Strains In Co-culture Research Articles

Naringenin-responsive riboswitch-based fluorescent biosensor module for Escherichia coli co-cultures.

The ability to design and construct combinatorial synthetic metabolic pathways has far exceeded our capacity for efficient screening and selection of the resulting microbial strains. The need for high-throughput rapid screening techniques is of upmost importance for the future of synthetic biology and metabolic engineering. Here we describe the development of an RNA riboswitch-based biosensor module with dual fluorescent reporters, and demonstrate a high-throughput flow cytometry-based screening method for identification of naringenin over producing Escherichia coli strains in co-culture. Our efforts helped identify a number of key operating parameters that affect biosensor performance, including the selection of promoter and linker elements within the sensor-actuator domain, and the effect of host strain, fermentation time, and growth medium on sensor dynamic range. The resulting biosensor demonstrates a high correlation between specific fluorescence of the biosensor strain and naringenin titer produced by the second member of the synthetic co-culture system. This technique represents a novel application for synthetic microbial co-cultures and can be expanded from naringenin to any metabolite if a suitable riboswitch is identified. The co-culture technique presented here can be applied to a variety of target metabolites in combination with the SELEX approach for aptamer design. Due to the compartmentalization of the two genetic constructs responsible for production and detection into separate cells and application as independent modules of a synthetic microbial co-culture we have subsequently reduced the need for re-optimization of the producer module when the biosensor is replaced or removed. Biotechnol. Bioeng. 2017;114: 2235-2244. © 2017 Wiley Periodicals, Inc.

Syntrophic Interactions Within a Butane-Oxidizing Bacterial Consortium Isolated from Puguang Gas Field in China.

Butane oxidation by the hydrocarbon degradation bacteria has long been described, but little is known about the microbial interaction in this process. To investigate this interaction, the efficiency of butane oxidation was estimated in monocultures and co-cultures of six strains of butane-oxidizing bacteria (BOB) and a butanol-oxidizing strain. Results showed that the butane degradation velocity was at least 26 times higher in the co-culture of the seven strains (228.50nmolh(-1)) than in the six individual monocultures (8.71nmolh(-1)). Gas chromatographic analysis of metabolites in the cultures revealed the accumulation of butanol in the monocultures of BOB strains but not in the co-culture with the butanol-oxidizing strain. These results evidenced a novel syntrophic association between BOB and butanol-oxidizing bacteria in the butane oxidation. The BOB strains oxidized butane into butanol, but this activity was inhibited by the accumulated butanol in monocultures, whereas the removal of butanol by the butanol-oxidizing strain in co-culture could eliminate the suppression and improve the butane degradation efficiency. In the co-culture, both BOB and butanol-oxidizing bacteria could grow and the time needed for butane complete removal was shortened from more than 192h to less than 4h. The unsuppressed effect of the co-culture was also consistent with the results of reverse transcription quantitative real-time PCR (RT-qPCR) of bmoX gene because increased expression of this gene was detected during the syntrophic growth compared with that in monoculture, pointing to the upregulation of bmoX in the syntrophic interaction.

Yeast Autolysis in Sparkling Wine Aging: Use of Killer and Sensitive Saccharomyces cerevisiae Strains in Co-Culture.

Sparkling wines produced by traditional method owe their characteristics to secondary fermentation and maturation that occur during a slow ageing in bottles. Yeast autolysis plays an important role during the sparkling wine aging. Using a combination of killer and sensitive yeasts is possible to accelerate yeast autolysis and reduce maturing time. killer and sensitive Saccharomyces cerevisiae strains, separately and in co-cultures, were inoculated in base wine and bottled on pilot-plant scale. Commercial Saccaromyces bayanus strain was also investigated. Protein free amino acid and polysaccharides contents and sensory analysis were determined on the wine samples at 3, 6 and 9 months of aging. Yeast autolysis that occurs during the production of sparkling wines, obtained with co-cultures of killer and sensitive strains, has influenced free amino acids, total protein and polysaccharides content after 3 months aging time: sparkling wines, produced without the use of these yeasts, have reached the same results only after 9 months aging time. These results demonstrate that killer and sensitive yeasts in co-culture can accelerate the onset of autolysis in enological conditions, and has a positive effect on the quality of the aroma and flavor of sparkling wine. This paper offers an interesting biotechnological method to reduce production time of sparkling wine with economical benefits for the producers. We revised all patents relating to sparkling wine considering only those of interest for our study.

Prebiotic preferences of human lactobacilli strains in co-culture with bifidobacteria and antimicrobial activity against Clostridium difficile.

To evaluate robustness, prebiotic utilization of Lactobacillus paracasei F8 and Lactobacillus plantarum F44 in mono- and co-cultures with Bifidobacterium breve 46 and Bifidobacterium animalis sub sp. lactis 8:8 and antimicrobial activity of co-culture against Clostridium difficile. The two Lactobacillus strains showed a high acid and bile tolerance. Lactobacillus plantarum F44 showed maximum growth in de Man Rogosa Sharpe basal broth with glucose and lactulose compared to growth in galacto-oligosaccharides (GOS) and isomalto-oligosaccharides (IMOS). In co-culture system, the amylolytic Bif.breve 46 stimulated the growth of a nonamylolytic Lact.paracasei F8, probably by producing intermediate metabolites of starch metabolism. A higher growth of four strains Lact.paracasei F8, Lact.plantarum F44, Bif.breve 46 and Bif.animalis ssp lactis 8:8 with different prebiotic combinations was found in a MRSC basal broth with SS (soluble starch) + IMOS + GOS and IMOS + GOS respectively. The two Lactobacillus strains exhibited a high antimicrobial activity against four clinical Cl.difficile strains and a hypervirulent NAP1/027strain and suppressed the toxin titres possibly through the production of organic acids and heat stable antimicrobial proteins when grown on glucose and through the production of acids when grown on prebiotics. Culture supernatants from synbiotic combinations inhibited the growth of the Cl.difficile NAP1/027 strain and its toxin titres. Lactobacillus paracasei F8, Lact.plantarum F44 exhibited potential probiotic properties. Further, the two Lactobacillus and two bifidobacteria strains were compatible with each other and exhibited high growth in co-cultures in presence of prebiotics and SS and antimicrobial activity against clinical Cl.difficile strains and a hypervirulent NAPI/027 strain. Results are promising for the development of a multi-strain synergistic synbiotic supplement for protection against Cl.difficile infection.

Effects of the probiotic Enterococcus faecium NCIMB 10415 on selected lactic acid bacteria and enterobacteria in co-culture.

Enterococcus faecium NCIMB 10415 is used as a probiotic for piglets and has been shown to modify the porcine intestinal microbiota. However, the mode of action of this probiotic modification is still unclear. One possible explanation is the direct growth inhibiting or stimulating effect of the probiotic on other indigenous bacteria. Therefore, the aim of the present study was to examine the growth interactions of the probiotic with different indigenous porcine bacteria in vitro. Reference strains were cultivated with the probiotic E. faecium strain NCIMB10415 (SF68) in a checkerboard assay with 102 to 105 cells/ml inoculum per strain. Growth kinetics were recorded for 8 h and used to determine specific growth of the co-cultures. Additionally, total DNA was extracted from the co-cultures at the end of the incubation to verify which strain in the co-culture was affected. Co-cultivation with eight Enterococcus spp. tester strains showed strain-specific growth differences. Three of four E. faecium strains were not influenced by the probiotic strain. PCR results showed reduced growth of the probiotic strain in co-culture with E. faecium DSM 6177. Three of four Enterococcus faecalis strains showed reduced specific growth in co-culture with the probiotic strain. However, E. faecalis DSM 20478 impaired growth of the probiotic E. faecium strain. The growth of Lactobacillus johnsonii DSM 10533 and Lactobacillus reuteri DSM 20016 was enhanced in co-culture with the probiotic strain, but co-cultivations with Lactobacillus mucosae DSM13345 or Lactobacillus amylovorus DSM10533 showed no differences. Co-cultures with the probiotic E. faecium showed no impact on the growth rate of four different enterobacterial reference strains (2 strains of Salmonella enterica and 2 strains of Escherichia coli), but PCR results showed reduced cell numbers for a pathogenic E. coli isolate at higher concentration of the probiotic strain. As the in vitro effect of the probiotic E. faecium on enterococci was strain specific and the growth of certain Lactobacillus spp. was enhanced by the probiotic, these results indicate a direct effect of the probiotic on certain members of the porcine gastro intestinal microbiota.

DCT protects human melanocytic cells from UVR and ROS damage and increases cell viability

Dopachrome tautomerase (DCT) is involved in the formation of the photoprotective skin pigment eumelanin and has also been shown to have a role in response to apoptotic stimuli and oxidative stress. The effect of DCT on UVR DNA damage responses and survival pathways in human melanocytic cells was examined by knockdown experiments using melanoma cells, neonatal foreskin melanoblasts (MB) in monoculture and in co-culture with human keratinocytes. MB cell strains genotyped as either MC1R WT or MC1R RHC homozygotes, which are known to be deficient in DCT, were transduced with lentivirus vectors for either DCT knockdown or overexpression. We found melanoma cell survival was reduced by DCT depletion and by UVR over time. UVR-induced p53 and pp53-Ser15 levels were reduced with DCT depletion. Knockdown of DCT in MC1R WT and MC1R RHC MB cells reduced their survival after UVR exposure, whereas increased DCT protein levels enhanced survival. DCT depletion reduced p53 and pp53-Ser15 levels in WM266-4 melanoma and MC1R WT MB cells, while MC1R RHC MB cells displayed variable levels. Both MC1R WT and RHC genotypes of MB cells were responsive to UVR at 3h with increases in both p53 and pp53-Ser15 proteins. MC1R WT MB cell strains in coculture with keratinocytes have an increased cell survival after UVR exposure when compared to those in monoculture, a protective effect which appears to be conferred by the keratinocytes.

Selective growth-inhibitory effect of 8-hydroxyquinoline towards Clostridium difficile and Bifidobacterium longum subsp. longum in co-culture analysed by flow cytometry.

The major risk factor for Clostridium difficile infection (CDI) is the use of antibiotics owing to the disruption of the equilibrium of the host gut microbiota. To preserve the beneficial resident probiotic bacteria during infection treatment, the use of molecules with selective antibacterial activity enhances the efficacy by selectively removing C. difficile. One of them is the plant alkaloid 8-hydroxyquinoline (8HQ), which has been shown to selectively inhibit clostridia without repressing bifidobacteria. Selective antimicrobial activity is generally tested by culture techniques of individual bacterial strains. However, the main limitation of these techniques is the inability to describe differential growth dynamics of more bacterial strains in co-culture within the same experiment. In the present study, we combined fluorescent in situ hybridization and flow cytometry to describe the changes in active and non-active cells of a mixed culture formed by the opportunistic pathogen C. difficile CECT 531 and the beneficial Bifidobacterium longum subsp. longum CCMDMND BL1 after exposure to 8HQ. It was observed that without 8HQ, the proportion of both strains was almost equal, oscillating between 22.7 and 77.9 % during a time lapse of 12 h, whereas with 8HQ the proportion of active C. difficile decreased after 4 h, and persisted only between 8.8 and 17.5 %. In contrast, bifidobacterial growth was not disturbed by 8HQ. The results of this study showed the selective inhibitory effect of 8HQ on clostridial and bifidobacterial growth dynamics, and the potential of this compound for the development of selective agents to control CDIs.

Applicability of a Lactobacillus amylovorus strain as co-culture for natural folate bio-enrichment of fermented milk

The ability of 55 strains from different Lactobacillus species to produce folate was investigated. In order to evaluate folic acid productivity, lactobacilli were cultivated in the folate-free culture medium (FACM). Most of the tested strains needed folate for growth. The production and the extent of vitamin accumulation were distinctive features of individual strains. Lactobacillus amylovorus CRL887 was selected for further studies because of its ability to produce significantly higher concentrations of vitamin (81.2±5.4μg/L). The safety of this newly identified folate producing strain was evaluated through healthy experimental mice. No bacterial translocation was detected in liver and spleen after consumption of CRL887 during 7 days and no undesirable side effects were observed in the animals that received this strain. This strain in co-culture with previously selected folate producing starter cultures (Lactobacillus bulgaricus CRL871, and Streptococcus thermophilus CRL803 and CRL415) yielded a yogurt containing high folate concentrations (263.1±2.4μg/L); a single portion of which would provide 15% of the recommended dietary allowance. This is the first report where a Lactobacillus amylovorus strain was successfully used as co-culture for natural folate bio-enrichment of fermented milk.

The physiological state of Lactoccocus lactis and Propionibacterium freudenreichii strains in co-cultures induced by low temperature and osmotic stress

The bacterial physiological state, type of interactions and changes in metabolism ofLactococcus lactis and Propionibacterium freudenreichii strains in co-culture were studied in skimmed milk in response to osmotic [3% (w/v) NaCl] and low temperature (10°C) stress during long-term incubation. Changes in the integrity of cell membrane were examined by LIVE/DEAD® BacLight™ staining, and culture viability and bacterial interactions studies were performed with the use of the plate count technique. The profiles of volatile organic compounds were assessed by static headspace-gas chromatography. During the stationary growth phase, the number of LIVE cells with intact membranes was reduced in the presence of NaCl in comparison with control conditions, and a longer adaptation phase was observed at 10°C. The viability of starter cultures was high at ~108to 109 CFU/ml at the end of the experiment in all tested conditions. Our results point to the possibility of commensalisms interactions between lactic acid and propionic acid bacteria. Prolonged culture incubation contributed to the accumulation of acetoin, and it enhanced acetic acid and propionic acid synthesis during the stationary growth phase of propionic acid bacteria. Key words: Lactococcus lactis, Propionibacterium freudenreichii, viability, volatiles compounds, osmotic stress, low temperature stress.

Enhancement of probiotic activity by S-layer protein of Lactobacillus plantarum D6 strain in coculture with L. plantarum D13

Among numerous lactic acid bacteria strains isolated from autochthonous smoked fresh cheeses, potential probiotic strains were selected according to strict probiotic selection criteria. Further research revealed that the strain MCD6 was actually a coculture of two Lactobacillus plantarum strains which were identified as L. plantarum D13 and L. plantarum D6, where L. plantarum D6 expresses surface S-layer proteins of approximately 45 kDa. Since S-layer proteins, to our knowledge, have never been identified among representatives of L. plantarum species, it was of our great interest to further characterise and study its functional role in probiotic activity. Hence, the S-layer functional role in probiotic activity of coculture L. plantarum D6 and L. plantarum D13 through the comparison of important functional activities of probiotic strains was evaluated. Aggregation and coaggregation abilities, adhesion to intestinal epithelial cells in vitro, pathogen exclusion and survival in simulated conditions of gastrointestinal tract and during freeze drying, before and after guanidine hydrochloride extraction of S-layer proteins were examined in coculture and monocultures of L. plantarum D13 and L. plantarum D6, respectively. As a result it was established that coculture of two L. plantarum strains enhances their probiotic activity due to the S-layer protein of L. plantarum D6 strain.

Proximity-Dependent Inhibition in Escherichia coli Isolates from Cattle

ABSTRACT We describe a novel proximity-dependent inhibition phenotype of Escherichia coli that is expressed when strains are cocultured in defined minimal media. When cocultures of “inhibitor” and “target” strains approached a transition between logarithmic and stationary growth, target strain populations rapidly declined >4 log CFU per ml over a 2-h period. Inhibited strains were not affected by exposure to conditioned media from inhibitor and target strain cocultures or when the inhibitor and target strains were incubated in shared media but physically separated by a 0.4-μm-pore-size membrane. There was no evidence of lytic phage or extracellular bacteriocin involvement, unless the latter was only present at effective concentrations within immediate proximity of the inhibited cells. The inhibitory activity observed in this study was effective against a diversity of E. coli strains, including enterohemorrhagic E. coli serotype O157:H7, enterotoxigenic E. coli expressing F5 (K99) and F4 (K88) fimbriae, multidrug-resistant E. coli , and commensal E. coli. The decline in counts of target strains in coculture averaged 4.8 log CFU/ml (95% confidence interval, 4.0 to 5.5) compared to their monoculture counts. Coculture of two inhibitor strains showed mutual immunity to inhibition. These results suggest that proximity-dependent inhibition can be used by bacteria to gain a numerical advantage when populations are entering stationary phase, thus setting the stage for a competitive advantage when growth conditions improve.

The prevalence of virulent clonal strains of mutans streptococci in vivo and co-culture succession of the strains in vitro—Virulence potential of mutans streptococci

Purpose:To examine selected putative virulent prop-erties of mutans streptococci in two groups with dif-ferent caries activity and to examine co-culture hy-bridization of the strains in vitro. Methods: A set of strains from caries-free subjects (115) and another set from caries-active subjects (165) were isolated. Each strain was characterized for three virulence determi-nants. The clinical bacteria were then cocultured by three strains exhibiting the highest levels of virulence. Isolate colonies of last filial generation bacteria were enrichment-incubated and estimated for virulence again. RAPD-PCR and MLEE analyses were processed for parental bacteria and last filial genera-tion one. Results: No difference associated with caries activity of the subjects from whom the isolates origi-nated. Virulent properties of a filial generation strains was not different in the same generation, but was very different from their parent strains. Conclu-sion: The coexist properties of virulent polyclonal strain of MS may hold in a very general conditional sense in a dental plaque ecosystem in vivo, however, one of the co-culture strains may became dominant and displa- ced the others as the result of continuous ecological succession in vitro.

E Unibus Plurum: Genomic Analysis of an Experimentally Evolved Polymorphism in Escherichia coli

Microbial populations founded by a single clone and propagated under resource limitation can become polymorphic. We sought to elucidate genetic mechanisms whereby a polymorphism evolved in Escherichia coli under glucose limitation and persisted because of cross-feeding among multiple adaptive clones. Apart from a 29 kb deletion in the dominant clone, no large-scale genomic changes distinguished evolved clones from their common ancestor. Using transcriptional profiling on co-evolved clones cultured separately under glucose-limitation we identified 180 genes significantly altered in expression relative to the common ancestor grown under similar conditions. Ninety of these were similarly expressed in all clones, and many of the genes affected (e.g., mglBAC, mglD, and lamB) are in operons coordinately regulated by CRP and/or rpoS. While the remaining significant expression differences were clone-specific, 93% were exhibited by the majority clone, many of which are controlled by global regulators, CRP and CpxR. When transcriptional profiling was performed on adaptive clones cultured together, many expression differences that distinguished the majority clone cultured in isolation were absent, suggesting that CpxR may be activated by overflow metabolites removed by cross-feeding strains in co-culture. Relative to their common ancestor, shared expression differences among adaptive clones were partly attributable to early-arising shared mutations in the trans-acting global regulator, rpoS, and the cis-acting regulator, mglO. Gene expression differences that distinguished clones may in part be explained by mutations in trans-acting regulators malT and glpK, and in cis-acting sequences of acs. In the founder, a cis-regulatory mutation in acs (acetyl CoA synthetase) and a structural mutation in glpR (glycerol-3-phosphate repressor) likely favored evolution of specialists that thrive on overflow metabolites. Later-arising mutations that led to specialization emphasize the importance of compensatory rather than gain-of-function mutations in this system. Taken together, these findings underscore the importance of regulatory change, founder genotype, and the biotic environment in the adaptive evolution of microbes.

Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors

Both cis- and trans-regulatory mutations contribute to gene expression divergence within and between species. To estimate their relative contributions, we examined two yeast strains, BY (a laboratory strain) and RM (a wild strain), for their gene-expression divergence by microarray. Using these data and published ChIP-chip data, we obtained a set of single-regulator-regulated genes that showed expression divergence between BY and RM. We randomly selected 50 of these genes for further study. We developed a step-by-step approach to assess the relative contributions of cis- and trans-variations to expression divergence by using pyrosequencing to quantify the mRNA levels of the BY and RM alleles in the same culture (co-culture) and in hybrid diploids. Forty genes showed expression divergence between the two strains in co-culture, and pyrosequencing of the BY/RM hybrid diploids showed that 45% (18/40) can be attributed to differences in trans-acting factors alone, 17.5% (7/40) mainly to trans-variations, 20% (8/40) to both cis- and trans-acting factors, 7.5% (3/40) mainly to cis-variations, and 10% (4/40) to cis-acting factors alone. In addition, we replaced the BY promoter by the RM promoter in each of 10 BY genes that were found from our microarray data to have expression divergence between BY and RM, and in each case our quantitative PCR analysis revealed a cis effect of the promoter replacement on gene expression. In summary, our study suggests that trans-acting factors play the major role in expression evolution between yeast strains, but the role of cis variation is also important.

Régulations métaboliques de Lactococcus lactis en culture pure ou mixte dans le lait

Metabolic regulation of Laetoeoeeus Jactis grown in pure or co-culture in milk. The cell responds to environmental changes by triggering or repressing the expression of its genes in order to adapt its metabolism to the new conditions. The measure of promoter activities could thus allow an indirect assessment of the extemal signais that the cell has integrated and the modification of its metabolic potential. We have developed a method using this idea to evaluate the bacterial metabolism independently of its extemalized products. Promoter activity is measured by following the expression of luciferases as reporter genes. Two different luciferase genes were used, luxAB from the bacteria Vibrio harveyi and lue from the eucaryote Photinus pyralis. The activity of the procaryotic and the eucaryotic enzymes is detectable by on-Iine measure- ment with whole cells when the cells provide the cofactors FMNH and ATP, respectively. This method is very sensitive, aIlowing the detection of weak promoter activity, or moderate transcription at low cell density. To demonstrate that this method is efficient, we studied promoter activities modulated by the presence of available amino acids with bacterial culture in milk. This allows us to see when the cells are starving, either in pure cultures or in mixed cultures with competing bac- teria. As the two luciferases can be detected independently in the same culture, this method should allow the study of the interaction between strains in coculture at the molecular level. © InralElsevier, Paris. metabolism Iluciferase 1 metabolic probe 1 mixte culture 1 Laetoeoeeus laetis/ milk