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Lactobacillales vs LAB (Lactic acid bacteria)

Lactobacillales vs LAB (Lactic acid bacteria)


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As far as I understand bacteria of order Lactobacillales are all LAB (Lactic acid bacteria). So often "Lactobacillales" and "LAB" are used interchangeably.

But I also thought that this is not the whole truth, because there are LAB which are not of order Lactobacillales.

Can anyone elaborate on this topic and is there a paper/review explaining the consensus on this topic?


Lactic acid fermentation is the most common type of fermentation among Eubacteria, and it's found on several genera.

Actually, regarding the fermentation types, we can say as a general rule:

  • Ethanol fermentation: found in Plants and Fungi.
  • Lactic acid fermentation: found in Bacteria and Animals.

That being said, according to the Todar's Online Textbook of Bacteriology,

Although many genera of bacteria produce lactic acid as a primary or secondary end-product of fermentation, the term Lactic Acid Bacteria is conventionally reserved for genera in the Order Lactobacillales.

And according to Lactic Acid Bacteria: Microbiological and Functional Aspects, Fourth Edition:

They [LAB] belong to the Phylum Firmicutes, Class Bacilli and Order Lactobacillales.

These genera are: Lactobacillus, Leuconostoc, Pediococcus, Lactococcus, Streptococcus, Carnobacterium, Enterococcus, Oenococcus, Tetragenococcus, Vagococcus and Weisella.

The problem here is that not all lactic acid producing bacteria are called a LAB. Therefore, Lactobacillales and LAB can be used interchangeably. However, you cannot say that all bacteria that perform lactic acid fermentation are LAB.

Sources:


Synthetic biology in probiotic lactic acid bacteria: At the frontier of living therapeutics

Genetic tools in LAB can be highly strain-specific and species-specific.

Genome-engineering tools have enabled engineering of more complex functions in LAB.

Therapeutics in development are largely focused on GI disorders and vaccines.

Advances in E. coli engineering provide a framework for future LAB engineering.

The trillions of microbes hosted by humans can dictate health or illness depending on a multitude of genetic, environmental, and lifestyle factors that help define the human ecosystem. As the human microbiota is characterized, so can the interconnectivity of microbe–host-disease be realized and manipulated. Designing microbes as therapeutic agents can not only enable targeted drug delivery but also restore homeostasis within a perturbed microbial community. Used for centuries in fermentation and preservation of food, lactic acid bacteria (LAB) have a long history of safe, and occasionally health promoting, interactions with the human gut, making them ideal candidates for engineered functionality. This review outlines available genetic tools, recent developments in biomedical applications, as well as potential future applications of synthetic biology to program LAB-based therapeutic systems.


Natural source

Lactobacilli are ubiquitous and normally harmless. In humans and animals, they are found in the intestinal tract and perform many beneficial functions, including immunomodulation, suppression of enteric pathogens and maintenance of intestinal flora. On the negative side, Lactobacilli decompose plant material and are responsible for spoiling vegetables, fruits, beverage and other nutrients. L. casei and L. brevis are two of the most common beer-spoilage organisms.

Certain lactobacilli like Lactobacillus delbrueckii are known to cause urinary tract infections.(2)


Materials and Methods

Whole-genome shotgun sequencing was carried out at the U.S. Department of Energy Joint Genome Institute. Genomes were sequenced to ≈8× depth and assembled by using Jazz, the Joint Genome Institute assembler (51). Gap closure was carried out at Fidelity Systems, Inc., by using direct genomic sequencing (52).

ORFs were identified with the GeneMarkS program (53). Gene functions were predicted by assigning predicted genes to COGs (www.ncbi.nlm.nih.gov/COG) by using the COGNITOR method (24) and by database searches conducted with the PSI-BLAST program (54). Transfer RNAs were predicted with the tRNAscan-SE program (55). LaCOGs were constructed by using previously described procedures (23, 56). Phylogenetic analysis was performed by using the least-square or maximum-likelihood methods, and gene gain/loss scenarios were reconstructed with a version of the weighted parsimony algorithm (29).

Additional methodological details and a detailed list of data deposition numbers are provided in Supporting Materials and Methods, which is published as supporting information on the PNAS web site.


Lactic acid bacteria vs. pathogens in the gastrointestinal tract of fish: a review

* Present address: Lisbeth Løvmo, Granåsveien 34, 7048 Trondheim, Norway.

Department of Marine Biotechnology, Norwegian College of Fishery Science, University of Tromsø, Tromsø, Norway

Department of Marine Biotechnology, Norwegian College of Fishery Science, University of Tromsø, Tromsø, Norway

† Present address: Yvonne Bakken, Skretting, 8450 Storkmarknes, Norway.

Fish Innate Immune System, Department of Cell Biology, University of Murcia, Murcia, Spain

Institute of Anatomy and Cell Biology, University of Bergen, Bergen, Norway

Institute of Marine Research, Bergen, Norway

School of Biomedical Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK

Department of Marine Biotechnology, Norwegian College of Fishery Science, University of Tromsø, Tromsø, Norway

Institute of Marine Research, Bergen, Norway

Department of Marine Biotechnology, Norwegian College of Fishery Science, University of Tromsø, Tromsø, Norway

* Present address: Lisbeth Løvmo, Granåsveien 34, 7048 Trondheim, Norway.

Department of Marine Biotechnology, Norwegian College of Fishery Science, University of Tromsø, Tromsø, Norway

Department of Marine Biotechnology, Norwegian College of Fishery Science, University of Tromsø, Tromsø, Norway

† Present address: Yvonne Bakken, Skretting, 8450 Storkmarknes, Norway.

Fish Innate Immune System, Department of Cell Biology, University of Murcia, Murcia, Spain

Institute of Anatomy and Cell Biology, University of Bergen, Bergen, Norway

Institute of Marine Research, Bergen, Norway

School of Biomedical Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK


Systems Biology – A Guide for Understanding and Developing Improved Strains of Lactic Acid Bacteria

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Research output : Contribution to journal › Journal article › Research › peer-review

T1 - Systems Biology – A Guide for Understanding and Developing Improved Strains of Lactic Acid Bacteria

N2 - Lactic Acid Bacteria (LAB) are extensively employed in the production of various fermented foods, due to their safe status, ability to affect texture and flavor and finally due to the beneficial effect they have on shelf-life. More recently, LAB have also gained interest as production hosts for various useful compounds, particularly compounds with sensitive applications, such as food ingredients and therapeutics. As for all industrial microorganisms, it is important to have a good understanding of the physiology and metabolism of LAB in order to fully exploit their potential, and for this purpose, many systems biology approaches are available. Systems metabolic engineering, an approach that combines optimization of metabolic enzymes/pathways at the systems level, synthetic biology as well as in silico model simulation, has been used to build microbial cell factories for production of biofuels, food ingredients and biochemicals. When developing LAB for use in foods, genetic engineering is in general not an accepted approach. An alternative is to screen mutant libraries for candidates with desirable traits using high-throughput screening technologies or to use adaptive laboratory evolution to select for mutants with special properties. In both cases, by using omics data and data-driven technologies to scrutinize these, it is possible to find the underlying cause for the desired attributes of such mutants. This review aims to describe how systems biology tools can be used for obtaining both engineered as well as non-engineered LAB with novel and desired properties.

AB - Lactic Acid Bacteria (LAB) are extensively employed in the production of various fermented foods, due to their safe status, ability to affect texture and flavor and finally due to the beneficial effect they have on shelf-life. More recently, LAB have also gained interest as production hosts for various useful compounds, particularly compounds with sensitive applications, such as food ingredients and therapeutics. As for all industrial microorganisms, it is important to have a good understanding of the physiology and metabolism of LAB in order to fully exploit their potential, and for this purpose, many systems biology approaches are available. Systems metabolic engineering, an approach that combines optimization of metabolic enzymes/pathways at the systems level, synthetic biology as well as in silico model simulation, has been used to build microbial cell factories for production of biofuels, food ingredients and biochemicals. When developing LAB for use in foods, genetic engineering is in general not an accepted approach. An alternative is to screen mutant libraries for candidates with desirable traits using high-throughput screening technologies or to use adaptive laboratory evolution to select for mutants with special properties. In both cases, by using omics data and data-driven technologies to scrutinize these, it is possible to find the underlying cause for the desired attributes of such mutants. This review aims to describe how systems biology tools can be used for obtaining both engineered as well as non-engineered LAB with novel and desired properties.


General Conclusion

The LAB are multifaceted microorganisms that have existed on earth for several millions of years, with tens of thousands of years of shared history with animals and humans. They have been used for the production of fermented foods for centuries, and more or less actively developed as probiotics for several decades (Figure 1). LAB may strongly be part of the health concept for livestock rearing and in food and feed production. An outstanding effort has been made these last years, using extended omics approaches, to build the knowledge and further tools to elucidate the contribution of LAB in health and diseases. We are now facing the daunting task of integrating of all this information for general application as well as for individual use (“my personalized LAB”). Indeed, separately, LAB can either contribute to induce Th1 or Th2 immune responses they may also induce specific or non-specific regulatory T cells, which may or may not be required by the host. Similarly, LAB have the potential to favor either weight loss or weight gain. LAB abundance is sometimes diminished or increased depending on diseases. The central role of LAB within the microbiota, providing antimicrobials, also raises the question of the control of ecological niches, which can be advantageous or not (Berstad et al., 2016 Hegarty et al., 2016). Berstad argued that ‘we should stop thinking of LAB as always being friendly.’ Indeed, few data exist on the long-term impact of LAB, considering their possible capacity to destabilize the microbiota, and the “paradox” to use them empirically in multiple pathologies and combined (metabolic, immune, psychological) disorders. Nevertheless, LAB are our obligate partners and we have to cope with these microorganisms. Dissociating the common and specific interactions of LAB strains, -species and -genera within the whole of the microbiota in which they partake is still necessary to identify regulatory mechanisms, respectively, involved in distinct organs, systems, and hosts. Definitely, integrative system biology approaches are required to achieve the ultimate goal of applying LAB for personalized medicine. It comprises using omics technologies on the LAB as well as on the host and including foodomics and nutrigenomics (Kussmann and Van Bladeren, 2011 Bordoni and Capozzi, 2014), together with appropriate basic and integrative models and tools (Fritz et al., 2013 Daniel et al., 2015 Papadimitriou et al., 2015) to appraise the overall functionality of LAB.

FIGURE 1. Schematic representation of the worldwide occurrence (left) and multiple health applications (right) of lactic acid bacteria.


Summary

Several studies have recently pointed towards an increased occurrence and prevalence of several taxa of the lactic acid bacteria (LAB) in the microbiota of the upper respiratory tract (URT) under healthy conditions versus disease. These include several species of the Lactobacillales such as Lacticaseibacillus casei, Lactococcus lactis and Dolosigranulum pigrum. In addition to physiological studies on their potential beneficial functions and their long history of safe use as probiotics in other human body sites, LAB are thus increasingly to be explored as alternative or complementary treatment for URT diseases. This review highlights the importance of lactic acid bacteria in the respiratory tract and their potential as topical probiotics for this body site. We focus on the potential probiotic properties and adaptation factors that are needed for a bacterial strain to optimally exert its beneficial activity in the respiratory tract. Furthermore, we discuss a range of in silico, in vitro and in vivo models needed to obtain better insights into the efficacy and adaptation factors specifically for URT probiotics. Such knowledge will facilitate optimal strain selection in order to conduct rigorous clinical studies with the most suitable probiotic strains. Despite convincing evidence from microbiome association and in vitro studies, the clinical evidence for oral or topical probiotics for common URT diseases such as chronic rhinosinusitis (CRS) needs further substantiation.


PTS-related phosphoglucosidases

The phosphoenolpyruvate (PEP)-dependent carbohydrate PTS (PEP : PTS) is a key mechanism of the bacterial sugar catabolism that directly couples substrate import with phosphorylation ( Fig. 1). The PEP : PTS is mainly encountered in obligately and facultatively anaerobic bacteria where it serves as a bioenergetically efficient alternative to active substrate import and ATP-dependent phosphorylation, as only one ATP equivalent has to be expended for both import and activation ( Postma et al., 1993). The phosphate group is transferred from the phosphoryl donor PEP to the sugar substrate by a cascade that involves the cytoplasmic proteins Enzyme I and HPr. The Enzyme II complex (EII), whose membrane-associated components are directly involved in substrate translocation (EIIC permeases) and phosphorylation (EIIB), represents the substrate-specific part of the cascade. Upon phosphorylation, the activated sugar (e.g. glucose 6-phosphate) can enter glycolysis directly ( Postma et al., 1993 Barabote & Saier, 2005). The PTS is mainly specific for hexoses. Since PEP does not occur as an intermediate in the phosphoketolase pathway of heterofermentative LAB, PEP : PTS appears solely associated with homolactic fermentation. PEP : PTS also has a key regulatory function in the mechanism of carbon catabolite repression (CCR). CCR ensures that in the presence of preferred substrates such as glucose, the metabolism of less favourable carbon sources is inhibited ( Deutscher et al., 2006). As described below, EIIA and HPr serve central regulatory roles in CCR of Gram-negative and Gram-positive bacteria, respectively.

Schematic representation of cellobiose import, phosphorylation and hydrolysis by the bacterial PEP-dependent carbohydrate PTS. PEP, an intermediate of glycolysis, serves as phosphoryl donor. The phospho group is transferred to the substrate via phospho-intermediates of the general proteins Enzyme I (EI), HPr and the carbohydrate-specific Enzyme II complex (EII). The substrate is translocated by the permease EIIC, and phosphorylated at the membrane by EIIB. Phosphorylated cellobiose is released into the cytoplasm and hydrolysed to glucose 6-phosphate and glucose by a phospho-β-glucosidase.

Schematic representation of cellobiose import, phosphorylation and hydrolysis by the bacterial PEP-dependent carbohydrate PTS. PEP, an intermediate of glycolysis, serves as phosphoryl donor. The phospho group is transferred to the substrate via phospho-intermediates of the general proteins Enzyme I (EI), HPr and the carbohydrate-specific Enzyme II complex (EII). The substrate is translocated by the permease EIIC, and phosphorylated at the membrane by EIIB. Phosphorylated cellobiose is released into the cytoplasm and hydrolysed to glucose 6-phosphate and glucose by a phospho-β-glucosidase.

Function and occurrence of phospho-β-glucosidases

β-Glucosides and disaccharides such as cellobiose and lactose can be metabolized via the PEP : PTS as well. In these cases, the phosphorylated glycoconjugates are hydrolysed by cytoplasmic phospho-β-glucosidases (EC 3.2.1.86) or phospho-β-galactosidases (EC 3.2.1.85) that usually do not possess hydrolytic activity towards non-phosphorylated substrates ( Fig. 1). Most known phosphoglucosidases/galactosidases have been assigned to GH 1. However, the differences between β-glucosidases and phospho-β-glucosidases of GH 1 are subtle and not yet completely resolved. It was shown that specificity for phosphorylated or nonphosphorylated substrates can depend on the exchange of only a few amino acid residues in the substrate binding pocket ( Marana, 2006 Hill & Reilly, 2008).

Together with the phosphoglycosidases, EII components form the selective part of the PTS. PTS-related glycosidase genes are frequently organized in operons with genes encoding EII (ABC) components specific for the corresponding substrate. The published genome of L. plantarum WCFS1 contains 11 genes putatively encoding GH 1 enzymes with phospho-β-glucosidase functionality. Nine of these genes were found adjacent to genes encoding β-glucoside/cellobiose-specific EII components ( Table 1). A recent crystallographic study ( Michalska et al., 2013) provided detailed insights into the substrate binding site of a phosphoglucosidase of L. plantarum (Pbg1, Table 1). Sequence comparison showed that the glycone (6-phosphate-glucopyranosyl) binding site is highly conserved in all L. plantarum phosphoglucosidases. Considerable sequence variations were reported for the aglycone binding sites and entry regions to the active site. It therefore appears that these operons ( Table 1) may not simply represent redundant systems, but are possibly specific for distinct β-glucosides.

Putative phospho-β-glucosidase genes of Lactobacillus plantarum WCFS1 (GenBank accession no. NC_004567) and their predicted organization in operons the information was obtained from the Prokaryotic Operon DataBase ( Taboada et al., 2012)


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