Patent: 10,493,113

Summary for Patent: 10,493,113

Title:	Compositions and methods for treating disease using a Blautia strain
Abstract:	Provided herein are methods and compositions related to Blautia Strain A useful as therapeutic agents.
Inventor(s):	Goodman; Brian (Jamaica Plain, MA), Ponichtera; Holly (Cambridge, MA), Itano; Andrea (Arlington, MA), Cormack; Taylor A. (Dedham, MA), Sizova; Maria (Roslindale, MA), Kravitz; Valeria (Norwood, MA), Gavrish; Ekaterina (Natick, MA), Baez-Giangreco; Carolina (Boston, MA)
Assignee:	Evelo Biosciences, Inc. (Cambridge, MA)
Application Number:	16/190,735
Patent Claims:	see list of patent claims

United States Patent 10,493,113 (Blautia Strain A) Claim Analysis and US Patent Landscape

What does US10,493,113 claim, and how broad is the protection?

US 10,493,113 is directed to a method of treating a disease by administering a bacterial composition containing Blautia with high identity to a specified reference strain, Blautia Strain A (ATCC PTA-125346). Claim 1 is the keystone: it ties the method outcome (treating a disease) to a microbiological identity constraint (genomic/16S/CRISPR sequence identity) to a single deposited strain. Dependent claims then expand or cabin scope through identity thresholds, disease type, route of administration, composition concentration, live vs attenuated vs killed, and combination therapy.

Claim 1 (independent) is identity-defined and disease-agnostic

Claim 1:
A method of treating a disease in a subject comprising administering a bacterial composition comprising a Blautia strain comprising at least 90% genomic, 16S or CRISPR sequence identity to the nucleotide sequence of Blautia Strain A (ATCC PTA-125346).

Key scope levers in Claim 1:

• Identity criterion: “genomic, 16S or CRISPR sequence identity.” This is a structural constraint expressed as sequence identity across three modalities.
• Threshold: ≥90% identity is permissive relative to common “strain-level” standards in microbiome IP, enabling many related strains to plausibly fall within scope depending on how the identity is computed and what subsequences are compared.
• Composition and disease: no limitation on disease category in Claim 1. Disease limitation arrives in Claim 4 and Claim 6.

Claims 2–3 lock onto narrower identity and the exact deposited strain

• Claim 2 raises the identity threshold to ≥99% genomic/16S/CRISPR identity.
• Claim 3 specifies the strain is Blautia Strain A (ATCC PTA-125346).

Business implication:

• The patent simultaneously claims (i) a catch-all identity band (≥90%) and (ii) a high-confidence band (≥99%), including the exact ATCC deposit.

Claims 4–7 define disease as immune disorders and cancer (with extensive lists)

• Claim 4: disease is an immune disorder.

• Immune disorder subclasses are enumerated in Claim 5 with a large, heterogeneous set spanning:

  • allergic and hypersensitivity conditions,
  • inflammatory bowel disease and colitis variants,
  • autoimmune diseases (e.g., Hashimoto’s, lupus, Sjogren’s),
  • systemic inflammatory and immune-mediated syndromes,
  • ocular immune disorders,
  • cardiovascular inflammatory conditions,
  • nervous system immune conditions,
  • skin immune disorders,
  • vasculitis and lymphatic inflammation,
  • and broad categories of immune-mediated infections (including C. difficile infection).

• Claim 6: disease is cancer.

• Claim 7: cancer is a long list covering hematologic malignancies and solid tumors (e.g., NHL, multiple myeloma, breast cancer, lung cancer, colon cancer, melanoma, pancreatic, etc.).

Business implication:

• Claim 5’s list is so broad that it functions like a coverage surface across most immune-mediated indications, with cancer coverage separately layered.

Claims 8–12 cover route and formulation type

• Claim 8: oral, rectal, intravenous, intratumoral, or subcutaneous administration.
• Claim 9: ≥50% of bacteria are Blautia Strain A.
• Claim 10: substantially all bacteria are Blautia Strain A.
• Claim 11: ≥1×10^6 CFUs of Blautia Strain A.
• Claim 12: live, attenuated, or killed bacteria.

Business implication:

• This is a route-flexible, status-flexible claim set. The “killed bacteria” option is important because it can support commercial strategies that avoid live culture regulatory and manufacturing constraints while still alleging infringement.

Claims 13–21 expand into combination therapy and include antibiotic/cancer co-therapies

• Claim 13: method further comprises an additional therapeutic.
• Claim 14: additional therapeutic can be any of a very large basket: immunosuppressants, DMARDs, NSAIDs, steroids, cytokine antagonists, TNF-axis drugs, biologics, JAK inhibitors, antibodies, vaccines, small molecules, chemotherapy agents (and more).
• Claim 15: additional therapeutic is an immunosuppressive agent.
• Claim 16: additional therapeutic is an antibiotic.
• Claim 17–18: additional therapeutic is a cancer therapeutic comprising a chemotherapy agent.
• Claims 19–21 further bracket the bacterial composition burden:
  • ≥50% Blautia strain in the composition (Claim 19),
  • substantially all (Claim 20),
  • ≥1×10^6 CFUs (Claim 21) (note: repeats CFU concept with “of the Blautia strain,” distinct from Claim 11’s “Blautia Strain A,” but functionally consistent).

Where are the likely infringement and enforcement “pressure points”?

1) The identity language can be both an anchor and an attack surface

The infringement inquiry will likely focus on:

• Which regions are compared for “genomic, 16S or CRISPR sequence identity.”
• How “identity” is computed (global vs local alignment, selected loci, read depth effects, trimming, primer bias).
• Whether a product’s Blautia strain is tested against the ATCC PTA-125346 reference nucleotide sequence.

From a claim-construction standpoint, “genomic identity” can be ambiguous in practice unless the spec defines alignment windows. “16S identity” is routinely measurable, but “≥90% 16S identity” can still include multiple biologically different strains depending on the hypervariable regions used. “CRISPR identity” depends on CRISPR spacer content, which can vary even among closely related isolates.

2) The composition definition is functional, not excipient-limited

Claims do not restrict:

• presence of other microbes (except percentage thresholds in dependent claims),
• carrier matrices, prebiotics, or dosing schedule mechanics.

The patent therefore gives room for multiple formulations to meet claim elements so long as the claimed Blautia strain identity and CFU and/or percentage requirements are satisfied.

3) Combination-therapy dependence may create multi-party liability questions

Claim 13 and Claim 14 require a concurrently administered “additional therapeutic.” In practice, combination regimens implicate:

• prescribers,
• pharmacy compounding / dispensing,
• sponsor protocols,
• and potentially product labels and clinical trial regimens.

If enforcement targets a sponsor marketing the Blautia product, defendants may argue that their product is not marketed “as part of” a specific claimed combination. The broad wording (“method further comprises administering an additional therapeutic”) is nevertheless compatible with standard oncology/immune disorder care pathways where drugs are co-administered.

4) Live vs killed bacteria expands design-around difficulty

Many microbial therapeutics can be “designed around” by switching to dead-cell products. Claim 12 directly blocks that route for the core claim set by allowing live, attenuated, or killed bacteria.

What is the practical “scope map” of the claim set?

The claims can be reduced to a few technical dimensions:

A. Strain definition

• Broad: ≥90% genomic/16S/CRISPR identity to PTA-125346 (Claim 1)
• Narrow: ≥99% identity (Claim 2)
• Exact: strain is PTA-125346 (Claim 3)

B. Disease category

• Immune disorders (Claim 4) with an extensive list (Claim 5)
• Cancer (Claim 6) with extensive lists (Claim 7)

C. Administration and product form

• Routes: oral, rectal, IV, intratumoral, subcutaneous (Claim 8)
• Composition: ≥50% Blautia, substantially all, or at least 1×10^6 CFU (Claims 9–11, 19–21)
• Viability status: live, attenuated, killed (Claim 12)

D. Combination therapy

• Any additional therapeutic from a wide basket (Claim 14), including:
  • immunosuppressive agents and DMARDs,
  • TNF inhibitors and biologics,
  • NSAIDs/steroids,
  • antibiotics,
  • vaccines,
  • and cancer therapeutics with chemotherapy agents (Claims 16–18).

How does the claim drafting strategy affect the US patent landscape?

Claim structure supports both product-level and regimen-level capture

US10,493,113 is a method-of-treatment claim set that nonetheless contains product-defining elements:

• strain identity to a specific ATCC deposit,
• CFU and fractional composition requirements,
• route and viability status,
• plus combination administration.

That structure often makes it harder to evade by changing:

• dosing route (Claim 8),
• bacterial viability (Claim 12),
• proportion (Claims 9–11, 19–20),
• and typical co-therapies (Claims 13–18).

Dependence on a single deposit can concentrate both validity and freedom-to-operate risk

Because the claims are tethered to ATCC PTA-125346, competitors trying to build around may attempt:

• different Blautia strains,
• materially lower identity,
• or non-Blautia consortia.

However, the broad ≥90% identity can pull in near-neighbors if sequence comparisons align favorably to the claimed identity metric.

Patent landscape: what “clusters” matter around this asset?

Without a full citation map of all family members and competing US filings in the same Blautia/strain-identity space, the landscape analysis can still be structured around the dominant US patent landscape dynamics that determine commercial freedom:

1) Microbiome and live biotherapeutic product (LBP) method claims

Most enforceable claims in this space tend to be:

• strain-specific (deposit number, accession, or exact sequence identity),
• indication-specific (immune disorders, IBD, cancer immunotherapy),
• dosage/route defined,
• and sometimes combination regimen dependent.

US10,493,113 fits that profile via:

• deposit tethering,
• immune disorder and cancer indication lists,
• route flexibility,
• CFU thresholds,
• and combination therapy categories.

2) Sequence-identity-defined strain patenting is increasingly central

This patent’s use of genomic/16S/CRISPR identity aligns with a broader trend: applicants increasingly use sequence identity language to claim:

• variants,
• close isolates,
• and derivative strains that preserve key genetic similarity.

In enforcement, this raises the bar for competitors: they must demonstrate identity below the threshold under the claim’s identity method or avoid the strain equivalence.

3) “Killed bacteria allowed” pushes against viability-based design-arounds

Many companies have used “non-live” forms to reduce overlap with LBPs. Claim 12 closes that gap for this asset by explicitly covering attenuated and killed bacteria.

4) Combination-therapy breadth targets regimen switching

Claim 14’s extensive therapeutic list attempts to prevent competitors from avoiding infringement by pairing the bacterial product with a different immunosuppressive, biologic, NSAID, antibiotic, or cancer regimen within typical clinical practice.

Critical assessment of claim robustness: where is the patent vulnerable?

Identity threshold mechanics can invite validity challenges or narrow construction

If the specification does not clearly define:

• alignment methodology for “genomic sequence identity,”
• how “nucleotide sequence” is mapped to a deposit reference for CRISPR identity,
• and whether percent identity is calculated over full length or selected regions,

then the claims may be attacked for:

• indefiniteness,
• lack of enablement for producing strains that satisfy the identity constraints across platforms,
• or lack of written description support for the breadth implied by “genomic/16S/CRISPR” alternatives.

These are not hypothetical in litigation risk. In microbial composition patents, identity mechanics often become central to claim construction and expert testimony.

Overbreadth across indications may collide with support/enablement

Claim 5 lists immune disorders across many organ systems and etiologies, including:

• allergic,
• autoimmune,
• inflammatory,
• infectious contexts,
• and a very broad “TNF-mediated inflammatory disease” category.

Claim 7 similarly spans wide cancer types. If the specification’s examples cover only a subset of these conditions, broad indication lists can create:

• support challenges,
• enablement challenges,
• or arguments that the claims are not commensurate with demonstrated efficacy.

Combination therapy basket may be challenged for “laundry list” breadth

Claim 14 includes many drugs and biologics, some of which are mechanistically unrelated. Broad lists in method-of-treatment patents can be challenged as overbroad relative to data demonstrating additive or synergistic effect, especially if the patent does not provide specific mechanistic linkage or clinical trial evidence across the entire list.

Commercial and R&D implications: how competitors likely respond

Likely design-around strategies

• Use a non-Blautia probiotic/bacterial consortium.
• Use a Blautia isolate with identity below 90% under the patent’s comparators.
• Avoid the claimed CFU or composition fraction if selling a mixed consortium product.
• Avoid the claimed route combination (though Claim 8’s route list is wide).
• Avoid concurrently administering a “listed additional therapeutic” where possible, though Claim 14’s basket is broad.

Likely litigation posture for competitors

• Contest the strain identity measurement (identity computation and alignment method).
• Narrow identity construction to avoid the “genomic/16S/CRISPR” alternative collapsing into a broad equivalence.
• Challenge breadth as unsupported by examples across immune disorder and cancer subtypes.
• Target combination therapy dependence if enforcement theory relies on specific co-therapies.

Key Takeaways

• US 10,493,113 claims a strain-identity-defined bacterial method using Blautia Strain A (ATCC PTA-125346), with a ≥90% identity threshold in Claim 1 and ≥99% plus exact deposit coverage in dependent claims.
• The indication scope is broad: immune disorders (extensive list) and cancer (extensive list), with route flexibility (oral/rectal/IV/intratumoral/subcutaneous) and viability flexibility (live/attenuated/killed).
• Dependent claims add practical enforcement hooks: Blautia fraction (≥50% or substantially all), dose (≥1×10^6 CFU), and combination therapy with a very large therapeutic basket.
• The main vulnerability is likely in identity-definition mechanics (how % identity is computed across genomic/16S/CRISPR) and in breadth vs support for the extensive immune/cancer indications and drug basket.

FAQs

1) What is the core infringement element in US 10,493,113?
Administering a bacterial composition containing a Blautia strain that meets the sequence identity requirement to Blautia Strain A (ATCC PTA-125346), tied to a method of treating an immune disorder or cancer (depending on dependent claim scope).

2) Does the patent require live bacteria?
No. Claim 12 allows live, attenuated, or killed Blautia bacteria.

3) How does the patent handle mixed bacterial compositions?
It includes dependent claims requiring ≥50% Blautia (by bacteria fraction) or substantially all Blautia, plus claims tied to ≥1×10^6 CFU Blautia.

4) Can infringement be avoided by changing routes of administration?
Not easily on the claim set provided. Claim 8 lists oral, rectal, intravenous, intratumoral, and subcutaneous routes.

5) Does the patent cover combination regimens?
Yes. Claims 13 and 14 require “additional therapeutic” co-administration, with a large list including immunosuppressants, TNF-axis agents, antibiotics, steroids/NSAIDs, and chemotherapy agents.

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References

[1] United States Patent 10,493,113. (2020). Method of treating disease using Blautia strains with sequence identity to Blautia Strain A (ATCC PTA-125346).

Details for Patent 10,493,113

Applicant	Tradename	Biologic Ingredient	Dosage Form	BLA	Approval Date	Patent No.	Expiredate
Eli Lilly And Company	HUMATROPE	somatropin	For Injection	019640	June 23, 1987	10,493,113	2038-11-14
Eli Lilly And Company	HUMATROPE	somatropin	For Injection	019640	October 16, 1986	10,493,113	2038-11-14
Eli Lilly And Company	HUMATROPE	somatropin	For Injection	019640	February 04, 1999	10,493,113	2038-11-14