Characterization of the gut microbiota of Kawasaki disease patients by metagenomic analysis

Kawasaki disease (KD) is an acute febrile illness of early childhood. Previous reports have suggested that genetic disease susceptibility factors, together with a triggering infectious agent, could be involved in KD pathogenesis; however, the precise etiology of this disease remains unknown. Additionally, previous culture-based studies have suggested a possible role of intestinal microbiota in KD pathogenesis. In this study, we performed metagenomic analysis to comprehensively assess the longitudinal variation in the intestinal microbiota of twenty-eight KD patients. Several notable bacterial genera were commonly extracted during the acute phase, whereas a relative increase in the number of Ruminococcus bacteria was observed during the non-acute phase of KD. The metagenomic analysis results based on bacterial species classification suggested that the number of sequencing reads with similarity to five Streptococcus spp. (S. pneumonia, pseudopneumoniae, oralis, gordonii, and sanguinis), in addition to patient-derived Streptococcus isolates, markedly increased during the acute phase in most patients. Streptococci include a variety of pathogenic bacteria and probiotic bacteria that promote human health; therefore, this further species discrimination could comprehensively illuminate the KD-associated microbiota. The findings of this study suggest that KD-related Streptococci might be involved in the pathogenesis of this disease

Antifungal activity of some medicinal plants on soybean seed-borne macrophomina phaseolina

Soybean Glycine max (L.) Merr. seeds, pods and seedlings are susceptible to fungal attackdue to its rich nutrient content. The most commonly isolated soybean (JS-335) seed-borne fungiwere Fusarium spp., Macrophomina phaseolina., Pythium spp., Aspergillus spp., Phoma spp., and Phomopsis spp. Macrophomina phaseolina is an important plant pathogenic fungus that causes charcoal rot of soybean and infects more than 500 hosts. In humid climates, the fungus causes a post emergence damping-off of soybean seedlings leading to 50 of crop losses. The objective ofthis work was to study the efficacy of the botanicals on soybean seed-borne Macrophomina phaseolina. Among the 10 botanicals screened, Datura metel (L.) methanol leaf extract showed the most promising activity against Macrophomina phaseolina

빙하 후퇴에 따른 극지역 토양 미생물의 군집 구조와 잠재적 기능의 천이 변화

학위논문(박사) -- 서울대학교대학원 : 자연과학대학 생명과학부, 2022. 8. 이은주.Glacier forelands have long fascinated ecologists and soil scientists by providing ideal places to study the patterns and processes of ecological succession. Previous studies on ecological succession in glacier forelands have focused mainly on the vegetation development or pedogenesis, but relatively less attention has been paid to microbial succession, especially in polar regions such as the High Arctic and Antarctica. In addition, former studies on microbial succession have typically focused on a single taxonomic group and often lack the examination on chemical turnover of organic substrates corresponding to biological turnover, resulting in a limited understanding of microbial succession in glacier forelands. In order to get a comprehensive understanding of microbial succession in glacier forelands of polar regions, this thesis aimed to investigate the successional changes of microbial communities in both the biological aspects (e.g., taxonomic compositions, functional profiles, and interactions between microbial groups) and the chemical aspects (e.g., diversity and compositional changes of dissolved organic matters). To acquire the knowledge on microbial community succession at the very early successional stages prior to plant colonization, the successional dynamics and assembly processes of bacterial and fungal communities were compared along a soil age gradient of 10 years on the Fourcade glacier foreland. Bacterial and fungal communities in recently deglaciated soils are largely decoupled from each other during succession and exert very divergent trajectories of succession and assembly under different selective forces. In addition to the study on successional patterns of microbial communities in unvegetated glacier forelands, the compositional changes of four different microbial communities (bacteria, fungi, protists, and archaea) and their interactions were investigated to gain a holistic view of microbial succession on a glacier foreland of the High Arctic along the 100 years of deglaciation. Overall, microbial community structures changed in a directional manner and environmental properties played a key role in the compositional changes following deglaciation. A higher proportion of the interactions between microbial groups in late than early soil-age gradients suggested that bacterial, fungal, and protistan communities less independently respond to glacier retreat along the soil-age gradient. Microbial succession involves not only changes in other biological communities but also at the same time changes in the diversity and composition of organic molecules mediated by biological processes. The successional dynamics of soil dissolved organic matter (DOM) and its relationship with microbial communities were examined following deglaciation in the High Arctic. The succession of DOM followed a distinct pattern from the patterns of microbial communities but is strongly associated with biological soil crusts (BSCs). Also, the abundance and richness of DOM molecule showed closer relationships with potential metabolic capability and in situ activity than the taxonomic structure of microbial communities. This thesis advanced the understanding of microbial succession in newly exposed glacier forelands of polar regions by providing the knowledge on not only successional dynamics of various microbial communities but also multitrophic interactions following soil-age gradient since deglaciation. Additionally, this study provides novel insights into interactions between organic compounds and microbial communities during succession. Consequently, these results can advance our understanding of belowground microbial succession in deglaciated terrains of polar regions.빙하 후퇴 지역 (glacier forelands)은 시간에 따른 생태학적 천이 과정 및 패턴을 연구하는데 이상적인 장소를 제공함으로써 지난 오랜 시간 동안 많은 생태학자와 토양학자들을 매료시켜왔다. 빙하 후퇴 지역에서 이루어진 생태적 천이 (ecological succession)에 대한 이전 연구들은 주로 식생 천이나 토양 발달에 초점을 맞추었으며 특히 고위도 북극이나 남극에서의 미생물 천이 (microbial succession)에 대한 연구는 많이 이루어지지 않았다. 또한 미생물 천이에 대한 이전 연구들은 주로 단일 분류군에 대해서만 초점을 맞추고 있으며 생물학적 변화에 상응하는 유기물의 화학적 변화에 대한 연구가 부족하여 이는 빙하 후퇴 지역에서의 미생물 천이에 대한 이해가 부족해지는 결과를 낳았다. 극지역 빙하 후퇴 지역에서의 미생물 천이에 대한 포괄적인 이해를 얻고자 본 연구는 미생물 천이의 생물학적 측면 (예를 들어, 군집의 구성, 기능적 프로파일, 미생물 그룹간의 상호작용)과 화학적 측면 (예를 들어, 용존 유기물의 다양성 및 구성의 변화)에서 연구하였다. 식물이 발달하기 이전의 극 초기 빙하 후퇴 지역에서의 미생물 천이에 대한 지식을 얻고자 세균 및 곰팡이 군집의 천이적 변화를 빙하가 후퇴한 지 약 10년여 지난 포케이드(Fourcade) 빙하 후퇴 지역에서 연구하였다. 그 결과, 극 초기 빙하 후퇴 지역에서 세균과 곰팡이 군집의 천이는 서로 분리되어 진행되며 서로 다른 선택적 요인의 영향으로 상반된 천이 패턴을 나타내었다. 극 초기 지역에서의 미생물 천이에 대한 연구에 이어, 미생물 천이를 전체적인 관점에서 이해하고자 고위도 북극에 위치한 약 100여년간 빙하가 후퇴한 지역에서 4개의 서로 다른 미생물 군집들 (세균, 진균, 원생생물 그리고 고세균)의 천이 패턴과 그들의 상관관계를 연구하였다. 종합적으로, 여러 미생물 군집의 구조는 빙하 후퇴 이후 시간에 따라 방향적으로 변화하였으며 이에 환경 요인들이 큰 영향을 주었다. 그리고 미생물 그룹들 간의 상관관계는 초기보다 후기에서 그 비중이 높았는데 이는 세균, 진균, 원생생물의 군집이 점차 덜 독립적으로 (보다 상호작용하며) 빙하 후퇴에 반응한다는 것을 시사한다. 미생물 천이는 다른 생물학적 군집의 천이 뿐만 아니라 동시에 생물학적 과정과 관련된 유기물의 다양성 및 구성적 변화를 함께 동반하기에, 토양의 용존 유기물의 천이 변화 및 미생물 군집간의 관계에 대해 연구를 고위도 북극의 빙하 후퇴 지역에서 진행하였다. 토양의 용존 유기물의 변화 패턴은 미생물의 천이와 다른 패턴을 나타내었으나 biological soil crusts (BSCs)의 발달과 강한 상관관계가 있었다. 그리고 용존 유기물의 양과 다양성은 미생물 군집의 분류학적 구조보다 미생물의 잠재적 대사능 (potential metabolic capability) 및 실제 물질 대사 능력 (in situ activity)과 보다 밀접한 관계를 나타내었다. 본 연구는 빙하 후퇴에 따른 다양한 미생물 군집들의 천이 패턴 및 이들의 상관관계 변화에 대한 지식을 제공함으로써 빙하 후퇴 지역의 미생물 천이에 대한 이해를 증진시켰다. 또한, 천이가 진행되는 동안 토양 유기물과 미생물 군집 간의 상호작용에 대한 새로운 관점을 제공하였다. 종합적으로, 본 연구를 통해 극지역 빙하 후퇴 지역 토양 밑의 미생물 천이에 대한 이해를 향상시킬 수 있었다.Chapter 1. General Introduction 1 1.1. Ecological succession in glacier forelands 1 1.2. Microbial succession in glacier forelands 3 1.3. Objectives of this study 6 Chapter 2. Early-stage successional dynamics of bacterial and fungal communities in a recently deglaciated terrain of the maritime Antarctica 10 2.1. Introduction 11 2.2. Materials and Methods 14 2.2.1. Site description and sampling strategy 14 2.2.2. Soil physicochemical analysis and meteorological data 16 2.2.3. Abundances of bacteria and fungi 17 2.2.4. DNA extraction, amplicon sequencing, and community analysis 20 2.2.5. Bioinformatics analysis 21 2.2.6. Statistical analyses 22 2.2.7. Null model analysis 26 2.2.8. Co-occurrence network analysis 27 2.3. Results 27 2.3.1. Soil geochemistry and microbial abundance 27 2.3.2. Microbial taxa 32 2.3.3. Microbial alpha- and beta-diversity 37 2.3.4. Key drivers of microbial beta-diversity 46 2.3.5. Biotic interactions within- and between-taxonomic groups 47 2.4. Discussion 52 Chapter 3. Successional dynamics of microbial communities along a 100-year deglaciation gradient in the High Arctic 60 3.1. Introduction 61 3.2. Materials and Methods 63 3.2.1. Site description and sampling strategy 63 3.2.2. Soil physicochemical analysis 66 3.2.3. Phospholipid fatty acid (PLFA) analysis 67 3.2.4. RNA/DNA isolation, cDNA synthesis, amplicon sequencing, and community analysis 68 3.2.5. Shotgun metagenomic sequencing 69 3.2.6. Annotation of microbial functional groups 70 3.2.7. Statistical analyses 71 3.2.8. Network analysis 72 3.3. Results 73 3.3.1. Soil physicochemical properties and microbial biomass 73 3.3.2. Taxonomic composition of RNA-based and DNA -based microbial communities 77 3.3.3. Changing trends of microbial taxa in RNA- and DNA-based microbial communities 80 3.3.4. Changes in putative functional profiles and functional potential along the chronosequence 86 3.3.5. Microbial alpha- and beta-diversity 91 3.3.6. Key drivers of microbial beta-diversity 97 3.3.7. Biotic interactions within- and between-taxonomic groups 101 3.4. Discussion 105 Chapter 4. Chemical succession of dissolved organic matter (DOM) molecules and its relation to microbial communities in a deglaciated foreland of the High Arctic 108 4.1. Introduction 109 4.2. Materials and Methods 116 4.2.1. Study site, soil sampling, soil physicochemical properties, and NDVI 116 4.2.2. Preparation of soil organic matter 116 4.2.3. FT-ICR MS analysis 117 4.2.4. Data processing and elemental composition assignments 117 4.2.5. Dissolved organic matter (DOM) chemodiversity and multivariate analysis 118 4.2.6. Chlorophyll a extraction 119 4.2.7. Long-read amplicon sequencing using LoopSeq 119 4.2.8. Statistical analyses 121 4.2.9. Network analysis 122 4.2.10. Community-level physiological profiles 123 4.3. Results 124 4.3.1. General characteristics of DOM compounds in the foreland of Midtre Lovénbreen 121 4.3.2. Changes in DOM characteristics along the gradient of time since deglaciation 121 4.3.3. Underlying mechanisms and primary drivers of DOM compositional changes 134 4.3.4. Network associations between N-containing DOM compounds and microbial OTUs 141 4.4. Discussion 151 Chapter 5. Conclusion 158 References 161 Appendix 179 Abstract in Korean(국문초록) 229박

Air Force Institute of Technology Research Report 2006

This report summarizes the research activities of the Air Force Institute of Technology’s Graduate School of Engineering and Management. It describes research interests and faculty expertise; lists student theses/dissertations; identifies research sponsors and contributions; and outlines the procedures for contacting the school. Included in the report are: faculty publications, conference presentations, consultations, and funded research projects. Research was conducted in the areas of Aeronautical and Astronautical Engineering, Electrical Engineering and Electro-Optics, Computer Engineering and Computer Science, Systems and Engineering Management, Operational Sciences, Mathematics, Statistics and Engineering Physics

Sustainable Agricultural Practices-Impact on Soil Quality and Plant Health

Agricultural practices involving the excessive use of chemical fertilizers and pesticides pose major risks to the environment and to human health. The development and adoption of sustainable ecofriendly agricultural management to preserve and enhance the physical, chemical, and biological properties of soils and improve agroecosystem functions is a challenge for both scientists and farmers. The Special Issue entitled “Sustainable Agricultural Practices—Impact on Soil Quality and Plant Health” is a collection of 10 original contributions addressing the state of the art of sustainable agriculture and its positive impact on soil quality. The content of this Special Issue covers a wide range of topics, including the use of beneficial soil microbes, intercropping, organic farming and its effects on soil bacteria and nutrient stocks, application of plant-based nematicides and zeolite amendments, sustainability in CH4 emissions, and the effect of irrigation, fertilization, and environmental conditions as well as land suitability on crop production

Diagnóstico de patógenos productores de mastitis mediante prueba AccuMast® en vacas seleccionadas por las técnicas CMT y Draminski en Ganadería San Gabriel, Departamento de Jinotega.

La mastitis bovina es una enfermedad recurrente en las diferentes explotaciones, causando pérdidas económicas significativas, principalmente los agentes involucrados son de origen bacteriano. Ganadería San Gabriel ubicada en el departamento de Jinotega tiene un tipo de explotación intensiva de ganado raza lechera Pardo Suizo Americano y Holstein, con una altura de 1112 msnm y una temperatura promedio de 24 °C. Con 104 vacas en producción generando 1,700 litros diarios en dos ordeños y un promedio por vaca de 16.34 litros. Los especímenes en estudio se seleccionaron mediante la prueba California Mastitis Test (CMT) y la prueba de conducción eléctrica Draminski. Los cuartos positivos a mastitis fueron cultivados durante 16 horas mediante la prueba AccuMast ®. Obteniendo los siguientes resultados: el 26% del hato dio positiva mastitis siendo los cuartos afectados izquierdo delantero (ID) 31.57%, Izquierdo trasero (IT) 26.51%, derecho trasero (DT) 21.06% derecho delantero (DD) 21.06% debido a un desajuste de la bomba de vacío y los pulsadores de las ordeñadoras, encontrando en los cultivos los patógenos Streptococcus Uberis (40.74%) Streptococcus spp. (33.33%) Staphylococcus spp. (18.51%) Staphylococcus haemolyticus (7.4%) E. Coli (3.7%) Klebsiella spp, Enterobacter spp, Serratia spp. (3.7%), adecuando el protocolo de tratamiento para la recuperación de los semovientes

Characterization of low pathogenic H5 subtype influenza viruses from Eurasia: Implications for the origin of highly pathogenic H5N1 viruses

Oral Presentations - Genetic and Antigenic EvolutionHighly pathogenic avian influenza (HPAI) H5N1 viruses are now endemic in many Asian countries. The immediate precursor of these HPAI viruses was recognized as A/Goose/Guangdong/1/96 (Gs/Gd)-like H5N1 HPAI viruses first detected in Guangdong in 1996. However, precursors of the Gs/GD-like viruses and their subsequent reassortants have not been fully determined. Here we characterize low pathogenic avian influenza (LPAI) H5 subtype viruses isolated from poultry and migratory birds in southern China and Europe from the 1970s to the 2000s. Phylogenetic analyses revealed that Gs/GD-like virus was likely derived from an LPAI H5 virus in migratory birds. However, its variants arose from multiple reassortments between Gs/GD-like virus and viruses from migratory birds, or with those Eurasian viruses isolated in the 1970s. It is of note that unlike HPAI H5N1 viruses, those recent LPAI H5 viruses have not become established in aquatic or terrestrial poultry. Phylogenetic analyses revealed the dynamic nature of the influenza gene pool in Eurasia with repeated transmissions between the eastern and western extremities of the continent. The data also shows reassortment between influenza viruses from domestic and migratory birds in this region that has contributed to the expanded diversity of the influenza gene pool among poultry in Eurasia ...postprin

Evaluation of Chlorinated Solvent Removal Efficiency among Three Wetland Plant Species: A Mesocom Study

Different species of plants need to be studied individually to compare the remediation efficiency of each species. This research will study three different wetland plants species and an unplanted control, under a laboratory setting. Each plant has a different characteristic favorable for chlorinated solvent degradation. Eleocharis erythropoda (Spike Rush) are plants with thin tube like leaves and large root mass. Carex comosa (Bearded Sedge) has broad leaves and Scirpus atrovirens (Green Bulrush) are broad leafed wetland plants with a long flowering stem during reproduction. PCE will be injected into the plant mesocosm and any possible PCE degradation will be observed. It is my hypothesis that PCE will be degraded into daughter products in all the mesocosms. However, the question will be which plant is the most efficient at chlorinated solvent degradation and is there difference between the planted reactors and the control reactors

Pseudomonas aeruginosa inhibits in-vitro Candida biofilm development

<p>Abstract</p> <p>Background</p> <p>Elucidation of the communal behavior of microbes in mixed species biofilms may have a major impact on understanding infectious diseases and for the therapeutics. Although, the structure and the properties of monospecies biofilms and their role in disease have been extensively studied during the last decade, the interactions within mixed biofilms consisting of bacteria and fungi such as <it>Candida spp</it>. have not been illustrated in depth. Hence, the aim of this study was to evaluate the interspecies interactions of <it>Pseudomonas aeruginosa </it>and six different species of <it>Candida </it>comprising <it>C. albicans</it>, <it>C. glabrata, C. krusei</it>, <it>C. tropicalis</it>, <it>C. parapsilosis</it>, and <it>C. dubliniensis </it>in dual species biofilm development.</p> <p>Results</p> <p>A significant reduction in colony forming units (CFU) of <it>C. parapsilosis </it>(90 min), <it>C. albicans </it>and <it>C. tropicalis </it>(90 min, 24 h and 48 h), <it>C. dubliniensis </it>and <it>C. glabrata</it>, (24 h and 48 h) was noted when co-cultured with <it>P. aeruginosa </it>in comparison to their monospecies counterparts (P < 0.05). A simultaneous significant reduction in <it>P. aeruginosa </it>numbers grown with <it>C. albicans </it>(90 min and 48 h), <it>C. krusei </it>(90 min, 24 h and 48 h),<it>C. glabrata</it>, (24 h and 48 h), and an elevation of <it>P. aeruginosa </it>numbers co-cultured with <it>C. tropicalis </it>(48 h) was noted (P < 0.05). When data from all <it>Candida spp</it>. and <it>P. aeruginosa </it>were pooled, highly significant mutual inhibition of biofilm formation was noted (<it>Candida </it>P < 0.001, <it>P. aeruginosa </it>P < 0.01). Scanning Electron Microscopy (SEM) and Confocal Laser Scanning Microscopy (CLSM) analyses confirmed scanty architecture in dual species biofilm in spite of dense colonization in monospecies counterparts.</p> <p>Conclusions</p> <p><it>P. aeruginosa </it>and <it>Candida </it>in a dual species environment mutually suppress biofilm development, both quantitatively and qualitatively. These findings provide a foundation to clarify the molecular basis of bacterial-fungal interactions, and to understand the pathobiology of mixed bacterial-fungal infections.</p

Scientific publications and presentations relating to planetary quarantine. Volume 5: The 1971 supplement

A bibliographic compilation, with approximately 200 listings, on planetary quarantine is presented. Also given are scientific publications, and presentations along with an author index