Pub Date : 2023-03-16DOI: 10.3389/frmbi.2023.1147082
Stefano Leo, O. F. Cetiner, Laure F. Pittet, N. Messina, W. Jakob, L. Falquet, N. Curtis, P. Zimmermann
Introduction The early-life intestinal microbiome plays a crucial role in the development and regulation of the immune system. Perturbations in its composition during this critical period have been linked to the development of allergic diseases. Objective This study aimed to investigate the association between the composition of the early-life intestinal microbiome and the presence of eczema in the first year of life using shotgun metagenomic sequencing and functional analyses (metabolic pathways). Methods Stool samples from 393 healthy term infants collected at 1 week of age were analyzed with shotgun metagenomic sequencing. Environmental and clinical data were prospectively collected using 3-monthly validated questionnaires. Participants were clinically assessed during study visits at 12 months of age. Eczema was diagnosed by the UK diagnostic tool and by a research nurse. Data analysis was stratified by delivery mode. Results Eczema was diagnosed in 16.4% (60/366) of participants by nurse diagnosis. Infants born by cesarean section (CS) with nurse-diagnosed eczema had a higher relative abundance of Escherichia, Shigella, Enterobacter, and Citrobacter and a lower relative abundance of Veillonella than CS-born infants without eczema. In addition, CS-born infants without eczema had a higher abundance of genes involved in lactic fermentation. Vaginally born infants with eczema had a higher relative abundance of Bacteroides and a lower abundance of Streptococcus. Conclusion There is an association between the bacterial composition of the intestinal microbiome at 1 week of age and the presence of eczema in the first 12 months of life. Graphical Abstract
{"title":"The association between the composition of the early-life intestinal microbiome and eczema in the first year of life","authors":"Stefano Leo, O. F. Cetiner, Laure F. Pittet, N. Messina, W. Jakob, L. Falquet, N. Curtis, P. Zimmermann","doi":"10.3389/frmbi.2023.1147082","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1147082","url":null,"abstract":"Introduction The early-life intestinal microbiome plays a crucial role in the development and regulation of the immune system. Perturbations in its composition during this critical period have been linked to the development of allergic diseases. Objective This study aimed to investigate the association between the composition of the early-life intestinal microbiome and the presence of eczema in the first year of life using shotgun metagenomic sequencing and functional analyses (metabolic pathways). Methods Stool samples from 393 healthy term infants collected at 1 week of age were analyzed with shotgun metagenomic sequencing. Environmental and clinical data were prospectively collected using 3-monthly validated questionnaires. Participants were clinically assessed during study visits at 12 months of age. Eczema was diagnosed by the UK diagnostic tool and by a research nurse. Data analysis was stratified by delivery mode. Results Eczema was diagnosed in 16.4% (60/366) of participants by nurse diagnosis. Infants born by cesarean section (CS) with nurse-diagnosed eczema had a higher relative abundance of Escherichia, Shigella, Enterobacter, and Citrobacter and a lower relative abundance of Veillonella than CS-born infants without eczema. In addition, CS-born infants without eczema had a higher abundance of genes involved in lactic fermentation. Vaginally born infants with eczema had a higher relative abundance of Bacteroides and a lower abundance of Streptococcus. Conclusion There is an association between the bacterial composition of the intestinal microbiome at 1 week of age and the presence of eczema in the first 12 months of life. Graphical Abstract","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81649994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-15DOI: 10.3389/frmbi.2023.1123064
P. Morgan, P. Parbie, Desmond Opoku Ntiamoah, A. A. Boadu, P. Asare, Ivy Naa Koshie Lamptey, Cecilia Nancy Gorman, Emmanuel Afreh, Adwoa Asante-Poku, I. Otchere, S. Aboagye, D. Yeboah-Manu
Background The gut microbiota is known to play a critical role in shaping the host immunity, and metabolism and influences the onset and progression of both communicable and non-communicable diseases. This study assessed the gut microbiome of tuberculosis (TB) cases with diabetes mellitus (DM) or HIV comorbidities before anti-TB therapy and after the intensive phase anti-TB therapy. Methods Ninety cases comprising 60 TB-only, 23 TB-DM, 7 TB-HIV were recruited, among which 35 TB-only, 10 TB-DM, 5 TB-HIV were also sampled after 2 months of anti-TB treatment. Total gut microbiome was detected by 16S rRNA gene sequencing of DNA extracted from collected stool specimen. The taxonomic and functional diversity of the different groups were compared in addition to changes that could occur after 2 months antibiotics use. Results Compared to the healthy controls, the gut microbiome of all the TB cohorts was characterized by a significant decreased alpha diversity and significant compositional changes. All the three TB cohorts were enriched with inflammatory related microorganisms of the genera Escherichia-shigella, Streptococcus, Enterococcus and Erysipelatoclostridium with depletion in beneficial taxa of the genera Faecalibacterium, Bifidobacterium and Clostridium. In pairwise comparison with the healthy controls, the TB-only cohort were enriched with Streptococcus and Erysipelatoclostridium, the TB-DM enriched with Bacteroides, and TB-HIV enriched with Escherichia-shigella, Dialister and Erysipelatoclostridium. After the intensive phase anti-TB therapy, there was general enrichment of the genera Erysipelotrichaceae_UCG 003, Veillonella and Fusobacterium. Conclusion Our findings show a dysbiotic gut microbiome and associated upregulation of inflammation related microorganism in gut microbiome of TB individuals with or without comorbidity.
{"title":"Gut microbiome variation in pulmonary TB patients with diabetes or HIV comorbidities","authors":"P. Morgan, P. Parbie, Desmond Opoku Ntiamoah, A. A. Boadu, P. Asare, Ivy Naa Koshie Lamptey, Cecilia Nancy Gorman, Emmanuel Afreh, Adwoa Asante-Poku, I. Otchere, S. Aboagye, D. Yeboah-Manu","doi":"10.3389/frmbi.2023.1123064","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1123064","url":null,"abstract":"Background The gut microbiota is known to play a critical role in shaping the host immunity, and metabolism and influences the onset and progression of both communicable and non-communicable diseases. This study assessed the gut microbiome of tuberculosis (TB) cases with diabetes mellitus (DM) or HIV comorbidities before anti-TB therapy and after the intensive phase anti-TB therapy. Methods Ninety cases comprising 60 TB-only, 23 TB-DM, 7 TB-HIV were recruited, among which 35 TB-only, 10 TB-DM, 5 TB-HIV were also sampled after 2 months of anti-TB treatment. Total gut microbiome was detected by 16S rRNA gene sequencing of DNA extracted from collected stool specimen. The taxonomic and functional diversity of the different groups were compared in addition to changes that could occur after 2 months antibiotics use. Results Compared to the healthy controls, the gut microbiome of all the TB cohorts was characterized by a significant decreased alpha diversity and significant compositional changes. All the three TB cohorts were enriched with inflammatory related microorganisms of the genera Escherichia-shigella, Streptococcus, Enterococcus and Erysipelatoclostridium with depletion in beneficial taxa of the genera Faecalibacterium, Bifidobacterium and Clostridium. In pairwise comparison with the healthy controls, the TB-only cohort were enriched with Streptococcus and Erysipelatoclostridium, the TB-DM enriched with Bacteroides, and TB-HIV enriched with Escherichia-shigella, Dialister and Erysipelatoclostridium. After the intensive phase anti-TB therapy, there was general enrichment of the genera Erysipelotrichaceae_UCG 003, Veillonella and Fusobacterium. Conclusion Our findings show a dysbiotic gut microbiome and associated upregulation of inflammation related microorganism in gut microbiome of TB individuals with or without comorbidity.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77201045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-06DOI: 10.3389/frmbi.2023.1085508
K. Barfod, J. Lui, Signe Schmidt Kjølner Hansen, Sreyoshee Sengupta, L. Zachariassen, A. K. Hansen, J. Sørli
Early-life changes to lung and gut microbiota have been linked to alterations in immune responses that may lead to pulmonary diseases later in life. Associations between early-life microbiota, germ-free status, lung gene expression, lung development and function are not well described. In this study, we compare early-life lung gene transcription under germ-free and different perinatal microbial exposures, and analyze with a predetermined focus on lung capacity and lung surfactant. We also analyze the later-in-life physiological measures of breathing patterns and lung surfactant function between the germ-free, gnotophoric and gnotobiotic offspring. To achieve this, we kept pregnant BALB/c germ-free mice in separate germ-free isolators until exposure to either A: no exposure (GF), B: Bifidobacterium animalis ssp. Lactis (BI04) or C: full cecum content harvested from other female SPF mice (Cecum). Subsequently, perinatally exposed offspring were used for the analyses. Lung tissue transcriptomics analysis was done at postnatal day 10 (PNday10) at the first phase of lung alveolar development. Head-out plethysmography for breathing pattern analysis was performed on the siblings at PNday23 followed by lung surfactant collection. The function of the collected lung surfactant was then analyzed ex vivo using the constrained drop surfactometer. Our results show that lung transcriptomics had differentially expressed genes related to surfactant turnover between groups and sex at PNday10. They also show that the GF and BI04 animals had lower respiratory rate than Cecum mice, or compared to age-matched specific pathogen-free (SPF) reference animals. We also see changes in lung surfactant function ex vivo. The overall conclusions are that 10-day-old GF mice do not have a markedly different lung gene transcription compared to gnotophoric or gnotobiotic mice, but genes related to surfactant metabolism are among the few differentially expressed genes. We show here for the first time that early-life microbiome status correlates with early-life surfactant-gene transcription and to later-in-life lung surfactant function and associated respiratory-rate changes in mice.
{"title":"The impact of bacterial exposure in early life on lung surfactant gene expression, function and respiratory rate in germ-free mice","authors":"K. Barfod, J. Lui, Signe Schmidt Kjølner Hansen, Sreyoshee Sengupta, L. Zachariassen, A. K. Hansen, J. Sørli","doi":"10.3389/frmbi.2023.1085508","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1085508","url":null,"abstract":"Early-life changes to lung and gut microbiota have been linked to alterations in immune responses that may lead to pulmonary diseases later in life. Associations between early-life microbiota, germ-free status, lung gene expression, lung development and function are not well described. In this study, we compare early-life lung gene transcription under germ-free and different perinatal microbial exposures, and analyze with a predetermined focus on lung capacity and lung surfactant. We also analyze the later-in-life physiological measures of breathing patterns and lung surfactant function between the germ-free, gnotophoric and gnotobiotic offspring. To achieve this, we kept pregnant BALB/c germ-free mice in separate germ-free isolators until exposure to either A: no exposure (GF), B: Bifidobacterium animalis ssp. Lactis (BI04) or C: full cecum content harvested from other female SPF mice (Cecum). Subsequently, perinatally exposed offspring were used for the analyses. Lung tissue transcriptomics analysis was done at postnatal day 10 (PNday10) at the first phase of lung alveolar development. Head-out plethysmography for breathing pattern analysis was performed on the siblings at PNday23 followed by lung surfactant collection. The function of the collected lung surfactant was then analyzed ex vivo using the constrained drop surfactometer. Our results show that lung transcriptomics had differentially expressed genes related to surfactant turnover between groups and sex at PNday10. They also show that the GF and BI04 animals had lower respiratory rate than Cecum mice, or compared to age-matched specific pathogen-free (SPF) reference animals. We also see changes in lung surfactant function ex vivo. The overall conclusions are that 10-day-old GF mice do not have a markedly different lung gene transcription compared to gnotophoric or gnotobiotic mice, but genes related to surfactant metabolism are among the few differentially expressed genes. We show here for the first time that early-life microbiome status correlates with early-life surfactant-gene transcription and to later-in-life lung surfactant function and associated respiratory-rate changes in mice.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88029862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-03DOI: 10.3389/frmbi.2023.1143303
A. Marsh, M. Azcarate-Peril, M. Aljumaah, Jessica Neville, Maryanne T. Perrin, L. Dean, M. Wheeler, Ian N Hines, R. Pawlak
{"title":"Corrigendum: Fatty acid profile driven by maternal diet is associated with the composition of human milk microbiota","authors":"A. Marsh, M. Azcarate-Peril, M. Aljumaah, Jessica Neville, Maryanne T. Perrin, L. Dean, M. Wheeler, Ian N Hines, R. Pawlak","doi":"10.3389/frmbi.2023.1143303","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1143303","url":null,"abstract":"","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78944440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-03DOI: 10.3389/frmbi.2023.1061193
Jacob Dehinsilu, Chrysi Sergaki, G. Amos, V. Fontana, M. Pirmohamed
The advent of immune checkpoint inhibitor therapy was a significant step in the development of treatments for cancer. It is, however, a double-edged sword. Immune related adverse events are the result of unleashing brakes on the immune system and affect many patients undergoing checkpoint inhibitor therapy, often being debilitating and occasionally lethal. It has been shown both in mice and in humans that the presence of certain families, genera and species of bacteria are associated with improved responses to checkpoint inhibitor therapy, whereas in their absence the response to therapy is often poor. Recent studies have demonstrated that immune related adverse events to checkpoint inhibitor therapy can be perturbed and perhaps predicted based on the composition and functional capacity of the gut microbiota and parts of the immune system. In the case of colitis associated with immune checkpoint inhibitor therapy, one interesting avenue of investigation is based on the activity of secretory immunoglobulin A (SIgA). Produced by plasma cells, IgA is present in high concentrations at the gut mucosa and is involved in both the maturation and maintenance of the microbiota as well as the development of IBD. Here we summarise the current literature surrounding the interplay between the gut microbiota and response to CPI therapy. Additionally, we overview the colonic immune system, paying particular attention to IgA, as a key component of the microbiota-immune system interaction.
{"title":"The interplay between the microbiome and colonic immune system in checkpoint inhibitor therapy","authors":"Jacob Dehinsilu, Chrysi Sergaki, G. Amos, V. Fontana, M. Pirmohamed","doi":"10.3389/frmbi.2023.1061193","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1061193","url":null,"abstract":"The advent of immune checkpoint inhibitor therapy was a significant step in the development of treatments for cancer. It is, however, a double-edged sword. Immune related adverse events are the result of unleashing brakes on the immune system and affect many patients undergoing checkpoint inhibitor therapy, often being debilitating and occasionally lethal. It has been shown both in mice and in humans that the presence of certain families, genera and species of bacteria are associated with improved responses to checkpoint inhibitor therapy, whereas in their absence the response to therapy is often poor. Recent studies have demonstrated that immune related adverse events to checkpoint inhibitor therapy can be perturbed and perhaps predicted based on the composition and functional capacity of the gut microbiota and parts of the immune system. In the case of colitis associated with immune checkpoint inhibitor therapy, one interesting avenue of investigation is based on the activity of secretory immunoglobulin A (SIgA). Produced by plasma cells, IgA is present in high concentrations at the gut mucosa and is involved in both the maturation and maintenance of the microbiota as well as the development of IBD. Here we summarise the current literature surrounding the interplay between the gut microbiota and response to CPI therapy. Additionally, we overview the colonic immune system, paying particular attention to IgA, as a key component of the microbiota-immune system interaction.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87840583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-02DOI: 10.3389/frmbi.2023.1078024
D. Naylor, Katherine Naasko, Montana L. Smith, Sneha P. Couvillion, C. Nicora, Jesse Trejo, S. Fransen, R. Danczak, R. Mcclure, K. Hofmockel, J. Jansson
Two factors that are well-known to influence soil microbiomes are the depth of the soil as well as the level of moisture. Previous works have demonstrated that climate change will increase the incidence of drought in soils, but it is unknown how fluctuations in moisture availability affect soil microbiome composition and functioning down the depth profile. Here, we investigated soil and wheatgrass rhizosphere microbiomes in a single common field setting under four different levels of irrigation (100%, 75%, 50%, and 25%) and three depths (0-5 cm, 5-15 cm, and 15-25 cm from the surface). We demonstrated that there is a significant interactive effect between depth and irrigation, where changes in soil moisture more strongly affect soil microbiomes at the surface layer than at deeper layers. This was true for not only microbiome community composition and diversity metrics, but also for functional profiles (transcriptomic and metabolomic datasets). Meanwhile, in rhizosphere communities the influence of irrigation was similar across the different depths. However, for the ‘Alkar’ wheatgrass cultivar, the rhizosphere microbial communities responded more strongly to changes in irrigation level than did the communities for the ‘Jose’ cultivar rhizosphere. The lessened response of deeper soil microbiomes to changes in irrigation may be due to higher incidence of slow-growing, stress-resistant microbes. These results demonstrate that the soil microbiome response to moisture content is depth-dependent. As such, it will be optimal for soil microbiome studies to incorporate deeper as well as surface soils, to get a more accurate picture of the soil microbiome response to stress.
{"title":"Interactive effects of depth and differential irrigation on soil microbiome composition and functioning","authors":"D. Naylor, Katherine Naasko, Montana L. Smith, Sneha P. Couvillion, C. Nicora, Jesse Trejo, S. Fransen, R. Danczak, R. Mcclure, K. Hofmockel, J. Jansson","doi":"10.3389/frmbi.2023.1078024","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1078024","url":null,"abstract":"Two factors that are well-known to influence soil microbiomes are the depth of the soil as well as the level of moisture. Previous works have demonstrated that climate change will increase the incidence of drought in soils, but it is unknown how fluctuations in moisture availability affect soil microbiome composition and functioning down the depth profile. Here, we investigated soil and wheatgrass rhizosphere microbiomes in a single common field setting under four different levels of irrigation (100%, 75%, 50%, and 25%) and three depths (0-5 cm, 5-15 cm, and 15-25 cm from the surface). We demonstrated that there is a significant interactive effect between depth and irrigation, where changes in soil moisture more strongly affect soil microbiomes at the surface layer than at deeper layers. This was true for not only microbiome community composition and diversity metrics, but also for functional profiles (transcriptomic and metabolomic datasets). Meanwhile, in rhizosphere communities the influence of irrigation was similar across the different depths. However, for the ‘Alkar’ wheatgrass cultivar, the rhizosphere microbial communities responded more strongly to changes in irrigation level than did the communities for the ‘Jose’ cultivar rhizosphere. The lessened response of deeper soil microbiomes to changes in irrigation may be due to higher incidence of slow-growing, stress-resistant microbes. These results demonstrate that the soil microbiome response to moisture content is depth-dependent. As such, it will be optimal for soil microbiome studies to incorporate deeper as well as surface soils, to get a more accurate picture of the soil microbiome response to stress.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83067824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-02-14DOI: 10.3389/frmbi.2022.1097124
A. Tadmor, Gita Mahmoudabadi, Helen Foley, R. Phillips
Viruses are a major component of the human microbiome, yet their diversity, lifestyles, spatiotemporal dynamics, and functional impact are not well understood. Elucidating the ecology of human associated phages may have a major impact on human health due to the potential ability of phages to modulate the abundance and phenotype of commensal bacteria. Analyzing 690 Human Microbiome Project metagenomes from 103 subjects sampled across up to 18 habitats, we found that despite the great interpersonal diversity observed among human viromes, humans harbor distinct phage families characterized by their shared conserved hallmark genes known as large terminase subunit (TerL) genes. Phylogenetic analysis of these phage families revealed that different habitats in the oral cavity and gut have unique phage community structures. Over a ~7-month timescale most of these phage families persisted in the oral cavity and gut, however, presence in certain oral habitats appeared to be transitory, possibly due to host migration within the oral cavity. Interestingly, certain phage families were found to be highly correlated with pathogenic, carriage and disease-related isolates, and may potentially serve as novel biomarkers for disease. Our findings shed new light on the core human virome and offer a metagenomic-independent way to probe the core virome using widely shared conserved phage markers.
{"title":"Identification and spatio-temporal tracking of ubiquitous phage families in the human microbiome","authors":"A. Tadmor, Gita Mahmoudabadi, Helen Foley, R. Phillips","doi":"10.3389/frmbi.2022.1097124","DOIUrl":"https://doi.org/10.3389/frmbi.2022.1097124","url":null,"abstract":"Viruses are a major component of the human microbiome, yet their diversity, lifestyles, spatiotemporal dynamics, and functional impact are not well understood. Elucidating the ecology of human associated phages may have a major impact on human health due to the potential ability of phages to modulate the abundance and phenotype of commensal bacteria. Analyzing 690 Human Microbiome Project metagenomes from 103 subjects sampled across up to 18 habitats, we found that despite the great interpersonal diversity observed among human viromes, humans harbor distinct phage families characterized by their shared conserved hallmark genes known as large terminase subunit (TerL) genes. Phylogenetic analysis of these phage families revealed that different habitats in the oral cavity and gut have unique phage community structures. Over a ~7-month timescale most of these phage families persisted in the oral cavity and gut, however, presence in certain oral habitats appeared to be transitory, possibly due to host migration within the oral cavity. Interestingly, certain phage families were found to be highly correlated with pathogenic, carriage and disease-related isolates, and may potentially serve as novel biomarkers for disease. Our findings shed new light on the core human virome and offer a metagenomic-independent way to probe the core virome using widely shared conserved phage markers.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82168810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-02-02DOI: 10.3389/frmbi.2022.1077151
A. van Belkum, P. Lisotto, W. Pirovano, S. Mongiat, Amine Zorgani, M. Gempeler, R. Bongoni, E. Klaassens
Both academia and dermatological and cosmetic industries have acknowledged that healthy skin microbiota contribute to overall skin integrity and well-being. This implies that formulations developed for personal care (skin, scalp, hair etc) or (medical and cosmetic) treatment need to be compatible with microbiota conservation or possibly even improvement. The various chemical and biological components and mixtures thereof intended for direct application to the skin should not extensively affect the qualitative and quantitative composition of the skin microbiota. A compound should promote beneficial microbes and inhibit pathogens. Compounds but also final products could be considered at least theoretically “microbiome friendly” while in some cases changes to the microbiota may even be considered beneficial. An important hurdle lies in the practical and methodological approaches to be used for defining microbiota inertia of compounds and formulations. Clear guidelines for assessing microbiome friendliness are lacking. We propose three testing concepts that may help to define microbiome friendliness based on the assessment of minimal microbiota perturbation and possibly elimination of potential pathogens. Methods to prove microbiome friendliness should ultimately be based upon (metagenomic rather than amplicon-based) next generation sequencing of naive versus compound- or final product-exposed skin microbiota in vivo, but preferably also including in vitro and ex vivo pre-screening methodologies to build an understanding of their consequences. As in many domains of microbiome research, the development of experimental process controls and internal standards, which are essentially lacking to date, should be taken as a future prerequisite. There is also a requirement from regulatory agencies to define and harmonize acceptance criteria.
{"title":"Being friendly to the skin microbiome: Experimental assessment","authors":"A. van Belkum, P. Lisotto, W. Pirovano, S. Mongiat, Amine Zorgani, M. Gempeler, R. Bongoni, E. Klaassens","doi":"10.3389/frmbi.2022.1077151","DOIUrl":"https://doi.org/10.3389/frmbi.2022.1077151","url":null,"abstract":"Both academia and dermatological and cosmetic industries have acknowledged that healthy skin microbiota contribute to overall skin integrity and well-being. This implies that formulations developed for personal care (skin, scalp, hair etc) or (medical and cosmetic) treatment need to be compatible with microbiota conservation or possibly even improvement. The various chemical and biological components and mixtures thereof intended for direct application to the skin should not extensively affect the qualitative and quantitative composition of the skin microbiota. A compound should promote beneficial microbes and inhibit pathogens. Compounds but also final products could be considered at least theoretically “microbiome friendly” while in some cases changes to the microbiota may even be considered beneficial. An important hurdle lies in the practical and methodological approaches to be used for defining microbiota inertia of compounds and formulations. Clear guidelines for assessing microbiome friendliness are lacking. We propose three testing concepts that may help to define microbiome friendliness based on the assessment of minimal microbiota perturbation and possibly elimination of potential pathogens. Methods to prove microbiome friendliness should ultimately be based upon (metagenomic rather than amplicon-based) next generation sequencing of naive versus compound- or final product-exposed skin microbiota in vivo, but preferably also including in vitro and ex vivo pre-screening methodologies to build an understanding of their consequences. As in many domains of microbiome research, the development of experimental process controls and internal standards, which are essentially lacking to date, should be taken as a future prerequisite. There is also a requirement from regulatory agencies to define and harmonize acceptance criteria.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78521261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-02-02DOI: 10.3389/frmbi.2022.1092771
I. Vacarean-Trandafir, Roxana-Maria Amărandi, I. Ivanov, Ş. Iacob, A. Muşină, Elena-Roxana Bărgăoanu, Mihail-Gabriel Dimofte
Introduction The intestinal microbiota is vital to human health, and has a profound influence on several biological processes including inflammation and pathogen resistance. Antibiotic intake greatly impacts bacterial diversity, can increase antibiotic resistance and impair the equilibrium between bacterial species. The key to grasping post-antibiotic effects on the gut microbiota rests on the implementation of a suitable procedure to isolate microbial DNA and a meticulous consideration of experimental sequencing artefacts. Methods We herein report the bacterial community dynamics of a cohort of 128 surgical oncology patients before and after the intravenous administration of cefuroxime, an antibiotic routinely used in surgical antibioprophylaxis with proven efficiency against both gram-positive and gram-negative bacteria. In our study, we analyzed patient fecal samples collected through rectal examination before and 7 days post cefuroxime treatment by employing a high-throughput sequencing assay which targets the V3–V4 region of the 16S rRNA gene. A first challenge in applying the study design was to extract an appropriate amount of DNA characteristic to the sampled microbiota, which implied the use of both mechanical (ceramic beads) and chemical (proteinase K, lysozyme and lysostaphin) lysis. Results Gut microbiota richness and composition was significantly different between the two groups, but most differences were determined by additional perioperative procedures, rather than antibioprophylaxis. Intestinal microbiota composition was not significantly changed one week post cefuroxime treatment when compared to pre-treatment condition for patients without mechanical bowel preparation, but some loss in taxonomic variety could be observed. Discussion Taken together, cefuroxime does not promote short-term dysbiosis in surgical patients without any additional perioperative procedures.
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