Microbiology - Journal Articles

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    Microbiota and metabolome dynamics induced by Shiga toxin-producing E. coli in an in vitro model of an infant’s colon
    (Shared Science Publishers OG, 2025-04-14) Izquierdo, Mariana; O’Sullivan, Deborah; Uriot, Ophélie; Brun, Morgane; Durif, Claude; Denis, Sylvain; Gallardo, Pablo; Gahan, Cormac G. M.; Etienne-Mesmin, Lucie; Blanquet-Diot, Stéphanie; Farfan, Mauricio J.; Agencia Nacional de Investigación y Desarrollo; Evaluation-orientation de la Coopération Scientifique; ECOS; Fondo Nacional de Desarrollo Científico y Tecnológico; Horizon 2020; Vicerrectoría de Investigación y Desarrollo; Universidad de Chile
    Shiga toxin-producing Escherichia coli (STEC) is a major food-borne pathogen causing human diseases ranging from diarrhea to life-threatening complications, mainly in young children. Colonization, virulence, and interactions of STEC strains with human gut microbiota are pivotal during infection but remain poorly described, particularly in children, the most affected population. In this work, we evaluated changes in the microbiota and metabolome composition in the in vitro gut model: Toddler ARtificial COLon (T-ARCOL) infected with EHEC O157:H7 strain EDL 933. Stool samples collected from children with STEC-positive diarrhea and stool from the same children after recovery from the diarrheal episode (n=5) were used to inoculate the T-ARCOL model. STEC colonization was progressively reduced throughout fermentation in T-ARCOL with diarrhea or recovery fecal samples. Beta diversity showed that the diarrhea-associated microbiota was significantly distinct from the recovery microbiota and exhibited a lower α-diversity. In contrast to recovery conditions, diarrheal conditions were characterized by an increased abundance of potential pathobionts such as members of the Clostridiaceae family and higher acetate, succinate, and N-acetylneuraminic acid levels. Our results provide new evidence of the impact of EHEC in the microbiota and metabolome dynamics in an in vitro gut model that could be useful in understanding their physiopathology in this at-risk population, considering inter-individual variabilities in gut microbiota.
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    Bacteroides maternus sp. nov., a novel species isolated from human faeces
    (Nature Research, 2025) da Silva Morais, Emilene; Grimaud, Ghjuvan M.; Warda, Alicja; Stephens, Niamh; Ross, R. Paul; Stanton, Catherine; IFF; Science Foundation Ireland
    A novel bacterial strain, MSB163, was isolated from the stool sample of a healthy mother, 4 weeks after giving birth via vaginal delivery. Taxonomic identification tools revealed that MSB163 belongs to the genus Bacteroides, but it is distinct from any currently known species. The closest related species is Bacteroides cellulosilyticus strain BFG- 250, with an average nucleotide identity (fastANI) of 94.51%. The genome length of MSB163 is 6,440,948 bp and the GC content 42.95%. Two plasmids were identified in the whole genome sequence. MSB163 is a Gram-negative, rod-shaped, non-motile anaerobic bacterium. The optimum growth conditions were at 37 °C, pH 7 and 0% (w/v) NaCl. The respiratory quinones were the menaquinones MK- 10 and MK- 11 and C15:0 ANTEISO was the major fatty acid. The predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phospholipid. According to the taxonomic results and physiological analysis, strain MSB163 represents a novel species of the genus Bacteroides, for which we propose the name Bacteroides maternus, since the type strain was isolated from the stool sample of a mother. B. maternus type strain (MSB163) sequencing can be accessed under the biosample ID SAMN3953129 on NCBI. The strain was deposited on BCCM/LMG Bacteria Collection under the accession number LMG 33,374 and Leibniz Institut DSMZ GMBH under the accession number DSM 117,047.
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    Host plasma microenvironment in immunometabolically impaired HIV infection leads to dysregulated monocyte function and synaptic transmission ex vivo
    (John Wiley and Sons Inc, 2025) Mikaeloff, Flora; Gelpi, Marco; Escós, Alejandra; Wang, Tianqi; Gupta, Soham; Olofsson, Anna; Akusjärvi, Sara Svensson; Schuster, Sabrina; Naval, Prajakta; Sood, Vikas; Nikouyan, Negin; Knudsen, Andreas D.; Vestad, Beate; Høgh, Julie; Hov, Johannes R.; Benfield, Thomas; Trøseid, Marius; Pawar, Vinay; Rucevic, Marijana; Benfeitas, Rui; Végvári, Ákos; O'Mahony, Liam; Savai, Rajkumar; Björkström, Niklas K.; Lourda, Magda; de Magalhães, João Pedro; Weiss, Siegfried; Mardinoglu, Adil; Varshney, Mukesh Kumar; Karlsson, Annika C.; Syed, Yasir Ahmed; Nielsen, Susanne D.; Neogi, Ujjwal; Swedish Research Council; Knut and Alice Wallenberg Foundation; Karolinska Instititute; Novo Nordic Foundation; Lundbeck Foundation; Augustinus Foundation; Region Hovedstaden; Rigshospitalet Research Council; Engineering and Physical Sciences Research Council; Hodge Foundation; Medical Research Foundation; Azeez Farooki award
    Risk stratification using multi-omics data deepens understanding of immunometabolism in successfully treated people with HIV (PWH) is inadequately explained. A personalized medicine approach integrating blood cell transcriptomics, plasma proteomics, and metabolomics is employed to identify the mechanisms of immunometabolic complications in prolonged treated PWH from the COCOMO cohort. Among the PWHs, 44% of PWH are at risk of experiencing immunometabolic complications identified using the network-based patient stratification method. Utilizing advanced machine learning techniques and a Bayesian classifier, five plasma protein biomarkers; Tubulin Folding Cofactor B (TBCB), Gamma-Glutamylcyclotransferase (GGCT), Taxilin Alpha (TXLNA), Pyridoxal Phosphate Binding Protein (PLPBP) and Large Tumor Suppressor Kinase 1 (LATS1) are identified as highly differentially abundant between healthy control (HC)-like and immunometabolically at-risk PWHs (all FDR<10−10). The personalized metabolic models predict metabolic perturbations, revealing disruptions in central carbon metabolic fluxes and host tryptophan metabolism in at-risk phenotype. Functional assays in primary cells and cortical forebrain organoids (FBOs) further validate this. Metabolic perturbations lead to persistent monocyte activation, thereby impairing their functions ex vivo. Furthermore, the chronic inflammatory plasma microenvironment contributes to synaptic dysregulation in FBOs. The endogenous plasma inflammatory microenvironment is responsible for chronic inflammation in treated immunometabolically complicated at-risk PWH who have a higher risk of cardiovascular and neuropsychiatric disorders.
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    Nano in micro: novel concepts in foodborne pathogen transmission and pathogenesis
    (Annual Reviews, 2024-12-02) Liu, Yue; Ma, Xuchuan; Cazzaniga, Monica; Gahan, Cormac G. M.; den Besten, Heidy M. W.; Abee, Tjakko; Science Foundation Ireland; Horizon 2020
    In this article, we highlight novel components of foodborne pathogens that influence their response, physiology, adaptation, and survival in the face of diverse stresses, and consequently have implications for their transmission in the food chain and their pathogenesis. Recent insights into the role of bacteriophages/prophages, bacterial extracellular vesicles, and bacterial microcompartments, which make up the emerging field we coined as “nano in micro,” are presented, together with the role of understudied food-relevant substrates in pathogen fitness and virulence. These new insights also lead to reflections on generally adopted laboratory conditions in the long-standing research field of adaptive stress response in foodborne pathogens. In addition, selected examples of the impact of diet and microbiota on intestinal colonization and host invasion are discussed. A final section on risk assessment presents an overview of tools for (kinetic) data modeling and perspectives for the implementation of information derived from whole-genome sequencing, combined with advancements in dose-response models and exposure assessments.
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    Associations between the gut microbiome, inflammation, and cardiovascular profiles in people with human immunodeficiency virus
    (Oxford University Press, 2025) MacCann, Rachel; Li, Junhui; Leon, Alejandro Abner Garcia; Negi, Riya; Alalwan, Dana; Tinago, Willard; Mcgettrick, Padraig; Cotter, Aoife G; Landay, Alan; Sabin, Caroline; O'toole, Paul W; Mallon, Patrick W. G; Barco, Elena Alvarez; Leon, Alejandro Garcia; Mcdermott, Aoife; Mcginty, Tara; Macken, Alan; Kavanagh, Eoin; Mccarthy, Geraldine; Sheehan, Gerard; Lambert, John; Powderly, William; Compston, Juliet; Health Research Board; Wellcome Trust; Health Service Executive; Health and Social Care, Research and Development Division, Northern Ireland; Science Foundation Ireland; Horizon Europe
    Background: Inflammation and innate immune activation are associated with chronic human immunodeficiency virus (HIV) infection, despite effective treatment. Although gut microbiota alterations are linked to systemic inflammation, their relationship with HIV infection the relationships between the gut microbiome, inflammation, and HIV remains unclear. Methods: The HIV UPBEAT Coronary Artery Disease sub-study evaluated cardiovascular disease (CVD) in people with and without HIV. Subclinical CVD was assessed using coronary computed tomography angiography (CCTA). Thirty-four biomarkers were measured using quantitative immunoassays. Stool samples underwent 16S rRNA sequencing. Differentially abundant species were identified by analysis of compositions of microbiomes with bias correction (ANCOM-BC) and correlated to biomarkers, diet, and CCTA outcomes using Spearman correlation. Results: Among 81 participants (median age, 51 years; 73% male), people with HIV (n = 44) had higher rates of hypercholesterolemia (P <. 025). Gut microbiome β-diversity differed significantly by HIV status. Enriched Bifidobacterium pseudocatenulatum, Megamonas hypermegale, and Selenomonas ruminantium correlated with lower plaque burden, while depleted Ruminococcus bromii correlated with higher plaque burden and fat intake. Depleted Bacteroides spp and Alistepes spp correlated with elevated biomarkers (D-dimer, CD40 ligand, C-reactive protein, and interferon-γ). Conclusions: Gut microbiota differences in people with HIV were linked to subclinical CVD, diet, and inflammation, highlighting the microbiome's role in cardiovascular risk in HIV infection.