@article{cen_rasmussen_2024, title={Exploring the Accuracy and Limits of Algorithms for Localizing Recombination Breakpoints}, volume={41}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msae133}, abstractNote={Abstract Phylogenetic methods are widely used to reconstruct the evolutionary relationships among species and individuals. However, recombination can obscure ancestral relationships as individuals may inherit different regions of their genome from different ancestors. It is, therefore, often necessary to detect recombination events, locate recombination breakpoints, and select recombination-free alignments prior to reconstructing phylogenetic trees. While many earlier studies have examined the power of different methods to detect recombination, very few have examined the ability of these methods to accurately locate recombination breakpoints. In this study, we simulated genome sequences based on ancestral recombination graphs and explored the accuracy of three popular recombination detection methods: MaxChi, 3SEQ, and Genetic Algorithm Recombination Detection. The accuracy of inferred breakpoint locations was evaluated along with the key factors contributing to variation in accuracy across datasets. While many different genomic features contribute to the variation in performance across methods, the number of informative sites consistent with the pattern of inheritance between parent and recombinant child sequences always has the greatest contribution to accuracy. While partitioning sequence alignments based on identified recombination breakpoints can greatly decrease phylogenetic error, the quality of phylogenetic reconstructions depends very little on how breakpoints are chosen to partition the alignment. Our work sheds light on how different features of recombinant genomes affect the performance of recombination detection methods and suggests best practices for reconstructing phylogenies based on recombination-free alignments.}, number={7}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Cen, Shi and Rasmussen, David A.}, year={2024}, month={Jul} }
 @article{pan_cen_yu_tian_zhao_zhang_chen_zhai_2021, title={Niche-Specific Adaptive Evolution of Lactobacillus plantarum Strains Isolated From Human Feces and Paocai}, volume={10}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85099731849&partnerID=MN8TOARS}, DOI={10.3389/fcimb.2020.615876}, abstractNote={Lactobacillus plantarum , a widely used probiotic in the food industry, exists in diverse habitats, which has led to its niche-specific genetic evolution. However, the relationship between this type of genetic evolution and the bacterial phenotype remains unclear. Here, six L. plantarum strains derived from paocai and human feces were analyzed at the genomic and phenotypic levels to investigate the features of adaptive evolution in different habitats. A comparative genomic analysis showed that 93 metabolism-related genes underwent structural variations (SVs) during adaptive evolution, including genes responsible for carbohydrate, lipid, amino acid, inorganic ion and coenzyme transport and metabolism, and energy production and conversion. Notably, seven virulence factor-related genes in strains from both habitats showed SVs — similar to the pattern found in the orthologous virulence genes of pathogenic bacteria shared similar niches, suggesting the possibility of horizontal gene transfer. These genomic variations further influenced the metabolic abilities of strains and their interactions with the commensal microbiota in the host intestine. Compared with the strains from feces, those from paocai exhibited a shorter stagnation period and a higher growth rate in a diluted paocai solution because of variations in functional genes. In addition, opposite correlations were identified between the relative abundances of L. plantarum strains and the genus Bifidobacterium in two media inoculated with strains from the two habitats. Overall, our findings revealed that the niche-specific genetic evolution of L. plantarum strains is associated with their fermentation abilities and physiological functions in host gut health. This knowledge can help guiding the exploration and application of probiotics from the specific niches-based probiotic exploitation.}, journal={Frontiers in Cellular and Infection Microbiology}, author={Pan, Q. and Cen, S. and Yu, L. and Tian, F. and Zhao, J. and Zhang, H. and Chen, W. and Zhai, Q.}, year={2021} }
 @article{wang_cen_wang_lee_zhao_zhang_chen_2020, title={Acetic acid and butyric acid released in large intestine play different roles in the alleviation of constipation}, volume={69}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85082865532&partnerID=MN8TOARS}, DOI={10.1016/j.jff.2020.103953}, abstractNote={Constipation is a disorder that affects people of all ages. Previous study showed Bifidobacterium spp. altered the faecal concentrations of short-chain fatty acids (SCFAs) while relieving constipation. Therefore, we speculated SCFAs might relieve constipation. We evaluated constipation-related indicators, SCFA levels and the faecal microbiota of constipated mice that were fed acylated starches derived from specific SCFAs for 1 month. It confirmed application of acylated starches resolved the issue of SCFAs absorption in small intestine by measuring the concentration of different SCFA in various tissues. Acetylated starch relieved constipation by increasing acetic acid-producing bacteria that were correlated positively with the small intestinal transit rate and water content of faeces, while butylated starch relieved constipation by increasing butyric acid-producing bacteria that were correlated negatively with the time to the first black stool defecation. These results indicated acetic acid and butyric acid play different roles in relieving constipation.}, journal={Journal of Functional Foods}, author={Wang, L. and Cen, S. and Wang, G. and Lee, Y.-K. and Zhao, J. and Zhang, H. and Chen, W.}, year={2020} }
 @article{yu_han_cen_duan_feng_xue_tian_zhao_zhang_zhai_et al._2020, title={Beneficial effect of GABA-rich fermented milk on insomnia involving regulation of gut microbiota}, volume={233}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85077514718&partnerID=MN8TOARS}, DOI={10.1016/j.micres.2020.126409}, abstractNote={Insomnia is a common health problem in modern societies. GABA, an inhibitory neurotransmitter, can promote relaxation and reduce anxiety. In this study, milk was fermented with Lactobacillus brevis DL1-11, a strain with high GABA-producing capacity. The potential beneficial effects of this fermented milk on anxiety and sleep quality were evaluated in animal experiments. Sixty mice were divided into control, non-GABA fermented milk (NGFM), low-dose GABA fermented milk (LGFM, 8.83 mg/kg.bw), medium-dose GABA fermented milk (MGFM, 16.67 mg/kg.bw), high-dose GABA fermented milk (HGFM, 33.33 mg/kg.bw) and diazepam groups. The results of open field test and elevated plus-maze test indicated decreases in anxiety behavior after oral HGFM administration. Moreover, mice in the HGFM group exhibited a significantly prolonged sleep time after an intraperitoneal injection of sodium pentobarbital and a shortened sleep latency after an intraperitoneal injection of sodium barbital. These results indicate a beneficial effect of HGFM on sleep. Additionally, significant increases in the relative abundances of Ruminococcus, Adlercreutzia and Allobaculum and the levels of some short-chain fatty acids (SCFAs), such as butyric acid, were observed in the HGFM group. The results suggest that GABA-fermented milk may improve sleep and the protective pathways may involve in regulation of gut microbiota and increase of SCFAs level.}, journal={Microbiological Research}, author={Yu, L. and Han, X. and Cen, S. and Duan, H. and Feng, S. and Xue, Y. and Tian, F. and Zhao, J. and Zhang, H. and Zhai, Q. and et al.}, year={2020} }
 @article{cen_yin_mao_zhao_zhang_zhai_chen_2020, title={Comparative genomics shows niche-specific variations of Lactobacillus plantarum strains isolated from human, Drosophila melanogaster, vegetable and dairy sources}, volume={35}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85082796592&partnerID=MN8TOARS}, DOI={10.1016/j.fbio.2020.100581}, abstractNote={Lactobacillus plantarum colonizes a range of natural habitat. A phylogenomic analysis showed little association between the range of habitats and diversity in the core-genome. However, the functional genetic features and evolutionary strategies used by L. plantarum to adapt to its niches have not been well investigated using statistical methods. In this study, 140 genomes of L. plantarum recorded in the NCBI database were subjected to comparative genomic analysis to evaluate the genetic diversity and elucidate the distinguishing features associated with the occupation of different niches, including humans, dairy products, Drosophila melanogaster and vegetables. Notably, the genome sizes and GC contents of strains isolated from D. melanogaster were markedly different. By aligning the genomes against the Clusters of Orthologous Groups of Proteins database, the Carbohydrate-Active Enzyme database, the Virulence Factor database and the Comprehensive Antibiotic Resistance database, statistically different functional genome profiles in strains from those 4 niches were determined, as well as correlations of some functional genes with the ability to adapt to a habitat. Based on these results, 20 strains of L. plantarum from human feces and Chinese pickles were isolated and their genomic features were analyzed. Subsequently, a machine learning model confirmed the consistency of functional features of L. plantarum in different niches. This study showed that although most L. plantarum strains were not native to their habitats and had distinct genetic backgrounds, this organism could undergo genomic variation in response to ecological constraints. Moreover, strains within the same niche tended to harbor similar functional genome profiles.}, journal={Food Bioscience}, author={Cen, S. and Yin, R. and Mao, B. and Zhao, J. and Zhang, H. and Zhai, Q. and Chen, W.}, year={2020} }
 @article{yu_duan_kellingray_cen_tian_zhao_zhang_gall_mayer_zhai_et al._2021, title={Lactobacillus plantarum-Mediated Regulation of Dietary Aluminum Induces Changes in the Human Gut Microbiota: an In Vitro Colonic Fermentation Study}, volume={13}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85087278244&partnerID=MN8TOARS}, DOI={10.1007/s12602-020-09677-0}, abstractNote={The gut microbiota has been identified as a target of toxic metals and a potentially crucial mediator of the bioavailability and toxicity of these metals. In this study, we show that aluminum (Al) exposure, even at low dose, affected the growth of representative strains from the human intestine via pure culture experiments. In vitro, Lactobacillus plantarum CCFM639 could bind Al on its cell surface as shown by electron microscopy and energy dispersive X-ray analysis. The potential of L. plantarum CCFM639 to reverse changes in human intestine microbiota induced by low-dose dietary Al exposure was investigated using an in vitro colonic fermentation model. Batch fermenters were inoculated with fresh stool samples from healthy adult donors and supplemented with 86 mg/L Al and/or 109 CFU of L. plantarum CCFM639. Al exposure significantly increased the relative abundances of Bacteroidetes (Prevotella), Proteobacteria (Escherichia), Actinobacteria (Collinsella), Euryarchaeota (Methanobrevibacter), and Verrucomicrobiaceae and decreased Firmicutes (Streptococcus, Roseburia, Ruminococcus, Dialister, Coprobacillus). Some changes were reversed by the inclusion of L. plantarum CCFM639. Alterations in gut microbiota induced by Al and L. plantarum CCFM639 inevitably led to changes in metabolite levels. The short-chain fatty acid (SCFAs) contents were reduced after Al exposure, but L. plantarum CCFM639 could elevate their levels. SCFAs had positive correlations with beneficial bacteria, such as Dialister, Streptococcus, Roseburia, and negative correlations with Erwinia, Escherichia, and Serratia. Therefore, dietary Al exposure altered the composition and structure of the human gut microbiota, and this was partially mitigated by L. plantarum CCFM639. This probiotic supplementation is potentially a promising and safe approach to alleviate the harmful effects of dietary Al exposure.}, number={2}, journal={Probiotics and Antimicrobial Proteins}, author={Yu, L. and Duan, H. and Kellingray, L. and Cen, S. and Tian, F. and Zhao, J. and Zhang, H. and Gall, G.L. and Mayer, M.J. and Zhai, Q. and et al.}, year={2021}, pages={398–412} }
 @article{zhai_shen_cen_zhang_tian_zhao_zhang_xue_chen_2020, title={Screening of: Lactobacillus salivarius strains from the feces of Chinese populations and the evaluation of their effects against intestinal inflammation in mice}, volume={11}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85078684504&partnerID=MN8TOARS}, DOI={10.1039/c9fo02116g}, abstractNote={Screening of <italic>Lactobacillus salivarius</italic> strains and the evaluation of their effects against intestinal inflammation in mice.}, number={1}, journal={Food and Function}, author={Zhai, Q. and Shen, X. and Cen, S. and Zhang, C. and Tian, F. and Zhao, J. and Zhang, H. and Xue, Y. and Chen, W.}, year={2020}, pages={221–235} }
 @article{zhai_cen_jiang_zhao_zhang_chen_2019, title={Disturbance of trace element and gut microbiota profiles as indicators of autism spectrum disorder: A pilot study of Chinese children}, volume={171}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85061188598&partnerID=MN8TOARS}, DOI={10.1016/j.envres.2019.01.060}, abstractNote={Autism spectrum disorder (ASD) is a neuro-developmental disorder that is characterized by impairments of reciprocal social interaction and restricted stereotyped repetitive behavior. The goal of the present study was to investigate the trace element and gut microbiota profiles of Chinese autistic children and screen out potential metallic or microbial indicators of the disease. One hundred and thirty-six children (78 with ASD and 58 healthy controls) aged from 3 to 7 years were enrolled. The levels of lead, cadmium, arsenic, copper, zinc, iron, mercury, calcium and magnesium in hair samples from the children were analyzed. Fecal samples were also collected and the children's gut microbiota profiles were characterized by 16s rRNA sequencing. Concentrations of lead, arsenic, copper, zinc, mercury, calcium and magnesium were significantly higher in the ASD group than in the control group. Linear discriminant analysis effect size analysis indicated that the relative abundance of nine genera was increased in the autistic children. Redundancy analysis showed that arsenic and mercury were significantly associated with Parabacteroides and Oscillospira in the gut. A random forest model was trained with high accuracy (84.00%) and the metallic and microbial biomarkers of ASD were established. Our results indicate significant alterations in the trace element and gut microbiota profiles of Chinese children with ASD and reveal the potential pathogenesis of this disease in terms of metal metabolism and gut microecology.}, journal={Environmental Research}, author={Zhai, Q. and Cen, S. and Jiang, J. and Zhao, J. and Zhang, H. and Chen, W.}, year={2019}, pages={501–509} }
 @article{zhai_wang_cen_zhao_zhang_tian_chen_2019, title={Modulation of the gut microbiota by a galactooligosaccharide protects against heavy metal lead accumulation in mice}, volume={10}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85067555561&partnerID=MN8TOARS}, DOI={10.1039/c9fo00587k}, abstractNote={GOS prevents Pb accumulation by modulating gut microbiota.}, number={6}, journal={Food and Function}, author={Zhai, Q. and Wang, J. and Cen, S. and Zhao, J. and Zhang, H. and Tian, F. and Chen, W.}, year={2019}, pages={3768–3781} }
 @article{zhai_cen_li_tian_zhao_zhang_chen_2018, title={Effects of Dietary Selenium Supplementation on Intestinal Barrier and Immune Responses Associated with Its Modulation of Gut Microbiota}, volume={5}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85058271225&partnerID=MN8TOARS}, DOI={10.1021/acs.estlett.8b00563}, abstractNote={Variations in selenium (Se) intake have been reported to affect the barrier function and immune responses in the gut. Previous studies mainly focused on the role of Se itself or its metabolites, while the influences of the Se-intake-related microbiota on gut health were not thoroughly studied. This study compared the effects of different dietary Se supplementation (Se-deficient, Se-adequate, and Se-supranutritional) on the gut microbiota of mice. Fecal microbiota transplantation (FMT) was further conducted to bypass the effect of Se itself and provided direct evidence that the effects of dietary Se supplementation on the intestinal barrier and immune responses are associated with its modulation of the gut microbiota. Deficient Se supplementation can result in a phenotype of gut microbiota that is more susceptible to dextran sulfate sodium (DSS)-induced colitis and Salmonella typhimurium infection. Sufficient or supranutritional Se intake can optimize the gut microbiota for protection against these intestinal dysfunctions.}, number={12}, journal={Environmental Science and Technology Letters}, author={Zhai, Q. and Cen, S. and Li, P. and Tian, F. and Zhao, J. and Zhang, H. and Chen, W.}, year={2018}, pages={724–730} }