Isolation of genomic DNAs from plants, fungi and bacteria using benzyl chloride

Does the genome of Sarcoleotia globosa encode a rich carbohydrate-active enzyme gene repertoire?

The lifestyles of the order Geoglossales (Geoglossomycetes, Ascomycota) remain largely unknown. Recent observations support ericoid mycorrhizal lifestyles, especially in cultured Sarcoleotia-related species. However, the currently known genomes of geoglossoid fungi encode fewer carbohydrate-active enzymes (CAZymes) in Pezizomycotina, in contrast to the abundant CAZyme repertoires found in well-known ericoid mycorrhizal fungi. The absence of assembled genomes for cultured geoglossoid fungi hinders our understanding of the genomic features related to their lifestyles. We hypothesize that the genome of Sarcoleotia globosa, a putative ericoid mycorrhizal fungus, encodes abundant CAZymes, consistent with its culturability. General features, such as smaller genome size and smaller number of genes, are shared between the genome of S. globosa strain NBRC 116039 and other geoglossalean genomes. However, the former had the most extensive CAZyme repertoire, with several enzyme families involved in plant cell wall degradation. Some of these CAZymes are not found in Geoglossales and closely related lineages. Nonetheless, the number of CAZymes from S. globosa was notably smaller than that previously reported in ericoid mycorrhizal fungi. This inconsistency may highlight not only ecophysiological variation among ericoid root mycobionts but also the specific evolution of lifestyles in Geoglossales.

Draft genome sequences of three xerophilic Aspergillus section Restricti species isolated from house dust in Japan

We present the nuclear and complete mitochondrial genome sequences of Aspergillus clavatophorus NBRC 116038, Aspergillus magnivesiculatus NBRC 116037, and Aspergillus verrucosus NBRC 115547T, all isolated from house dust in Japan. These sequence data are crucial for elucidating the evolutionary characteristics of section Restricti, a unique taxon comprising exclusively xerophilic species.

Genomic characteristics and phylogenetic relationships of Cutibacterium acnes breast milk isolates

BACKGROUND

Cutibacterium acnes is one of the most commonly found microbes in breast milk. However, little is known about the genomic characteristics of C. acnes isolated from breast milk. In this study, the sequencing and assembly results of 10 C. acnes isolates from breast milk were compared with the genomic data of 454 strains downloaded from NCBI, and the characteristics of breast milk isolates from various perspectives, including phylogeny, genomic characteristics, virulence genes, drug resistance genes, and carbohydrate utilization, were elucidated.

RESULTS

The findings of this study revealed no differences between the breast milk isolates and other isolates in terms of genomic features, phylogenetic relationships, virulence, and resistance-related genes. However, breast milk-derived isolates exhibited significantly lower copies of the carbohydrate metabolic enzyme genes GT5 and GT51 (P < 0.05) and a higher copy number of the GH31 gene (P < 0.05) than others. C. acnes primarily consists of three genetic branches (A, B, and C), which correspond to the three subspecies of C. acnes (C. acnes subsp. elongatum, C. acnes subsp. defendens, C. acnes subsp. acnes). The genetic differences between branches B and C were smaller than that between branch A. Branches A and B carry a higher number of copies of carbohydrate enzymes, including CE1, CE10, GH3, and CBM32 than branch C. Branches B and C possess the carbohydrate enzymes PL8 and GH23, which are absent in branch A. Core genes, core intergenic regions, and concatenated sequences of core genes and core intergenic regions were compared to construct a phylogenetic tree, and it was found that core intergenic regions could be used to describe phylogenetic relationships.

CONCLUSIONS

It is therefore speculated that the C. acnes in breast milk originates from the nipple or breast surface. This study provides a novel genetic basis for genetic differentiation of C. acnes isolates from breast milk.

Species Diversity and Distribution of Non-fumigatus Aspergillus Species in Ogasawara Islands, Japan

Aspergillus sections Flavi, Nigri, and Terrei are known as common causative agents of aspergillosis, followed by section Fumigati. A previous study investigated the distribution of section Fumigati in Izu and Ogasawara Islands and found that the dominant species changes depending on the soil environment. This study investigated the species diversity and distribution of sections Flavi, Nigri, and Terrei in Mukojima, Hahajima, and Chichijima of Ogasawara Islands and clarified whether the dominant species vary depending on the soil environment, as in section Fumigati. The strains were isolated from soil samples collected in 2019 and 2020 at 18 sites in three islands, including different landscapes, and species identification was based on the nucleotide sequence of the calmodulin gene. Overall, 172 strains were isolated from all sites and identified to seven section Flavi, five section Nigri, and three section Terrei species. Three section Flavi, three section Nigri, and one section Terrei species have been reported as causative agents of aspergillosis. Three sections were distributed in Chichijima and Hahajima, but only section Nigri was found in Mukojima. The frequency of occurrence of Aspergillus tamarii and Aspergillus nomiae belonging to section Flavi and Aspergillus niger and Aspergillus tubingensis belonging to section Nigri were > 60% in forests, including shrub forests, whereas that of Aspergillus floccosus belonging to section Terrei was > 40% in bare land and grassland. Aspergillus pseudonomiae belonging to section Flavi was isolated at > 40% frequency of occurrence regardless of the landscape. Thus, differences of soil environments affected the distribution of the dominant species belonging to three sections.

Genetic diversity and population structure of Alternaria alternata: An endophytic fungus isolated from various hosts

Alternaria alternata is a significant fungal species that can function as both an endophytic fungus and a pathogen in various plant tissues. Unlike pathogenic fungi, endophytic fungi enhance the growth of host plants through different mechanisms. Studying the genetic diversity of endophytic fungi can provide insights into their co-evolution with plants. In this research, the genetic diversity of A. alternata from different hosts was examined using ten pairs of ISSR primers. Seven of the ten primers generated scorable polymorphic bands (total of 65 bands with an average of 9.2 bands per primer) for molecular analysis. Genetic diversity parameters revealed that isolates from Gundelia tournefortii exhibited the highest genetic diversity (Na, Ne, I, and He values of 1.55, 1.45, 0.35, and 0.24, respectively), while isolates from Tamarix ramosissima showed lower diversity (Na, Ne, I, and He values of 1.18, 1.13, 0.11, and 0.07, respectively). Cluster analysis grouped the isolates into four clusters based on Jaccard similarity matrix and UPGMA method. Principal coordinate analysis (PCOA) supported the cluster analysis findings. Analysis of molecular variance (AMOVA) indicated a high level of genetic differentiation within populations (72 %), with only 28 % of diversity between populations. The genetic structure assessment revealed a relatively strong genetic structure among populations, suggesting the presence of a hidden sexual cycle or mitotic recombination as factors contributing to the high genetic differentiation among A. alternata populations.

Gut microbiota modulation and amino acid absorption by Lactiplantibacillus plantarum TWK10 in pea protein ingestion: TWK10 boosts hut microbiota, amino acid uptake

For vegetarians or vegan athletes, improving the utilization of plant-based protein and the absorption of amino acids is crucial. This study explored the impact of combining pea protein with Lactiplantibacillus plantarum TWK10 and resistance training on amino acid absorption and exercise performance. Sixteen male and sixteen female participants were randomly assigned to either a control group (20 g of pea protein without TWK10) or a TWK10 group (20 g of pea protein combined with 1 × 1010 colony-forming units of TWK10). After 28 days of supplementation combined with resistance exercise training three times per week. All subjects underwent body composition and muscle strength performance, plasma and fecal samples were collected for microbiota analysis and blood amino acid concentrations. The TWK10 group showed a significant increase in muscle thickness and improvements were observed in 1 repetition maximum bench press, explosive, anaerobic power output compared to before the intervention, and were significantly higher than those in the control group (p < 0.05). TWK10 supplementation significantly increased the area under the curve and maximum concentration of branched-chain amino acids, essential amino acids, and total amino acids (p < 0.05). Furthermore, TWK10 supplementation effectively increased the richness of gut bacterial families. Our study demonstrated that the TWK10 significant increase in the abundance of specific bacterial families in the gut, resulting in increased pea protein amino acid absorption. Moreover, increasing muscle mass and significantly improving muscle thickness, muscle strength, power, and anaerobic capacity.

Two novel Archaeorhizomyces species isolated from ericoid mycorrhizal roots and their association with ericaceous plants in vitro

Archaeorhizomyces is a diverse and ubiquitous genus of the subphylum Taphrinomycotina, which contains soil-inhabiting/root-associated fungi. Although ecological importance and root-associating lifestyles of Archaeorhizomyces can be postulated, morphological aspects of fungal body and root colonization are largely unknown due to the scarcity of cultures. We obtained three unidentified Archaeorhizomyces isolates from ericoid mycorrhizal (ErM) roots of Rhododendron scabrum and Rhododendron × obtusum collected in Japan. To advance our understanding of lifestyle of the genus, we investigated their general morphology, phylogeny, and in vitro root-colonizing ability in ericoid mycorrhizal hosts, Vaccinium virgatum and Rhododendron kaempferi. Some morphological characteristics, such as slow glowing white-to-creamy-colored colonies and formation of yeast-like or chlamydospore-like cells, were shared between our strains and two described species, Archaeorhizomycesfinlayi and Archaeorhizomyces borealis, but they were phylogenetically distant. Our strains were clearly distinguished as two undescribed species based on morphology and phylogenetic relationship. As seen in typical ErM fungi, both species frequently formed hyphal coils within vital rhizodermal cells of ErM plants in vitro. The morphology of hyphal coils was also different between species. Consequently, two novel species, Archaeorhizomyces notokirishimae sp. nov. and Archaeorhizomyces ryukyuensis sp. nov., were described.

Synergistic effect of two bacterial strains promoting anaerobic digestion of rice straw to produce methane

A large amount of agricultural waste causes global environmental pollution. Biogas production by microbial pretreatment is an important way to utilize agricultural waste resources. In this study, Sporocytophaga CG-1 (A, cellulolytic strain) was co-cultured with Bacillus clausii HP-1 (B, non-cellulolytic strain) to analyze the effect of pretreatment of rice straw on methanogenic capacity of anaerobic digestion (AD). The results showed that weight loss rate of filter paper of co-culture combination is 53.38%, which is 29.37% higher than that of A. The synergistic effect of B on A can promote its degradation of cellulose. The cumulative methane production rate of the co-culture combination was the highest (93.04 mL/g VS substrate), which was significantly higher than that of A, B and the control group (82.38, 67.28 and 67.70 mL/g VS substrate). Auxiliary bacteria can improve cellulose degradation rate by promoting secondary product metabolism. These results provide data support for the application of co-culture strategies in the field of anaerobic digestion practices.

Mining Tamarix ramosissima roots for endophytic growth promoting fungi to improve wheat root growth

Endophytic fungi are commonly found in the root endosphere and can enhance plant growth through various mechanisms. The aim of this study was to isolate cultivable endophytic fungi associated with the roots of Tamarix ramosissima and to evaluate their plant growth promoting properties. About 35 isolated fungal endophytes belonging to the Ascomycota from four different genera were isolated from the endosphere of T. ramosissima: Alternaria, Aspergillus, Fusarium and Talaromyces. These fungal endophytes showed different abilities to solubilize phosphate and produce indole-3-acetic acid (IAA). The fungal isolates of T. allahabadensis (T3) and A. niger (T4) showed different efficiency in solubilizing phosphate. Almost all fungal isolates were able to produce IAA, and the highest value (0.699 μg/ml) was found in the isolate of F. solani (T11). Inoculation of wheat seeds with endophytic fungi significantly increased the initial growth of wheat roots. The results showed that inoculation with the endophytic fungus A. fumigatus T15 significantly increased root length by 75%. The extensive root system of T. ramosissima may be due to symbiosis with IAA-producing endophytic fungi, which enhance root development and water uptake in dry conditions. These fungi can also boost soil phosphorus levels, promoting plant growth.

Supplementation with Lactiplantibacillus brevis GKEX Combined with Resistance Exercise Training Improves Muscle Mass, Strength Performance, and Body Fat Condition in Healthy Humans

In addition to maintaining good exercise and dietary habits, recent studies have shown that probiotics may have potential benefits for muscle mass and strength. It is worth noting that the effects may vary depending on the specific strains used. To date, no studies have analyzed the effects of Lactiplantibacillus brevis in this context. Here, we combine the L. brevis strain GKEX with resistance training to further understand its effects on muscle mass, thickness, performance, and fat loss. In a six-week intervention for a double-blind randomized trial, 52 healthy subjects were divided into two groups (10 male and 16 female participants in each group): a placebo group (two capsules/day, containing 0 CFU of GKEX per capsule) and a GKEX group (two capsules/day, containing 1 × 1010 CFU of GKEX per capsule). Before the intervention, no differences were observed between the two groups in any of the tests (body composition, muscle thickness, exercise performance, and blood parameters). However, supplementation with GKEX significantly improved muscle mass and thickness, as well as grip strength, muscle strength, and explosive performance, when compared to the associated parameters before the intervention. Additionally, GKEX supplementation promoted a reduction in the body fat percentage (p < 0.05). Through analysis of the change amount, we observed that GKEX supplementation yielded significantly improved benefits when compared to the placebo group (p < 0.05). In summary, our findings support the notion that a six-week resistance exercise training program combined with L. brevis GKEX supplementation has superior additive effects that enhance muscle mass and strength performance, while also reducing body fat percentage. This intervention can promote muscle gain and fat loss.

In Vitro Assessment of Postbiotic and Probiotic Commercial Dietary Supplements Recommended for Counteracting Intestinal Dysbiosis in Dogs

Many environmental aspects influence the preservation of a beneficial microbiome in dogs, and gut dysbiosis occurs when imbalances in the intestinal ecosystem cause functional changes in the microbial populations. The authors evaluated the effects of two specific commercial dietary supplements: a combination of a postbiotic and prebiotics (Microbiotal cane®) and a probiotic product (NBF 1®) recommended for counteracting intestinal dysbiosis in dogs, on the gut canine microbiota composition and its metabolic activities (production of short-chain fatty acids). The investigation was performed using an in vitro fermentation system inoculated with dog fecal samples. Microbiotal cane® promoted a more immediate increase in Lactobacillus spp. after the first 6 h of fermentation, whereas NBF 1® promoted the increase at the end of the process only. The two supplements supported an increase in the Bifidobacterium spp. counts only after 24 h. The in vitro abilities of Microbiotal cane® and NBF 1® to increase selectively beneficial bacterial groups producing acetic, propionic, and butyric acids suggest a possible positive effect on the canine gut microbiota, even if further in vivo studies are needed to confirm the beneficial effects on the intestinal health.

Talaromyces mellisjaponici sp. nov., a xerophilic species isolated from honey in Japan

Five isolates of a xerophilic Talaromyces species were obtained from honey in Japan. Molecular phylogenetic analysis based on a combined dataset for four regions (rRNA internal transcribed spacer, β-tubulin, calmodulin and RNA polymerase II second largest subunit) revealed that the strains formed an independent clade in section Trachyspermi, which is sister to Talaromyces affinitatimellis, Talaromyces basipetosporus and Talaromyces speluncarum. The strains and their relatives have different growth on creatine agar, yeast extract sucrose agar and dichloran 18 % glycerol agar, different branching patterns (mostly monoverticillate or biverticillate, less frequently divaricate or terverticillate), and different sizes and surface structures of conidia. Xerotolerance tests were also conducted using media adjusted to five different sucrose concentrations (0, 20, 40, 60 and 80 %). The colony diameters of the strains were larger than those of T. affinitatimellis, T. basipetosporus and T. speluncarum at each sucrose concentration. Altogether, the obtained morphological, molecular and physiological data allowed the proposal of Talaromyces mellisjaponici sp. nov. for this novel species, with NBRC 116048T as the type strain.

Aspergillus verrucosus sp. nov., a xerophilic species isolated from house dust and honey in Japan

Three strains of a xerophilic Aspergillus species were isolated from house dust and honey in Japan. A molecular phylogenetic analysis based on the combined dataset for four regions (internal transcribed spacer rDNA, calmodulin, β-tubulin, and RNA polymerase II second largest subunit) revealed that the strains formed an independent lineage, sister to Aspergillus halophilicus classified in section Restricti. Morphological comparisons show that the strains differ from A. halophilicus in three aspects: (i) the size of cleistothecia, as well as the surface structure and size of ascospores, (ii) the ability to grow on Harrold's agar and dichloran 18 % glycerol agar, and (iii) the lack of conidiophore formation on potato dextrose agar +20 % NaCl. These strains could be clearly distinguished from all known Aspergillus section Restricti species. Therefore, we consider it to be a novel species and propose the name Aspergillus verrucosus sp. nov. (NBRC 115547^T).

Effects of probiotic Lactiplantibacillus plantarum IMC 510 supplementation on metabolic factors in otherwise healthy overweight and obese individuals

AIMS

Probiotic supplementation approach offers the possibility to shape the gut microbiota (GM), enabling the development of innovative formulations able to improve intestinal well-being and consequently the related body weight modulation and energy metabolism. In the present clinical study, a new potential probiotic supplement based on Lactiplantibacillus plantarum IMC 510 was studied for weight management.

METHODS AND RESULTS

Quantitative characterization by qPCR of representative bacterial groups of GM was used to determine the microbiota modulation at different supplementation periods. Furthermore, measurement of the endpoints linked to weight control (body mass index, body weight, waist circumference) was assessed. Specific questionnaires to evaluate the impact on psychological and physiological point of view were performed. Results showed that after 90 days, Lact. plantarum IMC 510 supplementation brought an improvement in endpoints linked to weight control and healthy status, although no significant changes in the microbiota composition were reported for analysed bacterial groups, except for Lactobacillus spp. and Bifidobacterium spp.

CONCLUSIONS

We concluded that Lact. plantarum IMC 510 supplementation could be an interesting tool for weight management. More studies are needed to understand the impact on GM, for example, evaluating the production of short-chain fatty acids, since their important role in dietary metabolism. Further research is necessary to better elucidate the relationship between GM and overweight and the mechanism of action by which Lact. plantarum IMC 510 modifies body weight.

SIGNIFICANCE AND IMPACT OF THE STUDY

However, these promising outcomes represent a clear advantage of probiotic supplementation and identify a new potential probiotic as a novel and safe therapeutic approach in the obesity prevention and management.

Species Diversity based on Revised Systematics of Xerophilic Aspergillus section Restricti Isolated from Storage Rooms and Houses in Japan

Eighty-seven strains of Aspergillus section Restricti were isolated from five storage rooms (50 strains) and 21 houses (37 strains) between 2014 and 2020. Eleven species were identified based on their morphological characteristics and molecular phylogeny using the rRNA internal transcribed spacer (ITS) region, calmodulin (CaM), β-tubulin (benA), and RNA polymerase II second largest subunit (RPB2) sequences. A. penicillioides, which was known to cause the deterioration of cultural assets, was isolated at high frequency (73%) from the surfaces of 11 cultural assets in the storage rooms; A. clavatophorus and A. magnivesiculatus, which are closely related to A. penicillioides, were also isolated frequently (45 and 64%, respectively). Five species [A. clavatophorus (42.8%), A. penicillioides (42.8%), A. magnivesiculatus (14.3%), A. reticulatus (28.6%), and A. vitricola (28.6%)] were isolated from dust on the carpets in seven houses. Five species [A. clavatophorus (33.3%), A. penicillioides (55.5%), A. magnivesiculatus (44.4%), A. restrictus (44.4%), and A. gracilis (11.1%)] were isolated from dust on the bedding in nine houses. Using the taxonomic system described by Sklenář et al. (2017), five species (A. clavatophorus, A. magnivesiculatus, A. hordei, A. reticulatus, and A. glabripes) previously identified as A. penicillioides were confirmed as new to Japan.

Hydrogenophilus thiooxidans sp. nov., a moderately thermophilic chemotrophic bacterium unable to grow on hydrogen gas, isolated from hot spring microbial mats

A novel thermophilic chemotrophic bacterium, strain SS56T, was isolated from Nakabusa Hot Spring, Japan. The isolate was a rod-shaped (1.5–2.1×0.6–0.8 µm), Gram-stain-negative bacterium. The cells of this strain grew chemoheterotrophically under aerobic and anaerobic conditions. Autotrophic growth was observed with thiosulphate and elemental sulphur under aerobic conditions but not with H2 as the electron donor. Heterotrophic growth in the presence of O2 occurred on yeast extract, tryptone, polypeptone and organic acids. Strain SS56T used nitrite as an alternative electron acceptor under anaerobic chemoheterotrophic conditions. The isolate grew between 35 and 65 °C, with the optimum at 55 °C. The pH range for growth was pH 6.0–9.0; optimal growth occurred at pH 7.0–8.0. The 16S rRNA gene sequence of strain SS56T was 98.9% identical to that of Hydrogenophilus thermoluteolus TH-1T. The draft genome sequence of 2401804 bp for strain SS56T gave values of 53.7% for digital DNA–DNA hybridization, 92.9% for average nucleotide identity and 93.6% for average amino acid identity compared with the genome sequence of 2223143 bp for H. thermoluteolus TH-1T. Based on the information described above, strain SS56T (=DSM 111892T=JCM 34254T) is proposed as the type strain of a novel species, Hydrogenophilus thiooxidans sp. nov.

Isolation and Characterization of Commensal Bifidobacteria Strains in Gut Microbiota of Neonates Born Preterm: A Prospective Longitudinal Study

Bifidobacterial population dynamics were investigated using a longitudinal analysis of dominant species isolated from feces of neonates born preterm (singletons (n = 10), pairs of twins (n = 11)) from birth up to 16 months of age. We performed quantification, isolation, and identification of the dominant bifidobacteria strains. The genetic relationship of the isolates was investigated via pulsed field gel electrophoresis (PFGE) genotyping, and PCR was used to screen the specific genetic marker tet genes. Additionally, all of the isolated strains were phenotypically characterized by their response to gastro-intestinal stresses and the MIC determination of tetracycline. In the same individual, our results showed a turnover of the bifidobacteria dominant population not only at species but also at strain levels. In addition, we found clonally related strains between twins. A minority of strains were tolerant to gastric (6%) and intestinal (16%) stresses. Thirteen percent of the strains were resistant to tetracycline. This work is original as it provides insights at the strain level of the early life in vivo dynamics of gut microbiota bifidobacteria in preterm neonates. It highlights the need to take into consideration the fluctuation of bifidobacteria populations that may occur for one individual.

Construction of a fungal consortium for effective degradation of rice straw lignin and potential application in bio-pulping

To improve the lignin degradation efficiency, we established a co-culture consortium (LDFC) consisting of Trametes hirsuta BYL-3, Trametes versicolor BYL-7 and Trametes hirsuta BYL-8. The testing results showed that the constructed consortium showed improved the lignin degradation rate by fungi. The optimal cultivation conditions were mixture at 1:1:1 vol ratio of each fungus, 7% (w/v) of inoculum amount, culture temperature at 26 °C, pH was 6.9 and 10 days of culturing time. Under these conditions, the degradation rate of lignin was 39.7%, which was 9.3% higher than those before optimization (30.4%). Using rice straw for treatment by LDFC to papermaking, the paper tensile strength was 8 N, and the ring pressure index was 2.46 N·m/g, which meets the standards for the production of corrugated paper for packaging. These results indicate that LDFC has potential application value to convert rice straw resources for bio-pulping to make papers.

The accuracy and clinical impact of the morphological identification of Aspergillus species in the age of cryptic species: A single-centre study

BACKGROUND

Aspergillus spp. is identified morphologically without antifungal susceptibility tests (ASTs) in most clinical laboratories. The aim of this study was to examine the clinical impact of the morphological identification of Aspergillus spp. to ensure the adequate clinical management of Aspergillus infections.

PATIENTS/METHODS

Aspergillus isolates (n = 126) from distinct antifungal treatment-naïve patients with aspergillosis were first identified morphologically, followed by species-level identification via DNA sequencing. An AST for itraconazole (ITC) and voriconazole (VRC) was performed on each Aspergillus isolate.

RESULTS

Based on the genetic test results, morphology-based identification was accurate for >95% of the isolates at the species sensu lato level although the test concordance of Aspergillus spp. with low detection rates was low. The rates of cryptic species were found to be 1.2% among the isolates of A. fumigatus complex and 96.8% in the A. niger complex. Cryptic species with lower susceptibilities to antifungal drugs than sensu stricto species among the same Aspergillus section were as follows: The A. lentulus (n = 1) isolates had low susceptibilities to azoles among the A. fumigatus complex species (n = 86), and A. tubingensis isolates (n = 18) exhibited lower susceptibility to azoles among the A. niger complex species (n = 31).

CONCLUSION

Diagnostic accuracy was high at the A. fumigatus and A. niger complex level. However, in the presence of cryptic species, a solely morphological identification was insufficient. Particularly, ITC and VRC might be inappropriate for aspergillosis treatment when the A. niger complex is identified morphologically because it is possible that the Aspergillus isolate is A. tubingensis.

Supplementation with Lactiplantibacillus plantarum IMC 510 Modifies Microbiota Composition and Prevents Body Weight Gain Induced by Cafeteria Diet in Rats

Changes in functionality and composition of gut microbiota (GM) have been associated and may contribute to the development and maintenance of obesity and related diseases. The aim of our study was to investigate for the first time the impact of Lactiplantibacillus (L.) plantarum IMC 510 in a rat model of diet-induced obesity, specifically in the cafeteria (CAF) diet. This diet provides a strong motivation to voluntary overeat, due to the palatability and variety of selected energy-dense foods. The oral administration for 84 days of this probiotic strain, added to the CAF diet, decreased food intake and body weight gain. Accordingly, it ameliorated body mass index, liver and white adipose tissue weight, hepatic lipid accumulation, adipocyte size, serum parameters, including glycemia and low-density lipoprotein levels, in CAF fed rats, potentially through leptin control. In this scenario, L. plantarum IMC 510 showed also beneficial effects on GM, limiting the microbial imbalance established by long exposure to CAF diet and preserving the proportion of different bacterial taxa. Further research is necessary to better elucidate the relationship between GM and overweight and then the mechanism of action by which L. plantarum IMC 510 modifies weight. However, these promising results prompt a clear advantage of probiotic supplementation and identify a new potential probiotic as a novel and safe therapeutic approach in obesity prevention and management.

Bacterial and fungal communities of traditional fermented Chinese soybean paste (Doujiang) and their properties

Soybean paste (Doujiang) is one of the traditional fermented foods from China, fermented by various microorganisms. However, the microflora of Doujiang keeps little known. In this study, the microbial communities of seven kinds of representative Doujiang samples were investigated by both culture-independent and culture-dependent methods. We found that core OTUs among seven Doujiang samples were mainly from Bacillus, Pseudomonas, Candida, and Aspergillus according to Illumina sequencing. Every type of Doujiang sample harbored a different composition of microbial community. Doujiang LSJ and LBJ had the highest bacterial and fungal richness and diversity, respectively. The structure of microbial community was remarkably correlated with Doujiang properties-pH, and the content of total protein, soluble protein, amino acid, and total sugar (p < .05). Bacillus spp. were most frequently isolated bacterial species. Fungi of Monascus, Candida, and Aspergillus were also isolated. Eleven microbial strains showed high protease activities to degrade corn proteins, which can form obvious transparent hydrolytic circles in corn gluten meal medium plates. Therefore, microbial communities were supposed to tightly connect to Doujiang type and properties. It is possible to apply potential protein-degrading microbial strains to corn byproducts for protein production in the future study.

Isolation and Characterization of Nickel-Tolerant Trichoderma Strains from Marine and Terrestrial Environments

Nickel contamination is a serious environmental issue that requires immediate action. In this study, 23 strains of Trichoderma were isolated from terrestrial and marine environments and identified using a polyphasic approach of morphological characterization and ITS gene sequence analysis. The Trichoderma strains were tested for their tolerance and biosorption of nickel. Our results showed the growth of all Trichoderma strains on Trichoderma Selective Medium (TSM) with 50–1200-ppm nickel, indicating their tolerance of this heavy metal even at a relatively high concentration. Six Trichoderma strains (three isolated from terrestrial substrates and three from marine substates) had the highest radial growth on TSM with 50-ppm Ni. Among these fungal isolates, Trichoderma asperellum (S03) isolated from soil exhibited the best growth after 2 days of incubation. For the biosorption of nickel, the accumulation or uptake efficiency by the six selected Trichoderma was determined in Potato Dextrose Broth (PDB) supplemented with 50-ppm Ni using a Flame Atomic Absorption Spectrophotometer (AAS). The percent uptake efficiency of the three strains of T. asperellum (S03, S08, and LL14) was computed to be up to 66%, while Trichoderma virens (SG18 and SF22) and Trichoderma inhamatum (MW25) achieved up to 68% uptake efficiency. Observation of the Trichoderma strains with Scanning Electron Microscopy (SEM) before and after the absorption of nickel showed very minimal damage on the hyphal and conidial surface morphology, but changes in the colonial characteristics were observed. Our study highlighted the potential of terrestrial and marine strains of Trichoderma for the bioremediation of nickel pollution.

A capsule-associated gene of Cryptococcus neoformans, CAP64, is involved in pH homeostasis

The CAP64 gene is known to be involved in capsule formation in the basidiomycete yeast Cryptococcus neoformans. A null mutant of CAP64, Δcap64, lacks a capsule around the cell wall and its acidic organelles are not stained with quinacrine. In order to clarify whether the Cap64 protein indeed maintains vacuole or vesicle acidification, so that the vesicle containing the capsule polysaccharide or DBB substrate are transported to the cell membrane side, the relationship between CAP64 and intracellular transport genes and between CAP64 and enzyme-secretion activity were analysed. Laccase activity was higher in the Δcap64 strain than in the wild-type strain, and the transcriptional levels of SAV1 and VPH1 were also higher in the Δcap64 strain than in the wild-type strain. The intracellular localization of the Cap64 protein was analysed by overexpressing an mCherry-tagged Cap64 and observing its fluorescence. The Cap64 protein was accumulated within cells in a patch-like manner. The quinacrine-stained cells were observed to analyse the acidified cell compartments; quinacrine was found to be accumulated in a patch-like manner, with the patches overlapping the fluorescence of CAP64-mCherry fusion protein. Quinacrine was thus accumulated in a patch-like fashion in the cells, and the mCherry-tagged Cap64 protein position was consistent with the position of quinacrine accumulation in cells. These results suggest that CAP64 might be involved in intracellular acidification and vesicle secretion via exocytosis.

Effective methane production from the Japanese weed Gyougi-shiba (Cynodon dactylon) is accomplished by colocalization of microbial communities that assimilate water-soluble and -insoluble fractions

Weed, an abundant biomass, is considered unsuitable as a raw material for methane production. There are few reports on the anaerobic digestion of weeds without the addition of other organic wastes. To solve this problem, a methane-producing microbial community with weed as a sole feedstock was established. This study mainly focused on the degree of contribution between water-soluble and -insoluble fractions of the weed to methane production; thus, methane production from both fractions was tested separately. Methane production after 80-day batch cultures with whole weed, water-soluble and water-insoluble fractions was 184.5, 96.8 and 26.5 NmL g-1 dry matter (DM), respectively. The results of 16S rRNA gene amplicon sequence analysis revealed that Proteiniphilum saccharofermentans and several Methanobacterium species commonly dominated all cultures, whereas the population dynamics of minor species differed in every culture. Moreover, the remixed culture of microbial communities adapted to water-soluble and -insoluble fractions recovered methane production (252.4 NmL g-1 DM). Based on these results, it can be strongly inferred that colocalizing the minor species in water-soluble and -insoluble fractions is important for effective methane production.

Molecular epidemiology and antifungal susceptibilities of Cryptococcus species isolates from HIV and non-HIV patients in Southwest China

To investigated the molecular epidemiology and in vitro antifungal susceptibility of Cryptococcus isolates from West China Hospital from HIV and non-HIV patients between 2009 and 2015. A total of 132 C. neoformans and C. gattii were subjected to antifungal susceptibility testing by E-test method. Among the 132 isolates, 42 C. neoformans and C. gattii were analyzed by mating type and URA5-RFLP. A total of 113 C. neoformans and C. gattii were subjected to multi-locus sequence typing (MLST). MLST results revealed that ST5 was the major molecular type. The wild-type (WT) phenotype was seen in 91.5-100% of C. neoformans isolates for amphotericin B, 5-flucytosine, fluconazole, and voriconazole. However, 72.3% (94/130) of C. neoformans isolates were non-wild-type (non-WT) to itraconazole by E-test method. In the sixth study year, the geometric mean, MIC50 and MIC90 of fluconazole were the highest (P < 0.001). Among 132 patients. 52 were coinfected with HIV and 80 were HIV-negative. Isolates from HIV and non-HIV patients showed no differences in susceptibility to amphotericin B (P = 0.544), 5-flucytosine (P = 0.063), fluconazole (P = 0.570), voriconazole (P = 0.542), and itraconazole (P = 0.787). Our study showed that Cryptococcus in southwest China showed a low degree of genetic diversity. The increased MIC values of fluconazole are noted. Cryptococcus isolates from HIV and non-HIV patients have shown no differences in susceptibility to five antifungal agents.

Five Non-motile Dinotom Dinoflagellates of the Genus Dinothrix

Dinothrix paradoxa and Gymnodinium quadrilobatum are benthic dinoflagellates possessing diatom-derived tertiary plastids, so-called dinotoms. Due to the lack of available genetic information, their phylogenetic relationship remains unknown. In this study, sequencing of 18S ribosomal DNA (rDNA) and the rbcL gene from temporary cultures isolated from natural samples revealed that they are close relatives of another dinotom, Galeidinium rugatum. The morphologies of these three dinotoms differ significantly from each other; however, they share a distinctive life cycle, in which the non-motile cells without flagella are their dominant phase. Cell division occurs in this non-motile phase, while swimming cells only appear for several hours after being released from each daughter cell. Furthermore, we succeeded in isolating and establishing two novel dinotom strains, HG180 and HG204, which show a similar life cycle and are phylogenetically closely related to the aforementioned three species. The non-motile cells of strain HG180 are characterized by the possession of a hemispheroidal cell covered with numerous nodes, while those of the strain HG204 form aggregations consisting of spherical smooth-surface cells. Based on the similarity in life cycles and phylogenetic closeness, we conclude that all five species should belong to a single genus, Dinothrix, the oldest genus within this clade. We transferred Ga. rugatum and Gy. quadrilobatum to Dinothrix, and described strains HG180 and HG204 as Dinothrix phymatodea sp. nov. and Dinothrix pseudoparadoxa sp. nov.

Batch-Mode Analysis of Thermophilic Methanogenic Microbial Community Changes in the Overacidification Stage in Beverage Waste Treatment

Biogasification by methane fermentation is an important and effective way to utilize beverage wastes. Beverage wastes are good feedstocks for methane fermentation because of their richness in sugars and proteins, although overacidification and inhibition of methane production caused by high substrate loading often become problematic. This study investigated changes in microbial communities in the overacidification state of the thermophilic methane fermentation process with beverage waste by establishing a simulated batch culture. We assessed 20 mL-scale batch cultures using a simulant beverage waste mixture (SBWM) with different amounts of addition; high cumulative methane production was achieved by adding 5 mL of SBWM (11358 mg-chemical oxygen demand-COD/L of organic loading), and overacidification was observed by adding 10 mL of SBWM (22715 mg-COD/L of organic loading). The results of 16S rRNA amplicon sequence analysis using nanopore sequencer suggested that Coprothermobacter proteolyticus, Defluviitoga tunisiensis, Acetomicrobium mobile, and Thermosediminibacter oceani were predominantly involved in hydrolysis/acidogenesis/acetogenesis processes, whereas Methanothrix soehngenii was the major acetotrophic methane producer. A comparison of microbial population between the methane-producing cultures and overacidification cultures revealed characteristic population changes especially in some minor species under 0.2% of population. We concluded that careful monitoring of population changes of the minor species is a potential indicator for prediction of overacidification.

Feature-Based Molecular Networking Analysis of the Metabolites Produced by In Vitro Solid-State Fermentation Reveals Pathways for the Bioconversion of Epigallocatechin Gallate

Dark teas are prepared by a microbial fermentation process. Flavan-3-ol B-ring fission analogues (FBRFAs) are some of the key bioactive constituents that characterize dark teas. The precursors and the synthetic mechanism involved in the formation of FBRFAs are not known. Using a unique solid-state fermentation system with β-cyclodextrin inclusion complexation as well as targeted chromatographic isolation, spectroscopic identification, and Feature-based Molecular Networking on the Global Natural Products Social Molecular Networking web platform, we reveal that dihydromyricetin and the FBRFAs, including teadenol A and fuzhuanin A, are derived from epigallocatechin gallate upon exposure to fungal strains isolated from Fuzhuan brick tea. In particular, the strains from subphylum Pezizomycotina were key drivers for these B-/C-ring oxidation transformations. These are the same transformations seen during the fermentation process of dark teas. These discoveries set the stage to enrich dark teas and other food products for these health-promoting constituents.

Diversity of the diploid sequence type of Candida albicans clinical isolates from a tertiary-care hospital in Mwanza, Tanzania

Geographical strain variations of Candida albicans causing different clinical conditions in susceptible individuals have been reported. In this study, the distribution of diploid sequence type of C. albicans was investigated in Mwanza, Tanzania. A total of 64 C. albicans were selected on the basis of their antifungal susceptibility patterns, followed by multilocus sequence typing (MLST) to establish the circulating sequence types (STs). Forty-eight MLST were obtained out of 64 isolates amounting to 75% population structure differences. Out of these STs, 27 (56.3%) were new diploid ST types. C. albicans isolates with new ST were more diverse than isolates with known STs (27/29, 93.1% vs. 21/35, 60%, p 0.002). In conclusion, C. albicans from clinical specimens were highly diverse, with more than half of the detected diploid ST not previously reported in the MLST database, thus confirming the genetic differences of C. albicans from different geographical regions.

Quality and Probiotic Lactic Acid Bacteria Diversity of Rabbit Meat Bekasam-Fermented Meat

Rabbit meat bekasam is a traditional fermentation product from Indonesia. This study aimed to determine the chemical and microbiological characteristics of rabbit meat bekasam during the fermentation process in order to isolate, characterize (in vitro and in vivo), and identify lactic acid bacteria (LAB) as the probiotic candidate. The chemical contents of bekasam on 7-day fermentation were investigated in explorative and experimental methods in a completely randomized design. A proximate analysis reported a decrease in the moisture content, fat and carbohydrate content, and an increase in protein content. Also, lactic acid content was increased from 0.48% to 1.12%, and pH was decreased from 5.3 to 4.3. Other properties indicated different values, such as bacteria (2.75×10⁶ to 4.45×10⁷ CFU/g), total LAB (3.82×10⁶ to 4.67×10⁸ CFU/g), total yeast (9.89×10⁶ to 3.82×10⁸ CFU/g) and total mould (4.34×10¹ to 4.86×10³ CFU/g). The experiment produced nine LAB isolates, including two probiotics subjected to further 16S rRNA gene analysis, which indicated that Lactobacillus buchneri was the potential probiotic isolate. After being tested on BALB/c mice, L. buchneri could improve the immune system by inhibiting the growth of Coliform and Salmonella.

Wickerhamomyces psychrolipolyticus f.a., sp. nov., a novel yeast species producing two kinds of lipases with activity at different temperatures

Two yeast strains isolated from soil collected in Hokkaido, Japan, were found to secrete two extracellular lipases that exhibited activities at both 25 and 4 °C. Both strains could utilize olive oil, rapeseed oil, lard and fish oil as sole carbon sources. The similarity of the D1/D2 domain of the large subunit ribosomal RNA (LSU rRNA) sequence of these yeast strains to that of other yeasts in the GenBank database was very low (<96 %). The phylogenetic trees based on the LSU rRNA sequences and translation elongation factor-1-α (tef1-α) sequences indicated that both strains represented a member of the Wickerhamomyces /Candida clade. Sexual reproduction was not observed. The name Wickerhamomyces psychrolipolyticus f.a., sp. nov is proposed for this newly described yeast species producing cold-active lipases. This novel species is distinguishable from the type strains of other related species, Wickerhamomyces alni, Candida ulmi and Candida quercuum due to their abilities to grow at 4 to 30 °C, to produce lipase that is active also at 4 °C and to assimilate soluble starch.

Molecular identification and phytochemical screening of endophytic fungi isolated from Lithospermum officinale L. roots: A new source of shikonin

Endophytic fungi are microorganisms located in the inter- or intracellular compartments of plant tissues but with no harmful effects. They are considered a potential source of biological compounds. The present study was conducted to investigate the molecular identification of endophytic fungi isolated from the roots of Lithospermum officinale and their potential production of shikonin. Phylogenetic analysis was performed based on the Internal Transcribed Spacer (ITS) region and the isolates were classified into five genera as follows: Alternaria, Chaetosphaeronema, Fusarium, Mucor, and Trichoderma. The study on the methanol extracts of endophytic fungi indicated that total polyphenol content had a positive relationship with antioxidant activities and the highest antioxidant activity belonged to the methanol extracts of Fusarium tricinctum and Alternaria altenata. Then, to investigate the ability of the fungal isolates to produce shikonin, a naphthoquinone compound with high biological activity, the extracts were subjected to HPLC. The results obtained from HPLC-mass spectrometry showed that shikonin could be produced only by F. tricinctum. Thus, F. tricinctum isolated from the roots of L. officinale can be presented as a new source of shikonin.

A simplified quick microbial genomic DNA extraction via freeze-thawing cycles

Effective isolation of high-quality genomic DNA is one of the essential steps in molecular biology, biochemistry, and genetic studies. Here we describe a simplified procedure based on repeated freeze-thawing cycles to isolate genomic DNA from different organisms of microbes (Burkholderia pyrrocinia JK-SH007, Bacillus pumilus HRl0, Botrytis cinerea) and nematodes (Bursaphelenchus xylophilus). The DNA extraction buffer includes 10% of CTAB; 4% of NaCl (W/V); 20 mM of ethylenediamine tetraacetic acid; 100 mM of Tris-HCl, pH 8.0 and 1% of polyvinylpyrrolidone. The released DNA was purified from the mixture using a phenol/chloroform mixture and precipitated in 70% ethanol to remove proteins, carbohydrates, phenols, RNA, etc. Our method is a reproducible, simple, and rapid technique for routine DNA extractions from various microorganisms and nematodes. Furthermore, the low cost of this method could be an economic benefit to large-scale studies.

Antimicrobial activity of SYNBIO® probiotic formulation in pathogens isolated from chronic ulcerative lesions: in vitro studies

AIMS

Probiotics have the ability to enhance the immune system, produce anti-inflammatory action and promote wound healing process. The first aim of the study was to isolate pathogenic micro-organisms from sites of chronic ulcerative lesion. The second aim was to evaluate probiotic efficacy of SYNBIO^® (1:1 combination of Lactobacillus rhamnosus IMC 501^® and Lactobacillus paracasei IMC 502^® ) in counteracting wound infections.

METHODS AND RESULTS

Several bacterial pathogens were isolated from chronic ulcerative lesions and identified by morphological, biochemical and molecular techniques. SYNBIO^® probiotic formulation was investigated for its antimicrobial activity, minimum inhibitory concentration, co-aggregation and adherence capacity against the isolated pathogens. Moreover, SYNBIO was also tested in combination with some medical devices, using an in vitro model, in order to simulate a real ulcerative wound infection. Probiotic formulation demonstrated an inhibitory action against all the tested pathogens and their mixture (MIX), with an increased ability of co-aggregation during time. In addition, the adhesion percentage of probiotic micro-organisms to human keratinocyte (HaCaT cells) and human fibroblasts (NHF), calculated by an in vitro model, was 19% and 17% respectively, highlighting the possibility to create a protective environment preventing pathogens' biofilm formation in order to contrast infections.

CONCLUSIONS

SYNBIO^® probiotics showed a very good antimicrobial capacity and adhesion percentage to HaCaT cells and fibroblasts, giving the opportunity to be successfully used as complement to conventional therapies in the treatment of chronic ulcerative lesions.

SIGNIFICANCE AND IMPACT OF THE STUDY

A new therapeutic approach with probiotics (supplemented in topical applications, excluding side effects) able to eliminate pathogenic micro-organisms and improve healing of chronic ulcerative lesions.

Whole-Genome Bisulfite Sequencing and Epigenetic Variation in Cereal Methylomes

Whole-genome bisulfite sequencing (WGBS) is a technique used for the analysis of genome-wide DNA methylation patterns (DNA methylomes) at a single-base resolution. Here, I describe a simple DNA extraction method from rice endosperm and the universal protocol of WGBS, MethylC-sequencing library preparation. The use of benzyl chloride allows for the extraction of high-quality genomic DNA from starchy endosperm, while sodium bisulfite converts unmethylated cytosine to uracil, whereas methylated cytosine is unchanged. The bisulfite conversion of whole genome sequencing libraries before the final amplification step allows for the discrimination of methylated from unmethylated cytosines in a genome-wide manner.

Draft Genome Sequence of Zygosaccharomyces mellis CA-7, Isolated from Honey

In this study, we report the draft genome sequence of Zygosaccharomyces mellis CA-7, isolated from purchased honey imported from Canada. The 10.19-Mb genome contains 4,963 gene models. To our knowledge, this annotated genome sequence is the first from the species Z. mellis and will contribute to a better understanding of the osmotolerance of microorganisms in high-sugar products.

In this study, we report the draft genome sequence of Zygosaccharomyces mellis CA-7, isolated from purchased honey imported from Canada. The 10.19-Mb genome contains 4,963 gene models. To our knowledge, this annotated genome sequence is the first from the species Z. mellis and will contribute to a better understanding of the osmotolerance of microorganisms in high-sugar products.

Symbiotic Growth of a Thermophilic Sulfide-Oxidizing Photoautotroph and an Elemental Sulfur-Disproportionating Chemolithoautotroph and Cooperative Dissimilatory Oxidation of Sulfide to Sulfate

A thermophilic filamentous anoxygenic photosynthetic bacterium, Chloroflexus aggregans, is widely distributed in neutral to slightly alkaline hot springs. Sulfide has been suggested as an electron donor for autotrophic growth in microbial mats dominated with C. aggregans, but remarkable photoautotrophic growth of isolated C. aggregans has not been observed with sulfide as the sole electron source. From the idea that sulfide is oxidized to elemental sulfur by C. aggregans and the accumulation of elemental sulfur may have an inhibitory effect for the growth, the effects of an elemental sulfur-disproportionating bacterium that consumes elemental sulfur was examined on the autotrophic growth of C. aggregans, strain NA9-6, isolated from Nakabusa hot spring. A sulfur-disproportionating bacterium, Caldimicrobium thiodismutans strain TF1, also isolated from Nakabusa hot spring was co-cultured with C. aggregans. C. aggregans and C. thiodismutans were successfully co-cultured in a medium containing thiosulfate as the sole electron source and bicarbonate as the sole carbon source. Quantitative conversion of thiosulfate to sulfate and a small transient accumulation of sulfide was observed in the co-culture. Then the electron source of the established co-culture was changed from thiosulfate to sulfide, and the growth of C. aggregans and C. thiodismutans was successfully observed with sulfide as the sole electron donor for the autotrophic growth of the co-culture. During the cultivation in the light, simultaneous consumption and accumulation of sulfide and sulfate, respectively, were observed, accompanied with the increase of cellular DNAs of both species. C. thiodismutans likely works as an elemental sulfur scavenger for C. aggregans, and C. aggregans seems to work as a sulfide scavenger for C. thiodismutans. These results suggest that C. aggregans grows autotrophically with sulfide as the electron donor in the co-culture with C. thiodismutans, and the consumption of elemental sulfur by C. thiodismutans enabled the continuous growth of the C. aggregans in the symbiotic system. This study shows a novel symbiotic relationship between a sulfide-oxidizing photoautotroph and an elemental sulfur-disproportionating chemolithoautotroph via cooperative dissimilatory sulfide oxidation to sulfate.

Gut microbiota disorders cause type 2 diabetes mellitus and homeostatic disturbances in gut-related metabolism in Japanese subjects

Few studies have investigated the host-microbe metabolic axis in people with type 2 diabetes mellitus (T2DM). This study aimed to determine and compare the nutrient intakes and metabolic markers and to elucidate the relationships among these factors in Japanese T2DM patients and control individuals. Fifty-nine Japanese T2DM patients and 59 matched healthy control individuals participated in this study. We examined the differences regarding the participants’ dietary habits, microbiota, and fecal short-chain fatty acids, and analyzed the relationships between the gut microbiota and blood metabolic markers in the T2DM patients and the control subjects. The T2DM patients consumed more carbohydrates, and had lower fecal propionate and butyrate concentrations, larger fecal populations of Bifidobacterium spp. and bacteria of the order Lactobacillales, and smaller fecal Bacteroides spp. populations than the control individuals. In the T2DM patients, the level of Bifidobacterium spp. correlated negatively with the carbohydrate intake and the level of bacteria of the order Lactobacillales correlated negatively with the protein intake. T2DM patients have gut dysbiosis that may contribute to disease onset and influence its prognosis. Furthermore, homeostatic disturbances in the gut-related metabolism may underlie the pathogenesis of T2DM.

Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species

The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes, and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novo assembled a high-quality, haploid-phased genome. Here, we present our assembly, with a total length of 351 Mb, of which 92.2% was anchored onto 12 chromosomes. We detected 34,389 genes and 38.1% of the genome consisted of repetitive content. We validated our assembly by a comparative linkage analysis and by examining well-characterized gene families. This genome assembly will be a useful resource to exploit beneficial alleles found in O. longistaminata. Our results also show that it is possible to generate a high-quality, functionally complete rice genome assembly from moderate SMRT read coverage by exploiting synteny in a closely related Oryza species.

Stefan Reuscher et al. assembled the genome of an African wild rice species to facilitate breeding efforts and functional genomic studies. They used SMRT sequencing, chromosomal synteny between rice species, and a linkage map to assemble the 351 Mb genome into 12 chromosomes.

Biolistic-delivery-based transient CRISPR/Cas9 expression enables in planta genome editing in wheat

The current application of genome editing to crop plants is limited to cultivars that are amenable to in vitro culture and regeneration. Here, we report an in planta genome-editing which does not require callus culture and regeneration. Shoot apical meristems (SAMs) contain a subepidermal cell layer, L2, from which germ cells later develop during floral organogenesis. The biolistic delivery of gold particles coated with plasmids expressing CRISPR/Cas9 components designed to target TaGASR7 were bombarded into SAM-exposed embryos of imbibed seeds. Bombarded embryos showing transient GFP expression within SAM were selected and grown into adult plants. Mutations in the target gene were assessed in fifth-leaf tissue by cleaved amplified polymorphic sequence analysis. Eleven (5.2%) of the 210 bombarded plants carried mutant alleles, and the mutations of three (1.4%) of these were inherited in the next generation. Genotype analysis of T1 plants identified plants homozygous for the three homeologous genes, which were all derived from one T0 plant. These plants showed no detectable integration of the Cas9 and guide RNA genes, indicating that transient expression of CRISPR/Cas9 introduced the mutations. Together, our current method can be used to achieve in planta genome editing in wheat using CRISPR/Cas9 and suggests possible applications to other recalcitrant plant species and variations.

Ethylene-gibberellin signaling underlies adaptation of rice to periodic flooding

Most plants do poorly when flooded. Certain rice varieties, known as deepwater rice, survive periodic flooding and consequent oxygen deficiency by activating internode growth of stems to keep above the water. Here, we identify the gibberellin biosynthesis gene, SD1 (SEMIDWARF1), whose loss-of-function allele catapulted the rice Green Revolution, as being responsible for submergence-induced internode elongation. When submerged, plants carrying the deepwater rice-specific SD1 haplotype amplify a signaling relay in which the SD1 gene is transcriptionally activated by an ethylene-responsive transcription factor, OsEIL1a. The SD1 protein directs increased synthesis of gibberellins, largely GA₄, which promote internode elongation. Evolutionary analysis shows that the deepwater rice-specific haplotype was derived from standing variation in wild rice and selected for deepwater rice cultivation in Bangladesh.

Construction, heterologous expression, partial purification, and in vitro cytotoxicity of the recombinant plantaricin E produced by Lactococcus lactis against Enteropathogenic Escherichia coli K.1.1 and human cervical carcinoma (HeLa) cells

Lactobacillus plantarum produces bacteriocin called plantaricin that can kill or inhibit other bacteria. Plantaricin E (Pln E), a recombinant bacteriocin, has been successfully constructed and produced by a GRAS host, Lactococcus lactis. A polymerase chain reaction (PCR) overlapping technique has been used to construct a ligation of signal peptide gene, Pln A and bacteriocin encoding gene, Pln E. Furthermore, the fusion fragment were cloned into pNZ8148 vector and transformed into L. lactis NZ3900. Molecular expression study shows that recombinant L. lactis NZ3900 is able to express the mature pln E at transcription level with size of 168 bp. Plantaricin E is purified by ammonium sulphate precipitation followed by gel filtration chromatography. Purified fractions were proven to be active against Enteropathogenic Escherichia coli K.1.1. The other fractions of Pln E also have antibacterial activity against several Gram positive and Gram negative bacteria. Purified recombinant plantaricin E is 3.7 kDa in size. The cytotoxicity assay shows purified Pln E inhibits 46.949 ± 3.338% of HeLa cell lines on 10 ppm dose whilst the metabolite inhibits 53.487 ± 2.957% of HeLa cell line on 100 ppm dose. The IC₅₀ calculation of Pln E metabolite is 107.453 ppm, while the purified protein is 11.613 ppm.