Plant-Soil Systems
There are different ecosystems in the soil which are characterized by different types of microorganisms, grouped under the term microbiota. This includes bacteria, fungi, viruses, protozoa, and archea.
The microbiota conditions the functionality, bioactivity and health of a soil, and therefore plays a very important role in the development of crops since it affects plant growth.
Considering that the microbiota is affected by the use of inputs in agriculture: the study of possible changes in the microbiota over time is very important, to make precise agronomic decisions and carry out adequate fertilization, and thus increase:
To get this knowledge and making a functional analysis of the soil we use modern next generation sequencing techniques with metagenomic approaches and with the use of bioinformatics to process all the data for decision making.
Truffle Cultivation
Molecular Biology techniques can be used for the certification of mycorrhizal plants in nurseries dedicated to the production of this material and for the characterization of strains of ectomycorrhizae (see services-Characterization of clones or varietal identification by genotyping of microsatellite markers).
On the other hand, it has been shown that the genetic factor plays an important role in the aroma of the different strains of truffle, which may be due to the difference in the expression of the genes involved in the synthesis of aromatic compounds. In the cases in which these genes are known, their expression in the different strains could be studied using qPCR (technique, service). On the other hand, when the genes involved are not known, an attempt can be made to identify them using our RNA-seq service.
Not only the genetic factor determines the aroma of the truffle, some studies have shown that the microbiome that accompanies the collected truffles (mainly α-Proteobacteria, β-Proteobacteria, and Sphingobacteria) plays an important role, the characterization of the microbiome can be very useful to explain and maintain the specific aroma of truffles grown in specific areas. This can be done using our metabarcoding services.
Water-Irrigation – Fertigation
Accessibility to abundant sources of high-quality water for vegetable production is of vital importance to the agricultural sector. However, access to safe water is increasingly difficult in many parts of the world and this can lead to the use of water contaminated with microorganisms with the resulting risk to human and animal health.
Thanks to our help, the species present in different aquaculture systems such as oceanographic systems, fish farms, irrigation systems, etc., can be analyzed in order to find beneficial or harmful associations present in these waters.
Biocontrol and targeted biotization
Biotization is a metabolic response of plants grown in vitro to inoculation with microorganisms that leads to physiological and developmental changes that increase their resistance to abiotic and biotic stress.
An adequate characterization of the endophyte communities present in plants, together with studies that allow elucidating their role in the promotion of growth or in the response to biotic stress (tolerance to diseases, resistance against pathogens, etc.) and abiotic (phosphate solubilization, nitrogen assimilation, resistance to high / low temperatures …) allows for a directed biotization so that the plants are better prepared for the field.
Production chains
Contaminating microorganisms are introduced through raw materials, facilities, equipment and personnel in food production chains that can play an important role in food spoilage.
To control contaminating microorganisms, cleaning and environmental control practices are normally established, however, on many occasions, those microorganisms responsible for the deterioration of food and the origin of the pathogenic microorganisms are not known.
The use of DNA metabarcoding allows us to determine the identity of all the microorganisms present in food processing chains, which makes this technique a powerful tool in deterioration investigations, shelf life analysis and environmental control.
This technique will offer you several advantages over traditional methods of studying contaminating microorganisms:
On the other hand, by sequencing the whole genome, you can check whether the input and output samples are exactly the same.
Fermentative Processes
Many are the fermentation processes used in the food industry and in the production of beverages. In all of them, the microbiota that participates in the fermentation process or that can act as a contaminant in the process plays a very important role since it influences the taste, consistency and durability of the final product. It is currently unknown in most industry processes how endogenous and exogenous variables affect the gene expression of microorganisms and how they are related to the quality variables of the final product. In this sense, genomic information plays a key role in understanding these relationships and being able to find improvement actions at the industrial level.
Current DNA and mRNA sequencing techniques make it possible to determine the identity of all microorganisms present in a given fermentation process and even the metabolic pathways that are operating at a given time.
Taking cheese production as an example, the use of these techniques allows characterizing the microbiota of a production line, even quantifying each type of microorganism and determining whether there are contaminants. On the other hand, the use of metatranscriptomics, which consists of sequencing the mRNAs of all the genes of the microorganisms present in the mixture, followed by a bioinformatic analysis, makes it possible to identify the metabolic pathways that are expressed in different conditions of temperature, pH, humidity, etc. This is of vital importance because depending on the metabolic routes that are working, the organoleptic and physicochemical properties of the cheese will vary.
Therefore, it is essential to understand the positive and negative contributions of these microbial components to promote the growth of those that produce the desired characteristics and minimize the impact of microorganisms with undesirable effects.
Taking as an example one of the multiple elaborations that could be associated within this process, we find sectors such as cheese or wine, where the variation of the microbiota within a production line of the same product, varies substantially the physical, chemical and organoleptic properties of the final product.
Probiotics
Probiotics are defined as living microorganisms that, when supplied in adequate amounts, confer benefit on their host. The identification of microorganisms in probiotic products is of vital importance in product quality control and for public health. Typically, these products include lactic acid producing bacterial genera such as Lactobacillus, Bifidobacterium and Bacillus.
The use of modern metagenomic techniques has made it possible to identify healthy microorganisms, as well as others related to different diseases, which constitute the basis of probiotic products. On the other hand, companies dedicated to the production of these types of products could offer their customers greater confidence if they characterize their products and perform quality control in their workflows using modern metagenomics and metatranscriptomics techniques.
Drinking-bottled waters
Bottled water is an increasingly popular source of drinking water around the world. The latest EU Directive 2009/54 / EC defines natural mineral water as microbiologically healthy water of underground origin that is protected from all risk of contamination and can be clearly distinguished from other types of drinking water.
Additionally, disinfection or chemical treatment of natural mineral water is not permitted, however it is routinely tested for its number of culturable bacteria, including various marker organisms (Escherichia coli and other coliforms, fecal streptococci, Pseudomonas aeruginosa, and sporulated sulfite-reducing anaerobes). The largely untreated nature of natural mineral waters allows microorganisms in the source water aquifer and possibly the bottling plant (i.e. pipes and storage tanks) to act as inoculum to the bottle environment. A few days after bottling, these microorganisms begin to grow during the storage of natural mineral waters at room temperature.
This microbial growth in bottled waters is a well-known fact, but its composition and post-bottling dynamics have been little investigated using molecular techniques.
We make available to plants that produce bottled water, as well as other producers of drinking water, metagenomics techniques that rely on next-generation sequencing and bioinformatic techniques to characterize the composition of these waters, and ensure their safety and microbiological quality.
Ingredient identification
For the food industry it is key to be able to quickly and accurately determine the characteristics of the microorganisms in the ingredients of their products during their processing and, above all, in the final product.
Therefore, efficient techniques for simultaneous detection and quantification are required as in the case of DNA metabarcoding.
On the other hand, food fraud has been identified as a growing problem on a global scale with a significant economic, social, health and environmental impact. Genomics and the techniques adjacent to it are a fundamental tool for detecting possible cases of fraud. By using DNA barcoding it is possible to check the ingredients of which a certain food is composed. This method can be routinely implemented to check raw materials, traceability, and to detect adulterations or contamination along supply chains or to certify the finished product.
It can also be used to:
Evolution of canned products
Deterioration of canned foods occurs when the quality of the food deteriorates from its original properties observed at the time of processing. This generates enormous economic losses for both producers, intermediaries and consumers, also representing a risk to health.
Microbes are the most common cause of food spoilage and are ubiquitous, and their presence can go unnoticed.
With the use of modern DNA sequencing techniques, it is possible to study the microbial composition of canned foods in moments before and after canning, determining which are the contaminating microorganisms that cause food spoilage and even the effect of environmental factors on its development. The use of metatranscriptomics can even analyze which metabolic pathways and therefore which compounds are causing the deterioration that is occurring and which conditions favor them. This makes it possible to develop useful strategies to extend the life of the product, whether by making improvements in the canning process or in the conservation conditions.
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The applications of Molecular Biology techniques to agriculture are very diverse, here are some of them.
Farms
Farms that are dedicated to the cultivation of both plant and animal species, they can benefit from our services applied to herbaceous, shrub and tree species (see the Agriculture sector for more information),
and from our services for livestock and fish farming. Below, we offer you a summary of the services that you can use for both plant and animal species:
Our “Species identification by DNA metabarcoding” service can be especially useful for:
Livestock
Several of our services can benefit farms. For example, our paternity testing service with microsatellite molecular markers uses the “International Panel of Microsatellites for Cattle Parentage Testing” (ISAG Panel) recommended by the International Society for Animal Genetics (see Clone Characterization or varietal identification by genotyping microsatellite markers).
On the other hand, it is known that the microbiome present in the digestive system of ruminants plays an important role in the digestion of carbohydrates and nitrogen compounds. The quantitative and / or qualitative modification of the ruminal microflora causes abnormalities in the rumen, with the consequent affectation of the physiological and metabolic processes of the animal and the suffering of gastrointestinal disorders, weight loss, loss of appetite and even death. For this reason, the study of the microbial composition of the rumen can be very useful in the production of milk and meat. Our metabarcoding services can determine the microbial composition of the rumen in real time (see Species identification by DNA metabarcoding).
Farmers can also use our qPCR services to detect diseases caused by various microorganisms such as influenza and Mycoplasma hyopneumoniae in pigs or herpes virus 5 in cattle or similar diseases in sheep, cattle or other animals (see qPCR).
In the same way, an early selection of the individuals that interest us the most can be made based on the required characteristics, such as % pure breed, milk producers, body mass, etc.
On the other hand, with the use of metagenomics, viruses or other pathogens that have never been described before can be identified.
Zoos
In zoos, numerous species of mammals, birds, reptiles and fish coexist in numerous habitats.
Several of our services can benefit zoos.
For example, our service for the identification of microorganisms using metagenomics techniques has multiple applications for these facilities, such as those are present in the rumen of ruminants, the cecum or intestine of birds and primates, etc. thus being able to estimate your health status and correct your diet based on this information.
The identification of outbreaks of diseases of unknown origin that could be affecting a certain group of animals.
The microbiological analysis of the water where the animals live or that which is supplied to them.
The services of “Detection, tracking and monitoring of microorganisms by qPCR” that allows you to detect diseases in animals caused by viruses. Unlike other methods based on symptoms and signs of the disease, qPCR diagnosis is unequivocal since it is based on the detection of nucleic acids (DNA or RNA) specific to each virus.
Our services of “Characterization of clones or varietal identification by genotyping of microsatellite markers” and “Identification of SNPs” can be used to perform paternity and / or maternity tests, which serve as an argument for the reliability and credibility of the heard books of the different races.
Fish farms
Fish farms are facilities dedicated to the farming of fish and shellfish for commercial purposes, and the quality of the feed plays an essential role in the success of this business.
The gut microbiome of fish has been shown to play an integral role in host health by stimulating immune system development, assisting in nutrient acquisition, and overcoming opportunistic pathogens, and is influenced by feeding regimen. Among other findings, it has been shown that:
For all these reasons, it is evident that the study of the intestinal microbiota of fish is very important to create the most favorable conditions for their growth and health in fish farms.
bioSEQs offers you services for the identification and classification of microorganisms both in the intestinal tract of the fish and in the water where they are grown and the food that is supplied to them.
In addition, we offer you the services of “Detection, tracking and monitoring of microorganisms by qPCR” that allows you to detect diseases in fish caused by viruses and other pathogens as well as studies of genetic relationships through the use of “Characterization of clones or varietal identification by genotyping of microsatellite markers” which allows to obtain unique DNA patterns for the identification of animals.
Veterinary Clinics
Veterinary clinics are responsible for caring for the health of animals and diagnosing various diseases caused by different pathogens, many of them with similar symptoms, which makes diagnosis difficult. If we add to this, the fact that many of these diseases can be transmitted to humans, this means that guaranteed diagnostic methods are required.
From bioSEQs, the “Detection, tracking and monitoring of microorganisms by qPCR” allows us to detect a large number of diseases in animals.
On the other hand, the diagnosis of rare or infrequent diseases may require the identification of the microorganism performing massive sequencing through our service “Identification and Typing by sequencing the whole genome”.
In the case of diseases of the intestinal tract that affect, for example, herds of animals or poultry farms, it is possible to carry out metagenomic studies with our “Identification of species by DNA metabarcoding” service to analyze the microbial composition of this region and detect the presence of pathogenic microorganisms that could be associated with the diet.
Municipalities
The municipalities have among their responsibilities to maintain the hygiene of the cities. Although the hygienic and environmental culture of society has increased, there are still people who allow their pets to relieve themselves in the street and do not pick up excrement. For these reasons, there is increasing pressure for each animal to have a DNA profile by which it can be identified. Our “Characterization of clones or varietal identification by genotyping of microsatellite markers” service allows the development of DNA profiles for the unequivocal identification of animals even by their excrement, which would be of great help to identify pet owners who have failed to comply with civic responsibilities.
The applications of Molecular Biology and sequencing techniques to Animal Health and Genetics are very diverse, here are some of them:
Dermal Biomes
The skin in humans is known to be a reservoir for a large number of microorganisms, many of which help the immune system to counter attack by pathogenic microorganisms. This microbiome can be affected by the use of external use products such as soaps, shampoos, skin creams, makeup if these have been manufactured without taking into account their effect on this microbiota.
Our “Species identification by DNA metabarcoding” service allows us to identify the microbiome of the skin and estimate the beneficial or harmful effect that these products may have on it.
Bioproduction
Bioproduction is a combination of traditional engineering with applied biology, which makes it possible to obtain substances with high added value and high biological activity from the exploitation of living microorganisms.
This exploration can be done with the help of metagenomics and metatranscriptomics which is supported by the latest advances in next generation sequencing techniques.
bioSEQs offers its clients its metagenomics services focused on the discovery of new biological activities such as enzymatic activities, bioactive compounds and antibiotics, with potential use in the industry. We also offer the discovery of microorganisms for the industrial obtaining of active principles with functional activity and production of active molecules to develop treatments against diseases.
Magistral formula (Special prescriptions)
The magistral formula is the medicine prepared by the pharmacist for an individualized patient to fill a medical prescription.
Some of these formulations are for topical use for dermatological conditions such as skin creams, while others are for oral delivery. The efficiency of these formulations could be increased with knowledge of the microbiome of either the skin or the intestinal tract of individuals following a personalized medicine approach (see our service “Identification of species by DNA metabarcoding”).
Simulated Communities
Simulated communities are man-made mixtures of microorganisms to serve a specific purpose. For example, specific communities can be created for a probiotic product to correct the biome of a certain group of patients lacking in those specific microorganisms. This is also applicable to animals and plants.
In the same way, these communities can be created for many other purposes such as the production of products for the skin, the production of fertilizers, food or any other process in which living organisms intervene.
This always entails a study of the microbiome of the organism or process in question, for example with the use of our service of “Identification of species by DNA metabarcoding” for a correct design of the simulated community.
Pharmacies are dedicated to the sale of drugs for the prevention and treatment of diseases while parapharmacies and the associated industry are dedicated to the production and distribution of products indicated to preserve and improve health and well-being. Among these products you can find health and biocide products, intimate hygiene products, makeup, gels or creams for facial and dermo-aesthetic care, natural weight control formulations, diet and food products, among many others.
bioSEQs offers personalized services for both sectors.
Forest species
The forest system is currently facing a number of major challenges, including increasing demand for wood, and global climate change and associated threats. Adapting these systems in response to such challenges will require a multifaceted approach, in which the genomic sciences have an important role to play.
In keeping with these requirements, bioSEQs makes several services available to conservationists:
Ecosystem evolution
The ecosystem is like a great living being that changes over time, undergoing transformations that can lead to the replacement of one ecosystem by a different one.
Evolution is a fundamental process of the ecosystem. Studying the genomic variation of organisms can not only improve our understanding of evolutionary processes, but also the dynamics of contemporary and future ecosystems.
In the study of the evolution of ecosystems, several areas of genomics play a fundamental role, such as metagenomics (study of genetic material directly from environmental samples) that allows identifying all the component organisms of the ecosystem in a single analysis, functional genomics (understanding of gene function), comparative genomics (comparing genomes of different organisms), and population genomics (large-scale comparison of DNA sequences in populations).
bioSEQs offers services that are perfectly adjusted to the requirements of studies on the evolution of ecosystems:
Substrates – Organic fertilizers
Organic fertilizers are prepared from plant residues (leaves, crop residues, etc.), animals (manure from different species such as sheep, birds, bats, etc.) or other materials (such as kitchen waste, molasses, semolina, etc.). Due to their high content of organic matter and microorganisms, they improve the physical-chemical and biological properties of the soil.
The microbial composition must be controlled, both of the raw material and in each of its processes, controlling its evolution and allowing its handling and management throughout the entire process to improve and / or accelerate the decomposition of waste.
Our “Identification of species by DNA metabarcoding” service allows the identification and classification and quantification of all the microorganisms present in a mixture of fertilizers in a single analysis, which allows you to know which are the microorganisms with the greatest impact on the degradation of fertilizers and allows the design of experiments to know the impact of environmental factors on their development. Similarly, it is possible to determine the presence of pathogens in fertilizers.
Nurseries
Nurseries are special facilities in which young plants of various horticultural, agricultural or forestry species are grown under more or less controlled conditions.
bioSEQs offers various services that are tailored to the needs of nurseries.
Our “Identification of species by DNA metabarcoding” service can be very useful in the microbiological characterization of the soil, substrates or organic fertilizers that are used. In the same way, it can be used for the microbiological characterization of irrigation water.
On the other hand, our service of “Detection, tracking and monitoring of microorganisms by qPCR” allows the molecular diagnosis of diseases caused by bacteria, fungi, viruses, viroids and mycoplasmas, among others, and our service of “Characterization of clones or varietal identification by genotyping of microsatellite marker” makes it possible to determine the genetic homogeneity of the propagation material and offer a guarantee to customers on the material.
Treatment plants
Human activity in large cities generates a large amount of wastewater that must be treated and reused to protect people’s health and the quality of the environment.
Liquid effluents contain microorganisms, some pathogens, nutrients that stimulate the growth of aquatic plants, and organic matter that rapidly decomposes and generates odors and consumes dissolved oxygen in the water. They can also contain toxic compounds.
The anaerobic stabilization of the sludge generated in the primary treatment allows the production of organic fertilizers for use in agriculture. The efficiency of this process depends on the conditions in which it is carried out and on the microbial composition of these mixtures.
Similarly, in secondary treatment, microorganism processes are used to eliminate most of the organic matter.
The determination of the microbiomes present in these stages of the process is essential for their correct management and efficiency.
bioSEQs offers a “Species identification by DNA metabarcoding” service that allows the identification and characterization of all the microorganisms present in the different stages of the wastewater treatment process, which allows for better management. In addition, this service itself allows to determine the microbiological quality of the water, being able to detect viruses that are not detectable by other methods.
Aquifer wells
Aquifer wells or groundwater are a source of drinking water used throughout the world.
Sometimes these waters can be contaminated with microorganisms by human activity, such as the construction of septic tanks or agriculture.
With the use of our “Identification of species by DNA metabarcoding” service it is possible to determine the microbial population of these aquifers and ensure their safety and microbiological quality.
Rivers-Lakes-Marshes
Rivers, lakes and marshes are very important ecosystems from the ecological point of view, since they contain a great variety of animal and plant species and microorganisms, as well as being sources of water for human consumption, irrigation and industry.
Human activity has affected many of these ecosystems, through the construction of public works, settlements, the establishment of agricultural, industrial, and aquaculture zones, among other actions that degrade and transform them, which alters the ecosystem.
With the use of our “Species identification by DNA metabarcoding” service it is possible to determine the microbial population of these lakes, rivers or marshes, and ensure their safety and quality.
We offer services focused on different entities dedicated to the promotion of environmental policies, the study of the evolution of ecosystems or the treatment and recycling of waste.
Focused on eDNA (environmental DNA), our DNA metabarcoding service allows the taxonomic identification of organisms present in complex environmental samples such as soil, waste, marshes, rivers, etc. In addition, the service itself is very useful to analyze the microorganisms present in processes of decomposition of organic matter for the production of fertilizers, among other applications.
Agricultural biomass
Biomass is considered to be a group of renewable energy products and raw materials that originate from organic matter formed by biological means.
Through our service “Identification of species by DNA metabarcoding” it is possible to identify, classify and quantify all the microorganisms present in the different stages of biomass conversion, assigning roles to each of the microorganisms in the process of transformation of organic matter and identifying the metabolic routes responsible for the decomposition process at the same time that the best conditions can be determined to favor the process. Likewise, the joint use of metagenomics and meta-transcriptomics techniques allows us to identify the most efficient microorganisms and the most innovative enzymatic activities to accelerate processes.
Directed composting
Compost is made by the biological decomposition of organic products such as crop residues, animal manure, garbage, etc. Composting said remains is nothing more than imitating the fermentation process that occurs naturally in a forest floor, but accelerated and directed.
Compost is rich in nutrients, and used, for example, in gardens, horticulture, urban agriculture and organic farming.
Among the microorganisms that participate in the composting process we can find:
Because it is a process where a great variety of microorganisms participate, it is evident that the knowledge and proper management of their composition in the different stages of the process can help to accelerate it and give specific recommendations for the use of activators.
Using our “Identification of species by DNA metabarcoding” service it is possible to determine all the microorganisms present in a compost mixture at each stage, performing a characterization and quantification that allows you to better manage the process. In addition, the effect of environmental factors on the composition of microorganisms can be determined, and using metatranscriptomic techniques it is possible to determine which metabolic pathways are activated at any given time and therefore, to know which compounds are being transformed, enabling the evaluation of environmental factors on the activation of these routes.
Waste recovery
The valorization of a waste is to carry out its preparation to fulfill a particular function destined to increase its initial value.
This reduces the level of pollution on the planet, offers economic advantages to companies by reducing the costs of purchasing raw materials and creates new jobs in recycling plants.
The material recovery of waste containing organic matter is done through composting or anaerobic digestion in which the microbial composition of these mixtures plays a fundamental role to achieve a rapid and complete decomposition of organic matter.
bioSEQs through its “Identification of species by DNA metabarcoding” service can identify, classify and quantify all the microorganisms present in these mixtures and provide suggestions on how to enrich these mixtures for a better composting process.
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Agriculture, industry and human activity in general generate waste of various types that, if not reused, would accumulate on the planet. Fortunately, today there are several ways to reuse these raw materials and convert them into fertilizers, biofuels or electricity.
bioSEQs puts modern sequencing techniques at the service of organic fertilizer producing plants, biomass plants or waste recovery plants that allow identifying, classifying and quantifying the microorganisms in charge of these processes and giving recommendations on their best management.
Bioremediation is a branch of biotechnology that is responsible for all the processes that contribute to fully or partially recover a contaminated space through the use of living organisms.
It is carried out by means of natural autochthonous microorganisms or modified by biotechnology, by plants or specific enzymatic activities.
Ecotoxicology is the study of the effect of toxic chemical compounds on living beings, especially in terms of populations, communities and ecosystems. In those ecosystems in which the diversity of species has been affected by the effect of toxic compounds, ecotoxicological studies can provide information to take action and prevent further deterioration of the ecosystem and its restoration.
Thanks to the services of “Identification of species by DNA metabarcoding” and “Identification and typing by sequencing of the whole genome” and “Identification and characterization of genes by RNA seq” and the use of specific bioinformatic procedures, bioSEQs help in the identification of microorganisms and novel enzymatic activities for bioremediation as well as evaluating the effect of treatments on the composition and activity of the microbiota, for example during biostimulation processes. Furthermore, it allows evaluating the composition of organisms in different ecosystems in different periods of time and in the face of different degrees of contamination and in a single analysis, allowing rapid and efficient measures to be taken.
