Genetic Information Processing Research Articles

Label-free quantitative proteomic analysis of the mechanism of salt stress promoting selenium enrichment in Lactobacillus rhamnosus

Lactobacillus rhamnosus can metabolize selenite into organic selenium and Se0. In this paper, label-free quantitative proteomics was applied to explore the mechanism of salt stress promoting selenium enrichment of L.rhamnosus. 397 proteins were up-regulated and 147 proteins were down-regulated of selenium-enriched L.rhamnosus under salt stress. The differentially expressed proteins (DEPs) were mainly involved in metabolism, membrane transport and genetic information processing. The results of quantitative real-time PCR showed that gene opuA, metN, trxR and ldh of Se-enriched L.rhamnosus with salt stress were significantly up-regulated. However, the expression levels of gene luxS, groEL, dnaK and pgk were down-regulated. It was indicated that L.rhamnosus promoted part of amino acids combining with selenium into selenoamino acids with salt stress. Secondly, sodium chloride stimulated the expression of key enzymes involved in metabolism to provide energy for the process of Se-enrichment. In addition, NaCl induced the expression of enzymes and genes involved in the synthesis of selenoproteins. SignificanceIt was indicated that L.rhamnosus promoted part of amino acids combining with selenium into selenoamino acids with salt stress. Secondly, sodium chloride stimulated the expression of key enzymes involved in metabolism to provide energy for the process of Se-enrichment. In addition, NaCl induced the expression of enzymes and genes involved in the synthesis of selenoproteins.

Comparison of Gut Microbiota Diversity Between Captive and Wild Tokay Gecko (Gekko gecko).

Captive animals and wild animals may exhibit different characteristics due to the heterogeneity of their living environments. The gut microbiota play an important role in the digestion and absorption, energy metabolism, immune regulation, and physiological health of the host. However, information about the gut microbiota of captive and wild Gekko gecko is currently limited. To determine the difference in gut microbiota community composition, diversity, and structure between captive and wild geckos, we used the Illumina miseq platform to conduct high-throughput sequencing and bioinformatics analysis of the v3–v4 hypervariable region of 16S rRNA in 54 gecko samples. Our results showed that Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were the dominant gut microbiota phyla of the gecko. The dominant genera comprised mainly Pseudomonas, Burkholderia-caballeronia-paraburkholderia, Ralstonia, Romboutsia, and Bacteroides. Captive geckos had significantly higher alpha diversity and potential pathogenic bacteria than wild populations. Moreover, significant differences in beta diversity of gut microbiota were observed between two populations. Functional prediction analysis showed that the relative abundance of functional pathways of wild geckos was more higher in metabolism, genetic information processing and organismal system function than those in captive geckos. Total length significantly affected gut microbial community (R2 = 0.4527, p = 0.001) and explained 10.45% of the total variation for gut microbial community variance between two groups. These results may be related to differences in diet and living environment between two populations, suggesting that the management of captive populations should mimic wild environments to the greatest extent possible to reduce the impact on their gut microbiota.

Molecular mechanism of protein dynamic change in Pacific oyster (Crassostrea gigas) during depuration at different salinities uncovered by mass spectrometry-based proteomics combined with bioinformatics

Salinity stress during depuration of Pacific oysters (Crassostrea gigas) leads to degradation in quality; therefore, an understanding of the molecular mechanisms regulating dynamic changes during depuration is needed. Here, C. gigas was depurated for 72 h at salinities ranging from 26 to 38 g/L, a ± 10–20% fluctuation from that in the production area, and the gill proteomes were analyzed by sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS). Of the 1218 proteins analyzed, 241 were differentiating proteins (DPs). Salinity stress led to increased levels of DPs associated with glycolysis and the extracellular matrix–receptor interaction pathway, and decreased levels of DPs associated with the citric acid cycle, lipid metabolism, genetic information processing, and cell transformation, especially in oysters exposed to 38 g/L salinity (+20%). Controlling salinity fluctuation within ± 10% of the production area during depuration was conducive to maintaining quality in C. gigas.

Insights into the bacterial, fungal, and phage communities and volatile profiles in different types of Daqu

Daqu has a rich and diverse microbiota, giving them a suitable biotope for phages. However, the absolute abundances of bacteria and fungi, as well as the phage community characteristics in Daqu, remain unclear. In this study, the microbiota absolute abundance, indigenous phage composition and function, and volatile compound profiles of high-temperature Daqu (HTDQ), medium-temperature Daqu (MTDQ), and low-temperature Daqu (LTDQ) were investigated. Absolute microbiota quantification revealed that there were significant variations in microbial composition and absolute abundance across three types of Daqu. The absolute abundances of the top 30 bacterial genera in LTDQ, MTDQ, and HTDQ were 6.0 × 105, 5.3 × 104, 1.4 × 105 copies/ng DNA, while the top 30 fungal genera had 8.5 × 107, 2.1 × 106, and 6.2 × 105 copies/ng DNA, respectively. LTDQ were enriched in Pantoea, Staphylococcus, and Saccharomycopsis; MTDQ were dominated by Saccharopolyspora, Staphylococcus, Saccharomycopsis, and Aspergillus; HTDQ were dominated by Saccharopolyspora, Bacillus, Byssochlamys, and Saccharomycopsis. Volatile profile analysis revealed that LTDQ, MTDQ, and HTDQ comprised 68, 68, and 75 compounds, respectively, with 39 compounds shared by the three types. Fourteen volatile compounds were identified as highly discriminative features among three types of Daqu, which were closely related to Saccharopolyspora, Thermoactinomyces, Kroppenstedtia, Byssochlamys, and Thermomyces. Metaviromics indicated that Genomoviridae, Mimiviridae and Siphoviridae, and Parvoviridae were the dominant viruses in LTDQ, MTDQ, and HTDQ, respectively. The hosts of phages in Daqu mainly included Lactobacillus, Enterobacter, Pantoea, Bacillus, Pediococcus, and Staphylococcus. Phages may prey on numerous microbes living on Daqu via pathways such as genetic information processing, signaling and cellular processes, and replication and repair. This study highlights the use of absolute quantification to avoid misjudgment of differential taxa in comparative microbiome analysis and provides new insights into the phage community and function in Daqu.

Whole-plant corn silage improves rumen fermentation and growth performance of beef cattle by altering rumen microbiota.

In recent years, whole-plant corn silage has been widely used in China. Roughage is an important source of nutrition for ruminants and has an important effect on rumen microbiota, which plays an important role in animal growth performance and feed digestion. To better understand the effects of different silages on rumen microbiota, the effects of whole-plant corn silage or corn straw silage on growth performance, rumen fermentation products, and rumen microbiota of Simmental hybrid cattle were studied. Sixty healthy Simmental hybrid cattle were randomly divided into 2 groups with 6 replicates in each group and 5 cattle in each replicate. They were fed with whole-plant corn silage (WS) diet and corn straw silage (CS) diet respectively. Compared with corn straw silage, whole-plant corn silage significantly increased daily gain and decreased the feed intake-to-weight gain ratio (F/G) of beef cattle. Whole-plant corn silage also decreased the acetic acid in the rumen and the acetate-to-propionate ratio (A/P) compared with corn straw silage. On the genus level, the relative abundance of Prevotella_1 was significantly increased while the relative abundance of Succinivibrionaceae_UCG-002 was decreased in cattle fed whole-plant corn silage compared with those fed corn straw silage. Prevotella_1 was positively correlated with acetic acid and A/P. Succinivibrionaceae_UCG-002 was positively correlated with propionic acid and butyric acid, and negatively correlated with pH. Feeding whole-plant corn silage improved amino acid metabolism, nucleotide metabolism, and carbohydrate metabolism. Correlation analysis between rumen microbiota and metabolic pathways showed that Succinivibrionaceae_UCG-002 was negatively correlated with glycan biosynthesis and metabolism, metabolism of co-factors and vitamins, nucleotide metabolism, and translation while Prevotellaceae_UCG-003 was positively correlated with amino acid metabolism, carbohydrate metabolism, energy metabolism, genetic information processing, lipid metabolism, membrane transport, metabolism of cofactors and vitamins, nucleotide metabolism, replication and repair, and translation. Ruminococcus_2 was positively correlated with amino acid metabolism and carbohydrate metabolism. Feeding whole-plant corn silage can improve the growth performance and rumen fermentation of beef cattle by altering rumen microbiota and regulating the metabolism of amino acids, carbohydrates, and nucleotides. KEY POINTS: • Feeding whole-plant corn silage could decrease the F/G of beef cattle • Feeding whole-plant corn silage improves rumen fermentation in beef cattle • Growth performance of beef cattle is related to rumen microbiota and metabolism.

Identification of mutant p53-specific proteins interaction network using TurboID-based proximity labeling

BackgroundsAlthough several studies on mutant p53 reported cancer-promoting activities via “gain-of-function”, the mechanism underlying these differences in function between p53 R175H, R175P, and p53 wild-type (WT) remains unclear. MethodsLinking miniTurbo with p53 WT, R175H, and R175P, the expression of fusion and biotinylated proteins were assessed by Western blotting. The function and subcellular localization of fusion proteins were detected by apoptosis assay and immunofluorescence, respectively. Biotinylated proteins were analyzed by liquid chromatography-tandem mass spectrometry, followed by bioinformatics analysis. Small-scale pull-downs and Co-Immunoprecipitation were performed to validate the interaction between mutant or p53 WT and biotinylated proteins. ResultsThe fusion protein's cellular localization and function were consistent with those of previous studies on the corresponding p53. Comparative profiles of R175H versus WT showed that most of the interacting proteins belonged to the intracellular organelle lumen, and the pathways involved were metabolism and genetic information processing. Comparative profiles of R175P versus WT suggested that the majority of the interacting proteins belonged to the intracellular organelle lumen and the extracellular membrane-bounded organelle, and the pathways involved were metabolism and genetic information processing pathways. The comparison between R175H and R175P revealed that most interacting proteins belonged to the organelle lumen, and pathways involved were genetic information processing pathways. Finally, the mutation of p53 significantly altered the interaction with the target proteins were confirmed. ConclusionWe verified the reliability of the miniTurbo system and obtained candidate targets of mutant p53, which provided new thoughts on the mechanism of mutant p53 gain-of-function and new potential targets for cancer therapy.

Energy metabolism and genetic information processing mark major transitions in the life history of Scrippsiella acuminata (Dinophyceae)

Many dinoflagellates perform sexual reproduction and form cysts as a life history strategy to survive adverse environmental conditions and seed annual harmful algal blooms (HABs). The molecular mechanisms underpinning the life stage transitions can provide clues about how key environmental factors induce encystment and initiation of a HAB but are still poorly understood. Here, we conducted an integrated physiological and transcriptomic study to unravel the mechanisms in Scrippsiella acuminata. We established a culture from a bloom, induced cyst formation, and divided the process into four life stages. Transcriptomic analysis of these stages revealed 19,900 differentially expressed genes (DEGs). The expression of genes related to photosynthesis was significantly up-regulated from vegetative stage to immature cyst stage, consistent with the marked increase in cell contents of energy-storing macromolecules (carbohydrates and lipids). When proceeding to resting cysts, most photosynthesis genes were down-regulated while “genetic information processing” related genes were up-regulated. Comparing germinating cysts with resting cysts revealed 100 DEGs involved in energy metabolism, indicating a high energy requirement of germination. In addition, the transition from germinating cysts to vegetative cells featured up-regulation of photosynthesis. Our results demonstrate that energy storage and consumption play a pivotal role in cyst formation and germination respectively and genetic information processing is crucial in cyst dormancy.

Bacterial Community Composition and Function in a Tropical Municipal Wastewater Treatment Plant

Bacterial diversity and community composition are of great importance in wastewater treatment; however, little is known about the diversity and community structure of bacteria in tropical municipal wastewater treatment plants (WWTPs). Therefore, in this study, activated sludge samples were collected from the return sludge, anaerobic sludge, anoxic sludge, and aerobic sludge of an A2O WWTP in Haikou, China. Illumina MiSeq high-throughput sequencing was used to examine the 16S ribosomal RNA (rRNA) of bacteria in the samples. The microbial community diversity in this tropical WWTP was higher than in temperate, subtropical, and plateau WWTPs. Proteobacteria, Bacteroidota, Patescibacteria, and Chloroflexi were the dominant phyla. Nitrification bacteria Nitrosomonas, and Nitrospira were also detected. Tetrasphaera, instead of Candidatus Accumulibacter, were the dominant polyphosphate accumulating organisms (PAOs), while, glycogen accumulating organisms (GAOs), such as Candidatus Competibacter and Defluviicoccus were also detected. The bacterial community functions predicted by PICRUSt2 were related to metabolism, genetic information processing, and environmental information processing. This study provides a reference for the optimization of tropical municipal WWTPs.

Analysis of bacterial and fungal communities in fermented fish (pla-ra) from Northeast Thailand.

Our aim was to explore the microbial community composition (bacteria and fungi) of fermented fish (pla-ra) from Northeast Thailand. We also made functional predictions concerning these microbial communities. The association between the microbiota and odor intensity was also analyzed. Fourteen samples of 1-year fermented fish samples derived from seven local markets in Khon Kaen, Northeast Thailand were used. The microbial community composition of each was investigated by sequencing the V1-V9 regions of the 16S rRNA gene (bacteria) and the ITS gene (fungi) using an Illumina MiSeq platform. Functional prediction analysis was conducted through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) based on the use of the bacterial 16S rRNA gene sequences. The bacterial communities were rich, comprising 402 genera from 28 phyla, including such genera as Tetragenococcus, Staphylococcus, Virgibacillus, Lactobacillus and Lentibacillus. The fungal communities comprised 7 phyla and 60 genera, such as Heterobasidion, Densospora, Exophiala and Monascus. The bacterial community functional analysis revealed an association with six biological metabolic pathway categories (e.g., metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems and human diseases) with 17 subfunctions, showing the richness of bacterial community functions. Odor-association analysis revealed that Brevibacterium, Brachybacterium and Chromohalobacter were more abundant in the weak-odor group, while Noviherbaspirillum was more abundant in the strong-odor group. This study provides a preliminary analysis of pla-ra microbial community structure and function in popular traditional Thai foods. Functional prediction analysis might be helpful to improve our knowledge of the microbiota in fermented fish.

Time-Series Clustering of lncRNA-mRNA Expression during the Adipogenic Transdifferentiation of Porcine Skeletal Muscle Satellite Cells.

Skeletal muscle satellite cells (SMSCs), which are multifunctional muscle-derived stem cells, can differentiate into adipocytes. Long-chain non-coding RNA (lncRNA) has diverse biological functions, including the regulation of gene expression, chromosome silencing, and nuclear transport. However, the regulatory roles and mechanism of lncRNA during adipogenic transdifferentiation in muscle cells have not been thoroughly investigated. Here, porcine SMSCs were isolated, cultured, and induced for adipogenic differentiation. The expressions of lncRNA and mRNA at different time points during transdifferentiation were analysed using RNA-seq analysis. In total, 1005 lncRNAs and 7671 mRNAs showed significant changes in expression at differential differentiation stages. Time-series expression analysis showed that the differentially expressed (DE) lncRNAs and mRNAs were clustered into 5 and 11 different profiles with different changes, respectively. GO, KEGG, and REACTOME enrichment analyses revealed that DE mRNAs with increased expressions during the trans-differentiation were mainly enriched in the pathways for lipid metabolism and fat cell differentiation. The genes with decreased expressions were mainly enriched in the regulation of cell cycle and genetic information processing. In addition, 1883 DE mRNAs were regulated by 193 DE lncRNAs, and these genes were related to the controlling in cell cycle mainly. Notably, three genes in the fatty acid binding protein (FABP) family significantly and continuously increased during trans-differentiation, and 15, 13, and 11 lncRNAs may target FABP3, FABP4, and FABP5 genes by cis- or trans-regulation, respectively. In conclusion, these studies identify a set of new potential regulator for adipogenesis and cell fate and help us in better understanding the molecular mechanisms of trans-differentiation.

Physiological Effects and Transcriptomic Analysis of sbGnRH on the Liver in Pompano (Trachinotus ovatus).

Pompano (Trachinotus ovatus) is one of the important economic marine fishes in the south coast of China. At present, the research on the basic biology of pompano is relatively weak, which has seriously affected the development of this economic important fish. The liver is an important digestive and metabolic organ of fish which plays an important regulatory role in its growth and development. It is necessary to clarify the effects of sea bream gonadotropin releasing hormone (sbGnRH) on liver physiology and metabolic enzyme activity. The effects of sbGnRH peptides (10 ng/gbw) on the physiological and biochemical indices and metabolic enzyme activities of pompano liver were studied. It was found that after injection of 10 ng/gbw sbGnRH peptides, the contents of albumin, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, glucose, creatine kinase, iron, magnesium, aspartate aminotransferase, alanine aminotransferase and creatinine increased, while of cholesterol and calcium contents decreased. The activities of amylase, lipase, pyruvate kinase, acyl CoA oxidase, superoxide dismutase, phospholipid hydroperoxide glutathione peroxidase, catalase, glucose-6-phosphate dehydrogenase, fatty acid synthase and lipoprotein lipase increased, while the activities of malic enzyme, carnitine acyl, carnitine translocation, acetyl CoA carboxylase and malondialdehyde decreased. Three hours after the injection of different concentrations of sbGnRH peptides (0 and 10 ng/gbw), the transcriptome sequences of the two groups of livers were sequenced. After quality control and removal of some low-quality data, clean reads of 21,283,647、19,427,359、21,873,990、21,732,174、23,660,062 and 21,592,338 were obtained respectively. In this study, 99 genes were screened and identified as differentially expressed genes, including 77 up-regulated genes and 22 down-regulated genes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway analyses, these pathways and the typical genes involved can be divided into cellular processes, environmental information processing, genetic information processing, diseases, metabolism and organismal systems. The results from this study provide a the oretical basis for studying the effects of sbGnRH on the physiology, biochemistry and metabolic enzyme activities of liver in pompano.

Taxonomic and functional diversity of Dendrobium officinale microbiome in Danxia habitat.

Microbial communities that inhabit plants are crucial for plant survival and well-being including growth in stressful environments. The medicinal plant, Dendrobium officinale grows in the barren soils of the Danxia Habitat. However, the microbiome composition and functional potential for growth of this plant in this environment are still unexplored. In this study, we analysed the taxonomic and functional diversity of the D. officinale Microbiome by metagenomic sequencing of both rhizosphere and endosphere samples. A total of 155 phyla, 122 classes, 271 orders, 620 families and 2194 genera were identified from all samples. The rhizospheric microbes (DXRh) were mainly composed of Proteobacteria and Acidobacteria, while Basidiomycota and Ascomycota were the most dominant phyla in root endosphere (DXRo) and stem endosphere (DXS), respectively. Most of the dominant microbial communities had been reported to have diverse functional potentials that can help plant growth and development in stressful and nutrient-deprived ecological environmental. These include plant growth promoting rhizobacteria (PGPR) such as Massilia, Pseudomonas, Bradyrhizobium, Klebsiella, Streptomyces, Leclercia, Paenibacillus, Frankia and Enterobacter in the DXRh, Tulasnella and Serendipita in the DXRo, Colletotrichum and Burkholderia in the DXS and Paraburkholderia, Rhizophagus and Acetobacter in endosphere. Analysis using the KEGG, eggNOG and CAZy databases showed that metabolic pathways such as carbohydrate metabolism, amino acid metabolism, energy metabolism, genetic information processing and environmental information processing are significantly abundant, which may be related to the survival, growth and development of D. officinale in a stressful environment. We speculated that the microbial community with diverse taxonomic structures and metabolic functions inhabiting in different niches of plants supports the survival and growth of D. officinale in the stressful environment of Danxia Habitat. This study provided an important data resource for microbes associated with D. officinale and theoretical foundation for further studies.

De Novo assembly and annotation of the Pacific calico scallop (Argopecten ventricosus) transcriptome for immune-related gene discovery

Invertebrates' immune defense mechanisms play a critical role in pathogen recognition and elimination. De novo assembly and annotation of the Argopecten ventricosus transcriptome were performed for the immune-related gene identification. Scallops (height: 4.4 cm) were challenged with inactivated Vibrio parahaemolyticus IPNGS16. The RNA from different tissues was pooled for a single cDNA library construction sequenced by NextSeq 500 platform 2×75 paired‐end chemistry. Before de novo assembling with Trinity, reads were analyzed with FastQC, Trimmomatic, and Prinseq. Assembled sequences were analyzed by CD-HIT-EST and TransDecoder. The corresponding annotation was performed against NCBI-nr, RefSeq protein, and KAAS (KEGG) databases. The Trinity assembly yielded 107,516 contigs. TransDecoder yielded 25,285 sequences as CDSs of which, 16,123 were annotated against the NCBI-nr protein, most of them scored with Crassostrea gigas data. Gene ontology mapped sequences (15,262) were classified in molecular functions (~13,000), cellular components (~11,000), and biological processes (~13,000). The KAAS analysis showed biological categories for metabolism (13%), cellular processes (12%), genetic information processing (10%), organismal systems (19%), environmental information (13%), and human diseases (33 %). Within the organismal systems, 467 immune-related genes (KO) were identified. Sixty-four immune-related genes were annotated/blasted against the NCBI-nr and RefSeq protein databases. An RT-qPCR was performed to analyze the expression level of immune-related genes obtained in the transcriptome analysis in scallops (height 4.5 cm) treated with probiotic bacilli added to culture water. Bacilli significantly increased the expression of the HSP70 and PGRP genes. The gene transcripts analysis of A. ventricosus will better understand its immune response against pathogens in culture systems.

Whole Transcriptomic Profiling in Metastatic Liver Cancer With Distinct Molecular Signatures

PURPOSE Genomics landscape in liver cancer is one of the most revolutionizing platforms in the era of next generation sequencing (NGS). Understanding the intra- and inter-liver cancer heterogeneity has an important role in treatment decision-making. Herein, we present a whole transcriptomic based NGS with distinct molecular signatures in metastatic liver cancer tissues of orthotopic SCID mice. METHODS High throughput whole transcriptome sequencing was carried out using Illumina platform in ex vivo metastatic liver cancer tissues of orthotopic SCID mice. Healthy normal liver tissues were also subjected to NGS analysis. Pathway analysis was performed using all differentially expressed transcripts. RESULTS Approximately 35.4 million sequencing reads and approximately 28.2 million mapped reads were obtained from metastatic liver cancer tissue samples sequenced. We identified approximately 40,018 differently expressed genes. Distinct top 50 significantly differentially expressed transcripts expressed were observed. About 3,840 novel isoforms were identified. The mapping of the differentially expressed transcripts represented major metabolic pathways, immune-related pathways, cell growth-related pathways, the genes involved in metabolism, genetic information processing, and cellular processes. CONCLUSION It gives an insight into a better understanding of the molecular mechanisms relevant to liver tumorigenesis. The unique whole transcriptomic molecular signatures could provide an important data to predict the treatment response to molecular therapies in metastatic liver cancer.

Analysis of Phyllosphere Microorganisms and Potential Pathogens of Tobacco Leaves.

In the tobacco phyllosphere, some of the microbes may have detrimental effects on plant health, while many may be neutral or even beneficial. Some cannot be cultivated, so culture-independent methods are needed to explore microbial diversity. In this study, both metagenetic analysis and traditional culture-dependent methods were used on asymptomatic healthy leaves and symptomatic diseased leaves of tobacco plants. In the culture-independent analysis, asymptomatic leaves had higher microbial diversity and richness than symptomatic leaves. Both asymptomatic and symptomatic leaves contained several potentially pathogenic bacterial and fungal genera. The putative bacterial pathogens, such as species of Pseudomonas, Pantoea, or Ralstonia, and putative fungal pathogens, such as species of Phoma, Cladosporium, Alternaria, Fusarium, Corynespora, and Epicoccum, had a higher relative abundance in symptomatic leaves than asymptomatic leaves. FUNGuild analysis indicated that the foliar fungal community also included endophytes, saprotrophs, epiphytes, parasites, and endosymbionts. PICRUSt analysis showed that the dominant functions of the bacterial community in a symptomatic leaf were cellular processes and environmental information processing. In the other five foliar samples, the dominant functions of the bacterial community were genetic information processing, metabolism, and organismal systems. In the traditional culture-dependent method, 47 fungal strains were isolated from 60 symptomatic tobacco leaf fragments bearing leaf spots. Among them, 21 strains of Colletotrichum (29%), Xylariaceae (14%), Corynespora (14%), Pestalotiopsis (10%), Alternaria (10%), Epicoccum (10%), Byssosphaeria (5%), Phoma (5%), and Diaporthe (5%) all fulfilled Koch’s postulates and were found to cause disease on detached tobacco leaves in artificial inoculation tests. Symptoms on detached leaves caused by three strains of Corynespora cassiicola in artificial inoculation tests were similar to the original disease symptoms in the tobacco field. This study showed that the combined application of culture-dependent and independent methods could give comprehensive insights into microbial composition that each method alone did not reveal.

Research Note: The gut microbiota varies with dietary fiber levels in broilers

It is generally accepted the gut microbiota have a profound effect on the nutrition, health, and production in poultry. To deeply understand the gut microbiota composition with the dietary fiber level in broilers, we evaluated the cecal microbiota profiles feeding on different dietary fiber level with alfalfa as additive in Dahen broilers based on 16S rRNA gene sequencing and gas chromatography. As a result, the gut microbiota diversity was greatly accelerated with the dietary fiber level. The dietary fiber stimulated the growth of many intestinal communities such as Rikenellaceae RC9 gut group, Faecalibacterium, Prevotellaceae UCG 001 and Ruminococcaceae UCG 014, and led to an altered microbial function such as Carbohydrate metabolism and Genetic information processing. Meanwhile, we found the genera Anaerofilum and Dielma were significantly correlated with the production of short chain fatty acids (SCFAs). All these results provide a reference for the broilers gut microbiota changes with different dietary fiber level. The key role of the altered microbiota with the dietary fiber may mediate beneficial effects in broiler production, which also reflect the substantial potential of dietary fiber level in poultry.

Proteomic Response of Bacillus subtilis Spores under High Pressure Combined with Moderate Temperature and Random Peptide Mixture LK Treatment.

In this study, a method of Bacillus subtilis spore inactivation under high pressure (P, 200 MPa) combined with moderate temperature (T, 80 °C) and the addition of antimicrobial peptide LK (102 μg/mL) was investigated. Spores presented cortex hydrolysis and inner membrane (IM) damage with an 8.16 log reduction in response to treatment with PT-LK, as observed by phase-contrast and inverted fluorescence microscopy and flow cytometry (FCM) analysis. Furthermore, a tandem mass tag (TMT) quantitative proteomics approach was utilized because Liquid chromatography-tandem mass spectrometry (LC–MS/MS) analysis data were used. After treatment with PT-LK, 17,017 polypeptides and 3166 proteins were detected from B. subtilis spores. Among them, 78 proteins showed significant differences in abundance between the PT-LK-treated and control groups, with 49 proteins being upregulated and 29 proteins being downregulated in the PT-LK-treated group. Genetic information processing, metabolism, cellular process, and environmental information processing were the main mechanisms of PT-LK-mediated spore inactivation.

Bovine host genome acts on rumen microbiome function linked to methane emissions

Our study provides substantial evidence that the host genome affects the comprehensive function of the microbiome in the rumen of bovines. Of 1,107/225/1,141 rumen microbial genera/metagenome assembled uncultured genomes (RUGs)/genes identified from whole metagenomics sequencing, 194/14/337 had significant host genomic effects (heritabilities ranging from 0.13 to 0.61), revealing that substantial variation of the microbiome is under host genomic control. We found 29/22/115 microbial genera/RUGs/genes host-genomically correlated (|0.59| to |0.93|) with emissions of the potent greenhouse gas methane (CH4), highlighting the strength of a common host genomic control of specific microbial processes and CH4. Only one of these microbial genes was directly involved in methanogenesis (cofG), whereas others were involved in providing substrates for archaea (e.g. bcd and pccB), important microbial interspecies communication mechanisms (ABC.PE.P), host-microbiome interaction (TSTA3) and genetic information processes (RP-L35). In our population, selection based on abundances of the 30 most informative microbial genes provided a mitigation potential of 17% of mean CH4 emissions per generation, which is higher than for selection based on measured CH4 using respiration chambers (13%), indicating the high potential of microbiome-driven breeding to cumulatively reduce CH4 emissions and mitigate climate change.

Ecological impacts of sea-crossing bridge construction on local sediment microbiome in East China

With the increasing global human activities, local microbial communities will be dramatically changed and impaired. Sea-crossing bridges have been constructed worldwide with the rapid economic development. However, knowledge about impacts of bridge constructions on diversity and functional shifts of local microbiota is lacking. In the present study, high-throughput sequencing and bioinformatics were implemented to compare changes of microbial communities between sediments influenced by sea-crossing bridge construction (EG group) and the surrounding control sediments (CG group). High levels of beta diversity in EG group indicated environmental changes and bridge construction increased local microbial diversity. Comparative analyses revealed significant changes in microbial composition and abundance and a total of 17 indicator species were detected using LEfSe approach. The predicted functional attributes of microbiota revealed most of which were involved in metabolism, environmental and genetic information processing. Notably, annotated pathways involved in human diseases were significantly enriched in EG group, revealing potential deleterious effects of public health security influenced by bridge construction. For the first time, our study revealed significant changes in local microbial communities affected by sea-crossing bridge construction. We suggested local biodiversity and human health should be specifically noticed in engineering construction process. These results may greatly enhance our understanding of the microbial responses to marine infrastructure and civil engineering.

Effects of Host Plant and Insect Generation on Shaping of the Gut Microbiota in the Rice Leaffolder, Cnaphalocrocis medinalis.

Gut microbes in insects may play an important role in the digestion, immunity and protection, detoxification of toxins, development, and reproduction. The rice leaffolder Cnaphalocrocis medinalis (Guenée) (Lepidoptera: Crambidae) is a notorious insect pest that can damage rice, maize, and other gramineous plants. To determine the effects of host plants and generations on the gut microbiota of C. medinalis, we deciphered the bacterial configuration of this insect pest fed rice or maize for three generations by Illumina MiSeq technology. A total of 16 bacterial phyla, 34 classes, 50 orders, 101 families, 158 genera, and 44 species were identified in C. medinalis fed rice or maize for three generations. Host plants, insect generation, and their interaction did not influence the alpha diversity indices of the gut microbiota of C. medinalis. The dominant bacterial taxa were Proteobacteria and Firmicutes at the phylum level and Enterococcus and unclassified Enterobacteriaceae at the genus level. A number of twenty genera coexisted in the guts of C. medinalis fed rice or maize for three generations, and their relative abundances occupied more than 90% of the gut microbiota of C. medinalis. A number of two genera were stably found in the gut of rice-feeding C. medinalis but unstably found in the gut microbiota of maize-feeding C. medinalis, and seven genera were stably found in the gut of maize-feeding C. medinalis but unstably found in the gut of rice-feeding C. medinalis. In addition, many kinds of microbes were found in some but not all samples of the gut of C. medinalis fed on a particular host plant. PerMANOVA indicated that the gut bacteria of C. medinalis could be significantly affected by the host plant and host plant × generation. We identified 47 taxa as the biomarkers for the gut microbiota of C. medinalis fed different host plants by LEfSe. Functional prediction suggested that the most dominant role of the gut microbiota in C. medinalis is metabolism, followed by environmental information processing, cellular processes, and genetic information processing. Our findings will enrich the understanding of gut bacteria in C. medinalis and reveal the differences in gut microbiota in C. medinalis fed on different host plants for three generations.