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Biotechnology Journal Sep 2023Aerobic granular sludge (AGS) is a microbial aggregate with a biofilm structure. Thus, investigating AGS in the aspect of biofilm and microbial attachment at the genetic...
Aerobic granular sludge (AGS) is a microbial aggregate with a biofilm structure. Thus, investigating AGS in the aspect of biofilm and microbial attachment at the genetic level would help to reveal the mechanism of granule biofilm formation. In this work, a two-plasmid clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas)12a genome editing system was constructed to identify attachment genes for the first time in Stenotrophomonas AGS-1 from AGS. One plasmid contained a Cas12a cassette driven by an arabinose-inducible promoter, and another contained the specific crRNA and homologous arms (HAs). Acidaminococcus sp. Cas12a (AsCas12a) was adopted and proven to have mild toxicity (compared to Cas9) and strong cleavage activity for AGS-1. CRISPR/Cas12a-mediated rmlA knockout decreased attachment ability by 38.26%. Overexpression of rmlA in AGS-1 resulted in an increase of 30.33% in attachment ability. These results showed that the modulation of rmlA was an important factor for the biofilm formation of AGS-1. Moreover, two other genes (xanB and rpfF) were knocked out by CRISPR/Cas12a and identified as attachment-related genes in AGS-1. Also, this system could achieve point mutations. These data indicated that the CRISPR/Cas12a system could be an effective molecular platform for attachment gene function identification, which would be useful for the development of AGS in wastewater treatment.
Topics: CRISPR-Cas Systems; Sewage; Gene Editing; Plasmids; Bacterial Proteins
PubMed: 37288647
DOI: 10.1002/biot.202200596 -
Frontiers in Immunology 2023Immune checkpoint inhibitors have had a major impact on cancer treatment. Gut microbiota plays a major role in the cancer microenvironment, affecting treatment response....
INTRODUCTION
Immune checkpoint inhibitors have had a major impact on cancer treatment. Gut microbiota plays a major role in the cancer microenvironment, affecting treatment response. The gut microbiota is highly individual, and varies with factors, such as age and race. Gut microbiota composition in Japanese cancer patients and the efficacy of immunotherapy remain unknown.
METHODS
We investigated the gut microbiota of 26 patients with solid tumors prior to immune checkpoint inhibitor monotherapy to identify bacteria involved in the efficacy of these drugs and immune-related adverse events (irAEs).
RESULTS
The genera and were relatively common in the group showing efficacy towards the anti-PD-1 antibody treatment (effective group). The proportions of (P = 0.022) and (P = 0.049) were significantly higher in the effective group than in the ineffective group. In addition, the proportion of (P = 0.033) was significantly higher in the ineffective group. Next, they were divided into irAE and non-irAE groups. The proportions of (P = 0.001) and (P = 0.001) were significantly higher in the group with irAEs than in those without, while the proportions of (P = 0.013) and the unclassified (P = 0.027) were significantly higher in the group without irAEs than those with. Furthermore, within the Effective group, and (both P = 0.001) were more abundant in the subgroup with irAEs than in those without them. In contrast, (P = 0.021) and (P= 0.033) were statistically significantly more common in those without irAEs.
DISCUSSION
Our Study suggests that the analysis of the gut microbiota may provide future predictive markers for the efficacy of cancer immunotherapy or the selection of candidates for fecal transplantation for cancer immunotherapy.
Topics: Humans; Immune Checkpoint Inhibitors; Acidaminococcus; Neoplasms; Immunotherapy; Tumor Microenvironment
PubMed: 37207204
DOI: 10.3389/fimmu.2023.1164724 -
Clinical Nutrition (Edinburgh, Scotland) Jun 2023Previous studies have suggested that circulating 25-hydroxyvitamin D (25 [OH]D, VD) and the gut microbiota-bile acid axis play crucial roles in metabolic health....
BACKGROUND & AIMS
Previous studies have suggested that circulating 25-hydroxyvitamin D (25 [OH]D, VD) and the gut microbiota-bile acid axis play crucial roles in metabolic health. Exploring the mediating role of the gut microbiota-bile acid axis would improve our understanding of the mechanisms underlying the effects of VD on human metabolic health. This study examined the association between plasma 25(OH)D and the prevalence/incidence of metabolic syndrome (MetS) and the mediating role of the gut microbiota-bile acid axis.
METHODS
This prospective study included 3180 participants with plasma 25(OH)D data at baseline and 2966 participants with a 9-year follow-up. MetS was determined every three years. The gut microbiota was analyzed by 16S rRNA sequencing in 1752 participants, and targeted bile acid metabolites in feces were further determined in 974 participants using UPLC‒MS/MS at the middle of the study. Mediating roles of microbiota and bile acids in the VD-MetS associations were analyzed using mediation/path analyses adjusted for potential confounders.
RESULTS
Among the 2966 participants who were followed-up, 1520, 193, 647, and 606 were MetS-free (normal), recovered, had incident MetS, and had persistent MetS, respectively. The multivariable-adjusted ORs (95% CIs) of MetS prevalence were 0.65 (0.50, 0.84) for baseline MetS and 0.46 (0.33, 0.65) for 9-year persistent MetS in quartile 4 (compared to quartile 1) of plasma 25(OH)D (median: 37.7 vs. 19.6, ng/ml). The corresponding HR (95% CI) of 9-year MetS incidence was 0.71 (0.56, 0.90) (all P-trend < 0.05). Higher VD concentrations were associated with greater α-diversity of the gut microbiota, which was inversely correlated with MetS risk. The groups classified by VD and MetS status had significantly different β-diversity. Ruminiclostridium-6 and Christensenellaceae R-7 group were enriched in the high-VD group and were inversely associated with MetS. However, opposite associations were observed for Lachnoclostridium and Acidaminococcus. The overlapping differential microbial score (ODMS) developed from the four differential genera explained 12.2% of the VD-MetS associations (P = 0.015). Furthermore, the fecal bile acid score created from 11 differential bile acids related to ODMS and MetS mediated 34.2% of the association between ODMS and MetS (P = 0.029). Path analyses showed that the inverse association between plasma 25(OH)D and MetS could be mediated by the gut microbiota-bile acid axis.
CONCLUSIONS
The findings suggest that the gut microbiota-bile acid axis partially mediates the beneficial association between plasma 25(OH)D and the risk of persistent MetS and incident MetS in the Chinese population.
Topics: Adult; Humans; Metabolic Syndrome; Prospective Studies; Gastrointestinal Microbiome; Bile Acids and Salts; RNA, Ribosomal, 16S; Chromatography, Liquid; East Asian People; Tandem Mass Spectrometry; Vitamin D; Vitamins
PubMed: 37086617
DOI: 10.1016/j.clnu.2023.03.022 -
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 -
International Journal of Systematic and... Feb 2023The human gastrointestinal tract is inhabited by various microorganisms, including thousands of bacterial taxa that have yet to be cultured and characterized. In this...
The human gastrointestinal tract is inhabited by various microorganisms, including thousands of bacterial taxa that have yet to be cultured and characterized. In this report, we describe the isolation, cultivation, genotypic and phenotypic characterization and taxonomy of five novel anaerobic bacterial strains that were recovered during the massive cultivation and isolation of gut microbes from human faecal samples. On the basis of the polyphasic taxonomic results, we propose two novel genera and five novel species. They are sp. nov. (type strain NSJ-142=CGMCC 1.17903=KCTC 25346), sp. nov. (type strain NSJ-176=CGMCC 1.17933=KCTC 25355), gen. nov. sp. nov. (type strain NSJ-141=CGMCC 1.17902=KCTC 25345), gen. nov. sp. nov. (type strain NSJ-153=CGMCC 1.17915=KCTC 25350) and sp. nov. (type strain NSJ-152=CGMCC 1.17914=KCTC 25349).
Topics: Humans; Fatty Acids; Acidaminococcus; Phylogeny; DNA, Bacterial; RNA, Ribosomal, 16S; Base Composition; Bacterial Typing Techniques; Sequence Analysis, DNA; Firmicutes; Actinobacteria; Tenericutes; Feces; Phospholipids
PubMed: 36735588
DOI: 10.1099/ijsem.0.005648 -
Frontiers in Veterinary Science 2022It is of great importance to find antibiotic alternatives that can improve poultry performance and enhance immunity. Plant-derived extracts and their concentrates are...
INTRODUCTION
It is of great importance to find antibiotic alternatives that can improve poultry performance and enhance immunity. Plant-derived extracts and their concentrates are natural bioactive compounds that are widely and effectively applied as the antibiotic alternatives in animal industries. This study was conducted to investigate the effects of extract (YSE) on growth performance, serum biochemical parameters, immune function, intestinal morphology, and microbiota diversity of young pigeons.
METHODS
A total of 120 healthy White King pigeons (28 days old) with similar weight were randomly assigned to 4 treatments with six replicate cages. Each of the pigeons from 4 treatments was orally administrated with 0 (control), 5, 10, and 15 mg YSE per day, respectively.
RESULTS
The results showed that orally supplemental YSE had no significant effects ( > 0.05) on the growth performance and immune organ index of pigeons. The serum total protein and IgM contents in the 10 mg YSE group were significantly higher ( < 0.05) than those in the control group. Supplemental 10 and 15 mg YSE significantly lowered the level of serum total cholesterol ( < 0.05) and increased ( < 0.05) the villi height in the jejunum compared with the control group. Supplemental 5 and 10 mg YSE significantly decreased ( < 0.05) the level of serum alanine aminotransferase and the crypt depth in the ileum compared with the control group. The beta diversity showed a distinct difference in the ileum microbial composition between the control and the 10 mg YES group. YSE supplementation enriched the bacterial genera , and . Additionally, genus showed a significantly negative correlation with serum alanine aminotransferase ( = -0.618, = 0.043). genus showed a significantly negative correlation with cholesterol ( = -0.633, = 0.036). genus showed a significantly positive correlation with villi height in the jejunum ( = 0.751, = 0.008).
DISCUSSION
In conclusion, orally supplemental YSE could improve serum biochemistry, immunoglobulin contents, and intestinal morphology by regulating the composition of microbial community in the ileum of young pigeons.
PubMed: 36713856
DOI: 10.3389/fvets.2022.1077555 -
Food Chemistry Jun 2023The effects of superfine yak bone powder (YBP) on human gut microbiota (HGM) were investigated by in vitro digestion and fermentation combined with microbiomics and...
In vitro digestion and fermentation combined with microbiomics and metabolomics reveal the mechanism of superfine yak bone powder regulating lipid metabolism by altering human gut microbiota.
The effects of superfine yak bone powder (YBP) on human gut microbiota (HGM) were investigated by in vitro digestion and fermentation combined with microbiomics and metabolomics. Results showed that size reduction and protein structural degradation during digestion allowed superfine YBP to release more Ca than CaCO powders with similar particle size. Moreover, the indigestible YBP further influenced HGM and was associated with increased occurrence of beneficial bacteria such as Megasphaera spp., Megamonas spp., Acidaminococcus spp., and Prevotella spp. The altered HGM was associated with greater production of short-chain fatty acids with 4-6 carbon atoms. Furthermore, the indigestible YBP was associated with up-regulation of many lipid-related metabolites, including taurine, secondary bile acids, saturated long-chain fatty acids, and ω-3/ω-6 polyunsaturated fatty acids, which modulated favorably lipid metabolic pathways. These findings implied the potential activity of superfine YBP as a food fortifier in favorably altering HGM community structure and regulating lipid metabolism.
Topics: Animals; Humans; Cattle; Powders; Gastrointestinal Microbiome; Fermentation; Lipid Metabolism; Metabolomics; Fatty Acids, Volatile; Digestion; Feces
PubMed: 36652799
DOI: 10.1016/j.foodchem.2023.135441 -
Frontiers in Veterinary Science 2022The fermented feed has been used extensively as a growth promoter in agricultural animal production. However, the effects of fermented feed on swine gut microbiota are...
The fermented feed has been used extensively as a growth promoter in agricultural animal production. However, the effects of fermented feed on swine gut microbiota are still largely unknown. The work presented here aimed to investigate the growth performance and gut microbiota of nursery pigs receiving the LPF diet (10% and co-fermented feed + basal diet) compared with pigs receiving the NC diet (basal diet). The data showed LPF diet numerically improved average daily gain and significantly increased fecal acetate, butyrate, and total short-chain fatty acid (SCFA) concentrations. Furthermore, gut microbiota structure and membership significantly changed in response to the addition of fermented feed in the diet. Gut microbiota results indicated that LPF treatment significantly enriched SCFA-producing bacteria such as , and . Some of these bacteria also had anti-inflammatory and other beneficial functions. Overall, these findings suggested that and co-fermented feed benefited growth performance and established potential health impacts on the gut microbiota of nursery pigs.
PubMed: 36578437
DOI: 10.3389/fvets.2022.1076906 -
Nutrients Nov 2022Pre-clinical studies suggest that circulating oxylipins, i.e., the oxidation products of polyunsaturated fatty acids (PUFAs), modulate gut microbiota composition in...
Pre-clinical studies suggest that circulating oxylipins, i.e., the oxidation products of polyunsaturated fatty acids (PUFAs), modulate gut microbiota composition in mice, but there is no information available in humans. Therefore, this study aimed to investigate the relationship between omega-3 and omega-6 derived oxylipins plasma levels and fecal microbiota composition in a cohort of young adults. 80 young adults (74% women; 21.9 ± 2.2 years old) were included in this cross-sectional study. Plasma levels of oxylipins were measured using liquid chromatography-tandem mass spectrometry. Fecal microbiota composition was analyzed by V3-V4 16S rRNA gene sequencing. We observed that plasma levels of omega-3 derived oxylipins were positively associated with the relative abundance of genus ( phylum; rho ≥ 0.415, ≤ 0.009) and negatively associated with the relative abundance of genus (Proteobacteria phylum; rho ≥ -0.270, ≤ 0.041), respectively. Moreover, plasma levels of omega-6 derived oxylipins were negatively associated with the relative abundance of and genera ( phylum; all rho ≥ -0.263, ≤ 0.024), as well as , , and genera ( phylum; all rho ≥ -0.263, ≤ 0.024). Lastly, the ratio between omega-6 and omega-3 oxylipins plasma levels was negatively associated with the relative abundance of cluster IV genus ( phylum; rho = -0.334, = 0.004) and genus ( phylum; rho = -0.292, = 0.014). In conclusion, our results show that the plasma levels of omega-3 and omega-6 derived oxylipins are associated with the relative abundance of specific fecal bacteria genera.
Topics: Young Adult; Humans; Female; Mice; Animals; Adult; Male; RNA, Ribosomal, 16S; Cross-Sectional Studies; Oxylipins; Feces; Microbiota; Firmicutes; Bacteroidetes; Proteobacteria; Fatty Acids, Omega-3
PubMed: 36501021
DOI: 10.3390/nu14234991 -
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