Genetic Information Processing Research Articles

Comparative Proteomics of Resistant and Susceptible Strains of Frankliniella occidentalis to Abamectin.

Western flower thrips, Frankliniella occidentalis (Thysanoptera: Thripidae) is an invasive agricultural pest with developed resistance to abamectin in some strains due to frequent treatment with the pesticide. In this study, we examined differentially expressed proteins (DEPs) between abamectin-resistant (AbaR; under abamectin selective pressure) and susceptible strains (AbaS; without abamectin selective pressure) of F. occidentalis. Proteins were isolated from second instar larvae of both strains and separated via two-dimensional polyacrylamide gel electrophoresis. Nano-flow liquid chromatography-tandem mass spectrometry identified selected protein spot features. From 70 DEPs, 43 spot features were identified: A total of 23 showed an increase in abundance, and 20 were down-regulated in response to abamectin pressure. The enzymatic and structural proteins were classified into the functional groups of macromolecular metabolisms, signaling and cellular processes, immune system, genetic information processing, and exoskeleton-related proteins. The up-regulation of exoskeleton-related proteins may contribute to forming a thicker cuticle, potentially hindering abamectin penetration, which is an interesting finding that needs further investigation. Two novel proteins, triacylglycerol lipase and cuticle protein CPF 2, were only expressed in AbaR. This work provides insights into abamectin resistance mechanisms in F. occidentalis, which will provide important information for developing insecticide resistance management approaches for this pest.

Effects of Chenpi (Citrus reticulata cv. Chachiensis) on serum antioxidant enzymes, inflammatory factors, and intestinal health in Beagle dogs.

Ensuring companion animal welfare is a top priority for the pet industry and owners alike. The health of the pets can be directly and effectively improved through diet. Chenpi includes beneficial ingredients with proven anti-inflammatory, antioxidant, and immunomodulatory properties. The present investigation involved feeding snacks infused with Chenpi powder (CPP) to dogs for 42 days to examine the potential health benefits of CPP. The research evidenced a notable increase in serum superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) activity in dogs, accompanied by a decrease in malondialdehyde (MDA), interleukin-8 (IL-8), and interferon-gamma (IFN-γ) level. Additionally, CPP increased fecal scores and significantly reduced fecal odors due to inhibition of 3-methylindole, hydrogen sulfide (H2S), and ammonia nitrogen (NH4 +-N), and also raised the levels of fecal secretory immunoglobulin A (SIgA). Analysis of the microbial composition via 16S rRNA sequencing showed that CPP increased Bacteroidota and decreased Firmicutes in the gut flora at the phylum level. Functional prediction study of microbial communities also showed that the CPP group enriched metabolic and genetic information processing pathways. In addition, there were significant correlations between serum indicators and several significantly altered microorganisms. These findings suggest that CPP can potentially enhance the overall health of dogs by reducing fecal odorants, enhancing antioxidant and immunological capabilities, and modulating intestinal flora. This study establishes a solid scientific foundation regarding the application of CPP in functional pet foods.

16S rRNA Sequencing Analysis Uncovers Dose-Dependent Cupric Chloride Effects on Silkworm Gut Microbiome Composition and Diversity.

Copper-based pesticides are extensively used in agriculture, yet their impacts on beneficial insects remain poorly understood. Here, we investigate how cupric chloride exposure affects the gut microbiome of Bombyx mori, a model organism crucial for silk production. Using 16S rRNA sequencing, we analyzed the gut bacterial communities of fifth-instar silkworm larvae exposed to different concentrations of cupric chloride (0, 4, and 8 g/kg) in an artificial diet. The high-dose exposure dramatically altered the microbial diversity and community structure, where the Bacteroidota abundance decreased from 50.43% to 23.50%, while Firmicutes increased from 0.93% to 18.92%. A network analysis revealed complex interactions between the bacterial genera, with Proteobacteria and Firmicutes emerging as key players in the community response to copper stress. The functional prediction indicated significant shifts in metabolic pathways and genetic information processing in the high-dose group. Notably, the low-dose treatment induced minimal changes in both the taxonomic composition and predicted functions, suggesting a threshold effect in the microbiome response to copper exposure. Our findings provide novel insights into how agricultural chemicals influence insect gut microbiota and highlight potential implications for silkworm health and silk production. This work contributes to understanding the ecological impacts of copper-based pesticides and may inform evidence-based policies for their use in sericulture regions.

Unraveling the Molecular Mechanisms of Blueberry Root Drought Tolerance Through Yeast Functional Screening and Metabolomic Profiling.

Blueberry plants are among the most important fruit-bearing shrubs, but they have shallow, hairless roots that are not conducive to water and nutrient uptake, especially under drought conditions. Therefore, the mechanism underlying blueberry root drought tolerance should be clarified. Hence, we established a yeast expression library comprising blueberry genes associated with root responses to drought stress. High-throughput sequencing technology enabled the identification of 1475 genes potentially related to drought tolerance. A subsequent KEGG enrichment analysis revealed 77 key genes associated with six pathways: carbon and energy metabolism, biosynthesis of secondary metabolites, nucleotide and amino acid metabolism, genetic information processing, signal transduction, and material transport and catabolism. Metabolomic profiling of drought-tolerant yeast strains under drought conditions detected 1749 differentially abundant metabolites (DAMs), including several up-regulated metabolites (organic acids, amino acids and derivatives, alkaloids, and phenylpropanoids). An integrative analysis indicated that genes encoding several enzymes, including GALM, PK, PGLS, and PIP5K, modulate key carbon metabolism-related metabolites, including D-glucose 6-phosphate and β-D-fructose 6-phosphate. Additionally, genes encoding FDPS and CCR were implicated in terpenoid and phenylalanine biosynthesis, which affected metabolite contents (e.g., farnesylcysteine and tyrosine). Furthermore, genes for GST and GLT1, along with eight DAMs, including L-γ-glutamylcysteine and L-ornithine, contributed to amino acid metabolism, while genes encoding NDPK and APRT were linked to purine metabolism, thereby affecting certain metabolites (e.g., inosine and 3',5'-cyclic GMP). Overall, the yeast functional screening system used in this study effectively identified genes and metabolites influencing blueberry root drought tolerance, offering new insights into the associated molecular mechanisms.

Structural Analysis and Functional Prediction of Gut Microbiota in Wild and Cultured Striped Knifejaw (Oplegnathus fasciatus)

Understanding the role of gut microbiota in fish health is crucial for optimizing aquaculture practices and ensuring sustainable fish populations. In this study, the diversity and compositional differences of intestinal microbiota were comparatively analyzed between wild and cultured striped knifejaw (Oplegnathus fasciatus Kroyer, 1845). Using high-throughput 16S rDNA sequencing and bioinformatics, an in-depth investigation of the gut microbiota in both populations was conducted. The results revealed that the number of intestinal bacterial sequences was significantly higher in the cultured population than in the wild population. The study included 16 individuals from the wild population and 38 individuals from the cultured population, with an average weight of 67.7 ± 12.4 g and 44.9 ± 16.8 g, respectively. Alpha diversity analysis indicated that intestinal microbiota species richness and diversity were both greater in the cultured O. fasciatus. Furthermore, significant differences were observed in the intestinal bacterial communities between the two populations, with Pseudomonadota, Verrucomicrobia, and Bacillota dominating in the cultured population, whereas Pseudomonadota overwhelmingly dominated in the wild population. Functional prediction analysis revealed differences between the intestinal microbiota in pathways related to genetic and environmental information processing, as well as metabolism. This study provides critical data for understanding the structure and function of intestinal microbial communities in O. fasciatus and offers a theoretical foundation for optimizing farming strategies to improve fish health and growth performance.

Genome-wide identification, structural characterization and expression profiling of AP2/ERF gene family in bayberry (Myrica rubra)

BackgroundBayberry is the most economically significant fruit within the Myricaceae family, having high nutritional and medicinal value. The AP2/ERF family is a class of transcription factors found mainly in plants. However, the bayberry AP2/ERF gene family has not previously been studied.ResultsIn this study, 113 members of the bayberry AP2/ERF gene family were identified. According to the phylogenetic tree, the members of this group are divided into three subfamilies, namely AP2, ERF, and DREB. The gene structure and conserved motifs were analyzed. Chromosome localization showed that 95 genes were unevenly distributed on 8 chromosomes and 18 genes were located on the skeleton. Gene collinearity analysis of the bayberry AP2/ERF gene family showed 12 segmental duplication events, involving 21 AP2/ERFs. In addition, we further investigated the evolutionary relationship of the AP2/ERF gene family between bayberry and six other species. It was found that bayberry was most closely related to Populus trichocarpa and Malus pumila, with 153 and 141 homologous gene pairs, respectively. Cis-acting elements indicated that AP2/ERFs were related to phytohormone responses, light response, abiotic and biotic stress tolerance. Transcriptomic data showed that the expression pattern of AP2/ERF gene was different in bayberry space electric field treatment and at different stages of fruit development. The results of GO annotation revealed the biological processes, cellular component and molecular function that the AP2/ERF genes were involved. And KEGG enrichment analysis indicated that these genes were mainly clustered in genetic information processing and metabolism pathways.ConclusionsThe AP2/ERF gene was identified in the genome of bayberry, and its structure, conserved motif, and phylogenetic relationship were analyzed. These findings of this study serve as a reference for the genome-wide identification of the AP2/ERF gene family in other species and groundwork for future research on the function of AP2/ERF genes in bayberry.

Reductive soil disinfestation influences microbial aging of low-density polyethylene and polyhydroxyalkanoate microplastics and microbial communities in plastispheres

The extensive use of plastic products has led to the accumulation of microplastics (MPs) in agricultural soils, raising concerns about their fate in various environments. Reductive soil disinfestation (RSD) treatment is increasingly being adopted in various countries to address agricultural soil health issues. However, the treatment can alter the soil microbial environment, potentially affecting the fate of contaminants, including MPs. The effect of RSD on the aging of low-density polyethylene (LDPE) and polyhydroxyalkanoates (PHA) MPs was studied through an incubation experiment. The mechanism involved was further investigated by microbial community analysis. The characterization results shown that RSD treatment inhibited the aging of LDPE but promoted the aging of PHA. The results indicated that RSD reshaped the microbial community and reduced the relative abundance of lipid metabolism in the LDPE plastisphere, thereby hindering LDPE aging. Predicted functional genes in the plastispheres were primarily involved in metabolism (77.15–87.48%) and genetic information processing (8.774–12.62%). The enrichment of bacteria related to poly(3-hydroxybutyrate) depolymerase (phaZ) in the PHA plastisphere explained the higher aging degree of PHA during RSD. Some fungus also involved in the MPs aging, while some fungus pathogens can proliferate in the MPs plastispheres. The 3DEEM analysis indicated that PHA MPs aging increased tyrosine-like substances in soil extracts. These findings provide new insights into the ecological implications of RSD and enhance our understanding of microbial communities within plastispheres.

Stress-induced premature senescence in high five cell cultures: a principal factor in cell-density effects

The Baculovirus Expression Vector System (BEVS) is highly valued in vaccine development, protein engineering, and drug metabolism research due to its biosafety, operational convenience, rapid scalability, and capacity for self-assembling virus-like particles. However, increasing cell density at the time of inoculation severely compromises the production capacity of BEVS, resulting in the “cell density effect”. This study aimed to explore the mechanisms of the cell density effect through time-series analysis of transcriptomes and proteomes, with the goal of overcoming or alleviating the decline in productivity caused by increased cell density. The dynamic analysis of the omics of High Five cells under different CCI (cell density at infection) conditions showed that the impact of the “cell density effect” increased over time, particularly affecting genetic information processing, error repair, protein expression regulation, and material energy metabolism. Omics analysis of the growth stage of High Five cells showed that after 36 h of culture (cell density of about 1 × 106 cells/mL), the expression of ribosome-related proteins decreased, resulting in a rapid decrease in protein synthesis capacity, which was a key indicator of cell aging. Senescence verification experiments showed that cells began to show obvious early aging characteristics after 36 h, resulting in a decrease in the host cell’s ability to resist stress. Overexpression and siRNA inhibition studies showed that the ndufa12 gene was a potential regulatory target for restricting the “cell density effect”. Our results suggested that stress-induced premature senescence in High Five cell cultures, resulting in reduced energy metabolism and protein synthesis capabilities, was a critical factor contributing to cell density effects, and ultimately affecting virus production. In conclusion, this study provided new insights into managing virus production limitations due to cell density effects and offered innovative strategies to mitigate the adverse effects of cellular aging in biomanufacturing technologies.Graphical abstract

Genomic insights into bamboo witches' broom disease: pathogenicity and phytohormone biosynthesis in Aciculosporium take.

Bamboo witches' broom disease (WBD), caused by Aciculosporium take Miyake, devastates bamboo forests. Understanding the genome and pathogenic factors of pathogen is crucial for disease control. We employed single-molecule real-time sequencing, Illumina paired-end sequencing, and chromatin interaction mapping techniques to assemble the genome of A. take CCTCC-M2023413, analyze pathogenicity- and phytohormone-biosynthesis-related genes, and compare it to 12 other WBD pathogens. The genome of A. take is 59.24 Mb in size, with 54.32% repeats, 7 chromosomes, 7,105 protein-coding genes, 84 ribosomal RNAs, and 115 transfer RNAs. Predictive analysis of pathogenicity genes found 237 carbohydrate-active enzymes, 1,069 membrane transport proteins, 1,040 pathogen-host interaction genes, 315 virulence factors, and 70 effectors. Most of pathogenicity genes overlapped with repeat-rich regions. Additionally, 172 genes were linked to auxin biosynthesis, 53 to brassinosteroid biosynthesis, and 2 to cis-zeatin biosynthesis. Comparative genomic analysis identified 77 core orthogroups shared by 13 WBD pathogens, played roles in metabolites, genetic information processing, pathogenesis, cis-zeatin biosynthesis, lifespan, and quorum sensing. The miaA gene, crucial for cis-zeatin biosynthesis, is structurally conserved and sequence-diverse among 13 WBD pathogens, with upregulated expression during bamboo WBD pathogenesis. This highlights that cis-zeatin is significant contributor to host pathogenesis, and miaA is a new potential target for controlling WBD. This study provides important insights on preventing and controlling bamboo WBD.

Double effects of mitigating cyanobacterial blooms using modified clay technology: regulation and optimization of the microbial community structure.

Harmful algal blooms (HABs) are global hazards under global climate change and eutrophication conditions. Modified clay (MC) method is widely used to control HABs in Asian and American coastal waters. However, little research has been conducted on the underlying mechanisms by which MC controls blooms in freshwater environments. Herein, experiments and bioinformatics analyses were conducted for MC-based control of freshwater blooms in a closed water body with an area of approximately 240 m2 in the Fuchun River, China. Results revealed that the dominant bloom species were Microcystis, and an 87.68-97.01% removal efficiency of whole algal biomass was achieved after 3 h of MC treatment. The weaker zeta potentials of Microcystis species and hydrophilic groups such as O-H and P-O-P in the extracellular polymeric substances (EPS) surrounding Microcystis cells made them easier to be flocculated and removed by MC particles, and the relative abundance of Microcystis decreased to 29.12% and that of Cyanobium increased to 40.97%. Therefore, MC changes the cyanobacterial community structure, which is accompanied by the elimination of Microcystis sp. apical dominance and enhanced competition between Cyanobium and Microcystis in the phytoplankton community, increasing cyanobacterial community diversity. Under MC treatment, residual microorganisms, including cyanobacteria, had a high potential for DNA damage repair and were more likely to survive after being subjected to oxidative stress. In the meanwhile, the abundance of genes involved in genetic information processing, signal transduction, and photosynthesis was decreased indicating that the residual microbiome was week in proliferation and light energy harvesting. Therefore, accompanied with the destruction of Microcystis colonies, MC changes the function of cyanobacteria and phycosphere microbiome, further hindering bloom development. These findings illustrate that MC can regulate and optimize the microbial community structure through which MC controls cyanobacterial blooms in ecosystems.

Comparative transcriptome analysis of low- and high-latitude populations of Charybdis japonica under temperature stress

Global climate change has caused rapid temperature changes in marine environments. Understanding how marine organisms respond to temperature changes can help predict their richness of future biodiversity. In this study, we examined the gene expression levels and the difference in the pathways that are responsive to acute temperature stress in low- and high-latitude populations of the shore swimming crab, Charybdis japonica. The two populations of C. japonica were exposed to low- and high-temperature stresses (15°C and 28°C) and used for transcriptome sequencing. Genetic regulatory ability changes were compared to determine the diverse response of the two crab populations to temperature change. The gene expression levels and functional enrichment analysis showed that the low-latitude crab regulated more genes (938) that were mainly enriched in DNA replication and metabolic pathways, whereas the high-latitude crab regulated less genes (309) that were mainly enriched in genetic information processing at low-temperature stress. Furthermore, the low-latitude crab regulated less genes (33) that were mainly enriched in genetic information processing, whereas the high-latitude crab regulated more genes (280) that were mainly enriched in signal transduction and cellular process at high-temperature stress. These results implied that the low-latitude population was more resilient to high-temperature stress, while the high-latitude population was more resilient to low-temperature stress. This study enhances our understanding of how different geographic C. japonica populations respond to varying temperature environments in their living zone, which could be helpful for predicting future biodiversity trends of intertidal crustaceans under global climate change.

Effect of xylo-oligosaccharides on intestinal bacterial diversity in mice with spleen deficiency constipation.

To explore the effect of xylo-oligosaccharides on intestinal bacterial diversity in mice with spleen deficiency constipation. The 16S rDNA sequencing was used to identify microbiota composition in four groups, including the normal group (NG), the model group with spleen-deficiency constipation (SDC), XOS treated groups that include XOS1 groups treated XOS 0.05 g/mL•d, and XOS2 group treated XOS 0.1 g/mL•d. Chao1 and Shannon were used to conduct gut microbes diversity analysis. Linear discriminant analysis coupled with effect size measurements (LEfSe) was used to identify signature gut microbiota, and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) was used to predict the function of altered gut microbiota. Veen map indicated 245 common OTUs were identified from four groups. Especially, 9, 3, 0, and 19 unique OTUs were identified in NG, SDC, XOS1, and XOS2 groups, respectively. The Shannon index was evidently higher in NG group than in the other three groups (p < 0.05). We identified the occurrence of dominant bacterial groups including Bacteroidetes (25.5 ~ 49.9%), Firmicutes (25.4 ~ 39.3%), Proteobacteria (12.5 ~ 24.9%), Deferribacteres (1.6 ~ 19.2%), Cyanobacteria (0.3 ~ 1.8%), Verrucomicrobia (0.02 ~ 1.6%), Actinobacteria (0.01 ~ 0.5%), and Tenericutes (0.03 ~ 0.09%) at the four groups. The XOS2 group was characterized by a higher abundance of Peptostreptococcaceae, Intestinibacter, Aerococcaceae, and Facklamia. XOS1 group enriched in Deferribacteres, Mucispirillum, Deferribacterales, Deferribacteres, Lachnoclostridium, Rhodospirillaceae, and Rhodospirillales. Meanwhile, the SDC mice showed dramatic enrichment in Rikenellaceae, Lachnospiraceae, Rikenellaceae, Roseburia, and Alistipes, which were highly abundant in the NG group. XOS fed-mice evidently increase Deferribcteres abundance compared with NG and SDC groups. However, the abundance of Rikenellaceae was significantly reduced in XOS1 and XOS2 groups compared with NG and SDC groups. We identified that altered gut microbiotas by XOS treatment were associated with various metabolic pathways, including organismal systems, metabolism, human diseases, genetic information processing, and cellular processes. Our research indicated that XOS has the potential to recover intestinal bacteria and contribute to the treatment of spleen deficiency constipation.

Structural and functional differences of gut microbiota in Pomacea canaliculata from different geographical locations and habitats.

Gut microbiota is related to host fitness, and influenced by geographical locations and habitats. Pomacea canaliculata is a malignant invasive alien snail that threatens agricultural production and ecosystem functions worldwide. Clarifying the general rules of the gut microbial community structure and function of the snails in different geographical locations and habitats is of great significance for understanding their invasion at different spatial scales. This study used high-throughput sequencing technology to compare and analyze the differences in community structure and function of gut microbiota in P. canaliculata from five geographical locations (Liuzhou, Yulin, Nanning, Wuzhou, and Hezhou) and three different habitats (pond, paddy field, and ditch) in Guangxi Province. The results showed that intestinal microbial alpha diversity of P. canaliculata was higher in Liuzhou, Yulin, lower in Nanning, Wuzhou, Hezhou, and higher in ponds compared with paddy fields and ditches. The dominant phyla of gut microbiota in snails were Firmicutes, Cyanobacteria, Proteobacteria, Fusobacteriota, Bacteroidota, and the dominant genus was Lactococcus. The community structure of gut microbiota in snails varied significantly across different geographical locations and habitats, and the phyla Firmicutes, Cyanobacteria had significantly higher relative abundance in snails collected from Nanning and Yulin, respectively. Moreover, the relative abundance of gut functional microbiota associated with human disease in P. canaliculata was significantly affected by geographical locations and habitats, and with the highest abundance in ponds. However, the relative abundance of functional microbiota related to metabolism, genetic information processing, organizational system, environmental information processing, and cellular processes were only significantly affected by geographical locations. Collectively, geographical locations and habitats had significantly different effects on the community structure and function of gut microbiota in P. canaliculata, and the greater differences were caused by geographical locations rather than by habitats.

Exploring the effect of lipid loading on acidogenic fermentation of food waste: Insights from microbiome, quorum sensing and carbon metabolic pathway

The high lipid loading in food waste (FW) is widely regarded as one of the main bottlenecks in the traditional anaerobic digestion, but the effect of lipid on FW acidogenic fermentation has been historically ignored. This study attempted to reveal the influence of lipid loading on volatile fatty acids (VFAs) production and the corresponding synthesis mechanisms during FW acidogenic fermentation. The VFAs production reached 27.10 ± 1.00 g COD/L when the lipid loading comprised 25 % of the FW dry weight, increasing by 36.88 % compared to the CK group. Lactobacillus, with a relative abundance of 59.43 %, was the predominant genus under lipid loading. In quorum sensing (QS) system, the relative abundance of luxS that is involved in the biosynthetic pathway of the Autoinducer-2 (AI-2) signal molecule increased from 0.066 % to 0.10 % in the presence of lipid. The relative abundance of Genetic Information Processing increased from 16.36 % to 24.25 % under lipid loading, with up-regulation of Translation and Replication and repair. Lipid loading not only promoted the conversion of acetyl-CoA to acetic acid, as evidenced by a 1.36-fold increase in pta gene abundance, but also concurrently suppressed the consumption of acetic acid, reflected in the 96.83 % and 77.16 % decreases in ALDH and aldB abundance, thus accumulating acetic acid. Carbon emission was also constrained under lipid loading, in which the conversion from formate to CO2 and passing Tricarboxylic acid (TCA) cycle were restricted over 60 %. Together, lipid loading in FW represents a potential strategy for enhancing VFAs production in FW acidogenic fermentation.

Essential genes for Haemophilus parainfluenzae survival and biofilm growth.

Haemophilus parainfluenzae (Hp) is a Gram-negative, highly prevalent, and abundant commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the supragingival plaque biofilm. Little is known about how Hp interacts with its neighbors in healthy biofilms nor its mechanisms of pathogenesis as an opportunistic pathogen. To address this, we identified the essential genome and conditionally essential genes in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain (Hp 392) and oral isolate EL1 (Hp EL1), we show that the essential genomes of Hp 392 and Hp EL1 are composed of 395 (20%) and 384 (19%) genes, respectively. The core essential genome, consisting of 341 (17%) essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains. RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo habitat. This library presents a valuable tool for investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.IMPORTANCEHaemophilus parainfluenzae is a highly abundant human commensal microbe, present in most healthy individuals where it colonizes the mouth. H. parainfluenzae correlates with good oral health and may play a role in preservation of healthy host status. Also, H. parainfluenzae can cause opportunistic infections outside of the oral cavity. To date, little is known about how H. parainfluenzae colonizes the human host, despite being such a frequent and abundant part of our human microbiome. Here, we demonstrate the creation and use of a powerful tool, a TnSeq library, used to identify genes necessary for both the outright growth of this organism and also genes conditionally essential for growth in varying oxygen status which it can encounter in the human host. This tool and these data serve as a foundation for further study of this relatively unknown organism that may play a role in preserving human health.

Dysbiosis of the gut microbiota in glioblastoma patients and potential biomarkers for risk assessment

BackgroundThe significant death rate of glioblastoma is well-known around the world. The link between gut microbiota and glioma is becoming more studied. The goal of this study was to look at the relationships between intestinal flora and glioblastoma, and to provide a new perspective for the diagnosis as well as treatment of glioblastoma. MethodsFecal samples from 80 participants with glioblastoma (n = 40) and healthy individuals (n = 40) in this study were collected as well as analyzed utilizing 16S rRNA gene amplicon sequencing in order to characterize the gut microbial community. ResultsEach group has its own microbial community, and the microbial environment of glioblastoma patients had lower richness and evenness. The structure of gut microbiota community in glioblastoma patients showed profound changes, which includes the increase of pathogens in Fusobacteria and Bacteroidetes, and the reduction of probiotic bacteria in Firmicutes, Actinobacteria and Verrucomicrobia. Meanwhile, the significant correlations and clustering of OTUS (operational taxonomic units) in glioblastoma patients were discovered, and a biomarker panel (Fusobacterium, Escherichia/Shigella, Ruminococcus gnavus group, Lachnospira, Akkermansia, Parasutterella) had been used to discriminate the patients with glioblastoma from the healthy subjects (AUC: 0.80). Furthermore, the glioblastoma group exhibited multiple disturbed pathways through KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, particularly in genetic information processing. Moreover, the prediction of phenotypic characteristics of microbiome proposed that the glioblastoma patients might have more Gram-negative bacteria and opportunistic pathogens than the healthy controls. ConclusionsWhen compared to healthy people, glioblastoma sufferers have a different host-microbe interaction. Furthermore, certain types of intestinal flora could be regarded as biomarkers and drug targets for the diagnosis as well as treatment of glioblastomas.

Sediment microbial diversity, functional potentials, and antibiotic resistance pattern: a case study of Cochin Estuary core sediment.

Marine sediments are an important part of the marine environment and the world's greatest organic carbon source. Sediment microorganisms are important regulators of major geochemical and eco-environmental processes in marine environments, especially nutrient dynamics and biogeochemical cycles. Despite their importance, core marine microorganisms are virtually unknown due to a lack of consensus on how to identify them. Most core microbiotas have been characterized thus far based on species abundance and occurrence. The combined effects of habitat and depth on benthic bacterial communities and ecological functions were studied using "Next-Generation sequencing (NGS) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictive functional profiling" at the surface (0.2cm) and bottom depth (250cm) in a sediment core sample from Cochin Estuary, Kerala, India. The results showed that bacterial diversity and richness were significantly higher in the surface sediment sample with the most abundant phyla being Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes. The major metabolic functions were metabolism, followed by environmental information processing and genetic information processing. Antibiotic resistance genes between the surface and bottom samples help to understand the resistance pattern among multidrug resistance is the most prominent one. Among viruses, Siphoviridae is the dominant family, followed by Myoviridae. In the case of Archea, Crenarchaeota is dominant, whereas among eukaryotes phyla Streptophyta and Chordata were dominant in the surface and the bottom samples respectively.

Multiomics-Based Biocargo Components Analysis in Enterococcus faecium Membrane Vesicles.

Enterococcus spp. have been shown to have gastrointestinal tract protective functions; our recent results suggest that membrane vesicles (MVs) play an important role in the gastric protection of Enterococcus faecium (E. faecium). The specific function is determined by molecular compositions of MVs. To resolve biocargo components in E. faecium MVs (EfmMVs), MVs were isolated from E. faecium culture. Transcriptomics, label-free quantitative proteomics, and untargeted metabolomics were performed to obtain information about the complexity of ribonucleic acids (RNAs), proteins, and metabolites biocargo they carry, respectively. RNA-sequencing identified a total of 2122 transcripts. The top 20 transcripts accounted for 27.63% of total counts, which, including enzymes, participate in glycolysis, ribosomal proteins, DNA-directed RNA polymerases, protein-synthesizing relative enzymes, molecules associated with protein post-translational processing and transport, and peptidoglycan lyases. Label-free quantitative proteomics analysis identified a total of 711 proteins. The top 20 proteins accounted for 48.02% of all identified proteins, which including ribosomal proteins, enzymes participate in glycolysis, DNA-directed RNA polymerases, protein-synthesizing relative enzymes, peptidoglycan lyases, and autolysin. Untargeted metabolomics analysis identified a total of 519 metabolites. The top 20 metabolites accounted for 79.55% of all identified metabolites, which included amino acids, substrates, or products in the metabolism of amino acids, natural organic acids, products in the metabolism of organic acids, ketone compounds, and two other compounds. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that the identified biocargo components enriched in metabolism, genetic, and environmental information processing. Overall, we hope that the current exploration of multiple "-omics" analyses of this EfmMVs will provide useful information and further groundwork for future studies on E. faecium application.

Ultrasonic treatment can improve maize seed germination and abiotic stress resistance

Constant-frequency ultrasonic treatment helped to improve seed germination. However, variable-frequency ultrasonic treatment on maize seed germination were rarely reported. In this study, maize seeds were exposed to 20–40 kHz ultrasonic for 40 s. The germination percentage and radicle length of maize seeds increased by 10.4% and 230.5%. Ultrasonic treatment also significantly increased the acid protease, α-amylase, and β-amylase contents by 96.4%, 73.8%, and 49.1%, respectively. Transcriptome analysis showed that 11,475 differentially expressed genes (DEGs) were found in the ultrasonic treatment and control groups, including 5,695 upregulated and 5,780 downregulated. Metabolic pathways and transcription factors (TFs) were significantly enriched among DEGs after ultrasonic treatment. This included metabolism and genetic information processing, that is, ribosome, proteasome, and pyruvate metabolism, sesquiterpenoid, triterpenoid, and phenylpropanoid biosynthesis, and oxidative phosphorylation, as well as transcription factors in the NAC, MYB, bHLH, WRKY, AP2, bZIP, and ARF families. Variable-frequency ultrasonic treatment increased auxin, gibberellin, and salicylic acid by 5.5%, 37.3%, and 28.9%, respectively. Abscisic acid significantly decreased by 33.2%. The related DEGs were upregulated and downregulated to varying degrees. Seed germination under the abiotic stress conditions of salt stress (NaCl solution), drought (PEG solution), and waterlogging (water-saturated sand bed) under ultrasonic treatment were promoted, radicle length was significantly increased by 30.2%, 30.5%, and 27.3%, respectively; and germination percentage by 14.8%, 20.1%, and 21.6%, respectively. These findings provide new insight into the mechanisms through ultrasonic to promote maize seed germination.

Development and implementation of a core genome multilocus sequence typing scheme for Haemophilus influenzae.

Haemophilus influenzae is part of the human nasopharyngeal microbiota and a pathogen causing invasive disease. The extensive genetic diversity observed in H. influenzae necessitates discriminatory analytical approaches to evaluate its population structure. This study developed a core genome multilocus sequence typing (cgMLST) scheme for H. influenzae using pangenome analysis tools and validated the cgMLST scheme using datasets consisting of complete reference genomes (N = 14) and high-quality draft H. influenzae genomes (N = 2297). The draft genome dataset was divided into a development dataset (N = 921) and a validation dataset (N = 1376). The development dataset was used to identify potential core genes, and the validation dataset was used to refine the final core gene list to ensure the reliability of the proposed cgMLST scheme. Functional classifications were made for all the resulting core genes. Phylogenetic analyses were performed using both allelic profiles and nucleotide sequence alignments of the core genome to test congruence, as assessed by Spearman's correlation and ordinary least square linear regression tests. Preliminary analyses using the development dataset identified 1067 core genes, which were refined to 1037 with the validation dataset. More than 70% of core genes were predicted to encode proteins essential for metabolism or genetic information processing. Phylogenetic and statistical analyses indicated that the core genome allelic profile accurately represented phylogenetic relatedness among the isolates (R 2 = 0.945). We used this cgMLST scheme to define a high-resolution population structure for H. influenzae, which enhances the genomic analysis of this clinically relevant human pathogen.