Limosilactobacillus reuteri, 2021

Li, Fuyong, Cheng, Christopher C., Zheng, Jinshui, Liu, Junhong, Quevedo, Rodrigo Margain, Li, Junjie, Roos, Stefan, Gänzle, Michael G. & Walter, Jens, 2021, Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts, International Journal of Systematic and Evolutionary Microbiology (004644) 71 (2), pp. 1-21 : 18

DESCRIPTION OF LIMOSILACTOBACILLUS REUTERI SUBSP. KINNARIDIS SUBSP. NOV.

Limosilactobacillus reuteri subsp. kinnaridis (kin.na′ ri.dis. N.L. gen.n. kinnaridis of Kinnaris, referring to kinnaris, halfbird, half-woman creatures of South-East Asian mythology and reflecting occurrence of strains of this subspecies in birds and in humans. The name also reflects the use of this subspecies in probiotics, as according to south-east Asian mythology, Kinnaris are believed to come from the Himalayas and watch over the well-being of humans in times of trouble or danger).

L. reuteri strains clustered in lineage VI ( Fig. 3 ) belong to L. reuteri subsp. kinnaridis and they were isolated from poultry and humans [ 5, 7]. Strains of this subspecies have ANI values of 98.2–100.0% with each other and ANI values of 93.8–96.6 % with other L. reuteri strains belonging to different subspecies ( Fig. 4 ). Acid is produced from D-ribose, D-galactose, D-glucose, maltose, lactose, melibiose, sucrose, raffinose and potassium gluconate; acid production from L-arabinose, methylα- D-glucopyranoside and turanose is strain-specific; acid is not produced from D-xylose, D-fructose, D-mannose, aesculin, glycerol, erythritol, D-arabinose,L-xylose,D-adonitol, methyl β -Dxylopyranoside, L-sorbose,L-rhamnose, dulcitol, inositol, D-mannitol, D-sorbitol, methyl α- D-mannopyranoside, N -acetylglucosamine, amygdalin, arbutin, salicin, cellobiose, trehalose, inulin, melezitose, starch, glycogen, xylitol, gentiobiose, D-lyxose, D-tagatose, D-fucose, L-fucose, D-arabitol,L-arabitol, potassium 2-ketogluconate or potassium 5-ketogluconate. Phylogenetic analyses based on the core genes identified in this study ( Fig. 3 ) and a previous study [ 5], AFLP and MLSA (using concatenated sequences of ddl, pkt, leuS, gyrB, dltA, rpoA and recA genes) [ 7] indicate that strains clustered in this lineage are adapted to poultry and also occur in humans. Experimental test has revealed that strains of L. reuteri subsp. kinnaridis displayed elevated fitness in chickens but not in humans [ 5], suggesting that this subspecies is autochthonous of chicken and share an evolutionary history with poultry. Strains of this subspecies possess the pdu-cbi-cob-hem cluster (pdu cluster) [ 6, 8], which equips them with the ability to utilize 1,2-propanediol and glycerol as electron acceptors [ 16, 39, 40] and to produce the broad-spectrum antimicrobial compound reuterin [ 8, 34]. These strains are immunostimulatory; specifically, they stimulate the production of IL-7, IL-12 and IL-13, but suppress the production of IL-5 [ 34]. In addition, strains belonging to this subspecies synthesize folate de novo [ 34].

The type strain, AP3 T (=DSM 110703 T =LMG 31724 T), was isolated from the gastrointestinal tract of an Argus Pheasant, with a DNA G+C content of 38.6mol%.

Figures

Fig. 3. A maximum-likelihood phylogenetic tree reconstructed using core genes (n=100) identified from whole-genome sequences, showing the evolutionary relationships among six L. reuteri subspecies.The tree was reconstructed using 33 L. reuteri genomes available in public databases (n=6 for L. reuteri subsp. kinnaridis, n=2 for L. reuteri subsp. porcinus, n=5 for L. reuteri subsp. murium, n=10 for L. reuteri subsp. reuteri, n=5 for L. reuteri subsp. suis and n=5 for L. reuteri subsp. rodentium) and L. balticus BG-AF3-AT was used as an outgroup. Further information on the involved genome sequences is listed in Table S1. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. The tree was drawn with iTOL [54].

Fig. 4. Pairwise average nucleotide identity values (ANI; %) of genome sequences belonging to the same or different L. reuteri subspecies. ANI values within the same subspecies and between different subspecies were calculated for 33 L. reuteri genomes available in public databases (n=6 for L. reuteri subsp. kinnaridis, n=2 for L. reuteri subsp. porcinus, n=5 for L. reuteri subsp.murium, n=10for L. reuteri subsp.reuteri, n=5 for L. reuteri subsp. suis and n=5 for L. reuteri subsp. rodentium). Further information on the involved genome sequences is listed in Table S1.