Pub Date : 2023-10-25DOI: 10.3389/frmbi.2023.1212130
Katarzyna B. Miska, Monika Proszkowiec-Weglarz, Vinicius Buiatte, Mahmoud Mahmoud, Tyler Lesko, Mark C. Jenkins, Surinder Chopra, Alberto Gino Lorenzoni
Necrotic enteritis (NE) is a disease of the gastrointestinal tract that is common in broiler chickens and causes substantial economic losses to the poultry industry worldwide. The removal of many antimicrobials in poultry diets has driven the search for alternatives. The purpose of this study was to determine the microbiota changes in the cecal luminal (CE-L) and mucosal (CE-M) populations of broiler chickens undergoing clinical NE (co-infected with Eimeria maxima and Clostridium perfringens) while fed a diet containing a flavonoid rich corn (PennHFD1) or control diet using commercial corns. It was previously shown that chickens fed a diet high in flavonoids had improved performance parameters, lower mortality rate, and lower incidence of intestinal lesions. Flavonoids have been shown to have anti-bacterial, immuno-modulatory, and anti-inflammatory activity. The current study included four experimental groups: infected chickens fed commercial corn diet (CTRL-A) or PennHFD1 (CTRL-B) and infected chickens fed commercial corn diet (IF-A) or PennHFD1 (IF-B). We found that most of the microbiota changes were due to infection rather than diet. The alpha diversity in the IF chickens was lower in both CE-L and CE-M. The beta diversity of microbial communities was different between IF and CTRL chickens, as well as between CTRL-A and CTRL-B. The beta diversity of CTRL birds was more homogenous compared to IF samples. Taxonomic analysis showed a decrease in short chain fatty acid producing bacteria in IF birds. An increase in lactic acid producing bacteria, Escherichia coli , and Enterococcus cecorum was also observed in IF birds. It is possible that the effect of the high flavonoid corn on the microbiota was overcome by the effect of NE, or that the positive effects of increased flavonoids in NE-challenged birds are a result of mechanisms which do not involve the microbiota. The effects of high flavonoid corn on NE infections may be further investigated as a possible alternative to antimicrobials.
{"title":"Comparative analysis of microbiota in the ceca of broiler chickens with necrotic enteritis fed a commercial corn diet or with corn high in flavonoids (PennHFD1)","authors":"Katarzyna B. Miska, Monika Proszkowiec-Weglarz, Vinicius Buiatte, Mahmoud Mahmoud, Tyler Lesko, Mark C. Jenkins, Surinder Chopra, Alberto Gino Lorenzoni","doi":"10.3389/frmbi.2023.1212130","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1212130","url":null,"abstract":"Necrotic enteritis (NE) is a disease of the gastrointestinal tract that is common in broiler chickens and causes substantial economic losses to the poultry industry worldwide. The removal of many antimicrobials in poultry diets has driven the search for alternatives. The purpose of this study was to determine the microbiota changes in the cecal luminal (CE-L) and mucosal (CE-M) populations of broiler chickens undergoing clinical NE (co-infected with Eimeria maxima and Clostridium perfringens) while fed a diet containing a flavonoid rich corn (PennHFD1) or control diet using commercial corns. It was previously shown that chickens fed a diet high in flavonoids had improved performance parameters, lower mortality rate, and lower incidence of intestinal lesions. Flavonoids have been shown to have anti-bacterial, immuno-modulatory, and anti-inflammatory activity. The current study included four experimental groups: infected chickens fed commercial corn diet (CTRL-A) or PennHFD1 (CTRL-B) and infected chickens fed commercial corn diet (IF-A) or PennHFD1 (IF-B). We found that most of the microbiota changes were due to infection rather than diet. The alpha diversity in the IF chickens was lower in both CE-L and CE-M. The beta diversity of microbial communities was different between IF and CTRL chickens, as well as between CTRL-A and CTRL-B. The beta diversity of CTRL birds was more homogenous compared to IF samples. Taxonomic analysis showed a decrease in short chain fatty acid producing bacteria in IF birds. An increase in lactic acid producing bacteria, Escherichia coli , and Enterococcus cecorum was also observed in IF birds. It is possible that the effect of the high flavonoid corn on the microbiota was overcome by the effect of NE, or that the positive effects of increased flavonoids in NE-challenged birds are a result of mechanisms which do not involve the microbiota. The effects of high flavonoid corn on NE infections may be further investigated as a possible alternative to antimicrobials.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135168899","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 : 2023-10-19DOI: 10.3389/frmbi.2023.1231271
Petra Zimmermann
Introduction The nasopharynx harbours a diverse and dynamic microbial community, which plays an important role in maintaining the health and homeostasis of the respiratory tract, as well as in immune system development. Understanding factors that influence the composition of the nasopharyngeal microbiome in children and its association with diseases is of particular importance, as children are at a heightened risk for respiratory infections and other adverse health outcomes. Objectives This review systematically summarises studies which investigated the nasopharyngeal microbiome in children, including its dynamics, stability over time, and the influence of intrinsic and extrinsic factors on its composition. Methods MEDLINE was searched using the OVID interface. Original studies which investigated the nasopharyngeal microbiome using next generation sequencing in children were summarised. Results The search identified 736 studies, of which 77 were included. The studies show that the nasopharyngeal microbiome in children is dynamic and influenced by many external factors. A high abundance of Haemophilus , Moraxella , and Streptococcus and a low abundance of Corynebacterium and Dolosigranlum are associated with adverse health outcomes such as respiratory tract infections, wheezing and asthma exacerbations. Factors which have been identified as risk factors for these adverse health outcomes, such as being born by Caesarean section, not being breast-fed, having siblings, day-care attendance, and antibiotic exposure have been shown to be associated with the aforementioned features in the nasopharyngeal microbiome. Conclusion The association between specific nasopharyngeal microbial profiles and adverse health outcomes highlights the potential of the nasopharyngeal microbiome as a marker for identifying children at risk for disease and even more importantly, as an avenue for targeted interventions and preventive strategies.
{"title":"Exploring the microbial landscape of the nasopharynx in children: a systematic review of studies using next generation sequencing","authors":"Petra Zimmermann","doi":"10.3389/frmbi.2023.1231271","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1231271","url":null,"abstract":"Introduction The nasopharynx harbours a diverse and dynamic microbial community, which plays an important role in maintaining the health and homeostasis of the respiratory tract, as well as in immune system development. Understanding factors that influence the composition of the nasopharyngeal microbiome in children and its association with diseases is of particular importance, as children are at a heightened risk for respiratory infections and other adverse health outcomes. Objectives This review systematically summarises studies which investigated the nasopharyngeal microbiome in children, including its dynamics, stability over time, and the influence of intrinsic and extrinsic factors on its composition. Methods MEDLINE was searched using the OVID interface. Original studies which investigated the nasopharyngeal microbiome using next generation sequencing in children were summarised. Results The search identified 736 studies, of which 77 were included. The studies show that the nasopharyngeal microbiome in children is dynamic and influenced by many external factors. A high abundance of Haemophilus , Moraxella , and Streptococcus and a low abundance of Corynebacterium and Dolosigranlum are associated with adverse health outcomes such as respiratory tract infections, wheezing and asthma exacerbations. Factors which have been identified as risk factors for these adverse health outcomes, such as being born by Caesarean section, not being breast-fed, having siblings, day-care attendance, and antibiotic exposure have been shown to be associated with the aforementioned features in the nasopharyngeal microbiome. Conclusion The association between specific nasopharyngeal microbial profiles and adverse health outcomes highlights the potential of the nasopharyngeal microbiome as a marker for identifying children at risk for disease and even more importantly, as an avenue for targeted interventions and preventive strategies.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135730730","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 : 2023-10-03DOI: 10.3389/frmbi.2023.1248384
Qilin Yang, Jiancheng Wang, Dawei Zhang, Hui Feng, Tohir A. Bozorov, Honglan Yang, Daoyuan Zhang
Transgenic crops are increasingly prevalent worldwide, and evaluating their impact on soil microbial communities is a critical aspect of upholding environmental safety. Our previous research demonstrated that overexpression of ScALDH21 from desiccant-tolerant moss, Syntrichia caninervis , in cotton revealed multi-resistance to drought, salt, and biotic stresses. We conducted metabarcoding using high-throughput sequencing to evaluate the effect of ScALDH21 transgenic cotton on soil microbial communities. We further conducted soil tests to analyze the chemical properties of transgenic and non-transgenic cotton, including the total content and availability of chemical elements (K, P, and N), organic matter, and pH value. Both transgenic and non-transgenic cotton fields exhibited soil pH values higher than 8. The presence of transgenic cotton significantly enhanced the availability of available K and the total content of total P in the soil. Alpha and beta diversity indices of soil microbiota showed no difference between two transgenic and non-transgenic cotton groups. Dominant clades of fungal and bacterial genera were equivalent at the phylum and genus levels in all three groups. The correlation analysis of microbial communities and soil environmental factors revealed the absence of significant differences between transgenic and non-transgenic cotton genotypes. Functional predictions of soil microbial communities indicated that microbial community function did not show significant differences between transgenic and non-transgenic cotton samples. These findings are essential for evaluating the environmental effects of transgenic crops and supporting the secure implementation of transgenic cotton.
{"title":"Effects of multi-resistant ScALDH21 transgenic cotton on soil microbial communities","authors":"Qilin Yang, Jiancheng Wang, Dawei Zhang, Hui Feng, Tohir A. Bozorov, Honglan Yang, Daoyuan Zhang","doi":"10.3389/frmbi.2023.1248384","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1248384","url":null,"abstract":"Transgenic crops are increasingly prevalent worldwide, and evaluating their impact on soil microbial communities is a critical aspect of upholding environmental safety. Our previous research demonstrated that overexpression of ScALDH21 from desiccant-tolerant moss, Syntrichia caninervis , in cotton revealed multi-resistance to drought, salt, and biotic stresses. We conducted metabarcoding using high-throughput sequencing to evaluate the effect of ScALDH21 transgenic cotton on soil microbial communities. We further conducted soil tests to analyze the chemical properties of transgenic and non-transgenic cotton, including the total content and availability of chemical elements (K, P, and N), organic matter, and pH value. Both transgenic and non-transgenic cotton fields exhibited soil pH values higher than 8. The presence of transgenic cotton significantly enhanced the availability of available K and the total content of total P in the soil. Alpha and beta diversity indices of soil microbiota showed no difference between two transgenic and non-transgenic cotton groups. Dominant clades of fungal and bacterial genera were equivalent at the phylum and genus levels in all three groups. The correlation analysis of microbial communities and soil environmental factors revealed the absence of significant differences between transgenic and non-transgenic cotton genotypes. Functional predictions of soil microbial communities indicated that microbial community function did not show significant differences between transgenic and non-transgenic cotton samples. These findings are essential for evaluating the environmental effects of transgenic crops and supporting the secure implementation of transgenic cotton.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"155 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135739260","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 : 2023-10-02DOI: 10.3389/frmbi.2023.1218281
Hongyu Yao, Zeming Zhang, Nan Wu, Mengping Wang, Qian Wu, Hong Wu, Dapeng Zhao
The migratory bird’s gut microbiome composition and function change during the overwintering period, helping the host to adapt to different environments. Our study investigated the gut microbiome of migratory relict gulls ( Larus relictus ) in the early and late wintering stages from their overwintering grounds in Tianjin, China. We collected 24 and 29 fecal samples at the early and late stages, respectively, and analyzed the samples using high-throughput sequencing technology to find the relationship between diet, living environment, and gut microbiome of migratory birds. The results showed that the diversity and abundance of microbial communities (alpha diversity) increased during the overwintering period and significantly differed between both groups (beta diversity). Based on the gut microbial taxonomic composition, the relative abundance of Firmicutes decreased during the overwintering period, and Proteobacteria increased significantly. Furthermore, Catellicoccus and Breznakia were the main genera in both the early and late stages. Prediction of KEGG functions based on the PICRUSt2 method showed that changes in the gut microbiome resulted in an increased abundance of bacteria associated with amino acid metabolism, metabolism of cofactors and vitamins, energy metabolism, and environmental adaptation in the late stage. Differences in diet and environment at different stages during the overwintering period may have led to the differentiation of microbial communities, and their adaptive mechanisms need to be further investigated. This is the first in-depth study of the gut microbial composition of L. relictus during the overwintering period in northern China. These findings may contribute to the protection of migratory birds.
{"title":"Comparative analysis of intestinal flora at different overwintering periods in wild relict gulls (Larus relictus): first evidence from Northern China","authors":"Hongyu Yao, Zeming Zhang, Nan Wu, Mengping Wang, Qian Wu, Hong Wu, Dapeng Zhao","doi":"10.3389/frmbi.2023.1218281","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1218281","url":null,"abstract":"The migratory bird’s gut microbiome composition and function change during the overwintering period, helping the host to adapt to different environments. Our study investigated the gut microbiome of migratory relict gulls ( Larus relictus ) in the early and late wintering stages from their overwintering grounds in Tianjin, China. We collected 24 and 29 fecal samples at the early and late stages, respectively, and analyzed the samples using high-throughput sequencing technology to find the relationship between diet, living environment, and gut microbiome of migratory birds. The results showed that the diversity and abundance of microbial communities (alpha diversity) increased during the overwintering period and significantly differed between both groups (beta diversity). Based on the gut microbial taxonomic composition, the relative abundance of Firmicutes decreased during the overwintering period, and Proteobacteria increased significantly. Furthermore, Catellicoccus and Breznakia were the main genera in both the early and late stages. Prediction of KEGG functions based on the PICRUSt2 method showed that changes in the gut microbiome resulted in an increased abundance of bacteria associated with amino acid metabolism, metabolism of cofactors and vitamins, energy metabolism, and environmental adaptation in the late stage. Differences in diet and environment at different stages during the overwintering period may have led to the differentiation of microbial communities, and their adaptive mechanisms need to be further investigated. This is the first in-depth study of the gut microbial composition of L. relictus during the overwintering period in northern China. These findings may contribute to the protection of migratory birds.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135828290","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 : 2023-09-29DOI: 10.3389/frmbi.2023.1192773
Meghan A. Berryman, Eric W. Triplett, Johnny Ludvigsson
To determine the importance of Lactobacillus in shaping the human gut microbiome, the microbial composition of stools from 1,602 children between the ages of 0.3 months and 37.2 months was analyzed in a general population cohort in the All Babies in Southeast Sweden study. Lactobacillus colonized only 32% of the total pediatric population at an average relative abundance of 0.29%. Lactobacillus was age-dependent, decreasing in prevalence and relative abundance over time. The main determining factor for Lactobacillus colonization was whether the individual was actively breastfeeding. Following cessation of breastfeeding, Lactobacillus prevalence rapidly declined. However, within the actively breastfeeding cohort, 45.6% of the population remained uncolonized by Lactobacillus . The presence versus absence of Lactobacillus was determined to be human leukocyte antigen (HLA) dependent. Individuals with HLA DR15-DQ6.2 were 3.4 times more likely to be colonized by Lactobacillus than those without the haplotype, and those with HLA DR5-DQ7 were more likely to have zero Lactobacillus despite actively breastfeeding. These results suggest that HLA genetics should be considered when designing Lactobacillus -based probiotics.
{"title":"Human leukocyte antigen-dependent colonization of Lactobacillus in the early-life gut","authors":"Meghan A. Berryman, Eric W. Triplett, Johnny Ludvigsson","doi":"10.3389/frmbi.2023.1192773","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1192773","url":null,"abstract":"To determine the importance of Lactobacillus in shaping the human gut microbiome, the microbial composition of stools from 1,602 children between the ages of 0.3 months and 37.2 months was analyzed in a general population cohort in the All Babies in Southeast Sweden study. Lactobacillus colonized only 32% of the total pediatric population at an average relative abundance of 0.29%. Lactobacillus was age-dependent, decreasing in prevalence and relative abundance over time. The main determining factor for Lactobacillus colonization was whether the individual was actively breastfeeding. Following cessation of breastfeeding, Lactobacillus prevalence rapidly declined. However, within the actively breastfeeding cohort, 45.6% of the population remained uncolonized by Lactobacillus . The presence versus absence of Lactobacillus was determined to be human leukocyte antigen (HLA) dependent. Individuals with HLA DR15-DQ6.2 were 3.4 times more likely to be colonized by Lactobacillus than those without the haplotype, and those with HLA DR5-DQ7 were more likely to have zero Lactobacillus despite actively breastfeeding. These results suggest that HLA genetics should be considered when designing Lactobacillus -based probiotics.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135132314","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 : 2023-09-29DOI: 10.3389/frmbi.2023.1212255
Helen Marie Golder, Josh Rehberger, Alexandra Helena Smith, Elliot Block, Ian John Lean
Introduction Early-lactation Holstein cows ( n = 261) from 32 herds in three regions (Australia, California, and Canada) were previously categorized using a discriminant analysis model as being at a high (26.1% of cows), medium (26.8% of cows), or low risk (47.1% of cows) of ruminal acidosis. We aimed to investigate if (1) risk of acidosis would be associated with ruminal bacterial taxa and dietary nutrient components, (2) there would be individual or combinations of bacterial taxa associated with acidosis-risk groups, and (3) the abundance of bacterial taxa would be associated with the intake of dietary nutrient components. Methods Diets ranged from pasture supplemented with concentrates to total mixed rations. Bacteria 16S ribosomal DNA sequences from rumen samples collected < 3 hours after feeding via stomach tube were analyzed to determine bacterial presence. The relative abundance of each bacterial phylum and family was center log transformed and the transformed family data were subjected to two redundancy analysis biplots, one for acidosis risk group and one for region, to identify the 20 best-fit bacterial families from each respective redundancy analysis. A total of 29 unique families were identified when the lists of 20 families were combined from each redundancy analysis, and these 29 families were termed "influential" families." The association of acidosis-risk groups with the abundance of individual influential families was assessed by mixed models. Backward stepwise elimination mixed models were used to determine the bacterial taxa associated with each acidosis-risk group and the dietary nutrients associated with the abundance of the bacterial taxa. Results and discussion High-risk acidosis cows were associated with increased abundances of Anaerocella_f and Veillonellaceae and decreased abundances of several bacterial families with different characteristics. Five phyla: Firmicutes [odds ratio (OR) = 7.47 ± 7.43], Spirochaetes (OR = 1.28 ± 0.14), Lentisphaerae (OR = 0.70 ± 0.07), Planctomycetes (OR = 0.70 ± 0.09), and Tenericutes (OR = 0.44 ± 0.15), and nine families were associated with a higher risk of acidosis. Of the nine phyla identified to be of interest based on abundance and strength of association with acidosis-risk groups, all had one or more dietary nutrient that predicted their abundance. Sugar was the most frequently associated nutrient with the nine phyla, and was present in 78% (seven out of nine phyla) of the models; crude protein was present in 56% of models and crude fat was present in 44% of the models. Sugar and crude protein were most associated with the influential families and all but three families had one or more nutrient predictive of their abundance. Ruminal bacterial taxa are associated with ruminal acidosis; dietary sugar and crude protein are vital predictors of these and, thus, of ruminal acidosis risk.
{"title":"Ruminal bacterial communities differ in early-lactation dairy cows with differing risk of ruminal acidosis","authors":"Helen Marie Golder, Josh Rehberger, Alexandra Helena Smith, Elliot Block, Ian John Lean","doi":"10.3389/frmbi.2023.1212255","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1212255","url":null,"abstract":"Introduction Early-lactation Holstein cows ( n = 261) from 32 herds in three regions (Australia, California, and Canada) were previously categorized using a discriminant analysis model as being at a high (26.1% of cows), medium (26.8% of cows), or low risk (47.1% of cows) of ruminal acidosis. We aimed to investigate if (1) risk of acidosis would be associated with ruminal bacterial taxa and dietary nutrient components, (2) there would be individual or combinations of bacterial taxa associated with acidosis-risk groups, and (3) the abundance of bacterial taxa would be associated with the intake of dietary nutrient components. Methods Diets ranged from pasture supplemented with concentrates to total mixed rations. Bacteria 16S ribosomal DNA sequences from rumen samples collected &lt; 3 hours after feeding via stomach tube were analyzed to determine bacterial presence. The relative abundance of each bacterial phylum and family was center log transformed and the transformed family data were subjected to two redundancy analysis biplots, one for acidosis risk group and one for region, to identify the 20 best-fit bacterial families from each respective redundancy analysis. A total of 29 unique families were identified when the lists of 20 families were combined from each redundancy analysis, and these 29 families were termed \"influential\" families.\" The association of acidosis-risk groups with the abundance of individual influential families was assessed by mixed models. Backward stepwise elimination mixed models were used to determine the bacterial taxa associated with each acidosis-risk group and the dietary nutrients associated with the abundance of the bacterial taxa. Results and discussion High-risk acidosis cows were associated with increased abundances of Anaerocella_f and Veillonellaceae and decreased abundances of several bacterial families with different characteristics. Five phyla: Firmicutes [odds ratio (OR) = 7.47 ± 7.43], Spirochaetes (OR = 1.28 ± 0.14), Lentisphaerae (OR = 0.70 ± 0.07), Planctomycetes (OR = 0.70 ± 0.09), and Tenericutes (OR = 0.44 ± 0.15), and nine families were associated with a higher risk of acidosis. Of the nine phyla identified to be of interest based on abundance and strength of association with acidosis-risk groups, all had one or more dietary nutrient that predicted their abundance. Sugar was the most frequently associated nutrient with the nine phyla, and was present in 78% (seven out of nine phyla) of the models; crude protein was present in 56% of models and crude fat was present in 44% of the models. Sugar and crude protein were most associated with the influential families and all but three families had one or more nutrient predictive of their abundance. Ruminal bacterial taxa are associated with ruminal acidosis; dietary sugar and crude protein are vital predictors of these and, thus, of ruminal acidosis risk.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"70 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135245975","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 : 2023-09-27DOI: 10.3389/frmbi.2023.1094865
Mabel T. Wong, Camilla L. Nesbø, Weijun Wang, Marie Couturier, Vincent Lombard, Pascal Lapebie, Nicolas Terrapon, Bernard Henrissat, Elizabeth A. Edwards, Emma R. Master
Metagenomes of lignocellulose-degrading microbial communities are reservoirs of carbohydrate-active enzymes relevant to biomass processing. Whereas several metagenomes of natural digestive systems have been sequenced, the current study analyses metagenomes originating from an industrial anaerobic digester that processes effluent from a cellulose pulp mill. Both 16S ribosomal DNA and metagenome sequences were obtained following anaerobic cultivation of the digester inoculum on cellulose and pretreated (steam exploded) poplar wood chips. The community composition and profile of predicted carbohydrate-active enzymes were then analyzed in detail. Recognized lignocellulose degraders were abundant in the resulting cultures, including populations belonging to Clostridiales and Bacteroidales orders. Poorly defined taxonomic lineages previously identified in other lignocellulose-degrading communities were also detected, including the uncultivated Firmicutes lineage OPB54 which represented nearly 10% of the cellulose-fed enrichment even though it was not detected in the bioreactor inoculum. In total, 3580 genes encoding carbohydrate-active enzymes were identified through metagenome sequencing. Similar to earlier enrichments of animal digestive systems, the profile encoded by the bioreactor inoculum following enrichment on pretreated wood was distinguished from the cellulose counterpart by a higher occurrence of enzymes predicted to act on pectin. The majority (> 93%) of carbohydrate-active enzymes predicted to act on plant polysaccharides were identified in the metagenome assembled genomes, permitting taxonomic assignment. The taxonomic assignment revealed that only a small selection of organisms directly participates in plant polysaccharide deconstruction and supports the rest of the community.
{"title":"Taxonomic composition and carbohydrate-active enzyme content in microbial enrichments from pulp mill anaerobic granules after cultivation on lignocellulosic substrates","authors":"Mabel T. Wong, Camilla L. Nesbø, Weijun Wang, Marie Couturier, Vincent Lombard, Pascal Lapebie, Nicolas Terrapon, Bernard Henrissat, Elizabeth A. Edwards, Emma R. Master","doi":"10.3389/frmbi.2023.1094865","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1094865","url":null,"abstract":"Metagenomes of lignocellulose-degrading microbial communities are reservoirs of carbohydrate-active enzymes relevant to biomass processing. Whereas several metagenomes of natural digestive systems have been sequenced, the current study analyses metagenomes originating from an industrial anaerobic digester that processes effluent from a cellulose pulp mill. Both 16S ribosomal DNA and metagenome sequences were obtained following anaerobic cultivation of the digester inoculum on cellulose and pretreated (steam exploded) poplar wood chips. The community composition and profile of predicted carbohydrate-active enzymes were then analyzed in detail. Recognized lignocellulose degraders were abundant in the resulting cultures, including populations belonging to Clostridiales and Bacteroidales orders. Poorly defined taxonomic lineages previously identified in other lignocellulose-degrading communities were also detected, including the uncultivated Firmicutes lineage OPB54 which represented nearly 10% of the cellulose-fed enrichment even though it was not detected in the bioreactor inoculum. In total, 3580 genes encoding carbohydrate-active enzymes were identified through metagenome sequencing. Similar to earlier enrichments of animal digestive systems, the profile encoded by the bioreactor inoculum following enrichment on pretreated wood was distinguished from the cellulose counterpart by a higher occurrence of enzymes predicted to act on pectin. The majority (&gt; 93%) of carbohydrate-active enzymes predicted to act on plant polysaccharides were identified in the metagenome assembled genomes, permitting taxonomic assignment. The taxonomic assignment revealed that only a small selection of organisms directly participates in plant polysaccharide deconstruction and supports the rest of the community.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"105 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135579432","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 : 2023-09-22DOI: 10.3389/frmbi.2023.1242895
Kylie B. Bodle, Rebecca C. Mueller, Madeline R. Pernat, Catherine M. Kirkland
This study characterizes the effects of three commonly detected pharmaceuticals—diclofenac, erythromycin, and gemfibrozil—on aerobic granular sludge. Approximately 150 µg/L of each pharmaceutical was fed in the influent to a sequencing batch reactor for 80 days, and the performance of the test reactor was compared with that of a control reactor. Wastewater treatment efficacy in the test reactor dropped by approximately 30-40%, and ammonia oxidation was particularly inhibited. The relative abundance of active Rhodocyclaceae, Nitrosomonadaceae , and Nitrospiraceae families declined throughout exposure, likely explaining reductions in wastewater treatment performance. Pharmaceuticals were temporarily removed in the first 12 days of the test via both sorption and degradation; both removal processes declined sharply thereafter. This study demonstrates that aerobic granular sludge may successfully remove pharmaceuticals in the short term, but long-term tests are necessary to confirm if pharmaceutical removal is sustainable.
{"title":"Treatment performance and microbial community structure in an aerobic granular sludge sequencing batch reactor amended with diclofenac, erythromycin, and gemfibrozil","authors":"Kylie B. Bodle, Rebecca C. Mueller, Madeline R. Pernat, Catherine M. Kirkland","doi":"10.3389/frmbi.2023.1242895","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1242895","url":null,"abstract":"This study characterizes the effects of three commonly detected pharmaceuticals—diclofenac, erythromycin, and gemfibrozil—on aerobic granular sludge. Approximately 150 µg/L of each pharmaceutical was fed in the influent to a sequencing batch reactor for 80 days, and the performance of the test reactor was compared with that of a control reactor. Wastewater treatment efficacy in the test reactor dropped by approximately 30-40%, and ammonia oxidation was particularly inhibited. The relative abundance of active Rhodocyclaceae, Nitrosomonadaceae , and Nitrospiraceae families declined throughout exposure, likely explaining reductions in wastewater treatment performance. Pharmaceuticals were temporarily removed in the first 12 days of the test via both sorption and degradation; both removal processes declined sharply thereafter. This study demonstrates that aerobic granular sludge may successfully remove pharmaceuticals in the short term, but long-term tests are necessary to confirm if pharmaceutical removal is sustainable.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"78 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136060464","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 : 2023-09-21DOI: 10.3389/frmbi.2023.1249518
Ran Xu, Shuo Liu, Lu-yi Li, Ying Zhang, Guang-cheng Luo, Bo-qin Fang, Xin-jun Wang
Background Recent studies have suggested a possible association between gut microbiota and bipolar disorder (BD). However, observational studies are limited and there are variations between the gut microbiota taxa found in different studies. Therefore, we aimed to explore whether there is a causal relationship between gut microbiota and bipolar disorder at the genetic level and to reveal trends in the effect of influential gut microbiota on the development of bipolar disorder. Methods We conducted a Mendelian randomisation (MR) study of summary statistics from a genome-wide association study (GWAS) of gut microbiota and bipolar disorder. Inverse variance weighting (IVW) was used as the primary method of statistical analysis, while results from the MR-Egger method, weighted median, weighted mode, and MR multiplicity residuals and outliers (MR-PRESSO) tests were used for additional validation.Cochrane’s Q test, MR-Egger intercept test, and MR-PRESSO global test were used to test MR results for stability and reliability. Result We identified 13 gut microbial taxa causally associated with bipolar disorder. Betaproteobacteria, Acidaminococcaceae, Eubacterium xylanophilum group, Butyricimonas, Peptococcus, Prevotella 7, Roseburia, Terrisporobacter, Burkholderiales and Desulfovibrionales increased the risk of BD, whereas Candidatus Soleaferrea, Ruminiclostridium 5 and Victivallis decreased the risk of BD. The results of the MR analysis were shown to be reliable in the sensitivity analysis. Conclusion With the MR study, we analysed the causal relationship between 196 gut microbial taxa and bipolar disorder and also identified gut microbiota associated with the risk of developing bipolar disorder. Our findings provide new biomarkers and potential therapeutic targets for the prevention and treatment of BD.
{"title":"Causal effects of gut microbiota on the risk of bipolar disorder: a Mendelian randomization study","authors":"Ran Xu, Shuo Liu, Lu-yi Li, Ying Zhang, Guang-cheng Luo, Bo-qin Fang, Xin-jun Wang","doi":"10.3389/frmbi.2023.1249518","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1249518","url":null,"abstract":"Background Recent studies have suggested a possible association between gut microbiota and bipolar disorder (BD). However, observational studies are limited and there are variations between the gut microbiota taxa found in different studies. Therefore, we aimed to explore whether there is a causal relationship between gut microbiota and bipolar disorder at the genetic level and to reveal trends in the effect of influential gut microbiota on the development of bipolar disorder. Methods We conducted a Mendelian randomisation (MR) study of summary statistics from a genome-wide association study (GWAS) of gut microbiota and bipolar disorder. Inverse variance weighting (IVW) was used as the primary method of statistical analysis, while results from the MR-Egger method, weighted median, weighted mode, and MR multiplicity residuals and outliers (MR-PRESSO) tests were used for additional validation.Cochrane’s Q test, MR-Egger intercept test, and MR-PRESSO global test were used to test MR results for stability and reliability. Result We identified 13 gut microbial taxa causally associated with bipolar disorder. Betaproteobacteria, Acidaminococcaceae, Eubacterium xylanophilum group, Butyricimonas, Peptococcus, Prevotella 7, Roseburia, Terrisporobacter, Burkholderiales and Desulfovibrionales increased the risk of BD, whereas Candidatus Soleaferrea, Ruminiclostridium 5 and Victivallis decreased the risk of BD. The results of the MR analysis were shown to be reliable in the sensitivity analysis. Conclusion With the MR study, we analysed the causal relationship between 196 gut microbial taxa and bipolar disorder and also identified gut microbiota associated with the risk of developing bipolar disorder. Our findings provide new biomarkers and potential therapeutic targets for the prevention and treatment of BD.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"78 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136130085","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 : 2023-09-18DOI: 10.3389/frmbi.2023.1194516
Alejandro Ramirez Garcia, Anna Greppi, Florentin Constancias, Hans-Joachim Ruscheweyh, Julie Gasser, Katherine Hurley, Shana J. Sturla, Clarissa Schwab, Christophe Lacroix
Introduction Anaerobutyricum hallii is a human gut commensal that transforms the heterocyclic amine 2-amino-1-methyl-6-phenylimidazo [4,5-b] pyridine (PhIP), a carcinogen from cooked meat. The transformation mechanism involves the microbial production of acrolein from glycerol, and its conjugation with PhIP, thus blocking its mutagenic potential. A potential cancer prevention strategy could therefore involve supplementing complex human microbial communities with metabolically competent bacteria such as A. hallii that can deplete PhIP. However, it has not been established how the proportion of A. hallii in diverse healthy human gut microbial communities relates to functional capacity for PhIP transformation and, moreover, how supplementing microbiomes with A. hallii affects this function. Methods In this study, shotgun metagenomics was used to study taxonomic profiling, the abundance of glycerol/diol dehydratase ( gdh )-harboring taxa, the proportion of resident A. hallii , and the reconstruction of A. hallii population genomes in the fecal samples of 20 healthy young adult donors. Furthermore, the influence of supplementing 10 6 cells/mL of A. hallii DSM 3353 with diluted fecal microbiota was characterized. Results and discussion Six microbiota were assigned to Bacteroides , nine to Prevotella , and five to Ruminococcus by enterotype-associated clustering. The total number of gdh copies in the 20 fecal microbiota expressed per 10 10 bacterial cells ranged between 1.32 × 10 8 and 1.15 × 10 9 . Eighteen out of the 20 donors were dominated by A. hallii , representing between 33% and 94% of the total gdh relative abundance of the samples. The microbiota with low A. hallii abundance (i.e., with a relative abundance < 1%) transformed less PhIP than the microbiota with high A. hallii abundance (i.e., with a relative abundance > 1%). Furthermore, supplementing the low- A. hallii -abundant microbiota with glycerol significantly increased the PhIP transformation capacity after 6 h while reducing total short-chain fatty acid (SCFA) levels, which is most likely due to acrolein production. Although acetate decreased in all microbiota with glycerol and with the combination of glycerol and A. hallii , for most of the microbiomes, butyrate production increased over time. Thus, for a significant number of diverse healthy human fecal microbiomes, and especially when they have little of the taxa to start with, supplementing A. hallii increases PhIP transformation. These findings suggest the need to test in vivo whether supplementing microbiomes with A. hallii reduces PhIP exposure.
{"title":"Anaerobutyricum hallii promotes the functional depletion of a food carcinogen in diverse healthy fecal microbiota","authors":"Alejandro Ramirez Garcia, Anna Greppi, Florentin Constancias, Hans-Joachim Ruscheweyh, Julie Gasser, Katherine Hurley, Shana J. Sturla, Clarissa Schwab, Christophe Lacroix","doi":"10.3389/frmbi.2023.1194516","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1194516","url":null,"abstract":"Introduction Anaerobutyricum hallii is a human gut commensal that transforms the heterocyclic amine 2-amino-1-methyl-6-phenylimidazo [4,5-b] pyridine (PhIP), a carcinogen from cooked meat. The transformation mechanism involves the microbial production of acrolein from glycerol, and its conjugation with PhIP, thus blocking its mutagenic potential. A potential cancer prevention strategy could therefore involve supplementing complex human microbial communities with metabolically competent bacteria such as A. hallii that can deplete PhIP. However, it has not been established how the proportion of A. hallii in diverse healthy human gut microbial communities relates to functional capacity for PhIP transformation and, moreover, how supplementing microbiomes with A. hallii affects this function. Methods In this study, shotgun metagenomics was used to study taxonomic profiling, the abundance of glycerol/diol dehydratase ( gdh )-harboring taxa, the proportion of resident A. hallii , and the reconstruction of A. hallii population genomes in the fecal samples of 20 healthy young adult donors. Furthermore, the influence of supplementing 10 6 cells/mL of A. hallii DSM 3353 with diluted fecal microbiota was characterized. Results and discussion Six microbiota were assigned to Bacteroides , nine to Prevotella , and five to Ruminococcus by enterotype-associated clustering. The total number of gdh copies in the 20 fecal microbiota expressed per 10 10 bacterial cells ranged between 1.32 × 10 8 and 1.15 × 10 9 . Eighteen out of the 20 donors were dominated by A. hallii , representing between 33% and 94% of the total gdh relative abundance of the samples. The microbiota with low A. hallii abundance (i.e., with a relative abundance &lt; 1%) transformed less PhIP than the microbiota with high A. hallii abundance (i.e., with a relative abundance &gt; 1%). Furthermore, supplementing the low- A. hallii -abundant microbiota with glycerol significantly increased the PhIP transformation capacity after 6 h while reducing total short-chain fatty acid (SCFA) levels, which is most likely due to acrolein production. Although acetate decreased in all microbiota with glycerol and with the combination of glycerol and A. hallii , for most of the microbiomes, butyrate production increased over time. Thus, for a significant number of diverse healthy human fecal microbiomes, and especially when they have little of the taxa to start with, supplementing A. hallii increases PhIP transformation. These findings suggest the need to test in vivo whether supplementing microbiomes with A. hallii reduces PhIP exposure.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135206229","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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