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International Journal of Systematic and... Apr 2020The genus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of and on...
The genus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of and on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus into 25 genera including the emended genus , which includes host-adapted organisms that have been referred to as the group, and 23 novel genera for which the names , , , , , , , , , , , , , , , , , , , , , and are proposed. We also propose to emend the description of the family to include all genera that were previously included in families and . The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus encompassing species adapted to vertebrates (such as , , , , and ) or invertebrates (such as and ).
Topics: Bacterial Typing Techniques; DNA, Bacterial; Lactobacillaceae; Lactobacillus; Leuconostocaceae; Phylogeny; Sequence Analysis, DNA
PubMed: 32293557
DOI: 10.1099/ijsem.0.004107 -
Microbiology (Reading, England) Dec 2023The bacterial family (the lactobacilli) occupy a unique role in microbiology due to their beneficial role in both human cultural history and biology, from the food...
The bacterial family (the lactobacilli) occupy a unique role in microbiology due to their beneficial role in both human cultural history and biology, from the food preservation of hunter gatherers-turned-farmers, through the prevention of scurvy in seafarers exploring new worlds, and the health-promoting properties of species that colonize the human body as well as animals that are important for agriculture and pollination. The almost bewildering phenotypic and genomic complexity of the former genus was recently reconciled with molecular taxonomy and phylogeny to establish robust genera comprising the , whose main features are summarized in this Microbe Profile.
Topics: Lactobacillaceae; Probiotics
PubMed: 38088348
DOI: 10.1099/mic.0.001414 -
Nutrients Dec 2022probiotics contained in dietary supplements or functional foods are well-known for their beneficial properties exerted on host health and diverse pathological... (Review)
Review
probiotics contained in dietary supplements or functional foods are well-known for their beneficial properties exerted on host health and diverse pathological situations. Their capacity to improve inflammatory bowel disease (IBD) and regulate the immune system is especially remarkable. Although bacteria-host interactions have been thought to occur directly, the key role that extracellular vesicles (EVs) derived from probiotics play on this point is being unveiled. EVs are lipid bilayer-enclosed particles that carry a wide range of cargo compounds and act in different signalling pathways. Notably, these EVs have been recently proposed as a safe alternative to the utilisation of live bacteria since they can avoid the possible risks that probiotics may entail in vulnerable cases such as immunocompromised patients. Therefore, this review aims to give an updated overview of the existing knowledge about EVs from different strains, their mechanisms and effects in host health and different pathological conditions. All of the information collected suggests that EVs could be considered as potential tools for the development of future novel therapeutic approaches.
Topics: Humans; Lactobacillaceae; Extracellular Vesicles; Inflammatory Bowel Diseases; Lactobacillus; Immune System
PubMed: 36558455
DOI: 10.3390/nu14245296 -
Microbial Genomics Mar 2021Species belonging to the family are found in highly diverse environments and play an important role in fermented foods and probiotic products. Many of these species...
Species belonging to the family 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 harbour plasmids that encode important genes. In this study, we performed comparative genomic analysis of publicly available data for 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-thirds of the species had at least one plasmid-harbouring strain. Plasmid abundance and GC content were significantly lower in vertebrate-adapted species as compared to nomadic and free-living species. Hierarchical clustering highlighted the distinct nature of plasmids from the nomadic and free-living species than those from the vertebrate-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 the major facilitator superfamily were overrepresented on the plasmids of the vertebrate-adapted species. These genomic signatures correlate with the comparatively nutrient-depleted, stressful and dynamic environments of nomadic and free-living species and nutrient-rich and anaerobic environments of vertebrate-adapted species. Thus, these results indicate the contribution of the plasmids in the adaptation of lactobacilli to their respective habitats. This study also underlines the potential application of these plasmids in improving the technological and probiotic properties of lactic acid bacteria.
Topics: Adaptation, Physiological; Bacterial Proteins; DNA Repair; Genomics; Lactobacillaceae; Phylogeny; Plasmids; Recombination, Genetic; Species Specificity
PubMed: 33166245
DOI: 10.1099/mgen.0.000472 -
Probiotics and Antimicrobial Proteins Oct 2022Dyslipidemia, specifically abnormal levels of low-density lipoprotein cholesterol (LDL-C), is an important risk factor of cardiovascular disease. Evidence showing the...
Dyslipidemia, specifically abnormal levels of low-density lipoprotein cholesterol (LDL-C), is an important risk factor of cardiovascular disease. Evidence showing the promising abilities of probiotics to lower total cholesterol or LDL-C has, however, not yet convinced experts to recommend probiotic bacteria as treatment for blood lipid management. Therefore, there are opportunities for the development of new efficient cholesterol-lowering probiotics. Bile salt hydrolase (BSH) and feruloyl esterase (FAE) are bacterial enzymes proposed to explain the cholesterol-lowering capacity of some bacteria and have both been shown to be responsible for lipid reduction in vivo. Here, in order to select for cholesterol-lowering bacteria, 70 strains related to Lactobacillaceae were screened for BSH and FAE activities. Based on this two-way screening approach, two bacteria were selected and assessed for their capacity to assimilate cholesterol in vitro, another suggested mechanism. Lactobacillus acidophilus CL1285 showed BSH and FAE activity as well as capacity to assimilate cholesterol in vitro. Lactiplantibacillus plantarum CHOL-200 exhibited BSH activity and ability to assimilate cholesterol. These properties observed in vitro make both strains good probiotic candidates for the management of dyslipidemia. Further investigation is needed to assess their ability to reduce blood cholesterol in human trial.
Topics: Cholesterol; Cholesterol, LDL; Humans; Lactobacillaceae; Lactobacillus plantarum; Lipids; Probiotics
PubMed: 35704269
DOI: 10.1007/s12602-022-09959-9 -
Metallomics : Integrated Biometal... Aug 2023As the second most abundant transition element and a crucial cofactor for many proteins, zinc is essential for the survival of all living organisms. To maintain required...
As the second most abundant transition element and a crucial cofactor for many proteins, zinc is essential for the survival of all living organisms. To maintain required zinc levels and prevent toxic overload, cells and organisms have a collection of metal transport proteins for uptake and efflux of zinc. In bacteria, metal transport proteins are well defined for model organisms and many pathogens, but fewer studies have explored metal transport proteins, including those for zinc, in commensal bacteria from the gut microbiota. The healthy human gut microbiota comprises hundreds of species and among these, bacteria from the Lactobacillaceae family are well documented to have various beneficial effects on health. Furthermore, changes in dietary metal intake, such as for zinc and iron, are frequently correlated with changes in abundance of Lactobacillaceae. Few studies have explored zinc requirements and zinc homeostasis mechanisms in Lactobacillaceae, however. Here we applied a bioinformatics approach to identify and compare predicted zinc uptake and efflux proteins in several Lactobacillaceae genera of intestinal relevance. Few Lactobacillaceae had zinc transporters currently annotated in proteomes retrieved from the UniProt database, but protein sequence-based homology searches revealed that high-affinity ABC transporter genes are likely common, albeit with genus-specific domain features. P-type ATPase transporters are probably also common and some Lactobacillaceae genera code for predicted zinc efflux cation diffusion facilitators. This analysis confirms that Lactobacillaceae harbor genes for various zinc transporter homologs, and provides a foundation for systematic experimental studies to elucidate zinc homeostasis mechanisms in these bacteria.
Topics: Humans; Lactobacillaceae; Zinc; Metals; ATP-Binding Cassette Transporters; Bacteria; Computational Biology
PubMed: 37463796
DOI: 10.1093/mtomcs/mfad044 -
Archives of Microbiology Apr 2022The adhesion and aggregation are characteristic attributes of probiotic strains belonging to Lactobacillaceae genus. Due to these properties the host organisms can avoid...
The adhesion and aggregation are characteristic attributes of probiotic strains belonging to Lactobacillaceae genus. Due to these properties the host organisms can avoid colonisation of the intestinal tract by enteropathogenic bacteria. The presented research includes a comparison of the properties of various strains belonging to different Lactobacillaceae species and isolated from different sources The aim of this study was to investigate the ability of Lactocaseibacillus rhamnosus, Lactiplantibacillus plantarum, and Lactobacillus strains (L. acidophilus, L. gasseri, L. ultunensis) from probiotic products and clinical specimens to direct and competitive adherence to Caco-2 and HT-29 cell lines. Furthermore, the ability of lactobacilli and enteropathogenic bacteria, E. coli, E. faecalis, and S. Typhimurium, to auto- and co-aggregation was also investigated.The results showed that all tested strains adhered to Caco-2 and HT-29 cell lines. Though, the factor of adhesion depended on the species and origin of the strain. L. rhamnosus strains showed a lowest degree of adherence as compared to L. plantarum and Lactobacillus sp. strains. On the other side both, L. rhamnosus and L. acidophilus strains reduced the pathogenic bacteria in competition adherence test most effectively. All tested lactobacilli strains were characterised by auto- and co-aggregation abilities, to various degrees. The properties of Lactobacillaceae strains analysed in this study, like adhesion abilities, competitive adherence, auto- and co-aggregation, may affect the prevention of colonisation and elimination of pathogenic bacteria in gastrointestinal tract.
Topics: Bacterial Adhesion; Caco-2 Cells; Escherichia coli; Humans; Lactobacillaceae; Lactobacillus
PubMed: 35478049
DOI: 10.1007/s00203-022-02889-8 -
Microbial Biotechnology Jun 2023The S-layer or surface layer protein (SLP) is the most ancient biological envelope, highly conserved in several Bacteria and Archaea. In lactic acid bacteria (LAB), SLP...
The S-layer or surface layer protein (SLP) is the most ancient biological envelope, highly conserved in several Bacteria and Archaea. In lactic acid bacteria (LAB), SLP is only found in species belonging to the Lactobacillaceae family, many of them considered probiotic microorganisms. New reclassification of members within the Lactobacillaceae family (International Journal of Systematic and Evolutionary Microbiology, 2020, 70, 2782) and newly sequenced genomes demands an updated revision on SLP genes and domain organization. There is growing information concerning SLP occurrence, molecular biology, biophysical properties, and applications. Here, we focus on the prediction of slp genes within the Lactobacillaceae family, and specifically, on the neat interconnection between the two different modular SLP domain organizations and the new reclassified genera. We summarize the results in a concise tabulated manner to review the present knowledge on SLPs and discuss the most relevant and updated concepts regarding SLP sequence clustering. Our assessment is based on sequence alignments considering the new genera classification and protein domain definition with post-translational modifications. We analyse the difficulties encountered to resolve the SLPs 3D structure, describing the need for structure prediction approaches and the relation between protein structure and its anchorage mechanism to the cell wall. Finally, we enumerate new SLP applications regarding heterologous display, pathogen exclusion, immunostimulation, and metal binding.
Topics: Bacterial Proteins; Membrane Glycoproteins; Membrane Proteins; Lactobacillaceae
PubMed: 36752119
DOI: 10.1111/1751-7915.14230 -
International Journal of Food... Apr 2023Members of the family Lactobacillaceae, which now includes species formerly belonging to the genera Lactobacillus and Pediococcus, but also Leuconostocaceae, are of...
Members of the family Lactobacillaceae, which now includes species formerly belonging to the genera Lactobacillus and Pediococcus, but also Leuconostocaceae, are of foremost importance in food fermentations and spoilage, but also as components of animal and human microbiota and as potentially pathogenic microorganisms. Knowledge of the ecological distribution of a given species and genus is important, among other things, for the inclusion in lists of microorganisms with a Qualified Presumption of Safety or with beneficial use. The objective of this work is to use the data in FoodMicrobionet database to obtain quantitative insights (in terms of both abundance and prevalence) on the distribution of these bacteria in foods and food environments. We first explored the reliability of taxonomic assignments using the SILVA v138.1 reference database with full length and partial sequences of the 16S rRNA gene for type strain sequences. Full length 16S rRNA gene sequences allow a reasonably good classification at the genus and species level in phylogenetic trees but shorter sequences (V1-V3, V3-V4, V4) perform much worse, with type strains of many species sharing identical V4 and V3-V4 sequences. Taxonomic assignment at the genus level of 16S rRNA genes sequences and the SILVA v138.1 reference database can be done for almost all genera of the family Lactobacillaceae with a high degree of confidence for full length sequences, and with a satisfactory level of accuracy for the V1-V3 regions. Results for the V3-V4 and V4 region are still acceptable but significantly worse. Taxonomic assignment at the species level for sequences for the V1-V3, V3-V4, V4 regions of the 16S rRNA gene of members of the family Lactobacillaceae is hardly possible and, even for full length sequences, and only 49.9 % of the type strain sequences can be unambiguously assigned to species. We then used the FoodMicrobionet database to evaluate the prevalence and abundance of Lactobacillaceae in food samples and in food related environments. Generalist and specialist genera were clearly evident. The ecological distribution of several genera was confirmed and insights on the distribution and potential origin of rare genera (Dellaglioa, Holzapfelia, Schleiferilactobacillus) were obtained. We also found that combining Amplicon Sequence Variants from different studies is indeed possible, but provides little additional information, even when strict criteria are used for the filtering of sequences.
Topics: Humans; Animals; Lactobacillaceae; Phylogeny; RNA, Ribosomal, 16S; Reproducibility of Results; Bacteria
PubMed: 36841075
DOI: 10.1016/j.ijfoodmicro.2023.110124 -
Canadian Journal of Microbiology Jun 2022The 60 barcode sequence has been established as an informative target for microbial species identification. Applications of 60 barcode sequencing are supported by the...
The 60 barcode sequence has been established as an informative target for microbial species identification. Applications of 60 barcode sequencing are supported by the availability of "universal" PCR primers for amplification and a curated reference database of 60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the 60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 60 sequences representing 258/269 of the validly named species in , , and the 23 newer genera showed that 60-based sequence relationships were generally consistent with whole-genome-based phylogeny. Aligning or mapping full-length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, "universal" barcode amplification primers, and the inherent sequence diversity within the 60 barcode makes it a useful target for the detection and identification of lactobacilli, as defined by the latest taxonomic framework.
Topics: Chaperonin 60; DNA Primers; Lactobacillaceae; Lactobacillus; Phylogeny; Polymerase Chain Reaction
PubMed: 35230911
DOI: 10.1139/cjm-2021-0296