Effects of <i>T. gondii</i> infection on rat gut microbiota diversity.
<p><b>(A)</b> Rarefaction curves showing the relationship between gene richness and sequencing depth, indicating that microbial gene diversity reaches a plateau with increased sequencing effort. <b>(B–C)</b> Raincloud plots depicting richness and Shannon diversity index...
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2025
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| _version_ | 1849927625750872064 |
|---|---|
| author | Ji-Xin Zhao (22056386) |
| author2 | Wen-Bin Zheng (3328680) Shi-Chen Xie (10678094) He Ma (583317) Xiao-Tong Chen (4217488) Ying-Qian Gao (22683622) Lu-Yao Tang (22683625) Meng-Ting Yang (10714266) Fu-Long Nan (22056395) Jing Jiang (130103) Hany M. Elsheikha (6910232) Xiao-Xuan Zhang (610969) |
| author2_role | author author author author author author author author author author author |
| author_facet | Ji-Xin Zhao (22056386) Wen-Bin Zheng (3328680) Shi-Chen Xie (10678094) He Ma (583317) Xiao-Tong Chen (4217488) Ying-Qian Gao (22683622) Lu-Yao Tang (22683625) Meng-Ting Yang (10714266) Fu-Long Nan (22056395) Jing Jiang (130103) Hany M. Elsheikha (6910232) Xiao-Xuan Zhang (610969) |
| author_role | author |
| dc.creator.none.fl_str_mv | Ji-Xin Zhao (22056386) Wen-Bin Zheng (3328680) Shi-Chen Xie (10678094) He Ma (583317) Xiao-Tong Chen (4217488) Ying-Qian Gao (22683622) Lu-Yao Tang (22683625) Meng-Ting Yang (10714266) Fu-Long Nan (22056395) Jing Jiang (130103) Hany M. Elsheikha (6910232) Xiao-Xuan Zhang (610969) |
| dc.date.none.fl_str_mv | 2025-11-25T19:00:50Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pntd.0013768.g001 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/Effects_of_i_T_gondii_i_infection_on_rat_gut_microbiota_diversity_/30715239 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biochemistry Microbiology Cell Biology Genetics Physiology Ecology Immunology Computational Biology Biological Sciences not elsewhere classified Chemical Sciences not elsewhere classified showed negative associations quality reads produced oxidative stress response conducted metagenomic sequencing compositional changes coincided bile acid transformation aromatic compound processing 7 million genes rothia nasimurium </ lactobacillus intestinalis </ de novo </ untargeted serum metabolomics specific metabolic disruptions amino acid metabolism toxoplasma gondii </ limosilactobacillus reuteri </ lactobacillus johnsonii </ akkermansia muciniphila </ host systemic metabolism disrupts intestinal microbiota reuteri </ muciniphila </ johnsonii </ gondii </ host metabolism untargeted lc metabolic targets energy metabolism infection disrupts significant shifts reduced abundance rat model positively correlated pathways related novel microbial microbial diversity metabolites implicated marked reduction marked depletion key role immune modulation gut microbiota findings demonstrate enhanced glycan disease mechanisms comprehensive non community structure chronic stages active enzymes 18 sprague |
| dc.title.none.fl_str_mv | Effects of <i>T. gondii</i> infection on rat gut microbiota diversity. |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p><b>(A)</b> Rarefaction curves showing the relationship between gene richness and sequencing depth, indicating that microbial gene diversity reaches a plateau with increased sequencing effort. <b>(B–C)</b> Raincloud plots depicting richness and Shannon diversity index in <i>T. gondii</i>-infected and uninfected rats. Individual sample values are shown as dots, density plots represent the distribution, and box plots summarize the median and interquartile range. Statistical significance was determined using the Wilcoxon rank-sum test: *<i>P</i> < 0.05; *<i>*P</i> < 0.01; **<i>*P</i> < 0.001. <b>(D–E)</b> Principal coordinate analysis (PCoA) based on Bray–Curtis distances depicting differences in microbial community composition across infection stages. Ellipses represent 95% confidence intervals. Box plots adjacent to PCoA axes display sample scores for PCoA1 and PCoA2, with boxes indicating medians and interquartile ranges, and whiskers extending to 1.5 × the IQR. Overall and pairwise differences in community structure were assessed using PERMANOVA, with effect sizes shown in the upper right scatter plot. <i>P</i>-values were calculated using the adonis test with 1,000 permutations. LI: large intestine; SI: small intestine.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_53aef8a2c85c109d864856262b8764ae |
| identifier_str_mv | 10.1371/journal.pntd.0013768.g001 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30715239 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Effects of <i>T. gondii</i> infection on rat gut microbiota diversity.Ji-Xin Zhao (22056386)Wen-Bin Zheng (3328680)Shi-Chen Xie (10678094)He Ma (583317)Xiao-Tong Chen (4217488)Ying-Qian Gao (22683622)Lu-Yao Tang (22683625)Meng-Ting Yang (10714266)Fu-Long Nan (22056395)Jing Jiang (130103)Hany M. Elsheikha (6910232)Xiao-Xuan Zhang (610969)BiochemistryMicrobiologyCell BiologyGeneticsPhysiologyEcologyImmunologyComputational BiologyBiological Sciences not elsewhere classifiedChemical Sciences not elsewhere classifiedshowed negative associationsquality reads producedoxidative stress responseconducted metagenomic sequencingcompositional changes coincidedbile acid transformationaromatic compound processing7 million genesrothia nasimurium </lactobacillus intestinalis </de novo </untargeted serum metabolomicsspecific metabolic disruptionsamino acid metabolismtoxoplasma gondii </limosilactobacillus reuteri </lactobacillus johnsonii </akkermansia muciniphila </host systemic metabolismdisrupts intestinal microbiotareuteri </muciniphila </johnsonii </gondii </host metabolismuntargeted lcmetabolic targetsenergy metabolisminfection disruptssignificant shiftsreduced abundancerat modelpositively correlatedpathways relatednovel microbialmicrobial diversitymetabolites implicatedmarked reductionmarked depletionkey roleimmune modulationgut microbiotafindings demonstrateenhanced glycandisease mechanismscomprehensive noncommunity structurechronic stagesactive enzymes18 sprague<p><b>(A)</b> Rarefaction curves showing the relationship between gene richness and sequencing depth, indicating that microbial gene diversity reaches a plateau with increased sequencing effort. <b>(B–C)</b> Raincloud plots depicting richness and Shannon diversity index in <i>T. gondii</i>-infected and uninfected rats. Individual sample values are shown as dots, density plots represent the distribution, and box plots summarize the median and interquartile range. Statistical significance was determined using the Wilcoxon rank-sum test: *<i>P</i> < 0.05; *<i>*P</i> < 0.01; **<i>*P</i> < 0.001. <b>(D–E)</b> Principal coordinate analysis (PCoA) based on Bray–Curtis distances depicting differences in microbial community composition across infection stages. Ellipses represent 95% confidence intervals. Box plots adjacent to PCoA axes display sample scores for PCoA1 and PCoA2, with boxes indicating medians and interquartile ranges, and whiskers extending to 1.5 × the IQR. Overall and pairwise differences in community structure were assessed using PERMANOVA, with effect sizes shown in the upper right scatter plot. <i>P</i>-values were calculated using the adonis test with 1,000 permutations. LI: large intestine; SI: small intestine.</p>2025-11-25T19:00:50ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1371/journal.pntd.0013768.g001https://figshare.com/articles/figure/Effects_of_i_T_gondii_i_infection_on_rat_gut_microbiota_diversity_/30715239CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/307152392025-11-25T19:00:50Z |
| spellingShingle | Effects of <i>T. gondii</i> infection on rat gut microbiota diversity. Ji-Xin Zhao (22056386) Biochemistry Microbiology Cell Biology Genetics Physiology Ecology Immunology Computational Biology Biological Sciences not elsewhere classified Chemical Sciences not elsewhere classified showed negative associations quality reads produced oxidative stress response conducted metagenomic sequencing compositional changes coincided bile acid transformation aromatic compound processing 7 million genes rothia nasimurium </ lactobacillus intestinalis </ de novo </ untargeted serum metabolomics specific metabolic disruptions amino acid metabolism toxoplasma gondii </ limosilactobacillus reuteri </ lactobacillus johnsonii </ akkermansia muciniphila </ host systemic metabolism disrupts intestinal microbiota reuteri </ muciniphila </ johnsonii </ gondii </ host metabolism untargeted lc metabolic targets energy metabolism infection disrupts significant shifts reduced abundance rat model positively correlated pathways related novel microbial microbial diversity metabolites implicated marked reduction marked depletion key role immune modulation gut microbiota findings demonstrate enhanced glycan disease mechanisms comprehensive non community structure chronic stages active enzymes 18 sprague |
| status_str | publishedVersion |
| title | Effects of <i>T. gondii</i> infection on rat gut microbiota diversity. |
| title_full | Effects of <i>T. gondii</i> infection on rat gut microbiota diversity. |
| title_fullStr | Effects of <i>T. gondii</i> infection on rat gut microbiota diversity. |
| title_full_unstemmed | Effects of <i>T. gondii</i> infection on rat gut microbiota diversity. |
| title_short | Effects of <i>T. gondii</i> infection on rat gut microbiota diversity. |
| title_sort | Effects of <i>T. gondii</i> infection on rat gut microbiota diversity. |
| topic | Biochemistry Microbiology Cell Biology Genetics Physiology Ecology Immunology Computational Biology Biological Sciences not elsewhere classified Chemical Sciences not elsewhere classified showed negative associations quality reads produced oxidative stress response conducted metagenomic sequencing compositional changes coincided bile acid transformation aromatic compound processing 7 million genes rothia nasimurium </ lactobacillus intestinalis </ de novo </ untargeted serum metabolomics specific metabolic disruptions amino acid metabolism toxoplasma gondii </ limosilactobacillus reuteri </ lactobacillus johnsonii </ akkermansia muciniphila </ host systemic metabolism disrupts intestinal microbiota reuteri </ muciniphila </ johnsonii </ gondii </ host metabolism untargeted lc metabolic targets energy metabolism infection disrupts significant shifts reduced abundance rat model positively correlated pathways related novel microbial microbial diversity metabolites implicated marked reduction marked depletion key role immune modulation gut microbiota findings demonstrate enhanced glycan disease mechanisms comprehensive non community structure chronic stages active enzymes 18 sprague |