From field to fermentation: the origins of Lactococcus lactis and its domestication to the dairy environment

AcrR1, a novel TetR/AcrR family repressor, mediates acid and antibiotic resistance and nisin biosynthesis in Lactococcus lactis F44

Lactococcus lactis, widely used in the manufacture of dairy products, encounters various environmental stresses both in natural habitats and during industrial processes. It has evolved intricate machinery of stress sensing and defense to survive harsh stress conditions. Here, we identified a novel TetR/AcrR family transcription regulator, designated AcrR1, to be a repressor for acid and antibiotic tolerance that was derepressed in the presence of vancomycin or under acid stress. The survival rates of acrR1 deletion strain ΔAcrR1 under acid and vancomycin stresses were about 28.7-fold (pH 3.0, HCl), 8.57-fold (pH 4.0, lactic acid) and 2.73-fold (300 ng/mL vancomycin) as that of original strain F44. We also demonstrated that ΔAcrR1 was better able to maintain intracellular pH homeostasis and had a lower affinity to vancomycin. No evident effects of AcrR1 deletion on the growth and morphology of strain F44 were observed. Subsequently, we characterized that the transcription level of genes associated with amino acids biosynthesis, carbohydrate transport and metabolism, multiple drug resistance and DNA repair proteins significantly upregulated in ΔAcrR1 using transcriptome analysis and quantitative reverse transcription-PCR (qRT-PCR) assays. Additionally, AcrR1 could repress the transcription of nisin post-translational modification gene, nisC, leading to a 16.3% increase in nisin yield after AcrR1 deletion. Our results not only refined the knowledge of the regulatory mechanism of TetR/AcrR family regulator in L. lactis, but presented a potential strategy to enhance industrial production of nisin.

Infective endocarditis caused by Lactococcus garvieae: A case report and review of the literature

Lactococcus garvieae is a Gram-positive coccus that can be easily misidentified as Enterococcus spp. or streptococci. Infection with L. garvieae is associated with the consumption of raw fish and unpasteurized dairy products. Although rare, it can cause infective endocarditis (IE). Herein, we report a case in which aortic valve replacement (AVR) was required for IE caused by L. garvieae. A 79-year-old Japanese man with a history of hypertension, myocardial infarction, gastroesophageal reflux disease (GERD), and abdominal aortic aneurysm presented with loss of appetite, myalgia, and difficulty in moving. Physical examination revealed a diastolic murmur, an Osler's node on the right first toe, dental caries, and a palpable spleen, suggesting IE. Transthoracic echocardiography revealed a large, mobile vegetation on the aortic valve, which was associated with severe aortic regurgitation. Blood cultures revealed L. garvieae. The patient received antibiotic therapy, underwent AVR, and recovered without major complications. To date, 30 cases of L. garvieae-associated IE have been reported. We reviewed and summarized all cases of L. garvieae-associated IE including our case.

Technological and Enzymatic Characterization of Autochthonous Lactic Acid Bacteria Isolated from Viili Natural Starters

Viili, a Finnish ropy fermented milk, is traditionally manufactured through spontaneous fermentation, by mesophilic lactic acid bacteria and yeast-like fungi, or back-slopping. This study evaluated four natural viili starters as sources of lactic acid bacteria for dairy production. Back-slopping activation of the studied viili samples was monitored through pH and titratable acidity measurements and enumeration of mesophilic lactic acid bacteria. Sixty lactic acid bacteria isolates were collected, molecularly identified, and assayed for acidification performance, enzymatic activities, production of exopolysaccharides (EPSs), presence of the histidine decarboxylase (hdcA) gene of Gram-positive bacteria, and production of bacteriocins. A neat predominance of Lactococcus lactis emerged among the isolates, followed by Enterococcus faecalis, Enterococcus faecium, Enterococcus durans, Enterococcus lactis, and Lactococcus cremoris. Most isolates exhibited proteolytic activity, whereas only a few enterococci showed lipase activity. Five isolates identified as L. cremoris, L. lactis, and E. faecalis showed a good acidification performance. Most of the isolates tested positive for leucine arylamidase, whereas only one E. durans and two L. lactis isolates were positive for valine arylamidase. A few isolates also showed a positive reaction for beta-galactosidase and alpha- and beta-glucosidase. None of the isolates produced EPSs or bacteriocins. The hdcA gene was detected in five isolates identified as L. lactis and E. faecium. A few L. cremoris and L. lactis isolates for potential use as starter or adjunct cultures for dairy processing were finally identified.

The contribution of abortive infection to preventing populations of Lactococcus lactis from succumbing to infections with bacteriophage

In the dairy industry bacteriophage (phage) contamination significantly impairs the production and quality of products like yogurt and cheese. To combat this issue, the strains of bacteria used as starter cultures possess mechanisms that make them resistant to phage infection, such as envelope resistance, or processes that render them immune to phage infection, such as restriction-modification and CRISPR-Cas. Lactococcus lactis, used to manufacture cheese and other dairy products, can also block the reproduction of infecting phages by abortive infection (Abi), a process in which phage-infected cells die before the phage replicate. We employ mathematical-computer simulation models and experiments with two Lactococcus lactis strains and two lytic phages to investigate the conditions under which Abi can limit the proliferation of phages in L. lactis populations and prevent the extinction of their populations by these viruses. According to our model, if Abi is almost perfect and there are no other populations of bacteria capable of supporting the replication of the L. lactis phages, Abi can protect bacterial populations from succumbing to infections with these viruses. This prediction is supported by the results of our experiment, which indicate that Abi can help protect L. lactis populations from extinction by lytic phage infections. However, our results also predict abortive infection is only one element of L. lactis defenses against phage infection. Mutant phages that can circumvent the Abi systems of these bacteria emerge. The survival of L. lactis populations then depends on the evolution of envelope mutants that are resistant to the evolved host-range phage.

Assessing probiotic viability in mixed species yogurt using a novel propidium monoazide (PMAxx)-quantitative PCR method

Viability is a prerequisite for any therapeutic benefits associated with the ingestion of probiotic bacteria. Current culture-based techniques are inadequate for the enumeration of probiotics in mixed-species food products. This study utilized a quantitative PCR (qPCR) method coupled with propidium monoazide (PMAxx), and novel species-specific tuf gene primers to selectively enumerate Lacticaseibacillus rhamnosus, Bifidobacterium spp., and yogurt starter cultures in mixed-species probiotic yogurt. The method was optimized for PMAxx concentration and specificity and evaluated for efficiency and applicability. PMAxx-qPCR showed high specificity to the target organisms in mixed-species yogurt, quantifying only viable cells. The linear dynamic ranges were established over five to seven orders of magnitude. The assay was reliable with an efficiency of 91-99%, R2 values > 0.99, and a good correlation to the plate count method (r = 0.882). The results of this study demonstrate the high selectivity, improved lead time, and reliability of PMAxx-qPCR over the culture-dependent method, making it a valuable tool for inline viability verification during processing and improving probiotic quality assurance for processors and consumers.

Enhancing nutritional and sensory properties of plant-based beverages: a study on chickpea and Kamut® flours fermentation using Lactococcus lactis

The study aimed to set up a protocol for the production of a clean-label plant-based beverage (PBB), obtained by mixing chickpeas and Kamut® flours and using a commercial Lactococcus lactis (LL) as fermentation starter, and to characterize it, from nutritional, microbiological, textural, shelf-life, and sensory points of view. The effect of using the starter was evaluated comparing the LL-PBB with a spontaneously fermented beverage (CTRL-PBB). Both PBBs were high in proteins (3.89/100 g) and could be considered as sources of fiber (2.06/100 g). Notably, L. lactis fermentation enhanced the phosphorus (478 vs. 331 mg/kg) and calcium (165 vs. 117 mg/kg) concentrations while lowering the raffinose content (5.51 vs. 5.08 g/100 g) compared to spontaneous fermentation. Cell density of lactic acid bacteria increased by ca. two log cycle during fermentation of LL-PBB, whereas undesirable microbial groups were not detected. Furthermore, L. lactis significantly improved the beverage's viscosity (0.473 vs. 0.231 Pa s), at least for 10 days, and lightness. To assess market potential, we conducted a consumer test, presenting the LL-PBB in "plain" and "sweet" (chocolate paste-added) variants. The "sweet" LL-PBB demonstrated a higher acceptability score than its "plain" counterpart, with 88 and 78% of participants expressing acceptability and a strong purchase intent, respectively. This positive consumer response positions the sweet LL-PBB as a valuable, appealing alternative to traditional flavored yogurts, highlighting its potential in the growing plant-based food market.

The Impact of Goat Milk Pretreatment with Pulsed Electric Fields on Cheese Quality

To reduce the microbial load in goat's milk, which is less thermally stable than cow's milk, an alternative processing method was used in this study. This involved treating the milk with pulsed electric fields (PEFs) (at 10 kV·cm-1, with 50 µs pulses for 3 Hz) and then heat-treating it at 63 °C for 6.0 s, as well as using heat treatment alone at 75 °C for 3.4 s. Cheeses were made using both types of milk treatment, and samples were collected after 5, 15, and 25 days of ripening for DNA extraction and purification, followed by high-throughput sequencing on the MiSeq Illumina sequencing platform. Analysis of the bacterial populations in the two types of cheese using various diversity indices revealed no significant differences in species richness and abundance, although there was a trend for the PEF-treated cheese to have a less diverse set of species with an uneven distribution of relative abundance. However, when examining the composition of the microbial communities in the two types of cheese using Weighted UniFrac analysis and Analysis of Similarities, there were significant differences in the presence and abundance of various species, which could have implications for the development of starter cultures. Concerning physicochemical properties (pH, aw, moisture content, total acidity and L, and a and b color parameters), the results also reveal that, generally, no significant differences were found, except for the color parameter, where cheeses treated with PEF demonstrated more whiteness (L) and yellowness (b) during ripening. Sensory scores for typicity (caprylic, goaty, and acetic) increased over time, but between treatments, only small differences were perceived by panellists in cheese with 5 days of ripening. Concerning texture firmness and cohesiveness, the PEF+HT samples presented lower values than the HT samples, even over storage time. In general, concerning quality parameters, similar behavior was observed between the treatments during the ripening period.

Tartrolon sensing and detoxification by the Listeria monocytogenes timABR resistance operon

Listeria monocytogenes is a foodborne bacterium that naturally occurs in the soil. Originating from there, it contaminates crops and infects farm animals and their consumption by humans may lead to listeriosis, a systemic life-threatening infectious disease. The adaptation of L. monocytogenes to such contrastive habitats is reflected by the presence of virulence genes for host infection and other genes for survival under environmental conditions. Among the latter are ABC transporters for excretion of antibiotics produced by environmental competitors; however, most of these transporters have not been characterized. Here, we generated a collection of promoter-lacZ fusions for genes encoding ABC-type drug transporters of L. monocytogenes and screened this reporter strain collection for induction using a library of natural compounds produced by various environmental microorganisms. We found that the timABR locus (lmo1964-lmo1962) was induced by the macrodiolide antibiotic tartrolon B, which is synthesized by the soil myxobacterium Sorangium cellulosum. Tartrolon B resistance of L. monocytogenes was dependent on timAB, encoding the ATPase and the permease component of a novel ABC transporter. Moreover, transplantation of timAB was sufficient to confer tartrolon B resistance to Bacillus subtilis. Expression of the timABR locus was found to be auto-repressed by the TimR repressor, whose repressing activity was lost in the presence of tartrolon B. We also demonstrate that tartrolon sensitivity was suppressed by high external potassium concentrations, suggesting that tartrolon acts as potassium ionophore. Our results help to map the ecological interactions of an important human pathogen with its co-residing species within their joint natural reservoir.

Lactococcus lactis, a bacterium with probiotic functions and pathogenicity

Lactococcus lactis (L. lactis) is the primary organism for lactic acid bacteria (LAB) and is a globally recognized safe microorganism for the regulation of the intestinal micro-ecological balance of animals and improving the immune performance of the host. L. lactis is known to play a commercially important role in feed fortification, milk fermentation, and vaccine production, but pathogenic L. lactis has been isolated from many clinical cases in recent years, such as the brain of silver carp with Lactococcosis, the liver and spleen of diseased waterfowl, milk samples and padding materials with cow mastitis, and blood and urine from human patients with endocarditis. In dairy farming, where L. lactis has been used as a probiotic in the past, however, some studies have found that L. lactis can cause mastitis in cows, but the lack of understanding of the pathogenesis of mastitis in cows caused by L. lactis has become a new problem. The main objective of this review is to analyze the increasingly serious clinical mastitis caused by L. lactis and combined with the wide application of L. lactis as probiotics, to comprehensively discuss the characteristics and diversity of L. lactis.

Wild-type Lactococcus lactis producing bacteriocin-like prophage lysins

Introduction

Lactococcus is a genus of lactic acid bacteria used in the dairy industry as a starter. Lactococci have been found to produce altogether more than 40 different bacteriocins, ribosomally synthesized antimicrobial proteins. All known Lactococcus spp. bacteriocins belong to classes I and II, which are mainly heat-resistant peptides. No class III bacteriocins, bigger heat-sensitive proteins, including phage tail-like bacteriocins, have been found from the Lactococcus spp. Unlike phage tail-like bacteriocins, prophage lysins have not been regarded as bacteriocins, possibly because phage lysins contribute to autolysis, degrading the host's own cell wall.

Methods

Wild-type Lactococcus lactis strain LAC460, isolated from spontaneously fermented idli batter, was examined for its antimicrobial activity. We sequenced the genome, searched phage lysins from the culture supernatant, and created knock-out mutants to find out the source of the antimicrobial activity.

Results and discussion

The strain LAC460 was shown to kill other Lactococcus strains with protease- and heat-sensitive lytic activity. Three phage lysins were identified in the culture supernatant. The genes encoding the three lysins were localized in different prophage regions in the chromosome. By knock-out mutants, two of the lysins, namely LysL and LysP, were demonstrated to be responsible for the antimicrobial activity. The strain LAC460 was found to be resistant to the lytic action of its own culture supernatant, and as a consequence, the phage lysins could behave like bacteriocins targeting and killing other closely related bacteria. Hence, similar to phage tail-like bacteriocins, phage lysin-like bacteriocins could be regarded as a novel type of class III bacteriocins.

Biochemical hydrogen potential assay for predicting the patterns of the kinetics of semi-continuous dark fermentation

The performance and kinetics response of thermophilic semi-continuous dark fermentation (DF) of simulated complex carbohydrate-rich waste was investigated at various hydraulic retention times (HRT) (2, 2.5, and 3 d) and compared with data obtained from biochemical hydrogen potential assay (BHP). A culture of Thermoanaerobacterium thermosaccharolyticum was used as the inoculum and dominated both in BHP and semi-continuous reactor. Both the modified Gompertz and first-order models described the DF kinetics well (R² = 0.97-1.00). HRT of 2.5 d was found to be optimal in terms of maximum hydrogen production rate and hydrogen potential, which were 3.97 and 1.26 times higher, respectively, than in BHP. The hydrolysis constant was highest at HRT of 3 d and was closest to the value obtained in the BHP. Overall, BHP has been shown to be a useful tool for predicting H₂ potential and the hydrolysis constant, while the maximum H₂ production rate is greatly underestimated.

Queijo Serra da Estrela PDO Cheese: Investigation into Its Morpho-Textural Traits, Microbiota, and Volatilome

Queijo Serra da Estrela is a PDO Portuguese cheese produced through coagulation of raw ewe’s milk using cardoon (Cynara cardunculus L.) flowers. The present research was aimed at depicting an up-to-date and comprehensive overview of the microbiota of Queijo Serra da Estrela cheese. To this end, viable counting and metataxonomic analysis were carried out on cheeses sampled from four Portuguese artisan producers. Physico-chemical and morpho-textural analyses were also performed, together with the analysis of volatile organic compounds (VOCs). Finally, non-starter lactic acid bacteria (NSLAB) isolated from the cheeses were characterized for their enzymatic activities using a semi-quantitative method. According to the metataxonomic analysis, Lactococcus lactis and Lactococcus piscium were the species occurring at the highest relative abundance. The isolates collected from the cheeses were assigned to Enterococcus durans, Enterococcus faecalis, Enterococcus faecium, Enterococcus lactis, Levilactobacillus brevis, Latilactobacillus graminis, Leuconostoc mesenteroides, and the Lacticaseibacillus casei group. The enzymatic characterization of these cultures highlighted esterase, aminopeptidase, acid phosphatase, beta-galactosidase, alpha-glucosidase, and beta-glucosidase among the major enzymatic activities. Fungal populations were dominated by Debaryomyces hansenii and Kurtzmaniella zeylanoides; however, species rarely found in cheese (e.g., Candida boidinii, Vishniacozyma victoriae, and Starmerella) were also detected. The volatile compounds characterizing the analyzed cheeses were carboxylic acids and esters, followed by carbonyl compounds and alcohols.

Effect of Autochthonous Lactic Acid Bacteria-Enhanced Fermentation on the Quality of Suancai

The lactic acid bacteria (LABs) used for fermentation have an extremely vital impact on the quality of Suancai, a fermented vegetable. The bacterial diversity and metabolites of inoculated Suancai with LABs, including Lactiplantibacillus plantarum (Lb. plantarum), Levilactabacillus brevis (Lb. brevis), and Leuconostoc mesenteroides (Leu. mesenteroides), were investigated. The inoculation of LABs significantly decreased the pH and the content of nitrite. The Suancai inoculated with LABs had a higher content of the total titratable acidity (TTA) and organic acids than spontaneous fermentation. The LABs inoculation significantly influenced the bacterial community structures, which directly or indirectly caused changes of metabolites. The bacterial community profiles of Suancai inoculated with Lb. plantarum were more similar to spontaneous fermentation. The inoculation of Lb. plantarum, Lb. brevis, and Leu. mesenteroides could increase its abundance in Suancai. Whatever the species inoculated, Lb. plantarum was always the predominant bacterium in Suancai after fermentation. The inoculated LABs were positively correlated with most volatile compounds and amino acids. The inoculated LABs significantly improved the volatile compounds and amino acid content of Suancai. This study could contribute to understanding the function of starters in Suancai fermentation and promote the selection of applicable starters for high-quality Suancai production.

The plasmid-encoded lactose operon plays a vital role in the acid production rate of Lacticaseibacillus casei during milk beverage fermentation

Lacticaseibacillus casei is used extensively in the fermented milk-beverage industry as a starter culture. Acid production capacity during fermentation is the main criterion for evaluating starters although it is strain-dependent. In this study, the acid production rates of 114 L. casei strains were determined and then classified into high acid (HC), medium acid (MC), and low acid (LC) groups. Comparative genomics analysis found that the lac operon genes encoding the phosphoenolpyruvate-lactose phosphotransferase system (PTS^Lac) were located on plasmids in the HC strains; however, it is notable that the corresponding operons were located on the chromosome in LC strains. Real-time PCR analysis showed that the copy numbers of lac operon genes in HC strains were between 3.1 and 9.3. To investigate the relationship between copy number and acid production rate, the lac operon cluster of the HC group was constitutively expressed in LC strains. The resulting copy numbers of lac operon genes were between 15.8 and 18.1; phospho-β-galactosidase activity increased by 1.68–1.99-fold; and the acid production rates increased by 1.24–1.40-fold, which enhanced the utilization rate of lactose from 17.5 to 42.6% in the recombinant strains. The markedly increased expression of lac operon genes increased lactose catabolism and thereby increased the acid production rate of L. casei.

Phenotype testing, genome analysis, and metabolic interactions of three lactic acid bacteria strains existing as a consortium in a naturally fermented milk

This work reports the characterization of three lactic acid bacteria (LAB) strains -Lactococcus lactis LA1, Lactococcus cremoris LA10, and Lactiplantibacillus plantarum LA30- existing as a stable consortium in a backslopping-inoculated, naturally fermented milk (NFM). This study aimed at uncovering the biochemical and genetic basis of the stability of the consortium and the cooperativity among the strains during milk fermentation. All three strains were subjected to phenotyping, covering the utilization of carbohydrates, enzyme activity, and antibiotic resistance. The strains were grown in milk individually, as well as in all possible combinations, and the resulting fermented product was analyzed for sugars, organic acids, and volatile compounds. Finally, the genomes of the three strains were sequenced and analyzed for genes associated with technological and safety properties. As expected, wide phenotypic diversity was seen between the strains. Lactococcus cremoris LA10 was the only strain to reach high cell densities and coagulate milk alone after incubation at 22°C for 24 h; congruently, it possessed a gene coding for a PrtP type II caseinolytic protease. Compared to any other fermentation, acetaldehyde concentrations were greater by a factor of six when all three strains grew together in milk, suggesting that its production might be the result of an interaction between them. Lactococcus lactis LA1, which carried a plasmid-encoded citQRP operon, was able to utilize milk citrate producing diacetyl and acetoin. No genes encoding virulence traits or pathogenicity factors were identified in any of the strains, and none produced biogenic amines from amino acid precursors, suggesting them to be safe. Lactiplantibacillus plantarum LA30 was susceptible to tetracycline, although it harbors a disrupted antibiotic resistance gene belonging to the tetM/tetW/tetO/tetS family. All three strains contained large numbers of pseudogenes, suggesting that they are well adapted ("domesticated") to the milk environment. The consortium as a whole or its individual strains might have a use as a starter or as starter components for dairy fermentations. The study of simple consortia, such as that existing in this NFM, can help reveal how microorganisms interact with one another, and what influence they may have on the sensorial properties of fermented products.

Open pangenome of Lactococcus lactis generated by a combination of metagenome-assembled genomes and isolate genomes

Lactococcus lactis (L. lactis) is a well isolated and cultured lactic acid bacterium, but if utilizing the isolate genomes alone, the genome-based analysis of this taxon would be incomplete, because there are still uncultured strains in some ecological niches. In this study, we recovered 93 high-quality metagenome-assembled genomes (MAGs) of L. lactis from food and human gut metagenomes with a culture-independent method. We then constructed a unified genome catalog of L. lactis by integrating these MAGs with 70 publicly available isolated genomes. Having this comprehensive resource, we assessed the genomic diversity and phylogenetic relationships to further explore the genetic and functional properties of L. lactis. An open pangenome of L. lactis was generated using our genome catalog, consisting of 13,066 genes in total, from which 5,448 genes were not identified in the isolate genomes. The core genome-based phylogenetic analysis showed that L. lactis strains we collected were separated into two main subclades corresponding to two subspecies, with some uncultured phylogenetic lineages discovered. The species disparity was also indicated in PCA analysis based on accessory genes of our pangenome. These various analyzes shed further light on unexpectedly high diversity within the taxon at both genome and gene levels and gave clues about its population structure and evolution. Lactococcus lactis has a long history of safe use in food fermentations and is considered as one of the important probiotic microorganisms. Obtaining the complete genetic information of L. lactis is important to the food and health industry. However, it can naturally inhabit many environments other than dairy products, including drain water and human gut samples. Here we presented an open pan-genome of L. lactis constructed from 163 high-quality genomes obtained from various environments, including MAGs recovered from environmental metagenomes and isolate genomes. This study expanded the genetic information of L. lactis about one third, including more than 5,000 novel genes found in uncultured strains. This more complete gene repertoire of L. lactis is crucial to further understanding the genetic and functional properties. These properties may be harnessed to impart additional value to dairy fermentation or other industries.

Biodiversity of wild Lactococcus lactis and their geo-spatial relationship with the environment

Lactic acid bacteria are distributed in nature, isolating themselves from diverse ecosystems and presenting a wide metabolic biodiversity. In Corrientes (Argentina), artisanal cheeses and their specific environment are an important source of autochthonous lactic acid bacteria. The objective of this work was to establish associations between the phenotypic characteristics of strains of Lactococcus lactis subsp. lactis native from Corrientes with climatological data of the Province and the characteristics of the soil and the landscapes. Physiological and biochemical characterization data of Lactococcus lactis subsp. lactis isolated from the dairy environment and from different localities of Corrientes will be used. The strains were space-located through Google Earth, flood and drought events were evaluated using Standardized Precipitation Evapotranspiration Index, and soil composition data (A and Bt horizons) in the study areas were obtained from the experimental station National Institute of Agricultural Technology - Corrientes. A statistical analysis was applied to these results (Infostat Software, Di Rienzo et al. 2008). The resulting consists in three conglomerates, differentiating strains from soils coming from "flooded landscapes" and those from "sandy hills landscape". The analysis by main components highlighted the preference of strains from flooded landscapes by a saline-alkaline environment, affecting during periods of drought, and strains from sandy hills landscape by a low medium in salts and acid soil, directly during period of high humidity resulting from previous floods.

Lactic Acid Bacteria as Biocontrol Agents against Potato (Solanum tuberosum L.) Pathogens

Biological control offers an alternative to chemical pesticides, which are inconsistent with the global trend of “going green”. Biological control includes various approaches, from natural predators to biologically produced molecules. This article focuses on the selection of lactic acid bacteria (LAB) as biological control agents against potato pathogens. The scope included evaluating the antimicrobial activity of 100 LAB strains against ten phytopatogens (Pectobacterium carotovorum, Streptomyces scabiei, Fusarium oxysporum, Fusarium sambucinum, Alternaria solani, Alternaria, tenuissima, Alternaria alternata, Phoma exigua, Rhizoctonia solani, Colletotrichum coccodes) by cross-streak plate method. HPLC determined the metabolic profiles for the most active LAB strains, and lactic acid, acetic acid, propionic acid and ethanol were found in the largest quantities. The strain Lactiplantibacillus plantarum KB2 LAB 03 was finally selected and cultured on supplemented acid whey. After the selection in laboratory tests, the strain KB2 LAB 03 was assessed in situ on seed potatoes against phytopathogens. The test showed a 40–90% reduction of eight potato pathogens infestation; only F. sambucinum and F. oxysporum were not inhibited at all. L. plantarum KB2 LAB 03 was proposed as the potential biocontrol agent for the potato protection against phytopathogens.

Calcium Determines Lactiplantibacillus plantarum Intraspecies Competitive Fitness

The importance of individual nutrients for microbial strain robustness and coexistence in habitats containing different members of the same species is not well understood. To address this for Lactiplantibacillus plantarum in food fermentations, we performed comparative genomics and examined the nutritive requirements and competitive fitness for L. plantarum strains B1.1 and B1.3 isolated from a single sample of teff injera fermentation batter. Compared to B1.1 and other L. plantarum strains, B1.3 has a smaller genome, limited biosynthetic capacities, and large mobilome. Despite these differences, B1.3 was equally competitive with B1.1 in a suspension of teff flour. In commercially sourced, nutrient-replete MRS (cMRS) medium, strain B1.3 reached 3-fold-higher numbers than B1.1 within 2 days of passage. Because B1.3 growth and competitive fitness were poor in mMRS medium (here called mMRS), a modified MRS medium lacking beef extract, we used mMRS to identify nutrients needed for robust B1.3 growth. No improvement was observed when mMRS was supplemented with nucleotides, amino acids, vitamins, or monovalent metals. Remarkably, the addition of divalent metal salts increased the growth rate and cell yields of B1.3 in mMRS. Metal requirements were confirmed by inductively coupled plasma mass spectrometry, showing that total B1.3 intracellular metal concentrations were significantly (up to 2.7-fold) reduced compared to B1.1. Supplemental CaCl₂ conferred the greatest effect, resulting in equal growth between B1.1 and B1.3 over five successive passages in mMRS. Moreover, calcium supplementation reversed a B1.3 strain-specific, stationary-phase, flocculation phenotype. These findings show how L. plantarum calcium requirements affect competitive fitness at the strain level.

IMPORTANCE Ecological theory states that the struggle for existence is stronger between closely related species. Contrary to this assertion, fermented foods frequently sustain conspecific individuals, in spite of their high levels of phylogenetic relatedness. Therefore, we investigated two isolates of Lactiplantibacillus plantarum, B1.1 and B1.3, randomly selected from a single batch of teff injera batter. These strains spanned the known genomic and phenotypic range of the L. plantarum species, and in laboratory culture medium used for strain screening, B1.3 exhibited poor growth and was outcompeted by the more robust strain B1.1. Nonetheless, B1.1 and B1.3 were equally competitive in teff flour. This result shows how L. plantarum has adapted for coexistence in that environment. The capacity for the single macronutrient calcium to restore B1.3 competitive fitness in laboratory culture medium suggests that L. plantarum intraspecies diversity found in food systems is fine-tuned to nutrient requirements at the strain level.

Cassava Starch as an Effective Texture Corrector of Fat-Free Dairy Products Based on Symbiotic Starter Culture

Cassava starch can be an effective texture corrector for dairy products; however, the presence of a starchy taste in such products is undesirable. A possible solution to this problem can be the use of partially hydrolyzed cassava starch; complex microbial amylase preparations, for instance, Amylosubtilin® or Bacillus licheniformis amylases, can be used as an enzyme. The use of these enzyme preparations in low concentration allows it to obtain cassava starches with increased solubility, which can be easily used in the technology of dairy products. Starch is partially hydrolyzed by amylase preparations and does not significantly affect the chemical composition of the protein part of the Symbilact dairy product. Positive dynamics of the rheological and antioxidant properties of the low-fat dairy product “Symbilact” from the enzyme-modified cassava starch during storage were revealed in the researches. AT starches are more able to correct the structure, especially AT-0.5 and AT-1, but to a less extent increase antioxidant properties. As matter of a fact, BT starches exhibit higher antioxidant potential, but less structure correction.

Quorum sensing signals improve the power performance and chlortetracycline degradation efficiency of mixed-culture electroactive biofilms

Electroactive biofilms (EABs) play an important role in bioelectrochemical systems due to their abilities to generate electrons and perform extracellular electron transfer (EET). Here, we investigated the effects of quorum sensing (QS) signals on power output, chlortetracycline degradation, and structure of EABs in MFCs treating antibiotic wastewater. The voltage output of MFCs with C4-HSL and PQS increased by 21.57% and 13.73%, respectively, compared with that without QS signals. The chlortetracycline degradation efficiency in closed-circuit MFCs with C4-HSL and PQS increased by 56.53% and 50.04%, respectively, which resulted from the thicker biofilms, higher biomass, and stronger activities. Additionally, QS signals induced the heterogeneous distribution of EPS for a balance between self-protection and EET under environmental pressure. Geobacter prevailed by the addition of QS signals to resist high chlortetracycline concentration. Our results provided a broader understanding on regulating EABs within electrode interface to improve their performance for environmental remediation and clean energy development.

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The voltage output of MFCs was enhanced with the addition of QS signals

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QS signals increased the bioelectrochemical degradation efficiency of CTC

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EABs exhibited heterogeneity in composition and interaction by the QS signals

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QS signals induced a balance between self-protection and EET of EABs

Physiological Roles of Short-Chain and Long-Chain Menaquinones (Vitamin K2) in Lactococcus cremoris

Lactococcus cremoris and L. lactis are well known for their occurrence and applications in dairy fermentations, but their niche extends to a range of natural and food production environments. L. cremoris and L. lactis produce MKs (vitamin K2), mainly as the long-chain forms represented by MK-9 and MK-8, and a detectable number of short-chain forms represented by MK-3. The physiological significance of the different MK forms in the lifestyle of these bacterial species has not been investigated extensively. In this study, we used L. cremoris MG1363 to construct mutants producing different MK profiles by deletion of genes encoding (i) a menaquinone-specific isochorismate synthase, (ii) a geranyltranstransferase, and (iii) a prenyl diphosphate synthase. These gene deletions resulted in (i) a non-MK producer (ΔmenF), (ii) a presumed MK-1 producer (ΔispA), and (iii) an MK-3 producer (Δllmg_0196), respectively. By examining the phenotypes of the MG1363 wildtype strain and respective mutants, including biomass accumulation, stationary phase survival, oxygen consumption, primary metabolites, azo dye/copper reduction, and proteomes, under aerobic, anaerobic, and respiration-permissive conditions, we could infer that short-chain MKs like MK-1 and MK-3 are preferred to mediate extracellular electron transfer and reaction with extracellular oxygen, while the long-chain MKs like MK-9 and MK-8 are more efficient in aerobic respiratory electron transport chain. The different electron transfer routes mediated by short-chain and long-chain MKs likely support growth and survival of L. cremoris in a range of (transiently) anaerobic and aerobic niches including food fermentations, highlighting the physiological significance of diverse MKs in L. cremoris.

Diversity Analysis of Bacterial and Function Prediction in Hurunge From Mongolia

With the continuous infiltration of industrialization and modern lifestyle into pastoral areas, the types and processing capacity of Hurunge are decreasing, and the beneficial microbial resources contained in it are gradually disappearing. The preservation and processing of Hurunge are very important for herdsmen to successfully produce high-quality koumiss in the second year. Therefore, in this study, 12 precious Hurunge samples collected from Bulgan Province, Ovorkhangay Province, Arkhangay Province, and Tov Province of Mongolia were sequenced based on the V3–V4 region of the 16S rRNA gene, and the bacterial diversity and function were predicted and analyzed. There were significant differences in the species and abundance of bacteria in Hurunge from different regions and different production methods (p < 0.05). Compared with the traditional fermentation methods, the OTU level of Hurunge fermented in the capsule was low, the Acetobacter content was high and the bacterial diversity was low. Firmicutes and Lactobacillus were the dominant phylum and genus of 12 samples, respectively. The sample QHA contained Komagataeibacter with the potential ability to produce bacterial nanocellulose, and the abundance of Lactococcus in the Tov Province (Z) was significantly higher than that in the other three regions. Functional prediction analysis showed that genes related to the metabolism of bacterial growth and reproduction, especially carbohydrate and amino acid metabolism, played a dominant role in microorganisms. In summary, it is of great significance to further explore the bacterial diversity of Hurunge for the future development and research of beneficial microbial resources, promotion, and protection of the traditional ethnic dairy products.

Extracellular vesicle formation in Lactococcus lactis is stimulated by prophage-encoded holin-lysin system

Gram-positive bacterial extracellular membrane vesicles (EVs) have been drawing more attention in recent years. However, mechanistic insights are still lacking on how EVs are released through the cell walls in Gram-positive bacteria. In this study, we characterized underlying mechanisms of EV production and provide evidence for a role of prophage activation in EV release using the Gram-positive bacterium Lactococcus lactis as a model. By applying a standard EV isolation procedure, we observed the presence of EVs in the culture supernatant of a lysogenic L. lactis strain FM-YL11, for which the prophage-inducing condition led to an over 10-fold increase in EV production in comparison with the non-inducing condition. In contrast, the prophage-encoded holin-lysin knockout mutant YL11ΔHLH and the prophage-cured mutant FM-YL12 produced constantly low levels of EVs. Under the prophage-inducing condition, FM-YL11 did not show massive cell lysis. Defective phage particles were found to be released in and associated with holin-lysin-induced EVs from FM-YL11, as demonstrated by transmission electron microscopic images, flow cytometry and proteomics analysis. Findings from this study further generalized the EV-producing phenotype to Gram-positive L. lactis, and provide additional insights into the EV production mechanism involving prophage-encoded holin-lysin system. The knowledge on bacterial EV production can be applied to all Gram-positive bacteria and other lactic acid bacteria with important roles in fermentations and probiotic formulations, to enable desired release and delivery of cellular components with nutritional values or probiotic effects.

The gut microbiome of extremely preterm infants randomized to the early progression of enteral feeding

BACKGROUND

Early progression of feeding could influence the development of the gut microbiome.

METHODS

We collected fecal samples from extremely preterm infants randomized to receive either early (feeding day 2) or delayed (feeding day 5) feeding progression. After study completion, we compared samples obtained at three different time points (week 1, week 2, and week 3) to determine longitudinal differences in specific taxa between the study groups using unadjusted and adjusted negative binomial and zero-inflated mixed models. Analyses were adjusted for a mode of delivery, breastmilk intake, and exposure to antibiotics.

RESULTS

We analyzed 137 fecal samples from 51 infants. In unadjusted and adjusted analyses, we did not observe an early transition to higher microbial diversity within samples (i.e., alpha diversity) or significant differences in microbial diversity between samples (i.e., beta diversity) in the early feeding group. Our longitudinal, single-taxon analysis found consistent differences in the genera Lactococcus, Veillonella, and Bilophila between groups.

CONCLUSIONS

Differences in single-taxon analyses independent of the mode of delivery, exposure to antibiotics, and breastmilk feeding suggest potential benefits of early progression of enteral feeding volumes. However, this dietary intervention does not appear to increase the diversity of the gut microbiome in the first 28 days after birth.

TRIAL REGISTRATION

ClinicalTrials.gov identifier: NCT02915549.

IMPACT

Early progression of enteral feeding volumes with human milk reduces the duration of parenteral nutrition and the need for central venous access among extremely preterm infants. Early progression of enteral feeding leads to single-taxon differences in longitudinal analyses of the gut microbiome, but it does not appear to increase the diversity of the gut microbiome in the first 28 days after birth. Randomization in enteral feeding trials creates appealing opportunities to evaluate the effects of human milk diets on the gut microbiome.

Impact of lactic acid bacteria and their metabolites on the techno-functional properties and health benefits of fermented dairy products

After conversion of lactose to lactic acid, several biochemical changes occur such as enhanced protein digestibility, fatty acids release, and production of bioactive compounds etc. during the fermentation process that brings nutritional and quality improvement in the fermented dairy products (FDP). A diverse range of lactic acid bacteria (LAB) is being utilized for the development of FDP with specific desirable techno-functional attributes. This review contributes to the knowledge of basic pathways and changes during fermentation process and the current research on techniques used for identification and quantification of metabolites. The focus of this article is mainly on the metabolites responsible for maintaining the desired attributes and health benefits of FDP as well as their characterization from raw milk. LAB genera including Lactobacillus, Streptococcus, Leuconostoc, Pediococcus and Lactococcus are involved in the fermentation of milk and milk products. LAB species accrue these benefits and desirable properties of FDP producing the bioactive compounds and metabolites using homo-fermentative and heterofermentative pathways. Generation of metabolites vary with incubation and other processing conditions and are analyzed and quantified using highly advanced and sophisticated instrumentation including nuclear magnetic resonance, mass-spectrometry based techniques. Health benefits of FDP are mainly possible due to the biological roles of such metabolites that also cause technological improvements desired by dairy manufacturers and consumers.

Efficiency of a probiotic in carp lactococcosis in an in vitro experiment

The purpose of this article is to study the effect of the probiotic on experimental infections of carp's fingerlings with Lactococcus garvieae. Lactic acid bacteria (LAB) (Lactobacillus fermentum 24с, Pediococcus pentosaceus 10/9к, Lactobacillus paracasei 9c) for the probiotic were previously isolated from the intestines of mature carps from Maybalyk commercial fisheries, which provided fingerlings for this experiment too as well. The feed-contained probiotic was given to fish in the experimental group for 14 days before challenge with pathogen L. garvieae. Throughout ten days after the infection, death of the fish was regularly recorded in the group, where the probiotic was not given with the feeding. Ten days after, all fish in this group died. In the probiotic group, the mortality on the tenth day after the challenge with pathogen was 10%. It was concluded the effect of the probiotic is not due to antibacterial action to the pathogen. The effectiveness of the probiotic can be associated with the displacement of the pathogen, due to the competitive adhesion and/or more likely, with the activation of the immune response from the fish organism due to the addition of the probiotic to the feed.

Serra da Estrela PDO Cheese Microbiome as Revealed by Next Generation Sequencing

Serra da Estrela PDO cheese is the oldest traditional cheese manufactured in Portugal. In this work, its microbiome as well as the main raw materials used in cheese production, raw ewes’ milk and thistle flowers (Cynara cardunculus L.), were characterized using next generation sequencing. Samples were accordingly retrieved from a local producer over two consecutive production campaigns and at different time periods within each campaign. The bacterial and fungi communities associated with each matrix were accessed through sequencing of V3–V4 and Internal Transcribed Spacer 2 regions of rRNA gene amplicons, respectively. A high microbial diversity was found associated to each matrix, differing significantly (p < 0.05) from each other. Over 500 taxa were identified in each analyzed matrix, ranging from dominant (relative abundance > 1%), sub-dominant (0.01–1%) and rare taxa (<0.01%). Specifically, in cheese, 30 taxa were present in all analyzed samples (core taxa), including species of Leuconostoc spp. and Lactococcus spp. for bacteria and Candida spp., Debaryomyces spp. and Yarrowia spp. for fungi, that were cumulatively the most prevalent genera in Serra da Estrela PDO cheese (average relative abundance ≥10%). Ultimately, this characterization study may contribute to a better understanding of the microbial dynamics of this traditional PDO product, namely the influence of raw materials on cheese microbiome, and could assist producers interested in preserving the identity, quality and safety of Serra da Estrela PDO cheese.

Research opportunities: Traditional fermented beverages in Mexico. Cultural, microbiological, chemical, and functional aspects

In Mexico, close to 200 fermented products have been described, of which, approximately 20 are beverages. They were obtained through rustic and ancestral fermentation methods by different indigenous Mexican communities; most of them were used in ceremonies, agricultural work, and other occasions. For their elaboration, different substrates obtained from plants are used, where uncontrolled and low-scale spontaneous anaerobic fermentation occurs. In Mexico, some of these products are considered as nutritional sources and functional beverages; the study of those products has revealed the presence of multiple compounds of biological importance. Additionally, elder generations attribute healing properties against diverse illnesses to these beverages. The aim of this review is to highlight the available information on twelve traditional Mexican fermented beverages, their traditional uses, and their fermentation processes along with toxicological, chemical, nutritional, and functional studies as seen from different areas of investigation. In the literature, pulque, cocoa, and pozol were the beverages with the greatest amount of described health properties; sendechó and guarapo were less characterized. Polyphenols, gallic and ferulic acid, anthocyanins and saponins were the most abundant molecules in all beverages. Finally, it is important to continue this research in order to determine the microorganisms that are involved in the fermentation process, as well as the organoleptic and beneficial properties they lend to the traditional Mexican fermented beverages.

Microbial communities and volatile profile of Queijo de Azeitão PDO cheese, a traditional Mediterranean thistle-curdled cheese from Portugal

The production of ovine or caprine milk cheeses with thistle rennet is a common practice in the Mediterranean basin. The aim of the present study was to obtain information on bacteria and yeast communities harboured by Queijo de Azeitão PDO cheese through viable counting and, for the first time, via metataxonomic analysis. Moreover, solid phase microextraction (SPME) technique was applied to characterize Queijo de Azeitão PDO cheese volatile compounds. Nine cheese samples were collected from three different artisan producers located in Portugal. The results of physico-chemical analyses showed significant differences between producers, with mean values ranging from 5.40 ± 0.25 (Producer 1) to 6.00 ± 0.22 (Producer 2). As for TTA, Producer 1 showed the highest mean value attesting at 18.04 ± 6.57 mL of 0.1 M NaOH used to reach pH 8.3. Regarding lactic acid concentration, Producer 1 showed the highest mean value attesting at 0.488 ± 0.106 g 100 g^-1, whereas, for acetic acid, no significant differences were evidenced among producers with values comprised between 0.141 ± 0.021 g 100 g^-1 and 0.245 ± 0.016 g 100 g^-1. No significant differences were observed between overall mean values of the three producers for viable counts of presumptive lactococci, thermophilic cocci, presumptive lactobacilli, thermophilic lactobacilli and total mesophilic aerobes with values in the order of 7-8 log cfu g^-1. Moreover, no significant differences were evidenced for viable counts of coagulase-negative cocci, enterococci, Enterobacteriaceae and Pseudomonadaceae. As for eumycetes, cheeses from Producer 1 showed the lowest mean value (2.78 ± 2.42 log cfu g^-1) in respect with values detected in cheeses from Producer 2 and 3. Concerning microbiota and mycobiota of the analyzed cheeses, the alpha diversity index did not show any significant difference between the three producers in terms of composition and complexity of the microbial population. A simple composition was apparently shared by the three producers, whose cheese manufactures were dominated by the presence of Leuconostoc mesenteroides (37% of the relative frequency in average), Lactococcus lactis (29%), Lacticaseibacillus zeae (4.7%), Lentilactobacillus kefiri (4.4%), Serratia spp. (3.5%), Lactiplantibacillus plantarum (2.7%), and Latilactobacillus sakei (2.5%). The mycobiota composition showed the neat dominance of Yarrowia lipolytica (46.7% of the relative frequency in average), followed by Candida ethanolica (13.6%), Kurtzmaniella zeylanoides (9.4%), Geotrichum candidum (8.8%), Galactomyces geotrichum (8.7%), Kluyveromyces lactis (3.5%), and Geotrichum silvicola (2.7%). The volatile profile analysis allowed 24 different compounds to be identified: 7 acids, 7 esters, 4 alcohols, 3 ketones, 2 aromatic hydrocarbons, and 1 aldehyde. The most represented volatile organic compounds (VOCs) were 2-butanone, butanoic acid and hexanoic acid. A positive correlation between Len. kefiri and hexanoic acid and isopentyl isobutyrate was observed (P < 0.05), whereas Y. lipolytica displayed the highest number of positive correlations with 3-methyl-butanal, 2-pentanone and 2-pentanol (P < 0.05). To the authors' knowledge, this is the very first detection of Len. kefiri in a raw ewe's milk cheese coagulated with vegetable rennet.

A review on enzyme-producing lactobacilli associated with the human digestive process: From metabolism to application

Complex carbohydrates, proteins, and other food components require a longer digestion process to be absorbed by the lining of the alimentary canal. In addition to the enzymes of the gastrointestinal tract, gut microbiota, comprising a large range of bacteria and fungi, has complementary action on the production of digestive enzymes. Within this universe of "hidden soldiers", lactobacilli are extensively studied because of their ability to produce lactase, proteases, peptidases, fructanases, amylases, bile salt hydrolases, phytases, and esterases. The administration of living lactobacilli cells has been shown to increase nutrient digestibility. However, it is still little known how these microbial-derived enzymes act in the human body. Enzyme secretion may be affected by variations in temperature, pH, and other extreme conditions faced by the bacterial cells in the human body. Besides, lactobacilli administration cannot itself be considered the only factor interfering with enzyme secretion, human diet (microbial substrate) being determinant in their metabolism. This review highlights the potential of lactobacilli to release functional enzymes associated with the digestive process and how this complex metabolism can be explored to contribute to the human diet. Enzymatic activity of lactobacilli is exerted in a strain-dependent manner, i.e., within the same lactobacilli species, there are different enzyme contents, leading to a large variety of enzymatic activities. Thus, we report current methods to select the most promising lactobacilli strains as sources of bioactive enzymes. Finally, a patent landscape and commercial products are described to provide the state of art of the transfer of knowledge from the scientific sphere to the industrial application.

Effects of a Bioprocessed Soybean Meal Ingredient on the Intestinal Microbiota of Hybrid Striped Bass, Morone chrysops x M. saxatilis

The hybrid striped bass (Morone chrysops x M. saxatilis) is a carnivorous species and a major product of US aquaculture. To reduce costs and improve resource sustainability, traditional ingredients used in fish diets are becoming more broadly replaced by plant-based products; however, plant meals can be problematic for carnivorous fish. Bioprocessing has improved nutritional quality and allowed higher inclusions in fish diets, but these could potentially affect other systems such as the gut microbiome. In this context, the effects of bioprocessed soybean meal on the intestinal bacterial composition in hybrid striped bass were investigated. Using high-throughput sequencing of amplicons targeting the V1-V3 region of the 16S rRNA gene, no significant difference in bacterial composition was observed between fish fed a control diet, and fish fed a diet with the base bioprocessed soybean meal. The prominent Operational Taxonomic Unit (OTU) in these samples was predicted to be a novel species affiliated to Peptostreptococcaceae. In contrast, the intestinal bacterial communities of fish fed bioprocessed soybean meal that had been further modified after fermentation exhibited lower alpha diversity (p < 0.05), as well as distinct and more varied composition patterns, with OTUs predicted to be strains of Lactococcus lactis, Plesiomonas shigelloides, or Ralstonia pickettii being the most dominant. Together, these results suggest that compounds in bioprocessed soybean meal can affect intestinal bacterial communities in hybrid striped bass.

Microbiological and Metagenomic Characterization of a Retail Delicatessen Galotyri-Like Fresh Acid-Curd Cheese Product

This study evaluated the microbial quality, safety, and ecology of a retail delicatessen Galotyri-like fresh acid-curd cheese traditionally produced by mixing fresh natural Greek yogurt with ‘Myzithrenio’, a naturally fermented and ripened whey cheese variety. Five retail cheese batches (mean pH 4.1) were analyzed for total and selective microbial counts, and 150 presumptive isolates of lactic acid bacteria (LAB) were characterized biochemically. Additionally, the most and the least diversified batches were subjected to a culture-independent 16S rRNA gene sequencing analysis. LAB prevailed in all cheeses followed by yeasts. Enterobacteria, pseudomonads, and staphylococci were present as <100 viable cells/g of cheese. The yogurt starters Streptococcus thermophilus and Lactobacillus delbrueckii were the most abundant LAB isolates, followed by nonstarter strains of Lactiplantibacillus, Lacticaseibacillus, Enterococcus faecium, E. faecalis, and Leuconostoc mesenteroides, whose isolation frequency was batch-dependent. Lactococcus lactis isolates were sporadic, except for one cheese batch. However, Lactococcus lactis, Enterobacteriaceae, Vibrionaceae, Salinivibrio, and Shewanellaceae were detected at fairly high relative abundances culture-independently, despite the fact that their viable counts in the cheeses were low or undetectable. Metagenomics confirmed the prevalence of S. thermophilus and Lb. delbrueckii. Overall, this delicatessen Galotyri-like cheese product was shown to be a rich pool of indigenous nonstarter LAB strains, which deserve further biotechnological investigation.

A snapshot study of the microbial community dynamics in naturally fermented cow's milk

Natural fermentation of milk is a prerequisite in the production of traditional dairy products and is considered a bioresource of fermentative microorganisms and probiotics. To understand the microbial dynamics during distinct fermentative phases, the roles of different microbes, and the relationship between bacteria and fungi, microbial community dynamics was investigated by culture-dependent and culture-independent approaches. Natural, static fermentation of milk induces the formation of the underlying curds and the superficial sour cream (Zuohe in the Mongolian language). From an overall perspective, viable LAB increased remarkably. Yeast showed an initial increase in their abundance (from 0 hr to 24 hr), which was followed by a decrease, and mold was detected at the later stages of fermentation (after 68 hr). The observed trends in microbiota variation suggest an antagonistic interaction between bacteria (LAB) and fungi (yeast and mold). The beneficial bacterial and fungal genus and species (e.g., Lactococcus, Streptococcus, Leuconostoc, Dipodascus, Lactococcus lacti, Dipodascus australiensis) are gradually increased in concentration, and the potentially detrimental microbial genus and species (e.g., Acinetobacter, Pseudomonas, Fusarium, Aspergillus, Mortierella, Acinetobacter johnsonii, Fusarium solani) decrease during the decline of bacterial and fungi diversity from natural fermentation. The study of microbial community dynamics could make a great contribution to understand the mechanism of natural fermentation of milk and the formation of curds and Zuohe, and to discover the potentially fermentative microbes for industrial starter cultures.

Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety

The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of "synthetic" microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.

Group II Introns Generate Functional Chimeric Relaxase Enzymes with Modified Specificities through Exon Shuffling at Both the RNA and DNA Level

Group II introns are large self-splicing RNA enzymes with a broad but somewhat irregular phylogenetic distribution. These ancient retromobile elements are the proposed ancestors of approximately half the human genome, including the abundant spliceosomal introns and non-long terminal repeat retrotransposons. In contrast to their eukaryotic derivatives, bacterial group II introns have largely been considered as harmful selfish mobile retroelements that parasitize the genome of their host. As a challenge to this view, we recently uncovered a new intergenic trans-splicing pathway that generates an assortment of mRNA chimeras. The ability of group II introns to combine disparate mRNA fragments was proposed to increase the genetic diversity of the bacterial host by shuffling coding sequences. Here, we show that the Ll.LtrB and Ef.PcfG group II introns from Lactococcus lactis and Enterococcus faecalis respectively can both use the intergenic trans-splicing pathway to catalyze the formation of chimeric relaxase mRNAs and functional proteins. We demonstrated that some of these compound relaxase enzymes yield gain-of-function phenotypes, being significantly more efficient than their precursor wild-type enzymes at supporting bacterial conjugation. We also found that relaxase enzymes with shuffled functional domains are produced in biologically relevant settings under natural expression levels. Finally, we uncovered examples of lactococcal chimeric relaxase genes with junctions exactly at the intron insertion site. Overall, our work demonstrates that the genetic diversity generated by group II introns, at the RNA level by intergenic trans-splicing and at the DNA level by recombination, can yield new functional enzymes with shuffled exons, which can lead to gain-of-function phenotypes.

Temperature affects substrate-associated bacterial composition during Ganoderma lucidum hyphal growth

The growth of the well-known fungus Ganoderma lucidum is influenced by temperature, which has an impact on the associated microbial structure in the substrate. In this study, we analyzed the bacterial diversity of the substrate at different temperatures using next-generation sequencing technology. A total of 513 733 sequences from 15 samples were assigned to 19 bacterial phyla. The samples were dominated by Proteobacteria, followed by Firmicutes; the 2 phyla exhibited opposite changes with elevated temperature. Bacterial genera showed different abundances at different temperatures, in which Sediminibacterium maintained a stable abundance below 40 °C, while Ochrobactrum and Rhodococcus were enriched with elevated temperature and both showed their highest abundances at 40 °C. Functional prediction uncovered 39 identified KEGG pathways, and bacterial genes involved in the membrane transport pathway exhibited the highest abundance subject to heat (40 °C) during the growth of G. lucidum. In general, our findings illustrated the influence of temperatures on G. lucidum mycelial morphology and the bacterial community in the substrate, and the results will facilitate cultivation of this fungus.

Acute oral treatment with resveratrol and Lactococcus Lactis Subsp. Lactis decrease body weight and improve liver proinflammatory markers in C57BL/6 mice

The present study aimed to evaluate the effects of resveratrol, a nutraceutical polyphenol, and Lactococcus lactis (bacteria probiotic), on metabolic parameters and hepatic proinflammatory markers expression. C57BL/6 mice were divided into 4 groups: Standard (ST), Lactococcus lactis (LL), Resveratrol (RSV), and Lactococcus lactis plus resveratrol (LL + RSV). Lactococcus lactis and resveratrol were administered by orogastric gavage. Blood parameters were assessed (total cholesterol, triglycerides, ALT and AST). IL-6 mRNA expression was evaluated by Real-time PCR and TNF-α protein expression was assessed by immunohistochemistry. The main findings showed that resveratrol and Lactococcus lactis association decreased body weight, aspartate aminotransferase and total cholesterol levels. LL and LL + RSV decreased triglycerides levels and IL-6 and TNF-α expression. These results open a perspective of using resveratrol and Lactococcus lactis to improve metabolic parameters and Lactococcus lactis in preventing inflammation and the hepatic diseases development.

Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning

Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable of biological nitrogen fixation (BNF) without containing any of the proposed essential genes for this trait (nifHDKENB). To determine the genes in Lactococcus associated with this phenotype, we selected 70 lactococci from the dairy industry that are not known to be diazotrophic to conduct a comparative population genomic analysis. This showed that the diazotrophic lactococcal genomes were distinctly different from the dairy isolates. Examining the pangenome followed by genome-wide association study and machine learning identified genes with the functions needed for BNF in the maize isolates that were absent from the dairy isolates. Many of the putative genes received an ‘unknown’ annotation, which led to the domain analysis of the 135 homologs. This revealed genes with molecular functions needed for BNF, including mucilage carbohydrate catabolism, glycan-mediated host adhesion, iron/siderophore utilization, and oxidation/reduction control. This is the first report of this pathway in this organism to underpin BNF. Consequently, we proposed a model needed for BNF in lactococci that plausibly accounts for BNF in the absence of the nif operon in this organism.

Lactococcus lactis and Resveratrol Decrease Body Weight and Increase Benefic Gastrointestinal Microbiota in Mice

BACKGROUND

The microbiome is now known for its important role in whole-body homeostasis. A dysbiosis of the normal microbiota is correlated with metabolic disorders. In this sense, the search for compounds able to modulate the microbiome is needed. Resveratrol, a natural compound found in grapes seems to be a promising candidate.

OBJECTIVE

In this study, our motivation was to evaluate the effects of the association between Resveratrol and Lactococcus lactis, a probiotic, on the composition of the gastrointestinal microbiota and body weight of mice.

METHODS

Twenty female mice were divided into 4 groups: (1) standard diet, (2) standard diet plus Lactococcus lactis, (3) standard diet plus resveratrol, and (4) standard diet plus Lactococcus lactis and resveratrol. At the end of the treatment period, samples of blood, mucus, stomach, and small and large intestines were collected for analysis. Total levels of Immunoglobulin A and Immunoglobulin E, Lac+ and Lac- bacteria and Lactobacillus were measured.

RESULTS

The main results indicate that the association between resveratrol and probiotics was able to decrease mice body weight, as compared to the other groups, in addition to decrease the number of Lac- bacteria and increasing the number of Lac+ bacteria. The levels of secretory IgA were also decreased, compared to the animals treated with only probiotics or resveratrol.

CONCLUSION

We observed potential synergism between Resveratrol and Lactococcus lactis mainly in modulating the stomach and intestinal microbiota.

An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far?

The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.

Lactococcus carnosus sp. nov. and Lactococcus paracarnosus sp. nov., two novel species isolated from modified-atmosphere packaged beef steaks

As part of a study investigating the spoilage microbiome of modified-atmosphere packaged beef from Germany, four novel strains of lactic acid bacteria were isolated and subsequently taxonomically characterized by a polyphasic approach, which revealed that they could not be assigned to known species. The isolates were Gram-staining-positive, coccoid, facultatively anaerobic, non-motile, catalase-negative and oxidase-negative. Morphological, physiological and phylogenetic analysis revealed a distinct lineage within the genus Lactococcus , with Lactococcus piscium and Lactococcus plantarum as closest relatives. Results indicated that they represented two different novel species with two strains, (TMW 2.1612T/TMW 2.1613 and TMW 2.1615T/TMW 2.1614), respectively. The two strains of both novel species shared identical 16S rRNA gene sequences but a MLSA allowed their intraspecies differentiation. The 16S rRNA gene sequences of TMW 2.1612T and TMW 2.1615T had a similarity of 99.85 % to each other and a similarity of 99.85 and 99.78 % the most closely related type strain of Lactococcus piscium , respectively. However, the ANIb value between the respective type strains TMW 2.1612T and TMW 2.1615T, and the type strain of Lactococcus piscium was only 94.3 and 92.0 %, respectively, and 92.9 % between TMW 2.1612T and TMW 2.1615T. The in silico DDH estimate value between the respective type strain TMW 2.1612T and TMW 2.1615T and the most closely related type strain of Lactococcus piscium was only 59.9 and 48.9 %, respectively, and 51.1 % between TMW 2.1612T and TMW 2.1615T. Peptidoglycan type of strain TMW 2.1612T is Lys–Thr–Ala and major fatty acids are summed feature 8 and C16 : 0. Peptidoglycan type of strain TMW 2.1615T is Lys–Ala and major fatty acids are C16 : 0, C19 : 0cyclo ω8c and summed feature 8. On the basis of polyphasic evidence, the meat isolates represent two novel species of the genus Lactococcus , for which the names Lactococcus carnosus sp. nov and Lactococcus paracarnosus sp. nov are proposed. The designated respective type strains are TMW 2.1612T (=DSM 111016T =CECT 30115T) and TWM 2.1615T (=DSM 111017T =CECT 30116T).

In Vivo Imaging with Genetically Encoded Redox Biosensors

Redox reactions are of high fundamental and practical interest since they are involved in both normal physiology and the pathogenesis of various diseases. However, this area of research has always been a relatively problematic field in the context of analytical approaches, mostly because of the unstable nature of the compounds that are measured. Genetically encoded sensors allow for the registration of highly reactive molecules in real-time mode and, therefore, they began a new era in redox biology. Their strongest points manifest most brightly in in vivo experiments and pave the way for the non-invasive investigation of biochemical pathways that proceed in organisms from different systematic groups. In the first part of the review, we briefly describe the redox sensors that were used in vivo as well as summarize the model systems to which they were applied. Next, we thoroughly discuss the biological results obtained in these studies in regard to animals, plants, as well as unicellular eukaryotes and prokaryotes. We hope that this work reflects the amazing power of this technology and can serve as a useful guide for biologists and chemists who work in the field of redox processes.

Isolation and Evaluation of Anti-Listeria Lactococcus lactis from Vegetal Sources

This chapter describes methods used to isolate, identify, and partially characterize lactic acid bacteria (LAB) which exhibit inhibitory activity against Listeria monocytogenes from foods. Vegetal (plant based) sources are rich in naturally occurring LAB and therefore provide an easily accessible source of strains with potential antimicrobial activity for use in food-processing applications. From our previous work, the majority of LAB with inhibitory activity against L. monocytogenes were identified as generally recognized as safe (GRAS) Lactococcus lactis. Although these bacteria are most commonly known for their role in industrial dairy fermentations, they are believed to have originally derived from natural plant-based habitats. These isolates with anti-Listeria activity were all found to carry the genes involved in the production of nisin, which is an approved food-grade preservative (E234). These isolates may find various applications for in situ production of nisin allowing control of L. monocytogenes in various fermented and non-fermented foods and other environments.