Our guest today is Dr Ozan Gundogdu for a deeper dive into the food borne pathogen Campylobacter and how genomics has informed the field over the past 20 years since the publication of the first reference genome in 1999.

Ozan leads the foodborne enteric pathogen group at the London school of hygiene and tropical medicine. Where they study the physiology and pathogenesis of Campylobacter and other related enteric microorganisms like Listeria and Vibrio. His background is in Molecular Biology and Computer Science and he completed his PhD at LSHTM (London School of Hygiene & Tropical Medicine) in 2011.
www.lshtm.ac.uk/aboutus/people/gundogdu.ozan

63 A dive into Campylobacter genomics

We’re continuing our series where we examine a particular microbial species in some depth. We’re talking about mycobacterium tuberculosis, the forgotten pandemic. 

Our guests are Dr. Suzie Hingley-Wilson Lecturer in Bacteriology at the University of Surrey, Dr. Dany Beste Senior Lecturer in Microbial Metabolism at the University of Surrey and Dr. Conor Meehan assistant professor in molecular microbiology at the University of Bradford.

64 Mycobacterium tuberculosis: the forgotten pandemic

We’re continuing our series where we examine a particular microbial species in some depth. We’re continuing our look at Mycobacterium tuberculosis, focusing more on bioinformatics, genomics and typing. 

Our guests are Dr. Suzie Hingley-Wilson Lecturer in Bacteriology at the University of Surrey, Dr. Dany Beste Senior Lecturer in Microbial Metabolism at the University of Surrey and Dr. Conor Meehan assistant professor in molecular microbiology at the University of Bradford.

65 Genomics of Mycobacterium tuberculosis

Today we’re talking about some exciting new developments in the area of comparative genomics. We are joined by Dr. Zamin Iqbal who is a Research Group Leader at the European Bioinformatics Institute and Dr. Grace Blackwell who is jointly at the European Bioinformatics Institute, in Zam’s group and Nick Thomson’s team at Wellcome Sanger Institute

77 Genomics for a new era

We are joined by Dr Robert Petit from the Wyoming Public Health Laboratory who is talking to us about BACTOPIA, a bioinformatics workflow specifically for bacterial genomes.

Docs: https://bactopia.github.io/ 
Repo: https://github.com/bactopia/bactopia/
Pub: https://doi.org/10.1128/mSystems.00190-20

72 Bactopia and using workflow managers in bioinformatics  part 1

What are the major challenges for getting AMR genomics into the clinic? 
This was the question poised to a panel of experts at the 7th Microbial Bioinformatics hackathon run in conjunction with JPIAMR, PHA4GE and CLIMB.

The panel were: Mark Pallen from the Quadram Institute Bioscience, UK, Finlay Maguire from Dalhousie University, Canada, Anthony Underwood from the Centre for genomic pathogen surveillance, UK and Clement Tsui from the Weill Cornell Medicine, Qatar. Andrew Page was the Chair, supported by Lee Katz.

76 What are the major challenges for getting AMR genomics into the clinic?

We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2.  Find out more at https://github.com/CDCgov/datasets-sars-cov-2

* Previous paper for bacterial datasets can be found at https://peerj.com/articles/3893/
* Jill can be found on Twitter at @JillHagey and jvhagey.github.io
* Lingzi can be found on LinkedIn at https://www.linkedin.com/in/lingzi-xiaoli-27b87174/

80 Benchmark datasets for SARS-CoV-2

For the first time ever all 3 MicroBinfies are together in person to record an episode. We are joined by Torsten Seemann for a conversation about how what we do in research can get lost in translation when applied to public health. We discuss what we did with SARS-CoV-2 genomics and somehow end up chatting about geography and language.  Hope you enjoy.

95 Lost in Translation with Torsten Seemann

We interview Frank Ambrosio.  He is embarking on a lifestyle of nomadic bioinformatics, living his best life.

* https://www.linkedin.com/in/francis-ambrosio/

In this episode of the MicroBinfie podcast, Frank Ambrosio, a bioinformatician working for Theiagen as a traveling bioinformatician, joins co-hosts Andrew Nabil and Lee to talk about his journey into bioinformatics.

Frank shares how he transitioned from being a lab technician and microbiologist to analyzing his own data and pursuing a master's program in bioinformatics at Georgia Tech. He also discusses his experience working at the CDC, where he gained exposure to different laboratories working on tuberculosis, biodefense research and development, surveillance-oriented production laboratories for strep genomes, and the division of HIV/AIDS prevention.

Frank gives tips for aspiring bioinformaticians, recommending that early career scientists focus on applying for contracting agencies at the CDC to gain valuable experience and eventually become full-time employees. He also suggests starting with a virtual machine and a cloud-based IDE like Google Cloud and VS Code for ease of use and reliability.

The conversation then moves onto Frank's nomadic lifestyle as a traveling bioinformatician, and his desire to connect with the public health community worldwide. Frank shares his recent experience meeting collaborators in Mozambique and the importance of building personal connections with colleagues in public health for collaboration and support.

Frank concludes by discussing his approach to routines while traveling and how he uses his Google calendar to plan out his days and weeks. He emphasizes the importance of flexibility and adaptability as a traveling bioinformatician, and his eagerness to continue meeting new people and building connections in the public health community.

Moving on to Frank's lifestyle as a digital nomad bioinformatician, he explains how he enjoys enhanced flexibility, better quality of life, and the ability to work anywhere in the world. However, he also highlights that this lifestyle model could be challenging, particularly for those who prefer greater stability and predictability.

Nabil wonders how possible it would be for bioinformaticians to engage in mentoring and education while working as digital nomads. Frank acknowledges the concerns but highlights that he has been fortunate enough to maintain his mentor relationships remotely. He talks about how working with someone on a project can facilitate a stronger and more rewarding mentor-mentee relationship.

The hosts note that flexibility is not new to bioinformatics and that technological advancement is making it easier to find intelligent people worldwide to join in the missions of organizations like the CDC. Frank reflects on his future, reserving the potential to remain with his current institution, Theiagen. He remains optimistic about the potential of these digital collaborations and is open to new opportunities to help the global bioinformatics community.

98 Nomadic bioinformatics with Frank

Over the past few weeks scientists have been swapping Twitter for Mastodon. Our very own Nabil-Fareed Alikhan talks about his experience with setting up and running a Mastodon server called https://mstdn.science which is one of the places where scientists have moved over to.  We are joined by Emma Hodcroft to get an independent scientists view on the whole thing.

In the MicroBinfie podcast, Andrew and Nabil discuss the migration of academics from Twitter to a new platform called Mastodon, with Nabil playing a significant role in this shift. According to Nabil, Mastodon is a free and open web application designed for micro-blogging. It enables integration and communication between servers, allowing the users to follow, reply, or read content from other servers.

The migration happened after Elon Musk bought Twitter and made significant changes that concerned people about freedom of speech and democracy. In response, Nabil and Duncan set up their own Mastodon instance called https://mstdn.science initially planning to create a social network for bioinformaticians, microbial genomics people, and tech-savvy microbiologists. Expected to have only 50-100 users, many more scientists, including Nobel Laureates, journals, and scientists from other disciplines, joined, and Nabil's instance now has almost 2000 users.

Meanwhile, other instances around science, like genomic.social or ecoevo.social, also saw a surge in sign-ups. In terms of resources, Nabil and Duncan's virtual server have almost 2000 users costing around £100 per 1000 users, depending on how much interaction and following goes on.

The Mastodon network replicates content from other instances, spawning many jobs, even if a user's account doesn't change much. Nabil does not limit which instances of Mastodon communicate with his site but does block domains serving unwanted or unsafe content. Even though the Mastodon network can crash and burn, Nabil thinks it could still work in the long run.

The podcast contributors suggest that Twitter's recent changes have left some users feeling dissatisfied, leading them to Mastodon, which is a decentralized social media platform. Some dodgy servers have been blocked by Mastodon for moderation, and people have moved from Twitter to Mastodon as a total replacement for Twitter. Mastodon has become a "sign" for fed-up users.

According to Emma, who recently moved from Twitter to Mastodon, Mastodon is a hedge against Twitter's unknown future. Mastodon's decentralized platform allows for a shift of power towards content and interaction, not available in a centrally controlled platform. Mastodon may not replace Twitter as a one-for-one replacement, but it fits certain use cases, such as a place for academics to complain about papers.

Mastodon's success is not dependent on Twitter's fate but rather on what "crazy ideas" Twitter comes up with in the future, Emma argues. While Mastodon may never be quite the same as Twitter, it could be even better.

94 The great scientific Mastodon migration

We are back talking about systematics, and SeqCode;  a nomenclatural code for prokaryotes described from sequence data. 
Marike Palmer is a  Postdoctoral researcher in the School of Life Sciences at the University of Nevada Las Vegas and Miguel Rodriguez is an Assistant Professor of Bioinformatics at the University of Innsbruck in the departments of Microbiology and the Digital Science Center (DiSC).

Link to paper: https://www.nature.com/articles/s41564-022-01214-9 
History paper: https://www.sciencedirect.com/science/article/pii/S0723202022000121

They discussed the SeqCode, a nomenclature code for Prokaryotes described from sequence data. The SeqCode was created to provide a specific nomenclature code for previously uncultivated organisms. Palmer explained that the impetus for the SeqCode was the need to accommodate previously uncultivated organisms under a specific nomenclature code. She emphasized that the SeqCode was written to allow any peer-reviewed publication, but noted that the authors have designed three paths of validation in the SeqCode. They hope that anyone proposing a name will work with the curriculum team to ensure the best quality descriptions, names, etymology, and solidification. 

Rodriguez discussed the SeqCode's governance, which is already in place, and they have made them public so that anyone interested can join the SeqCode community. The governance structure comprises an executive board, committees, and working groups. The position's co-opted members hold some of the committees of these committees, while some are chosen by ballot.

The hosts sought to clarify the relationship between the Isme Society, which is backing the SeqCode, and the wider field in general. Rodriguez explained that ISME is simply providing support as an umbrella organization for the SeqCode. 

Palmer and Rodriguez clarified that the SeqCode is not a competing code but rather a parallel one that aims to accommodate previously uncultivated organisms. The SeqCode was created to provide a specific nomenclature code for previously uncultivated organisms. Palmer noted that most scientists culture prokaryotes not for naming but to advance their knowledge of these organisms through physiology experiments. They emphasized that the new system is the result of a long collaborative effort that involved many different viewpoints and philosophies.

The episode also discussed the practical requirements for naming under the new system, which include standards for the completeness and contamination levels required in the genome sequence data. Palmer noted that while the 16S rRNA gene sequence was not required for naming, it was recommended for improved accuracy in cross-talk between different taxonomies. The conversation highlighted the importance and challenges of naming microorganisms and the ongoing efforts to create a system that is inclusive of all microorganisms, both cultivated and uncultivated.

Rodriguez and Palmer also discussed the SeqCode, a nature code for naming prokaryotes described from sequence data. They agreed that high-quality genomes should be the main control types to ensure the system builds up rather than breaks down. They noted the challenge of obtaining full genomes of some organisms, such as obligate intracellular parasites but suggested obtaining housekeeping genes as a potential solution. They further explained the technical issue of estimating completeness or contamination for many taxa, but Palmer confirmed that registering a name on the SeqCode registry requires adding such estimates. 

It emphasized the importance of collaboration within the scientific community and the need to create a system that is inclusive of all microorganisms. It also highlighted the challenges inherent in the process of naming microorganisms but demonstrated that it is an ongoing process, and that scientists are working to create a system that is accurate, practical, and beneficial for all.

108 SeqCode: a nomenclatural code for prokaryotes described from sequence data

Andrew and Lee are at the Global Microbial Identifier conference (GMI13) in Vancouver Canada. We talk to Dr William Hsiao, one of the organisers of the conference.

112 Global Microbial Identifier conference with Will Hsiao

125 Kostas Konstantinidis returns to talk to us about ANI and metagenomics

Nabil and Lee have a quick chat about minimum spanning trees (MST).

Eburst paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-152

127 Minimum spanning trees

In this episode of the Micro Binfie podcast, host Andrew Page talks with Dr. Erin Young, a bioinformatician at the Utah Public Health Laboratory, recorded during the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. Erin shares her journey from researching hereditary cancer predisposition to her current role in public health bioinformatics, which she entered through a prestigious CDC and APHL fellowship. The conversation delves into her work with bacterial pathogens, particularly in tracking antimicrobial resistance in organisms like Klebsiella. Erin discusses the tools she uses for genome typing, such as MASH, FastANI, and SKA, and her innovative research on the accuracy of long-read sequencing technologies like Nanopore for detecting antimicrobial resistance genes. She also provides a preview of her upcoming poster for ASM, where she examines how Nanopore reads can be used effectively in public health microbiology. This episode offers a fascinating look at how bioinformatics and genomics are advancing the fight against infectious diseases.

133 The Role of Bioinformatics in Public Health and Disease Outbreaks

In this episode of the Podcast, hosts Lee Katz and Andrew Page delve into the intricacies of clinical metagenomics. Joined by experts Torsten Seemann and Finlay Maguire, they explore the challenges and methodologies involved in identifying pathogens in clinical samples when traditional diagnostic methods fail. They discuss the types of samples analyzed, the impact of low DNA concentrations, and the complexities of sequencing data interpretation. The conversation highlights the importance of interdisciplinary collaboration between bioinformaticians and clinicians in managing difficult infections. Despite the hurdles, clinical metagenomics is presented as a complementary tool aiding in diagnosis, emphasizing the need for genomic literacy among healthcare professionals.

140 Exploring Clinical Metagenomics

On this episode we are joined by Sara Zufan to discuss her PhD journey and recent projects. The episode covers various research experiences and challenges in the field, including the rapid detection of AMR using nanopore sequencing, COVID-19 projects, hepatitis A outbreak investigations, and Lassa virus surveillance in Liberia. The guests share insights into their professional journeys, their experiences working across different continents, and the future of microbial bioinformatics research.

139 Lassa virus genomics

In a two-part discussion, the hosts analyze the movie Contagion from their expert perspectives, focusing on the film's portrayal of epidemiology and genomics. They note that the movie compresses timelines for dramatic effect, speeding up the virus's spread and the response to it, and that decisions about managing a crisis are based on societal values, not just science.

In part one, the hosts discuss the movie's depiction of the R0 value. They note that while this explanation is useful for the audience, it is unlikely that an epidemiologist would need to explain this concept to other epidemiologists. The group notes that the MEV1 virus is modeled on the real-life Nipah virus and comment on a scene where the genome of the virus is described as being 15 to 19 kilobases in length with 6 to 10 genes. They also discuss the movie's depiction of virus isolation and the unrealistic speed with which the initial assessment of the virus occurs. The podcasters touch upon the BSL4 lab and how the film depicts how the scientists behave. They also discuss the character of Matt Damon, who is exposed to the virus but does not get sick, and is an example of an asymptomatic carrier.

In part two, the bioinformaticians examine the "genome dashboard" scene, noting the software's informative interface, which includes an alignment panel, protein structure, and a recombination map. They also discuss a scene where a phylogenetic tree is used to determine a change in the R0 value. They find this unrealistic because the tree is just a picture that doesn't accurately represent how a virus spreads. The group discusses how the bioinformatician is depicted in the film as moving in and out of the lab, which may have been realistic in 2011 but is less so in the present day. They discuss how the CDC is portrayed in the film, noting scenes that were filmed at the actual CDC, as well as their experiences at the CDC. The podcasters note the movie is very US-centric and that many international partners would be involved in solving a global pandemic.

136 Contagion part 1

Andrew, Lee, Torsten, and Fin muse over the future of MLST, Illumina, and Nanopore at the ASM NGS Hackathon

141 hackathon panel

The crew talks about the genomeqc ecosystem. Check it out at https://happykhan.github.io/qualibact/

Errata: The project name was chaned to qualibact and is no longer genomeqc as mentioned on the episode.

142 - Microbinfie - genomeqc

143 - where we catch up on our professional lives

Nabil and Lee bring a guest host Clint to talk with some of the people behind Pathoplexus http://pathoplexus.org/ 

* Dr. Emma Hodcroft - https://pathoplexus.org/about/eb
* Dr. Theo Sanderson - https://pathoplexus.org/about/development-team
* Mr. Arthur Shem Kasambula - https://pathoplexus.org/about/development-team 

144 - micro binfie Pathoplexus part 1

145 - micro binfie Pathoplexus part 2

Andrew, Nabil, and Lee debate about NextFlow!

146 - NextFlow debate 1

147 - NextFlow debate 2

Final part of our discussion/debate on NextFlow

148 - NextFlow debate 3

In this episode we identify areas of “Peak-bioinformatics”. There are a lot of existing bioinformatics software out there - more often than not the new tool you want to write already exists or a new tool cannot effectively improve. We discuss this in terms of genome assembly, read mapping and phylogenetics. 

Question and comments? microbinfie@gmail.com

SHOW NOTES
Generally, novel software is not needed if:
There are a plethora of existing tools
The problem is more or less solved or its been shown to be unsolvable
The underlying technology or problem is now obsolete and/or superceded by other methods. 

Multiple sequence aligners:
MAFFT https://mafft.cbrc.jp/alignment/software/
MUSCLE  https://www.drive5.com/muscle/ 
Whole genome aligners:
Mauve  http://darlinglab.org/mauve/mauve.html
Mugsy http://mugsy.sourceforge.net/
Sibellia  http://bioinf.spbau.ru/sibelia
Parsnp https://github.com/marbl/parsnp

Assemblers:
SPADES https://github.com/ablab/spades
Skesa  https://github.com/ncbi/SKESA
Velvet https://www.ebi.ac.uk/~zerbino/velvet/
Abyss https://github.com/bcgsc/abyss
Edena  http://www.genomic.ch/edena.php
Ray http://denovoassembler.sourceforge.net/

Long read assemblies
HGAP https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP-2.0
Flye https://github.com/fenderglass/Flye
Canu https://github.com/marbl/canu
Ra https://www.biorxiv.org/content/10.1101/656306v1
Unicycler  https://github.com/rrwick/Unicycler

Read mapping
BWA http://bio-bwa.sourceforge.net/ 
Bowtie2 http://bio-bwa.sourceforge.net/
Minimap2 https://github.com/lh3/minimap2 (BWA better for short reads: https://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa)
BBtools https://jgi.doe.gov/data-and-tools/bbtools/
BLAST/BLAT: https://genome.ucsc.edu/FAQ/FAQblat.html
SMALT https://www.sanger.ac.uk/science/tools/smalt-0
Snippy https://github.com/tseemann/snippy
Phenix:  https://github.com/phe-bioinformatics/PHEnix

Variant callers
GATK: https://software.broadinstitute.org/gatk/
VIPR: https://www.viprbrc.org/brc/home.spg?decorator=vipr  
Varscan2  http://varscan.sourceforge.net/

Workflow managers
Bespoke example https://github.com/VertebrateResequencing/vr-codebase
Snakemake. https://snakemake.readthedocs.io/en/stable/
Nextflow  https://www.nextflow.io/
Galaxy  https://usegalaxy.org/
Bpipe  https://github.com/ssadedin/bpipe

Phylogenetics:
Raxml - Raxml-NG https://cme.h-its.org/exelixis/software.html 
IQTREE http://www.iqtree.org/ 
FastTree http://www.microbesonline.org/fasttree/ 
BEAST 1&2 https://www.beast2.org/ 
RevBayes  https://revbayes.github.io/

Metagenomics
Taxonomic classification: Megan, Kraken, SIGMA, MIDAS, metaphlan2, mOTUs. 
Assemblers: MetaSpades, metaflye, MEGAHIT, MetaVelvet, a lot of single isolate assemblers have been tweaked to run on metagenomes.
https://github.com/lskatz/Kalamari

AMR
https://github.com/arpcard/amr_curation
https://food-safety-bioinformatics-hackathon.github.io/AMR-protocols/
ABRICATE https://github.com/tseemann/abricate 
ARIBA https://www.sanger.ac.uk/science/tools/ariba 
Too many detection tools:
https://docs.google.com/spreadsheets/d/18XGWpDiaE249qQKDAL7gdBCka0Z1drpA_s3FElfMJe0/edit#gid=0

Other mentioned resources
Mentioned Recent review. 
Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B (2011) A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies. PLoS ONE 6(3): e17915. https://doi.org/10.1371/journal.pone.0017915
The Assemblerthon: https://assemblathon.org/
Blog post describing that BWA better for short reads: https://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa
The science web: https://thescienceweb.wordpress.com/2015/03/23/each-bioinformatician-to-have-their-own-personal-short-read-aligner-by-2016/

01 What bioinformatics software not to write part 1

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00 Trailer

14 La resistance lives on: The AMR deep dive

Invasive non-typhoidal Salmonella is a significant public health challenge in Africa. We talk to Abdoulie Kanteh and Grant Mackenzie about their work in The Gambia, and their use of genomics to understand the serovars in circulation.

Manuscript: https://www.biorxiv.org/content/10.1101/2021.02.18.431831v2

50 Atypical invasive non-typhoidal Salmonella in The Gambia

We are joined by Peter van Heusden to discuss all the latest developments in SARS-CoV-2 genomics, particularly around tools and resources. We also discuss the challenges of building and sharing data in large scale sequencing endeavours.

Tools and resources: 
Nextalign github.com/nextstrain/nextclade/releases

COG mutation explorer http://sars2.cvr.gla.ac.uk/cog-uk/

Grinch https://cov-lineages.org

New US tool for variants: https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html 
https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/global-variant-map.html 

Online lineage assignment: https://pangolin.cog-uk.io/

CoronaHiT paper published: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00839-5

49 SARS-CoV-2 Tools and resources update

Microbial Bioinformatics is a rapidly changing field marrying computer science and microbiology. Join us as we share some tips and tricks we’ve learnt over the years. If you’re student just getting to grips to the field, or someone who just wants to keep tabs on the latest and greatest - this podcast is for you. 

The hosts are Dr. Lee Katz from the Centres for Disease Control and Prevention (US), Dr. Nabil-Fareed Alikhan from the University of Oxford (UK), and Prof. Andrew Page from Theiagen Genomics (UK) and bring together years of experience in microbial bioinformatics.

The opinions expressed here are our own and do not necessarily reflect the views of Centres for Disease Control and Prevention, University of Oxford or Theiagen Genomics.

Intro music : Werq - Kevin MacLeod (incompetech.com)
Licensed under Creative Commons: By Attribution 3.0 License
http://creativecommons.org/licenses/by/3.0/

Outro music : Scheming Weasel (faster version) - Kevin MacLeod (incompetech.com)
Licensed under Creative Commons: By Attribution 3.0 License
http://creativecommons.org/licenses/by/3.0/

Question and comments? microbinfie@gmail.com

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