microbiome-based therapies, the possibilities are vast and exciting.

For more information on microbiome sequencing types and methodologies, visit Clinical Microbiomics today.

Microbiome Statistics FAQs

How big is the microbiome industry?

The microbiome industry is rapidly expanding, driven by significant investments and advancements in research. In 2021, the global microbiome sequencing market was valued at $859.4 million and is projected to reach $3,417.09 million by 2031, growing at a compound annual growth rate (CAGR) of 14.8%. The human microbiome market size in 2023 was valued at $842.36 million, with an estimated market value of $6.47 billion by 2032, growing at a CAGR of 25.7% from 2024 to 2032.

How many microbiome companies are there?

While the exact number of microbiome companies varies, the industry includes numerous key players focusing on different aspects of microbiome research and application. Companies are leveraging the vast potential of microbiome and metabolomics data to develop innovative solutions in health and disease management. The rise in the number of startups and established firms entering the market highlights the growing recognition of the importance of human gut microbiota and its role in human health.

What is microbiome engineering?

Microbiome engineering involves the manipulation of microbial communities to achieve desired health outcomes. This field encompasses various techniques, including the modification of bacterial species and the use of operational taxonomic units to understand and influence microbiome composition. By accounting for environmental factors and utilizing advanced statistical methods, researchers can enhance downstream statistical analysis to develop targeted therapies and improve gut health.

What are microbiome-based therapeutics?

Microbiome-based therapeutics are treatments developed to modulate the human microbiota for improved health outcomes. These therapies include probiotics, prebiotics, and biotherapeutics like GUT-108, which have shown promise in reversing conditions such as colitis. By harnessing the power of microbiome and metabolomics data, researchers can create personalized treatments that address specific bacterial imbalances and leverage the complex interactions within the gut microbiota to combat diseases.