Translational Microbiome Research and Pandemic Preparedness – Lars Engstrand group

Microbiome Exploration and Development for Intervention (MEDI) and National Pandemic Centre (NPC) are research under the Engstrand group, with a focus on translational microbiome research and pandemic preparedness. MEDI studies the impact of the microbiome on human health and disease, while NPC conducted large-scale sequencing during the pandemic and currently collaborates on pandemic preparedness related R&D projects. Research in Amir Saei Lab and Juan Du Lab also belongs to Engstrand group.

Part of the:
Lars Engstrand

Lars Engstrand group

In the Engstrand group, we have established a highly effective translational scientific environment, with a broad interdisciplinary approach to the interface between epidemiology and the microbiological, immunological and genetic aspects of chronic diseases. Our goal is to clarify the pathogenic mechanisms within the fields of gastroenterology, women’s health and cancer, define what is a normal and healthy microbiome, and to improve the prospects for primary prevention.

Lars Engstrand is heading the division, and Microbiome Exploration, Development for Intervention, MEDI, consists of:
Culturomics - Valerie Valeriano
Bioinformatics – Fredrik Boulund
Labcore – Maike Seifert
Project Management and Support – Marica Ekström
Womans Health – Ina Schuppe Koistinen. 

The division also includes National Pandemic center NPC – Jessica Alm,  as well as the labs of Amir Saei and Juan Du.

Publications

Selected publications

All publications from group members

Staff and contact

Group leader

All members of the group

Engstrand lab MEDI

Microbiome Exploration and Development for Intervention MEDI

MEDI builds on a deep understanding of translational microbiome research and has established a broad base of technical, biological, clinical, and epidemiological platforms to study complex microbial communities in well-defined human materials.
 

Access to Sweden´s population registers combined with biological material obtained in large clinical prospective studies provide the centre with many opportunities for drug discovery, disease intervention and prevention. An infrastructure has been built for DNA/RNA extraction and sequencing as well as for microbial cultures of human samples.
 

In March 2020, the National Pandemic Centre (NPC) was started as a Covid-19 diagnostic laboratory as a separate unit to offer large-scale analysis of SARS-CoV-2. Since 2021, NPC has grown and developed to continuously contribute to better preparedness and national preparation for unforeseen events with large-scale impacts on society.  NPC currently conducts research projects related to diagnostics and large-scale analysis platforms, often in collaboration with the majority of national and international partners. Moreover, NPC has a national collaboration with Biobank Sweden for the storage of 1.5 million Covid-19 samples.
 

Today, MEDI and NPC are two organisations within the Engstrand research group where resources and expertise from both centres are partially shared.

National Pandemic Centre (NPC)

Ny rutin ger forskare tillgång till 1,5 miljoner covid-19-prover som förvaras på KI
Photo: evelina björninen

Ny rutin ger forskare tillgång till 1,5 miljoner covid-19-prover som förvaras på KI

Biobank Sverige har tillsammans med regionerna och Nationellt Pandemicenter (NPC) vid KI tagit fram en ny process som ger forskare tillgång till 1,5 miljoner covid-19-prover. Proverna förvaras vid NPC på KI och ansökan om att ta del av proverna kräver etiskt godkännande.

Sveriges Radio: "Postcovid – var står vi nu?", November 29 2022
Picture from Sveriges Radio Studio Photo: Jessica Alm

Sveriges Radio: "Postcovid – var står vi nu?", November 29 2022

I dag möts man sällan av rubriker om överbelamrade IVA-avdelningar, presskonferenser om restriktioner eller prognoser för när pandemin kommer vara över. Annat var det för bara ett år sedan, nu är det som om pandemin är bortblåst för de allra flesta av oss. Men så finns det de som blev kvar, de som drabbades av postcovid och fortfarande lider i sviterna av covid-19-viruset. Hur är läget för patienterna, forskningen och viruset nu?

Read more NPC News

Juan Du Lab

Juan Du Lab work in the field of translational microbiome research, with a special focus on virus-bacteria and host-microbe interactions, aiming to create opportunities for the development of novel therapies. Using an in vitro healthy gut microbiota system, we have demonstrated the protective role of the gut microbiota against the growth of antibiotic-resistant pathogens. We have also examined the prevalence of different HPV types and the vaginal microbiome, and explored the microbiome's role in potential cancer progression.

Juan Du Lab group picture
Juan Du Lab. Photo: Laura Poole

Research description   

Project 1: Cohort study: Swedish Cancer Microbiome project (SCANMi)

The SCANMi project comprises cohorts from head and neck cancer (HNC), cervical cancer (CC), ovarian cancer (OC), and breast cancer (BC), which are the most common cancer types worldwide. The hypothesis is that the microbiome of the gut, oral, vagina, and tumor will be altered according to differences in immune system, cancer stage, and treatments. Certain commensal bacterial species are expected to be more abundant and relate to a stronger immune response, less inflammation, and better clinical outcomes. It paves the way for more personalized and precise cancer treatments that take into account individual microbiome compositions.

Project 2: Harnessing the power of the vaginal microbiome to combat Human Papillomavirus (HPV) infections and related diseases

Vaginal microbes and HPV share the same biological niche. We and others have previously found that bacterial vaginosis is associated with a higher risk of HPV infection. It is also essential to identify commensal bacteria/probiotics e.g. /Lactobacillus, / that have the potential to combat HPV infection and related diseases. We employ state-of-the-art laboratory analyses to gain mechanistic insights into the interplay between vaginal microbes and HPV.

Additionally, we are investigating the carcinogenic mechanisms of microbes that are related to cancer. Furthermore, we possess a large clinical bacterial biobank that enables us to compare and distinguish the best candidates for potential anti-HPV and anti-cancer treatment.

Project 3: Using commensal bacteria and their metabolites to combat antibiotic resistant pathogens

Antimicrobial-resistant bacterial infections have become a global burden, and currently, new antibiotic discovery streams are extremely limited. My group studies the interaction between pathogens and commensal bacteria to determine the crucial role played by commensal bacteria from our gut microbiota and their derived metabolites in pathogen clearance. This proposal will generate valuable data on microbiome-pathogen interactions, both in vitro and in vivo. My long-term goal is to establish a platform for systematic screening of the gut microbiota, which can provide significant value for future treatments of microbiota-related diseases.

Project 4: Gut/Vagina-microbiota 3D model for host-microbiota interaction

We aim to establish an in vitro 3D co-culture platform using a hydrogel system that mimics the morphology of the human small intestine and vagina. This platform will serve as a foundation for co-culturing human small intestine cell lines or vaginal cell lines with human microbiota, enabling us to evaluate the interactions between the host and microbiota. Additionally, we will test our hypotheses using ex vivo explants of cervix tissues.

 

Lab members

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Juan Du

Associate Professor
+46852482539
Department of Microbiology, Tumor and Cell Biology
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Fabricio Romero Garcia

PhD candidate
Department of Microbiology, Tumor and Cell Biology

Yichan Zhang

PostDoc
Department of Microbiology, Tumor and Cell Biology

Yilin Ren

Affiliated to Research
Department of Microbiology, Tumor and Cell Biology

Paarkavi Udayakumar

Affiliated to Research
Department of Microbiology, Tumor and Cell Biology

Daniel Hunde

Affiliated
Department of Microbiology, Tumor and Cell Biology;Department of Women's and Children's Health
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Åsa Sjöling

Professor
Department of Microbiology, Tumor and Cell Biology
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Jonatan Martin Rodriguez

Senior Research Specialist
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Enrique Joffré

Affiliated to Research

Elisabeth Norin

Affiliated to Research
Department of Microbiology, Tumor and Cell Biology

Amir Saei Lab

Photo: N/A

Dr. Amir Saei’s team integrates chemical proteomics, metabolomics, and computational strategies to uncover the intricate interplay between metabolites, proteins, diet, and gut microbiota in different metabolic disease states. By developing and leveraging innovative tools—including the Proteome Integral Solubility Alteration (PISA) assay and the multifaceted PISA-REX platform—we provide unprecedented insights into protein expression, stability, and redox regulation, which will revolutionize the understanding of metabolite interactome, key biological processes, and disease mechanisms.

Metabolite-protein interactions in disease

Understanding the molecular basis of metabolic diseases has become critical for the development of next-generation therapeutic strategies. Combining advanced proteomics with systems biology and classical biochemical approaches, we seek to identify and validate therapeutic targets and biomarkers in metabolic and neoplastic diseases. In our long view of our studies, these findings are meant to be translational in the area of precision therapies and diagnostics, enhancing patient outcomes and quality of life. 

Next generation microbiome-mimetic therapeutics

Our team studies the complex interplay between host cells, microbiome, and microbial metabolites in the gut using data-driven approaches including machine learning. We envision the development of novel modalities including small molecule drugs targeting host proteins as well as antibiotics and precision probiotics targeting pathogens. 

Saei Lab Research.
Photo: Amir Saei

Development of novel proteomics tools

The propelling engine for our studies is chemical proteomics that can be used for studying the interaction of molecular entities with proteins. We have developed multiple techniques and methodologies including Proteome Integral Solubility Alteration (PISA) assay and its automated version OPTI-PISA, PISA-REX, ProTargetMiner, SIESTA, GAPPIS and AFDIP. These tools can be employed for identification of targets for drugs, antibiotics, and metabolites, for discovery of enzyme substrates and for pinpointing mechanistic proteins involved in disease pathobiology. Developments in meta-proteomics strategies will also be one of the key areas of focus. 

Overcoming antibiotic resistance in ESKAPE pathogens

We have established a consortium spanning several research labs and aim to develop an AI-based bio-chemo-informatics pipeline on multidimensional proteome signatures for overcoming antibiotic resistance in ESKAPE pathogens. This will lead to the discovery of novel combination treatments and antibiotics.

Diagnostics and biomarker discovery through deep plasma proteome profiling

Leveraging the specific interaction of phosphatidylcholine with high abundance plasma proteins such as albumin, we fish the proteins using nanoparticles for deep plasma proteome profiling. This scalable technology enables the quantification of thousands of plasma proteins in large cohorts. 

Lab members

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Amir Ata Saei

Assistant Professor
Department of Microbiology, Tumor and Cell Biology
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Aleksandra Wielento

Postdoctoral Studies
Department of Microbiology, Tumor and Cell Biology

Hanna Hjärpsgård

Phd Student
Department of Microbiology, Tumor and Cell Biology
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Xueyao Wang

Phd Student
Department of Women's and Children's Health;Department of Microbiology, Tumor and Cell Biology

Marcel Esen

Other
Department of Microbiology, Tumor and Cell Biology

Dimitrios Karadedos

Other
Department of Microbiology, Tumor and Cell Biology

Affiliated and Collaborating Research Groups

Collaborations

National collaborators

International collaborators

Affiliated Researchers

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Hanna Danielsson

Phd Student
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Justine Debelius

Affiliated to Research
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Daniel Globisch

Affiliated to Research
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Luisa Warchavchik Hugerth

Affiliated to Research
Keywords:
Cell and Molecular Biology Medical Biotechnology (Focus on Cell Biology (incl. Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Microbiology in the Medical Area
Content reviewer:
Lars Engstrand
Marica Ekström
29-04-2025