Microbiology Journal Club


Weekly meeting of faculty and students in the Field of Microbiology and beyond. In these colloquia, participants discuss contemporary or seminal papers in the field of microbiology. Student objectives are (1) to evolve our critical reading, analysis, and presentation skills, (2) to expand our horizons and explore areas of microbiology that we otherwise would not, as we (3) discuss current progress in the field with faculty and peers.  Journal club is led by Dr. Esther Angert (era23@cornell.edu) and co-organized by graduate student volunteers.

The Microbiology Journal Club will meet on Tuesdays from 12:00-1:00 in M01 Stocking Hall. Students may enroll for credit under course number BioMI 79100.


Fall 2019

Tues, December 10: Imachi, Hiroyuki, et al. Isolation of an archaeon at the prokaryote-eukaryote interface (2019) https://doi.org/10.1101/726976

Tues, December 3: Mason, Charles J., et al. Plant defenses interact with insect enteric bacteria by initiating a leaky gut syndrome. PNAS 116 (32): 15991-15996 (2019) https://doi.org/10.1073/pnas.1908748116

Tues, November 26: Matthey, Noemie, et al. Neighbor predation linked to natural competence fosters the transfer of large genomic regions in Vibrio cholerae. eLife 2019;8:e48212 https://doi.org/10.7554/eLife.48212

Tues, November 19: Hsu, Bryan B., et al. Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model. Cell Host & Microbe 25(6): 803-814 (2019) https://doi.org/10.1016/j.chom.2019.05.001

Tues, November 12: North, Olesia I., et al. Phage tail fibre assembly proteins employ a modular structure to drive the correct folding of diverse fibres. Nat Microbiol 4, 1645-1653 (2019) https://doi.org/10.1038/s41564-019-0477-7

Tues, November 5: Muchnikov, Nikolai V., et al. Inducible asymmetric cell division and cell differentiation in a bacterium. Nat Chem Biol 15, 925-931 (2019) https://doi.org/10.1038/s41589-019-0340-4 

Tues, October 29: Qian, Xin-Xin, et al., 2019. Juxtaposed membranes underpin cellular adhesion and display unilateral cell division of multicellular magnetotactic prokatryotes. Society for Applied Microbiology. https://doi.org/10.1111/1462-2920.14710.

Tues, October 22: Lai, Ghee Chuan, et al., 2017. The mecillinam resistance reveals a role for peptidoglycan endopeptidases in stumulating cell wall synthesis in Escherichia coli. PLoS Genet 13(7): e1006934. https://doi.org/10.1371/journal.pgen.1006934

Tues, October 8: Mitra, Avishek, et al., 2019. Heme and hemoglobin utilization by Mycobacterium tuberculosis. Nature Communications 10, 4260.

Tues, October 1: Din, M. Oman, et al., 2016. Synchronized cycles of bacterial lysis for in vivo delivery. Nature 536, 81-85.

Tues, Sept 24: Benson, Meredith A., et al., 2014. Evolution of hypervirulence by a MRSA clone through acquisition of a transposable elementMolecular Microbiology 93(4): 664-681.

Tues, Sept 10: Barchewitz, Tino et al., 2019. Non-canonical localization of RubisCO under high light conditions in the toxic cyanobacterium Microcystic aeruginose PCC7806.

Tues, Sept 3: Organizational Meeting


Spring 2019

Tues, May 7: Varble A et al., 2019. Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci. Nature Microbiology: https://doi.org/10.1038/s41564-019-0400-2.

Tues, Apr 23: ​Zeevi D. et al., 2019. Structural variation in the gut microbiome associates with host health. Nature 568, 43-48.

Tues, Apr 16: ​White E. C. et al., 2018. Manipulation of host and parasite microbiotas: survival strategies during chronic nematode infection. Science Advances, 4(3).

Tues, Mar 26: Pasolli, E. et al., 2019. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell, 176(3): 649-662.

Tues, Mar 19: Borges, A. L., et al., 2018. Bacteriophage Cooperation Suppresses CRISPR-Cas3 and Cas9 Immunity. Cell 174, 917-925.

Tues, Mar 12: Melnyk, R.A. et al., 2019. Convergent gain and loss of genomic islands drive lifestyle changes in plant-associated Pseudomonas. The ISME Journal. https://doi.org/10.1038/s41396-019-0372-5

Tues, Mar 5: Duval, M et al., 2018. HflXr, a homolog of a ribosome-splitting factor mediates antibiotic resistance. Proceedings of the National Academy of Sciences, 115(52): 13359-13364.

Tues, Feb 19: Smits, S.A. et al., 2017. Seasonal cycling in the gut microbiome of the Hazda hunter-gatherers of Tanzania. Science, 357:6353(802-806).

Tues, Jan 29: Yang, S. et al., 2018. Biodegradation of polystyrene wastes in yellow mealworms (larvae of Tenebrio molitor Linnaeus): Factors affecting biodegradation rates and the ability of polystyrene-fed larvae to complete their life cycle. Chemosphere: 191: 979-989.

Fall 2018

Tues, Dec 4: Shukla, S. P. et al., 2018. Microbiome-assisted carrion preservation aids larval development a burying beetle. Proceedings of the National Academy of Sciences, 115(44): 11274-11279.

Tues, Nov 27: Jacobson A et al., 2018. A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection. Cell Host & Microbe, 24(2): 296-307.

​Tues, Nov 20: ​Gao, X et al., 2017. Evolution of host adaptation in the Salmonella typhoid toxin. Nature Microbiology 2(12), 1592-1599.

Tues, Nov 13: ​Mehta, A. P. et al., 2018. Engineering yeast endosymbionts as a step toward the evolution of mitochondria. Proceedings of the National Academy of Sciences, 201813143; DOI:10.1073/pnas.1813143115.

Tues, Nov 6: ​Nikoh, N. et al, 2018. mbio.asm.org/content/9/3/e00890-18Genomic Insight into Symbiosis-Induced Insect Color Change by a Facultative Bacterial Endosymbiont, “Candidatus Rickettsiella viridis”.  mBio, 9 (3) e00890-18; doi:10.1128/mBio.00890-18.

Tues, Oct 30: Radlinski L, et al. (2017). Pseudomonas aeruginosa exoproducts determine antibiotic efficacy against Staphylococcus aureus. PLoS Biol 15(11): e2003981.

Tues, Oct 23: Ellison, C. K. et al., 2018. Retraction of DNA-bound type IV competence pili initiates DNA uptake during natural transformation in Vibrio cholerae. Nature Microbiology 3, 773-780.

Tues, Oct 16: Dar, D. and Sorek, R. (2018). Extensive reshaping of bacterial operons programmed by mRNA decay. PLoS Genetics, 14(4): e1007354.

Tues, Oct 9:  No meeting, Fall Break

Tues, Oct 2: Brophy, J. A. N. et al. (2018). Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria. Nature Microbiology, 3:1043-1053.

​Tues, Sept 25: Fisher, R. M. et al. (2017). The evolution of host-symbiont dependence. Nature Communications, 8:15973.

Tues, Sept 18: Yip, D.Z. et al. (2018). Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populous deltoides). New Phytologist, doi: 10.1111/nph:15346.

Tues, Sept 11: Hynes, A.P. et al. (2018). Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins. Nat Commun 9:2919.

Tues, Sept 4: Van der Henst, C. et al. (2018) Molecular insights into Vibrio cholerae’s intra-amoebal host-pathogen interactions. Nat Commun 9(1):3460

Tues, Aug 28: Organizational Meeting


Spring 2018

Tues, May 3:
Freeman, S. et. al. (2014) Active learning increases student performance in science, engineering, and mathematics. PNAS 111 (23) 8410-841.

Tues, Apr 24:
Lieberman, T., et. al. (2016). Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosisNature Medicine Letters 22:1470-1474

Tues, Apr 17:
Rohschild, D., et. al. (2018). Environment dominates over host genetics in shaping human gut microbiota. Nature 555: 210-215.

Tues, Apr 3:
Schroeder JW, Randall JR, Hirst WG, O’Donnell ME, Simmons LA. (2017) Mutagenic cost of ribonucleotides in bacterial DNA.  Proc Natl Acad Sci U S A. 114:11733-11738.

Tues, Mar 20:
Figueroa, et. al. (2017) Metagenomics-guided analysis of microbial chemolithoautrophic phosphite oxidation yields evidence of a seventh natural CO2 fixation pathway. PNAS 201715549 

Tues, Mar 13:
Fischer, et. al. (2017) Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior. eLIFE 6: e1885

Tues, Mar 6:
Zhang, et. al. (2018) Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium. Cell Host & Microbe 23:169-176
Zhang, et. al. (2017) Identification and characterization of a novel botulinum neurotoxinNature Communications 8:14130

Tues, Feb 27:
Espaillat, et. al. (2016) Chemometric analysis of bacterial peptidoglycan reveals atypical modifications that empower the cell wall against predatory enzymes and fly innate immunity. 
JACS 138:9193

​Tues, Feb 20:
No meeting, February Break

Tues, Feb 13:
Gray, et. al. (2016) Intercellular communication and conjugation are mediated by ESX secretion systems in mycobacteria.
 Science 354:631

Tues, Feb 6:
Cho et al (2016) 
Bacterial cell wall biogenesis is mediated by SEDS and PBP polymerase families functioning semi-autonomously.  Nature Microbiology 19:16172

Tues, Jan 30:
Organizational meeting

Fall 2017

Tuesday, November 28:
Parks et al. (2017) Recovery of nearly 8000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology 2:1533-42.

Tuesday, Nov 21:
Anbutsu, et. al. Small genome symbiont underlies cuticle hardness in beetles. PNAS, Sept, 2017

Tuesday, Nov 14:
Rotaru et al (2014) ​Direct Interspecies Electron Transfer between Geobacter metallireducens and Methanosarcina barkeri. Applied and Environmental Microbiology, epub ahead of print.
Rotaru et al (2013) A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane. Royal Society of Chemistry, 7:408-15.

Tuesday, Nov 7:
Genetic characterization of mycobacterial L,D-transpeptidases​.
Microbiology, 2014.
A Role for the Class A Penicillin-Binding Protein PonA2 in the Survival of Mycobacterium smegmatis under Conditions of Nonreplication.
​Journal of Bacteriology, 2010.

Tuesday, Oct 31:
Chamakura, et al (2017) A viral protein antibiotic inhibits lipid II flippase activity. Nature Microbiology 2:1480-4.

Tuesday, Oct 24:
​Ellison, et. al. (2017) Obstruction of pilus retraction stimulates bacterial surface sensing. BioRXiv.

Tuesday, Oct 17:
Peter Diebold and Joe Peters will be leading the discussion about the key findings from three papers (below) in preparation for our Thursday seminar speaker, Laura Hug from the University of Waterloo:
Hug, L. A., Baker, B. J., Anantharaman, K., Brown, C. T., Probst, A. J., Castelle, C. J., et al. (2016). A new view of the tree of life. Nature Microbiology, 1–6. http://doi.org/10.1038/nmicrobiol.2016.48
Brown, C. T., Hug, L. A., Thomas, B. C., Sharon, I., Castelle, C. J., Singh, A., et al. (2015). Unusual biology across a group comprising more than 15% of domain Bacteria. Nature, 523(7559), 208–211. http://doi.org/10.1038/nature14486
Lennon, C. W., Stanger, M., & Belfort, M. (2016). Protein splicing of a recombinase intein induced by ssDNA and DNA damage. Genes & Development, 30(24), 2663–2668. http://doi.org/10.1101/gad.289280.116

Tuesday, Oct 10:
No meeting, Fall Break

Tuesday, Oct 3:
Ionescu et al. (2017)Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum. Nature Communications 8:455 doi: 10.1038/s41467-017-00342-9

Tuesday, Sept 26:
Woznica, Gerdt,King et al. (2017) Mating in the Closest Living Relatives of Animals Is Induced by a Bacerial Chondroitinase. Cell  170:1175-1183 doi: p1175-1183.e11

Tuesday, Sept 19:
Erdmann et al. (2017) A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells. Nature Microbiology  doi:10.1038/s41564-017-0009-2​

Tuesday, Sept 12:
Cohen et al. (2017) Commensal bacteria make GPCR ligands that mimic human signalling molecules.
Nature 549:48-53. doi: 10.1038/nature23874

Tuesday, Aug 29:
​Organizational meeting

Spring 2017 semester:

May 8: 
Dodd MS, Papineau D, Grenne T, Slack JF, Rittner M, Pirajno F, O’Neil J, Little CT. (2017) Evidence for early life in Earth’s oldest hydrothermal vent precipitates. Nature. 543(7643):60-64.

May 2: 
Papenfort K, Silpe JE, Schramma KR, Cong JP, Seyedsayamdost MR, Bassler BL. (2017) Vibrio cholerae autoinducer-receptor pair that controls biofilm formation. Nat Chem Biol. 2017 May;13(5):551-557.

April 25: 
Boedeker C, Schüler M, Reintjes G, Jeske O, van Teeseling MC, Jogler M, Rast P, Borchert D, Devos DP, Kucklick M, Schaffer M, Kolter R, van Niftrik L, Engelmann S, Amann R, Rohde M, Engelhardt H, Jogler C. Determining the bacterial cell biology of Planctomycetes. Nat Commun. 2017 Apr 10;8:14853.

April 11: 
Hodak and Galan (2012) ASalmonella Typhi homologue of bacteriophage muramidases controls typhoid toxin secretion. EMBO Reports 4:95-1

March 28: 
Peng W, de Vries RP, Grant OC, et al.(2017) “Recent H3N2 Viruses Have Evolved Specificity for Extended, Branched Human-type Receptors, Conferring Potential for Increased Activity

March 14: 
Dodd MS, Papineau D, Grenne T, Slack JF, Rittner M, Pirajno F, O’Neil J, Little CTS (2017) Evidence for early life in Earth’s oldest hydrothermal vent precipitates. Nature 543:60-64

March 7:
Carini P, Marsden PJ, Leff JW Morgan EE, Strickland MS Fierer N. (2017) Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nat Microbiol. 2:1642.

February 28:
Leinweber A, Fredrik Inglis R, Kummerli R. (2107) Cheating fosters species co-existence in well-mixed bacterial communities. ISME J. doi: 10.1038/ismej.2016.195. [Epub ahead of print]

February 14:
Lamberte LE, Baniulyte G, Singh SS, Stringer AM, Bonocora RP, Stracy M, Kapanidis AN, Wade JT, Grainger DC. (2017) Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase. Nat Microbiol. 2:16249. doi: 10.1038/nmicrobiol.2016.249.

February 7:
Research presentation by Angert Lab on recent field work conducted at Lizard Island, Australia

January 31:
Organizational meeting