Article
Immunology
Meghan A. Berryman, Patricia L. Milletich, Joseph R. Petrone, Luiz F. W. Roesch, Jorma Ilonen, Eric W. Triplett, Johnny Ludvigsson
Summary: This study demonstrates the significant influence of autoimmune-associated genetic factors on the colonization of common Bifidobacterium strains in the gut. HLA DR1-DQ5 is proposed as a protective haplotype associated with increased Bifidobacterium abundance. These findings suggest that HLA genetics should be considered when designing probiotics for individuals at high genetic risk for autoimmune diseases.
JOURNAL OF AUTOIMMUNITY
(2022)
Article
Cell Biology
Sanzhima Garmaeva, Anastasia Gulyaeva, Trishla Sinha, Andrey N. Shkoporov, Adam G. Clooney, Stephen R. Stockdale, Johanne E. Spreckels, Thomas D. S. Sutton, Lorraine A. Draper, Bas E. Dutilh, Cisca Wijmenga, Alexander Kurilshikov, Jingyuan Fu, Colin Hill, Alexandra Zhernakova
Summary: The study found that there is a high diversity of gut virome composition in healthy adults, with individual viromes stable at the family level but varying significantly at the genera and species levels. Lower initial diversity of the human gut virome leads to a more pronounced effect of dietary intervention on its composition.
Review
Biotechnology & Applied Microbiology
Jungyeon Kim, Yong-Su Jin, Kyoung Heon Kim
Summary: L-fucose is an important metabolite in human-gut microbiome interactions. It is continuously produced by humans and delivered to the gut, where gut microorganisms metabolize it and produce short-chain fatty acids. Recent studies have shown that the carbon flux in L-fucose metabolism by gut microorganisms is different from other sugar metabolisms due to cofactor imbalance and low energy synthesis efficiency. The large amounts of short-chain fatty acids produced during microbial L-fucose metabolism are used by epithelial cells to recover the energy used up during L-fucose synthesis. This review provides an overview of microbial L-fucose metabolism and discusses the potential use of genetically engineered probiotics for disease treatment and prevention by modulating fucose metabolism.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Review
Food Science & Technology
Prasoon Kumar, Rajeshwari Sinha, Pratyoosh Shukla
Summary: This article discusses the crucial role of AI-assisted synthetic biology in modulating probiotics and improving human gut microbiome health. AI techniques help in understanding the genomic data of the gut microbiome and provide opportunities and challenges for the development of synthetic biology.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Article
Multidisciplinary Sciences
Akshit Goyal, Tong Wang, Veronika Dubinkina, Sergei Maslov
Summary: Combining ecology-based computational methods and optimization techniques, GutCP predicts a large number of experimentally untested cross-feeding interactions in the human gut microbiome. It has the potential to improve microbial community models and predict the metabolic profile of the gut.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Evy Maas, John Penders, Koen Venema
Summary: Most studies on the human gut microbiota focus on bacteria, but recent research indicates that intestinal fungi are also important for maintaining health. This study analyzed the mycobiome of healthy individuals and its interaction with the bacterial component of the microbiome. The results showed a lower diversity of fungi compared to bacteria, with significant inter-individual variation. Positive correlations were observed between certain fungi and bacteria, including those associated with alleviating inflammatory bowel disease. Further research is needed to investigate the importance of these correlations and distinguish between gut colonizers and transient species.
Editorial Material
Microbiology
Bryan B. Hsu
Summary: The gut microbiome is a complex system with bacteria, bacteriophages, and other microbial members playing important roles. Recent studies have shown associations between the composition of resident phage communities and human health and disease, but the mechanisms of these associations remain unclear.
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.
Review
Microbiology
E. Daniel Leon, M. Pilar Francino
Summary: The interaction between the immune system and the gastrointestinal microbiota is crucial for maintaining intestinal homeostasis. Secretory immunoglobulin A (SIgA), the principal antibody produced in the gastrointestinal mucosa, plays an important role in modulating the gut microbiota. SIgA molecules can bind to different antigens on bacterial surfaces and exhibit cross-species reactivity, which helps in regulating and promoting beneficial members of the microbiota.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Immunology
Sonakshi Rastogi, Sneha Mohanty, Sapna Sharma, Prabhanshu Tripathi
Summary: This review summarizes the recent progress in understanding the effects of dietary metabolites, particularly short-chain fatty acids (SCFAs), on the gut-lung axis and its impact on lung health. The role of the gut-lung axis in SARS-CoV-2 mediated inflammation is also highlighted. By analyzing global research progress and knowledge gaps, the study predicts future research directions.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
Lauren E. Fuess, Stijn den Haan, Fei Ling, Jesse N. Weber, Natalie C. Steinel, Daniel Bolnick
Summary: This study explores the correlations between gene expression and microbiome composition in laboratory-raised fish, highlighting the strong positive associations between microbial alpha diversity and host immune gene expression. Additionally, 15 microbial families are found to be highly correlated with host gene expression, particularly with immune processes. These findings support the understanding of intimate links between host immunity and gut microbiome composition in nonmodel vertebrate species.
Article
Gastroenterology & Hepatology
Naoyoshi Nagata, Tadashi Takeuchi, Hiroaki Masuoka, Ryo Aoki, Masahiro Ishikane, Noriko Iwamoto, Masaya Sugiyama, Wataru Suda, Yumiko Nakanishi, Junko Terada-Hirashima, Moto Kimura, Tomohiko Nishijima, Hiroshi Inooka, Tohru Miyoshi-Akiyama, Yasushi Kojima, Chikako Shimokawa, Hajime Hisaeda, Fen Zhang, Yun Kit Yeoh, Siew C. Ng, Naomi Uemura, Takao Itoi, Masashi Mizokami, Takashi Kawai, Haruhito Sugiyama, Norio Ohmagari, Hiroshi Ohno
Summary: This study investigates the interrelationships among gut microbes, metabolites, and cytokines in COVID-19 and its complications, and validates the results with follow-up data. The results show multiple correlations between COVID-19-related microbes, gut metabolites, and inflammatory cytokine dynamics, especially in severe disease and pneumonia. The study also confirms the concordance of altered metabolites in COVID-19 with their corresponding microbial functional genes.
Article
Biochemistry & Molecular Biology
Susan Hromada, Yili Qian, Tyler B. Jacobson, Ryan L. Clark, Lauren Watson, Nasia Safdar, Daniel Amador-Noguez, Ophelia S. Venturelli
Summary: This study explores the principles of gut microbiome colonization resistance to the pathogen Clostridioides difficile, demonstrating a strong negative interaction between C. difficile and other species, inhibition mechanisms such as environment acidification and resource competition were identified. Increasing the initial density of C. difficile can increase its abundance in the community, but the maximum achievable abundance is determined by the community context.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Immunology
Rachel L. G. Maus, Alexey A. Leontovich, Raymond M. Moore, Zachary Fogarty, Ruifeng Guo, Tara M. Davidson, Burak Tekin, Chathu Atherton, Jill M. Schimke, Betty A. Dicke, Benjamin J. Chen, Svetomir N. Markovic
Summary: This study used a spatial characterization method to evaluate tumor-immune interactions and found that the cellular composition of tumor and immune cell subsets in the tumor core was not associated with recurrence, but the spatial patterns were significantly different. It was also found that a cluster enriched with tumor and dendritic cells was associated with no recurrence. Further analysis found an enrichment of CTL-dendritic cell interactions in patients with no recurrence and CTL-macrophage interactions in patients with recurrence.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
Lokanand Koduru, Meiyappan Lakshmanan, Shawn Hoon, Dong-Yup Lee, Yuan Kun Lee, Dave Siak-Wei Ow
Summary: The incidence and prevalence of inflammatory disorders are increasing globally, and gut microbiome-based therapeutics offer potential for ameliorating chronic inflammation. However, these therapeutics are largely experimental and lack a clear mechanistic basis, limiting the development of precision probiotics.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Virology
Francisco Murilo Zerbini, Stuart G. Siddell, Arcady R. Mushegian, Peter J. Walker, Elliot J. Lefkowitz, Evelien M. Adriaenssens, Poliane Alfenas-Zerbini, Bas E. Dutilh, Maria Laura Garcia, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Malgorzata Lobocka, Hanna M. Oksanen, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Nobuhiro Suzuki, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani
Summary: Following the ICTV Ratification Vote in March 2021, a standard two-part binomial nomenclature is now the standard for naming virus species. The adoption of this new nomenclature is still in its early stages, making it timely to clarify the distinction between viruses and virus species and provide guidelines for their correct naming and writing.
ARCHIVES OF VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sean Meaden, Ambarish Biswas, Ksenia Arkhipova, Sergio E. Morales, Bas E. Dutilh, Edze R. Westra, Peter C. Fineran
Summary: This study analyzes metagenomic data from diverse ecosystems and finds that viral abundance and diversity are major ecological factors that drive the selection and maintenance of CRISPR-Cas in microbial ecosystems. The study also suggests that CRISPR-Cas systems offer limited protection when targeting a diverse viral community.
Article
Engineering, Environmental
Ernestina Hauptfeld, Jordi Pelkmans, Terry T. Huisman, Armin Anocic, Basten L. Snoek, F. A. Bastiaan von Meijenfeldt, Jan Gerritse, Johan van Leeuwen, Gert Leurink, Arie van Lit, Ruud van Uffelen, Margot C. Koster, Bas E. Dutilh
Summary: Biodegradation is a sustainable and cost-effective solution for groundwater pollution. In this study, the microbial populations involved in the biodegradation of poly-contaminants in a heavily contaminated groundwater pipeline were investigated. The microbial communities were analyzed using genome-resolved metagenomic analysis, revealing the changing microbial communities in a highly effective groundwater treatment system.
Article
Multidisciplinary Sciences
Patrick A. de Jonge, Koen Wortelboer, Torsten P. M. Scheithauer, Bert-Jan H. van den Born, Aeilko H. Zwinderman, Franklin L. Nobrega, Bas E. Dutilh, Max Nieuwdorp, Hilde Herrema
Summary: The authors characterize gut viromes in individuals with metabolic syndrome and discover a widespread family of gut bacteriophages named Candidatus Heliusviridae. The gut viromes of individuals with metabolic syndrome exhibit decreased richness and diversity and are enriched in phages infecting Streptococcaceae and Bacteroidaceae while depleted in those infecting Bifidobacteriaceae. The identification of the Candidatus Heliusviridae provides a starting point for studying the effects of phages on gut bacteria and their role in metabolic syndrome.
NATURE COMMUNICATIONS
(2022)
Article
Virology
Dann Turner, Andrey N. Shkoporov, Cedric Lood, Andrew D. Millard, Bas E. Dutilh, Poliane Alfenas-Zerbini, Leonardo J. van Zyl, Ramy K. Aziz, Hanna M. Oksanen, Minna M. Poranen, Andrew M. Kropinski, Jakub Barylski, J. Rodney Brister, Nina Chanisvili, Rob A. Edwards, Francois Enault, Annika Gillis, Petar Knezevic, Mart Krupovic, Ipek Kurtboke, Alla Kushkina, Rob Lavigne, Susan Lehman, Malgorzata Lobocka, Cristina Moraru, Andrea Moreno Switt, Vera Morozova, Jesca Nakavuma, Alejandro Reyes Munoz, Janis Rumnieks, B. L. Sarkar, Matthew B. Sullivan, Jumpei Uchiyama, Johannes Wittmann, Tong Yigang, Evelien M. Adriaenssens
Summary: This article summarizes the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses from March 2021 to March 2022. It provides an overview of the new classifications proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. The taxonomy of bacterial viruses underwent significant changes, including the abolition of the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae, as well as the order Caudovirales, and the establishment of a binomial nomenclature system for species. Additionally, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
ARCHIVES OF VIROLOGY
(2023)
Article
Virology
Francisco Murilo Zerbini, Stuart G. Siddell, Elliot J. Lefkowitz, Arcady R. Mushegian, Evelien M. Adriaenssens, Poliane Alfenas-Zerbini, Donald M. Dempsey, Bas E. Dutilh, Maria Laura Garcia, R. Curtis Hendrickson, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Malgorzata Lobocka, Hanna M. Oksanen, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Donald B. Smith, Nobuhiro Suzuki, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani
Summary: This article reports on changes to virus taxonomy and nomenclature approved by the International Committee on Taxonomy of Viruses (ICTV) in April 2023. All ICTV members were invited to vote on 174 taxonomic proposals and a revision of the ICTV Statutes that had been approved by the ICTV Executive Committee in July 2022. Majority approval was obtained for all proposals and the revised ICTV Statutes. A significant change was the renaming of existing species according to the binomial format and the classification of gene transfer agents (GTAs) as viriforms. In total, one class, seven orders, 31 families, 214 genera, and 858 species were created.
ARCHIVES OF VIROLOGY
(2023)
Article
Ecology
Jose L. Lopez, Arista Fourie, Sanne W. M. Poppeliers, Nikolaos Pappas, Juan J. Sanchez-Gil, Ronnie de Jonge, Bas E. Dutilh
Summary: The root microbiome is shaped by plant root activity, which selects specific microbial taxa from the surrounding soil. Understanding the traits that make bacteria successful in the rhizosphere is critical for developing sustainable agriculture solutions.
Article
Gastroenterology & Hepatology
Carlijn E. Bruggeling, Maarten te Groen, Daniel R. Garza, Famke van Heeckeren Tot Overlaer, Joyce P. M. Krekels, Basma-Chick Sulaiman, Davy Karel, Athreyu Rulof, Anne R. Schaaphok, Daniel L. A. H. Hornikx, Iris D. Nagtegaal, Bas E. Dutilh, Frank Hoentjen, Annemarie Boleij
Summary: This prospective cohort study found that colonic bacterial biofilms are common in ulcerative colitis (UC) and may increase the risk of dysplasia through oncogenic traits. Moreover, the study also found that bacterial composition is associated with biofilms and dysplasia risk. The presence of biofilms is not significantly associated with dysplasia in UC, while ClbB is independently associated with dysplasia and FadA and Fusobacteriales are associated with a decreased risk of dysplasia in UC.
JOURNAL OF CROHNS & COLITIS
(2023)
Review
Biotechnology & Applied Microbiology
Stuart G. Siddell, Donald B. Smith, Evelien Adriaenssens, Poliane Alfenas-Zerbini, Bas E. Dutilh, Maria Laura Garcia, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Elliot J. Lefkowitz, Malgorzata Lobocka, Arcady R. Mushegian, Hanna M. Oksanen, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Nobuhiro Suzuki, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani, F. Murilo Zerbini
Summary: The International Committee on Taxonomy of Viruses (ICTV) is responsible for the development and oversight of virus taxonomy. It approves and ratifies taxonomic proposals and maintains a list of approved virus names. The ICTV has a democratic decision-making process with approximately 180 members who vote on proposals. Taxon-specific Study Groups, comprised of over 600 scientists, provide expertise and contribute to taxonomic proposals.
JOURNAL OF GENERAL VIROLOGY
(2023)
Article
Virology
Liliane S. S. Oliveira, Alejandro Reyes, Bas E. E. Dutilh, Arthur Gruber
Summary: The study developed protocols for the rational design of profile HMMs, which can automatically identify informative sequence motifs and construct profile HMMs. These methods were applied to detect and classify different viral groups and related transposable elements.
Article
Biochemistry & Molecular Biology
Simon E. Roux, Antonio Pedro Camargo, Felipe H. Coutinho, Shareef M. Dabdoub, Bas E. Dutilh, Stephen Nayfach, Andrew Tritt
Summary: The extraordinary diversity of viruses infecting bacteria and archaea can be studied through metagenomics. However, metagenome-derived viral sequences lack key information about host association. We introduce iPHoP, a framework that integrates multiple methods to predict host taxonomy for a range of uncultivated viruses, while maintaining a low false discovery rate. Using a large dataset from the IMG/VR database, iPHoP shows promise in providing extensive host prediction for uncultivated viruses.
Article
Ecology
F. A. Bastiaan von Meijenfeldt, Paulien Hogeweg, Bas E. Dutilh
Summary: Defining the niche of a microorganism is challenging because it depends on an objective definition of the environment. In this study, researchers used the community a microorganism resides in as the environment and developed a quantitative measure called social niche breadth. They found that social generalists have a more diverse and open genome compared to social specialists, and observed two distinct evolutionary strategies for specialists in different habitats.
NATURE ECOLOGY & EVOLUTION
(2023)
Correction
Virology
Francisco Murilo Zerbini, Stuart G. Siddell, Elliot J. Lefkowitz, Arcady R. Mushegian, Evelien M. Adriaenssens, Poliane Alfenas-Zerbini, Donald M. Dempsey, Bas E. Dutilh, Maria Laura Garcia, R. Curtis Hendrickson, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Malgorzata Lobocka, Hanna M. Oksanen, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Donald B. Smith, Nobuhiro Suzuki, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani
ARCHIVES OF VIROLOGY
(2023)
Article
Ecology
Daniel R. Garza, F. A. Bastiaan von Meijenfeldt, Bram van Dijk, Annemarie Boleij, Martijn A. Huynen, Bas E. Dutilh
Summary: We introduce a computational framework for analyzing and interpreting pan-reactomes that provides novel insights into the ecological and evolutionary drivers of pan-genome dynamics.
BMC ECOLOGY AND EVOLUTION
(2022)
Meeting Abstract
Gastroenterology & Hepatology
Carlijn Bruggeling, Maarten te Groen, Daniel Garza, Joyce Krekels, Iris D. Nagtegaal, Bas E. Dutilh, Frank Hoentjen, Annemarie Boleij