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2018年中国质谱学术大会（CMSC2018）

作者： Liang Qiao Yi Yang Ding Cheng Yu Lin Peter Horvatovich Department of Chemistry Fudan University Research School of Computer Science College of Engineering and Computer ScienceThe Australian National University Department of Pharmacy University of Groningen

bacterial typing is of great importance in clinical diagnosis, environmental monitoring, food safety analysis, and biological research. Matrix-assisted laser desorption/ionization mass spectrometry(MALDI-MS) is now widely used to analyze bacterial samples. identification of bacteria at the species level can be realized by matching the mass spectra of samples against a library of mass spectra of known bacteria. Nevertheless, in order to reasonably type bacteria, identification accuracy should be further improved. We have developed a set of bioinformatics tools for bacterial identification using MALDI-TOF mass spectra. For isolated pure cultures, our approach combines new measures for spectra similarity and a novel bootstrapping assessment. [1] We tested our approach on a general data set containing the mass spectra of 1741 strains of bacteria and another challenging data set containing 250 strains, including 40 strains in the Bacillus cereus group that were previously claimed to be impossible to resolve by MALDI-MS. With the bootstrapping assessment, we achieved much more reliable predictions at both the genus and species level, and enabled to resolve the Bacillus cereus group. For bacterial mixtures, the framework is a combination of a synthetic mixture model based on a non-negative linear combination of candidate reference spectra and a statistical assessment by in silico generated spectra via a jackknife resampling. [2] Ninety-seven model bacterial mixture samples and 8 co-cultured blind-coded bacterial mixture samples, containing up to 6 strains in varied ratios in each sample, together with a reference database containing the mass spectra of 1081 strains, were used to validate the framework. High sensitivity(>80%, with error rate bacterial colonies, which is time-consuming and not possible for many species and strains

关键词： MALDI-TOF MS bacterial identification bioinformatics statistical assessment

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Comprehensive characterization of indoor airborne bacterial profile

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Journal of Environmental Sciences 2009年第8期21卷 1148-1152页

作者： P. L. Chan P. H. F. Yu Y. W. Cheng C. Y. Chan P. K. Wong Department of Biology The Chinese University of Hong Kong Department of Applied Biology and Chemical Technology The Hong Kong Polytechnic University Department of Microbiology The Chinese University of Hong Kong

This is the first detailed characterization of the airborne bacterial profiles in indoor environments. Two restaurants were selected for this study. Fifteen genera of bacteria were isolated from each restaurant and identified by three different bacterial identification systems including MIDI, Biolog and Riboprinter. The dominant bacteria of both restaurants were Gram-positive bacteria in which Micrococcus and Bacillus species were the most abundant. Most bacteria identified were representative species of skin and respiratory tract of human, and soil. Although the bacterial levels in these two restaurants were below the limit of the Hong Kong Indoor Air Quality Objective （HKIAQO） Level 1 standard （i.e., 〈 500 cfu/m^3）, the majority of these bacteria were opportunistic pathogens. These results suggested that the identity of airborne bacteria should also be included in the IAQ to ensure there is a safety guideline for the public.

关键词： airborne bacterial profile bacterial identification indoor air quality

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BioCluster:Tool for identification and Clustering of Enterobacteriaceae Based on Biochemical Data

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Genomics, Proteomics & Bioinformatics 2015年第3期13卷 192-199页

作者： Ahmed Abdullah S.M.Sabbir Alam Munawar Sultana M.Anwar Hossain Department of Microbiology University of Dhaka

Presumptive identifcation of different Enterobaeteriaeeae species is routinely achieved based on biochemical properties. Traditional practice includes manual comparison of each biochem- ical property of the unknown sample with known reference samples and inference of its identity based on the maximum similarity pattern with the known samples. This process is labor- intensive, time-consuming, error-prone, and subjective. Therefore, automation of sorting and sim- ilarity in calculation would be advantageous. Here we present a MATLAB-based graphical user interface （GUI） tool named BioCluster. This tool was designed for automated clustering and iden- tification of Enterobacteriaceae based on biochemical test results. In this tool, we used two types of algorithms, i.e., traditional hierarchical clustering （HC） and the Improved Hierarchical Clustering （IHC）, a modified algorithm that was developed specifically for the clustering and identification of within this species. IHC takes into account the variability in result of 1-47 biochemical tests family. This tool also provides different options to optimize the clus- tering in a user-friendly way. Using computer-generated synthetic data and some real data, we have demonstrated that BioCluster has high accuracy in clustering and identifying enterobacterial species based on biochemical test data. This tool can be freely downloaded at http：//***/ biocluster/.

关键词： bacterial identification Enterobacteriaceae Biochemical properties Clustering tool identification tool Hierarchy algorithm

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A VIBRIO ANGUILLARUM STRAIN ASSOCIATED WITH SKIN ULCER ON CULTURED FLOUNDER, PARALICHTHYS OLIVACEUS

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Chinese Journal of Oceanology and Limnology 2001年第4期19卷 319-326页

作者：莫照兰谭训刚徐永立张培军中科院海洋所实验海洋生物学开放实验室山东青岛 266071

The characteristics of a bacterium strain M3, isolated from cultured flounder Paralichthys olivaceus with remarkable external sign of skin ulcer during an epizootic outbreak, indicated that the bacterium belonged to the species Vibrio anguillarum . Challenge by I.M. (intramuscular injection), bath, and oral administration with M3 showed that it was highly pathogenic for Paralichthys olivacues . The LD 50 dose was 5.144×10 3 CFU/ per fish infection by I.M. injection. Recovered inoculated bacteria from the surviving fish revealed that the asymptomatic carriers could be a latent contagious source. Study of the effect of bacterial culture CFS (cell free supernatant) showed that the exotoxins produced by M3 play an important role in its pathogenicity for flounder. The resistance of M3 to 36 out of 41 antibiotics indicated that the bacterial disease outbreak was mainly attributable to the frequent and excessive use of antimicrobial agents; and that vaccination would be an effective precaution against bacterial disease.

关键词： flounder Paralichthys olivaceus bacterial identification Vibrio anguillarum pathogenicity LD 50 antibiotic sensitivity

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Gram-Positive Bacteria Associated with Rice in China and Their Antagonists Against the Pathogens of Sheath Blight and Bakanae Disease in Rice

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Rice science 2005年第3期12卷 213-218页

作者： Luo Jin-yan XIE Guan-lin LI Bin Luo Yuan-chan ZHAO Li-han WANG Xiao LIU Bo LI Wen State Key Laboratory of Rice Biology Zhejiang University Hangzhou 310029 China Center ofBiotechnology Fujian Academy of Agricultural Science Fuzhou 350003 China

It is necessary to understand the bacterial populations associated with rice so as to provide more information and natural resources for effective management of major diseases in rice. A survey on screening and identification of gram-positive bacteria was conducted during 1998 2004. Seven hundred and fifty-six rice samples were collected from Zhejiang, Jiangsu, Fujian and Yunnan Provinces, China. Over 1000 bacterial isolates were isolated and tested for colony morphology, pathogenicity, and some characteristics of bacteriology including Gram staining, fluorescent pigment on Kings medium B and microscopic observation for endospore. Together with five standard reference strains, 74 representative gram-positive bacterial isolates were confirmed by Biolog and gas chromatographic analysis of fatty acid methyl esters. Five bacterial species of Bacillus and other three genera were identified and isolates from Bacillus sublitis and Bacillus megaterium, exhibited the most effective inhibition against the pathogens of sheath blight and bakanae disease of rice. A few isolates from Bacillus pumilus and Bacillus megaterium showed weak virulent on rice together with some virulent isolates, risk should be considered when isolates from these species were screened for biocontrol agents.

关键词： bacterial identification bacterial population antagonistic bacteria sheath blight bakanae disease rice

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Establishment of Molecular Biological Method for identification of Bacteria by 16S rDNA and gyrB Gene

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Asian Agricultural Research 2023年第4期15卷 21-25页

作者： Xiaxia HOU Yunxia WANG Cuizhi LI Zhiyong LU Inner Mongolia Yili Industrial Group Co. Ltd.Hohhot 010110China

[Objectives]The paper was to establish a molecular biological method for identification of bacterial strains.[Methods]The thalli of standard bacterial strains existing in the laboratory were collected and genomic DNA was extracted for amplification of 16S rDNA and gyrB *** 16S rDNA and gyrB gene sequences were obtained after *** were aligned and analyzed via EzBioCloud and NCBI database,and phylogenetic trees were constructed to determine the species relationship of ***,they were compared with known strains.[Results]This method could identify 5 standard strains accurately to the species *** 16S rDNA and gyrB gene sequences were aligned and analyzed in EzBioCloud database and NCBI *** strain with the max score was consistent with the known *** the query cover and ident were both above 99%.[Conclusions]The established molecular biological method for identification of bacterial strains by 16S rDNA and gyrB gene has good accuracy,which effectively solves the problem that the laboratory identification of bacteria relies on traditional methods and the accuracy can not be guaranteed,and further improves the identification ability of laboratory bacterial strains.

关键词： 16S rDNA gyrB bacterial identification Molecular biological method

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