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Frontiers in Microbiology 2021Acute myocardial infarction (AMI) continues as the main cause of morbidity and mortality worldwide. Interestingly, emerging evidence highlights the role of gut...
Acute myocardial infarction (AMI) continues as the main cause of morbidity and mortality worldwide. Interestingly, emerging evidence highlights the role of gut microbiota in regulating the pathogenesis of coronary heart disease, but few studies have systematically assessed the alterations and influence of gut microbiota in AMI patients. As one approach to address this deficiency, in this study the composition of fecal microflora was determined from Chinese AMI patients and links between gut microflora and clinical features and functional pathways of AMI were assessed. Fecal samples from 30 AMI patients and 30 healthy controls were collected to identify the gut microbiota composition and the alterations using bacterial 16S rRNA gene sequencing. We found that gut microflora in AMI patients contained a lower abundance of the phylum and a slightly higher abundance of the phylum compared to the healthy controls. Chao1 ( = 0.0472) and PD-whole-tree ( = 0.0426) indices were significantly lower in the AMI versus control group. The AMI group was characterized by higher levels of the genera , , , and , and lower levels of , , , , and as compared to that in the healthy controls ( < 0.05). The common metabolites of these genera are mostly short-chain fatty acids, which reveals that the gut flora is most likely to affect the occurrence and development of AMI through the short-chain fatty acid pathway. In addition, our results provide the first evidence revealing remarkable differences in fecal microflora among subgroups of AMI patients, including the STEMI vs. NSTEMI, IRA-LAD vs. IRA-Non-LAD and Multiple (≥2 coronary stenosis) vs. Single coronary stenosis groups. Several gut microflora were also correlated with clinically significant characteristics of AMI patients, including LVEDD, LVEF, serum TnI and NT-proBNP, Syntax score, counts of leukocytes, neutrophils and monocytes, and fasting serum glucose levels. Taken together, the data generated enables the prediction of several functional pathways as based on the fecal microfloral composition of AMI patients. Such information may enhance our comprehension of AMI pathogenesis.
PubMed: 34295318
DOI: 10.3389/fmicb.2021.680101 -
Scientific Reports Oct 2023Type 2 Diabetes Mellitus has reached epidemic levels globally, and several studies have confirmed a link between gut microbial dysbiosis and aberrant glucose homeostasis...
Uncovering the relationship between gut microbial dysbiosis, metabolomics, and dietary intake in type 2 diabetes mellitus and in healthy volunteers: a multi-omics analysis.
Type 2 Diabetes Mellitus has reached epidemic levels globally, and several studies have confirmed a link between gut microbial dysbiosis and aberrant glucose homeostasis among people with diabetes. While the assumption is that abnormal metabolomic signatures would often accompany microbial dysbiosis, the connection remains largely unknown. In this study, we investigated how diet changed the gut bacteriome, mycobiome and metabolome in people with and without type 2 Diabetes.1 Differential abundance testing determined that the metabolites Propionate, U8, and 2-Hydroxybutyrate were significantly lower, and 3-Hydroxyphenyl acetate was higher in the high fiber diet compared to low fiber diet in the healthy control group. Next, using multi-omics factor analysis (MOFA2), we attempted to uncover sources of variability that drive each of the different groups (bacterial, fungal, and metabolite) on all samples combined (control and DM II). Performing variance decomposition, ten latent factors were identified, and then each latent factor was tested for significant correlations with age, BMI, diet, and gender. Latent Factor1 was the most significantly correlated. Remarkably, the model revealed that the mycobiome explained most of the variance in the DM II group (12.5%) whereas bacteria explained most of the variance in the control group (64.2% vs. 10.4% in the DM II group). The latent Factor1 was significantly correlated with dietary intake (q < 0.01). Further analyses of the impact of bacterial and fungal genera on Factor1 determined that the nine bacterial genera (Phocaeicola, Ligilactobacillus, Mesosutterella, Acidaminococcus, Dorea A, CAG-317, Caecibacter, Prevotella and Gemmiger) and one fungal genus (Malassezia furfur) were found to have high factor weights (absolute weight > 0.6). Alternatively, a linear regression model was fitted per disease group for each genus to visualize the relationship between the factor values and feature abundances, showing Xylose with positive weights and Propionate, U8, and 2-Hydroxybutyrate with negative weights. This data provides new information on the microbially derived changes that influence metabolic phenotypes in response to different diets and disease conditions in humans.
Topics: Humans; Diabetes Mellitus, Type 2; Gastrointestinal Microbiome; Dysbiosis; Propionates; Multiomics; Metabolomics; Bacteria; Eating; Hydroxybutyrates
PubMed: 37863978
DOI: 10.1038/s41598-023-45066-7 -
Gut Microbes 2020Our objective was to investigate the relationship between the gut microbiota and anthropometric measurements among 248 participants from the Health Effects of Arsenic...
Our objective was to investigate the relationship between the gut microbiota and anthropometric measurements among 248 participants from the Health Effects of Arsenic Longitudinal Study (HEALS) in Bangladesh. Our cohort represents a unique population that allows for the investigation of the gut microbiota and anthropometric measurements in lean individuals. We measured height, weight, arm, thigh, hip, and waist circumferences, and collected fecal samples. Microbial DNA was extracted from the stool samples and sequenced by 16S rRNA gene sequencing. We examined associations between relative abundance of individual bacterial taxa from phylum to genus levels and anthropometric measurements. We found that higher BMI, mid-upper arm circumference, waist circumference, and waist-to-hip ratio were associated with a lower alpha diversity of fecal bacteria. Relative abundance of the genus and the family were inversely related to all measurements after correction for multiple testing. Relative abundance of genus and family were also associated with several measurements. The positive associations of the genus with BMI, as well as waist and hip circumferences, were stronger in women than in men. Our data in this lean Bangladeshi population found a correlation between and leanness, as measured using multiple anthropometric measures.
Topics: Anthropometry; Bacteria; Bangladesh; Body Mass Index; Body Weight; Clostridiales; Cohort Studies; Cross-Sectional Studies; Feces; Female; Gastrointestinal Microbiome; Humans; Longitudinal Studies; Male; Middle Aged; RNA, Ribosomal, 16S; Thinness; Waist Circumference; Waist-Hip Ratio
PubMed: 31138061
DOI: 10.1080/19490976.2019.1614394 -
The Journal of Biological Chemistry Apr 2020Cas12a (Cpf1) is an RNA-guided endonuclease in the bacterial type V-A CRISPR-Cas anti-phage immune system that can be repurposed for genome editing. Cas12a can bind and...
Cas12a (Cpf1) is an RNA-guided endonuclease in the bacterial type V-A CRISPR-Cas anti-phage immune system that can be repurposed for genome editing. Cas12a can bind and cut dsDNA targets with high specificity , making it an ideal candidate for expanding the arsenal of enzymes used in precise genome editing. However, this reported high specificity contradicts Cas12a's natural role as an immune effector against rapidly evolving phages. Here, we employed high-throughput cleavage assays to determine and compare the native cleavage specificities and activities of three different natural Cas12a orthologs (FnCas12a, LbCas12a, and AsCas12a). Surprisingly, we observed pervasive sequence-specific nicking of randomized target libraries, with strong nicking of DNA sequences containing up to four mismatches in the Cas12a-targeted DNA-RNA hybrid sequences. We also found that these nicking and cleavage activities depend on mismatch type and position and vary with Cas12a ortholog and CRISPR RNA sequence. Our analysis further revealed robust nonspecific nicking of dsDNA when Cas12a is activated by binding to a target DNA. Together, our findings reveal that Cas12a has multiple nicking activities against dsDNA substrates and that these activities vary among different Cas12a orthologs.
Topics: Acidaminococcus; Bacterial Proteins; Base Pair Mismatch; Base Sequence; CRISPR-Associated Proteins; CRISPR-Cas Systems; DNA; DNA Cleavage; Endodeoxyribonucleases; Francisella; Gene Editing; Gene Expression
PubMed: 32161115
DOI: 10.1074/jbc.RA120.012933 -
The American Journal of Clinical... Mar 2023Dietary patterns high in healthy minimally processed plant foods play an important role in modulating the gut microbiome and promoting cardiometabolic health. Little is...
BACKGROUND
Dietary patterns high in healthy minimally processed plant foods play an important role in modulating the gut microbiome and promoting cardiometabolic health. Little is known on the diet-gut microbiome relationship in US Hispanics/Latinos, who have a high burden of obesity and diabetes.
OBJECTIVE
In a cross-sectional analysis, we sought to examine the relationships of 3 healthy dietary patterns-the alternate Mediterranean diet (aMED), the Healthy Eating Index (HEI)-2015, and the healthful plant-based diet index (hPDI)-with the gut microbiome in US Hispanic/Latino adults, and to study the association of diet-related species with cardiometabolic traits.
METHODS
The Hispanic Community Health Study/Study of Latinos is a multi-site community-based cohort. At baseline (2008-2011), diet was assessed by using 2, 24-hour recalls. Shotgun sequencing was performed on stool samples collected in 2014-17 (n = 2444). Analysis of Compositions of Microbiomes 2 (ANCOM2) was used to identify the associations of dietary pattern scores with gut microbiome species and functions, adjusting for sociodemographic, behavioral, and clinical covariates.
RESULTS
Better diet quality according to multiple healthy dietary patterns was associated with a higher abundance of species from class Clostridia, including [Eubacterium] eligens, Butyrivibrio crossotus, and Lachnospiraceae bacterium TF01-11, but functions related to better diet quality differed for the dietary patterns (e.g., aMED with pyruvate:ferredoxin oxidoreductase, hPDI with L-arabinose/lactose transport). Poorer diet quality was associated with a higher abundance of Acidaminococcus intestini and with functions of manganese/iron transport, adhesin protein transport, and nitrate reduction. Some healthy diet pattern-enriched Clostridia species were related to more favorable cardiometabolic traits such as lower triglycerides and waist-to-hip ratio.
CONCLUSIONS
Healthy dietary patterns in this population are associated with a higher abundance of fiber-fermenting Clostridia species in the gut microbiome, consistent with previous studies in other racial/ethnic groups. Gut microbiota may be involved in the beneficial effect of higher diet quality on cardiometabolic disease risk.
Topics: Humans; Cardiovascular Diseases; Cross-Sectional Studies; Gastrointestinal Microbiome; Hispanic or Latino; Public Health; Diet, Healthy
PubMed: 36872018
DOI: 10.1016/j.ajcnut.2022.11.020 -
European Journal of Biochemistry Aug 19811. Glutaconate CoA-transferase catalyses the transfer of CoAS- from acetyl-CoA preferentially to (E)-glutaconate, but glutarate, (R)-2-hydroxyglutarate, acrylate and...
1. Glutaconate CoA-transferase catalyses the transfer of CoAS- from acetyl-CoA preferentially to (E)-glutaconate, but glutarate, (R)-2-hydroxyglutarate, acrylate and propionate are also good acceptors. No reaction was observed with (Z)-glutaconate and C4-dicarboxylic acids. 2. The product of the reaction of acetyl-CoA with (E)-glutaconate is the 1-isomer of glutaconyl-CoA, i.e. the thiol ester is conjugated with the double bond. Other results indicate, however, that with (R)-2-hydroxyglutarate as substrate both possible isomers are generated. 3. Glutaconate CoA-transferase was purified from cell-free extracts of Acidaminococcus fermentans to apparent homogeneity and crystallized. The relative molecular mass of the enzyme is approximately 275000. It consists of two different polypeptide chains (M, 32000 and 34000). On the catalytic pathway a thiolester is formed between CoASH and a carboxylate of the smaller polypeptide chain. 4. The structural and functional relationships between glutaconate CoA-transferase and other CoA-transferases are discussed. 5. Glutaconate CoA-transferase is also present in other bacteria fermenting glutamate via hydroxyglutarate. Experiments with an antiserum against the enzyme indicate that the transferase is necessary for the decarboxylation of glutaconate but not for the dehydration of (R)-2-hydroxyglutarate.
Topics: Acyl Coenzyme A; Coenzyme A; Coenzyme A-Transferases; Crystallization; Glutarates; Gram-Negative Anaerobic Bacteria; Kinetics; Molecular Weight; Substrate Specificity; Sulfhydryl Reagents; Sulfurtransferases
PubMed: 6945182
DOI: 10.1111/j.1432-1033.1981.tb06404.x -
Journal of Bacteriology May 1969Acidaminococcus gen. n. and the type species Acidaminococcus fermentans sp. n. were described. Amino acids, of which glutamic acid is the most important, could serve as...
Acidaminococcus gen. n. and the type species Acidaminococcus fermentans sp. n. were described. Amino acids, of which glutamic acid is the most important, could serve as the sole energy source for growth. Acetic and butyric acids and CO(2) were produced; propionic acid and hydrogen were not produced. Amino acid media supporting growth and the amino acid and vitamin requirements were described. Glucose was frequently not fermented or was weakly catabolized. Derivative products from glucose autoclaved in media, but not glucose itself, stimulated or were required for growth in amino acid media. A wide range of polyols and carbohydrates were not attacked. Lactate, fumarate, malate, succinate, citrate, and pyruvate were not used as energy sources for growth. Pyruvate completely suppressed growth. Cytochrome oxidase and benzidine reactions were negative; catalase, indole, acetyl methyl carbinol, and H(2)S were not produced; nitrate and sulfonthalein indicators were not reduced; ammonia was produced; gelatin liquefaction was negative or slow and partial; vancomycin (7.5 mug/ml) was resisted. Acidaminococcus was different from Veillonella in morphology, serology, nutrition, utilization of substrates, and accumulation of products in media supporting growth; Acidaminococcus resembled Peptococcus in utilization of glutamic acid and accumulation of similar products, but the two genera differed in morphology, gram reaction, serology, guanine plus cytosine content of deoxyribonucleic acid, and nutrition.
Topics: Aldehydes; Amino Acids; Bacteria; Culture Media; DNA, Bacterial; Glucose; Glutamates; Veillonella; Vitamins
PubMed: 5784223
DOI: 10.1128/jb.98.2.756-766.1969 -
BMC Biology Apr 2022The CRISPR-Cas12a (formerly Cpf1) system is a versatile gene-editing tool with properties distinct from the broadly used Cas9 system. Features such as recognition of...
BACKGROUND
The CRISPR-Cas12a (formerly Cpf1) system is a versatile gene-editing tool with properties distinct from the broadly used Cas9 system. Features such as recognition of T-rich protospacer-adjacent motif (PAM) and generation of sticky breaks, as well as amenability for multiplex editing in a single crRNA and lower off-target nuclease activity, broaden the targeting scope of available tools and enable more accurate genome editing. However, the widespread use of the nuclease for gene editing, especially in clinical applications, is hindered by insufficient activity and specificity despite previous efforts to improve the system. Currently reported Cas12a variants achieve high activity with a compromise of specificity. Here, we used structure-guided protein engineering to improve both editing efficiency and targeting accuracy of Acidaminococcus sp. Cas12a (AsCas12a) and Lachnospiraceae bacterium Cas12a (LbCas12a).
RESULTS
We created new AsCas12a variant termed "AsCas12a-Plus" with increased activity (1.5~2.0-fold improvement) and specificity (reducing off-targets from 29 to 23 and specificity index increased from 92% to 94% with 33 sgRNAs), and this property was retained in multiplex editing and transcriptional activation. When used to disrupt the oncogenic BRAF mutant, AsCas12a-Plus showed less off-target activity while maintaining comparable editing efficiency and BRAF cancer cell killing. By introducing the corresponding substitutions into LbCas12a, we also generated LbCas12a-Plus (activity improved ~1.1-fold and off-targets decreased from 20 to 12 while specificity index increased from 78% to 89% with 15 sgRNAs), suggesting this strategy may be generally applicable across Cas12a orthologs. We compared Cas12a-Plus, other variants described in this study, and the reported enCas12a-HF, enCas12a, and Cas12a-ultra, and found that Cas12a-Plus outperformed other variants with a good balance for enhanced activity and improved specificity.
CONCLUSIONS
Our discoveries provide alternative AsCas12a and LbCas12a variants with high specificity and activity, which expand the gene-editing toolbox and can be more suitable for clinical applications.
Topics: Acidaminococcus; CRISPR-Cas Systems; Endonucleases; Gene Editing; Proto-Oncogene Proteins B-raf
PubMed: 35468792
DOI: 10.1186/s12915-022-01296-1 -
Frontiers in Nutrition 2022Recent research suggest that gut microbiome may play a fundamental role in athlete's health and performance. Interestingly, nutrition can affect athletic performance by...
BACKGROUND
Recent research suggest that gut microbiome may play a fundamental role in athlete's health and performance. Interestingly, nutrition can affect athletic performance by influencing the gut microbiome composition. Among different dietary patterns, ketogenic diet represents an efficient nutritional approach to get adequate body composition in athletes, however, some concerns have been raised about its potential detrimental effect on gut microbiome. To the best of our knowledge, only one study investigated the effect of ketogenic diet on the gut microbiome in athletes (elite race walkers), whilst no studies are available in a model of mixed endurance/power sport such as soccer. This study aimed to investigate the influence of a ketogenic Mediterranean diet with phytoextracts (KEMEPHY) diet on gut microbiome composition in a cohort of semi-professional soccer players.
METHODS
16 male soccer players were randomly assigned to KEMEPHY diet (KDP = 8) or western diet (WD = 8). Body composition, performance measurements and gut microbiome composition were measured before and after 30 days of intervention by 16S rRNA amplicon sequencing. Alpha-diversity measures and PERMANOVA was used to investigate pre-post differences in the relative abundance of all taxonomic levels (from phylum to genus) and Spearman's correlations was used to investigate associations between microbial composition and macronutrient intake. Linear discriminant analysis was also performed at the different taxonomic levels on the post-intervention data.
RESULTS
No differences were found between pre and post- dietary intervention for microbial community diversity: no significant effects of time ( = 0.056, ES = 0.486 and = 0.129, ES = 0.388, respectively for OTUs number and Shannon's ENS), group ( = 0.317, ES = 0.180 and = 0.809, ES = 0.047) or time × group ( = 0.999, ES = 0.01 and = 0.230, ES = 0.315). paired Wilcoxon test showed a significant time × group effect for ( = 0.021, ES = 0.578), which increased in the WD group (median pre: 1.7%; median post: 2.3%) and decreased in the KEMEPHY group (median pre: 4.3%; median post: 1.7%). At genus level, the linear discriminant analysis in the post intervention differentiated the two groups for genus (pertaining to the phylum), and genera, all more abundant in the WD group, and for (order, family, and genus), genera (pertaining to the Marinifilaceae family), and genus, all more abundant in the KEMEPHY group.
CONCLUSIONS
Our results demonstrate that 30 days of KEMEPHY intervention, in contrast with previous research on ketogenic diet and gut microbiome, do not modify the overall composition of gut microbiome in a cohort of athletes. KEMEPHY dietary pattern may represent an alternative and safety tool for maintaining and/or regulating the composition of gut microbiome in athletes practicing regular exercise. Due to the fact that not all ketogenic diets are equal, we hypothesized that each version of ketogenic diet, with different kind of nutrients or macronutrients partitioning, may differently affect the human gut microbiome.
PubMed: 36386948
DOI: 10.3389/fnut.2022.979651 -
Animals : An Open Access Journal From... Nov 2020The gut microbiota in sows is important for the health of the host, and potential benefits may also be transferred to piglets during pregnancy. Therefore, systematic...
The gut microbiota in sows is important for the health of the host, and potential benefits may also be transferred to piglets during pregnancy. Therefore, systematic studies investigating the changes in the gut microbiota of sows are needed to elucidate the microbial compositions and functions. This study was conducted at 12 time points to investigate the temporal variations in gut microbiota on Days 27, 46, 64, 81, 100, and 113 during gestation (G) and Days 3, 5, 7, 10, 14, and 21 during lactation (L). Results suggested that the gut microbiota changed across the perinatal period with microbial function and abundance varying between the prenatal and postnatal periods. The alpha diversity was higher in the postnatal period than in the prenatal period. Thirty-eight genera were distributed between the two periods with , , , and r being enriched in the prenatal period while , , , , , , , were enriched in the postnatal period. Analysis done at the different time points of the prenatal period suggested that Days 27 and 113 had more microbial biomarkers than other days. , , and were enriched on the 27th day, while bacteria belonging to the and were enriched on the 113th day. On the other hand, , , , and unclassified were enriched three days after delivery. Predicted microbial KO functions were also more enriched on Day 27 of the gestation period and Day 3 of the lactation period. Random forest, a machine learning method, was used to identify the top five important genera of , , , , and , while the most important function was arginine and proline metabolism. These systematic results provide important information for the gut microbiota of sows.
PubMed: 33266170
DOI: 10.3390/ani10122254