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Bioscience of Microbiota, Food and... 2022Chronic inflammation caused by gut dysbiosis is associated with the pathophysiology of metabolic disease. Synbiotics are useful for ameliorating gut dysbiosis; however,...
Chronic inflammation caused by gut dysbiosis is associated with the pathophysiology of metabolic disease. Synbiotics are useful for ameliorating gut dysbiosis; however, it remains unclear what types of bacteria act as key markers for synbiotic-driven improvement of chronic inflammation. Here, we performed a post hoc analysis of a 24-week randomized controlled study using synbiotics to investigate the association between gut microbiota and inflammatory markers. We characterized the responders who showed lower interleukin-6 (IL-6) levels in response to synbiotic supplementation among 86 obese patients with type 2 diabetes mellitus. In our baseline analysis, the relative abundances of and correlated positively with IL-6, lipopolysaccharide binding protein (LBP), and high-sensitivity C-reactive protein (Hs-CRP) levels. The relative abundance of correlated positively with LBP and Hs-CRP levels, and that of correlated positively with LBP levels. Based on our responder analysis, patients with higher body mass indices (over 30 kg/m on average), low abundances of and at baseline and 24 weeks, and minimal changes in the relative abundance of and Shannon index from baseline showed decreased IL-6 levels compared with baseline. However, glycemic control in responders was unchanged. In conclusion, we identified four bacterial species (, , , ) related to chronic inflammation and predictive markers ( and severity of obesity) in responders to synbiotic supplementation among obese patients with type 2 diabetes.
PubMed: 35854696
DOI: 10.12938/bmfh.2021-081 -
Microbiology Spectrum Aug 2022The gastrointestinal microbiota members produce α-l-fucosidases that play key roles in mucosal, human milk, and dietary oligosaccharide assimilation. Here, 36 open...
The gastrointestinal microbiota members produce α-l-fucosidases that play key roles in mucosal, human milk, and dietary oligosaccharide assimilation. Here, 36 open reading frames (ORFs) coding for putative α-l-fucosidases belonging to glycosyl hydrolase family 29 (GH29) were identified through metagenome analysis of breast-fed infant fecal microbiome. Twenty-two of those ORFs showed a complete coding sequence with deduced amino acid sequences displaying the highest degree of identity with α-l-fucosidases from Bacteroides thetaiotaomicron, Bacteroides caccae, Phocaeicola vulgatus, Phocaeicola dorei, Ruminococcus gnavus, and Streptococcus parasanguinis. Based on sequence homology, 10 α-l-fucosidase genes were selected for substrate specificity characterization. The α-l-fucosidases Fuc18, Fuc19A, Fuc35B, Fuc39, and Fuc1584 showed hydrolytic activity on α1,3/4-linked fucose present in Lewis blood antigens and the human milk oligosaccharide (HMO) 3-fucosyllactose. In addition, Fuc1584 also hydrolyzed fucosyl-α-1,6--acetylglucosamine (6FN), a component of the core fucosylation of -glycans. Fuc35A and Fuc193 showed activity on α1,2/3/4/6 linkages from H type-2, Lewis blood antigens, HMOs and 6FN. Fuc30 displayed activity only on α1,6-linked l-fucose, and Fuc5372 showed a preference for α1,2 linkages. Fuc2358 exhibited a broad substrate specificity releasing l-fucose from all the tested free histo-blood group antigens, HMOs, and 6FN. This latest enzyme also displayed activity in glycoconjugates carrying lacto--fucopentaose II (Le) and lacto--fucopentaose III (Le) and in the glycoprotein mucin. Fuc18, Fuc19A, and Fuc39 also removed l-fucose from neoglycoproteins and human α-1 acid glycoprotein. These results give insight into the great diversity of α-l-fucosidases from the infant gut microbiota, thus supporting the hypothesis that fucosylated glycans are crucial for shaping the newborn microbiota composition. α-l-Fucosyl residues are frequently present in many relevant glycans, such as human milk oligosaccharides (HMOs), histo-blood group antigens (HBGAs), and epitopes on cell surface glycoconjugate receptors. These fucosylated glycans are involved in a number of mammalian physiological processes, including adhesion of pathogens and immune responses. The modulation of l-fucose content in such processes may provide new insights and knowledge regarding molecular interactions and may help to devise new therapeutic strategies. Microbial α-l-fucosidases are exoglycosidases that remove α-l-fucosyl residues from free oligosaccharides and glycoconjugates and can be also used in transglycosylation reactions to synthesize oligosaccharides. In this work, α-l-fucosidases from the GH29 family were identified and characterized from the metagenome of fecal samples of breastfed infants. These enzymes showed different substrate specificities toward HMOs, HBGAs, naturally occurring glycoproteins, and neoglycoproteins. These novel glycosidase enzymes from the breast-fed infant gut microbiota, which resulted in a good source of α-l-fucosidases, have great biotechnological potential.
Topics: Animals; Blood Group Antigens; Fucose; Gastrointestinal Microbiome; Glycoconjugates; Humans; Infant; Infant, Newborn; Mammals; Metagenome; Milk, Human; Oligosaccharides; Polysaccharides; alpha-L-Fucosidase
PubMed: 35943155
DOI: 10.1128/spectrum.01775-22 -
Frontiers in Cellular and Infection... 2020Many studies have explored changes in the gut microbiome associated with HIV infection, but the consistent pattern of changes has not been clarified. Men who have sex... (Meta-Analysis)
Meta-Analysis
Many studies have explored changes in the gut microbiome associated with HIV infection, but the consistent pattern of changes has not been clarified. Men who have sex with men (MSM) are very likely to be an independent influencing factor of the gut microbiome, but relevant research is still lacking. We conducted a meta-analysis by screening 12 published studies of 16S rRNA gene amplicon sequencing of gut microbiomes related to HIV/AIDS (six of these studies contain data that is relevant and available to MSM) from NCBI and EBI databases. The analysis of gut microbiomes related to HIV infection status and MSM status included 1,288 samples (HIV-positive (HIV+) individuals, = 744; HIV-negative (HIV-) individuals, = 544) and 632 samples (MSM, = 328; non-MSM, = 304), respectively. The alpha diversity indexes, beta diversity indexes, differentially enriched genera, differentially enriched species, and differentially enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways related to gut microbiomes were calculated. Finally, the overall trend of the above indicators was evaluated. Our results indicate that HIV+ status is associated with decreased alpha diversity of the gut microbiome. MSM status is an important factor that affects the study of HIV-related gut microbiomes; that is, MSM are associated with alpha diversity changes in the gut microbiome regardless of HIV infection, and the changes in the gut microbiome composition of MSM are more significant than those of HIV+ individuals. A consistent change in , and was found in HIV+ individuals and MSM. The differential expression of the gut microbiome may be accompanied by changes in functional pathways of carbohydrate metabolism, amino acid metabolism, and lipid Metabolism. This study shows that the changes in the gut microbiome are related to HIV and MSM status. Importantly, MSM status may have a far greater impact on the gut microbiome than HIV status.
Topics: Bacteroides; Female; Gastrointestinal Microbiome; HIV Infections; Homosexuality, Male; Humans; Male; Prevotella; RNA, Ribosomal, 16S; Sexual Behavior; Sexual and Gender Minorities
PubMed: 33102244
DOI: 10.3389/fcimb.2020.00434 -
Journal of Applied Microbiology Jul 2011To develop species-specific monitoring techniques for rapid detection of Bacteroides and Parabacteroides inhabiting the mouse intestine by fluorescence in situ...
Design of species-specific oligonucleotide probes for the detection of Bacteroides and Parabacteroides by fluorescence in situ hybridization and their application to the analysis of mouse caecal Bacteroides-Parabacteroides microbiota.
AIMS
To develop species-specific monitoring techniques for rapid detection of Bacteroides and Parabacteroides inhabiting the mouse intestine by fluorescence in situ hybridization.
METHODS AND RESULTS
The specificity of oligonucleotide probes was evaluated by fluorescence whole-cell hybridization. Oligonucleotide probes specific for each species hybridized only with the target bacteria. Using these probes, caecal Bacteroides-Parabacteroides microbiota of conventional mice and specific pathogen-free (SPF) mice from three different breeders were analysed. It was shown that Bacteroides acidifaciens Group-1, Group-2 and Group-3 were dominant in conventional mice and SPF mice from two out of three breeders. Bacteroides vulgatus and Parabacteroides distasonis were detected in one of these two SPF breeding colonies in addition to Bact. acidifaciens. SPF mice of the remaining breeder harboured characteristic Bacteroides-Parabacteroides microbiota, consisting of Bacteroides sp. ASF519 and Bacteroides caccae.
CONCLUSIONS
Bacteroides acidifaciens is the dominant and most typical species in the mouse Bacteroides-Parabacteroides microbiota. The Group-3 was identified as a novel group and revealed to occupy a major niche together with Bact. acidifaciens Group-1 and Group-2.
SIGNIFICANCE AND IMPACT OF THE STUDY
The species-specific probe set developed in this study was the efficient tool for rapid detection of target bacterial groups inhabiting the mouse intestine. The results of this study provide important new information on the mouse Bacteroides-Parabacteroides community.
Topics: Animals; Bacteriological Techniques; Bacteroidetes; Cecum; Feces; In Situ Hybridization, Fluorescence; Male; Mice; Mice, Inbred BALB C; Oligonucleotide Probes; RNA, Bacterial; RNA, Ribosomal, 16S; Species Specificity; Specific Pathogen-Free Organisms
PubMed: 21535330
DOI: 10.1111/j.1365-2672.2011.05039.x -
MedRxiv : the Preprint Server For... May 2023Metal exposures are associated with gut microbiome (GM) composition and function, and exposures early in development may be particularly important. Considering the role...
BACKGROUND
Metal exposures are associated with gut microbiome (GM) composition and function, and exposures early in development may be particularly important. Considering the role of the GM in association with many adverse health outcomes, understanding the relationship between prenatal metal exposures and the GM is critically important. However, there is sparse knowledge of the association between prenatal metal exposure and GM later in childhood.
OBJECTIVES
This analysis aims to identify associations between prenatal lead (Pb) exposure and GM composition and function in children 9-11 years old.
METHODS
Data come from the Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS) cohort based in Mexico City, Mexico. Prenatal metal concentrations were measured in maternal whole blood drawn during the second and third trimesters of pregnancy. Stool samples collected at 9-11 years old underwent metagenomic sequencing to assess the GM. This analysis uses multiple statistical modeling approaches, including linear regression, permutational analysis of variance, weighted quantile sum regression (WQS), and individual taxa regressions, to estimate the association between maternal blood Pb during pregnancy and multiple aspects of the child GM at 9-11 years old, adjusting for relevant confounders.
RESULTS
Of the 123 child participants in this pilot data analysis, 74 were male and 49 were female. Mean prenatal maternal blood Pb was 33.6(SE=2.1) ug/L and 34.9(SE=2.1) ug/L at second and third trimesters, respectively. Analysis suggests a consistent negative relationship between prenatal maternal blood Pb and the GM at age 9-11, including measures of alpha and beta diversity, microbiome mixture analysis, and individual taxa. The WQS analysis showed a negative association between prenatal Pb exposure and the gut microbiome, for both second and third trimester exposures (2Tβ=-0.17,95%CI=[-0.46,0.11]; 3Tβ=-0.17,95%CI=[-0.44,0.10]). Ruminococcus gnavus, Bifidobacterium longum, Alistipes indistinctus, Bacteroides caccae, and Bifidobacterium bifidum all had weights above the importance threshold from 80% or more of the WQS repeated holdouts in association with both second and third trimester Pb exposure.
DISCUSSION
Pilot data analysis suggests a negative association between prenatal Pb exposure and the gut microbiome later in childhood; however, additional investigation is needed.
PubMed: 37214901
DOI: 10.1101/2023.05.10.23289802 -
Frontiers in Microbiology 2023Metal exposures are associated with gut microbiome (GM) composition and function, and exposures early in development may be particularly important. Considering the role...
BACKGROUND
Metal exposures are associated with gut microbiome (GM) composition and function, and exposures early in development may be particularly important. Considering the role of the GM in association with many adverse health outcomes, understanding the relationship between prenatal metal exposures and the GM is critically important. However, there is sparse knowledge of the association between prenatal metal exposure and GM later in childhood.
OBJECTIVES
This analysis aims to identify associations between prenatal lead (Pb) exposure and GM composition and function in children 9-11 years old.
METHODS
Data come from the Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS) cohort based in Mexico City, Mexico. Prenatal metal concentrations were measured in maternal whole blood drawn during the second and third trimesters of pregnancy. Stool samples collected at 9-11 years old underwent metagenomic sequencing to assess the GM. This analysis uses multiple statistical modeling approaches, including linear regression, permutational analysis of variance, weighted quantile sum regression (WQS), and individual taxa regressions, to estimate the association between maternal blood Pb during pregnancy and multiple aspects of the child GM at 9-11 years old, adjusting for relevant confounders.
RESULTS
Of the 123 child participants in this pilot data analysis, 74 were male and 49 were female. Mean prenatal maternal blood Pb was 33.6 (SE = 2.1) ug/L and 34.9 (SE = 2.1) ug/L at second and third trimesters, respectively. Analysis suggests a consistent negative relationship between prenatal maternal blood Pb and the GM at age 9-11, including measures of alpha and beta diversity, microbiome mixture analysis, and individual taxa. The WQS analysis showed a negative association between prenatal Pb exposure and the gut microbiome, for both second and third trimester exposures (2Tβ = -0.17, 95%CI = [-0.46,0.11]; 3Tβ = -0.17, 95%CI = [-0.44,0.10]). , , , , and all had weights above the importance threshold from 80% or more of the WQS repeated holdouts in association with both second and third trimester Pb exposure.
DISCUSSION
Pilot data analysis suggests a negative association between prenatal Pb exposure and the gut microbiome later in childhood; however, additional investigation is needed.
PubMed: 37426026
DOI: 10.3389/fmicb.2023.1193919 -
ISME Communications Aug 2022The infant gut microbiome has lifelong implications on health and immunity but there is still limited understanding of the microbiome differences and similarities...
The infant gut microbiome has lifelong implications on health and immunity but there is still limited understanding of the microbiome differences and similarities between children in low- and middle-income countries (LMICs) vs. high-income countries (HICs). Here, we describe and compare the microbiome profile of children aged under 48 months in two urban areas: Maputo, Mozambique and Atlanta, USA using shotgun metagenomics. The gut microbiome of American children showed distinct development, characterized by higher alpha diversity after infancy, compared to the same age group of African children, and the microbiomes clustered separately based on geographic location or age. The abundances of antibiotic resistance genes (ARGs) and virulence factors (VFs) were significantly higher in Maputo children, driven primarily by several primary and opportunistic pathogens. Most notably, about 50% of Maputo children under the age of two were positive for enterotoxigenic (ETEC) and typical enteropathogenic (EPEC) Escherichia coli diagnostic genes while none of the Atlanta age-matched children showed such a positive signal. In contrast, commensal species such as Phocaeicola vulgatus and Bacteroides caccae were more abundant in Atlanta, potentially reflecting diets rich in animal protein and susceptibility to inflammatory diseases. Overall, our results suggest that the different environments characterizing the two cities have significant, distinctive signatures on the microbiota of children and its development over time. Lack of safe water, sanitation, and hygiene (WASH) conditions and/or unsafe food sources may explain the higher enteric pathogen load among children in Maputo.
PubMed: 37938667
DOI: 10.1038/s43705-022-00154-z -
Molecular Medicine (Cambridge, Mass.) May 2021To evaluate the taxonomic composition of the gut microbiome in gout patients with and without tophi formation, and predict bacterial functions that might have an impact...
OBJECTIVE
To evaluate the taxonomic composition of the gut microbiome in gout patients with and without tophi formation, and predict bacterial functions that might have an impact on urate metabolism.
METHODS
Hypervariable V3-V4 regions of the bacterial 16S rRNA gene from fecal samples of gout patients with and without tophi (n = 33 and n = 25, respectively) were sequenced and compared to fecal samples from 53 healthy controls. We explored predictive functional profiles using bioinformatics in order to identify differences in taxonomy and metabolic pathways.
RESULTS
We identified a microbiome characterized by the lowest richness and a higher abundance of Phascolarctobacterium, Bacteroides, Akkermansia, and Ruminococcus_gnavus_group genera in patients with gout without tophi when compared to controls. The Proteobacteria phylum and the Escherichia-Shigella genus were more abundant in patients with tophaceous gout than in controls. Fold change analysis detected nine genera enriched in healthy controls compared to gout groups (Bifidobacterium, Butyricicoccus, Oscillobacter, Ruminococcaceae_UCG_010, Lachnospiraceae_ND2007_group, Haemophilus, Ruminococcus_1, Clostridium_sensu_stricto_1, and Ruminococcaceae_UGC_013). We found that the core microbiota of both gout groups shared Bacteroides caccae, Bacteroides stercoris ATCC 43183, and Bacteroides coprocola DSM 17136. These bacteria might perform functions linked to one-carbon metabolism, nucleotide binding, amino acid biosynthesis, and purine biosynthesis. Finally, we observed differences in key bacterial enzymes involved in urate synthesis, degradation, and elimination.
CONCLUSION
Our findings revealed that taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.
Topics: Biodiversity; Computational Biology; Dysbiosis; Gastrointestinal Microbiome; Gout; Humans; Metagenome; Metagenomics; Protein Interaction Mapping; Protein Interaction Maps; Uric Acid
PubMed: 34030623
DOI: 10.1186/s10020-021-00311-5 -
Pharmaceutics Sep 2022Our previous clinical trial showed that a novel concentrated herbal extract formula, YH1 ( and Shen-Ling-Bai-Zhu-San), improved blood glucose and lipid control. This...
Our previous clinical trial showed that a novel concentrated herbal extract formula, YH1 ( and Shen-Ling-Bai-Zhu-San), improved blood glucose and lipid control. This pilot observational study investigated whether YH1 affects microbiota, plasma, and fecal bile acid (BA) compositions in ten untreated male patients with type 2 diabetes (T2D), hyperlipidemia, and a body mass index ≥ 23 kg/m. Stool and plasma samples were collected for microbiome, BA, and biochemical analyses before and after 4 weeks of YH1 therapy. As previous studies found, the glycated albumin, 2-h postprandial glucose, triglycerides, total cholesterol, and low-density lipoprotein cholesterol levels were significantly improved after YH1 treatment. Gut microbiota revealed an increased abundance of the short-chain fatty acid-producing bacteria and . Furthermore, YH1 inhibited specific phylotypes of bile salt hydrolase-expressing bacteria, including , , and . Stool tauro-conjugated BA levels increased after YH1 treatment. Plasma total BAs and 7α-hydroxy-4-cholesten-3-one (C4), a BA synthesis indicator, were elevated. The reduced deconjugation of BAs and increased plasma conjugated BAs, especially tauro-conjugated BAs, led to a decreased glyco- to tauro-conjugated BA ratio and reduced unconjugated secondary BAs. These results suggest that YH1 ameliorates T2D and hyperlipidemia by modulating microbiota constituents that alter fecal and plasma BA compositions and promote liver cholesterol-to-BA conversion and glucose homeostasis.
PubMed: 36145605
DOI: 10.3390/pharmaceutics14091857 -
3 Biotech Jun 2020The gut microbial diversity of Thai people was investigated between two large cohorts, adult and elderly subjects, from the middle region of Thailand; the cohorts were...
The gut microbial diversity of Thai people was investigated between two large cohorts, adult and elderly subjects, from the middle region of Thailand; the cohorts were divided into different age groups of healthy adult 73 and elderly subjects 47. The diversities of the groups were characterized using a pyrosequencing technique with primers targeting the V6-V8 region of the 16S rRNA gene, and a significant decrease in the and ratio from 7.3 to 4.5 was observed with increased age The microbiota of the adult and elderly groups had a significantly higher abundance of the phylum , including the three species , and , and the phylum containing the four species , , and . showed no significant differences between the two groups. Eleven species belonging to , and were shared by at least 90% of all subjects and defined as core gut microbiota of healthy Thai, among which a high abundance of was particularly characterized in Thai elderly individuals. Multiple linear regression analysis of age, gender, BMI and diet consumption frequency showed the correlation of age with and . Rice consumption frequency showed a significant positive correlation with , while no correlation was found for other factors. Taken together, in the gut of Thai adults, decreased and increased with age, while rice consumption increased the abundance of . These link of age and food, especially rice carbohydrate, to gut microbiota and health could be ultimately proposed as the Thai feature.
PubMed: 32537376
DOI: 10.1007/s13205-020-02265-7