Genetically Modified Microorganisms - Subtopic Landscape

A synthetic biology perspective

The subset of SynBio – genetically modified microorganisms related patents were further investigated to identify subtopics and assess trending areas. The topic model leverages a hybrid approach based on the optimised extractive summary for each publication. Using a combination of topic discovery via fine-tuned transformer based deep learning and ground truth cross referencing via keyword and classification codes. The process enables a patent to belong to more than one topic for accurate multi-classification trends, accounting for multiple invention embodiments. Please see the topic model page for further details regarding the topic model methodology to avoid duplication here.

Subtopic counts

The identified subtopics within the topic are shown in figure 1. The topics are ranked based on the total number of published applications since 2015. A patent application can be counted more than once as it can belong to multiple topics.

In figure 1, the analysis enables multilabel classification for each patent application, to account for multiple invention embodiments. Since 2015, approx.43% of the GMOs dataset was classified in the bacteria subtopic. Approx 40.8% of the dataset was classified in the viral subtopic. Yeast also represents an important microorganism within the field, with 18.1% of documents classified here and 13.4% of documents classified in the E.Coli subtopic, Food & probiotics (13.4%) and biofuels (4.8%) are important areas for GMOs research and development. E.coli is identified as a key microorganism in synthetic biology for efficiency of growth and established genetic engineering, whilst adeno-associated virus (AAV – 20.6%) is a leading platform for gene therapy due to its effectiveness in therapeutic gene delivery.

Bacillus type bacteria (5.9%) have diverse applications but are recognised biocontrol agents in agriculture, acting as versatile cell factories. Bacillus thuringiensis naturally produces insecticidal toxins and is a prominent biocide used in pest control. Bacillus subtilis has a highly efficient protein secretion system and adaptable metabolism, unsurprisingly it has diverse applications as a cell factory producing chemicals, enzymes and antimicrobials. The Corynebacterium species and in particular Corynebacterium glutamicum, has great potential for producing high value chemicals and is an emerging host for expressing heterologous proteins. Algal biofuels could become one of the highest energy and carbon efficient bioproduction methods.

The GMOs subtopic publication year trends are shown in figure 2. Publication trends discussed below are based on EP A1/A2 applications, identified patents can belong to more than one subtopic due to multiple invention embodiments.

In figure 2 the fastest growing subtopics identified of note and based on compound annual growth rates during 2016-24 were Adeno-Associated Virus & Adenovirus (31.7%), Saccharomyces Cerevisiae (28.9%), Corynebacterium (26%), Viral (25.9%), Bacillus species (19.6%) and fungal / yeast isolates (18.7%).

Subtopic top 20 assignees distributions (published since 2015)

The patent portfolios of the top 20 assignees within the dataset are analysed in figure 3. The portfolios are restricted to publications during 2015-24, mapped to the subtopics identified, the counts represent total EPO publications.

The heatmap in figure 3 reveals the distribution of the top 20 assignees since 2015, publications can be assigned to more than one subtopic, reflecting multiple invention embodiments. CJ CHEILJEDANG have a large distribution in the bacteria subtopic (345 publications) and this appears to be heavily influenced by the Corynebacterium subtopic (201 publications). DANISCO & NOVOZYMES are leading assignees within the biofuel subtopic and the Bacillus species subtopic. The food and probiotics subtopic is led by CHR HANSEN (63 publications) & DSM IP ASSETS (50 publications).

The analysis does not account for earlier publications prior to 2015, which may have contributed to companies developing market share, etc. and potential licensing and acquisitions (subsidiaries). The analysis is an informative guide as some specific subtopics have strict content boundaries to enable differentiation, whilst others are broader to capture more generic areas.