A novel species-specific PCR assay for identifying Lactobacillus fermentum

Immune and microbiome modulatory effects of Limosilactobacillus fermentum NCDC 400 in an immunocompromised mouse model

The present study was aimed to assess and validate the safety and functional efficacy of an indigenous probiotic strain Limosilactobacillus fermentum NCDC 400 (hereafter, LFN400) in an immunocompromised murine model. The study included four groups; a normal control (NC) group without immune suppression; an experimental model control (MC) with immune suppression induced via intraperitoneal cyclophosphamide (Cy) administration; and two MC groups orally administered with either low dose (LD) or high dose (HD) of LFN400 at dose 108 and 1010 CFU/mouse/day, respectively, for 15-days. Both control groups received normal saline as placebo control. LFN400 improved specific experimental characteristics including hematological and serum biochemical markers. Compared to MC group, LFN400-fed groups showed markedly (P < 0.05) decreased arrays of detrimental caecal enzymes. We did not observe instances of bacterial translocation of LFN400 from gut to bloodstream or extra-intestinal organs. LFN400 intake significantly (P < 0.05) enhanced spleen cell differentiation, immune and oxidative stress markers, and restored Cy-induced histopathological changes in multiple tissues, including the spleen. There was no genotoxic effect of LFN400 on bone marrow cells. Although not statistically significant, LFN400 feeding moderately increased gut microbiome diversity, supporting the growth of beneficial saccharolytic microorganisms and reducing the presence of pathobionts. The findings demonstrate that the probiotic strain LFN400 possesses in vivo safety and immunomodulatory potency and thus should be considered a potential candidate for future human clinical studies.

Recent and Advanced DNA-Based Technologies for the Authentication of Probiotic, Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) Fermented Foods and Beverages

The authenticity of probiotic products and fermented foods and beverages that have the status of protected designation of origin (PDO) or geographical indication (PGI) can be assessed via numerous methods. DNA-based technologies have emerged in recent decades as valuable tools to achieve food authentication, and advanced DNA-based methods and platforms are being developed. The present review focuses on the recent and advanced DNA-based techniques for the authentication of probiotic, PDO and PGI fermented foods and beverages. Moreover, the most promising DNA-based detection tools are presented. Strain- and species-specific DNA-based markers of microorganisms used as starter cultures or (probiotic) adjuncts for the production of probiotic and fermented food and beverages have been exploited for valuable authentication in several detection methods. Among the available technologies, propidium monoazide (PMA) real-time polymerase chain reaction (PCR)-based technologies allow for the on-time quantitative detection of viable microbes. DNA-based lab-on-a-chips are promising devices that can be used for the on-site and on-time quantitative detection of microorganisms. PCR-DGGE and metagenomics, even combined with the use of PMA, are valuable tools allowing for the fingerprinting of the microbial communities, which characterize PDO and PGI fermented foods and beverages, and they are necessary for authentication besides permitting the detection of extra or mislabeled species in probiotic products. These methods, in relation to the authentication of probiotic foods and beverages, need to be used in combination with PMA, culturomics or flow cytometry to allow for the enumeration of viable microorganisms.

Evaluation of heat-inactivated Limosilactobacillus fermentum CCFM1139 and its supernatant for the relief of experimental periodontitis in rats

Periodontitis is a chronic inflammatory disease induced by subgingival microbial dysbiosis, characterised by inflammation of the soft tissues of the periodontium and progressive loss of alveolar bone. Limosilactobacillus fermentum CCFM1139 is a probiotic with the potential to relieve periodontitis in vitro and in vivo. Due to the cost of active strain in production applications, we considered the effectiveness of bacterial components and metabolites in alleviating experimental periodontitis. Therefore, this study investigated the effect of heat-inactivated Limosilactobacillus fermentum CCFM1139 and its supernatant in the development of experimental periodontitis through animal experiments. The results showed that active, heat-inactivated Limosilactobacillus fermentum CCFM1139 and its supernatant all significantly reduced IL-1β levels in gingival tissue and serum (p < 0.05). Micro-computed tomography (micro CT) analysis showed that the active and heat-inactivated Limosilactobacillus fermentum CCFM1139 reduced alveolar bone loss in rats with periodontitis by 25.6% and 15.9% respectively (p < 0.05), with no change in percentage of bone volume (p > 0.05). In histomorphometric analysis, active Limosilactobacillus fermentum CCFM1139 showed better results in reducing alveolar bone loss and reducing inflammatory cell recruitment at the second molar. In addition, there was no significant difference in the number of tartrate-resistant acid phosphatase (TRAP) positive cells after in all experimental groups (p > 0.05). Therefore, heat-inactivated Limosilactobacillus fermentum CCFM1139 or its supernatant also have the ability to relieve periodontitis, and their alleviating effect may focus on the regulation of inflammatory response.

Quantitative analysis of salivary and biofilm bacteria associated with cavitated and non-cavitated carious lesions in pre-school children

OBJECTIVE

To quantify and compare Streptococcus mutans (S. mutans) and Lactobacillus fermentum (L. fermentum) in saliva and biofilm of caries-free children to those with cavitated and non-cavitated lesions.

DESIGN

One hundred and thirty-five 3-4 years old children were grouped (n = 45 in each group) according to their caries status: Clinical examination was done by a calibrated examiner. Biofilm and saliva were collected to quantify the microorganisms using qRT-PCR. The decayed-missing-filled surfaces (dmfs) was calculated by adding the number of decayed (ICDAS-II score 3-6), filled (ICDAS-II score 7 and 8) and missing (ICDAS-II score 9) surfaces due to caries. The correlation between the bacterial amounts and the number of carious surfaces was evaluated using Spearman's correlation coefficient. The levels and proportions of the microorganisms were compared using the Kruskal-Wallis test at an α-level of 0.05.

RESULTS

The quantity of S. mutans and L. fermentum was significantly higher in saliva and biofilm of children with cavitated lesions, followed by those with non-cavitated lesions and the lowest in caries-free children. Also, salivary and biofilm S. mutans, along with biofilm L. fermentum levels, significantly correlated with the number of non-cavitated surfaces; while salivary and biofilm S. mutans and L. fermentum levels significantly correlated with the number of cavitated surfaces. Additionally, dmfs scores significantly correlated with the salivary and biofilm S. mutans and L. fermentum levels.

CONCLUSIONS

S. mutans and L. fermentum in saliva and biofilm samples are associated with caries lesion severity.

Molecular Identification and Selection of Probiotic Strains Able to Reduce the Serum TMAO Level in Mice Challenged with Choline

Trimethylamine oxide (TMAO) originates from trimethylamine (TMA), which is oxidized in the liver by hepatic flavin-containing monooxygenases (FMO3). TMA is produced by its dietary precursors such as choline, carnitine, and phosphatidylcholine by gut microbiota. TMAO attracts attention, identified as a novel and independent risk factor for promoting obesity, atherosclerosis and cardiovascular disease (CVD), chronic kidney disease (CKD), insulin tolerance, and colon cancer. Probiotics have been considered as live microorganisms, providing benefits to their host when they are given in sufficient quantities and administered continuously. The objective of this study is to suggest a method to select potential probiotic strains to reduce the serum concentration of TMAO in mice fed with choline. In this work, we chose three lactobacilli with strong adherence capability, and fed multistrain formula (MF) to the mice challenged with choline. On days 7, 14, and day 28, it was found that the MF-containing L. amylovorus LAM1345, Lpb. plantarum LP1145, and Lim. fermentum LF33 showed a significant reduction in serum TMAO and TMA levels. For the single strains, LP1145 reduced TMAO on days 14 and 28, and strain LAM1345 reduced TMAO significantly on days 7 and day 14. For strain LF1143 from strain LF33, it showed no significant effect on TMAO and TMA. Thus, MF showed the best effect, which may be due to the additive and synergetic effect and the contribution of strain LP1145 and LAM1345. Finally, for the LAM1345 and LP1145 strains, we used molecular identification and typing methods to assure that these two strains are unique strains. The methods used for LAM 1345 were leader peptidase A (lepA) gene analysis and phylogenetic analysis, while for strain LP 1145and other strains of Lpb. plantarum subsp. plantarum sequences were compared using the whole-genome multilocus sequence typing (wgMLST) method.

Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

Background

Lactobacillus species are used as probiotics and play an important role in fermented food production. However, use of 16S rRNA gene sequences as standard markers for the differentiation of Lactobacillus species offers a very limited scope, as several species of Lactobacillus share similar 16S rRNA gene sequences. In this study, we developed a rapid and accurate method based on comparative genomic analysis for the identification of 37 Lactobacillus species that are commonly used in probiotics and fermented foods.

Results

To select species-specific sequences or genes, a total of 180 Lactobacillus genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S–23S rRNA gene. Selected unique genes were obtained using comparative genomic analysis and all genes were confirmed to be specific for 52,478,804 genomes via in silico analysis; they were found not to be strain-specific, but to exist in all strains of the same species. Species-specific primer pairs were designed from the selected 16S–23S rRNA gene sequences or unique genes of species. The specificity of the species-specific primer pairs was confirmed using reference strains, and the accuracy and efficiency of the polymerase chain reaction (PCR) with the standard curve were confirmed. The PCR method developed in this study is able to accurately differentiate species that were not distinguishable using the 16S rRNA gene alone. This PCR assays were designed to detect and identify 37 Lactobacillus species. The developed method was then applied in the monitoring of 19 probiotics and 12 dairy products. The applied tests confirmed that the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label.

Conclusions

The method developed in this study is able to rapidly and accurately distinguish different species of Lactobacillus, and can be used to monitor specific Lactobacillus species in foods such as probiotics and dairy products.

Assessing the Safety and Efficacy of Lactobacillus plantarum MTCC 5690 and Lactobacillus fermentum MTCC 5689 in Colitis Mouse Model

Probiotic lactobacilli have an unprecedented history of safe use, although some cases of infections have raised concerns about their safety, and hence, a rigorous screening of any new strain even of Lactobacillus is a must in order to study possible adverse interactions with the host, particularly under unhealthy conditions. The present study was, therefore, undertaken to investigate the safety as well as therapeutic efficacy of probiotic Lactobacillus plantarum MTCC 5690 and L. fermentum MTCC 5689 strains in dextran sodium sulfate (DSS)-induced colitis mouse model. Both MTCC 5690 and MTCC 5689 did not induce any detrimental effect on the colitic mice, as was reflected by normal colon and caecum length, blood biochemistry, hematology, and absence of inflammation. Although translocation of both the strains was observed in extraintestinal organs, probiotic-fed mice had significantly improved intestinal permeability and decreased myeloperoxidase (MPO) activity. Probiotic interventions also led to an improved health index and better growth of colitis mice compared to colitis animals with no probiotic intervention. These results point towards the safe use of L. plantarum MTCC 5690 and L. fermentum MTCC 5689 as biotherapeutics for amelioration of inflammatory conditions after establishing their efficacy in human clinical trials.

Viability and Composition Validation of Commercial Probiotic Products by Selective Culturing Combined with Next-Generation Sequencing

The consumption of dietary supplements to treat health complications or to improve overall health conditions has become a globally increasing trend that leads to the development of a large number of health-related novel products and expands the associated manufacturing industries around the world. In the current study, we applied selective culturing combined with next-generation sequencing to examine the microbial viability in terms of its culturability on culture medium, composition, and possible contamination in the selected 17 commercial probiotic products sold in the mainland China market. Additionally, the relative abundance of each individual bacterial content was also evaluated by using the generated sequencing reads. The tested probiotic product samples were subjected to Illumina HiSeq-2000 sequencing platform and thoroughly analyzed by the in-house developed bioinformatics pipeline. The comprehensive culturing and sequencing analysis revealed both viability and composition inaccuracy among the several tested probiotic products, however, no contaminant was identified during the analysis. Among the total, five probiotic products (29.41%) were found with an inaccurate or lower colony-forming unit (CFU) counts on culture media while four probiotic products (23.52%) have inaccurately labeled classification. This study provides an ideal qualitative and quantitative assessment approach, which can be used as a diagnostic tool for the accurate assessment of commercial probiotic supplements.

Geographical location specific composition of cultured microbiota and Lactobacillus occurrence in human breast milk in China

Breast milk bacteria play an important role in the early development of the gut microbiota and the immune system. Dominant living bacteria of 89 healthy Chinese women from 11 cities in five regions were analysed by broad-range yeast extract, casitone, and fatty acid and de Man, Rogosa, and Sharpe-based culturing coupled with 16S rRNA sequence and quantitative polymerase chain reaction. Principal coordinate analysis showed that human breast milk samples were classified into three groups, driven by Enterococcus (abundance in group 1, 63.13%), Streptococcus (abundance in group 2, 68.16%) and Staphylococcus (abundance in group 3, 55.17%). The microbiota profile was highly region-specific. Samples from the Northwest and North of China showed higher alpha diversity compared to other regions (p < 0.05). Staphylococcus, Streptococcus, and Enterococcus were the dominant genera in all samples. Lactobacillus had a high occurrence in samples from the Northwest and North, dominated by Lactobacillus reuteri and Lactobacillus gasseri. Samples of mothers with a high postpartum body mass index showed more Staphylococcus and less Lactobacillus and Streptococcus. Staphylococcus was negatively correlated with Lactobacillus and Streptococcus. The mode of delivery also affected the composition of microbiota, even after culture. These findings indicate differences between the North and South, provide effective information for collection of samples in which Lactobacillus is the predominant genus, and lower the detection limit for small amounts of bacteria.

Screening for gum-producing Lactic acid bacteria in Oil palm (Elaeis guineensis) and raphia palm (Raphia regalis) sap from South-West Nigeria

Lactic acid bacteria have wide applications in food processing. Lactic acid bacteria produced exopolysaccharides (EPS) which could be used as possible replacer for commercial stabilizer and thickeners produced by nonfood grade bacteria. Seventy-two samples of Oil and Raphia palm sap were collected in eighteen locations across South-Western Nigeria and screened for exopolysaccharide production in 6% sucrose agar using streaked plate method. Four hundred EPS-producing bacteria (EPB) isolated were clustered based on morphological characteristics into two broad groups and preliminary screened for EPS-producing capacity. Twenty representative of EPB were selected from the broad groups for tentative identification by API 50CHL and 10 high yielding EPB were selected for large-scale EPS production. Each strain was inoculated into 6% sucrose broth with 3% (v/v) preculture grown overnight in a 1.5 ml flask and incubated at 37°C for 72 hr. The EPSs were purified and freeze-dried prior to quantification of yields. EPS-producing bacteria were identified as Leuconostoc lactis, Lactobacillus fermentum, Lactobacillus delbrueckii ssp. lactis, L. delbrueckii ssp. delbrueckii, Lactobacillus acidophilus, Lactobacillus plantarum, Lactobacillus crispatus, and Leuconostoc mesenteroides ssp. mesenteroides/dextranicum. EPS yield ranged from 132-810.75 mg/L and EPS-producing potential of lactic acid bacteria (LAB) strains ranged; 36% (132-245 mg/L), 36% (250-460 mg/L), and 28% (461-820 mg/L). L. plantarum had the highest EPS yield of 810.75 mg/L whereas L. crispatus had the least yield 242.5 mg/L. These results suggest that majority of LAB in palm wine saps are gum-producing bacteria. Leuconostoc and Lactobacillus were the most abundant LAB found in this study while L. plantarum could have applications as potential starter cultures for the production of exopolysaccharides (EPS) at industrial level.

Developing novel species-specific DNA markers for PCR-based species identification of the Lactobacillus sakei group

Identification of members of the Lactobacillus sakei group (LSG) by common phenotypic and genotypic methods is generally inadequate and time-consuming. The objective of this study was to develop novel species-specific primers based on sequence-characterized amplified region (SCAR) markers using random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) analysis. Three species-specific fragments were gel-purified, cloned and sequenced after preliminary screening of 80 random primers. Accordingly, three pairs of primers Lcur-F/R, Lgram-F/R and Lsakei-F/R were designed based on single species-specific bands (281, 278 and 472 bp) that were obtained from Lactobacillus curvatus, Lactobacillus graminis and L. sakei, respectively. The specificities of these primer pairs were confirmed in 21 LSG strains and 31 nontarget Lactobacillus strains. In addition, the detection limits for each primer pair were approx. 10⁵ , 10⁴ and 10⁶ cells per gram of meat samples spiked with L. curvatus, L. graminis and L. sakei, respectively. In conclusion, we have successfully developed a rapid, accurate and effective PCR-based method for identification of species in the LSG.

SIGNIFICANCE AND IMPACT OF THE STUDY

Neither phenotypic nor the most commonly used genotypic method (16S rRNA gene sequencing) provides sufficient resolution for accurate identification of the Lactobacillus sakei group. A sequence-characterized amplified region method developed in this study provides a rapid, cost-effective way to detect the member of the L. sakei group in meat sample.

Effect of fermented milk containing Lactobacillus rhamnosus SD11 on oral microbiota of healthy volunteers: A randomized clinical trial

The aims of this study were to evaluate whether short-term consumption of fermented milk containing Lactobacillus rhamnosus SD11 affected levels of oral microbiota in vivo and whether L. rhamnosus SD11 could colonize in the human mouth. We also monitored for potential side effects of the probiotic. The applicability of using L. rhamnosus SD11 compared with Lactobacillus bulgaricus as a starter culture for fermented milk was evaluated. After informed consent, 43 healthy young adults were recruited and randomly assigned to either the probiotic or control group and received fermented milk containing L. rhamnosus SD11 or L. bulgaricus, respectively, once daily for 4 wk. The numbers of mutans streptococci, lactobacilli, and total bacteria in saliva were counted at baseline and then after 4 and 8 wk. An oral examination was performed at baseline and after 8 wk. The persistence of L. rhamnosus SD11 was investigated by DNA fingerprinting using arbitrary primer-PCR. Results demonstrated that statistically significant reductions in mutans streptococci and total bacteria were observed in the probiotic group compared with the control group, and the number of lactobacilli was significantly increased in both groups after receiving fermented milks. Lactobacillus rhamnosus SD11 could be detected (in >80% of subjects) up to 4 wk following cessation of dosing among subjects in the probiotic group. No side effects were reported. Thus, L. rhamnosus SD11 could be used as a starter culture for fermented milk. Daily consumption of L. rhamnosus SD11-containing fermented milk for 4 wk may have beneficial effects on oral health by reducing salivary levels of mutans streptococci. The probiotic was apparently able to colonize the oral cavity for a longer time than previously reported. However, the potential benefits of probiotic L. rhamnosus SD11 on oral health require further evaluation with a larger group of volunteers in a longer-term study.

Antiviral Probiotics: A New Concept in Medical Sciences

In recent decades, probiotics have shown beneficial effects on animal and human health. Probiotics can protect the host against several health threats, including infectious diseases. Before 1995, researchers believed that the effect of probiotics was only on gut microbiota which can restore the gut flora and thus prevent pathogenic bacteria from triggering gastroenteritis. Recent studies have shown that the immunomodulatory activity is the most important mechanism of action of probiotics. From this information, researchers started to evaluate the effect of some immunobiotics, not only on pathogenic bacteria but also on viruses, including enteric and respiratory viruses. Several studies have confirmed the potential antiviral activity of some probiotics due to the immunomodulatory effect. These studies were conducted on humans (clinical trials) and in animal models. In this chapter, probiotics with antiviral effect against respiratory and enteric viruses will be presented and discussed, as well as their mechanisms of action.

DNA-based culture-independent analysis detects the presence of group a streptococcus in throat samples from healthy adults in Japan

Background

Group A Streptococcus (GAS; Streptococcus pyogenes) causes a range of mild to severe infections in humans. It can also colonize healthy persons asymptomatically. Therefore, it is important to study GAS carriage in healthy populations, as carriage of it might lead to subsequent disease manifestation, clonal spread in the community, and/or diversification of the organism. Throat swab culture is the gold standard method for GAS detection. Advanced culture-independent methods provide rapid and efficient detection of microorganisms directly from clinical samples. We investigated the presence of GAS in throat swab samples from healthy adults in Japan using culture-dependent and culture-independent methods.

Results

Two throat swab samples were collected from 148 healthy volunteers. One was cultured on selective medium, while total DNA extracted from the other was polymerase chain reaction (PCR) amplified with two GAS-specific primer pairs: one was a newly designed 16S rRNA-specific primer pair, the other a previously described V-Na⁺-ATPase primer pair. Although only 5 (3.4 %) of the 148 samples were GAS-positive by the culture-dependent method, 146 (98.6 %) were positive for the presence of GAS DNA by the culture-independent method. To obtain serotype information by emm typing, we performed nested PCR using newly designed emm primers. We detected the four different emm types in 25 (16.9 %) samples, and these differed from the common emm types associated with GAS associated diseases in Japan. The different emm types detected in the healthy volunteers indicate that the presence of unique emm types might be associated with GAS carriage.

Conclusions

Our results suggest that culture-independent methods should be considered for profiling GAS in the healthy hosts, with a view to obtaining better understanding of these organisms. The GAS-specific primers (16S rRNA and V-Na⁺-ATPase) used in this study can be used to estimate the maximum potential GAS carriage in people.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0858-5) contains supplementary material, which is available to authorized users.

Probiotic attributes of Lactobacillus fermentum isolated from human feces and dairy products

The objective of this study was to characterize native Lactobacillus fermentum isolates for their probiotic attributes. Accordingly, 12 L. fermentum isolates selected from indigenous fermented dairy products and infant fecal samples were evaluated for their probiotic properties by in vitro and PCR methods. The cultures exhibited high tolerance to acid and bile as well as survival in simulated transit fluids (above 70 %). Cell surface hydrophobicity was in the range of 0.55-57.69 % for xylene and 0.45-77.12 % for hexadecane, whereas auto-aggregation ranged between 9 and 62 %. Isolates exhibited efficient binding to mucin and fibronectin, bile salt hydrolase activity, cholesterol assimilation (49-76 %), and radical scavenging activity (37-77 %). The isolates demonstrated antibacterial activity against Listeria monocytogenes Scott A and Micrococcus luteus ATCC 9341. Molecular fingerprinting and identification of the isolates were achieved by PCR with GTG5 as well as 16S rRNA, phenylalanyl-tRNA synthetase alpha subunit (pheS), and RNA polymerase alpha subunit (rpoA) genes. This revealed the genomic diversity of the isolates from the two sources. Gene-specific amplification of probiotic marker genes was attained by PCR-based methods, and resultant products were sequenced. Multiple sequence alignment of the probiotic marker genes using bioinformatics revealed similarity to completely sequenced genomes of L. fermentum CECT 5716 and IFO 3956 with a few variations in mucin-binding protein gene sequences. Isolates designated as L. fermentum MCC 2759 and L. fermentum MCC 2760 showed the best probiotic attributes with high survival in simulated gastrointestinal fluids, in vitro adhesion, cholesterol reduction, and high antioxidative potential. Thus, these cultures could be potential probiotic candidates for application as functional foods.

Assessment of the fecal lactobacilli population in patients with hepatitis B virus-related decompensated cirrhosis and hepatitis B cirrhosis treated with liver transplant

This study aims to provide an overview of the diversity of intestinal Lactobacillus among Chinese patients with hepatitis B virus (HBV)-related decompensated cirrhosis and who received liver transplant for hepatitis B cirrhosis. Fecal samples were collected from 38 healthy volunteers, 61 patients with HBV-related decompensated cirrhosis (group LC) and 74 patients who had liver transplant for hepatitis B cirrhosis (group LT). Quantitative polymerase chain reaction technology with species-specific primers was applied to investigate lactobacilli 16S rDNA in crude DNA, extracted from fecal samples. Software package Statistical Package for the Social Sciences and Palaeontological Statistics for Windows was used to analyze the data. Lactobacilli population of the two patient groups was different from the healthy control subjects, principal differences being marked decrease in the population of Lactobacillus rhamnosus (p < 0.001 for both patient groups) and reduction in the frequency of Lactobacillus fermentus (p < 0.001 for group LC and p < 0.01 for group LT). Our findings on the frequency of lactobacilli population suggested decreased diversity in groups LC and LT (compared with the healthy controls (p < 0.001 and p < 0.01, respectively)). Patients tended to have less complex fecal lactobacilli composition than the healthy controls, especially in the group LC.

Complete genomic sequence of the Lactobacillus temperate phage LF1

Bacteriophage LF1, a newly isolated temperate phage from a mitomycin-C-induced lysate of wild type Lactobacillus fermentum, was found to contain a double-strand DNA of 42,606 base pairs (bp) with a G+C content of 45%. Bioinformatic analysis of the phage genome revealed 57 putative open reading frames (ORFs). The predicted protein products of ORFs were determined and described. According to morphological analysis by transmission electron microscopy (TEM), LF1 has an isometric head and a non-contractile tail, indicating that it belongs to the family Siphoviridae. The temperate phage LF1 has a good genetic mosaic relationship with ΦPYB5 in the packaging module. To our knowledge, this is first report of genomic sequencing and characterization of temperate phage LF1 from wild-type L. fermentum isolated from Kimchi in Korea.

Identification and characterisation of lactobacilli isolated from Kimere, a spontaneously fermented pearl millet dough from Mbeere, Kenya (East Africa)

The objective of the study was to isolate potential probiotic lactobacilli from Kimere, a pearl millet dough prepared in the Mbeere community of Kenya, East Africa, by fermentation for 18-24 hours. Kimere samples, collected from 11 different homesteads in Mbeere, showed average pH values of 3.63±0.29. Counts of presumptive lactobacilli were 8.52±0.02 log10 colony forming units per gram, respectively. 48 presumptive Lactobacillus isolates were characterised and identified by biochemical and molecular methods. Lactobacillus fermentum (46 isolates) was the dominant Lactobacillus species detected. Analysis of strain diversity with pulsed-field gel electrophoresis indicated relatively large biodiversity among L. fermentum isolates. All L. fermentum isolates were able to grow in MRS medium containing 0.3% ox gall. Twelve of them were able to grow in the presence of 3% ox gall, and of these 60% survived incubation at pH 3 in the presence of 2 mg pepsin per ml for three hours.