Explore the vast range of titles available.

Several probiotic-marketed formulations available for the consumers contain live lactic acid bacteria and/or bifidobacteria. The multispecies product commercialized as VSL#3 has been used for treating various gastro-intestinal disorders. However, like many other products, the bacterial strains present in VSL#3 have only been characterized to a limited extent and their efficacy as well as their predicted mode of action remain unclear, preventing further applications or comparative studies. In this work, the genomes of all eight bacterial strains present in VSL#3 were sequenced and characterized, to advance insights into the possible mode of action of this product and also to serve as a basis for future work and trials. Phylogenetic and genomic data analysis allowed us to identify the 7 species present in the VSL#3 product as specified by the manufacturer. The 8 strains present belong to the species Streptococcus thermophilus, Lactobacillus acidophilus, Lactobacillus paracasei, Lactobacillus plantarum, Lactobacillus helveticus, Bifidobacterium breve and B. animalis subsp. lactis (two distinct strains). Comparative genomics revealed that the draft genomes of the S. thermophilus and L. helveticus strains were predicted to encode most of the defence systems such as restriction modification and CRISPR-Cas systems. Genes associated with a variety of potential probiotic functions were also identified. Thus, in the three Bifidobacterium spp., gene clusters were predicted to encode tight adherence pili, known to promote bacteria-host interaction and intestinal barrier integrity, and to impact host cell development. Various repertoires of putative signalling proteins were predicted to be encoded by the genomes of the Lactobacillus spp., i.e. surface layer proteins, LPXTG-containing proteins, or sortase-dependent pili that may interact with the intestinal mucosa and dendritic cells. Taken altogether, the individual genomic characterization of the strains present in the VSL#3 product confirmed the product specifications, determined its coding capacity as well as identified potential probiotic functions.

During aging of human skin, a number of intrinsic and extrinsic factors cause the alteration of the skin’s structure, function and cutaneous physiology. Many studies have investigated the influence of the skin microbiome on these alterations, but the molecular mechanisms that dictate the interplay between these factors and the skin microbiome are still not fully understood. To obtain more insight into the connection between the skin microbiome and the human physiological processes involved in skin aging, we performed a systematic study on interconnected pathways of human and bacterial metabolic processes that are known to play a role in skin aging. The bacterial genes in these pathways were subsequently used to create Hidden Markov Models (HMMs), which were applied to screen for presence of defined functionalities in both genomic and metagenomic datasets of skin-associated bacteria. These models were further applied on 16S rRNA gene sequencing data from skin microbiota samples derived from female volunteers of two different age groups (25–28 years (‘young’) and 59–68 years (‘old’)). The results show that the main bacterial pathways associated with aging skin are those involved in the production of pigmentation intermediates, fatty acids and ceramides. This study furthermore provides evidence for a relation between skin aging and bacterial enzymes involved in protein glycation. Taken together, the results and insights described in this paper provide new leads for intervening with bacterial processes that are associated with aging of human skin.

The most sophisticated survival strategy Bacillus subtilis employs is the differentiation of a subpopulation of cells into highly resistant endospores. To examine the expression patterns of non‐sporulating cells within heterogeneous populations, we used buoyant density centrifugation to separate vegetative cells from endospore‐containing cells and compared the transcriptome profiles of both subpopulations. This demonstrated the differential expression of various regulons. Subsequent single‐cell analyses using promoter‐ gfp fusions confirmed our microarray results. Surprisingly, only part of the vegetative subpopulation highly and transiently expresses genes encoding the extracellular proteases Bpr (bacillopeptidase) and AprE (subtilisin), both of which are under the control of the DegU transcriptional regulator. As these proteases and their degradation products freely diffuse within the liquid growth medium, all cells within the clonal population are expected to benefit from their activities, suggesting that B. subtilis employs cooperative or even altruistic behavior. To unravel the mechanisms by which protease production heterogeneity within the non‐sporulating subpopulation is established, we performed a series of genetic experiments combined with mathematical modeling. Simulations with our model yield valuable insights into how population heterogeneity may arise by the relatively long and variable response times within the DegU autoactivating pathway. Synopsis When environmental conditions become unfavorable, the Gram‐positive model bacterium Bacillus subtilis is able to employ a number of adaptive responses, such as competence development for DNA uptake, endospore formation and the production and secretion of proteolytic enzymes (Dubnau and Lovett, 2002 ; Piggot and Losick, 2002 ; Tjalsma et al , 2004 ). Activation of the competence or sporulation pathway occurs only in part of the population (Cahn and Fox, 1968 ; Hadden and Nester, 1968 ; Chung et al , 1994 ). As there are clearly two distinguishable cell types in both cases, this phenotypic variation was described as exhibiting bistability (Fujita et al , 2005 ; Maamar and Dubnau, 2005 ; Smits et al , 2005 ; Veening et al , 2005 ). As most gene expression experiments in the stationary growth phase have been performed on the basis of population‐wide studies, little is known about the gene expression profiles of the specific subpopulations. Previous genome‐wide studies on sporulating cultures might have masked non‐sporulation‐related gene expression and putative additional levels of heterogeneity (Fawcett et al , 2000 ; Eichenberger et al , 2004 ). To reveal the expression patterns of non‐sporulating cells within isogenic sporulating cultures of B. subtilis , both a genome‐wide and a single‐cell approach were used. First, we developed a method to separate endospore‐containing cells from vegetative cells using buoyant density gradient centrifugation. The transcriptomes of the resulting subpopulations were compared using DNA‐microarray technology. This analysis revealed the occurrence of substantial heterogeneity in gene expression patterns within the isogenic B. subtilis culture. Cells either sporulate or activate a number of adaptive regulatory networks such as motility and competence development. Subsequent single‐cell analyses using promoter‐GFP fusions confirmed the microarray results and, surprisingly, revealed further heterogeneity within the non‐sporulating subpopulation (Figure 2). Only part of the cells within the vegetative subpopulation highly and transiently expresses genes encoding the extracellular proteases Bpr (bacillopeptidase) and AprE (subtilisin), both of which are under the control of the DegU transcriptional regulator (Figure 1A ). These extracellular proteases are known to act as scavenging enzymes and degrade large, complex proteins to smaller peptides, which can subsequently be taken up again as a new source of nutrients. Since these proteases and the products of their degradation activity freely disperse within the (liquid) growth medium, all cells within the clonal population are expected to benefit from their activities, indicating that B. subtilis might employ cooperative or altruistic behavior. To obtain more mechanistic insights into how such heterogeneity is generated, we performed a series of genetic experiments and developed a quantitative mathematical model that accurately describes our (genetic) observations. Our data show that degU transcription is heterogeneous and gradually increases with time in a unimodal distribution. Autoactivation of DegU is critical in reaching high levels of aprE transcription. Furthermore, phosphorylation of Spo0A, the master sporulation transcription factor, is also required to relieve the aprE promoter from repression of a number of transcriptional regulators (e.g. AbrB and SinR). Our experimental data suggest a time‐window model of how heterogeneity of aprE gene expression is generated. The temporal window for aprE expression opens when at least two conditions are satisfied. Firstly, environmental signals result in phosphorylation of Spo0A and de‐repression of negative repressors such as AbrB and SinR. Because only part of the population reaches the Spo0A∼P levels that are required to relieve the aprE promoter, only part of the population is primed to activate aprE gene expression. Secondly, an increase in the DegU phosphorylation rate (or decrease in the dephosphorylation rate) results in a higher probability of activating the degU autostimulatory loop. Thus, only cells that have high levels of both Spo0A∼P and DegU∼P will highly express aprE (Figure 1B ). The aprE expression window closes when the gradual increase of Spo0A∼P reaches the level required to initiate endospore formation (Fujita and Losick, 2005 ) and may also be affected by additional factors such as cell death or induced DegU proteolysis. Using this information, we built a qualitative mathematical model that constitutes a logic AND circuit involving the bistable sporulation pathway and the DegU autoactivation pathway (DegU system). Our model and experimental data support the hypothesis that, in the late stationary phase, the DegU system functions with parameters where only the fully activated state is operational. However, positive feedback in the system with the potential to demonstrate bistability results in slow and stochastically variable transitions from the ‘OFF’ to the ‘ON’ state. Simulations of the integrative model yield valuable insights into how aprE population heterogeneity arises from the relatively long and variable response times within the DegU system and makes testable experimental predictions. Within a late stationary phase culture of Bacillus subtilis, three distinct subpopulations of cells can be distinguished: 1) cells that sporulate, 2) cells that do not, or only to low levels express the extracellular proteases Bpr and AprE, 3) cells that highly express extracellular proteases. Heterogeneous expression of these proteases is established by a logic AND gate via the DegU and Spo0A regulatory proteins. A mathematical model was constructed which accurately describes our genetic observations and makes testable predictions of the system. Advanced time‐lapse microscopy confirms our modeling predictions on variable and long response times in aprE activation.

[This corrects the article DOI: 10.1371/journal.pone.0192452.].

The presence of bacterial spores in cocoa powders is inevitable due to the cocoa bean fermentation process, during which members of the genera Bacillus and Geobacillus are typically present. Spores are a concern in heat-treated foods when they survive heat treatments and the finished product supports germination, growth, and potentially toxin production. In this study, available methods for the enumeration of total mesophilic and thermophilic spores (TMS and TTS, respectively) were evaluated, leading to the recommendation of one global method specifically for cocoa powders. The proposed method was validated during a ring test on seven selected cocoa powders and applied during routine analyses on commercial powders. The method includes dilution of cocoa powder using buffered peptone water, heating at 80°C for 10 min for TMS and TTS counts, and heating at 100°C for 30 min for a heat-resistant (HR) spore count. Tryptic soy agar is used as a recovery medium with a maximal concentration of cocoa powder of 2.5 mg/mL (to prevent growth inhibition) and a nonnutrient agar overlay to prevent swarming of bacteria. Plates are incubated for at least 72 h at 30°C for recovery of mesophilic bacteria and 55°C for thermophilic bacteria. Suitable alternatives to specific method parameters are provided. Median values of total spore concentrations are low (<400 CFU/g for TMS and <75 CFU/g for TTS), and concentrations of HR spores are very low (<5 CFU/g). Importantly, the relation between concentrations of HR spores in cocoa powder and incidence of spoilage of heat-treated beverages containing cocoa is currently unclear. In the powders included in this study, Bacillus subtilis and Bacillus licheniformis were the predominant spore-forming species identified (49 and 39%, respectively). Both species are known for high variability in spore heat resistance. The development of reliable and sensitive molecular methods is therefore required to assess the risk of spoilage caused by spores present in cocoa powders.

Prevalence of anaemia among Nigerian toddlers is reported to be high, and may cause significant morbidity, affects brain development and function, and results in weakness and fatigue. Although, iron fortification can reduce anaemia, yet the effect on gut microbiota is unclear. This open-label randomised study in anaemic malnourished Nigerian toddlers aimed to decrease anaemia without affecting pathogenic gut bacteria using a multi-nutrient fortified dairy-based drink. The test product was provided daily in different amounts (200, 400 or 600 mL, supplying 2.24, 4.48 and 6.72 mg of elemental iron, respectively) for 6 months. Haemoglobin, ferritin, and C-reactive protein concentrations were measured to determine anaemia, iron deficiency (ID) and iron deficiency anaemia (IDA) prevalence. Faecal samples were collected to analyse gut microbiota composition. All three dosages reduced anaemia prevalence, to 47%, 27% and 18%, respectively. ID and IDA prevalence was low and did not significantly decrease over time. Regarding gut microbiota, Enterobacteriaceae decreased over time without differences between groups, whereas Bifidobacteriaceae and pathogenic E. coli were not affected. In conclusion, the multi-nutrient fortified dairy-based drink reduced anaemia in a dose-dependent way, without stimulating intestinal potential pathogenic bacteria, and thus appears to be safe and effective in treating anaemia in Nigerian toddlers.

Here, we report the draft genomes of five strains of Geobacillus spp., one Caldibacillus debilis strain, and one draft genome of Anoxybacillus flavithermus, all thermophilic spore-forming Gram-positive bacteria.

Here, we report the draft genomes of twelve isolates of five different Bacillus species, all spore-forming, Gram-positive bacteria.

Here, we report the draft genome sequences of 10 isolates of Bacillus subtilis, a spore forming Gram-positive bacterium. The strains were selected from food products and produced spores with either high or low heat resistance.

During aging of human skin, a number of intrinsic and extrinsic factors cause the alteration of the skin's structure, function and cutaneous physiology. Many studies have investigated the influence of the skin microbiome on these alterations, but the molecular mechanisms that dictate the interplay between these factors and the skin microbiome are still not fully understood. To obtain more insight into the connection between the skin microbiome and the human physiological processes involved in skin aging, we performed a systematic study on interconnected pathways of human and bacterial metabolic processes that are known to play a role in skin aging. The bacterial genes in these pathways were subsequently used to create Hidden Markov Models (HMMs), which were applied to screen for presence of defined functionalities in both genomic and metagenomic datasets of skin-associated bacteria. These models were further applied on 16S rRNA gene sequencing data from skin microbiota samples derived from female volunteers of two different age groups (25-28 years ('young') and 59-68 years ('old')). The results show that the main bacterial pathways associated with aging skin are those involved in the production of pigmentation intermediates, fatty acids and ceramides. This study furthermore provides evidence for a relation between skin aging and bacterial enzymes involved in protein glycation. Taken together, the results and insights described in this paper provide new leads for intervening with bacterial processes that are associated with aging of human skin.