Methods Guide for Microbial

Whole-Genome Sequencing
Sequence hundreds of organisms simultaneously, generate accurate
reference genomes, and perform comparative genomic studies

For Research Use Only. Not for use in diagnostic procedures.

Introduction
Microbial whole-genome sequencing (WGS) is an important method for characterizing or
assembling genomes of novel organisms, finishing genomes of known organisms, or comparing
genomes across multiple samples. Sequencing entire bacterial, viral, and other microbial
genomes is important for generating accurate reference genomes, for microbial identification, and
enables comparative genomic studies.
Unlike capillary sequencing or PCR-based approaches, next-generation sequencing (NGS) allows
microbiology researchers to sequence hundreds of organisms simultaneously. Additionally, NGS
can identify low-frequency variants and genome rearrangements that may be missed or are too
expensive to identify using other methods.
Use microbial WGS to:
• Analyze entire genomes and mobile genetic elements from microbial isolates and
cultures comprehensively
• Sequence whole genomes directly from primary samples through targeted resequencing
• Discover new variants and detect low-frequency quasispecies in culture or clinical samples with
an improved lower limit of detection compared to traditional methods
• Sequence multiple organisms in parallel using high-capacity NGS systems

For Research Use Only. Not for use in diagnostic procedures. 2

 De novo microbial genome sequencing
De novo WGS involves assembling a genome without the use of a genomic reference
and is often used to sequence novel microbial genomes. Illumina sequencing systems
provide exceptional raw read accuracy, read length, and read depth for high-quality
draft and complete microbial genome assemblies.

Microbial whole-genome resequencing

Microbial whole-genome resequencing involves sequencing the entire genome of a
bacteria, virus, or other microbe, and comparing the sequence to that of a known
reference. Generating rapid and accurate microbial genome sequence information is
critical for detecting low frequency mutations, finding key deletions and insertions, and
discovering other genetic changes among microbial strains.

Sequencing isolates or primary samples

Sample type and previous knowledge of organisms of interest will determine the best
sequencing method to use. For microbial isolates, WGS of DNA or whole-transcriptome
sequencing (WTS) of RNA is recommended. These methods can detect known targets
or offer hypothesis-free analysis of the sample. When analyzing complex primary
samples, a hypothesis-driven, targeted resequencing approach like amplicon or
enrichment sequencing is recommended when the target organism is either known
or suspected. Hypothesis-free sequencing of complex primary samples requires
approaches like shotgun metagenomics or metatranscriptomic sequencing.

Methods for sequencing isolates and primary samples

Isolate Primary sample

DNA DNA
Target RNA RNA
(prokaryotes, eukaryotes, (prokaryotes, eukaryotes,
Organism (viruses only) (viruses only)
and DNA viruses) and DNA viruses)
Targeted DNA amplicon Targeted RNA amplicon
Known
sequencing sequencing
WGS WTSa Custom DNA enrichment RNA enrichment metagenomic
Suspected
metagenomic sequencing sequencing
Unknown Shotgun metagenomics Metatranscriptomic sequencinga
a. With optional ribosomal RNA (rRNA) depletion.

For Research Use Only. Not for use in diagnostic procedures. 3

Applications
NGS has opened new doors in microbial genomics, revealing fresh insight into how microbes impact humans
and the environment. The power to generate accurate reference genomes for microbial identification and/or other
comparative genomic studies has widespread applications.

• Discover new microbes, including viruses

• Characterize difficult-to-culture organisms
• Investigate and understand outbreaks from infectious disease, antibiotic resistance, or foodborne pathogens
• Enable synthetic biology solutions to harness the power of nature to solve problems in medicine, manufacturing,
and agriculture
• Analyze human, plant, animal, and environmental samples for beneficial microbes and pathogens
• Monitor quality in industrial bioprocess and vector quality control (QC)
• Discover new enzymes and metabolic functions for industrial or medical use with systematic bioprospecting

Bacterial species change over time through various mechanisms, such as horizontal gene transfer and coevolution
with other organisms. High-resolution gene sequencing can inform a wide range of studies, including mutagenesis,
directed evolution, the spatial and temporal dynamics of epidemics, and mechanisms of disease transmission.

Uncover new taxa and biology

Extremophiles

Dr. Brian Hedlund uses microbial WGS to learn more about the unique microbes that populate hot springs. Through
his multidisciplinary approach to the topic, Dr. Hedlund is discovering major new groups of life that have never been
explored by science before. These organisms likely diverged from known lineages of microbes over a billion years
ago. Thanks to genomics, he is discovering new classes of organisms, learning how to work with difficult-to-culture
microbes, and learning new insights about microbial life in general.

Watch the video at illumina.com/company/video-hub/nH3dGo-DZTk.html.

Infectious disease outbreaks and epidemiology

Ebola

Dr. Pardis Sabeti wants to empower public health communities and try to stop the next Ebola epidemic before it
starts. To do this, she advocates using microbial WGS to identify infectious threats and track their spread in real time.
She, along with her partners and sponsors, including Illumina, have successfully overcome many challenges and
delivered and installed three sequencing systems in West Africa.

Watch the video at illumina.com/company/news-center/feature-articles/adventures-in-genomics--the-fight-against-

ebola.html.

Tuberculosis

In their paper, “Use of Whole Genome Sequencing to Determine the Microevolution “WGS provided
of Mycobacterium tuberculosis during an Outbreak,” Kato-Maeda et al a link between
demonstrated how WGS analysis of all M. tuberculosis isolates from a hospital cases that did not
outbreak of tuberculosis enabled researchers to trace the outbreak, uncovering the otherwise have an
source and determining the directionality of transmission. epidemiologic link.”
Read the article at journals.plos.org/plosone/article?id=10.1371/journal. – Kato-Maeda et al
pone.0058235.

For Research Use Only. Not for use in diagnostic procedures. 4

Antibiotic resistance detection and managing the spread
MRSA (methicillin-resistant Staphylococcus aureus) “WGS seems promising in
outbreak investigations,
Bartels et al used WGS to analyze a Methicillin-resistant Staphylococcus and might add information
aureus (MRSA) outbreak in a neonatal ward and cases in the community, on the spread of outbreak
suggesting that WGS can potentially fill in gaps in epidemiological data. clones outside the hospital
setting, where the connection
Read the article at ncbi.nlm.nih.gov/pubmed/25955776. between patients is frequently
not clear.” – Bartels et al

Foodborne pathogen surveillance and outbreak investigations

IZSLER Parma laboratory provides diagnostic and testing services for animal disease diagnostic testing, including
zoonoses, official controls on food and feedstuffs, epidemiological and analytical support to health authorities for
the design and management of official prevention and eradication plans, monitoring and surveillance of animal and
zoonotic diseases for foodborne diseases, and applied and basic research in infectious diseases.
Read the article at illumina.com/content/dam/illumina-marketing/documents/icommunity/pongolini-izsler-interview-
miseq-micro-770-2015-033.pdf.

Harness the power of microbes to improve medicine, agriculture, and manufacturing

Synthetic biology is a growing field that involves redesigning organisms for useful purposes by engineering them
to have new abilities. Researchers and companies around the world are harnessing the power of nature to solve
problems in medicine, manufacturing, and agriculture. WGS is a foundational technology for this area of research
and applied outcomes, enabling organism engineers to use many approaches, such as gene editing or synthetic
gene synthesis, to build complex metabolic pathways in microorganisms designed to perform high-value functions.
Applied applications include living medicines, cultured ingredients, enhanced agricultural microbiomes, and use in
biosecurity initiatives.

Improve food and drug development and QC

Microbes are used in many food production processes, like cheese, wine, and beer. Microbes can be analyzed and
characterized to understand how they influence important quality traits and must be closely monitored and managed
to ensure that these traits of interest are maintained. WGS enables discovery of new strains that can provide new
quality traits in food production and monitoring and quality control of strains in use.

Similarly, in biopharmaceutical research, risk monitoring is a key aspect in research and product development. WGS
allows researchers to track cell line stability and conduct biosafety monitoring.

Yeast in beer

An international group of scientists, yeast producers, and brewers sequenced 96 yeast strains to learn how genetics
can influence the flavor of beer. Their findings could help brewers make better beers.

Read the Cell article at cell.com/cell/fulltext/S0092-8674(16)31071-6.

For Research Use Only. Not for use in diagnostic procedures. 5

How it works
Microbial WGS has three basic steps: library preparation, sequencing, and analysis. During library preparation, DNA is
fragmented and probes containing Illumina sequencing adapters hybridize to each fragment. Each individual fragment
is then sequenced and the resulting nucleotide-level data is analyzed to generate an accurate reference genome,
compare variations within and between species, and differentiate between organisms.

Illumina solutions for microbial WGS

Prepare library Sequence Analyze and report

Illumina DNA Prep iSeq 100 System Local Run Manager Software
Nextera XT DNA Library Prep Kit MiniSeq System
Resequencing
MiSeq System
BaseSpace Sequence Hub
NextSeq 550 System
NextSeq 2000 System DRAGEN RNA Pathogen Detection

NovaSeq 6000 System BWA Aligner, Pisces Variant Caller,

SRST2, SPAdes, Bacterial Analysis
Pipeline, Velvet de novo Assembly, Prokka
Genome Annotation

Illumina Informatics Solutions

Local Run Manager, BaseSpace Sequence Hub
Run management | Analysis | Reporting
BaseSpace Clarity LIMS

Training Service contracts Professional services

Customer site training Tiered service plans Proof-of-Concept Service

Illumina DNA Prep iSeq 100 System Standard application functional testing
Nextera XT DNA Library Prep Kit MiniSeq System with your samples
MiSeq System
NextSeq 550 System
NextSeq 2000 System
NovaSeq 6000 System

For Research Use Only. Not for use in diagnostic procedures. 6

 Step 1 Choose a library prep method

Illumina recommends two library preparation kits for microbial WGS studies: Illumina DNA Prep and Nextera™ XT DNA
Library Prep. Illumina DNA Prep provides a faster workflow with fewer steps. Nextera XT DNA Library Prep requires
less input material and can generate longer insert sizes for sequencing.

Library prep kit Illumina DNA Prep Nextera XT DNA Library Prep Kit
Most important to me Simple and versatile sample-to-data workflow Less hands-on time and longer insert protocol
Least important to me PCR-free workflow Amplicons < 300 bp in length
Input quantity 1-500 ng 1 ng DNA
Multiplexing 384 samples 384 samples
Assay time 3-4 hrs ~5.5 hrs
Hands-on time 1.5 hrs a
15 min
Target insert size ~350 bp 300 bp-1.5 kb
Diversity ≥ 1B unique fragments ≥ 1B unique fragments
Genome coverage Complete Complete
Mechanism of action Bead-linked transposome Enzymatic DNA fragmentation
a. Denotes total workflow time, including DNA extraction, library preparation, and library normalization/pooling steps

Illumina DNA Prep*

Save time and reduce hands-on touch points with On-Bead Tagmentation, producing sequencing-ready libraries in
less than three hours. Simplify daily operations with a kit that supports a broad DNA input range (1-500 ng), multiple
DNA input types, and use with small (bacteria, Archaea, viruses, plasmids) to large genomes (human, plant, mouse).
Libraries prepared with Illumina DNA Prep are compatible with all Illumina sequencing systems.

Learn more at illumina.com/illumina-dna-prep.

Nextera XT DNA Library Prep Kits

Generate sequencing-ready libraries from small genomes (bacteria, Archaea, viruses), amplicons, and plasmids
in less than 90 minutes with only 15 minutes of hands-on time. Nextera XT DNA Library Prep Kits simultaneously
fragment input DNA and tags the fragments with sequencing adapters in a single-tube enzymatic reaction.
Nextera XT DNA Library Prep Kits require as little as 1 ng of input, supporting a wide array of sample types. Bead-
based normalization eliminates the need for library quantification before pooling and sequencing. Libraries prepared
with Nextera XT Kits are compatible with all Illumina sequencing systems.

Learn more at illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-xt-dna.html.

* Formerly available as the Nextera DNA Flex Library Preparation Kit

For Research Use Only. Not for use in diagnostic procedures. 7

 Step 2 Choose a sequencing system

Sequencing system selection begins with identifying the best flow cell type and read length to support given
applications while matching data output, time to results, and price per sample to meet study needs.

iSeq 100 NextSeq 550 NextSeq 2000 NovaSeq 6000

System MiniSeq System MiSeq System
System System System System
High-throughput
Flexible benchtop High-
sequencing
Speed, accuracy, sequencing throughput,
Affordability Simplicity and power and
Most important and simplicity for far- system for exome, low-cost
and instrument flexibility to scale
to me reaching applications in transcriptome, and sequencing for
efficiency affordability based on your
microbiology whole-genome production-scale
project or workflow
sequencing genomics
needs
Bacterial
genome 1 - 1536; using
1 - 384; limited by
samples 1-4 1-18 1-24 1-384 all 4 lanes of
available indexes
processed/ S4 flow cell
flow cella
Onboard
— —
informatics
Benchtop
—
system
Production-
scale — — — — —
capabilities
Flow cell Mid-output/ Standard v2, Micro v2, Mid-output/
Standard P2, P3 SP, S1, S2, S4
options High-output Nano v2, Standard v3 High-output
Flow cells
1 1 1 1 1 1 or 2
processed/run
a. Sample numbers may depend on genome size, read depth, and specific flow cell output. Calculations based on 5 Mb genome and 1M reads.

iSeq™ 100 System

With the lowest price, smallest footprint, and fastest run
time of any Illumina instrument, the iSeq 100 System offers
an affordable option for researchers to expand the scope of
iSeq 100 System flow cell options and specifications their research. Sequence microbes, targeted genes, RNA
Flow cell type i1a transcripts, and more at the push of a button.
Output/run 144 Mb-1.2 Gb
• Lowest Illumina sequencing system cost
Reads/run 4M
• Suitable for small sample batches
Max read length 2 × 150 bp • Fixed throughput and read length
Cycles 300 • Suitable for microbial WGS and amplicon sequencing
a. The i1 flow cell is included in the iSeq 100 Reagents; this is a
ready-to-use cartridge prefilled with all the reagents needed for
sequencing. Simply load the reagent cartridge directly onto the Learn more at illumina.com/iSeq.
iSeq 100 System and start a run.

For Research Use Only. Not for use in diagnostic procedures. 8

MiniSeq™ System
Applying industry-leading sequencing technology in a simple, small,
affordable system, the MiniSeq System supports a broad range of
targeted DNA and RNA applications for examining single genes or entire
pathways. An intuitive user interface, load-and-go operation, and onboard
data analysis make it easy to learn and easy to use.

• Affordable to acquire
• Suitable for moderate sample batches
• Range of throughput and read length
• Suitable for microbial WGS and amplicon sequencing

Learn more at illumina.com/miniseq.

MiniSeq System flow cell options and specifications

Flow cell type Mid-output High-output
Output/run 2.1-2.4 Gb 1.7-1.9 Gb 3.3-3.8 Gb 6.6-7.5 Gb
Reads/run 8M 25M 25M 25M
Max read length 2 × 150 bp 1 × 75 bp 2 × 75 bp 2 × 150 bp
Cycles 300 75 150 300

MiSeq™ System
Combining speed, high-quality data, and the longest read
lengths from Illumina, the MiSeq System is ideal for sequencing
targeted panels, amplicons, and small genomes.

• Suitable for moderate sample batches

• Range of throughput and offers the longest read lengths of
any Illumina benchtop system
• Suitable for many microbial sequencing applications,
including WGS

Learn more at illumina.com/miseq.

MiSeq System flow cell options and specifications

Flow cell type Standard v2 Micro v2 Nano v2 Standard v3
Output/run 0.75-0.85 Gb 4.5-5.1 Gb 7.5-8.5 Gb 1.2 Gb 0.3 Gb 0.5 Gb 3.3-3.8 Gb 13.2-15 Gb
Reads/run 15M 15M 15M 4M 1M 1M 25M 25M
Max read length 2 × 25 bp 2 × 150 bp 2 × 250 bp 2 × 150 bp 2 × 150 bp 2 × 250 bp 2 × 75 bp 2 × 300 bp
Cycles 50 300 500 300 300 500 150 600

For Research Use Only. Not for use in diagnostic procedures. 9

 NextSeq™ 550 System
The NextSeq 550 System delivers the power of high-throughput sequencing
with the simplicity of a benchtop sequencer, transforming exome,
transcriptome, and whole-genome sequencing into everyday research
tools. High-quality data combined with versatile, streamlined DNA-to-data
workflows enables low- and high-throughput studies supporting a range of
project sizes and applications.

• Suitable for high sample batches

• Range of throughput and read lengths
• Suitable for many microbial sequencing applications, including WGS,
shotgun metagenomic sequencing, and metatranscriptomic sequencing

Learn more at illumina.com/systems/sequencing-platforms/nextseq.html.

NextSeq 550 System flow cell options and specifications

Flow cell type Mid-output v2.5 High-output v2.5
Output/run 16-19 Gb 32-39 Gb 25-30 Gb 50-60 Gb 100-120 Gb
Reads/run 130M 130M 400M 400M 400M
Max read length 2 × 75 bp 2 × 150 bp 1 × 75 bp 2 × 75 bp 2 × 150 bp
Cycles 150 300 75 150 300

NextSeq 2000 System

The NextSeq 2000 System enables researchers to explore current
and emerging applications with higher efficiency and fewer restraints.
The cost-efficient, high-throughput system delivers accurate results for
emerging applications of increasing complexity. Combining a streamlined
workflow with onboard informatics, this easy-to-use benchtop system
makes NGS accessible to novice and expert users.

• Suitable for high sample batches

• Fixed throughput and read lengths
• Suitable for many microbial sequencing applications,
including WGS, shotgun metagenomic sequencing, and
metatranscriptomic sequencing
• On-board integrated informatics with DRAGEN™ Bio-IT Platform for
rapid secondary analysis

Learn more at illumina.com/nextseq2000.

NextSeq 2000 System flow cell options and specifications

Flow cell type P2 P3
Output/run 40 Gb 80 Gb 120 Gb 110 Gb 220 Gb 330 Gb
Reads/run 400M 400M 400M 1.1B 1.1B 1.1B
Max read length 2 × 50 bp 2 × 100 bp 2 × 150 bp 2 × 50 bp 2 × 100 bp 2 × 150 bp
Cycles 100 200 300 100 200 300

For Research Use Only. Not for use in diagnostic procedures. 10

 NovaSeq™ 6000 System
The NovaSeq 6000 System unleashes groundbreaking innovations that build upon
proven Illumina sequencing by synthesis (SBS) chemistry. Get scalable throughput
and flexibility for virtually any sequencing method, genome, and scale of project.
Applications requiring large amounts of data can now be completed in a more
cost-effective manner. For additional flexibility, the NovaSeq Xp workflow supports
individual lane loading for sequencing different libraries in each flow cell lane. When
combined with lower output flow cells, the same instrument can be used for less
data intensive methods.

• High-throughput sequencing with unprecedented throughput at the lowest cost

per sample for any Illumina sequencing system
• Range of throughput and read lengths
• Suitable for many microbial sequencing applications including WGS, shotgun
metagenomic sequencing, and metatranscriptomic sequencing

Learn more at illumina.com/systems/sequencing-platforms/novaseq.html.

NovaSeq 6000 System flow cell options and specifications

Flow cell type SP S1 S2 S4
Output/run 80 Gb 250 Gb 400 Gb 167 Gb 333 Gb 500 Gb 417 Gb 833 Gb 1250 Gb 3000 Gb
Reads/run 800M 800M 800M 1600M 1600M 1600M 4100M 4100M 4100M 10,000M
Cycles 100 300 500 100 200 300 100 200 300 300
Output per flow cell
2 × 50 bp 65-80 Gb 134-167 Gb 333-417 Gb N/A
2 × 100 bp 134-167 Gb 266-333 Gb 667-833 Gb 1600-2000 Gb
2 × 150 bp 200-250 Gb 400-500 Gb 1000-1250 Gb 2400-3000 Gb
2 × 250 bp 325-400 Gb N/A N/A N/A
N/A = not applicable

For Research Use Only. Not for use in diagnostic procedures. 11

 Step 3 Add biological context

Analyze whole-genome data with Local Run Manager Software or BaseSpaceTM Sequence Hub Apps.

Learn more, including example data sets, workflows, and supported file types at illumina.com/basespace.

Pathogen detection

DRAGEN RNA Pathogen Detection App†

• Uses a combined human and virus reference to analyze pathogen data and create
consensus FASTAs
• Creates pathogen coverage plots
• Offers integrated QC metrics

BWA† ‡ Aligner and Pisces Variant Caller

• Performs read alignment and mutation detection for any genome with a known reference sequence.
If none is available, the pipeline can still be used to analyze bacteria, fungi, or viruses after de novo
assembly

SRST2†
• Reports the presence of sequence types (STs) from a multilocus sequence typing (MLST) database
and/or reference genes from a database of sequences for virulence genes, resistance genes, and
plasmid replicons

Bacterial Analysis Pipeline

• Identifies species, MLST, plasmids, virulence, and antimicrobial resistance genes in bacteria

Isolate sequencing and assembly

Assembly workflow§
• Assembles small genomes (< 20 Mb); best suited for the assembly of bacterial genomes,
such as E. coli
• Uses the EMBL Velvet algorithm and writes assembly results in FASTA format

SPAdes Genome Assembler

• Assembles genomes from standard bacterial isolates and single-cell multiple displacement
amplification (MDA) preparations

† BaseSpace Labs Apps are developed using an accelerated development process to make them available to BaseSpace users faster than conventional Illumina Apps.
Illumina may provide support for BaseSpace Labs Apps at its sole discretion. BaseSpace Labs Apps are provided AS IS without any warranty of any kind. BaseSpace
Labs Apps are used at the user’s sole risk. Illumina is not responsible for any loss of data, incorrect results, or any costs, liabilities, or damages that may result from the use
of a BaseSpace Labs App. For inquiries or feedback for this application, to provide a feature request, or to get support, email [email protected].
‡ BWA: Burrows-Wheeler Aligner
§ Available through Local Run Manager

For Research Use Only. Not for use in diagnostic procedures. 12

Gene annotation

Prokka Genome Annotation†

• Annotates genes and identifies coding sequences in prokaryotic genomes
• Does not annotate eukaryotic genomes

Commercial third-party apps

bioMérieux EPISEQ
• Integrates comprehensive applications for microbiological research and routine applications
• Combines information from various genomic and phenotypic sources into one global database and conducts
combined analyses

Learn more at applied-maths.com/applications.

ChunLab TrueBac ID
• Uses whole-genome sequences to identify >12,000 species for microbial applications in research, applied, and
industrial settings

Learn more at truebacid.com.

† BaseSpace Labs Apps are developed using an accelerated development process to make them available to BaseSpace users faster than conventional Illumina Apps.
Illumina may provide support for BaseSpace Labs Apps at its sole discretion. BaseSpace Labs Apps are provided AS IS without any warranty of any kind. BaseSpace
Labs Apps are used at the user’s sole risk. Illumina is not responsible for any loss of data, incorrect results, or any costs, liabilities, or damages that may result from the
use of a BaseSpace Labs App. For inquiries or feedback for this application, to provide a feature request, or to get support, email [email protected].

For Research Use Only. Not for use in diagnostic procedures. 13

Services and support
Illumina consulting services provide laboratories with direct access to experienced Illumina teams to
jump start successful sequencing workflow implementation.

Training
Onsite customer training courses provide detailed, hands-on training on
Illumina library preparation solutions in the customer’s laboratory. Participants
will receive expert instruction and best practice guidance for performing and
troubleshooting the basic protocol. By the end of the course participants
will be able to prepare libraries efficiently and consistently for use on Illumina
sequencing systems. Standard and personalized workflow training options are
available.

Learn more at illumina.com/services/instrument-services-training/training.

html.

Service contracts
A standard 1-year base warranty is included with every new Illumina instrument
purchase, along with installation and basic applications training. Illumina
also offers several tiered services plans to upgrade the base warranty to
an enhanced service level or extend service coverage beyond the 1-year
warranty. These plans are designed to optimize the customer experience and
to protect instrument investment. Illumina Product Support Services Plans help
researchers maximize performance and productivity with reliable, high-quality
results at various cost-effective levels.

Learn more at illumina.com/services/instrument-services-training/product-

support-services/service-plans.html.

Professional services
The Proof-of-Concept (POC) Service will run a subset of your samples with your
desired system and application in a real-world demonstration of how Illumina
NGS can empower your laboratory. Receive in-person consultation pre-POC
to establish POC needs and goals, POC sequencing services of your samples
at the Illumina Service Lab, and in-person consultation post-POC to review
sequencing run QC, data, and reports based on your samples.

Contact your local account manager to learn more.

For Research Use Only. Not for use in diagnostic procedures. 14

Ordering information
Library prep kits

Product Catalog no.

Illumina DNA Prep
Illumina DNA Prep (M), Tagmentation (24 samples) 20018704
Illumina DNA Prep (M), Tagmentation (96 samples) 20018705
Flex Lysis Reagent Kit 20018706
Nextera DNA CD Indexes (24 indexes, 24 samples) 20018707
Nextera DNA CD Indexes (96 indexes, 96 samples) 20018708
Nextera XT DNA Library Prep
Nextera XT DNA Library Prep Kit (24 samples) FC-131-1024
Nextera XT DNA Library Prep Kit (96 samples) FC-131-1096
Nextera XT Index Kit (24 indexes, 96 samples) FC-131-1001
Nextera XT Index Kit (96 indexes, 384 samples) FC-131-1002
TruSeq TM
Dual Index Sequencing Primer Kit, single read FC-121-1003
TruSeq Dual Index Sequencing Primer Kit, paired-end read PE-121-1003
Nextera XT DNA Library Prep Kit training at customer site TR-204-0009

Sequencing Systems

System Catalog no.

iSeq 100 System 20021532
MiniSeq System SY-420-1001
MiSeq System SY-410-1003
NextSeq 550 System SY-415-1002
NextSeq 2000 System 20038897
NovaSeq 6000 System 20012850

Data analysis
Product Catalog no.
BaseSpace Sequence Hub Professional Annual Subscription 20042109
BaseSpace Sequence Hub Enterprise Annual Subscription 15066411

For Research Use Only. Not for use in diagnostic procedures. 15

References
1. McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3). pii: e00031-18. doi:
10.1128/mSystems.00031-18.
2. McDonald D1, Price MN, Goodrich J, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.
ISME J. 2012;6(3):610-8. doi: 10.1038/ismej.2011.139.
3. Illumina. (2016) Sequencing a mouthful of microbes. Accessed April 29, 2020.
4. Data calculations on file. Illumina, Inc., 2017.
5 American Gut Project. American Gut – What’s in your gut? San Diego, CA. Accessed May 5, 2020.
6. Illumina. (2015) Microbes and metagenomics in human health. Accessed April 29, 2020.
7. Earth Microbiome Project. https://earthmicrobiome.org/. Accessed May 5, 2020.
8. Thompson LR, Sanders JG, McDonald D, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017;551:457-463. doi:10.1038/
nature24621.
9. Hospital Microbiome Project. http://built-envi.com/portfolio/hospital-microbiome-project/. Accessed May 5, 2020.
10. Illumina. 16S Metagenomic Sequencing Library Preparation. Accessed April 29, 2020.
11. Klindworth A, Pruesse E, Schweer T, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next‐generation sequencing‐based diversity
studies. Nucleic Acids Res. 2013;41(1):e1.
12. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol.
2007;73(16):5261-7.

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For Research Use Only. Not for use in diagnostic procedures.
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