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Nutrients Sep 2023Cystic Fibrosis-related gut dysbiosis (CFRGD) has become a recognised complication in children with this condition, and current evidence remains insufficient to guide...
Cystic Fibrosis-related gut dysbiosis (CFRGD) has become a recognised complication in children with this condition, and current evidence remains insufficient to guide the selection of probiotic strains for supplementation treatments. The aim of this study was to characterise the effect of three probiotic strains on CFRGD by means of a dynamic in vitro simulation of the colonic fermentation (SHIME). The configuration of the system included three bioreactors colonised with the faecal inoculum of a child with cystic fibrosis. For 20 days, each bioreactor was supplied daily with either (ATCC 53103 TM), (DSM 17938) or (DSM 22266). The baseline microbiota was characterised by a high abundance of , and genera. After 20 days of supplementation, and reduced significantly, and the three strains led to increased and and decreased , with some of these changes being maintained 10 days after ceasing supplementation. The metabolic activity remained unaltered in terms of short-chain fatty acids, but branched-chain fatty acids showed a significant decrease, especially with . Additionally, ammonia decreased at 20 days of supplementation, and lactate continuously increased with the three strains. The effects on colonic microbiota of , or were established, including increased beneficial bacteria, such as , and beneficial metabolites such as lactate; and on the other hand, a reduction in pathogenic genera, including or and branched-chain fatty acids, overall supported their use as probiotics in the context of CFRGD.
Topics: Child; Humans; Lactobacillaceae; Cystic Fibrosis; Limosilactobacillus reuteri; Lactic Acid; Dysbiosis; Faecalibacterium; Fatty Acids; Microbiota
PubMed: 37686878
DOI: 10.3390/nu15173846 -
BMC Pregnancy and Childbirth Feb 2022The primary purpose of the study is to determine the variation of gut microbiota composition between first (T1) and third trimester (T3); gestational diabetes mellitus... (Comparative Study)
Comparative Study Observational Study
BACKGROUND
The primary purpose of the study is to determine the variation of gut microbiota composition between first (T1) and third trimester (T3); gestational diabetes mellitus (GDM) and non-gestational diabetes mellitus (NGDM); and also within a different category of Body Mass Index (BMI) of selected pregnant Malaysian women.
METHODS
A prospective observational study on selected 38 pregnant Malaysian women attending a tertiary medical centre was carried out. Those with preexisting diabetes, metabolic syndrome or any other endocrine disorders were excluded. GDM was determined using oral glucose tolerance test (OGTT) while BMI was stratified as underweight, normal, pre-obese and obese. Fecal samples were then collected during the first trimester (T1) and the third trimester (T3). The V3-V4 region of 16S rRNA gene amplicon libraries were sequenced and analyzed using QIIME (version 1.9.1) and METAGENassist.
RESULTS
Twelve women (31.6%) were diagnosed as GDM. A trend of lower α-diversity indices in GDM, pre-obese and obese pregnant women were observed. Partial Least Squares Discriminant Analysis (PLS-DA) shows a clustering of gut microbiota according to GDM status and BMI, but not by trimester. Genera Acidaminococcus, Clostridium, Megasphaera and Allisonella were higher, and Barnesiella and Blautia were lower in GDM group (P < 0.005). Obese patients had gut microbiota that was enriched with bacteria of Negativicutes and Proteobacteria class such as Megamonas, Succinatimonas and Dialister (P < 0.005). The normal and mild underweight profiles on the other hand had a higher bacteria from the class of Clostridia (Papillibacter, Oscillibacter, Oscillospira, Blautia, Dorea) and Bacteroidia (Alistipes, Prevotella, Paraprevotella) (P < 0.005).
CONCLUSION
The prevalence and variation of several key bacteria from classes of Negativicutes, Clostridia and Proteobacteria has potential metabolic links with GDM and body weight during pregnancy which require further functional validation.
Topics: Adult; Analysis of Variance; Bacteria; Body Mass Index; DNA, Bacterial; Diabetes, Gestational; Female; Gastrointestinal Microbiome; Humans; Least-Squares Analysis; Malaysia; Microbiota; Pregnancy; Pregnancy Trimesters; Pregnant Women; Principal Component Analysis; Prospective Studies
PubMed: 35209853
DOI: 10.1186/s12884-022-04472-x -
Frontiers in Veterinary Science 2021The gut microbiome plays important roles in maintaining host health, and inappropriate use of antibiotics can cause imbalance, which may contribute to serious disease....
The gut microbiome plays important roles in maintaining host health, and inappropriate use of antibiotics can cause imbalance, which may contribute to serious disease. However, despite its promise, using metagenomic sequencing to explore the effects of colistin on gut microbiome composition in pig has not been reported. Herein, we evaluated the roles of colistin in gut microbiome modulation in pigs. Metagenomic analysis demonstrated that overall microbial diversity was higher in the colistin group compared with the control group. Antibiotic Resistance Genes Database analysis demonstrated that following colistin treatment, expression levels of , and were significantly upregulated, indicating that colistin may induce transformation of antibiotic resistance genes. Colistin also affected the microbiome distribution patterns at both genus and phylum levels. In addition, at the species level, colistin significantly reduced the abundance of , and and enhanced the abundance of and compared to the control group. Gene Ontology analysis demonstrated that following treatment with colistin, metabolic process, cellular process, and single-organism process were the dominant affected terms. Kyoto Encyclopedia of Genes and Genomes analysis showed that oxidative phosphorylation, protein processing in endoplasmic reticulum, various types of N-glycan biosynthesis, protein processing in endoplasmic reticulum, pathogenic infection, and mitogen-activated protein kinase signaling pathway-yeast were the dominant signaling pathways in the colistin group. Overall, our results suggested that colistin affects microbial diversity and may modulate gut microbiome composition in pig, potentially providing novel strategy or antibiotic rationalization pertinent to human and animal health.
PubMed: 34277753
DOI: 10.3389/fvets.2021.663820 -
Scientific Reports Mar 2021In the present study, we characterized the distinctive signatures of the gut microbiota (GM) from overweight/obese patients (OB), and normal-weight controls (NW), both...
In the present study, we characterized the distinctive signatures of the gut microbiota (GM) from overweight/obese patients (OB), and normal-weight controls (NW), both of Sardinian origin. Fecal bacterial composition of 46 OB patients (BMI = 36.6 ± 6.0; F/M = 40/6) was analyzed and compared to that of 46 NW subjects (BMI = 21.6 ± 2.1; F/M = 41/5), matched for sex, age and smoking status, by using 16S rRNA gene sequencing on MiSeq Illumina platform. The gut microbial community of OB patients exhibited a significant decrease in the relative abundance of several Bacteroidetes taxa (i.e. Flavobacteriaceae, Porphyromonadaceae, Sphingobacteriaceae, Flavobacterium, Rikenella spp., Pedobacter spp., Parabacteroides spp., Bacteroides spp.) when compared to NW; instead, several Firmicutes taxa were significantly increased in the same subjects (Lachnospiraceae, Gemellaceae, Paenibacillaceae, Streptococcaceae, Thermicanaceae, Gemella, Mitsuokella, Streptococcus, Acidaminococcus spp., Eubacterium spp., Ruminococcus spp., Megamonas spp., Streptococcus, Thermicanus, Megasphaera spp. and Veillonella spp.). Correlation analysis indicated that body fatness and waist circumference negatively correlated with Bacteroidetes taxa, while Firmicutes taxa positively correlated with body fat and negatively with muscle mass and/or physical activity level. Furthermore, the relative abundance of several bacterial taxa belonging to Enterobacteriaceae family, known to exhibit endotoxic activity, was increased in the OB group compared to NW. The results extend our knowledge on the GM profiles in Italian OB, identifying novel taxa linking obesity and intestine.
Topics: Adult; Bacteria; Female; Gastrointestinal Microbiome; Humans; Italy; Male; Middle Aged; Obesity; RNA, Bacterial; RNA, Ribosomal, 16S
PubMed: 33750881
DOI: 10.1038/s41598-021-84928-w -
Evidence-based Complementary and... 2021To evaluate the prebiotic effects of polysaccharide (CPP) on human gut bacteria in vitro.
OBJECTIVE
To evaluate the prebiotic effects of polysaccharide (CPP) on human gut bacteria in vitro.
METHODS
Codonopsis Radix was extracted with water at 100°C, and the extract was precipitated by 80% ethanol to obtain CPP. Human fresh fecal samples were collected from three healthy adults and used to ferment CPP. The fermented samples were collected to be analyzed by 16S rRNA sequencing.
RESULTS
The results showed that CPP exhibited significantly the stimulation on the growth of genus of human gut bacteria ( < 0.05). Although CPP also exhibited regulative trends on the genera including , , , and , no significant differences were observed ( > 0.05), which was likely associated with the limited samples ( = 3).
CONCLUSION
CPP has the potential to stimulate the growth of of the human gut bacteria and to be benefit to human health.
PubMed: 33859715
DOI: 10.1155/2021/9524913 -
Genetics Jan 2022The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas universe continues to expand. The type II CRISPR-Cas system from Streptococcus pyogenes...
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas universe continues to expand. The type II CRISPR-Cas system from Streptococcus pyogenes (SpyCas9) is the most widely used for genome editing due to its high efficiency in cells and organisms. However, concentrating on a single CRISPR-Cas system imposes limits on target selection and multiplexed genome engineering. We hypothesized that CRISPR-Cas systems originating from different bacterial species could operate simultaneously and independently due to their distinct single-guide RNAs (sgRNAs) or CRISPR-RNAs (crRNAs), and protospacer adjacent motifs (PAMs). Additionally, we hypothesized that CRISPR-Cas activity in zebrafish could be regulated through the expression of inhibitory anti-CRISPR (Acr) proteins. Here, we use a simple mutagenesis approach to demonstrate that CRISPR-Cas systems from S. pyogenes (SpyCas9), Streptococcus aureus (SauCas9), Lachnospiraceae bacterium (LbaCas12a, previously known as LbCpf1) are orthogonal systems capable of operating simultaneously in zebrafish. CRISPR systems from Acidaminococcus sp. (AspCas12a, previously known as AsCpf1) and Neisseria meningitidis (Nme2Cas9) were also active in embryos. We implemented multichannel CRISPR recording using three CRISPR systems and show that LbaCas12a may provide superior information density compared with previous methods. We also demonstrate that type II Acrs (anti-CRISPRs) are effective inhibitors of SpyCas9 in zebrafish. Our results indicate that at least five CRISPR-Cas systems and two anti-CRISPR proteins are functional in zebrafish embryos. These orthogonal CRISPR-Cas systems and Acr proteins will enable combinatorial and intersectional strategies for spatiotemporal control of genome editing and genetic recording in animals.
Topics: Gene Editing
PubMed: 34735006
DOI: 10.1093/genetics/iyab196 -
Journal of Dairy Science May 2024Methane is a potent greenhouse gas produced during the ruminal fermentation and is associated with a loss of feed energy. Therefore, efforts to reduce methane emissions...
Methane is a potent greenhouse gas produced during the ruminal fermentation and is associated with a loss of feed energy. Therefore, efforts to reduce methane emissions have been ongoing in the last decades. Methane production is highly influenced by factors such as the ruminal microbiome and host genetics. Previous studies have proposed to use the ruminal microbiome to reduce long-term methane emissions, as ruminal microbiome composition is a moderately heritable trait and genetic improvement accumulates over time. Lactation stage is another important factor that might influence methane production but potential associations with the ruminal microbiome have not been evaluated previously. This study sought to examine the changes in ruminal microbiome over the lactation period of primiparous Holstein cows differing in methane intensity and estimate the heritability of the abundance of relevant microorganisms. Ruminal content samples from 349 primiparous Holstein cows with 14 - 378 d in milk were collected from May 2018 to June 2019. Methane intensity (MI) of each cow was calculated as methane concentration/milk yield. Up to 64 taxonomic features (TF) from 20 phyla had a significant differential abundance between cows with low and high MI early in lactation, 16 TF during mid lactation, and none late in lactation. Taxonomical features within the Firmicutes, Proteobacteria, Melainabacteria, Cyanobacteria, Bacteroidetes and Actinobacteria phyla were associated to low MI, whereas eukaryotic TF and those within the Euryarchaeota, Verrucomicrobia, Kiritimatiellaeota, Lentisphaerae phyla were associated to high MI. Out of the 60 TF that were found to be differentially abundant between early and late lactation in cows with low MI, 56 TF were also significant when cows with low and high MI were compared in the first third of the lactation. In general, microbes associated with low MI were more abundant early in lactation (e.g., Acidaminococcus, Aeromonas and Weimeria genera) and showed low to moderate heritabilities (0.03 to 0.33). These results suggest some potential to modulate the rumen microbiome composition through selective breeding for lower MI. Differences in the ruminal microbiome of cows with extreme MI levels likely result from variations in the ruminal physiology of these cows and were more noticeable early in lactation probably due to important interactions between the host phenotype and environmental factors associated to that period. Our results suggest that the ruminal microbiome evaluated early in lactation may be more precise for MI difference, and hence, this should be considered to optimize sampling periods to establish a reference population in genomic selection scenarios.
PubMed: 38788852
DOI: 10.3168/jds.2023-24552 -
Toxins Jul 2021Sarcopenia is a prevalent condition in chronic kidney disease (CKD). We determined gut microbiota (gMB) composition in CKD patients with or without sarcopenia....
Association of Sarcopenia and Gut Microbiota Composition in Older Patients with Advanced Chronic Kidney Disease, Investigation of the Interactions with Uremic Toxins, Inflammation and Oxidative Stress.
Sarcopenia is a prevalent condition in chronic kidney disease (CKD). We determined gut microbiota (gMB) composition in CKD patients with or without sarcopenia. Furthermore, we investigated whether in these patients, there was any association between gMB, uremic toxins, inflammation and oxidative stress. We analyzed gMB composition, uremic toxins (indoxyl sulphate and p-cresyl sulphate), inflammatory cytokines (interleukin 10, tumor necrosis factor α, interleukin 6, interleukin 17, interleukin 12 p70, monocyte chemoattractant protein-1 and fetuin-A) and oxidative stress (malondialdehyde) of 64 elderly CKD patients (10 < eGFR < 45 mL/min/1.73 m, not on dialysis) categorized as sarcopenic and not-sarcopenic. Sarcopenia was defined according to European Working Group on Sarcopenia in Older People 2 criteria. Sarcopenic patients had a greater abundance of the and families and of , , , and genera. They had a lower abundance of the and families and of and genera. GMB was associated with uremic toxins, inflammatory cytokines and MDA. However, uremic toxins, inflammatory cytokines and MDA were not different in sarcopenic compared with not-sarcopenic individuals, except for interleukin 10, which was higher in not-sarcopenic patients. In older CKD patients, gMB was different in sarcopenic than in not-sarcopenic ones. Several bacterial families and genera were associated with uremic toxins and inflammatory cytokines, although none of these latter substantially different in sarcopenic versus not-sarcopenic patients.
Topics: Aged; Bacteria; Gastrointestinal Microbiome; Humans; Indican; Inflammation; Interleukin-6; Malondialdehyde; Middle Aged; Oxidative Stress; Renal Dialysis; Renal Insufficiency, Chronic; Sarcopenia; Uremia; Uremic Toxins
PubMed: 34357944
DOI: 10.3390/toxins13070472 -
BioRxiv : the Preprint Server For... May 2024Somatic genome editing in mouse models has increased our understanding of the effects of genetic alterations in areas ranging from neuroscience to cancer biology and...
Somatic genome editing in mouse models has increased our understanding of the effects of genetic alterations in areas ranging from neuroscience to cancer biology and beyond. However, existing models are limited in their ability to create multiple targeted edits. Thus, our understanding of the complex genetic interactions that underlie development, homeostasis, and disease remains incomplete. Cas12a is an RNA-guided endonuclease with unique attributes that enable simple targeting of multiple genes with crRNA arrays containing tandem guides. To accelerate and expand the generation of complex genotypes in somatic cells, we generated transgenic mice with Cre-regulated and constitutive expression of enhanced Cas12a (enAsCas12a). In these mice, enAsCas12a-mediated somatic genome editing robustly generated compound genotypes, as exemplified by the initiation of diverse cancer types driven by homozygous inactivation of trios of tumor suppressor genes. We further integrated these modular crRNA arrays with clonal barcoding to quantify the size and number of tumors with each array, as well as the efficiency of each crRNA. These Cas12a alleles will enable the rapid generation of disease models and broadly facilitate the high-throughput investigation of coincident genomic alterations in somatic cells .
PubMed: 38496463
DOI: 10.1101/2024.03.07.583774 -
Frontiers in Physiology 2023Liver transplantation (LTx) is the most effective treatment for end-stage liver diseases. Gut microorganisms influence the host physiology. We aim to profile the...
Liver transplantation (LTx) is the most effective treatment for end-stage liver diseases. Gut microorganisms influence the host physiology. We aim to profile the dynamics of gut microbiota in the perioperative period and a 1-year follow-up of LTx recipients in Northeast China. A total of 257 fecal samples were longitudinally collected from 85 LTx patients using anal swabs from pre-LTx to 1-year post-LTx. A total of 48 fecal samples from end-stage liver disease patients without LTx served as the control. 16S rRNA sequencing was used to analyze gut microbiota diversity, bacterial genera, phenotype classification, and metabolic pathways. The diversity of gut microbiota decreased significantly after transplantation, accompanied by a profound change in the microbial structure, which is characterized by increased abundance of facultative anaerobic bacteria dominated by g_ and reduced anaerobic bacteria composition. Predicted functional analysis also revealed disturbances in the metabolic pathway of the gut microbiota. After LTx, the diversity of microbiota gradually recovered but to a less preoperative level after 1 year of recovery. Compared with pre-transplantation, the microbiome structure was characterized by an increase in and after 1 year of transplantation. LTx and perioperative treatment triggered gut microbial dysbiosis. The gut microbiota was restructured after LTx to near to but significantly differed from that of pre-LTx.
PubMed: 38187130
DOI: 10.3389/fphys.2023.1266635