Era7 bioinformatics and_the_microbiome_november_2016

November 2016
www.era7bioinformatics.com
info@era7.com
@Era7bioinfo
The Microbiome
in Era7 Bioinformatics.

Era7 Bioinformatics is
The Bacterial Genomics Company
and
a leader in Microbiome Analysis

The Microbiome Revolution era
started officially on May 13th 2016

This date The White House announced the
launching of The National Microbiome Initiative

And Era7 was there!
Our CEO Eduardo Pareja was invited to
the Launching of the National
Microbiome Initiative

Microbiome became one of the White
House Important Initiatives:
• Precision Medicine Initiative
• Cancer Moonshot
• National Microbiome Initiative

National Microbiome Initiative definition:
“Microbiomes are the communities of
microorganisms that live on or in people,
plants, soil, oceans, and the atmosphere.
Microbiomes maintain healthy function of
these diverse ecosystems, inﬂuencing
human health, climate change, food
security, and other factors”

And not only The White House thinks
that The Microbiome is a revolution

The Microbiome contains many kinds
of microorganisms but the more
frequently analysed are Bacteria and
Archaea

Bacteria
are all
over the
World ……

In the Sea

In
the soil

In the Air

And in all
living
organisms

The Microbiome has got a great interest
recently:
• Humans: in different parts of the body
• Environmental: soils, water, oceans ….
• Industrial: farms, food …..
• Places: Hospitals, tools, phones, trains…

Microbiome in PubMed

The Human Microbiome has been
called:
“ The Second Genome “
“ The Last Organ “

Human Microbiome facts:
• 100 times more genes than the Human Genome
• 1.5 Kilograms
• 10 times more bacteria cells than human cells in our
body

More than 10% of the small
molecules in the blood come from
the gut microbiome

Human Microbiomes, many places to
analyse:
• Mouth
• Gut
• Skin
• Urinary Tract
• Airways
• Vagina
• Human Milk
• ………………………..

A healthy Microbiome is needed
and a “bad” Microbiome is related
with diseases

• Obesity
• Type 1 Diabetes
• Type 2 Diabetes
• Colon cancer
• Asthma
• Atherosclerosis
• Autism
• Autoimmunity
• Cardiovascular Disease
• Crohn
• Cystic Fibrosis
Not exhaustive list of health conditions related with Gut
Microbiome:
• Skin disorders
• Inflammation
• Fe deficiency
• Multiple Sclerosis
• Obesidad
• Rheumatoid Arthritis
• Parkinson
• Sarcoidosis
• Stroke
• AIDS

The Microbiome shapes The Immune System
Some examples:
• Mice do not have Blood-Brain barrier when their gut is
sterile.
• In Cancer Immunotherapy in mice, results depend on
the Microbiome composition
• In mice, Stroke recovery depends on The Microbiome
composition as demonstrated after antibiotics treatment

The Human Microbiome is closely related
with The Immune System and, thus, in Era7
Bioinformatics we can also do:
• HLA typing
• TCR repertoire
• BCR repertoire

We have several approaches to
analyse The Microbiome
• 16S and 18S
• Shotgun metagenomics
• Other targeted sequencing

16S and 18S taxonomic profiling
With 16S sequencing you get info from
bacteria and archaea. Is much more cheaper
than Shotgun approach and very good results
can be obtained.

We offer two approaches:
• illumina approach
• PacBio approach

illumina approach:
You get information from 16S rRNA gene v3
and v4 variable regions sequencing an
amplicon

PacBio approach:
You get information from full length 16S sRNA
gene sequencing an amplicon containing all
the 9 variable regions:

In any approach, illumina or PacBio,
our MG7 pipeline and DB7 reference
database get the best results that
each technology can provide

Shotgun approach:
All the DNA present in the metagenomics
sample is sequenced and analysed:
You get information from all kinds of
organisms but sequencing and analysis cost
is higher

Shotgun approach:
Era7 Bioinformatics uses different pipelines
adapted to the objective of the analysis.

There are also many things influencing the
Microbiome:
• Antibiotics
• Diet
• Genome
• Immune System
• Exercise
• Pets
• Infections
• Age
• Jet-Lag
• ………..

Era7 has a very specialised
and multidisciplinary team
• Mathematicians
• Software engineers
• Biochemists
• Microbiologists
• Medical Doctors

Data Information Knowledge
Era7 is based in Cloud Computing

Microbiome Biomarkers will be
applied very soon to Clinics
Era7 Bioinformatics is developing EHR integration
and new rich interactive visualisations for
clinicians in the context of our R&D project
“Cardiobiome”

El Microbioma de la Boca
Podría estar involucrado en algunos Infartos Agudos
de Miocardio
Proyecto CARDIOBIOME

Cardiobiome project:
• Cloud Microbiome analysis integrated
with Electronic Health Record (EHR)
• New rich interactive visualisation tools
designed for clinicians
• Microbiome analysis of Acute Myocardial
Infarction as a proof of concept

In Era7, we are expert in
Microbiome based - Precision and
Personalised Medicine Integrated
with Immunogenomics

• Era7 is present in The United States in
Cambridge Massachusetts
• Era7 has its own specially designed methods for
Microbiome analysis: MG7 and DB7
• Era7 team is very experienced in Genomics Big
Data analysis
• Era7 team is based in knowledge and in research

Era7 Bioinformatics has done Microbiome
analysis projects for:
• Biotech Companies
• Pharma Companies
• Agri-food companies
• Research Centres
• Universities
• Hospitals

Era7 has launched recently a
portal with Microbiome related
information , from references to
news and simple tools:
www.themicrobiome.com

¿ Qué queremos hacer ?
El Portal “The Microbiome”
como elemento de Marketing

SERVICE MG7

MG7 Bioinformatics analysis for 16S
MG7 is a complete analysis tool developed by Era7
Bioinformatics oriented to provide taxonomic
assignment results for big sets of sequences.
MG7 pipelines of analysis are continuously being
updated with the newest approaches.

Our rRNA reference database DB7
We have built our reference database DB7 of 16S and
18S sequences based on the complete RNAcentral
release 5 . RNAcentral is a general database for all the
types of non coding RNA maintained by RNAcentral
Consortium

Our taxonomic assignment algorithm is
exhaustive
We compare each read against all the sequences of
our DB7 database. The taxonomic assignment for each
read is based on the results of BLASTN of each read
against our DB7 database.

Our algorithm for taxonomic assignment provides
results for two diﬀerent assignment approaches:
• Best Blast Hit (BBH)
• Lowest Common Ancestor (LCA)

MG7 provides a rich set of deliverables with 4 diﬀerent
types of abundance values for each of the 2
approaches (BBH and LCA) to evaluate the frequencies
of bacterial and archaeal organisms:
• direct values and cumulative abundance values
• absolute counts and abundance percentages
DELIVERABLES of MG7 Bioinformatics
analysis for 16S

Best BLAST Hit (BBH):
• Direct Assignment, Absolute Values
• Direct Assignment, Percentage Values
• Cumulative Assignment, Absolute Values
• Cumulative Assignment, Percentage Values
Lowest Common Ancestor Algorithm (LCA):
• Direct Assignment, Absolute Values
• Direct Assignment, Percentage Values
• Cumulative Assignment, Absolute Values
• Cumulative Assignment, Percentage Values
analysis for 16S

MG7 provides a rich set of deliverables including tables
per sample, per groups of samples, global, per ranks:
• Abundance tables per sample
• All the ranks in a complete table
• Abundances for each rank
• Abundance tables per each deﬁned group of samples
• Abundance tables for all the samples together
analysis for 16S

MG7 provides a rich set of deliverables including
Analysis of diversity indexes
The Shannon-Wiener and Simpson’s diversity
indexes are calculated for each sample.
analysis for 16S

Comparison of groups of samples
We provide statistical analysis for the study of
diﬀerences between groups of samples. We use for it
open tools based on R software from CRAN (The
Comprehensive R Archive Network). In each case we
apply the most appropriate approaches.
analysis for 16S

Some types of statistical analysis provided for the
comparison of groups of samples:
• Univariate statistics (fold change analysis, t-tests, volcano plots, one-way
ANOVA, correlation analysis)
• Multivariate statistics (principal component analysis , partial least
squares discriminant analysis)
• Clustering (dendrograms, heatmaps, K-means clustering, self organizing
feature maps)
• Supervised classiﬁcation (random forests, support vector machine)
analysis for 16S

Charts and Reports that MG7 provides
Diﬀerent types of charts with the possibility of providing
interactive visualizations (See our research project
BIOGRAPHIKA about interactive visualizations)
Complete results in compliant formats
Technical reports ready to scientiﬁc publication
analysis for 16S

MG7 workﬂow for 16S
• Our Reference database DB7
• Exhaustive taxonomic assignment
for each read
• Two diﬀerent taxonomic
assignment approaches, Best Blast
Hit (BBH) and Lowest Common
Ancestor (LCA)
• A complete set of deliverables

SERVICE MG7
for full-length 16S taxonomic proﬁling with PacBio

Full-length 16S taxonomic proﬁling with PacBio
and Era7 Bioinformatics MG7
• 100% of the hypervariable regions
• Obtaining 16S full gene sequences
• More speciﬁc taxonomic assignments

Our service of
Taxonomic Profiling
with PacBio:
Primer position in
16S gene. Includes
v1 to v9 regions
Taken from
www.themicrobiome.com

Check our
SlideShare
Presentation:
Taxonomic
Profiling with
PacBio

From DNA or from already sequenced raw data

Regardless your platform of
preference…
We can also provide further tailored
interpretation services based in our
Bio4j bioinformatics platform

Bio4j is a bioinformatics graph based DB
including most data available in:
- UniProt (SwissProt + Trembl)
- UniRef (50,90,100)
- Gene Ontology (GO)
- RefSeq
- NCBI taxonomy
- Enzyme DB
Big Data:
- 2.000.000.000 relationships
- 400.000.000 nodes
- 1.000.000.000 properties

Bio4j was
selected by
Google for the
Google
Summer of
Code 2014

Era7 Bioinformatics can also do data
integration with other -omics results
and design specialised databases for
your results and tailored visualisation
tools

In summary, with Era7 Bioinformatics
you will have a very specialised team
using a wonderful pipeline and the
possibility of obtaining tailored
approaches, databases and and data
integration.

Thanks for your
attention !
info@era7.com

@Era7bioinfo

Era7 bioinformatics and_the_microbiome_november_2016

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