​Lab Meeting

Our lab meeting will be held every Monday 9am this semester (20200-2021).

Every week, one student will give a "formal" presentation on her/his project, and three students will lead the discussion of a paper each.

Presenters and discussion leaders must upload the files to the Nut Share.

If you have more questions, please contact Xiangyin Chen. 

Since 2020, you will find all papers discussed in our Jounal Club on Mendeley Group

2019.05.23

Presentation: Jiaqiang Wu

Journal Club: Qinglin Wang, Zijing Zhang, Qina Cao

• Robertson et al. 2019 Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models. Cell Reports https://doi.org/10.1016/j.celrep.2019.04.023

• Holder et al. 2018 Dietary Emulsifiers Consumption Alters Anxiety-Like and Social-Related Behaviors in Mice in A Sex-Dependent Manner. Scientific Reports https://doi.org/10.1038/s41598-018-36890-3

• Gao et al. 2018 Antibiotics-Induced Modulation of Large Intestinal Microbiota Altered Aromatic Amino Acid Profile and Expression of Neurotransmitters in the Hypothalamus of Piglets. 
  Journal of Neurochemistry https://doi.org/10.1111/jnc.14333

2019.05.16

Presentation: Xiaohuan Mu, Haolin Qu

Journal Club: Haoyu Lang, Jieni Wang, Huihui Sun, Tianjin Cui

• Wang et al. 2019 Assessing the Viability of Transplanted Gut Microbiota by Sequential Tagging with D-Amino Acid-Based Metabolic Probes. Nature Communications https://doi.org/10.1038/s41467-019-09267-x

• Pacheco et al. 2018 Costless Metabolic Secretions as Drivers of Interspecies Interactions in Microbial Ecosystems Interspecies Interactions in Microbial Ecosystems. Nature Communications https://doi.org/10.1038/s41467-018-07946-9

• Ronda et al. 2018 Metagenomic Engineering of the Mammalian Gut Microbiome in situ.
  Nature Methods https://doi.org/10.1038/s41592-018-0301-y

• Maori et al. 2019 A Transmissible RNA Pathway in Honey Bee. Cell Reports https://doi.org/10.1016/j.celrep.2019.04.073

2019.05.10

Presentation: Huijuan Duan

Journal Club: Qinglin Wang, Zijing Zhang, Jiaqiang Wu, Qina Cao

• Saffouri et al. 2019 Small Intestinal Microbial Dysbiosis Unerlies Symptoms Associated with Functional Gastrointestinal Disorders. Nature Communication https://doi.org/10.1038/s41467-019-09964-7

• Baker et al. 2018 Horizontal Antimicrobial Resistance Transfer Drives Epidemics of Multiple Shigella Species.
  Nature Communication https://doi.org/10.1038/s41467-018-03949-8

• Han et al. 2018 Agricultural Risk fACTORS influence Microbial Ecology in Honghu Lake.                                
  Genomics Proteomics Bioinformatics https://doi.org/10.1016/j.gpb.2018.04.008

• Wong et al. 2019 Early Life Stress Disrupts Intestinal Homeostasis via NGF-TrkA Signaling.
  Nature Communication https://doi.org/10.1038/s41467-019-09744-3

2019.04.24

Presentation: Tianjin Cui

Journal Club: Qinglin Wang, Jieni Wang, Huihui Sun, Xiaohuan Mu

• Schulfer et al. 2019 The impact of Early-Life Sub-therapeutic Antibiotic Treatment (STAT) on Excessive Weight Is Robust despite Transfer Microbes. ISME https://doi.org/10.1038/s41396-019-0349-4

• Hochstein et al. 2019 The Deposit Feeder Capitella telex Has A Unique and Relatively Complex Microbiome Likely Supporting Its Ability to Degrade Pollutants. 
  Science of the Total Environment https://doi.org/10.1016/j.scitotenv.2019.03.255

• Baker et al. 2019 Klebsiella and Providencia Emerge as Long Survivors Following Long-Term Starvation of Oral Microbiota. PNAS https://doi.org/10.1073/pnas.1820594116

• Guo et al. 2018 Metagenomic Study Suggests That the Gut Microbiota of the Giant Panda (Ailuropoda melanoleuca) May Not Be Specialized for Fiber Fermentation. Frontiers in Microbiology https://doi.org/10.3389/fmicb.2018.00229

2019.04.18

Presentation: Qina Cao

Journal Club: Haoyu Lang, Zijing Zhang, Jiaqiang Wu, Huijuan Duan

• Labed et al. 2018 Intestinal Epithelial Wnt Signaling Mediates Acetylchline-Triggered Host Defense against Infection. Immunity https://doi.org/10.1016/j.immuni.2018.04.017

• Knowles et al. 2019 Species Identity Dominates over Environment in Shaping the Microbiota of Small Mammals.
  Ecology Letters https://doi.org/10.1111/ele.13240

• Poole et al. 2019 Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes.                                
  Cell Host & Microbe https://doi.org/10.1016/j.chom.2019.03.001

• Fouhy et al. 2019 Perinatal Factors Affect the Gut Microbiota up to Four Years after Birth.
  Nature Communication https://doi.org/10.1038/s41467-019-09252-4

2019.04.11

Presentation: Jieni Wang

Journal Club: Haoyu Lang, Tianjin Cui, Huihui Sun, Xiaohuan Mu

• Martino et al. 2018 Bacterial Adaptation to the Host's Diet Is a Key Evolutionary Force Shaping Drosophila-Lactobacillus Symbiosis. Cell Host & Microbe https://doi.org/10.1016/j.chom.2018.06.001

• Velazquez et al. 2019 Endogenous Enterobacteriaceae Underlie Variation in Susceptibility to Salmonella Infection. Nature Microbiology https://doi.org/10.1038/s41564-019-0407-8

• Ross et al. 2018 Comprehensive Skin Microbiome Analysis Reveals the Uniqueness of Human Skin and Evidence for Phylosymbiosis within the Class Mammalia. PNAS https://doi.org/10.1073/pnas.1801302115

• Brito et al. 2019 Transmission of Human-Associated Microbiota along Family and Social Networks.
  Nature Microbiology https://doi.org/10.1038/s41564-019-0409-6

2019.04.05

Presentation: Zijing Zhang

Journal Club: Qinglin Wang, Qina Cao, Jiaqiang Wu, Huijuan Duan

• Goldford et al. 2018 Emergent Simplicity in Microbial Community Assembly. Science https://doi.org/10.1126/science.aat1168

• Iszatt et al. 2019 Environmental Toxicants in Breast Milk of Norwegian Mothers and Gut Bacteria Composition and Metabolites in Their Infant at 1 Month. Microbiome https://doi.org/10.1186/s40168-019-0645-2

• Chen et al. 2019 Drosophila Histone Demethylase KDM5 Regulates Social Behavior through Immune Control and Gut Microbiota Maintenance. Cell Host & Microbe https://doi.org/10.1016/j.chom.2019.02.003

• Zeevi et al. 2019 Structural Variation in the Gut Microbiome Associates with Host Health.
  Nature https://doi.org/10.1038/s41586-019-1065-y

2019.03.20

Presentation: Huihui Sun

Journal Club: Haoyu Lang, Tianjin Cui, Jieni Wang, Xiaohuan Mu

• Jacobson et al. 2018 A Gut  Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection. Cell Host & Microbe https://doi.org/10.1016/j.chom.2018.07.002

• Litvak et al. 2019 Commensal Enterobacteriaceae Protect against Salmonella Colonization through Oxygen Competition. Cell Host & Microbe https://doi.org/10.1016/j.chom.2018.12.003

• Kniazeva et al. 2019 Rhizobium Induced DNA Damage in Caenorhabditis elegant Intestinal cells. 
  PNAS https://doi.org/10.1073/pnas.1815656116

• Regan et al. 2018 Characterisation of the British Honey Bee Metagenome.
  Nature Communications https://doi.org/10.1038/s41467-018-07426-0

2019.03.14

Presentation: Qinglin Wang

Journal Club: Zijing Zhang, Qina Cao, Jiaqiang Wu, Huijuan Duan

• Valles-Colomer et al. 2018 The Neuroactive Potential of the Human Gut Microbiota in Quality of Life and Depression.     Nature Microbiology https://doi.org/10.1038/s41564-018-0377-x

• De Filippis et al. 2019 Distinct Genetic and Functional Traits of Human Intestinal Prevotella copra Strains Are Associated with Different Habitual Diets. Cell Host & Microbe https://doi.org/10.1016/j.chom.2019.01.004

• Augustin et al. 2017 A Secreted Antibacterial Neuropeptide Shapes the Microbiome of Hydra. 
  Nature Communications https://doi.org/10.1038/s41467-017-00625-1

• Zhou et al. 2019 Selective Colonization Ability of Human Fecal Microbes in Different Mouse Gut Environments. 
  ISME https://doi.org/10.1038/s41396-018-0312-9

2019.03.07

Presentation: Haoyu Lang

Journal Club: Tianlin Cui, Xiaohuan Mu, Jieni Wang, Huihui Sun

• Guittar et al. 2019 Trait-Based Community Assembly and Succession of the Infant Gut Microbiome.                                   Nature Communications https://doi.org/10.1038/s41467-019-08377-w

• Jiang et al. 2019 Invertible Promoters  Mediate Bacterial Phase Variation, Antibiotic Resistance, and Host Adaption in the Gut. Science https://doi.org/10.1126/science.aau5238

• Kim et al. 2019 Genomic Insights from Monoglobus pectinilyticus: A Pectin-Degrading Specialist Bacterium in the Human Colon. ISME https://doi.org/10.1038/s41396-019-0363-6

• Ellegaard et al. 2019 Genomic Diversity Landscape of the Honey Bee Gut Microbiota. Nature Communications https://doi.org/10.1038/s41467-019-08303-0

2019.01.16

Journal Club: Tianlin Cui, Zijing Zhang, Qina Cao, Qinglin Wang

• Trible et al. 2017 Orco Mutagenesis Causes Loss of Antennal Lobe Glomeruli and Impaired Social Behavior in Ants.     Cell https://doi.org/10.1016/j.cell.2017.07.001

• Mets et al. 2018 Regulation of Acetate Metabolism and Coordination with the TCA Cycle via A Processed Small RNA.  PNAS https://doi.org/10.1073/pnas.1815288116

• Moeller et al. 2017 Dispersal Limitation Promotes the Diversification of the Mammalian Gut Microbiota.                     PNAS https://doi.org/10.1073/pnas.1700122114

• Gospocic et al. 2017 The Neuropeptide Corazonin Controls Social Behavior and Identity in Ants.                                       Cell https://doi.org/10.1016/j.cell.2017.07.014

2019.01.09

Presentation: Tianlin Cui

Journal Club: Jieni Wang, Huihui Sun, Haoyu Lang

• Fu et al. 2018 Tracking Vibrio cholerae Cell-Cell Interactions during Infection Reveals Bacterial Population Dynamics within Intestinal Microenvironments. Cell Host & Microbe https://doi.org/10.1016/j.chom.2017.12.006

• Ruppé et al. 2019 Prediction of Intestinal Resistome by A Three-Dimensional Structure-Based Method.                     Nature Microbiology  https://doi.org/10.1038/s41564-018-0292-6

• Waldschmitt et al. 2018 The Regenerating Family Member 3 β Instigates IL- 17A-Mediated Neutrophil Recruitment Downstream of NOD1/2 Signalling for Controlling Colonisation Resistance Independently of Microbiota Community Structure. Mucosai Immunity https://doi.org/10.1136/gutjnl-2018-316757

2019.01.02

Presentation: Qina Cao

Journal Club: Zijing Zhang, Jiaqiang Wu, Qinglin Wang

• Motta et al. 2018 Glyphosate Perturb the Gut Microbiota of Honey Bees. PNAS https://doi.org/10.1073/pnas.1803880115

• Kolodny et al. 2018 Coordinated Change at the Colony Level in Fruit Bat Fur Microbiomes through Time for. Nature Ecology & Evolution  https://doi.org/10.1038/s41559-018-0731-z

• Robinson et al. 2018 Experimental Bacterial Adaptation to the Zebrafish Gut Reveals A Primary Role for Immigration. PLOS Biology https://doi.org/10.1371/journal.pbio.2006893

2018.12.19

Presentation: Jieni Wang

Journal Club: Tianlin Cui, Huihui Sun

• Strandwitz et al. 2018 GABA-Modulating Bacteria of the Human Gut Microbiota.
  Nature Microbiology  https://doi.org/10.1038/s41564-018-0307-3j

• Jang et al. 2018 Evidence for Interplay among Antibacterial-Induced Gut Microbiota Disturbance, Neuro-Inflammation, and Anxiety in Mice. Mucosal Immunology  https://doi.org/10.1038/s41385-018-0042-3

2018.12.19

Presentation: Zijing Zhang

Journal Club: Qinglin Wang, Jiaqiang Wu, Qina Cao

• Jha et al. 2018 Gut Microbiome Transition across A Lifestyle Gradient in Himalaya.
  PLOS Biology  https://doi.org/10.1371/journal.pbio.2005396

• Gould et al. 2018 Microbiome Interactions Shape Host Fitness. PNAS  https://doi.org/10.1073/pnas.1809349115

• Suarez et al. 2018 Gut Vagal Sensory Signaling Regulates Hippocampus Function through Multi-Order Pathways.         Nature Communication https://doi.org/10.1038/s41467-018-04639-1

2018.12.12

Journal Club: Tianlin Cui, Haoyu Lang, Huihui Sun

• Beardmore et al. 2018 Drug-Mediated Metabolic Tipping between Antibiotic Resistant States in A Mixed-Species Community. Nature Ecology & Evolution  https://doi.org/10.1038/s41559-018-0582-7

• Kokou et al. 2018 Host Genetic Selection for Cold Tolerance Shapes Microbiome Composition and Modulates Its Response to Temperature. ELife  https://doi.org/10.7554/eLife.36398

• Perofsky et al. 2018 Terrestriality and Bacterial Transfer: A Comparative Study of Gut Microbiomes in Sympatric Malagasy Mammals. ISME https://doi.org/10.1038/s41396-018-0251-5

2018.12.05

Presentation: Qinglin Wang

Journal Club: Qina Cao, Jieni Wang, Jiaqiang Wu

• Reese et al. 2018 Microbial Nitrogen Limitation in the Mammalian Large Intestine.
  Nature Microbiology  https://doi.org/10.1038/s41564-018-0267-7

• Olson et al. 2018 The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet. Cell  https://doi.org/10.1016/j.cell.2018.04.027

• Tso et al. 2018 Experimental Evolution of A Fungal Pathogen into A Gut Symbiont.           Science https://doi.org/10.1126/science.aat0537

2018.11.28

Presentation: Huihui Sun

Journal Club: Zijing Zhang, Tianlin Cui, Haoyu Lang

• Solden et al. 2018 Interspecies Cross-Feeding Orchestrates Carbon Degradation in the Rumen Ecosystem.
  Nature Microbiology  https://doi.org/10.1038/s41564-018-0225-4

• Connolly et al. 2018 Host-Associated Niche Metabolism Controls Enteric Infection through Fine-Tuning the Regulation of Type 3 Secretion. Nature Communications  https://doi.org/10.1038/s41467-018-06701-4

• Pifer et al. 2018 Redox, Amino Acid, and Fatty Acid Metabolism Intersect with Bacterial Virulence in the Gut.                    PNAS https://doi.org/10.1073/pnas.1813451115

2018.11.14

Presentation: Jiaqiang Wu

Journal Club: Qinzhi Su, Jieni Wang, Qina Cao, Qinglin Wang

• Stewart et al. 2018 Temporal Development of the Gut Microbiome in Early Childhood from the TEDDY Study.
  Nature  https://doi.org/10.1038/s41586-018-0617-x

• Bäumler et al. 2016 Interactions Between the Microbiota and Pathogenic Bacteria in the Gut.
  Nature  https://doi.org/10.1038/nature18849

• Dura ́ n et al. 2018 Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival.
  Cell https://doi.org/10.1016/j.cell.2018.10.020

• Walters et al. 2018 Sarcosine Is Uniquely Modulated by Aging and Dietary Restriction in Rodents and Humans.
  Cell Report https://doi.org/10.1016/j.celrep.2018.09.065

2018.11.05

Presentation: Haoyu Lang

Journal Club: Zijing Zhang, Huihui Sun, Chenyi Li, Tianlin Cui

• Schretter et al. 2018 A Gut Microbial Factor Modulates Locomotor Behaviour in Drosophila. Nature https://doi.org/10.1038/s41586-018-0634-9

• Goyal et al. 2018 Multiple Stable States in Microbial Communities Explained by the Stable Marriage Problem. ISME https://doi.org/10.1038/s41396-018-0222-x

• Wang et al. 2018 Antiepileptic Drug Carbamazepine Promotes Horizontal Transfer of Plasmid-Borne Multi-Antibiotic Resistance Genes Within and Across Bacterial Genera. ISME https://doi.org/10.1038/s41396-018-0275-x

• Bueno et al. 2018 Anaerobic Nitrate Reduction Divergently Governs Population Expansion of the Enteropathogen Vibrio Cholerae. Nature Microbiology https://doi.org/10.1038/s41564-018-0253-0

2018.10.31

Presentation: Qina Cao

Journal Club: Jiaqiang Wu, Qinglin Wang, Qinzhi Su, Jieni Wang

• Leventhal et al. 2018 Strain-Level Diversity Drives Alternative Community Types in Millimetre-Scale Granular Biofilms. Nature Microbiology https://doi.org/10.1038/s41564-018-0242-3

• Vandeputte et al. 2017 Quantitative Microbiome Profiling Links Gut Community Variation to Microbial Load. Nature https://doi.org/10.1038/nature24460

• Han et al. 2018 A Neural Circuit for Gut-Induced Reward. Cell https://doi.org/10.1016/j.cell.2018.08.049

• Pärnänen et al. 2018 Maternal Gut and Breast Milk Microbiota Affect Infant Gut Antibiotic Resistome and Mobile Genetic Elements. Nature Communications https://doi.org/10.1038/s41467-018-06393-w

2018.10.22

Presentation: Tianlin Cui, Qing Guo

2018.10.15

Presentation: Zijing Zhang

Journal Club: Huihui Sun, Chenyi Li, Haoyu Lang, Qina Cao

• Lundsgaard et al. 2019 Mechanisms Preserving Insulin Action during High Dietary Fat Intake. Cell Metabolism https://doi.org/10.1016/j.cmet.2018.08.022

• Sharma et al. 2018 Mannose Alters Gut Microbiome, Prevents Diet- Induced Obesity, and Improves Host Metabolism. Cell Reports https://doi.org/10.1016/j.celrep.2018.08.064

• Piewngam et al. 2018 Pathogen Elimination by Probiotic Bacillus via Signalling Interference. Nature https://doi.org/10.1038/s41586-018-0616-y

• Ju et al. 2018 Wastewater Treatment Plant Resistomes Are Shaped by Bacterial Composition, Genetic Exchange, and Upregulated Expression in The Effluent Microbiomes. ISME https://doi.org/10.1038/s41396-018-0277-8

2018.10.08

Presentation: Jieni Wang

Journal Club: Jiaqiang Wu, Qinglin Wang, Qinzhi Su, Tianlin Cui

• Zierer et al. 2018 The Fecal Metabolome as A Functional Readout of The Gut Microbiome. Nature Genetics https://doi.org/10.1038/s41588-018-0135-7

• Pärnänen et al. 2018 Maternal Gut and Breast Milk Microbiota Affect Infant Gut Antibiotic Resistome and Mobile Genetic Elements. Nature Communications https://doi.org/10.1038/s41467-018-06393-w

• Adamowicz et al. 2018 Cross-Feeding Modulates Antibiotic Tolerance in Bacterial Communities. ISME Journal https://doi.org/10.1038/s41396-018-0212-z

• Martı ́nez et al. 2018 Experimental Evaluation of The Importance of Colonization History in Early-Life Gut Microbiota Assembly. ELife https://doi.org/10.7554/elife.36521

2018.09.24

Presentation: Huihui Sun

Journal Club: Jieni Wang, Jiaqiang Wu, Zijing Zhang

• Suez et al. 2018 Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell https://doi.org/10.1016/j.cell.2018.08.047

• Zmora et al. 2018 Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features. Cell https://doi.org/10.1016/j.cell.2018.08.041

• Light et al. 2018 A Flavin-Based Extracellular Electron Transfer Mechanism in Diverse Gram-Positive Bacteriasoil Viral Ecology along A Permafrost Thaw Gradient. Nature https://doi.org/10.1038/s41586-018-0498-z

2018.09.17

Presentation: Jiaqing Wu, Haoyu Lang

Journal Club: Tianlin Cui, Qinan Cao, Chenyi Li, Qinzhi Su

• Sanchez et al. 2018 Cooperative Metabolic Adaptations in the Host Can Favor Asymptomatic Infection and Select for Attenuated Virulence in an Enteric Pathogen. Cell https://doi.org/10.1016/j.cell.2018.07.016

• Deschasaux et al. 2018 Depicting the Composition of Gut Microbiota in A Population with Varied Ethnic Origins but Shared Geography. Nature Medicine https://doi.org/10.1038/s41591-018-0160-1

• Emerson et al. 2018 Host-Linked Soil Viral Ecology along A Permafrost Thaw Gradient. Nature Microbiology https://doi.org/10.1038/s41564-018-0190-y

• Fulde et al. 2018 Neonatal Selection by Toll-Like Receptor 5 Influences Long-Term Gut Microbiota Composition. Nature  https://doi.org/10.1038/s41586-018-0395-5