GigaScience Press

Chris Hunter

#### FUNC on Safari: Functional Metagenomics conference 2024 at Skukuza, Kruger National Park, South Africa (2nd -- 5th June 2024) {#func-on-safari-functional-metagenomics-conference-2024-at-skukuza-kruger-national-park-south-africa-2nd-5th-june-2024}

::: {#attachment_5791 .wp-caption .aligncenter style="width: 810px"}
![ Functional Metagenomics conference FMG24 participants group
photo](http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/participants-FMG24-small-1024x703.jpg){.wp-image-5791
fetchpriority="high" decoding="async"
aria-describedby="caption-attachment-5791" width="800" height="549"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/participants-FMG24-small-1024x703.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/participants-FMG24-small-300x206.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/participants-FMG24-small-768x527.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/participants-FMG24-small-1536x1055.jpg 1536w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/participants-FMG24-small-2048x1406.jpg 2048w"
sizes="(max-width: 800px) 100vw, 800px"}

FMG24 participants group photo, taken outside the conference centre at
Skukuza rest camp.
:::

GigaScience Press were [once
again](https://doi.org/10.59350/7dd55-0c961) proud sponsors of
the [Functional Metagenomics conference](https://fmg2024.carlamani.com/)
(FMG24). Functional Metagenomics is an area of interest for the journal,
particularly via [our MetaFUNC thematic
series](https://academic.oup.com/gigascience/pages/functional_metagenomics_series).
This, the 6th installment of the conference, was held in South Africa at
the Skukuza rest camp inside the famous Kruger National Park in South
Africa, from June 2nd-5th. I was lucky enough to be able to attend again
(see the [write-up of the 2019
edition](http://gigasciencejournal.com/blog/func-in-the-fjords-functional-metagenomics-2019/))
on behalf of *GigaScience*.

::: {#attachment_5790 .wp-caption .alignleft style="width: 410px"}
![](http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/local-dancers-small-300x200.jpg){.wp-image-5790
decoding="async" aria-describedby="caption-attachment-5790" width="400"
height="267"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/local-dancers-small-300x200.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/local-dancers-small-1024x683.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/local-dancers-small-768x512.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/local-dancers-small-1536x1024.jpg 1536w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/local-dancers-small-2048x1365.jpg 2048w"
sizes="(max-width: 400px) 100vw, 400px"}

Traditional music and dance performance
:::

The conference opened on the Sunday evening with local music and dance
performances and a few brief words from the local host [Prof. Don
Cowan](https://www.up.ac.za/microbial-ecology-and-genomics/article/1928624/prof-don-cowan)
(University of Pretoria) to welcome us all to South Africa. Every day
included a multitude of great speakers on various topics, below I
highlight just a few of them, interspersed with important networking
event coverage.

::: {#attachment_5793 .wp-caption .alignright style="width: 410px"}
![](http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/Alex-300x174.jpg){.wp-image-5793
decoding="async" aria-describedby="caption-attachment-5793" width="400"
height="232"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/Alex-300x174.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/Alex-1024x594.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/Alex-768x446.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/Alex-1536x892.jpg 1536w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/Alex-2048x1189.jpg 2048w"
sizes="(max-width: 400px) 100vw, 400px"}

Alexander Wentzel (SINTEF) speaking at FMG24
:::

The main event kicked off with a keynote talk from another of the
organisers [Alexander
Wentzel](https://www.sintef.no/en/all-employees/employee/alexander.wentzel/)
(SINTEF) describing the progress of bioprospecting efforts in Norway.
[SINTEF](https://www.sintef.no/en/) utilise both data-driven approaches
(e.g shotgun metagenome sequencing with bioinformatic analysis) as well
as more traditional functional approaches (e.g. cloning and screening
for traits of interest). Recognising the advantages of both approaches;
with the rapid growth in sequencing technologies allowing a greater
ability to mine the various sources for known or very similar genes, but
the functional screening enabling the discovery of more diverse gene
products that have the desired actions. Alex gave an overview of some of
the ongoing projects at SINTEF and how they are utilising the more
advanced screening techniques of microfluidics (covered in more detail
by later presenters).

[Marla Trindade](https://imbm.co.za/staff/senior-lecturer/) (University
of Western Cape) took us on a journey of discovery of biosurfactants and
explained the ever growing utility (and thus market) for these microbial
compounds. Biosurfactants are surfactants of biological origin (usually
microbial). They can be any compound that reduces the surface tension
between two media (liquid-liquid, liquid-gas, or liquid-solid).
Surfactants are common compounds found in detergents and cleaning
agents. The use of biosurfactants is more desireable than chemical
surfactants from a marketing point of view as they are considered "Eco"
friendly. In addition, they could be safely used in an even wider range
of products, including beauty and food products.  
For a change of tack, [Eran Elhaik](https://www.eranelhaiklab.org/)
(Lund University) demonstrated the ability to use metagenomic sequencing
as a rudamentary bio-tracing method. Using geographially informative
taxa (GITs) he can employ a machine learning approach to determine the
geographic origin of items. The approach seems to have some promise for
things that are not disturbed too much, or where you have a good deal of
data for a given origin, but the accuracy and certainty still needs some
improvements.

Moving back to functional screening experiments, [Gabrielle
Potocki-Veronese](https://www.toulouse-biotechnology-institute.fr/en/gabrielle-potocki-veronese/)
(University of Toulouse) presented their use of microfluidic approaches
that are proving so useful at scalling up functional screening, in this
case to help identify novel glycosides.

::: {#attachment_5802 .wp-caption .alignleft style="width: 310px"}
![](http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/sunset-300x200.jpg){.wp-image-5802
.size-medium loading="lazy" decoding="async"
aria-describedby="caption-attachment-5802" width="300" height="200"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/sunset-300x200.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/sunset-1024x683.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/sunset-768x512.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/sunset-1536x1024.jpg 1536w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/sunset-2048x1365.jpg 2048w"
sizes="(max-width: 300px) 100vw, 300px"}

The sunset in Kruger national park
:::

We rounded out the first day with a sunset safari drive followed by a
bush brai (BBQ in the bush!) where we exchanged stories of who saw what.
One group (not mine-hence no photo) having a close encounter with a
Rhino!  
  
[Florian Hollfelder](https://www.bioc.cam.ac.uk/research/hollfelder)
(University of Cambridge) is one of the leading experts in the
application of microfluidics to functional metagenomics, he presented an
overview of recent work on utilising ultra high throughput microfluics
combined with sequencing to aid directed evolution of enzmes (as seen in
his recent paper on
[biorXiv](https://doi.org/10.1101/2024.04.08.588565)).  
Later that day [Liisa Van
Vliet](https://www.linkedin.com/in/liisa-van-vliet-9959565/?originalSubdomain=uk)
(University of Cambridge) also from the Hollfelder group, presented the
technical advancements of the various microfluid screening methods that
are now possible and in regular use in their lab, allowing the screening
of up to 10^7^ variants per day!  
Whilst [Trevor Charles](https://uwaterloo.ca/biology/profile/tcharles)
(Friend of *GigaScience* and series editor of the [Functional
metagenomics
series](https://academic.oup.com/gigascience/pages/functional_metagenomics_series))
was unable to attend the conference on this occasion, he was able to
deputise a couple of members of his group to come in his stead. [Delaney
Nash](https://uwaterloo.ca/environmental-virology-ecology-research-group/contacts/delaney-nash)
(University of Waterloo) explained the nuances of mosaic end
tagmentation technique that they are using to explore antimicrobial
resistance genes in wastewater, and [Aranksha
Thakor](https://www.linkedin.com/in/aranksha-thakor-352863162)
(University of Waterloo), also studying wastewater, demonstrated the
optimsed construction of metagenomics libraries using Cosmids.

::: {#attachment_5796 .wp-caption .alignright style="width: 179px"}
![](http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/hippo-169x300.jpg){.wp-image-5796
.size-medium loading="lazy" decoding="async"
aria-describedby="caption-attachment-5796" width="169" height="300"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/hippo-169x300.jpg 169w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/hippo-576x1024.jpg 576w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/hippo-768x1365.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/hippo-864x1536.jpg 864w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/hippo-1152x2048.jpg 1152w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/hippo.jpg 1350w"
sizes="(max-width: 169px) 100vw, 169px"}

Hippo on the putting green! \#extreamegolfing
:::

Dinner on the second evening, was hosted at the local golf club. Where
members can  play at their own risk....there are no fences stopping the
wildlife roaming the fairways! Thankfully we were only there for dinner
in the enclosed dining area, but the view from the veranda showed us the
sort of obstacles that could wander on to the course.....see hippo photo
to right!

[Prof Stephanie
Burton](https://www.linkedin.com/in/stephanie-burton-71122658)
(University of Pretoria), gave a thought provoking presentation on the
impact of AI and digital technologies on the academic research
environment (see also our [recent
post](http://gigasciencejournal.com/blog/riddles-of-the-sphinx-research-integrity/)
from the WCRI conference related to AI in the research environment).
There is no point in trying to put that genie back in its bottle,
instead academia need to embrace it and learn how to teach (students and
staff) how to utilise it responsibly, whilst understanding its
limitations.  
[Grace Ijoma](https://www.linkedin.com/in/grace-ijoma-9767141b)
(University of South Africa) made two appearances as speaker, once on
the water quality (or lack of) in two artifical lakes in the Gauteng
province. They used metagenomics to demonstrate the level of pathogens
present in those water bodies to prompt the government to  take remidial
action. The second was a very brief account of the isolation and
sequencing of a novel fungi associated with white rot on decaying
wood.  
[Michael
Wittenberg](https://science.uct.ac.za/department-mcb/contacts/michael-wittenberg)
(University of Cape Town) is investigating the microbiomes of seasonal
resurrection plants, a fascinating group of plants that have the ability
to change their behaviour across seasons depending on levels of
desication. His research is looking into the potential of the
rhizosphere to influence this behvaviour.

::: {#attachment_5792 .wp-caption .alignleft style="width: 310px"}
![](http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/Don-300x205.jpg){.wp-image-5792
.size-medium loading="lazy" decoding="async"
aria-describedby="caption-attachment-5792" width="300" height="205"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/Don-300x205.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/Don-1024x700.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/Don-768x525.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/Don-1536x1050.jpg 1536w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/Don-2048x1400.jpg 2048w"
sizes="(max-width: 300px) 100vw, 300px"}

Don Cowan speaking at FMG24
:::

Fittingly, the local host, Don Cowan, presented the closing keynote on
the changing face of functional metagenomics. After a brief jaunt
through the ages summarising metgenomics from its first mention in the
[literature](https://doi.org/10.1128/mmbr.68.4.669-685.2004) in 1998 to
the present day. Don went on to speculate on the future of this
conference series, by a simple show of hands, it was clear that there is
indeed a desire to continue the FMG Conference series in some shape or
format, so watch this space!

 

And finally, what sort of a trip to Kruger National Park would it have
been without some wildlife photos!

::: {#attachment_5839 .wp-caption .aligncenter style="width: 810px"}
![selection of animal
photos](http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/montage-4-blog.png){.wp-image-5839
loading="lazy" decoding="async"
aria-describedby="caption-attachment-5839" width="800" height="386"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/montage-4-blog.png 1240w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/montage-4-blog-300x145.png 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/montage-4-blog-1024x494.png 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2024/06/montage-4-blog-768x370.png 768w"
sizes="(max-width: 800px) 100vw, 800px"}

A selection of animal photos from Kruger national park whilst attending
FMG24
:::

The post [FUNC on Safari: the 6th International Conference on Functional
Metagenomics
(FMG24)](http://gigasciencejournal.com/blog/6th-international-conference-on-functional-metagenomics-fmg24/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


FUNC on Safari: Functional Metagenomics conference 2024 at Skukuza, Kruger National Park, South Africa (2nd – 5th June 2024)     FMG24 participants group photo, taken outside the conference centre at Skukuza rest camp.  GigaScience Press were once again proud sponsors of the Functional Metagenomics conference (FMG24). Functional Metagenomics is an area of interest for the journal, particularly via our MetaFUNC thematic series.

FUNC on Safari: the 6th International Conference on Functional Metagenomics (FMG24)

Scott Edmunds

***Following our efforts promoting open science and ["community
genomics"](http://gigasciencejournal.com/blog/community-genomes-from-the-peoples-parrot-to-crowdfernding/){target="_blank"
rel="noreferrer noopener"} projects that have included the** [**"Peoples
Parrot"**](http://www.bio-itworld.com/2012/09/28/peoples-parrot-first-community-sponsored-genome.html)[**,**](http://blogs.biomedcentral.com/gigablog/2014/06/16/guest-posting-lets-crowdfund-a-fern-genome-that-will-blow-your-mind/){target="_blank"
rel="noreferrer noopener"} **[community
cactus](http://gigasciencejournal.com/blog/guest-posting-help-crowdfund-community-cactus/),
and our very own [Bauhinia
Genome](https://blogs.biomedcentral.com/on-biology/2015/11/24/help-investigate-genetic-mystery-hong-kongs-floral-emblem-bauhinia-flower/),
today we have a guest posting from the
[Transbiome](https://en.goteo.org/project/transbiome) team. Who are
working on new community driven research program using crowdfunding and
co-creation to discover the diversity of the neo-vaginal microbiome.**
**We've covered another example of a [community
microbiome](http://gigasciencejournal.com/blog/community-microbiomes-chatting-scat-kittybiomes-holly-ganz/)
project on cats (see [Kittybiome](https://youtu.be/TmZ3t93trOA)), but
like the microbiome datasets we've been publishing (including these two
new Data Release papers in GigaByte presenting [urinary
microbiome](https://doi.org/10.46471/gigabyte.9) and the [microbiome
from bone-loss](https://doi.org/10.46471/gigabyte.12) patients) this
work should have direct implications for human health.** **As a great
example of participant-centered research, unsurprising as two of the
Open Humans team are involved (see [their
paper](https://doi.org/10.1093/gigascience/giz076) in GigaScience),**
**the Transbiome team explain more about their project, and how they
need your help to make the study happen.***

<figure class="wp-block-image size-large is-resized">
<img
src="http://gigasciencejournal.com/blog/wp-content/uploads/2021/03/transbiome1.png"
class="wp-image-3788" loading="lazy" decoding="async"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2021/03/transbiome1.png 923w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/03/transbiome1-300x168.png 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/03/transbiome1-768x431.png 768w"
sizes="(max-width: 692px) 100vw, 692px" width="692" height="389"
alt="transbiome" />
</figure>

# What's the Transbiome? {#whats-the-transbiome .wp-block-heading}

Trans women who have a gender affirmation surgery gain a new organ --
the neo-vagina. Following the surgery it becomes host to its own
microbiome that colonizes this new organ! But what bacteria and fungi
make up this new microbiome? Good question, because no one really knows
right now! And, given that there's many different techniques to perform
gender affirmation surgeries -- with different tissues being used to
construct the neo-vagina -- it might well be the case that different
surgery techniques, methods of post-operative care and other factors
influence the composition of the microbiome! 

That's why our *Transbiome* study -- which is led by a team that is
majority trans -- will investigate the fungal and bacterial neo-vaginal
microbiome. We aim to map out the diversity of the microbiome and also
see if there are correlations between different external factors such as
surgery technique and the type of microbiome that establishes itself.

# Why is this important? {#why-is-this-important .wp-block-heading}

The microbial flora of cis-women's vagina has been studied extensively.
That's why we know how bacterial vaginosis and yeast infections occur
and how we can treat them. And it doesn't stop there: The vaginal
microbiome has also been linked to conditions like neoplasia and the
risk to develop cancer! 

Trans women's can suffer from (neo-)vaginal infections in the same way
as cis-women. But as we lack even basic knowledge about how their
microbiome looks like, they currently can't get access to the same
gynecological care as cis-women. By providing a survey of the
neo-vaginal microbiome we will help to provide the basic research that
is necessary to improve trans healthcare in the future!

# How are you planning to do this? {#how-are-you-planning-to-do-this .wp-block-heading}

Our goal is to work closely with 50 trans women from across Europe. We
will send them a sampling kit that allows them to easily and safely
collect a microbiome sample from the privacy of their own home. Along
with the sampling they will fill out a short survey about the surgery
technique used, what they did for post-operative care and some other
parameters -- like whether they suffered from infections. These samples
and answers are then sent back to us anonymously. 

Those microbiome samples will then be sequenced for both the 16s rRNA
for bacterial taxa and ITS sequencing for fungal taxa, each at around
50,000 sequencing reads per sample. This, paired with the number of
participants, should allow us to get a good first picture of how diverse
the neo-vaginal microbiome is between participants and also see if there
are particular types that cluster together based on the secondary
characteristics. 

<figure class="wp-block-image size-large is-resized">
<img
src="http://gigasciencejournal.com/blog/wp-content/uploads/2021/03/transbiome3-1.png"
class="wp-image-3791" loading="lazy" decoding="async"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2021/03/transbiome3-1.png 859w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/03/transbiome3-1-300x173.png 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/03/transbiome3-1-768x442.png 768w"
sizes="(max-width: 644px) 100vw, 644px" width="644" height="371" />
</figure>

# Help us to Crowdfund {#help-us-to-crowdfund .wp-block-heading}

Our *Transbiome* study will not only provide basic knowledge but it
happens in a context where it can be a promising first step to enable
better gynecological care for trans women. We will share the individual
data generated from each sample with the participant -- and of course
also share the deidentified raw data to enable the broadest possible
re-use of it. Using the same CC0 Public Domain Dedication that
*GigaScience* mandates to maximise reuse, all scientific outputs such as
publications will also be made available and will be released under open
licenses.

But to make this happen we need your help: As the *Transbiome* started
as a participant-driven student project we rely on
[crowdfunding](https://en.goteo.org/invest/transbiome) to make this
study happen. With around €4,000 we can already analyze the first 20
samples, with the optimum funding we will be able to do the full 50
samples. Any contribution you might be able to do -- no matter how small
-- brings us a step further to this! And please also share our project
with your friends and colleagues! 

<figure
class="wp-block-embed-youtube wp-block-embed is-type-video is-provider-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio">
<div class="wp-block-embed__wrapper">
<div class="iframe">
<div id="player">

</div>
<div class="player-unavailable">
<h1 id="ein-fehler-ist-aufgetreten." class="message">Ein Fehler ist
aufgetreten.</h1>
<div class="submessage">
<a href="https://www.youtube.com/watch?v=zm2bGosytdE"
target="_blank">Sieh dir dieses Video auf www.youtube.com an</a> oder
aktiviere JavaScript, falls es in deinem Browser deaktiviert sein
sollte.
</div>
</div>
</div>
</div>
</figure>

**To make this happen please help with crowdfunding and finding
potential participants via the project page here:
<https://en.goteo.org/project/transbiome>**

The post [Guest Posting: Help Crowdfund the
Transbiome](http://gigasciencejournal.com/blog/transbiome-guest-post/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


<em>
 <strong>
  Following our efforts promoting open science and “community genomics” projects that have included the
 </strong>
 <strong>
  “Peoples Parrot”
 </strong>
 <strong>
  ,
 </strong>
 <strong>
  community cactus, and our very own Bauhinia Genome, today we have a guest posting from the Transbiome team.
 </strong>
</em>

Guest Posting: Help Crowdfund the Transbiome

**The mock metagenome, MAGs and breaking the first rule of Long Read
Club**

::: {#attachment_2866 .wp-caption .alignright style="width: 310px"}
![mock
metagenome](http://gigasciencejournal.com/blog/wp-content/uploads/2019/05/NickLoman-300x225.jpg){.size-medium
.wp-image-2866 loading="lazy" decoding="async"
aria-describedby="caption-attachment-2866" width="300" height="225"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/05/NickLoman-300x225.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/05/NickLoman-768x576.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/05/NickLoman-1024x768.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/05/NickLoman.jpg 2048w"
sizes="(max-width: 300px) 100vw, 300px"}

Nick showing us some of his experiments with an [early]{dobid="hdw"}
[antecedent]{dobid="hdw"} Short Read Club...
:::

Out [today in *GigaScience*](https://doi.org/10.1093/gigascience/giz043)
is a new "mock metagenome" Data Note from the Nick Loman lab in
Birmingham showcasing the latest long-read sequencing technologies from
Oxford Nanopore. Having published the first nanopore *E. coli* genome
[with us in 2014](https://doi.org/10.1186/2047-217X-3-22) showcasing the
then new MinION, this new benchmark  presents long read metagenomics
datasets from Oxford Nanopore's new PromethION sequencer. In one of our
long running series of author Q&As Nick Loman and first author Sam
Nicholls give us the lowdown on the importance of the mock metagenome,
open science, MAGs, and how this work is part of a new Long Read Club.

**What does a mock metagenomics dataset give you that you can't get from
"real-world" datasets? Why are these community standards important?**

Mock communities are really useful for both lab and bioinformatics
"positive controls".

Because the community has gram-negative, gram-positive and two types of
yeast cells, it can be used to check that DNA extractions have worked
properly. Some kits will fail to lyse some of the cells and they will
simply be missing from your experiment! Having a gold standard reference
for each genome is really useful for assessing how well bioinformatics
aligners and de novo assemblers are working. And the use of known taxa
and abundances in invaluable for assessing taxonomic assignment
pipelines.

In this case, to keep pace with such changes and to ensure robustness of
results, it is incredibly helpful to have validated, known "gold
standard" datasets. In this case we used a commercially-available ["mock
community" from
Zymo](https://www.zymoresearch.com/blogs/blog/zymobiomics-microbial-standards-optimize-your-microbiomics-workflow):
real cells, in known abundances, comprised of 10 different microbes.

As genomics is moving into real-world uses such as in the clinic, it is
even more vital that experiments are conducted correctly and sequencing
and bioinformatics pipelines can be validated. We are trying to help the
community design accepted best practices for long read metagenomics.

Our paper is a starting point for a longer-term goal to generate
reliable trusted data sets, and make them [freely
available](http://dx.doi.org/10.5524/100580) for the community.

**This example presents large amounts of long-read sequencing data, so
what does this technology bring to the field of metagenomics?**

Metagenomics is a very exciting technique, and the field has really
taken off in recent years, and has been used for diverse applications
including diagnosis for clinical microbiology, the discovery of new
genes and species with potentially industrial biotechnology
applications, and for studies of microbial diversity: for example, whole
new swathes of the Tree of Life, such as the Candidate Phyla Radiation
were [discovered using
metagenomics](http://dx.doi.org/10.1038/s41564-017-0083-5)!

The field is enthusiastic about being able to recover whole genome
information directly from samples without the need for culture, and
so-called metagenome-assembed genomes (MAGs) are being collected at an
increasing pace. MAGs are usually made by sorting sequence reads or
contigs with similar composition or coverage into genome 'bins'.
However, these binned MAGs can be fragmented, miss important genes and
end up being contaminated with sequences from related species.

::: {#attachment_2867 .wp-caption .alignleft style="width: 310px"}
![mock
microbiome](http://gigasciencejournal.com/blog/wp-content/uploads/2019/05/giz043fig1-300x278.jpeg){.size-medium
.wp-image-2867 loading="lazy" decoding="async"
aria-describedby="caption-attachment-2867" width="300" height="278"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/05/giz043fig1-300x278.jpeg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/05/giz043fig1.jpeg 549w"
sizes="(max-width: 300px) 100vw, 300px"}

Output of the PromethION & GridION sequencers (source: Nicholls et al.).
:::

In comparison to short-read high-yield platforms where read lengths are
limited between 100 and 300 bp, single-molecule long-read platforms can
sequence much longer fragments of DNA: with read lengths averaging over
10 Kbp, with over 2 Mbp reported by the community. Long reads simply
hold much more information, making them a powerful tool for
metagenomics. For example, their increased information content offers
more evidence for sequencing mapping against references, or taxonomic
databases. Additionally, longer reads are key in bridging repetitive
structures within and between genomes.

We think long reads can help with this problem: particularly as the cost
of generating long reads has recently dropped dramatically (in our paper
we show outputs of \~15Gb from a single MinION flowcell, and \~150Gb
from the PromethION flowcells). However, there's not a clear view on the
best way to analyse long read metagenomic data as it's such a new field.

**You gather Oxford Nanopore PromethION, GridION and Illumina data, so
what do you see from these comparisons, and what do you hope users will
get from this mock metagenome data?**

The goal of this work was to make available a really deep long read
dataset for the two [Zymo mock community
standards](https://www.zymoresearch.com/blogs/blog/zymobiomics-microbial-standards-optimize-your-microbiomics-workflow).

[These datasets](https://lomanlab.github.io/mockcommunity/) can be used
for a wealth of comparisons: between the evenly-distributed and
log-distributed samples, and between the Oxford Nanopore GridION and
PromethION platforms too. The Illumina short-read data demonstrates that
high-quality short-reads cannot adequately assemble the communities
alone, but are useful for polishing our long-read assemblies to a high
consensus accuracy (although we found that polishing long-read nanopore
data alone with Racon and Medaka does a very good job too).

Our work also benefits from the recent release of PacBio data for some
of the isolates in this community from Chris Mason and Alexa McIntyre.
These genomes now permit us to make a reliable estimate of the
correctness of the assemblies we generate, both in terms of base quality
and assembly structure.

We are really hoping that users will take parts (or all!) of our data
and use it to develop and validate new laboratory and software pipelines
for long-read metagenomics. We've taken care to ensure we are up to date
with the latest ONT software including the newest "flip-flop model"
Guppy basecaller, the quite recent wtdbg2 assembler, and current
polishing strategies (Racon, Medaka, Pilon). This is a nice
demonstration of what can be achieved with long-read metagenomics, but
this is just the beginning and there will be  plenty more to come!

**The Oxford Nanopore PromethION is a pretty new beast, so what does
this platform allow you to do that previous sequencing technologies were
not able to do? Especially for the field of metagenomics.**

PromethION data is quite sparse at the moment and to our knowledge this
is the first metagenomics PromethION dataset to be released. To make a
simple analogy, it's like having a more powerful microscope. Using the
PromethION, we see 10-fold increases in coverage for each of the genomes
in the community compared to exactly the same library when sequenced on
the GridION. This level of resolution permits us to assemble some of the
lower abundance organisms from the log-distributed community and to
detect organisms at extremely low abundance with more confidence. This
will be crucial for some applications where important community members
are not the highest abundance in the sample. We also are able to
demonstrate that the PromethION data are of similar quality to the
GridION when run on the same library, giving confidence that this beast
may be useful.

**Can you tell us about the [Long Read
Club](https://www.longreadclub.org/), and what does this work contribute
to it?**

![mock
metagenome](http://gigasciencejournal.com/blog/wp-content/uploads/2019/05/longreadclub-300x272.jpg){.alignright
.size-medium .wp-image-2863 loading="lazy" decoding="async" width="300"
height="272"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/05/longreadclub-300x272.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/05/longreadclub.jpg 475w"
sizes="(max-width: 300px) 100vw, 300px"}The first rule of Long Read Club
is you don't talk about Long Read Club...!

If we were to break that rule, we'd tell you that [Long Read
Club](https://www.longreadclub.org/) is part of a recently funded
Wellcome Trust Technology Development Award to Nick here in Birmingham,
and Matt Loose at the University of Nottingham. The goal is to help the
genomics community at large achieve finished-quality complete genomes
from long-reads, routinely and at scale. Our work here is a small
stepping stone contributing towards the future of long-read
metagenomics. We've shown that long-read based assemblies are getting
close to the single-contig finished quality genomes that one would
expect to get from isolate sequencing directly, and we'd like to think
that we're sharing the best extraction, sequencing and bioinformatics
protocols currently available.

Most importantly, Long Read Club is a Club, so the core idea is to share
our knowledge with each-other and the wider community. Our reads,
software and analyses are open access and open source, because we want
everybody to be able to achieve really very long reads indeed.

**All the [data](http://dx.doi.org/10.5524/100580), snakemake
[workflows](https://github.com/LomanLab/mockcommunity) and
[protocols](http://dx.doi.org/10.17504/protocols.io.x9tfr6n.) are
provided openly without restriction, and your lab have been big
advocates of open source approaches to science (e.g., [the
Tweenome](http://gigasciencejournal.com/blog/tweenome-on-film-excellent-video-on-crowdsourcing-killer-outbreaks/)).
Have you seen the benefits of this first hand?**

We have! [The paper itself](https://doi.org/10.1093/gigascience/giz043)
features recently published data from Alexa McIntyre et al's [recent
*Nature Communications*
paper](http://dx.doi.org/10.1038/s41467-019-08289-9) that included
PacBio isolate sequencing of eight of the ten organisms in the two
ZymoBIOMICS community standards, which was generously shared with us
ahead of publication; allowing us to perform robust comparisons of our
long-read nanopore assemblies against orthogonal long-read PacBio
assemblies. We are very grateful for their early data sharing, not least
because it allowed us to respond to a request from the reviewers to
include assembly comparisons in this manuscript.

Last month, Mikhail Kolmogorov and Jeffrey Yuan (et al.) [published the
Flye assembler in *Nature
Biotechnology*](https://www.nature.com/articles/s41587-019-0072-8). Over
the past year, Mikhail and Jeffrey have been developing a metagenomic
assembly mode for Flye ('metaFlye') -- [a preprint has just been made
available](https://doi.org/10.1101/637637) -- and have shown it works
really well using the Zymo mock community data. We actually made the
first version of this dataset available only a few weeks after
generating it and released it at last September's Genome Science
meeting. It's gratifying to know that there are developers taking our
data and working to develop and validate new methods for long-read
metagenomics. If you're interested, you can hear more about Flye from
Mikhail and Jeffrey in their recent [Long Read Club
episode](https://www.youtube.com/watch?v=It5KXnPBnbg).

We want to make everything we do available for everyone to use and
improve. The MinION has helped to democratise sequencing and in the past
couple of years we've seen huge improvement in long-read technology, but
it is natural that it takes time for a new field to figure out the best
way to analyse data. Making our ideas,
[protocols](https://www.protocols.io/groups/long-read-club) and software
open means we can accelerate science and work with the genomics
community to make long-read metagenomics robust, scalable and
scientifically-accurate for everyone.

**Further Reading  
**Nicholls SM, Quick JC, T Shuiquan, Loman NJ. Ultra-deep, long-read
nanopore sequencing of mock microbial community standards.
*GigaScience*. 2019
doi:[10.1093/gigascience/giz043](https://doi.org/10.1093/gigascience/giz043)

**Further Watching**  
Watch the latest updates for the Long Read Club on their youtube
channel: <https://www.youtube.com/c/longreadclub>

The post [Mock the Metagenome. Author Q&A with Nick Loman & Sam
Nicholls](http://gigasciencejournal.com/blog/mock-metagenome/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


<strong>
 The mock metagenome, MAGs and breaking the first rule of Long Read Club
</strong>
Nick showing us some of his experiments with an early antecedent Short Read Club…  Out today in
<em>
 GigaScience
</em>
is a new “mock metagenome” Data Note from the Nick Loman lab in Birmingham showcasing the latest long-read sequencing technologies from Oxford Nanopore.

Rogue Scholar Posts

FUNC on Safari: the 6th International Conference on Functional Metagenomics (FMG24)

Guest Posting: Help Crowdfund the Transbiome

Mock the Metagenome. Author Q&A with Nick Loman & Sam Nicholls