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Dive into the research topics where Marcel Martínez-Porchas is active.

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Featured researches published by Marcel Martínez-Porchas.


The Scientific World Journal | 2012

World Aquaculture: Environmental Impacts and Troubleshooting Alternatives

Marcel Martínez-Porchas; Luis Rafael Martínez-Córdova

Aquaculture has been considered as an option to cope with the world food demand. However, criticisms have arisen around aquaculture, most of them related to the destruction of ecosystems such as mangrove forest to construct aquaculture farms, as well as the environmental impacts of the effluents on the receiving ecosystems. The inherent benefits of aquaculture such as massive food production and economical profits have led the scientific community to seek for diverse strategies to minimize the negative impacts, rather than just prohibiting the activity. Aquaculture is a possible panacea, but at present is also responsible for diverse problems related with the environmental health; however the new strategies proposed during the last decade have proven that it is possible to achieve a sustainable aquaculture, but such strategies should be supported and proclaimed by the different federal environmental agencies from all countries. Additionally there is an urgent need to improve legislation and regulation for aquaculture. Only under such scenario, aquaculture will be a sustainable practice.


Critical Reviews in Biotechnology | 2017

From microbes to fish the next revolution in food production

Luis Rafael Martínez-Córdova; Marcel Martínez-Porchas; Maurício Gustavo Coelho Emerenciano; Anselmo Miranda-Baeza; Teresa Gollas-Galván

Increasing global population and the consequent increase in demand for food are not a new story. Agroindustrial activities such as livestock help meet this demand. Aquaculture arose decades ago and revolutionized the agroindustrial activity as a significant food generator. However, like livestock, aquaculture is based on finite resources and has been accused of being unsustainable. Abandoning aquaculture is not an option considering the food, foreign exchange, and employment it generates, and therefore must be reinvented. Among the many alternatives suggested to make aquaculture more sustainable, microorganisms have been highlighted as a direct food source for cultured fish and crustaceans, a strategy that promises to revolutionize aquaculture by eliminating waste. Considering waste, as part of a cycle, it can increase stock densities and reduce emissions of contaminants and operational costs.


The Scientific World Journal | 2012

Production response and digestive enzymatic activity of the Pacific white shrimp Litopenaeus vannamei (Boone, 1931) intensively pregrown in microbial heterotrophic and autotrophic-based systems.

Manuel de Jesús Becerra-Dorame; Marcel Martínez-Porchas; Luis Rafael Martínez-Córdova; Martha Elisa Rivas-Vega; José Antonio López-Elías; Marco A. Porchas-Cornejo

Shrimp postlarvae were reared into different microcosm systems without water exchange; a traditional system based on simple fertilization to improve microalgae concentration (control), an autotrophic system (AS) based on the promotion of biofloc and biofilm by the addition of fertilizer and artificial substrates and a heterotrophic system (HS) based on the promotion of heterotrophic bacteria by the addition of nitrogenous and carbonaceous sources and artificial substrates. Better growth performance and survival were registered in shrimp from the AS and HS compared to the control. Feed conversion ratios were below 0.7 for all treatments, but AS and HS were significantly lower than the control. Regarding digestive performance, no significant differences were observed for trypsin, amylase and lipase activities among AS and control shrimp; however, shrimp from HS showed a higher trypsin and amylase activities, suggesting a higher digestive activity caused by the presence of microbial bioflocs. The presence of biofilm and bioflocs composed by either autotrophic or heterotrophic organisms in combination with formulated feed improved the growth performance and survival of shrimp. Apparently, such combination fits the nutritional requirements of shrimp.


PeerJ | 2017

How conserved are the conserved 16S-rRNA regions?

Marcel Martínez-Porchas; Enrique Villalpando-Canchola; Luis Enrique Ortiz Suarez; Francisco Vargas-Albores

The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123) were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers) were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%). Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker.


Helgoland Marine Research | 2017

Bacterial biota of shrimp intestine is significantly modified by the use of a probiotic mixture: a high throughput sequencing approach

Francisco Vargas-Albores; Marco A. Porchas-Cornejo; Marcel Martínez-Porchas; Enrique Villalpando-Canchola; Teresa Gollas-Galván; Luis Rafael Martínez-Córdova

The use of probiotics is a common practice of current shrimp aquaculture. Despite the immunophysiological responses that have been measured in shrimp exposed to probiotics, no information is currently available on the effect of this practice on the intestinal microbiota. The objective of this work was to evaluate the effect of a probiotic mixture on the intestinal microbiota of shrimp cultured under farm conditions. A culture-independent method based on high-throughput-sequencing (16S rRNA) was used to examine intestinal bacterial communities. A traditional system (without probiotics) was used as the reference. Targeted metagenomics analysis revealed that the probiotic mixture was based on bacteria in the phyla Proteobacteria and Firmicutes. A total of 23 species of bacteria were detected in the probiotic mixture; of these, 11 were detected in the intestine of shrimp reared in both systems, and 12 were novel for the system. Eight of the novel species were detected in shrimp cultured with the probiotic mixture; however, none of these novel species were related to marine or inclusively aquacultural environments, and only one (Bacillus subtilis) was recognized as probiotic for shrimp. The use of the probiotic mixture modified the bacterial profile of the shrimp intestine; however, most of the bacteria incorporated into the intestine were nonindigenous to the marine environment with no previous evidence of probiotic effects on any marine organism. The use of this probiotic mixture may represent a risk of causing environmental imbalances, particularly because farms using these types of probiotic mixtures discharge their effluents directly into the ocean without prior treatment.


Journal of Microbiological Methods | 2016

Studying long 16S rDNA sequences with ultrafast-metagenomic sequence classification using exact alignments (Kraken).

Fabiola Valenzuela-González; Marcel Martínez-Porchas; Enrique Villalpando-Canchola; Francisco Vargas-Albores

Ultrafast-metagenomic sequence classification using exact alignments (Kraken) is a novel approach to classify 16S rDNA sequences. The classifier is based on mapping short sequences to the lowest ancestor and performing alignments to form subtrees with specific weights in each taxon node. This study aimed to evaluate the classification performance of Kraken with long 16S rDNA random environmental sequences produced by cloning and then Sanger sequenced. A total of 480 clones were isolated and expanded, and 264 of these clones formed contigs (1352 ± 153 bp). The same sequences were analyzed using the Ribosomal Database Project (RDP) classifier. Deeper classification performance was achieved by Kraken than by the RDP: 73% of the contigs were classified up to the species or variety levels, whereas 67% of these contigs were classified no further than the genus level by the RDP. The results also demonstrated that unassembled sequences analyzed by Kraken provide similar or inclusively deeper information. Moreover, sequences that did not form contigs, which are usually discarded by other programs, provided meaningful information when analyzed by Kraken. Finally, it appears that the assembly step for Sanger sequences can be eliminated when using Kraken. Kraken cumulates the information of both sequence senses, providing additional elements for the classification. In conclusion, the results demonstrate that Kraken is an excellent choice for use in the taxonomic assignment of sequences obtained by Sanger sequencing or based on third generation sequencing, of which the main goal is to generate larger sequences.


Developmental and Comparative Immunology | 2017

Crustins are distinctive members of the WAP-containing protein superfamily: An improved classification approach

Francisco Vargas-Albores; Marcel Martínez-Porchas

Crustins are considered effector molecules of innate immunity in arthropods, and classification schemes have been proposed over the last 10 years. However, classification problems have emerged: for example, proteins that have been well identified as members of a particular category have also been classified as crustins. Therefore, the objective of this manuscript was to analyze and, based on solid arguments, improve the original proposed nomenclature to make crustins a distinctive group of antibacterial proteins. The presence of WAP or 4DSC domain has been considered a distinctive feature of crustins; however, several antibacterial proteins containing WAP domains have been detected in diverse taxonomic groups (including mammals). Here, we present evidence supporting the idea that the Cys-rich region and the 4DSC domain can be considered a signature of crustins and, together with some distance arrangements occurring within this 12-Cys region, yield enough information for the classification of these proteins. Herein, the core characteristics to be considered for classification purposes are the length of the Gly-rich region and the repetitive tetrapeptides occurring within this region; these characteristics are then hierarchically followed by the F and A distances located within the 4DSC domain. Finally, the proposed system considers the crustin signature as the common structure in all members, which is a differentiator from other proteins containing WAP domains, separating crustins as a well-distinguished member of the superfamily of WAP-domain containing proteins.


Heliyon | 2016

Significant loss of sensitivity and specificity in the taxonomic classification occurs when short 16S rRNA gene sequences are used

Marcel Martínez-Porchas; Enrique Villalpando-Canchola; Francisco Vargas-Albores

The classification performance of Kraken was evaluated in terms of sensitivity and specificity when using short and long 16S rRNA sequences. A total of 440,738 sequences from bacteria with complete taxonomic classifications were downloaded from the high quality ribosomal RNA database SILVA. Amplicons produced (86,371 sequences; 1450 bp) by virtual PCR with primers covering the V1–V9 region of the 16S-rRNA gene were used as reference. Virtual PCŔs of internal fragments V3–V4, V4–V5 and V3–V5 were performed. A total of 81,523, 82,334 and 82,998 amplicons were obtained for regions V3–V4, V4–V5 and V3–V5 respectively. Differences in depth of taxonomic classification were detected among the internal fragments. For instance, sensitivity and specificity of sequences classified up to subspecies level were higher when the largest internal fraction (V3–V5) was used (54.0 and 74.6% respectively), compared to V3–V4 (45.1 and 66.7%) and V4–V5 (41.8 and 64.6%) fragments. Similar pattern was detected for sequences classified up to more superficial taxonomic categories (i.e. family, order, class…). Results also demonstrate that internal fragments lost specificity and some could be misclassified at the deepest taxonomic levels (i.e. species or subspecies). It is concluded that the larger V3–V5 fragment could be considered for massive high throughput sequencing reducing the loss of sensitivity and sensibility.


Latin American Journal of Aquatic Research | 2012

Effect of alternative mediums on production and proximate composition of the microalgae Chaetoceros muelleri as food in culture of the copepod Acartia sp.

Luis Rafael Martínez-Córdova; Alfredo Campaña-Torres; Marcel Martínez-Porchas; José Antonio López-Elías; Celia Olivia García-Sifuentes

Microalgae Chaetoceros muelleri was cultured in three different mediums consisting on an agricultural fertilizer (Agr-F), aquacultural fertilizer (Aq-F) and a conventional medium (F/2, control). These microalgae were later used as natural food to culture the copepod Acartia sp. The productive response and chemical proximate composition of microalgae and copepods were monitored. Growth rate and final cell concentration were higher in microalgae cultured in Agr-F compared to the control. In addition, the final biomass and cellular concentration were also the highest in Agr-F. Microalgae from Agr-F and Aq-F had higher carbohydrate and lower protein contents than those in the control. No differences in lipid and ash contents were observed. Regarding copepod production, higher densities and fecundity indexes were observed for those fed with microalgae previously cultured in Agr-F and Aq-F, compared to the control. The adult- nauplii ratio was also higher in copepods fed on microalgae from Agr-F compared to Aq-F and control. Copepods fed on Agr-F and Aq-F microalgae, had higher protein content compared to those fed on control microalgae; carbohydrates were higher in copepods fed on Agr-F as compared to Aq-F microalgae. No differences in lipid and ash contents were registered. Agr-F and Aq-F were adequate alternative mediums to produce C. muelleri, which produced higher quality microalgae that increased the copepod production.


Revista De Biologia Marina Y Oceanografia | 2011

Studies on the bioremediation capacity of the adult black clam, Chione fluctifraga, of shrimp culture effluents

Luis Rafael Martínez-Córdova; José Antonio López-Elías; Marcel Martínez-Porchas; Tamara Bernal-Jaspeado; Anselmo Miranda-Baeza

Resumen es: La almeja negra, Chione fluctifraga, puede ser utilizada para biorremediar efluentes de descarga en cultivos de camaron. Con este proposito se evaluo dur...

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Teresa Gollas-Galván

Spanish National Research Council

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Francisco Vargas-Albores

Spanish National Research Council

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Marco A. Porchas-Cornejo

Spanish National Research Council

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Jorge Hernández-López

Spanish National Research Council

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Alfredo Campaña-Torres

Spanish National Research Council

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Fernando Mendoza-Cano

Spanish National Research Council

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