Variation and interaction mechanism between active components in Rheum officinale and rhizosphere soil microorganisms under drought stress / 中国中药杂志

To explore the changes and the reaction mechanisms between soil microecological environment and the content of secon-dary metabolites of plants under water deficit, this study carried out a pot experiment on the 3-leaf stage seedlings of Rheum officinale to analyze their response mechanism under different drought gradients(normal water supply, mild, moderate, and severe drought). The results indicated that the content of flavonoids, phenols, terpenoids, and alkaloids in the root of R. officinale varied greatly under drought stresses. Under mild drought stress, the content of substances mentioned above was comparatively high, and the content of rutin, emodin, gallic acid, and(+)-catechin hydrate in the root significantly increased. The content of rutin, emodin, and gallic acid under severe drought stress was significantly lower than that under normal water supply. The number of species, Shannon diversity index, richness index, and Simpson index of bacteria in the rhizosphere soil were significantly higher than those in blank soil, and the number of microbial species and richness index decreased significantly with the aggravation of drought stresses. In the context of water deficit, Cyanophyta, Firmicutes, Actinobacteria, Chloroflexi, Gemmatimonadetes, Streptomyces, and Actinomyces were the dominant bacteria in the rhizosphere of R. officinale. The relative content of rutin and emodin in the root of R. officinale was positively correlated with the relative abundance of Cyanophyta and Firmicutes, and the relative content of(+)-catechin hydrate and(-)-epicatechin gallate was positively correlated with the relative abundance of Bacteroidetes and Firmicutes. In conclusion, appropriate drought stress can increase the content of secondary metabolites of R. officinale from physiological induction and the increase in the association with beneficial microbe.

Effect of Different Cultivation Modes on Microbial Diversity and Secondary Metabolites of Rhizosphere Soil of Gentiana crassicaulis / 中国实验方剂学杂志

ObjectiveTo investigate the effects of different cultivation modes on the yield of Gentiana crassicaulis and its microbial diversity and secondary metabolite content in the rhizosphere soil. MethodWith G. crassicaulis of different cultivation modes and its rhizosphere soil as the research objects， the composition of bacterial and fungal communities， dominant bacteria， and differential microorganisms in the rhizosphere soil were analyzed by high-throughput sequencing technology. HPLC was used to determine the content of iridoids in G. crassicaulis with different cultivation modes. ResultCompared with plastic film mulching， planting without mulch and intercropping of peony， white kidney bean， potato， and corn increased the yield of fresh products by 16.11%-17.68%， 22.48%-26.34%， 29.37%-32.19%， 34.82%-36.57%， and 35.34%-39.71%， respectively， and increased the yield of dry products by 19.75%-23.17%， 25.86%-29.32%， 30.18%-34.94%， 35.22%-39.87%， and 39.72%-43.73%. The total content of four iridoids， including gentiopicrin， loganic acid， sweroside， and swertiamarin， increased by 10.17%-37.83%， 5.93%-47.44%， 9.09%-28.84%， and 10.71%-28.57%， respectively. The diversity of bacterial and fungal communities in the rhizosphere soil increased significantly （P<0.05）. The relative abundance of pathogenic bacteria such as Sordariomycetes， Leotiomycetes， Tremellomycetes， Eurotiomycetes， Fusarium， and Cladophialophora decreased， and the proportions of beneficial bacteria such as Proteobacteria， Acidobacteria， and Actinobacteriota increased and they gradually became the dominant bacteria. ConclusionDifferent cultivation modes can affect the yield of G. crassicaulis and its microbial diversity and iridoid content in the rhizosphere soil. Cultivation without mulch and intercropping patterns have certain advantages， which can provide theoretical references for the planting of G. crassicaulis.

Analysis of microbial diversity in the midgut of Haemaphysalis longicornis infected with severe fever with thrombocytopenia syndrome virus / 中国热带医学

@#Abstract: Objective　To investigate the composition and diversity of midgut microbial community of Haemaphysalis longicornis infected with severe fever with thrombocytopenia syndrome virus (SFTSV)． Methods　The midgut DNA of three group Haemaphysalis longicornis infected with SFTSV was extracted, and the 16S rDNA gene of the sample was sequenced by HiSeq platform. The composition and diversity of endosymbiotic microbial community were clarified by OTU cluster analysis and alpha diversity analysis. Results　The midgut microbial clusters of the three groups infected with SFTSV were 143, 113, 163 OTUs respectively; the sparsity curve and abundance grade curve showed that the data had sufficient sequencing depth, and the midgut of Haemaphysalis longicornis infected with SFTSV was rich in microbial composition, but the species distribution was uneven. The analysis of microbial community composition showed that Proteobacteria, Firmicutes and Actinobacteria were the main dominant bacteria at the phyla level. At the class level, Gammaproteobacteria, Bacilli, Betaproteobacteria and Actinomycetia were the main dominant bacteria. At the order level, Legionellales, Bacillales, Burkholderiales and Actinomycetales were the main dominant orders. At the family level, Coxiellaceae, Bacillaceae, Moraxellaceae and Rhodococcaceae were the main dominant families. At the genus level, the relative abundance of Coxiella was the highest, followed by Aeribaillus and Azonexus. Alpha diversity analysis showed that the average Shannon index was 139.67, the average Simpson index was 0.48, the average Chao index was 145.06, and the average ACE index was 147.11. Conclusions　The species diversity of intestinal microorganisms in Haemaphysalis longicornis infected with SFTSV is rich. The results provide a basis for further exploring the interaction between intestinal microbes of Haemaphysalis longicornis and SFTSV and developing new ideas for the prevention and control of ticks and tick-borne diseases.

Distribution characteristics of antibiotic resistance genes in the domestic water of residents in Haimen， Jiangsu Province / 上海预防医学

ObjectiveAntibiotic resistance genes （ARGs） have received wide attention all over the world. The purpose of this study was to explore the bacterial community structure， the types and levels of antibiotic resistance genes in a water body in east China， and to compare and analyze the characteristics of microbial species distribution and antibiotic resistance gene distribution in various water environments. MethodsA total of 10 households in Haimen City， Jiangsu Province were selected and their surrounding water environment samples were collected. 21 water samples including river water （4）， Mingou water （9） and well water （8） were collected for metagenomics sequencing， assembled with MetaWRAP， annotated with CARD database， and analyzed with R software. ResultsIn various water bodies， the dominant bacteria phyla was Proteobacteria， the dominant bacteria genera were Deuterostomia， Pseudomonas， Flavobacteriales and Streptomycetaceae. The ARGs annotated were mainly composed of quinolones， aminoglycosides， macrolides and beta-lactams antibiotic resistance genes. The top four relative abundance of resistance genes were macB， RanA， evgS and TxR， The average absolute abundance and expression of resistance genes in well water and Mingou water were higher than those in river water. ConclusionMultiple ARGs are detected to varying degrees in well water， river water， and Mingou water bodies， and the expression of resistance genes in well water and Mingou water bodies is higher than that in river water bodies， possibly due to human production and living activities.

Study on Changes of Microorganisms and Volatile Components in Aquilariae Lignum Resinatum with Different Aging Years / 中国实验方剂学杂志

ObjectiveThis study aims to investigate the changes in fungal community diversity and volatile components during the aging process of Aquilariae Lignum Resinatum and explore the internal relationship between them. MethodAquilariae Lignum Resinatum samples with different aging years were collected. High-throughput sequencing was employed to analyze the fungal diversity and abundance， and α and β diversity indicators were calculated to reveal the composition and dynamic changes of the fungal community. In addition， the essential oils of Aquilariae Lignum Resinatum with different aging years were extracted， separated， and identified by two-dimensional gas chromatography-high resolution time-of-flight mass spectrometry. ResultA total of 61 compounds were identified from the volatile components of five groups of Aquilariae Lignum Resinatum samples， including 2 monoterpenes， 24 sesquiterpenoids， 1 diterpene， 13 aromatic hydrocarbons， 9 alkanes， and 12 other compounds. Among them， the volatile compounds isolated from the sample aged for 1 year had the largest number， and those from the sample aged for 2 years accounted for the largest proportion of the total components. The internal transcribed spacer（ITS） amplicon sequencing revealed that the fungi in the five groups of samples belonged to 162 genera. Kirschsteiniothelia， Aspergillus， Lasiodiplodia， Phaeoacremonium， and Trichoderma were the dominant fungal genera. The fungal diversity in the Aquilariae Lignum Resinatum sample aged for 4 years was significantly higher than that in the samples aged for 0 to 3 years. ConclusionThe volatile component content and composition of Aquilariae Lignum Resinatum altered dramatically during aging. The aging of Aquilariae Lignum Resinatum was accompanied by the increasing fungal diversity， decreasing relative content of aromatic hydrocarbons， and increasing relative content of sesquiterpenoids. In general， aging was beneficial to the transformation of sesquiterpenoids and the enrichment of fungi.

Efecto de los cultivos de cobertura invernales sobre el microbioma del suelo: revisión sistemática de la literatura / Effect of winter cover crops on the soil microbiome: a systematic literature review

Resumen La inclusión de cultivos de cobertura invernales (CCI) en un sistema de siembra directa (SD) en reemplazo del barbecho constituye una alternativa promisoria para mejorar la salud del suelo y contribuir a la sustentabilidad ambiental de los sistemas agrícolas. Esta revisión ofrece un panorama integral de los efectos sobre el microbioma del suelo que tiene la introducción de CCI en rotación con cultivos de verano en sistemas de SD vs. el barbecho desnudo. Se realizó una búsqueda sistemática de la literatura que reporta los efectos de los CCI sobre los parámetros de abundancia, actividad y diversidad microbiana del suelo. Combinando 7 criterios de búsqueda se seleccionaron y analizaron 22 trabajos. El conjunto de resultados de esos trabajos muestra que la actividad enzimática del suelo se ve favorecida con la inclusión de CCI en la rotación, principalmente si estos se componen de leguminosas y mezclas de especies. Más de la mitad de esos trabajos reportan una mayor biomasa microbiana con CCI que con barbecho. Además, se advierte que los efectos de los CCI sobre los parámetros microbianos son independientes de la duración de los ensayos. Sin embargo, aún se necesitan más investigaciones básicas que permitan reducir la heterogeneidad entre estudios y comprender las complejas interacciones que ocurren entre los CCI y el microbioma del suelo.

Abstract The inclusion of winter cover crops (WCC) in no-till (NT) systems in replacement of bare fallow is a promising alternative to improve soil health and consequently, contribute to environmental sustainability of agricultural systems. This review provides a comprehensive evaluation of the effects of the use of WCC in rotation with summer cash crops under NT systems on the soil microbiome versus bare fallows. A systematic literature search was conducted to evaluate the impact of WCC on microbial parameters indicative of abundance, activity and diversity. Twenty-two papers were selected based on seven combined criteria. The results of this review show that enzyme activities in soil are enhanced with the inclusion of WCC in the rotation, particularly those that include legumes and mix of species. ln general, more than half of the analyzed papers report higher microbial biomass in soils with WCC than in bare fallow. Interestingly, the effects of WCC on microbial parameters are independent of the duration of the experiments. However, more basic research is necessary to reduce the heterogeneity of the studies and to better understand the complexity of the interactions between WCC and the soil microbiome.

Microorganisms: the secret agents of the biosphere, and their key roles in biotechnology / Micro-organismos: os agentes secretos da biosfera, e seus papéis determinantes na biotecnologia

Abstract We present a survey of projects that have been funded by FAPESP under the BIOTA-Microorganisms program. These projects generated a wide variety of results, including the identification of novel antibacterial-producing microorganisms, the characterization of novel microbial enzymes for industrial applications, taxonomic classification of novel microorganisms in several environments, investigation of the soil and mangrove microbial ecosystems and its influence on endangered plant species, and the sequencing of novel metagenome-assembled genomes. The results surveyed demonstrate the importance of microorganisms in environments that play important roles in human activities as well as the potential that many of these microorganisms have in contributing to biotechnological applications crucial for human survival in the 21st century.

Resumo Apresentamos um levantamento comentado de projetos financiados pelo programa BIOTA-Micro-organismos. Estes projetos geraram uma variada gama de resultados, incluindo a identificação de novos micro-organismos produtores de compostos antibacterianos, a caracterização de novas enzimas microbianas para usos industriais, classificação taxonômica de novos micro-organismos presentes em diversos ambientes, investigação de ecossistemas microbianos em solos e mangues e sua influência sobre plantas ameaçadas, e o sequenciamento de vários novos genomas microbianos derivados de metagenomas. Os resultados descritos demonstram o papel-chave de micro-organismos em ecossistemas importantes para atividades humanas, assim como o potencial que vários desses micro-organismos tem de contribuir para aplicações biotecnológicas cruciais para a sobrevivência humana no século 21.

Molecular Techniques to Study Microbial Wastewater Communities

Abstract wastewater treatment (WT) is of major importance on modern cities, removing wastewater pollutants resultant from anthropogenic activities. The unique abilities of microbes to degrade organic matter, remove nutrients and transform toxic compounds into harmless products make them essential players in waste treatment. The microbial diversity determines the metabolic pathways that may occur in WT and quality of treated wastewater. Therefore, understanding WT microbial community structure, distribution, and metabolic functioning is essential for development and optimization of efficient microbial engineering systems. Since cultivation methods can only detect a small fraction of the microbial diversity, the use of culture-independent molecular methods has circumvented this issue, allowing unprecedented access to genes and genomes used for microbial composition and function evaluation. Traditional approaches like RAPD, DGGE, ARDRA, RISA, SSCP, T-RFLP, and FISH and modern approaches like microarray, qPCR, and metagenomics are essential techniques for identifying and depicting the total microbial community structure and their interaction with environmental and biotic factors. Thus, this review describes traditional and state of the art molecular techniques which provide insights into phylogenetic and functional activities of microbial assemblages in a WT system.

Effects of viral infection and microbial diversity on patients with sepsis: A retrospective study based on metagenomic next-generation sequencing / 世界急诊医学杂志（英文）

@#BACKGROUND: The study aims to investigate the performance of a metagenomic next-generation sequencing (NGS)-based diagnostic technique for the identification of potential bacterial and viral infections and effects of concomitant viral infection on the survival rate of intensive care unit (ICU) sepsis patients. METHODS: A total of 74 ICU patients with sepsis who were admitted to our institution from February 1, 2018 to June 30, 2019 were enrolled. Separate blood samples were collected from patients for blood cultures and metagenomic NGS when the patients’ body temperature was higher than 38 °C. Patients’ demographic data, including gender, age, ICU duration, ICU scores, and laboratory results, were recorded. The correlations between pathogen types and sepsis severity and survival rate were evaluated. RESULTS: NGS produced higher positive results (105 of 118; 88.98%) than blood cultures (18 of 118; 15.25%) over the whole study period. Concomitant viral infection correlated closely with sepsis severity and had the negative effect on the survival of patients with sepsis. However, correlation analysis indicated that the bacterial variety did not correlate with the severity of sepsis. CONCLUSIONS: Concurrent viral load correlates closely with the severity of sepsis and the survival rate of the ICU sepsis patients. This suggests that prophylactic administration of antiviral drugs combined with antibiotics may be beneficial to ICU sepsis patients.

Effect of management (ecological and conventional) on functional groups of soil microorganisms in coffee agroecosystems with different resilience to climate variability, Colombia

The effect of management (ecological and conventional) on functional groups of microorganisms of soil in agroecosystems with different resilience scores reported to climate variability in Anolaima, Colombia was evaluated. Were found clustering associated with management and cellulolytic bacteria and fungi abundances. No differences found in diversity of phosphate solubilizing or nitrogen-fixing microorganisms, related to management. The diversity of microbial functional groups was affected by the climatic condition of sampling season. Management was relevant in relationships between resilience scores to climate variability and cellulolytic microorganisms; in ecological agroecosystems, biodiversity knowledge, agroecological main structure, and the participation of farmers in organizations were important.

Advance in study on 16S rRNA gene sequencing technology in oral microbial diversity / 中南大学学报(医学版)

The 16S rRNA gene is the most commonly used molecular marker for identifying microorganisms. It is used in sequencing technology, including the first-generation, the second-generation, and the third-generation sequencing technology. A large number of studies on the 16S rRNA gene have contributed to a deeper understanding of oral microbial diversity. In the healthy oral cavity, there is microbial diversity in time and space. With the occurrence or development of oral diseases such as caries, periodontal disease, or halitosis, the microbial diversity will be changed.

Effects of different application methods of Bacillus subtilis agent on soil microbial diversity and growth of muskmelon / 生物工程学报

Continuous planting of muskmelon and excessive application of chemical fertilizers have caused a series of problems, such as imbalance of the soil micro-ecological environment, serious soil-borne diseases and yield loss. Application of Bacillus subtilis agent is an important way to improve soil micro-ecological environment, prevent soil-borne diseases, and promote plant growth. In this study, B. subtilis was used as experimental agent to analyze the effects of different application methods on the soil microbial diversity and growth of muskmelon in greenhouse. The number of culturable microorganisms in soil was measured by dilution-plate method. The diversity of soil uncultivated microorganisms was determined by Illumina Miseq sequencing technology. The yield of muskmelon was measured by weighing method. The number of culturable bacteria in the root irrigation, hole application and dipping root application groups was higher than that of the control in different muskmelon growth stages, but there was no significant difference among the three different application methods. The number of soil fungi from B. subtilis agent treatment groups in flowering stage was significantly lower in comparison to the control group. However, B. subtilis agent treatment did not cause significant difference on soil fungi number at the fruiting and pulling stage. Diversity analysis of uncultured microorganisms showed that the Shannon index values of bacteria were higher and Simpson index values were lower respectively in the three B. subtilis treatment groups than that in the control. Moreover, the dipping root treatment produced the lowest Shannon index value and the highest Simpson index value of fungi. NMDS and cluster analysis showed that B. subtilis agents dipping root treatment significantly affected the bacterial and fungal flora, both of which were clustered into one independent branch. The application of B. subtilis agents, especially dipping root treatment, significantly decreased the abundance of Bacteroidetes, increased the abundance of Actinobacteria and Acidobacteria. The B. subtilis agent treatment didn't produce significant effect on the diversity of fungal flora except Chytridiomycota. The height, stem diameter and leaf area of muskmelon increased by applying B. subtilis agents, and dipping root treatment produced the most significant effect. As a new type of environmental protection fertilizer, B. subtilis agent can increase the number of soil culturable microorganisms, improve soil microbial diversity, and promote growth and yield. This study would provide a scientific basis for the rational application of B. subtilis.

Association Study Between Rhizoma Gastrodia elata Brown-rot and Soil Microbial Communities / 中国实验方剂学杂志

Objective:To study the microbial community composition and diversity of brown-rot Gastrodia elata and its surface soil，in order to explain the relationship between brown-rot G. elata and soil microflora in G. elata planting process and provide theoretical basis for revealing the reasons of G. elata brown-rot disease. Method:Used internal transcribed spacer region（ITS） and 16S rDNA high-throughput sequencing technologies to detect the microbial diversity，community structure composition and community structure similarity of fungi and bacteria in healthy tuber，Brown-rot tuber，healthy soil and Brown-rot soil. Result:Compared with health groups，the number of fungi and bacteria operational taxonomic units（OTUs） was increased in brown-rot G. elata and its soil， and the abundance and diversity of fungi and bacteria in brown-rot G. elata soil were significantly decreased. The diversity of fungi in the tubers of brown-rot G. elata was significantly reduced，while the diversity of bacteria was significantly decreased. At the genus level， Mortierella was dominant fungi genus in healthy tuber and healthy soil，which was reduced 7.62% and 15.75% respectively in brown-rot tuber and brown-rot soil. And the dominant bacteria genus was Bradyrhizobium and Burkholderia-Paraburkholderia respectively. Ilyonectria was dominant fungi genus in brown-rot tuber and brown-rot soil，the dominant bacteria genus was Serratia and Bradyrhizobium respectively. Conclusion:The fungal flora in the tuber of brown-rot G. elata had a very high degree of similarity to that in the surrounding soil. These results indicated that the change of soil microbial fungal community caused the occurrence of G. elata brown-rot disease to a certain extent. And the pathogenic fungal Ilyonectria was dominant genus in fungi community of brown-rot tuber and brown-rot soil. Ilyonectria may have the main G. elata brown-rot disease pathogen.

Analysis of intestinal patients' flora changes with severe pneumonia based on 16SrDNA sequencing technology / 中华危重病急救医学

Objective@#To investigate the characteristics of gut microbiota dysbosis in patients with severe pneumonia using 16SrDNA sequencing.@*Methods@#A prospective observational research was conducted. The stool samples retained by natural defecation or enema within 2 days after hospital were collected from 16 patients with severe pneumonia admitted to department of intensive care unit (ICU) of General Hospital of Ningxia Medical University from June to December in 2018 and 10 persons for physical exam were enrolled as the healthy control group. The 16SrDNA sequencing technology was used to detect fecal flora and analyze biological information.@*Results@#① 1 015 475 effective sequences were obtained from the stool samples from the severe pneumonia group and the healthy control group. Using 16SrDNA method, it was found that the average effective length of the sample sequence was 458.35 bp and the average sequence number of the total samples was 39 056.73. ② Analysis of α diversity of gut microbiota showed that, compared with the healthy control group, the Ace index, Chao index and the Shannon index of gut microbiota diversity in the severe pneumonia group were significantly decreased [Ace index: 167.23 (143.14, 211.26) vs. 227.71 (214.53, 247.05), Chao index: 152.38 (138.09, 182.54) vs. 228.25 (215.49, 248.95), Shannon index: 2.37 (1.68, 2.89) vs. 3.39 (3.03, 3.63), all P < 0.01], and the Simpson index was significantly increased [0.21 (0.11, 0.33) vs. 0.07 (0.06, 0.12), P < 0.01], which indicated the gut microbiota diversity of the severe pneumonia group was decreased. ③ Analysis of β diversity of gut microbiota, principal coordinate analysis (PCoA) showed that gut microbiota structural with the healthy control group was similar, while that in the severe pneumonia group was different. Adonis analysis showed that the structural of the gut microflora revealing significant differences between the severe pneumonia group and the healthy control group (R2 = 0.061, P = 0.05). ④ Analysis of phylum difference gut microflora showed that, compared with the healthy control group, the proportion of Firmicutes in severe pneumonia group was decreased [27.36 (18.12, 39.28)% vs. 52.25 (38.36, 63.82)%, P = 0.02], the proportions of Actinobacterias, Synergistetes and Fusobacterias were increased [2.30 (0.30, 4.80)% vs. 0.02 (0.00, 0.06)%, 0.36 (< 0.01, 0.57)% vs. < 0.01 (< 0.01, < 0.01)%, 0.01 (< 0.01, 0.08)% vs. < 0.01 (< 0.01, < 0.01)%, all P < 0.05]. ⑤ Analysis of genus difference gut microflora showed that, the proportions of Bifidobacterium, Ruminococcus, Pseudobutyrivibrio, Coprococcus, Lachnospira and Prevotella in the severe pneumonia group were significantly lower than those in healthy control group [0.18 (0.01, 0.25)% vs. 3.40 (0.46, 5.78)%, 0.01 (< 0.01, 0.29)% vs. 2.26 (0.84, 4.86)%, 0.01 (< 0.01, 0.02)% vs. 2.73 (1.87, 5.74)%, 0.02 (< 0.01, 0.07)% vs. 0.80 (0.50, 2.32)%, < 0.01 (< 0.01, < 0.01)% vs. 0.88 (0.33, 2.08)%, 0.02 (< 0.01, 0.31)% vs. 7.74 (0.07, 36.27)%, all P < 0.05]; the proportions of Escherichia and Enterococcus in the severe pneumonia group were higher than those in healthy control group, but there was no difference between the two groups [2.00 (0.57, 10.23)% vs. 1.16 (0.23, 2.68)%, 0.02 (< 0.01, 0.42)% vs. < 0.01 (< 0.01, 0.04)%, both P > 0.05]; the proportions of Fusobacterium and Staphylococcus in severe pneumonia group were significantly higher than those in healthy control group [0.01 (< 0.01, 0.08)% vs. < 0.01 (< 0.01, < 0.01)%, 0.01 (< 0.01, 0.02)% vs. < 0.01 (< 0.01, < 0.01)%, both P < 0.05].@*Conclusion@#Gut microbiota dysbiosis in patients with severe pneumonia shows that the abundance and diversity decrease, structure of intestinal flora changes, and beneficial symbiotic bacteria decrease and pathogenic bacteria increase, which may be associated with the occurrence and development of severe pneumonia.

Analysis of intestinal patients' flora changes with severe pneumonia based on 16SrDNA sequencing technology / 中华危重病急救医学

Objective To investigate the characteristics of gut microbiota dysbosis in patients with severe pneumonia using 16SrDNA sequencing. Methods A prospective observational research was conducted. The stool samples retained by natural defecation or enema within 2 days after hospital were collected from 16 patients with severe pneumonia admitted to department of intensive care unit (ICU) of General Hospital of Ningxia Medical University from June to December in 2018 and 10 persons for physical exam were enrolled as the healthy control group. The 16SrDNA sequencing technology was used to detect fecal flora and analyze biological information. Results ① 1015475 effective sequences were obtained from the stool samples from the severe pneumonia group and the healthy control group. Using 16SrDNA method, it was found that the average effective length of the sample sequence was 458.35 bp and the average sequence number of the total samples was 39056.73. ② Analysis of α diversity of gut microbiota showed that, compared with the healthy control group, the Ace index, Chao index and the Shannon index of gut microbiota diversity in the severe pneumonia group were significantly decreased [Ace index: 167.23 (143.14, 211.26) vs. 227.71 (214.53, 247.05), Chao index: 152.38 (138.09, 182.54) vs. 228.25 (215.49, 248.95), Shannon index:2.37 (1.68, 2.89) vs. 3.39 (3.03, 3.63), all P < 0.01], and the Simpson index was significantly increased [0.21 (0.11, 0.33) vs. 0.07 (0.06, 0.12), P < 0.01], which indicated the gut microbiota diversity of the severe pneumonia group was decreased. ③ Analysis of β diversity of gut microbiota, principal coordinate analysis (PCoA) showed that gut microbiota structural with the healthy control group was similar, while that in the severe pneumonia group was different. Adonis analysis showed that the structural of the gut microflora revealing significant differences between the severe pneumonia group and the healthy control group (R2 = 0.061, P = 0.05). ④ Analysis of phylum difference gut microflora showed that, compared with the healthy control group, the proportion of Firmicutes in severe pneumonia group was decreased [27.36 (18.12, 39.28)％ vs. 52.25 (38.36, 63.82)％, P = 0.02], the proportions of Actinobacterias, Synergistetes and Fusobacterias were increased [2.30 (0.30, 4.80)％ vs. 0.02 (0.00, 0.06)％, 0.36 (< 0.01, 0.57)％ vs. < 0.01 (< 0.01, < 0.01)％, 0.01 (< 0.01, 0.08)％ vs. < 0.01 (< 0.01, < 0.01)％, all P < 0.05]. ⑤ Analysis of genus difference gut microflora showed that, the proportions of Bifidobacterium, Ruminococcus, Pseudobutyrivibrio, Coprococcus, Lachnospira and Prevotella in the severe pneumonia group were significantly lower than those in healthy control group [0.18 (0.01, 0.25)％ vs. 3.40 (0.46, 5.78)％, 0.01 (< 0.01, 0.29)％ vs. 2.26 (0.84, 4.86)％, 0.01 (< 0.01, 0.02)％ vs. 2.73 (1.87, 5.74)％, 0.02 (< 0.01, 0.07)％vs. 0.80 (0.50, 2.32)％, < 0.01 (< 0.01, < 0.01)％ vs. 0.88 (0.33, 2.08)％, 0.02 (< 0.01, 0.31)％ vs. 7.74 (0.07, 36.27)％, all P < 0.05]; the proportions of Escherichia and Enterococcus in the severe pneumonia group were higher than those in healthy control group, but there was no difference between the two groups [2.00 (0.57, 10.23)％ vs. 1.16 (0.23, 2.68)％, 0.02 (< 0.01, 0.42)％ vs. < 0.01 (< 0.01, 0.04)％, both P > 0.05]; the proportions of Fusobacterium and Staphylococcus in severe pneumonia group were significantly higher than those in healthy control group [0.01 (< 0.01, 0.08)％ vs. < 0.01 (< 0.01, < 0.01)％, 0.01 (< 0.01, 0.02)％ vs. < 0.01 (< 0.01, < 0.01)％, both P < 0.05]. Conclusion Gut microbiota dysbiosis in patients with severe pneumonia shows that the abundance and diversity decrease, structure of intestinal flora changes, and beneficial symbiotic bacteria decrease and pathogenic bacteria increase, which may be associated with the occurrence and development of severe pneumonia.

A preliminary study on the origin of neonatal intestinal microbiota during cesarean section / 中国实用妇科与产科杂志

OBJECTIVE: To explore the composition of microbial communities in vagina and intestine of the mother,the placenta and the neonatal meconium after cesarean section and to analyze the origin of neonatal intestinal microbiota.METHODS: Samples of intestine,vagina and placenta and neonatal meconium from 4 women who underwent cesarean section in Yan'an Hospital of Kunming City in October 2016 were collected.The high-throughput sequencing technology was used to sequence the 16 S rRNA gene,and the composition of the microbial communities and the relationship among the samples were analyzed.RESULTS: Firstly,comparing the number of OTUs in different samples,it was found that the number in placenta was the highest,followed by the intestine and vagina,and the least was in the neonatal meconium.Secondly,each sample was analyzed by PCA clustering,and it was found that the neonatal meconium was affected least by individual differences but the vagina was affected most.The intestinal and placental microbial communities had certain similarities.Finally,comparing the microbial community composition of each sample,it was found that the highest abundance in the neonatal meconium and placenta was Proteobacteria,and in the intestine and vagina it was the Firmicutes.CONCLUSION: During the caesarean section,maternal microbiota transfer may be from the mother's intestine to the placenta and then to the infant's intestine.

Clinical investigation of gut microbiota dysbiosis in septic patients / 中华急诊医学杂志

Objective To investigate the characteristics of gut microbiota dysbosis in septic and non-septic patients in ICU.Methods A prospective observational research was conducted.Ten septic patients(septic group),ten patients without sepsis(non-septic group) were admitted to Department of Critical Care Medicine of General Hospital of Ningxia Medical University from February 2017 to June 2017 were enrolled.And ten healthy persons was enrolled as control group.Stool samples were collected from septic and non-septic patients within two days following admission to the intensive care unit (ICU);healthy persons' was random.High throughput 16S rRNA gene sequencing technology was used to detect fecal bacterium of three groups.Acute Physiology and Chronic Health Evaluation Ⅱ (APACHE Ⅱ) score,Sequential Organ Failure Assessment (SOFA) score of patients were recorded on the first day after admission to ICU.Results Compared with the control group,the α diversity of gut microbiota in non-septic and septic groups showed a downward trend,the [3 diversity showed that the structure of gut microbiota in non-septic and the septic groups was significant different,and the individual differences were more obvious.At the level of phylum,compared with the control group,the proportion of Firmicutes+Bacteroidetes in non-septic and septic groups decreased significantly(P=0.013,0.028),and the proportion of Proteobacteria increased(P=0.017,0.026),while the proportion of Fusobacteria just increased in the non-septic group(P ＜ 0.01).At the level of genus,compared with the control group,the proportion of beneficial symbiotic genus in non-septic and septic groups can be seen decreased,such as Ruminococcus(P=0.045,0.026),Pseudobutyrivibrio(P=0.009,＜ 0.01),Anaerostipes(P=0.011,0.003),Coprococcus(P=0.045,0.011),Phascolarctobacterium(P=0.008,0.022),Subdoligranulum(P=0.006,0.026).The proportion of Lactobacillus,Dorea,Faecalibacterium,Roseburia and Blautia showed downward trend in non-septic and septic groups,but only the decline of Lactobacillus in non-septic group had statistical difference(P=0.005),and the decline of Dorea,Faecalibacterium,Roseburia and Blautia in septic group had statistical differences(P=0.037,0.038,0.002 and 0.017,respectively).The proportion of conditional pathogenic Fusobacterium,Actinomyces,Peptstreptococcus,Streptococcus increased in non-septic group(P=0.001,0.019,0.011 and 0.014,respectively),the proportion of pathogenic Staphylococcus(P=0.035,0.006),Enterococcus(P=0.001,0.001),Anaerococcus(P=0.006,0.006) and Bacillus(both P ＜ 0.01) increased in non-septic and septic groups.Conclusions Gut microbiota dysbiosis occured in septic and non-septic patients in the ICU,and showed that diversity decreased,structure of intestinal flora changed,obligate anaerobic bacteria decreased,facultative anaerobic bacteria increased,benefical symbiotic bacteria decreased,pathogenic bacteria increased and can be the dominate genus.

Oral microbiological diversity in patients with salivary adenoid cystic carcinoma / 华西口腔医学杂志

OBJECTIVE@#The aim of this study was to identify the differences in microbial diversity and community in patients with salivary adenoid cystic carcinoma (SACC).@*METHODS@#Saliva was collected from 13 patients with SACC confirmed by histopathological diagnosis and 10 healthy control subjects. Total metagenomic DNA was extracted. The DNA amplicons of the V3-V4 hypervariable regions of the 16S rRNA gene were generated and subjected to high-throughput sequencing. Microbial diversity and community structure were analyzed with Mothur software.@*RESULTS@#A total of 16 genera of dominant bacteria in the SACC group were found, including Streptococcus (36.68%), Neisseria (8.55%), Prevotella_7 (7.53%), and Veillonella (6.37%), whereas 15 dominant bacteria in the control group were found, including Streptococcus (18.41%), Neisseria (18.20%), Prevotella_7 (8.89%), Porphyromonas (6.20%), Fusobacterium (5.86%) and Veillonella (5.82%). The statistically different phyla between the two groups were Firmicutes, Proteobacteria and Fusobacterium (P<0.05). The statistically different genera between the two groups were Streptococcus, Neisseria and Porphyromonas (P<0.05), and Capnocytophaga was only detected in patients with SACC.@*CONCLUSIONS@#Significant differences were observed in the oral microorganisms between the two groups.

Diversity of Gut Microbiota in Patients with Acute Traumatic Complete Spinal Cord Injury / 中国康复理论与实践

Objective:To Compare and analyze the gut microbiota and biochemical indexes between patients with acute traumatic complete spinal cord injury and healthy subjects. Methods:From May, 2017 to May, 2018, a total of 44 patients with acute traumatic complete spinal cord injury (patient group) and 33 healthy controls (control group) were included. The clinical data and fresh blood, urine and fecal samples of the two groups were collected. The V3-V4 region of 16S rRNA gene was sequenced and analyzed. Results:The abundance of gut microbiota was higher in the patient group than in the control group, and the structural composition was different. Compared with the control group, the expression of Bacteroidetes decreased (P < 0.05), and the expression of Actinobacteria, Proteobacteria, Synergistetes, Saccharibacteria and Cyanobacteria increased in the patient group (P < 0.05). The serum glucose, low density lipoprotein, triglyceride and total cholesterol were significantly higher in the patient group than in the control group (P < 0 05). There was a significant correlation between these elevated markers and intestinal microbial community structure (P < 0.05). Conclusion:There is gut microbiota dysbiosis in patients with acute traumatic complete spinal cord injury, and the changes of the microbiota are related to the elevation of some serum biomarkers.

Proteolytic and lipolytic potential of Pseudomonas spp. from goat and bovine raw milk / Potencial proteolítico e lipolítico de espécies de Pseudomonas do leite cru caprino e bovino

Pseudomonas, the main genus of gram-negative microorganisms isolated from milk, is psychrotrophic, biofilm-forming, and thermo-resistant deteriorating enzyme producers. The aim of this study was to quantify Pseudomonas spp. in goat's and cow's milk produced in the Paraná state, Brazil, to evaluate the deteriorating activity of the isolates at mesophilic and psychrotrophic conditions and to identify, at the species level, the isolates with alkaline metalloprotease (aprX gene) production potential. Microbiological, biochemical and molecular methods were used for isolating, confirming and identifying of isolates. The mean counts were 1.6 (±6.3)x104 and 0.89(±3)x102 CFU/mL for goat and bovine milk samples, respectively, immediately after milking. Of the Pseudomonas colonies isolated from goat milk (n=60), 91.7% showed proteolytic potential when incubated at 35°C/48 h and 80% at 7°C/10 days, and lipolytic potential was observed in 95% of the isolates incubated in mesophilic and 78.3% at refrigeration conditions. From the isolates of bovine milk (n=20), 35% showed proteolytic activity only when incubated at 35°C/48 h, and lipolytic potential was observed in 25% of the isolates incubated at 7°C/10d and 35°C/48h. It was observed that 83.3% and 25% of the isolates genetically confirmed as Pseudomonas spp. of goat and bovine milk showed the potential for alkaline metalloprotease production, with the species P. azotoformans, P. koreensis, P. gessardii, P. monteilii and P. lurida being the most frequent in goat milk and P. aeruginosa the only species identified in cow milk.(AU)

Pseudomonas é o principal gênero de micro-organismos Gram negativos isolados do leite, são psicrotróficos, formadores de biofilmes e produtores de enzimas deteriorantes termodúricas. O objetivo do presente trabalho foi quantificar Pseudomonas spp. no leite de cabras e vacas produzido no estado do Paraná, Brasil, avaliar a atividade deteriorante em temperatura mesofílica e psicrotrófica e identificar, em nível de espécie, os isolados com potencial de produção de metaloprotease alcalina (geneaprX). Foram utilizados métodos microbiológicos, bioquímicos e moleculares para isolamento, confirmação e identificação dos isolados. As contagens médias foram de 1,6 (±6,3) x 104 e 0,9 (±3) x 102 UFC/mL para as amostras de leite caprino e bovino, respectivamente. Dos isolados de Pseudomonas do leite de cabra (n=60), 91,7% demonstraram potencial proteolítico quando incubadas a 35°C/48h e 80% a 7°C/10dias e lipolíticos em 95% dos isolados incubados em mesofilia e em 78,3% dos incubados em temperatura de refrigeração. Dos isolados do leite bovino (n=20), foi verificada atividade proteolítica de 35% apenas quando incubadas a 35°C/48h e lipolítica em 25% dos isolados incubados a 7°C/10d e 35°C/48h. Foi observado que 83,3% e 25% dos isolados confirmados geneticamente como Pseudomonas spp. do leite caprino e bovino, respectivamente, apresentaram o potencial de produção de metaloprotease alcalina, sendo as espécies P. azotoformans, P. koreensis, P. gessardii, P. monteilii e P. lurida as mais frequentes no leite de cabras e P. aeruginosa a única identificada do leite de vacas.(AU)