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WO2025201672A1 - Mélange de hmo et de micro-organisme transitionnel de bifidobacterium longum - Google Patents

Mélange de hmo et de micro-organisme transitionnel de bifidobacterium longum

Info

Publication number
WO2025201672A1
WO2025201672A1 PCT/EP2024/084924 EP2024084924W WO2025201672A1 WO 2025201672 A1 WO2025201672 A1 WO 2025201672A1 EP 2024084924 W EP2024084924 W EP 2024084924W WO 2025201672 A1 WO2025201672 A1 WO 2025201672A1
Authority
WO
WIPO (PCT)
Prior art keywords
transitional
longum
composition
suitably
lacto
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
PCT/EP2024/084924
Other languages
English (en)
Inventor
Claire Laurence Lucie Marie BOULANGE
Jean-Baptiste CAVIN
Eleonora CIARLO
Stéphane DUBOUX
Cheong Kwet Choy KWONG CHUNG
Mario NOTI
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Societe des Produits Nestle SA
Nestle SA
Original Assignee
Societe des Produits Nestle SA
Nestle SA
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Societe des Produits Nestle SA, Nestle SA filed Critical Societe des Produits Nestle SA
Publication of WO2025201672A1 publication Critical patent/WO2025201672A1/fr
Pending legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Classifications

    • A—HUMAN NECESSITIES
    • A23—FOODS OR FOODSTUFFS; TREATMENT THEREOF, NOT COVERED BY OTHER CLASSES
    • A23L—FOODS, FOODSTUFFS OR NON-ALCOHOLIC BEVERAGES, NOT OTHERWISE PROVIDED FOR; PREPARATION OR TREATMENT THEREOF
    • A23L33/00—Modifying nutritive qualities of foods; Dietetic products; Preparation or treatment thereof
    • A23L33/40—Complete food formulations for specific consumer groups or specific purposes, e.g. infant formula
    • A—HUMAN NECESSITIES
    • A23—FOODS OR FOODSTUFFS; TREATMENT THEREOF, NOT COVERED BY OTHER CLASSES
    • A23L—FOODS, FOODSTUFFS OR NON-ALCOHOLIC BEVERAGES, NOT OTHERWISE PROVIDED FOR; PREPARATION OR TREATMENT THEREOF
    • A23L33/00—Modifying nutritive qualities of foods; Dietetic products; Preparation or treatment thereof
    • A23L33/10—Modifying nutritive qualities of foods; Dietetic products; Preparation or treatment thereof using additives
    • A23L33/135—Bacteria or derivatives thereof, e.g. probiotics
    • A—HUMAN NECESSITIES
    • A23—FOODS OR FOODSTUFFS; TREATMENT THEREOF, NOT COVERED BY OTHER CLASSES
    • A23L—FOODS, FOODSTUFFS OR NON-ALCOHOLIC BEVERAGES, NOT OTHERWISE PROVIDED FOR; PREPARATION OR TREATMENT THEREOF
    • A23L33/00—Modifying nutritive qualities of foods; Dietetic products; Preparation or treatment thereof
    • A23L33/20—Reducing nutritive value; Dietetic products with reduced nutritive value
    • A23L33/21—Addition of substantially indigestible substances, e.g. dietary fibres
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/702—Oligosaccharides, i.e. having three to five saccharide radicals attached to each other by glycosidic linkages
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria
    • A61K35/741—Probiotics
    • A61K35/744—Lactic acid bacteria, e.g. enterococci, pediococci, lactococci, streptococci or leuconostocs
    • A61K35/745—Bifidobacteria
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
    • A61P11/06—Antiasthmatics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • A61P31/16—Antivirals for RNA viruses for influenza or rhinoviruses

Definitions

  • Infancy especially the first weeks, 3 months, 6 months or 12 months of life is a critical period for the establishment of a balanced gut microbiota. It is known that the modulation of the gut microbiota during infancy can prospectively have a great influence on future health status. For example the gut flora can have influence on the development of a strong immune system, normal growth and even on the development of obesity later in life.
  • the gut microbiota and its evolution during the development of the infant is, however, a fine balance between the presence and prevalence (amount) of many populations of gut bacteria.
  • Some gut bacteria are classified as "generally positive” while other ones are “generally negative” (or pathogenic) as to their effect on the overall health of the infant.
  • probiotics in particular from the Lactobacillus and Bifidobacterium genus, support protection against respiratory tract infections.
  • the role of probiotics in viral respiratory tract infections was reviewed by Lehtoranta and co-workers (Lehtoranta et al, Eur J Clin Microbiol Infect Dis, 2014;33; 1289-1302).
  • the weaning period has been described as a non-redundant window for immune imprinting (Cahenzli et al., Cell Host Microbe, 2013, 14(5), 559-70; Olszak et al., Science, 2012, 336(6080): 489-93; Nabhani et al., Immunity, 2019, 50(5), 1276-1288).
  • Healthy immune imprinting promotes appropriate immune responses against environmental challenges, including infections. Due to the loss of Bifidobacterium species in the infant gut and low breast-feeding rates, there is a need to provide infants with both HMOs and HMO-utilizing bacteria such as a Bifidobacterium longum transitional microorganism and/or B. longum subsp. infantis to support a healthy microbiome for long-term health. Additionally, there are limited means to prevent or treat viral infections. There are limited numbers of effective antiviral drugs, for example drugs used to treat HIV and influenza, and the primary method to control viral disease is vaccination which is intended to prevent outbreaks by building immunity to a virus or a family of viruses.
  • Bifidobacterium longum subsp microorganisms B. longum transitional
  • B. longum transitional Bifidobacterium longum subsp microorganisms
  • the inventors have shown that the B. longum transitional microorganisms are capable of modulating levels of protective cytokines (e.g.
  • IL-6 and/or short-chain fatty acids (SCFAs); and modulating gut barrier permeability, for example following an insult or exacerbation to gut barrier permeability.
  • synbiotic intervention a Bifidobacterium longum transitional microorganism in combination with a mix of human milk oligosaccharides
  • synbiotic intervention B.
  • infantis in combination with a mix of human milk oligosaccharides in early life provides protection from virus-induced bronchiolitis and promotes a sustained immune benefit into adulthood (as assessed by reduced susceptibility to pollution-enhanced allergic airway inflammation).
  • the present inventors have shown that synbiotic interventions resulted in a rapid resolution of virus-induced lung inflammation and appropriate lung tissue remodeling upon clearance of the virus.
  • the present invention is based, at least in part, on the provision of a novel Bifidobacterium longum transitional microorganism strain.
  • This B. longum transitional strain is referred to herein as NCC 5025; and was deposited with the Collection Nationale de Cultures de Micro- organisms (CNCM), Institute Pasteur by SOCIÉTÉ DES PRODUITS NESTLÉ S.A according to the Budapest Treaty on the 29th of March 2023 receiving the deposit number CNCM I-5942.
  • CNCM Collection Nationale de Cultures de Micro- organisms
  • the present B. longum transitional strain is considered to have several advantageous characteristics which make it particularly suited for supporting the transition between a milk- based diet and solid in infants and young children, for example when used as a probiotic or as part of a synbiotic.
  • the present B. longum transitional strain may provide one or more of the following advantages: a ) free of antibiotic resistance to the set of antibiotics considered relevant by EFSA; b) a unique Carbohydrate Active EnZyme (CaZy) profile, including the presence of a GH43 subfamily 17 enzyme, that was not characterized to date in the B. longum species; c) advantageous growth on 3-FL; without wishing to be bound by theory, this capacity is believed to render the present B.
  • the present B. longum transitional strain competitive in the weaning infant gut environment; d ) advantageous growth on a set of food derived fibers (e.g. inulin and arabinan).
  • a set of food derived fibers e.g. inulin and arabinan.
  • the present B. longum transitional strain is particularly adapted to the weaning period and may perform in this environment better than other B. longum transitional strains.
  • the present B. longum transitional strain may perform better on a diet containing food derived fiber (e.g. in adulthood) than other B. longum transitional strains.
  • the present invention provides a composition comprising a Bifidobacterium longum transitional microorganism and a HMO mixture consisting of 2'- fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3- FL) and/or lacto-N-neotetraose (LNnT), wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I-5942 and/or has at least one identifying characteristic of the B.
  • ANI Average Nucleotide Identity
  • the invention provides a composition comprising a Bifidobacterium longum transitional microorganism and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N- neotetraose (LNnT) for use in preventing, reducing the risk of and/or treating an infection in a subject, wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I
  • ANI Average Nucleotide Identity
  • the invention provides a composition comprising a Bifidobacterium longum transitional microorganism and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N- neotetraose (LNnT) for use in promoting a long-term immune benefit in a subject, wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of
  • the invention provides a composition comprising a Bifidobacterium longum transitional microorganism and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N- neotetraose (LNnT) for use in i) preventing and/or reducing the risk of allergen sensitisation and/or ii) preventing and/or reducing the risk of developing a respiratory condition in a subject, wherein the Bifidobacterium longum transition
  • the composition or combination further comprises a Bifidobacterium longum subsp. infantis and/or Bifidobacterium lactis microorganism.
  • the present inventors have also surprisingly found that the combination of 6HMOs with three probiotics (B. l. iuvenis + B. lactis + B. infantis) significantly increased the levels of indole-3- propionic acid as compared to the 6HMOs in combination with either B. l. iuvenis alone or with B. lactis + B. infantis.
  • Indole-3-propionic acid is a microbial derived metabolite that is linked with immune benefits (Li et al., Front. Pharmacol., 2021, 12: 769501).
  • the present invention provides a composition comprising a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp.
  • the invention provides a combination of a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp. infantis and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'- sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT), wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I-5942 and/or has at least one
  • ANI Average Nucleotide Identity
  • the invention provides a composition comprising a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp. infantis and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'- sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT) for use in preventing, reducing the risk of and/or treating an infection in a subject, wherein the Bifidobacterium longum transitional microorganism has an Average Nucleot
  • the infection is a viral infection.
  • the invention provides a composition comprising a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp.
  • infantis and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'- sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT) for use in promoting a long-term immune benefit in a subject, wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I-5942 and/or has at least one identifying characteristic of the B.
  • ANI Average Nucleotide Identity
  • the invention provides a composition comprising a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp. infantis and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'- sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT) for use in i) preventing and/or reducing the risk of allergen sensitisation and/or ii) preventing and/or reducing the risk of developing a respiratory condition in a subject
  • the composition is for use in preventing and/or reducing the risk of allergen sensitisation in a subject. In some embodiments, the composition is for use in preventing and/or reducing the risk of developing a respiratory condition in a subject.
  • the invention provides a composition comprising a Bifidobacterium longum transitional microorganism and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N- neotetraose (LNnT) for use in preventing and/or reducing the risk of developing asthma in a subject, wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I-5942 and/or has at least one identifying characteristic of the B.
  • ANI Average Nucle
  • the invention provides a composition comprising a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp. infantis and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'- sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT) for use in preventing and/or reducing the risk of developing asthma in a subject, wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide
  • the invention further provides a prebiotic for use in preventing and/or reducing the risk of an infection in a subject by promoting the growth and/or survival of a Bifidobacterium longum transitional microorganism in the gut of the infant or young child, wherein the prebiotic is a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT), and wherein the Bifidobacterium longum transitional microorganism has an Average Nucle
  • the invention also provides a combination of a Bifidobacterium longum transitional microorganism and a HMO mixture for use in preventing, reducing the risk of, and/or treating an infection in a subject; wherein the HMO mixture consists of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N- neotetraose (LNnT), and wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 98% with CNC
  • ANI Average Nucleotide Identity
  • the infection is a viral infection.
  • the invention provides a combination of a Bifidobacterium longum transitional microorganism and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N- neotetraose (LNnT) for use in promoting a long-term immune benefit in a subject, wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least
  • the HMO mixture consists of 2’-FL, DFL, LNT, 6SL, 3SL, 3-FL, and LNnT.
  • the HMO mixture consists essentially of: i. 31 wt% to 82 wt% of 2’-FL, preferably 41wt% to 70 wt%; ii. 10 wt% to 27 wt% of LNT, preferably 14 wt% to 23 wt%; iii. 4 wt% to 11 wt% of DFL, preferably 6 wt% to 10 wt%; and iv. 9 wt% to 34 wt% of 6SL and 3SL combined, preferably 11 wt% to 29 wt%.
  • the composition is in the form of a nutritional composition.
  • the nutritional composition is selected from an infant formula, a starter infant formula, a follow-on or follow-up formula, a baby food, an infant cereal composition, a growing-up-milk, a fortifier such as a human milk fortifier, or a supplement.
  • the subject is an infant, a young child or a child.
  • the subject is an infant or a young child.
  • longum transitional strain NCC5001 was promoted in a complex gut microbiota community by pectin (sugar beet) and arabinogalactan (larch wood).
  • Figure 9 - Growth of B. longum transitional strain NCC5002 was promoted in a complex gut microbiota community by arabinogalactan (larch wood) and starch (potato).
  • Figure 13 Growth ratios of 3-FL over 2’-FL of B. longum transitional strains and B. longum subsp. infantis LMG 11588.
  • Figure 14 Schematic of model of early life viral airway infection and pollution enhanced allergic airway inflammation.
  • Figure 15 Early life nutritional intervention with synbiotic (B. infantis + 6HMOs) reduces virus- induced lung pathology.
  • Figures 16 and 17 Early life nutritional intervention with synbiotic (B. infantis + 6HMOs) promotes sustained immune benefits into adulthood.
  • Figure 18 Early life nutritional intervention with synbiotic (B. infantis + 5HMOs) promotes anti-viral immune responses at peak of infection and reduces virus-induced lung inflammation.
  • Figure 19 Schematics of the experimental set up for a preclinical model for efficacy testing of B. longum transitional strain in infection model.
  • Figure 21 The effect of the combination of B. l. iuvenis (Bj) with B. infantis (Bi), B. lactis (Bl) and 6 HMOs on boosting a microbial derived metabolite that is linked with immune benefits.
  • Figure 22 Carbohydrate-Active Enzymes (CAZymes) harbored by B. longum transitional strains, including NCC 5025.
  • Figure 23 The genetic region of NCC 5025 encompassing the unique GH43_17 encoding gene.
  • Figure 24 Growth profile of B. longum transitional strains, including NCC 5025 on 3-FL as sole carbon source. The final panel represents the obtained growth rates k for each tested strain.
  • Figure 25 Growth profile of different B. longum transitional strains on A) Inulin and B) Arabinan as a substrate. Detailed Description of the invention All percentages are by weight unless otherwise stated.
  • Mammals include but are not limited to murines, simians, humans, farm animals, sport animals and pets.
  • the term “infant” means a human subject under the age of 12 months or an age equivalent non-human animal.
  • the terms “young child” or “toddler” as used herein may mean a human subject aged between 12 months and 5 years of age. Suitably, a “young child” may refer to an age equivalent non- human animal.
  • the term “child” means a human child aged between three and twelve years. Preferably, the term “child” means a child aged between three and six years.
  • a "preterm” or "premature” subject means an infant or young child who was not born at term. Generally it refers to an infant or young child born prior 36 weeks of gestation.
  • SGA small for gestational age
  • SGA intrauterine growth restriction
  • IUGR intrauterine growth restriction
  • low birth weight it should be understood as any body weight under 2500g at birth.
  • complementary feeding period can be interchangeably used and refer to the period during which the milk, either breast milk or formula, is substituted by other foods in the diet of an infant or a young child.
  • the infant or the young child is typically moved or transitioned gradually from exclusive milk-feeding, either breast feeding or formula feeding, to mixed diet comprising milk and/or solid foods.
  • the transitional period depends on the infant or young child but typically falls between about 4 months and about 18 months of age, such as between about 6 and about 18 months of age, but can in some instances extend up to about 24 months or more.
  • composition or “nutritional composition” refer to any kind of composition or formulation that provides a nutritional benefit to an individual and that may be safely consumed by a human or an animal.
  • a nutritional composition may be in solid (e.g. powder), semi-solid or liquid form and may comprise one or more macronutrients, micronutrients, food additives, water, etc.
  • the nutritional composition may comprise the following macronutrients: a source of proteins, a source of lipids, a source of carbohydrates and any combination thereof.
  • the nutritional composition may comprise the following micronutrients: vitamins, minerals, fiber, phytochemicals, antioxidants, prebiotics, probiotics, bioactives, metabolites (e.g. butyrate, Docosahexaenoic acid (DHA), Eicosapentaenoic acid (EPA), Gamma-Linolenic acid (GLA)) and any combination thereof.
  • the composition may also contain food additives such as stabilizers (when provided in liquid or solid form) or emulsifiers (when provided in liquid form). The amount of the various ingredients (e.g.
  • the oligosaccharides can be expressed in g/100 g of composition on a dry weight basis when it is in a solid form, e.g. a powder, or as a concentration in g/L of the composition when it refers to a liquid form (this latter also encompasses liquid composition that may be obtained from a powder after reconstitution in a liquid such as milk, water, e.g. a reconstituted infant formula or follow-on/follow-up formula or infant cereal product or any other formulation designed for infant or young child nutrition).
  • a nutritional composition can be formulated to be taken enterally, orally, parenterally, or intravenously, and it usually includes one of more nutrients selected from: a lipid or fat source, a protein source, and a carbohydrate source.
  • a nutritional composition is for oral use.
  • the nutritional composition is a “synthetic nutritional composition”.
  • synthetic nutritional composition means a mixture obtained by chemical and/or biological means.
  • infant formula refers to a foodstuff intended for particular nutritional use by infants during the first months of life and satisfying by itself the nutritional requirements of this category of person (Article 2(c) of the European Commission Directive 91/321/EEC 2006/141/EC of 22 December 2006 on infant formulae and follow-on formulae). It also refers to a nutritional composition intended for infants and as defined in Codex Alimentarius (Codex STAN 72-1981) and Infant Specialities (incl. Food for Special Medical Purpose).
  • infant formula encompasses both “starter infant formula” and “follow-up formula” or “follow-on formula”. A “follow-up formula” or “follow-on formula” is given from the 6th month onwards.
  • the expression “baby food” means a foodstuff intended for particular nutritional use by infants or young children during the first years of life.
  • infant cereal composition means a foodstuff intended for particular nutritional use by infants or young children during the first years of life.
  • growing-up milk (or GUM) refers to a milk-based drink generally with added vitamins and minerals, that is intended for young children or children.
  • fortifier refers to liquid or solid nutritional compositions suitable for fortifying or mixing with human milk, infant formula, growing-up milk or human breast milk fortified with other nutrients.
  • the fortifier can be administered after dissolution in human breast milk, in infant formula, in growing-up milk or in human breast milk fortified with other nutrients or otherwise it can be administered as a stand-alone composition.
  • the milk fortifier can be also identified as being a “supplement”.
  • the term “metabolize” is used herein to mean that a substrate can by broken down, adsorbed and/or utilized by a microorganism.
  • the substrate may promote and/or contribute to the growth and/or survival of the microorganism.
  • the term “capable of metabolizing the glycan substrate” may mean that the B.
  • the longum transitional strain encodes at least one CAZyme which is capable of utilizing the glycan substrate.
  • the CAZyme may be capable of catalyzing the hydrolysis of a glycosidic bond within the glycan substrate.
  • the B. longum transitional strain may encode at least one, at least two, at least three, at least four or at least five CAZymes that are capable of utilizing the glycan substrate.
  • the term “capable of metabolizing the glycan substrate” may mean that the glycan substrate (or a fiber or ingredient comprising the glycan substrate) is capable of promoting growth and/or survival of the B. longum transitional strain (e.g.
  • growth and/or survival of the B. longum transitional strain may be determined by measuring the abundance of 16S rDNA – for example using PCR methods.
  • An illustrative assay for measuring growth of a B. longum transitional strain in the presence of glycan substrates is provided in the present examples.
  • the glycan substrate is capable of being metabolized by the B longum transitional microorganism.
  • the glycan substrate may be capable of promoting growth and/or survival of the B. longum transitional strain.
  • longum transitional strain may be determined by e.g. anaerobic culture of the B. longum transitional strain with the glycan substrate to be tested. Growth and/or survival of the B. longum transitional strain may be determined by measuring bacteria cell number, cell density (e.g. measured by optical density) and/or the abundance of 16S rDNA – for example using PCR methods. An illustrative assay for measuring growth of a B. longum transitional strain in the presence of glycan substrates is provided in the Examples. A glycan substrate capable of promoting growth and/or survival of the B. longum transitional strain may increase the number of B.
  • a glycan substrate capable of promoting growth and/or survival of the B. longum transitional strain may increase the number of B. longum transitional bacteria in an anaerobic culture by a statistically significant amount (e.g. p-value ⁇ 0.05 as determined by one-way ANOVA) compared to the number of B. longum transitional bacteria in a control anaerobic culture which does not comprise the glycan substrate.
  • a “glycan substrate” refers to a glycan that can be metabolized by a microorganism.
  • a glycan substrate may be, for example, a glycoconjugate, oligo- or polysaccharide.
  • Glycoconjugate glycans may comprise N-linked glycans or O-linked glycans within glycoproteins and proteoglycans, or glycolipids.
  • an O-linked glycan may comprise a protein or peptide where the oxygen atom of a serine or threonine residue is linked to a monosaccharide, oligo- or polysaccharide as in the case with glycosaminoglycans (GAGs).
  • glycan substrates are cellulose, which is a glycan composed of ⁇ -1,4-linked D-glucose, and chitin, which is a glycan composed of ⁇ -1,4-linked N-acetyl-D-glucosamine.
  • Glycans may be homo- or heteropolymers of monosaccharide residues and can be linear or branched.
  • “Glycan substrate” as used herein encompasses, for example, oligosaccharides and polysaccharides.
  • the “oligosaccharide” may refer to a carbohydrate that has greater than 2 but relatively few monosaccharide units (typically 3, 4, 5, 6, and up to 10).
  • Exemplary oligosaccharides include, but are not limited to, fructo-oligosaccharides, galacto-oligosaccharides (raffinose, stachyose, verbascose), maltooligosaccharides, gentio-oligosaccharides, cellooligosaccharides, milk oligosaccharides (e.g., those present in secretions from mammary glands), isomalto- oligosaccharides, lactosucrose, mannooligosaccharides, melibiose-derived oligosaccharides, pectic oligosaccharides, xylo-oligosaccharides.
  • polysaccharide may refer to a carbohydrate that has more than ten monosaccharide units.
  • exemplary polysaccharides include, but are not limited to, starch, arabinogalactan, laminarin, chrysolaminarin, xylan, arabinoxylan, mannan, fucoidan and galactomannan. It is to be understood that there is not a precise cut-off or distinction between the terms oligosaccharide and polysaccharide, nor is such a distinction necessary to practice the invention.
  • GAG glycosaminoglycan
  • mucopolysaccharide refers to long linear polysaccharides consisting of repeating disaccharide units (i.e. two-sugar units).
  • the repeating two-sugar unit consists of a uronic sugar and an amino sugar, with the exception of keratan, where in the place of the uronic sugar it has galactose.
  • GAGs are classified into four groups based on core disaccharide structures. “Mucins”, as used herein, may refer to a family of high molecular weight, heavily glycosylated proteins (glycoconjugates).
  • HMO human milk oligosaccharide(s). These carbohydrates are highly resistant to enzymatic hydrolysis, indicating they may display essential functions not directly related to their caloric value. It has been especially illustrated they play a vital role in the early development of infants and young children, such as the maturation of the immune system. Many different kinds of HMOs are found in the human milk.
  • Each individual oligosaccharide is based on a combination of glucose, galactose, sialic acid (N- acetylneuraminic acid), fucose and/or N-acetylglucosamine with many and varied linkages between them, thus accounting for the enormous number of different oligosaccharides in human milk – over 130 such structures have been identified so far. Almost all of them have a lactose moiety at their reducing end while sialic acid and/or fucose (when present) occupy the terminal position at the non-reducing ends.
  • the HMOs can be divided as non-fucosylated (neutral) or fucosylated (neutral) and sialylated (acidic) and non-sialylated molecules, respectively.
  • fucosylated oligosaccharide refers to an oligosaccharide having a fucose residue. It has a neutral nature.
  • Some examples are 2’-fucosyllactose (2’-FL), 3-fucosyllactose (3-FL), difucosyllactose (DiFL), lacto-N-fucopentaose (e.g.
  • lacto-N-fucopentaose I lacto-N- fucopentaose II, lacto-N-fucopentaose III, lacto-N-fucopentaose V)
  • lacto-N-fucohexaose lacto-N-difucohexaose I, fucosyllacto-N-hexaose, fucosyllacto-N-neohexaose, difucosyllacto- N-hexaose I, difucosyllacto-N-neohexaose II and any combination thereof.
  • Fucosylated oligosaccharides represents the largest fraction of human milk with 2’-FL constituting up to 30% of the total HMOs. Fucosylated oligosaccharides are thought to reduce the risk of infections and inflammations and to boost growth and metabolic activity of specific commensal microbes reducing inflammatory response.
  • the expression “N-acetylated oligosaccharide(s)” encompasses both “N-acetyl-lactosamine” and “oligosaccharide(s) containing N-acetyl-lactosamine”. They are neutral oligosaccharides having an N-acetyl-lactosamine residue.
  • LNT lacto-N-tetraose
  • para- lacto-N-neohexaose para-LNnH
  • LNnT lacto-N-neotetraose
  • DSLNT disialyllacto-N- tetraose
  • lacto-N-hexaose lacto-N- neohexaose, para- lacto-N-hexaose, para-lacto-N-neohexaose, lacto-N-octaose, lacto-N- neooctaose, iso- lacto-N-octaose, para- lacto-N-octaose and lacto-N-decaose.
  • the expressions “at least one fucosylated oligosaccharide” and “at least one N-acetylated oligosaccharide” should be understood as “at least one type of fucosylated oligosaccharide” and “at least one type of N-acetylated oligosaccharide”.
  • the term “sialylated oligosaccharide” refers to an oligosaccharide having a charged sialic acid residue. It has an acidic nature. Some examples are 3’-sialyllactose (3-SL), 6’-sialyllactose (6- SL), sialyllacto-N-tetraose (Lst – e.g.
  • a Bifidobacterium longum transitional microorganism and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT) is effective for preventing and/or reducing the risk of developing infection is surprising.
  • 2’-FL 2'-fucosyllactose
  • DFL difucosyllactose
  • LNT lacto-N-tetraose
  • 6SL 6'-sialyllactose
  • 3SL 3'-sialyll
  • the invention provides a composition comprising a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp. infantis and 2'-fucosyllactose (2’- FL), wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I-5942 and/or has at least one identifying characteristic of the B. longum transitional strain deposited under deposit number CNCM I- 5942.
  • the composition further comprises Bifidobacterium longum subsp. infantis and/or Bifidobacterium lactis.
  • the composition further comprises Bifidobacterium longum subsp. infantis.
  • the composition further comprises Bifidobacterium lactis.
  • the composition further comprises Bifidobacterium longum subsp. infantis and Bifidobacterium lactis.
  • the present inventors have also surprisingly found that symbiotic intervention with the combination of 6HMO with three probiotic strains (namely, B. l. iuvenis, B. infantis and B. lactis) increased the levels of metabolite indole-3-propionic acid by comparison to 6HMO with B. l. iuvenis alone or 6HMO with the two strains B. infantis and B. lactis.
  • the invention provides a composition comprising a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp. infantis and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP- I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT), wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I-5942 and/or has at least one identifying characteristic of the B.
  • ANI Average Nucleotide Identity
  • the invention provides a nutritional composition comprising a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp. infantis and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N- tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N- fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT), wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I-5942 and/or
  • ANI Average Nucleotide Identity
  • the invention provides a combination comprising or consisting of a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp.
  • the combination consists of the Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp. infantis and a HMO mixture consisting of 2'-fucosyllactose (2’- FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N- neotetraose (LNnT).
  • 2'-fucosyllactose 2'-fucosyllactose
  • DFL difucosyllactose
  • LNT lacto-N-tetraose
  • 6SL 6'-sialyllactose
  • the composition further comprises Bifidobacterium lactis.
  • the combination comprises or consists of the Bifidobacterium longum transitional microorganism, a HMO mixture, Bifidobacterium longum subsp.
  • HMO mixture consists of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N- neotetraose (LNnT).
  • 2’-FL 2'-fucosyllactose
  • DFL difucosyllactose
  • LNT lacto-N-tetraose
  • 6SL 6'-sialyllactose
  • 3SL 3'-sialyllactose
  • lacto-N-fucopentaose I lacto-N-fucopentaose I
  • the combination consists of the Bifidobacterium longum transitional microorganism, and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT).
  • the combination includes Bifidobacterium longum subsp.
  • the combination includes Bifidobacterium lactis.
  • the combination includes Bifidobacterium longum subsp. infantis and Bifidobacterium lactis.
  • Bifidobacterium longum transitional microorganism Bifidobacterium longum subsp microorganisms of a clade that is present in the gut microbiome of the transitional feeding period of mammals, particularly humans, have previously been identified.
  • B. longum microorganisms belonging to this clade are referred to herein as Bifidobacterium longum transitional (B. longum transitional) and are also known in the art as B. longum subsp. iuvenis. B.
  • NCC 5000, NCC 5001, NCC 5002, NCC 5003 and NCC 5004 were deposited with the CollectionInstitut de cultures de micro- organisms (CNCM), Institute Pasteur (INSTITUT PASTEUR, 25 RUE DU DOCTEUR ROUX, F-75724 PARIS CEDEX 15, FRANCE) by SOCIÉTÉ DES PRODUITS NESTLÉ S.A according to Budapest Treaty on 11th of May 2021 receiving the deposit numbers CNCM I-5683, CNCM I-5684, CNCM I-5685, CNCM I-5686 and CNCM I-5687, respectively.
  • US provisional patent application 63/216127 it was shown that the B.
  • longum transitional microorganisms are greater in relative abundance during the transitional feeding period (e.g. weaning period) than either B. longum subsp. infantis (B. infantis) or B. longum subsp longum. Indeed, the relative abundance of B. longum subsp. infantis decreases at the beginning of the transitional feeding period until the end of the transitional feeding period while B. longum subsp. longum begins to increase in abundance. Vatanen et al.
  • B. longum subsp. iuvenis strain NCC 5025 was deposited with the Collection Nationale de Cultures de Micro-organisms (CNCM), Institute Pasteur by SOCIÉTÉ DES PRODUITS NESTLÉ S.A according to Budapest Treaty on the 29 th of March 2023 receiving the deposit number CNCM I-5942.
  • CNCM Collection Nationale de Cultures de Micro-organisms
  • the Bifidobacterium longum transitional microorganism for use according to the invention has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I-5942 and/or has at least one identifying characteristic of the B. longum transitional strain deposited under deposit number CNCM I-5942.
  • the Bifidobacterium longum transitional microorganism for use according to the invention has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I-5942.
  • the Bifidobacterium longum transitional microorganism for use according to the invention has at least one identifying characteristic of the B. longum transitional strain deposited under deposit number CNCM I-5942.
  • the Bifidobacterium longum transitional microorganism for use according to the invention has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I-5942 and has at least one identifying characteristic of the B. longum transitional strain deposited under deposit number CNCM I-5942.
  • the B. longum subsp. iuvenis may be B. longum subsp. iuvenis NCC 5025.
  • the B. longum transitional microorganism may be a Bifidobacterium longum transitional microorganism strain deposited with CNCM under deposit number CNCM I-5942 or a B. longum transitional strain having at least one identifying characteristic of the B.
  • an identifying characteristic of the present B. longum transitional strain may refer to one or more of the phenotypic or genotypic characteristics described herein.
  • the present invention provides a B. longum transitional microorganism strain which has an Average Nucleotide Identity (ANI) of at least 99% to the B. longum transitional strain deposited with the CNCM under deposit number CNCM I-5942.
  • ANI Average Nucleotide Identity
  • longum transitional strain has an ANI of at least at least 99.0%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, or at least 99.9%, compared to the B. longum strain deposited with the CNCM under deposit number CNCM I-5942.
  • the B. longum transitional strain has an ANI of at least 99.9% compared to the B. longum strain deposited with the CNCM under deposit number CNCM I-5942.
  • the B. longum transitional strain has an ANI of at least 99.9% compared to the B. longum strain deposited with the CNCM under deposit number CNCM I-5942.
  • the B. longum transitional strain has an ANI of at least 99.9% compared to the B. longum strain deposited with the CNCM under deposit number CNCM I-5942.
  • longum transitional strain has an ANI of at least 98.1%, at least 98.2%, at least 98.3%, at least 98.4%, of at least 98.5%, of at least 98.6%, of at least 98.6 %, of at least 98.7 %, of at least 98.8 %, of at least 98.9 %, of at least 99 %, of at least 99.1 %, of at least 99.2 %, of at least 99.3 %, of at least 99.4 %, of at least 99.5 %, of at least 99.6 %, of at least 99.7 %, of at least 99.8 %, or of at least 99.9 % compared to the B.
  • the B. longum transitional strain has an ANI of at least 98.4%, of at least 98.5%, of at least 98.6%, of at least 98.6 %, of at least 98.7 %, of at least 98.8 %, of at least 98.9 %, of at least 99 %, of at least 99.1 %, of at least 99.2 %, of at least 99.3 %, of at least 99.4 %, of at least 99.5 %, of at least 99.6 %, of at least 99.7 %, of at least 99.8 %, or of at least 99.9 % compared to the B.
  • longum strain deposited with the CNCM under deposit number CNCM I- 5942 has at least one identifying characteristics of the B. longum transitional strain deposited under deposit number CNCM I-5942 – as described herein.
  • Methods for sequencing microbial genomes are well known in the art (see e.g. Segerman; Front. Cell. Infect. Microbiol.; 2020; 10; Article 527102 & Donkor; Genes; 2013; 4(4); 556-572).
  • metagenomics methods may be used. Suitable metagenomics methods may be performed using shotgun sequencing data, for example.
  • the ANI between two bacterial genomes can be determined, for example, by averaging the nucleotide identity of orthologous genes identified as bidirectional best hits (BBHs).
  • Protein-coding genes of a first genome (Genome A) and second genome (Genome B) are compared at the nucleotide level using a similarity search tool, for example, NSimScan (Novichkov et al., Bioinformatics 32(15): 2380-23811 (2016)). The results are then filtered to retain only the BBHs that display at least 70% sequence identity over at least 70% of the length of the shorter sequence in each BBH pair.
  • the ANI of Genome A to Genome B is defined as the sum of the percent identity times the alignment length for all BBHs, divided by the sum of the lengths of the BBH genes.
  • the B. longum transitional microorganism for use in the present invention is isolated from a human.
  • the B. longum transitional microorganism is not of the subspecies B. longum subsp. longum or B. longum subsp. infantis.
  • the B. longum transitional microorganism is provided as a probiotic.
  • the B. longum transitional microorganism is provided in a composition.
  • the composition or combination according to the invention may contain from 10 3 to 10 12 cfu of the B.
  • the B. longum transitional microorganism is administered to the subject in an amount of at least about 10 6 cfu/day, at least about 10 7 cfu/day, or at least about 108 cfu/day.
  • the B. longum transitional microorganism is administered to the subject in an amount of about 10 12 cfu/day or less, about 10 11 cfu/day or less, or about 10 10 cfu/day or less. In one embodiment, the B.
  • antibiotics in addition, the wide-spread use of antibiotics means that it is increasingly challenging to provide bacterial strains that do not have transferrable resistance to one or more EFSA relevant antibiotics. It is known that a single gene may instill antibiotic resistance against a particular antibiotic, and that bacteria can transfer genes through horizontal gene transfer via conjugation, transduction or transformation. Accordingly, it is known that antibiotic resistance may be transferred between bacteria via horizontal gene transfer; including in the gut microbiome. It is therefore advantageous that the present B. longum transitional strain does not harbor transferrable antibiotic resistance to one or more antibiotics as this reduces the risk of the antibiotic resistance being transferred to other components of the microbiome when the present B. longum transitional strain is used as a probiotic.
  • the present B. Longum transitional strain may lack a tet(W) gene.
  • the present B. longum transitional strain may lack a tet(W) gene encoding a polypeptide shown as SEQ ID NO: 1 or a variant which shares at least 80% sequence identity to SEQ ID NO: 1.
  • the variant may share at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identity with SEQ ID NO: 1.
  • Longum transitional strain may lack a tet(Q) gene.
  • the present B. longum transitional strain may lack a tet(Q) gene encoding a polypeptide shown as SEQ ID NO: 2 or a variant which shares at least 80% sequence identity to SEQ ID NO: 2.
  • the variant may share at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identity with SEQ ID NO: 2.
  • the present B. Longum transitional strain may lack an erm(X) gene.
  • the present B. Longum transitional strain may lack an erm(X) gene which encodes a protein comprising SEQ ID NO: 4 or a variant which shares at least 80% sequence identity to SEQ ID NO: 4.
  • the variant may share at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identity with SEQ ID NO: 4.
  • SEQ ID NO: 4 MSAYGHGRHENGQNFLTNHKIINSIIDLVKQTSGPIIEIGPGSGALTHPMAHLGRAITAVEVDAKLAAKLTQETS SAAVEVVHDDFLNFRLPATPCVIVGNIPFHLTTAILRKLLHAPAWTDAVLLMQWEVARRRAGVGASTMMTAQWSP WFTFHLGSRVPRTAFRPQPNVDGGILVIRRVGDPKIPIEQRKAFQAMVHTVFTARGRGIGEILRRAGLFSSRSET QSWLRSRGIDPATLPPRLHTNDWIDLFQVTGSSLPHHRPISPSGSSQRPPQQKNRSRRR Resistance to streptomycin may be afforded by a mutation within the rpSL gene which encodes a ribosomal S12 protein.
  • the present B. Longum transitional strain may have an A residue a position 128 of the rpSL gene.
  • the present B. Longum transitional strain does not comprise a G128A mutation in the rpSL gene.
  • An illustrative rpSL gene sequence comprising an A at position 128 is shown as SEQ ID NO: 5.
  • the present B. longum transitional strain may lack a crmX gene.
  • the present B. longum transitional strain may lack a crmX gene encoding a polypeptide comprising SEQ ID NO: 6 or a variant which shares at least 80% sequence identity to SEQ ID NO: 6.
  • the variant may share at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identity with SEQ ID NO: 6.
  • Carbohydrate-Active Enzymes are responsible for the synthesis and breakdown of glycoconjugates, oligo- and polysaccharides. They typically correspond to 1-5% of the genes in the living organism. Glycoconjugates, oligo- and polysaccharides play essential roles in many biological functions, for example as structure and energy reserve components and in many intra- and intercellular events.
  • the Carbohydrate Active Enzyme (CAZy) classification is a sequence-based family classification system that correlates with the structure and molecular mechanism of CAZymes (www.cazy.org).
  • CAZymes include glycoside hydrolyases (GH), glycosyltransferases (GT), polysaccharide lyases (PL), carbohydrate esterases (CE), and carbohydrate-binding module families (CBM) GHs catalyze the hydrolysis of glycosidic bonds between two or more carbohydrates or between a carbohydrate and a non-carbohydrate moiety. In most cases, the hydrolysis of the glycosidic bond is catalyzed by two amino acid residues of the enzyme: a general acid (proton donor) and a nucleophile/base. Depending on the spatial position of these catalytic residues, hydrolysis occurs via overall retention or overall inversion of the anomeric configuration.
  • GH glycoside hydrolyases
  • GT glycosyltransferases
  • PL polysaccharide lyases
  • CE carbohydrate esterases
  • CBM carbohydrate-binding module families
  • a GH classification system is provided by the CAZy classification.
  • GHs are divided into families based on molecular function (e.g., GH1, GH2, GH3, GH4, etc.). These families are then further divided into subfamilies based on subgroups found within a family that share a more recent ancestor and, typically more uniform in molecular function (e.g., GH13_1, GH13_2, GH13_3, GH13_4, etc.).
  • the present B. Longum transitional strain encodes a glycosyl hydrolase family 43_17 (GH43_17) enzyme.
  • GH43_17 comprises both ⁇ -L-arabinofuranosidase (EC 3.2.1.55) and endo- ⁇ -1,4-xylanase (EC 3.2.1.8) activities, with capacity to breakdown complex carbohydrates like arabinan, arabinogalactan, and arabinoxylan.
  • the GH43_17 gene comprises SEQ ID NO: 7 or a sequence with at least 60% sequence identity to SEQ ID NO: 7.
  • the GH43_17 gene comprises a sequence with at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 7.
  • the B. Longum transitional strain comprises a GH43_22 gene encoding a protein shown as SEQ ID NO: 11 or a sequence with at least 80% sequence identity to SEQ ID NO: 11m and a GH43_22 gene encoding a protein shown as SEQ ID NO: 12, or a sequence with at least 80% sequence identity to SEQ ID NO: 12.
  • the protein may comprise a sequence with at least 85%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 11 or 12 SEQ ID NO: 11 MKHWKKMAASLVAISTMMAVVPTTYAMESEDSQPQTTDTATVQTTKAAEPTLLASWDFTGKNGTTNSAIADSTGK YNLTLKDGAKIEQYGDRSTNEALSLRGDGQYAQIDDQLFKDAGDSFTLEFASKTRHDDSGKFFSFIVGKDGSNDA NTTDQANANKYLMFYNSKTAIKGVISNNNWGNEQGSKVTVSGNDNSWADYKIVVDGTNLAVFRNNALIIFKANTG IKMSDLGATTAYIGKSFYSVDEYWNGAMDDIKVYRGADLTMPTAVAISGTGVVNNKLTLIEKDSTKLTATVTPDD AVSKNVTWSSSDESVAKVAADGTVTGVKAGTATITATTELGGVKAELP
  • Longum transitional strain comprises a glycosyl hydrolase family 43_27 (GH43_27) gene.
  • the GH43_27 gene comprises SEQ ID NO: 13 or a sequence with at least 60% sequence identity to SEQ ID NO: 13.
  • the GH43_27 gene comprises a sequence with at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 13.
  • Longum transitional strain comprises a glycosyl hydrolase family 43_29 (GH43_29) gene.
  • the GH43_29 gene comprises SEQ ID NO: 15 or a sequence with at least 60% sequence identity to SEQ ID NO: 15.
  • the GH43_29 gene comprises a sequence with at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 15.
  • the protein may comprise a sequence with at least 85%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 16.
  • SEQ ID NO: 16 MSFHVSAQSVRAVAGGLVAAATLLSGLALAPTAMAADSATADNAPSVAGHAYNELPYNNPDVTVTQIDNSALPSY MRNPIGQNEGIDTPNDLSQNYYSADASALSYDGKLFVFTGHDEASPDYGSFNMKDWGVYVTDEDGLNQGKWTHYK TIAKADLFSWATGDGAYAGQVVADDNGTPSDTSDDWFYYVPVKDKASEAAGQDPFAIGVAKSKSPLGPWKDTIG KPLLTTSQTQIETIDPAFFVDEDGTGYLHFGTFGTQLAIKMKKDATTGRTSYTEVETKADGTTPNLHTMKDADSN ANGPKGFFEAAWVFRKGDTYYNVYDGGKPGSGTATCVESNYQACIQYST
  • Longum transitional strain comprises a glycosyl hydrolase family 121 (GH121) gene.
  • the GH121 gene comprises SEQ ID NO: 17 or a sequence with at least 60% sequence identity to SEQ ID NO: 17.
  • the GH121 gene comprises a sequence with at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 17.
  • Longum transitional strain comprises a GH43_17 gene and one or more genes selected from a GH43_22, GH43_27, GH43_29 and GH121 gene as defined herein.
  • the B. Longum transitional strain comprises a GH43_17, GH43_22, GH43_27, GH43_29 and GH121 gene as defined herein.
  • one or more of the arabinan-degrading GHs described herein comprises a signal peptide.
  • a ‘signal peptide’ may refer to a short amino acid sequence, typically present at the N-terminus of a polypeptide, which allows the polypeptide to be secreted out of abacterial cell.
  • a ‘primary degrader’ may refer to a bacterium that is capable of depolymerizing specific polysaccharides to mono-, di-, and oligosaccharides that they can take up and ferment themselves to acidic end products such as acetate or lactate.
  • the GH43_22, GH43_27, GH43_29, GH_121, GH43_24 and/or GH30_5 enzyme may comprise a signal peptide.
  • each of the GH43_22, GH43_27, GH43_29, GH_121, GH43_24 and GH30_5 enzymes may comprise a signal peptide.
  • the present B. longum transitional strain comprises a glycosyl hydrolase family gene that encodes a CAZyme that targets arabinogalactans.
  • the present B. longum transitional strain comprises a glycosyl hydrolase family 43_24 (GH43_24) gene.
  • the GH43_24 gene comprises SEQ ID NO: 19 or a sequence with at least 60% sequence identity to SEQ ID NO: 19.
  • the GH43_24 gene comprises a sequence with at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 19.
  • SEQ ID NO: 19 ATGAAGATAAACAATAAGGGCAAGGGCGCTCTTATCGCGGCAATTACCGCCGCGGCAACGCTATTGTCATGCGGG CTGGCCGCTGCAAGTGCCAGTGCGGCAGGTGTGAATTACCTGCCTACCATCGGCCAAGTGCCGACATACACCAAG TTCCAGCCCACAGCCGATCCGGGCAAGAACGCTAGCGATTACTTCCAGCCATATTGGTATGCCAAGAACGCCAAT GATAATGGCGGCACACACATCCAAGCGCACGGTGGCCAAGTGGTCAAGGTTGGCGACGCCTACTACTGGTATGGC GAAGACCGTTCTAACGGTTACGACAACAGCCCCGGTGTTCATGCTTATATGTCGACAGATCTATACAACTGGACC GATCTTGGTGTGGCGCTGCGTGCGGTGACC
  • the protein may comprise a sequence with at least 85%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 20.
  • SEQ ID NO: 20 MKINNKGKGALIAAITAAATLLSCGLAAASASAAGVNYLPTIGQVPTYTKFQPTADPGKNASDYFQPYWYAKNAN DNGGTHIQAHGGQVVKVGDAYYWYGEDRSNGYDNSPGVHAYMSTDLYNWTDLGVALRAVTSKSQLTDKSNADYAY FDKAYNLTKSDGSVDAAKADAIFPYLNTNPDQDGDGAVDSVQGIFERPKIIYNKKNKQYVLWWHSDGSTTPGGSN YARALAGVAVSDNPAGPFTMVGAYRLPNQNNWKEAAGNPSWGENGDSRDMTVFVDPKDDSAYVLYSSEANATLYI AKLNDDYTNVVKTTNVDQSEGQKQYSADGQYPYILADATT
  • longum transitional strain comprises a glycosyl hydrolase family 127 (GH127) gene.
  • the GH127 gene comprises SEQ ID NO: 21 or a sequence with at least 60% sequence identity to SEQ ID NO: 21.
  • the GH127 gene comprises a sequence with at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 21.
  • the protein may comprise a sequence with at least 85%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 22.
  • SEQ ID NO: 22 MNVTITSPFWKRRRDQIVESVIPYQWGVMNDEIDTTVPDDPAGNQLADSKSHAVANLKVAAGELDDEFHGMVFQD SDVYKWLEEAAYALAYHPDPELKALCDRTVDLIARAQQPDGYLDTPYQIKSGVWADRPRFSLIQQSHEMYVMGHY IEAAVAYHQVTGNEQALEVAKKMADCLDANFGPEEGKIHGADGHPEIELALAKLYEETGEKRYLTLSQYLIDVRG QDPQFYTKQLKALNGDNIFPDLGFYKPTYFQAAEPVRDQQTADGHAVRVGYLCTGVAHVGRLLGDRGLIDTAKRF WTNIVARRMYVTGAIGSTHVGESFTYDYDLPNDTMYGETCASVAMSMFAQQMLDLE
  • longum transitional strain comprises a glycosyl hydrolase family 30_5 (GH30_5) gene.
  • the GH30_5 gene comprises SEQ ID NO: 23 or a sequence with at least 60% sequence identity to SEQ ID NO: 23.
  • the GH30_5 gene comprises a sequence with at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 23.
  • the protein may comprise a sequence with at least 85%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 24.
  • SEQ ID NO: 24 MKVLSKSLAAMVAAATLVGGGAFAVAGTAYAADNDAITVTPNPWYANSFDGWGTSLAWFANATGSLGEESAITTN LGDDASKAKAVEYGKQLREQFYQSIFGDEGLDLNMARYNVGGGNASDVAYGYPFMRQGAAVPGTWKDDATGSGTY GNGVTTKQADKDKLAAAFDPTDDNQYDFSKSAAQDWWIERGATGDNPDITDVEAFANSAPWFLTNSGYATGGRNS GSNNLANPEKFAQYMAKNVEHLESLGANVDTVEPFNESETSYWGTPGDMASKYTDESDDNTKLINNYWDKYYSDK DKSVTPYANALKKPQEGMHVSNAQQQQTITALAEALKDNDDTIIAATDATNSADFVKS
  • longum transitional strain comprises a glycosyl hydrolase family 43_32 (GH42_32) gene.
  • the GH42_32 gene comprises SEQ ID NO: 25 or a sequence with at least 60% sequence identity to SEQ ID NO: 25.
  • the GH42_32 gene comprises a sequence with at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 25.
  • the protein may comprise a sequence with at least 85%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 26.
  • SEQ ID NO: 26 MTATISNGVSASYSPAEDELGAADPTALLAESGDLKPLAERTYTNPVPYADGKSHTAPDPFVLKYRDLYYCYATD EHGILVSTSPDMVHWTSHGFCYTEAGRRNFWAPSVILINGVFHMYFSNMPAEETDTHTEIMRVAVSEDPLGPFEK KAELFNTFAIDSQVVYGDDGQLYLLYADNQVTGLSDDRPGTSVMIDRLVTPYSRENKPRPLIVPTMDEEIFARNR FGDGRDWHTVEGATYFAYRDRAFITYSANAYEHEDYFVGYSYAQLPNKQADAHIDQLDWTKQLNENRFDPLLIRS PKVEGTGHNSIVKAPNAVDDWIVYHGRNADDELYVGTEQRVMRIDPLYYAEGGLDTPGPTAAAQSAPLYG
  • the longum transitional strain comprises one or more genes selected from a GH43_24, GH127, GH30_5, and GH 43_32 gene as defined herein.
  • the B. longum transitional strain comprises a GH43_17 gene and one or more selected from a GH43_24, GH127, GH30_5, and GH 43_32 gene as defined herein.
  • the B. longum transitional strain comprises a GH43_17, GH43_24, GH127, GH30_5, and GH 43_32 gene as defined herein.
  • the B. longum transitional strain comprises a GH43_17, GH43_24, GH127, GH30_5, and GH 43_32 gene as defined herein.
  • longum transitional strain comprises a GH43_17, GH43_22, GH43_27, GH43_29, GH121, GH43_24, GH127, GH30_5, and GH 43_32 gene as defined herein.
  • the B. longum transitional strain comprises a GH43_17, GH43_22, GH43_27, GH43_29, GH121, GH43_24, GH127, GH30_5, GH 43_32, as defined herein.
  • GH43_17 gene cluster Suitably, the B.
  • longum transitional strain may comprise one or more genes encoding for a family 31 glucosidase (GH31), an ABC transporter, a Lac-I type regulator, a MFS transporter and/or an AraC family transcriptional regulator.
  • the present B. longum transitional strain comprises a glycosyl hydrolase family 31 (GH31) gene.
  • the GH31 gene comprises SEQ ID NO: 27 or a sequence with at least 60% sequence identity to SEQ ID NO: 27.
  • the GH31 gene comprises a sequence with at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 27.
  • the gene may encode a polypeptide with at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 32.
  • the gene may encode a polypeptide with at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 33.
  • the gene may encode a polypeptide with at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 34.
  • the longum transitional strain comprises a Lac-I type regulator gene.
  • the Lac-I type regulator gene comprises SEQ ID NO: 35 or a sequence with at least 60% sequence identity to SEQ ID NO: 35.
  • the Lac-I type regulator gene comprises a sequence with at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 35.
  • the protein may comprise a sequence with at least 85%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 36.
  • SEQ ID NO: 36 MVTINDVAREAGVSKTTVSFVLSGSRPVAAATEQRIREAMDRLGYTVNHAARSLSTSKTMTIAVVTSN RQDAYFDIARGTYINGLSRAAAETGYDMLITNDPDGSATENACQSHKADGLVFLDVRQNDPRVPIAAE
  • SGIPTVSLGVPVNPMNLDVVDTDFTDMAASTMRTLHDAGHRRVSVITLSSRVIAEQLNDTARFLREIE RSGERLGMHATIRHCSTRPGIIDTDIARILDGRGEDTAFVIHNESAVLVFRRAVEHRGLRIPEDISVI AINEKQMSDALYLPYSAYENDVELVTQSAVNTLVDRIEHPELTPTRTLIKASYIDRDSVANI Suitably, the present B.
  • longum transitional strain comprises a facilitator superfamily (MFS) gene.
  • MFS facilitator superfamily
  • the MFS gene comprises SEQ ID NO: 37 or a sequence with at least 60% sequence identity to SEQ ID NO: 37.
  • the MFS gene comprises a sequence with at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 37.
  • the protein may comprise a sequence with at least 85%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 38.
  • SEQ ID NO: 38 MAEFHYAIGHFHCAGHRIGCSGIPGQLALQRADDCFGITLTALVGAWLTGKLASILSRKTVALIGAGGMLLFGLL PYFVHSSLAAVIAFSALMGVCLGFINNVLPTLISVHYEGDERQSIMGQQVAVASIGAMVFMTVAGKLATAQWYHA YLIYLFAAVVLVVCAFTLPTKNGETDEAGRIQGTGPSASIREVMTGKLWFLVVAGFFFLLANNAYSNNLSLLVEQ RGLGDAGTAGLISTIGQFGGLLAGLCVGLMVRFVKNHLLMVGFIVEGLSLLLLGCSASLPLLIIGSFFAGAGLSI YYAQAPFLVTVIEKPYLIPLGIAAMTTANALGGFASPVLVNAINGLFGSHAAGAMFIGAAIALAGAVALGVSGF
  • the longum transitional strain comprises an AraC family transcriptional regulator gene.
  • the AraC gene comprises SEQ ID NO: 39 or a sequence with at least 60% sequence identity to SEQ ID NO: 39.
  • the AraC gene comprises a sequence with at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to SEQ ID NO: 39.
  • the Bifidobacterium lactis has at least 99.9% ANI to Bifidobacterium lactis CNCM 1-3446.
  • Bifidobacterium lactis CNCM 1-3446 was deposited with the Collection Nationale de Cultures de Microorganismes (CNCM), Institut Pasteur (INSTITUT PASTEUR, 25 RUE DU DOCTEUR ROUX, F-75724 PARIS CEDEX 15, FRANCE) by NESTEC S.A. (NESTEC S.A., AVENUE NESTLE 55, CH-1800 VEVEY) according to the Budapest Treaty on 7 th June 2005 receiving the deposit number CNCM 1-3446.
  • composition or combination according to the invention may contain from 10 3 to 10 12 cfu of Bifidobacterium lactis, more preferably between 10 7 and 10 12 cfu such as between 10 8 and 1010 cfu of Bifidobacterium lactis per g of composition or combination on a dry weight basis.
  • the Bifidobacterium lactis is administered to the subject in an amount of at least about 10 6 cfu/day, at least about 10 7 cfu/day, or at least about 10 8 cfu/day.
  • the Bifidobacterium lactis is administered to the subject in an amount of about 1012 cfu/day or less, about 10 11 cfu/day or less, or about 10 10 cfu/day or less. In one embodiment, the Bifidobacterium lactis is viable.
  • the invention provides a composition comprising a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp. infantis and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'- sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT) for use in preventing, reducing the risk of and/or treating an infection in a subject, wherein the Bifidobacterium longum transitional microorganism has an Average Nucleo
  • the invention provides a composition comprising a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp. infantis, Bifidobacterium lactis and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT) for use in preventing, reducing the risk of and/or treating an infection in a subject, wherein the Bifidobacterium longum transition
  • the invention provides a nutritional composition comprising a Bifidobacterium longum transitional microorganism and a HMO mixture consisting of 2'- fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3- FL) and/or lacto-N-neotetraose (LNnT) for use in preventing, reducing the risk of, and/or treating an infection in a subject, wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I
  • ANI Average Nucleotide Identity
  • the invention provides a nutritional composition comprising a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp. infantis and a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N- tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N- fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT) for use in preventing, reducing the risk of, and/or treating an infection in a subject, wherein the Bifidobacterium longum transitional microorganism has an Average Nu
  • the invention provides a method of preventing, reducing the risk of and/or treating an infection in a subject, wherein the method comprises administering a nutritional composition according to the invention to the subject.
  • the composition or nutritional composition is for use in preventing and/or reducing the risk of an infection in a subject.
  • the invention also provides a combination of a Bifidobacterium longum transitional microorganism and a HMO mixture for use in preventing, reducing the risk of and/or treating an infection in a subject; wherein the HMO mixture consists of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT), and wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I-5942 and/or has at least one identifying characteristic of the B.
  • ANI Average Nucleotide Identity
  • the invention also provides a combination of a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp. infantis and a HMO mixture for use in preventing, reducing the risk of and/or treating an infection in a subject; wherein the HMO mixture consists of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT) and wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I-5942 and/
  • ANI Average Nucleotide Identity
  • the invention provides a combination of a Bifidobacterium longum transitional microorganism, Bifidobacterium longum subsp. infantis, Bifidobacterium lactis, and a HMO mixture for use in preventing, reducing the risk of and/or treating an infection in a subject; wherein the HMO mixture consists of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally 3- fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT), and wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (
  • the invention provides the use of a combination according to the invention for the manufacture of a medicament for preventing, reducing the risk of and/or treating an infection in a subject.
  • the invention provides a method of preventing, reducing the risk of and/or treating an infection in a subject, wherein the method comprises administering a combination according to the invention to the subject.
  • the composition or nutritional composition is for use in preventing and/or reducing the risk of an infection in a subject.
  • the Bifidobacterium longum transitional microorganism may be a Bifidobacterium longum transitional microorganism as described herein.
  • the HMO mixture may be a HMO mixture as described herein.
  • the Bifidobacterium longum subsp. infantis may be a Bifidobacterium longum subsp. infantis as described herein.
  • the Bifidobacterium lactis may be a Bifidobacterium lactis as described herein.
  • the combination (e.g. of a Bifidobacterium longum transitional microorganism and a HMO mixture) may be provided in any form as described herein.
  • the combination may be provided in a composition as described herein.
  • the B. longum transitional microorganism and HMO mixture may be administered separately, simultaneously or sequentially.
  • longum transitional microorganism and HMO mixture may be administered in a combined composition.
  • the B. longum transitional microorganism, HMO mixture, Bifidobacterium longum subsp. infantis and/or Bifidobacterium lactis may be administered separately, simultaneously or sequentially.
  • the B. longum transitional microorganism, HMO mixture, Bifidobacterium longum subsp. infantis and Bifidobacterium lactis may be administered in a combined composition.
  • infantis and/or Bifidobacterium lactis and a HMO mixture may be referred to as a “synbiotic”.
  • “Infection”, as used herein, may refer to a disease or disorder caused by an infectious agent or pathogen (including symptoms thereof).
  • “Preventing”, as used herein, may refer to administering the composition and/or combination and/or prebiotic of the invention to a subject who has not yet contracted an infection and/or who is not showing any symptoms of the infection to prevent or impair the cause of the disease or to reduce or prevent development of at least one symptom associated with the disease.
  • the subject may have a predisposition for, or be thought to be at risk of developing, the disease.
  • “Reducing the risk of an infection” may refer to administering the composition and/or combination and/or prebiotic of the invention to a subject who has not yet contracted an infection and/or who is not showing any symptoms of the infection to reduce the likelihood of the infant or young child developing a disease caused by infectious agent or pathogen.
  • the administration may prevent or impair the cause of the disease or reduce or prevent development of at least one symptom associated with the disease.
  • the subject may have a predisposition for, or be thought to be at risk of developing, the disease.
  • treating or “treatment”, it is meant a decrease of the duration and/or of the severity of a physical state, a condition or their consequences (e.g. a decrease or elimination of symptoms of the condition).
  • Treatment also encompasses to reduce, alleviate or eliminate one or more symptoms associated with the disease, disorder or condition which is being treated and/or to slow down, reduce or block the progression of the disease, disorder or condition which is being treated.
  • the prevention and/or the treatment of a physical state, a condition or their consequences can occur during the treatment (i.e. during the administration of the composition of the present invention, either immediately after the start of the administration or some time after, e.g. some days or weeks after the start). But it can also encompass the prevention and/or the treatment later in life.
  • the term “later in life” encompasses the effect after the termination of the intervention or treatment.
  • the effect “later in life” can be from 1 week to several months, or even years, for example from 2 to 4 weeks, from 2 to 6 weeks, from 2 to 8 weeks, from 1 to 6 months or from 2 to 12 months.
  • the effect “later in life” can be from 12 months to 12 years, such as from 2 years to 10 years, or from 4 years to 5 years, after the termination of the intervention or treatment.
  • the effect “later in life” lasts until the subject is at least 5 years of age, such as at least 10 years of age, at least 20 years of age or at least 30 years of age.
  • the present use to prevent and/or reduce the risk of an infection may be referred to as a prophylactic use to delay or prevent the onset of the symptoms of the infection and/or reduce the number or severity of symptoms of the infection.
  • administering the composition and/or combination and/or prebiotic of the invention to a subject may reduce the magnitude and/or amount of symptoms of an infection caused by the infectious agent or pathogen.
  • the present composition and/or combination and/or prebiotic may be administered to an infant, young child or child.
  • the present composition and/or combination and/or prebiotic may prevent and/or reduce the risk of an infection in a subject.
  • the composition and/or combination and/or prebiotic may increase the levels of short- chain fatty acids (SFCA) in the subject.
  • the SCFA may be selected from acetate (Ethanoate, C1:0), butyrate (Butanonate, C4:0) and/or propionate (Propanoate, C3:0).
  • SCFAs are produced when dietary fiber is fermented in the colon. SCFAs have diverse physiological roles in body functions; they can affect the production of lipids, energy and vitamins; affect appetite and cardiometabolic health; and have roles in lowering blood pressure in experimental models.
  • Influenza B virus (IBV) and Influenza C virus (ICV) primarily infect humans
  • Influenza D virus (IDV) is found in cattle and pigs.
  • IAV and IBV circulate in humans and cause seasonal epidemics, and ICV causes a mild infection, primarily in children. IDV can infect humans but is not known to cause illness.
  • influenza viruses are primarily transmitted through respiratory droplets produced from coughing and sneezing. Transmission through aerosols and intermediate objects and surfaces contaminated by the virus also occur.
  • Respiratory syncytial virus (RSV) a negative-sense, single-stranded RNA virus. It is the single most common cause of respiratory hospitalization in infants, with infection rates typically higher during the cold winter months, causing bronchiolitis.
  • compositions, combination and/or prebiotic of the invention is, in particular, effective for use in the treatment and/or prevention of a viral infection in a subject.
  • the composition, combination and/or prebiotic of the invention is particularly effective in treating, preventing, reducing the risk of contracting and/or reducing the symptoms of a viral infection caused by RSV.
  • composition of the invention is particularly preferred for use in treating, preventing, reducing the risk of contracting and/or reducing the symptoms of RSV- induced bronchiolitis or RSV-induced pneumonia.
  • the invention further provides a prebiotic for use in preventing, reducing the risk of and/or treating an infection in a subject by promoting the growth of a Bifidobacterium longum transitional microorganism in the gut of the subject, wherein the prebiotic is a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'- sialyllactose (6SL), and 3'-sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT), and wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 98% with CNCM I-5942 and/or
  • the invention provides the use of a prebiotic for the manufacture of a medicament for preventing, reducing the risk of and/or treating an infection in a subject by promoting the growth of a Bifidobacterium longum transitional microorganism in the gut of the infant or young child, wherein the prebiotic is a HMO mixture consisting of 2'-fucosyllactose (2’-FL), difucosyllactose (DFL), lacto-N-tetraose (LNT), 6'-sialyllactose (6SL), and 3'- sialyllactose (3SL), and optionally lacto-N-fucopentaose I (LNFP-I), 3-fucosyllactose (3-FL) and/or lacto-N-neotetraose (LNnT), and wherein the Bifidobacterium longum transition
  • the HMO mixture may be as defined herein.
  • the prebiotic is for use in preventing and/or reducing the risk of an infection in a subject.
  • the subject is an infant or a young child.
  • the composition and/or combination of the invention may further comprise a prebiotic (i.e. in addition to the HMO mixture as described herein).
  • the prebiotic is a glycan substrate. Glycan Substrate / Carbohydrate-Active Enzymes (CAZymes)
  • the B. longum transitional microorganisms encode a profile of Carbohydrate-Active Enzymes (CAZymes).
  • targeting these CAZymes by, for example, providing the HMO mixture as described herein and/or suitable glycan substrates in the form of a prebiotic, may promote the growth and/or survival of the Bifidobacterium longum transitional microorganisms in the gut microbiota of an infant or young child.
  • promoting the growth and/or survival of the B longum transitional microorganism may refer to increasing the number and/or concentration of the B longum transitional microorganism in the gut microbiota.
  • the prebiotic for use in the present invention may comprise a glycan substrate that is capable of being degraded by a CAzyme as described herein.
  • the prebiotic for use in the present invention may comprise a combination of glycan substrates that is capable of being degraded by a CAZyme as described herein. Suitable glycan substrates are known in the art.
  • the combination of glycan substrates may comprise at least 2, at least 4, at least 10, at least 20, at least 30, at least 40 or at least 50 glycan substrates.
  • the prebiotic may comprise at least 2, at least 4, at least 10, at least 20, or at least 30 glycan substrates.
  • the glycan substrate may be a complex carbohydrate like arabinan, arabinogalactan, and arabinoxylan.
  • the glycan substrate may comprise or consist of pectin, arabinogalactan and/or starch.
  • the glycan substrate may comprise or consist of pectin.
  • the glycan substrate may comprise or consist of arabinogalactan.
  • the glycan substrate may comprise or consist of starch.
  • the present B. longum transitional microorganism grows well on a set of food derived fibres (e.g. inulin and arabinan).
  • the glycan substrate may comprise or consist of inluin.
  • the glycan substrate may comprise or consist of arabinan.
  • the glycan substrate may comprise or consist of inulin and arabinan.
  • the glycan substrate is provided in the form of a dietary fiber.
  • the dietary fiber may be a prebiotic fiber.
  • the glycan substrate may be comprised in an ingredient, for example a dietary ingredient.
  • the pectin may be comprised in fruit or vegetable pectin.
  • suitable ingredients comprising pectin include, but are not limited to, fruits (e.g., apple, pear), vegetables, legumes (peas), and roots (e.g., sugar beet).
  • Suitable purified fibers comprising arabinogalactan include peach pectin.
  • the pectin extracted from sugar beet contains arabinan, galactans and arabinogalactans and may be provided as an ingredient.
  • the arabinogalactan may be comprised in fruit or vegetable pectin.
  • suitable ingredients comprising arabinogalactan include, but are not limited to, fruits, vegetables, whole grain cereals and sea weed dietary fiber.
  • Suitable purified fibers comprising arabinogalactan include peach pectin, larch wood arabinogalactan, and Arabic gum.
  • the arabinogalactan may be provided in larch wood arabinogalactan.
  • the starch may be comprised in resistant-starch from cereals (whole grains), legumes, vegetables (e.g., corn) and roots (e.g., potato).
  • Illustrative suitable ingredients comprising starch include, but are not limited to, corn.
  • Suitable purified fibers comprising starch include high amylose starch and resistant dextrin.
  • the starch may be provided in a potato, corn or other ingredient.
  • the starch may be comprised in a potato ingredient.
  • the prebiotic comprises one or more additional HMO(s).
  • the additional HMO(s) is/are different to those provided in the HMO mixture as described herein.
  • the additional HMO(s) is/are capable of being metabolized by the B longum transitional microorganism.
  • the additional HMO(s) may be capable of promoting growth and/or survival of the B. longum transitional strain.
  • HMOs capable of promoting growth and/or survival of the B. longum transitional strain may be determined by e.g. anaerobic culture of the B. longum transitional strain with the HMO to be tested. Growth and/or survival of the B.
  • a HMO capable of promoting growth and/or survival of the B. longum transitional strain may increase the number of B. longum transitional bacteria in an anaerobic culture by a statistically signifiicant amount (e.g. p-value ⁇ 0.05 as determined by one-way ANOVA) compared to the number of B. longum transitional bacteria in a control anaerobic culture which does not comprise the HMO.
  • the HMO may be a fucosylated oligosaccharide (i.e. an oligosaccharide having a fucose residue; e.g.
  • 3-fucosyllactose (3-FL), difucosyllactose (DiFL), lacto-N-fucopentaose (e.g. lacto-N-fucopentaose II, lacto-N-fucopentaose III, lacto-N-fucopentaose V), lacto-N- fucohexaose, lacto-N-difucohexaose I, fucosyllacto-N-hexaose, fucosyllacto-N-neohexaose, difucosyllacto-N-hexaose I, difucosyllacto-N-neohexaose II and any combination thereof), an N-acetylated oligosaccharide (e.g.
  • para-lacto-N-neohexaose para-LNnH
  • LNnT lacto-N- neotetraose
  • DSLNT disialyllacto-N-tetraose
  • lacto-N-hexaose lacto-N-neohexaose
  • para- lacto-N-hexaose para-lacto-N-neohexaose
  • lacto-N-octaose lacto-N- neooctaose
  • sialylated oligosaccharide e.g.
  • the subject is an infant. In one embodiment, the subject is a young child. In one embodiment, the subject is a child.
  • the composition or combination according to the invention is for use in infants, young children or children. It is particularly adapted for infants under 6 months of age. In general, formula-fed infants have an underdeveloped immune system compared with adults and are more prone to viral infections than breastfed, and the younger the infant is, the less developed the immune system.
  • the composition or combination in for use infants, young children or children having a fragile or unbalanced microbiota or dysbiosis of microbiota such as preterm infants, infants born by Caesarean-section, infants born small for gestational age or with low birth weight, hospitalized infants/young children/children, infants/young children/children treated or having been treated by antibiotics and/or infants/young children/children suffering or having suffered from gut infection and/or gut inflammation.
  • the composition or combination of the invention may be even more beneficial to infants born with possibly impaired gut microbiota or fragile infants/young children/children (such as prematurely born infants and/or infants born by C-section).
  • composition or combination of the invention can be administered (or given or fed) at an age and for a period that depends on the needs.
  • the infants or young children are 0-36 months of age, such as 0-12 months or 0-6 months of age. It is foreseen that the composition or combination of the invention may be even more beneficial to infants just after birth (0-4 weeks or 0-8 weeks) as their intestinal tract may be more fragile.
  • the composition (e.g. nutritional composition) or combination according to the invention can be for use before and/or during the weaning period.
  • the composition (e.g. nutritional composition) or combination according to the invention is for use in a subject at risk and/or in need.
  • the subject at risk and/or in need may be bottle-fed and/or formula-fed.
  • the composition or combination of the invention is given to the subject as a supplementary composition to the mother's milk.
  • the subject receives the mother's milk during at least the first 2 weeks, first 1, 2, 4, or 6 months.
  • the composition e.g.
  • the composition of the invention is given to the subject after such period of mother's nutrition, or is given together with such period of mother's milk nutrition.
  • the composition or combination is given to the subject as the sole or primary nutritional composition during at least one period of time, e.g. after the 1 st , 2 nd or 4 th month of life, during at least 1, 2, 4 or 6 months.
  • the nutritional composition of the invention is a complete nutritional composition (fulfilling all or most of the nutritional needs of the subject).
  • the nutrition composition of the invention is a supplement or a fortifier intended for example to supplement human milk or to supplement an infant formula or a follow- on formula.
  • Nutritional composition In some embodiments, the composition of the invention is in the form of a nutritional composition.
  • the nutritional composition according to the invention can be for example an infant formula, a starter infant formula, a follow-on or follow-up formula, a growing-up milk, a baby food, an infant cereal composition, a fortifier such as a human milk fortifier, or a supplement.
  • the composition of the invention is an infant formula, a fortifier or a supplement that may be intended for the first 4 or 6 months of age.
  • the nutritional composition of the invention is an infant formula.
  • the nutritional composition of the present invention is a fortifier.
  • the fortifier can be a breast milk fortifier (e.g.
  • the nutritional composition when the nutritional composition is a supplement, it can be provided in the form of unit doses. In such cases it is particularly useful to define the amount of oligosaccharides and probiotics in terms of daily dose to be administered to the infant or young child.
  • the nutritional composition when the nutritional composition is a supplement, it may comprise the HMO mixture as described herein and the Bifidobacterium longum subsp microorganism, and no other additional nutrient on top of the excipients necessary to obtain a stable nutritional composition.
  • the nutritional composition of the present invention can be in solid (e.g. powder), liquid or gelatinous form.
  • the nutritional composition is a supplement, wherein the supplement is in powder form and provided in a sachet, preferably a sachet with 0.1 to 20 g per sachet, for example 1 to 10 g per sachet, or in the form of a syrup, preferably a syrup with a total solid concentration of 5 to 75 g/100 mL (5 to 75% (w/v)).
  • the supplement when it is in powder form, it may comprise a carrier. It is however preferred that the supplement is devoid of a carrier.
  • the components are preferably dissolved or suspended in water acidified with citrate.
  • the nutritional composition according to the invention is a hypoallergenic composition.
  • composition according to the invention is a hypoallergenic nutritional composition.
  • Other ingredients may also comprise other types of oligosaccharide(s), polysaccharides and/or a fiber(s) and/or a precursor(s) thereof.
  • Suitable probiotic bacterial strains include Lactobacillus rhamnosus ATCC 53103 available from Valio Oy of Finland under the trademark LGG, Lactobacillus rhamnosus CGMCC 1.3724, Lactobacillus paracasei CNCM I-2116, Lactobacillus johnsonii CNCM I-1225, Streptococcus salivarius DSM 13084 sold by BLIS Technologies Limited of New Zealand under the designation KI2, B. longum CNCM I-2618 (B.
  • the protein amount can be between 2.4 and 4 g/100kcal or more than 3.6 g/100kcal. In some other embodiments the protein amount can be below 2.0 g per 100 kcal, e.g. between 1.8 to 2 g/100 kcal, or in an amount below 1.8 g per 100 kcal.
  • Protein sources based on whey, casein and mixtures thereof may be used as well as protein sources based on soy. As far as whey proteins are concerned, the protein source may be based on acid whey or sweet whey or mixtures thereof and may include alpha-lactalbumin and beta-lactoglobulin in any desired proportions.
  • hydrolysed means in the context of the present invention a protein which has been hydrolysed or broken down into its component amino acids.
  • the proteins may be either fully or partially hydrolysed. It may be desirable to supply partially hydrolysed proteins (degree of hydrolysis between 2 and 20%), for example for infants or young children believed to be at risk of developing cow’s milk allergy.
  • the hydrolysis process may be carried out as desired and as is known in the art.
  • whey protein hydrolysates may be prepared by enzymatically hydrolysing the whey fraction in one or more steps. If the whey fraction used as the starting material is substantially lactose free, it is found that the protein suffers much less lysine blockage during the hydrolysis process.
  • At least 70% of the proteins are hydrolysed, preferably at least 80% of the proteins are hydrolysed, such as at least 85% of the proteins are hydrolysed, even more preferably at least 90% of the proteins are hydrolysed, such as at least 95% of the proteins are hydrolysed, particularly at least 98% of the proteins are hydrolysed. In a particular embodiment, 100% of the proteins are hydrolysed.
  • the proteins of the nutritional composition are hydrolyzed, fully hydrolyzed or partially hydrolyzed.
  • the degree of hydrolysis (DH) of the protein can be between 8 and 40, or between 20 and 60 or between 20 and 80 or more than 10, 20, 40, 60, 80 or 90.
  • the protein component can alternatively be replaced by a mixture or synthetic amino acid, for example for preterm or low birth weight infants.
  • the nutritional composition or the growing-up milk according to the invention is a hypoallergenic composition.
  • the composition according to the invention is a hypoallergenic nutritional composition or growing-up milk.
  • the nutritional composition according to the present invention generally contains a carbohydrate source. This is particularly preferable in the case where the nutritional composition of the invention is an infant formula.
  • any carbohydrate source conventionally found in infant formulae such as lactose, sucrose, saccharose, maltodextrin, starch and mixtures thereof may be used although one of the preferred sources of carbohydrates is lactose.
  • the nutritional composition according to the present invention generally contains a source of lipids. This is particularly relevant if the nutritional composition of the invention is an infant formula.
  • the lipid source may be any lipid or fat which is suitable for use in infant formulae.
  • Some suitable fat sources include palm oil, structured triglyceride oil, high oleic sunflower oil and high oleic safflower oil, medium-chain-triglyceride oil.
  • the essential fatty acids linoleic and ⁇ -linolenic acid may also be added, as well small amounts of oils containing high quantities of preformed arachidonic acid and docosahexaenoic acid such as fish oils or microbial oils.
  • the fat source may have a ratio of n-6 to n-3 fatty acids of about 5:1 to about 15:1; for example about 8:1 to about 10:1.
  • the nutritional composition of the invention may also contain all vitamins and minerals understood to be essential in the daily diet and in nutritionally significant amounts. Minimum requirements have been established for certain vitamins and minerals.
  • Examples of minerals, vitamins and other nutrients optionally present in the composition of the invention include vitamin A, vitamin B1, vitamin B2, vitamin B6, vitamin B12, vitamin E, vitamin K, vitamin C, vitamin D, folic acid, inositol, niacin, biotin, pantothenic acid, choline, calcium, phosphorous, iodine, iron, magnesium, copper, zinc, manganese, chlorine, potassium, sodium, selenium, chromium, molybdenum, taurine, and L-carnitine. Minerals are usually added in salt form. The presence and amounts of specific minerals and other vitamins will vary depending on the intended population.
  • the nutritional composition of the invention may contain emulsifiers and stabilisers such as soy, lecithin, citric acid esters of mono- and di-glycerides, and the like.
  • the nutritional composition of the invention may also contain other substances which may have a beneficial effect such as lactoferrin, nucleotides, nucleosides, and the like.
  • the nutritional composition of the invention may also contain carotenoid(s). In some particular embodiments of the invention, the nutritional composition of the invention does not comprise any carotenoid.
  • Manufacture of a nutritional composition The nutritional composition according to the invention may be prepared in any suitable manner. A composition will now be described by way of example.
  • a formula such as an infant formula may be prepared by blending together the protein source, the carbohydrate source and the fat source in appropriate proportions. If used, the emulsifiers may be included at this point. The vitamins and minerals may be added at this point but they are usually added later to avoid thermal degradation. Any lipophilic vitamins, emulsifiers and the like may be dissolved into the fat source prior to blending. Water, preferably water which has been subjected to reverse osmosis, may then be mixed in to form a liquid mixture. The temperature of the water is conveniently in the range between about 50°C and about 80°C to aid dispersal of the ingredients. Commercially available liquefiers may be used to form the liquid mixture.
  • the oligosaccharide(s) may be added at this stage, especially if the final product is to have a liquid form. If the final product is to be a powder, they may likewise be added at this stage if desired.
  • the liquid mixture is then homogenised, for example in two stages.
  • the liquid mixture may then be thermally treated to reduce bacterial loads, by rapidly heating the liquid mixture to a temperature in the range between about 80°C and about 150°C for a duration between about 5 seconds and about 5 minutes, for example. This may be carried out by means of steam injection, an autoclave or a heat exchanger, for example a plate heat exchanger. Then, the liquid mixture may be cooled to between about 60°C and about 85°C for example by flash cooling.
  • the supplement may further contain protective hydrocolloids (such as gums, proteins, modified starches), binders, film forming agents, encapsulating agents/materials, wall/shell materials, matrix compounds, coatings, emulsifiers, surface active agents, solubilizing agents (oils, fats, waxes, lecithins etc.), adsorbents, carriers, fillers, co-compounds, dispersing agents, wetting agents, processing aids (solvents), flowing agents, taste masking agents, weighting agents, jellifying agents and gel forming agents.
  • protective hydrocolloids such as gums, proteins, modified starches
  • binders film forming agents, encapsulating agents/materials, wall/shell materials, matrix compounds, coatings, emulsifiers, surface active agents, solubilizing agents (oils, fats, waxes, lecithins etc.), adsorbents, carriers, fillers, co-compounds, dispersing agents, wetting agents, processing aid
  • composition or combination according to any one of the preceding clauses wherein the Bifidobacterium longum transitional microorganism has an Average Nucleotide Identity (ANI) of at least 99% with Bifidobacterium longum strain deposited with the CNCM under deposit number CNCM I-5942. 11. The composition or combination according to any one of the preceding clauses, wherein the B. longum transitional microorganism is not resistant to any one of tetracycline and erythromycin. 12. The composition or combination according to any one of the preceding clauses, wherein the B. longum transitional microorganism is not resistant to any one of tetracycline, erythromycin, clindamycin and ampicillin. 13.
  • ANI Average Nucleotide Identity
  • NCC 5025 possesses a unique CAZyme profile. Its genome encodes five different CAZymes that target arabinans (GH43_22, GH43_27, GH43_29, GH121, and the exclusive GH43_17), compared to UCD399 and BSM11-5, which encode four and the rest of the B. longum transitional genomes which encode either three or fewer of these CAZymes ( Figure 22).
  • This unique region contains a family 31 glucosidase (GH31; NCC5025_001581), followed by an ABC transporter (NCC5025_001580-001578), a Lac-I type regulator (NCC5025_001577), a GH43_17 enzyme (NCC5025_001576), a MFS transporter (NCC5025_001575) and an AraC family transcriptional regulator (NCC5025_001574) (see Figure 23 and Table 7).
  • NCC 5025 has the highest growth rate on 3FL, indicating that this strain is the best adapted to this substrate (see Figure 24).
  • 3-FL is the human milk oligosaccharide that shows the greatest increase in the human breast milk during the period of transition between milk-based diet and solid food (Plows, J.F., et al., Longitudinal Changes in Human Milk Oligosaccharides (HMOs) Over the Course of 24 Months of Lactation. J Nutr, 2021.151(4): p.876-882), hence these results show an advantage of NCC 5025 for an application during this period.
  • Example 16 Growth of NCC 5025 on high molecular weight food fibers The inventors tested if the NCC 5025 strain had the capacity to grow on related high molecular weight fibers. For that purpose, selected B.
  • NCC 5002, NCC 5004, NCC 5025 longum transitional strains (NCC 5002, NCC 5004, NCC 5025, respectively) were grown on the above mentioned MRSc medium without sugar, to which 5 g/L% of arabinan (arabinan from Sugar-beet pulp from Megazyme) or Inulin (Orafti HSI from Beneo,) was added. Growth assays were performed in a BioLector XT microbioreactor system (m2p-labs GmbH, Baesweiler, Germany), using 48 flowerplate inserted in an anaerobic chamber for 50h (2ml volume per well, agitation at 600 rpm, CO2 atmosphere, 37°C). Growth was followed over time by continuous measurement of the scattered light at 620 nm.
  • B. longum transitional NCC 5025 had a particular ability to grow on inulin (average size of DP6-8, Tsatsaragkou et al.; Foods 2021, 10(5), 951) and high molecular weight arabinan.
  • B. longum transitional NCC 5025 grew faster (faster doubling time) and to a higher final yield.
  • the NCC 5025 strain was the only to grow (see Figure 25).
  • longum transitional NCC 5025 is clearly distinguished from previously isolated B. l. j uvenis strains, and shares 98.4% ANI to the strains previously isolated from Bangladeshi infants (Vatanen et al.2022; as above); b) This is the only B. longum transitional strain to date to be free of antibiotic resistance to the set of antibiotics considered relevant by EFSA; c) B. longum transitional NCC 5025 has a unique Carbohydrate Active EnZyme (CaZy) profile, including the presence of a GH43 subfamily 17 enzyme, that was not characterized t o date in the B. longum species. d) B. longum transitional NCC 5025 grows particularly well on 3-FL; e) B.
  • CaZy Carbohydrate Active EnZyme
  • longum transitional NCC 5025 grows the well on a set of food derived fibers (e.g. inulin and arabinan). Overall, the data suggest that this strain is particularly adapted to the weaning period and may perform in this environment better than other B. longum transitional strains. As well, our data suggest that on a diet containing food derived fiber (e.g. in adulthood), this strain may as well perform better than other B. longum transitional strains. All publications mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described methods and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention.

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Abstract

La présente invention concerne une composition comprenant un microorganisme transitionnel Bifidobacterium longum et un mélange d'oligosaccharides du lait maternel (HMO) composé de 2'-fucosyllactose (2'-FL), de difucosyllactose (DFL), de lacto-N-tétraose (LNT), de 6'-sialyllactose (6SL) et de 3'-sialyllactose (3SL), et éventuellement de lacto-N-fucopentaose I (LNFP-I), de 3-fucosyllactose (3-FL) et/ou de lacto-N-néotétraose (LNnT), le microorganisme transitionnel Bifidobacterium longum présentant une identité nucléotidique moyenne (ANI) d'au moins 98 % avec CNCM I-5942. L'invention concerne également l'utilisation de la composition pour prévenir, pour réduire le risque et/ou pour traiter une infection chez un sujet. L'invention concerne en outre la composition destinée à être utilisée pour favoriser un bénéfice immunitaire à long terme chez un sujet, pour prévenir et/ou réduire le risque de sensibilisation aux allergènes, pour prévenir et/ou réduire le risque de développer une affection respiratoire chez un sujet et/ou pour prévenir et/ou réduire le risque de développer l'asthme chez un sujet.
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