Despite the numerous fecal microbiota transplantation trials that have been carried out, knowledge about the actual composition of a “healthy microbiota” remains scarce. The aim of this research was to describe the differences in the composition of oral and fecal microbiotas in a super-donor. The microbiota analysis was done using next-generation sequencing of the V3 and V4 regions of the bacterial 16S rRNA gene. The biodiversity found in the mouth was very rich, with 56 species identified, and there was a predominance of the genera Veillonella , Haemophilus , and Streptococcus . It is worth mentioning the presence (2.33%) of Fusobacterium nucleatum in the mouth. In feces, the genera Bacteroides and Faecalibacterium predominated, with the species F. prausnitzii being the most abundant. This analysis shows that the diversity of the microbiota of a super-donor plays a fundamental role in the effectiveness of its product in fecal matter transplantation. This suggests that transplanted gut microorganisms have the ability to maintain or recover health in a dynamic process between the microbiota and the host. Our findings encourage further research which will result in the development of bacterial therapies in infectious and inflammatory diseases.
{"title":"Case Report: Oral and fecal microbiota in a super-donor: the healthy microbiota paradigm for fecal transplantation","authors":"Nayeli Ortiz-Olvera, Edith A. Fernández-Figueroa, Jesús Argueta-Donohué, Haydee Miranda-Ortíz, Erika Ruiz-García","doi":"10.3389/frmbi.2023.1219960","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1219960","url":null,"abstract":"Despite the numerous fecal microbiota transplantation trials that have been carried out, knowledge about the actual composition of a “healthy microbiota” remains scarce. The aim of this research was to describe the differences in the composition of oral and fecal microbiotas in a super-donor. The microbiota analysis was done using next-generation sequencing of the V3 and V4 regions of the bacterial 16S rRNA gene. The biodiversity found in the mouth was very rich, with 56 species identified, and there was a predominance of the genera Veillonella , Haemophilus , and Streptococcus . It is worth mentioning the presence (2.33%) of Fusobacterium nucleatum in the mouth. In feces, the genera Bacteroides and Faecalibacterium predominated, with the species F. prausnitzii being the most abundant. This analysis shows that the diversity of the microbiota of a super-donor plays a fundamental role in the effectiveness of its product in fecal matter transplantation. This suggests that transplanted gut microorganisms have the ability to maintain or recover health in a dynamic process between the microbiota and the host. Our findings encourage further research which will result in the development of bacterial therapies in infectious and inflammatory diseases.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"63 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135884532","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 : 2023-09-12DOI: 10.3389/frmbi.2023.1208166
Linda Simon Paulo, George Msema Bwire, K. Klipstein-Grobusch, Appolinary Kamuhabwa, Gideon Kwesigabo, Pilly Chillo, Folkert W. Asselbergs, Virissa C. Lenters
Introduction As Sub-Saharan Africa (SSA) undergoes rapid urbanization changes in diet and lifestyle have contributed to a rise in non-communicable diseases (NCDs) across the region. Changes in gut microbiota which play an important role in human health may be an underlying driving factor. While evidence suggests that the gut microbiota differs between the extreme levels of economic development (least vs highly developed), it is not well-established which factors along the urbanization gradient are most influential, especially for SSA. This systematic review analyzed published articles from SSA countries that examined the differences in the composition and diversity of gut microbiota along the urbanization gradient. The findings of this review have important implications for understanding the impact of urbanization on human health in the SSA. Methods Peer-reviewed articles that examined the link between the urbanization gradient, dietary patterns, and gut microbiota using culture-independent techniques were included in the review. Results A total of 3,265 studies were identified and screened. Eighty-nine (89) studies underwent full-text review, and 23 studies were extracted and included for final analysis. Among these studies, it was observed that hunter-gatherers had high alpha diversity (within-person variation) and beta diversity (between-person variation) in their gut microbiota compared to rural and urban residents in SSA. However, there were inconsistent differences between rural and urban at the individual taxa levels, potentially due to limited statistical power and large variability in the study techniques and designs. Similarly, there were no clear differences in the relative abundance of genera across the urbanization gradient. Additionally, both diet and intestinal parasites were associated with the composition and diversity of the gut microbiota. Conclusion The review revealed there are variations in both alpha and beta diversity of the gut microbiota across the urbanization gradient with a higher diversity observed in rural areas. However, we did not observe significant differences in the relative abundance at phyla or genus levels consistently across the urbanization gradient. Moreover, our findings suggest that the mode of subsistence, diet, and intestinal parasites play a role in shaping the composition and diversity of the gut microbiota in SSA. Systematic review registration https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021251006 , identifier CRD42021251006.
{"title":"Urbanization gradient, diet, and gut microbiota in Sub-Saharan Africa: a systematic review","authors":"Linda Simon Paulo, George Msema Bwire, K. Klipstein-Grobusch, Appolinary Kamuhabwa, Gideon Kwesigabo, Pilly Chillo, Folkert W. Asselbergs, Virissa C. Lenters","doi":"10.3389/frmbi.2023.1208166","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1208166","url":null,"abstract":"Introduction As Sub-Saharan Africa (SSA) undergoes rapid urbanization changes in diet and lifestyle have contributed to a rise in non-communicable diseases (NCDs) across the region. Changes in gut microbiota which play an important role in human health may be an underlying driving factor. While evidence suggests that the gut microbiota differs between the extreme levels of economic development (least vs highly developed), it is not well-established which factors along the urbanization gradient are most influential, especially for SSA. This systematic review analyzed published articles from SSA countries that examined the differences in the composition and diversity of gut microbiota along the urbanization gradient. The findings of this review have important implications for understanding the impact of urbanization on human health in the SSA. Methods Peer-reviewed articles that examined the link between the urbanization gradient, dietary patterns, and gut microbiota using culture-independent techniques were included in the review. Results A total of 3,265 studies were identified and screened. Eighty-nine (89) studies underwent full-text review, and 23 studies were extracted and included for final analysis. Among these studies, it was observed that hunter-gatherers had high alpha diversity (within-person variation) and beta diversity (between-person variation) in their gut microbiota compared to rural and urban residents in SSA. However, there were inconsistent differences between rural and urban at the individual taxa levels, potentially due to limited statistical power and large variability in the study techniques and designs. Similarly, there were no clear differences in the relative abundance of genera across the urbanization gradient. Additionally, both diet and intestinal parasites were associated with the composition and diversity of the gut microbiota. Conclusion The review revealed there are variations in both alpha and beta diversity of the gut microbiota across the urbanization gradient with a higher diversity observed in rural areas. However, we did not observe significant differences in the relative abundance at phyla or genus levels consistently across the urbanization gradient. Moreover, our findings suggest that the mode of subsistence, diet, and intestinal parasites play a role in shaping the composition and diversity of the gut microbiota in SSA. Systematic review registration https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021251006 , identifier CRD42021251006.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135886043","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 : 2023-09-08DOI: 10.3389/frmbi.2023.1217820
J. G. Gonçalves-Nobre, Inês Gaspar, Diogo Alpuim Costa
Breast cancer (BC) is one of the most prevalent cancers worldwide. Fortunately, BC treatment has taken a huge turn in the last few years. Despite these advances, one of the main issues related to systemic treatment remains the management of its side effects, including cardiotoxicity. In this regard, we highlight the irreversible dose-dependent cardiotoxicity of anthracyclines related to oxidative stress and the reversible cardiotoxicity with trastuzumab, whose mechanism is still poorly understood. Moreover, the combination of anthracyclines and trastuzumab further exacerbate the myocardial damage. More recently, altered gut microbiota composition has been linked to the long-term effects of cancer therapy, including the potential connection between treatment-related microbial changes and cardiotoxicity. Bacteroides spp., Coriobacteriaceae_UGC-002, and Dubosiella have already been reported as bacterial species with deleterious effects on the myocardium, mainly due to the promotion of inflammation. On the other hand, Alloprevotella, Rickenellaceae_RC9, Raoultella planticola, Klebsiella pneumoniae, and Escherichia coli BW25113 can induce cardioprotection, predominantly by increasing anti-inflammatory cytokines, promoting intestinal barrier integrity and early metabolization of doxorubicin. Herein, we explore the role of gut microbiota in the development of cardiotoxicity, as well as future perspectives to decrease the risk of cardiotoxicity associated with BC treatment.
{"title":"Anthracyclines and trastuzumab associated cardiotoxicity: is the gut microbiota a friend or foe? – a mini-review","authors":"J. G. Gonçalves-Nobre, Inês Gaspar, Diogo Alpuim Costa","doi":"10.3389/frmbi.2023.1217820","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1217820","url":null,"abstract":"Breast cancer (BC) is one of the most prevalent cancers worldwide. Fortunately, BC treatment has taken a huge turn in the last few years. Despite these advances, one of the main issues related to systemic treatment remains the management of its side effects, including cardiotoxicity. In this regard, we highlight the irreversible dose-dependent cardiotoxicity of anthracyclines related to oxidative stress and the reversible cardiotoxicity with trastuzumab, whose mechanism is still poorly understood. Moreover, the combination of anthracyclines and trastuzumab further exacerbate the myocardial damage. More recently, altered gut microbiota composition has been linked to the long-term effects of cancer therapy, including the potential connection between treatment-related microbial changes and cardiotoxicity. Bacteroides spp., Coriobacteriaceae_UGC-002, and Dubosiella have already been reported as bacterial species with deleterious effects on the myocardium, mainly due to the promotion of inflammation. On the other hand, Alloprevotella, Rickenellaceae_RC9, Raoultella planticola, Klebsiella pneumoniae, and Escherichia coli BW25113 can induce cardioprotection, predominantly by increasing anti-inflammatory cytokines, promoting intestinal barrier integrity and early metabolization of doxorubicin. Herein, we explore the role of gut microbiota in the development of cardiotoxicity, as well as future perspectives to decrease the risk of cardiotoxicity associated with BC treatment.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"60 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80452799","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 : 2023-08-17DOI: 10.3389/frmbi.2023.1206961
Rafael S. Oliveira, Otávio H. B. Pinto, B. Quirino, Mayanne A M de Freitas, F. Thompson, C. Thompson, R. Kruger
The Great Amazon Reef System (GARS) is an extensive biogenic reef influenced by a plume layer of sediments. This creates an extreme environment where light is reduced, thus affecting physicochemical properties as well as living organisms such as sponges and their microbiomes. The sponge’s microbiome has numerous ecological roles, like participation in biogeochemical cycles and host nutrition, helping the sponge thrive and contributing to the ecosystem. Also, sponges and sponge-associated microorganisms are rich sources of bioactive compounds, and their products are applied in different areas, including textile, pharmaceutical, and food industries. In this context, metagenome-assembled genomes (MAG), obtained from GARS sponges microbiota, were analyzed to predict their ecological function and were prospected for biotechnological features. Thus, in this work, tissues of GARS sponges were collected, their metagenomes were sequenced and assembled, and 1,054 MAGs were recovered. Ten of those MAGs were selected based on their taxonomic classification in the candidate phylum Latescibacterota and this group’s abundance in GARS sponges. The workflow consisted of MAG’s quality definition, taxonomic classification, metabolic reconstruction, and search for bioactive compounds. Metabolic reconstruction from medium to high-quality MAGs revealed genes related to degradation and synthesis pathways, indicating functions that may be performed by GARS sponge-associated Latescibacterota. Heterotrophy, a recurring attribute in Latescibacterota that might be crucial for GARS sponge holobiont nutrition, was verified by the presence of genes related to respiration and fermentation. Also, the analyzed bacteria may contribute to the host’s survival in multiple ways, including host protection via defense systems; aid in nutrient consumption by breaking complex substrates and producing essential nutrients like vitamins and certain amino acids; and detoxification of mercury, arsenic, ammonia, and hydrogen sulfide. Additionally, genes linked to persistent organic pollutant degradation, including glyphosate, and biogeochemical cycles reactions, such as ammonification, sulfate reduction, thiosulfate disproportionation, phosphorus remineralization, and complex organic matter degradation, were identified, suggesting the participation of these Latescibacterota in bioremediation and nutrient cycling. Finally, the investigated MAGs contain genes for numerous bioactive compounds, including industrial enzymes, secondary metabolites, and biologically active peptides, which may have biotechnological value.
{"title":"Genome-resolved metagenomic analysis of Great Amazon Reef System sponge-associated Latescibacterota bacteria and their potential contributions to the host sponge and reef","authors":"Rafael S. Oliveira, Otávio H. B. Pinto, B. Quirino, Mayanne A M de Freitas, F. Thompson, C. Thompson, R. Kruger","doi":"10.3389/frmbi.2023.1206961","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1206961","url":null,"abstract":"The Great Amazon Reef System (GARS) is an extensive biogenic reef influenced by a plume layer of sediments. This creates an extreme environment where light is reduced, thus affecting physicochemical properties as well as living organisms such as sponges and their microbiomes. The sponge’s microbiome has numerous ecological roles, like participation in biogeochemical cycles and host nutrition, helping the sponge thrive and contributing to the ecosystem. Also, sponges and sponge-associated microorganisms are rich sources of bioactive compounds, and their products are applied in different areas, including textile, pharmaceutical, and food industries. In this context, metagenome-assembled genomes (MAG), obtained from GARS sponges microbiota, were analyzed to predict their ecological function and were prospected for biotechnological features. Thus, in this work, tissues of GARS sponges were collected, their metagenomes were sequenced and assembled, and 1,054 MAGs were recovered. Ten of those MAGs were selected based on their taxonomic classification in the candidate phylum Latescibacterota and this group’s abundance in GARS sponges. The workflow consisted of MAG’s quality definition, taxonomic classification, metabolic reconstruction, and search for bioactive compounds. Metabolic reconstruction from medium to high-quality MAGs revealed genes related to degradation and synthesis pathways, indicating functions that may be performed by GARS sponge-associated Latescibacterota. Heterotrophy, a recurring attribute in Latescibacterota that might be crucial for GARS sponge holobiont nutrition, was verified by the presence of genes related to respiration and fermentation. Also, the analyzed bacteria may contribute to the host’s survival in multiple ways, including host protection via defense systems; aid in nutrient consumption by breaking complex substrates and producing essential nutrients like vitamins and certain amino acids; and detoxification of mercury, arsenic, ammonia, and hydrogen sulfide. Additionally, genes linked to persistent organic pollutant degradation, including glyphosate, and biogeochemical cycles reactions, such as ammonification, sulfate reduction, thiosulfate disproportionation, phosphorus remineralization, and complex organic matter degradation, were identified, suggesting the participation of these Latescibacterota in bioremediation and nutrient cycling. Finally, the investigated MAGs contain genes for numerous bioactive compounds, including industrial enzymes, secondary metabolites, and biologically active peptides, which may have biotechnological value.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"112 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79403803","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 : 2023-08-15DOI: 10.3389/frmbi.2023.1222089
Rebecca Gudka, I. Nyinoh
Autism spectrum disorders (ASDs) are complex neurobiological conditions with poor long-term outcomes and limited treatment options. The microbiota–gut–brain axis indicates a pathway by which the gut microbiota links to ASDs. Fecal microbial transplantation (FMT), whereby the gut microbiota is replaced with that of a healthy individual, shows promise for the treatment of neurobiological conditions. This review examines the current evidence for the use of FMT as a therapeutic for ASD.ASDs and their associated gastrointestinal symptoms are improved with FMT, potentially due to the engraftment of features of a healthy gut. Longer treatment regimens that include daily maintenance doses appear to be the most effective long-term therapeutic option, with benefits persisting 2 years post-intervention. Evidence is mixed regarding the use of preparatory treatments. Considering the sex bias in ASD research, small sample sizes and the lack of placebo control arms, randomized controlled trials would be of benefit to the evidence base regarding the use of FMT as a therapeutic option for ASD.FMT is a promising new therapeutic for ASD, but the evidence base is in its infancy.
{"title":"Fecal microbial transplantation as a novel therapeutic for autism spectrum disorders: a review of the current literature","authors":"Rebecca Gudka, I. Nyinoh","doi":"10.3389/frmbi.2023.1222089","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1222089","url":null,"abstract":"Autism spectrum disorders (ASDs) are complex neurobiological conditions with poor long-term outcomes and limited treatment options. The microbiota–gut–brain axis indicates a pathway by which the gut microbiota links to ASDs. Fecal microbial transplantation (FMT), whereby the gut microbiota is replaced with that of a healthy individual, shows promise for the treatment of neurobiological conditions. This review examines the current evidence for the use of FMT as a therapeutic for ASD.ASDs and their associated gastrointestinal symptoms are improved with FMT, potentially due to the engraftment of features of a healthy gut. Longer treatment regimens that include daily maintenance doses appear to be the most effective long-term therapeutic option, with benefits persisting 2 years post-intervention. Evidence is mixed regarding the use of preparatory treatments. Considering the sex bias in ASD research, small sample sizes and the lack of placebo control arms, randomized controlled trials would be of benefit to the evidence base regarding the use of FMT as a therapeutic option for ASD.FMT is a promising new therapeutic for ASD, but the evidence base is in its infancy.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74753677","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 : 2023-08-15DOI: 10.3389/frmbi.2023.1204988
E. Guduk, M. Hall, G. Zanton, A. Steinberger, P. Weimer, G. Suen, K. Weigel
We evaluated the influence of diets differing in non-fiber carbohydrates and rumen-degradable protein (RDP) levels on changes in the ruminal bacterial populations in lactating Holstein cows. In all, 12 ruminally cannulated cows were assigned to diets with high or low RDP levels. Within each RDP level, molasses was substituted for corn grain at a concentration of 0%, 5.25%, or 10.5% of diet dry matter in a replicated 3 × 3 Latin square design with 28-day periods. Liquid and solid rumen digesta fractions collected at the end of each period underwent 16S rRNA gene sequencing to identify operational taxonomic units and were analyzed for short-chain fatty acids. Protein degradability affected 6 bacterial genera, whereas carbohydrate alteration impacted 13 genera (p < 0.05). Of the 30 genera with the highest relative abundance, 26 differed by digesta fraction (p < 0.05), with Bacteroidetes genera showing a greater abundance in solids and Firmicutes genera demonstrating a greater prevalence in liquids. Regarding relative abundances, with increasing molasses, Succiniclasticum decreased in liquid (p < 0.05), and CF231, YRC22, Clostridium, Desulfovibrio, BF311, and Oscillospira increased in solids (p < 0.05). In contrast, at higher RDP levels, Succiniclasticum increased while YRC22 and Pseudobutyrivibrio decreased in solids (p < 0.05). Genera with abundances found to be correlated with fermentation products in the liquid included Shuttleworthia, Treponema, Lachnospira, and Schwartzia, which typically have lower relative abundances, showing strong positive correlations with molar proportions (mol%) of propionate, butyrate, and valerate (p < 0.05), and negative correlations with pH and acetate mol% (p < 0.05). Fibrobacter was positively correlated with lactate mol% (p < 0.05). Butyrate mol% exhibited a quadratic increase as molasses increased (p = 0.017), and lactate mol% rose with increased RDP levels (p = 0.042). No treatment effects were detected for pH propionate and valerate mol%; however, we observed a tendency (p = 0.075) for a quadratic effect of molasses treatment on the mol% of acetate. These findings substantiate the pivotal role of diet in shaping rumen microbiota and metabolism, elucidating a nuanced relationship between dietary components, bacterial community structure, and metabolic output. This offers a more detailed understanding of rumen function and the potential for high-precision dietary management in lactating cows.
{"title":"Characterization of rumen microbiota in lactating Holstein cows fed molasses versus corn grain at two levels of rumen-degradable protein","authors":"E. Guduk, M. Hall, G. Zanton, A. Steinberger, P. Weimer, G. Suen, K. Weigel","doi":"10.3389/frmbi.2023.1204988","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1204988","url":null,"abstract":"We evaluated the influence of diets differing in non-fiber carbohydrates and rumen-degradable protein (RDP) levels on changes in the ruminal bacterial populations in lactating Holstein cows. In all, 12 ruminally cannulated cows were assigned to diets with high or low RDP levels. Within each RDP level, molasses was substituted for corn grain at a concentration of 0%, 5.25%, or 10.5% of diet dry matter in a replicated 3 × 3 Latin square design with 28-day periods. Liquid and solid rumen digesta fractions collected at the end of each period underwent 16S rRNA gene sequencing to identify operational taxonomic units and were analyzed for short-chain fatty acids. Protein degradability affected 6 bacterial genera, whereas carbohydrate alteration impacted 13 genera (p < 0.05). Of the 30 genera with the highest relative abundance, 26 differed by digesta fraction (p < 0.05), with Bacteroidetes genera showing a greater abundance in solids and Firmicutes genera demonstrating a greater prevalence in liquids. Regarding relative abundances, with increasing molasses, Succiniclasticum decreased in liquid (p < 0.05), and CF231, YRC22, Clostridium, Desulfovibrio, BF311, and Oscillospira increased in solids (p < 0.05). In contrast, at higher RDP levels, Succiniclasticum increased while YRC22 and Pseudobutyrivibrio decreased in solids (p < 0.05). Genera with abundances found to be correlated with fermentation products in the liquid included Shuttleworthia, Treponema, Lachnospira, and Schwartzia, which typically have lower relative abundances, showing strong positive correlations with molar proportions (mol%) of propionate, butyrate, and valerate (p < 0.05), and negative correlations with pH and acetate mol% (p < 0.05). Fibrobacter was positively correlated with lactate mol% (p < 0.05). Butyrate mol% exhibited a quadratic increase as molasses increased (p = 0.017), and lactate mol% rose with increased RDP levels (p = 0.042). No treatment effects were detected for pH propionate and valerate mol%; however, we observed a tendency (p = 0.075) for a quadratic effect of molasses treatment on the mol% of acetate. These findings substantiate the pivotal role of diet in shaping rumen microbiota and metabolism, elucidating a nuanced relationship between dietary components, bacterial community structure, and metabolic output. This offers a more detailed understanding of rumen function and the potential for high-precision dietary management in lactating cows.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88950677","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 : 2023-08-09DOI: 10.3389/frmbi.2023.1199766
Josué Rodríguez-Ramos, Angela Oliverio, Mikayla A. Borton, Robert Danczak, Birgit M. Mueller, Hanna Schulz, Jared Ellenbogen, Rory M. Flynn, Rebecca A. Daly, LeAundra Schopflin, Michael Shaffer, Amy Goldman, Joerg Lewandowski, James C. Stegen, Kelly C. Wrighton
Although river ecosystems constitute a small fraction of Earth’s total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae , which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.
{"title":"Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream","authors":"Josué Rodríguez-Ramos, Angela Oliverio, Mikayla A. Borton, Robert Danczak, Birgit M. Mueller, Hanna Schulz, Jared Ellenbogen, Rory M. Flynn, Rebecca A. Daly, LeAundra Schopflin, Michael Shaffer, Amy Goldman, Joerg Lewandowski, James C. Stegen, Kelly C. Wrighton","doi":"10.3389/frmbi.2023.1199766","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1199766","url":null,"abstract":"Although river ecosystems constitute a small fraction of Earth’s total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae , which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"58 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135652426","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 : 2023-08-02DOI: 10.3389/frmbi.2023.1194705
Alexandra von Münchow, Sarah Torp Yttergren, R. R. Jakobsen, N. Lúthersson, A. K. Hansen, F. Lindenberg
The prevalence of Equine Metabolic Syndrome and insulin dysregulation is increasing in the horse population. Insulin dysregulation is a risk factor for laminitis, which has significant welfare consequences for the horse. Current treatment strategies for Equine Metabolic Syndrome have variable effects on insulin sensitivity. Findings suggest that gut microbiota plays an important role in gastrointestinal barrier protection and metabolic diseases. Dietary supplementation with oligosaccharides has been shown to increase the production of short-chain fatty acids and induce changes in the gut microbiota, with an increase in insulin sensitivity.We hypothesized that dietary oligosaccharide supplementation would ameliorate insulin dysregulation in horses with Equine Metabolic Syndrome.Fifteen horses were included in a cross-over study including two feed supplementations periods with oligosaccharide supplementation or calcium carbonate. Before and after each period plasma insulin, endotoxin, serum amyloid A, and blood glucose concentrations were measured during an oral sugar test and fecal samples were collected.Oligosaccharide supplementation significantly reduced insulin in geldings (p = 0.02). Overall, none of the dominating bacterias changed significantly in relative Δ-abundance. In the gut microbiota of mares, the Akkermansia genus and Clostridiaceae family were significantly more abundant. Within-sample bacterial diversity of horses with insulin concentrations > 60 mIU/L was significantly greater when compared to horses < 60 mIU/L. Horses with insulin concentrations > 60 mIU/L and horses with previous laminitis had a significantly greater beta diversity.Cut-off values for oligosaccharide feed supplementation/placebo dosing instead of dosing by g/kg body weight; owner compliance; single blood sample in oral sugar test; inter-horse variationThis study demonstrated that oligosaccharide supplementation could improve insulin dysregulation in geldings with Equine Metabolic Syndrome suggesting that sex susceptibility might be a factor to consider. Additionally, a tendency of reduction of obesity-associated bacteria was observed. Furthermore, the diversity of the gut microbiota was significantly dependent on laminitis status and insulin concentrations. However, more studies on the effects of oligosaccharide supplementation on insulin dysregulation are needed to improve the dietary management of horses with Equine Metabolic Syndrome.
{"title":"Oligosaccharide feed supplementation reduces plasma insulin in geldings with Equine Metabolic Syndrome","authors":"Alexandra von Münchow, Sarah Torp Yttergren, R. R. Jakobsen, N. Lúthersson, A. K. Hansen, F. Lindenberg","doi":"10.3389/frmbi.2023.1194705","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1194705","url":null,"abstract":"The prevalence of Equine Metabolic Syndrome and insulin dysregulation is increasing in the horse population. Insulin dysregulation is a risk factor for laminitis, which has significant welfare consequences for the horse. Current treatment strategies for Equine Metabolic Syndrome have variable effects on insulin sensitivity. Findings suggest that gut microbiota plays an important role in gastrointestinal barrier protection and metabolic diseases. Dietary supplementation with oligosaccharides has been shown to increase the production of short-chain fatty acids and induce changes in the gut microbiota, with an increase in insulin sensitivity.We hypothesized that dietary oligosaccharide supplementation would ameliorate insulin dysregulation in horses with Equine Metabolic Syndrome.Fifteen horses were included in a cross-over study including two feed supplementations periods with oligosaccharide supplementation or calcium carbonate. Before and after each period plasma insulin, endotoxin, serum amyloid A, and blood glucose concentrations were measured during an oral sugar test and fecal samples were collected.Oligosaccharide supplementation significantly reduced insulin in geldings (p = 0.02). Overall, none of the dominating bacterias changed significantly in relative Δ-abundance. In the gut microbiota of mares, the Akkermansia genus and Clostridiaceae family were significantly more abundant. Within-sample bacterial diversity of horses with insulin concentrations > 60 mIU/L was significantly greater when compared to horses < 60 mIU/L. Horses with insulin concentrations > 60 mIU/L and horses with previous laminitis had a significantly greater beta diversity.Cut-off values for oligosaccharide feed supplementation/placebo dosing instead of dosing by g/kg body weight; owner compliance; single blood sample in oral sugar test; inter-horse variationThis study demonstrated that oligosaccharide supplementation could improve insulin dysregulation in geldings with Equine Metabolic Syndrome suggesting that sex susceptibility might be a factor to consider. Additionally, a tendency of reduction of obesity-associated bacteria was observed. Furthermore, the diversity of the gut microbiota was significantly dependent on laminitis status and insulin concentrations. However, more studies on the effects of oligosaccharide supplementation on insulin dysregulation are needed to improve the dietary management of horses with Equine Metabolic Syndrome.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84260610","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 : 2023-07-28DOI: 10.3389/frmbi.2023.1180565
M. Mulinge, Sylvia Mwanza, H. M. Kabahweza, D. Wamalwa, R. Nduati
Preterm infants encounter an unnatural beginning to life, with housing in neonatal intensive care units (NICUs) where they are exposed to antibiotics. Although the effectiveness of antibiotics in infection control is well established, the short- and long-term unintended effects on the microbiota of preterm infants receiving antibiotic treatment are yet to be quantified. Our aim was to investigate the unintended consequences of NICU antibiotics on preterm infants’ gut microbiota. We searched three electronic databases—Embase, PubMed, and Scopus—for records from 2010 to October 2022. Eligibility criteria included intervention and observational studies that collected stool samples and analyzed microbiota data on the effect of antibiotics on the gut microbiota of preterm infants using 16S rRNA sequencing. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed, and the quality of the studies was judged using the Cochrane Collaboration Tool for assessing risk of bias (RoB2) for clinical trials, while non-randomized studies were assessed using the Newcastle–Ottawa Scale (NOS). The initial searches yielded 7,605 papers, of which 21 were included in the review. The selected studies examined 3,669 stool samples that were collected longitudinally from 878 preterm infants in seven different countries. Preterm infants exposed to antibiotics had a reduced bacterial diversity, an increased relative abundance of pathogenic bacteria such as Enterobacteriaceae, and a decrease or absence of symbiotic bacteria such as Bifidobacterium spp., which have been shown to assist in immunity development. Antibiotic discontinuation restored diversity, with variances linked to the antibiotic spectrum and treatment duration in some but not all cases. Breastfeeding confounded the association between antibiotic use and dysbiosis. Intriguingly, the reduction of γ-aminobutyric acid (GABA), a crucial neurotransmitter for early brain development, was linked to the depletion of Veillonella spp. Despite the apparent benefits of using antibiotics on preterm infants, we conclude that they should be used only when absolutely necessary and for a short period of time. Mothers’ milk is recommended to hasten the restoration of disrupted microbiota.
{"title":"The impact of neonatal intensive care unit antibiotics on gut bacterial microbiota of preterm infants: a systematic review","authors":"M. Mulinge, Sylvia Mwanza, H. M. Kabahweza, D. Wamalwa, R. Nduati","doi":"10.3389/frmbi.2023.1180565","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1180565","url":null,"abstract":"Preterm infants encounter an unnatural beginning to life, with housing in neonatal intensive care units (NICUs) where they are exposed to antibiotics. Although the effectiveness of antibiotics in infection control is well established, the short- and long-term unintended effects on the microbiota of preterm infants receiving antibiotic treatment are yet to be quantified. Our aim was to investigate the unintended consequences of NICU antibiotics on preterm infants’ gut microbiota. We searched three electronic databases—Embase, PubMed, and Scopus—for records from 2010 to October 2022. Eligibility criteria included intervention and observational studies that collected stool samples and analyzed microbiota data on the effect of antibiotics on the gut microbiota of preterm infants using 16S rRNA sequencing. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed, and the quality of the studies was judged using the Cochrane Collaboration Tool for assessing risk of bias (RoB2) for clinical trials, while non-randomized studies were assessed using the Newcastle–Ottawa Scale (NOS). The initial searches yielded 7,605 papers, of which 21 were included in the review. The selected studies examined 3,669 stool samples that were collected longitudinally from 878 preterm infants in seven different countries. Preterm infants exposed to antibiotics had a reduced bacterial diversity, an increased relative abundance of pathogenic bacteria such as Enterobacteriaceae, and a decrease or absence of symbiotic bacteria such as Bifidobacterium spp., which have been shown to assist in immunity development. Antibiotic discontinuation restored diversity, with variances linked to the antibiotic spectrum and treatment duration in some but not all cases. Breastfeeding confounded the association between antibiotic use and dysbiosis. Intriguingly, the reduction of γ-aminobutyric acid (GABA), a crucial neurotransmitter for early brain development, was linked to the depletion of Veillonella spp. Despite the apparent benefits of using antibiotics on preterm infants, we conclude that they should be used only when absolutely necessary and for a short period of time. Mothers’ milk is recommended to hasten the restoration of disrupted microbiota.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84837707","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 : 2023-07-26DOI: 10.3389/frmbi.2023.1192316
R. Yamamura, Kumi Y. Inoue, K. Nishino, S. Yamasaki
Gut microbiota has been reported to be closely related to host energy metabolism and immunity, and thus influence the development and progression of various human diseases. To date, the gut microbial metabolites such as short-chain fatty acids, defensins, cathelicidins, and lactoferrin in feces have been investigated as biomarkers associated with various disease conditions. In this review, we introduce intestinal and fecal pH, which is relatively easy and rapid to measure compared to the composition of the gut microbiota and its metabolites. In particular, this review presents the distribution of pH in the human body, its role and clinical significance, and various factors that affect intestinal and fecal pH, including the gut microbiota and its metabolites.
{"title":"Intestinal and fecal pH in human health","authors":"R. Yamamura, Kumi Y. Inoue, K. Nishino, S. Yamasaki","doi":"10.3389/frmbi.2023.1192316","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1192316","url":null,"abstract":"Gut microbiota has been reported to be closely related to host energy metabolism and immunity, and thus influence the development and progression of various human diseases. To date, the gut microbial metabolites such as short-chain fatty acids, defensins, cathelicidins, and lactoferrin in feces have been investigated as biomarkers associated with various disease conditions. In this review, we introduce intestinal and fecal pH, which is relatively easy and rapid to measure compared to the composition of the gut microbiota and its metabolites. In particular, this review presents the distribution of pH in the human body, its role and clinical significance, and various factors that affect intestinal and fecal pH, including the gut microbiota and its metabolites.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"71 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86244957","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}
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