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 : 19-20

DESCRIPTION OF LIMOSILACTOBACILLUS REUTERI SUBSP. RODENTIUM SUBSP. NOV.

Limosilactobacillus reuteri subsp. rodentium (ro.den′ ti.um. L. pl. gen. n. rodentium of gnawing animals, reflecting adaptation of the subspecies to rodents).

L. reuteri strains clustered in lineage III ( Fig. 3 ) belong to L. reuteri subsp. rodentium and were mainly isolated from rodents [ 5 – 7]. Strains of this subspecies have ANI values of 96.1–98.9 % with each other and ANI values of 93.8–96.3% 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 and D-xylose is strain-specific; acid is not produced from D-fructose, D-mannose, methyl α- D-glucopyranoside, aesculin, glycerol, erythritol, D-arabinose, L-xylose, D-adonitol, methyl β -D-xylopyranoside, 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, turanose, 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 including the sourdough isolates are rodent-specific. Strains of L. reuteri subsp. rodentium displayed elevated fitness in mice through the colonization and biofilm formation on the forestomach epithelium [ 5, 7, 11], suggesting adaptive evolution with rodents that led to host specificity. Large surface proteins (>750 aa) exist among strains belonging to this subspecies, which involve in epithelial adhesion and biofilm formation [ 6]. A xylose operon is highly conserved for this subspecies, especially for strains originating from rodents [ 6], and thus most strains of this subspecies could metabolize xylose that is an important substrate for gut bacteria [ 51]. In addition, strains of this subspecies produce the enzyme urease for acid resistance and rarely produce the antimicrobial compound reuterin [ 6, 8]. Sourdough isolates of this subspecies (LTH2584, TMW1.106, TMW1.112 and TMW1.656) produce reutericyclin, a unique antimicrobial tetramic acid with activity against Gram-positive bacteria [ 52].

The type strain, 100-23 T (=DSM 17509 T =CIP 109821 T), was isolated from the rat gastrointestinal tract [ 11, 53], with a DNA G+C content of 38.7mol%.

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.