0000000000320111
AUTHOR
Vicente Pérez-brocal
Severity-Related Changes of Bronchial Microbiome in Chronic Obstructive Pulmonary Disease
ABSTRACT Bronchial colonization by potentially pathogenic microorganisms (PPMs) is often demonstrated in chronic obstructive pulmonary disease (COPD), but culture-based techniques identify only a portion of the bacteria in mucosal surfaces. The aim of the study was to determine changes in the bronchial microbiome of COPD associated with the severity of the disease. The bronchial microbiome of COPD patients was analyzed by 16S rRNA gene amplification and pyrosequencing in sputum samples obtained during stable disease. Seventeen COPD patients were studied (forced expiratory volume in the first second expressed as a percentage of the forced vital capacity [FEV 1 %] median, 35.0%; interquartile…
Beyond cells – The virome in the human holobiont
Viromics, or viral metagenomics, is a relatively new and burgeoning field of research that studies the complete collection of viruses forming part of the microbiota in any given niche. It has strong foundations rooted in over a century of discoveries in the field of virology and recent advances in molecular biology and sequencing technologies. Historically, most studies have deconstructed the concept of viruses into a simplified perception of viral agents as mere pathogens, which demerits the scope of large-scale viromic analyses. Viruses are, in fact, much more than regular parasites. They are by far the most dynamic and abundant entity and the greatest killers on the planet, as well as th…
Symbionts and Pathogens: What is the Difference?
The ecological relationships that organisms establish with others can be considered as broad and diverse as the forms of life that inhabit and interact in our planet. Those interactions can be considered as a continuum spectrum, ranging from beneficial to detrimental outcomes. However, this picture has revealed as more complex and dynamic than previously thought, involving not only factors that affect the two or more members that interact, but also external forces, with chance playing a crucial role in this interplay. Thus, defining a particular symbiont as mutualist or pathogen in an exclusive way, based on simple rules of classification is increasingly challenging if not unfeasible, since…
Immunity and other defenses in pea aphids, Acyrthosiphon pisum
Background Recent genomic analyses of arthropod defense mechanisms suggest conservation of key elements underlying responses to pathogens, parasites and stresses. At the center of pathogen-induced immune responses are signaling pathways triggered by the recognition of fungal, bacterial and viral signatures. These pathways result in the production of response molecules, such as antimicrobial peptides and lysozymes, which degrade or destroy invaders. Using the recently sequenced genome of the pea aphid (Acyrthosiphon pisum), we conducted the first extensive annotation of the immune and stress gene repertoire of a hemipterous insect, which is phylogenetically distantly related to previously ch…
The respiratory virome in chronic obstructive pulmonary disease
Aim: To characterize the respiratory virome in moderate/severe chronic obstructive pulmonary disease (COPD) patients using metagenomics, with healthy subjects as the reference. Patients & Methods: Sputum COPD samples were collected during stability and exacerbations with negative usual-care microbiologic analysis. Results: Eukaryotic viruses from the Anelloviridae, Herpesviridae and Retroviridae families and phages from the Shiphoviridae family were commonly found in COPD, and the respiratory virome in stability and noninfectious exacerbations showed a substantial similarity. DNA viruses with the highest relative abundance in COPD are Anelloviridae. Conclusion: These results support a …
Comparative analysis of two genomic regions among four strains of Buchnera aphidicola, primary endosymbiont of aphids
Preliminary analysis of two selected genomic regions of Buchnera aphidicola BCc, the primary endosymbiont of the cedar aphid Cinara cedri, has revealed a number of interesting features when compared with the corresponding homologous regions of the three B. aphidicola genomes previously sequenced, that are associated with different aphid species. Both regions exhibit a significant reduction in length and gene number in B. aphidicola BCc, as it could be expected since it possess the smallest bacterial genome. However, the observed genome reduction is not even in both regions, as it appears to be dependent on the nature of their gene content. The region fpr-trxA, that contains mainly metabolic…
Advanced strategy to exploit wine-making waste by manufacturing antioxidant and prebiotic fibre-enriched vesicles for intestinal health.
Grape extract-loaded fibre-enriched vesicles, nutriosomes, were prepared by combining antioxidant extracts obtained from grape pomaces and a prebiotic, soluble fibre (Nutriose®FM06). The nutriosomes were small in size (from ∼140 to 260 nm), homogeneous (polydispersity index < 0.2) and highly negative (∼ −79 mV). The vesicles were highly stable during 12 months of storage at 25 °C. When diluted with warmed (37 °C) acidic medium (pH 1.2) of high ionic strength, the vesicles only displayed an increase of the mean diameter and a low release of the extract, which were dependent on Nutriose concentration. The formulations were highly biocompatible and able to protect intestinal cells (Caco-2) fro…
Additional file 2 of Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile
Additional file 2. Alignments of the mimetic amino acid motif of the α-MSH, the ClpB from E. coli str K12 and the predicted ORFs from each sequence of the samples 1, 30 and 143.
Interkingdom Gut Microbiome and Resistome of the Cockroach Blattella germanica
Cockroaches are intriguing animals with two coexisting symbiotic systems, an endosymbiont in the fat body, involved in nitrogen metabolism, and a gut microbiome whose diversity, complexity, role, and developmental dynamics have not been fully elucidated. In this work, we present a metagenomic approach to study Blattella germanica populations not treated, treated with kanamycin, and recovered after treatment, both naturally and by adding feces to the diet, with the aim of better understanding the structure and function of its gut microbiome along the development as well as the characterization of its resistome.
The microbiome in respiratory medicine: current challenges and future perspectives
The healthy lung has previously been considered to be a sterile organ because standard microbiological culture techniques consistently yield negative results. However, culture-independent techniques report that large numbers of microorganisms coexist in the lung. There are many unknown aspects in the field, but available reports show that the lower respiratory tract microbiota: 1) is similar in healthy subjects to the oropharyngeal microbiota and dominated by members of the Firmicutes, Bacteroidetes and Proteobacteria phyla; 2) shows changes in smokers and well-defined differences in chronic respiratory diseases, although the temporal and spatial kinetics of these changes are only partially…
Obesity-associated deficits in inhibitory control are phenocopied to mice through gut microbiota changes in one-carbon and aromatic amino acids metabolic pathways
Gut: first published.
Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile
[Background]: The chaperone ClpB, a bacterial protein, is a conformational antigen-mimetic of α-melanocyte-stimulating hormone (α-MSH) implicated in body weight regulation in mice. We here investigated the potential associations of gut bacterial ClpB-like gene function with obesity status and gut microbiota in humans.
Presence of Blastocystis in gut microbiota is associated with cognitive traits and decreased executive function.
Growing evidence implicates the gut microbiome in cognition. Blastocystis is a common gut single-cell eukaryote parasite frequently detected in humans but its potential involvement in human pathophysiology has been poorly characterized. Here we describe how the presence of Blastocystis in the gut microbiome was associated with deficits in executive function and altered gut bacterial composition in a discovery (n = 114) and replication cohorts (n = 942). We also found that Blastocystis was linked to bacterial functions related to aromatic amino acids metabolism and folate-mediated pyrimidine and one-carbon metabolism. Blastocystis-associated shifts in bacterial functionality translated into …
Cross-regional view of functional and taxonomic microbiota composition in obesity and post-obesity treatment shows country specific microbial contribution
This work was supported by CONICYT-Chile through the FONDECYT [n° 3160525] (DM) and by Universidad San Sebastián, and by grants to AM from the Spanish Ministry of Economy and Competitiveness (projects SAF2012-31187, SAF2013-49788-EXP, SAF2015-65878-R), Carlos III Health Institute (Projects PIE14/00045 and AC15/00022), Generalitat Valenciana (Project PrometeoII/2014/065 and Prometeo/2018/A/133), Asociación Española Contra el Cancer (Project AECC 2017-1485) and co-financed by the European Regional Development Fund (ERDF).
Estudios de epidemiología molecular en población inmigrante en España
Fundamentos: La epidemiología molecular es una nueva disciplina que permite la integración de la información sobre la variabilidad genética de patógenos infecciosos con su difusión en la población y subgrupos de la misma incluyendo, por ejemplo, las mutaciones de resistencia a antibióticos y antivirales. El objetivo es conocer qué posibles diferencias existe en las características genéticas de los agentes infecciosos que afectan a las poblaciones inmigrante y autóctoctona en España. Métodos: Se revisaron artículos originales publicados entre 1998-2013, con las palabras clave "epidemiología molecular", "tipado molecular", "secuenciación", "inmigrante", "España". Resultados: De un total de 26…
Elevated circulating levels of succinate in human obesity are linked to specific gut microbiota
Gut microbiota-related metabolites are potential clinical biomarkers for cardiovascular disease (CVD). Circulating succinate, a metabolite produced by both microbiota and the host, is increased in hypertension, ischemic heart disease, and type 2 diabetes. We aimed to analyze systemic levels of succinate in obesity, a major risk factor for CVD, and its relationship with gut microbiome. We explored the association of circulating succinate with specific metagenomic signatures in cross-sectional and prospective cohorts of Caucasian Spanish subjects. Obesity was associated with elevated levels of circulating succinate concomitant with impaired glucose metabolism. This increase was associated wit…
Additional file 1 of Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status
Additional file 1: Supplementary Table 1. Clinical characteristics of subjects after 1-year follow-up according to the gender and menopausal status.
The respiratory microbiome in bronchial mucosa and secretions from severe IgE-mediated asthma patients
Altres ajuts: This work was supported by Fundació Catalana de Neumología (FUCAP) and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias(CIBERES). CIBERES is an initiative of the Instituto de Salud Carlos III. The bronchial microbiome in chronic lung diseases presents an abnormal pattern, but its microbial composition and regional differences in severe asthma have not been sufficiently addressed. The aim of the study was to describe the bacterial community in bronchial mucosa and secretions of patients with severe chronic asthma chronically treated with corticosteroids in addition to usual care according to Global Initiative for Asthma. Bacterial community composition was…
Evolution of the Secondary Symbiont “Candidatus Serratia symbiotica” in Aphid Species of the Subfamily Lachninae ▿†
ABSTRACT Buchnera aphidicola BCc, the primary endosymbiont of the aphid Cinara cedri (subfamily Lachninae), is losing its symbiotic capacity and might be replaced by the coresident “ Candidatus Serratia symbiotica.” Phylogenetic and morphological analyses within the subfamily Lachninae indicate two different “ Ca . Serratia symbiotica” lineages and support the longtime coevolution of both symbionts in C. cedri .
Additional file 5 of Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status
Additional file 5: Supplementary Table 5. MRM parameters for determination of steroids and isotopically labelled standards by LC–MS/MS.
Identification of the Weevil immune genes and their expression in the bacteriome tissue
Abstract Background Persistent infections with mutualistic intracellular bacteria (endosymbionts) are well represented in insects and are considered to be a driving force in evolution. However, while pathogenic relationships have been well studied over the last decades very little is known about the recognition of the endosymbionts by the host immune system and the mechanism that limits their infection to the bacteria-bearing host tissue (the bacteriome). Results To study bacteriome immune specificity, we first identified immune-relevant genes of the weevil Sitophilus zeamais by using suppressive subtractive hybridization (SSH) and then analyzed their full-length coding sequences obtained b…
Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status
[Background]: Gonadal steroid hormones have been suggested as the underlying mechanism responsible for the sexual dimorphism observed in metabolic diseases. Animal studies have also evidenced a causal role of the gut microbiome and metabolic health. However, the role of sexual dimorphism in the gut microbiota and the potential role of the microbiome in influencing sex steroid hormones and shaping sexually dimorphic susceptibility to disease have been largely overlooked. Although there is some evidence of sex-specific differences in the gut microbiota diversity, composition, and functionality, the results are inconsistent. Importantly, most of these studies have not taken into account the go…
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
Abstract Background The main limitations in the analysis of viral metagenomes are perhaps the high genetic variability and the lack of information in extant databases. To address these issues, several bioinformatic tools have been specifically designed or adapted for metagenomics by improving read assembly and creating more sensitive methods for homology detection. This study compares the performance of different available assemblers and taxonomic annotation software using simulated viral-metagenomic data. Results We simulated two 454 viral metagenomes using genomes from NCBI's RefSeq database based on the list of actual viruses found in previously published metagenomes. Three different ass…
Bronchial microbiome, PA biofilm-forming capacity and exacerbation in severe COPD patients colonized by P. aeruginosa
Aim: The bronchial microbiome of severe chronic obstructive pulmonary disease patients colonized by Pseudomonas aeruginosa was analyzed using 16S rRNA gene sequencing to identify differences related to biofilm-forming capacity. Patients & methods: Patient sputum samples from 21 patients were studied. Results: Statistically significant differences related to biofilm-forming capacity were only found for genera with relative abundances <1%, and Fusobacterium was over-represented when biofilm-forming capacity was high. Genera with relative abundances >50% which increased from baseline were observed in 10/14 exacerbations, but corresponded to Pseudomonas only in three episodes, while …
Bronchial microbiome of severe COPD patients colonised by Pseudomonas aeruginosa
The bronchial microbiome in severe COPD during stability and exacerbation in patients chronically colonised by Pseudomonas aeruginosa (PA), has not been defined. Our objective was to determine the characteristics of the bronchial microbiome of severe COPD patients colonised and not colonised by P. aeruginosa and its changes during exacerbation. COPD patients with severe disease and frequent exacerbations were categorised according to chronic colonisation by P. aeruginosa. Sputum samples were obtained in stability and exacerbation, cultured, and analysed by 16S rRNA gene amplification and pyrosequencing. Sixteen patients were included, 5 of them showing chronic colonisation by P. aeruginosa.…
Profiling of Protein Degraders in Cultures of Human Gut Microbiota
Unabsorbed proteins reach the colon and are fermented by the microbiota, yielding a variety of harmful metabolites. In the present study, a 16S rRNA gene survey identified the bacterial taxa flourishing in 11 batch fermentations with proteins and peptones as the sole fermentable substrates, inoculated with the feces of six healthy adults. Organic acids, ammonia, and indole resulting from protein breakdown and fermentation accumulated in all of the cultures. Analysis of differential abundances among time-points identified Enterobacteriaceae, Burkholderiaceae, and Desulfovibrionaceae (including Esherichia-Shigella, Sutterella, Parasutterella, and Bilophila) among the bacteria that especially …
Chronic Obstructive Pulmonary Disease Lung Microbiota Diversity May Be Mediated by Age or Inhaled Corticosteroid Use
We read with great interest the paper by Garcia-Nunez et al. ([1][1]) published in the December 2014 issue of this journal, where the authors investigated the sputum microbiota of chronic obstructive pulmonary disease (COPD) patients. The authors found decreased microbial diversity in patients with
Plasmids in the aphid endosymbiont Buchnera aphidicola with the smallest genomes. A puzzling evolutionary story
Buchnera aphidicola, the primary endosymbiont of aphids, has undergone important genomic and biochemical changes as an adaptation to intracellular life. The most important structural changes include a drastic genome reduction and the amplification of genes encoding key enzymes for the biosynthesis of amino acids by their translocation to plasmids. Molecular characterization through different aphid subfamilies has revealed that the genes involved in leucine and tryptophan biosynthesis show a variable fate, since they can be located on plasmids or on the chromosome in different lineages. This versatility contrasts with the genomic stasis found in three distantly related B. aphidicola strains …
Isolation in small populations of Wayampi Amerindians promotes endemicity and homogenisation of their faecal virome, but its distribution is not entirely random
The isolated community of the Wayampi Amerindians has been extensively studied for the presence of beta lactamase-producing enterobacteria and their gut microbiota. However, no information about their virome was available. This study tries to establish potential associations between the virome and diverse epidemiological data, through the metagenomic study of the faecal prophages and DNA viruses from 31 samples collected in 2010. Taxonomic assignments, composition, abundance and diversity analyses were obtained to characterise the virome and were compared between groups according to several demographic, environmental and medical data. Prophages outnumbered viruses. Composition and abundance…
Study of the Viral and Microbial Communities Associated With Crohn's Disease: A Metagenomic Approach
OBJECTIVES: This study aimed to analyze and compare the diversity and structure of the viral and microbial communities in fecal samples from a control group of healthy volunteers and from patients affected by Crohn's disease (CD). METHODS: Healthy adult controls (n=8) and patients affected by ileocolic CD (n=11) were examined for the viral and microbial communities in their feces and, in one additional case, in the intestinal tissue. Using two different approaches, we compared the viral and microbial communities in several ways: by group (patients vs. controls), entity (viruses vs. bacteria), read assembly (unassembled vs. assembled reads), and methodology (our approach vs. an existing pipe…
A genomic reappraisal of symbiotic function in the aphid/Buchnera symbiosis: reduced transporter sets and variable membrane organisations.
International audience; Buchnera aphidicola is an obligate symbiotic bacterium that sustains the physiology of aphids by complementing their exclusive phloem sap diet. In this study, we reappraised the transport function of different Buchnera strains, from the aphids Acyrthosiphon pisum, Schizaphis graminum, Baizongia pistaciae and Cinara cedri, using the re-annotation of their transmembrane proteins coupled with an exploration of their metabolic networks. Although metabolic analyses revealed high interdependencies between the host and the bacteria, we demonstrate here that transport in Buchnera is assured by low transporter diversity, when compared to free-living bacteria, being mostly bas…
Retrospective case-control study of viral pathogen screening in proliferative verrucous leukoplakia lesions.
Objective This study aimed to survey the presence of known oncoviruses in oral biopsies from patients diagnosed with the aetiologically undetermined proliferative verrucous leukoplakia and compare results to those from milder oral leukoplakia (OL) cases, oral squamous cell carcinoma, a common outcome of the lesions of interest, and healthy controls. Design Blind, retrospective, case–control study. Setting A stomatology unit in an academic Hospital and a Public Health laboratory. Participants Forty patients were divided in four groups. Ten patients had been diagnosed with proliferative verrucous leukoplakia, 10 with OL and 10 with OSCC, and 10 were healthy subjects. Main outcome measures The…
Obesity status and obesity-associated gut dysbiosis effects on hypothalamic structural covariance
[Background]: Functional connectivity alterations in the lateral and medial hypothalamic networks have been associated with the development and maintenance of obesity, but the possible impact on the structural properties of these networks remains largely unexplored. Also, obesity-related gut dysbiosis may delineate specific hypothalamic alterations within obese conditions. We aim to assess the effects of obesity, and obesity and gut-dysbiosis on the structural covariance differences in hypothalamic networks, executive functioning, and depressive symptoms.
Metagenomic Survey of the Highly Polyphagous Anastrepha ludens Developing in Ancestral and Exotic Hosts Reveals the Lack of a Stable Microbiota in Larvae and the Strong Influence of Metamorphosis on Adult Gut Microbiota
We studied the microbiota of a highly polyphagous insect, Anastrepha ludens (Diptera: Tephritidae), developing in six of its hosts, including two ancestral (Casimiroa edulis and C. greggii), three exotic (Mangifera indica cv. Ataulfo, Prunus persica cv. Criollo, and Citrus x aurantium) and one occasional host (Capsicum pubescens cv. Manzano), that is only used when extreme drought conditions limit fruiting by the common hosts. One of the exotic hosts (“criollo” peach) is rife with polyphenols and the occasional host with capsaicinoids exerting high fitness costs on the larvae. We pursued the following questions: (1) How is the microbial composition of the larval food related to the composit…
Metagenomic Analysis of Crohn's Disease Patients Identifies Changes in the Virome and Microbiome Related to Disease Status and Therapy, and Detects Potential Interactions and Biomarkers.
Background The aim of this study was to survey the bacterial and viral communities in different types of samples from patients with Crohn's disease (CD) at different stages of the disease to relate their distribution with the origin and progression of this disorder. Methods A total of 42 fecal samples and 15 biopsies from 20 patients with CD and 20 healthy control individuals were collected for bacterial 16S rRNA gene profiling and DNA/RNA virome metagenomic analysis through 454 pyrosequencing. Their composition, abundance, and diversity were analyzed, and comparisons of disease status, patient status, and sample origin were used to determine statistical differences between the groups. Resu…
New Insights on the Evolutionary History of Aphids and Their Primary Endosymbiont Buchnera aphidicola
Since the establishment of the symbiosis between the ancestor of modern aphids and their primary endosymbiont,Buchnera aphidicola, insects and bacteria have coevolved. Due to this parallel evolution, the analysis of bacterial genomic features constitutes a useful tool to understand their evolutionary history. Here we report, based on data fromB. aphidicola, the molecular evolutionary analysis, the phylogenetic relationships among lineages and a comparison of sequence evolutionary rates of symbionts of four aphid species from three subfamilies. Our results support previous hypotheses of divergence ofB. aphidicolaand their host lineages during the early Cretaceous and indicate a closer relati…
Coexistence of Wolbachia with Buchnera aphidicola and a Secondary Symbiont in the Aphid Cinara cedri
ABSTRACT Intracellular symbiosis is very common in the insect world. For the aphid Cinara cedri , we have identified by electron microscopy three symbiotic bacteria that can be characterized by their different sizes, morphologies, and electrodensities. PCR amplification and sequencing of the 16S ribosomal DNA (rDNA) genes showed that, in addition to harboring Buchnera aphidicola , the primary endosymbiont of aphids, C. cedri harbors a secondary symbiont (S symbiont) that was previously found to be associated with aphids (PASS, or R type) and an α-proteobacterium that belongs to the Wolbachia genus. Using in situ hybridization with specific bacterial probes designed for symbiont 16S rDNA seq…
Functional Metagenomics of the Bronchial Microbiome in COPD
Altres ajuts: Sociedad Catalana de Neumología; Fundació Catalana de Neumología; Fundació Parc Tauli; Marató de TV3; Sociedad Española de Neumología y Cirugía Torácica; Fundación Menarini; Generalitat Valenciana (Spain) [Prometeo/2009/092] i Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES) The course of chronic obstructive pulmonary disease (COPD) is frequently aggravated by exacerbations, and changes in the composition and activity of the microbiome may be implicated in their appearance. The aim of this study was to analyse the composition and the gene content of the microbial community in bronchial secretions of COPD patients in both stability and exacerbati…
LSC Abstract – Functional metagenomics of respiratoy microbiome in exacerbated COPD
Background: The course of COPD is frequently aggravated by exacerbations. New molecular techniques have suggested that many bacterial groups, not only the common COPD pathogens, could trigger the exacerbations. Objective: to analyze the microbial community and the gene content of samples obtained during stability and exacerbation of COPD patients. Method: 16S rRNA was pyrosequenced to obtain the taxonomic information. The metabolic information was obtained with the Metagenomics RAST server (MG-RAST) with KEGG database. Results: 8 severe COPD patients were included. At genus level, 68 different OTUs were found. No significant differences in the relative abundance of any of the detected gener…
The Gut Metagenome Changes in Parallel to Waist Circumference, Brain Iron Deposition, and Cognitive Function.
Context Microbiota perturbations seem to exert modulatory effects on emotional behavior, stress-, and pain-modulation systems in adult animals; however, limited information is available in humans. Objective To study potential relationships among the gut metagenome, brain microstructure, and cognitive performance in middle-aged, apparently healthy, obese and nonobese subjects after weight changes. Design This is a longitudinal study over a 2-year period. Setting A tertiary public hospital. Patients or other participants Thirty-five (18 obese) apparently healthy subjects. Intervention(s) Diet counseling was provided to all subjects. Obese subjects were followed every 6 months. Main outcome me…
The analysis of the oral DNA virome reveals which viruses are widespread and rare among healthy young adults in Valencia (Spain).
We have analysed oral wash samples from 72 healthy young adults in Valencia (Spain) for a metagenomic analysis through the construction of shotgun libraries and high-throughput-sequencing. The oral viral communities have been taxonomically characterised as well as and the gene content from the latter. The majority of viruses are found in few individuals, with single occurrences being the most widespread ones, whereas universally distributed viruses, while present, are relatively rare, with bacteriophages from families Siphoviridae and Myoviridae, and Streptococcus phages, as well as the eukaryotic viral family Herpesviridae amongst the most widespread viruses. No significant differences wer…
The intestinal mycobiota and its relationship with overweight, obesity and nutritional aspects
[Background]: The fungal community of the gastrointestinal tract has recently become of interest, and knowledge of its relationship with the development of obesity is scarce. The present study aimed to evaluate the cultivable fungal fraction from the microbiota and to analyze its relationship with obesity.
Additional file 3 of Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status
Additional file 3: Supplementary Table 3. DESeq2 results for the differential expressed bacterial taxa between post-menopausal women and men.
Additional file 1: Table S1. of The respiratory microbiome in bronchial mucosa and secretions from severe IgE-mediated asthma patients
Relative abundance (median, IQR) of all genera detected in BB and BA samples. (XLSX 32 kb)
Additional file 2 of Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status
Additional file 2: Supplementary Table 2. DESeq2 results for the differential expressed bacterial taxa between pre-menopausal women and men.
Additional file 6 of Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status
Additional file 6: Supplementary Figure 1. Associations of gut microbiota composition in non-obese and obese subjects and bacterial families with gender and menopause status. Alpha diversity indices in a) non-obese and b) obese individuals. Beta diversity in non-obese subjects measured by c)Bray-Curtis and d) weighted unifrac. Beta diversity in obese subjects measured by e) Bray-Curtis and f) weighted unifrac. Overall differences in the microbiome composition among groups were assessed by PERMANOVA using 1000 permutations and pairwise differences between groups were assessed using the pairwise.adonis function adjusted for Bonferroni correction. *,P < 0.05; **, P < 0.01.g) Volcano plot…
Additional file 4 of Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status
Additional file 4: Supplementary Table 4. DESeq2 results for the differential expressed bacterial taxa between pre-menopausal women and post-menopausal women.
Additional file 1 of Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile
Additional file 1. Top 10 bacterial taxa (family level) contributing reads to the gut bacterial ClpB-like function, in absolute and relative figures per sample.
Additional file 7 of Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status
Additional file 7: Supplementary Figure 2. Associations of gut microbiota functionality with gender and menopause status in non-obese subjects. a) Fold change for the significant differential KEGG pathways between pre-menopausal women and men, and b) pre- and post-menopausal women, identified by DESeq2 adjusting for age and obesity status. Bars are colored according to the Benjamini-Hochberg corrected p values (pFDR).
Additional file 8 of Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status
Additional file 8: Supplementary Figure 3. Gender and menopausal status differences in gonadal steroids according to the obesity status. Boxplots for the concentrations of progestin,androgens, and estrogens converted to base 10 logarithmic values. Differences among groups were analyzed by a Kruskal-Wallis test, and pair-wise comparisons were assessed by the Wilcoxon test. Significant differences are highlighted in bold italics.
Additional file 3 of Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile
Additional file 3. Alignments. Alignment motif of the α-MSH and percentage of identity between the E. coli motif and the identified microbial counterparts in each sequence. Bacterial family identity: Average identity of the epitope in each bacterial family compared to the motif in E. coli as well as the distribution of families through the samples according to their degree of homology.
Additional file 9 of Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status
Additional file 9: Supplementary Figure 4. Gut microbial associations with circulating testosterone concentrations. a) Permutation tests for the goodness-of-fit (R2Y) and goodness of prediction (Q2Y) for the O-PLS model predicting plasma testosterone levels from bacterial families in non-obese individuals. b) Significant gut bacterial families identified by O-PLS modeling. c) Permutation tests for the goodness-of-fit (R2Y) and goodness of prediction (Q2Y) for the O-PLS model predicting plasma testosterone levels after 1-year follow-up from bacterial families at baseline in humans. d) Significant gut bacterial families identified by O-PLS modeling. e) Permutation tests for the goodness-of-fi…