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Functional Characterization of Lactic Acid Bacteria

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 29037

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Dr. Franca Rossi

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Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy
Interests: food safety; food microbiology; microbial genetics and physiology; gene cloning; antibiotic resistance; foodborne pathogens; bacteriocins; food microbial ecology; fermentation and ripening; gene expression
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Dear Colleagues,

Lactic Acid Bacteria (LAB), comprising the most relevant bacterial species in technological and health promoting applications and belonging to the genera Lactobacillus, Lactococcus, Streptococcus, Enterococcus as well as other less characterized lineages, merit research efforts to exploit at best their potential to improve human life.

Despite the fact that much literature is available on their taxonomic dissection, with an endless series of new species descriptions, rearrangements and genotype distinction, studies on their ability to carry out desired activities in food production and in vivo have regarded very few strains of a small number of species, mostly those already in use as probiotics. Nevertheless, among the hundreds of species described, for example, in the genus Lactobacillus and related organisms, many are not characterized at all on the physiological and functional viewpoint and for some even ecology is little known since only a few strains have been described to date.

Therefore, this special issue is aimed at collecting articles that deepen knowledge on the functional roles of so far little studied species or intra-species groups of LAB. Applicative studies linking strain performance in the food technology or probiotic ambits with genetic background and expression regulation of gene products involved in desired activities are welcome. Also studies on the intra-species variability in those activities, demonstrating at the same time the absence of risk characters, are of interest.

In the articles to be submitted a precise definition of the taxonomic affiliation of the microorganisms studied by sequencing of genetic markers is required.

Review articles regarding the above topics will also be taken into consideration.

This special issue aims to contribute suggestions on how to enlarge the application of LAB, also those less studied to date, to protect human health directly, or indirectly, by improving food safety and animal wellness.

Dr. Franca Rossi
Guest Editor

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Keywords

Lactic Acid Bacteria
Lactobacillus
Lactococcus
Streptococcus
Enterococcus
function
characterization
application
food safety
genetic features
gene regulation
ecology
immunostimulation

Published Papers (11 papers)

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Editorial

Jump to: Research, Review

5 pages, 187 KiB

Open AccessEditorial

Special Issue “Functional Characterization of Lactic Acid Bacteria”: Editorial

by Franca Rossi

Microorganisms 2023, 11(5), 1190; https://doi.org/10.3390/microorganisms11051190 - 01 May 2023

Viewed by 985

Abstract

Lactic acid bacteria (LAB) are a diverse group of microorganisms of the order Lactobacillales in the Bacillota phylum, subdivision Bacilli, comprising, at this stage of taxonomic descriptions six families (Aerococcaceae, Carnobacteriaceae, Enterococcaceae, Lactobacillaceae, Leuconostocaceae and Streptococcaceae) [...] Full article

(This article belongs to the Special Issue Functional Characterization of Lactic Acid Bacteria)

Research

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13 pages, 2276 KiB

Open AccessArticle

Variability of Genetic Characters Associated with Probiotic Functions in Lacticaseibacillus Species

by Franca Rossi, Carmela Amadoro, Maria Luigia Pallotta and Giampaolo Colavita

Microorganisms 2022, 10(5), 1023; https://doi.org/10.3390/microorganisms10051023 - 13 May 2022

Cited by 3 | Viewed by 1919

Abstract

This study aims to explore the intra-species distribution of genetic characteristics that favor the persistence in the gastrointestinal tract (GIT) and host interaction of bacteria belonging to species of the Lacticaseibacillus genus. These bacterial species comprise commercial probiotics with the widest use among consumers and strains naturally occurring in GIT and in fermented food. Since little is known about the distribution of genetic traits for adhesion capacity, polysaccharide production, biofilm formation, and utilization of substrates critically important for survival in GIT, which influence probiotic characteristics, a list of genetic determinants possibly involved in such functions was created by a search for specific genes involved in the above aspects in the genome of the extensively characterized probiotic L. rhamnosus GG. Eighty-two gene loci were retrieved and their presence and variability in other Lacticaseibacillus spp. genomes were assessed by alignment with the publicly available fully annotated genome sequences of L. casei, L. paracasei, L. rhamnosus, and L. zeae. Forty-nine of these genes were found to be absent in some strains or species. The remaining genes were conserved and covered almost all the functions considered, indicating that all strains of the genus may exert some probiotic effects. Among the variable loci, a taurine utilization operon and a α-L-fucosidase were examined for the presence/absence in 26 strains isolated from infant feces by PCR-based tests. Results were variable among the isolates, though their common origin indicated the capacity to survive in the intestinal niche. This study indicated that the capacity to exert probiotic actions of Lacticaseibacillus spp. depends on a conserved set of genes but variable genetic factors, whose role is only in part elucidated, are more numerous and can explain the enhanced probiotic characteristics for some strains. The selection of the most promising probiotic candidates to be used in food is feasible by analyzing the presence/absence of a set of variable traits. Full article

(This article belongs to the Special Issue Functional Characterization of Lactic Acid Bacteria)

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16 pages, 2556 KiB

Open AccessArticle

Probiotic Properties of Lactic Acid Bacteria with High Conjugated Linoleic Acid Converting Activity Isolated from Jeot-Gal, High-Salt Fermented Seafood

by Nho-Eul Song, Na-Jeong Kim, Young-Hun Kim and Sang-Ho Baik

Microorganisms 2021, 9(11), 2247; https://doi.org/10.3390/microorganisms9112247 - 28 Oct 2021

Cited by 10 | Viewed by 2108

Abstract

Conjugated linoleic acid (CLA) isomers are potent health-promoting fatty acids. This study evaluated the probiotic properties of 10 strains of high CLA-producing lactic acid bacteria (LAB) isolated from Jeot-gal, a high-salt, fermented seafood. Two isolates, Lactiplantibacillus plantarum JBCC105683 and Lactiplantibacillus pentosus JBCC105676, produced the largest amounts of CLA (748.8 and 726.9 μg/mL, respectively). Five isolates, L. plantarum JBCC105675, L. pentosus JBCC105676, L. pentosus JBCC105674, L. plantarum JBCC105683, and Lactiplantibacillus paraplantarum JBCC105655 synthesized more cis-9, trans-11-CLA than trans-10, cis-12-CLA (approximately 80:20 ratio). All the strains survived severe artificial acidic environments and showed antimicrobial activity and strong adhesion capability to Caco-2 cells as compared to the commercial strain Lactocaseibacillus rhamnosus GG. Among them, Pediococcus acidilactici JBCC105117, L. paraplantarum JBCC105655, and L. plantarum JBCC105683 strongly stimulated the immunological regulatory gene PMK-1 and the host defense antimicrobial peptide gene clec-60 in Caenorhabditis elegans. Moreover, three strains showed a significant induction of tumor necrosis factor-α, interleukin (IL)-1β, IL-6, IL-12, and IL-10 production in RAW 264.7 macrophages, indicating that they were promising candidates for probiotics with high CLA-converting activity. Our results indicate that the newly isolated CLA-producing LAB might be useful as a functional probiotic with beneficial health effects that modulate the immune system. Full article

(This article belongs to the Special Issue Functional Characterization of Lactic Acid Bacteria)

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12 pages, 2437 KiB

Open AccessArticle

Identification of Potential Citrate Metabolism Pathways in Carnobacterium maltaromaticum

by Heng Li, Nancy E. Ramia, Frédéric Borges, Anne-Marie Revol-Junelles, Finn Kvist Vogensen and Jørgen J. Leisner

Microorganisms 2021, 9(10), 2169; https://doi.org/10.3390/microorganisms9102169 - 18 Oct 2021

Cited by 5 | Viewed by 2527

Abstract

In the present study, we describe the identification of potential citrate metabolism pathways for the lactic acid bacterium (LAB) Carnobacterium maltaromaticum. A phenotypic assay indicated that four of six C. maltaromaticum strains showed weak (Cm 6-1 and ATCC 35586) or even delayed (Cm 3-1 and Cm 5-1) citrate utilization activity. The remaining two strains, Cm 4-1 and Cm 1-2 gave negative results. Additional analysis showed no or very limited utilization of citrate in media containing 1% glucose and 22 or 30 mM citrate and inoculated with Cm 6-1 or ATCC 35586. Two potential pathways of citrate metabolism were identified by bioinformatics analyses in C. maltaromaticum including either oxaloacetate (pathway 1) or tricarboxylic compounds such as isocitrate and α-ketoglutarate (pathway 2) as intermediates. Genes encoding pathway 1 were present in two out of six strains while pathway 2 included genes present in all six strains. The two potential citrate metabolism pathways in C. maltaromaticum may potentially affect the sensory profiles of milk and soft cheeses subjected to growth with this species. Full article

(This article belongs to the Special Issue Functional Characterization of Lactic Acid Bacteria)

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15 pages, 2093 KiB

Open AccessArticle

Comparative Genomic Analysis Determines the Functional Genes Related to Bile Salt Resistance in Lactobacillus salivarius

by Qiqi Pan, Xudan Shen, Leilei Yu, Fengwei Tian, Jianxin Zhao, Hao Zhang, Wei Chen and Qixiao Zhai

Microorganisms 2021, 9(10), 2038; https://doi.org/10.3390/microorganisms9102038 - 27 Sep 2021

Cited by 8 | Viewed by 2265

Abstract

Lactobacillus salivarius has drawn attention because of its promising probiotic functions. Tolerance to the gastrointestinal tract condition is crucial for orally administrated probiotics to exert their functions. However, previous studies of L. salivarius have only focused on the bile salt resistance of particular strains, without uncovering the common molecular mechanisms of this species. Therefore, in this study, we expanded our research to 90 L. salivarius strains to explore their common functional genes for bile salt resistance. First, the survival rates of the 90 L. salivarius strains in 0.3% bile salt solutions were determined. Comparative genomics analysis was then performed to screen for the potential functional genes related to bile salt tolerance. Next, real-time polymerase chain reaction and gene knockout experiments were conducted to further verify the tolerance-related functional genes. The results indicated that the strain-dependent bile salt tolerance of L. salivarius was mainly associated with four peptidoglycan synthesis-related genes, seven phosphotransferase system-related genes, and one chaperone-encoding gene involved in the stress response. Among them, the GATase1-encoding gene showed the most significant association with bile salt tolerance. In addition, four genes related to DNA damage repair and substance transport were redundant in the strains with high bile salt tolerance. Besides, cluster analysis showed that bile salt hydrolases did not contribute to the bile salt tolerance of L. salivarius. In this study, we determined the global regulatory genes, including LSL_1568, LSL_1716 and LSL_1709, for bile salt tolerance in L. salivarius and provided a potential method for the rapid screening of bile salt-tolerant L. salivarius strains, based on PCR amplification of functional genes. Full article

(This article belongs to the Special Issue Functional Characterization of Lactic Acid Bacteria)

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16 pages, 1759 KiB

Open AccessArticle

Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese

by Werner Ruppitsch, Andjela Nisic, Patrick Hyden, Adriana Cabal, Jasmin Sucher, Anna Stöger, Franz Allerberger and Aleksandra Martinović

Microorganisms 2021, 9(8), 1612; https://doi.org/10.3390/microorganisms9081612 - 28 Jul 2021

Cited by 12 | Viewed by 2942

Abstract

In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank. Full article

(This article belongs to the Special Issue Functional Characterization of Lactic Acid Bacteria)

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15 pages, 1659 KiB

Open AccessArticle

Oligosaccharide Metabolism and Lipoteichoic Acid Production in Lactobacillus gasseri and Lactobacillus paragasseri

by Tsukasa Shiraishi, Shintaro Maeno, Sayoko Kishi, Tadashi Fujii, Hiroki Tanno, Katsuaki Hirano, Takumi Tochio, Yasuhiro Tanizawa, Masanori Arita, Shin-ichi Yokota and Akihito Endo

Microorganisms 2021, 9(8), 1590; https://doi.org/10.3390/microorganisms9081590 - 26 Jul 2021

Cited by 7 | Viewed by 2939

Abstract

Lactobacillus gasseri and Lactobacillus paragasseri are human commensal lactobacilli that are candidates for probiotic application. Knowledge of their oligosaccharide metabolic properties is valuable for synbiotic application. The present study characterized oligosaccharide metabolic systems and their impact on lipoteichoic acid (LTA) production in the two organisms, i.e., L. gasseri JCM 1131^T and L. paragasseri JCM 11657. The two strains grew well in medium with glucose but poorly in medium with raffinose, and growth rates in medium with kestose differed between the strains. Oligosaccharide metabolism markedly influenced their LTA production, and apparent molecular size of LTA in electrophoresis recovered from cells cultured with glucose and kestose differed from that from cells cultured with raffinose in the strains. On the other hand, more than 15-fold more LTA was observed in the L. gasseri cells cultured with raffinose when compared with glucose or kestose after incubation for 15 h. Transcriptome analysis identified glycoside hydrolase family 32 enzyme as a potential kestose hydrolysis enzyme in the two strains. Transcriptomic levels of multiple genes in the dlt operon, involved in D-alanine substitution of LTA, were lower in cells cultured with raffinose than in those cultured with kestose or glucose. This suggested that the different sizes of LTA observed among the carbohydrates tested were partly due to different levels of alanylation of LTA. The present study indicates that available oligosaccharide has the impact on the LTA production of the industrially important lactobacilli, which might influence their probiotic properties. Full article

(This article belongs to the Special Issue Functional Characterization of Lactic Acid Bacteria)

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14 pages, 1945 KiB

Open AccessArticle

Analysis and Reconstitution of the Menaquinone Biosynthesis Pathway in Lactiplantibacillus plantarum and Lentilactibacillus buchneri

by Nisit Watthanasakphuban, Ludovika Jessica Virginia, Dietmar Haltrich and Clemens Peterbauer

Microorganisms 2021, 9(7), 1476; https://doi.org/10.3390/microorganisms9071476 - 09 Jul 2021

Cited by 7 | Viewed by 2647

Abstract

In Lactococcus lactis and some other lactic acid bacteria, respiratory metabolism has been reported upon supplementation with only heme, leading to enhanced biomass formation, reduced acidification, resistance to oxygen, and improved long-term storage. Genes encoding a complete respiratory chain with all components were found in genomes of L. lactis and Leuconostoc mesenteroides, but menaquinone biosynthesis was found to be incomplete in Lactobacillaceae (except L. mesenteroides). Lactiplantibacillus plantarum has only two genes (menA, menG) encoding enzymes in the biosynthetic pathway (out of eight), and Lentilactobacillus buchneri has only four (menA, menB, menE, and menG). We constructed knock-out strains of L. lactis defective in menA, menB, menE, and menG (encoding the last steps in the pathway) and complemented these by expression of the extant genes from Lactipl. plantarum and Lent. buchneri to verify their functionality. Three of the Lactipl. plantarum biosynthesis genes, lpmenA1, lpmenG1, and lpmenG2, as well as lbmenB and lbmenG from Lent. buchneri, reconstituted menaquinone production and respiratory growth in the deficient L. lactis strains when supplemented with heme. We then reconstituted the incomplete menaquinone biosynthesis pathway in Lactipl. plantarum by expressing six genes from L. lactis homologous to the missing genes in a synthetic operon with two inducible promoters. Higher biomass formation was observed in Lactipl. plantarum carrying this operon, with an OD₆₀₀ increase from 3.0 to 5.0 upon induction. Full article

(This article belongs to the Special Issue Functional Characterization of Lactic Acid Bacteria)

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8 pages, 241 KiB

Open AccessArticle

Genomic Comparison of Lactobacillus casei AP and Lactobacillus plantarum DR131 with Emphasis on the Butyric Acid Biosynthetic Pathways

by Widodo Widodo, Aditya Lutfe Ariani, Donny Widianto and Dietmar Haltrich

Microorganisms 2021, 9(2), 425; https://doi.org/10.3390/microorganisms9020425 - 19 Feb 2021

Cited by 6 | Viewed by 3348

Abstract

Butyric acid is known to possess anticarcinogenic and antioxidative properties. The local lactic acid bacteria (LAB) strains Lactobacillus casei AP isolated from the digestive tract of healthy Indonesian infants and L. plantarum DR131 from indigenous fermented buffalo milk (dadih) can produce butyric acid in vitro. However, the genes and metabolic pathways involved in this process remain unknown. We sequenced and assembled the 2.95-Mb L. casei AP and 4.44-Mb L. plantarum DR131 draft genome sequences. We observed that 98% of the 2870 protein-coding genes of L. casei AP and 97% of the 3069 protein-coding genes of L. plantarum DR131 were similar to those of an L. casei strain isolated from infant stools and an L. plantarum strain in sheep milk, respectively. Comparison of the genome sequences of L. casei AP and L. plantarum DR131 led to the identification of genes encoding butyrate kinase (buk) and phosphotransbutyrylase (ptb), enzymes involved in butyric acid synthesis in L. casei AP. In contrast, a medium-chain thio-esterase and type 2 fatty acid synthase facilitated butyric acid synthesis in L. plantarum DR131. Our results provide new insights into the physiological behavior of the two LAB strains to facilitate their use as probiotics. Full article

(This article belongs to the Special Issue Functional Characterization of Lactic Acid Bacteria)

12 pages, 1917 KiB

Open AccessArticle

Improvement of Fermentation Quality in the Fermented Total Mixed Ration with Oat Silage

by Hong Yang, Bing Wang, Qing Zhang, Hui Cheng and Zhu Yu

Microorganisms 2021, 9(2), 420; https://doi.org/10.3390/microorganisms9020420 - 18 Feb 2021

Cited by 9 | Viewed by 3128

Abstract

The use of the fermented total mixed ration (FTMR) is a promising approach for the preservation of homogeneous feed, but changes during fermentation and links with the bacterial community of FTMR are not fully understood. This study investigated the effects of adding oat silage (OS) to the fermented total mixed ration (FTMR) in terms of fermentation, chemical composition, and the bacterial community. The fermentation quality of FTMR with 22% OS was greatly improved, as demonstrated by decreases in the butyric acid concentration, a lower lactic acid/acetic acid ratio, a larger population of lactic acid bacteria (LAB), and quicker spoilage yeast death. Further examination of the effects of various ensiling days on nutritive values showed stable crude protein and nonprotein nitrogen (NPN) contents. The concentrations of acetic acid, propionic acid, and ammonia–nitrogen (NH₃–N) were increased following all FTMR treatments after 15 d, while the concentration of water-soluble carbohydrates (WSC) was decreased. More heterofermentative LAB, such as Lentilactobacillus buchneri, Lentilactobacillus brevis, and Companilactobacillus versmoldensis were found after adding 11% and 22% OS. Moreover, the addition of 22% OS caused a marked increase in both bacterial richness and diversity, dominated by the Lactobacillus genus complex. Among species of the Lactobacillus genus complex, the occurrence of Loigolactobacillus coryniformis was positively correlated with lactic acid, NPN, and NH₃–N concentrations, suggesting its potential role in altering the fermentation profiles. Full article

(This article belongs to the Special Issue Functional Characterization of Lactic Acid Bacteria)

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Review

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16 pages, 2987 KiB

Open AccessReview

The Effect of Recombinant Protein Production in Lactococcus lactis Transcriptome and Proteome

by Gabriel A. Monteiro and Sofia O. D. Duarte

Microorganisms 2022, 10(2), 267; https://doi.org/10.3390/microorganisms10020267 - 25 Jan 2022

Cited by 1 | Viewed by 2829

Abstract

Lactococcus lactis is a food-grade, and generally recognized as safe, bacterium, which making it ideal for producing plasmid DNA (pDNA) or recombinant proteins for industrial or pharmaceutical applications. The present paper reviews the major findings from L. lactis transcriptome and proteome studies, with an overexpression of native or recombinant proteins. These studies should provide important insights on how to engineer the plasmid vectors and/or the strains in order to achieve high pDNA or recombinant proteins yields, with high quality standards. L. lactis harboring high copy numbers of plasmids for DNA vaccines production showed altered proteome profiles, when compared with a smaller copy number plasmid. For live mucosal vaccination applications, the cell-wall anchored antigens had shown more promising results, when compared with intracellular or secreted antigens. However, previous transcriptome and proteome studies demonstrated that engineering L. lactis to express membrane proteins, mainly with a eukaryotic background, increases the overall cellular burden. Genome engineering strategies could be used to knockout or overexpress the pinpointed genes, so as to increase the profitability of the process. Studies about the effect of protein overexpression on Escherichia coli and Bacillus subtillis transcriptome and proteome are also included. Full article

(This article belongs to the Special Issue Functional Characterization of Lactic Acid Bacteria)

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