0000000001254522
AUTHOR
Francisco Montero
Metabolic complementation in bacterial communities: Necessary conditions and optimality
Bacterial communities may display metabolic complementation, in which different members of the association partially contribute to the same biosynthetic pathway. In this way, the end product of the pathway is synthesized by the community as a whole. However, the emergence and the benefits of such complementation are poorly understood. Herein, we present a simple model to analyze the metabolic interactions among bacteria, including the host in the case of endosymbiotic bacteria. The model considers two cell populations, with both cell types encoding for the same linear biosynthetic pathway. We have found that, for metabolic complementation to emerge as an optimal strategy, both product inhib…
MOESM9 of In vivo fluorescent cercariae reveal the entry portals of Cardiocephaloides longicollis (Rudolphi, 1819) Dubois, 1982 (Strigeidae) into the gilthead seabream Sparus aurata L.
Additional file 9: Table S9. Evaluation of the effect of dyes on cercarial infectivity and metacercarial encystment success.
Additional file 3 of Considerations on the taxonomy and morphology of Microcotyle spp.: redescription of M. erythrini van Beneden & Hesse, 1863 (sensu stricto) (Monogenea: Microcotylidae) and the description of a new species from Dentex dentex (L.) (Teleostei: Sparidae)
Additional file 3: Table S3. Metrical data for Microcotyle erythrini (sensu stricto) and other species of Microcotyle in sparid fishes in the Mediterranean Sea and North-East Atlantic. Measurements are in micrometres expressed as ranges, except where a single value was provided.
Additional file 2: of Come rain or come shine: environmental effects on the infective stages of Sparicotyle chrysophrii, a key pathogen in Mediterranean aquaculture
Table S2. Larval longevity and behaviour of S. chrysophrii by replicate at each temperature. (DOCX 15 kb)
MOESM8 of In vivo fluorescent cercariae reveal the entry portals of Cardiocephaloides longicollis (Rudolphi, 1819) Dubois, 1982 (Strigeidae) into the gilthead seabream Sparus aurata L.
Additional file 8: Table S8. Evaluation of the effect of sub-regions of fish’s surface on cercarial density.
MOESM2 of In vivo fluorescent cercariae reveal the entry portals of Cardiocephaloides longicollis (Rudolphi, 1819) Dubois, 1982 (Strigeidae) into the gilthead seabream Sparus aurata L.
Additional file 2: Table S2. Evaluation of the effect of different NB concentrations on cercarial survival.
A genome-scale study of metabolic complementation in endosymbiotic consortia: the case of the cedar aphid
AbstractBacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their tiny metabolic allies. These nutritional complementations sustain themselves on a diversity of metabolite exchanges between the cell host and the reduced yet highly specialized bacterial metabolism –which, for instance, overproduces a small set of essential amino acids and vitamins. A well-known case of metabolic complementation is provided by the cedar aphidCinara cedrithat harbors two co-primary endosymbionts,Buchnera aphidicolaBCc andCa.Serratia …
MOESM5 of In vivo fluorescent cercariae reveal the entry portals of Cardiocephaloides longicollis (Rudolphi, 1819) Dubois, 1982 (Strigeidae) into the gilthead seabream Sparus aurata L.
Additional file 5: Table S5. Evaluation of the effect of CFSE concentration treatment on cercarial activity.
Structural analyses of a hypothetical minimal metabolism
By integrating data from comparative genomics and large-scale deletion studies, we previously proposed a minimal gene set comprising 206 protein-coding genes. To evaluate the consistency of the metabolism encoded by such a minimal genome, we have carried out a series of computational analyses. Firstly, the topology of the minimal metabolism was compared with that of the reconstructed networks from natural bacterial genomes. Secondly, the robustness of the metabolic network was evaluated by simulated mutagenesis and, finally, the stoichiometric consistency was assessed by automatically deriving the steady-state solutions from the reaction set. The results indicated that the proposed minimal …
Nature lessons: the whitefly bacterial endosymbiont is a minimal amino acid factory with unusual energetics
Reductive genome evolution is a universal phenomenon observed in endosymbiotic bacteria in insects. As the genome reduces its size and irreversibly losses coding genes, the functionalities of the cell system, including the energetics processes, are more restricted. Several energetic pathways can also be lost. How do these reduced metabolic networks sustain the energy needs of the system? Among the bacteria with reduced genomes Candidatus Portiera aleyrodidarum, obligate endosymbiont of whiteflies, represents an extreme case since lacks several key mechanisms for ATP generation. Thus, to analyze the cell energetics in this system, a genome-scale metabolic model of this endosymbiont was const…
MOESM1 of In vivo fluorescent cercariae reveal the entry portals of Cardiocephaloides longicollis (Rudolphi, 1819) Dubois, 1982 (Strigeidae) into the gilthead seabream Sparus aurata L.
Additional file 1: Table S1. Evaluation of the effect of fish’s flank on cercarial attachment success.
Determinism and contingency shape metabolic complementation in an endosymbiotic consortium
Bacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their tiny metabolic allies. These nutritional complementations sustain themselves on a diversity of metabolite exchanges between the cell host and the reduced yet highly specialized bacterial metabolism-which, for instance, overproduces a small set of essential amino acids and vitamins. A well-known case of metabolic complementation is provided by the cedar aphid Cinara cedri that harbors two co-primary endosymbionts, Buchnera aphidicola BCc and Ca. Serratia sym…
MOESM7 of In vivo fluorescent cercariae reveal the entry portals of Cardiocephaloides longicollis (Rudolphi, 1819) Dubois, 1982 (Strigeidae) into the gilthead seabream Sparus aurata L.
Additional file 7: Table S7. Evaluation of the effect of major regions of fish’s surface on cercarial density.
Additional file 4 of Considerations on the taxonomy and morphology of Microcotyle spp.: redescription of M. erythrini van Beneden & Hesse, 1863 (sensu stricto) (Monogenea: Microcotylidae) and the description of a new species from Dentex dentex (L.) (Teleostei: Sparidae)
Additional file 4: Table S4. Metrical data from descriptions of Microcotyle spp. similar to M. erythrini (sensu stricto) from Mediterranean non-sparid or non-Mediterranean fishes. Measurements are in micrometres expressed as ranges, except where a single value was provided.
MOESM4 of In vivo fluorescent cercariae reveal the entry portals of Cardiocephaloides longicollis (Rudolphi, 1819) Dubois, 1982 (Strigeidae) into the gilthead seabream Sparus aurata L.
Additional file 4: Table S4. Evaluation of the effect of CFSE different concentrations on cercarial survival.
Additional file 5: of Come rain or come shine: environmental effects on the infective stages of Sparicotyle chrysophrii, a key pathogen in Mediterranean aquaculture
Table S5. Parameters of embryonic development of S. chrysophrii by replicate at each light regime. (DOC 36 kb)
Additional file 8: of Come rain or come shine: environmental effects on the infective stages of Sparicotyle chrysophrii, a key pathogen in Mediterranean aquaculture
Table S8. Larval longevity and behaviour of S. chrysophrii by replicate at different salinities and temperatures. (DOCX 15 kb)
Additional file 6: of Come rain or come shine: environmental effects on the infective stages of Sparicotyle chrysophrii, a key pathogen in Mediterranean aquaculture
Table S6. Larval longevity and behaviour of S. chrysophrii by replicate at each light regime. (DOCX 13 kb)
Additional file 3: of Come rain or come shine: environmental effects on the infective stages of Sparicotyle chrysophrii, a key pathogen in Mediterranean aquaculture
Table S3. Parameters of embryonic development of S. chrysophrii by replicate at each pH level. (DOC 37 kb)
MOESM6 of In vivo fluorescent cercariae reveal the entry portals of Cardiocephaloides longicollis (Rudolphi, 1819) Dubois, 1982 (Strigeidae) into the gilthead seabream Sparus aurata L.
Additional file 6: Table S6. Evaluation of the effect of dyes on cercarial survival and activity.
Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach.
Genome-scale metabolic models usually contain inconsistencies that manifest as blocked reactions and gap metabolites. With the purpose to detect recurrent inconsistencies in metabolic models, a large-scale analysis was performed using a previously published dataset of 130 genome-scale models. The results showed that a large number of reactions (~22%) are blocked in all the models where they are present. To unravel the nature of such inconsistencies a metamodel was construed by joining the 130 models in a single network. This metamodel was manually curated using the unconnected modules approach, and then, it was used as a reference network to perform a gap-filling on each individual genome-s…
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti
Abstract Background Metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. Although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed. Results We introduce a general definition of gap metabolite that allows its detection in a straightforward manner. Moreover, a method for the detection of Unconnected Modules, defined as isolated sets of blocked reactions connect…
Additional file 7: of Come rain or come shine: environmental effects on the infective stages of Sparicotyle chrysophrii, a key pathogen in Mediterranean aquaculture
Table S7. Parameters of embryonic development of S. chrysophrii by replicate at different salinities and temperatures. (DOC 45 kb)
Additional file 1 of Considerations on the taxonomy and morphology of Microcotyle spp.: redescription of M. erythrini van Beneden & Hesse, 1863 (sensu stricto) (Monogenea: Microcotylidae) and the description of a new species from Dentex dentex (L.) (Teleostei: Sparidae)
Additional file 1: Table S1. Mean genetic divergence (uncorrected p-distance in % and number of pairwise nucleotide differences in parentheses) estimated for the partial cox1 sequence pairs within- (along the diagonal, emboldened) and among species of Microcotyle (below the diagonal).
Additional file 4: of Come rain or come shine: environmental effects on the infective stages of Sparicotyle chrysophrii, a key pathogen in Mediterranean aquaculture
Table S4. Larval longevity and behaviour of S. chrysophrii by replicate at each pH level. (DOCX 13 kb)
Additional file 1: of Come rain or come shine: environmental effects on the infective stages of Sparicotyle chrysophrii, a key pathogen in Mediterranean aquaculture
Table S1. Parameters of embryonic development of S. chrysophrii by replicate at each temperature. (DOCX 15 kb)
MOESM3 of In vivo fluorescent cercariae reveal the entry portals of Cardiocephaloides longicollis (Rudolphi, 1819) Dubois, 1982 (Strigeidae) into the gilthead seabream Sparus aurata L.
Additional file 3: Table S3. Evaluation of the effect of NB concentration treatment on cercarial activity.
MOESM10 of In vivo fluorescent cercariae reveal the entry portals of Cardiocephaloides longicollis (Rudolphi, 1819) Dubois, 1982 (Strigeidae) into the gilthead seabream Sparus aurata L.
Additional file 10: Table S10. Evaluation of the effect of fish’s head sub-regions on cercarial density.
Additional file 2 of Considerations on the taxonomy and morphology of Microcotyle spp.: redescription of M. erythrini van Beneden & Hesse, 1863 (sensu stricto) (Monogenea: Microcotylidae) and the description of a new species from Dentex dentex (L.) (Teleostei: Sparidae)
Additional file 2: Table S2. Pairwise nucleotide differences among species of Microcotyle for the partial 28S rDNA sequences, including Bivagina pagrosomi.