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

Fuyong Li; Christopher C. Cheng; Jinshui Zheng; Junhong Liu; Rodrigo Margain Quevedo; Junjie Li; Stefan Roos; Michael G. Gänzle; Jens Walter

doi:10.1099/ijsem.0.004644

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

Fuyong Li
, Christopher C. Cheng
, Jinshui Zheng
, Junhong Liu
, Rodrigo Margain Quevedo
, Junjie Li
, Stefan Roos
, Michael G. Gänzle
, Jens Walter

Research output: Contribution to journal › Article › peer-review

Abstract

Ten strains, BG-AF3-A^T, pH52_RY, WF-MT5-A^T, BG-MG3-A, Lr3000^T, RRLNB_1_1, STM3_1^T, STM2_1, WF-MO7-1^T and WF-MA3-C, were isolated from intestinal or faecal samples of rodents, pheasant and primate. 16S rRNA gene analysis identified them as Limosilactobacillus reuteri. However, average nucleotide identity and digital DNA–DNA hybridization values based on whole genomes were below 95 and 70%, respectively, and thus below the threshold levels for bacterial species delineation. Based on genomic, chemotaxonomic and morphological analyses, we propose five novel species with the names Limosilactobacil-lus balticus sp. nov. (type strain BG-AF3-A^T=DSM 110574^T=LMG 31633^T), Limosilactobacillus agrestis sp. nov. (type strain WF-MT5-A^T=DSM 110569^T=LMG 31629^T), Limosilactobacillus albertensis sp. nov. (type strain Lr3000^T=DSM 110573^T=LMG 31632^T), Limosilactobacillus rudii sp. nov. (type strain STM3_1^T=DSM 110572^T=LMG 31631^T) and Limosilactobacillus fastidiosus sp. nov. (type strain WF-MO7-1^T=DSM 110576^T=LMG 31630^T). Core genome phylogeny and experimental evidence of host adaptation of strains of L. reuteri further provide a strong rationale to consider a number of distinct lineages within this species as subspe-cies. Here we propose six subspecies of L. reuteri: L. reuteri subsp. kinnaridis subsp. nov. (type strain AP3^T=DSM 110703^T=LMG 31724^T), L. reuteri subsp. porcinus subsp. nov. (type strain 3c6^T=DSM 110571^T=LMG 31635^T), L. reuteri subsp. murium subsp. nov. (type strain lpuph1^T=DSM 110570^T=LMG 31634^T), L. reuteri subsp. reuteri subsp. nov. (type strain F 275^T=DSM 20016^T=ATCC 23272^T), L. reuteri subsp. suis subsp. nov. (type strain 1063^T=ATCC 53608^T=LMG 31752^T) and L. reuteri subsp. rodentium subsp. nov. (type strain 100-23^T=DSM 17509^T=CIP 109821^T).

Original language	English
Article number	004644
Pages (from-to)	1-21
Number of pages	21
Journal	International Journal of Systematic and Evolutionary Microbiology
Volume	71
Issue number	2
DOIs	https://doi.org/10.1099/ijsem.0.004644
Publication status	Published - 2021

Keywords

Evolution
Host adaptation
Limosilactobacillus reuteri subspecies
Novel Limosilactobacillus species
Phylogenetic lineages

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Li, F., Cheng, C. C., Zheng, J., Liu, J., Quevedo, R. M., Li, J., Roos, S., Gänzle, M. G., & Walter, J. (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, 71(2), 1-21. Article 004644. https://doi.org/10.1099/ijsem.0.004644

Li, Fuyong ; Cheng, Christopher C. ; Zheng, Jinshui et al. / 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. In: International Journal of Systematic and Evolutionary Microbiology. 2021 ; Vol. 71, No. 2. pp. 1-21.

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title = "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",

abstract = "Ten strains, BG-AF3-AT, pH52\_RY, WF-MT5-AT, BG-MG3-A, Lr3000T, RRLNB\_1\_1, STM3\_1T, STM2\_1, WF-MO7-1T and WF-MA3-C, were isolated from intestinal or faecal samples of rodents, pheasant and primate. 16S rRNA gene analysis identified them as Limosilactobacillus reuteri. However, average nucleotide identity and digital DNA–DNA hybridization values based on whole genomes were below 95 and 70\%, respectively, and thus below the threshold levels for bacterial species delineation. Based on genomic, chemotaxonomic and morphological analyses, we propose five novel species with the names Limosilactobacil-lus balticus sp. nov. (type strain BG-AF3-AT=DSM 110574T=LMG 31633T), Limosilactobacillus agrestis sp. nov. (type strain WF-MT5-AT=DSM 110569T=LMG 31629T), Limosilactobacillus albertensis sp. nov. (type strain Lr3000T=DSM 110573T=LMG 31632T), Limosilactobacillus rudii sp. nov. (type strain STM3\_1T=DSM 110572T=LMG 31631T) and Limosilactobacillus fastidiosus sp. nov. (type strain WF-MO7-1T=DSM 110576T=LMG 31630T). Core genome phylogeny and experimental evidence of host adaptation of strains of L. reuteri further provide a strong rationale to consider a number of distinct lineages within this species as subspe-cies. Here we propose six subspecies of L. reuteri: L. reuteri subsp. kinnaridis subsp. nov. (type strain AP3T=DSM 110703T=LMG 31724T), L. reuteri subsp. porcinus subsp. nov. (type strain 3c6T=DSM 110571T=LMG 31635T), L. reuteri subsp. murium subsp. nov. (type strain lpuph1T=DSM 110570T=LMG 31634T), L. reuteri subsp. reuteri subsp. nov. (type strain F 275T=DSM 20016T=ATCC 23272T), L. reuteri subsp. suis subsp. nov. (type strain 1063T=ATCC 53608T=LMG 31752T) and L. reuteri subsp. rodentium subsp. nov. (type strain 100-23T=DSM 17509T=CIP 109821T).",

keywords = "Evolution, Host adaptation, Limosilactobacillus reuteri subspecies, Novel Limosilactobacillus species, Phylogenetic lineages",

author = "Fuyong Li and Cheng, \{Christopher C.\} and Jinshui Zheng and Junhong Liu and Quevedo, \{Rodrigo Margain\} and Junjie Li and Stefan Roos and G{\"a}nzle, \{Michael G.\} and Jens Walter",

note = "Publisher Copyright: {\textcopyright} 2021 The Authors.",

year = "2021",

doi = "10.1099/ijsem.0.004644",

language = "English",

volume = "71",

pages = "1--21",

journal = "International Journal of Systematic and Evolutionary Microbiology",

issn = "1466-5026",

publisher = "Microbiology Society",

number = "2",

}

Li, F, Cheng, CC, Zheng, J, Liu, J, Quevedo, RM, Li, J, Roos, S, Gänzle, MG & Walter, J 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, vol. 71, no. 2, 004644, pp. 1-21. https://doi.org/10.1099/ijsem.0.004644

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. / Li, Fuyong; Cheng, Christopher C.; Zheng, Jinshui et al.
In: International Journal of Systematic and Evolutionary Microbiology, Vol. 71, No. 2, 004644, 2021, p. 1-21.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - 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

AU - Li, Fuyong

AU - Cheng, Christopher C.

AU - Zheng, Jinshui

AU - Liu, Junhong

AU - Quevedo, Rodrigo Margain

AU - Li, Junjie

AU - Roos, Stefan

AU - Gänzle, Michael G.

AU - Walter, Jens

PY - 2021

Y1 - 2021

N2 - Ten strains, BG-AF3-AT, pH52_RY, WF-MT5-AT, BG-MG3-A, Lr3000T, RRLNB_1_1, STM3_1T, STM2_1, WF-MO7-1T and WF-MA3-C, were isolated from intestinal or faecal samples of rodents, pheasant and primate. 16S rRNA gene analysis identified them as Limosilactobacillus reuteri. However, average nucleotide identity and digital DNA–DNA hybridization values based on whole genomes were below 95 and 70%, respectively, and thus below the threshold levels for bacterial species delineation. Based on genomic, chemotaxonomic and morphological analyses, we propose five novel species with the names Limosilactobacil-lus balticus sp. nov. (type strain BG-AF3-AT=DSM 110574T=LMG 31633T), Limosilactobacillus agrestis sp. nov. (type strain WF-MT5-AT=DSM 110569T=LMG 31629T), Limosilactobacillus albertensis sp. nov. (type strain Lr3000T=DSM 110573T=LMG 31632T), Limosilactobacillus rudii sp. nov. (type strain STM3_1T=DSM 110572T=LMG 31631T) and Limosilactobacillus fastidiosus sp. nov. (type strain WF-MO7-1T=DSM 110576T=LMG 31630T). Core genome phylogeny and experimental evidence of host adaptation of strains of L. reuteri further provide a strong rationale to consider a number of distinct lineages within this species as subspe-cies. Here we propose six subspecies of L. reuteri: L. reuteri subsp. kinnaridis subsp. nov. (type strain AP3T=DSM 110703T=LMG 31724T), L. reuteri subsp. porcinus subsp. nov. (type strain 3c6T=DSM 110571T=LMG 31635T), L. reuteri subsp. murium subsp. nov. (type strain lpuph1T=DSM 110570T=LMG 31634T), L. reuteri subsp. reuteri subsp. nov. (type strain F 275T=DSM 20016T=ATCC 23272T), L. reuteri subsp. suis subsp. nov. (type strain 1063T=ATCC 53608T=LMG 31752T) and L. reuteri subsp. rodentium subsp. nov. (type strain 100-23T=DSM 17509T=CIP 109821T).

AB - Ten strains, BG-AF3-AT, pH52_RY, WF-MT5-AT, BG-MG3-A, Lr3000T, RRLNB_1_1, STM3_1T, STM2_1, WF-MO7-1T and WF-MA3-C, were isolated from intestinal or faecal samples of rodents, pheasant and primate. 16S rRNA gene analysis identified them as Limosilactobacillus reuteri. However, average nucleotide identity and digital DNA–DNA hybridization values based on whole genomes were below 95 and 70%, respectively, and thus below the threshold levels for bacterial species delineation. Based on genomic, chemotaxonomic and morphological analyses, we propose five novel species with the names Limosilactobacil-lus balticus sp. nov. (type strain BG-AF3-AT=DSM 110574T=LMG 31633T), Limosilactobacillus agrestis sp. nov. (type strain WF-MT5-AT=DSM 110569T=LMG 31629T), Limosilactobacillus albertensis sp. nov. (type strain Lr3000T=DSM 110573T=LMG 31632T), Limosilactobacillus rudii sp. nov. (type strain STM3_1T=DSM 110572T=LMG 31631T) and Limosilactobacillus fastidiosus sp. nov. (type strain WF-MO7-1T=DSM 110576T=LMG 31630T). Core genome phylogeny and experimental evidence of host adaptation of strains of L. reuteri further provide a strong rationale to consider a number of distinct lineages within this species as subspe-cies. Here we propose six subspecies of L. reuteri: L. reuteri subsp. kinnaridis subsp. nov. (type strain AP3T=DSM 110703T=LMG 31724T), L. reuteri subsp. porcinus subsp. nov. (type strain 3c6T=DSM 110571T=LMG 31635T), L. reuteri subsp. murium subsp. nov. (type strain lpuph1T=DSM 110570T=LMG 31634T), L. reuteri subsp. reuteri subsp. nov. (type strain F 275T=DSM 20016T=ATCC 23272T), L. reuteri subsp. suis subsp. nov. (type strain 1063T=ATCC 53608T=LMG 31752T) and L. reuteri subsp. rodentium subsp. nov. (type strain 100-23T=DSM 17509T=CIP 109821T).

KW - Evolution

KW - Host adaptation

KW - Limosilactobacillus reuteri subspecies

KW - Novel Limosilactobacillus species

KW - Phylogenetic lineages

UR - https://www.scopus.com/pages/publications/85101576724

U2 - 10.1099/ijsem.0.004644

DO - 10.1099/ijsem.0.004644

M3 - Article

C2 - 33533708

AN - SCOPUS:85101576724

SN - 1466-5026

VL - 71

SP - 1

EP - 21

JO - International Journal of Systematic and Evolutionary Microbiology

JF - International Journal of Systematic and Evolutionary Microbiology

IS - 2

M1 - 004644

ER -

Li F, Cheng CC, Zheng J, Liu J, Quevedo RM, Li J et al. 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. 2021;71(2):1-21. 004644. doi: 10.1099/ijsem.0.004644

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