Inflammatory diseases in felines

Abstract

The presently disclosed subject matter relates to an in vitro method for diagnosing or tracking an inflammatory disease in a feline. The disclosed subject matter also relates to compounds and compositions thereof for the treatment of inflammatory diseases in felines.

Description

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS

[0002] This application claims priority from European application No. 22202920.9, filed on October 21, 2022, the entire contents of which are incorporated herein by reference.

[0003] Sequence Listing

[0004] This application contains a sequence listing, which has been submitted in XML format via EFS-Web and is hereby incorporated by reference in its entirety. This XML copy was created on September 29, 2023, is named 069269_0650_SL.xml, and is 2757 bytes in size. Technical Field

[0005] The presently disclosed subject matter relates to the field of diagnosis and tracking of inflammatory diseases in felines, particularly pet animals such as cats.

[0006] More specifically, the presently disclosed subject matter relates to the field of diagnosis and tracking of feline atopic syndrome (FAS), including feline atopic skin syndrome (FASS), flea allergy dermatitis (FAD), feline food allergy (FFA), and related conditions.

[0007] The presently disclosed subject matter also relates to compounds and compositions thereof for treating inflammatory diseases in felines. Background Art

[0008] The complex human gut microbiome has been extensively studied over the past five decades. Studies have shown that the microbiome is influenced, both significantly and subtly, by diverse environmental factors and diseases, including systemic inflammatory diseases. Long-term human diseases such as obesity, inflammatory bowel disease, allergic rhinitis, and atopic dermatitis have been reported to be associated with the microbiome, but the causal relationship remains controversial. Current research focuses on understanding its preventive role in infancy and the bacterial strains associated with allergic conditions in adults.

[0009] Specifically, atopic dermatitis is a chronic inflammatory skin disease that begins in early childhood and is often the first manifestation of atopy. Depending on the presence of commensal intestinal bacteria, the inappropriate T helper cell type 2 (Th2) immune response that predominates at birth matures into a Th1 immune response that predominates in infancy and adulthood. The microbiome has a well-documented role in human atopic dermatitis, particularly the association of dysbiosis with an increased risk of atopy.

[0010] American adults with allergies, particularly to nuts and seasonal pollen, have a low-diversity gut microbiome, with a decrease in Clostridiales and an increase in Bacteroidetes. This dysbiosis may help improve the treatment or prevention of allergies (Hua et al.; Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project; ebioMedicine, 2016).

[0011] Under certain conditions, it is speculated that intestinal homeostasis in other non-human mammals may also be disrupted. For example, dysbiosis may occur with reduced bacterial diversity, loss of beneficial bacteria, and overgrowth of pathogens. Because changes in the microbiome often accompany disease, it is conceivable that microbiome profiles could be used as biomarkers for diagnosis and / or monitoring in the future, as reported in the fecal microbiome of dogs (Lin et al.; An ambient temperature collection and stabilization strategy for canine microbiota studies; Nature, 2020).

[0012] Inflammatory diseases, particularly those caused by feline allergic diseases, are common in cats (Halliwell et al.; Feline allergic diseases: introduction and proposed nomenclature; Veterinary Dermatology, 2021). Feline atopic skin syndrome (FASS) is an inflammatory and pruritic skin syndrome in cats that presents with a spectrum of reactivity that may be related to IgE antibodies to environmental allergens (Richard Halliwell; Immunopathogenesis of the feline atopic syndrome; Veterinary Dermatology, 2021).

[0013] The skin lesions of FASS vary in appearance and include miliary dermatitis (MD), spontaneous alopecia / hypotrichosis (SIAH), head and neck pruritus (HNP), and eosinophilic granuloma complex (EGC) (Santoro et al.; Clinical signs and diagnosis of feline atopic syndrome: detailed guidelines for a correct diagnosis; Veterinary Dermatology, 2021).

[0014] In felines, a new understanding of the role of the gut microbiota and the rapid development of next-generation sequencing have also enabled the acquisition of these microbial data (Lyu et al.; Past, Present, and Future of Gastrointestinal Microbiota Research in Cats; Front. Microbiol., 2020). Similar to other mammals, the vast majority (over 99%) of the cat's gastrointestinal (GI) microbiota is composed of the dominant bacterial phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria.

[0015] One study showed a correlation between the severity of chronic enteropathy in cats and an increase in Enterobacteriaceae (Simpson; Chapter 10 - The Role of the Microbiota in Feline Inflammatory Bowel Disease; August's Consultations in Feline Internal Medicine, Vol. 7, 2016).

[0016] Increases in Bifidobacteriales and Lactobacillaceae were further associated with feline immunodeficiency virus infection in one study (Weese et al., The rectal microbiota of cats infected with feline immunodeficiency virus infection and uninfected controls; Veterinary Microbiology, 2015).

[0017] Therefore, new biomarkers are needed for detecting inflammatory diseases in felines, particularly cats.

[0018] There is also a need for compounds and compositions for treating these inflammatory diseases in non-human mammals, including felines.

[0019] The presently disclosed subject matter is directed to satisfying the aforementioned needs. Summary of the Invention

[0020] A first major aspect of the presently disclosed subject matter relates to an in vitro method for diagnosing or tracking an inflammatory disease in a feline, the method comprising the step of determining the presence of Bacteroides vulgatus or Helicobacter canis in a feline digestive tract sample; wherein: an increase in the level of Bacteroides vulgatus indicates the onset of an inflammatory disease, a decrease in the level of Helicobacter canis indicates the onset of an inflammatory disease, and / or an increase in the ratio of Bacteroides vulgatus to Helicobacter canis indicates an inflammatory disease.

[0021] In certain embodiments, the method includes the step of determining the level of Bacteroides vulgaris present in a digestive tract sample.

[0022] In certain embodiments, the method comprises the step of determining the level of Helicobacter caninum in a digestive tract sample.

[0023] In certain embodiments, the method comprises the step of determining the levels of Bacteroides vulgaris and Helicobacter caninum in a digestive tract sample.

[0024] In certain embodiments, the inflammatory disease is selected from the group consisting of: allergic diseases, inflammatory skin diseases, inflammatory digestive tract diseases, and respiratory diseases. In certain embodiments, the inflammatory disease is feline atopic syndrome (FAS). In certain embodiments, the inflammatory disease is selected from the group consisting of: feline atopic skin syndrome (FASS), flea allergy dermatitis (FAD), and feline food allergy (FFA). In certain embodiments, the inflammatory disease is feline atopic skin syndrome (FASS).

[0025] In certain embodiments, the inflammatory disease is selected from the group consisting of miliary dermatitis (MD), spontaneous alopecia / hypotrichosis (SIAH), head and neck pruritus (HNP), and eosinophilic granuloma complex (EGC).

[0026] In certain embodiments, the digestive tract sample is selected from the list consisting of a stool sample, a stomach sample, a saliva sample, or a fraction thereof; in particular a stool sample or a fraction thereof.

[0027] In certain embodiments, the feline is selected from the list consisting of cheetahs, cougars, jaguars, leopards, lions, lynxes, ligers, tigers, panthers, bobcats, ocelots, saber-toothed cats, caracals, servals, and cats; particularly wild cats and domestic cats, including their bred species and hybrids; most preferably domestic cats.

[0028] In certain embodiments, the feline is selected from the group consisting of: Abyssinian, Aegean, American Bobtail, American Curl, American Ringtail, American Shorthair, American Wirehair, Aphrodite Giant, Arabian Mau, Asian, Asian Semi-longhair, Australian Mist, Balinese, Bambino, Bengal, Birman, Bombay, Brazilian Shorthair, British Longhair, British Shorthair, Burmese, Burmilla, California Spangled, and more. Spangled, Chantilly-Tiffany, Chartreux, Chausie, Colorpoint Shorthair, Cornish Rex, Cymric, Manx Longhair, Long-haired Manx, Cyprus, Devon Rex, Donskoy, Don Sphynx, Dragon Li, Chinese Li Hua, Dwelf, Egyptian Mau, European Shorthair, Exotic Shorthair, Foldex, German Rex, Havana Brown), Highlander, Himalayan, Colorpoint Persian, Japanese Bobtail, Javanese, Colorpoint LonghairLonghair, Kanaani, Khao Manee, Kinkalow, Korat, Korean Bobtail, Korn Ja, Kurilian Bobtail, Kuril Islands Bobtail, Lambkin, LaPerm, Lykoi, Maine Coon, Manx, Mekong Bobtail, Minskin, Minuet, Munchkin, Nebelung, Norwegian Forest Cat, Ocicat, Ojos Azules, Oregon Rex, Oriental Bicolor, Oriental Longhair Longhair, Oriental Shorthair, Persian, Peterbald, Pixie-bob, Ragamuffin, Liebling, Ragdoll, Raas, Russian Blue, Russian White, Russian Black, Russian Tabby, Sam Sawet, Savannah, Scottish Fold, Selkirk Rex, Serengeti, Serrade Petit, Siamese, Siberian, Siberian Forest Cat, Neva Siberian Forest Cat Masquerade), Singapura, Snowshoe, Sokoke, Somali, Sphynx, Suphalak, Thai, Thai Lilac, Thai Blue Point, Thai LilacPoint, Tonkinese, Toybob, Toyger, Turkish Angora, Turkish Van, Turkish Vankedisi, Ukrainian Levkoy and York Chocolate.

[0029] In certain embodiments, the step of determining the level of occurrence of Bacteroides vulgaris or Helicobacter caninum comprises detecting, preferably quantifying, all or part of a nucleic acid sequence of said Bacteroides vulgaris or Helicobacter caninum.

[0030] A second main aspect of the presently disclosed subject matter relates to a compound or composition thereof selected from the list consisting of: a corticosteroid, particularly a glucocorticoid or a mineralocorticosteroid; ciclosporin; oclatinib; an H1-receptor blocking antihistamine; an essential fatty acid selected from the group consisting of linoleic acid, linolenic acid, and arachidonic acid; palmitoylethanolamide (PEA); and combinations thereof;

[0031] The invention relates to a method for treating an inflammatory disease in a feline animal characterized by increased levels of Bacteroides vulgaris in the digestive tract, decreased levels of Helicobacter canis in the digestive tract, and / or an increased ratio of Bacteroides vulgaris to Helicobacter canis in the digestive tract. DETAILED DESCRIPTION

[0032] The bacterial species Bacteroides vulgaris and Helicobacter canis are known to be present in the intestinal microbiota of felines, particularly domestic cats. However, this disclosure reports for the first time that these two species, Bacteroides vulgaris and Helicobacter canis, exhibit differential prevalence in a group of cats with feline atopic skin syndrome (FASS). This regulation is unexpected given the lack of research on the relationship between the feline gut microbiota and inflammatory diseases, such as FASS.

[0033] Thus, this disclosure reports:

[0034] - Increased levels of Bacteroides vulgaris (e.g. above reference values, such as in healthy individuals) indicating the development of inflammatory disease, and / or

[0035] - a reduced level of Helicobacter caninum (e.g. below a reference value, such as in healthy individuals) indicates the development of an inflammatory disease, and / or

[0036] - An increased level of the ratio of Bacteroides vulgaris to Helicobacter canis (eg when compared to a healthy individual or to the same individual in a previous / healthier state) is indicative of the development of an inflammatory disease.

[0037] In particular, the regulation of Helicobacter canis, which was less prevalent in the FASS group, was unexpected because this bacterial strain had been previously described in other studies in both patients with diarrhea and healthy subjects, including Foley et al. (Isolation of Helicobacteri canis from a Colony of bengal Cats with Endemic Diarrhea; Journal of Clinical Microbiology; 1999) and Stanley et al. (Helicobacter canis sp. nov., a new species from dogs: an integrated study of phenotype and genotype; J. Gen. Microbiol. 1993).

[0038] Without wishing to be bound by theory, the present disclosure believes that the above modulations constitute novel biomarkers for feline inflammatory diseases, including symptoms associated with Feline Atopic Syndrome (FAS) and Feline Atopic Skin Syndrome (FASS).

[0039] The present disclosure also discloses compounds and compositions for use in treating inflammatory diseases in a subpopulation of felines characterized by:

[0040] - Increased levels of Bacteroides vulgaris compared to reference values, and / or

[0041] - a decrease in the level of Helicobacter caninum compared to a reference value, and / or

[0042] -The ratio of Bacteroides vulgaris to Helicobacter caninum increased.

[0043] Specifically, the present disclosure further discloses compounds and compositions for treating inflammatory diseases in a subpopulation of felines characterized by:

[0044] - Increased levels of Bacteroides vulgaris compared to reference values, and / or

[0045] - a decrease in the level of Helicobacter caninum compared to a reference value, and / or

[0046] -The ratio of Bacteroides vulgaris to Helicobacter caninum increased.

[0047] More specifically, the present disclosure discloses compounds and compositions that have been previously reported to be effective in treating allergic diseases, inflammatory skin diseases, inflammatory digestive tract diseases and / or respiratory diseases, and preferably are effective in treating feline atopic syndrome (FAS), which is believed to be particularly relevant to an identified subgroup of felines.

[0048] The presently disclosed subject matter also discloses a method for treating an inflammatory disease in a feline, the method comprising the steps of: a) determining, in the digestive tract of the feline, particularly in a digestive tract sample of the feline, an increase in the level of Bacteroides vulgaris in the digestive tract, a decrease in the level of Helicobacter canis in the digestive tract, and / or an increase in the ratio of Bacteroides vulgaris to Helicobacter canis in the digestive tract; and b) administering to the feline at least one compound or composition selected from the group consisting of a corticosteroid, particularly a glucocorticoid or a mineralocorticoid, cyclosporine, oclacitinib, an H1 receptor blocking antihistamine, an essential fatty acid selected from the group consisting of linoleic acid, linolenic acid and arachidonic acid, palmitoylethanolamine (PEAum) and / or a combination thereof.

[0049] For purposes of clarity and not limitation, the detailed description of the presently disclosed subject matter is divided into the following subsections:

[0050] 1. Definitions; and

[0051] 2. Diagnostic methods.

[0052] 1. Definition

[0053] The terms used in this specification generally have their ordinary meanings in the art, in the context of the present invention, and in the specific context in which each term is used. Certain terms are discussed below or elsewhere in the specification to provide additional guidance to practitioners when describing the methods and compositions of the present invention and how to prepare and use them. The following definitions are provided for this specification, including the claims.

[0054] As used in the specification and the appended claims, the singular forms "a," "an," and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "a compound" includes a mixture of compounds.

[0055] As used herein, the terms “include,” “including,” “comprises,” “comprising” or any other variations thereof are intended to cover a non-exclusive inclusion such that a process, method, article, or apparatus that comprises a list of elements includes not only those elements but may include other elements not expressly listed or inherent to such process, method, article, or apparatus.

[0056] In the detailed description herein, references to "an embodiment," "an embodiment," "one embodiment," "in various embodiments," etc. indicate that the embodiment may include a particular feature, structure, or characteristic, but every embodiment may not necessarily include the particular feature, structure, or characteristic. Furthermore, such phrases do not necessarily refer to the same embodiment. Furthermore, when a particular feature, structure, or characteristic is described in conjunction with an embodiment, whether or not explicitly described, it is considered within the knowledge of those skilled in the art to affect such feature, structure, or characteristic in conjunction with other embodiments. After reading the description, it will be clear to those skilled in the relevant art how to implement the present disclosure in alternative embodiments.

[0057] The term "about" or "approximately" means within an acceptable error range for a particular value as determined by one skilled in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, according to practice in the art, "about" can mean within 3 or more standard deviations. Alternatively, "about" can mean a range of up to 20%, preferably up to 10%, more preferably up to 5%, and still more preferably up to 1% of a given value.

[0058] As used herein, the term "treating" or "treatment" in this context means to administer or consume a composition according to the present disclosure for the purpose of curing, resolving, alleviating, relieving, reducing, altering, remedying, alleviating, improving or affecting a condition according to the present disclosure, a symptom of a condition, or preventing or delaying the onset of symptoms or complications, or arresting or inhibiting the further development of a condition in a statistically significant manner.

[0059] As used herein, the term "inflammatory disease" refers to any disease / disorder associated with inflammation, without limitation, including diseases / disorders associated with one selected from allergic (or atopic) diseases, inflammatory skin diseases, inflammatory digestive tract diseases, and respiratory diseases. For example, the term may encompass one or more of the following conditions and syndromes: atopic disease, feline atopic syndrome (FAS), feline atopic skin syndrome (FASS), feline asthma, and feline food allergy (FFA). The term also includes allergic dermatitis, allergic enteritis, and asthma.

[0060] As used herein, the term "atopy" or "atopic disease" refers to the generally accepted definition without limitation. The main characteristic of atopic disease is a susceptibility to allergic diseases affecting the skin. Therefore, the term encompasses any clinical dermatitis hypersensitivity reaction associated with a genetic predisposition to produce immunoglobulin E (IgE) antibodies to environmental proteins, such as pollen, house dust mites, and food allergens.

[0061] As used herein, the term "feline atopic syndrome" or "FAS" is used in the broadest sense to encompass allergic diseases of the skin, gastrointestinal tract, and respiratory tract, as described by Halliwell et al. (Feline allergic diseases: introduction and proposed nomenclature; Veterinary Dermatology, 2021). Thus, the term encompasses allergic dermatitis associated with environmental allergens, food allergies, and asthma that may be associated with IgE antibodies. Thus, the term encompasses inflammatory diseases selected from the group consisting of feline atopic skin syndrome (FASS), flea allergy dermatitis (FAD), feline food allergy (FFA), and feline asthma.

[0062] As used herein, the term "feline atopic skin syndrome" or "FASS" refers to the generally accepted definition without limitation. Thus, the term encompasses allergic skin diseases associated with environmental allergies. More specifically, it may encompass one or more of the following conditions: miliary dermatitis (MD), spontaneous alopecia / hypotrichosis (SIAH), head and neck pruritus (HNP), eosinophilic granuloma complex (EGC). In particular, FASS is often associated with an inflammatory and pruritic skin syndrome (such as that found in cats). Food allergies and flea allergies can both lead to this syndrome.

[0063] As used herein, "feline asthma" refers to the generally accepted definition without limitation. Thus, the term encompasses eosinophilic inflammatory diseases that affect the bronchioles and cause spontaneous, reversible bronchoconstriction and airway remodeling, which manifest as acute respiratory distress or chronic cough and expiratory wheezing, and may be associated with IgE antibodies to inhaled allergens.

[0064] As used herein, "feline food allergy" refers to the generally accepted definition without limitation. Thus, the term encompasses clinical manifestations resulting from allergen-specific reactions to ingested food, including those of FASS.

[0065] As used herein, the term "corticosteroid" refers to any corticosteroid hormone, without limitation, including naturally occurring corticosteroids and synthetic corticosteroids. Thus, the term particularly encompasses glucocorticoids or mineralocorticoids, without limitation to a specific route of administration. Thus, in the absence of contrary indications, the term encompasses topical, inhaled, and systemic corticosteroids (e.g., glucocorticoids).

[0066] As used herein, " glucocorticoid " refers to a steroid capable of binding to a glucocorticoid receptor, without limitation. These compounds encompass but are not limited to dexamethasone, a medicament containing dexamethasone, cortivazol (cortivazol), hydrocortisone, methylprednisolone, paramethasone, prednisone, prednisolone, prednylidene (prednylidene), cortisone, budesonide, betamethasone, beclomethasone, mometasone furoate, fluticasone, flunisolide, triamcinolone acetonide, methylprednisone, derivatives and salts thereof. Other instantiations of glucocorticoid include dexamethasone base, dexamethasone sodium phosphate, dexamethasone hemisuccinate, dexamethasone sodium succinate, dexamethasone succinate and dexamethasone acetate.

[0067] As used herein, the term "cyclosporine" or "cyclosporin" or "cyclosporin" or "cyclosporin A" refers to the compound with CAS number 59865-13-3 and its salts; thus, it may include microemulsions and liquid forms thereof.

[0068] As used herein, the term "oclatinib" refers to the compound with CAS number 1208319-26-9 and its salts.

[0069] As used herein, the term "H1 receptor blocking antihistamine" or "H1 antagonist" or "H1 blocker" refers to a compound that is capable of blocking the action of histamine on the H1 receptor, and thus may encompass H1 antihistamines, including compounds selected from the group consisting of loratadine, cetirizine, cyproheptadine, chlorpheniramine, clemastine, and salts thereof.

[0070] As used herein, the term "essential fatty acids" refers to those fatty acids that are considered essential for felines (e.g., cats) because they cannot be synthesized from non-fat sources such as carbohydrates or proteins. Essential fatty acids for felines (e.g., cats) include linoleic acid, linolenic acid, and arachidonic acid.

[0071] As used herein, the term "feline" or "Felidae" refers to members of the family Felidae; including, but not limited to, the subfamilies Felinae, Pantherinae, and Acinonychinae; the genera Caracal, Catopuma, Felis, Herpailurus, Leopardus, Leptailurus, Lynx, Oncifenac, and Ocelot. elis), Oreailurus, Otocolobus, Prionailurus, Profelis, Puma, Neofelis, Panthera, Pardofelis, and Uncia; species: felis, lybica, jubatus, caracal, badia, bieti, chausie, and safari cats. ), Sand cat (margarita), Black-footed cat (nigripes), European wildcat (silvestris), Gordon's wildcat (gordonii), Slender-waisted cat (yaguarondi), Jaguar cat (pardalis), Small tabby cat (tigrinus), Long-tailed tiger cat (wiedi), Serval, Canada lynx (canadensis), Eurasian lynx (lynx), Iberian lynx (pardinus), Bobcat (rufus), Pampas cat (colocolo), Joe's cat (geoffrey), As used herein, cat encompasses both wild and domestic cats, with domestic cats being the most preferred.

[0072] The present disclosure relates particularly to domestic cat breeds. In the context of the present disclosure, domestic cat breeds particularly contemplated may include, or consist of, breeds recognized by The International Cat Association (TICA). Examples of cat breeds contemplated herein include breeds selected from the list consisting of: Abyssinian, Aegean, American Bobtail, American Curl, American Ringtail, American Shorthair, American Wirehair, Aphrodite Giant, Arabian Mau, Asian, Asian Semi-Longhair, Australian Mist, Balinese, Babine Noire, Bengal, Birman, Bombay, Brazilian Shorthair, British Longhair, British Shorthair, Burmese, Bombay, California Spangled, Chadli-Tiffany, Chartres, African Lion, Colorpoint Shorthair, Cornish Rex, Welsh, Manx Longhair, Long-haired Manx, Cyprus, Devon Rex, Donskoy, Don Sphynx, and many more. Sphynx), Tabby, Chinese Tabby, Dwarf (Dwelf), Egyptian Mau, European Shorthair, Exotic Shorthair, Scottish Fold, German Rex, Havana Brown, Highlander, Himalayan, Colorpoint Persian, Japanese Bobtail, Javanese, Colorpoint Longhair, Kanani, Diamond-eyed Khao Manee, Kinkalow, Korat, Korean Bobtail, Korn Ja, Kurilian Bobtail, Kuril Islands Bobtail, Lambeau, Lapwing, Lycoris, Maine Coon, Manx, Mekong Bobtail, Minus Golden, Minuet, Munchkin, Nevadan, Norwegian Forest Cat, Ocicat, Ojos Azules), Oregon Rex, Oriental Bicolor, Oriental Longhair, Oriental Shorthair, Persian, Peterbald, North American Shorthair, Ragamuffin, Liebling, Ragdoll, Russian Blue, Russian White, Russian Black, Russian Tabby, Samsawet, Savannah, Scottish Fold, Selkirk Rex, Serengeti, Serrade Petit, Siamese, Siberian, Siberian Forest Cat, Neva Masquerade, Singapura, Snowshoe, Kenyan, Somali, Canadian Sphynx, Suphalak, Thai, Thai Lilac, Thai Blue PointPoint), Thai Lilac Point, Tonkinese, Toy Bobtail, Toyger, Turkish Angora, Turkish Van, Turkish Vankedisi, Ukrainian Levkoy, York Chocolate.

[0073] As used herein, the term "food product" or "food composition" or "diet" or "foodstuff" may refer to, for example, but not limited to, food, diet, food supplement, liquid and / or materials that may contain protein, carbohydrates and / or crude fat. For example, the term may also refer to supplementary substances or additives, such as minerals, vitamins and flavorings (see Merriam-Webster's Collegiate Dictionary, 10th edition, 1993). These food compositions or products may be nutritionally complete, or not nutritionally complete.

[0074] As used herein, the term "gastrointestinal sample" can refer to any sample or portion thereof that is readily obtained from the gastrointestinal tract, including the entire digestive tract from the mouth to the anus, and thus can include the upper digestive tract, the lower digestive tract, and combinations thereof; thus, it can include any biological sample or portion thereof obtained from the mouth, stomach, small intestine, colon, cecum, rectum, or anus. Thus, a gastrointestinal sample according to the present disclosure can include, or consist of, a gastric, colorectal, duodenal, or rectal sample, or a portion thereof.

[0075] As used herein, the terms "stool sample," "stool sample," and "stool" are used interchangeably.

[0076] Therefore, suitable nucleic acid samples, for example suitable nucleic acid gastrointestinal samples, can include or consist of nucleic acid samples obtained from stool samples or parts thereof. Stool samples are commonly used in the art to sample intestinal microbiota. Preferred nucleic acid samples can be nucleic acid samples obtained from suitable stool samples.

[0077] Methods for obtaining stool samples from subjects are known in the art and include, but are not limited to, rectal swabs, stool collection, and ground or environmental sampling of animal defecation (e.g., pens on commercial animal farms). Suitable stool samples can be freshly obtained or have been stored at appropriate temperatures and conditions known in the art.

[0078] Thus, as used herein, the term "gastrointestinal sample" can encompass a nucleic acid sample (eg, a nucleic acid stool sample) comprising one or more ("plurality") heterogeneous nucleic acids produced by the subject's gut microbiota.

[0079] A gastrointestinal sample according to the present disclosure may comprise or consist of a stool sample or a portion thereof.

[0080] Gastrointestinal samples suitable for study using the methods of the present application include, but are not limited to, samples of intestinal contents and / or mucosal biopsies obtained directly by invasive techniques such as surgery, rectal or intestinal sampling by colonoscopy-type procedures, or other means. Most preferably, the sample is obtained by a less invasive method, such as a stool sample.

[0081] Methods for extracting nucleic acids from gastrointestinal samples (e.g., feces / stool samples) are also well known in the art. Depending on the type and sensitivity of the data acquisition component, the nucleic acid in the nucleic acid sample may or may not be amplified before being used as input. When amplification is required, nucleic acid can be amplified from the nucleic acid sample by polymerase chain reaction (PCR). The method for carrying out PCR is well known in the art. The selection of nucleic acid or nucleic acid region to be amplified has been discussed above. The nucleic acid in the nucleic acid sample can also be fluorescently labeled or chemically labeled, fragmented, or otherwise modified before sequencing or hybridization with an array, as routinely performed in the art.

[0082] As used herein, the term "microbiome" refers to the collection of genomes of all microorganisms, including bacteria, viruses, and fungi; in particular, all bacteria and their genetic elements (genomes) within a defined environment, such as the gut of a host, the latter being referred to as the "gut microbiome." Thus, a gut microbiome profile can represent the presence, absence, or abundance of one or more bacterial taxa identified in a gut biosample; bacterial metabolites in the gut biosample; proteins in the gut biosample; or nucleic acids in the gut biosample.

[0083] Microbial taxa can be defined at any taxonomic level, including phylum, class, order, family, genus, species, strain, or a combination thereof. Those skilled in the art will appreciate that while higher resolution taxonomy (e.g., genus, species, or strain) may generally be more predictive, in some cases, using a higher level of taxonomy may improve the performance of the system.

[0084] According to the present disclosure, the bacteria, bacterial metabolites and the proteins and / or the nucleic acids are derived from Helicobacter canis and / or Bacteroides vulgaris. According to some preferred embodiments, the intestinal microbiome profile can be determined based on analysis of nucleic acids, in particular amplification products of DNA and / or RNA of the intestinal microbiota, for example, based on analysis of amplification products of genes encoding one or more small subunit rRNAs and / or based on analysis of proteins and / or metabolites present in a biological sample (e.g., a gastrointestinal sample). The intestinal microbiome profile can be "compared" using a variety of statistical analysis programs.

[0085] As used herein, the term "operational taxonomic unit" ("OTU") refers to a terminal leaf in a phylogenetic tree that is defined by a specific gene sequence and all sequences that share sequence identity with that sequence at the species level. One or more bacteria comprise an OTU or multiple different OTUs, also encompassing strains, species, genera, families, or orders of bacteria. The specific gene sequence may be a 16S rRNA sequence or a portion of a 16S rRNA sequence, or may be a functionally conserved housekeeping gene that is widely present in the eubacterial kingdom. OTUs typically have at least 95%, 96%, 97%, 98%, or 99% sequence identity; preferably at least 97% sequence identity. OTUs are typically defined by comparing sequences between organisms. Sequences with less than 95% sequence identity are generally not considered to constitute part of the same OTU.

[0086] As used herein, "16S rRNA" may be the 16S rRNA itself, or may be the genomic sequence from which the corresponding 16S rRNA is derived. 16S rRNA can be sequenced using primers / probes directed against the V3-V4 hypervariable region, such as DNA or RNA probes, such as the DNA probes of SEQ ID No. 1 and SEQ ID No. 2.

[0087] Suitable nucleic acids for taxonomic classification are generally distributed in the intestinal microorganism colony being queried, so that analysis can be performed. According to some embodiments, nucleic acid has both conserved regions and the region of at least one experience variation. There is at least one variable region to allow enough diversification to provide classification tools, and there is conserved region to enable design of suitable primers (if necessary) for amplification and / or probes for hybridization, for the various taxa of the different classification levels from a single strain to a whole door. Although any suitable nucleic acid known in the art can be used, it will be understood by those skilled in the art that the selection of nucleic acid to be amplified or nucleic acid region may be different because of environment. In some embodiments, the nucleic acid being queried is a small subunit ribosomal RNA gene. For bacterial colony, the V district of 16s rRNA gene, particularly V3 and / or V4 district of 16s rRNA gene are suitable, although other suitable regions are known in the art. Guidance for selecting suitable 16S rRNA regions to be amplified can be found in the art, including Guo F et al., PLOS One 8(10)e76185, 2013; Soergel DAW et al., ISME Journal 6:1440, 2012; and Hamady M et al., Genome Res. 19:1141, 2009. For example, the 16S rRNA of the present disclosure can be a partial 16S rRNA nucleic acid sequence or a full-length 16S rRNA nucleic acid sequence.

[0088] When the level of bacteria (e.g. Helicobacter caninum and / or Bacteroides vulgaris) is determined by determining nucleic acids, e.g. DNA and / or RNA from one or more intestinal microbiota, it is preferably achieved by determining one or more regions of the 16S rRNA of said one or more bacteria, in particular the V region and / or determining one or more OTUs of said bacteria.

[0089] Suitable nucleic acids for classification may include nucleic acids encoding polypeptides that can be assigned to functional groups known in the art.The current technology is not limited to any one classification scheme.

[0090] As used herein, " identity percentage " or " sequence identity " between two proteins or nucleic acid sequences (depending on applicable circumstances) represent identical amino acids or bases between two sequences to be compared that obtain after optimal comparison, for example the percentage of nucleotides or nucleosides, residues, and this percentage is pure statistics, and the difference between the two sequences is randomly distributed along its length. The comparison of sequence is traditionally carried out by comparing sequences after optimal comparison, and described comparison can be carried out by fragment or by using " comparison window ".Except manual comparison, the local homology algorithm of Smith and Waterman (1981) can also be used, by the local homology algorithm of Neddleman and Wunsch (1970), by the similarity search method of Pearson and Lipman (1988) or by using computer software (GAP, BESTFIT, FASTA and TFASTA in the Wisconsin Genetics software package, Genetics Computer Group, 575 Science Dr., Madison, WI, or by comparing software BLAST NR or BLAST P) to compare the best comparison of sequences.

[0091] The percent identity between two sequences is determined by comparing two optimally aligned sequences, wherein the sequences to be compared may have additions or deletions compared to the reference sequence to achieve optimal alignment between the two sequences. The percent identity is calculated by determining the number of positions at which the amino acid residues are identical between the two sequences, preferably between the two complete sequences, dividing the number of identical positions by the total number of positions in the comparison window, and multiplying the result by 100 to obtain the percent identity between the two sequences.

[0092] After obtaining the sample, the type and / or quantity (e.g., occurrence rate or abundance) of at least one bacterium of interest (e.g., Helicobacter caninum and / or Bacteroides vulgaris) in the sample is determined according to any method known to those skilled in the art. In addition, the total amount of bacteria can be determined, and then the fractional percentage (e.g., relative amount, ratio, distribution, frequency, percentage, etc.) of each constituent bacterium in the total amount can be calculated. The result is typically correlated with at least one appropriate control result, such as a control result for the same parameter obtained from an asymptomatic individual / feline (negative control) and / or an individual / feline known to have an inflammatory disease of interest (positive control) or an individual / feline that has an inflammatory disease of interest and is being or has been treated (whether successful or unsuccessful).

[0093] As used herein, modulation of the level of Bacteroides vulgaris or Helicobacter caninum for a given subject / individual is determined based on a reference value; it can correspond to an increase or a decrease based on said reference value.

[0094] As used herein, "an increase in the level of Bacteroides vulgaris" or "an increase in the level of Helicobacter caninum" above a reference value may encompass any statistically significant increase over the reference value. It will be readily understood herein that the level of increase will necessarily depend on the detection method and the reference value considered. For example, the increase in the level of a reference value may be at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100% or at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, or at least 100-fold higher than the reference value.

[0095] As used herein, "a reduction in the level of Bacteroides vulgaris" or "a reduction in the level of Helicobacter caninum" below a reference value may encompass any statistically significant reduction below the reference value. It will be readily understood herein that the level of reduction will necessarily depend on the detection method and the reference value considered. For example, a reduction in the level of a reference value may be at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100% below the reference value, or at least 1 / 2, at least 1 / 3, at least 1 / 4, at least 1 / 5, at least 1 / 6, at least 1 / 7, at least 1 / 8, at least 1 / 9, at least 10, or at least 100 times lower than the reference value.

[0096] 2. Diagnostic methods

[0097] According to a first main embodiment, the presently disclosed subject matter thus relates to an in vitro method for diagnosing or following an inflammatory disease in a feline, comprising the step of determining the level of presence of Bacteroides vulgatus or Helicobacter canis in a sample of the digestive tract of the feline, wherein:

[0098] - Increased levels of Bacteroides vulgaris suggestive of inflammatory disease, and / or

[0099] - reduced levels of Helicobacter canis indicate the development of inflammatory disease, and / or

[0100] - Increased ratio of Bacteroides vulgaris to Helicobacter caninum

[0101] Indicates inflammatory disease.

[0102] According to a particular embodiment, the in vitro method comprises the step of determining the level of occurrence of Bacteroides vulgaris in a sample of the digestive tract.

[0103] According to a particular embodiment, the in vitro method comprises the step of determining the level of presence of Helicobacter caninum in a sample of the digestive tract.

[0104] According to a particular embodiment, the in vitro method comprises the step of determining the levels of occurrence of Bacteroides vulgaris and Helicobacter caninum in a sample of the digestive tract.

[0105] According to a particular embodiment of the in vitro method, said inflammatory disease is selected from the list consisting of allergic diseases, inflammatory skin diseases, inflammatory digestive tract diseases and respiratory tract diseases.

[0106] According to a specific embodiment of the in vitro method, said inflammatory disease is Feline Atopic Syndrome (FAS).

[0107] According to a specific embodiment of the in vitro method, the inflammatory disease is selected from the group consisting of: feline atopic skin syndrome (FASS), flea allergy dermatitis (FAD), feline food allergy (FFA).

[0108] According to a specific embodiment of the in vitro method, said inflammatory disease is Feline Atopic Skin Syndrome (FASS).

[0109] According to a specific embodiment of the in vitro method, the inflammatory disease is selected from the group consisting of: miliary dermatitis (MD), spontaneous alopecia / hypotrichosis (SIAH), head and neck pruritus (HNP), and eosinophilic granuloma complex (EGC).

[0110] According to a specific embodiment of the in vitro method, the digestive tract sample is selected from the list consisting of: a stool sample, a stomach sample, a saliva sample, or a fraction thereof; in particular a stool sample or a fraction thereof.

[0111] According to a specific embodiment of the in vitro method, the feline is selected from the list consisting of: cheetah, cougar, jaguar, leopard, lion, lynx, liger, tiger, panther, bobcat, ocelot, saber-toothed tiger, caracal, serval and cat; in particular wild cats and domestic cats, including their breeding species and hybrids; most preferably domestic cats.

[0112] According to a specific embodiment of the in vitro method, the feline is selected from the group consisting of: Abyssinian, Aegean, American Bobtail, American Curl, American Ringtail, American Shorthair, American Wirehair, Aphrodite Giant, Arabian, Asian, Asian Semi-Longhair, Australian Mist, Balinese, Babine, Bengal, Birman, Bombay, Brazilian Shorthair, British Longhair, British Shorthair, Burmese, Bombay, California Spangled, Chadli-Tiffany, Chartres, African Lion, Colorpoint Shorthair, Cornish Rex, Welsh, Manx Longhair, Long-haired Manx, Cyprus, Devon Rex, Donskoy, Don Sphynx, etc. Sphynx), Tabby, Chinese Tabby, Dwarf (Dwelf), Egyptian Mau, European Shorthair, Exotic Shorthair, Scottish Fold, German Rex, Havana Brown, Highlander, Himalayan, Colorpoint Persian, Japanese Bobtail, Javanese, Colorpoint Longhair, Kanani, Diamond-eyed Khao Manee, Kinkalow, Korat, Korean Bobtail, Korn Ja, Kurilian Bobtail, Kuril Islands Bobtail, Lambeau, Lapwing, Lycoris, Maine Coon, Manx, Mekong Bobtail, Minus Golden, Minuet, Munchkin, Nevadan, Norwegian Forest Cat, Ocicat, Ojos Azules), Oregon Rex, Oriental Bicolor, Oriental Longhair, Oriental Shorthair, Persian, Peterbald, North American Shorthair, Ragamuffin, Liebling, Ragdoll, Russian Blue, Russian White, Russian Black, Russian Tabby, Samsawet, Savannah, Scottish Fold, Selkirk Rex, Serengeti, Serrade Petit, Siamese, Siberian, Siberian Forest Cat, Neva Masquerade, Singapura, Snowshoe, Kenyan, Somali, Canadian Sphynx, Suphalak, Thai, Thai Lilac, Thai Blue Point, Thai Lilac PointPoint), Tonkinese, Toy Bobtail, Toyger, Turkish Angora, Turkish Van, Turkish Vankedisi, Ukrainian Levkoy, York Chocolate.

[0113] According to a specific embodiment, the in vitro method comprises the step of determining the level of occurrence of Bacteroides vulgaris or Helicobacter caninum, comprising determining, preferably quantifying, all or part of the nucleic acid sequence of said Bacteroides vulgaris or Helicobacter caninum.

[0114] According to some specific embodiments of the in vitro method for diagnosing or tracking an inflammatory disease, the method comprises the step of contacting a digestive tract sample or a portion thereof, such as a feces / stool sample, with one or more probes capable of specifically hybridizing to one or more nucleic acid sequences of the gut microbiome, in particular Bacteroides vulgaris and / or Helicobacter pylori canis.

[0115] According to some specific embodiments of the in vitro method for diagnosing or tracking an inflammatory disease, the method comprises the step of detecting and / or isolating probes that specifically hybridize to gut microbiome nucleic acid sequences in the sample.

[0116] According to some specific embodiments of the in vitro method for diagnosing or tracking an inflammatory disease, the method comprises the step of sequencing the nucleic acid sequence of the gut microbiome that is likely to be present in a digestive tract sample.

[0117] According to some specific embodiments of the in vitro method for diagnosing or tracking an inflammatory disease, the method comprises the step of comparing the gut microbiome nucleic acid sequence with a database comprising reference gut microbiome nucleic acid sequences, in particular reference gut microbiome nucleic acid sequences from Bacteroides vulgaris and / or Helicobacter caninum.

[0118] According to some specific embodiments of the in vitro method for diagnosing or tracking an inflammatory disease, the method comprises the following steps:

[0119] a) contacting a digestive tract sample or a portion thereof with one or more probes capable of specifically hybridizing to one or more nucleic acid sequences of the gut microbiome, in particular Bacteroides vulgaris and / or Helicobacter pylori canis;

[0120] b) optionally detecting and / or isolating probes that specifically hybridize to gut microbiome nucleic acid sequences in the sample;

[0121] c) sequencing the gut microbiome nucleic acid sequences that hybridize to the one or more probes; and

[0122] d) comparing the sequence from (c) to a database comprising reference gut microbiome nucleic acid sequences, in particular from Bacteroides vulgaris and / or Helicobacter caninum.

[0123] 3. Compounds, compositions and methods of treatment

[0124] According to a second main embodiment, the presently disclosed subject matter is directed to a compound or composition thereof, e.g., a food composition, for use in a method of treating an inflammatory disease in a feline characterized by increased levels of Bacteroides vulgaris in the digestive tract, decreased levels of Helicobacter canis in the digestive tract, and / or an increased ratio of Bacteroides vulgaris to Helicobacter canis in the digestive tract.

[0125] According to a second main embodiment, the present invention relates to a compound or a composition thereof selected from the list consisting of:

[0126] -Corticosteroids, especially glucocorticoids or mineralocorticoids;

[0127] -Cyclosporin;

[0128] -oclatinib;

[0129] -H1 receptor blocking antihistamines;

[0130] - essential fatty acids selected from linoleic acid, linolenic acid and arachidonic acid;

[0131] -- Palmitoylethanolamide (PEA), such as ultramicronized PEA;

[0132] - and their combinations;

[0133] The invention relates to a method for treating an inflammatory disease in a feline animal characterized by increased levels of Bacteroides vulgaris in the digestive tract, decreased levels of Helicobacter canis in the digestive tract, and / or an increased ratio of Bacteroides vulgaris to Helicobacter canis in the digestive tract.

[0134] According to a specific embodiment, the compound for use according to the present disclosure or composition thereof is a food composition, which may or may not be nutritionally complete; for example a food additive.

[0135] According to a specific embodiment, the compound for use according to the present disclosure or composition thereof is used in a method of treating an inflammatory disease in a feline, wherein the inflammatory disease is feline atopic skin syndrome (FASS).

[0136] The presently disclosed subject matter also relates to a method for treating an inflammatory disease in a feline characterized by increased levels of Bacteroides vulgaris in the digestive tract, decreased levels of Helicobacter canis in the digestive tract, and / or an increased ratio of Bacteroides vulgaris to Helicobacter canis in the digestive tract.

[0137] The presently disclosed subject matter also relates to a method for treating an inflammatory disease in a feline, comprising the step of administering to the feline at least one compound or composition selected from the group consisting of a corticosteroid, particularly a glucocorticoid or a mineralocorticoid, cyclosporine, oclacitinib, an H1 receptor blocking antihistamine, an essential fatty acid selected from the group consisting of linoleic acid, linolenic acid, and arachidonic acid, palmitoylethanolamine (PEAum), and / or combinations thereof.

[0138] The present disclosure also relates to a method for treating an inflammatory disease in a feline animal, the method comprising the following steps:

[0139] a) determining in the digestive tract of a feline, particularly in a feline digestive tract sample, that Bacteroides vulgaris is increased in the digestive tract, that Helicobacter canis is decreased in the digestive tract, and / or that the ratio of Bacteroides vulgaris to Helicobacter canis is increased; and

[0140] b) administering to the feline at least one compound or composition selected from the group consisting of: corticosteroids, particularly glucocorticoids or mineralocorticoids, cyclosporine, oclacitinib, H1 receptor blocking antihistamines, essential fatty acids selected from the group consisting of linoleic acid, linolenic acid and arachidonic acid, palmitoylethanolamine (PEAum), and / or combinations thereof.

[0141] Example

[0142] The present disclosure is illustrated by the following examples and is not limited in any way to these examples.

[0143] Materials & Methods

[0144] Research group

[0145] Animals were recruited in France by four ECVD veterinarians and three (Fr)CertAVP (VD) veterinarians. Twenty feline referrals with feline atopic skin syndrome were admitted to the clinic. Clinical signs were consistent with miliary dermatitis (MD) and / or spontaneous alopecia / hypotrichosis (SIAH) and / or head and neck pruritus (HNP) and / or eosinophilic granuloma complex (EGC). To be included in the study, patients had to be older than 9 months and younger than 12 years of age and receive appropriate topical antiparasitic treatment for flea control and deworming. There were no visible or cytological signs of active bacterial and yeast infections. Patients were also required to be free of diarrhea and not have taken any medications within 14 days prior to the clinic visit and sampling. Twenty-one healthy cats were recruited as a control group. These cats were of the same age group and were receiving routine antiparasitic treatment. They had no clinical signs of disease, suffered from any systemic chronic diseases, or received any medications. Cats with any signs of skin disease were excluded from enrollment.

[0146] Sample collection and DNA extraction

[0147] Samples were collected from FASS and healthy cats using the provided sterile swabs and clear tubes (Isohelix DAN oral swabs, Harrietsham, Kent, UK, reference number SK-1S). Each swab was pre-moistened with sterile saline solution and gently inserted into the rectum until the entire collection portion disappeared through the anus. The swab was then rotated ten times and subsequently removed. The end of each swab was stored in a sterile Eppendorf tube and labeled with a permanent marker. The tubes were frozen at -20°C and kept at the clinic until shipped to -80°C for storage and analysis.

[0148] Rectal swabs were extracted using a Macherey-Nagel Soil Kit using Lysis Buffer SL1 and Enhancer SX. DNA quantity and quality were assessed prior to analysis and stored at −20°C.

[0149] Amplification and sequencing

[0150] To assess the bacterial microbiota, two bacterial analyses were performed:

[0151] -Axiom Microbiome Array, using Applied Biosystems TM Axiom TMDetect biochemistry, query the non-polymorphic sequences in the family conserved regions and target specific regions in the NCBI database sequences. It detects more than 12,000 species, including archaea, bacteria, fungi, protozoa, and viruses. For RNA samples, according to the guidance in the Axiom Microbiome Array User Guide, reverse transcription reactions were performed using Superscript VILO. The cDNA extracted from the samples was used as the substrate for Axiom whole genome amplification. The RNA samples were not treated with DNase, so any DNA in the total nucleic acid preparation would be carried into the whole genome amplification. According to the instructions of the manufacturer (Thermo Fisher, Waltham, MA), the arrays were hybridized, washed, and scanned on a GeneTitan multi-channel instrument in an automated manner. 96-well plates were used to run various clinical and spiked samples to evaluate the sensitivity and applicability of the arrays in clinical samples, as reported by Thissen et al. (Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis. PLoS ONE. 2019).

[0152] PCR amplification of the V3-V4 hypervariable region of the 16S rRNA gene. Library preparation was carried out according to the standard instructions of the 16S Metagenomic Sequencing Library Preparation protocol. A hypervariable region (V3-V4 region) of the bacterial 16S rRNA gene was amplified using DNA aliquots isolated from each sample. In each sample, the V3-V4 region of the 16S rRNA gene was amplified by targeting the V3-V4 hypervariable region using the following primers: "forward" (TACGGGAGGCAGCAG) (SEQ ID No. 1) and "reverse" (CCAGGGTATCTAATCC) (SEQ ID No. 2). Subsequently, the resulting amplicon (456 bp) was subjected to high-throughput sequencing using the MiSeq platform. All low-quality (<Q20) end bases were removed using Trimmomatic (v0.35), thus only retaining high-quality reads. All quality-controlled sequencing results and metadata used in the project have been submitted to the Sequence Read Archive (SRA) NCBI database (accession number PRJNA554535).

[0153] Microarray data analysis

[0154] Microarray data were analyzed using MiDAS software (Axiom Microbial Detection Analysis Software) (Thermo Fisher), which is based on the LLNL-developed Composite Likelihood Maximization Method (CLiMax) algorithm. The Axiom MiDAS platform performs single-sample analysis on CEL files from Axiom Microbiome Arrays and automatically generates a comprehensive analysis summary in an easy-to-use software package. Probes with signal intensities above the 99th percentile of random control probe intensities and detection of greater than 20% of target-specific probes were considered positive. MiDAS uses an initial score and a conditional score to determine the likelihood that a target is present. The initial score is the log-likelihood ratio of the target being present in the sample (if no other targets are present) to the absence of any target in the sample. Based on the probes observed when the sample is queried using the Axiom Microbiome Array, this value provides information about the maximum possible contribution of the target to the overall model of the sample. The conditional score provides the actual contribution of each target to the sample model; it is the log-likelihood of the model with the target compared to the model without the target. Since the conditional score takes into account the presence of other targets, if there are common probes between targets, the conditional score may be lower than the initial score for a given target.

[0155] 16S data analysis

[0156] By using FLASH (v1.2.11) to the high-quality readings filtered are spliced.The script multiple_join_paired_ends.py of QIIME (1.8.0) is used to assemble 16S rRNA amplicon.In addition, the barcode of mismatch and the sequence of length less than threshold value (200 bases) are also removed.Use UCHIME (v4.2) to remove chimeric sequences, provide effective label (high-quality sequence) for downstream microbial diversity analysis.These readings filtered through quality use QIIME script (pick_de_novo_otus.py) to implement VSEARCH (v2.4.2) for Silva (v123) and Greengenes (gg13.8) reference database, use de novo OTU to select and taxonomic distribution clustering as operational taxonomic unit (OTU; 97% identity). Representative sequences were classified and annotated by the Naive Bayesian classification algorithm of the RDP classifier (v2.2) as reported in Ahmad et al. (Analysis of gut microbiota of obese individuals with type 2 diabetes and healthy individuals; PLoS ONE. 2019).

[0157] result

[0158] The primary objective of this study was to compare the gut microbiota of healthy cats and cats with feline atopic skin syndrome (FASS) to determine whether the loss of diversity associated with the atopic state in humans and dogs is also present in cats; and, if applicable, to identify significant differences in the gut microbiota between the two groups. The last two groups identified in the study (healthy versus atopic / allergic or FASS) are reported below.

[0159] Table 1 Analysis of patient characteristics

[0160] FASS (N=14) Healthy (N=12) Unadjusted p-value Median age 4.50 3.00 0.054 Gender, number of females (%) 11(79％) 7(58％) 0.401 Lifespan, indoor quantity (%) 5(36％) 6(50％) 0.692 Number of castrations (%) 14(100％) 6(50％) 0.004 Variety, quantity (%) 0.261 -Abyssinian cat 1(7％) 0(0％) -BLH 1(7％) 0(0％) -DSH 12(68％) 8(67％) -Maine Coon 0(0％) 1(8％) -Savannah cat 0(0％) 1(8％) -Siamese cat 0(0％) 1(8％) -Siberian cat 0(0％) 1(8％)

[0161] Table 1 reports the main characteristics of the two groups. No significant differences were observed, with the exception of the castrated cats, where only 50% of the cats in the control group were castrated. This imbalance in the ratio is related to the recruitment of healthy cats at the time of castration. Deusch et al. (“A Longitudinal Study of the Feline Faecal Microbiome Identifies Changes into Early Adulthood Irrespective of Sexual Development”; PLOS ONE; 2015) demonstrated that the gut microbiota in cats is quite stable from 9 months of age (the youngest cat in our study was 9 months old). Furthermore, it was demonstrated that neither sex, castration, nor age at castration influenced the gut microbiota. However, there were no statistically significant differences in the bacterial ratios between castrated and intact cats.

[0162] Therefore, the two groups were found to be comparable for further study.

[0163] Statistical analysis based on microarray detection found that among the 30 most common bacterial strains, the prevalence of Helicobacter canis and Bacteroides vulgaris was significantly different between the two groups (healthy group and allergic group).

[0164] Table 2: Regulation of two species in the healthy and FASS groups

[0165] <![CDATA[ FASS (N=14) ]]> <![CDATA[ Healthy (N=12) ]]> <![CDATA[ Unadjusted p-value ]]> Bacteroides vulgaris 13(93％) 6(50％) 0.026 Helicobacter canis 2(14％) 7(58％) 0.038

[0166] H. canis was found to be absent in 60% of healthy cats and present in 14% of FASS (unadjusted p-value: 0.038 = statistically significant).

[0167] Bacteroides vulgaris was found to be absent in 50% of healthy cats and present in almost 100% of FASS (unadjusted p-value: 0.026 = statistically significant).

[0168] ***

[0169] Although the subject matter of the present disclosure and advantages thereof have been described in detail, it should be understood that various changes, substitutions and modifications may be made without departing from the spirit and scope of the present invention as defined by the appended claims. In addition, the scope of the present application is not intended to be limited to the specific embodiments of the processes, machines, manufactures, compositions of matter, devices, methods and steps described in the specification. Those of ordinary skill in the art will readily understand from the disclosure of the disclosed subject matter that, according to the subject matter of the present disclosure, existing or future processes, machines, manufactures, compositions of matter, devices, methods or steps that perform substantially the same functions as the corresponding embodiments described herein or achieve substantially the same results may be used. Therefore, the appended claims are intended to include such processes, machines, manufactures, compositions of matter, devices, methods or steps within their scope. Patents, patent applications, publications, product descriptions and schemes are cited in this application, and their disclosures are incorporated herein by reference in their entirety for all purposes.

Claims

1. An in vitro method for diagnosing or tracking an inflammatory disease in a feline animal, the method comprising the step of determining the presence of Bacteroides vulgatus or Helicobacter canis in a sample from the digestive tract of the feline animal; wherein: (a) Increased levels of Bacteroides vulgaris indicate the development of inflammatory diseases, and / or (b) a decrease in the level of Helicobacter caninum indicates the development of an inflammatory disease, and / or (c) Increased levels of the ratio of Bacteroides vulgaris to Helicobacter canis indicate inflammatory disease.

2. The in vitro method according to claim 1, comprising the step of determining the level of occurrence of Bacteroides vulgaris in a sample of the digestive tract thereof.

3. The in vitro method according to claim 1, comprising the step of determining the level of occurrence of Helicobacter canis in a sample of the digestive tract thereof.

4. The in vitro method according to claim 1, comprising the step of determining the levels of Bacteroides vulgaris and Helicobacter caninum in a digestive tract sample.

5. The in vitro method according to any one of the preceding claims, wherein the inflammatory disease is selected from the list consisting of allergic diseases, inflammatory skin diseases, inflammatory digestive tract diseases and respiratory tract diseases.

6. The in vitro method according to any one of the preceding claims, wherein the inflammatory disease is feline atopic syndrome (FAS).

7. The in vitro method according to any one of the preceding claims, wherein the inflammatory disease is selected from the group consisting of: Feline Atopic Skin Syndrome (FASS), Flea Allergy Dermatitis (FAD), or Feline Food Allergy (FFA).

8. The in vitro method according to any one of the preceding claims, wherein the inflammatory disease is Feline Atopic Skin Syndrome (FASS).

9. The in vitro method according to any one of the preceding claims, wherein the inflammatory disease is selected from the group consisting of miliary dermatitis (MD), spontaneous alopecia / hypotrichosis (SIAH), head and neck pruritus (HNP), or eosinophilic granuloma complex (EGC).

10. The in vitro method according to any of the preceding claims, wherein the digestive tract sample is selected from the list consisting of: a stool sample, a stomach sample, a saliva sample, and fractions thereof; in particular a stool sample or a fraction thereof.

11. The in vitro method according to any one of the preceding claims, wherein the feline is selected from the list consisting of: cheetah, puma, jaguar, leopard, lion, lynx, liger, tiger, panther, bobcat, ocelot, saber-toothed cat, caracal, serval and cat; in particular wild cats and domestic cats, including their bred species and hybrids; most preferably domestic cats.

12. The in vitro method according to any one of the preceding claims, wherein the feline is selected from the list consisting of: Abyssinian, Aegean, American Bobtail, American Curl, American Ringtail, American Shorthair, American Wirehair, Cyprus, Arabian, Asian, Asian Semi-Longhair, Australian Mist, Balinese, Babine Noire, Bengal, Birman, Bombay, Brazilian Shorthair, British Longhair, British Shorthair, Burmese, Pomeranian, California Spangled, Chadli-Tiffany, Chatterjee, Cats such as the Belgian cat, the African lion cat, the key shorthair cat, the Cornish Rex cat, the Welsh cat, the Isle of Man longhair cat, the longhaired Isle of Man cat, the Cyprus cat, the Devon Rex cat, the Donskoy cat, the Don Sphynx cat, the tabby cat, the Chinese tabby cat, the dwarf cat, the Egyptian mau, the European shorthair cat, the exotic shorthair cat, the Scottish Fold cat, the German Rex cat, the Havana brown cat, the Highlander cat, the Himalayan cat, the key color Persian cat, the Japanese Bobtail cat, the Javanese cat, the key color longhair cat, the Kanani cat, the Diamond Eyed cat, the King Karaoke cat, the Korat cat, the Korean Bobtail cat, the Kornja cat, and the Kuril Bobtail cat. Cats, Kuril Island Bobtail, Lamb, Lapwing, Wolf, Maine Coon, Manx, Mekong Bobtail, Minsk Golden, Minute, Munchkin, Nevadan, Norwegian Forest Cat, Ocicat, Oasis, Oregon Rex, Oriental Bicolor, Oriental Longhair, Oriental Shorthair, Persian, Peterbald, North American Shorthair, Ragamuffin, Liebling, Ragdoll, Russian Blue, Russian White, Russian Black, Russian Tabby, Sam Savit, Savannah, Scottish Fold, Selkirk Rex, Serengeti, Sierra Leone, Siamese, Siberian, Siberian Forest Cat, Neva Siberian Forest Cat, Singapura, Snowshoe, Kenyan, Somali, Canadian Sphynx, Supalak, Thai, Thai Lilac, Thai Blue Point, Thai Lilac Point, Tonkinese, Toy Bobtail, Toyger, Turkish Angora, Turkish Van, Turkish Van Cordis, Ukrainian Levkoy, and Yorkie Chocolate.

13. The in vitro method according to any one of the preceding claims, wherein the step of determining the level of occurrence of Bacteroides vulgaris or Helicobacter caninum comprises detecting, preferably quantifying, all or part of the nucleic acid sequence of said Bacteroides vulgaris or Helicobacter caninum.

14. A compound or composition thereof selected from the group consisting of: (a) corticosteroids, particularly glucocorticoids or mineralocorticoids; (b) cyclosporine; (c) oclatinib; (d) H1 receptor blocking antihistamines; (e) an essential fatty acid selected from the group consisting of linoleic acid, linolenic acid, and arachidonic acid; (f) palmitoylethanolamide (PEA); and (g) combinations thereof; The invention relates to a method for treating an inflammatory disease in a feline animal characterized by increased levels of Bacteroides vulgaris in the digestive tract, decreased levels of Helicobacter canis in the digestive tract, and / or an increased ratio of Bacteroides vulgaris to Helicobacter canis in the digestive tract.

15. A compound according to the preceding claim, or a composition thereof, for use in a method of treating an inflammatory disease in a feline species, said inflammatory disease being Feline Atopic Skin Syndrome (FASS).

16. A method for treating an inflammatory disease in a feline, the method comprising the steps of: a) determine that in the digestive tract of felines, particularly in feline digestive tract samples, Increased levels of Bacteroides vulgaris in the digestive tract, decreased levels of Helicobacter canis in the digestive tract, and / or an increased ratio of Bacteroides vulgaris to Helicobacter canis in the digestive tract; and b) administering to the feline at least one compound or composition selected from the group consisting of: corticosteroids, particularly glucocorticoids or mineralocorticoids, cyclosporine, oclacitinib, H1 receptor blocking antihistamines, essential fatty acids selected from the group consisting of linoleic acid, linolenic acid and arachidonic acid, palmitoylethanolamine (PEAum), and / or combinations thereof.