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Agricultural Risk Factors Influence microbial Ecology in Honghu Lake

Genomics, Proteomics & Bioinformatics 2019年第1期17卷 76-90页

作者： Maozhen Han Melissa Dsouza Chunyu Zhou Hongjun Li Junqian Zhang Chaoyun Chen Qi Yao Chaofang Zhong Hao Zhou Jack A Gilbert Zhi Wang Kang Ning Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Key Laboratory of Bioinformatics and Molecularimaging Department of Bioinformatics and Systems Biology College of Life Science and Technology Huazhong University of Science and Technology Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei Institute of Geodesy and GeophysicsChinese Academy of Sciences The Microbiome Center Department of Surgery University of Chicago Argonne National Laboratory Biosciences Division Marine Biological Laboratory State Key Laboratory of Water Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences

Agricultural activities, including stock-farming, planting industry, and fish aquaculture,can affect the physicochemical and biological characters of freshwater lakes. However, the effects of pollution producing by agricultural activities on microbial ecosystem of lakes remain unclear.Hence, in this work, we selected Honghu Lake as a typical lake that is influenced by agriculture activities. We collected water and sediment samples from 18 sites, which span a wide range of areas from impacted and less-impacted areas. We performed a geospatial analysis on the composition of microbial communities associated with physicochemical properties and antibiotic pollution of samples. The co-occurrence networks of water and sediment were also built and analyzed. Our results showed that the microbial communities of impacted and less-impacted samples of water were largely driven by the concentrations of TN, TP, NO_3^--N, and NO_2^--N, while those of sediment were affected by the concentrations of Sed-OM and Sed-TN. Antibiotics have also played important roles in shaping these microbial communities: the concentrations of oxytetracycline and tetracycline clearly reflected the variance in taxonomic diversity and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Furthermore, for samples from both water and sediment, large differences of network topology structures between impacted and less-impacted were also observed. Our results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu Lake.

关键词： Freshwater microbial communities Agriculture activities Antibiotics Human impact

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microbial transglutaminase should be considered as an environmental inducer of celiac disease

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World Journal of Clinical Cases 2019年第22期7卷 3912-3914页

作者： Aaron Lerner Torsten Matthias AESKU.KIPP Institute

Due to the recent interest in food additives that can act as triggering factors in autoimmune diseases including celiac disease(CD),the present letter to the editor expands on the microbial transglutaminase(mTG).It is heavily consumed by a plethora of food processing industries as“glue of proteins”thus improving product’s stability,texture and shelf life.However,more and more information is accumulated lately,questioning its safety.Its cross-linked gliadin complexes are immunogenic in CD.The enzyme increases gliadin uptake,is transported in a trans-epithelial way and deposited below the enterocyte’s line,has antiphagocytic activity,enhances intestinal permeability and creates luminal resistant isopeptide bonds.No doubt that mTG is beneficial to food industries but a caveat to public health is highly recommended.

关键词： microbial transglutaminase Transglutaminase 2 Celiac disease Processedfood Food additive Food industry Immunogenicity Pathogenicity Food safety Publichealth

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Relationship between intestinal microbial dysbiosis and primary liver cancer

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Hepatobiliary & Pancreatic Diseases International 2019年第2期18卷 149-157页

作者： Lei Zhang Yong-Na Wu Tuo Chen Cheng-Hui Ren Xun Li Guang-Xiu Liu Key Laboratory of Desert and Desertification Northwest Institute of Eco-Environment and Resources Chinese Academy of Sciences Key Laboratory of Extreme Environmental microbial Resources and Engineering of Gansu Province University of Chinese Academy of Sciences The First Clinical Medical College Lanzhou University The First Hospital of Lanzhou University Lanzhou University Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province

Background: Intestinal microbial dysbiosis is involved in liver disease pathogenesis. However, its role in primary liver cancer(PLC), particularly in hepatocarcinogenesis remains unclear. The present study aimed to study the changes in intestinal flora at various stages of PLC and clarify the relationship between intestinal microbes and PLC. Methods: Twenty-four patients with PLC(PLC group), 24 patients with liver cirrhosis(LC group), and 23 healthy control individuals(HC group) were enrolled from October 2016 to October 2017. Stool specimens of the participants were collected and the genomic DNA of fecal bacteria was isolated. High-throughput pyrosequencing of 16 S r DNA was used to identify differences in gut bacterial diversity among HC, LC, and PLC groups. We also analyzed the relationship between clinical factors and intestinal microorganisms in LC and PLC groups. Results: Diversity of Firmicutes tended to decrease from the HC to LC and PLC groups at the phylum level. Among species, Enterobacter ludwigii displayed an increasing trend in the PLC group, wherein the relative abundance of Enterobacter ludwigii in the PLC group was 100 times greater than that in the HC and LC groups. The ratio of Firmicutes/Bacteroidetes was significantly decreased with the disease progression. In addition, the linear discriminant analysis effect size method indicated that Clostridia were predominant in the gut microbiota of the HC group, whereas Enterococcaceae, Lactobacillales, Bacilli and Gammaproteobacteria may be used as diagnostic markers of PLC. Redundancy analysis showed a correlation between intestinal microbial diversity and clinical factors AST, ALT, and AFP. Veillonella showed a significant positive correlation with AFP in the PLC group, whereas Subdoligranulum showed a negative correlation with AFP. Conclusions: This study indicates that dysbiosis of the gut microbiota might be involved in PLC development and progression.

关键词： Gut microbiota microbial dysbiosis Hepatocarcinogenesis 16S rDNA

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microbial Contents and Antibiotics Susceptibilities from Hand Washing Stations during COVID-19 Pandemic in Lagos, Nigeria

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Advances in Infectious Diseases 2023年第1期13卷 54-65页

作者： Tajudeen Akanji Bamidele Bamidele Tolulope Odumosu Princess Temitope Adenola James Ameh Joseph Anejo-Okopi Adesola Zaidat Musa Babatunde Osoba Oliver Chukwujekwu Ezechi Babatunde Lawal Salako Nigerian Institute of Medical Research Yaba Nigeria University of Lagos Akoka Nigeria University of Queensland School of Veterinary Science Brisbane Australia Microbiology Department Federal University of Health Sciences Otukpo Nigeria Ministry of Health Lagos Nigeria

The COVID-19 pandemic put every government in the globe on red alert;safety protocol and long-standing infection prevention and control (IPC) measures such as hand and oral hygiene, social/ physical distancing, use of face mask were rigorously enforced. This study evaluated microbial (bacterial, fungal) contents of rinsate, bowl water, water from tap, and the neighborhood drainage in selected hand washing stations in Agege, Alimosho, Mainland, Island and Shomolu local government areas (LGAs) in Lagos, Nigeria. The identities of bacterial isolates were confirmed with 16S rRNA sequencing while the fungi were identified by colonial appearances. The antibiotics susceptibility testing (AST) of the bacteria against structurally unrelated antibiotics was performed and interpreted according to standard guidelines. Sixty-seven (67) bacterial and fifty-one (51) fungal isolates were recovered from mainly water bucket with tap and rinsates across all the LGAs. There were marked microbial loads (some too numerous to count at 10-3 dilution) across Alimosho, Lagos Island and Mainland. Forty (40) representative bacterial isolates were selected for 16S rRNA sequencing. The occurrence of microbial isolates in the samples was at varying degrees;Klebsiella spp. (37.5%), Bacillus spp. (32.5%), Enterobacter spp. (17.5%), were the predominant bacteria while Aspergillus spp. (46.2%), yeasts (34.6%), Sporothrix schenckii (11.5%) and Penicillium spp. (7.7%) constituted the fungal isolates. The biological weapon, B. anthracis was recovered from a water bucket with tap in Alimosho. The antibiotics susceptibility testing of the bacteria showed high degrees of resistance profile;45 (69.2%) to ampicillin, 41.5% amoxicillin/clavulanate while 47.6% were resistant to two (2) or more antibiotics. This study demonstrated high microbial load during the pandemic at the study LGAs, presence of environmental commensals reputed for debilitating opportunistic infections in man and risk of passing heavy load of these potential pathogens to the

关键词： microbial Antibiotics Handwashing COVID-19 Rinsates

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A comprehensive census of lake microbial diversity on a global scale

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Science China(Life Sciences) 2019年第10期62卷 1320-1331页

作者： Jian Yang Hongchen Jiang Hailiang Dong Yongqin Liu State Key Laboratory of Biogeology and Environmental Geology China University of GeosciencesWuhan 430074China State Key Laboratory of Biogeology and Environmental Geology China University of GeosciencesBeijing 100083China Department of Geology and Environmental Earth Science Miami UniversityOxfordOhio 45056USA Institute of Tibetan Plateau Research Chinese Academy of SciencesBeijing 100101China

Despite recent interest in microbial diversity and community structure of lakes across various spatial scales, a global biogeographic distribution pattern and its controlling factors have not been fully disclosed. Here, we compiled and analyzed 88,334,735 environmental 16S rRNA sequences from 431 lakes across a wide range of geographical distance and environmental conditions(in particular, salinity, 0–373.3 gL^–1). Our results showed that lake sediments inhabit significantly(ANOVA: Pmicrobial communities than lake waters. Non-metric dimensional scaling(NMDS) ordinations indicated that microbial community compositions differed distinctly among sample types(freshwater vs. saline, water vs. sediment) and geographic locations. Mantel and partial Mantel tests showed that microbial community composition in lake water was significantly(P=0.001) correlated with geographic distance, salinity, and pH. Statistical analyses based on neutral community and null models indicated that stochastic processes may play predominant roles in shaping the microbial biogeographic distribution patterns in the studied global lake waters. The dispersal-related stochasticity(e.g., homogenizing dispersal) exhibited a stronger influence on the distribution of microbial community in freshwater lakes than in saline lakes. Overall, this work expands our understanding of the impact of geographic distance, environmental conditions, and stochastic processes on microbial distribution in global lakes.

关键词： microbial biogeography lakes geographic distance environmental factors stochastic processes

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microbial Geochemical Characteristics of the Coalbed Methane in the Shizhuangnan Block of Qinshui Basin, North China and their Geological Implications

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Acta Geologica Sinica(English Edition) 2019年第3期93卷 660-674页

作者： LI Yang SHI Wei TANG Shuheng School of Energy Resource China University of GeosciencesBeijing 100083China Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism Ministry of EducationBeijing 100083China Key Laboratory of Strategy Evaluation for Shale Gas Ministry of Land and ResourcesBeijing 100083China

Methanogens and sulfate reducing bacteria were detected by the 16SrRNA sequencing of coalbed methane(CBM)co-produced water in the south of the Qinshui Basin,which is indicative of the presence of secondary biological gas in the south of this basin,in contradiction to the previous understanding of thermogenic gas.This work systematically collected water samples from the CBM wells in the Shizhuangnan Block and analyzed the microbial geochemical characteristics from the aspects of water ions,hydrogen and oxygen isotopes,dissolved inorganic carbon and microbial diversity.It is shown that the Shizhuangnan Block has a nearly SN-trending monoclinic structure,and the elevation of coal seam decreases gradually from the east to west.Because of the water blocking effect of Sitou fault in the west,the precipitation flowed from the east to west,and gradually transited to stagnant flow area.The concentration variation of some ions such as Na^+,K^+,Ca2^+,Mg2^+,Cl^-,HCO3^-and total dissolved solids(TDS)suggest the variation of redox condition in the coal reservoir water.The 16SrDNA sequencing analysis of the collected water samples detected the presence of methanogens and sulfate reduction bacteria.The presence of methane production zone and sulfate methane transition zone(SMTZ)was identified.The effect of methanogens in the methane production zone leads to an increase in the methane concentration,resulting in a high gas content in the study area.In the SMTZ,most methane is consumed by anaerobic oxidation due to high sulfate concentrations.

关键词： CBM co-produced water microbial geochemistry sulfate methane transition zone Shizhuangnan Block

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Effects of spaceflight and simulated microgravity on microbial growth and secondary metabolism

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Military Medical Research 2018年第4期5卷 335-349页

作者： Bing Huang Dian-Geng Li Ying Huang Chang-Ting Liu Nanlou Respiratory Diseases Department Chinese PLA General Hospital/Chinese PLA Postgraduate Medical School State Key Laboratory of microbial Resources Institute of Microbiology Chinese Academy of Sciences

Spaceflight and ground-based microgravity analog experiments have suggested that microgravity can affect microbial growth and metabolism. Although the effects of microgravity and its analogs on microorganisms have been studied for more than 50 years, plausible conflicting and diverse results have frequently been reported in different experiments, especially regarding microbial growth and secondary metabolism. Until now, only the responses of a few typical microbes to microgravity have been investigated; systematic studies of the genetic and phenotypic responses of these microorganisms to microgravity in space are still insufficient due to technological and logistical hurdles. The use of different test strains and secondary metabolites in these studies appears to have caused diverse and conflicting results. Moreover, subtle changes in the extracellular microenvironments around microbial cells play a key role in the diverse responses of microbial growth and secondary metabolisms. Therefore, "indirect" effects represent a reasonable pathway to explain the occurrence of these phenomena in microorganisms. This review summarizes current knowledge on the changes in microbial growth and secondary metabolism in response to spaceflight and its analogs and discusses the diverse and conflicting results. In addition, recommendations are given for future studies on the effects of microgravity in space on microbial growth and secondary metabolism.

关键词： microbial growth Secondary metabolism Spaceflight Microgravity Simulated microgravity Microgravity analogs

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Gclust:A Parallel Clustering Tool for microbial Genomic Data

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Genomics, Proteomics & Bioinformatics 2019年第5期17卷 496-502页

作者： Ruilin Li Xiaoyu He Chuangchuang Dai Haidong Zhu Xianyu Lang Wei Chen Xiaodong Li Dan Zhao Yu Zhang Xinyin Han Tie Niu Yi Zhao Rongqiang Cao Rong He Zhonghua Lu Xuebin Chi Weizhong Li Beifang Niu Computer Network Information Center Chinese Academy of SciencesBeijing 100190China University of Chinese Academy of Sciences Beijing 100190China Center of Scientific Computing Applications&Research Chinese Academy of SciencesBeijing 100190China Guizhou University School of Medicine Guiyang 550025China J.Craig Venter Institute La JollaCA 92037USA

The accelerating growth of the public microbial genomic data imposes substantial burden on the research community that uses such resources.Building databases for non-redundant reference sequences from massive microbial genomic data based on clustering analysis is essential.However,existing clustering algorithms perform poorly on long genomic sequences.In this article,we present Gclust,a parallel program for clustering complete or draft genomic sequences,where clustering is accelerated with a novel parallelization strategy and a fast sequence comparison algorithm using sparse suffix arrays(SSAs).Moreover,genome identity measures between two sequences are calculated based on their maximal exact matches(MEMs).In this paper,we demonstrate the high speed and clustering quality of Gclust by examining four genome sequence datasets.Gclust is freely available for non-commercial use at https://***/niu-lab/gclust.We also introduce a web server for clustering user-uploaded genomes at http://***/gclust.

关键词： microbial genome clustering Parallelization Sparse suffix array Maximal exact match Segment extension

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Piglet gut microbial shifts early in life:causes and effects

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Journal of Animal Science and Biotechnology 2019年第3期10卷 519-528页

作者： Robin B.Guevarra Jun Hyung Lee Sun Hee Lee Min-Jae Seok Doo Wan Kim Bit Na Kang Timothy J.Johnson Richard E.Isaacson Hyeun Bum Kim Department of Animal Resources Science Dankook UniversityCheonan 31116South Korea National Institute of Animal Science Rural Development AdministrationCheonan 55365South Korea Abbvie Bioresearch Center AbbvieWorcesterMA 01605USA Department of Veterinary and Biomedical Sciences University of MinnesotaSt.PaulMN 55108USA

The gut microbiome has long been known to play fundamentally important roles in the animal health and the well-being of its host. As such, the establishment and maintenance of a beneficial gut microbiota early in life is crucial in pigs, since early gut colonizers are pivotal in the establishment of permanent microbial community structures affecting the health and growth performance of pigs later in life. Emphasizing this importance of early gut colonizers, it is critical to understand the factors impacting the establishment of the piglet gut microbiome at weaning. Factors include, among others, diet, in-feed antibiotics, probiotics and prebiotic administration. The impact of these factors on establishment of the gut microbiome of piglets at weaning includes effects on piglet gut microbial diversity, structure, and succession. In this review, we thoroughly reviewed the most recent findings on the piglet gut microbiome shifts as influenced by weaning, and how these microbiome changes brought about by various factors that have been shown to affect the development of microbiota in piglets. This review will provide a general overview of recent studies that can help to facilitate the design of new strategies to modulate the gut microbiome in order to enhance gastrointestinal health, growth performance and well-being of piglets.

关键词： microbial diversity Next generation sequencing 16S rRNA Swine microbiota Weaning

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Molecular underpinnings for microbial extracellular electron transfer during biogeochemical cycling of earth elements

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Science China(Life Sciences) 2019年第10期62卷 1275-1286页

作者： Yongguang Jiang Meimei Shi Liang Shi Department of Biological Sciences and Technology School of Environmental StudiesChina University of GeosciencesWuhan 430074 China State Key Laboratory of Biogeology and Environmental Geology China University of GeosciencesWuhan 430074China

microbial extracellular electron transfer(EET) is electron exchanges between the quinol/quinone pools in microbial cytoplasmic membrane and extracellular substrates. Microorganisms with EET capabilities are widespread in Earth hydrosphere, such as sediments of rivers, lakes and oceans, where they play crucial roles in biogeochemical cycling of key elements, including carbon,nitrogen, sulfur, iron and manganese. Over the past 12 years, significant progress has been made in mechanistic understanding of microbial EET at the molecular level. In this review, we focus on the molecular mechanisms underlying the microbial ability for extracellular redox transformation of iron, direct interspecies electron transfer as well as long distance electron transfer mediated by the cable bacteria in the hydrosphere.

关键词： microbial extracellular electron transfer molecular mechanisms multiheme c-type cytochrome conductive nanowires, direct interspecies electron transfer cable bacteria biogeochemical cycling of elements Earth hydrosphere

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