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EP-4739326-A2 - PRODUCTION & SECRETION OF AUXIN-LIKE MOLECULES IN BACTERIA

EP4739326A2EP 4739326 A2EP4739326 A2EP 4739326A2EP-4739326-A2

Abstract

The present invention relates to modified bacteria and plasmids (e.g. conjugative plasmids) which are engineered to express auxins and auxin-like molecules (ALMs), to pharmaceutical compositions containing them and their use in the treatment of various metabolic and cardiovascular diseases.

Inventors

  • SEMSEY, Szabolcs
  • SØNDBERG, Emilie
  • MUNCK, Christian
  • KOULOUKTSIS, Andreas

Assignees

  • SNIPR Biome ApS

Dates

Publication Date
20260513
Application Date
20240704

Claims (1)

  1. Claims 1. A modified bacterium, or a plasmid (e.g. conjugative plasmid), for producing and secreting one or more Auxin Like Molecules (ALMs), wherein the bacterium or plasmid comprises one or more heterologous genes for the biosynthesis of said one or more ALMs, and wherein: a. the bacterium further comprises a heterologous gene encoding an exporter which is capable of exporting said one or more ALMs out of the bacterium; or b. the plasmid further comprises a heterologous gene encoding an exporter which is capable of exporting said one or more ALMs out of a bacterium which comprises said plasmid and which bacterium produces and secretes said one or more ALMs. 2. A modified bacterium, or a plasmid (e.g. conjugative plasmid), for secreting one or more Auxin Like Molecules (ALMs), wherein: a. the bacterium comprises one or more genes for the production of said one or more ALMs and further comprises a heterologous gene encoding an exporter which is capable of exporting said one or more ALMs out of the bacterium; or b. the plasmid comprises a heterologous gene encoding an exporter which is capable of exporting said one or more ALMs out of a bacterium which comprises said plasmid, and the bacterium which comprises said plasmid comprises one or more genes for the production of said one or more ALMs. 3. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 1 or claim 2, wherein the one or more ALMs is an auxin, for example an auxin selected from the group consisting of indole-3-acetic acid (IAA), indole-3-butyric acid (IBA) and indole-3-proprionic acid (IPA). 4. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 1 or claim 2, wherein the one or more ALMs is selected from indole-3-pyruvic acid (IPyA), indole-3- acetaldehyde (lAAId), indole-3-lactic acid (ILA), indole-3-acrylic acid (IA), indole-3-carboxylic acid (ICA) and indole-3-ethanol. 5. A modified bacterium, or a plasmid (e.g. conjugative plasmid), for producing and secreting an Auxin Like Molecule (ALM) which is indole-3-butyric acid (IBA), wherein the bacterium or plasmid comprises one or more heterologous gene(s) for the biosynthesis of IBA, and wherein: a. the bacterium further comprises a heterologous gene encoding an exporter which is capable of exporting IBA out of the bacterium; or b. the plasmid further comprises a heterologous gene encoding an exporter which is capable of exporting IBA out of a bacterium which comprises said plasmid and produces and secretes IBA. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 5, wherein the one or more heterologous gene(s) for the biosynthesis of IBA are selected from: A. a gene for the conversion of tryptophan to tryptamine (optionally a gene which is tryptophan decarboxylase (tot)), a gene for the conversion of tryptamine to indole-3- acetaldehyde (lAAId) (optionally a gene which is monoamine oxidase (tynA)), a gene for the conversion of lAAId to IAA (optionally a gene selected from indole-3-acetaldehyde dehydrogenase (jadl) and Indole-3-acetaldehyde oxidase (aaol)), and optionally a gene for the conversion of IAA to IBA (optionally a gene which is IBA synthetase); B. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to tryptamine (optionally a gene which is tryptophan decarboxylase (tot)), a gene for the conversion of tryptamine to indole-3-acetaldehyde (lAAId) (optionally a gene which is monoamine oxidase (tynA)), a gene for the conversion of lAAId to IAA (optionally a gene selected from indole-3-acetaldehyde dehydrogenase (jadl) and Indole-3-acetaldehyde oxidase (aao7)), and optionally a gene for the conversion of IAA to IBA (optionally a gene which is IBA synthetase); C. a gene for the conversion of tryptophan to indole-3-pyruvic acid (IPyA) (optionally a gene selected from L-tryptophan oxidase (sta(J), L-tryptophan aminotransferase (aro9), aspartate aminotransferase (aspC), L-tryptophan-pyruvate aminotransferase (taal) and tryptophan dehydrogenase (trpDH)), a gene for the conversion of IPyA to lAAId (optionally a gene which is indole-3-pyruvate decarboxylase (jpdC)), a gene for the conversion of lAAId to IAA (optionally a gene selected from iadl and aaol), and optionally a gene for the conversion of IAA to IBA (optionally a gene which is IBA synthetase); D. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to indole-3-pyruvic acid (IPyA) (optionally a gene selected from L-tryptophan oxidase (sta(J), L-tryptophan aminotransferase (aro9), aspartate aminotransferase (aspC), L-tryptophan-pyruvate aminotransferase (taal) and tryptophan dehydrogenase (trpDH)), a gene for the conversion of IPyA to lAAId (optionally a gene which is indole-3-pyruvate decarboxylase (jpdC)), a gene for the conversion of lAAId to IAA (optionally a gene selected from iadl and aaol), and optionally a gene for the conversion of IAA to IBA (optionally a gene which is IBA synthetase); E. a gene for the conversion of tryptophan to indole-3-pyruvic acid (IPyA) (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to IAA (optionally a gene which is an indole-3-pyruvate monooxygenase (e.g. selected from YUC genes, yuc2, and yuc6)), and optionally a gene for the conversion of IAA to IBA (optionally a gene which is IBA synthetase); F. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to indole-3-pyruvic acid (IPyA) (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to IAA (optionally a gene which is an indole-3-pyruvate monooxygenase (e.g. selected from YUC genes, yuc2, and yuc6)), and optionally a gene for the conversion of IAA to IBA (optionally a gene which is IBA synthetase); G. a gene for the conversion of tryptophan to indole-3-acetamide (IAM) (optionally a gene which is tryptophan 2-monooxygenase {iaaM}), a gene for the conversion of IAM to IAA (optionally a gene which is indoleacetamide hydrolase (JaaH)), and optionally a gene for the conversion of IAA to IBA (optionally a gene which is IBA synthetase); H. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to indole-3-acetamide (IAM) (optionally a gene which is tryptophan 2-monooxygenase {iaaM)), a gene for the conversion of IAM to IAA (optionally a gene which is indoleacetamide hydrolase (JaaH)), and optionally a gene for the conversion of IAA to IBA (optionally a gene which is IBA synthetase); I. a gene for the conversion of tryptophan to indole-3-acetaldoximine (lAOx) (optionally a gene selected from tryptophan N-monooxygenase (CYP79B2) and tryptophan N- monooxygenase (CYP79B3)), a gene for the conversion of lAOx to indole-3-acetonitrile (IAN) (optionally a gene which is indoleacetaldoxime dehydratase (CYP71A13)), a gene for the conversion of IAN to IAA (optionally a gene which is a nitrilase (e.g. selected from nitl, nit2 and nitB), and optionally a gene for the conversion of IAA to IBA (optionally a gene which is IBA synthetase); J. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to indole-3-acetaldoximine (lAOx) (optionally a gene selected from tryptophan N-monooxygenase (CYP79B2) and tryptophan N- monooxygenase (CYP79B3)), a gene for the conversion of lAOx to indole-3-acetonitrile (IAN) (optionally a gene which is indoleacetaldoxime dehydratase (CYP71A13)), a gene for the conversion of IAN to IAA (optionally a gene which is a nitrilase (e.g. selected from nitl, nit2 and nitB), and optionally a gene for the conversion of IAA to IBA (optionally a gene which is IBA synthetase); K. a gene for the conversion of tryptophan to indole-3-acetaldoximine (lAOx) (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to indole- 3-acetonitrile (IAN) (optionally a gene which is CYP71A13), a gene for the conversion of IAN to IAM (optionally a gene which is nitrile hydratase (nthABj), a gene for the conversion of IAM to IAA (optionally a gene which is iaaH), and optionally a gene for the conversion of IAA to IBA (optionally a gene which is IBA synthetase); L. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to indole-3-acetaldoximine (lAOx) (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to indole-3- acetonitrile (IAN) (optionally a gene which is CYP71A13), a gene for the conversion of IAN to IAM (optionally a gene which is nitrile hydratase (nthAB)}, a gene for the conversion of IAM to IAA (optionally a gene which is iaaH), and optionally a gene for the conversion of IAA to IBA (optionally a gene which is IBA synthetase); M. any combination of pathways A to L; and N. any part of pathways A to L. 7. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any one of claims 1 to 3, or 5 or 6, wherein the auxin is IBA and wherein the heterologous gene encoding an exporter which is capable of exporting IBA encodes a protein selected from: (i) an auxin efflux carrier (AEC) family protein transporter, (for example an AEC family protein transporter from a bacterial species); and (ii) an ABC family protein transporters (for example an ABC family protein transporter from a plant species, such as an ABC-PDR sub-family protein transporter, e.g. from a plant species). 8. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 7, wherein the heterologous gene encoding an exporter which is capable of exporting IBA encodes a protein selected from PXA1/ABCD1, ABCG36, ABCG37, and ABCG36/PDR8/PEN3. 9. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any one of claims 1 to 3, or 5 or 6, wherein the auxin is IBA, and wherein the heterologous gene encoding an exporter which is capable of exporting IBA encodes a protein which is TOBI. 10. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any preceding claim, wherein the exporter is from an Arabidopsis species, e.g. from Arabidopsis thaliana. 11. A modified bacterium, or a plasmid (e.g. conjugative plasmid), for producing and secreting an Auxin Like Molecule (ALM) which is indole-3-acetic acid (IAA), wherein the bacterium comprises one or more heterologous gene(s) for the biosynthesis of IAA, and wherein: a. the bacterium further comprises a heterologous gene encoding an exporter which is capable of exporting IAA out of the bacterium; or b. the plasmid further comprises a heterologous gene encoding an exporter which is capable of exporting IAA out of a bacterium which comprises said plasmid and produces and secretes IAA. 12. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 11, wherein the one or more heterologous gene(s) for the biosynthesis of IAA are selected from: A. a gene for the conversion of tryptophan to tryptamine (optionally a gene which is tryptophan decarboxylase (tot)), a gene for the conversion of tryptamine to indole-3- acetaldehyde (lAAId) (optionally a gene which is monoamine oxidase (tynA)), a gene for the conversion of lAAId to IAA (optionally a gene selected from indole-3-acetaldehyde dehydrogenase (jadl) and Indole-3-acetaldehyde oxidase (aaoZ)); B. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to tryptamine (optionally a gene which is tryptophan decarboxylase (tot)), a gene for the conversion of tryptamine to indole-3-acetaldehyde (lAAId) (optionally a gene which is monoamine oxidase (tynA)), a gene for the conversion of lAAId to IAA (optionally a gene selected from indole-3-acetaldehyde dehydrogenase (jadl) and Indole-3-acetaldehyde oxidase (aaoZ)); C. a gene for the conversion of tryptophan to indole-3-pyruvic acid (IPyA) (optionally a gene selected from L-tryptophan oxidase (staO), L-tryptophan aminotransferase (aro9), aspartate aminotransferase (aspC), L-tryptophan-pyruvate aminotransferase (taal) and tryptophan dehydrogenase (trpDH)), a gene for the conversion of IPyA to lAAId (optionally a gene which is indole-3-pyruvate decarboxylase (ipdC)), a gene for the conversion of lAAId to IAA (optionally a gene selected from iadl and aaol)} D. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to indole-3-pyruvic acid (IPyA) (optionally a gene selected from L-tryptophan oxidase (staO), L-tryptophan aminotransferase (aro9), aspartate aminotransferase (aspC), L-tryptophan-pyruvate aminotransferase (taal) and tryptophan dehydrogenase (trpDH)), a gene for the conversion of IPyA to lAAId (optionally a gene which is indole-3-pyruvate decarboxylase (ipdC)), a gene for the conversion of lAAId to IAA (optionally a gene selected from iadl and aaol)} E. a gene for the conversion of tryptophan to indole-3-pyruvic acid (IPyA) (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to IAA (optionally a gene which is an indole-3-pyruvate monooxygenase (e.g. selected from YUC genes, yuc2, and /vc6)); F. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to indole-3-pyruvic acid (IPyA) (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to IAA (optionally a gene which is an indole-3-pyruvate monooxygenase (e.g. selected from YUC genes, yuc2, and yuc6))} G. a gene for the conversion of tryptophan to indole-3-acetamide (IAM) (optionally a gene which is tryptophan 2-monooxygenase (iaaM)), a gene for the conversion of IAM to IAA (optionally a gene which is indoleacetamide hydrolase (iaaH)),- H. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to indole-3-acetamide (IAM) (optionally a gene which is tryptophan 2-monooxygenase (JaaM)}, a gene for the conversion of IAM to IAA (optionally a gene which is indoleacetamide hydrolase (JaaHyy, I. a gene for the conversion of tryptophan to indole-3-acetaldoximine (lAOx) (optionally a gene selected from tryptophan N-monooxygenase {CYP79B2} and tryptophan N- monooxygenase {CYP79B3}}, a gene for the conversion of lAOx to indole-3-acetonitrile (IAN) (optionally a gene which is indoleacetaldoxime dehydratase {CYP71A13}}, a gene for the conversion of IAN to IAA (optionally a gene which is a nitrilase (e.g. selected from nitl, nit2ax\d nit3y J. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to indole-3-acetaldoximine (lAOx) (optionally a gene selected from tryptophan N-monooxygenase (CYP79B2) and tryptophan N- monooxygenase {CYP79BB}), a gene for the conversion of lAOx to indole-3-acetonitrile (IAN) (optionally a gene which is indoleacetaldoxime dehydratase (CYP71A13)), a gene for the conversion of IAN to IAA (optionally a gene which is a nitrilase (e.g. selected from nitl, nit2ax\d nit3y K. a gene for the conversion of tryptophan to indole-3-acetaldoximine (lAOx) (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to indole- 3-acetonitrile (IAN) (optionally a gene which is CYP71A13), a gene for the conversion of IAN to IAM (optionally a gene which is nitrile hydratase (nthABj), a gene for the conversion of IAM to IAA (optionally a gene which is iaaHy, L. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to indole-3-acetaldoximine (lAOx) (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to indole-3- acetonitrile (IAN) (optionally a gene which is CYP71A13), a gene for the conversion of IAN to IAM (optionally a gene which is nitrile hydratase (jithAB)), and a gene for the conversion of IAM to IAA (optionally a gene which is iaaHy, M. any combination of pathways A to L; and N. any part of pathways A to L. 13. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 12, wherein the one or more heterologous gene(s) for the biosynthesis of IAA comprise: i. Indole-3-pyruvate decarboxylase (jpdCy ii. Tryptophan-pyruvate aminotransferase 1 (taaiy and iii. Indole-3-acetaldehyde dehydrogenase (jadl). 14. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 13, wherein; i. the ipdC\s from a Pantoea species, e.g. from Pantoea agglomerans, optionally having the nucleic acid sequence of SEQ ID No:41; and/or ii. the taal is from an Arabidopsis species, e.g. from Arabidopsis tha/iana, optionally having the nucleic acid sequence of SEQ ID No:40; and/or iii. the iadl is from an UstHago species, e.g. from UstHago maydis, optionally having the nucleic acid sequence of SEQ ID No:42. 15. A modified bacterium, or a plasmid (e.g. conjugative plasmid), for producing and secreting an Auxin Like Molecules (ALM) which is indole-3-propionic acid (IPA), wherein the bacterium or plasmid comprises one or more heterologous genes for the biosynthesis of IPA, and wherein: a. the bacterium further comprises a heterologous gene encoding an exporter which is capable of exporting IPA out of the bacterium; or b. the plasmid further comprises a heterologous gene encoding an exporter which is capable of exporting IPA out of a bacterium which comprises said plasmid and produces and secretes IPA. 16. The modified bacterium, or the plasmid (e.g. conjugative plasmid) according to claim 15, wherein the one or more heterologous gene(s) for the biosynthesis of IPA is selected from: A. a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to indole-3-lactic acid (ILA) (optionally a gene selected from hcxB, Idh4&c\d f/dH), a gene for the conversion of ILA to indole-3-acrylic acid (IA) (optionally genes which are f/dAIBC), and a gene for the conversion of IA to IPA (optionally a gene which is acdAy, B. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to ILA (optionally a gene selected from hcxB, Idh4 and f/dH), a gene for the conversion of ILA to IA (optionally genes which are f/dAIBC), and a gene for the conversion of IA to IPA (optionally a gene which is acdAy C. a gene for the conversion of tryptophan to IA (optionally a gene which is tryptophan ammonia lyase ( WAL)), and a gene for the conversion of IA to IPA (optionally a gene which is acdAy D. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to IA (optionally a gene which is l/l/AL); and a gene for the conversion of IA to IPA (optionally a gene which is acdAy E. any combination of pathways A to D; and F. any part of pathways A to D. 17. A modified bacterium, or a plasmid (e.g. conjugative plasmid), for producing and secreting an Auxin Like Molecule (ALM) which is indole-3-pyruvic acid (IPyA), wherein the bacterium or plasmid comprises one or more heterologous genes for the biosynthesis of IPyA, and wherein: a. the bacterium further comprises a heterologous gene encoding an exporter which is capable of exporting IPyA out of the bacterium; or b. the plasmid further comprises a heterologous gene encoding an exporter which is capable of exporting IPyA out of a bacterium which comprises said plasmid and produces and secretes IPyA. 18. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 17, wherein the one or more heterologous gene(s) for the biosynthesis of IPyA is selected from: A. a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH),- and B. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), and a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH). 19. A modified bacterium, or a plasmid (e.g. conjugative plasmid), for producing and secreting an Auxin Like Molecules (ALM) which is indole-3-acetaldehyde (lAAId), wherein the bacterium or plasmid comprises one or more heterologous genes for the biosynthesis of lAAId, and wherein: a. the bacterium further comprises a heterologous gene encoding an exporter which is capable of exporting lAAId out of the bacterium; or b. the plasmid further comprises a heterologous gene encoding an exporter which is capable of exporting lAAId out of a bacterium which comprises said plasmid and produces and secretes lAAId. 20. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 19, wherein the one or more heterologous gene(s) for the biosynthesis of lAAId is selected from: A. a gene for the conversion of tryptophan to tryptamine (optionally a gene which is tdc) and a gene for the conversion of tryptamine to lAAId (optionally a gene which is tynA),- B. a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH) and a gene for the conversion of IPyA to lAAId (optionally a gene which is ipdCy, C. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to tryptamine (optionally a gene which is tdc) and a gene for the conversion of tryptamine to lAAId (optionally a gene which is tynA); D. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH} and a gene for the conversion of IPyA to lAAId (optionally a gene which is ipdCy E. any combination of pathways A to D; and F. any part of pathways A to D. 21. A modified bacterium, or a plasmid (e.g. conjugative plasmid), for producing and secreting an Auxin Like Molecules (ALM) which is indole-3-lactic acid (ILA), wherein the bacterium or plasmid comprises one or more heterologous genes for the biosynthesis of ILA, and wherein: a. the bacterium further comprises a heterologous gene encoding an exporter which is capable of exporting ILA out of the bacterium; or b. the plasmid further comprises a heterologous gene encoding an exporter which is capable of exporting ILA out of a bacterium which comprises said plasmid and produces and secretes ILA. 22. The modified bacterium, or the plasmid (e.g. conjugative plasmid) according to claim 21, wherein the one or more heterologous gene(s) for the biosynthesis of ILA are selected from: A. a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH}, and a gene for the conversion of IPyA to ILA (optionally a gene selected from hcxB, Idh4&c\d f/dHy B. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB}, a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH}, and a gene for the conversion of IPyA to ILA (optionally a gene selected from hcxB, Idh4&c\d f/dHy, and C. any part of pathway A or B. 23. A modified bacterium, or a plasmid (e.g. conjugative plasmid), for producing and secreting an Auxin Like Molecules (ALM) which is indole-3-acrylic acid (IA), wherein the bacterium or plasmid comprises one or more heterologous genes for the biosynthesis of IA, and wherein: a. the bacterium further comprises a heterologous gene encoding an exporter which is capable of exporting IA out of the bacterium; or b. the plasmid further comprises a heterologous gene encoding an exporter which is capable of exporting IA out of a bacterium which comprises said plasmid and produces and secretes IA. 24. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 23, wherein the one or more heterologous gene(s) for the biosynthesis of IA are selected from: A. a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH}, a gene for the conversion of IPyA to ILA (optionally a gene selected from hcxB, Idh4 and fldH), and a gene for the conversion of ILA to IA (optionally genes which are fldAIBCy, B. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to ILA (optionally a gene selected from hcxB, Idh4&c\d fldH), and a gene for the conversion of ILA to IA (optionally genes which are fldABCy, C. a gene for the conversion of tryptophan to IA (optionally a gene which is WALy, D. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB) and a gene for the conversion of tryptophan to IA (optionally a gene which is WAL); and E. any part of pathway A or B. 25. A modified bacterium, or a plasmid (e.g. conjugative plasmid), for producing and secreting an Auxin Like Molecules (ALM) which is indole-3-carboxylic acid (ICA), wherein the bacterium or plasmid comprises one or more heterologous genes for the biosynthesis of ICA, and wherein: c. the bacterium further comprises a heterologous gene encoding an exporter which is capable of exporting ICA out of the bacterium; or d. the plasmid further comprises a heterologous gene encoding an exporter which is capable of exporting ICA out of a bacterium which comprises said plasmid and produces and secretes ICA. 26. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 25, wherein the one or more heterologous gene(s) for the biosynthesis of ICA are selected from: A. a gene for the conversion of tryptophan to tryptamine (optionally a gene which is tdc), a gene for the conversion of tryptamine to lAAId (optionally a gene which is tynA), a gene for the conversion of lAAId to IAA (optionally a gene selected from iadl and aaol), a gene for the conversion of IAA to skatole (optionally a gene which is indoleacetate decarboxylase (IAD)), a gene for the conversion of skatole to indole-3-methanol (IM) (optionally a gene which is tryptophan side chain oxidase ( TSO)), a gene for the conversion of IM to indole-3-carboxaldehyde (IAID) (optionally a gene which is tryptophan side chain oxidase ( TSO)), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),- B. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to tryptamine (optionally a gene which is tdc), a gene for the conversion of tryptamine to lAAId (optionally a gene which is tynA), a gene for the conversion of lAAId to IAA (optionally a gene selected from iadl and aaol), a gene for the conversion of IAA to skatole (optionally a gene which is indoleacetate decarboxylase (IAD)), a gene for the conversion of skatole to indole-3-methanol (IM) (optionally a gene which is tryptophan side chain oxidase ( TSO)), a gene for the conversion of IM to indole-3-carboxaldehyde (IAID) (optionally a gene which is tryptophan side chain oxidase ( TSO)), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol)} C. a gene for the conversion of tryptophan to tryptamine (optionally a gene which is tdc), a gene for the conversion of tryptamine to lAAId (optionally a gene which is tynA), a gene for the conversion of lAAId to IAA (optionally a gene selected from iadl and aaol), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol)} D. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to tryptamine (optionally a gene which is tdc), a gene for the conversion of tryptamine to lAAId (optionally a gene which is tynA), a gene for the conversion of lAAId to IAA (optionally a gene selected from iadl and aaol), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol)} E. a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to lAAId (optionally a gene which is ipdC), a gene for the conversion of lAAId to IAA (optionally a gene selected from iadl and aaol), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IM (optionally a gene which is TSO), a gene for the conversion of IM to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol)} F. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to lAAId (optionally a gene which is ipdC), a gene for the conversion of lAAId to IAA (optionally a gene selected from iadl and aaol), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IM (optionally a gene which is TSO), a gene for the conversion of IM to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol)} G. a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to lAAId (optionally a gene which is ipdC), a gene for the conversion of lAAId to IAA (optionally a gene selected from iadl and aaol), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol)} H. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to lAAId (optionally a gene which is ipdC), a gene for the conversion of lAAId to IAA (optionally a gene selected from iadl and aaol), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),' I. a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to IAA (optionally a gene which is an indole-3-pyruvate monooxygenase (e.g. selected from K/Cgenes, yuc2, and yuc6)), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IM (optionally a gene which is TSO), a gene for the conversion of IM to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),' J. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to IAA (optionally a gene which is an indole-3-pyruvate monooxygenase (e.g. selected from KtCgenes, yuc2, and yuc6)), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IM (optionally a gene which is TSO), a gene for the conversion of IM to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),' K. a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to IAA (optionally a gene which is an indole-3-pyruvate monooxygenase (e.g. selected from K/Cgenes, yuc2, and yuc6)), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),' L. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to IPyA (optionally a gene selected from staO, aro9, aspC, taal and trpDH), a gene for the conversion of IPyA to IAA (optionally a gene which is an indole-3-pyruvate monooxygenase (e.g. selected from KtCgenes, yuc2, and yuc6)), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),' M. a gene for the conversion of tryptophan to IAM (optionally a gene which is iaaM), a gene for the conversion of IAM to IAA (optionally a gene which is iaaH), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IM (optionally a gene which isTSO), a gene for the conversion of IM to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),- N. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to IAM (optionally a gene which is iaaM), a gene for the conversion of IAM to IAA (optionally a gene which is iaaH), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IM (optionally a gene which isTSO), a gene for the conversion of IM to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),- O. a gene for the conversion of tryptophan to IAM (optionally a gene which is iaaM), a gene for the conversion of IAM to IAA (optionally a gene which is iaaH), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),- P. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to IAM (optionally a gene which is iaaM), a gene for the conversion of IAM to IAA (optionally a gene which is iaaH), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),- Q. a gene for the conversion of tryptophan to lAOx (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to IAN (optionally a gene which is CYP71A13), a gene for the conversion of IAN to IAA (optionally a gene selected from nitl, nit2 and nitB), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IM (optionally a gene which is TSO), a gene for the conversion of IM to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),- R. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to lAOx (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to IAN (optionally a gene which is CYP71A13), a gene for the conversion of IAN to IAA (optionally a gene selected from nitl, nit2 and nitB), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IM (optionally a gene which is TSO), a gene for the conversion of IM to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),- S. a gene for the conversion of tryptophan to lAOx (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to IAN (optionally a gene which is CYP71A13), a gene for the conversion of IAN to IAA (optionally a gene selected from nitl, nit2 and nitB), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol)} T. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to lAOx (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to IAN (optionally a gene which is CYP71A13), a gene for the conversion of IAN to IAA (optionally a gene selected from nitl, nit2 and nitB), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol)} U. a gene for the conversion of tryptophan to lAOx (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to IAN (optionally a gene which is CYP71A13), a gene for the conversion of IAN to IAM (optionally a gene which is nitrile hydratase (jithAB)), a gene for the conversion of IAM to IAA (optionally a gene which is iaaH), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IM (optionally a gene which is TSO), a gene for the conversion of IM to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol)} V. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to lAOx (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to IAN (optionally a gene which is CYP71A13), a gene for the conversion of IAN to IAM (optionally a gene which is nitrile hydratase (jithAB)), a gene for the conversion of IAM to IAA (optionally a gene which is iaaH), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IM (optionally a gene which is TSO), a gene for the conversion of IM to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol)} W. a gene for the conversion of tryptophan to lAOx (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to IAN (optionally a gene which is CYP71A13), a gene for the conversion of IAN to IAM (optionally a gene which is nthAB), a gene for the conversion of IAM to IAA (optionally a gene which is iaaH), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),- X. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to lAOx (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to IAN (optionally a gene which is CYP71A13), a gene for the conversion of IAN to IAM (optionally a gene which is nthAB), a gene for the conversion of IAM to IAA (optionally a gene which is iaaH), a gene for the conversion of IAA to skatole (optionally a gene which is IAD), a gene for the conversion of skatole to IAID (optionally a gene which is TSO), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),- Y. a gene for the conversion of tryptophan to lAOx (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to IAN (optionally a gene which is cytochrome P450 monooxygenase {CYP71A13)), a gene for the conversion of IAN to IAID (optionally a gene which is CYP71B6), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),- Z. a gene for the conversion of indole to tryptophan (optionally a gene which is trpB), a gene for the conversion of tryptophan to lAOx (optionally a gene selected from CYP79B2 and CYP79B3), a gene for the conversion of lAOx to IAN (optionally a gene which is cytochrome P450 monooxygenase {CYP71A13)), a gene for the conversion of IAN to IAID (optionally a gene which is CYP71B6), and a gene for the conversion of IAID to ICA (optionally a gene selected from iadl and aaol),- PA. any combination of pathways A to Z; and BB. any part of pathways A to Z. 27. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any preceding claim, wherein the one or more heterologous genes for the biosynthesis of said one or more ALMs are each or all under the control of one or more constitutive promoter(s). 28. A modified bacterium, or a plasmid (e.g. conjugative plasmid), for the biosynthesis of an Auxin Like Molecule (ALM) which is indole-3-acetic acid (IAA), comprising heterologous genes for the biosynthesis of IAA, which heterologous genes encode: i. Indole-3-pyruvate decarboxylase (jpdC) from a Pantoea species, e.g. from Pantoea aggiomerans, optionally having the nucleic acid sequence of SEQ ID No:41; ii. Tryptophan-pyruvate aminotransferase 1 {taal) from an Arabidopsis species, e.g. from Arabidopsis thaiiana, optionally having the nucleic acid sequence of SEQ ID No:40; and iii. Indole-3-acetaldehyde dehydrogenase {iadl) from an Ustiiago species, e.g. from Ustiiago maydis, optionally having the nucleic acid sequence of SEQ ID No:42; wherein heterologous genes (i) to (iii) are each or all under the control of one or more constitutive promoter(s). 29. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 28, wherein: a. the bacterium further comprises a heterologous gene encoding an exporter which is capable of exporting IAA out of the bacterium; or b. the plasmid further comprises a heterologous gene encoding an exporter which is capable of exporting IAA out of a bacterium which comprises said plasmid and produces and secretes IAA. 30. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any preceding claim, wherein the heterologous gene encoding an exporter which is capable of exporting said one or more ALMs (e.g. IAA) is under the control of a constitutive promoter. 31. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any preceding claim, wherein the one or more heterologous gene(s) for the biosynthesis of said one or more ALMs (e.g. IAA) are comprised within an operon under the control of a single constitutive promoter. 32. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 31, wherein the ALM is IAA, and wherein the one or more heterologous gene(s) for the biosynthesis of IAA comprised within the operon comprise the following genes in downstream order: i. Indole-3-pyruvate decarboxylase (jpdQ, optionally from a Pantoea species, e.g. from Pantoea aggiomerans, further optionally having the nucleic acid sequence of SEQ ID No:41; ii. Tryptophan-pyruvate aminotransferase 1 (taal), optionally from an Arabidopsis species, e.g. from Arabidopsis thaiiana, further optionally having the nucleic acid sequence of SEQ ID No:40; and iii. Indole-3-acetaldehyde dehydrogenase (jadl), optionally from an Ustiiago species, e.g. from Ustiiago maydis, further optionally having the nucleic acid sequence of SEQ ID No:42. 33. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 31 or claim 32, wherein the one or more heterologous gene(s) for the biosynthesis of said one or more ALMs (e.g. IAA) and the heterologous gene encoding an exporter which is capable of exporting said one or more ALMs (e.g. IAA) are comprised within an operon under the control of a single constitutive promoter. 34. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any one of claims 27 to 33, wherein the constitutive promoter is a strong constitutive promoter having an Anderson score >0.4 (e.g. >0.5), e.g. a tac promoter, for example a Pc-tga promoter having the sequence of SEQ ID No: 1. 35. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 34, wherein the promoter is a promoter selected from a RelB, Bo/A, Hya, YiaG&cxd a RpoH promoter, such as a promoter selected from a RelB promoter sequence, o70; a Bo/A promoter sequence, oS, o70; a Hya promoter sequence, oS, o70; a YiaG promoter sequence, oS; a RpoH promoter sequence Pl, o70; a RpoH promoter sequence P2, aS; a RpoH promoter sequence P3, o24; a RpoH promoter sequence P4, o70; a RpoH promoter sequence P5, o70; and a /^/-/promoter sequence P6, o54, in particular a promoter having a nucleotide sequence selected from any one of Seq ID Nos: 65 to 74, or a nucleotides sequence having 90% (or 95%) homology thereto. 36. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any one of claims 33 to 35, wherein the one or more heterologous gene(s) for the biosynthesis of said one or more ALMs (e.g. IAA) and the heterologous gene encoding an exporter which is capable of exporting said one or more ALMs (e.g. IAA) comprised within the operon comprise the following genes in downstream order: i. Indole-3-pyruvate decarboxylase (jpdQ, optionally from a Pantoea species, e.g. from Pantoea agglomerans, further optionally having the nucleic acid sequence of SEQ ID No:41; ii. Tryptophan-pyruvate aminotransferase 1 (taal), optionally from an Arabidopsis species, e.g. from Arabidopsis thaiiana, further optionally having the nucleic acid sequence of SEQ ID No:40; and iii. Indole-3-acetaldehyde dehydrogenase (jadl), optionally an Ustiiago species, e.g. from Ustiiago maydis, further optionally having the nucleic acid sequence of SEQ ID No:42; and iv. the heterologous gene encoding an exporter of IAA, optionally wherein the operon is comprised by the chromosome of the modified bacterium. 37. The modified bacterium according to any preceding claim, wherein the bacterium further comprises a modification in an endogenous tryptophanase (f/7<aXI) and/or tnaC which reduces expression (or prevents expression) of said tnaA and/or tnaC, e.g. the bacterium further comprises a deletion of one or more nucleotides in an endogenous tnaA and/or tnaC which prevents or reduces (e.g. prevents) transcription or expression of said tnaA and/or tnaC, such as a deletion which comprises at least the nucleotides which, when transcribed, express a TnaC peptide. 38. The modified bacterium according to any preceding claim, wherein the bacterium further comprises a modification in an endogenous tryptophan transcriptional repressor (trpR) gene which reduces expression (or prevents expression) of said trpR, e.g. the bacterium further comprises a deletion of one or more nucleotides in an endogenous ftp/? gene which prevents ore reduces (e.g. prevents) transcription or expression of said trpR. 39. The modified bacterium according to any preceding claim, wherein the one or more heterologous gene(s) for the biosynthesis of said one or more ALMs (e.g. IAA) are all comprised by the chromosome of said modified bacterium. 40. The modified bacterium according to any preceding claim, wherein the heterologous gene encoding an exporter which is capable of exporting said one or more ALMs (e.g. IAA) is comprised by the chromosome of said modified bacterium. 41. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any preceding claim, wherein: a. the bacterium is a gram negative bacterium; or b. the plasmid is capable of being conjugatively transferred to a recipient bacterial cell, such as a gram negative recipient bacterial cell. 42. The modified bacterium according to any preceding claim, or the plasmid (e.g. conjugative plasmid) according to claim 41, wherein the bacterium or bacterial cell is a strain selected from any of the strains in Table 3. 43. The modified bacterium according to any preceding claim, or the plasmid (e.g. conjugative plasmid) according to claim 41 or claim 42, wherein the bacterium or bacterial cell is an E. coli strain, for example an E. coH\x<w\ phylogroup A, Bl and/or E, or an E. coli strain which is present in a probiotic product, such as colinfant New Born (e.g. strain AO 34/86) or symbioflor2 (e.g. strain Gl/2, G4/9, G5, G6/7, and G8, in particular strain G6/7), or Mutaflor (e.g. E. co//Nissle). 44. The modified bacterium or the plasmid (e.g. conjugative plasmid) according to any preceding claim, wherein the bacterium or bacterial cell strain has been engineered to remove some or all (e.g. all) prophage genes present in the bacterium or bacterial cell genome, or wherein the bacterium or bacterial cell strain is devoid of some or all (e.g. all) prophage genes. 45. The modified bacterium or the plasmid (e.g. conjugative plasmid) according to any preceding claim, wherein the bacterium or bacterial cell strain has been engineered to remove any identified pathogenicity factors (such as htyA, htyB, htyC and/or htyDor any combination thereof) present in the bacterium or bacterial cell genome, or wherein the bacterium or bacterial cell strain is devoid of pathogenicity factors (such as htyA, htyB, htyC and/or htyDor any combination thereof). 46. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any one of claims 43 to 45, wherein the bacterium or bacterial cell is a strain belonging to a genera selected from Bifidobacterium, Bacteroides, Lactobacillus, Lacticaseibaciiius, Lactipiantibaciiius, Levilactobacillus, Ligilactobacillus, Limosilactobacillus and Lactococcus, (e.g. a species which is selected from Bifidobacterium iongum, Bifidobacterium breve, Bifidobacterium adoiescentis, Bacteroides uniformis, Bacteroides vuigatus, Bacteroides theta iotaomicron, Lactobacillus gasseri, Lacticaseibaciiius paracasei, Lactipiantibaciiius plantarum, Levilactobacillus brevis, Ligilactobacillus saliva rius, Limosilactobacillus reuteri and Lactococcus iactid), in particular a strain belonging to a Bifidobacterium genus or a Bacteroides genus (e.g. a species which is selected from Bifidobacterium iongum, Bifidobacterium breve, Bifidobacterium adoiescentis, Bacteroides uniformis, Bacteroides vuigatus and Bacteroides thetaiotaomicrori). A7. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any preceding claim, wherein the bacterium or plasmid does not comprise any heterologous genes for the biosynthesis of tryptophan, for example genes encoding one or more genes selected from trpA, trpB, trpC, trpD&cxd trpE, for example all of trpA, trpC, trpD&cxd trpE. 48. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any preceding claim, wherein the bacterium or plasmid comprises no other heterologous genes other than: I. the one or more heterologous gene(s) for the biosynthesis of said one or more ALMs (e.g. IAA); and/or II. the heterologous gene encoding an exporter which is capable of exporting said one or more ALMs (e.g. IAA); III. optionally the kill switch(es); and IV. optionally any heterologous or modified auxotrophy genes. 49. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any one of claims 1 to 6 or 11 to 27 or 29 to 45, wherein the heterologous gene encoding an exporter which is capable of exporting said one or more ALMs (e.g. IAA) encodes an auxin efflux protein, for example an exporter selected from: (i) an auxin efflux carrier (AEC) family protein transporter (for example an AEC family protein from a bacterial species); (ii) a PIN family protein transporter (for example a PIN family protein transporter from a plant species); and (iii) an ABC family protein transporter, such as an ABCD subfamily protein transporter or an ABCB subfamily protein transporter, e.g. an ABCB-PGP sub-family protein transporter (for example where the ABC family protein transporter is from a plant species). 50. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 49, wherein the exporter is an AEC family protein transporter. 51. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 49 or claim 50, wherein the auxin efflux protein is from a Pantoea species, e.g. Pantoea agglomerans. 52. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any one of claims 49 to 51, wherein the heterologous gene encoding the exporter comprises the nucleotide sequence of SEQ ID No: 2. 53. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to claim 49, wherein the exporter of IAA is a PIN transporter (e.g. PIN2 or PIN7), optionally wherein the PIN transporter is from a plant species (e.g. from an Arabidopsis species, e.g. from Arabidopsis thaiiana), or wherein the heterologous gene encoding the exporter comprises the nucleotide sequence of SEQ ID No: 3. 54. The modified bacterium according to any preceding claim, wherein the bacterium comprises a kill switch, and/or wherein the bacterium includes an auxotrophy, such as deletion of thyA. 55. The modified bacterium, or the plasmid (e.g. conjugative plasmid), according to any preceding claim, wherein production of the one or more ALMs is comparable, for example is statistically similar or is within statistical error at 30 °C and at 37 °C in vitro. 56. The modified bacterium according to any preceding claim, wherein the bacterium is capable of maintaining a stable level of colonisation in a mouse model for at least 5 days (for example at least 6, or at least 7 or at least 8 days), optionally as measured by number of colony-forming units (CFU) in feces. 57. The modified bacterium according to claim 56, wherein the level of colonisation is at least (about) lxio 4 CFU/g feces, at least (about) lxio 5 CFU/g feces, for example at least (about) lxio 6 CFU/g feces, or at least (about) lxio 7 CFU/g feces, or at least (about) lxio 8 CFU/g feces. 58. The modified bacterium according to any preceding claim, wherein the bacterium is capable of producing IAA in a mouse model for at least 24 hours (for example at least 48 hours, or at least 72 hours or at least 96 hours), optionally by measuring IAA levels in feces. 59. The modified bacterium according to claim 58, wherein the IAA levels are at least (about) 10 nmol/g feces, for example at least (about) 15 nmol/g feces, or at least (about) 20 nmol/g feces. 60. The modified bacterium according to any one of claims 56 to 59, wherein the measurements are conducted in an in vivo mouse model, for example conducted as described for group 6 in Example 4.2.2. 61. A host bacterial cell comprising a plasmid as defined in any one of claims 1 to 38 or claims 41 to 60, optionally wherein the plasmid is a conjugative plasmid, and optionally wherein the host bacterial cell is a bacterium as defined in any one of claims 41 to 46. 62. A pharmaceutical composition comprising a modified bacterium as defined in any one of claims 1 to 60, or comprising a host bacterial cell as defined in claim 61, and a pharmaceutically acceptable excipient or carrier. 63. The pharmaceutical composition according to claim 62, which is formulated for oral or rectal administration, preferably oral administration, for example formulated as a capsule or coated tablet. 64. The pharmaceutical composition according to claim 62 or claim 63, which is a lyophilised formulation or is an encapsulated formulation to be released in the lower gut of a subject, for example in the small intestine or large intestine of a subject. 65. The pharmaceutical composition according to claim 64, which is formulated as an enteric late release capsule. 66. The pharmaceutical composition according to any one of claims 54 to 57, wherein the formulation comprises freeze dried modified bacteria or host cells. 67. The pharmaceutical composition according to any one of claims 62 to 66, wherein the formulation comprises (approximately) lxlO 9 colony forming units (CFU)/gram of a modified bacterium as defined in any one of claims 1 to 60 or host bacterial cell as defined in claim 61. 68. A method of producing an ALM (e.g. IAA) in the gut of a subject, comprising administering to said subject a modified bacterium as defined in any one of claims 1 to 60, a host bacterial cell as defined in claim 61, or a pharmaceutical composition as defined in any one of claims 62 to 67. 69. A method of treating a metabolic disease, such as a cardiovascular metabolic disease, optionally selected from leaky gut, type 1 diabetes, type 2 diabetes (including complications of type 1 and type 2 diabetes, e.g. insulin sensitivity in type 2 diabetes), metabolic syndrome, Bardet-Biedel syndrome, Prader-Willi syndrome, non-alcoholic fatty liver disease, tuberous sclerosis; Albright hereditary osteodystrophy; brain-derived neurotrophic factor (BDNF) deficiency, Single-minded 1 (SIM1) deficiency, leptin deficiency, leptin receptor deficiency, pro-opiomela nocorti n (POMC) defects, proprotein convertase subtilisin/kexin type 1 (PCSK1) deficiency, Src homology 2B1 (SH2B1) deficiency, pro-hormone convertase 1/3 deficiency, melanocortin-4-receptor (MC4R) deficiency, Wilms tumor, aniridia, genitourinary anomalies, and mental retardation (WAGR) syndrome, pseudohypoparathyroidism type 1A, Fragile X syndrome, Borjeson-Forsmann- Lehmann syndrome, Alstrom syndrome, Cohen syndrome, and ulnar-mammary syndrome (in particular selected from metabolic syndrome, type 2 diabetes (including complications of type 2 diabetes, e.g. insulin sensitivity in type 2 diabetes), and non-alcoholic fatty liver disease), said method comprising administering to a subject in need thereof a modified bacterium as defined in any one of claims 1 to 60, a host bacterial cell as defined in claim 61, or a pharmaceutical composition as defined in any one of claims 62 to 67. 70. The modified bacterium as defined in any one of claims 1 to 60, the host bacterial cell as defined in claim 61, or the pharmaceutical composition as defined in any one of claims 62 to 67, for use as a medicament. 71. The modified bacterium as defined in any one of claims 1 to 60, a host bacterial cell as defined in claim 61, or a pharmaceutical composition as defined in any one of claims 62 to 67, for use in the treatment of a metabolic disease, such as a cardiovascular metabolic disease, optionally selected from leaky gut, type 1 diabetes, type 2 diabetes (including complications of type 1 and type 2 diabetes, e.g. insulin sensitivity in type 2 diabetes), metabolic syndrome, Bardet-Biedel syndrome, Prader-Willi syndrome, non-alcoholic fatty liver disease, tuberous sclerosis; Albright hereditary osteodystrophy; brain-derived neurotrophic factor (BDNF) deficiency, Single-minded 1 (SIM1) deficiency, leptin deficiency, leptin receptor deficiency, pro-opiomela nocorti n (POMC) defects, proprotein convertase subtilisin/kexin type 1 (PCSK1) deficiency, Src homology 2B1 (SH2B1) deficiency, pro-hormone convertase 1/3 deficiency, melanocortin-4-receptor (MC4R) deficiency, Wilms tumor, aniridia, genitourinary anomalies, and mental retardation (WAGR) syndrome, pseudohypoparathyroidism type 1A, Fragile X syndrome, Borjeson-Forsmann- Lehmann syndrome, Alstrom syndrome, Cohen syndrome, and ulnar-mammary syndrome (in particular selected from metabolic syndrome, type 2 diabetes (including complications of type 2 diabetes, e.g. insulin sensitivity in type 2 diabetes), and non-alcoholic fatty liver disease). 72. A method of treating or preventing a cancers, in particular colorectal cancer (CRC) and/or pancreatic cancer, e.g. pancreatic ductal adenocarcinoma (PDAC), said method comprising administering to a subject in need thereof a modified bacterium as defined in any one of claims 1 to 60, a host bacterial cell as defined in claim 61, or a pharmaceutical composition as defined in any one of claims 62 to 67, whereby the cancer is treated or prevented, and optionally wherein the subject is receiving a chemotherapy (e.g. concurrently, before or after administration of the bacterium, the plasmid (e.g. conjugative plasmid), the host cell or the pharmaceutical formulation. 73. A method of treating or preventing non-alcoholic fatty liver disease (NAFLD), said method comprising administering to a subject in need thereof a modified bacterium as defined in any one of claims 1 to 60, a host bacterial cell as defined in claim 61, or a pharmaceutical composition as defined in any one of claims 62 to 67, whereby the NAFLD is treated or prevented. 74. A method of improving insulin resistance, lipid metabolism, oxidative stress and/or inflammatory stress, said method comprising administering to a subject in need thereof a modified bacterium as defined in any one of claims 1 to 60, a host bacterial cell as defined in claim 61, or a pharmaceutical composition as defined in any one of claims 62 to 67, whereby the insulin resistance, lipid metabolism, oxidative stress and/or inflammatory stress is improved. 75. The method or use according to any one of claims 69 to 74, wherein the or a subject is administered a course of antibiotics within one month (for example within 2 weeks, within one week, e.g. within 5, 4 or 3 days, in particular within 34 hours) of receiving a first dose of the modified bacterium, the host cell, or the pharmaceutical composition. 76. The method or use according to claim 75, wherein the antibiotic treatment is selected from an aminoglycoside (e.g. amikacin, liposomal amikacin, gentamicin, plazomicin and tobramycin), a £- lactam inhibitor (e.g. ceftolozane and cilastatin), a p-lactamase inhibitor (e.g. avibactam, clavulanate, clavulanic acid, salbactam, tazobactam, relebactam and vaborbactam), a carbapenem (e.g. doripenem, ertapenem, imipenem, and meropenem), a cephalosporin (e.g. cefaclor, cefadroxil, cefazolin, cefdinir, cefditoren, cefepime, cefiderocol, cefixime, cefotaxime, cefotetan, cefoxitin, cefpodoxime, cefprozil, ceftaroline, ceftazidime, ceftibuten, ceftizoxime, ceftriaxone, cefuroxime and cephalexin), a fluoroquinolone (e.g. ciprofloxacin, delafloxacin, gemifloxacin, levofloxacin and moxifloxacin), a folate pathway inhibitor (e.g. sulfisoxazole, sulfamethoxazole and trimethoprim), a fosfomycin (e.g. fosfomycin), a glycopeptide (e.g. dalbavancin, oritavancin, telavancin and vancomycin), a glycocycline (e.g. tigecycline), a ketolide (e.g. telithromycine), a lincosamide (e.g. clindamycin), a lipopeptide (e.g. daptomycin), a macrocyclic (e.g. fidaxomicin) macrolide (e.g. azithromycin, clarithromycin and erythromycin), a monobactam (e.g. aztreonam), a nitrofuran (e.g. nitrofurantoin), a nitroimidazole (e.g. metronidazole and tinidazole), a nucleoside analog (e.g. molnupiravir and remdesivir), an oxazolidinone (e.g. linezolid and tedizolid), penicillin (e.g. amoxicillin, ampicillin, dicloxacillin, nafcillin, oxacillin, penicillin G, penicillin V, piperacillin and ticarcillin), a phenicol (e.g. chloramphenicol), a polyene (e.g. amphotericin B, liposomal amphotericin B and amphotericin B lipid complex), polymerase acidic endonuclease inhibitor (e.g. baloxavir marboxil), a polymyxin (e.g. colistimethate, colistin and polymyxin B), a pleuromutilin (e.g. lefamulin), a protease inhibitor (e.g. nirmatrelvir), rifampin, a streprogramin (e.g. quinupristin and dalfopristin), a tetracycline (e.g. eravacycline, minocycline, omadacycline and tetracycline), or combinations thereof. 77. A method of producing a modified bacterium as defined in any one of claims 1 to 60, wherein the heterologous genes are comprised by the chromosome of said bacterium, said method comprising the use of recombineering to introduce the heterologous genes into the chromosome of the bacterium, optionally wherein the one or more heterologous gene(s) for the biosynthesis of said one or more ALMs (e.g. IAA) are as defined in any one of claims 6, 12 to 26, 28, 32 or 36; and/or optionally wherein the heterologous gene encoding an exporter which is capable of exporting said one or more ALMs (e.g. IAA) is as defined in any of claims 7 to 10 or claims 49 to 53; and/or optionally wherein the promoter is as defined in claim 34 or claim 35, and propagating said bacterium; and optionally formulating said bacterium into a pharmaceutical composition (optionally a pharmaceutical composition as defined in any of claims 62 to 67); and optionally packaging said pharmaceutical composition with instructions for use (optionally for the treatment of any of the diseases defined in claim 69).

Description

PRODUCTION & SECRETION OF AUXIN-LIKE MOLECULES IN BACTERIA Background Metabolic disorders have gradually become public health-threatening problems with an estimated incidence of around 1/4 worldwide. Strategies and therapeutic attention are demanded to prevent metabolic disorders, particularly type 2 diabetes (T2D), obesity, and non-alcoholic fatty liver disease (NAFLD). Gut microbiome dysbiosis has been associated with these metabolic disorders, resulting in an inflammatory state due to increased permeability of the intestinal epithelium (Taleb, Frontiers in Immunology, 10:2113, 2019). The intestinal epithelium is maintained by the presence of tight and adherence junctions in the epithelial cells and serves as a protective barrier against external substances. However, in inflammatory diseases, this barrier can become dysfunctional, leading to increased permeability and the movement of microbial components such as lipopolysaccharide (LPS) into the bloodstream. This can result in observed inflammation, which is implicated in the development of cardiometabolic diseases. Recent evidence has linked indole-3-acetic acid (IAA), a gut microbiota-derived metabolite from dietary tryptophan, with resistance to liver damage and steatosis in mice (Ji et al., Nutrient 11:2062, 2019; Li et al., Frontiers in Pharmacology, 12:769501, 2021), and improved epithelial barrier function in mice (Laurans et al., Nature Medicine, 24:1113, 2018) and piglets (Liang et al., Frontiers in Microbiology, 9:1736, 2018). In humans, decreased levels of tryptophan and IAA, and increased levels of kynurenine, have been observed in the fecal samples from patients with obesity and T2D compared to healthy subjects, and similarly a change in tryptophan metabolism towards more kynurenine and less IAA in people with obesity and T2D (Laurans et al., 2018, supra; Natividad et al., Cell Metabolism, 28:737, 2018). IAA and other tryptophan-derived compounds have previously been characterized as aryl hydrocarbon receptor (AHR) agonists, establishing a direct effect of the gut microbiome and its metabolites on intestinal homeostasis. In vitro data demonstrated that IAA induces activation of the aryl hydrocarbon receptor (AHR) in intestinal immune cells, increasing the production of anti- inflammatory interleukins like IL-17 and IL-22, which are important for antimicrobial immunity and mucosal barrier integrity (Laurans et al., 2018, supra). Moreover, IAA has been shown to attenuate lipogenesis in hepatocytes induced by cytokine and free fatty acids (Krishnan et al., Cell Reports, 23:1099, 2018). Whilst IAA is a key auxin, in the treatment of cardiometabolic diseases, other auxin-like molecules may have therapeutic benefits. Other tryptophan-derived metabolites have been shown to regulate intestinal barrier function, and contributing to an anti-inflammatory environment in the gut epithelium. Those include indole-3-propionic acid (IPA) (Lanis et al., Mucosal Immunology 10:1133, 2017), indole-3-acetaldehyde (IAAld), or indole-3-pyruvate (IPyA) (Scott et al., PNAS, 117:19376, 2020). Specifically, IPyA has been shown to prevent chronic inflammation in the colon by activating AHR (Aoki et al., The Journal of Immunology, 15(201), 3683, 2018) and IPA protected against indomethacin-induced intestinal injury (Venkatesh et al, Immunity, 41:296, 2014). Indole-3-butyric acid (IBA) significantly inhibited the LPS-induced upregulation of IL-4 and IL-6 mRNA (Zhen et al, Journal of Asthma and Allergy, 15:117, 2022). Romasi & Lee, J. Microbiol. Biotechnol., 23(12), 1726-1736, 2013, doi: http://dx.doi.org/ 10.4014/jmb.1308.08082 discloses lAA-producing E coH comprising ipdC, aspC&cxd iadl genes. WO2017/123418 (Synlogic, Inc) discloses inter alia genetic circuits for inclusion in bacteria for the production of indole metabolites and derivatives. WO2021/242897 (Synlogic, Inc) discloses gene cassettes for producing IAA which are operably linked to an inducible promoter. There remains a need for efficient in situ production of auxins and auxin like molecules which have a beneficial effect in vivo, for example in the gut microbiome. Summary The inventors have advantageously realised that increased levels of secretion of Auxin-Like Molecules (ALMs) can be achieved by modifying bacteria to include various heterologous exporters. As is known in the art, diffusion of molecules through bacterial membrane(s) (both gram-negative and gram-positive bacteria) can limit the amount of a particular molecule which diffuses to the local environment. Without being bound by theory, in general, bacterial membrane(s) are hydrophobic, so the more hydrophilic the small molecule is, the less likely it is to be able to cross the membrane. However, certain molecules which are detrimental to the cell (for example toxins, bacteriocins, etc) are exported more often, along with certain molecules which provide specific extra-cellular functions (such as molecules associated with quorum sensing, iron acquis