BØPosphere – January 2023

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bioRxiv

An Automated Scientist to Design and Optimize Microbial Strains for the Industrial Production of Small Molecules

2023-01-03

DOI:10.1101/2023.01.03.521657

A. H. Singh, B. B. Kaufmann-Malaga, J. A. Lerman, D. P. Dougherty, Y. Zhang, A. L. Kilbo, E. H. Wilson, C. Y. Ng, O. Erbilgin, K. A. Curran, C. D. Reeves, J. E. Hung, S. Mantovani, Z. A. King, M. Ayson, J. R. Denery, C.-W. Lu, P. Norton, C. Tran, D. M. Platt, J. R. Cherry, S. S. Chandran, A. L. Meadows

Affiliations

Amyris

Meet 𝐋𝐢𝐥𝐚 – an Automated Scientist built by the Amyris crew to do E.coli and Yeast metabolic engineering by DBTL cycles. Lila has made 100s of biosynthesis strains. Perhaps she is going to make your PhD students feel a bit sad
https://biorxiv.org/content/10.1101/2023.01.03.521657v1…

2023-01-06

In labs where microbes were bred,
To synthesize molecules, it’s said,
Lila came to the fore,
Automating much more,
A scientist’s dream sped ahead.

Nature biotechnology

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine.

2023-01-19

PubMed:36658342; DOI:10.1038/s41587-022-01628-0

Almut Heinken¹, Johannes Hertel¹, Geeta Acharya², Dmitry A Ravcheev¹, Malgorzata Nyga³, Onyedika Emmanuel Okpala⁴, Marcus Hogan¹, Stefanía Magnúsdóttir⁵, Filippo Martinelli¹, Bram Nap¹, German Preciat⁶, Janaka N Edirisinghe⁷, Christopher S Henry⁸, Ronan M T Fleming¹, Ines Thiele⁹

Affiliations

School of Medicine, University of Galway, Galway, Ireland
Integrated BioBank of Luxembourg, Dudelange, Luxembourg
University of Luxembourg, Esch-sur-Alzette, Luxembourg
Czech University of Life Sciences Prague, Prague, Czech Republic
Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
Computation Institute, University of Chicago, Chicago, IL, USA
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
School of Medicine, University of Galway, Galway, Ireland.

A resource of microbial metabolic models reveals how an individual’s gut microbiome influences drug metabolism

2023-03-31

In the world of microbes unseen,
A complex dance of health convene,
Precision medicine’s plea,
Incorporates microbiome’s glee,
AGORA2’s knowledge, vast and keen.

Strains and molecules, all in view,
Modeling’s art, complex and true,
Gut organisms in array,
Drug transformations come to sway,
AGORA2 shines, its insights grew.

Genome-scale reconstructions engage,
Microbial roles in health’s wide stage,
Drug efficacy, safety’s quest,
AGORA2 stands its toughest test,
Aiding personalized medical sage.

With colorectal patients in its scope,
AGORA2’s predictions give hope,
Metabolic insights intertwined,
Age, sex, BMI, a truth defined,
A future where microbes help us cope.

FBA-classic

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Metabolic engineering

A nutrition algorithm to optimize feed and medium composition using genome-scale metabolic models.

2023-01-29

PubMed:36724839; DOI:10.1016/j.ymben.2023.01.010

Bronson R Weston¹, Ines Thiele²

Affiliations

School of Medicine, University of Galway, Galway, H91 TK33, Ireland; Ryan Institute, University of Galway, Galway, H91 TK33, Ireland
School of Medicine, University of Galway, Galway, H91 TK33, Ireland; Ryan Institute, University of Galway, Galway, H91 TK33, Ireland; Discipline of Microbiology, University of Galway, Galway, H91 TK33, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland, Cork, T12 K8AF, Ireland.

Sydney Brenner once said that the most important omics is economics. Most flux balance analysis methods optimize with physiology-related parameters in mind (product yield, biomass yield or growth rate), while fewer consider what matters to impact the real world: the multiplication of profit margin (does revenue exceed costs?) and asset turnover (the ratio of revenue to capex).

The algorithm from Thiele’s lab considers price when optimizing for nutrition. For example with salmon farming we want to maximize for revenue from salmon (biomass) and minimize costs (nitrogen waste). Authors discuss limitations, such as dietary restrictions, such as a maximum. It cannot solve a minimax or maximin problem. They also discuss applications.

In silico, a quest takes its place,
To optimize feeds with great grace,
With GEM’s linear flair,
In metabolic affairs,
New insights on nutrition we embrace.

Microbial cell factories

Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii.

2023-01-17

PubMed:36650525; DOI:10.1186/s12934-022-02004-y

Haoyang Yao¹, Sanjeev Dahal¹, Laurence Yang²

Affiliations

Department of Chemical Engineering, Queen’s University, 19 Division St, Kingston, K7L 2N9, Canada
Department of Chemical Engineering, Queen’s University, 19 Division St, Kingston, K7L 2N9, Canada.

Excited to share this work I was a part of. In this study, we extended the Chlamydomonas reinhardtii metabolic model to create a protein-constrained metabolic model.

2023-01-21

Metabolic engineering

CHOGlycoNET: Comprehensive glycosylation reaction network for CHO cells.

2023-01-04

PubMed:36610518; DOI:10.1016/j.ymben.2022.12.009

Pavlos Kotidis¹, Roberto Donini², Johnny Arnsdorf³, Anders Holmgaard Hansen³, Bjørn Gunnar Rude Voldborg³, Austin W T Chiang⁴, Stuart M Haslam², Michael Betenbaugh⁵, Ioscani Jimenez Del Val⁶, Nathan E Lewis⁷, Frederick Krambeck⁸, Cleo Kontoravdi⁹

Affiliations

Sargent Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, UK.
Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
Department of Pediatrics, University of California, San Diego, CA, 92093, USA
Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
School of Chemical & Bioprocess Engineering, University College, Dublin, D04 V1W8, Ireland
Department of Pediatrics, University of California, San Diego, CA, 92093, USA; Department of Bioengineering, University of California, San Diego, CA, 92093, USA
ReacTech Inc., 810 Cameron Street, Alexandria, VA, 22314, USA
Sargent Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, UK.

Immensely proud of alumnus Pavlos Kotidis who received the Chris Hewitt Rising Star award from @ESACTUK this week for his contributions to animal cell technology @Pavlos_kot @ImperialChemEng @GSK

2023-01-14

metabolic-engineering

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bioRxiv

Engineering Escherichia coli to produce aromatic chemicals from ethylene glycol

2023-01-08

DOI:10.1101/2023.01.08.523183

S. Panda, J. F. J. Zhou, M. Feigis, E. Harrison, X. Ma, V. Fung, R. Mahadevan, K. Zhou

Affiliations

National University of Singapore

bioRxiv

The pGinger family of expression plasmids

2023-01-23

DOI:10.1101/2023.01.23.524619

A. N. Pearson, M. Thompson, L. Kirkpatrick, C. Ho, K. M. Vuu, L. Waldburger, J. D. Keasling, P. M. Shih

Affiliations

UC Berkeley

resources

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STAR protocols

ImmCellFie: A user-friendly web-based platform to infer metabolic function from omics data.

2023-01-25

PubMed:36853701; DOI:10.1016/j.xpro.2023.102069

Helen O Masson¹, David Borland², Jason Reilly², Adrian Telleria², Shalki Shrivastava², Matt Watson², Luthfi Bustillos², Zerong Li³, Laura Capps², Benjamin P Kellman⁴, Zachary A King¹, Anne Richelle³, Nathan E Lewis⁵, Kimberly Robasky⁶

Affiliations

Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
Renaissance Computing Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
Department of Pediatrics, UC San Diego, La Jolla, CA 92093, USA
Bioinformatics and Systems Biology Program, UC San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, UC San Diego, La Jolla, CA 92093, USA
Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, UC San Diego, La Jolla, CA 92093, USA.
Renaissance Computing Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel H0069ll, NC 27514, USA; School of Information and Library Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Health and Informatics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

human-health

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Nature microbiology

Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome.

2023-01-12

PubMed:36635575; DOI:10.1038/s41564-022-01293-8

William F Kindschuh¹, Federico Baldini¹, Martin C Liu¹, Jingqiu Liao¹, Yoli Meydan¹, Harry H Lee¹, Almut Heinken², Ines Thiele², Christoph A Thaiss³, Maayan Levy⁴, Tal Korem⁵

Affiliations

Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
School of Medicine, University of Ireland, Galway, Galway, Ireland
Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.

Very happy to finally see this published @NatureMicrobiol with @MaayanLevy_Lab, studying the vaginal metabolome during pregnancy and in preterm birth. Work led by the fantastic @WilliamKindsch1, @FedBld and Martin Liu.

Short thread of key results:

2023-01-12

ACS synthetic biology

A Universal Strategy to Promote Secretion of G+/G- Bacterial Extracellular Vesicles and Its Application in Host Innate Immune Responses.

2023-01-02

PubMed:36592614; DOI:10.1021/acssynbio.2c00583

Yilan Liu¹, Jinjin Chen¹, Kaushik Raj¹, Lauren Baerg², Nayanan Nathan³, Dana J Philpott³, Radhakrishnan Mahadevan¹

Affiliations

Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada

Frontiers in microbiology

Characterization of Klebsiella pneumoniae bacteriophages, KP1 and KP12, with deep learning-based structure prediction.

2023-01-24

PubMed:36762092; DOI:10.3389/fmicb.2022.990910

Youngju Kim¹, Sang-Mok Lee², Linh Khanh Nong², Jaehyung Kim², Seung Bum Kim³, Donghyuk Kim²

Affiliations

Optipharm Inc., Cheongju-si, Chungcheongbuk-do, Republic of Korea
School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
Department of Microbiology and Molecular Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea

Scientific reports

Identifying metabolic shifts in Crohn’s disease using’ omics-driven contextualized computational metabolic network models.

2023-01-05

PubMed:36604447; DOI:10.1038/s41598-022-26816-5

Philip Fernandes¹, Yash Sharma¹, Fatima Zulqarnain¹, Brooklyn McGrew¹, Aman Shrivastava¹, Lubaina Ehsan¹, Dawson Payne¹, Lillian Dillard¹, Deborah Powers¹, Isabelle Aldridge¹, Jason Matthews², Subra Kugathasan², Facundo M Fernández³, David Gaul³, Jason A Papin⁴, Sana Syed⁵

Affiliations

Department of Pediatrics, Division of Gastroenterology, Hepatology & Nutrition, University of Virginia School of Medicine & UVA Child Health Research Center, University of Virginia, MR-4 Bldg, 409 Lane Rd., Charlottesville, VA, 22908, USA
Division of Pediatric Gastroenterology, Emory Children’s Center, Atlanta, GA, USA
Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
Department of Pediatrics, Division of Gastroenterology, Hepatology & Nutrition, University of Virginia School of Medicine & UVA Child Health Research Center, University of Virginia, MR-4 Bldg, 409 Lane Rd., Charlottesville, VA, 22908, USA.
Department of Pediatrics, Division of Gastroenterology, Hepatology & Nutrition, University of Virginia School of Medicine & UVA Child Health Research Center, University of Virginia, MR-4 Bldg, 409 Lane Rd., Charlottesville, VA, 22908, USA.

An in-silico omics-driven approach was used to identify and characterize metabolic shifts Crohn’s disease, work by @PIFF_MD @yashsharma0906 @SyedLabGI_AI and colleagues

2023-01-17

Current research in microbial sciences

Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess.

2023-01-09

PubMed:36685102; DOI:10.1016/j.crmicr.2023.100180

Monika Kumaraswamy¹, Alison Coady², Richard Szubin³, Thomas Cs Martin⁴, Bernhard Palsson¹, Victor Nizet¹, Jonathan M Monk¹

Affiliations

Collaborative to Halt Antibiotic-Resistant Microbes (CHARM), University of California San Diego, La Jolla, CA 92093, USA
Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA

physiology

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NAR genomics and bioinformatics

Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli .

2023-01-20

PubMed:36685725; DOI:10.1093/nargab/lqad006

Joon Young Park¹, Sang-Mok Lee¹, Ali Ebrahim², Zoe K Scott-Nevros¹, Jaehyung Kim¹, Laurence Yang³, Anand Sastry², Sang Woo Seo⁴, Bernhard O Palsson², Donghyuk Kim¹

Affiliations

School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
Department of Chemical Engineering, Queen’s University, Kingston, Canada
School of Chemical and Biological Engineering, and Interdisciplinary Program in Bioengineering, and Institute of Chemical Processes, and Bio-MAX Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea

You probably know much about the regulation of carbon metabolism, but how about nitrogen? The interaction of two key transcription factors (Nac and NtrC) and their regulatory role in E. coli has been revealed. https://bit.ly/3Rfpt7T @NIHFunding @UCSDJacobs

2023-01-30

non-microbe-hosts

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Microbiology spectrum

A Machine Learning Approach Reveals a Microbiota Signature for Infection with Mycobacterium avium subsp. paratuberculosis in Cattle.

2023-01-19

PubMed:36656029; DOI:10.1128/spectrum.03134-22

Sang-Mok Lee¹, Hong-Tae Park², Seojoung Park¹, Jun Ho Lee², Danil Kim³, Han Sang Yoo², Donghyuk Kim¹

Affiliations

School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
Department of Farm Animal Medicine, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea

BØPosphere – January 2023

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