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EP-4739321-A1 - PROBIOTIC COMPOSITION COMPRISING VIABLE KLEBSIELLA SP. STRAIN ARO112 AS THE ONLY INGREDIENT OR IN COMBINATION WITH SCFA PRODUCING BACTERIA

EP4739321A1EP 4739321 A1EP4739321 A1EP 4739321A1EP-4739321-A1

Abstract

The invention relates to probiotic compositions comprising viable bacteria of Klebsiella strain ARO112, optionally for use as a therapeutic medicament. Compositions of the invention are provided for use in preventing, or treating dysbiosis, intestinal inflammation, infection with intestinal pathogens, or intestinal inflammatory diseases such Crohn's disease, or ulcerative colitis.

Inventors

  • DE BIVAR XAVIER, Karina
  • CABRAL, Vitor
  • ALMEIDA DE OLIVEIRA, Ana

Assignees

  • Fundação GIMM - Gulbenkian Institute for Molecular Medicine

Dates

Publication Date
20260513
Application Date
20240705

Claims (20)

  1. 1 . A probiotic composition comprising as the only active bacterial ingredient viable Klebsiella sp. strain ARO112 bacteria, wherein the Klebsiella sp. strain ARO112 bacteria are characterized by a genome >90% similarto the genome of the Klebsiella sp. ARO112 strain deposited in the Sequence Read Archive (SRA) of the NCBI database under the BioProject ID. PRJNA590204.
  2. 2. The probiotic composition according to claim 1 , wherein the Klebsiella sp. strain ARO112 bacteria comprise the genome of the Klebsiella sp. ARO112 strain deposited in the Sequence Read Archive (SRA) of the NCBI database under the BioProject ID. PRJNA590204.
  3. 3. A probiotic composition comprising viable: (i) Klebsiella sp. bacteria; and (ii) short-chain fatty acid (SCFA) producing bacteria.
  4. 4. The probiotic composition according to claim 3, wherein the short-chain fatty acid (SCFA) is butyrate, optionally wherein the butyrate producing bacteria are selected from a group of bacterial families consisting of: Lachnospiraceae, Ruminococcaceae, Oscillospiraceae, Butyricicoccaceae, and Bacteroidaceae .
  5. 5. The probiotic composition according to either claim 3 or claim 4, wherein the Klebsiella sp. bacteria comprise Klebsiella sp. strain ARO112 bacteria, and wherein the Klebsiella sp. strain ARO112 bacteria are characterized by a genome >90% similar to the genome of the Klebsiella sp. ARO112 strain deposited in the Sequence Read Archive (SRA) of the NCBI database under the BioProject ID. PRJNA590204.
  6. 6. The probiotic composition according to any one of claims 3-5, wherein the Klebsiella sp. strain ARO112 bacteria comprise the genome of the Klebsiella sp. ARO112 strain deposited in the Sequence Read Archive (SRA) of the NCBI database under the BioProject ID. PRJNA590204.
  7. 7. The probiotic composition according to any one of claims 1-6, for use as a medicament.
  8. 8. The probiotic composition according to any one of claims 1-6, for use in: (i) promoting bacterial diversity in mammals or in a human subject; and/or (ii) preventing, or treating intestinal dysbiosis in a human subject.
  9. 9. The probiotic composition according to any one of claims 1-6, for use in preventing, or treating intestinal inflammation in a human subject.
  10. 10. A probiotic composition comprising as the only active bacterial ingredient viable Klebsiella sp. bacteria for use in preventing, or treating intestinal inflammation in a mammalian subject, particularly a human subject.
  11. 11 . A probiotic composition comprising as the only active bacterial ingredient viable Klebsiella sp. bacteria for use in: (i) increasing the relative abundance of butyrate producers in the gut of a subject, and/or (ii) increasing the amount of butyrate in the gut of a subject.
  12. 12. The probiotic composition for use according to claim 11 , wherein the butyrate producers have been depleted by antibiotics.
  13. 13. The probiotic composition according to any one of claims 10-12, wherein the Klebsiella sp. bacteria comprise Klebsiella sp. strain ARO112 bacteria, and wherein the Klebsiella sp. strain ARO112 bacteria are characterized by a genome >90% similar to the genome of the Klebsiella sp. ARO112 strain deposited in the Sequence Read Archive (SRA) of the NCBI database under the BioProject ID. PRJNA590204.
  14. 14. The probiotic composition according to any one of claims 10-13, wherein the Klebsiella sp. strain ARO112 bacteria comprise the genome of the Klebsiella sp. ARO112 strain deposited in the Sequence Read Archive (SRA) of the NCBI database under the BioProject ID. PRJNA590204.
  15. 15. The probiotic composition according to any one of claims 1-6, for use in preventing, or treating an intestinal infection by a pathogenic bacterial species in a human subject.
  16. 16. The probiotic composition for use according to claim 15, wherein the pathogenic bacterial species is a member of the phylum Proteobacteria (Pseudomonadota).
  17. 17. The probiotic composition for use according to either claim 15 or claim 16, wherein the pathogenic bacterial species is an antibiotic-resistant bacterial species, particularly a multidrug resistant bacterial species.
  18. 18. The probiotic composition for use according to any one of claims 15-17, wherein the pathogenic bacterial species is: a member of a genus selected from Escherichia, Citrobacter, Salmonella, or Vibrio. Clostridioides difficile, a vancomycin-resistant Enterococcus species; and/or a multi-drug resistant species of pathogenic bacteria selected from Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species, and E. coli.
  19. 19. The probiotic composition for use according to any one of claims 15-18, wherein the pathogenic bacterial species is Vibrio cholerae, adherent-invasive E. coli (AIEC), enterohemorrhagic Escherichia coli (EHEC), enteroaggregative E. coli (EAEC), enteropathogenic E. coli (EPEC) or uropathogenic E. coli (UPEC), particularly wherein the pathogenic bacteria is the AIEC E. coli strain LF82.
  20. 20. The probiotic composition for use according to any one of claims 7 to 19, for use in a human subject who has received a therapeutic course of antibiotics in the previous month, particularly in the previous 48 hours, optionally wherein the therapeutic course of antibiotics comprises vancomycin, gentamicin, metronidazole, ciprofloxacin, and/or rifaximin.

Description

PROBIOTIC COMPOSITION COMPRISING VIABLE KLEBSIELLA SP. STRAIN ARO112 AS THE ONLY INGREDIENT OR IN COMBINATION WITH SCFA PRODUCING BACTERIA Field The present invention relates to a probiotic composition comprising Klebsiella strain ARO112, and a probiotic composition for use as a medicament, particularly in the prevention or treatment of dysbiosis, intestinal inflammation or bacterial infection. Background Inflammatory Bowel Diseases (IBD) are a group of multi-factorial pathologies with an etiology involving genetic predisposition, and/or environmental influences. The limited treatment options available focus on the common symptoms that greatly diminish patients’ quality of life. Three symptoms emerge as the core of a disease cycle that afflict IBD patients, increased and persistent intestinal inflammation, gut microbiota imbalances, and susceptibility to recurrent intestinal infection. Intestinal inflammatory flares are frequent in IBD, for which patients take antibiotics or antiinflammatory medication. These drugs, however, can have a detrimental effect on the intestinal microbiota, and may exacerbate a proinflammatory intestinal environment (Santana, 2022). An additional effect of an imbalanced microbiota is the consequent loss of natural protection that a balanced microbiota provides and subsequent increase in susceptibility to infection, often by Enterobacteriaceae bacteria, like the adherent-invasive Escherichia coli (AIEC), which can also induce inflammatory bouts (Small, 2013). The gold-standard treatment against bacterial infections is still antibiotic therapy, which leads to further intestinal microbiota imbalances with consequent increase in susceptibility to infection. This intricate and self-sustained disease cycle exponentiates the chronicity of IBD, leaving patients constantly in a disease-treatment-disease state, in need of novel and efficient approaches that can complement current treatments disrupting this burdening cycle. Probiotics have long been suggested as complementary or alternative approaches to current treatments for intestinal diseases, but few cases have been shown to be efficient for complex pathologies, like IBD. Probiotic bacteria have been suggested for IBD treatment (Carmen, 2011), however, current probiotics are not known to target the diverse symptoms described above to be critical for IBD. Furthermore, therapeutic probiotics have encountered lack of efficacy when tested in patients, rather than in laboratory conditions, which can be explained by some frequent caveats: 1) probiotic strains are foreign to the target microbiota, therefore unable to colonize long enough to actuate effects; 2) probiotic bacteria persistently colonize imbalanced microbiota communities, not allowing for natural microbiota recovery of diversity to occur (Suez, 2018); 3) probiotic bacterial strains can contribute to the increase of antibiotic resistance transfer (Montassier, 2021). Probiotics have been shown to delay microbiota recovery after antibiotic treatment, lingering in the microbiota for long periods of time (Suez, 2018). Furthermore, AIEC infection has been shown to hinder microbiota recovery in IBD, even upon a strong therapy, like fecal microbiota transplant (Zhilu 2021). Escherichia coli Nissle 1917 (EcN) has long been used as probiotic strain and has been touted as a potential therapy for IBD (Schultz, 2008). The common probiotic strain EcN has shown partial effect on AIEC growth in in vitro assays (Huebner 2011). None of the aforementioned probiotic therapies were tested in an inflammatory context, which is particularly susceptible to dysbiosis, nor have been studied in the presence of AIEC, which, as mentioned above, drives lingering dysbiosis and hinders recovery. One recent approach found promising results with a GMO EcN strain in an inflammatory context, however genetically modified organisms face steep regulatory hurdles (Zhou 2022). In previous work, the inventors identified a commensal intestinal bacterium, Klebsiella sp. ARO112, that provided limited colonization resistance against colonization with a E. coli K-12 MG1655 strain in a streptomycin-induced intestinal dysbiosis murine model (Oliveira, 2020). However, the effect on pathogen numbers was partial, and as with other probiotics, it was unclear whether such displacement could be achieved in an inflammatory environment resembling an IBD patient, or whether the intervention had a positive or negative impact on microbial diversity, and local inflammation. Furthermore, Klebsiella sp. ARO112 is a member of the Klebsiella genus comprising many opportunistic pathogens such as K. pneumoniae and K. oxytoca, and the safety regarding pathogenesis and virulence of the Klebsiella sp. ARO112 is unknown. For Enterobacteriaceae in general, one of the most challenging and problematic characteristics is the easy acquisition of antibiotic resistances from other members of the community, namely by horizontal gene transfer events, like pl