Workflow Solutions for Microbiome Research Applications

Microbiome Detection

Try New Metagenomics Software Platform

  • Our in-house Metagenomic Software is a cloud-based application that does not require annual licenses or complicated downloads but is an intuitive software tool with updated sequencing databases as well as comprehensive taxonomic classifications. At the end of your data analysis, we provide a downloadable HTML report that is interactive and dynamic to generate publication ready figures that can be shared with your collaborators. Access to this platform is free for the remainder of 2020.

  • If you need to outsource your microbiome samples for sequencing and metabolite detection, the NEW Microbiome multi-omic platform offers service packages for 16S and Whole Genome Sequencing in Metagenomic analysis and offerings will be available soon for metabolomics, transcriptomics and proteomics. It’s simple, ship us the samples and we will perform the sample prep, library prep, sequencing and bioinformatics. You can track the status of your project online at all times and we will perform a comprehensive consultation with R&D plus bioinformatic experts to ensure that you have full access to the data as well as the understanding of the statistical analysis parameters.

As a microbiome researcher, you already appreciate how next generation tools have revolutionized the study of metagenomics and can boost research efforts for more accurate analysis of microbes. Standardization is essential in microbiome analysis in order to generate accurate and valid data. We support metagenomics and microbiomics workflows by improving reproducibility and allowing for reliable comparison of results. Our growing portfolio of reagents for microbiome research will support your efforts to reveal the role of the microbiome in human, animal, environmental health.

  • MetaPolyzyme is a mixture of 6 enzymes that is intended for isolation of total DNA for metagenomics studies. Adapted from an initial formulation devised by leaders in the field, MetaPolyzyme was evaluated and developed in consultation and collaboration with the
    Association of Biomolecular Resource Facilities (ABRF) Metagenomics and Microbiome Research Group (MMRG).
  • For contamination-free DNA analysis, we provide DNA-free enzymes
  • For microbial community characterization and DNA preparation, we offer growth media by microorganism and microbial media
  • To avoid bias and increase the reproducibility of next generation sequencing and metagenomics analysis, we provide individual DNA standards and inactivated bacteria standards
  • For microbiome detection and isolation, we offer antibodies that are highly specific to bacteria and bacterial components, such as toxins, unique proteins and lipopolysaccharides
  • To further understand in vitro host/microbe interactions, we have a large selection of effector molecules that can be added to 3D models or co-cultured cells and be analyzed via metabolomics, proteomics or transcriptomics.


 What exactly are microbiomes?

Host-associated microbial communities exist in humans, animals, plants, the earth, oceans and the atmosphere1. Microorganisms live all over the human body – inside and out. These microbes consist of trillions of different coexisting bacteria, fungi, viruses, and archaea that can be helpful or harmful to our health, depending on how many there are and where they reside, such as in the mouth, gut, or on the skin3. Microbiome refers to the collective genomes or genetic material of microbes. The human microbiome refers to the collection of microbiomes of the human body, which varies considerably from one person to another and among different anatomical sites5. Factors that can influence the microbiome include diet, lifestyle, genetics, anatomical site, antibiotics and pathogens.

 

The role of human microbiota

Microbial communities can be either beneficial or detrimental to host health. The human microbiome programs the immune system, provides nutrients, controls digestion, attacks pathogens, and naturally protects the body by maintaining the right balance among microbes. There is growing evidence that diet can influence gut microbiome and improve health6.

However, diseases can occur when the microbiome becomes imbalanced. It is still not certain whether an altered microbiome is a cause or consequence of disease5. Obesity and autism have been linked to an increased abundance of certain microorganisms in the gastrointestinal microbiota. The oral microbiome has been linked to cardiovascular disease. In fact there is some evidence that support that alterations to the composition of the microbiome can even affect our mood, sleep, and mental health, leading to anxiety and depression6. Other conditions that have been shown to be correlated include allergies, diabetes, cancer, infectious diseases, or even chronic inflammation1. However, as stated earlier, it is not completely understood if the presence of certain microbes causes a disease or if a person with a type of disease has this type of microbiome because of the disease.

 

Why is microbiome research important?

The microbiome provides biomarkers for disease. Understanding the host-microbe pathways in microbiome research has great diagnostic value for disease prevention, detection and management5. Potential therapeutic solutions, including personalized medicine, can be developed to influence how we respond to certain drugs, supplement traditional medical treatment and support the body in protecting itself. Whether for treating cancer, metabolic diseases, gastrointestinal disorders or cardiovascular illnesses, the human microbiome can be manipulated to manage diseases.

 

Advancements in microbiome research

Due to the sheer number and diversity of the trillions of different microbes, identifying and studying the genetic profile of microbes can be a daunting task. In addition, some microbes can be difficult to isolate, culture and study. Microbiome analysis determines the composition and function of microorganism communities in particular locations, which can then be characterized as microbiome modulators4. The initial focus of microbiome research was compositional 6(FN: Zeevi D,), based on detecting as many microbes as possible. Early DNA sequencing technologies, such as the Sanger method, involved the cultivation of microbiota and then sequencing a single DNA fragment at a time, which was time-consuming and limited, and more appropriate for analyzing complex microbial communities3.

Many microbial studies concentrate on amplifying a marker gene, usually the 16S rRNA gene, which is present in all living organisms, therefore making it the preferred gene for analyzing microbial communities. With technological advancements in metagenomics making it possible to sequence all genomic DNA within a single sample3, more efficient and affordable methods have emerged. High-throughput sequencing tools, such as next generation sequencing (NGS) have proven to be highly effective in microbiome analysis due to their scalability and speed, in particular for detection of microbes that are not culturable. NGS enables millions of DNA fragments to be sequenced per run. This culture-independent process expedites the discovery and analysis of novel and rare microbes.

Targeted sequencing in metagenomics enables focused research on individual genes, or a subset of genes, or genomic regions by isolating and sequencing them. This NGS approach allows for cost-efficient and timely analysis of a smaller data set in specific areas of interest. Therefore, targeted microbiome sequencing can be used to concentrate on biomarkers of certain diseases in order to develop therapies accordingly. Common applications include cancer gene sequencing, bacterial identification such as the 16S ribosomal RNA gene, early detection and intervention in rare genetic diseases and conditions, and research on specific drug development.

Metagenome sequencing, or whole-genome shotgun sequencing (WGS) is an untargeted method to comprehensively study all microbial genomes in a given complex sample, for instance to discover unculturable microorganisms, detect the abundance of microbes in distinct environments and analyze microbe diversity. This method allows for parallel sequencing of DNA fragments taken from the complete gene repertoire in a microbial population.

Microbiome researchers are now able to better study the activity of microbes within complex communities, take entire community dynamics into consideration and understand their functionality: what are the connections between microbes and host health and how they interact6. As DNA sequencing technology continues to advance, it will fundamentally change the future of genetic diagnosis and advanced clinical diagnostics.

 

References

Read Abstract

1- Tools for the Microbiome: Nano and Beyond

Biteen JS, Blainey PC, Cardon ZG, et al. Tools for the Microbiome: Nano and Beyond. ACS Nano. 2016;10(1):6–37. doi:10.1021/acsnano.5b07826
The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks.... Read more

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2- Emerging Technologies for Gut Microbiome Research

Arnold JW, Roach J, Azcarate-Peril MA. Emerging Technologies for Gut Microbiome Research. Trends Microbiol. 2016 Nov;24(11):887-901. doi: 10.1016/j.tim.2016.06.008.
Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological.... Read more

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3- The Hoops, Hopes, and Hypes of Human Microbiome Research

Bik EM. The Hoops, Hopes, and Hypes of Human Microbiome Research. Yale J Biol Med. 2016;89(3):363–373. Published 2016 Sep 30.
Recent developments in sequencing methods and bioinformatics analysis tools have greatly enabled the culture-independent analysis of complex microbial communities associated with environmental samples, plants, and animals. This has led to a spectacular.... Read more

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4- A clinician's guide to microbiome analysis

Claesson, M., Clooney, A. & O'Toole, P. A clinician's guide to microbiome analysis. Nat Rev Gastroenterol Hepatol 14, 585–595 (2017). https://doi.org/10.1038/nrgastro.2017.97
Microbiome analysis involves determining the composition and function of a community of microorganisms in a particular location. For the gastroenterologist, this technology opens up a rapidly evolving set of challenges and opportunities for generating.... Read more

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5- Genomic approaches to studying the human microbiota

Weinstock GM. Genomic approaches to studying the human microbiota. Nature. 2012;489(7415):250–256. doi:10.1038/nature1155
The human body is colonized by a vast array of microbes, which form communities of bacteria, viruses and microbial eukaryotes that are specific to each anatomical environment. Every community must be studied as a whole because many organisms have never been.... Read more

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6- Personalized Nutrition by Prediction of Glycemic Responses

Zeevi D, Korem T, Zmora N, et al. Personalized Nutrition by Prediction of Glycemic Responses. Cell. 2015;163(5):1079–1094. doi:10.1016/j.cell.2015.11.001
Elevated postprandial blood glucose levels constitute a global epidemic and a major risk factor for prediabetes and type II diabetes, but existing dietary methods for controlling them have limited efficacy. Here, we continuously monitored week-long glucose levels in an.... Read more