Importance of lactobacilli in food and feed biotechnology

Isolation and Characterization of New Probiotic Strains From Chinese Babies

GOALS

The aims of this study were to isolate, to identify, and to characterize new potential probiotic strains from the feces of Chinese neonates.

BACKGROUND

Probiotic strains approved in China for use in infants were declared to originate from the human gut of Western subjects. Diet is listed among the main factors affecting the composition of the human gut along with other factors such as genetics, lifestyle, and health status. On the basis of this, the lifestyle of mothers, including dietary habits, could have an impact on the bacterial strains that colonize the gut of their babies.

STUDY

Starting from fecal samples, plated onto selective media, of 26 babies, a total of 38 Lactobacillus and 45 Bifidobacterium colonies were isolated and subcultured, identified at the specie level with the partial sequencing of the 16S ribosomal RNA gene, and assessed for safety according to international guidelines for probiotics and European guidance. Only 6 Lactobacillus and 5 Bifidobacterium spp. were included for further analysis for the evaluation of survival rate within the gastrointestinal tract and for adhesive properties on the Caco-2 cell line. Some tests for prebiotic metabolism and growth on reconstituted skimmed milk were also performed.

RESULTS

Three Lactobacillus strains and 1 Bifidobacterium strain showing interesting adhesive abilities were included in the in vitro immune-stimulatory test with dendritic cells. Among these isolates, the Bifidobacterium breve 2TA showed the most interesting probiotic properties.

CONCLUSIONS

The results obtained led to the identification of 4 new potential probiotic strains from Chinese babies to be submitted to further investigations about their metabolic and functional features.

Evaluation of probiotic Lactobacillus plantarum against foodborne pathogens and its fermentation potential in improving Lolium multiflorum silage quality

The objective of this study was to isolate the lactic acid bacteria from fermented silage sample and analyze their antibacterial activities, probiotic properties, and fermentation potential in silage. Eleven lactic acid bacteria (LAB) were selected based on distinct morphologies and preliminary studies. Cell-free supernatant (CFS) was then prepared from the selected strains for antibacterial analysis. L-30 strain and its CFS showed highest inhibition (> 10 mm) against tested foodborne pathogens as compared to other strains. Hereafter, the strain L-30 was named as KCC-30 and used for further studies. KCC-30 can survive in the harsh conditions of GIT such as low pH ( 2) and bile salt environment (oxgal) than standard L. plantarum KACC-91016 (pH 2: 27.2% vs 20.5%; oxgal: 72.3% vs 57.7%, both p < 0.05). In addition, KCC-30 exhibited strong auto-aggregation (68.3% vs 51.5%) and co-aggregation (33% vs 23.9%) properties. For silage experiment, KCC-30 treatment did not alter the nutrient profiles of silage. At the same time, KCC-30 treatment increased the lactic acid content of silage as compared to untreated silage (5.55 DM% vs 3.11 DM%). An increase of lactic acid content in the silage is due to higher lactic acid bacteria population in KCC-30 treated silage (15.33 × 10⁷ CFU/g vs 7.66 × 10⁷ CFU/g) than untreated silage (p < 0.05). Overall data suggested that KCC-30 exhibited strong probiotic potential and improved the quality of Lolium multiflorum silage by increasing the lactic acid level. Therefore, KCC-30 could be considered as potential strain to improve the fermentation quality of L. multiflorum silage.

Identification and Classification for the Lactobacillus casei Group

Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA–DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories. Currently, genome-based comparisons, including average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), are commonly applied to bacterial taxonomy as alternatives to the gold standard method for the demarcating phylogenetic relationships. To establish quick and accurate methods for identifying strains in the L. casei group at the species and subspecies levels, we developed species- and subspecies-specific identification methods based on housekeeping gene sequences and whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral pattern analysis. By phylogenetic analysis based on concatenated housekeeping gene sequences (dnaJ, dnaK, mutL, pheS, and yycH), 53 strains were separated into four clusters corresponding to the four species: L. casei, L. paracasei and L. rhamnosus, and Lactobacillus chiayiensis sp. nov. A multiplex minisequencing assay using single nucleotide polymorphism (SNP)-specific primers based on the dnaK gene sequences and species-specific primers based on the mutL gene sequences provided high resolution that enabled the strains at the species level to be identified as L. casei, L. paracasei, and L. rhamnosus. By MALDI-TOF MS analysis coupled with an internal database and ClinProTools software, species- and subspecies-level L. casei group strains were identified based on reliable scores and species- and subspecies-specific MS peaks. The L. paracasei strains were distinguished clearly at the subspecies level based on subspecies-specific MS peaks. This article describes the rapid and accurate methods used for identification and classification of strains in the L. casei group based on housekeeping gene sequences and MALDI-TOF MS analysis as well as the novel speciation of this group including L. chiayiensis sp. nov. and ‘Lactobacillus zeae’ by genome-based methods.

Isolation of antibacterial protein from Lactobacillus spp. and preparation of probiotic curd

The study was aimed to isolate antagonistic lactobacilli and the molecules responsible for their antagonistic ability from curd. Preparation of probiotic curd and the ability of the selected lactobacilli to suppress the pathogen therein was also assessed. All the 116 isolates were identified as Lactobacillus spp. based on morphological, biochemical and curdling assays. Five of these lactobacilli (Lb-17, Lb-33, Lb-108, Lb-112, and Lb-N3) were found most promising to inhibit all test pathogens (Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Salmonella typhi and Shigella sonnei). The cell-free culture supernatants of these five lactobacilli were recorded as thermo-tolerant when subjected to heat treatment at 100 °C for 20 min. The loss in the activity after protease treatment indicated the proteinaceous nature of the antimicrobial molecule present in the culture supernatants. Active protein (19 kDa) produced by lactobacilli was confirmed by SDS-PAGE followed by agar-overlay method. Antibiotic sensitivity assay revealed that the selected Lactobacillus spp. isolates were resistant to methicillin and vancomycin. Probiotic curd prepared by using Lb-108 and Lb-N3 was found to be superior to rest of the three isolates based on organoleptic tests and shelf-life. Complete inhibition of all the test pathogens in curd was shown by Lb-108 and Lb-N3. Inhibition spectrum, production of thermostable protein and preparation of quality curd suggest Lb-108 and Lb-N3 as promising candidates to prepare probiotic curd.

Role of Lactobacillus reuteri in Human Health and Diseases

Lactobacillus reuteri (L. reuteri) is a well-studied probiotic bacterium that can colonize a large number of mammals. In humans, L. reuteri is found in different body sites, including the gastrointestinal tract, urinary tract, skin, and breast milk. The abundance of L. reuteri varies among different individuals. Several beneficial effects of L. reuteri have been noted. First, L. reuteri can produce antimicrobial molecules, such as organic acids, ethanol, and reuterin. Due to its antimicrobial activity, L. reuteri is able to inhibit the colonization of pathogenic microbes and remodel the commensal microbiota composition in the host. Second, L. reuteri can benefit the host immune system. For instance, some L. reuteri strains can reduce the production of pro-inflammatory cytokines while promoting regulatory T cell development and function. Third, bearing the ability to strengthen the intestinal barrier, the colonization of L. reuteri may decrease the microbial translocation from the gut lumen to the tissues. Microbial translocation across the intestinal epithelium has been hypothesized as an initiator of inflammation. Therefore, inflammatory diseases, including those located in the gut as well as in remote tissues, may be ameliorated by increasing the colonization of L. reuteri. Notably, the decrease in the abundance of L. reuteri in humans in the past decades is correlated with an increase in the incidences of inflammatory diseases over the same period of time. Direct supplementation or prebiotic modulation of L. reuteri may be an attractive preventive and/or therapeutic avenue against inflammatory diseases.

In Vitro and in Vivo Selection of Potentially Probiotic Lactobacilli From Nocellara del Belice Table Olives

Table olives are increasingly recognized as a vehicle as well as a source of probiotic bacteria, especially those fermented with traditional procedures based on the activity of indigenous microbial consortia, originating from local environments. In the present study, we report characterization at the species level of 49 Lactic Acid Bacteria (LAB) strains deriving from Nocellara del Belice table olives fermented with the Spanish or Castelvetrano methods, recently isolated in our previous work. Ribosomal 16S DNA analysis allowed identification of 4 Enterococcus gallinarum, 3 E. casseliflavus, 14 Leuconostoc mesenteroides, 19 Lactobacillus pentosus, 7 L. coryniformis, and 2 L. oligofermentans. The L. pentosus and L. coryniformis strains were subjected to further screening to evaluate their probiotic potential, using a combination of in vitro and in vivo approaches. The majority of them showed high survival rates under in vitro simulated gastro-intestinal conditions, and positive antimicrobial activity against Salmonella enterica serovar Typhimurium, Listeria monocytogenes and enterotoxigenic Escherichia coli (ETEC) pathogens. Evaluation of antibiotic resistance to ampicillin, tetracycline, chloramphenicol, or erythromycin was also performed for all selected strains. Three L. coryniformis strains were selected as very good performers in the initial in vitro testing screens, they were antibiotic susceptible, as well as capable of inhibiting pathogen growth in vitro. Parallel screening employing the simplified model organism Caenorhabditis elegans, fed the Lactobacillus strains as a food source, revealed that one L. pentosus and one L. coryniformis strains significantly induced prolongevity effects and protection from pathogen-mediated infection. Moreover, both strains displayed adhesion to human intestinal epithelial Caco-2 cells and were able to outcompete foodborne pathogens for cell adhesion. Overall, these results are suggestive of beneficial features for novel LAB strains, which renders them promising candidates as starters for the manufacturing of fermented table olives with probiotic added value.

Probiotic and anti-inflammatory potential of Lactobacillus rhamnosus 4B15 and Lactobacillus gasseri 4M13 isolated from infant feces

A total of 22 Lactobacillus strains, which were isolated from infant feces were evaluated for their probiotic potential along with resistance to low pH and bile salts. Eight isolates (L. reuteri 3M02 and 3M03, L. gasseri 4M13, 4R22, 5R01, 5R02, and 5R13, and L. rhamnosus 4B15) with high tolerance to acid and bile salts, and ability to adhere to the intestine were screened from 22 strains. Further, functional properties of 8 Lactobacillus strains, such as anti-oxidation, inhibition of α-glucosidase activity, cholesterol-lowering, and anti-inflammation were evaluated. The properties were strain-specific. Particularly, two strains of L. rhamnosus, 4B15 (4B15) and L. gasseri 4M13 (4M13) showed considerably higher anti-oxidation, inhibition of α-glucosidase activity, and cholesterol-lowering, and greater inhibition of nitric oxide production than other strains. Moreover, the two selected strains substantially inhibited the release of inflammatory mediators such as TNF-α, IL-6, IL-1β, and IL-10 stimulated the treatment of RAW 264.7 macrophages with LPS. In addition, whole genome sequencing and comparative genomic analysis of 4B15 and 4M13 indicated them as novel genomic strains. These results suggested that 4B15 and 4M13 showed the highest probiotic potential and have an impact on immune health by modulating pro-inflammatory cytokines.

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level

Although complete genome sequences hold particular value for an accurate description of core genomes, the identification of strain-specific genes, and as the optimal basis for functional genomics studies, they are still largely underrepresented in public repositories. Based on an assessment of the genome assembly complexity for all lactobacilli, we used Pacific Biosciences' long read technology to sequence and de novo assemble the genomes of three Lactobacillus helveticus starter strains, raising the number of completely sequenced strains to 12. The first comparative genomics study for L. helveticus—to our knowledge—identified a core genome of 988 genes and sets of unique, strain-specific genes ranging from about 30 to more than 200 genes. Importantly, the comparison of MiSeq- and PacBio-based assemblies uncovered that not only accessory but also core genes can be missed in incomplete genome assemblies based on short reads. Analysis of the three genomes revealed that a large number of pseudogenes were enriched for functional Gene Ontology categories such as amino acid transmembrane transport and carbohydrate metabolism, which is in line with a reductive genome evolution in the rich natural habitat of L. helveticus. Notably, the functional Clusters of Orthologous Groups of proteins categories “cell wall/membrane biogenesis” and “defense mechanisms” were found to be enriched among the strain-specific genes. A genome mining effort uncovered examples where an experimentally observed phenotype could be linked to the underlying genotype, such as for cell envelope proteinase PrtH3 of strain FAM8627. Another possible link identified for peptidoglycan hydrolases will require further experiments. Of note, strain FAM22155 did not harbor a CRISPR/Cas system; its loss was also observed in other L. helveticus strains and lactobacillus species, thus questioning the value of the CRISPR/Cas system for diagnostic purposes. Importantly, the complete genome sequences proved to be very useful for the analysis of natural whey starter cultures with metagenomics, as a larger percentage of the sequenced reads of these complex mixtures could be unambiguously assigned down to the strain level.

Tailor-made exopolysaccharides-CRISPR-Cas9 mediated genome editing in Paenibacillus polymyxa

Application of state-of-the-art genome editing tools like CRISPR-Cas9 drastically increase the number of undomesticated micro-organisms amenable to highly efficient and rapid genetic engineering. Adaptation of these tools to new bacterial families can open up entirely new possibilities for these organisms to accelerate as biotechnologically relevant microbial factories, also making new products economically competitive. Here, we report the implementation of a CRISPR-Cas9 based vector system in Paenibacillus polymyxa, enabling fast and reliable genome editing in this host. Homology directed repair allows for highly efficient deletions of single genes and large regions as well as insertions. We used the system to investigate the yet undescribed biosynthesis machinery for exopolysaccharide (EPS) production in P. polymyxa DSM 365, enabling assignment of putative roles to several genes involved in EPS biosynthesis. Using this simple gene deletion strategy, we generated EPS variants that differ from the wild-type polymer not only in terms of monomer composition, but also in terms of their rheological behavior. The developed CRISPR-Cas9 mediated engineering approach will significantly contribute to the understanding and utilization of socially and economically relevant Paenibacillus species and extend the polymer portfolio.

Lactobacillus allii sp. nov. isolated from scallion kimchi

A novel strain of lactic acid bacteria, WiKim39^T, was isolated from a scallion kimchi sample consisting of fermented chili peppers and vegetables. The isolate was a Gram-positive, rod-shaped, non-motile, catalase-negative and facultatively anaerobic lactic acid bacterium. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain WiKim39^T belonged to the genus Lactobacillus, and shared 97.1–98.2 % pair-wise sequence similarities with related type strains, Lactobacillus nodensis, Lactobacillus insicii, Lactobacillus versmoldensis, Lactobacillus tucceti and Lactobacillus furfuricola. The G+C content of the strain based on its genome sequence was 35.3 mol%. The ANI values between WiKim39^T and the closest relatives were lower than 80 %. Based on the phenotypic, biochemical, and phylogenetic analyses, strain WiKim39^T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus allii sp. nov. is proposed. The type strain is WiKim39^T (=KCTC 21077^T=JCM 31938^T).

Secretome of Intestinal Bacilli: A Natural Guard against Pathologies

Current studies of human gut microbiome usually do not consider the special functional role of transient microbiota, although some of its members remain in the host for a long time and produce broad spectrum of biologically active substances. Getting into the gastrointestinal tract (GIT) with food, water and probiotic preparations, two representatives of Bacilli class, genera Bacillus and Lactobacillus, colonize epithelium blurring the boundaries between resident and transient microbiota. Despite their minor proportion in the microbiome composition, these bacteria can significantly affect both the intestinal microbiota and the entire body thanks to a wide range of secreted compounds. Recently, insufficiency and limitations of pure genome-based analysis of gut microbiota became known. Thus, the need for intense functional studies is evident. This review aims to characterize the Bacillus and Lactobacillus in GIT, as well as the functional roles of the components released by these members of microbial intestinal community. Complex of their secreted compounds is referred by us as the "bacillary secretome." The composition of the bacillary secretome, its biological effects in GIT and role in counteraction to infectious diseases and oncological pathologies in human organism is the subject of the review.

Inhibitory substances production by Lactobacillus plantarum ST16Pa cultured in hydrolyzed cheese whey supplemented with soybean flour and their antimicrobial efficiency as biopreservatives on fresh chicken meat

Cheese whey, the main byproduct of the dairy industry, is one of the most worrisome types of industrial waste, not only because of its abundant annual global production but also because it is a notable source of environmental pollution. However, cheese whey can serve as a raw material for the production of biocomposites. In this context, in this study, we assayed the production of a bacteriocin-like inhibitory substance (BLIS) and lactate by culturing Lactobacillus plantarum ST16Pa in hydrolyzed fresh cheese whey. The process was improved by studying the enzymatic hydrolysis of cheese whey as well as its supplementation with soybean flour under microaerophilic or anaerobic conditions. Thus, the highest values of BLIS (7367.23 arbitrary units [AU]/mL) and lactate yield (Ylactate/lactose=1.39g/g) were achieved after addition of 10g/L soybean flour in microaerophilia. These conditions were successfully scaled up in a bioreactor because during complete anaerobiosis at 150rpm, L. plantarum ST16Pa attained considerable cell growth (3.14g/L), lactate concentration (14.33g/L), and BLIS activity (8082.56AU/mL). In addition, the cell-free supernatant resulting from this bioprocess showed high biopreservative efficiency in chicken breast fillets artificially contaminated with Enterococcus faecium 711 during 7days of refrigerated storage, thus indicating the potential use of this BLIS as a biopreservative in the food industry.

Effect of dietary Clostridium butyricum on growth, intestine health status and resistance to ammonia stress in Pacific white shrimp Litopenaeus vannamei

The present study evaluated the effect of dietary Clostridium butyricum (CB) on growth, intestine microstructure, intestine digestive and immune function, intestine short-chain fatty acids (SCFA) content and body composition of Pacific white shrimp Litopenaeus vannamei. The shrimp was fed for 56 d with diets containing different levels of C. butyricum (1 × 10⁹ cfu/g): 0% (Control), 0.25% (CB1), 0.5% (CB2) and 1.0% (CB3) as treatment groups, followed by an acute ammonia stress test for 72 h. The results indicated that dietary supplementation of C. butyricum decreased the feed conversion rate (FCR) and increased the growth performance of shrimp. Compared with the control group, after shrimp fed with C. butyricum 56 d, intestine amylase and protease activity in the three C. butyricum group increased, while lipase activity was only affected in the CB1 and CB2 group. Total antioxidant capacity (T-AOC) content, lysozyme (LSZ) activity, and the relative expression level of Toll and immune deficiency (Imd) gene all increased in three C. butyricum groups. Inducible nitric oxide synthase (iNOS) activity increased in the CB2 and CB3 group, heat shock protein 70 (HSP70) gene expression level increased in the CB3 group, while nitric oxide (NO) content was not affected by C. butyricum. After shrimp exposed to ammonia stress, intestine immune biochemical parameters (T-AOC, LSZ, iNOS and NO) and genes (HSP70, Toll and Imd) expression level of C. butyricum group was higher than that of the control. HE stain showed that C. butyricum increased the intestine epithelium height of L. vannamei. These results revealed that C. butyricum could improve the growth performance, increased intestine SCFA content and body crude protein content, modulated intestine digestive capacity, and enhanced intestine immune function of L. vannamei against ammonia stress.

Insight into Potential Probiotic Markers Predicted in Lactobacillus pentosus MP-10 Genome Sequence

Lactobacillus pentosus MP-10 is a potential probiotic lactic acid bacterium originally isolated from naturally fermented Aloreña green table olives. The entire genome sequence was annotated to in silico analyze the molecular mechanisms involved in the adaptation of L. pentosus MP-10 to the human gastrointestinal tract (GIT), such as carbohydrate metabolism (related with prebiotic utilization) and the proteins involved in bacteria-host interactions. We predicted an arsenal of genes coding for carbohydrate-modifying enzymes to modify oligo- and polysaccharides, such as glycoside hydrolases, glycoside transferases, and isomerases, and other enzymes involved in complex carbohydrate metabolism especially starch, raffinose, and levan. These enzymes represent key indicators of the bacteria's adaptation to the GIT environment, since they involve the metabolism and assimilation of complex carbohydrates not digested by human enzymes. We also detected key probiotic ligands (surface proteins, excreted or secreted proteins) involved in the adhesion to host cells such as adhesion to mucus, epithelial cells or extracellular matrix, and plasma components; also, moonlighting proteins or multifunctional proteins were found that could be involved in adhesion to epithelial cells and/or extracellular matrix proteins and also affect host immunomodulation. In silico analysis of the genome sequence of L. pentosus MP-10 is an important initial step to screen for genes encoding for proteins that may provide probiotic features, and thus provides one new routes for screening and studying this potentially probiotic bacterium.

Production of Protein Concentrate and 1,3-Propanediol by Wheat-Based Thin Stillage Fermentation

Fermentation of wheat with yeast produces thin stillage (W-TS) and distiller's wet grains. A subsequent fermentation of W-TS (two-stage fermentation, TSF) with endemic bacteria at 25 and 37 °C decreased glycerol and lactic acid concentrations, while 1,3-propanediol (1,3-PD) and acetic acid accumulated with greater 1,3-PD and acetic acid produced at 37 °C. During TSF, W-TS colloids coagulated and floated in the fermentation medium producing separable liquid and slurry fractions. The predominant endemic bacteria in W-TS were Lactobacillus panis, L. gallinarum, and L. helveticus, and this makeup did not change substantially as fermentation progressed. As nutrients were exhausted, floating particles precipitated. Protein contents of slurry and clarified liquid increased and decreased, respectively, as TSF progressed. The liquid was easily filtered through an ultrafiltration membrane. These results suggested that TSF is a novel method for W-TS clarification and production of protein concentrates and 1,3-PD from W-TS.

Effect of the dietary probiotic Clostridium butyricum on growth, intestine antioxidant capacity and resistance to high temperature stress in kuruma shrimp Marsupenaeus japonicus

A 56-day feeding trial followed by an acute high temperature stress test were performed to evaluate the effect of dietary probiotic Clostridium butyricum (CB) on growth performance and intestine antioxidant capacity of kuruma shrimp Marsupenaeus japonicus. Shrimp were randomly allocated in 9 tanks (30 shrimp per tank) and triplicate tanks were fed with diets containing different levels of C. butyricum (1×10⁹ cfu/g): 0mgg^-1 feed (Control), 100mgg^-1 feed (CB-100), 200mgg^-1 feed (CB-200) as treatment groups. The results indicated that dietary supplementation of C. butyricum increased the growth performance and decreased the feed conversion rate (FCR) of shrimp in the CB-100 group. HE stain showed that C. butyricum increased the intestine epithelium height of M. japonicus. C. butyricum supplemented in diets decreased·O₂^- generation capacity and malondialdehyde (MDA) content, and increased total antioxidant capacity (T-AOC), catalase (CAT) and peroxidase (POD) activity and the expression level of heat shock protein 70 (hsp70) and metallothionein (mt) gene in intestine of shrimp cultured under normal condition for 56 d, while no significant changes in glutathione peroxidase (GPx) activity and ferritin gene expression level. After shrimp exposed to high temperature stress 48h, the lower level of·O₂^- generation capacity and MDA content, and the higher level survival, activities of T-AOC, CAT, GPx and POD, as well as hsp70, ferritin and mt gene expression level were found in intestine of two C. butyricum groups. These results revealed that C. butyricum could improve the growth performance, increase intestine antioxidant capacity of M. japonicus against high temperature stress, and could be a potential feed additive in shrimp aquaculture.

Functional proteomics within the genus Lactobacillus

Lactobacillus are mainly used for the manufacture of fermented dairy, sourdough, meat, and vegetable foods or used as probiotics. Under optimal processing conditions, Lactobacillus strains contribute to food functionality through their enzyme portfolio and the release of metabolites. An extensive genomic diversity analysis was conducted to elucidate the core features of the genus Lactobacillus, and to provide a better comprehension of niche adaptation of the strains. However, proteomics is an indispensable "omics" science to elucidate the proteome diversity, and the mechanisms of regulation and adaptation of Lactobacillus strains. This review focuses on the novel and comprehensive knowledge of functional proteomics and metaproteomics of Lactobacillus species. A large list of proteomic case studies of different Lactobacillus species is provided to illustrate the adaptability of the main metabolic pathways (e.g., carbohydrate transport and metabolism, pyruvate metabolism, proteolytic system, amino acid metabolism, and protein synthesis) to various life conditions. These investigations have highlighted that lactobacilli modulate the level of a complex panel of proteins to growth/survive in different ecological niches. In addition to the general regulation and stress response, specific metabolic pathways can be switched on and off, modifying the behavior of the strains.

Study of Streptococcus thermophilus population on a world-wide and historical collection by a new MLST scheme

We analyzed 178 Streptococcus thermophilus strains isolated from diverse products, from around the world, over a 60-year period with a new multilocus sequence typing (MLST) scheme. This collection included isolates from two traditional cheese-making sites with different starter-use practices, in sampling campaigns carried out over a three years period. The nucleotide diversity of the S. thermophilus population was limited, but 116 sequence types (ST) were identified. Phylogenetic analysis of the concatenated sequences of the six housekeeping genes revealed the existence of groups confirmed by eBURST analysis. Deeper analyses performed on 25 strains by CRISPR and whole-genome analysis showed that phylogenies obtained by MLST and whole-genome analysis were in agreement but differed from that inferred by CRISPR analysis. Strains isolated from traditional products could cluster in specific groups indicating their origin, but also be mixed in groups containing industrial starter strains. In the traditional cheese-making sites, we found that S. thermophilus persisted on dairy equipment, but that occasionally added starter strains may become dominant. It underlined the impact of starter use that may reshape S. thermophilus populations including in traditional products. This new MLST scheme thus provides a framework for analyses of S. thermophilus populations and the management of its biodiversity.

Fermented Aloreña Table Olives as a Source of Potential Probiotic Lactobacillus pentosus Strains

A collection of 31 Lactobacillus pentosus strains isolated from naturally fermented Aloreña green table olives were screened in depth in the present study for their probiotic potential. Several strains could be considered promising probiotic candidates since they showed good growth capacity and survival under simulated gastro-intestinal conditions (acidic pH of 1.5, up to 4% of bile salts and 5 mM of nitrate), good ability to auto-aggregate which may facilitate their adhesion to host cells as multiple aggregates and the subsequent displacement of pathogens. Moreover, co-aggregation of lactobacilli with pathogenic bacteria was shown with Listeria innocua, Staphylococcus aureus, Escherichia coli, and Salmonella Enteritidis as good defense strategy against gut and food pathogens. Furthermore, they exhibited adherence to intestinal and vaginal cell lines, such property could be reinforced by their capacity of biofilm formation which is also important in food matrices such as the olive surface. Their antagonistic activity against pathogenic bacteria by means of acids and plantaricins, and also their different functional properties may determine their efficacy not only in the gastro-intestinal tract but also in food matrices. Besides their ability to ferment several prebiotics, the new evidence in the present study was their capacity to ferment lactose which reinforces their use in different food matrices including dairy as a dietary adjunct to improve lactose digestibility. Lactobacillus pentosus CF2-10N was selected to have the best probiotic profile being of great interest in further studies. In conclusion, spontaneous fermented Aloreña table olives are considered a natural source of potential probiotic L. pentosus to be included as adjunct functional cultures in different fermented foods.

Tetracycline Resistance Patterns of Lactobacillus buchneri Group Strains

Lactobacilli are applied as starter cultures for controlled fermentation in the production of food and feed. Among other lactobacilli, members of the Lactobacillus buchneri group are used in fermented milk, wine, and silage. Most of the L. buchneri species used for the manufacturing of food or feed are already on the list for qualified presumption of safety status and are recommended as biological agents by the European Food Safety Authority. Consequently, new strains intended as food or feed additives do not require any additional safety check than confirming the absence of transferable antibiotic resistance determinants. Of these determinants, tetracycline resistance genes are especially predominant in lactobacilli. Within this study, a total of 128 strains belonging to the L. buchneri group ( L. buchneri , L. diolivorans , L. farraginis , L. hilgardii , L. kefiri , L. kisonensis , L. otakiensis , L. parabuchneri , L. parafarraginis , L. parakefiri , L. rapi , L. senioris , and L. sunkii ) were examined for their susceptibility to tetracycline. Tetracycline MICs were assessed by the broth microdilution method according to ISO 10932/IDF 223. Subsequently, the presence of tetracycline resistance genes was investigated by using PCR. In addition, selected strains were tested for a broader range of tetracycline resistance genes by using a microarray technique. Applying the tetracycline cutoff values defined by European Food Safety Authority for heterofermentative and obligately homofermentative lactobacilli, 96.9% of the strains would have been categorized as tetracycline resistant. However, none of the tested tetracycline resistance genes could be detected by PCR or microarray analysis. Furthermore, the MIC distribution of all strains was unimodal and at the high end of the tested tetracycline concentration range (4 to 256 μg/ml). Thus, these data suggest that tetracycline resistance in the L. buchneri group strains is intrinsic, which complies with the requirements defined in the qualified presumption of safety outline.

Complete genome sequence of Lactobacillus plantarum LZ206, a potential probiotic strain with antimicrobial activity against food-borne pathogenic microorganisms

Lactobacilli strains have been considered as important candidates for manufacturing "natural food", due to their antimicrobial properties and generally regarded as safe (GRAS) status. Lactobacillus plantarum LZ206 is a potential probiotic strain isolated from raw cow milk, with antimicrobial activity against various pathogens, including Gram-positive bacteria (Staphylococcus aureus and Listeria monocytogenes), Gram-negtive bacteria (Escherichia coli and Salmonella enterica), and fungus Candida albicans. To better understand molecular base for its antimicrobial activity, entire genome of LZ206 was sequenced. It was revealed that genome of LZ206 contained a circular 3,212,951-bp chromosome, two circular plasmids and one predicted linear plasmid. A plantaricin gene cluster, which is responsible for bacteriocins biosynthesis and could be associated with its broad-spectrum antimicrobial activity, was identified based on comparative genomic analysis. Whole genome sequencing of L. plantarum LZ206 might facilitate its applications to protect food products from pathogens' contamination in the dairy industry.

Microbial Diversity and Biochemical Analysis of Suanzhou: A Traditional Chinese Fermented Cereal Gruel

Suanzhou as a traditional Chinese gruel is fermented from proso millet and millet. The biochemical analysis showed Suanzhou had relatively high concentrations of lactic acid, acetic acid, and free amino acids. The metagenomics of Suanzhou were studied, with the analysis of the V4 region of 16S rRNA gene, the genera Lactobacillus and Acetobacter were found dominant with the average abundance of 58.2 and 24.4%, respectively; and with the analysis of the ITS1 region between 18S and 5.8S rRNA genes, 97.3% of the fungal community was found belonging to the genus Pichia and 2.7% belonging to five other genera. Moreover, the isolates recovered from 59 Suanzhou samples with various media were identified with the 16S rRNA or 18S rRNA gene analyses. Lactobacillus fermentum (26.9%), L. pentosus (19.4%), L. casei (17.9%), and L. brevis (16.4%) were the four dominant Lactobacillus species; Acetobacter lovaniensis (38.1%), A. syzygii (16.7%), A. okinawensis (16.7%), and A. indonesiensis (11.9%) were the four dominant Acetobacter species; and Pichia kudriavzevii (55.8%) and Galactomyces geotrichum (23.1%) were the two dominant fungal species. Additionally, L. pentosus p28-c and L. casei h28-c1 were selected for the fermentations mimicking the natural process. Collectively, our data demonstrate that Suanzhou is a nutritional food high in free amino acids and organic acids. Diverse Lactobacillus, Acetobacter, and yeast species are identified as the dominant microorganisms in Suanzhou. The isolated strains can be further characterized and used as starters for the industrial production of Suanzhou safely.

Use of Potential Probiotic Lactic Acid Bacteria (LAB) Biofilms for the Control of Listeria monocytogenes, Salmonella Typhimurium, and Escherichia coli O157:H7 Biofilms Formation

Use of probiotic biofilms can be an alternative approach for reducing the formation of pathogenic biofilms in food industries. The aims of this study were (i) to evaluate the probiotic properties of bacteriocinogenic (Lactococcus lactis VB69, L. lactis VB94, Lactobacillus sakei MBSa1, and Lactobacillus curvatus MBSa3) and non-bacteriocinogenic (L. lactis 368, Lactobacillus helveticus 354, Lactobacillus casei 40, and Weissela viridescens 113) lactic acid bacteria (LAB) isolated from Brazilian’s foods and (ii) to develop protective biofilms with these strains and test them for exclusion of Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella Typhimurium. LAB were tested for survival in acid and bile salt conditions, surface properties, biosurfactant production, β-galactosidase and gelatinase activity, antibiotic resistance and presence of virulence genes. Most strains survived exposure to pH 2 and 4% bile salts. The highest percentages of auto-aggregation were obtained after 24 h of incubation. Sixty-seven percentage auto-aggregation value was observed in W. viridescens 113 and Lactobacillus curvatus MBSa3 exhibited the highest co-aggregation (69% with Listeria monocytogenes and 74.6% with E. coli O157:H7), while the lowest co-aggregation was exhibited by W. viridescens 113 (53.4% with Listeria monocytogenes and 38% with E. coli O157:H7). Tests for hemolytic activity, bacterial cell adherence with xylene, and drop collapse confirmed the biosurfactant-producing ability of most strains. Only one strain (L. lactis 368) produced β-galactosidase. All strains were negative for virulence genes cob, ccf, cylLL, cylLs, cyllM, cylB, cylA and efaAfs and gelatinase production. The antibiotic susceptibility tests indicated that the MIC for ciprofloxacin, clindamycin, gentamicin, kanamycin, and streptomycin did not exceed the epidemiological cut-off suggested by the European Food Safety Authority. Some strains were resistant to one or more antibiotics and resistance to antibiotics was species and strain dependent. In the protective biofilm assays, strains L. lactis 368 (bac-), Lactobacillus curvatus MBSa3 (bac+), and Lactobacillus sakei MBSa1 (bac+) resulted in more than six log reductions in the pathogens counts when compared to the controls. This effect could not be attributed to bacteriocin production. These results suggest that these potential probiotic strains can be used as alternatives for control of biofilm formation by pathogenic bacteria in the food industry, without conferring a risk to the consumers.

Comparative genome analysis of the candidate functional starter culture strains Lactobacillus fermentum 222 and Lactobacillus plantarum 80 for controlled cocoa bean fermentation processes

Background

Lactobacillus fermentum 222 and Lactobacillus plantarum 80, isolates from a spontaneous Ghanaian cocoa bean fermentation process, proved to be interesting functional starter culture strains for cocoa bean fermentations. Lactobacillus fermentum 222 is a thermotolerant strain, able to dominate the fermentation process, thereby converting citrate and producing mannitol. Lactobacillus plantarum 80 is an acid-tolerant and facultative heterofermentative strain that is competitive during cocoa bean fermentation processes. In this study, whole-genome sequencing and comparative genome analysis was used to investigate the mechanisms of these strains to dominate the cocoa bean fermentation process.

Results

Through functional annotation and analysis of the high-coverage contigs obtained through 454 pyrosequencing, plantaricin production was predicted for L. plantarum 80. For L. fermentum 222, genes encoding a complete arginine deiminase pathway were attributed. Further, in-depth functional analysis revealed the capacities of these strains associated with carbohydrate and amino acid metabolism, such as the ability to use alternative external electron acceptors, the presence of an extended pyruvate metabolism, and the occurrence of several amino acid conversion pathways. A comparative genome sequence analysis using publicly available genome sequences of strains of the species L. plantarum and L. fermentum revealed unique features of both strains studied. Indeed, L. fermentum 222 possessed genes encoding additional citrate transporters and enzymes involved in amino acid conversions, whereas L. plantarum 80 is the only member of this species that harboured a gene cluster involved in uptake and consumption of fructose and/or sorbose.

Conclusions

In-depth genome sequence analysis of the candidate functional starter culture strains L. fermentum 222 and L. plantarum 80 revealed their metabolic capacities, niche adaptations and functionalities that enable them to dominate the cocoa bean fermentation process. Further, these results offered insights into the cocoa bean fermentation ecosystem as a whole and will facilitate the selection of appropriate starter culture strains for controlled cocoa bean fermentation processes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1927-0) contains supplementary material, which is available to authorized users.

The effect of lactic acid bacterial starter culture and chemical additives on wilted rice straw silage

Lactic acid bacteria (LAB) are suitable for rice straw silage fermentation, but have been studied rarely, and rice straw as raw material for ensiling is difficult because of its disadvantages, such as low nutrition for microbial activities and low abundances of natural populations of LAB. So we investigated the effect of application of LAB and chemical additives on the fermentation quality and microbial community of wilted rice straw silage. Treatment with chemical additives increased the concentrations of crude protein (CP), water soluble carbohydrate (WSC), acetic acid and lactic acid, reduced the concentrations of acid detergent fiber (ADF) and neutral detergent fiber (NDF), but did not effectively inhibit the growth of spoilage organisms. Inoculation with LABs did not improve the nutritional value of the silage because of poor growth of LABs in wilted rice straw. Inoculation with LAB and addition of chemical materials improved the quality of silage similar to the effects of addition of chemical materials alone. Growth of aerobic and facultatively anaerobic bacteria was inhibited by this mixed treatment and the LAB gradually dominated the microbial community. In summary, the fermentation quality of wilted rice straw silage had improved by addition of LAB and chemical materials.

Bioactivity characterization of Lactobacillus strains isolated from dairy products

This study aimed to find candidate strains of Lactobacillus isolated from sheep dairy products (yogurt and ewe colostrum) with probiotic and anticancer activity. A total of 100 samples were randomly collected from yogurt and colostrum and 125 lactic acid bacteria were isolated. Of these, 17 Lactobacillus strains belonging to five species (L. delbrueckii, L. plantarum, L. rhamnosus, L. paracasei, and L. casei) were identified. L. plantarum 17C and 13C, which isolated from colostrums, demonstrated remarkable results such as resistant to low pH and high concentrations of bile salts, susceptible to some antibiotics and good antimicrobial activity that candidate them as potential probiotics. Seven strains (1C, 5C, 12C, 13C, 17C, 7M, and 40M), the most resistant to simulated digestion, were further investigated to evaluate their capability to adhere to human intestinal Caco-2 cells. L. plantarum 17C was the most adherent strain. The bioactivity assessment of L. plantarum 17C showed anticancer effects via the induction of apoptosis on HT-29 human cancer cells and negligible side effects on one human epithelial normal cell line (FHs 74). The metabolites produced by this strain can be used as alternative pharmaceutical compounds with promising therapeutic indices because they are not cytotoxic to normal mammalian cells.

Improving Oenococcus oeni to overcome challenges of wine malolactic fermentation

Oenococcus oeni is crucial for winemaking, bringing stabilization, deacidification, and sensory impacts through malolactic fermentation (MLF) to most wine styles. The poor nutritional make-up of wine together with typically low processing temperatures and pH and high ethanol content and sulfur dioxide (SO2) hinder O. oeni growth and activity. Production delays and interventions with starter cultures and nutritional supplements have significant cost and quality implications; thus, optimization of O. oeni has long been a priority. A range of optimization strategies, some guided by detailed characterization of O. oeni, have been exploited. Varying degrees of success have been seen with classical strain selection, mutagenesis, gene recombination, genome shuffling, and, most recently, directed evolution (DE). The merits, limitations, and future prospects of each are discussed.

Inhibition of pathogenic and spoilage bacteria by a novel biofilm-forming Lactobacillus isolate: a potential host for the expression of heterologous proteins

BACKGROUND

Bacterial biofilms are a preferred mode of growth for many types of microorganisms in their natural environments. The ability of pathogens to integrate within a biofilm is pivotal to their survival. The possibility of biofilm formation in Lactobacillus communities is also important in various industrial and medical settings. Lactobacilli can eliminate the colonization of different pathogenic microorganisms. Alternatively, new opportunities are now arising with the rapidly expanding potential of lactic acid bacteria biofilms as bio-control agents against food-borne pathogens.

RESULTS

A new isolate Lactobacillus plantarum PA21 could form a strong biofilm in pure culture and in combination with several pathogenic and food-spoilage bacteria such as Salmonella enterica, Bacillus cereus, Pseudomonas fluorescens, and Aeromonas hydrophila. Exposure to Lb. plantarum PA21 significantly reduced the number of P. fluorescens, A. hydrophila and B. cereus cells in the biofilm over 2-, 4- and 6-day time periods. However, despite the reduction in S. enterica cells, this pathogen showed greater resistance in the presence of PA21 developed biofilm, either in the planktonic or biofilm phase. Lb. plantarum PA21 was also found to be able to constitutively express GFP when transformed with the expression vector pMG36e which harbors the gfp gene as a reporter demonstrating that the newly isolated strain can be used as host for genetic engineering.

CONCLUSION

In this study, we evaluate the ability of a new Lactobacillus isolate to form strong biofilm, which would provide the inhibitory effect against several spoilage and pathogenic bacteria. This new isolate has the potential to serve as a safe and effective cell factory for recombinant proteins.

In Vitro Properties of Potential Probiotic Indigenous Lactic Acid Bacteria Originating from Traditional Pickles

The suitable properties of potential probiotic lactic acid bacteria (LAB) strains (preselected among 153 strains on the basis of their potential technological properties) isolated from traditional Çubuk pickles were examined in vitro. For this purpose, these strains (21 Lactobacillus plantarum, 11 Pediococcus ethanolidurans, and 7 Lactobacillus brevis) were tested for the ability to survive at pH 2.5, resistance to bile salts, viability in the presence of pepsin-pancreatin, ability to deconjugate bile salts, cholesterol assimilation, and surface hydrophobicity properties. Most of the properties tested could be assumed to be strain-dependent. However, L. plantarum and L. brevis species were found to possess desirable probiotic properties to a greater extent compared to P. ethanolidurans. In contrast to P. ethanolidurans strains, the tested L. plantarum and L. brevis strains exhibited bile salt tolerance, albeit to different extent. All tested strains showed less resistance to intestinal conditions than gastric juice environment. Based on the survival under gastrointestinal conditions, 22 of the 39 strains were selected for further characterization. The eight strains having the highest cholesterol assimilation and surface hydrophobicity ratios could be taken as promising probiotic candidates for further in vivo studies, because of the strongest variations found among the tested strains with regard to these properties.

Characterization of the spoilage lactic acid bacteria in "sliced vacuum-packed cooked ham"

The lactic acid bacteria are involved with food fermentation and in such cases with food spoilage. Considering the need to reduce the lactic acid bacteria growth in meat products, the aim of this work was to enumerated and investigated the lactic acid bacteria present on sliced vacuum-packed cooked ham stored at 4 °C and 8 °C for 45 days by phenotypic and molecular techniques. The quantification showed that the lactic acid bacteria were present from the first day with mean count of 1.98 log cfu/g for the four batches analyzed. The lactic acid bacteria grew rapidly on the samples, and plate counts around 7.59 log cfu/g and 8.25 log cfu/g were detected after 45 days of storage at 4 °C and 8 °C, respectively; storage temperatures studied showed significant influence on the microorganism in study growth. The predominant lactic acid bacteria associated with the spoilage samples at one day of storage includes Lactobacillus sp., the phenotypic overlap Leuconostoc / Weissella sp. and Enterococcus sp. At 45 days of storage at 4 and 8 °C the mainly specie was Lactobacillus curvatus , following by Lactobacillus sakei and Leuconostoc mesentereoides ; the Enterococcus sp. was not present in the samples.