Phenotypic, Technological, Safety, and Genomic Profiles of Gamma-Aminobutyric Acid-Producing Lactococcus lactis and Streptococcus thermophilus Strains Isolated from Cow's Milk.

Gamma-aminobutyric acid (GABA)-producing lactic acid bacteria (LAB) can be used as starters in the development of GABA-enriched functional fermented foods. In this work, four GABA-producing strains each of Lactococcus lactis and Streptococcus thermophilus species were isolated from cow's milk, and their phenotypic, technological, and safety profiles determined. Genome analysis provided genetic support for the majority of the analyzed traits, namely, GABA production, growth in milk, and the absence of genes of concern. The operon harboring the glutamate decarboxylase gene (gadB) was chromosomally encoded in all strains and showed the same gene content and gene order as those reported, respectively, for L. lactis and S. thermophilus. In the latter species, the operon was flanked (as in most strains of this species) by complete or truncated copies of insertion sequences (IS), suggesting recent acquisition through horizontal gene transfer. The genomes of three L. lactis and two S. thermophilus strains showed a gene encoding a caseinolytic proteinase (PrtP in L. lactis and PrtS in S. thermophilus). Of these, all but one grew in milk, forming a coagulum of good appearance and an appealing acidic flavor and taste. They also produced GABA in milk supplemented with monosodium glutamate. Two L. lactis strains were identified as belonging to the biovar. diacetylactis, utilized citrate from milk, and produced significant amounts of acetoin. None of the strains showed any noticeable antibiotic resistance, nor did their genomes harbor transferable antibiotic resistance genes or genes involved in toxicity, virulence, or pathogenicity. Altogether these results suggest that all eight strains may be considered candidates for use as starters or components of mixed LAB cultures for the manufacture of GABA-enriched fermented dairy products.

Antibiotic Resistance/Susceptibility Profiles of Staphylococcus equorum Strains from Cheese, and Genome Analysis for Antibiotic Resistance Genes.

In food, bacteria carrying antibiotic resistance genes could play a prominent role in the spread of resistance. Staphylococcus equorum populations can become large in a number of fermented foods, yet the antibiotic resistance properties of this species have been little studied. In this work, the resistance/susceptibility (R/S) profile of S. equorum strains (n = 30) from cheese to 16 antibiotics was determined by broth microdilution. The minimum inhibitory concentration (MIC) for all antibiotics was low in most strains, although higher MICs compatible with acquired genes were also noted. Genome analysis of 13 strains showed the S. equorum resistome to be composed of intrinsic mechanisms, acquired mutations, and acquired genes. As such, a plasmidic cat gene providing resistance to chloramphenicol was found in one strain; this was able to provide resistance to Staphylococcus aureus after electroporation. An msr(A) polymorphic gene was identified in five strains. The Mrs(A) variants were associated with variable resistance to erythromycin. However, the genetic data did not always correlate with the phenotype. As such, all strains harbored a polymorphic fosB/fosD gene, although only one acquired copy was associated with strong resistance to fosfomycin. Similarly, a plasmid-associated blaR1-blaZI operon encoding a penicillinase system was identified in five ampicillin- and penicillin G-susceptible strains. Identified genes not associated with phenotypic resistance further included mph(C) in two strains and norA in all strains. The antibiotic R/S status and gene content of S. equorum strains intended to be employed in food systems should be carefully determined.

Phenotypic and Safety Assessment of the Cheese Strain Lactiplantibacillus plantarum LL441, and Sequence Analysis of its Complete Genome and Plasmidome.

This work describes the phenotypic typing and complete genome analysis of LL441, a dairy Lactiplantibacillus plantarum strain. LL441 utilized a large range of carbohydrates and showed strong activity of some carbohydrate-degrading enzymes. The strain grew slowly in milk and produced acids and ketones along with other volatile compounds. The genome of LL441 included eight circular molecules, the bacterial chromosome, and seven plasmids (pLL441-1 through pLL441-7), ranging in size from 8.7 to 53.3 kbp. Genome analysis revealed vast arrays of genes involved in carbohydrate utilization and flavor formation in milk, as well as genes providing acid and bile resistance. No genes coding for virulence traits or pathogenicity factors were detected. Chromosome and plasmids were packed with insertion sequence (IS) elements. Plasmids were also abundant in genes encoding heavy metal resistance traits and plasmid maintenance functions. Technologically relevant phenotypes linked to plasmids, such as the production of plantaricin C (pLL441-1), lactose utilization (pLL441-2), and bacteriophage resistance (pLL441-4), were also identified. The absence of acquired antibiotic resistance and of phenotypes and genes of concern suggests L. plantarum LL441 be safe. The strain might therefore have a use as a starter or starter component in dairy and other food fermentations or as a probiotic.

Directed Recovery and Molecular Characterization of Antibiotic Resistance Plasmids from Cheese Bacteria.

Resistance to antimicrobials is a growing problem of worldwide concern. Plasmids are thought to be major drivers of antibiotic resistance spread. The present work reports a simple way to recover replicative plasmids conferring antibiotic resistance from the bacteria in cheese. Purified plasmid DNA from colonies grown in the presence of tetracycline and erythromycin was introduced into plasmid-free strains of Lactococcus lactis, Lactiplantibacillus plantarum and Lacticaseibacillus casei. Following antibiotic selection, the plasmids from resistant transformants were isolated, analyzed by restriction enzyme digestion, and sequenced. Seven patterns were obtained for the tetracycline-resistant colonies, five from L. lactis, and one each from the lactobacilli strains, as well as a single digestion profile for the erythromycin-resistant transformants obtained in L. lactis. Sequence analysis respectively identified tet(S) and ermB in the tetracycline- and erythromycin-resistance plasmids from L. lactis. No dedicated resistance genes were detected in plasmids conferring tetracycline resistance to L. casei and L. plantarum. The present results highlight the usefulness of the proposed methodology for isolating functional plasmids that confer antibiotic resistance to LAB species, widen our knowledge of antibiotic resistance in the bacteria that inhabit cheese, and emphasize the leading role of plasmids in the spread of resistance genes via the food chain.

Antibiotic Susceptibility Profiles of Lactic Acid Bacteria from the Human Vagina and Genetic Basis of Acquired Resistances.

Lactic acid bacteria can act as reservoirs of antibiotic resistance genes that can be ultimately transferred to pathogens. The present work reports on the minimum inhibitory concentration (MIC) of 16 antibiotics to 25 LAB isolates of five Lactobacillus and one Bifidobacterium species from the human vagina. Acquired resistances were detected to kanamycin, streptomycin, chloramphenicol, gentamicin, and ampicillin. A PCR analysis of lactobacilli failed to identify genetic determinants involved in any of these resistances. Surprisingly, a tet(W) gene was detected by PCR in two Bifidobacterium bifidum strains, although they proved to be tetracycline-susceptible. In agreement with the PCR results, no acquired genes were identified in the genome of any of the Lactobacillus spp. strains sequenced. A genome analysis of B. bifidum VA07-1AN showed an insertion of two guanines in the middle of tet(W) interrupting the open reading frame. By growing the strain in the presence of tetracycline, stable tetracycline-resistant variants were obtained. An amino acid substitution in the ribosomal protein S12 (K43R) was further identified as the most likely cause of VA07-1AN being streptomycin resistance. The results of this work expand our knowledge of the resistance profiles of vaginal LAB and provide evidence for the genetic basis of some acquired resistances.

Fermented foods in a global age: East meets West.

Fermented foods and alcoholic beverages have long been an important part of the human diet in nearly every culture on every continent. These foods are often well-preserved and serve as stable and significant sources of proteins, vitamins, minerals, and other nutrients. Despite these common features, however, many differences exist with respect to substrates and products and the types of microbes involved in the manufacture of fermented foods and beverages produced globally. In this review, we describe these differences and consider the influence of geography and industrialization on fermented foods manufacture. Whereas fermented foods produced in Europe, North America, Australia, and New Zealand usually depend on defined starter cultures, those made in Asia and Africa often rely on spontaneous fermentation. Likewise, in developing countries, fermented foods are not often commercially produced on an industrial scale. Although many fermented products rely on autochthonous microbes present in the raw material, for other products, the introduction of starter culture technology has led to greater consistency, safety, and quality. The diversity and function of microbes present in a wide range of fermented foods can now be examined in detail using molecular and other omic approaches. The nutritional value of fermented foods is now well-appreciated, especially in resource-poor regions where yoghurt and other fermented foods can improve public health and provide opportunities for economic development. Manufacturers of fermented foods, whether small or large, should follow Good Manufacturing Practices and have sustainable development goals. Ultimately, preferences for fermented foods and beverages depend on dietary habits of consumers, as well as regional agricultural conditions and availability of resources.

Effect of different starter cultures on chemical and microbial parameters of buckwheat honey fermentation.

The aim of this study was to analyze the microbiology of buckwheat honey fermentation inoculated with different starter cultures by culturing and PCR-DGGE, taking as a model for comparison a spontaneously fermented batch. The inoculants tested were (i) cider lees (from a cider factory), (ii) sourdough (from a bakery), and (iii) a commercial Saccharomyces cerevisiae strain. The results of the culturing and culture-independent techniques agreed well and detected the same dominant species along the fermentations. Our results suggest that S. cerevisiae strains, which constituted a majority population in all batches including the uninoculated one, carried out the fermentations. The highest microbial diversity was found at the beginning of the fermentation in the uninoculated batch; this contained in addition to S. cerevisiae bacteria (Paracoccus sp., Staphylococcus sp., and Bacillus sp.) and yeast (Candida sp.) species. Candida sp. was also common in batches inoculated with sourdough and cider lees cultures. Lactobacillus species were found throughout the fermentation of the sourdough-inoculated batch. Basic chemical analysis and testing trials demonstrated that the overall sensory acceptance of the four meads were highly similar. Yeast and bacteria isolated in this study could serve as a source of technologically relevant microorganisms for mead production.

Bacterial communities and metabolic activity of faecal cultures from equol producer and non-producer menopausal women under treatment with soy isoflavones.

BACKGROUND: Isoflavones are polyphenols with estrogenic activity found mainly in soy and soy-derived products that need to be metabolised in the intestine by the gut bacteria to be fully active. There is little knowledge about isoflavone bioconversion and equol production in the human intestine. In this work, we developed an in vitro anaerobic culture model based on faecal slurries to assess the impact of isoflavone supplementation on the overall intestinal bacterial composition changes and associated metabolic transformations. RESULTS: In the faecal anaerobic batch cultures of this study bioconversion of isoflavones into equol was possible, suggesting the presence of viable equol-producing bacterial taxa within the faeces of menopausal women with an equol producer phenotype. The application of high-throughput DNA sequencing of 16S rRNA gene amplicons revealed the composition of the faecal cultures to be modified by the addition of isoflavones, with enrichment of some bacterial gut members associated with the metabolism of phenolics and/or equol production, such as Collinsella, Faecalibacterium and members of the Clostridium clusters IV and XIVa. In addition, the concentration of short-chain fatty acids (SCFAs) detected in the isoflavone-containing faecal cultures was higher in those inoculated with faecal slurries from equol-producing women. CONCLUSIONS: This study constitutes the first step in the development of a faecal culturing system with isoflavones that would further allow the selection and isolation of intestinal bacterial types able to metabolize these compounds and produce equol in vitro. Although limited by the low number of faecal cultures analysed and the inter-individual bacterial diversity, the in vitro results obtained in this work tend to indicate that soy isoflavones might provide an alternative energy source for the increase of equol-producing taxa and enhancement of SCFAs production. SCFAs and equol are both considered pivotal bacterial metabolites in the triggering of intestinal health-related beneficial effects.

Relationships between the genome and some phenotypical properties of Lactobacillus fermentum CECT 5716, a probiotic strain isolated from human milk.

Lactobacillus fermentum CECT 5716, isolated from human milk, has immunomodulatory, anti-inflammatory, and anti-infectious properties, as revealed by several in vitro and in vivo assays, which suggests a strong potential as a probiotic strain. In this work, some phenotypic properties of L. fermentum CECT 5716 were evaluated, and the genetic basis for the obtained results was searched for in the strain genome. L. fermentum CECT 5716 does not contain plasmids and showed neither bacteriocin nor biogenic amine biosynthesis ability but was able to produce organic acids, glutathione, riboflavin, and folates and to moderately stimulate the maturation of mouse dendritic cells. No prophages could be induced, and the strain was sensitive to all antibiotics proposed by European Food Safety Authority (EFSA) standards, while no transmissible genes potentially involved in antibiotic resistance were detected in its genome. Globally, there was an agreement between the phenotype properties of L. fermentum CECT 5716 and the genetic information contained in its genome.

Impact of next generation sequencing techniques in food microbiology.

Understanding the Maxam-Gilbert and Sanger sequencing as the first generation, in recent years there has been an explosion of newly-developed sequencing strategies, which are usually referred to as next generation sequencing (NGS) techniques. NGS techniques have high-throughputs and produce thousands or even millions of sequences at the same time. These sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and those present in small numbers. In specific applications, NGS provides a complete inventory of all microbial operons and genes present or being expressed under different study conditions. NGS techniques are revolutionizing the field of microbial ecology and have recently been used to examine several food ecosystems. After a short introduction to the most common NGS systems and platforms, this review addresses how NGS techniques have been employed in the study of food microbiota and food fermentations, and discusses their limits and perspectives. The most important findings are reviewed, including those made in the study of the microbiota of milk, fermented dairy products, and plant-, meat- and fish-derived fermented foods. The knowledge that can be gained on microbial diversity, population structure and population dynamics via the use of these technologies could be vital in improving the monitoring and manipulation of foods and fermented food products. They should also improve their safety.

Safety evaluation of an extension of use of the food enzyme thermolysin from the non-genetically modified Anoxybacillus caldiproteolyticus strain AE-TP.

The food enzyme thermolysin (EC. 3.4.24.27) is produced with the non-genetically modified Anoxybacillus caldiproteolyticus strain AE-TP by Amano Enzyme Inc. A safety evaluation of this food enzyme was made previously, in which EFSA concluded that this food enzyme did not give rise to safety concerns when used in eight food manufacturing processes. Subsequently, the applicant has requested to extend its use to one additional process, to withdraw two processes and to revise the use levels. In this assessment, EFSA updated the safety evaluation of this food enzyme for use in a total of seven food manufacturing processes. The dietary exposure to the food enzyme-total organic solids (TOS) was calculated to be up to 0.989 mg TOS/kg body weight (bw) per day in European populations. When combined with the no observed adverse effect level reported in the previous opinion (700 mg TOS/kg bw per day, the mid-dose tested), the Panel derived a revised margin of exposure of at least 708. Based on the data provided for the previous evaluation and the revised margin of exposure in the present evaluation, the Panel concluded that this food enzyme does not give rise to safety concerns under the revised intended conditions of use.

Safety evaluation of an extension of use of the food enzyme oryzin from the non-genetically modified Aspergillus ochraceus strain AE-P.

The food enzyme oryzin (EC 3.4.21.63) is produced with the non-genetically modified Aspergillus ochraceus strain AE-P by Amano Enzyme Inc. A safety evaluation of this food enzyme was made previously, in which EFSA concluded that this food enzyme did not give rise to safety concerns when used in nine food manufacturing processes. Subsequently, the applicant has requested to extend its use to one additional process, to withdraw two food processes and to revise the use levels. In this assessment, EFSA updated the safety evaluation of this food enzyme when used in a total of eight food manufacturing processes. The dietary exposure to the food enzyme-total organic solids (TOS) was calculated to be up to 0.354 mg TOS/kg body weight (bw) per day in European populations. When combined with the no observed adverse effect level reported in the previous opinion (1862 mg TOS/kg bw per day, the highest dose tested), the Panel derived a margin of exposure of at least 5260. Based on the data provided for the previous evaluation and the revised margin of exposure in the present evaluation, the Panel concluded that this food enzyme does not give rise to safety concerns under the revised intended conditions of use.

Safety evaluation of the food enzyme lysophospholipase from the genetically modified Trichoderma reesei strain DP-Nyc81.

The food enzyme lysophospholipase (2-lysophosphatidylcholine acylhydrolase, EC 3.1.1.5) is produced with the genetically modified Trichoderma reesei strain DP-Nyc81 by Genencor International B.V. The genetic modifications do not give rise to safety concerns. The food enzyme is free from viable cells of the production organism and its DNA. It is intended to be used in the processing of cereals and other grains for the production of glucose syrups and other starch hydrolysates. Since residual amounts of food enzyme-total organic solids are removed during these food manufacturing processes, dietary exposure was not calculated and toxicological studies were considered unnecessary. A search for the identity of the amino acid sequence of the food enzyme to known allergens was made and no match was found. The Panel considered that the risk of allergic reactions upon dietary exposure cannot be excluded, but the likelihood is low. Based on the data provided, the Panel concluded that this food enzyme does not give rise to safety concerns, under the intended conditions of use.

Safety of feed additives consisting of microcrystalline cellulose and carboxymethyl cellulose for all animal species (International Cellulosics Association).

Following a request from the European Commission, the EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on the safety of microcrystalline cellulose and carboxymethyl cellulose as technological feed additives for all animal species. In its previous opinions on the safety and efficacy of the products, the FEEDAP Panel could not conclude on proper identification and characterisation as required for a feed additive. The occurrence of potential toxic impurities could also not be assessed. Based on the new data provided, the feed additives microcrystalline cellulose and carboxymethyl cellulose were properly identified and characterised and were shown to meet the specifications set for their use as food additives. Therefore, the conclusions of the safety reached in the previous opinions for microcrystalline cellulose and carboxymethyl cellulose meeting the food additive specifications apply to the microcrystalline cellulose and carboxymethyl cellulose under assessment as feed additives. The additives are considered safe for all animal species, the consumer and the environment. In the absence of data, the FEEDAP Panel is not in the position to conclude on the safety for the user.

Efficacy of a feed additive consisting of carvacrol (Nimicoat®) for weaned piglets (Techna France Nutrition).

Following a request from the European Commission, the Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on the efficacy of a feed additive consisting of carvacrol (Nimicoat®) as a zootechnical feed additive for weaned piglets at the recommended use level of 250 mg/kg complete feed. In a previous assessment, three efficacy trials and one tolerance-efficacy trial were assessed. Only one of the efficacy trials was considered to support the efficacy at the recommended use level. The applicant provided amendments to two previously submitted studies and a new trial. The amendments to the previously submitted studies did not change the conclusions from the previous assessment. The new efficacy study showed a significant improvement of the zootechnical parameters. Two studies showed positive and significant effects on the performance of the weaned piglets when the additive was administered at 250 mg/kg feed. Due to the lack of sufficient data, the FEEDAP Panel is not in the position to conclude on the efficacy of the additive for the target species.

Assessment of the feed additive consisting of Bacillus velezensisATCC PTA-6737 (PB6) for turkeys for fattening and turkeys reared for breeding for the renewal of its authorisation and the modification of the conditions of the authorisation for other growing poultry species (Kemin Europe N.V).

Following a request from the European Commission, the Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on Bacillus velezensis ATCC PTA-6737 as a zootechnical additive (functional group: gut-flora stabiliser) in the context of the renewal of the authorisation for turkeys for fattening and turkeys reared for breeding. The applicant is also requesting to modify the target species in the current authorisations to 'all growing poultry', the increase of the recommended use level in chickens for fattening, chickens reared for laying and minor poultry species except minor poultry for laying from 1 × 107 to 1 × 108 CFU/kg complete feed and the compatibility of the additive with halofuginone. The applicant provided evidence that the additive currently in the market complies with the conditions of the authorisation. There was no new evidence that would lead to reconsider previous conclusions. Therefore, the FEEDAP Panel concluded that the additive remains safe for all poultry species for fattening and reared for laying/breeding, the consumers and the environment under the current authorised conditions of use. The additive is not irritant to the skin and eyes, but it should be considered a respiratory sensitiser. The Panel could not conclude on the skin sensitisation potential of the additive. The Panel concluded that the additive has a potential to be efficacious as a zootechnical additive for poultry for fattening and reared for laying/breeding under the proposed conditions of use.

Assessment of the feed additive consisting of Pediococcus pentosaceus DSM 14021 for all animal species for the renewal of its authorisation (Chr. Hansen A/S).

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the assessment of the application for renewal of Pediococcus pentosaceus DSM 14021, a technological additive for all animal species. The applicant has provided evidence that the additive currently on the market complies with the existing conditions of authorisation. The Panel concluded that the additive remains safe for all animal species, consumers and the environment under the authorised conditions of use. Regarding user safety, the Panel considers that any exposure through skin and respiratory tract is considered a risk. The Panel cannot conclude on the eye irritation potential of the additive due to the lack of data. There is no need for assessing the efficacy of the additive in the context of the renewal of the authorisation.

Assessment of the feed additive consisting of Patent Blue V for all non-food-producing animal species for the renewal of its authorisation (Versele-Laga NV).

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the safety and efficacy of Patent Blue V as a sensory feed additive for non-food-producing animals. The additive is already authorised for use with non-food-producing animals. The applicant has not provided evidence that the additive currently on the market complies with the existing conditions of authorisation. The FEEDAP Panel cannot conclude whether the additive remains safe for the target species due to the non-compliance with the specifications and the lack of adequate data on the potential aneugenicity of the additive. In the absence of data, the FEEDAP Panel cannot conclude on the potential of the additive to be a dermal and eye irritant nor a dermal and respiratory sensitiser. Since the potential genotoxicity of the additive was not ruled out, the exposure to the additive of the unprotected users should be minimised. The Panel retains that the previously made conclusion on the efficacy remains valid.

Safety and efficacy of a feed additive consisting of l-isoleucine produced with Corynebacterium glutamicum CGMCC 20437 for all animal species (Eppen Europe SAS).

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the safety and efficacy of l-isoleucine produced by fermentation with Corynebacterium glutamicum CGMCC 20437 as a nutritional feed additive for use in feed and in water for drinking for all animal species. The production strain is non-genetically modified, qualifies for the QPS approach to safety assessment when used for production purposes, is susceptible to the relevant antibiotics and contains no antimicrobial resistance genes of concern. No viable cells of the production strain were detected in the final product. The additive does not give rise to any safety concern regarding the production strain. l-Isoleucine produced by fermentation with Corynebacterium glutamicum CGMCC 20437 is considered safe for the target species, the consumer and the environment. Regarding the use in water, the EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) reiterates its concerns over the safety for the target species of l-isoleucine administered simultaneously via water for drinking and feed owing to the risk of nutritional imbalances and hygienic reasons. In the absence of data, the FEEDAP Panel is not in a position to conclude on the potential of l-isoleucine produced by fermentation with Corynebacterium glutamicum CGMCC 20437 to be irritant to skin and/or eyes, or as a dermal sensitiser. Due to the high dusting potential, exposure by inhalation is likely. l-Isoleucine produced by fermentation with Corynebacterium glutamicum CGMCC 20437 is considered as an efficacious source of the essential amino acid l-isoleucine for non-ruminant animal species. For the supplemental l-isoleucine to be as efficacious in ruminants as in non-ruminant species, it would require protection against degradation in the rumen.

Safety for the user of the feed additive consisting of ferric tyrosine chelate (TYFER™) for chickens, turkeys and minor poultry species for fattening or reared for laying/breeding (Akeso Biomedical, Inc).

Following a request from the European Commission, the Panel on Additives and Products or Substances used in Animal Feed (FEEDAP Panel) was asked to deliver a scientific opinion on the safety for the users of the feed additive consisting of ferric tyrosine chelate (TYFER™) when used as a zootechnical additive for chickens, turkeys and minor poultry species for fattening or reared for laying/breeding. The European Commission request follows a previous opinion of the FEEDAP Panel. In that opinion, the Panel identified several risks for the users of the additive; it was listed that it posed a risk to users by inhalation, should be considered as an irritant to skin, eyes and mucous membranes, and also that, due to its nickel content, should be considered as a dermal and respiratory sensitiser. In the current application, the applicant proposed a maximum content of nickel (50 mg/kg). No changes in the manufacturing process have been reported by the applicant. In the absence of new data, the FEEDAP Panel reiterates its previous conclusion that the additive should be as an irritant to skin, eyes and mucous membranes and as a dermal and respiratory sensitiser.