Review
Biochemical Research Methods
Matteo Comin, Barbara Di Camillo, Cinzia Pizzi, Fabio Vandin
Summary: The study of microbial communities relies on comparing metagenomic next-generation sequencing data sets, facing challenges such as species identification and quantification, computation of distances between samples, and identification of features associated with a phenotype. Solutions involve reference-based methods using a database of reference genomes and reference-free methods working directly on sequencing reads.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Microbiology
Stefan Panaiotov, Yordan Hodzhev, Borislava Tsafarova, Vladimir Tolchkov, Reni Kalfin
Summary: This study quantified the culturable part of blood microbiota in healthy individuals using a specific culturing method and medium. The results showed differences in microbial composition between cultured and non-cultured samples, providing insights into the blood microbiota. Further optimization and testing of culturing conditions and media are suggested for better characterization of blood microbiota in both healthy and diseased individuals.
Article
Multidisciplinary Sciences
Rachel Gilroy, Joy Leng, Anuradha Ravi, Evelien M. Adriaenssens, Aharon Oren, Dave Baker, Roberto M. La Ragione, Christopher Proudman, Mark J. Pallen
Summary: By using metagenomic sequencing on thoroughbred equine faecal samples, this study provides new insights into the bacterial, archaeal and bacteriophage components of the horse gut microbiome. The resulting datasets serve as an important resource for future high-resolution taxonomic and functional studies on the equine gut microbiome.
Article
Agriculture, Dairy & Animal Science
Mariya Gryaznova, Yuliya Smirnova, Inna Burakova, Polina Morozova, Ekaterina Nesterova, Mariya Gladkikh, Evgeny Mikhaylov, Mikhail Syromyatnikov
Summary: This study aimed to investigate the composition of the microbiome in newborn piglets with diarrhea to identify relevant markers of the disease. The results showed no bacterial and eukaryotic aberrations in the fecal microbiome of diarrheal piglets but higher levels of bacterial diversity, which may be associated with dysbacteriosis and inflammation. Additionally, an increase in the abundance of Bacteroides B40-8 phage was observed in the observation group, while an increase in the abundance of Escherichia virus BP4 was found in the healthy group.
Review
Biochemistry & Molecular Biology
Konstantina Athanasopoulou, Panagiotis G. G. Adamopoulos, Andreas Scorilas
Summary: Over 10(14) symbiotic microorganisms in a healthy human body are responsible for important synthesis and support of the immune system. However, microbial deregulation can lead to various diseases. The human gastrointestinal tract is a favorable environment for diverse microbes. The gut microbiome, the largest microbiome community in the human body, has been extensively studied for its medical significance. Advances in sequencing techniques have enabled the detection of microbiomes and opened new avenues in studying human microbiota. The present review emphasizes the complexity of the gastrointestinal tract microbiome and its implications in cellular homeostasis and human diseases.
Review
Microbiology
Sven Kleine Bardenhorst, Tom Berger, Frank Klawonn, Marius Vital, Andre Karch, Nicole Ruebsamen
Summary: Reproducibility in microbiome studies is hindered by a lack of consensus on data analysis strategies. The complex nature of microbiome data, combined with increasingly sophisticated research questions, requires more advanced analytical methods. Current analysis strategies in microbiome studies show significant heterogeneity, particularly in differential abundance testing, indicating a need for better guidance in analyzing increasingly complex research questions.
Article
Health Care Sciences & Services
Souad Kartti, Houda Bendani, Nasma Boumajdi, El Mehdi Bouricha, Oumaima Zarrik, Hajar EL Agouri, Mohamed Fokar, Youssef Aghlallou, Rachid EL Jaoudi, Lahcen Belyamani, Basma Elkhannoussi, Azeddine Ibrahimi
Summary: This study analyzed the differences in bacterial composition between tumor and adjacent tissues in breast cancer patients in Morocco. The results showed that tumor tissues had a higher abundance of Bacilli and Actinobacteria, while adjacent tissues had a higher abundance of Gammaproteobacteria. Additionally, different microbial communities were identified in different breast cancer subtypes. These findings have implications for diagnosis and treatment strategies for breast cancer.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Article
Microbiology
Clarisse Marotz, Kellen J. Cavagnero, Se Jin Song, Daniel McDonald, Stephen Wandro, Greg Humphrey, MacKenzie Bryant, Gail Ackermann, Edgar Diaz, Rob Knight
Summary: This study reanalyzed data from a large sample storage study, confirming that 95% ethanol is an effective, practical, and cost-effective preservative that can preserve samples at room temperature for weeks. It also identified the optimal ratio of 95% ethanol to sample in stool and saliva samples, providing a solution that enables crowdsourcing microbiome studies and lowers the barrier for collecting diverse samples.
Article
Biodiversity Conservation
Y. Zeng, Y. Pu, L. L. Niu, J. B. Deng, D. Zeng, K. R. Amato, Y. Li, Y. Zhou, Y. C. Lin, J. Wang, L. Q. Wu, B. H. Chen, K. C. Pan, B. Jing, X. Q. Ni
Summary: High throughput sequencing of gut microbiota is an important tool for understanding the nutrition and health of the host, especially for wildlife conservation and management. A study on the gastrointestinal tract of golden snub-nosed monkey, green monkey, and ring-tailed lemur revealed differences in microbial composition and function across non-human primate species and gastrointestinal segments. This information can greatly improve our knowledge of host-gut microbe interactions and contribute to conservation interventions and animal care protocols in the wild and captivity.
GLOBAL ECOLOGY AND CONSERVATION
(2022)
Article
Microbiology
Ellen E. Higginson, M. Abu Sayeed, Joana Pereira Dias, Vignesh Shetty, Mamatha Ballal, Sunil Kumar Srivastava, Ian Willis, Firdausi Qadri, Gordon Dougan, Ankur Mutreja
Summary: Enterotoxigenic Escherichia coli (ETEC) is a significant cause of diarrhea in children in low- and middle-income countries. However, these bacteria are often identified in both patients and healthy controls. The gut microbiome may play a role in the resistance or progression to ETEC infection. In this study, the researchers analyzed the gut microbiomes of individuals in Bangladesh infected with ETEC, both symptomatically and asymptomatically. Symptomatic patients had higher bacterial burden, were more likely to be coinfected with other pathogenic bacteria, and had a higher prevalence of antimicrobial resistance genes. The composition of the gut microbiome was different between symptomatic and asymptomatic individuals, providing insight into the impact of the gut microbiome in intestinal infections.
Article
Microbiology
Florencia Velez-Cortes, Harris Wang
Summary: Bacterially secreted proteins are crucial for the functioning of bacterial cells and communities. In this study, a computational pipeline was used to predict and analyze the bacterial metasecretome of the human gut, revealing the presence of diverse families of secreted carbohydrate-active enzymes and their distribution across taxonomic groups. By mapping secreted proteins to metagenomic data from endoscopic sampling of the human gastrointestinal tract, specific regions were identified where resident microbes secrete glycosidases. The comprehensive analysis of the metasecretome provides valuable insights for microbiome research and understanding the impact of gut bacteria on human health.
Article
Parasitology
Xue-Ling Zhang, Yuan-Ping Deng, Tian Yang, Le-Yan Li, Tian-Yin Cheng, Guo-Hua Liu, De-Yong Duan
Summary: This study characterized the midgut microbiome of Rhipicephalus microplus ticks from China using metagenomic methods. The results showed that the midgut microbiome consists not only of bacteria but also eukaryotes and viruses. The gene functions of the midgut microflora were found to be involved in various metabolic pathways and infectious diseases.
PARASITES & VECTORS
(2022)
Article
Biochemistry & Molecular Biology
Andria Constantinou, Katarzyna Polak-Witka, Marios Tomazou, Anastasis Oulas, Varvara Kanti, Rolf Schwarzer, Johannes Helmuth, Anke Edelmann, Ulrike Blume-Peytavi, George M. Spyrou, Annika Vogt
Summary: This study investigated the bacterial composition of scalp skin and hair follicles in patients with FFA, LPP, AAc, and healthy individuals, finding dysbiosis in the bacterial communities of FFA and LPP patients and observed molecular signals associated with increased expression in lesional sites. This suggests the need for further research on the role of exogenous factors and molecular interactions in disease onset and propagation.
Review
Microbiology
Imane Allali, Regina E. Abotsi, Lemese Ah. Tow, Lehana Thabane, Heather J. Zar, Nicola M. Mulder, Mark P. Nicol
Summary: There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. Local leadership, capacity building, intra-continental collaboration, and national government investment are needed in microbiome research within Africa.
Article
Biochemistry & Molecular Biology
Concepcion Sanchez-Cid, Romie Tignat-Perrier, Laure Franqueville, Laurence Delauriere, Trista Schagat, Timothy M. Vogel
Summary: Next-generation sequencing techniques have increased our understanding of the soil microbiome, but there are biases in each step of soil metagenomics that affect the accurate definition of the microbiome and its function. This study compared the effects of DNA extraction and sequencing depth on bacterial richness discovery in soil samples. The results showed that sequencing depth had a greater influence on bacterial richness discovery at both the taxonomical and functional levels. Optimizing the soil metagenomics workflow is necessary to improve the accuracy of metagenomic comparisons and soil microbiome profiles.
Article
Infectious Diseases
Heimo Lagler, Christine Bangert, Tamara Quint, Zoe Osterreicher, Alina Nussbaumer-Proll, Sabine Eberl, Maria Weber, Matthias Karer, Morten O. A. Sommer, Markus Zeitlinger
Summary: This study compared three commonly used methods for sampling Staphylococcus aureus on atopic dermatitis skin lesions and investigated the effectiveness of skin disinfection. The results showed significant differences in quantifying S. aureus load between different sampling methods, highlighting the importance of method selection. Skin disinfection led to a reduction in S. aureus load, but complete eradication was not achieved. This data suggests the need for further clinical studies on the effectiveness of topical anti-staphylococcal antibiotics and consideration of alternative disinfection regimes in atopic dermatitis patients.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2022)
Article
Chemistry, Medicinal
Sang-Woo Lee, Kim Tai Tran, Ruben Vazquez-Uribe, Charlotte Held Gotfredsen, Mads Hartvig Clausen, Blanca Lopez Mendez, Guillermo Montoya, Anders Bach, Morten Otto Alexander Sommer
Summary: CRISPR/Cas9 activity can be controlled by a small-molecule ligand identified in this study, which inhibits Cas9:gRNA complex formation by directly binding to apo-Cas9. These molecules may serve as Cas9 modulators in various applications.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Review
Pharmacology & Pharmacy
Shivani Singh, Anne Weiss, James Goodman, Marie Fisk, Spoorthy Kulkarni, Ing Lu, Joanna Gray, Rona Smith, Morten Sommer, Joseph Cheriyan
Summary: This article reviews the pharmacology and scientific rationale for repurposing niclosamide, an anti-helminth drug, for the treatment of COVID-19. It highlights the drug's potent antiviral activity and its pleiotropic effects in preclinical and early clinical studies. The advantages and rationale for nebulized and intranasal formulations of niclosamide are also discussed, along with an overview of ongoing clinical trials.
BRITISH JOURNAL OF PHARMACOLOGY
(2022)
Article
Multidisciplinary Sciences
Karl Alex Hedin, Vanessa Emily Rees, Hongbin Zhang, Vibeke Kruse, Ruben Vazquez-Uribe, Morten Otto Alexander Sommer
Summary: This study established a robust mouse model for studying the colonisation of Saccharomyces boulardii, finding that antibiotic treatment significantly increased the colonisation levels and duration of S. boulardii in mice. The findings suggest that the antibiotic cocktail used in the study is an advantageous tool for studying S. boulardii-based probiotics and advanced microbiome therapeutics.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Sailesh Malla, Eric van der Helm, Behrooz Darbani, Stefan Wieschalka, Jochen Foerster, Irina Borodina, Morten Otto Alexander Sommer
Summary: The lack of an active export system limits the accumulation and purification of intracellular products in industrial bio-based production processes. In this study, a novel L-lysine exporter belonging to the uncharacterized EamA superfamily was identified using metagenomic functional selection. This exporter significantly improved L-lysine tolerance and enhanced the yield and production of L-lysine in an industrial strain. This approach allows for the discovery of novel exporters and can be used to increase the productivity of bioprocesses with toxicity limitations.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Pharmacology & Pharmacy
Hitesh P. Gelli, Ruben Vazquez-Uribe, Morten Otto Alexander Sommer
Summary: Using cell-penetrating peptides (CPPs) is an effective strategy to improve drug absorption. Among the 9 most promising CPPs studied, 4 of them significantly increased the paracellular permeability of the intestinal barrier without compromising cellular health. Furthermore, these 4 CPPs also affected the growth of the majority of tested commensal strains.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Dermatology
Jonathan I. I. Silverberg, Lars E. E. French, Richard B. B. Warren, Bruce Strober, Kim Kjoller, Morten O. A. Sommer, Philippe Andres, Jakob Felding, Anne Weiss, Deniz Tutkunkardas, Tine Skak-Nielsen, Emma Guttman
Summary: This study examined the PDE4 enzymatic activity and anti-inflammatory effects of orismilast in vitro, ex vivo, and in vivo. The results showed that orismilast selectively and potently inhibited PDE4 and demonstrated broad-spectrum anti-inflammatory activity. These findings support the clinical development of oral orismilast as a novel treatment option for chronic inflammatory skin diseases.
JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY
(2023)
Article
Dermatology
Richard B. B. Warren, Bruce Strober, Jonathan I. I. Silverberg, Emma Guttman, Philippe Andres, Jakob Felding, Deniz Tutkunkardas, Kim Kjoller, Morten O. A. Sommer, Lars E. E. French
Summary: This study aimed to examine the efficacy and safety of orismilast for psoriasis treatment. The phase 2a trial found that orismilast significantly improved the condition of patients with psoriasis. The phase 1 trial tested new formulations to minimize gastrointestinal adverse reactions.
JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Rebecca M. Lennen, Hyun Gyu Lim, Kristian Jensen, Elsayed T. Mohammed, Patrick V. Phaneuf, Myung Hyun Noh, Sailesh Malla, Rosa A. Borner, Ksenia Chekina, Emre Ozdemir, Ida Bonde, Anna Koza, Jerome Maury, Lasse E. Pedersen, Lars Y. Schoning, Nikolaus Sonnenschein, Bernhard O. Palsson, Alex T. Nielsen, Morten O. A. Sommer, Markus J. Herrgard, Adam M. Feist
Summary: This study used an automated platform to evolve Escherichia coli to grow optimally in the presence of 11 industrial chemicals and uncovered the tolerance mechanisms. The results showed that cells are tolerized through frequent mutation of membrane transporters, cell wall-associated proteins, transcription and translation machineries, and stress signaling proteins. Osmotic stress plays a significant role in tolerance, and pre-tolerized starting isolates can greatly enhance the subsequent production of chemicals.
METABOLIC ENGINEERING
(2023)
Article
Immunology
Anne Weiss, Rodinde Hendrickx, Eva Stensgaard, Mads Jellingso, Morten O. A. Sommer
Summary: Immunocompromised patients, including dialysis and kidney transplant patients, have faced an increased risk of mortality due to COVID-19 despite available countermeasures. Additional protection measures are necessary for this vulnerable population.
Article
Biotechnology & Applied Microbiology
Karl Alex Hedin, Vibeke Kruse, Ruben Vazquez-Uribe, Morten Otto Alexander Sommer
Summary: The human gastrointestinal tract plays a crucial role in human health and microorganisms engineered for therapeutic purposes have emerged as a novel approach to managing diseases. To prevent the spread of these microorganisms outside the treated individual, safe and robust biocontainment strategies are necessary.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Akanksha Rajput, Siddharth M. Chauhan, Omkar S. Mohite, Jason C. Hyun, Omid Ardalani, Leonie J. Jahn, Morten O. A. Sommer, Bernhard O. Palsson
Summary: Lactobacillaceae is an important microbial family in the food industry. Through a comprehensive pangenome analysis, we found the characteristics of core, accessory, and rare genomes, as well as a richness of biosynthetic gene clusters.
Article
Multidisciplinary Sciences
Sarunas Tumas, Trine Sundebo Meldgaard, Troels Holger Vaaben, Sara Suarez Hernandez, Annemette Tengstedt Rasmussen, Ruben Vazquez-Uribe, Sine Reker Hadrup, Morten O. A. Sommer
Summary: In this study, we optimized the delivery of biologically active IL-2 using engineered E. coli Nissle 1917. The engineered strain showed high biological activity of microbially produced IL-2 (mi-IL2) in vitro and demonstrated strong immune cell activation in a 3D tumor spheroid model. Furthermore, the engineered strain selectively colonized tumors in a murine CT26 tumor model and resulted in a modest reduction in tumor growth rate and increased levels of IL-2 in the tumor. This study provides a workflow for researchers interested in utilizing E. coli Nissle for microbial therapy against cancer.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Chrysoula Dimopoulou, Mareike Bongers, Mikael Pedersen, Martin Bahl, Morten O. A. Sommer, Martin F. Laursen, Tine R. Licht
Summary: We successfully transferred the ability to produce the health-beneficial microbial metabolite indole lactic acid (ILA) into Escherichia coli, and demonstrated its expression in vitro and in vivo. The expanding knowledge of gut microbiota's metabolic activities and their impact on health has led to growing interest in engineered probiotics. Tryptophan metabolites, especially ILA, are potential therapeutic agents with multiple beneficial effects. Our study engineered an E. coli strain that produces ILA and showed its robust production in a mouse model, offering efficient options for therapeutic interventions against gastrointestinal inflammation.
FEMS MICROBIOLOGY LETTERS
(2023)
Article
Endocrinology & Metabolism
Valeria Iannone, Ambrin Farizah Babu, Johnson Lok, Carlos Gomez-Gallego, Giuseppe D'Auria, Ruben Vazquez-Uribe, Troels Holger Vaaben, Mareike Bongers, Santtu Mikkonen, Maija Vaittinen, Ida Tikkanen, Mikko Kettunen, Anton Klavus, Ratika Sehgal, Dorota Kaminska, Jussi Pihlajamaki, Kati Hanhineva, Hani El-Nezami, Morten Otto Alexander Sommer, Marjukka Kolehmainen
Summary: This study found that Escherichia coli Nissle 1917 expressing aldafermin, combined with dietary changes, can alleviate symptoms of MASLD, including reducing body weight, liver steatosis, plasma aspartate aminotransferase, and plasma cholesterol levels. RNA sequencing and metabolomics analysis revealed the downregulation of amino acid metabolism and related receptor signaling pathways, which may be implicated in the reduction of hepatic steatosis and insulin resistance.
MOLECULAR METABOLISM
(2023)