John F. Baines
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View article: A global survey of taxa-metabolic associations across mouse microbiome communities
A global survey of taxa-metabolic associations across mouse microbiome communities Open
Host-microbiota mutualism is rooted in the exchange of dietary and metabolic molecules. Microbial diversity broadens the metabolite pool, with each taxon contributing distinct compounds in varying proportions. In the human microbiome, high…
View article: Bacterial metabolite patterns of infants receiving multi-strain probiotics and risk of late-onset sepsis
Bacterial metabolite patterns of infants receiving multi-strain probiotics and risk of late-onset sepsis Open
The effect of multi-strain probiotics containing Bifidobacterium longum (B. longum) on late-onset sepsis (LOS) risk in very-low-birth-weight infants (VLBWIs; birth weight < 1,500 g) remains uncertain. In a single-center study, we analyzed …
View article: Immunization reveals a key role of Enterobacterial ClpB protein in the development of host anorexia
Immunization reveals a key role of Enterobacterial ClpB protein in the development of host anorexia Open
Anorexia nervosa (AN) is a psychiatric disease of unknown etiology. Recently, caseinolytic protease B (ClpB), produced by Enterobacteriaceae, was identified as an antigen mimetic of α-melanocyte-stimulating hormone (α-MSH), an anorexigenic…
View article: Convergent genomic responses of human gut bacteria to variations in industrialization
Convergent genomic responses of human gut bacteria to variations in industrialization Open
Summary To what extent gut bacteria respond to the distinct ecological pressures imposed by human lifestyle remains unclear. Here, we investigate how genomic adaptation in gut bacteria differ between industrialized and non-industrialized h…
View article: Long-Term Intestinal Epithelial Remodeling Induced by Acute Protein-Energy Malnutrition
Long-Term Intestinal Epithelial Remodeling Induced by Acute Protein-Energy Malnutrition Open
Protein-energy malnutrition (PEM) is a global health burden with lasting effects that extend well beyond the initial nutrient deficiency. To systematically investigate the long-term effects of a single episode of PEM on the structure and f…
View article: The Influence of Omega‐3 Fatty Acids and Probiotics on Hippocampal Inflammation and Glial Cells in a Chronic Anorexia Nervosa Rat Model
The Influence of Omega‐3 Fatty Acids and Probiotics on Hippocampal Inflammation and Glial Cells in a Chronic Anorexia Nervosa Rat Model Open
Objective Anorexia nervosa (AN) is a severe eating disorder associated with brain volume reduction, glial cell loss, microbiome alterations, and dysregulated pro‐inflammatory mechanisms. However, the underlying cellular mechanisms remain i…
View article: Gut Microbiota Modulates and Predicts Disease Severity in Experimental Pemphigoid Disease
Gut Microbiota Modulates and Predicts Disease Severity in Experimental Pemphigoid Disease Open
Pemphigoid diseases (PD) are autoimmune blistering diseases with reported alterations in skin and gut microbiota, though their causal contribution to disease pathophysiology remains unclear. Using a passive model of bullous pemphigoid-like…
View article: Mouse model validity for studying the impact of tobacco smoke on the human gut microbiota assessed via <i>in silico</i> and experimental approaches
Mouse model validity for studying the impact of tobacco smoke on the human gut microbiota assessed via <i>in silico</i> and experimental approaches Open
Considering the high inter-individual variation in humans and the well-controlled conditions in mice, our results suggest that mice, despite the identified limitations, most likely represent a suitable model for studying specific processes…
View article: Gut Microbiome Structure and Progression in Multiple Sclerosis: A Meta-Analysis Across 14 COHORTS
Gut Microbiome Structure and Progression in Multiple Sclerosis: A Meta-Analysis Across 14 COHORTS Open
The gut microbiome is increasingly implicated in multiple sclerosis (MS), yet findings across studies remain inconsistent due to small sample sizes and methodological variability. We performed the largest MS microbiome meta-analysis to dat…
View article: Multi-omics analysis highlights the link of aging-related cognitive decline with systemic inflammation and alterations of tissue-maintenance
Multi-omics analysis highlights the link of aging-related cognitive decline with systemic inflammation and alterations of tissue-maintenance Open
Aging-related cognitive decline is associated with changes across different tissues and the gut microbiome, including dysfunction of the gut-brain axis. However, only few studies have linked multi-organ alterations to cognitive decline dur…
View article: Rapid genetic diversification of <i>Bacteroides thetaiotaomicron</i> in mono-associated mice revealed through deep population-level sequencing
Rapid genetic diversification of <i>Bacteroides thetaiotaomicron</i> in mono-associated mice revealed through deep population-level sequencing Open
Bacteria often feature short generation times and large populations, thereby allowing them to quickly evolve and adapt to new environments. Although it is known that gut bacteria can evolve on relatively short time scales, the extent of ge…
View article: Antibiotic‐Induced Microbial Dysbiosis Worsened Outcomes in the Activity‐Based Anorexia Model
Antibiotic‐Induced Microbial Dysbiosis Worsened Outcomes in the Activity‐Based Anorexia Model Open
Objective Anorexia nervosa (AN) is a complex psychiatric disorder characterized by persistent dieting and reduced food intake, leading to significantly low body weight. Dysbiosis in the gut microbiome of patients with AN has been suggested…
View article: Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice
Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice Open
Aging is accompanied by considerable changes in the gut microbiome, yet the molecular mechanisms driving aging and the role of the microbiome remain unclear. Here we combined metagenomics, transcriptomics and metabolomics from aging mice w…
View article: Enterobacterial caseinolytic protease B (ClpB) and ClpB antibodies in adolescents with anorexia nervosa
Enterobacterial caseinolytic protease B (ClpB) and ClpB antibodies in adolescents with anorexia nervosa Open
View article: Exploring new Bacteroidota strains: Functional Diversity and Probiotic Characteristics
Exploring new Bacteroidota strains: Functional Diversity and Probiotic Characteristics Open
Bacteroidota, a diverse phylum of bacteria, are increasingly recognized for their significant contributions to host health, particularly through their antimicrobial and probiotic properties. This study investigates the functional diversity…
View article: Meeting Report on “10th Anniversary Symposium on Inflammatory Skin Disease”
Meeting Report on “10th Anniversary Symposium on Inflammatory Skin Disease” Open
View article: House Mice in the Atlantic Region: Genetic Signals of Their Human Transport
House Mice in the Atlantic Region: Genetic Signals of Their Human Transport Open
Background/Objectives: The colonization history of house mice reflects the maritime history of humans that passively transported them worldwide. We investigated western house mouse colonization in the Atlantic region through studies of mit…
View article: Evolutionary Medicine for Chronic Inflammatory Diseases of the Gut: More Than a Clinical Fantasy?
Evolutionary Medicine for Chronic Inflammatory Diseases of the Gut: More Than a Clinical Fantasy? Open
View article: The need for guidance in antidepressant drug development: Revisiting the role of the forced swim test and tail suspension test
The need for guidance in antidepressant drug development: Revisiting the role of the forced swim test and tail suspension test Open
Depressive disorders are one of the most common mental disorders globally and progress in treating these disorders has been hampered, in part, by a lack of suitable nonclinical efficacy tests. Two common tests used in nonclinical efficacy …
View article: Fecal microbiota transplantation of patients with anorexia nervosa did not alter flexible behavior in rats
Fecal microbiota transplantation of patients with anorexia nervosa did not alter flexible behavior in rats Open
Objective Patients with anorexia nervosa (AN) are often anxious, display inflexible behavior and disrupted reward processing. Emerging evidence suggests that gut dysbiosis in patients contributes to the disease phenotype and progression. M…
View article: Long-Term Dynamics of Serum α-MSH and α-MSH-Binding Immunoglobulins with a Link to Gut Microbiota Composition in Patients with Anorexia Nervosa
Long-Term Dynamics of Serum α-MSH and α-MSH-Binding Immunoglobulins with a Link to Gut Microbiota Composition in Patients with Anorexia Nervosa Open
Introduction: Immunoglobulins (Ig) reactive with α-melanocyte-stimulating hormone (α-MSH), an anorexigenic neuropeptide, are present in humans and were previously associated with eating disorders. In this longitudinal study involving patie…
View article: Mitochondrial DNA variants and microbiota: An experimental strategy to identify novel therapeutic potential in chronic inflammatory diseases
Mitochondrial DNA variants and microbiota: An experimental strategy to identify novel therapeutic potential in chronic inflammatory diseases Open
We previously demonstrated that mice carrying natural mtDNA variants of the FVB/NJ strain (m.7778 G>T in the mt-Atp8 gene in mitochondrial complex V), namely C57BL/6 J-mtFVB/NJ (B6-mtFVB), exhibited (i) partial protection from e…
View article: Cytokine and Microbiome Changes in Adolescents with Anorexia Nervosa at Admission, Discharge, and One-Year Follow-Up
Cytokine and Microbiome Changes in Adolescents with Anorexia Nervosa at Admission, Discharge, and One-Year Follow-Up Open
Anorexia nervosa (AN) is a severe eating disorder that predominantly affects females and typically manifests during adolescence. There is increasing evidence that serum cytokine levels are altered in individuals with AN. Previous research …
View article: The archaeome in metaorganism research, with a focus on marine models and their bacteria–archaea interactions
The archaeome in metaorganism research, with a focus on marine models and their bacteria–archaea interactions Open
Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often rem…
View article: Longitudinal analysis of the gut microbiome in adolescent patients with anorexia nervosa: microbiome-related factors associated with clinical outcome
Longitudinal analysis of the gut microbiome in adolescent patients with anorexia nervosa: microbiome-related factors associated with clinical outcome Open
There is mounting evidence regarding the role of gut microbiota in anorexia nervosa (AN). Previous studies have reported that patients with AN show dysbiosis compared to healthy controls (HCs); however, the underlying mechanisms are unclea…
View article: Functional host-specific adaptation of the intestinal microbiome in hominids
Functional host-specific adaptation of the intestinal microbiome in hominids Open
View article: Additional file 2 of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development
Additional file 2 of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development Open
R code used for the integrated analysis shown in Fig. 5a. (R 1 kb)
View article: Additional file 14 of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development
Additional file 14 of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development Open
Methylation levels of microbiota- (CONV-R versus GF) and development-dependent (W1 versus W4 versus W12/16) DMPs. Hierarchical clustering resulted in ten DMP groups. (XLSX 203 kb)
View article: Additional file 17 of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development
Additional file 17 of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development Open
List of differentially expressed genes (CONV-R versus GF) that also contain DMPs as depicted in Additional file 13. (XLSX 45 kb)
View article: Additional file 8 of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development
Additional file 8 of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development Open
Alternative splicing events (total and only significant events in CONV-R versus GF) in the three developmental stages. (XLSX 9 kb)