Browsing by Author "Tang, Le"

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    Defining natural species of bacteria: clear-cut genomic boundaries revealed by a turning point in nucleotide sequence divergence
    (BioMed Central, 2013-07-18) Tang, Le; Li, Yang; Deng, Xia; Johnston, Randal N; Liu, Gui-Rong; Liu, Shu-Lin
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    E. coli diversity: low in colorectal cancer
    (2020-04-06) Tang, Le; Zhou, Yu-Jie; Zhu, Songling; Liang, Gong-Da; Zhuang, He; Zhao, Man-Fei; Chang, Xiao-Yun; Li, Hai-Ning; Liu, Zheng; Guo, Zhi-Rong; Liu, Wei-Qiao; He, Xiaoyan; Wang, Chun-Xiao; Zhao, Dan-Dan; Li, Jia-Jing; Mu, Xiao-Qin; Yao, Bing-Qing; Li, Xia; Li, Yong-Guo; Duo, Li-Bo; Wang, Li; Johnston, Randal N; Zhou, Jin; Zhao, Jing-Bo; Liu, Gui-Rong; Liu, Shu-Lin
    Abstract Background Escherichia coli are mostly commensals but also contain pathogenic lineages. It is largely unclear whether the commensal E. coli as the potential origins of pathogenic lineages may consist of monophyletic or polyphyletic populations, elucidation of which is expected to lead to novel insights into the associations of E. coli diversity with human health and diseases. Methods Using genomic sequencing and pulsed field gel electrophoresis (PFGE) techniques, we analyzed E. coli from the intestinal microbiota of three groups of healthy individuals, including preschool children, university students, and seniors of a longevity village, as well as colorectal cancer (CRC) patients, to probe the commensal E. coli populations for their diversity. Results We delineated the 2280 fresh E. coli isolates from 185 subjects into distinct genome types (genotypes) by PFGE. The genomic diversity of the sampled E. coli populations was so high that a given subject may have multiple genotypes of E. coli, with the general diversity within a host going up from preschool children through university students to seniors. Compared to the healthy subjects, the CRC patients had the lowest diversity level among their E. coli isolates. Notably, E. coli isolates from CRC patients could suppress the growth of E. coli bacteria isolated from healthy controls under nutrient-limited culture conditions. Conclusions The coexistence of multiple E. coli lineages in a host may help create and maintain a microbial environment that is beneficial to the host. As such, the low diversity of E. coli bacteria may be associated with unhealthy microenvironment in the intestine and hence facilitate the pathogenesis of diseases such as CRC.
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    Genetic boundaries delineate the potential human pathogen Salmonella bongori into discrete lineages: divergence and speciation
    (2019-12-04) Wang, Xiaoyu; Zhu, Songling; Zhao, Jian-Hua; Bao, Hong-Xia; Liu, Huidi; Ding, Tie-Min; Liu, Gui-Rong; Li, Yong-Guo; Johnston, Randal N; Cao, Feng-Lin; Tang, Le; Liu, Shu-Lin
    Abstract Background Salmonella bongori infect mainly cold-blooded hosts, but infections by S. bongori in warm-blooded hosts have been reported. We hypothesized that S. bongori might have diverged into distinct phylogenetic lineages, with some being able to infect warm-blooded hosts. Results To inspect the divergence status of S. bongori, we first completely sequenced the parakeet isolate RKS3044 and compared it with other sequenced S. bongori strains. We found that RKS3044 contained a novel T6SS encoded in a pathogenicity island-like structure, in addition to a T6SS encoded in SPI-22, which is common to all S. bongori strains so far reported. This novel T6SS resembled the SPI-19 T6SS of the warm-blooded host infecting Salmonella Subgroup I lineages. Genomic sequence comparisons revealed different genomic sequence amelioration events among the S. bongori strains, including a unique CTAG tetranucleotide degeneration pattern in RKS3044, suggesting non-overlapping gene pools between RKS3044 and other S. bongori lineages/strains leading to their independent accumulation of genomic variations. We further proved the existence of a clear-cut genetic boundary between RKS3044 and the other S. bongori lineages/strains analyzed in this study. Conclusions The warm-blooded host-infecting S. bongori strain RKS3044 has diverged with distinct genomic features from other S. bongori strains, including a novel T6SS encoded in a previously not reported pathogenicity island-like structure and a unique genomic sequence degeneration pattern. These findings alert cautions about the emergence of new pathogens originating from non-pathogenic ancestors by acquiring specific pathogenic traits.