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Gut microbiota and differential GENES-maintained homeostasis is key to maintaining health of individuals with Yang-deficiency constitution

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Journal of Traditional Chinese Medicine 2022年第1期42卷 96-101页

作者： ZHANG Huixiang WANG Limei GUO Jipeng WANG Jiai ZHANG Qianqian WANG Yutao LIU Xun ZHANG Lihuan SHI Lanlan WU Hongxiang CAO Xue Institute of Neuroscience Basic Medical CollegeKunming Medical UniversityKunming 650500China Department of Laboratory Animal Science Kunming Medical UniversityKunming 650500China Department of Laboratory Animal Science Kunming Medical UniversityState Key Laboratory for Conservation and Utilization of Bio-Resources in YunnanYunnan UniversityKunming 650500Chin Faculty of Rehabilitation Medicine Kunming Medical UniversityKunming 650500China School of Electrical and Information Technology Yunnan Minzu UniversityKunming 650500China School of Medicine Kunming UniversityKunming 650214China Basic Medical College Kunming Medical UniversityKunming 650500China Department of Anatomy Histology and EmbryologyBasic Medical CollegeKunming Medical UniversityKunming 650500China

OBJECTIVE:Yang-deficiency constitution(YADC)is a common unbalanced constitution that predisposes individuals to certain diseases.However,not all people with YADC manifest develop diseases.This calls for delineation of the underlying molecular mechanisms.Previous studies suggested that the gut microbiota and gene differential expression should be considered.METHODS:In the present study,we compared profiles of gut microbiota between four healthy YADC individuals and those of five healthy balanced constitution(BC)counterparts,based on 16 S r RNA gene sequence analysis.Furthermore,YADC relevant GENES identified by comparing 62 healthy YADC and 58 healthy BC individuals in total to perform intersection analysis,functional clustering and pathway enrichment analyses.RESULTS:The levels of harmful gut microbiota(Prevotellaceae,LDA score>4.0,P=0.0141)and beneficial gut microbiota(Ruminococcaceae,LDA score>4.0,P=0.0025,Faecalibacterium,LDA score>4.0,P=0.0484)were both elevated in healthy YADC individuals.Also,we found that the specific metabolic pathway with 2,6-Dichloro-p-hydroquinone 1,2-Dioxygenase(Pcp A)as the core in gut microbiota and the glutathione transferase activity has been enriched by YADC relevant GENES in healthy YADC individuals were both responsible for the detoxification of halogenated aromatic hydrocarbon substances.CONCLUSIONS:Both beneficial and harmful factors had been detected in healthy YADC individuals,functionally,they may have triggered homeostasis to maintain the health of individuals with YADC.The homeostasis may be maintained by beneficial and harmful factors from gut flora and GENES.Future studies are expected to focus on halogenated aromatic hydrocarbons and their detoxification processes.

关键词： Yang deficiency physical constitution theory health promotion gastrointestinal microbiome GENES hydrocarbons aromatic homeostasis

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Distribution and relationship between antimicrobial resistance GENES and heavy metals in surface sediments of Taihu Lake,China

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Journal of Environmental Sciences 2019年第3期31卷 323-335页

作者： Okugbe E.Ohore Felix Gyawu Addo Songhe Zhang Nini Han Kwaku Anim-Larbi Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes College of Environment Hohai University

Heavy metals, pharmaceuticals, and other wastes released into the environment can significantly influence environmental antibiotic resistance. We investigated the occurrence of 22 antimicrobial resistance GENES(ARGs) and 10 heavy metal concentrations, and the relationship between ARGs and heavy metals in surface sediment from seven sites of Lake Taihu. The results showed significant correlations(p GENES, but the strength of interaction was diminished with increasing depth. For most of the heavy metals, the concentration of elements in the top sediments was higher than that in other depths.Tetracycline resistance GENES(tet(A), tet(B), tet(D), tet(E) and tet(O), β-lactam resistance GENES(SHV, TEM, CTX, OXA and OXY) and sulfonamide resistance GENES(sulA, sul1, sul2, sul3 and int-1) were detected. They showed a trend which inferred a statistically significant increase followed by decreases in the relative abundance of these ARGs(normalized to 16 S rRNA GENES) with increasing depth. This study revealed that tet(A), tet(O), TEM, OXY, int-1, sul1 and sul3 were widespread in surface sediments with high abundance, indicating that these GENES deserve more attention in future work.

关键词： Antibiotic resistance GENES Heavy metals Surface sediments Taihu Lake Wastewater treatment plants Pollution

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Fate of antibiotics and antibiotic resistance GENES in a full-scale restaurant food waste treatment plant:Implications of the roles beyond heavy metals and mobile genetic elements

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Journal of Environmental Sciences 2019年第11期31卷 17-34页

作者： Pinjing He Zhuofeng Yu Liming Shao Yizhou Zhou Fan Lü State Key Laboratory of Pollution Control and Resource Reuse Tongji University Shanghai 200092 China Institute of Waste Treatment and Reclamation Tongji University Shanghai 200092 China Centre for the Technology Research and Training on Household Waste in Small Towns & Rural Area Ministry of Housing and Urban-Rural Development of PR China(MOHURD) China Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092 China

Is our food safe and free of the crisis of antibiotics and antibiotic resistance (AR)?And will the derived food waste (FW) impose AR risk to the environment after biological treatment? This study used restaurant FW leachates flowing through a 200 tons-waste/day biological treatment plant as a window to investigate the fate of antibiotics and antibiotic-resistance GENES (ARGs) during the acceptance and treatment of FW.Sulfonamides (sulfamethazine,sulfamethoxazole) and quinolones (ciprofloxacin,enrofloxacin,ofloxacin) were detected during FW treatment,while tetracyclines,macrolides and chloramphenicols were not observable.ARGs encoding resistance to sulfonamides,tetracyclines and macrolides emerged in FW leachates.Material flow analysis illustrated that the total amount of antibiotics (except sulfamethazine) and ARGs were constant during FW treatment processes.Both the concentration and total amount of most antibiotics and ARGs fluctuated during treatment,physical processes (screening,centrifugation,solid-liquid and oil-water separation) did not decrease antibiotic or ARGs concentrations or total levels permanently;the affiliated wastewater treatment plant appeared to remove sulfonamides and most ARGs concentrations and total amount.Heavy metals Ni,Co and Cu were important for disseminating antibiotics concentrations and MGEs for distributing ARGs concentrations.Humic substances (fulvic acids,hydrophilic fractions),C-associated and N-associated contents were essential for the distribution of the total amounts of antibiotics and ARGs.Overall,this study implied that human food might not be free of antibiotics and ARGs,and FW was an underestimated AR pool with various determinants.Nonetheless,derived hazards of FW could be mitigated through biological treatment with well-planned daily operations.

关键词： Food waste Biological treatment Anaerobic digestion Antibiotics Antibiotic resistance GENES Material flow analysis

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Vertical response of microbial community and degrading GENES to petroleum hydrocarbon contamination in saline alkaline soil

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Journal of Environmental Sciences 2019年第7期31卷 80-92页

作者： Qinglong Liu Jingchun Tang Xiaomei Liu Benru Song Meinan Zhen Nicholas J.Ashbolt College of Environmental Science and Engineering Nankai University Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education) Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation School of Public Health University of Alberta

A column microcosm was conducted by amending crude oil into Dagang Oilfield soil to simulate the bioremediation process. The dynamic change of microbial communities and metabolic GENES in vertical depth soil from 0 to 80 cm were characterized to evaluate the petroleum degradation potential of indigenous microorganism. The influence of environmental variables on the microbial responds to petroleum contamination were analyzed. Degradation extent of 42.45% of n-alkanes(C8–C40) and 34.61% of 16ΣPAH were reached after 22 weeks. Relative abundance of alkB, nah, and phe gene showed about 10-fold increment in different depth of soil layers. Result of HTS profiles demonstrated that Pseudomonas, Marinobacter and Lactococcus were the major petroleum-degrading bacteria in0–30 and 30–60 cm depth of soils. Fusarium and Aspergillus were the dominant oil-degrading fungi in the 0–60 cm depth of soils. In 60–80 cm deep soil, anaerobic bacteria such as Bacteroidetes, Lactococcus, and Alcanivorax played important roles in petroleum degradation.Redundancy analysis(RDA) and correlation analysis demonstrated that petroleum hydrocarbons(PHs) as well as soil salinity, clay content, and anaerobic conditions were the dominant effect factors on microbial community compositions in 0–30, 30–60, and 60–80 cm depth of soils, respectively.

关键词： Column microcosm Molecular analyses Petroleum hydrocarbons Microbial community Catabolic GENES Saline alkaline soil

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Occurrence and distribution of antibiotic resistance GENES in the sediments of the East China Sea bays

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Journal of Environmental Sciences 2019年第7期31卷 156-167页

作者： Jiayu Chen Zhiguo Su Tianjiao Dai Bei Huang Qinglin Mu Yongming Zhang Donghui Wen School of Environmental and Geography Sciences Shanghai Normal University College of Environmental Sciences and Engineering Peking University Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station

The coastal area of the East China Sea has experienced rapid urbanization and industrialization in China since 1980 s, resulting in severe pollution of its environments.Antibiotic resistance GENES(ARGs) are regarded as a kind of emerging pollutant with potential high risk. The sediment samples were collected from Hangzhou Bay(HB),Xiangshan Bay(XB), and Taizhou Bay(TB) to investigate the spatial occurrence and distribution of 27 ARGs and class I integron–integrase gene(intI1) in the coastal area of the East China Sea. The PCR results showed the frequent presence of 11 ARGs and intI1 in the sediments of the three bays. The qPCR results further showed that sulfonamide resistance was the most prevalent ARG type and antibiotic target replacement and protection were the most important resistance mechanisms in the sediments. Regarding the subtype of ARGs, sulI, tetW, and dfrA13 were the most abundant ARGs, in which sulI was higher in TB(based on both the absolute and relative abundances) and dfrA13 was higher in HB(based on the relative abundances). The network analysis revealed that intI1 had significant correlations with tetC, sulI, sulII, and blaPSE-1. Oil was the key connected factor, which had positive connections with sulI, sulII, and blaPSE-1. In addition, the joint effect of heavy metals and nutrients & organic pollutants might be crucial for the fate of ARGs in the coastal sediments.

关键词： Antibiotic resistance GENES (ARGs) Class I integron–integrase gene(intI1) the East China Sea sediment

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Occurrence of human pathogenic bacteria carrying antibiotic resistance GENES revealed by metagenomic approach: A case study from an aquatic environment

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Journal of Environmental Sciences 2019年第6期31卷 248-256页

作者： Renjun Zhou Shenzheng Zeng Dongwei Hou Jian Liu Shaoping Weng Jianguo He Zhijian Huang State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering School of MarineSciences Sun Yat-sen University School of Life Sciences Sun Yat-sen University

Antibiotic resistance GENES(ARGs), human pathogenic bacteria(HPB), and HPB carrying ARGs are public issues that pose a high risk to aquatic environments and public health. Their diversity and abundance in water, intestine, and sediments of shrimp culture pond were investigated using metagenomic approach. A total of 19 classes of ARGs, 52 HPB species, and 7 species of HPB carrying ARGs were found. Additionally, 157, 104, and 86 subtypes of ARGs were detected in shrimp intestine, pond water, and sediment samples, respectively. In all the samples, multidrug resistance GENES were the highest abundant class of ARGs. The dominant HPB was Enterococcus faecalis in shrimp intestine, Vibrio parahaemolyticus in sediments, and Mycobacterium yongonense in water, respectively. Moreover, E. faecalis(contig Intestine_364647)and Enterococcus faecium(contig Intestine_80272) carrying efr A, efr B and ANT(6)-Ia were found in shrimp intestine, Desulfosaricina cetonica(contig Sediment_825143) and Escherichia coli(contig Sediment_188430) carrying mex B and APH(3′)-IIa were found in sediments, and Laribacter hongkongensis(contig Water_478168 and Water_369477), Shigella sonnei(contig Water_880246),and Acinetobacter baumannii(contig Water_525520) carrying sul1, sul2, ere A, qac H, OXA-21, and mph D were found in pond water. Mobile genetic elements(MGEs) analysis indicated that horizontal gene transfer(HGT) of integrons, insertion sequences, and plasmids existed in shrimp intestine, sediment, and water samples, and the abundance of integrons was higher than that of other two MGEs. The results suggested that HPB carrying ARGs potentially existed in aquatic environments, and that these contributed to the environment and public health risk evaluation.

关键词： Antibiotic resistance GENES Human pathogenic bacteria Mobile genetic elements Aquatic environment

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Abundance of antibiotic resistance GENES and their association with bacterial communities in activated sludge of wastewater treatment plants: Geographical distribution and network analysis

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Journal of Environmental Sciences 2019年第8期31卷 24-38页

作者： Haihan Zhang Huiyan He Shengnan Chen Tinglin Huang Kuanyu Lu Zhonghui Zhang Rong Wang Xueyao Zhang Hailong Li Key Laboratory of Northwest Resource Environment and Ecology MOE Xi'an University of Architecture and Technology Shaanxi Key Laboratory of Environmental Engineering Xi'an University of Architecture and Technology Xi'an Environmental Monitoring Center Research Institute of Applied Biology Shanxi University

Wastewater treatment plants(WWTPs) are deemed reservoirs of antibiotic resistance GENES(ARGs). Bacterial phylogeny can shape the resistome in activated sludge. However, the co-occurrence and interaction of ARGs abundance and bacterial communities in different WWTPs located at continental scales are still not comprehensively understood. Here, we applied quantitative PCR and Miseq sequence approaches to unveil the changing profiles of ARGs(sul1, sul2, tet W, tet Q, tet X), int I1 gene, and bacterial communities in 18 geographically distributed WWTPs. The results showed that the average relative abundance of sul1 and sul2 GENES were 2.08 × 10^(-1) and 1.32 × 10^(-1) copies/16 S rRNA copies, respectively. The abundance of tet W gene was positively correlated with the Shannon diversity index(H′), while both studied sul GENES had significant positive relationship with the int I1 gene. The highest average relative abundances of sul1, sul2, tet X, and int I1 GENES were found in south region and oxidation ditch system. Network analysis found that 16 bacterial genera co-occurred with tet W gene. Co-occurrence patterns were revealed distinct community interactions between aerobic/anoxic/aerobic and oxidation ditch systems. The redundancy analysis model plot of the bacterial community composition clearly demonstrated that the sludge samples were significant differences among those from the different geographical areas,and the shifts in bacterial community composition were correlated with ARGs. Together,these findings from the present study will highlight the potential risks of ARGs and bacterial populations carrying these ARGs, and enable the development of suitable technique to control the dissemination of ARGs from WWTPs into aquatic environments.

关键词： Antibiotic resistance GENES Activate sludge Bacterial community Network analysis Mobile genetic elements

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Bioinformatic identification of key candidate GENES and pathways in axon regeneration after spinal cord injury in zebrafish

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Neural Regeneration Research 2020年第1期15卷 103-111页

作者： Jia-He Li Zhong-Ju Shi Yan Li Bin Pan Shi-Yang Yuan Lin-Lin Shi Yan Hao Fu-Jiang Cao Shi-Qing Feng Department of Orthopedics Tianjin Medical University General HospitalTianjinChina Department of Orthopedics the Affiliated Hospital of Xuzhou Medical UniversityXuzhouJiangsu ProvinceChina Tianjin Neurological Institute Key Laboratory of Post-Neuroinjury Neurorepair and Regeneration in Central Nervous SystemMinistry of Education and Tianjin CityTianjinChina

Zebrafish and human genomes are highly homologous;however,despite this genomic similarity,adult zebrafish can achieve neuronal proliferation,regeneration and functional restoration within 6–8 weeks after spinal cord injury,whereas humans cannot.To analyze differentially expressed zebrafish GENES between axon-regenerated neurons and axon-non-regenerated neurons after spinal cord injury,and to explore the key GENES and pathways of axonal regeneration after spinal cord injury,microarray GSE56842 was analyzed using the online tool,GEO2R,in the Gene Expression Omnibus database.Gene ontology and protein-protein interaction networks were used to analyze the identified differentially expressed GENES.Finally,we screened for GENES and pathways that may play a role in spinal cord injury repair in zebrafish and mammals.A total of 636 differentially expressed GENES were obtained,including 255 up-regulated and 381 down-regulated differentially expressed GENES in axon-regenerated neurons.Gene Ontology and Kyoto Encyclopedia of GENES and Genomes enrichment results were also obtained.A protein-protein interaction network contained 480 node GENES and 1976 node connections.We also obtained the 10 hub GENES with the highest correlation and the two modules with the highest score.The results showed that spectrin may promote axonal regeneration after spinal cord injury in zebrafish.Transforming growth factor beta signaling may inhibit repair after spinal cord injury in zebrafish.Focal adhesion or tight junctions may play an important role in the migration and proliferation of some cells,such as Schwann cells or neural progenitor cells,after spinal cord injury in zebrafish.Bioinformatic analysis identified key candidate GENES and pathways in axonal regeneration after spinal cord injury in zebrafish,providing targets for treatment of spinal cord injury in mammals.

关键词： axonal regeneration differentially expressed GENES focal adhesions Gene Ontology Kyoto Encyclopedia of GENES and Genomes neural regeneration protein-protein interaction network signaling pathway spectrin tight junctions transforming growth factor beta Wnt signaling pathway

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Bioinformatics analyses of differentially expressed GENES associated with spinal cord injury:a microarray-based analysis in a mouse model

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Neural Regeneration Research 2019年第7期14卷 1262-1270页

作者： Lei Guo Jing Lv Yun-Fei Huang Ding-Jun Hao Ji-Jun Liu Department of Spinal Surgery Honghui HospitalXi'an Jiaotong University Department of Clinical Laboratory Honghui HospitalXi'an Jiaotong University

Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new opportunity for investigating diagnosis,treatment,and prognosis of spinal cord injury.However,differentially expressed GENES are not consistent among studies,and many key GENES and signaling pathways have not yet been accurately studied.GSE5296 was retrieved from the Gene Expression Omnibus DataSet.Differentially expressed GENES were obtained using R/Bioconductor software(expression changed at least two-fold;P GENES and Animal Transcription Factor Database for predicting potential transcription factors.The resulting transcription regulatory protein interaction network was mapped to screen representative GENES and investigate their diagnostic and therapeutic value for disease.In total,this study identified 109 GENES that were upregulated and 30 that were downregulated at 0.5,4,and 24 hours,and 3,7,and 28 days after spinal cord injury.The number of downregulated GENES was smaller than the number of upregulated GENES at each time point.Database for Annotation,Visualization and Integrated Discovery analysis found that many inflammation-related pathways were upregulated in injured spinal cord.Additionally,expression levels of these inflammation-related GENES were maintained for at least 28 days.Moreover,399 regulation modes and 77 nodes were shown in the protein-protein interaction network of upregulated differentially expressed GENES.Among the 10 upregulated differentially expressed GENES with the highest degrees of distribution,six GENES were transcription factors.Among these transcription factors,ATF3 showed the greatest change.ATF3 was upregulated within 30 minutes,and its expression levels remained high at28 days after spinal cord injury.These key GENES screened by bioin

关键词： nerve regeneration spinal cord injury differentially expressed GENES bioinformatics analyses Database for Annotation,Visualization and Integrated Discovery analysis inflammation Kyoto Encyclopedia of GENES and Genomes pathway microarray transcription factors neural regeneration

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Comprehensive transcriptome analysis based on RNA sequencing identifies critical GENES for lipopolysaccharide-induced epididymitis in a rat model

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Asian Journal of Andrology 2019年第6期21卷 605-611页

作者： Xin Song Nan-He Lin You-Lin Wang Bin Chen Hong-Xiang Wang Kai Hu Department of Urology Shanghai Institute of AndrologyRenji HospitalShanghai Jiao Tong University School of MedicineShanghai 200001China.

Epididymitis is a comm only diagnosed disease associated with male infertility.However,little is known about the molecules that are involved in its development.This study was to identify critical GENES associated with lipopolysaccharide-induced epididymitis and an a lyze the molecular mecha nism of epididymitis through RNA sequencing.Experime ntal epididymitis models were generated by administering male Sprague-Dawley rats'lipopolysaccharide.A total of 1378 differentially expressed GENES,including 531 upregulated and 847 down regulated gen es,were identified in the epididymitis model rats compared with those in sham-operated rats by RNA seque ncing.Fun ctional enrichme nt an a lyses suggested that the upregulated GENES were markedly enriched in inflammati on.related biological processes,as well as in the tumor necrosis factor(TNF)signaling pathway,cytokine-cytokine receptor interactions,complement and coagulation cascades,and in the chemokine signalipathway.Four downregulated GENES(collagen type XXVⅢalpha 1 chain[Col28α1],cyclirndependent kinase-like 1[Cdkl1],phosphoserine phosphatase[Psph],and fatty acid desaturase 2[Fads2])and ten upregulated GENES(CCAAT/enhancer-binding protein beta[Cebp0],C-X-C motif chemokine receptor 2[Cxcr2],interleukin 11[ll11],C-C motif chemokine ligand 20[Ccl20],nuclear factor-kappa-B inhibitor alpha[NfKbia],claudin 4[Cldn4],matrix metallopeptidase 9[Mmp9],heat shock 70 kDa protein 8[Hspa8],intercellular cell adhesion molecule-1[Icam1],and Jun)were successfully confirmed by real-time polymerase chai n reaction.Wester n blot dem on strated that CDKL1 was decreased,while MMP9 and NFKBIA were increased in the experimental model group compared with those in the sham-operated group.Our study sheds new light on the understand!ng of the early response of the epididymis during bacterial epididymitis.

关键词： differentially expressed GENES epididymitis inflammation lipopolysaccharide

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