A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

Zheng, Jinshui; Wittouck, Stijn; Salvetti, Elisa; Franz, Charles M. A. P.; Harris, Hugh M. B.; Mattarelli, Paola; O’Toole, Paul W.; Pot, Bruno; Vandamme, Peter; Walter, Jens; Watanabe, Koichi; Wuyts, Sander; Felis, Giovanna E.; Gänzle, Michael G.; Lebeer, Sarah

doi:10.1099/ijsem.0.004107

Cited by 3,175 publications

(1,848 citation statements)

References 315 publications

(431 reference statements)

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“…Here we acknowledge newly reclassi cation and genera naming of some Lactobacillus spp. listed in this study (e.g., Lactobacillus fermentum as Limosilactobacillus fermentum and Lactobacillus mucosae as Limosilactobacillus mucosae) [49]. For consistency, older species names are being used here.…”

Section: Methodsmentioning

confidence: 99%

Recombinant Bacteriophage LysKB317 Endolysin Mitigates Lactobacillus Infection of Corn Mash Fermentations

Bischoff

Rich

et al. 2020

Preprint

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Background Commercial ethanol fermentation facilities traditionally rely on antibiotics for bacterial contamination control. Here we demonstrate an alternative approach to treat contamination using a novel peptidoglycan hydrolase (LysKB317) isolated from a bacteriophage, EcoSau. This endolysin was specially selected against Lactobacillus strains that were isolated as contaminants from a fuel ethanol plant. The LysKB317 gene was recombinantly expressed in Escherichia coli as a 33 kDa purified enzyme. Results In turbidity reduction assays, the recombinant enzyme was subjected to a panel of 32 bacterial strains and was active against 28 bacterial strains representing one species of Acetobacter, eight species of Lactobacillus, one species of Pediococcus, three species of Streptococcus, and one species of Weissella. The activity of LysKB317 was optimal around pH 6, but it has broad activity and stability from pH 4.5 – 7.5 up to at least 48 h. Maximum activity was observed at 50°C up to at least 72 hrs. In addition, LysKB317 was stable in 30% ethanol up to at least 72 hrs. In experimentally infected corn mash fermentations, 1 µM endolysin reduced bacterial load by 3-log fold change, while 0.01 µM reduced bacteria by 2-log fold change. Concentration of fermentation products (ethanol, residual glucose, lactic acid, and acetic acids) for infected cultures treated with ≥ 0.01 µM LysKB317 were similar to uncontaminated controls. Conclusion Exogenously added LysKB317 endolysin is functional in conditions typically found in fuel ethanol fermentations tanks and may be developed as an alternative to antibiotics for contamination control during fuel ethanol fermentations.

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Section: Methodsmentioning

confidence: 99%

Recombinant Bacteriophage LysKB317 Endolysin Mitigates Lactobacillus Infection of Corn Mash Fermentations

Bischoff

Rich

et al. 2020

Preprint

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“…Since antibiotic resistance is one of the safety concerns associated with LAB used for human streptogramin (1), and vancomycin (1). The presence of lmrB has been previously shown in L.…”

Section: Antibiotic Resistancementioning

confidence: 96%

“…Till March 2019, NCBI prokaryotic genome database was found to have complete genome sequences for 282 strains under the genus defined as Lactobacillus before its reclassification into several genera (1). With the current classification, this data includes 24 of the 26 genera under the Lactobacillaceae family.…”

Section: Data Collection and General Characterizationmentioning

confidence: 99%

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Plasmids encode niche-specific traits inLactobacillaceae

Davray

Deo

Kulkarni

2020

Preprint

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The species of family Lactobacillaceae are found in highly diverse environments and play an important role in fermented foods and probiotic products. Many of these species have been individually reported to harbor plasmids that encode important genes. In this study, we performed comparative genomic analysis of the publically available data of 512 plasmids from 282 strains represented by 51 species of this family and correlated the genomic features of plasmids with the ecological niches in which these species are found. Two-third of the species had at least one plasmid-harboring strain. Plasmid abundance and GC content were significantly lower in the host-adapted species as compared to the nomadic and free-living species. Hierarchical clustering (HCL) highlighted the distinct nature of plasmids from the nomadic and free-living species than those from the host-adapted species. EggNOG assisted functional annotation revealed that genes associated with transposition, conjugation, DNA repair and recombination, exopolysaccharide production, metal ion transport, toxin-antitoxin system, and stress tolerance were significantly enriched on the plasmids of the nomadic and in some cases nomadic and free-living species. On the other hand, genes related to anaerobic metabolism, ABC transporters, and major facilitator superfamily were found to be overrepresented on the plasmids of the host-adapted species. These genomic signatures are correlated to the comparatively nutrient-depleted, stressful and dynamic environments of nomadic and free-living species and nutrient-rich and anaerobic environments of the host-adapted species. Thus, these results indicate the contribution of the plasmids in the adaptation of lactobacilli to the respective habitats. This study also underlines the potential application of these plasmids in improving the technological and probiotic properties of lactic acid bacteria.

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“…GTDB [88] has applied the designation Lactobacillus_H, which cannot be incorporated into a well-formed binomial. However, according to Zheng et al [98] Limosilactobacillus encompasses other species classi ed by GTDB within this provisional genus A bacterial species cultured from chicken faeces and assigned to this genus and delineated as a species by analysis of its genome sequence. GTDB [88] has given this species the alphanumerical designation sp002278035.…”

Section: Description Of Bacillus Norwichensis Sp Novmentioning

confidence: 99%

A Genomic Blueprint of the Chicken Gut Microbiome

Gilroy¹,

Ray²,

Getino³

et al. 2020

Preprint

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Background: The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to deliver a genomic blueprint of this complex microbial community. Results: We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n=582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes This represents the most comprehensive view of the chicken gut associated microbiome to date, encompassing dozens of novel candidate bacterial genera and hundreds of novel candidate species. Keen to provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured bacterial isolates from faeces to deliver 282 whole genome sequences, incorporating thirty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii.Conclusions: Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provides a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.

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A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

Cited by 3,175 publications

References 315 publications

Recombinant Bacteriophage LysKB317 Endolysin Mitigates Lactobacillus Infection of Corn Mash Fermentations

Recombinant Bacteriophage LysKB317 Endolysin Mitigates Lactobacillus Infection of Corn Mash Fermentations

Plasmids encode niche-specific traits inLactobacillaceae

A Genomic Blueprint of the Chicken Gut Microbiome

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