KITP: Forum on Microbial Metabolism
(Jan 14 - Mar 18, 2021)
Coordinators: Terry Hwa, Boris Shraiman, and Alfred Spormann

Forum Overview | Talks | References | PodcastXML | Schedule |

Learning Material

1/14 Alfred Spormann: Tutorial 1 Fundamentals of Microbial Life, Physical-chemical structure of the environment, rate-yield trade off, fitness and selection

This manuscript provides some general review on growth and how some common celluar constraints induce trade-offs in metabolic strategies and growth parameters.
Helling, Vargas, and Adams
A classical paper describing experimentally the speciation of E. coli under constant and competitive conditions into 2 variants based on altered use of the resource glucose. Also useful to understand niche partitioning in experimental evolution using a glucose-limited chemostat.
Pfeiffer & Bonhoefer 02
Theoretical paper describing the arising of rate-yield trade offs from thermodynamic principles. Includes also the effect of the physical-chemical structure of the environment on the expression of a rate or yield phenotype.
Kreft 06
Evolution of cooperation in structured environments as a conseqeunce of rate-yield trade off.
Costa et al 06
Rate yield trade off driving speciation in nitrification. This paper is useful for the context of the talk by Sebastian Luecker.
Video: Alfred Spormann, Oxidation state of carbon
Very useful tutorial on how to look ate organic substrates and metabolites in energy metabolism. Everyone should be familiar with that.
Video: Alfred Spormann, Oxidation state of S and N compounds
As above but for sulfur and nitrogen compounds
Video: Alfred Spormann, Redoxpotential
This is a very useful tutorial for understanding the flux and properties of metabolic ‘electrons’. A must.

1/28 Uwe Sauer: Central metabolism and growth-lag tradeoff

Chubokov et al, 2014
Coordination of microbial metabolism
Gerosa and Sauer 2011
Regulation and control of metabolic fluxes in microbes

2/04 Bernhard Schink: Syntrophic microbial interactions

Schink, B.: Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61, 262- 280 (1997)
A classical review covering the entire field of syntrophy and interspecies electron transfer in methanogenic degradation.
Schink, B., D. Montag, A. Keller, N. Muller: Hydrogen or formate - alternative key players in methanogenic degradation. Environ. Microbiol. Rep. 9, 189-202 (2017)
A short review discussing the pros and cons of hydrogen versus formate as electron carriers in methanogenic degradation.
Schmidt, A., N. Muller, B. Schink, D. Schleheck: A proteomic view at the biochemistry of syntrophic butyrate oxidation in Syntrophomonas wolfei. Plos One (2013)
Our present-day understanding of reversed electron transport in syntrophic fatty acid oxidation.
Keller, A., B. Schink, N. Muller: Energy-conserving enzyme systems active during syntrophic acetate oxidation in the thermophilic bacterium Thermacetogenium phaeum. Front. Microbiol. Volume 10, Article Number: 2785 Nov 29 (2019)
Our concept of energy conservation and reversed electron transport in thermophilic syntrophic acetate oxidation.

2/11 Andreas Baumler: Metabolic strategies of pathogens in the human gut

Rogers, A., Tsolis, R. M., & Baumler, A. J. (2020). Salmonella versus the Microbiome. Microbiology and molecular biology reviews : MMBR, 85(1), e00027-19.
A recent review article that covers the topic of my lecture
Winter, S. E., Thiennimitr, P., Winter, M. G., Butler, B. P., Huseby, D. L., Crawford, R. W., Russell, J. M., Bevins, C. L., Adams, L. G., Tsolis, R. M., Roth, J. R., & Baumler, A. J. (2010). Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature, 467(7314), 426-429.
The first evidence that intestinal inflammation generates an electron acceptor for Salmonella growth in the lumen
Winter, S. E., Winter, M. G., Xavier, M. N., Thiennimitr, P., Poon, V., Keestra, A. M., Laughlin, R. C., Gomez, G., Wu, J., Lawhon, S. D., Popova, I. E., Parikh, S. J., Adams, L. G., Tsolis, R. M., Stewart, V. J., & Baumler, A. J. (2013). Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science (New York, N.Y.), 339(6120), 708-711.
The article shows that intestinal inflammation promotes luminal growth of nitrate reducing bacteria
Rivera-Chavez, F., Zhang, L. F., Faber, F., Lopez, C. A., Byndloss, M. X., Olsan, E. E., Xu, G., Velazquez, E. M., Lebrilla, C. B., Winter, S. E., & Baumler, A. J. (2016). Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella. Cell host & microbe, 19(4), 443-454.
The article shows that the action of Salmonella virulence factors increase oxygen availability in the gut lumen
Velazquez, E.M., Nguyen, H., Heasley, K.T. et al. (2019) Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection. Nat Microbiol 4, 1057-1064.
The article shows how competition contributes with closely related bacteria to colonization resistance against Salmonella

2/25 Sebastian Luecker: Complete nitrification by a single microorganism

van Kessel, M.A.H.J., D.R. Speth, M. Albertsen, P.H. Nielsen, H.J.M. Op den Camp, B. Kartal, M.S.M. Jetten, S. Lucker (2015). Complete nitrification by a single microorganism. Nature 528(7583): 555-559.
One of the two original articles first describing the identification of complete ammonia-oxidizing (comammox) bacteria. For the second article, which was published in the same issue of Nature, see here.
Sakoula, D., H. Koch, J. Frank, M.S.M. Jetten, M.A.H.J. van Kessel, S. Lu?cker (2020). Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification. The ISME Journal.
This study describes the enrichment and physiological characterisation of a novel comammox Nitrospira.
Daims, H., S. Lucker, M. Wagner (2016). A new perspective on microbes formerly known as nitrite-oxidizing bacteria. Trends in Microbiology 24(9): 699-712.
A review article summarising major findings forming our current understanding of the physiology and diversity of nitrite-oxidizing bacteria, including comammox Nitrospira.
Singer, E., Wagner, M. & Woyke, T. (2017). Capturing the genetic makeup of the active microbiome in situ. The ISME Journal 11: 1949?1963.
A recent review on methods available to link function to identity for uncultivated microorganisms.

3/04 Cornelia Welte: Microbial C1 metabolism

Thauer et al 1977
A seminal review in which you can find most ΔGs for anaerobic metabolic processes
Welte & Deppenmeier 2014
A review on the bioenergetics of methanogenesis
Kurth et al 2020
Our latest review on knowledge gaps in the metabolism of methanogenesis
Timmers et al 2017
This article deals with the reversibility of the methanogenesis / anaerobic methanotrophy pathway
Evans et al 2019
Interesting review providing a broader view on archaea that contain the key gene of methanogenesis/methanotrophy, mcr, but are probably doing different metabolic processes with it