Absolute abundance unveilsBasidiobolusas a cross-domain bridge indirectly bolstering gut microbiome homeostasis DOI Creative Commons
Mitra Ghotbi, Jason Stajich, Jason Dallas

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 28, 2024

Abstract The host microbiome is integral to metabolism, immune function, and resilience against pathogens. However, reliance on relative abundance (RA) estimate host-associated microbiomes introduces compositional biases, while limited tools for absolute (AA) quantification hinder broader applications. To address these challenges, we developed DspikeIn ( https://github.com/mghotbi/DspikeIn ), an R package paired with a versatile wet-lab methodology AA quantification. Using RA compare core distributions across herpetofauna orders their natural histories revealed starkly distinct results, driven by aggregate effects, including inherited biases in additional multifactorial influences. Focusing two closely related Desmognathus species demonstrated that enhanced resolution differential analyses minimized false discovery rates (FDR) when identifying enriched taxa gut microbiomes. Keystone identified through network associations also differed between data. For example, Lactococcus Cetobacterium were members Anura Caudata, Basidiobolus Mortierella Chelonia Squamata, facilitating adaptation diverse environments, insights undetectable AA-based analysis further removing the subnetwork increased negative interactions, highlighting its role promoting homeostasis cross-domain connectivity. Despite low redundancy, node exhibited high betweenness, efficiency, degree, serving as critical bridge linking disconnected nodes or modules indirectly supporting stability, consistent Burt’s structural hole theory. represents transformative tool research, enabling transition from delivering more accurate, consistent, comparable results studies. Graphical abstract cheatsheet

Language: Английский

Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications DOI Creative Commons
Rine Christopher Reuben, Cármen Torres

World Journal of Microbiology and Biotechnology, Journal Year: 2025, Volume and Issue: 41(2)

Published: Jan. 18, 2025

Mammalian milk contains a variety of complex bioactive and nutritional components microorganisms. These microorganisms have diverse compositions functional roles that impact host health disease pathophysiology, especially mastitis. The advent use high throughput omics technologies, including metagenomics, metatranscriptomics, metaproteomics, metametabolomics, as well culturomics in microbiome studies suggest strong relationships between phenotype signatures While single undoubtedly contributed to our current understanding mastitis, they often provide limited information, targeting only biological viewpoint which is insufficient system-wide information necessary for elucidating the footprints molecular mechanisms driving mastitis dysbiosis. Therefore, integrating multi-omics approach research could generate new knowledge, improve structural ecosystem, insights sustainable control management.

Language: Английский

Citations

1
Modulation of the Neuro–Cancer Connection by Metabolites of Gut Microbiota DOI Creative Commons
Alice Njolke Mafe, Dietrich Büsselberg

Biomolecules, Journal Year: 2025, Volume and Issue: 15(2), P. 270 - 270

Published: Feb. 12, 2025

The gut-brain-cancer axis represents a novel and intricate connection between the gut microbiota, neurobiology, cancer progression. Recent advances have accentuated significant role of microbiota metabolites in modulating systemic processes that influence both brain health tumorigenesis. This paper explores emerging concept metabolite-mediated modulation within connection, focusing on key such as short-chain fatty acids (SCFAs), tryptophan derivatives, secondary bile acids, lipopolysaccharides (LPS). While microbiota's impact immune regulation, neuroinflammation, tumor development is well established, gaps remain grasping how specific contribute to neuro-cancer interactions. We discuss with potential implications for neurobiology cancer, indoles polyamines, which yet be extensively studied. Furthermore, we review preclinical clinical evidence linking dysbiosis, altered metabolite profiles, tumors, showcasing limitations research gaps, particularly human longitudinal studies. Case studies investigating microbiota-based interventions, including dietary changes, fecal transplantation, probiotics, demonstrate promise but also indicate hurdles translating these findings therapies. concludes call standardized multi-omics approaches bi-directional frameworks integrating microbiome, neuroscience, oncology develop personalized therapeutic strategies patients.

Language: Английский

Citations

1
mimicINT: A workflow for microbe-host protein interaction inference DOI Creative Commons
Sébastien A. Choteau,

Kevin Maldonado,

Aurélie Bergon

et al.

F1000Research, Journal Year: 2025, Volume and Issue: 14, P. 128 - 128

Published: Jan. 27, 2025

Background The increasing incidence of emerging infectious diseases is posing serious global threats. Therefore, there a clear need for developing computational methods that can assist and speed up experimental research to better characterize the molecular mechanisms microbial infections. Methods In this context, we developed mimicINT, an open-source workflow large-scale protein-protein interaction inference between microbe human by detecting putative mimicry elements mediating with host proteins: short linear motifs (SLiMs) host-like globular domains. mimicINT exploits these infer proteins using known templates domain-domain SLiM-domain templates. also provides (i) robust Monte-Carlo simulations assess statistical significance SLiM detection which suffers from false positives, (ii) specificity filter account differences motif-binding domains same family. We have made available via web server. Results two use cases, identify potential interfaces in experimentally detected pathogenic Escherichia coli type-3 secreted effectors biologically relevant interactions Marburg virus proteins. Conclusions be instrumental understand details microbe-host interactions.

Language: Английский

Citations

0
Probiotics and Synbiotics: Applications, Benefits, and Mechanisms for the Improvement of Human and Ecological Health DOI Creative Commons

Ankita Bhatia,

Deeksha Sharma,

Jyoti Mehta

et al.

Journal of Multidisciplinary Healthcare, Journal Year: 2025, Volume and Issue: Volume 18, P. 1493 - 1510

Published: March 1, 2025

Abstract: This review explores the multifaceted roles and applications of probiotics, emphasizing their significance in maintaining enhancing host health through microbial interactions. It includes concept holobionts symbiotic relationships between hosts microbiomes, illustrating how various microbiota can enhance immunity, support growth, prevent diseases. delves into customization probiotics using molecular genomic techniques, focusing Enterococcus, Bifidobacterium , Lactobacillus species. Furthermore, it discusses effects symbiotics which aids survivability beneficial probiotics. The role microbes gut is emphasized, noting its impact on preventing diseases a stable community. potential therapeutic value ability to treat gastrointestinal diseases, as well strengthen immune system reduce number free radicals that are present body. Additionally, secondary metabolites produced by bacteria gut, such bacteriocins exopolysaccharides, effect human, particularly tract. concludes addressing use traditional medicine novel applications, including treatment endangered wildlife species human ailments. Keywords: health, microbiota, metabolites, synergistic

Language: Английский

Citations

0
mimicINT: A workflow for microbe-host protein interaction inference DOI Creative Commons
Sébastien A. Choteau,

Kevin Maldonado,

Aurélie Bergon

et al.

F1000Research, Journal Year: 2025, Volume and Issue: 14, P. 128 - 128

Published: March 28, 2025

Background The increasing incidence of emerging infectious diseases is posing serious global threats. Therefore, there a clear need for developing computational methods that can assist and speed up experimental research to better characterize the molecular mechanisms microbial infections. Methods In this context, we developed mimicINT, an open-source workflow large-scale protein-protein interaction inference between microbe human by detecting putative mimicry elements mediating with host proteins: short linear motifs (SLiMs) host-like globular domains. mimicINT exploits these infer proteins using known templates domain-domain SLiM-domain templates. also provides (i) robust Monte-Carlo simulations assess statistical significance SLiM detection which suffers from false positives, (ii) specificity filter account differences motif-binding domains same family. We have made available via web server. Results two use cases, identify potential interfaces in experimentally detected pathogenic Escherichia coli type-3 secreted effectors biologically relevant interactions Marburg virus proteins. Conclusions be instrumental understand details microbe-host interactions.

Language: Английский

Citations

0
The Role of the Microbiome and of Radiotherapy-Derived Metabolites in Breast Cancer DOI Open Access
Lourdes Herrera‐Quintana, Héctor Vázquez‐Lorente, Rafael Cardoso Maciel Costa Silva

et al.

Cancers, Journal Year: 2024, Volume and Issue: 16(21), P. 3671 - 3671

Published: Oct. 30, 2024

The gut microbiome has emerged as a crucial player in modulating cancer therapies, including radiotherapy. In the case of breast cancer, interplay between and radiotherapy-derived metabolites may enhance therapeutic outcomes minimize adverse effects. this review, we explore bidirectional relationship cancer. We explain how composition influences progression treatment response, its treatments influence composition. A dual role for is explored article, highlighting both their benefits potential hazards. By integrating genomics, metabolomics, bioinformatics tools, present comprehensive overview these interactions. study provides real-world insight through studies clinical trials, while innovations such probiotics, dietary interventions are examined to modulate effectiveness. Moreover, ethical considerations patient perspectives discussed, ensuring understanding subject. Towards revolutionizing strategies improving outcomes, review concludes with future research directions. It also envisions metabolite into personalized therapy.

Language: Английский

Citations

3
Microbiome and Mucosal Immunity in the Intestinal Tract DOI Open Access

Hannes Ahrend,

Anja Buchholtz,

Matthias B. Stope

et al.

In Vivo, Journal Year: 2024, Volume and Issue: 39(1), P. 17 - 24

Published: Dec. 31, 2024

The human bowel is exposed to numerous biotic and abiotic external noxious agents. Accordingly, the digestive tract frequently involved in malfunctions within organism. Together with commensal intestinal flora, it regulates immunological balance between inflammatory defense processes immune tolerance. Pathological changes this system often cause chronic diseases including Crohn's disease ulcerative colitis. This review article highlights complex interaction microorganisms, microbiome, epithelium-localized local system. main functions of microbiome include (i) protection against pathogenic microbial colonization, (ii) maintenance barrier function epithelium, (iii) degradation absorption nutrients (iv) active regulation immunity. consists primarily macrophages, antigen-presenting cells, natural killer cells. These cells regulate are turn regulated by signaling factors epithelial microbiome. Deregulated responses play an important role can lead both reduced activity pathologically increased harmful microorganisms. aspects have become focus attention recent years. It therefore consider immunological-microbial context diagnosis treatment diseases. A promising holistic approach would most comprehensive possible status patient, at time diagnostics during therapy.

Language: Английский

Citations

1
Absolute abundance unveilsBasidiobolusas a cross-domain bridge indirectly bolstering gut microbiome homeostasis DOI Creative Commons
Mitra Ghotbi, Jason Stajich, Jason Dallas

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 28, 2024

Abstract The host microbiome is integral to metabolism, immune function, and resilience against pathogens. However, reliance on relative abundance (RA) estimate host-associated microbiomes introduces compositional biases, while limited tools for absolute (AA) quantification hinder broader applications. To address these challenges, we developed DspikeIn ( https://github.com/mghotbi/DspikeIn ), an R package paired with a versatile wet-lab methodology AA quantification. Using RA compare core distributions across herpetofauna orders their natural histories revealed starkly distinct results, driven by aggregate effects, including inherited biases in additional multifactorial influences. Focusing two closely related Desmognathus species demonstrated that enhanced resolution differential analyses minimized false discovery rates (FDR) when identifying enriched taxa gut microbiomes. Keystone identified through network associations also differed between data. For example, Lactococcus Cetobacterium were members Anura Caudata, Basidiobolus Mortierella Chelonia Squamata, facilitating adaptation diverse environments, insights undetectable AA-based analysis further removing the subnetwork increased negative interactions, highlighting its role promoting homeostasis cross-domain connectivity. Despite low redundancy, node exhibited high betweenness, efficiency, degree, serving as critical bridge linking disconnected nodes or modules indirectly supporting stability, consistent Burt’s structural hole theory. represents transformative tool research, enabling transition from delivering more accurate, consistent, comparable results studies. Graphical abstract cheatsheet

Language: Английский

Citations

1