Bacterium is dominant microflora population in human oral cavity, and the novel species and novel genus were discovered and named one after another. This article reviewed the major biological characteristics of 5 novel genus and 16 novel species isolated from the human oral cavity from 2009 to 2012.
Bacteria ; classification ; isolation & purification ; Humans ; Mouth

82 cases of pneumonia patients in the community and 3 cases at the hospital aged 62 in average, randomly collected were diagnosed bacteriologically using the samples gathered endoscopically which underwent a quantified culture and the antibiogramme was made by the method of dispersion on ager disk. Results showed that the pathogenes were mainly streptococci then gram(-) bacilli, sensitive with classic beta-lactam antibiotic group. The previous treatment by antibiotic before bacterical detection affected dramatically on the antibiotic sensitivity of pathogenic bacteria, especially with betalactam antibiotic, commonly used now a day.
Pneumonia/classification ; Classification ; Anti-Bacterial Agents ; Bacteria ; Case reports

Microbiome is a novel research field related with a variety of chronic inflamatory diseases. Technically, there are two major approaches to analysis of microbiome: metataxonome by sequencing the 16S rRNA variable tags, and metagenome by shot-gun sequencing of the total microbial (mainly bacterial) genome mixture. The 16S rRNA sequencing analyses pipeline includes sequence quality control, diversity analyses, taxonomy and statistics; metagenome analyses further includes gene annotation and functional analyses. With the development of the sequencing techniques, the cost of sequencing will decrease, and big data analyses will become the central task. Data standardization, accumulation, modeling and disease prediction are crucial for future exploit of these data. Meanwhile, the information property in these data, and the functional verification with culture-dependent and culture-independent experiments remain the focus in future research. Studies of human microbiome will bring a better understanding of the relations between the human body and the microbiome, especially in the context of disease diagnosis and therapy, which promise rich research opportunities.
Bacteria ; classification ; Humans ; Metagenome ; Microbiota ; RNA, Ribosomal, 16S

Homoacetogens are a group of microorganisms with application potential to produce chemicals and biofuels by the bioconversion of synthesis gas. In this study, we collected waste activated sludge samples to screen homoacetogens by Hungate anaerobic technique, and studied the effect of pH on acetate and alcohol production from H2/CO2 gas. The mixed culture contained Clostridium ljungdahlii, Lysinibacillus fusiformis and Bacillus cereus. Acetate concentration achieved 31.69 mmol/L when the initial pH was 7. The mixed culture containing homoacetogen could converting H2/CO2 to acetate, which provides an efficient microbial resource for the bioconversion of synthesis gas.
Acetates ; chemistry ; Bacteria ; classification ; Biofuels ; Carbon Dioxide ; Hydrogen ; Sewage ; microbiology

Air Pollution ; analysis ; Bacteria ; classification ; isolation & purification ; China ; Cities

Aquilaria sinensis can generate agarwood, which is closely related with endophyte. Up to now, studies mainly focused on the effects of endophytic fungi on agarwood formation, but studies about endophytic bacteria are rarely reported. In our research, the T-RFs and Shannon index of endophytic bacteria in samples of agarwood increase. The number of distinctive T-RFs fragments of corresponding samples in the same group accounted for more than 60% the number of total T-RFs fragments. In samples of no-agarwood, the dominant bacterial population are Anoxybacillus, Clostridium, Candidatus endobugula, Lysinibacillus. In samples of agarwood, the dominant bacterial population are Clostridium, Lysinibacillus, Luteimonas, phytoplasma. Besides, there are. specific T-RFs fragment in samples of agarwood and no-agarwood respectively. When we perform cluster analysis, we found samples of agarwood highly gather together and samples of no-agarwood highly gather together. This means community of endophytic bacteria emerge significant and regular changes during agarwood formation, which may be result of agarwood production, or maybe it is important reason of agarwood production. In this paper, we obtain more comprehensive and accurate community of endophytic bacteria in Aquilaria sinensis and it's variation during agarwood formation using T-RFLP, which is first study of effects of endophytic bacteria on agarwood formation, and will help to exploit resource of endophytic bacteria more reasonably.
Bacteria ; classification ; genetics ; isolation & purification ; Biodiversity ; Endophytes ; classification ; genetics ; isolation & purification ; Thymelaeaceae ; microbiology ; Wood ; microbiology

Gastrodia elata is a heterotrophic plant that needed to be symbiotic with Armillaria. The obstacle of continuous cropping in G. elata is serious during the G. elata cultivation, and the mechanism of obstacle in G. elata continuous cropping had not been solved. The planting of G. elata-Phallus impudicus is a new sequential planting pattern adopted in Guizhou province, but the effect of the cultivation on soil microbial community structure is still unclear. In this study, we collected four soil samples for the research including the soil without planted G. elata as control(CK), rhizosphere soil samples tightly adhering to the G. elata surface(GE), rhizosphere soil samples tightly adhering to Armillaria which was symbiotic with G. elata(AGE), the rhizosphere soil of P. impudicus planting after G. elata cultivation(PI). In order to explore the mechanism, the research study on the soil of G. elata-P. impudicus by using ITS and 16 S rDNA high-throughput sequencing technologies to detect soil microbial community structure including fungi and bacteria in the soil of CK, AGE, GE and PI. OTU clustering and PCA analysis of soil samples showed that the soil microbial diversity was relatively similar in AGE and GE. And the soil microbial in PI and CK clustered together. The results showed that AGE and GE had similar soil microbial diversity, as well as PI and CK. Compared with CK, the soil microbial diversity and abundance in AGE and GE were significantly increased. But the microbial diversity and abundance decreased in PI compared with AGE and GE. The annotation indicated that the abundance of Basidiomycota, Acidobacteria and Chloroflexi decreased, and that of Ascomycota, Zygomycota and Proteobacteria increased in AGE and GE compared with CK. In contrast to AGE and GE, PI was the opposite. The abundance of Basidiomycota, Acidobacteria and Chloroflexi increased in PI compared with AGE and GE. The abundance of microorganisms in the soil of PI and CK was similar. In addition, the co-culture of Armillaria and P. impudicus indicated that P. impudicus had obvious antagonistic effects on the growth of Armillaria. Therefore, it is speculated that the mechanism of G. elata-P. impudicus planting pattern related to the change of soil microbial. And we supposed that P. impudicus might inhibit the growth of Armillaria and change the soil microbial community structure and the abundance of soil microbial. And the soil microbial community structure was restored to a state close to that of uncultivated G. elata. Thus, the structure of soil microbial community planting G. elata could be restored by P. impudicus planting.
Agaricales/growth & development* ; Bacteria/classification* ; Fungi/classification* ; Gastrodia/microbiology* ; Microbiota ; Rhizosphere ; Soil Microbiology

OBJECTIVETo differentiate closely related pathogenic bacteria via phylogenetic method on the basis of gyrB gene sequences.

METHODSGyrB sequences of 19 strains of E.coli, 13 Shigella spp. 2 Aeromonas caviae, 2 Aeromonas hydrophilia,1 Aeromonas veronii were determined and combined with sequences retrieved from public databases to construct phylogenetic trees. For each sequence tested, the identification deduced from the clustering relation of sequences was compared with the phenetic identification.

RESULTSAll the tested sequences, except those of Shigella boydii and Shigella dysenteriae, were corresponded with the 5 closest sequences on the tree at the species level. While the BLAST queries returned some other bacteria organisms or undetermined entries.

CONCLUSIONPhylogenetics displays good discriminative power in bacterial sequences differentiation.

Aeromonas ; classification ; genetics ; Bacteria ; classification ; genetics ; Bacterial Typing Techniques ; DNA Gyrase ; genetics ; DNA, Bacterial ; genetics ; Escherichia coli ; classification ; genetics ; Phylogeny ; Sequence Analysis, DNA ; Shigella ; classification ; genetics

OBJECTIVETo study the population structure and ecological distribution of the rhizosperic microorganisms of Angelica sinensis.

METHODThe isolation, culture and identification of microorganisms were studied by the biological methods, and the achieved data were analyzed by the statistical methods for analysis of species diversity.

RESULTWith the growing stages of A. sinensis from Min county of Gansu province, Heqing of Yunnan province and Baoxing of Sichuan province, the quantity of rhizosperic microorganisms increased; and it had reduced since October. In the area of Min county Gansu province, the number ratio of bacteria and fungi was higher than that in the other two areas. In addition, the population diversity and dynamic change were different in three areas. In the area of Min county Gansu province, the number of dominant microbial populations and the population diversities of bacteria, actinomyces and fungi in the rhizosphere were greater than those in the other two areas.

CONCLUSIONThe microecological system and microbial population structure in the rhizosphere of Min county Gansu province were stable. And it was suitable for the growth of A. sinensis in this area.

Angelica sinensis ; microbiology ; Bacteria ; classification ; isolation & purification ; Biodiversity ; Fungi ; classification ; isolation & purification ; Plant Roots ; microbiology ; Soil Microbiology

A high-content GABA was found in Sojae Semen Praeparatum(SSP), which is a famous traditional Chinese medicine and officially listed in Chinese Pharmacopoeia. To screen out and identify GABA-producing microbes from samples at different time points during the fermenting process of SSP, traditional microbiological methods combined with molecular biological methods were used to study the predominant GABA-producing microorganisms existing in the fermenting process of SSP. This study would lay a foundation for further studying the processing mechanism of SSP. The fermenting process of SSP was based on Chinese Pharmacopoeia(2010 edition), and samples were taken at different time points during the fermenting process of SSP. The bacteria and fungi from samples at different time points in the fermenting process of SSP were cultured, isolated and purified by selective medium, and dominant strains were selected. The dominant bacteria were cultured in the designated liquid medium to prepare the fermentation broths, and GABA in the fermentation broth was qualitatively screened out by thin-layer chromatography. The microbial fermentation broth with GABA spots in the primary screening was quantitatively detected by online pre-column derivatization and high performance liquid chromatography established in our laboratory. GABA-producing microorganisms were screened out from predominant strains, and their GABA contents in fermentation broth were determined. The DNA sequences of GABA-producing bacteria and fungi were amplified using 16S rDNA and 18S rDNA sequences by PCR respectively. The amplified products were sequenced, and the sequencing results were identified through NCBI homology comparison. Molecular biological identification was made by phylogenetic tree constructed by MEGA 7.0 software. Through the homology comparison of NCBI and the construction of phylogenetic tree by MEGA 7.0 software, nine GABA-producing microorganisms were screened out and identified in this study. They were Bacillus subtilis, Enterococcus faecium, E. avium, Aspergillus tamarii, A. flavus, A. niger, Cladosporium tenuissimum, Penicillium citrinum and Phanerochaete sordida respectively. For the first time, nine GABA-producing microorganisms were screened out and identified in the samples at different time points during the fermenting process of SSP in this study. The results indicated that multiple predominant GABA-producing microorganisms exist in the fermenting process of SSP and may play an important role in the formation of GABA.
Bacteria ; classification ; metabolism ; Chromatography, High Pressure Liquid ; Fermentation ; Fungi ; classification ; metabolism ; Phylogeny ; Seeds ; microbiology ; Soybeans ; microbiology ; gamma-Aminobutyric Acid ; biosynthesis