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In reference to the patent: US 4,210,672

The abstract contains the phrase:

Yogurt is prepared with a mixture of milk powder and novel Lactobacillus thermophilus (also known as Bacillus coagulans) spores that have specific characteristics ...

L. thermophilus is not Bacillus coagulans.

In several other places in the specification, the two names are conflated. The claims mention only Bacillus coagulans.

How does this error affect the validity of the patent claims?

1

There are several important considerations regarding the validity of this patent. First, the patent is already expired (it was granted from July 1, 1980 to July 1, 1997). However, I think this is an interesting case for several other reasons, so let’s ignore the expiration date for the remainder of this answer.

The bacterial names cited in this patent must be considered in the context of the state of bacterial nomenclature on the priority date of the patent. Bacterial (now Prokaryotic, to include the Archaea) nomenclature is governed by an international organization, the International Committee on Systematic Bacteriology (now the International Committee on Systematics of Prokaryotes). The application was filed on December 30, 1977, which was after the publication of the First Draft Approved Lists of Bacterial Names Int J Syst Bacteriol October 1976, 26(4):563–599, the list that effectively reset the nomenclature of the Bacteria (and ultimately the Archaea as well). The names on the Approved Lists were (at the time of publication of the lists) considered to have been validly published at the time of publication of the list. When the final Approved List was published, it retroactively made the of names on the previous lists valid on January 1, 1980 (note that this occurred after the filing date of the application, but prior to the patent grant date; since we are dealing with the priority date, we consider the valid publication of these names to be the date of publication of the list which they appeared on, i.e., October 1976).

However, the interpretation of the state of these names is not quite that simple, as this patent also claims the benefit of an earlier application:

Continuation-in-part of Ser. No. 672,959, Apr. 2, 1976, abandoned.

This complicates things for this discussion, because a continuation-in-part affects the priority date of the patent based on the content of the application of which it first appeared. The material added to the newer application may be interpreted to have the latter priority date (December 30, 1977) instead of the former priority date (April 2, 1976). In order to determine what priority date applies to the bacterial names cited in the patent grant, we need to compare the original patent application documents (Appl. No. 866,396 and Appl. No. 672,959). Unfortunately, although patent grant full text is available from the USPTO from 1976–present, the application full text is only available from the USPTO from 2001–present. It should be possible to obtain copies on request to the USPTO.

In lieu of having the original applications available, we can attempt to determine whether the interpretation of the names prior to the publication of the Approved List would differ from the the interpretation of the names after publication of the Approved List.

The good news is that the applicable Code of Nomenclature is unambiguous in this case. Both names fall under the jurisdiction of the International Code of Nomenclature of Bacteria (1975 Revision), applicable from January 1, 1976 until January 1, 1992 (publication of the 1990 Revision).

Rule 24a of the 1975 Revision establishes the appropriate context for interpreting the published names (see p24–25):

Rule 24a

Valid publication of names (or epithets) which are in accordance with the Rules of this Code dates from the date of publication of the Code.

After 1 January 1980, priority of publication shall date from 1 January 1980. On that date all names published prior to 1 January 1980 and included in the Approved Lists of Bacterial Names of the ICSB shall be treated for all nomenclatural purposes as though they had been validly published for the first time on that date, the existing types being retained (but see Rule 24b).

Note 1. Names of bacteria in the various taxonomic categories validly published up to 31 December 1977 will be assessed by the Judicial Commission with the assistance of taxonomic experts. Lists of names will be prepared together with the names of the authors who originally proposed the names. When approved by the ICSB these Approved Lists of Bacterial Names will be published in the IJSB before 1 January 1980. Names validly published under this Code between 1 January 1978 and 1 January 1980 will be added to the Approved Lists of Bacterial Names.

After 1 January 1980, no further names will be added to the lists. Those names validly published prior to 1 January 1980 but not included in the approved lists will have no further standing in nomenclature. They will not be added to the lists of nomina rejicienda and will thus be available for reuse for the naming of new taxa.

The Approved Lists of Bacterial Names will contain for each name a reference to an effectively published description and the type whenever possible. In the case of species or subspecies, if a type strain is available, it will be listed by its designation, and the culture collection(s) from which it may be obtained will be indicated. If such a strain is not available, a reference strain or reference material will be listed if possible.

Note 2. These approved lists may contain more than one name attached to the same type (objective synonyms) since the names on the lists will represent those names which are considered reasonable in the present state of bacteriological nomenclature and taxonomy and represent the views of many bacteriologists who may hold different taxonomic opinions.

Note 3. Synonyms may be objective synonyms, i.e., more than one name has been associated with the same type, or subjective synonyms, i.e., different names have been associated with different types that in the opinion of the bacteriologist concerned belong to the same taxon. The synonym first published is known as the senior synonym, and later synonyms are known as junior synonyms.

Publication of objective synonyms in the lists does not affect bacterial nomenclature any more than does the valid publication of objective synonyms in different works in the bacteriological literature at present.

Examples: Objective synonymsNocardia rhodochrous and Mycobacterium rhodochrous. Subjective synonyms–Luedemann (IJSB [1971] 21:240–247) regards Micromonospora fusca Jensen 1932 as a subjective synonym of Micromonospora purpureochromogenes (Waksman and Curtis 1916) Luedemann 1971. These two species have different types.

Rule 24b

If two names compete for priority and if both names date from 1 January 1980 on an approved list, the priority shall be determined by the date of the original publication of the name before 1 January 1980.

As you can see from Rule 24a and its examples, the Bacteriological Code in effect at the time of the priority date of the patent was able to accommodate multiple taxonomic opinions, even in cases where the type [strains] of the species were not identical (different organisms) via subjective synonyms.

If we examine the Approved Lists (1976, 1978, 1979, 1980, and the 1989 Amended List), we find that Bacillus coagulans Hammer 1915 was included on the Approved Lists, and the type strain ATCC® 7050™ (=NRS 609 =NCIB 9365 =NCTC 10334) was isolated and originally described in 1915:

Hammer B. W. Bacteriological studies on the coagulation of evaporated milk. Iowa Agr Exp Sta Res Bull 1915; 19:119–131.

We now have a type strain and a published description of Bacillus coagulans that is consistent in the context of both December 30, 1977 and April 2, 1976.

However, we will find that “Lactobacillus thermophilus” is absent from the Approved Lists. This means that the authors of the Approved Lists were unable to establish a type strain and authoritative description of the species.

Now, we could scour the historical literature to establish a definition (description) of “Lactobacillus thermophilus” as it would have been interpreted on December 30, 1977 and/or April 2, 1976. Or, we could make the assumption that since the authors of the Approved Lists (ones skilled in the art) were not able to find an appropriate assertion of authority for the name, that one did not exist.

Therefore, we can also come to the conclusion that in 1976 or 1977, interpreting the names cited in the patent in light of Rule 24a of the Bacteriological Code (1975 Revision) would lead one skilled in the art [of microbiology] to come to the conclusion that the inventors of the patent are establishing an (or referring to an earlier) objective synonym or subjective synonym between “Lactobacillus thermophilus” and Bacillus coagulans. Indeed, we see in the patent a non-patent reference to Fundamentals of Microbiology, 8th Ed., 1968 (pp. 394–396). Note the typos in the author and publisher names (“Frebisher” vs. Frobisher, “Sanders” vs. Saunders).

The above reference may establish a synonym between these two species. That is one text that I do not have on hand at the moment, but I will attempt to verify it.

In line with our (assumed) contemporary definition of “Lactobacillis thermophilus” the specification of the patent states:

Among the lactic bacilli, i.e. the lactic acid-producing bacilli contemplated in the present invention, there exists so many strains which generate spores in the natural world that they hitherto have been known as Lactobacillis thermophilus. However, as pointed out above, microorganisms which generate spores should either be classified as Bacillus or Clostridium and the name of Lactobacillus is technically improper. Indeed, recent studies have led the scientific world to abandon the term Lactobacillus thermophilus and to more properly name it Bacillus coagulans. Accordingly, while the term Lactobacillus thermophilus and Bacillus coagulans may in some cases be used interchangably [sic] throughout the instant specification, it should be understood that the latter is the more technically correct nomenclature in connection with the understanding of such microorganisms.

This gives us a fairly unambiguous definition of “Lactobacillis thermophilus”, and although we still do not have an authoritative reference for a circumscription of the specific set of strains, we can use the qualifier “microorganisms which generate spores”. This definition, however, may be interpreted as overly broad by one skilled in the art.

Finally, assuming that we have suitable definitions for these species in their contemporary context, we can begin to interpret the claims of the patent:

What is claimed is:

  1. A product of a dry material consisting essentially of a major amount of milk powder and a minor amount of the spores of a Bacillus coagulans having highly thermobiotic characteristics, the bacillus having characteristics such that:

    (a) the spores are able to exist in boiling water at 100° C. for more than two minutes;

    (b) the spores have the capacity to generate germ cells in a period no longer than five hours;

    (c) the germ cells have the capacity such that lactic acid fermentation occurs rapidly within four hours at about 50° C.;

    (d) the germ cells have characteristics such that the coagulation of milk occurs in a period no longer than five hours after the germ cells are formed;

    (e) the germ cells have the capacity to produce lactic acid in the final medium in a concentration more than 0.8%, and

    (f) the germ cells have the capacity to produce a final pH in the culture medium of a fermentation process of below 4.0.

  2. A product of a dry material according to claim 1, wherein the spores of the Bacillus coagulans are the spores of Bacillus EC-1, Species No. 2,930.

  3. A product of a dry material according to claim 1, wherein the germ cells of the Bacillus coagulans have the capacity to effect lactic acid fermentation within about three hours.

  4. A method of producing yogurt comprising adding boiling water to the material of claim 1 and permitting the resulting composition to ferment.

  5. A method according to claim 4, wherein after the addition of the boiling water, the resulting composition is permitted to ferment at a temperature of 40°–55° C. for about seven hours.

There is one independent claim (Claim 1), which establishes the identity of organisms based on their characteristics.

Claim 2 refers to a specific isolated strain of Bacillus, which would be unambiguous if it were possible to determine where that strain was preserved.

From the specification:

An example of such bacteria used in the present invention is EC-1 bacterium, (Species No. 2,930), which species has been deposited at the Fermentation Institute of Japan, which is a public depository located at No. 8-1, Inage Higashi 5-chome, Chiba City, Chiba Prefecture, Japan.

Great, so now we know where the EC-1 strain is held. Unfortunately, the deposit was made at the Fermentation Institute of Japan prior to the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure (April 28, 1977), which went into effect May 1, 1981.

As it turns out, there doesn’t seem to be a “Fermentation Institute of Japan”. This is likely a translation artifact of Institute for Fermentation [IFO] (Osaka, Japan), which will lead to another dead-end since that collection was terminated years ago and merged with the National Institute of Technology and Evaluation Biological Resource Center (NBRC). Although this collection allows search via IFO accession, a search on 2930 (IFO 2930) turns up no results. The accession is therefore a dead end, and the EC-1 strain may be considered to be unavailable. The loss of this strain likely occurred during the transition from IFO to NBRC under the Budapest Treaty (which would apply to 16 of the 17 years of the patent grant), but this would be difficult to verify.

An article from 2005 offers some additional perspective on The preparation of the Approved Lists of Bacterial Names:

I was responsible for suggesting the basic document to work from, and compiling names from this. This was the 8th edition of Bergey’s Manual of Determinative Bacteriology (Buchanan & Gibbons, 1974), because it covered all bacteria, contained good descriptions and usually listed type strains. It was felt that this volume contained most of the secure information on names of bacteria.

Finally, in Bergey’s Manual of Determiniative Bacteriology, 8th ed. we find the following statement (p 577):

The following, included in The Manual, 7th ed., are here excluded from Lactobacillus:

  1. ...
  2. ...
  3. Strains whose descriptions are consistent with the original description of L. thermophilus Ayers and Johnson 1924, 291 produce endospores, catalase and cytochromes that are probably very similar, if not identical, to Bacillus coagulans (Sharpe, 1962; Kitahara and Suzuki, 1963).
  4. ...

Now we have an appropriate link to the historical literature. From Bergey’s Manual of Determiniative Bacteriology, 7th ed., p 547:

Lactobacillus thermophilus Ayers and Johnson, 1924. (Jour. Bact., 9, 1924, 291.)

ther.mo'phi.lus. Gr. noun therme heat; Gr. adj. philus loving; M.L. adj. thermophilus heat-loving.

Description of Ayers and Johnson supplemented from Charlton (Jour. Dairy Sci., 15, 1932, 393).

Rods 0.5 by 3.0 microns. Non-motile (Charlton). Stain irregularly. Gran-positive.

Gelatin stab: No liquefaction.

Agar plate: Small colonies.

Agar slant: Slight, translucent growth (Charlkton).

Broth: Turbid (Charlton).

Litmus milk: Acid.

Acid from glucose, lactose, sucrose, starch and trace from glycerol; no acid from salicin, mannitol, raffinose or inulin (Ayers and Johnson). Acid from fructose, galactose, mannose, maltose, raffinose and dextrin; no acid from arabinose, xylose, glycerol, rhamnose, salicin, inulin or mannitol. Dextro rotatory lactic acid formed (Charlton).

Nitrites not produced from nitrates (Charlton).

Facultatively anaerobic. Grows best aerobically.

Temperature relations: Optimum, between 50° and 62.8° C. Minimum, 30° C. Maximum, 65° C. Thermal death point, 71° C. for 30 minutes or 82° C. for 2½ minutes.

This is the thermophilic lactobacillus obtained from pasteurized milk which causes pin-point colonies on agar plates.

Source: Isolated from pasteurized milk.

Habitat: Known only from pasteurized milk.

In short, I believe that your assertion that the two names should not be conflated is incorrect, but there are some deeper issues with this particular patent that cover multiple legal and scientific codes. Unfortunately, my investigation into these problems has run in to multiple dead-ends regarding the availability of documentation at the USPTO and the culture collections. This patent is a great example (the best I have seen yet) of a patent system, scientific field and political sphere in a state of transition.

I hope that I have addressed your question. If not, please let me know and I will be happy to expand on this answer.

Other References Cited

Lapage S. P., Sneath P. H. A., Lessel E. F., Skerman V. B. D., Seeliger H. P. R. and Clark W. A. (editors) (1975). International Code of Nomenclature of Bacteria. Washington, DC: American Society for Microbiology.

Fundamentals of Microbiology, 8th Ed. Frobisher M., Hinsdill R., Crabtree K. T. and Goodheart C. R. (editors). W. B. Saunders, Co., London, 1968 (pp. 394–396).

Sneath P. H. A. (2005). The preparation of the Approved Lists of Bacterial Names. Int J Syst Evol Microbiol 55(6):2247–2249.

Buchanan, R. E.& Gibbons, N. R. (editors) (1974). Bergey’s Manual of Determinative Bacteriology, 8th edn. Baltimore: Williams & Wilkins.

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