Polyphasic taxonomy, a consensus approach to bacterial systematics.

The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae 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 Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae 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 Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).

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.

Lactic acid bacteria of foods and their current taxonomy.

Lactic acid bacteria (LAB) constitute a group of gram-positive bacteria united by a constellation of morphological, metabolic, and physiological characteristics The general description of the bacteria included in the group is gram-positive, nonsporing, nonrespiring cocci or rods, which produce lactic acid as the major end product during the fermentation of carbohydrates The LAB term is intimately associated with bacteria involved in food and feed fermentation, including related bacteria normally associated with the (healthy) mucosal surfaces of humans and animals The boundaries of the group have been subject to some controversy, but historically the genera Lactobacillus, Leuconostoc, Pediococcus, and Streptococcus form the core of the group Taxonomic revisions of these genera and the description of new genera mean that LAB could, in their broad physiological definition, comprise around 20 genera However, from a practical, food-technology point of view, the following genera are considered the principal LAB: Aerococcus, Carnobacterium, Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Oenococcus, Pediococcus, Streptococcus, Tetragenococcus, Vagococcus, and Weissella The genus Bifidobacterium, often considered in the same context as the genuine lactic acid bacteria and sharing some of their typical features, is phylogenetically unrelated and has a unique mode of sugar fermentation The classification of lactic acid bacteria into different genera is largely based on morphology, mode of glucose fermentation, growth at different temperatures, configuration of the lactic acid produced, ability to grow at high salt concentrations, and acid or alkaline tolerance Chemotaxonomic markers such as fatty acid composition and constituents of the cell wall are also used in classification In addition, the present taxonomy relies partly on true phylogenetic relationships,

Lactic acid bacteria: classification and physiology.

Lactobacilli are Gram-positive, non-spore-forming, rods or coccobacilli with a G+C content of DNA usually below 50 mol%. They are strictly fermentative, aero-tolerant or anaerobic, aciduric or acidophilic and have complex nutritional requirements (e.g. for carbohydrates, amino acids, peptides, fatty acid esters, salts, nucleic acid derivatives, and vitamins). They do not synthesize porphyrinoids and thus, are devoid of heme-dependent activities. Strains of some species can use porphorinoids from the environment and exhibit activities of catalase, nitrite reduction or even cytochromes (Meisel, 1991). Pseudo-catalase is formed in strains of Lb. mali. With glucose as a carbon source lactobacilli may be either homofermentative, producing more than 85% lactic acid, or hetero-fermentative, producing lactic acid, CO2, ethanol (and/or acetic acid) in equimolar amounts. In the presence of oxygen or other oxidants increased amounts of acetate may be produced at the expense of lactate or ethanol, whereby one additional mole of ATP is gained via the acetate kinase reaction. Thus, variations in the metabolic end products may occur. Various compounds (e.g. citrate, malate, tartrate, quinolate, nitrate, nitrite, etc.) may be metabolized, and used as energy source (e.g. via building up a proton motive force) or electron acceptors.

The genus Lactobacillus

The microflora of sourdough preparations was investigated by examining the physiological characteristics, whole-cell protein patterns, and 16S rRNA sequences of Lactobacillus isolates. Strains isolated from sourdough were placed in the species Lactobacillus brevis, Lactobacillus sanfrancisco, and Lactobacillus reuteri. 16S rRNA sequences were determined for L. brevis, Lactobacillus fructivorans, Lactobacillus fermentum, L. sanfrancisco, and L. reuteri, and oligonucleotide probes for fast specific identification of these sourdough lactobacilli were deduced. The physiological characteristics, protein patterns, and 16S rRNA sequences of these organisms were compared with data for other sourdough lactobacilli and additional reference strains. Strains of a Lactobacillus species were isolated from rye sourdough; these strains may account for most of the flora in sourdough made from wheat or rye. These organisms were differentiated from other sourdough lactobacilli by their protein pattern, 16S rRNA sequence, G+C content, and physiological properties. The 16S rRNA sequence of this species was determined, and we constructed a phylogenetic tree which reflected the relationships of this species to other lactobacilli. This organism is closely related to L. reuteri. A new Lactobacillus species, Lactobacillus pontis, is proposed. The type strain is L. pontis LTH 2587 (= DSM 8475 = LMG 14187). We describe a general strategy in which a polyphasic approach was used to characterize a new species.

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Identification of lactobacilli from sourdough and description of Lactobacillus-pontis sp-nov.

Sourdough has played a significant role in human nutrition and culture for thousands of years and is still of eminent importance for human diet and the bakery industry. Lactobacillus sanfranciscensis is the predominant key bacterium in traditionally fermented sourdoughs. The genome of L. sanfranciscensis TMW 1.1304 isolated from an industrial sourdough fermentation was sequenced with a combined Sanger/454-pyrosequencing approach followed by gap closing by walking on fosmids. The sequencing data revealed a circular chromosomal sequence of 1,298,316 bp and two additional plasmids, pLS1 and pLS2, with sizes of 58,739 bp and 18,715 bp, which are predicted to encode 1,437, 63 and 19 orfs, respectively. The overall GC content of the chromosome is 34.71%. Several specific features appear to contribute to the ability of L. sanfranciscensis to outcompete other bacteria in the fermentation. L. sanfranciscensis contains the smallest genome within the lactobacilli and the highest density of ribosomal RNA operons per Mbp genome among all known genomes of free-living bacteria, which is important for the rapid growth characteristics of the organism. A high frequency of gene inactivation and elimination indicates a process of reductive evolution. The biosynthetic capacity for amino acids scarcely availably in cereals and exopolysaccharides reveal the molecular basis for an autochtonous sourdough organism with potential for further exploitation in functional foods. The presence of two CRISPR/cas loci versus a high number of transposable elements suggests recalcitrance to gene intrusion and high intrinsic genome plasticity.

/pdf/genomic-analysis-reveals-lactobacillus-sanfranciscensis-as-e9o3akpyup.pdf

Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs.

The utilisation of glucose and maltose was investigated with Lactobacillus strains isolated from sourdough starters. These preparations have been in continuous use for a long period to produce sourdough from rye, wheat and sorghum. The major metabolic products formed by resting cells from glucose or maltose were lactate, ethanol and acetate. Upon fermentation of maltose, resting cells of Lactobacillus sanfrancisco, L. reuteri, L. fermentum and Lactobacillus ep. released up to 13.8 mM glucose after 8 h. The ratio of released glucose per mol of utilised maltose was up to 1:1. Glucose formation was high when starved cells of L. sanfrancisco and Lactobacillus sp. were used. This is consistent with maltose utilisation via maltose phosphorylase which phosphorylates maltose without the expenditure of ATP and thus allows the cell to waste glucose in the presence of abundant maltose. The glucose formed may be utilised by the lactobacilli or other microorganisms, e.g. yeasts. However, the release of glucose into the medium by sourdough lactobacilli prevents competitors from utilising the abundant maltose by glucose repression. In strains of L. sanfrancisco, maltose utilisation was very effective and not subject to glucose repression. Therefore, they overgrow other microorganisms sharing this habitat. Wild isolates of L. sanfrancisco were initially unable to grow on glucose. Upon growth on maltose such strains required adaptation times of up to 150 h to grow on glucose. After subsequent transfer of glucose-grown cells to fresh medium the strains resumed growth both on glucose or maltose. They readily lost their ability to grow on glucose upon exposure to maltose. L. sanfrancisco exhibited biphasic growth characteristics on media containing glucose, maltose or both carbon sources. Evidence is provided that biphasic growth and metabolite formation are dependent on the redox potential.

Utilisation of maltose and glucose by lactobacilli isolated from sourdough

Sorghum flour was fermented in the traditional way for Kisra production. Wet or dry preparations of fermented sorghum dough from Sudanese households were employed as inocula. Microbiological and chemical analysis was performed throughout the fermentation process. Cell counts reached values of up to 9 × 108 cfu/g and contained >99% lactobacilli. Strains of Lactobacillus fermentum, L. reuteri and L. amylovorus or L. fermentum and L. amylovorus were found as dominant organisms in doughs inoculated with wet or dry sorghum dough preparations, respectively. The ratios of the lactobacilli remained constant after up to four consecutive fermentations. After inoculation with the dry dough preparation the yeast Candida krusei was detected at 106 cfu/g. During the fermentation the pH declined from 5.5 to values of approximately 3.4. The maltose content of the dough decreased continuously, wheraas glucose was accumulated as an intermediate. The relative content of most amino acids in the doughs did not significantly change during the fermentation. However, the concentrations of cysteine and methionine decreased, whereas threonine was enriched in the dough.

Georg Böcker

Papers

Identification of lactobacilli from sourdough and description of Lactobacillus-pontis sp-nov.

Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs.

Utilisation of maltose and glucose by lactobacilli isolated from sourdough

Microbiological and chemical analysis of fermented sorghum dough for Kisra production