Study on Microbial Community Succession and Functional Analysis during Biodegradation of Mushroom Residue

In this study, 16S rRNA high-throughput sequencing technology was used to analyze the composition and diversity of bacterial and fungal communities in mushroom residue samples at different composting stages. During the composting process, the maximum temperature in the center of the pile can reach 52.4°C, and the temperature above 50°C has been maintained for about 8 days. The results showed that Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, and Chloroflexi were the main microorganisms in the composting process, accounting for 98.9%-99.7% of the total bacteria. Furthermore, in order to obtain the protein expressed in each stage of composting, the nonstandard quantitative method (label free) was used to analyze it quantitatively by mass spectrometry, anda total of 22815 proteins were identified. It indicated that the number of identified proteins related to cellulose decomposition and the number of differentially expressed proteins were significantly enriched, and the functional proteins related to cellulose decomposition had significant stage correspondence.

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Analysis of the structure of bacterial and fungal communities in disease suppressive and disease conducive tobacco-planting soils in China

Soil Research ◽

10.1071/sr19204 ◽

2020 ◽

Vol 58 (1) ◽

pp. 35

Author(s):

Lin Gao ◽

Rui Wang ◽

Jiaming Gao ◽

Fangming Li ◽

Guanghua Huang ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Soil Samples ◽

Fungal Communities ◽

Sequencing Technology ◽

Operational Taxonomic Units ◽

Tobacco Cultivation ◽

Bacteria And Fungi ◽

Disease Suppressive Soil ◽

Conducive Soil

To clarify the differences between microbial communities resident in disease suppressive soil (DSS) and disease conducive soil (DCS) in tobacco cultivation, representative soil samples were collected from tobacco plantations in Shengjiaba, China, and the structure and diversity of the resident bacterial and fungal communities were analysed using high-throughput sequencing technology. Our results showed a greater number of operational taxonomic units associated with bacteria and fungi in DSS than in DCS. At the phylum level, abundances of Chloroflexi, Saccharibacteria, Firmicutes, and Planctomycetes in DSS were lower than in DCS, but abundance of Gemmatimonadetes was significantly higher. Abundances of Zygomycota and Chytridiomycota were higher in DSS than DCS, but abundance of Rozellomycota was significantly lower. At the genus level, abundances of 18 bacterial and nine fungal genera varied significantly between DSS and DCS. Relative abundances of Acidothermus, Microbacterium, Curtobacterium, and Colletotrichum were higher in DCS than DSS. The Shannon and Chao1 indices of DSS microbial communities were higher than those of DCS communities. High microbial diversity reduces the incidence of soil-borne diseases in tobacco plantations and promotes the formation of DSSs.

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Aerosol Concentrations and Fungal Communities Within Broiler Houses in Different Broiler Growth Stages in Summer

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.775502 ◽

2021 ◽

Vol 8 ◽

Author(s):

Guozhong Chen ◽

Di Ma ◽

Qingrong Huang ◽

Wenli Tang ◽

Maolian Wei ◽

...

Keyword(s):

High Throughput Sequencing ◽

Particle Diameter ◽

Growth Period ◽

Diversity Indices ◽

Fungal Communities ◽

Diameter Distribution ◽

Growth Stages ◽

Human Beings ◽

Sequencing Technology ◽

Poultry Houses

Fungal aerosols in broiler houses are important factors that can harm the health of human beings and broiler. To determine the composite characteristics and changes in fungal aerosols in broiler houses during different broiler growth stages in summer. We analyzed the species, concentration and particle diameter distribution characteristics of the aerosols in poultry houses using an Andersen sampler and internal transcribed spacer 1 (ITS1) high-throughput sequencing technology. The concentration of fungal aerosols in the poultry houses increased as the ages of the broiler increased, which was also accompanied by gradual increases in the variety and diversity indices of the fungal communities in the air of the poultry houses. During the entire broiler growth period, the dominant genera in the fungal aerosols in the poultry houses included Trichosporon, Candida, Aspergillus, Cladosporium and Alternaria. These fungi may be harmful to the health of poultry and human beings, so permanent monitoring of microbial air quality in chicken houses is necessary.

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Clinical Application of High-throughput Sequencing Technology for the Diagnosis of Patients With Severe Infection

Case Medical Research ◽

10.31525/ct1-nct04217252 ◽

2020 ◽

Author(s):

Keyword(s):

Clinical Application ◽

High Throughput ◽

High Throughput Sequencing ◽

Severe Infection ◽

Sequencing Technology

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Fungal Diversity in the Phyllosphere of Pinus heldreichii H. Christ—An Endemic and High-Altitude Pine of the Mediterranean Region

Diversity ◽

10.3390/d12050172 ◽

2020 ◽

Vol 12 (5) ◽

pp. 172 ◽

Cited By ~ 3

Author(s):

Jelena Lazarević ◽

Audrius Menkis

Keyword(s):

High Altitude ◽

Bark Beetles ◽

Fungal Pathogens ◽

High Throughput Sequencing ◽

Fungal Communities ◽

High Quality ◽

The Balkans ◽

Fungal Community Structure ◽

Growing Conditions ◽

Coniferous Tree Species

Pinus heldreichii is a high-altitude coniferous tree species naturaly occurring in small and disjuncted populations in the Balkans and southern Italy. The aim of this study was to assess diversity and composition of fungal communities in living needles of P. heldreichii specifically focusing on fungal pathogens. Sampling was carried out at six different sites in Montenegro, where 2-4 year-old living needles of P. heldreichii were collected. Following DNA isolation, it was amplified using ITS2 rDNA as a marker and subjected to high-throughput sequencing. Sequencing resulted in 31,831 high quality reads, which after assembly were found to represent 375 fungal taxa. The detected fungi were 295 (78.7%) Ascomycota, 79 (21.0%) Basidiomycota and 1 (0.2%) Mortierellomycotina. The most common fungi were Lophodermium pinastri (12.5% of all high-quality sequences), L. conigenum (10.9%), Sydowia polyspora (8.8%), Cyclaneusma niveum (5.5%), Unidentified sp. 2814_1 (5.4%) and Phaeosphaeria punctiformis (4.4%). The community composition varied among different sites, but in this respect two sites at higher altitudes (harsh growing conditions) were separated from three sites at lower altitudes (milder growing conditions), suggesting that environmental conditions were among major determinants of fungal communities associated with needles of P. heldreichii. Trees on one study site were attacked by bark beetles, leading to discolouration and frequent dieback of needles, thereby strongly affecting the fungal community structure. Among all functional groups of fungi, pathogens appeared to be an important component of fungal communities in the phyllosphere of P. heldreichii, especially in those trees under strong abiotic and biotic stress.

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Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherichia coli biofilm formation in co-culture

Proteome Science ◽

10.1186/s12953-021-00172-0 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Huiyi Song ◽

Ni Lou ◽

Jianjun Liu ◽

Hong Xiang ◽

Dong Shang

Keyword(s):

Escherichia Coli ◽

Proteomic Analysis ◽

Biofilm Formation ◽

Lactobacillus Rhamnosus ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

Label Free ◽

Quantitative Proteomic Analysis ◽

E Coli ◽

Protein Ubiquitination

Abstract Background Escherichia coli (E. coli) is the principal pathogen that causes biofilm formation. Biofilms are associated with infectious diseases and antibiotic resistance. This study employed proteomic analysis to identify differentially expressed proteins after coculture of E. coli with Lactobacillus rhamnosus GG (LGG) microcapsules. Methods To explore the relevant protein abundance changes after E. coli and LGG coculture, label-free quantitative proteomic analysis and qRT-PCR were applied to E. coli and LGG microcapsule groups before and after coculture, respectively. Results The proteomic analysis characterised a total of 1655 proteins in E. coli K12MG1655 and 1431 proteins in the LGG. After coculture treatment, there were 262 differentially expressed proteins in E. coli and 291 in LGG. Gene ontology analysis showed that the differentially expressed proteins were mainly related to cellular metabolism, the stress response, transcription and the cell membrane. A protein interaction network and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the differentiated proteins were mainly involved in the protein ubiquitination pathway and mitochondrial dysfunction. Conclusions These findings indicated that LGG microcapsules may inhibit E. coli biofilm formation by disrupting metabolic processes, particularly in relation to energy metabolism and stimulus responses, both of which are critical for the growth of LGG. Together, these findings increase our understanding of the interactions between bacteria under coculture conditions.

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The Banana Root Endophytome: Differences between Mother Plants and Suckers and Evaluation of Selected Bacteria to Control Fusarium oxysporum f.sp. cubense

Journal of Fungi ◽

10.3390/jof7030194 ◽

2021 ◽

Vol 7 (3) ◽

pp. 194

Author(s):

Carmen Gómez-Lama Cabanás ◽

Antonio J. Fernández-González ◽

Martina Cardoni ◽

Antonio Valverde-Corredor ◽

Javier López-Cepero ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Canary Islands ◽

High Throughput Sequencing ◽

Fungal Communities ◽

Phenological Stage ◽

Mother Plants ◽

Fusarium Wilt Of Banana ◽

Identification And Characterization

This study aimed to disentangle the structure, composition, and co-occurrence relationships of the banana (cv. Dwarf Cavendish) root endophytome comparing two phenological plant stages: mother plants and suckers. Moreover, a collection of culturable root endophytes (>1000) was also generated from Canary Islands. In vitro antagonism assays against Fusarium oxysporum f.sp. cubense (Foc) races STR4 and TR4 enabled the identification and characterization of potential biocontrol agents (BCA). Eventually, three of them were selected and evaluated against Fusarium wilt of banana (FWB) together with the well-known BCA Pseudomonas simiae PICF7 under controlled conditions. Culturable and non-culturable (high-throughput sequencing) approaches provided concordant information and showed low microbial diversity within the banana root endosphere. Pseudomonas appeared as the dominant genus and seemed to play an important role in the banana root endophytic microbiome according to co-occurrence networks. Fungal communities were dominated by the genera Ophioceras, Cyphellophora, Plecosphaerella, and Fusarium. Overall, significant differences were found between mother plants and suckers, suggesting that the phenological stage determines the recruitment and organization of the endophytic microbiome. While selected native banana endophytes showed clear antagonism against Foc strains, their biocontrol performance against FWB did not improve the outcome observed for a non-indigenous reference BCA (strain PICF7).

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Label-Free Comparative Proteomics of Differentially Expressed Mycobacterium tuberculosis Protein in Rifampicin-Related Drug-Resistant Strains

Pathogens ◽

10.3390/pathogens10050607 ◽

2021 ◽

Vol 10 (5) ◽

pp. 607

Author(s):

Nadeem Ullah ◽

Ling Hao ◽

Jo-Lewis Banga Ndzouboukou ◽

Shiyun Chen ◽

Yaqi Wu ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Drug Targets ◽

Control Strategies ◽

Multidrug Resistant ◽

Differentially Expressed ◽

Effective Control ◽

Drug Resistant ◽

Differentially Expressed Proteins ◽

Label Free ◽

Candidate Target

Rifampicin (RIF) is one of the most important first-line anti-tuberculosis (TB) drugs, and more than 90% of RIF-resistant (RR) Mycobacterium tuberculosis clinical isolates belong to multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. In order to identify specific candidate target proteins as diagnostic markers or drug targets, differential protein expression between drug-sensitive (DS) and drug-resistant (DR) strains remains to be investigated. In the present study, a label-free, quantitative proteomics technique was performed to compare the proteome of DS, RR, MDR, and XDR clinical strains. We found iniC, Rv2141c, folB, and Rv2561 were up-regulated in both RR and MDR strains, while fadE9, espB, espL, esxK, and Rv3175 were down-regulated in the three DR strains when compared to the DS strain. In addition, lprF, mce2R, mce2B, and Rv2627c were specifically expressed in the three DR strains, and 41 proteins were not detected in the DS strain. Functional category showed that these differentially expressed proteins were mainly involved in the cell wall and cell processes. When compared to the RR strain, Rv2272, smtB, lpqB, icd1, and folK were up-regulated, while esxK, PPE19, Rv1534, rpmI, ureA, tpx, mpt64, frr, Rv3678c, esxB, esxA, and espL were down-regulated in both MDR and XDR strains. Additionally, nrp, PPE3, mntH, Rv1188, Rv1473, nadB, PPE36, and sseA were specifically expressed in both MDR and XDR strains, whereas 292 proteins were not identified when compared to the RR strain. When compared between MDR and XDR strains, 52 proteins were up-regulated, while 45 proteins were down-regulated in the XDR strain. 316 proteins were especially expressed in the XDR strain, while 92 proteins were especially detected in the MDR strain. Protein interaction networks further revealed the mechanism of their involvement in virulence and drug resistance. Therefore, these differentially expressed proteins are of great significance for exploring effective control strategies of DR-TB.

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Identification of sex differentiation-related microRNA and long non-coding RNA in Takifugu rubripes gonads

Scientific Reports ◽

10.1038/s41598-021-83891-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hongwei Yan ◽

Qi Liu ◽

Jieming Jiang ◽

Xufang Shen ◽

Lei Zhang ◽

...

Keyword(s):

Sex Determination ◽

High Throughput Sequencing ◽

Sex Differentiation ◽

Mature Mirnas ◽

Takifugu Rubripes ◽

Sequencing Technology ◽

Non Coding Rna ◽

Differentially Expressed Mirnas ◽

Tiger Pufferfish ◽

Long Non Coding Rna

AbstractAlthough sex determination and differentiation are key developmental processes in animals, the involvement of non-coding RNA in the regulation of this process is still not clarified. The tiger pufferfish (Takifugu rubripes) is one of the most economically important marine cultured species in Asia, but analyses of miRNA and long non-coding RNA (lncRNA) at early sex differentiation stages have not been conducted yet. In our study, high-throughput sequencing technology was used to sequence transcriptome libraries from undifferentiated gonads of T. rubripes. In total, 231 (107 conserved, and 124 novel) miRNAs were obtained, while 2774 (523 conserved, and 2251 novel) lncRNAs were identified. Of these, several miRNAs and lncRNAs were predicted to be the regulators of the expression of sex-related genes (including fru-miR-15b/foxl2, novel-167, novel-318, and novel-538/dmrt1, novel-548/amh, lnc_000338, lnc_000690, lnc_000370, XLOC_021951, and XR_965485.1/gsdf). Analysis of differentially expressed miRNAs and lncRNAs showed that three mature miRNAs up-regulated and five mature miRNAs were down-regulated in male gonads compared to female gonads, while 79 lncRNAs were up-regulated and 51 were down-regulated. These findings could highlight a group of interesting miRNAs and lncRNAs for future studies and may reveal new insights into the function of miRNAs and lncRNAs in sex determination and differentiation.

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