Welcome to the Ludington Lab

Ecosystems fluctuate over time. For example, in a forest trees fall, seeds grow, and sometimes forest fires burn it all down. Microbial ecosystems experience similar fluctuations but on a much faster time scale. Taking advantage of the fast time scale and ease of setting up a controlled experiment, we study complex ecological dynamics that arise from microbial community interactions. Our research group investigates basic ecological principles in the context of gnotobiotic Drosophila melanogaster microbiomes in order to understand the complicated and often complex relationship between microbiome and host.

1. Gut microbial ecology modulates fly health. Using gnotobiotic flies and a battery of physiological and fitness assays, we study the effects of gut microbial community ecology on host cell physiology.

2. Metabolic crossfeeding influences community ecology of the gut microbiota. Using both gnotobiotic flies and high throughput in vitro growth assays, we study the microbial interactions that shape the fly gut microbiota.

3. Stochastic population dynamics in the microbiome influence host physiology. We have developed single fly feeding and monitoring techniques to measure microbial populations in the gut. Using these approaches, we are studying basic principles of colonization and stability in the context of host physiology and disease ecology.


Testing the role of intraflagellar transport in flagellar length control using length-altering mutants of Chlamydomonas K Wemmer, W Ludington, WF Marshall Philosophical Transactions of the Royal Society B 375 (1792), 20190159	2020
Bellymount enables longitudinal, intravital imaging of abdominal organs and the gut microbiota in adult Drosophila LAJ Koyama, A Aranda-Díaz, YH Su, S Balachandra, JL Martin, ... PLoS Biology 18 (1), e3000567	2020
Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance AD Andrés, B Obadia, D Ren, T Tani, ZF Hallberg, GZ Tüzün, ... eLife 9	2020
Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance A Aranda-Díaz, B Obadia, R Dodge, T Thomsen, ZF Hallberg, ZT Güvener, ... eLife 9	2020
*Cluster partitions and fitness landscapes of the Drosophila* fly microbiome H Eble, M Joswig, L Lamberti, WB Ludington Journal of mathematical biology 79 (3), 861-899**	2019
Combinatorial ecology in the simple fruit fly gut microbiome A Gould, V Zhang, L Lamberti, E Jones, B Obadia, N Korasidis, ... APS Meeting Abstracts	2019
Microbiome interactions shape host fitness AL Gould, V Zhang, L Lamberti, EW Jones, B Obadia, N Korasidis, ... Proceedings of the National Academy of Sciences 115 (51), E11951-E11960	2018
Microbial quantity impacts Drosophila nutrition, development, and lifespan ES Keebaugh, R Yamada, B Obadia, WB Ludington, WJ William Iscience 4, 247-259	2018
Diet influences host–microbiota associations in Drosophila B Obadia, ES Keebaugh, R Yamada, WB Ludington, WJ William Proceedings of the National Academy of Sciences 115 (20), E4547-E4548	2018
High dimensional microbiome interactions shape the host fitness landscape A Gould, V Zhang, L Lamberti, E Jones, B Obadia, A Gavryushkin, ... Bulletin of the American Physical Society 63	2018
Chronic ethanol ingestion impairs Drosophila melanogaster health in a microbiome-dependent manner JA Chandler, LV Innocent, IL Huang, JL Yang, MB Eisen, WB Ludington BioRxiv, 217240	2018
Probabilistic invasion underlies natural gut microbiome stability B Obadia, ZT Güvener, V Zhang, JA Ceja-Navarro, EL Brodie, WW Ja, ... Current Biology 27 (13), 1999-2006. e8	2017
MICROBIALLY-MEDIATED ALCOHOL RESISTANCE: A MODEL SYSTEM USING FRUIT FLIES, THEIRMICROBIOTA, AND INGESTED ALCOHOL JA Chandler, D Rosenthal, A Jain, M Eisen, W Ludington ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH 41, 304A-304A	2017
Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater WB Ludington, TD Seher, O Applegate, X Li, JI Kliegman, C Langelier, ... PloS one 12 (4)	2017
Maternal IgG and IgA antibodies dampen mucosal T helper cell responses in early life MA Koch, GL Reiner, KA Lugo, LSM Kreuk, AG Stanbery, E Ansaldo, ... Cell 165 (4), 827-841	2016
Stable host gene expression in the gut of adult Drosophila melanogaster with different bacterial mono-associations C Elya, V Zhang, WB Ludington, MB Eisen PloS one 11 (11)	2016
Invasion Dynamics in the Fly Gut Microbiota. B Obadia, T Guvener, V Zhang, WB Ludington MOLECULAR BIOLOGY OF THE CELL 27	2016
A systematic comparison of mathematical models for inherent measurement of ciliary length: how a cell can measure length and volume WB Ludington, H Ishikawa, YV Serebrenik, A Ritter, RA Hernandez-Lopez, ... Biophysical journal 108 (6), 1361-1379	2015
Avalanche-like behavior in ciliary import WB Ludington, KA Wemmer, KF Lechtreck, GB Witman, WF Marshall Proceedings of the National Academy of Sciences 110 (10), 3925-3930	2013
Organelle size equalization by a constitutive process WB Ludington, LZ Shi, Q Zhu, MW Berns, WF Marshall Current Biology 22 (22), 2173-2179	2012
Flagellar length control in Chlamydomonas reinhardtii, experimental and mathematical approaches WB Ludington UCSF	2011
The Flagellar Length Control System W Ludington, K Wemmer, B Engel, E Kannegaard, W Marshall MOLECULAR BIOLOGY OF THE CELL 22	2011
IFT and precursor pool regeneration in long and short flagella mutants of Chlamydomonas reinhardtii. K Wemmer, W Ludington, E Kannegaard, H Rego, WF Marshall MOLECULAR BIOLOGY OF THE CELL 22	2011
How the Flagellum Measures Its Length WB Ludington, BD Engel, WF Marshall Biophysical Journal 98 (3), 721a	2010
Intraflagellar transport particle size scales inversely with flagellar length: revisiting the balance-point length control model BD Engel, WB Ludington, WF Marshall Journal of Cell Biology 187 (1), 81-89	2009
Automated analysis of intracellular motion using kymographs in 1, 2, and 3 dimensions WB Ludington, WF Marshall Three-Dimensional and Multidimensional Microscopy: Image Acquisition and …	2009
fester, A candidate allorecognition receptor from a primitive chordate SV Nyholm, E Passegue, WB Ludington, A Voskoboynik, K Mitchel, ... Immunity 25 (1), 163-173	2006
Isolation and characterization of a protochordate histocompatibility locus AW De Tomaso, SV Nyholm, KJ Palmeri, KJ Ishizuka, WB Ludington, ... Nature 438 (7067), 454-459	2005
*Genetic variation in Mastocarpus papillatus* (Rhodophyta) in central California using amplified fragment length polymorphisms WB LUDINGTON, KA CALLICOTT, AW DETOMASO Plant species biology 19 (2), 107-113**	2004
*Paup^. phylogenetic Analysis Using Parsimony (^* and other methods) Paup^. phylogenetic Analysis Using Parsimony (^ and other methods), 2000 RV SNYDER, PDL GIBBS, A PALACIOS, L ABIY, R DICKEY, JV LOPEZ, ... Phycological research 49 (3), 251-261**	2001

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Welcome to the Ludington Lab