December 1st, 2020: I was invited to give a 2-hour class for the "Metabolic Pathways Engineering in Bacteria course" part of the Graduate Program In Biochemical Science UNAM Mexico.
gas, us 85% Dark matter Direct detection: Underground LZ experiment Indirect detection. Fermi Gamma-Ray Space Telescope Particle coliders: ATLAS experiment Culturable taxa 15% 99% Microbial dark matter Direct detection: Omics: Metagenomics, Metaproteomics, Metatranscriptomics Next generation Physiology Next generation Bioprospecting 1% Pharmaceutical, Industrial, Medicine, Model organisms
3 4 Origin of metagenomis Human microbiome Ocean microbiome New tree of life First Asgard culture Archaea tree of life Next Generation Physiology Jan Feb May
Primeros habitantes en el planeta Oxigenaron la atmósfera primitiva Dieron lugar a organismos multicelulares Han modificado (y continuan) la biogeoquímica del planeta Son la base fundamental de cualquier ecosistema Son los primeros en responder ante perturbaciones ambientales Cruciales para entender cambio climático global
Metaproteomics, Metatranscriptomics Next generation Physiology Next generation Bioprospecting 1% 03 Inferencia de metabolismo ¿Cómo analizar lo que no ha sido descrito?
speed, data processing, reproducibility) What do we need to improve efficiency of data processing? Biological data interpretation (evaluate, compare and analyze complex data in a large scale)
metabolismo For a given system, multiple sources (and possible types) of data are available and we want to study them integratively to improve knowledge discovery 1 MEBS
on biological meaningful regions (specific metabolic machineries) Does is it really work? Data integration 03 Inferencia de metabolismo For a given system, multiple sources (and possible types) of data are available and we want to study them integratively to improve knowledge discovery Prior Knowledge 1 2 MEBS
large-scale metabolic machineries? To reduce the solution space and/or to focus the analysis on biological meaningful regions (specific metabolic machineries) Does is it really work? Data integration 03 Inferencia de metabolismo For a given system, multiple sources (and possible types) of data are available and we want to study them integratively to improve knowledge discovery Prior Knowledge 1 2 3 Available data MEBS
large-scale metabolic machineries? To reduce the solution space and/or to focus the analysis on biological meaningful regions (specific metabolic machineries) Does is it really work? Data integration 03 Inferencia de metabolismo For a given system, multiple sources (and possible types) of data are available and we want to study them integratively to improve knowledge discovery Prior Knowledge 1 2 3 Available data 4 Mathematical model MEBS
large-scale metabolic machineries? To reduce the solution space and/or to focus the analysis on biological meaningful regions (specific metabolic machineries) Does is it really work? Data integration 03 Inferencia de metabolismo For a given system, multiple sources (and possible types) of data are available and we want to study them integratively to improve knowledge discovery Prior Knowledge 1 2 3 Available data 4 Mathematical model MEBS Single Informative Value
large-scale metabolic machineries? To reduce the solution space and/or to focus the analysis on biological meaningful regions (specific metabolic machineries) Does is it really work? Data integration 03 Inferencia de metabolismo For a given system, multiple sources (and possible types) of data are available and we want to study them integratively to improve knowledge discovery Prior Knowledge 1 2 3 Available data 4 Mathematical model MEBS Single Informative Value Improves efficiency of data processing?
de metabolismo Assembly Protein coding genes MEBS Entropy-based Scores Visualization Tree of life Metabolic clustering Time series Geographical potential
Sulfur cycle geographical potential De Anda et al., 2017 GigaScience C,O,N,S,Fe potential across 2 year period of time De Anda et al., 2018 Front. Microbiol 2k Deltaproteobacteria metabolism inference Langwig et al., Metabolic discovery of novel branches of the tree of life Carlton et al., De Anda et al., Appler et al.,
Castelán-Sánchez et al., 2019 Structure and function of communities hypersaline environment Anaerobic phenanthrene degrading bacteria characterization Kraiselburd et al., 2019 Environ Micro Marine bone degrading microbiome Borcher et al., 2020 Preprint Castelán-Sánchez et al., 2019
Metagenome Controlled conditions C and Energy Source Microbial interactions Environmental variables No prior knowledge C and Energy Source Only at the time of sampling Environmental variables Enrichment Sequencing
for all living things. Energy source Phototrophs Chemotrophs Chemoheterotrophs Chemoautotrophs Photoheterotrophs Photoautotrophs Organic compounds CO2 Chemical Light Carbon source Organic compounds CO2 Carbon source
for all living things. Energy source Phototrophs Chemotrophs Chemoheterotrophs Chemoautotrophs Photoheterotrophs Photoautotrophs Organic compounds CO2 Chemical Light Carbon source Organic compounds CO2 Carbon source O2 Not O2 Organic Inorganic Final e- acceptor Yes NO H20 to reduce CO2
CH 3 NH 2 CH 3 CH 3 CH 3 OH C R Dimethylsulfide (DMS) CH 3 S CH 3 CH 3 NH 2 CH 3 Important components of the global C, N, S Are derived from different sources such as phytoplankton, plants, and the decay of organic matter Abundant in the oceans, atmosphere and sediments Methylated compounds 03 Inferencia de metabolismo De Anda et al. in review Nature Comm.
Gb por muestra) ~ 3000 MAGs + 551 MAGs Dowmbroski et al., 2018 Woodcroft et al Nature 2018 Emerson et al., Nat Micro 2018 Tsagaraki et al., 2918 Degradación de materia orgánica Permafrost en Suecia 214 muestras 1529 MAGs Permafrost: Cambio climático 2540 MAGs 47 Nuevos linajes a nivel de Phylum Análisis detallado de la interacción de los ciclos biogeoquímicos a nivel de genomas De Anda et al., In Progres Anantharaman, K. et al., 2016 Nature commun Acuíferos Sitios contaminados 03 Inferencia de metabolismo
CP9 Asgard Análisis integral degradación de carbono Gong et al. Langwig et al. Rambo et al. Carlton, Vazquez et al Appler et al. De Anda et al. 03 Inferencia de metabolismo
Deltaproteobacteria Protein-level comparison of nearly 2,000 Deltaproteobacteria reveals new ecological and biogeochemical roles Langwig M, De Anda et al., ISME submitted
The first genome of this group was reconstructed from sediments near the Loki’s Castle hydrothermal vent field in the North Atlantic Ocean and was subsequently named Lokiarchaeota Lokiarchaeota Asgard archaea are the descendants of the archaeal host involved in eukaryogenesis 03 Inferencia de metabolismo Asgard Emme et al., 2017 Nature Reviews
fermentation or by anaerobic and aerobic respiration Odinarchaeum may be a thermophilic fermentative heterotroph Lokiarchaeota and Thorarchaeota can probably use organic compounds and hydrogen The Wood–Ljungdahl pathway (WLP) allows the reduction of carbon dioxide to acetyl-coenzyme A (CoA) and can be used to support both autotrophic carbon fixation and, when linked to chemiosmotic processes, energy conservation. Spang et al Nat Microbiol, 2019
Lopez-Garcia in 1998 and 2006 which invokes two bacterial and one archaeal partner(s) in the origin of the eukaryotic cell; that is, first, a syntrophic relationship was established between a fermentative deltaproteobacterium and a hydrogen-dependent archaeal methanogen, which was incorporated into the cytoplasm of the bacterium through endosymbiosis. Subsequently, a second endosymbiosis event led to the uptake of a facultative aerobic alphaproteobacterium, which was suggested to have oxidized organic compounds and hydrocarbons produced by the host. Although this model can explain the origin of the nucleus from the archaeal endosymbiont, it currently lacks support from genomic and phylogenomic analyse 03 Inferencia de metabolismo Syntrophic hypothesis Methanogen Delta Alpha Spang et al Nat Microbiol, 2019
Müller in 1998 which suggests that a symbiosis between a strictly autotrophic hydrogen-dependent methanogenic archaeon and an H2-producing and CO2-producing alphaproteobacterium led to the origin of the eukaryotic cell. 03 Inferencia de metabolismo Hydrogen hypothesis Methanogen Alphaproteobacterium Spang et al Nat Microbiol, 2019
of the updated hydrogen hypothesis based on the first analysis of the metabolic repertoire of Lokiarchaeum, which suggests that the archaeal host was an autotrophic hydrogen-dependent acetogen rather than a methanogen Spang et al Nat Microbiol, 2019
based on comparative analysis of the metabolic repertoire encoded by the various members of the Asgard archaea. This model suggests that a metabolic syntrophy between anaerobic ancestral Asgard archaea and facultative anaerobic alphaproteobacteria has provided the selective force for the establishment of a stable symbiotic interaction that has subsequently led to the origin of the eukaryotic cell. 03 Inferencia de metabolismo Reverse flow model Spang et al Nat Microbiol, 2019