Microbial communities such as those residing in the human gut are highly diverse and complex, and many with important implications for health and diseases. The effects and functions of these microbial communities are determined not only by their species compositions and diversities but also by the dynamic intra- and inter-cellular states at the transcriptional level. Powerful and scalable technologies capable of acquiring single-microbe-resolution RNA sequencing information in order to achieve a comprehensive understanding of complex microbial communities together with their hosts are therefore utterly needed. Here we report the development and utilization of a droplet-based smRNA-seq (single-microbe RNA sequencing) method capable of identifying large species varieties in human samples, which we name smRandom-seq2. Together with a triple-module computational pipeline designed for the bacteria and bacteriophage sequencing data by smRandom-seq2 in four human gut samples, we established a single-cell level bacterial transcriptional landscape of human gut microbiome, which included 29,742 single microbes and 329 unique species. Distinct adaptive response states among species in Prevotella and Roseburia genera and intrinsic adaptive strategy heterogeneity in Phascolarctobacterium succinatutens were uncovered. Additionally, we identified hundreds of novel host-phage transcriptional activity associations in the human gut microbiome. Our results indicated that smRandom-seq2 is a high-throughput and high-resolution smRNA-seq technique that is highly adaptable to complex microbial communities in real-world situations and promises new perspectives in the understanding of human microbiomes.
Humans ; Gastrointestinal Microbiome/genetics* ; Bacteriophages/physiology* ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, RNA/methods* ; Bacteria/virology*

Phages also known as bacteria viruses, are recognized as the most abundant and diverse microbes. This diversity is adapting to the selective pressures such as the prevalence of the phage resistance mechanisms of bacteria. Phages invade and lyse bacterial through six steps (adsorption, injection, replication, transcription translation, assemble, release). Bacteria evolve to many anti-phage mechanisms to avoid phage infection and lysis. This paper focus on a variety of anti-phage mechanisms of bacteria.
Bacteria ; genetics ; virology ; Bacterial Physiological Phenomena ; Bacteriophages ; genetics ; physiology ; DNA Replication ; Evolution, Molecular ; Virus Attachment

OBJECTIVETo study the distribution of pathogenic microorganisms in different genders, age groups and seasons in children with community-acquired pneumonia (CAP) and the relationship between the distribution of pathogenic microorganisms and clinical features.

METHODSA total of 1,155 children with CAP were enrolled, among whom there were 670 boys and 485 girls, with a mean age of 3.1±2.8 years (range: one month to 14 years). Indirect immunofluorescence assay, particle agglutination test, enzyme-linked immunosorbent assay, colloidal gold method. and bacterial culture were applied to determine common respiratory pathogenic microorganisms in sputum, throat swabs, blood samples, bronchoalveolar lavage fluid, and urine.

RESULTSA total of 758 specimens (65.63%) were tested positive by pathogen detection. The top three dominant pathogens were Mycoplasma pneumoniae (MP, 43.64%), bacteria (15.12%), and respiratory syncytial virus (RSV, 9.26%), and the rate of mixed infection was 16.02%. The rates of MP infection between boys and girls with CAP were different (40.8% vs 47.6%; P<0.05). The MP detection rate was the highest in the age group of 6-14 years (77.4%) and the lowest in children younger than 1 year (11.2%), while the detection rates of bacteria and RSV were the highest in children younger than 1 year (21.2% and 17.2%, respectively). The MP detection rate was significantly higher in summer and autumn than in winter and spring, while the detection rates of bacteria and RSV in summer and autumn were significantly lower than those in winter and spring. Among children who were MP positive, fever, chills, cough, crackles were more likely to appear; children with RSV infection were more likely to have wheezes; children with bacterial infection were less likely to have cough. Serum levels of C-reactive protein and procalcitonin were associated with bacterial infection (OR=1.747 and 1.418, respectively; both P<0.05).

CONCLUSIONSMP plays a more and more important role in the pathogenic microorganisms of CAP in children. Prevalence and outbreaks of MP infection among children should be alerted in summer and autumn. There are differences in the detection rate of various pathogenic microorganisms in CAP children with various age groups. The clinical features of children with CAP caused by different pathogenic microorganisms are different.

Adolescent ; Bacteria ; isolation & purification ; C-Reactive Protein ; analysis ; Child ; Child, Preschool ; Community-Acquired Infections ; microbiology ; virology ; Female ; Humans ; Infant ; Male ; Pneumonia ; microbiology ; virology ; Respiratory Syncytial Viruses ; isolation & purification ; Seasons

Bacteriolysis ; physiology ; Bacteriophages ; genetics ; isolation & purification ; physiology ; England ; Gram-Negative Bacteria ; virology ; Humans ; International Cooperation

Bacteria ; isolation & purification ; Community-Acquired Infections ; etiology ; microbiology ; virology ; Humans ; Pneumonia ; etiology ; microbiology ; virology

Six diseases have been found after disease surveys on Notopterygium incisum in Gansu province during 2004 to 2007. They were brown spot (Ascochyta levistici), powdery mildew (Erysiphe heraclei), grey spot (Alternaria sp. ; Alternaria burnsii), leaf spot (Septoria dearnessii), angular leaf spot (Pleospora sp.), leaf streak (Phoma sp.), bacterial angular leaf spot and a virus disease. Bacterial angular leaf spot and powdery mildew are the urgent problems waiting to be solved effectively. All these diseases were reported for the first time in China.
Apiaceae ; microbiology ; virology ; Ascomycota ; isolation & purification ; pathogenicity ; Bacteria ; isolation & purification ; pathogenicity ; China ; Plant Diseases ; microbiology ; virology ; Viruses ; isolation & purification ; pathogenicity

One type of important plant disease resistance, gene-for-gene resistance, is resulted from the interactions between products of the pathogen avirulence (Avr) genes and their matching plant resistance (R) genes. Avr genes have been cloned from a variety of pathogens including fungi, bacteria, viruses and oomycetes. No significant homology is found between sequences of the most cloned Avr genes and those of known proteins or between those of themselves. However, significant homology has been found between sequences of the cloned R genes and those of known proteins or between those of themselves. R proteins consist of similar domains. It has been reported that hypersensitive cell death and resistance, which are induced by interactions between products of different Avr/R gene pairs consisting of similar R genes but different Avr genes, are distinct in development speed, strength, and organ and tissue specificity. Avr genes have dual functions: Pathogens containing Avr genes are avirulent to plants carrying the matching R genes, while they are virulent in race, strain, pathovar or species-specific way to plants without carrying the matching R genes.
Bacteria ; genetics ; pathogenicity ; Fungi ; genetics ; pathogenicity ; Gene Expression ; Genes, Bacterial ; physiology ; Genes, Fungal ; physiology ; Genes, Viral ; physiology ; Plant Diseases ; genetics ; microbiology ; virology ; Plant Viruses ; genetics ; pathogenicity ; Virulence